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Dear Norbert,
    Object Image is very useful for those of us working with stacks of
confocal images. In particular, the tools for dynamically re-slicing  in
alternate x-z and y-z planes is extremely helpful. There are two items
that would be most helpful -
1) if the x-z and y-z planes could be rescaled to reflect a larger gap
between slices than a single pixel
2) Is there a version that allows cutting a stack on a bias in the x-z
and y-z planes?

Many thanks,
Harvey
--
Harvey J. Karten, M.D.
Dept. of Neurosciences
University of California at San Diego
La Jolla, CA 92093-0608
Phone (Voice): 619-534-4938
FAX:  619-534-6602
EMail: HJKarten@ucsd.edu
Alternate Email: kartenh@sdsc.edu
Retina Information System: http://www-cajal.ucsd.edu



From nih-image-request@io.ece.drexel.edu Wed Mar 10 11:48 EST 1999
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Does anyone have any experience with the Sound Vision SV-micro digital
camera?  It sounds pretty good. 10 bit image depth, B & W or color, the
ability to shut off auto gain/contrast and about 2k.  What is wrong with it?

Paul Lampe, Ph.D.
(plampe@fred.fhcrc.org)

Fred Hutchinson Cancer Research Center
1100 Fairview Ave N.  DE-320
P.O. Box 19024
Seattle, WA 98109-1024
(206) 667-4123
Fax (206) 667-2537



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Harvey,
the interactive 3D slicer already supports non-cubic ("tall") voxels. The
hight of a voxel can be entered in the stacks menu: "Stack info:
slicespacing". Is this  what you mean by gaps between slices?

Non-orthogonal slicing is not (yet?) supported. A work-around for more
freedom in vertical slicing could be to use several  (around z axis)
rotated copies of the same stack, e.g. 'Stack -30 deg', Stack 0 deg', Stack
30 deg'. Three stacks, as in this example, are enough to keep the spatial
distortion below 3.4%, (exactly: 1-cos(15deg)).

Then you could switch by macro between the coordinate systems, e.g.
  SelectWindow('Stack 30 deg');
  Slice3d;

Hope I got you right...

Norbert Vischer                  University of Amsterdam
Scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



From nih-image-request@io.ece.drexel.edu Wed Mar 10 13:37 EST 1999
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Date: Wed, 10 Mar 1999 14:27:12 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: Stacks
Cc: Janet Szczesny <szczesny@umich.edu>
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>My images are 8-bit images, all of the same size. The RAM is 240 MB.  I
>don't actually know how to create the stacks.  I tried to perform the
>stack by opening one image and choosing Windows to Stack which resulted in
>a message that read: " All windows must be
>closed before making a new stack."
>What is the correct procedure for stacking images?

One way is to use the Open command with "Open All" checked to open all the
images and then to use the Windows to Stack command to convert the images
to a stack. Before starting, to avoid error messages, make sure all windows
are closed. This method is limited to 250 images (1000 in V1.62). The
images may open in the wrong order, in which case you will need to use one
of the other methods.

Another way is to use a macro something like this:

    macro 'Open TIFF Series...';
    Var
        i:integer;
    begin
        for i:=0 to 99999 do
            Open('frame', i:3, '.tif');
    end;

This method requires that the file names include a numeric sequence (e.g.
file001, file002, file003, ...).

A third way is to use the File>Acquire>All as Stack command in ImageJ
(http://rsb.info.nih.gov/ij/) and save the resulting stack in TIFF format.

-wayne



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Dear All, 

I have recently started writing my own macros for image analysis but I have 
encountered some basic problems due to my long abstincence from Pascal (11 
years...).  Hence I wonder if there is a more detailed help manual on Scion 
Image (I am PC-bound...) especially on the macro language other than the one 
provided with the program to 'kick-start' me.  So if anybody has written a tutorial 
or something like this for class use etc. and made it public, I would greatly 
appreciate the URL for it or the file.  

Thanks a lot

Dietrich



_________________________________________
Dietrich Ruehlmann, Ph.D.
Human Blood Vessel Laboratory
Vancouver Vascular Biology Research Center
St. Paul's Hospital, University of British Columbia
1081 Burrard Street
Vancouver, BC
Canada, V6Z 1Y6
Tel : 001-604-682-2344  Ext. 2782/3056
Fax : 001-604-631-5351
http://confo.pulmonary.ubc.ca/~dietrich/


From nih-image-request@io.ece.drexel.edu Wed Mar 10 16:29 EST 1999
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        "Dietrich Ruehlmann" <druehlmann@prl.pulmonary.ubc.caprl.pulmonary.ubc.ca>
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me too!?


From nih-image-request@io.ece.drexel.edu Wed Mar 10 18:28 EST 1999
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The simplest way to stack images is to open all your TIFF images 
first then select 'Windows to stack' in the STACKS Menu. They will 
automatically be made into a stack which can then be manipulated 
using other commands in the STACK menu. The < and > keys let you 
scroll through the stack.
Just make sure all your images are the same size initially, and be 
aware they will be renumbered sequentially. Stack commands are 
explained on p48 of the manual.

Good Luck
---------------------------------------------------------------------- 
----------
Cathy Gorrie
Scientific Officer

School of Anatomy
UNSW, Kensington
Sydney 2052
Australia

ph   	9385 2462
fax 	9313 6252


From nih-image-d-request@io.ece.drexel.edu Thu Mar 11 06:20 EST 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #58
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 58

Today's Topics:
  Re: Object-Image                      [ "Harvey J. Karten" <hjkarten@ucsd.e ]
  Re: nih-image-d Digest V99 #57        [ Paul Lampe <plampe@fred.fhcrc.org> ]
  Re: Object-Image                      [ Norbert Vischer <vischer@bio.uva.nl ]
  Re: Stacks                            [ Wayne Rasband <wayne@codon.nih.gov> ]
  NIH image for beginners               [ "Dietrich Ruehlmann" <druehlmann@pr ]
  Re: NIH image for beginners           [ "Jared L. Rifkin" <jared_rifkin@qc. ]
  Re: Stacks                            [ Cathy Gorrie <C.Gorrie@unsw.edu.au> ]

------------------------------

Date: Wed, 10 Mar 1999 07:14:03 -0800
From: "Harvey J. Karten" <hjkarten@ucsd.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Object-Image
Message-ID: <36E68C3B.45EEDCF7@ucsd.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Dear Norbert,
    Object Image is very useful for those of us working with stacks of
confocal images. In particular, the tools for dynamically re-slicing  in
alternate x-z and y-z planes is extremely helpful. There are two items
that would be most helpful -
1) if the x-z and y-z planes could be rescaled to reflect a larger gap
between slices than a single pixel
2) Is there a version that allows cutting a stack on a bias in the x-z
and y-z planes?

Many thanks,
Harvey
--
Harvey J. Karten, M.D.
Dept. of Neurosciences
University of California at San Diego
La Jolla, CA 92093-0608
Phone (Voice): 619-534-4938
FAX:  619-534-6602
EMail: HJKarten@ucsd.edu
Alternate Email: kartenh@sdsc.edu
Retina Information System: http://www-cajal.ucsd.edu

------------------------------

Date: Wed, 10 Mar 1999 08:35:32 -0800
From: Paul Lampe <plampe@fred.fhcrc.org>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #57
Message-Id: <l03010d00b30c4f0e9791@[140.107.54.131]>
Content-Type: text/plain; charset="us-ascii"

Does anyone have any experience with the Sound Vision SV-micro digital
camera?  It sounds pretty good. 10 bit image depth, B & W or color, the
ability to shut off auto gain/contrast and about 2k.  What is wrong with it?

Paul Lampe, Ph.D.
(plampe@fred.fhcrc.org)

Fred Hutchinson Cancer Research Center
1100 Fairview Ave N.  DE-320
P.O. Box 19024
Seattle, WA 98109-1024
(206) 667-4123
Fax (206) 667-2537

------------------------------

Date: Wed, 10 Mar 1999 18:25:39 +0100
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Object-Image
Message-Id: <l03110704b30c567be27a@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

Harvey,
the interactive 3D slicer already supports non-cubic ("tall") voxels. The
hight of a voxel can be entered in the stacks menu: "Stack info:
slicespacing". Is this  what you mean by gaps between slices?

Non-orthogonal slicing is not (yet?) supported. A work-around for more
freedom in vertical slicing could be to use several  (around z axis)
rotated copies of the same stack, e.g. 'Stack -30 deg', Stack 0 deg', Stack
30 deg'. Three stacks, as in this example, are enough to keep the spatial
distortion below 3.4%, (exactly: 1-cos(15deg)).

Then you could switch by macro between the coordinate systems, e.g.
  SelectWindow('Stack 30 deg');
  Slice3d;

Hope I got you right...

Norbert Vischer                  University of Amsterdam
Scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: Wed, 10 Mar 1999 14:27:12 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Cc: Janet Szczesny <szczesny@umich.edu>
Subject: Re: Stacks
Message-Id: <v03007802b30c60169c6c@[128.231.99.220]>
Content-Type: text/plain; charset="us-ascii"

>My images are 8-bit images, all of the same size. The RAM is 240 MB.  I
>don't actually know how to create the stacks.  I tried to perform the
>stack by opening one image and choosing Windows to Stack which resulted in
>a message that read: " All windows must be
>closed before making a new stack."
>What is the correct procedure for stacking images?

One way is to use the Open command with "Open All" checked to open all the
images and then to use the Windows to Stack command to convert the images
to a stack. Before starting, to avoid error messages, make sure all windows
are closed. This method is limited to 250 images (1000 in V1.62). The
images may open in the wrong order, in which case you will need to use one
of the other methods.

Another way is to use a macro something like this:

    macro 'Open TIFF Series...';
    Var
        i:integer;
    begin
        for i:=0 to 99999 do
            Open('frame', i:3, '.tif');
    end;

This method requires that the file names include a numeric sequence (e.g.
file001, file002, file003, ...).

A third way is to use the File>Acquire>All as Stack command in ImageJ
(http://rsb.info.nih.gov/ij/) and save the resulting stack in TIFF format.

-wayne

------------------------------

Date: Wed, 10 Mar 1999 11:20:55 -0800
From: "Dietrich Ruehlmann" <druehlmann@prl.pulmonary.ubc.ca>
To: nih-image@io.ece.drexel.edu
Subject: NIH image for beginners
Message-Id: <199903101922.LAA09936@FEV1.pulmonary.ubc.ca>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7BIT

Dear All, 

I have recently started writing my own macros for image analysis but I have 
encountered some basic problems due to my long abstincence from Pascal (11 
years...).  Hence I wonder if there is a more detailed help manual on Scion 
Image (I am PC-bound...) especially on the macro language other than the one 
provided with the program to 'kick-start' me.  So if anybody has written a tutorial 
or something like this for class use etc. and made it public, I would greatly 
appreciate the URL for it or the file.  

Thanks a lot

Dietrich



_________________________________________
Dietrich Ruehlmann, Ph.D.
Human Blood Vessel Laboratory
Vancouver Vascular Biology Research Center
St. Paul's Hospital, University of British Columbia
1081 Burrard Street
Vancouver, BC
Canada, V6Z 1Y6
Tel : 001-604-682-2344  Ext. 2782/3056
Fax : 001-604-631-5351
http://confo.pulmonary.ubc.ca/~dietrich/

------------------------------

Date: Wed, 10 Mar 99 16:16:24 -0500
From: "Jared L. Rifkin" <jared_rifkin@qc.edu>
To: <nih-image@io.ece.drexel.edu>,
        "Dietrich Ruehlmann" <druehlmann@prl.pulmonary.ubc.caprl.pulmonary.ubc.ca>
Subject: Re: NIH image for beginners
Message-ID: <52DCC3972BC@qc1.qc.edu>
Content-Type: text/plain; charset="US-ASCII"

me too!?

------------------------------

Date: Thu, 11 Mar 1999 10:19:50 +1100
From: Cathy Gorrie <C.Gorrie@unsw.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Re: Stacks
Message-Id: <v04104401b30cabeb6443@[129.94.30.216]>
Content-Type: text/plain; charset="us-ascii" ; format="flowed"

The simplest way to stack images is to open all your TIFF images 
first then select 'Windows to stack' in the STACKS Menu. They will 
automatically be made into a stack which can then be manipulated 
using other commands in the STACK menu. The < and > keys let you 
scroll through the stack.
Just make sure all your images are the same size initially, and be 
aware they will be renumbered sequentially. Stack commands are 
explained on p48 of the manual.

Good Luck
---------------------------------------------------------------------- 
----------
Cathy Gorrie
Scientific Officer

School of Anatomy
UNSW, Kensington
Sydney 2052
Australia

ph   	9385 2462
fax 	9313 6252

--------------------------------
End of nih-image-d Digest V99 Issue #58
***************************************

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- Eye on Imaging -
May 26-28 
1999


Sponsored by the Microscopical Society of Canada
We are pleased to annouce the 26th annual meeting of the Microscopical
Society of Canada. This spring meeting will be taking place for three days,
May 26-28, 1999, on the campus of the University of Guelph in Guelph,
Ontario.
Many interesting speakers have agreed to participate including Dr. John Russ
(a frequent contributor to this list), Dr. P.C. Cheng (multi-photon
microscopy and microscope construction) , Dr. Chris Yip (AFM), Dr. Nestor
Zaluzec (Tele-Presence microscopy), Dr. Nick White (3-D quantitative
analysis and multi-photon microscopy) and Dr. Brian Kaye (Fractal analysis)
amongst others.
We are also offering a variety of afternoon workshops.
Please visit our web siter for information and registration packages:
http://www.uoguelph.ca/botany/rootlab/msc99.htm
Please pass this link along to anybody that may be interested.
Hope you can make it,
    Regards,
                Ken
--
Ken Baker M.Sc.
Microscopy, Imaging, Analysis
kwb@bserv.com
519-853-4787

--MS_Mac_OE_3003993008_821299_MIME_Part
Content-type: text/html; charset="US-ASCII"
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<HTML>
<HEAD>
<TITLE>First Announcement - Microscopical Society of Canada - 1999 - Eye on=
 Imaging</TITLE>
</HEAD>
<BODY BGCOLOR=3D"#FFFFFF">
<P ALIGN=3DCENTER>
<B>- Eye on Imaging -<BR>
May 26-28 <BR>
1999<BR>
</B>
<P>
<BR>
<BR>
<P ALIGN=3DCENTER>
<B>Sponsored by the Microscopical Society of Canada<BR>
</B>
<P>
We are pleased to annouce the 26th annual meeting of the Microscopical Soci=
ety of Canada. This spring meeting will be taking place for three days, May =
26-28, 1999, on the campus of the University of Guelph in Guelph, Ontario. <=
BR>
Many interesting speakers have agreed to participate including Dr. John Rus=
s (a frequent contributor to this list), Dr. P.C. Cheng (multi-photon micros=
copy and microscope construction) , Dr. Chris Yip (AFM), Dr. Nestor Zaluzec =
(Tele-Presence microscopy), Dr. Nick White (3-D quantitative analysis and mu=
lti-photon microscopy) and Dr. Brian Kaye (Fractal analysis) amongst others.=
<BR>
We are also offering a variety of afternoon workshops. <BR>
Please visit our web siter for information and registration packages:<BR>
<FONT COLOR=3D"#0000FF"><U>http://www.uoguelph.ca/botany/rootlab/msc99.htm<BR=
>
</U></FONT>Please pass this link along to anybody that may be interested.<B=
R>
Hope you can make it,<BR>
&nbsp;&nbsp;&nbsp;&nbsp;Regards,<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;Ken<BR>
<P ALIGN=3DCENTER>
-- <BR>
<P>
<FONT SIZE=3D"1">Ken Baker M.Sc.<BR>
Microscopy, Imaging, Analysis<BR>
kwb@bserv.com<BR>
519-853-4787<BR>
</FONT>
</BODY>
</HTML>

--MS_Mac_OE_3003993008_821299_MIME_Part--


From nih-image-request@io.ece.drexel.edu Thu Mar 11 11:13 EST 1999
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Date: Thu, 11 Mar 1999 07:57:57 -0800 (PST)
From: Mark Vivino <mvivino@yahoo.com>
Subject: Re: NIH image for beginners
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---Dietrich Ruehlmann <druehlmann@prl.pulmonary.ubc.ca> wrote:

> I have recently started writing my own macros for image analysis but
I have 
> encountered some basic problems due to my long abstincence from
Pascal (11 
> years...).  Hence I wonder if there is a more detailed help manual
on Scion 
> Image (I am PC-bound...) especially on the macro language other than
the one 
> provided with the program to 'kick-start' me.  So if anybody has
written a tutorial 
> or something like this for class use etc. and made it public, I
would greatly 
> appreciate the URL for it or the file.  

Somewhat dated but still valid (except my email)

http://rsb.info.nih.gov/nih-image/more-docs/InsideImage/inside.html

Mark
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-request@io.ece.drexel.edu Thu Mar 11 12:15 EST 1999
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From: "Ryan, Fiona - Technician Mechanical Engineering"
	 <Fiona.Ryan@IT-Tallaght.ie>
To: NIH-Queries <nih-image@io.ece.drexel.edu>
Subject: XY data from NIH image traces to Finite Element or CAD Package
Date: Thu, 11 Mar 1999 16:49:13 -0000
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Hi,
 I was wondering if it is possible to extract automatically XY data from the
edges of bones
>picked up in the CT images and importedinto NIH.
>
>I need the XY data of the profiles of each of the bones, but it seems that
I
>have to trace the edges and record the XY data at each increment manually.
>
>I would greatly appreciate if anyone could advise me on how to overcome his
problem. The data will eventually be used
>to create Finite Element models of the bones, so I need to get profile data
into a CAD or FE software package

>Thanks for your time. in advance

> Regards,
> Fiona 
> 
> Fiona Ryan
> Mechanical Engineering Technician,
> I.T.Tallaght
> Tallaght,
> Dublin 24.
> Tel *:- 	+353 1 4042567
> Fax :-	+353 1 4042504
> E-Mail* :- Fiona.Ryan@it-tallaght.ie
> 
> 
> 


From nih-image-request@io.ece.drexel.edu Thu Mar 11 14:11 EST 1999
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Date: Thu, 11 Mar 1999 14:02:48 -0800
To: nih-image@io.ece.drexel.edu
From: Michael Cammer <cammer@aecom.yu.edu>
Subject: Re: Pausing Macros
In-Reply-To: <Pine.GSO.3.95qL.990305161115.14620A-100000@bonjour.cc.colu
 mbia.edu>
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In the past I've simply had one macro stop, the user  does the ROI thing,
and then  the user presses a key to run the next macro.  Inelegant, but it
works.


********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************


From nih-image-request@io.ece.drexel.edu Thu Mar 11 18:14 EST 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: Fiona.Ryan@IT-Tallaght.ie, nih-image@io.ece.drexel.edu
Date:          Fri, 12 Mar 1999 10:09:02 +1100
Subject:       Re: XY data from NIH image traces to Finite Element or CAD 
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Fiona,
If you have a ROI in NIH-Image to mark the boundaries eg by autoWand with 
densitySlice or by manual selection eg with polygon tool, then a simple 
macro can access the xyCoordinates array for use or output to text. Also, 
you can saveAs Outline which records the coords in binary if you can decode 
this with a simple program.

Better still, Object-Image, an extention of NIH-Image by Norbert Vischer is 
available via http://simon.bio.uva.nl/object-image.html. This will allow 
export of sets of outlines as Rotator format ascii text files of coords.
With Object-Image & Rotator you can quickly get 3D reconstruction Rotation 
displays.

Greg Joss

>From: "Ryan, Fiona - Technician Mechanical Engineering"
>	 <Fiona.Ryan@IT-Tallaght.ie>
>To: NIH-Queries <nih-image@io.ece.drexel.edu>
>Subject: XY data from NIH image traces to Finite Element or CAD Package
>Date: Thu, 11 Mar 1999 16:49:13 -0000
>
>Hi,
> I was wondering if it is possible to extract automatically XY data from 
>the edges of bones
>>picked up in the CT images and importedinto NIH.
>>
>>I need the XY data of the profiles of each of the bones, but it seems 
>that I
>>have to trace the edges and record the XY data at each increment 
>manually.
>>
>>I would greatly appreciate if anyone could advise me on how to overcome 
>his problem. The data will eventually be used
>>to create Finite Element models of the bones, so I need to get profile 
>data into a CAD or FE software package
>
>>Thanks for your time. in advance
>
>> Regards,
>> Fiona 
>> 
>> Fiona Ryan
>> Mechanical Engineering Technician,
>> I.T.Tallaght
>> Tallaght,
>> Dublin 24.
>> Tel *:- 	+353 1 4042567
>> Fax :-	+353 1 4042504
>> E-Mail* :- Fiona.Ryan@it-tallaght.ie
>> 
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Thu Mar 11 18:55 EST 1999
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Date: Thu, 11 Mar 1999 15:47:03 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: : ;
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Dear Norbert and Greg,
 Thank you for the detailed responses. the first thing I found was that
the version of Object-Image I was using from the Zippy server was one
version old. I did
not have the RoiToObject command.
You were correct in interpreting that I am trying to create identical roi
objects on all slices in a stack.  Fortunately Greg's concern is not an
issue, the little buggers aren't moving.  

I can now define Objects and their clones on the first image of a stack
then replicate that cell on all subsequent slices of the stack. My next
macro steps through the stack and measures mean intensities of these
regions.  

 It appears that the nObjects function delivers the total number of clones
of all Objects in the Cell.  If this was intentional, then a command to
deliver just the number of Objects in a Cell would be most helpful.  
Since there were only 2 object classes, I could simply write their names
into the macro.  It could be much easier to loop without writing in Object
names if there was a function that came back with the number of Objects
only.

Does the Histogram function work with data in User Columns?  

thanks again, and if my questions are obviously spelled out in the docs,
no way will I ever find them.  

Glen


Glen MacDonald
   Research Scientist
Hearing Research Laboratories of the
Virginia Merrill Bloedel Hearing Research Center
Box 35-7923
University of Washington
Seattle, WA  98195-7923
(206) 616-4156
glenmac@u.washington.edu

//The box said "Requires Windows95, or better." so I bought a
Macintosh."//


From nih-image-d-request@io.ece.drexel.edu Fri Mar 12 03:16 EST 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #59
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 59

Today's Topics:
  First Announcement - Microscopical S  [ "Ken Baker" <kwb@bserv.com> ]
  Re: NIH image for beginners           [ Mark Vivino <mvivino@yahoo.com> ]
  XY data from NIH image traces to Fin  [ "Ryan, Fiona - Technician Mechanica ]
  Re: Pausing Macros                    [ Michael Cammer <cammer@aecom.yu.edu ]
  Re: XY data from NIH image traces to  [ GJOSS@rna.bio.mq.edu.au ]
  Unidentified subject!                 [ "G. Macdonald" <glenmac@u.washingto ]
  Re: objects...                        [ Norbert Vischer <vischer@bio.uva.nl ]

------------------------------

Date: Thu, 11 Mar 1999 10:30:07 -0500
From: "Ken Baker" <kwb@bserv.com>
To: nih-image@io.ece.drexel.edu
CC: George Harauz <gharauz@uoguelph.ca>
Subject: First Announcement - Microscopical Society of Canada - 1999 - Eye
	 on Imaging
Message-Id: <199903111535.KAA17595@bserv.com>
Content-type: multipart/alternative;
   boundary="MS_Mac_OE_3003993008_821299_MIME_Part"

> THIS MESSAGE IS IN MIME FORMAT. Since your mail reader does not understand
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--MS_Mac_OE_3003993008_821299_MIME_Part
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- Eye on Imaging -
May 26-28 
1999


Sponsored by the Microscopical Society of Canada
We are pleased to annouce the 26th annual meeting of the Microscopical
Society of Canada. This spring meeting will be taking place for three days,
May 26-28, 1999, on the campus of the University of Guelph in Guelph,
Ontario.
Many interesting speakers have agreed to participate including Dr. John Russ
(a frequent contributor to this list), Dr. P.C. Cheng (multi-photon
microscopy and microscope construction) , Dr. Chris Yip (AFM), Dr. Nestor
Zaluzec (Tele-Presence microscopy), Dr. Nick White (3-D quantitative
analysis and multi-photon microscopy) and Dr. Brian Kaye (Fractal analysis)
amongst others.
We are also offering a variety of afternoon workshops.
Please visit our web siter for information and registration packages:
http://www.uoguelph.ca/botany/rootlab/msc99.htm
Please pass this link along to anybody that may be interested.
Hope you can make it,
    Regards,
                Ken
--
Ken Baker M.Sc.
Microscopy, Imaging, Analysis
kwb@bserv.com
519-853-4787

--MS_Mac_OE_3003993008_821299_MIME_Part
Content-type: text/html; charset="US-ASCII"
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<HTML>
<HEAD>
<TITLE>First Announcement - Microscopical Society of Canada - 1999 - Eye on=
 Imaging</TITLE>
</HEAD>
<BODY BGCOLOR=3D"#FFFFFF">
<P ALIGN=3DCENTER>
<B>- Eye on Imaging -<BR>
May 26-28 <BR>
1999<BR>
</B>
<P>
<BR>
<BR>
<P ALIGN=3DCENTER>
<B>Sponsored by the Microscopical Society of Canada<BR>
</B>
<P>
We are pleased to annouce the 26th annual meeting of the Microscopical Soci=
ety of Canada. This spring meeting will be taking place for three days, May =
26-28, 1999, on the campus of the University of Guelph in Guelph, Ontario. <=
BR>
Many interesting speakers have agreed to participate including Dr. John Rus=
s (a frequent contributor to this list), Dr. P.C. Cheng (multi-photon micros=
copy and microscope construction) , Dr. Chris Yip (AFM), Dr. Nestor Zaluzec =
(Tele-Presence microscopy), Dr. Nick White (3-D quantitative analysis and mu=
lti-photon microscopy) and Dr. Brian Kaye (Fractal analysis) amongst others.=
<BR>
We are also offering a variety of afternoon workshops. <BR>
Please visit our web siter for information and registration packages:<BR>
<FONT COLOR=3D"#0000FF"><U>http://www.uoguelph.ca/botany/rootlab/msc99.htm<BR=
>
</U></FONT>Please pass this link along to anybody that may be interested.<B=
R>
Hope you can make it,<BR>
&nbsp;&nbsp;&nbsp;&nbsp;Regards,<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;Ken<BR>
<P ALIGN=3DCENTER>
-- <BR>
<P>
<FONT SIZE=3D"1">Ken Baker M.Sc.<BR>
Microscopy, Imaging, Analysis<BR>
kwb@bserv.com<BR>
519-853-4787<BR>
</FONT>
</BODY>
</HTML>

--MS_Mac_OE_3003993008_821299_MIME_Part--

------------------------------

Date: Thu, 11 Mar 1999 07:57:57 -0800 (PST)
From: Mark Vivino <mvivino@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH image for beginners
Message-ID: <19990311155757.26008.rocketmail@web510.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

---Dietrich Ruehlmann <druehlmann@prl.pulmonary.ubc.ca> wrote:

> I have recently started writing my own macros for image analysis but
I have 
> encountered some basic problems due to my long abstincence from
Pascal (11 
> years...).  Hence I wonder if there is a more detailed help manual
on Scion 
> Image (I am PC-bound...) especially on the macro language other than
the one 
> provided with the program to 'kick-start' me.  So if anybody has
written a tutorial 
> or something like this for class use etc. and made it public, I
would greatly 
> appreciate the URL for it or the file.  

Somewhat dated but still valid (except my email)

http://rsb.info.nih.gov/nih-image/more-docs/InsideImage/inside.html

Mark
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com

------------------------------

Date: Thu, 11 Mar 1999 16:49:13 -0000
From: "Ryan, Fiona - Technician Mechanical Engineering"
	 <Fiona.Ryan@IT-Tallaght.ie>
To: NIH-Queries <nih-image@io.ece.drexel.edu>
Subject: XY data from NIH image traces to Finite Element or CAD Package
Message-ID: <D7FFC2BFF870D211A89600A0C9DD656C4A2995@gpo.it-tallaght.ie>
Content-Type: multipart/mixed;
	boundary="----_=_NextPart_000_01BE6BDF.180C2722"

This message is in MIME format. Since your mail reader does not understand
this format, some or all of this message may not be legible.

------_=_NextPart_000_01BE6BDF.180C2722
Content-Type: text/plain

Hi,
 I was wondering if it is possible to extract automatically XY data from the
edges of bones
>picked up in the CT images and importedinto NIH.
>
>I need the XY data of the profiles of each of the bones, but it seems that
I
>have to trace the edges and record the XY data at each increment manually.
>
>I would greatly appreciate if anyone could advise me on how to overcome his
problem. The data will eventually be used
>to create Finite Element models of the bones, so I need to get profile data
into a CAD or FE software package

>Thanks for your time. in advance

> Regards,
> Fiona 
> 
> Fiona Ryan
> Mechanical Engineering Technician,
> I.T.Tallaght
> Tallaght,
> Dublin 24.
> Tel *:- 	+353 1 4042567
> Fax :-	+353 1 4042504
> E-Mail* :- Fiona.Ryan@it-tallaght.ie
> 
> 
> 

------------------------------

Date: Thu, 11 Mar 1999 14:02:48 -0800
From: Michael Cammer <cammer@aecom.yu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Pausing Macros
Message-Id: <3.0.5.32.19990311140248.009a93b0@mailserver.aecom.yu.edu>
Content-Type: text/plain; charset="us-ascii"

In the past I've simply had one macro stop, the user  does the ROI thing,
and then  the user presses a key to run the next macro.  Inelegant, but it
works.


********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************

------------------------------

Date:          Fri, 12 Mar 1999 10:09:02 +1100
From: GJOSS@rna.bio.mq.edu.au
To: Fiona.Ryan@IT-Tallaght.ie, nih-image@io.ece.drexel.edu
Subject:       Re: XY data from NIH image traces to Finite Element or CAD 
Message-ID: <1A2D68D71B4@rna.bio.mq.edu.au>

Fiona,
If you have a ROI in NIH-Image to mark the boundaries eg by autoWand with 
densitySlice or by manual selection eg with polygon tool, then a simple 
macro can access the xyCoordinates array for use or output to text. Also, 
you can saveAs Outline which records the coords in binary if you can decode 
this with a simple program.

Better still, Object-Image, an extention of NIH-Image by Norbert Vischer is 
available via http://simon.bio.uva.nl/object-image.html. This will allow 
export of sets of outlines as Rotator format ascii text files of coords.
With Object-Image & Rotator you can quickly get 3D reconstruction Rotation 
displays.

Greg Joss

>From: "Ryan, Fiona - Technician Mechanical Engineering"
>	 <Fiona.Ryan@IT-Tallaght.ie>
>To: NIH-Queries <nih-image@io.ece.drexel.edu>
>Subject: XY data from NIH image traces to Finite Element or CAD Package
>Date: Thu, 11 Mar 1999 16:49:13 -0000
>
>Hi,
> I was wondering if it is possible to extract automatically XY data from 
>the edges of bones
>>picked up in the CT images and importedinto NIH.
>>
>>I need the XY data of the profiles of each of the bones, but it seems 
>that I
>>have to trace the edges and record the XY data at each increment 
>manually.
>>
>>I would greatly appreciate if anyone could advise me on how to overcome 
>his problem. The data will eventually be used
>>to create Finite Element models of the bones, so I need to get profile 
>data into a CAD or FE software package
>
>>Thanks for your time. in advance
>
>> Regards,
>> Fiona 
>> 
>> Fiona Ryan
>> Mechanical Engineering Technician,
>> I.T.Tallaght
>> Tallaght,
>> Dublin 24.
>> Tel *:- 	+353 1 4042567
>> Fax :-	+353 1 4042504
>> E-Mail* :- Fiona.Ryan@it-tallaght.ie
>> 
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Thu, 11 Mar 1999 15:47:03 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: : ;
Subject: Unidentified subject!
Message-ID: <Pine.A41.4.05.9903101414490.22246-100000@homer01.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear Norbert and Greg,
 Thank you for the detailed responses. the first thing I found was that
the version of Object-Image I was using from the Zippy server was one
version old. I did
not have the RoiToObject command.
You were correct in interpreting that I am trying to create identical roi
objects on all slices in a stack.  Fortunately Greg's concern is not an
issue, the little buggers aren't moving.  

I can now define Objects and their clones on the first image of a stack
then replicate that cell on all subsequent slices of the stack. My next
macro steps through the stack and measures mean intensities of these
regions.  

 It appears that the nObjects function delivers the total number of clones
of all Objects in the Cell.  If this was intentional, then a command to
deliver just the number of Objects in a Cell would be most helpful.  
Since there were only 2 object classes, I could simply write their names
into the macro.  It could be much easier to loop without writing in Object
names if there was a function that came back with the number of Objects
only.

Does the Histogram function work with data in User Columns?  

thanks again, and if my questions are obviously spelled out in the docs,
no way will I ever find them.  

Glen


Glen MacDonald
   Research Scientist
Hearing Research Laboratories of the
Virginia Merrill Bloedel Hearing Research Center
Box 35-7923
University of Washington
Seattle, WA  98195-7923
(206) 616-4156
glenmac@u.washington.edu

//The box said "Requires Windows95, or better." so I bought a
Macintosh."//

------------------------------

Date: Fri, 12 Mar 1999 09:03:36 +0100
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: objects...
Message-Id: <l03010d00b30e687485a4@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

Glen,

In some cases, you have the choice to address things alternatively by
numbers or strings. For example, GetValue('myColumn', 13) is equal to
GetValue(1, 13) if 'myColumn' is the first column. I could think about to
implement this method in more cases. Meanwhile, a work-around could be the
use of indexable strings,  using concat(string, index). Perhaps you could
tell more precisely what you want to index? Is it the command
SwitchToObject(string)?


>Does the Histogram function work with data in User Columns?
>

Histograms of results can only be made from object result columns.
The sequence

  InitStaticColumn('abc');
  for n := 1 to rcount do
    SetValue('abc', n, rUser1[n]);

will copy column User1 to column abc.
You also can think about to put your  userdata directly into a object
result column. Look at the commands InitColumn, InitStaticColumn,
MakeColumn, MakeStaticColumn, and SetValue.

>thanks again, and if my questions are obviously spelled out in the docs,
>no way will I ever find them.

Just option-doubleclick any keyword in the macro text and you'll get its
description in the online help. This also works for standard NIH commands.
Also, look in the "Help" or "?" Menu.

Example: option-doubleclick on 'MakeNewWindow', and you get the description:

MakeNewWindow('Name')
  Creates a new image window. Use SetNewSize to specify
  the size of the new window.

Norbert

--------------------------------
End of nih-image-d Digest V99 Issue #59
***************************************

From nih-image-request@io.ece.drexel.edu Fri Mar 12 03:17 EST 1999
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Resent-Date: Fri, 12 Mar 1999 03:17:01 -0500 (EST)
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In-Reply-To: 
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Date: Fri, 12 Mar 1999 09:03:36 +0100
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: objects...
Resent-Message-ID: <"4Annz1.0.cM6.rgCws"@io>
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Glen,

In some cases, you have the choice to address things alternatively by
numbers or strings. For example, GetValue('myColumn', 13) is equal to
GetValue(1, 13) if 'myColumn' is the first column. I could think about to
implement this method in more cases. Meanwhile, a work-around could be the
use of indexable strings,  using concat(string, index). Perhaps you could
tell more precisely what you want to index? Is it the command
SwitchToObject(string)?


>Does the Histogram function work with data in User Columns?
>

Histograms of results can only be made from object result columns.
The sequence

  InitStaticColumn('abc');
  for n := 1 to rcount do
    SetValue('abc', n, rUser1[n]);

will copy column User1 to column abc.
You also can think about to put your  userdata directly into a object
result column. Look at the commands InitColumn, InitStaticColumn,
MakeColumn, MakeStaticColumn, and SetValue.

>thanks again, and if my questions are obviously spelled out in the docs,
>no way will I ever find them.

Just option-doubleclick any keyword in the macro text and you'll get its
description in the online help. This also works for standard NIH commands.
Also, look in the "Help" or "?" Menu.

Example: option-doubleclick on 'MakeNewWindow', and you get the description:

MakeNewWindow('Name')
  Creates a new image window. Use SetNewSize to specify
  the size of the new window.

Norbert



From nih-image-request@io.ece.drexel.edu Fri Mar 12 09:56 EST 1999
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Date: Fri, 12 Mar 1999 14:27:17 +0000
From: Stamatis Pagakis <spagaki@nimr.mrc.ac.uk>
Subject: Source for quick-time
In-reply-to: <1A2D68D71B4@rna.bio.mq.edu.au>
To: nih-image@io.ece.drexel.edu
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Does anyone know where I can find the latest version of quick time for the
mac?  Is it free?

Thank you

*-----------------*------------------*----------------------*---------------*

>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <
>Confocal and Image Analysis Laboratory             Tel: +44 (0)181 913 8675 <
>Membrane Biology                                Mobile: 0370 654288         <
>National Institute for Medical Research    Switchboard: 0181 9593666 x2621  <
>The Ridgeway                                   Message: x2219, x2622        <
>Mill Hill, London NW7 1AA                          FAX: +44 (0)181 906 4477 <


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                   NIH-image Mailing List Help 
                   ---------------------------
     


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Archive
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used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
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2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
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From nih-image-d-request@io.ece.drexel.edu Sat Mar 13 05:17 EST 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #60
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 60

Today's Topics:
  Source for quick-time                 [ Stamatis Pagakis <spagaki@nimr.mrc. ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]

------------------------------

Date: Fri, 12 Mar 1999 14:27:17 +0000
From: Stamatis Pagakis <spagaki@nimr.mrc.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Source for quick-time
Message-id: <Pine.SGI.4.10.9903121425130.12216-100000@membo2.nimr.mrc.ac.uk>
Content-type: TEXT/PLAIN; charset=US-ASCII

Does anyone know where I can find the latest version of quick time for the
mac?  Is it free?

Thank you

*-----------------*------------------*----------------------*---------------*

>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <
>Confocal and Image Analysis Laboratory             Tel: +44 (0)181 913 8675 <
>Membrane Biology                                Mobile: 0370 654288         <
>National Institute for Medical Research    Switchboard: 0181 9593666 x2621  <
>The Ridgeway                                   Message: x2219, x2622        <
>Mill Hill, London NW7 1AA                          FAX: +44 (0)181 906 4477 <

------------------------------

Date: Sat, 13 Mar 1999 05:05:01 -0500 (EST)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199903131005.FAA03673@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
                   ---------------------------
     


nih-image-d-request@biomed.drexel.edu  - Aministration for Digest
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     *********************************************************
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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

--------------------------------
End of nih-image-d Digest V99 Issue #60
***************************************

From nih-image-request@io.ece.drexel.edu Sat Mar 13 10:54 EST 1999
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From: Mansoor@nso1.uchc.edu (Mansoor,George)
To: mvivino@yahoo.com (Mark Vivino), nih-image@io.ece.drexel.edu
Message-ID: <1999Mar13.103700.1274.1740154@msgate.uchc.edu>
X-Mailer: Microsoft Mail via PostalUnion/SMTP (v2.2 Build 22006)
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Organization: UConn Health Center, 263 Farmington Ave, Farmington CT, USA
Date: Sat, 13 Mar 1999 10:33:46 -0500
Subject: Re: NIH image for beginners
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I have posted a request before regarding a project that IM doing. Has anyone 
done any work on the best methods to identify a vessel edge? And how to 
automate the measurment of vessels. These are retinal photographs and are in 
rgb color. Manually measurment appears to cause a lot of error. Is there a 
macro to identify the acttula vessel edge?

 ----------
From: Mark Vivino
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH image for beginners
Date: Thursday, March 11, 1999 10:57AM



 ---Dietrich Ruehlmann <druehlmann@prl.pulmonary.ubc.ca> wrote:

> I have recently started writing my own macros for image analysis but
I have
> encountered some basic problems due to my long abstincence from
Pascal (11
> years...).  Hence I wonder if there is a more detailed help manual
on Scion
> Image (I am PC-bound...) especially on the macro language other than
the one
> provided with the program to 'kick-start' me.  So if anybody has
written a tutorial
> or something like this for class use etc. and made it public, I
would greatly
> appreciate the URL for it or the file.

Somewhat dated but still valid (except my email)

http://rsb.info.nih.gov/nih-image/more-docs/InsideImage/inside.html

Mark
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-d-request@io.ece.drexel.edu Sun Mar 14 06:11 EST 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #61
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 61

Today's Topics:
  Re: NIH image for beginners           [ Mansoor@nso1.uchc.edu (Mansoor,Geor ]

------------------------------

Date: Sat, 13 Mar 1999 10:33:46 -0500
From: Mansoor@nso1.uchc.edu (Mansoor,George)
To: mvivino@yahoo.com (Mark Vivino), nih-image@io.ece.drexel.edu
Subject: Re: NIH image for beginners
Message-ID: <1999Mar13.103700.1274.1740154@msgate.uchc.edu>
Content-Type: text/plain; charset="US-ASCII"

I have posted a request before regarding a project that IM doing. Has anyone 
done any work on the best methods to identify a vessel edge? And how to 
automate the measurment of vessels. These are retinal photographs and are in 
rgb color. Manually measurment appears to cause a lot of error. Is there a 
macro to identify the acttula vessel edge?

 ----------
From: Mark Vivino
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH image for beginners
Date: Thursday, March 11, 1999 10:57AM



 ---Dietrich Ruehlmann <druehlmann@prl.pulmonary.ubc.ca> wrote:

> I have recently started writing my own macros for image analysis but
I have
> encountered some basic problems due to my long abstincence from
Pascal (11
> years...).  Hence I wonder if there is a more detailed help manual
on Scion
> Image (I am PC-bound...) especially on the macro language other than
the one
> provided with the program to 'kick-start' me.  So if anybody has
written a tutorial
> or something like this for class use etc. and made it public, I
would greatly
> appreciate the URL for it or the file.

Somewhat dated but still valid (except my email)

http://rsb.info.nih.gov/nih-image/more-docs/InsideImage/inside.html

Mark
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com

--------------------------------
End of nih-image-d Digest V99 Issue #61
***************************************

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Date: Sun, 14 Mar 1999 18:12:39 -0500 (EST)
From: Glenn Holm <KARUZIS@wccf.mit.edu>
Subject: Looking for Pseudocolor lookup tables
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Hi computer imagers,

I am pseudocolorizing some data we have of cellular responses from striatum of 
rats learning a T-maze from Ann Graybiel's tetrode recording project. What I 
am looking for is any "standard" pseudocolor tables used by imagers to colorize
0-255 grey levels into RGB values. 

I can apply a standard spectrum from 0 to 255 
running from magenta (255 0 255 RGB) through blue, cyan, green, yellow to red 
(255 0 0) or start with blue and go to red in a linear way. What this produces 
is colors that are mostly in the middle. What I think imagers must be using 
are tables weighted toward the red and blue, so transitions show up better. I 
can play with my tables in Excel to boost the red and blue ends and then apply 
them using Paint Shop Pro - which I am using for this because it uses palette 
files with ASCII values.

What I was wondering was if you have or know where 
I can find any standard tables, preferably of numerical RGB values used by the 
pros in the field, especially those who colorize biomedical data.

------------------------------------------------------------------
|Glenn Holm                       <mailto:karuzis@wccf.mit.edu>  |
|Graybiel Lab                    (617)253-5780;fax (617)253-1599 |
|M.I.T Dept. of Brain + Cog. Sci.        Cambridge, MA 02139     |
------------------------------------------------------------------


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Date: Mon, 15 Mar 1999 09:06:12 -0700
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From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
Subject: Re: Looking for Pseudocolor lookup tables
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>Hi computer imagers,
>
>I am pseudocolorizing some data we have of cellular responses from
>striatum of
>rats learning a T-maze from Ann Graybiel's tetrode recording project. What I
>am looking for is any "standard" pseudocolor tables used by imagers to
>colorize
>0-255 grey levels into RGB values.
>
>I can apply a standard spectrum from 0 to 255
>running from magenta (255 0 255 RGB) through blue, cyan, green, yellow to red
>(255 0 0) or start with blue and go to red in a linear way. What this
>produces
>is colors that are mostly in the middle. What I think imagers must be using
>are tables weighted toward the red and blue, so transitions show up better. I
>can play with my tables in Excel to boost the red and blue ends and then
>apply
>them using Paint Shop Pro - which I am using for this because it uses palette
>files with ASCII values.
>
>What I was wondering was if you have or know where
>I can find any standard tables, preferably of numerical RGB values used by
>the
>pros in the field, especially those who colorize biomedical data.
>
>------------------------------------------------------------------
>|Glenn Holm                       <mailto:karuzis@wccf.mit.edu>  |
>|Graybiel Lab                    (617)253-5780;fax (617)253-1599 |
>|M.I.T Dept. of Brain + Cog. Sci.        Cambridge, MA 02139     |
>------------------------------------------------------------------

My inclination is to say that the real pros don't colorize their data...
For the rest you are talking presentation here, which totally depends on
the taste of you and your audience. The 'rainbow' rolor table is used a lot
in meteorology, to indicate cold to hot (blue to red),but also
wind-directions, etc., and I like the fire-1 in NIH for elevation/3d
rendering prictures. For the rest it is really up to your own taste.

Arnout



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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 62

Today's Topics:
  Looking for Pseudocolor lookup table  [ Glenn Holm <KARUZIS@wccf.mit.edu> ]
  Re: Looking for Pseudocolor lookup t  [ Arnout Ruifrok <arnout@odin.mdacc.t ]

------------------------------

Date: Sun, 14 Mar 1999 18:12:39 -0500 (EST)
From: Glenn Holm <KARUZIS@wccf.mit.edu>
To: nih-image@io.ece.drexel.edu
Subject: Looking for Pseudocolor lookup tables
Message-id: <01J8TVT4UP788X2R82@wccf.mit.edu>
Content-type: TEXT/PLAIN
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Hi computer imagers,

I am pseudocolorizing some data we have of cellular responses from striatum of 
rats learning a T-maze from Ann Graybiel's tetrode recording project. What I 
am looking for is any "standard" pseudocolor tables used by imagers to colorize
0-255 grey levels into RGB values. 

I can apply a standard spectrum from 0 to 255 
running from magenta (255 0 255 RGB) through blue, cyan, green, yellow to red 
(255 0 0) or start with blue and go to red in a linear way. What this produces 
is colors that are mostly in the middle. What I think imagers must be using 
are tables weighted toward the red and blue, so transitions show up better. I 
can play with my tables in Excel to boost the red and blue ends and then apply 
them using Paint Shop Pro - which I am using for this because it uses palette 
files with ASCII values.

What I was wondering was if you have or know where 
I can find any standard tables, preferably of numerical RGB values used by the 
pros in the field, especially those who colorize biomedical data.

------------------------------------------------------------------
|Glenn Holm                       <mailto:karuzis@wccf.mit.edu>  |
|Graybiel Lab                    (617)253-5780;fax (617)253-1599 |
|M.I.T Dept. of Brain + Cog. Sci.        Cambridge, MA 02139     |
------------------------------------------------------------------

------------------------------

Date: Mon, 15 Mar 1999 09:06:12 -0700
From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Looking for Pseudocolor lookup tables
Message-Id: <v03102800b312df21134e@[143.111.62.105]>
Content-Type: text/plain; charset="us-ascii"

>Hi computer imagers,
>
>I am pseudocolorizing some data we have of cellular responses from
>striatum of
>rats learning a T-maze from Ann Graybiel's tetrode recording project. What I
>am looking for is any "standard" pseudocolor tables used by imagers to
>colorize
>0-255 grey levels into RGB values.
>
>I can apply a standard spectrum from 0 to 255
>running from magenta (255 0 255 RGB) through blue, cyan, green, yellow to red
>(255 0 0) or start with blue and go to red in a linear way. What this
>produces
>is colors that are mostly in the middle. What I think imagers must be using
>are tables weighted toward the red and blue, so transitions show up better. I
>can play with my tables in Excel to boost the red and blue ends and then
>apply
>them using Paint Shop Pro - which I am using for this because it uses palette
>files with ASCII values.
>
>What I was wondering was if you have or know where
>I can find any standard tables, preferably of numerical RGB values used by
>the
>pros in the field, especially those who colorize biomedical data.
>
>------------------------------------------------------------------
>|Glenn Holm                       <mailto:karuzis@wccf.mit.edu>  |
>|Graybiel Lab                    (617)253-5780;fax (617)253-1599 |
>|M.I.T Dept. of Brain + Cog. Sci.        Cambridge, MA 02139     |
>------------------------------------------------------------------

My inclination is to say that the real pros don't colorize their data...
For the rest you are talking presentation here, which totally depends on
the taste of you and your audience. The 'rainbow' rolor table is used a lot
in meteorology, to indicate cold to hot (blue to red),but also
wind-directions, etc., and I like the fire-1 in NIH for elevation/3d
rendering prictures. For the rest it is really up to your own taste.

Arnout

--------------------------------
End of nih-image-d Digest V99 Issue #62
***************************************

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Date: Mon, 15 Mar 1999 09:36:49 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: QuickTime
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You can upgrade to QuickTime 3 for free at:

http://www.apple.com/quicktime/

The QTPro package is $30, which adds some editing and export features.  

Regards,
Glen

Glen MacDonald
   Research Scientist
Hearing Research Laboratories of the
Virginia Merrill Bloedel Hearing Research Center
Box 35-7923
University of Washington
Seattle, WA  98195-7923
(206) 616-4156
glenmac@u.washington.edu



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Date: Mon, 15 Mar 1999 17:57:42 +0000
From: Stamatis Pagakis <spagaki@nimr.mrc.ac.uk>
Subject: Re: QuickTime
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On Mon, 15 Mar 1999, G. Macdonald wrote:

> The QTPro package is $30, which adds some editing and export features.  
> 
Thanks-- I got the standard version but it does not show the movie
continously, which is what I want to do, but it runs through only once.
Do you know if this feature is included in the QTPro package?

Thanks

*-----------------*------------------*----------------------*---------------*
>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <
>Confocal and Image Analysis Laboratory             Tel: +44 (0)181 913 8675 <
>Membrane Biology                                Mobile: 0370 654288         <
>National Institute for Medical Research    Switchboard: 0181 9593666 x2621  <
>The Ridgeway                                   Message: x2219, x2622        <
>Mill Hill, London NW7 1AA                          FAX: +44 (0)181 906 4477 <


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Subject: Re: QuickTime
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Pro has no control over this.  It is in the movie software. If you play a
movie with MoviePlayer, MoviePlay etc. there are options in the menu for
play every frame and loop which sounds like what you want.  Dave

>On Mon, 15 Mar 1999, G. Macdonald wrote:
>
>> The QTPro package is $30, which adds some editing and export features.
>>
>Thanks-- I got the standard version but it does not show the movie
>continously, which is what I want to do, but it runs through only once.
>Do you know if this feature is included in the QTPro package?
>
>Thanks
>
>*-----------------*------------------*----------------------*---------------*
>>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <
>>Confocal and Image Analysis Laboratory             Tel: +44 (0)181 913 8675 <
>>Membrane Biology                                Mobile: 0370 654288         <
>>National Institute for Medical Research    Switchboard: 0181 9593666 x2621  <
>>The Ridgeway                                   Message: x2219, x2622        <
>>Mill Hill, London NW7 1AA                          FAX: +44 (0)181 906 4477 <


Dr. David Knecht
Department of Molecular and Cell Biology
University of Connecticut
75 N. Eagleville Rd.
U-125
Storrs, CT 06269
Knecht@uconnvm.uconn.edu
860-486-2200
860-486-4331 (fax)



From nih-image-request@io.ece.drexel.edu Mon Mar 15 21:15 EST 1999
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Message-ID: <36EDB80A.C03E743E@siso.fo.usp.br>
Date: Mon, 15 Mar 1999 22:46:51 -0300
From: "Ruy G. Jaeger" <rgjaeger@fo.usp.br>
Organization: Faculdade de Odontologia USP
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>From Ruy Jaeger
University of Sao Paulo
Brazil



I am having a problem using NIH Image,  Scion LG-3 board and a shutter
drive.  I have not been able to use
the trigger  capability of LG-3  board.  I am working with image
acquisition of living cells, in order to make
movies of them.  However, this acquisition must be synchronized with a
light shutter.  Thus, each image is acquired at  the
same moment that the shutter opens to allow the light passage.

I unsuccessfully tried this acquisition several times with  Scion
Image.  I checked "external trigger"
in the video control dialog box, and I also checked "trigger each frame"
in the "make a movie" dialog box.

I also tried different macros from user macros directory at NIH web
site, such as fluorescence macro and time-lapse-video macro, with no
success

I am not sure whether this is a software or hardware problem.  What I do
know is that acquisition and make a movie
commands work just fine when external triggering is not checked, so I
assume that there is no connection problem of  the board
and the video camera of my scope.

Is it a hardware problem?   My triggering hardware is a Uniblittz
shutter (with Sync capability) with a T132 shutter controller.  Maybe  I
am connecting the cables to  the wrong switches either in the board or
in the shutter driver.

I connect the shutter's BNC sync output to LG3 trigger cable.  After
that, I connect the BNC output of my camera control
(Dage MTI CCD 72) to any of black and white inputs of Scion LG3 (these
directions are provided by both Uniblitz and Scion)



I look forward to receive any suggestion.

Ruy Jaeger


--
================================================================
Ruy G. Jaeger, DDS, MSD, PhD   School of Dentistry
Av. Prof Lineu Prestes 2227   University of So Paulo
So Paulo SP CEP 05508-900  BRAZIL
Phone  55-11-8187912   FAX  55-11-8187413
e-mail rgjaeger@siso.fo.usp.br
================================================================



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unsubscribe

Get Your Private, Free Email at http://www.hotmail.com


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------------------------------

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nih-image-d Digest				Volume 99 : Issue 63

Today's Topics:
  Re: QuickTime                         [ "G. Macdonald" <glenmac@u.washingto ]
  Re: QuickTime                         [ Stamatis Pagakis <spagaki@nimr.mrc. ]
  Re: QuickTime                         [ David Knecht <knecht@uconnvm.uconn. ]
  Problems with Scion LG3 and Uniblitz  [ "Ruy G. Jaeger" <rgjaeger@fo.usp.br ]
  unsubscribe                           [ "lynn huynh" <supershiny@hotmail.co ]

------------------------------

Date: Mon, 15 Mar 1999 09:36:49 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: QuickTime
Message-ID: <Pine.A41.4.05.9903150922150.133178-100000@homer07.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

You can upgrade to QuickTime 3 for free at:

http://www.apple.com/quicktime/

The QTPro package is $30, which adds some editing and export features.  

Regards,
Glen

Glen MacDonald
   Research Scientist
Hearing Research Laboratories of the
Virginia Merrill Bloedel Hearing Research Center
Box 35-7923
University of Washington
Seattle, WA  98195-7923
(206) 616-4156
glenmac@u.washington.edu

------------------------------

Date: Mon, 15 Mar 1999 17:57:42 +0000
From: Stamatis Pagakis <spagaki@nimr.mrc.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: QuickTime
Message-id: <Pine.SGI.4.10.9903151754540.21307-100000@membo2.nimr.mrc.ac.uk>
Content-type: TEXT/PLAIN; charset=US-ASCII

On Mon, 15 Mar 1999, G. Macdonald wrote:

> The QTPro package is $30, which adds some editing and export features.  
> 
Thanks-- I got the standard version but it does not show the movie
continously, which is what I want to do, but it runs through only once.
Do you know if this feature is included in the QTPro package?

Thanks

*-----------------*------------------*----------------------*---------------*
>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <
>Confocal and Image Analysis Laboratory             Tel: +44 (0)181 913 8675 <
>Membrane Biology                                Mobile: 0370 654288         <
>National Institute for Medical Research    Switchboard: 0181 9593666 x2621  <
>The Ridgeway                                   Message: x2219, x2622        <
>Mill Hill, London NW7 1AA                          FAX: +44 (0)181 906 4477 <

------------------------------

Date: Mon, 15 Mar 1999 14:23:21 -0500
From: David Knecht <knecht@uconnvm.uconn.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: QuickTime
Message-Id: <l03130302b3130e6fae07@[137.99.71.142]>
Content-Type: text/plain; charset="us-ascii"

Pro has no control over this.  It is in the movie software. If you play a
movie with MoviePlayer, MoviePlay etc. there are options in the menu for
play every frame and loop which sounds like what you want.  Dave

>On Mon, 15 Mar 1999, G. Macdonald wrote:
>
>> The QTPro package is $30, which adds some editing and export features.
>>
>Thanks-- I got the standard version but it does not show the movie
>continously, which is what I want to do, but it runs through only once.
>Do you know if this feature is included in the QTPro package?
>
>Thanks
>
>*-----------------*------------------*----------------------*---------------*
>>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <
>>Confocal and Image Analysis Laboratory             Tel: +44 (0)181 913 8675 <
>>Membrane Biology                                Mobile: 0370 654288         <
>>National Institute for Medical Research    Switchboard: 0181 9593666 x2621  <
>>The Ridgeway                                   Message: x2219, x2622        <
>>Mill Hill, London NW7 1AA                          FAX: +44 (0)181 906 4477 <


Dr. David Knecht
Department of Molecular and Cell Biology
University of Connecticut
75 N. Eagleville Rd.
U-125
Storrs, CT 06269
Knecht@uconnvm.uconn.edu
860-486-2200
860-486-4331 (fax)

------------------------------

Date: Mon, 15 Mar 1999 22:46:51 -0300
From: "Ruy G. Jaeger" <rgjaeger@fo.usp.br>
To: NIH Image mail list <nih-image@io.ece.drexel.edu>
Subject: Problems with Scion LG3 and Uniblitz shutter driver
Message-ID: <36EDB80A.C03E743E@siso.fo.usp.br>
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

>From Ruy Jaeger
University of Sao Paulo
Brazil



I am having a problem using NIH Image,  Scion LG-3 board and a shutter
drive.  I have not been able to use
the trigger  capability of LG-3  board.  I am working with image
acquisition of living cells, in order to make
movies of them.  However, this acquisition must be synchronized with a
light shutter.  Thus, each image is acquired at  the
same moment that the shutter opens to allow the light passage.

I unsuccessfully tried this acquisition several times with  Scion
Image.  I checked "external trigger"
in the video control dialog box, and I also checked "trigger each frame"
in the "make a movie" dialog box.

I also tried different macros from user macros directory at NIH web
site, such as fluorescence macro and time-lapse-video macro, with no
success

I am not sure whether this is a software or hardware problem.  What I do
know is that acquisition and make a movie
commands work just fine when external triggering is not checked, so I
assume that there is no connection problem of  the board
and the video camera of my scope.

Is it a hardware problem?   My triggering hardware is a Uniblittz
shutter (with Sync capability) with a T132 shutter controller.  Maybe  I
am connecting the cables to  the wrong switches either in the board or
in the shutter driver.

I connect the shutter's BNC sync output to LG3 trigger cable.  After
that, I connect the BNC output of my camera control
(Dage MTI CCD 72) to any of black and white inputs of Scion LG3 (these
directions are provided by both Uniblitz and Scion)



I look forward to receive any suggestion.

Ruy Jaeger


--
================================================================
Ruy G. Jaeger, DDS, MSD, PhD   School of Dentistry
Av. Prof Lineu Prestes 2227   University of So Paulo
So Paulo SP CEP 05508-900  BRAZIL
Phone  55-11-8187912   FAX  55-11-8187413
e-mail rgjaeger@siso.fo.usp.br
================================================================

------------------------------

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From nih-image-request@io.ece.drexel.edu Tue Mar 16 07:06 EST 1999
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From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: Quicktime looping
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<moovie looping>
>Pro has no control over this.  It is in the movie software. If you play a
>movie with MoviePlayer, MoviePlay etc. there are options in the menu for
>play every frame and loop which sounds like what you want.  Dave

Although it is in the app, it can be switched off by Pro. So with Pro the
movieplayer 3.0 does have a 'loop' menu command.

ard



From nih-image-request@io.ece.drexel.edu Tue Mar 16 17:28 EST 1999
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Date: Tue, 16 Mar 1999 17:13:23 -0500
From: Tong Liu <liut@EM.AGR.CA>
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Subject: Import quicktime in QTCapture.java
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I tried to compile ImageJ plugins (source code is downloaded from "codon.nih.ov") using jdk1.2. It gives complie errors like:
 Class quicktime.app.image.ImagePresenter not found in import
in QTCapture.java

So I think I need a quicktime.class.
Where can I get this quicktime.class?
Thanks.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           


From nih-image-request@io.ece.drexel.edu Tue Mar 16 17:47 EST 1999
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To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: Import quicktime in QTCapture.java
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>I tried to compile ImageJ plugins (source code is downloaded from
>"codon.nih.ov") using jdk1.2. It gives complie errors like:
> Class quicktime.app.image.ImagePresenter not found in import
>in QTCapture.java

The QTCapture plug-in requires QuickTime for Java available from
http://www.apple.com/quicktime/qtjava/.  The plug-in needs a lot more work
so don't expect it to do very much.

-wayne



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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 64

Today's Topics:
  Quicktime looping                     [ Ard Jonker <a.jonker@amc.uva.nl> ]
  Import quicktime in QTCapture.java    [ Tong Liu <liut@EM.AGR.CA> ]
  Re: Import quicktime in QTCapture.ja  [ Wayne Rasband <wayne@codon.nih.gov> ]

------------------------------

Date: Tue, 16 Mar 1999 12:31:24 +0100
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Quicktime looping
Message-Id: <l03130307b313f0eb43fd@[145.117.43.50]>
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<moovie looping>
>Pro has no control over this.  It is in the movie software. If you play a
>movie with MoviePlayer, MoviePlay etc. there are options in the menu for
>play every frame and loop which sounds like what you want.  Dave

Although it is in the app, it can be switched off by Pro. So with Pro the
movieplayer 3.0 does have a 'loop' menu command.

ard

------------------------------

Date: Tue, 16 Mar 1999 17:13:23 -0500
From: Tong Liu <liut@EM.AGR.CA>
To: nih-image@io.ece.drexel.edu
Subject: Import quicktime in QTCapture.java
Message-Id: <s6ee914f.017@EM.AGR.CA>
Content-Type: text/plain
Content-Disposition: inline

I tried to compile ImageJ plugins (source code is downloaded from "codon.nih.ov") using jdk1.2. It gives complie errors like:
 Class quicktime.app.image.ImagePresenter not found in import
in QTCapture.java

So I think I need a quicktime.class.
Where can I get this quicktime.class?
Thanks.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           

------------------------------

Date: Tue, 16 Mar 1999 18:47:02 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Import quicktime in QTCapture.java
Message-Id: <v03007800b3148e4cd630@[128.231.99.220]>
Content-Type: text/plain; charset="us-ascii"

>I tried to compile ImageJ plugins (source code is downloaded from
>"codon.nih.ov") using jdk1.2. It gives complie errors like:
> Class quicktime.app.image.ImagePresenter not found in import
>in QTCapture.java

The QTCapture plug-in requires QuickTime for Java available from
http://www.apple.com/quicktime/qtjava/.  The plug-in needs a lot more work
so don't expect it to do very much.

-wayne

--------------------------------
End of nih-image-d Digest V99 Issue #64
***************************************

From nih-image-request@io.ece.drexel.edu Wed Mar 17 18:40 EST 1999
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Date: Wed, 17 Mar 1999 16:48:12 -0500
From: Janet Szczesny <szczesny@umich.edu>
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 I was wondering if anyone knew of an image analysis program, commercial
or not, that allows for a 3-D reconstruction of a subject that can be
viewed on the computer monitor as a 3-D image.
In my case, the subject is a piece of tissue that has been serial
sectioned and I would like to measure a structure within that piece of
tissue.

Thanks for any help you can provide!   Janet Szczesny


From nih-image-request@io.ece.drexel.edu Wed Mar 17 18:43 EST 1999
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Susanne Richardson, M.Sc
Correct-o-Text
www.correctotext.qc.ca
(418)-684-9080



From nih-image-request@io.ece.drexel.edu Wed Mar 17 19:12 EST 1999
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Dear Imagineers,
I've checked all the documentation and maybe I've missed it but:
Is there an upper limit of RAM that NIH Image can address?  

Before I go out and spend a bunch on RAM I thought it might be prudent to ask!

Jeff Linn


From nih-image-request@io.ece.drexel.edu Wed Mar 17 20:11 EST 1999
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From: g2803kmaxs@umbsky.cc.umb.edu
Date: Wed, 17 Mar 1999 19:59:15 -0500
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Hi,

I am a masters student at the University of South Carolina working on the
morphological analysis of hybridization between two species of Thalassoma (a
marine fish).  I have about 43 pictures scanned onto my computer and am trying
to use NIH Imaging to quantitatively analyze the color patterns on each
picture.  The purpose of this analysis is to construct a phylogentic tree based
on coloration and color patterns and see if it matches the molecular tree I
am in the process of constructing.  I am unable to open/import my images of the
fish into the imaging program.  Although the picture will sometimes open in the
imaging program, it is about 100 times larger than the original photo.  
If there is any way I can do this analysis with the NIH Imaging system, please let me know
where I can find instructions.  If it cannot be used, do you know of another
computer program that may be useful?

Thank you very much for any information.
Kimberlee Maxson
G2803kmaxs@umbsky.cc.umb.edu
 


From nih-image-request@io.ece.drexel.edu Wed Mar 17 22:14 EST 1999
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Date: Wed, 17 Mar 1999 22:07:20 -0500
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Perhaps I'm missing something in the manual but is there no way to
reduce the size of an image on the monitor to less than 1:1?  If one
needs to obtain a  line profile from an image of, say, 3000 pixels wide,
how does one get the image reduced to fit on the screen?  Zoom seems to
work in the positive mode of 1:2, 1:4, 1:16, etc. magnifications but not
the negative to yield 2:1, 4:1 16:1 reductions.


From nih-image-request@io.ece.drexel.edu Wed Mar 17 22:44 EST 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: jtwilley@sprynet.com, nih-image@io.ece.drexel.edu
Date:          Thu, 18 Mar 1999 14:37:27 +1100
Subject:       Reducing the Displayed Size of an Image
Priority: normal
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>Date: Wed, 17 Mar 1999 22:07:20 -0500
>From: John Twilley <jtwilley@sprynet.com>
>X-Mailer: Mozilla 4.04 [en] (Win95; U)
>MIME-Version: 1.0
>To: nih-image@io.ece.drexel.edu
>Subject: Reducing the Displayed Size of an Image
>
>Perhaps I'm missing something in the manual but is there no way to
>reduce the size of an image on the monitor to less than 1:1?  If one
>needs to obtain a  line profile from an image of, say, 3000 pixels wide,
>how does one get the image reduced to fit on the screen?  Zoom seems to
>work in the positive mode of 1:2, 1:4, 1:16, etc. magnifications but not
>the negative to yield 2:1, 4:1 16:1 reductions.
>
John, 
"scale-to-fit-window( options menu will do just that.

However, if you want accurate selections with large or zoomed images, be 
aware that you can alternate scroll(hand) and selection tools extending an 
existing straight line selection from either end or an existing rectanular 
selection from the bottom left corner so that one end of the selection may 
be well off screen to cover the 3000 pixels.

This can be made more convenient than by toolbar menu by using simple 
single key macros to invoke the selectTool command.

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


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To: szczesny@umich.edu, nih-image@io.ece.drexel.edu
Date:          Thu, 18 Mar 1999 14:51:57 +1100
Subject:       Re: 3-D Reconstruction
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>Date: Wed, 17 Mar 1999 16:48:12 -0500
>From: Janet Szczesny <szczesny@umich.edu>
>To: nih-image@io.ece.drexel.edu
>CC: nih-image-d@io.ece.drexel.edu
>Subject: 3-D Reconstruction
>
> I was wondering if anyone knew of an image analysis program, commercial
>or not, that allows for a 3-D reconstruction of a subject that can be
>viewed on the computer monitor as a 3-D image.
>In my case, the subject is a piece of tissue that has been serial
>sectioned and I would like to measure a structure within that piece of
>tissue.
>
>Thanks for any help you can provide!   Janet Szczesny

NIH-Image can do quite a good job via the "project" in Stacks menu.

Better still, Object-Image, an extention of NIH-Image by Norbert Vischer is 
available via http://simon.bio.uva.nl/object-image.html. This will allow 
export of sets of outlines as Rotator format ascii text files of coords.
With Object-Image & Rotator you can quickly get 3D reconstruction Rotation 
displays.

With tissue sections it is important to have reference threads imbedded in 
the tissue (or some other method) to being able to properly register 
successive sections.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Wed Mar 17 23:07 EST 1999
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Organization:  Dept. of Biological Sciences
To: g2803kmaxs@umbsky.cc.umb.edu, nih-image@io.ece.drexel.edu
Date:          Thu, 18 Mar 1999 15:01:04 +1100
Subject:       Re: Analysis of Fish
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>	Wed, 17 Mar 1999 20:09:17 -0500 (EST)
>Resent-Date: Wed, 17 Mar 1999 20:09:17 -0500 (EST)
>From: g2803kmaxs@umbsky.cc.umb.edu
>Date: Wed, 17 Mar 1999 19:59:15 -0500
>To: NIH-IMAGE@io.ece.drexel.edu
>Message-ID: <009D5439.18F5BD40.902@umbsky.cc.umb.edu>
>Subject: Analysis of Fish
>
>Hi,
>
>I am a masters student at the University of South Carolina working on the
>morphological analysis of hybridization between two species of Thalassoma 
>(a
>marine fish).  I have about 43 pictures scanned onto my computer and am 
>trying
>to use NIH Imaging to quantitatively analyze the color patterns on each
>picture.  The purpose of this analysis is to construct a phylogentic tree 
>based
>on coloration and color patterns and see if it matches the molecular tree 
>I
>am in the process of constructing.  I am unable to open/import my images 
>of the
>fish into the imaging program.  Although the picture will sometimes open 
>in the
>imaging program, it is about 100 times larger than the original photo.  
>If there is any way I can do this analysis with the NIH Imaging system, 
>please let me know
>where I can find instructions.  If it cannot be used, do you know of 
>another
>computer program that may be useful?
>
>Thank you very much for any information.
>Kimberlee Maxson
>G2803kmaxs@umbsky.cc.umb.edu

You apparently scanned your images at too high a resolution. 
If your file format is tiff and you can allocate sufficient memory to 
NIH-Image (by changeing memory allocation via Finder(Get 
Information(preferred size) you should be able to read image and then scale 
down using "scale&rotate" in edit menu.
Alternatively you can rescan at a lower resolution.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Wed Mar 17 23:24 EST 1999
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>From: JLinn24538@aol.com
>Message-ID: <8193d4da.36f03fc8@aol.com>
>Date: Wed, 17 Mar 1999 18:50:32 EST
>To: nih-image@io.ece.drexel.edu
>Subject: Maximum Memory for NIH Image
>
>Dear Imagineers,
>I've checked all the documentation and maybe I've missed it but:
>Is there an upper limit of RAM that NIH Image can address?  
>
>Before I go out and spend a bunch on RAM I thought it might be prudent to 
>ask!
>
>Jeff Linn
>

166 MB allocated certainly works.
It is my understanding that 512MB would work but I haven't tried it.
256 PAL frames 768x512 is < 100MB,
so I am not sure you would want to go much over 166 MB in practice?

You could test by using virtual memory if you really wanted.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Thu Mar 18 03:41 EST 1999
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From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: 3-D Reconstruction
Date: Thu, 18 Mar 1999 09:29:01 +0100
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Hi!

I have used NIH-Image in order to make 3D reconstructions of plant
cells. 


Gary.


>-----Original Message-----
>From:	Janet Szczesny [SMTP:szczesny@umich.edu]
>Sent:	17. mars 1999 22:48
>To:	nih-image@io.ece.drexel.edu
>Cc:	nih-image-d@io.ece.drexel.edu
>Subject:	3-D Reconstruction
>
> I was wondering if anyone knew of an image analysis program, commercial
>or not, that allows for a 3-D reconstruction of a subject that can be
>viewed on the computer monitor as a 3-D image.
>In my case, the subject is a piece of tissue that has been serial
>sectioned and I would like to measure a structure within that piece of
>tissue.
>
>Thanks for any help you can provide!   Janet Szczesny
>


From nih-image-request@io.ece.drexel.edu Thu Mar 18 05:10 EST 1999
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From: Gary Chinga <gary.chinga@pfi.no>
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Subject: watershed...
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Hei!

I am trying to separate particles on an image. I know we can use the
Watershed method and I have the following procedure: Make a distance
image by summation of subsequent erosions of the original binary image.
Invert the final image (black particles in white background). But by
using the watershed rutine the image disappear and if I not invert the
image I get a separation of the background.

My question is: Can I use the watershed on distance images or I only
have to use binary  images. Any suggestions?

Gary.


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unsubscribe


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Date: Thu, 18 Mar 1999 11:58:08 +0000
From: Sven Pfeiffer <spfeiff@nimr.mrc.ac.uk>
Subject: Undo
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Dear All,

   the question I have concerns the macro command 'Undo'. After drawing a
line into a stack slice with MoveTo and LineTo in a called procedure, I
can't use Undo in the macro body to get rid of this line again. Is there any
solution to this problem ?

Thank's for all the help

Sven

*****************************************************
The National Institute for Medical Research
Division of Mammalian Development
The Ridgeway, Mill Hill
London, NW7 1AA

Tel: +44(0)181 959 3666 ext.2017
Fax: +44(0)181 913 8543
*****************************************************


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unsubscribe nih-image


From nih-image-request@io.ece.drexel.edu Thu Mar 18 09:53 EST 1999
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Subject: Unsubscribing procedure??!!
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Can someone tell me the correct procedure for unsubscribing to this list,
including the correct email address to do so?

Thanks very much

BILL MASON


From nih-image-d-request@io.ece.drexel.edu Thu Mar 18 09:55 EST 1999
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Subject: nih-image-d Digest V99 #65
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 65

Today's Topics:
  3-D Reconstruction                    [ Janet Szczesny <szczesny@umich.edu> ]
  unsubscribe                           [ Susanne <g1rrtrem@drs.crchul.ulaval ]
  Maximum Memory for NIH Image          [ JLinn24538@aol.com ]
  Analysis of Fish                      [ g2803kmaxs@umbsky.cc.umb.edu ]
  Reducing the Displayed Size of an Im  [ John Twilley <jtwilley@sprynet.com> ]
  Reducing the Displayed Size of an Im  [ GJOSS@rna.bio.mq.edu.au ]
  Re: 3-D Reconstruction                [ GJOSS@rna.bio.mq.edu.au ]
  Re: Analysis of Fish                  [ GJOSS@rna.bio.mq.edu.au ]
  Re: Maximum Memory for NIH Image      [ GJOSS@rna.bio.mq.edu.au ]
  RE: 3-D Reconstruction                [ Gary Chinga <gary.chinga@pfi.no> ]
  watershed...                          [ Gary Chinga <gary.chinga@pfi.no> ]
  Unidentified subject!                 [ Bill Mason <wtm@lsr.co.uk> ]
  Undo                                  [ Sven Pfeiffer <spfeiff@nimr.mrc.ac. ]
  Unidentified subject!                 [ Bill Mason <wtm@lsr.co.uk> ]
  Unsubscribing procedure??!!           [ Bill Mason <wtm@lsr.co.uk> ]

------------------------------

Date: Wed, 17 Mar 1999 16:48:12 -0500
From: Janet Szczesny <szczesny@umich.edu>
To: nih-image@io.ece.drexel.edu
CC: nih-image-d@io.ece.drexel.edu
Subject: 3-D Reconstruction
Message-ID: <36F0231B.465E7E98@umich.edu>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

 I was wondering if anyone knew of an image analysis program, commercial
or not, that allows for a 3-D reconstruction of a subject that can be
viewed on the computer monitor as a 3-D image.
In my case, the subject is a piece of tissue that has been serial
sectioned and I would like to measure a structure within that piece of
tissue.

Thanks for any help you can provide!   Janet Szczesny

------------------------------

Date: Wed, 17 Mar 1999 05:56:15 -0500
From: Susanne <g1rrtrem@drs.crchul.ulaval.ca>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <v04003a00b2e477bb5d33@[205.205.174.215]>
Content-Type: text/plain; charset="us-ascii"

Susanne Richardson, M.Sc
Correct-o-Text
www.correctotext.qc.ca
(418)-684-9080

------------------------------

Date: Wed, 17 Mar 1999 18:50:32 EST
From: JLinn24538@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Maximum Memory for NIH Image
Message-ID: <8193d4da.36f03fc8@aol.com>
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Dear Imagineers,
I've checked all the documentation and maybe I've missed it but:
Is there an upper limit of RAM that NIH Image can address?  

Before I go out and spend a bunch on RAM I thought it might be prudent to ask!

Jeff Linn

------------------------------

Date: Wed, 17 Mar 1999 19:59:15 -0500
From: g2803kmaxs@umbsky.cc.umb.edu
To: NIH-IMAGE@io.ece.drexel.edu
Subject: Analysis of Fish
Message-ID: <009D5439.18F5BD40.902@umbsky.cc.umb.edu>

Hi,

I am a masters student at the University of South Carolina working on the
morphological analysis of hybridization between two species of Thalassoma (a
marine fish).  I have about 43 pictures scanned onto my computer and am trying
to use NIH Imaging to quantitatively analyze the color patterns on each
picture.  The purpose of this analysis is to construct a phylogentic tree based
on coloration and color patterns and see if it matches the molecular tree I
am in the process of constructing.  I am unable to open/import my images of the
fish into the imaging program.  Although the picture will sometimes open in the
imaging program, it is about 100 times larger than the original photo.  
If there is any way I can do this analysis with the NIH Imaging system, please let me know
where I can find instructions.  If it cannot be used, do you know of another
computer program that may be useful?

Thank you very much for any information.
Kimberlee Maxson
G2803kmaxs@umbsky.cc.umb.edu
 

------------------------------

Date: Wed, 17 Mar 1999 22:07:20 -0500
From: John Twilley <jtwilley@sprynet.com>
To: nih-image@io.ece.drexel.edu
Subject: Reducing the Displayed Size of an Image
Message-ID: <36F06DE8.80FF75AE@sprynet.com>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Perhaps I'm missing something in the manual but is there no way to
reduce the size of an image on the monitor to less than 1:1?  If one
needs to obtain a  line profile from an image of, say, 3000 pixels wide,
how does one get the image reduced to fit on the screen?  Zoom seems to
work in the positive mode of 1:2, 1:4, 1:16, etc. magnifications but not
the negative to yield 2:1, 4:1 16:1 reductions.

------------------------------

Date:          Thu, 18 Mar 1999 14:37:27 +1100
From: GJOSS@rna.bio.mq.edu.au
To: jtwilley@sprynet.com, nih-image@io.ece.drexel.edu
Subject:       Reducing the Displayed Size of an Image
Message-ID: <2375BF563B2@rna.bio.mq.edu.au>

>Date: Wed, 17 Mar 1999 22:07:20 -0500
>From: John Twilley <jtwilley@sprynet.com>
>X-Mailer: Mozilla 4.04 [en] (Win95; U)
>MIME-Version: 1.0
>To: nih-image@io.ece.drexel.edu
>Subject: Reducing the Displayed Size of an Image
>
>Perhaps I'm missing something in the manual but is there no way to
>reduce the size of an image on the monitor to less than 1:1?  If one
>needs to obtain a  line profile from an image of, say, 3000 pixels wide,
>how does one get the image reduced to fit on the screen?  Zoom seems to
>work in the positive mode of 1:2, 1:4, 1:16, etc. magnifications but not
>the negative to yield 2:1, 4:1 16:1 reductions.
>
John, 
"scale-to-fit-window( options menu will do just that.

However, if you want accurate selections with large or zoomed images, be 
aware that you can alternate scroll(hand) and selection tools extending an 
existing straight line selection from either end or an existing rectanular 
selection from the bottom left corner so that one end of the selection may 
be well off screen to cover the 3000 pixels.

This can be made more convenient than by toolbar menu by using simple 
single key macros to invoke the selectTool command.

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date:          Thu, 18 Mar 1999 14:51:57 +1100
From: GJOSS@rna.bio.mq.edu.au
To: szczesny@umich.edu, nih-image@io.ece.drexel.edu
Subject:       Re: 3-D Reconstruction
Message-ID: <237998B29B8@rna.bio.mq.edu.au>

>Date: Wed, 17 Mar 1999 16:48:12 -0500
>From: Janet Szczesny <szczesny@umich.edu>
>To: nih-image@io.ece.drexel.edu
>CC: nih-image-d@io.ece.drexel.edu
>Subject: 3-D Reconstruction
>
> I was wondering if anyone knew of an image analysis program, commercial
>or not, that allows for a 3-D reconstruction of a subject that can be
>viewed on the computer monitor as a 3-D image.
>In my case, the subject is a piece of tissue that has been serial
>sectioned and I would like to measure a structure within that piece of
>tissue.
>
>Thanks for any help you can provide!   Janet Szczesny

NIH-Image can do quite a good job via the "project" in Stacks menu.

Better still, Object-Image, an extention of NIH-Image by Norbert Vischer is 
available via http://simon.bio.uva.nl/object-image.html. This will allow 
export of sets of outlines as Rotator format ascii text files of coords.
With Object-Image & Rotator you can quickly get 3D reconstruction Rotation 
displays.

With tissue sections it is important to have reference threads imbedded in 
the tissue (or some other method) to being able to properly register 
successive sections.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date:          Thu, 18 Mar 1999 15:01:04 +1100
From: GJOSS@rna.bio.mq.edu.au
To: g2803kmaxs@umbsky.cc.umb.edu, nih-image@io.ece.drexel.edu
Subject:       Re: Analysis of Fish
Message-ID: <237C0BD26A5@rna.bio.mq.edu.au>

>	Wed, 17 Mar 1999 20:09:17 -0500 (EST)
>Resent-Date: Wed, 17 Mar 1999 20:09:17 -0500 (EST)
>From: g2803kmaxs@umbsky.cc.umb.edu
>Date: Wed, 17 Mar 1999 19:59:15 -0500
>To: NIH-IMAGE@io.ece.drexel.edu
>Message-ID: <009D5439.18F5BD40.902@umbsky.cc.umb.edu>
>Subject: Analysis of Fish
>
>Hi,
>
>I am a masters student at the University of South Carolina working on the
>morphological analysis of hybridization between two species of Thalassoma 
>(a
>marine fish).  I have about 43 pictures scanned onto my computer and am 
>trying
>to use NIH Imaging to quantitatively analyze the color patterns on each
>picture.  The purpose of this analysis is to construct a phylogentic tree 
>based
>on coloration and color patterns and see if it matches the molecular tree 
>I
>am in the process of constructing.  I am unable to open/import my images 
>of the
>fish into the imaging program.  Although the picture will sometimes open 
>in the
>imaging program, it is about 100 times larger than the original photo.  
>If there is any way I can do this analysis with the NIH Imaging system, 
>please let me know
>where I can find instructions.  If it cannot be used, do you know of 
>another
>computer program that may be useful?
>
>Thank you very much for any information.
>Kimberlee Maxson
>G2803kmaxs@umbsky.cc.umb.edu

You apparently scanned your images at too high a resolution. 
If your file format is tiff and you can allocate sufficient memory to 
NIH-Image (by changeing memory allocation via Finder(Get 
Information(preferred size) you should be able to read image and then scale 
down using "scale&rotate" in edit menu.
Alternatively you can rescan at a lower resolution.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date:          Thu, 18 Mar 1999 15:17:56 +1100
From: GJOSS@rna.bio.mq.edu.au
To: JLinn24538@aol.com, nih-image@io.ece.drexel.edu
Subject:       Re: Maximum Memory for NIH Image
Message-ID: <238088F3536@rna.bio.mq.edu.au>

>From: JLinn24538@aol.com
>Message-ID: <8193d4da.36f03fc8@aol.com>
>Date: Wed, 17 Mar 1999 18:50:32 EST
>To: nih-image@io.ece.drexel.edu
>Subject: Maximum Memory for NIH Image
>
>Dear Imagineers,
>I've checked all the documentation and maybe I've missed it but:
>Is there an upper limit of RAM that NIH Image can address?  
>
>Before I go out and spend a bunch on RAM I thought it might be prudent to 
>ask!
>
>Jeff Linn
>

166 MB allocated certainly works.
It is my understanding that 512MB would work but I haven't tried it.
256 PAL frames 768x512 is < 100MB,
so I am not sure you would want to go much over 166 MB in practice?

You could test by using virtual memory if you really wanted.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Thu, 18 Mar 1999 09:29:01 +0100
From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: 3-D Reconstruction
Message-ID: <c=NO%a=_%p=pfi%l=PFINT1-990318082901Z-2742@pfint1.pfi.no>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

Hi!

I have used NIH-Image in order to make 3D reconstructions of plant
cells. 


Gary.


>-----Original Message-----
>From:	Janet Szczesny [SMTP:szczesny@umich.edu]
>Sent:	17. mars 1999 22:48
>To:	nih-image@io.ece.drexel.edu
>Cc:	nih-image-d@io.ece.drexel.edu
>Subject:	3-D Reconstruction
>
> I was wondering if anyone knew of an image analysis program, commercial
>or not, that allows for a 3-D reconstruction of a subject that can be
>viewed on the computer monitor as a 3-D image.
>In my case, the subject is a piece of tissue that has been serial
>sectioned and I would like to measure a structure within that piece of
>tissue.
>
>Thanks for any help you can provide!   Janet Szczesny
>

------------------------------

Date: Thu, 18 Mar 1999 10:47:29 +0100
From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: watershed...
Message-ID: <c=NO%a=_%p=pfi%l=PFINT1-990318094729Z-2759@pfint1.pfi.no>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

Hei!

I am trying to separate particles on an image. I know we can use the
Watershed method and I have the following procedure: Make a distance
image by summation of subsequent erosions of the original binary image.
Invert the final image (black particles in white background). But by
using the watershed rutine the image disappear and if I not invert the
image I get a separation of the background.

My question is: Can I use the watershed on distance images or I only
have to use binary  images. Any suggestions?

Gary.

------------------------------

Date: Thu, 18 Mar 1999 10:31:36 +0000
From: Bill Mason <wtm@lsr.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <3.0.32.19990318103131.006af15c@mail-server>
Content-Type: text/plain; charset="us-ascii"

unsubscribe

------------------------------

Date: Thu, 18 Mar 1999 11:58:08 +0000
From: Sven Pfeiffer <spfeiff@nimr.mrc.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Undo
Message-id: <0F8S002N5HDVQ0@ns2.nimr.mrc.ac.uk>
Content-type: text/plain; charset=ISO-8859-1
Content-transfer-encoding: 7bit

Dear All,

   the question I have concerns the macro command 'Undo'. After drawing a
line into a stack slice with MoveTo and LineTo in a called procedure, I
can't use Undo in the macro body to get rid of this line again. Is there any
solution to this problem ?

Thank's for all the help

Sven

*****************************************************
The National Institute for Medical Research
Division of Mammalian Development
The Ridgeway, Mill Hill
London, NW7 1AA

Tel: +44(0)181 959 3666 ext.2017
Fax: +44(0)181 913 8543
*****************************************************

------------------------------

Date: Thu, 18 Mar 1999 11:59:56 +0000
From: Bill Mason <wtm@lsr.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <3.0.32.19990318115952.009b8458@mail-server>
Content-Type: text/plain; charset="us-ascii"

unsubscribe nih-image

------------------------------

Date: Thu, 18 Mar 1999 14:29:48 +0000
From: Bill Mason <wtm@lsr.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Unsubscribing procedure??!!
Message-Id: <3.0.32.19990318142942.006a5b80@mail-server>
Content-Type: text/plain; charset="us-ascii"

Can someone tell me the correct procedure for unsubscribing to this list,
including the correct email address to do so?

Thanks very much

BILL MASON

--------------------------------
End of nih-image-d Digest V99 Issue #65
***************************************

From nih-image-request@io.ece.drexel.edu Thu Mar 18 10:19 EST 1999
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Date: Thu, 18 Mar 1999 08:55:00 -0700
To: nih-image@io.ece.drexel.edu
From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
Subject: Re: watershed...
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>Hei!
>
>I am trying to separate particles on an image. I know we can use the
>Watershed method and I have the following procedure: Make a distance
>image by summation of subsequent erosions of the original binary image.
>Invert the final image (black particles in white background). But by
>using the watershed rutine the image disappear and if I not invert the
>image I get a separation of the background.
>
>My question is: Can I use the watershed on distance images or I only
>have to use binary  images. Any suggestions?
>
>Gary.

 Using a routine like you use (repeated erosion) will give you a
'chessboard' distance, not a euclidian distance, wich is closer to the
physical distance. So if you want to measure a distance, you better use
'EDM'. For watershed segmentation you have to start with a binary image.
The watershed routine will use euclidian mapping to grow your objects from
the ultimate points, keeping the objects separated at the 'watershed'. So
in short: you have to use a binary image, and do the watershed operation on
that image.

Arnout



From nih-image-request@io.ece.drexel.edu Thu Mar 18 10:35 EST 1999
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Date: Thu, 18 Mar 1999 16:09:23 +0100
From: Thomas Ehmer <thomas.ehmer@urz.uni-heidelberg.de>
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The object image - expansion seems to fit also my problems, but we don't
use macintosh
is this tool also available for WinNT / Win95 ?

thanks
Thomas Ehmer


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unsubscribe nih-image


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From: Jan Lund <JANL@lundbeck.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Unsubscribing procedure??!!
Date: Thu, 18 Mar 1999 16:11:48 +0100
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Hi Bill.

U R welcome.

The address is : nih-image@io.ece.drexel.edu


rgds

Jan
                  ~"""~
                ( @ @ )
---------oOO----(_)----OOo-------------
|                  Jan Lund                         |
|   Elektronik og PC supporter     |
|     Farmakologisk forskning       |
|                                                             |
|       JANL@Lundbeck.Com        |
|         36 30 13 11 Lok. 2374          |
-----------------------------------------------


> ----------
> From: 	Bill Mason[SMTP:wtm@lsr.co.uk]
> Reply To: 	nih-image@io.ece.drexel.edu
> Sent: 	18. marts 1999 15:29
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	Unsubscribing procedure??!!
> 
> Can someone tell me the correct procedure for unsubscribing to this list,
> including the correct email address to do so?
> 
> Thanks very much
> 
> BILL MASON
> 


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subscribe nih-image

-----------------------------------------------------------------
Dr.Tatiana S. Karpova
Research Associate
Department of Cell Biology and Physiology
Washington Univ School of Medicine
Box 8228, 660 S Euclid Ave. St. Louis, MO  63110

Tel: (314) 362-4606
Fax:(314)362 74 63
tkarpova@cellbio.wustl.edu
World Wide Web site: http://www.cooperlab.wustl.edu/

for FedEx/UPS Shipping:
Dept. of Cell Biology
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St. Louis, MO 63110



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From nih-image-request@io.ece.drexel.edu Thu Mar 18 11:51 EST 1999
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Unsubscribe

*************************************
Naguib Mechawar
Sc. neurologiques
Universit de Montral
*************************************



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The following instructions were copied from the "ADMIN: list commands". Hope
this helps.

Unsubscribe
-----------
To unsubscribe to the list, send E-mail to
nih-image-request@biomed.drexel.edu.
The Subject of the message should contain "unsubscribe".

As in:  To: nih-image-request@biomed.drexel.edu
  Subject: unsubscribe

--

Ken Baker M.Sc.
Microscopy, Imaging, Analysis
4943, Fourth Line Erin
RR 2
Acton, Ontario
Canada
L7J-2L8

--

KWB@bserv.com
519-853-4787



----------
>From: Bill Mason <wtm@lsr.co.uk>
>To: nih-image@io.ece.drexel.edu
>Subject: unsubscribe nih-image
>Date: Thu, Mar 18, 1999, 10:57 AM
>

>
> 


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unsubscribe please


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NIH Image versions at least since 1.60 will work with up to 650 Mb,system 
7.5.5, 7.6 and 8.1 on a 9600/200MP. We've
been merging confocal z-series images into z-series montages and then
projecting rotations of them.  

Regards,
Glen


Glen MacDonald
   Research Scientist
Hearing Research Laboratories of the
Virginia Merrill Bloedel Hearing Research Center
Box 35-7923
University of Washington
Seattle, WA  98195-7923
(206) 616-4156
glenmac@u.washington.edu

//The box said "Requires Windows95, or better." so I bought a Macintosh.//



From nih-image-request@io.ece.drexel.edu Thu Mar 18 17:42 EST 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: thomas.ehmer@urz.uni-heidelberg.de, nih-image@io.ece.drexel.edu
Date:          Fri, 19 Mar 1999 9:26:32 +1100
Subject:       Re: 3d- reconcstruction.
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>Date: Thu, 18 Mar 1999 16:09:23 +0100
>From: Thomas Ehmer <thomas.ehmer@urz.uni-heidelberg.de>
>To: nih-image@io.ece.drexel.edu
>Subject: 3d- reconcstruction.
>
>The object image - expansion seems to fit also my problems, but we don't
>use macintosh
>is this tool also available for WinNT / Win95 ?
>
>thanks
>Thomas Ehmer
>
I am afraid not; unless you wanted to get imvolved with Mac emulators.

However the NIH-Image stack facilities are the basis of 3D reconstruction 
and the "project" facilities are quite useful.

I have used Scions Win version of Image quite effectively for student 
introductory training in imaging but cant recall how well "project" 
facilities are implemented in that version.

Certainly worth a try if you are stuck with Win as Scion-Image is freely 
available.

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


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Date: Thu, 18 Mar 1999 14:52:33 -0800 (PST)
From: Lesley Weston <lesley@interchange.ubc.ca>
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For some applications, such as time-lapse movies, where you need to manipulate
huge stacks,you want all the memory you can get. We bought all the RAM we could
afford (164M) and used virtual memory to push it up to 600M. NIH seems to be
able to handle this much. Hope this helps.

Lesley Weston.



On Thu, 18 Mar 1999 GJOSS@rna.bio.mq.edu.au wrote:

> >From: JLinn24538@aol.com
> >Message-ID: <8193d4da.36f03fc8@aol.com>
> >Date: Wed, 17 Mar 1999 18:50:32 EST
> >To: nih-image@io.ece.drexel.edu
> >Subject: Maximum Memory for NIH Image
> >
> >Dear Imagineers,
> >I've checked all the documentation and maybe I've missed it but:
> >Is there an upper limit of RAM that NIH Image can address?  
> >
> >Before I go out and spend a bunch on RAM I thought it might be prudent to 
> >ask!
> >
> >Jeff Linn
> >
> 
> 166 MB allocated certainly works.
> It is my understanding that 512MB would work but I haven't tried it.
> 256 PAL frames 768x512 is < 100MB,
> so I am not sure you would want to go much over 166 MB in practice?
> 
> You could test by using virtual memory if you really wanted.
> Greg Joss,
> School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
> Macquarie University,          Email gjoss@rna.bio.mq.edu.au
> North Ryde, (Sydney,) NSW 2109, Australia
> 
> 


From nih-image-request@io.ece.drexel.edu Thu Mar 18 18:11 EST 1999
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To: spfeiff@nimr.mrc.ac.uk, nih-image@io.ece.drexel.edu
Date:          Fri, 19 Mar 1999 9:56:08 +1100
Subject:       Re: Undo (bug in NIH & Object Image)
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>Date: Thu, 18 Mar 1999 11:58:08 +0000
>From: Sven Pfeiffer <spfeiff@nimr.mrc.ac.uk>
>Subject: Undo
>To: nih-image@io.ece.drexel.edu
>
>Dear All,
>
>   the question I have concerns the macro command 'Undo'. After drawing a
>line into a stack slice with MoveTo and LineTo in a called procedure, I
>can't use Undo in the macro body to get rid of this line again. Is there 
>any
>solution to this problem ?
>
>Thank's for all the help
>
>Sven
>
>*****************************************************
>The National Institute for Medical Research
>Division of Mammalian Development
>The Ridgeway, Mill Hill
>London, NW7 1AA
>
>Tel: +44(0)181 959 3666 ext.2017
>Fax: +44(0)181 913 8543
>*****************************************************
>

Sven,
There is some peculiar bug here.

Either construction:

macro'test/0';begin moveto(0,0);lineTo(256,256);undo;end

or

procedure line;begin moveto(0,0);lineTo(256,256);end

macro'test/0';begin line;undo;end

behave peculiarly.

There seems to be some "first time" bug that occurs here.
If an image or stack is created and the macro loaded; first invokations 
leave the line on the image or slice. After repeated invokation with manual 
clear of image, the undo then takes effect correctly in followon 
invokations until you quit and initialise. Then the initial malfunction is 
present again.

Problem occurs with both in NIH & Object Image.

Drawing and removing a line in a macro seems like an odd thing to do so I 
wonder why but... :-)

A simple workaround would be
selectAll;copy; {draw line...};paste;  {ie using clipboard}
or else use duplicate('temp'); to preserve a copy for later paste.





Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Thu Mar 18 20:11 EST 1999
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From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: Big Images, memory limits and what to do
Date: Fri, 19 Mar 1999 11:56:14 +1100
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1. I you have an image which is too big for the screen and want to look at
all of it and do a line trace.

Solution.
Scale to fit window. 
Then if you want it smaller still grab the bottom right hand conrner and
drag it as small as you like.

If Image objects about not enough memory, give it more. Also set the undo
buffer in the prefs control panel.
The limit would be about (2 or 4 Gb) I think as the manual says an Image can
be as big as you like but for editing you can only cut, copy paste bits as
wide as 4096 pixels, but these can be as long as you like.
So an Image could be 4000 wide and 40,000 long.
With a current G3 you could have 1Gb of Ram and as much Virtual RAM as you
want on the disc.

I have had Image running with 300 Mb without any dramas.
Best wishes
Noel Goldsmith


From nih-image-request@io.ece.drexel.edu Thu Mar 18 20:19 EST 1999
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Subject: Help debugging plug-ins
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Hi,
I see that this has been asked about several years ago, but my problem is
now and I am sure the technology and how you do it might have evolved, and I
wonder if anyone can offer advice about good techniques to debug an image
grabbing plug-in.
I have the source code,  which I did not write. I have the Image source code
(which Wayne wrote and did a great job) , I have Macsbug for the G3. 
I have the libraries for the card and the driver.
I have Code warrior,
I have tried to put Macsbug on the G3 and if it crashes out from a normal
app it drops into Macsbug.
Image crashes so infrequently I had to use a more unstable app.
The symptoms are that the use of the plug-in results in a lock up of the G3
on a somewhat random basis. But most often if the disc is writing or reading
(read making a noise) when an image is asked for.

When I use the plug-in with Image and it locks up the system, the mouse
freezes and it takes a three finger restart to get it up. And it doesn't
drop into Macsbug.
So how do I get Macsbug to work here?
Do I need some lines in the code for debugging?
Any advice would be really nice.
Thank you
Noel Goldsmith


From nih-image-request@io.ece.drexel.edu Thu Mar 18 20:49 EST 1999
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Date: Fri, 19 Mar 1999 12:35:56 +1100
To: nih-image@io.ece.drexel.edu
From: Steve Martin <s.martin@physio.unimelb.EDU.AU>
Subject: Re: Help debugging plug-ins
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Hi Noel,

one idea that crossed my mind is that your plug-in is stuck at Apples mail
address ( a.k.a. 1 infinite loop). I think this would not invoke macsbug,
but would produce the symptoms you describe.

Some messages from various segments of the code ('hi mum, I reached the
device driver loading code!', etc.) might be one way to narrow down the
search. If you have the MSL C Sioux library in your project, you can simple
writeLn('my message') and it will be appended to the console out window. Or
you may be able to write to Image's little status/message(?) window down on
the left depending on where your code is executing at the time.

hth

Steve

At 12:06 PM +1100 on 19/3/99, Goldsmith, Noel wrote:
> Hi,
> I see that this has been asked about several years ago, but my problem is
> now and I am sure the technology and how you do it might have evolved, and I
> wonder if anyone can offer advice about good techniques to debug an image
> grabbing plug-in.
> I have the source code,  which I did not write. I have the Image source code
> (which Wayne wrote and did a great job) , I have Macsbug for the G3.
> I have the libraries for the card and the driver.
> I have Code warrior,
> I have tried to put Macsbug on the G3 and if it crashes out from a normal
> app it drops into Macsbug.
> Image crashes so infrequently I had to use a more unstable app.
> The symptoms are that the use of the plug-in results in a lock up of the G3
> on a somewhat random basis. But most often if the disc is writing or reading
> (read making a noise) when an image is asked for.
>
> When I use the plug-in with Image and it locks up the system, the mouse
> freezes and it takes a three finger restart to get it up. And it doesn't
> drop into Macsbug.
> So how do I get Macsbug to work here?
> Do I need some lines in the code for debugging?
> Any advice would be really nice.
> Thank you
> Noel Goldsmith


From nih-image-d-request@io.ece.drexel.edu Fri Mar 19 02:45 EST 1999
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From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199903190745.CAA12786@io.ece.drexel.edu>
Subject: nih-image-d Digest V99 #66
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 66

Today's Topics:
  Re: watershed...                      [ Arnout Ruifrok <arnout@odin.mdacc.t ]
  Unidentified subject!                 [ Bill Mason <wtm@lsr.co.uk> ]
  3d- reconcstruction.                  [ Thomas Ehmer <thomas.ehmer@urz.uni- ]
  RE: Unsubscribing procedure??!!       [ Jan Lund <JANL@lundbeck.com> ]
  Unidentified subject!                 [ Tatiana Karpova <tkarpova@cellbio.w ]
  unsubscribe nih-image                 [ Bill Mason <wtm@lsr.co.uk> ]
  unsubscribe                           [ mechawan@ERE.UMontreal.CA (Naguib M ]
  Re: unsubscribe nih-image             [ "Ken Baker" <kwb@bserv.com> ]
  unsubscribe                           [ "Trevillian, Cristy" <C.J.Trevillia ]
  Re:RAM Limit                          [ "G. Macdonald" <glenmac@u.washingto ]
  Re: 3d- reconcstruction.              [ GJOSS@rna.bio.mq.edu.au ]
  Re: Undo (bug in NIH & Object Image)  [ GJOSS@rna.bio.mq.edu.au ]
  Re: Maximum Memory for NIH Image      [ Lesley Weston <lesley@interchange.u ]
  Big Images, memory limits and what t  [ "Goldsmith, Noel" <Noel.Goldsmith@d ]
  Help debugging plug-ins               [ "Goldsmith, Noel" <Noel.Goldsmith@d ]
  Re: Help debugging plug-ins           [ Steve Martin <s.martin@physio.unime ]
  Re: nih-image-d Digest V99 #65        [ Ard Jonker <a.jonker@amc.uva.nl> ]

------------------------------

Date: Thu, 18 Mar 1999 08:55:00 -0700
From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: watershed...
Message-Id: <v03102800b316d13bc891@[143.111.62.105]>
Content-Type: text/plain; charset="us-ascii"

>Hei!
>
>I am trying to separate particles on an image. I know we can use the
>Watershed method and I have the following procedure: Make a distance
>image by summation of subsequent erosions of the original binary image.
>Invert the final image (black particles in white background). But by
>using the watershed rutine the image disappear and if I not invert the
>image I get a separation of the background.
>
>My question is: Can I use the watershed on distance images or I only
>have to use binary  images. Any suggestions?
>
>Gary.

 Using a routine like you use (repeated erosion) will give you a
'chessboard' distance, not a euclidian distance, wich is closer to the
physical distance. So if you want to measure a distance, you better use
'EDM'. For watershed segmentation you have to start with a binary image.
The watershed routine will use euclidian mapping to grow your objects from
the ultimate points, keeping the objects separated at the 'watershed'. So
in short: you have to use a binary image, and do the watershed operation on
that image.

Arnout

------------------------------

Date: Thu, 18 Mar 1999 15:08:09 +0000
From: Bill Mason <wtm@lsr.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <3.0.32.19990318150803.01b74c40@mail-server>
Content-Type: text/plain; charset="us-ascii"

unsubscribe nih-image

------------------------------

Date: Thu, 18 Mar 1999 16:09:23 +0100
From: Thomas Ehmer <thomas.ehmer@urz.uni-heidelberg.de>
To: nih-image@io.ece.drexel.edu
Subject: 3d- reconcstruction.
Message-ID: <36F11723.F57A0C33@urz.uni-heidelberg.de>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

The object image - expansion seems to fit also my problems, but we don't
use macintosh
is this tool also available for WinNT / Win95 ?

thanks
Thomas Ehmer

------------------------------

Date: Thu, 18 Mar 1999 16:11:48 +0100
From: Jan Lund <JANL@lundbeck.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Unsubscribing procedure??!!
Message-ID: <F11D1722DDC1D111A2AD08002BB76BF40109DB7F@LUDK0009>
Content-Type: text/plain

Hi Bill.

U R welcome.

The address is : nih-image@io.ece.drexel.edu


rgds

Jan
                  ~"""~
                ( @ @ )
---------oOO----(_)----OOo-------------
|                  Jan Lund                         |
|   Elektronik og PC supporter     |
|     Farmakologisk forskning       |
|                                                             |
|       JANL@Lundbeck.Com        |
|         36 30 13 11 Lok. 2374          |
-----------------------------------------------


> ----------
> From: 	Bill Mason[SMTP:wtm@lsr.co.uk]
> Reply To: 	nih-image@io.ece.drexel.edu
> Sent: 	18. marts 1999 15:29
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	Unsubscribing procedure??!!
> 
> Can someone tell me the correct procedure for unsubscribing to this list,
> including the correct email address to do so?
> 
> Thanks very much
> 
> BILL MASON
> 

------------------------------

Date: Thu, 18 Mar 1999 09:37:56 -0600
From: Tatiana Karpova <tkarpova@cellbio.wustl.edu>
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <v03110701b316ce43907a@[128.252.206.41]>
Content-Type: text/plain; charset="us-ascii"

subscribe nih-image

-----------------------------------------------------------------
Dr.Tatiana S. Karpova
Research Associate
Department of Cell Biology and Physiology
Washington Univ School of Medicine
Box 8228, 660 S Euclid Ave. St. Louis, MO  63110

Tel: (314) 362-4606
Fax:(314)362 74 63
tkarpova@cellbio.wustl.edu
World Wide Web site: http://www.cooperlab.wustl.edu/

for FedEx/UPS Shipping:
Dept. of Cell Biology
Washington University School of Medicine
4566 Scott Ave.
St. Louis, MO 63110

------------------------------

Date: Thu, 18 Mar 1999 15:57:59 +0000
From: Bill Mason <wtm@lsr.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe nih-image
Message-Id: <3.0.32.19990318155753.01b7dd78@mail-server>
Content-Type: text/plain; charset="us-ascii"


------------------------------

Date: Thu, 18 Mar 1999 11:26:28 -0500 (EST)
From: mechawan@ERE.UMontreal.CA (Naguib MECHAWAR)
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <v01550100b316939106ef@[132.204.55.198]>
Content-Type: text/plain; charset="iso-8859-1"
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Unsubscribe

*************************************
Naguib Mechawar
Sc. neurologiques
Universit de Montral
*************************************

------------------------------

Date: Thu, 18 Mar 1999 11:59:24 -0500
From: "Ken Baker" <kwb@bserv.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: unsubscribe nih-image
Message-Id: <199903181646.LAA20285@bserv.com>
Content-type: text/plain; charset="US-ASCII"
Content-transfer-encoding: 7bit

The following instructions were copied from the "ADMIN: list commands". Hope
this helps.

Unsubscribe
-----------
To unsubscribe to the list, send E-mail to
nih-image-request@biomed.drexel.edu.
The Subject of the message should contain "unsubscribe".

As in:  To: nih-image-request@biomed.drexel.edu
  Subject: unsubscribe

--

Ken Baker M.Sc.
Microscopy, Imaging, Analysis
4943, Fourth Line Erin
RR 2
Acton, Ontario
Canada
L7J-2L8

--

KWB@bserv.com
519-853-4787



----------
>From: Bill Mason <wtm@lsr.co.uk>
>To: nih-image@io.ece.drexel.edu
>Subject: unsubscribe nih-image
>Date: Thu, Mar 18, 1999, 10:57 AM
>

>
> 

------------------------------

Date: Fri, 19 Mar 1999 07:44:17 +1300
From: "Trevillian, Cristy" <C.J.Trevillian@massey.ac.nz>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: unsubscribe
Message-ID: <E325DED913AED111B6480000F878317D01147C35@its-xchg1.massey.ac.nz>
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unsubscribe please

------------------------------

Date: Thu, 18 Mar 1999 11:37:19 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re:RAM Limit
Message-ID: <Pine.A41.4.05.9903181129580.162208-100000@homer15.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

NIH Image versions at least since 1.60 will work with up to 650 Mb,system 
7.5.5, 7.6 and 8.1 on a 9600/200MP. We've
been merging confocal z-series images into z-series montages and then
projecting rotations of them.  

Regards,
Glen


Glen MacDonald
   Research Scientist
Hearing Research Laboratories of the
Virginia Merrill Bloedel Hearing Research Center
Box 35-7923
University of Washington
Seattle, WA  98195-7923
(206) 616-4156
glenmac@u.washington.edu

//The box said "Requires Windows95, or better." so I bought a Macintosh.//

------------------------------

Date:          Fri, 19 Mar 1999 9:26:32 +1100
From: GJOSS@rna.bio.mq.edu.au
To: thomas.ehmer@urz.uni-heidelberg.de, nih-image@io.ece.drexel.edu
Subject:       Re: 3d- reconcstruction.
Message-ID: <24A2E9A5692@rna.bio.mq.edu.au>

>Date: Thu, 18 Mar 1999 16:09:23 +0100
>From: Thomas Ehmer <thomas.ehmer@urz.uni-heidelberg.de>
>To: nih-image@io.ece.drexel.edu
>Subject: 3d- reconcstruction.
>
>The object image - expansion seems to fit also my problems, but we don't
>use macintosh
>is this tool also available for WinNT / Win95 ?
>
>thanks
>Thomas Ehmer
>
I am afraid not; unless you wanted to get imvolved with Mac emulators.

However the NIH-Image stack facilities are the basis of 3D reconstruction 
and the "project" facilities are quite useful.

I have used Scions Win version of Image quite effectively for student 
introductory training in imaging but cant recall how well "project" 
facilities are implemented in that version.

Certainly worth a try if you are stuck with Win as Scion-Image is freely 
available.

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date:          Fri, 19 Mar 1999 9:56:08 +1100
From: GJOSS@rna.bio.mq.edu.au
To: spfeiff@nimr.mrc.ac.uk, nih-image@io.ece.drexel.edu
CC: Wayne Rasband <wayne@CODON.NIH.GOV>, Norbert Vischer <vischer@bio.uva.nl>
Subject:       Re: Undo (bug in NIH & Object Image)
Message-ID: <24AACD3045E@rna.bio.mq.edu.au>

>Date: Thu, 18 Mar 1999 11:58:08 +0000
>From: Sven Pfeiffer <spfeiff@nimr.mrc.ac.uk>
>Subject: Undo
>To: nih-image@io.ece.drexel.edu
>
>Dear All,
>
>   the question I have concerns the macro command 'Undo'. After drawing a
>line into a stack slice with MoveTo and LineTo in a called procedure, I
>can't use Undo in the macro body to get rid of this line again. Is there 
>any
>solution to this problem ?
>
>Thank's for all the help
>
>Sven
>
>*****************************************************
>The National Institute for Medical Research
>Division of Mammalian Development
>The Ridgeway, Mill Hill
>London, NW7 1AA
>
>Tel: +44(0)181 959 3666 ext.2017
>Fax: +44(0)181 913 8543
>*****************************************************
>

Sven,
There is some peculiar bug here.

Either construction:

macro'test/0';begin moveto(0,0);lineTo(256,256);undo;end

or

procedure line;begin moveto(0,0);lineTo(256,256);end

macro'test/0';begin line;undo;end

behave peculiarly.

There seems to be some "first time" bug that occurs here.
If an image or stack is created and the macro loaded; first invokations 
leave the line on the image or slice. After repeated invokation with manual 
clear of image, the undo then takes effect correctly in followon 
invokations until you quit and initialise. Then the initial malfunction is 
present again.

Problem occurs with both in NIH & Object Image.

Drawing and removing a line in a macro seems like an odd thing to do so I 
wonder why but... :-)

A simple workaround would be
selectAll;copy; {draw line...};paste;  {ie using clipboard}
or else use duplicate('temp'); to preserve a copy for later paste.





Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Thu, 18 Mar 1999 14:52:33 -0800 (PST)
From: Lesley Weston <lesley@interchange.ubc.ca>
To: nih-image@io.ece.drexel.edu
Subject: Re: Maximum Memory for NIH Image
Message-ID: <Pine.GSO.3.95q.990318142340.7007A-100000@interchange.ubc.ca>
Content-Type: TEXT/PLAIN; charset=US-ASCII

For some applications, such as time-lapse movies, where you need to manipulate
huge stacks,you want all the memory you can get. We bought all the RAM we could
afford (164M) and used virtual memory to push it up to 600M. NIH seems to be
able to handle this much. Hope this helps.

Lesley Weston.



On Thu, 18 Mar 1999 GJOSS@rna.bio.mq.edu.au wrote:

> >From: JLinn24538@aol.com
> >Message-ID: <8193d4da.36f03fc8@aol.com>
> >Date: Wed, 17 Mar 1999 18:50:32 EST
> >To: nih-image@io.ece.drexel.edu
> >Subject: Maximum Memory for NIH Image
> >
> >Dear Imagineers,
> >I've checked all the documentation and maybe I've missed it but:
> >Is there an upper limit of RAM that NIH Image can address?  
> >
> >Before I go out and spend a bunch on RAM I thought it might be prudent to 
> >ask!
> >
> >Jeff Linn
> >
> 
> 166 MB allocated certainly works.
> It is my understanding that 512MB would work but I haven't tried it.
> 256 PAL frames 768x512 is < 100MB,
> so I am not sure you would want to go much over 166 MB in practice?
> 
> You could test by using virtual memory if you really wanted.
> Greg Joss,
> School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
> Macquarie University,          Email gjoss@rna.bio.mq.edu.au
> North Ryde, (Sydney,) NSW 2109, Australia
> 
> 

------------------------------

Date: Fri, 19 Mar 1999 11:56:14 +1100
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: Big Images, memory limits and what to do
Message-Id: <F98649A5EE8ED11190160000F802756598D013@exchvic3.dsto.defence.gov.au>
Content-Type: text/plain;
	charset="windows-1252"

1. I you have an image which is too big for the screen and want to look at
all of it and do a line trace.

Solution.
Scale to fit window. 
Then if you want it smaller still grab the bottom right hand conrner and
drag it as small as you like.

If Image objects about not enough memory, give it more. Also set the undo
buffer in the prefs control panel.
The limit would be about (2 or 4 Gb) I think as the manual says an Image can
be as big as you like but for editing you can only cut, copy paste bits as
wide as 4096 pixels, but these can be as long as you like.
So an Image could be 4000 wide and 40,000 long.
With a current G3 you could have 1Gb of Ram and as much Virtual RAM as you
want on the disc.

I have had Image running with 300 Mb without any dramas.
Best wishes
Noel Goldsmith

------------------------------

Date: Fri, 19 Mar 1999 12:06:57 +1100
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: Help debugging plug-ins
Message-Id: <F98649A5EE8ED11190160000F802756598D014@exchvic3.dsto.defence.gov.au>
Content-Type: text/plain;
	charset="windows-1252"

Hi,
I see that this has been asked about several years ago, but my problem is
now and I am sure the technology and how you do it might have evolved, and I
wonder if anyone can offer advice about good techniques to debug an image
grabbing plug-in.
I have the source code,  which I did not write. I have the Image source code
(which Wayne wrote and did a great job) , I have Macsbug for the G3. 
I have the libraries for the card and the driver.
I have Code warrior,
I have tried to put Macsbug on the G3 and if it crashes out from a normal
app it drops into Macsbug.
Image crashes so infrequently I had to use a more unstable app.
The symptoms are that the use of the plug-in results in a lock up of the G3
on a somewhat random basis. But most often if the disc is writing or reading
(read making a noise) when an image is asked for.

When I use the plug-in with Image and it locks up the system, the mouse
freezes and it takes a three finger restart to get it up. And it doesn't
drop into Macsbug.
So how do I get Macsbug to work here?
Do I need some lines in the code for debugging?
Any advice would be really nice.
Thank you
Noel Goldsmith

------------------------------

Date: Fri, 19 Mar 1999 12:35:56 +1100
From: Steve Martin <s.martin@physio.unimelb.EDU.AU>
To: nih-image@io.ece.drexel.edu
Subject: Re: Help debugging plug-ins
Message-Id: <v04011702b31758a75f60@[128.250.109.214]>
Content-Type: text/plain; charset="us-ascii"

Hi Noel,

one idea that crossed my mind is that your plug-in is stuck at Apples mail
address ( a.k.a. 1 infinite loop). I think this would not invoke macsbug,
but would produce the symptoms you describe.

Some messages from various segments of the code ('hi mum, I reached the
device driver loading code!', etc.) might be one way to narrow down the
search. If you have the MSL C Sioux library in your project, you can simple
writeLn('my message') and it will be appended to the console out window. Or
you may be able to write to Image's little status/message(?) window down on
the left depending on where your code is executing at the time.

hth

Steve

At 12:06 PM +1100 on 19/3/99, Goldsmith, Noel wrote:
> Hi,
> I see that this has been asked about several years ago, but my problem is
> now and I am sure the technology and how you do it might have evolved, and I
> wonder if anyone can offer advice about good techniques to debug an image
> grabbing plug-in.
> I have the source code,  which I did not write. I have the Image source code
> (which Wayne wrote and did a great job) , I have Macsbug for the G3.
> I have the libraries for the card and the driver.
> I have Code warrior,
> I have tried to put Macsbug on the G3 and if it crashes out from a normal
> app it drops into Macsbug.
> Image crashes so infrequently I had to use a more unstable app.
> The symptoms are that the use of the plug-in results in a lock up of the G3
> on a somewhat random basis. But most often if the disc is writing or reading
> (read making a noise) when an image is asked for.
>
> When I use the plug-in with Image and it locks up the system, the mouse
> freezes and it takes a three finger restart to get it up. And it doesn't
> drop into Macsbug.
> So how do I get Macsbug to work here?
> Do I need some lines in the code for debugging?
> Any advice would be really nice.
> Thank you
> Noel Goldsmith

------------------------------

Date: Fri, 19 Mar 1999 08:37:11 +0100
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Cc: GJOSS@rna.bio.mq.edu.au
Subject: Re: nih-image-d Digest V99 #65
Message-Id: <l03130301b317ae735478@[145.117.43.50]>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 8bit

Greg Joss wrote:

>However, if you want accurate selections with large or zoomed images, be 
>aware that you can alternate scroll(hand) and selection tools extending an 
>existing straight line selection from either end or an existing rectanular 
>selection from the bottom left corner so that one end of the selection may 
>be well off screen to cover the 3000 pixels.

Do you mean that I can extend a, say, 500x500 selection to a 600x500 selection by appropriately clicking in the lower lefthand corner of the marching ants rectangle? As far as I could see, it either moves the marching ants without extending it, or it generates a whole new selection if you click just outside the marching ants.

I know shift-clicking could add an extra 500x100 box to the 500x500 box, but that is not what I mean.

Ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156

--------------------------------
End of nih-image-d Digest V99 Issue #66
***************************************

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Greg Joss wrote:

>However, if you want accurate selections with large or zoomed images, be 
>aware that you can alternate scroll(hand) and selection tools extending an 
>existing straight line selection from either end or an existing rectanular 
>selection from the bottom left corner so that one end of the selection may 
>be well off screen to cover the 3000 pixels.

Do you mean that I can extend a, say, 500x500 selection to a 600x500 selection by appropriately clicking in the lower lefthand corner of the marching ants rectangle? As far as I could see, it either moves the marching ants without extending it, or it generates a whole new selection if you click just outside the marching ants.

I know shift-clicking could add an extra 500x100 box to the 500x500 box, but that is not what I mean.

Ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156



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From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: Re: nih-image-d Digest V99 #65
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>   the question I have concerns the macro command 'Undo'. After drawing a
>line into a stack slice with MoveTo and LineTo in a called procedure, I
>can't use Undo in the macro body to get rid of this line again. Is there any
>solution to this problem ?

use line roi (rather than the line painting tool), copy the contents, paint it (fill it or draw outline) for whatever reason, do what you have to do, then paste the original contents back into the selection and your line is gone. 

ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156



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Unsubscribe


From nih-image-request@io.ece.drexel.edu Fri Mar 19 06:37 EST 1999
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Message-ID: <c=NO%a=_%p=pfi%l=PFINT1-990319112145Z-2930@pfint1.pfi.no>
From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: watershed...
Date: Fri, 19 Mar 1999 12:21:45 +0100
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Well, I am going to answer my own question. I am using the Scion Image
program and it doesnt seem to be as reliable as the NIH image program.
The watershed and distance map commands dont perform the required
operations. 

Gary.


>-----Original Message-----
>From:	Gary Chinga 
>Sent:	18. mars 1999 10:47
>To:	nih-image@io.ece.drexel.edu
>Subject:	watershed...
>
>Hei!
>
>I am trying to separate particles on an image. I know we can use the
>Watershed method and I have the following procedure: Make a distance image by
>summation of subsequent erosions of the original binary image. Invert the
>final image (black particles in white background). But by using the watershed
>rutine the image disappear and if I not invert the image I get a separation
>of the background.
>
>My question is: Can I use the watershed on distance images or I only have to
>use binary  images. Any suggestions?
>
>Gary.


From nih-image-request@io.ece.drexel.edu Fri Mar 19 07:47 EST 1999
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Date: Fri, 19 Mar 1999 06:28:00 -0600
From: Michael Herron <herro001@maroon.tc.umn.edu>
Reply-To: Michael J Herron <herro001@maroon.tc.umn.edu>
Organization: U of MN, Medicine, Infectious Diseases
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All,

I have this all-plastic microscope slide that
fluoresces at about 488 or so, and it's really nice to use as a
calibration slide for day-to-day intensity measurements.  The only trouble
is that I have only one and it is forever being borrowed.  On the slide I
read Delta Vision, but that is the only clue to lead me to the company
that sells these things.  I can't seem to make headway on the web, so I
was wondering if anyone knew where I might pick some up, especially if I
can get slides that light up at various wavelengths on out to infrared.

Thanks,
Mike

-- 

   _________________________________________________
     /  Michael J. Herron                          /
    /     U of MN,Medicine/Infectious Diseases    /
   /        herro001@maroon.tc.umn.edu           /
  /           http://128.101.243.213            /
 /_____________________________________________/


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Unsubscribe me, please.
 +-----------------------------------------------------------+ 
 | Dr. Jos Armando Escamilla Bencomo                        |
 | Centro de Investigacin Cientfica de Yucatn A.C.        |
 | P.O. Box 87 Cordemex Mrida Yucatn 97310 Mxico          |
 | ph    (52-99) 81-39-14    fax   (52-99) 81-39-00          |
 | email: jae@cicy.cicy.mx                                   |
 | http://www.cicy.mx/unidades/biologia/personal/armando.html|
 +-----------------------------------------------------------+ 


From nih-image-request@io.ece.drexel.edu Fri Mar 19 11:52 EST 1999
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On Fri, 19 Mar 1999, Michael Herron wrote:

> 
> I have this all-plastic microscope slide that
> fluoresces at about 488 or so, and it's really nice to use as a
> calibration slide for day-to-day intensity measurements.  The only trouble
> is that I have only one and it is forever being borrowed.  On the slide I
> read Delta Vision, but that is the only clue to lead me to the company
> that sells these things.  I can't seem to make headway on the web, so I
> was wondering if anyone knew where I might pick some up, especially if I
> can get slides that light up at various wavelengths on out to infrared.


Applied Precision, Inc
1040 12th Ave. N. W.
Issaquah, WA 98028-8929

v: 425.557.1000
f: 425.557.1055

http://www.api.com

*-----------------*------------------*----------------------*---------------*

>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <
>Confocal and Image Analysis Laboratory             Tel: +44 (0)181 913 8675 <
>Membrane Biology                                Mobile: 0370 654288         <
>National Institute for Medical Research    Switchboard: 0181 9593666 x2621  <
>The Ridgeway                                   Message: x2219, x2622        <
>Mill Hill, London NW7 1AA                          FAX: +44 (0)181 906 4477 <


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From: David Ehrhardt <ehrhardt@camelot.Stanford.EDU>
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I have one of these slides too, it comes from Applied Precision, which
makes the DeltaVision restoration microscopy system (sometimes called
deconvolution microscopy). Their WEB site is
http://www.api.com/dvsystems.html.  I do not know if they sell the slides,
but I suspect that they do not.  

-David 


> All,
> 
> I have this all-plastic microscope slide that
> fluoresces at about 488 or so, and it's really nice to use as a
> calibration slide for day-to-day intensity measurements.  The only trouble
> is that I have only one and it is forever being borrowed.  On the slide I
> read Delta Vision, but that is the only clue to lead me to the company
> that sells these things.  I can't seem to make headway on the web, so I
> was wondering if anyone knew where I might pick some up, especially if I
> can get slides that light up at various wavelengths on out to infrared.
> 
> Thanks,
> Mike
> 
> -- 
> 
>    _________________________________________________
>      /  Michael J. Herron                          /
>     /     U of MN,Medicine/Infectious Diseases    /
>    /        herro001@maroon.tc.umn.edu           /
>   /           http://128.101.243.213            /
>  /_____________________________________________/
> 
> 

David Ehrhardt				
Carnegie Institution of Washington
Department of Plant Biology		Phone (650) 325-1521 x261
260 Panama St., Stanford, CA 94305	FAX (650) 325-6857



From nih-image-request@io.ece.drexel.edu Fri Mar 19 17:49 EST 1999
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From: David Linker <dtlinker@u.washington.edu>
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Subject: Re: Help debugging plug-ins
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It is possible to use the Codewarrior debugger for plugin code. I did it
several years ago when I had to, but I have forgotten the details. I
beleive that there were some instructions in the codewarrior documentation.

If you do this, you can use the features of the Codewarrior debugger to
single step, set breakpoints, etc.

It might help.

DTL

--On Fri, Mar 19, 1999 12:06 PM +1100 "Goldsmith, Noel"
<Noel.Goldsmith@dsto.defence.gov.au> wrote:

> Hi,
> I see that this has been asked about several years ago, but my problem is
> now and I am sure the technology and how you do it might have evolved,
> and I wonder if anyone can offer advice about good techniques to debug an
> image grabbing plug-in.
> I have the source code,  which I did not write. I have the Image source
> code (which Wayne wrote and did a great job) , I have Macsbug for the G3. 
> I have the libraries for the card and the driver.
> I have Code warrior,
> I have tried to put Macsbug on the G3 and if it crashes out from a normal
> app it drops into Macsbug.
> Image crashes so infrequently I had to use a more unstable app.
> The symptoms are that the use of the plug-in results in a lock up of the
> G3 on a somewhat random basis. But most often if the disc is writing or
> reading (read making a noise) when an image is asked for.
> 
> When I use the plug-in with Image and it locks up the system, the mouse
> freezes and it takes a three finger restart to get it up. And it doesn't
> drop into Macsbug.
> So how do I get Macsbug to work here?
> Do I need some lines in the code for debugging?
> Any advice would be really nice.
> Thank you
> Noel Goldsmith
> 





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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #67
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 67

Today's Topics:
  Re: nih-image-d Digest V99 #65        [ Ard Jonker <a.jonker@amc.uva.nl> ]
  Unsubscribe                           [ "Jason Pickering" <J.P.Pickering@ct ]
  RE: watershed...                      [ Gary Chinga <gary.chinga@pfi.no> ]
  No subject was specified.             [ Michael Herron <herro001@maroon.tc. ]
  unsubscribe                           [ szele@rascal.med.harvard.edu (Franc ]
  unsubscribe                           [ jose escamilla <jae@cicy.cicy.mx> ]
  Re: No subject was specified.         [ Stamatis Pagakis <spagaki@nimr.mrc. ]
  Re: No subject was specified.         [ David Ehrhardt <ehrhardt@camelot.St ]
  Re: Help debugging plug-ins           [ David Linker <dtlinker@u.washington ]
  Tracking Translating Cells            [ Vikas Prabhakar <vp@duke.edu> ]

------------------------------

Date: Fri, 19 Mar 1999 08:44:19 +0100
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Cc: spfeiff@nimr.mrc.ac.uk
Subject: Re: nih-image-d Digest V99 #65
Message-Id: <l03130302b317b05dc7ce@[145.117.43.50]>
Content-Type: text/plain; charset="us-ascii"

>   the question I have concerns the macro command 'Undo'. After drawing a
>line into a stack slice with MoveTo and LineTo in a called procedure, I
>can't use Undo in the macro body to get rid of this line again. Is there any
>solution to this problem ?

use line roi (rather than the line painting tool), copy the contents, paint it (fill it or draw outline) for whatever reason, do what you have to do, then paste the original contents back into the selection and your line is gone. 

ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156

------------------------------

Date: Fri, 19 Mar 1999 11:11:01 +0100
From: "Jason Pickering" <J.P.Pickering@ct.utwente.nl>
To: nih-image@io.ece.drexel.edu
Subject: Unsubscribe
Message-Id: <199903191013.AA08750@ct.utwente.nl>
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Unsubscribe

------------------------------

Date: Fri, 19 Mar 1999 12:21:45 +0100
From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: watershed...
Message-ID: <c=NO%a=_%p=pfi%l=PFINT1-990319112145Z-2930@pfint1.pfi.no>
Content-Type: text/plain; charset="us-ascii"
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Well, I am going to answer my own question. I am using the Scion Image
program and it doesnt seem to be as reliable as the NIH image program.
The watershed and distance map commands dont perform the required
operations. 

Gary.


>-----Original Message-----
>From:	Gary Chinga 
>Sent:	18. mars 1999 10:47
>To:	nih-image@io.ece.drexel.edu
>Subject:	watershed...
>
>Hei!
>
>I am trying to separate particles on an image. I know we can use the
>Watershed method and I have the following procedure: Make a distance image by
>summation of subsequent erosions of the original binary image. Invert the
>final image (black particles in white background). But by using the watershed
>rutine the image disappear and if I not invert the image I get a separation
>of the background.
>
>My question is: Can I use the watershed on distance images or I only have to
>use binary  images. Any suggestions?
>
>Gary.

------------------------------

Date: Fri, 19 Mar 1999 06:28:00 -0600
From: Michael Herron <herro001@maroon.tc.umn.edu>
To: NIH Image Mailing List <nih-image@io.ece.drexel.edu>
Subject: No subject was specified.
Message-Id: <36F24283.5AEBA537@maroon.tc.umn.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

All,

I have this all-plastic microscope slide that
fluoresces at about 488 or so, and it's really nice to use as a
calibration slide for day-to-day intensity measurements.  The only trouble
is that I have only one and it is forever being borrowed.  On the slide I
read Delta Vision, but that is the only clue to lead me to the company
that sells these things.  I can't seem to make headway on the web, so I
was wondering if anyone knew where I might pick some up, especially if I
can get slides that light up at various wavelengths on out to infrared.

Thanks,
Mike

-- 

   _________________________________________________
     /  Michael J. Herron                          /
    /     U of MN,Medicine/Infectious Diseases    /
   /        herro001@maroon.tc.umn.edu           /
  /           http://128.101.243.213            /
 /_____________________________________________/

------------------------------

Date: Fri, 19 Mar 1999 10:13:57 +0500
From: szele@rascal.med.harvard.edu (Francis Szele)
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <v01510101b3178d412c78@[134.174.160.60]>
Content-Type: text/plain; charset="us-ascii"

Unsubscribe me, please.

------------------------------

Date: Fri, 19 Mar 1999 10:06:01 -0600
From: jose escamilla <jae@cicy.cicy.mx>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <199903191606.KAA01489@cicy.cicy.mx>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Unsubscribe me, please.
 +-----------------------------------------------------------+ 
 | Dr. Jos Armando Escamilla Bencomo                        |
 | Centro de Investigacin Cientfica de Yucatn A.C.        |
 | P.O. Box 87 Cordemex Mrida Yucatn 97310 Mxico          |
 | ph    (52-99) 81-39-14    fax   (52-99) 81-39-00          |
 | email: jae@cicy.cicy.mx                                   |
 | http://www.cicy.mx/unidades/biologia/personal/armando.html|
 +-----------------------------------------------------------+ 

------------------------------

Date: Fri, 19 Mar 1999 16:30:27 +0000
From: Stamatis Pagakis <spagaki@nimr.mrc.ac.uk>
To: Michael Herron <herro001@maroon.tc.umn.edu>
Cc: NIH Image Mailing List <nih-image@io.ece.drexel.edu>
Subject: Re: No subject was specified.
Message-id: <Pine.SGI.4.10.9903191629310.1373-100000@membo2.nimr.mrc.ac.uk>
Content-type: TEXT/PLAIN; charset=US-ASCII

On Fri, 19 Mar 1999, Michael Herron wrote:

> 
> I have this all-plastic microscope slide that
> fluoresces at about 488 or so, and it's really nice to use as a
> calibration slide for day-to-day intensity measurements.  The only trouble
> is that I have only one and it is forever being borrowed.  On the slide I
> read Delta Vision, but that is the only clue to lead me to the company
> that sells these things.  I can't seem to make headway on the web, so I
> was wondering if anyone knew where I might pick some up, especially if I
> can get slides that light up at various wavelengths on out to infrared.


Applied Precision, Inc
1040 12th Ave. N. W.
Issaquah, WA 98028-8929

v: 425.557.1000
f: 425.557.1055

http://www.api.com

*-----------------*------------------*----------------------*---------------*

>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <
>Confocal and Image Analysis Laboratory             Tel: +44 (0)181 913 8675 <
>Membrane Biology                                Mobile: 0370 654288         <
>National Institute for Medical Research    Switchboard: 0181 9593666 x2621  <
>The Ridgeway                                   Message: x2219, x2622        <
>Mill Hill, London NW7 1AA                          FAX: +44 (0)181 906 4477 <

------------------------------

Date: Fri, 19 Mar 1999 12:15:56 -0800 (PST)
From: David Ehrhardt <ehrhardt@camelot.Stanford.EDU>
To: Michael Herron <herro001@maroon.tc.umn.edu>
cc: NIH Image Mailing List <nih-image@io.ece.drexel.edu>
Subject: Re: No subject was specified.
Message-ID: <Pine.GUL.3.95.990319121023.6191B-100000@camelot.Stanford.EDU>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I have one of these slides too, it comes from Applied Precision, which
makes the DeltaVision restoration microscopy system (sometimes called
deconvolution microscopy). Their WEB site is
http://www.api.com/dvsystems.html.  I do not know if they sell the slides,
but I suspect that they do not.  

-David 


> All,
> 
> I have this all-plastic microscope slide that
> fluoresces at about 488 or so, and it's really nice to use as a
> calibration slide for day-to-day intensity measurements.  The only trouble
> is that I have only one and it is forever being borrowed.  On the slide I
> read Delta Vision, but that is the only clue to lead me to the company
> that sells these things.  I can't seem to make headway on the web, so I
> was wondering if anyone knew where I might pick some up, especially if I
> can get slides that light up at various wavelengths on out to infrared.
> 
> Thanks,
> Mike
> 
> -- 
> 
>    _________________________________________________
>      /  Michael J. Herron                          /
>     /     U of MN,Medicine/Infectious Diseases    /
>    /        herro001@maroon.tc.umn.edu           /
>   /           http://128.101.243.213            /
>  /_____________________________________________/
> 
> 

David Ehrhardt				
Carnegie Institution of Washington
Department of Plant Biology		Phone (650) 325-1521 x261
260 Panama St., Stanford, CA 94305	FAX (650) 325-6857

------------------------------

Date: Fri, 19 Mar 1999 14:33:57 -0800
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Help debugging plug-ins
Message-ID: <1249992.3130842837@huginn.medicine.washington.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

It is possible to use the Codewarrior debugger for plugin code. I did it
several years ago when I had to, but I have forgotten the details. I
beleive that there were some instructions in the codewarrior documentation.

If you do this, you can use the features of the Codewarrior debugger to
single step, set breakpoints, etc.

It might help.

DTL

--On Fri, Mar 19, 1999 12:06 PM +1100 "Goldsmith, Noel"
<Noel.Goldsmith@dsto.defence.gov.au> wrote:

> Hi,
> I see that this has been asked about several years ago, but my problem is
> now and I am sure the technology and how you do it might have evolved,
> and I wonder if anyone can offer advice about good techniques to debug an
> image grabbing plug-in.
> I have the source code,  which I did not write. I have the Image source
> code (which Wayne wrote and did a great job) , I have Macsbug for the G3. 
> I have the libraries for the card and the driver.
> I have Code warrior,
> I have tried to put Macsbug on the G3 and if it crashes out from a normal
> app it drops into Macsbug.
> Image crashes so infrequently I had to use a more unstable app.
> The symptoms are that the use of the plug-in results in a lock up of the
> G3 on a somewhat random basis. But most often if the disc is writing or
> reading (read making a noise) when an image is asked for.
> 
> When I use the plug-in with Image and it locks up the system, the mouse
> freezes and it takes a three finger restart to get it up. And it doesn't
> drop into Macsbug.
> So how do I get Macsbug to work here?
> Do I need some lines in the code for debugging?
> Any advice would be really nice.
> Thank you
> Noel Goldsmith
> 

------------------------------

Date: Sat, 20 Mar 1999 00:06:00 -0500 (EST)
From: Vikas  Prabhakar <vp@duke.edu>
To: nih-image@io.ece.drexel.edu
Subject: Tracking Translating Cells
Message-ID: <Pine.SOL.3.91.990319235928.17623A-100000@teer13.acpub.duke.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I study rolling velocities of monocytes interacting with endothelium and 
implications in atherosclerosis.  I was wondering if anyone is aware of 
any literature discussing methods to track the motion of translating cells.
Also, is there a superior commercial software package to track such cells?
Thanks in advance.

Vikas Prabhakar

--------------------------------
End of nih-image-d Digest V99 Issue #67
***************************************

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Date: Sat, 20 Mar 1999 00:06:00 -0500 (EST)
From: Vikas  Prabhakar <vp@duke.edu>
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I study rolling velocities of monocytes interacting with endothelium and 
implications in atherosclerosis.  I was wondering if anyone is aware of 
any literature discussing methods to track the motion of translating cells.
Also, is there a superior commercial software package to track such cells?
Thanks in advance.

Vikas Prabhakar


From nih-image-request@io.ece.drexel.edu Sat Mar 20 07:58 EST 1999
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To: nih-image@io.ece.drexel.edu
From: Cheryll & Wade Schuette <schuette@s.imap.itd.umich.edu>
Subject: Re: Tracking Translating Cells
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At 12:06 AM 3/20/99 -0500, you wrote:
>I study rolling velocities of monocytes interacting with endothelium and 
>implications in atherosclerosis.  I was wondering if anyone is aware of 
>any literature discussing methods to track the motion of translating cells.
>Also, is there a superior commercial software package to track such cells?
>Thanks in advance.
>
>Vikas Prabhakar
>

I wrote such software using NIH-Image for a previous position.
The code is proprietary, but I'd be glad to discuss the issues
and share ideas.

Ref: "An Automated High Capacity Data Capture and Analysis System for the 
in vitro Assessment of Leukocyte Adhesion Under Shear-stress Conditions", 
by Joseph Low, Debra Killner, and Wade Schuette, Journal of Immunological 
Methods 194: 59-70 (1996). 

Cheryll & Wade Schuette
2345 Stone Road
Ann Arbor MI 48105
734-763-8278


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To: nih-image@io.ece.drexel.edu (NIH Image)
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I am using Scion Image to analyze particle motion.  I have a stack of 
images and would like to superimpose these images into one picture to track 
the motion of the particle. Does anyone know how to do this. Thanks for 
the help.  

Dave

dws@seas.upenn.edu


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------------------------------

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nih-image-d Digest				Volume 99 : Issue 68

Today's Topics:
  Re: Tracking Translating Cells        [ Cheryll & Wade Schuette <schuette@s ]
  Object trace                          [ "DAVID W SCHMIDTKE" <dws@seas.upenn ]

------------------------------

Date: Sat, 20 Mar 1999 07:45:54 -0500
From: Cheryll & Wade Schuette <schuette@s.imap.itd.umich.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Tracking Translating Cells
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At 12:06 AM 3/20/99 -0500, you wrote:
>I study rolling velocities of monocytes interacting with endothelium and 
>implications in atherosclerosis.  I was wondering if anyone is aware of 
>any literature discussing methods to track the motion of translating cells.
>Also, is there a superior commercial software package to track such cells?
>Thanks in advance.
>
>Vikas Prabhakar
>

I wrote such software using NIH-Image for a previous position.
The code is proprietary, but I'd be glad to discuss the issues
and share ideas.

Ref: "An Automated High Capacity Data Capture and Analysis System for the 
in vitro Assessment of Leukocyte Adhesion Under Shear-stress Conditions", 
by Joseph Low, Debra Killner, and Wade Schuette, Journal of Immunological 
Methods 194: 59-70 (1996). 

Cheryll & Wade Schuette
2345 Stone Road
Ann Arbor MI 48105
734-763-8278

------------------------------

Date: Sat, 20 Mar 1999 14:14:22 -0500 (EST)
From: "DAVID W SCHMIDTKE" <dws@seas.upenn.edu>
To: nih-image@io.ece.drexel.edu (NIH Image)
Subject: Object trace
Message-Id: <199903201914.OAA10591@blue.seas.upenn.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit

I am using Scion Image to analyze particle motion.  I have a stack of 
images and would like to superimpose these images into one picture to track 
the motion of the particle. Does anyone know how to do this. Thanks for 
the help.  

Dave

dws@seas.upenn.edu

--------------------------------
End of nih-image-d Digest V99 Issue #68
***************************************

From nih-image-request@io.ece.drexel.edu Sun Mar 21 18:22 EST 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: a.jonker@amc.uva.nl, nih-image@io.ece.drexel.edu
Date:          Mon, 22 Mar 1999 10:12:46 +1100
Subject:       Re: extending a rectangular selection.
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>Date: Fri, 19 Mar 1999 08:37:11 +0100
>To: nih-image@io.ece.drexel.edu
>From: Ard Jonker <a.jonker@amc.uva.nl>
>Subject: Re: nih-image-d Digest V99 #65
>Cc: GJOSS@rna.bio.mq.edu.au
>
>Greg Joss wrote:
>
>>However, if you want accurate selections with large or zoomed images, be 
>>aware that you can alternate scroll(hand) and selection tools extending 
>>an existing straight line selection from either end or an existing 
>>rectanular selection from the bottom left corner so that one end of the 
>>selection may be well off screen to cover the 3000 pixels.
>
>Do you mean that I can extend a, say, 500x500 selection to a 600x500 
>selection by appropriately clicking in the lower lefthand corner of the 
>marching ants rectangle? As far as I could see, it either
>moves the marching ants without extending it, or it generates a whole new 
>selection if you click just outside the marching ants.
>
>I know shift-clicking could add an extra 500x100 box to the 500x500 box, 
>but that is not what I mean.
>
>Ard
>
>dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
>Dep of Cell Biology and Histology  |Meibergdreef 15
>Faculty of Medicine                |1105 AZ Amsterdam
>University of Amsterdam            |The Netherlands
>tel +31 20 566 5304                |fax +31 20 697 4156
>
Except for my silly slip of keying "bottom left corner" when it should have 
been "bottom RIGHt corner", yes, you "can extend a, say, 500x500 selection 
to a 600x500 selection".

In the bottom RIGHT corner of the marching ants rectangle of the selection 
is displayed a small (5x5 pixel) black square. If you drag within this 
square, the top left corner remains anchored while the bottom right can be 
extended (modified) at will. This allows you to alternate between 
selection, scroll(hand), magnifying glass tools so that selections can be 
made/modified with pixel accuracy even on a 4096 pixel wide image and with 
pixels magnified so that the mouse can be accurately positioned for the 
selection. The anchoring of top left and freedom of the bottom right can be 
accomodated in the occassional case where the top must be determined by the 
right hand side by also dragging within the selection (not in the black 
square bottom-left-corner) so that the whole selection is dragged. A simple 
iteration to set (top) left, (bottom) right, top right, top left, bottom 
(right) will be readily achieved with a little practice.
Alternately, in this special case, you might prefer to flip the image 
horizontally.

If you do this type activity in a production mode, then single key macros 
to selectTool's are convenient.

Greg
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: Noel.Goldsmith@dsto.defence.gov.au, nih-image@io.ece.drexel.edu
Date:          Mon, 22 Mar 1999 10:49:45 +1100
Subject:       Re: Big Images, memory limits and what to do
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>From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
>To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
>Subject: Big Images, memory limits and what to do
>Date: Fri, 19 Mar 1999 11:56:14 +1100
>
>1. I you have an image which is too big for the screen and want to look at
>all of it and do a line trace.
>
>Solution.
>Scale to fit window. 
>Then if you want it smaller still grab the bottom right hand conrner and
>drag it as small as you like.
>
>If Image objects about not enough memory, give it more. Also set the undo
>buffer in the prefs control panel.
>The limit would be about (2 or 4 Gb) I think as the manual says an Image 
>can
>be as big as you like but for editing you can only cut, copy paste bits as
>wide as 4096 pixels, but these can be as long as you like.
>So an Image could be 4000 wide and 40,000 long.
>With a current G3 you could have 1Gb of Ram and as much Virtual RAM as you
>want on the disc.
>
>I have had Image running with 300 Mb without any dramas.
>Best wishes
>Noel Goldsmith
>

Noel, 

Thanks for tip, I had not previously picked up on:
>Scale to fit window. 
>Then if you want it smaller still grab the bottom right hand conrner and
>drag it as small as you like.

I hadn't realised that, after "Scale to fit window", draging the window 
corner rescales the image as well as reducing the image window.

However, my experience with image size is a liitle different to yours:
> but these can be as long as you like.
>So an Image could be 4000 wide and 40,000 long.

With 120 MB allocated to image and 40960K to clipboard,
the following macro
macro'/0test';var w,h,wp,hp,n:integer;begin w:=8;h:=1024;hp:=h;
while h=hp do begin h:=h+h/2;
if n>0 then dispose;n:=n+1; 
setnewsize(w,h);makeNewWindow('temp');
getPicsize(wp,hp);
showMessage(n,'\',h,'\',hp);
end;
end

terminates with
7
17496
16383
in info window.

with h:=h+h/2; :
4
16384
16383

I have also found that I cannot 'import' images longer than about 20K even 
if only 1 wide. 

Greg.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Sun Mar 21 23:25 EST 1999
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To: "DAVID W SCHMIDTKE" <dws@seas.upenn.edu>, nih-image@io.ece.drexel.edu
Date: Mon, 22 Mar 1999 15:11:28 +1100
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Date forwarded: 	Sat, 20 Mar 1999 14:24:45 -0500 (EST)
Subject:        	Object trace
To:             	nih-image@io.ece.drexel.edu (NIH Image)
Date sent:      	Sat, 20 Mar 1999 14:14:22 -0500 (EST)
From:           	"DAVID W SCHMIDTKE" <dws@seas.upenn.edu>
Forwarded by:   	nih-image@io.ece.drexel.edu
Send reply to:  	nih-image@io.ece.drexel.edu

> I am using Scion Image to analyze particle motion.  I have a stack of 
> images and would like to superimpose these images into one picture to track 
> the motion of the particle. Does anyone know how to do this. Thanks for 
> the help.  
> 
> Dave
> 
> dws@seas.upenn.edu
> 
You can quite simply "project" the images onto a composite stack using the 
"project(stacks menu" in Scion or NIH-Image on the IBM PC or Mac.

You may need to persist with your efforts to get a proper understanding of 
project parameters as it is designed to do more sophisticated projections than 
you want so that the excess of options can be a little confusing at first.
The main aspect to keep in mind is that project is written with black as the 
expected transparent background (inverse to Image) so that you may find it 
easier to invert your image. ie the things you want to see should be bright (ie 
lower pixel value) on a dark (higher pixel value) background.

For your purpose, set total rotation to 0 so that the projection stack will be only 
one slice (you are not looking for a rotating 3D view).

Set surface opacity=0 so that you can see through all layers.

upper/lower transparency bounds can be used in an analogous way to 
setDensitySlice to control the intensity range of the visible objects as opposed 
to the background to be made transparent.



Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


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Date: Mon, 22 Mar 1999 09:55:25 -0800
From: "Zuccala David" <zuccala@cris.enel.it>
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> I am using Scion Image to analyze particle motion.  I have a stack of
> images and would like to superimpose these images into one picture to track
> the motion of the particle. Does anyone know how to do this. Thanks for
> the help.
> 
> Dave
> 
> dws@seas.upenn.edu

Dear David,
open your stack, do "Stack to windows" to get a set of separate images,
and try the following simple macro that I wrote for Scion Image:

macro 'Minimum'
  { Applies the min operator to all open images } 
var
  N, i, Result: integer;
begin
  N := nPics;  { number of open images }
  if N<2 then Exit('I need at least 2 images');
  ImageMath('min', 1, 2, 1, 0, 'Result');  { minimum between the first 2
images }
  Result := PidNumber;  { Pid of the active image ('Result') }
  for i:=3 to N do begin
    ImageMath('min', i, Result, 1, 0, Result);
  end
end;


The macro supposes that your particle be white on a black background
(gray level of the particle less than the background gray level). If
not, invert your images or change "min" into "max" in the macro.
Hope this helps.
David

*****************************************************
David Zuccala'
ENEL RICERCA - Polo Idraulico e Strutturale              
v. Pozzobonelli, 6       ph.: + 39 02 7224.3587
I - 20162 Milano         fax: + 39 02 7224.3530
                         e-mail: zuccala@cris.enel.it


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From: Cheryll & Wade Schuette <schuette@s.imap.itd.umich.edu>
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At 02:14 PM 3/20/99 -0500, you wrote:
>I am using Scion Image to analyze particle motion.  I have a stack of 
>images and would like to superimpose these images into one picture to track 
>the motion of the particle. Does anyone know how to do this. Thanks for 
>the help.  
>
>Dave

The answers posted so far assume, I think, that the images in your stack
are identically aligned (registered), and the only thing moving is the
particle.   Is that a valid assumption, or is there also some camera or
background jitter or motion that needs to be compensated for as well?

Wade

Cheryll & Wade Schuette
2345 Stone Road
Ann Arbor MI 48105
734-763-8278


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Dear Doctor Pagakis:
Molecular Probes makes plastic beads incorporated with fluorescin (and other
markers) that fluoresce at known relative intensities for use in calibrating
data. The kits include mounting media for mounting the beads on slides.
These may be what you need.

--------------------------------------------
William J. Clerici, Ph.D.
Associate Professor
Rm. C-236, Department of Surgery
Division of Otolaryngology-HNS
University of Kentucky Chandler Medical Center
800 Rose Street
Lexington, KY 40536-0084
           ------------------
Telephone: (606) 257-5097
      (lab): (606) 257-6020
      FAX: (606) 257-5096
      e-mail: bcler1@pop.uky.edu
--------------------------------------------


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------------------------------

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nih-image-d Digest				Volume 99 : Issue 69

Today's Topics:
  Re: extending a rectangular selectio  [ GJOSS@rna.bio.mq.edu.au ]
  Re: Big Images, memory limits and wh  [ GJOSS@rna.bio.mq.edu.au ]
  Re: Object trace                      [ "Greg Joss" <gjoss@rna.bio.mq.edu.a ]
  Re: Object trace                      [ "Zuccala David" <zuccala@cris.enel. ]
  Re: Object trace                      [ Cheryll & Wade Schuette <schuette@s ]
  Re: No subject was specified.         [ "Bill Clerici, Ph.D." <bcler1@pop.u ]

------------------------------

Date:          Mon, 22 Mar 1999 10:12:46 +1100
From: GJOSS@rna.bio.mq.edu.au
To: a.jonker@amc.uva.nl, nih-image@io.ece.drexel.edu
Subject:       Re: extending a rectangular selection.
Message-ID: <292FD1C5888@rna.bio.mq.edu.au>

>Date: Fri, 19 Mar 1999 08:37:11 +0100
>To: nih-image@io.ece.drexel.edu
>From: Ard Jonker <a.jonker@amc.uva.nl>
>Subject: Re: nih-image-d Digest V99 #65
>Cc: GJOSS@rna.bio.mq.edu.au
>
>Greg Joss wrote:
>
>>However, if you want accurate selections with large or zoomed images, be 
>>aware that you can alternate scroll(hand) and selection tools extending 
>>an existing straight line selection from either end or an existing 
>>rectanular selection from the bottom left corner so that one end of the 
>>selection may be well off screen to cover the 3000 pixels.
>
>Do you mean that I can extend a, say, 500x500 selection to a 600x500 
>selection by appropriately clicking in the lower lefthand corner of the 
>marching ants rectangle? As far as I could see, it either
>moves the marching ants without extending it, or it generates a whole new 
>selection if you click just outside the marching ants.
>
>I know shift-clicking could add an extra 500x100 box to the 500x500 box, 
>but that is not what I mean.
>
>Ard
>
>dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
>Dep of Cell Biology and Histology  |Meibergdreef 15
>Faculty of Medicine                |1105 AZ Amsterdam
>University of Amsterdam            |The Netherlands
>tel +31 20 566 5304                |fax +31 20 697 4156
>
Except for my silly slip of keying "bottom left corner" when it should have 
been "bottom RIGHt corner", yes, you "can extend a, say, 500x500 selection 
to a 600x500 selection".

In the bottom RIGHT corner of the marching ants rectangle of the selection 
is displayed a small (5x5 pixel) black square. If you drag within this 
square, the top left corner remains anchored while the bottom right can be 
extended (modified) at will. This allows you to alternate between 
selection, scroll(hand), magnifying glass tools so that selections can be 
made/modified with pixel accuracy even on a 4096 pixel wide image and with 
pixels magnified so that the mouse can be accurately positioned for the 
selection. The anchoring of top left and freedom of the bottom right can be 
accomodated in the occassional case where the top must be determined by the 
right hand side by also dragging within the selection (not in the black 
square bottom-left-corner) so that the whole selection is dragged. A simple 
iteration to set (top) left, (bottom) right, top right, top left, bottom 
(right) will be readily achieved with a little practice.
Alternately, in this special case, you might prefer to flip the image 
horizontally.

If you do this type activity in a production mode, then single key macros 
to selectTool's are convenient.

Greg
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date:          Mon, 22 Mar 1999 10:49:45 +1100
From: GJOSS@rna.bio.mq.edu.au
To: Noel.Goldsmith@dsto.defence.gov.au, nih-image@io.ece.drexel.edu
Subject:       Re: Big Images, memory limits and what to do
Message-ID: <29397CD16DF@rna.bio.mq.edu.au>

>From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
>To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
>Subject: Big Images, memory limits and what to do
>Date: Fri, 19 Mar 1999 11:56:14 +1100
>
>1. I you have an image which is too big for the screen and want to look at
>all of it and do a line trace.
>
>Solution.
>Scale to fit window. 
>Then if you want it smaller still grab the bottom right hand conrner and
>drag it as small as you like.
>
>If Image objects about not enough memory, give it more. Also set the undo
>buffer in the prefs control panel.
>The limit would be about (2 or 4 Gb) I think as the manual says an Image 
>can
>be as big as you like but for editing you can only cut, copy paste bits as
>wide as 4096 pixels, but these can be as long as you like.
>So an Image could be 4000 wide and 40,000 long.
>With a current G3 you could have 1Gb of Ram and as much Virtual RAM as you
>want on the disc.
>
>I have had Image running with 300 Mb without any dramas.
>Best wishes
>Noel Goldsmith
>

Noel, 

Thanks for tip, I had not previously picked up on:
>Scale to fit window. 
>Then if you want it smaller still grab the bottom right hand conrner and
>drag it as small as you like.

I hadn't realised that, after "Scale to fit window", draging the window 
corner rescales the image as well as reducing the image window.

However, my experience with image size is a liitle different to yours:
> but these can be as long as you like.
>So an Image could be 4000 wide and 40,000 long.

With 120 MB allocated to image and 40960K to clipboard,
the following macro
macro'/0test';var w,h,wp,hp,n:integer;begin w:=8;h:=1024;hp:=h;
while h=hp do begin h:=h+h/2;
if n>0 then dispose;n:=n+1; 
setnewsize(w,h);makeNewWindow('temp');
getPicsize(wp,hp);
showMessage(n,'\',h,'\',hp);
end;
end

terminates with
7
17496
16383
in info window.

with h:=h+h/2; :
4
16384
16383

I have also found that I cannot 'import' images longer than about 20K even 
if only 1 wide. 

Greg.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Mon, 22 Mar 1999 15:11:28 +1100
From: "Greg Joss" <gjoss@rna.bio.mq.edu.au>
To: "DAVID W SCHMIDTKE" <dws@seas.upenn.edu>, nih-image@io.ece.drexel.edu
Subject: Re: Object trace
Message-Id: <199903220411.PAA26170@llymarch.bio.mq.edu.au>

Date forwarded: 	Sat, 20 Mar 1999 14:24:45 -0500 (EST)
Subject:        	Object trace
To:             	nih-image@io.ece.drexel.edu (NIH Image)
Date sent:      	Sat, 20 Mar 1999 14:14:22 -0500 (EST)
From:           	"DAVID W SCHMIDTKE" <dws@seas.upenn.edu>
Forwarded by:   	nih-image@io.ece.drexel.edu
Send reply to:  	nih-image@io.ece.drexel.edu

> I am using Scion Image to analyze particle motion.  I have a stack of 
> images and would like to superimpose these images into one picture to track 
> the motion of the particle. Does anyone know how to do this. Thanks for 
> the help.  
> 
> Dave
> 
> dws@seas.upenn.edu
> 
You can quite simply "project" the images onto a composite stack using the 
"project(stacks menu" in Scion or NIH-Image on the IBM PC or Mac.

You may need to persist with your efforts to get a proper understanding of 
project parameters as it is designed to do more sophisticated projections than 
you want so that the excess of options can be a little confusing at first.
The main aspect to keep in mind is that project is written with black as the 
expected transparent background (inverse to Image) so that you may find it 
easier to invert your image. ie the things you want to see should be bright (ie 
lower pixel value) on a dark (higher pixel value) background.

For your purpose, set total rotation to 0 so that the projection stack will be only 
one slice (you are not looking for a rotating 3D view).

Set surface opacity=0 so that you can see through all layers.

upper/lower transparency bounds can be used in an analogous way to 
setDensitySlice to control the intensity range of the visible objects as opposed 
to the background to be made transparent.



Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Mon, 22 Mar 1999 09:55:25 -0800
From: "Zuccala David" <zuccala@cris.enel.it>
To: nih-image@io.ece.drexel.edu
Subject: Re: Object trace
Message-ID: <36F6840D.72B1@cris.enel.it>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

> I am using Scion Image to analyze particle motion.  I have a stack of
> images and would like to superimpose these images into one picture to track
> the motion of the particle. Does anyone know how to do this. Thanks for
> the help.
> 
> Dave
> 
> dws@seas.upenn.edu

Dear David,
open your stack, do "Stack to windows" to get a set of separate images,
and try the following simple macro that I wrote for Scion Image:

macro 'Minimum'
  { Applies the min operator to all open images } 
var
  N, i, Result: integer;
begin
  N := nPics;  { number of open images }
  if N<2 then Exit('I need at least 2 images');
  ImageMath('min', 1, 2, 1, 0, 'Result');  { minimum between the first 2
images }
  Result := PidNumber;  { Pid of the active image ('Result') }
  for i:=3 to N do begin
    ImageMath('min', i, Result, 1, 0, Result);
  end
end;


The macro supposes that your particle be white on a black background
(gray level of the particle less than the background gray level). If
not, invert your images or change "min" into "max" in the macro.
Hope this helps.
David

*****************************************************
David Zuccala'
ENEL RICERCA - Polo Idraulico e Strutturale              
v. Pozzobonelli, 6       ph.: + 39 02 7224.3587
I - 20162 Milano         fax: + 39 02 7224.3530
                         e-mail: zuccala@cris.enel.it

------------------------------

Date: Mon, 22 Mar 1999 06:00:09 -0500
From: Cheryll & Wade Schuette <schuette@s.imap.itd.umich.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Object trace
Message-Id: <3.0.5.32.19990322060009.00977380@s.imap.itd.umich.edu>
Content-Type: text/plain; charset="us-ascii"

At 02:14 PM 3/20/99 -0500, you wrote:
>I am using Scion Image to analyze particle motion.  I have a stack of 
>images and would like to superimpose these images into one picture to track 
>the motion of the particle. Does anyone know how to do this. Thanks for 
>the help.  
>
>Dave

The answers posted so far assume, I think, that the images in your stack
are identically aligned (registered), and the only thing moving is the
particle.   Is that a valid assumption, or is there also some camera or
background jitter or motion that needs to be compensated for as well?

Wade

Cheryll & Wade Schuette
2345 Stone Road
Ann Arbor MI 48105
734-763-8278

------------------------------

Date: Mon, 22 Mar 1999 09:11:06 -0500 (EST)
From: "Bill Clerici, Ph.D." <bcler1@pop.uky.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: No subject was specified.
Message-Id: <2.2.16.19990322091104.344f647c@pop.uky.edu>
Content-Type: text/plain; charset="us-ascii"

Dear Doctor Pagakis:
Molecular Probes makes plastic beads incorporated with fluorescin (and other
markers) that fluoresce at known relative intensities for use in calibrating
data. The kits include mounting media for mounting the beads on slides.
These may be what you need.

--------------------------------------------
William J. Clerici, Ph.D.
Associate Professor
Rm. C-236, Department of Surgery
Division of Otolaryngology-HNS
University of Kentucky Chandler Medical Center
800 Rose Street
Lexington, KY 40536-0084
           ------------------
Telephone: (606) 257-5097
      (lab): (606) 257-6020
      FAX: (606) 257-5096
      e-mail: bcler1@pop.uky.edu
--------------------------------------------

--------------------------------
End of nih-image-d Digest V99 Issue #69
***************************************

From nih-image-request@io.ece.drexel.edu Mon Mar 22 11:33 EST 1999
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Hi NIH-Imagers

I have a request for advice from NIH-Image experts. I am trying to use NIH-Image to analyse EM 
serial section stacks of nuclei. However, I do not have any true fiducial markers, and will need 
to register the sections as best I can by using structures such as nuclear outline, nucleolar 
outline, coiled bodies etc. I would like to do this by eye - flipping back and forth between each 
section and the next one  while moving the next to align it. I think only x-y translational 
alignment  is needed. Any ideas about how NIH-Image could do this? Thanks.

Peter Shaw  John Innes Centre, Norwich, UK. 01603-452571
peter.shaw@bbsrc.ac.uk


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Peter,

We have used the 'Paste Control' and/or the 'Live Paste' features in
NIH-Image with a lot of success.  We can superimpose the current image with
the previous image to line up the relvant features.

Joel


>Hi NIH-Imagers
>
>I have a request for advice from NIH-Image experts. I am trying to use
>NIH-Image to analyse EM
>serial section stacks of nuclei. However, I do not have any true fiducial
>markers, and will need
>to register the sections as best I can by using structures such as nuclear
>outline, nucleolar
>outline, coiled bodies etc. I would like to do this by eye - flipping back
>and forth between each
>section and the next one  while moving the next to align it. I think only
>x-y translational
>alignment  is needed. Any ideas about how NIH-Image could do this? Thanks.
>
>Peter Shaw  John Innes Centre, Norwich, UK. 01603-452571
>peter.shaw@bbsrc.ac.uk


****************************************************************************

CunhaLab, UCSF                          |
Mount Zion Cancer Center, Box 0540      |
2340 Sutter Street, Room S241	        | Tel:     (415) 476-6746
San Francisco, CA 94115    	        | Fax:     (415) 502-2270



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Hi,
I take adjacent overlapping images and would like to align and add them
to a larger montage automatically.
Has anyone done something similar and can give me some hints?
Thank you for any help!

Ralf






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Date: Mon, 22 Mar 1999 11:31:59 -0700
From: Peter Guthrie <Peter.Guthrie@hsc.utah.edu>
Subject: NIH Animations to Windows Powerpoint
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I know aspects of this have been discussed, but I have not yet found a
satisfactory solution to this porblem.

I have a variety of movies I have made in nih-image (generally calcium
imaging) which I need to be able to play in PowerPoint on a Windows
computer.  I can save the movies in quicktime from nih-image, flatten them
with MoviePlayer (2.5.1), and play them on the Windows machine with Apple's
Quicktime Player.  The problem comes with trying to import them into
PowerPoint.  Some of the movies will import and play fine; others will not.
>From !!long and repeated!! discussions with Microsoft, it is clear that if
the movie will not play in their Media Player, then it will not play in
PowerPoint.

I have tried to convert them to MPEG using Sparkle (2.4.5) with marginal
success.  Sometimes the movie looks OK, sometimes, it will lock up the
Windows Media Player.  I have tried converting to AVI movies using TRMOOV
(which works sometimes) and using the Asymetrix Digital Video Producer
(which sometimes works), but have not found any conversion system which
will work with all Macintosh Quicktime movies.  The only thing I am fairly
confident will always work is to convert the movies to individual frames,
convert the frames to jpeg files, and reassemble the frames into an AVI
movie using AVIConstructor on the Windows computer.

Does anyone have a better way (using freeware, shareware, or even
commercial software)?  Does anyone know if using a different version of
Quicktime, MoviePlayer, or Sparkle might be more successful?

Thanks


Peter Guthrie
Department of Neurobiology & Anatomy
University of Utah School of Medicine
50 N Medical Drive
Salt Lake City, UT  84132
(801) 581-8336       (801) 581-4233 fax
Peter.Guthrie@hsc.utah.edu



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Hello Peter,
As an alternative you can use Photoshop to cut and paste individual images
as "layers". The transparency of the image "layer" can be reduced to allow
rotational or X-Y alignment to underlying reference points in the image
"layer" below. The now aligned image can be cut and paste and used in NIH as
you please. Hope this helps.
--
Ken Baker M.Sc.
Microscopy, Imaging, Analysis
--
KWB@bserv.com
519-853-4787



----------
>From: "peter.shaw" <peter.shaw@bbsrc.ac.uk>
>To: nih-image@io.ece.drexel.edu
>Subject: registration of serial sections
>Date: Mon, Mar 22, 1999, 9:48 AM
>

> Hi NIH-Imagers
>
> I have a request for advice from NIH-Image experts. I am trying to use
> NIH-Image to analyse EM
> serial section stacks of nuclei. However, I do not have any true fiducial
> markers, and will need
> to register the sections as best I can by using structures such as nuclear
> outline, nucleolar
> outline, coiled bodies etc. I would like to do this by eye - flipping back
> and forth between each
> section and the next one  while moving the next to align it. I think only
> x-y translational
> alignment  is needed. Any ideas about how NIH-Image could do this? Thanks.
>
> Peter Shaw  John Innes Centre, Norwich, UK. 01603-452571
> peter.shaw@bbsrc.ac.uk
>
> 


From nih-image-request@io.ece.drexel.edu Mon Mar 22 17:42 EST 1999
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From: GJOSS@rna.bio.mq.edu.au
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>Subject: registration of serial sections
>To: nih-image@io.ece.drexel.edu
>Date: Mon, 22 Mar 99 14:48:42 +0000
>
>Hi NIH-Imagers
>
>I have a request for advice from NIH-Image experts. I am trying to use 
>NIH-Image to analyse EM 
>serial section stacks of nuclei. However, I do not have any true fiducial 
>markers, and will need 
>to register the sections as best I can by using structures such as nuclear 
>outline, nucleolar 
>outline, coiled bodies etc. I would like to do this by eye - flipping back 
>and forth between each 
>section and the next one  while moving the next to align it. I think only 
>x-y translational 
>alignment  is needed. Any ideas about how NIH-Image could do this? Thanks.
>
>Peter Shaw  John Innes Centre, Norwich, UK. 01603-452571
>peter.shaw@bbsrc.ac.uk
>
>
As Joel Brody stated the key to this is the use of 'Paste Control' which 
offers blend,replace and particularly XOR options. XOR will cause a paste 
of unregististed but identical scenes to turn all white (0) when 
registration is achieved. For similar scenes, the edge differences will be 
very clear when nearly registered. You can switch paste mode to copy or 
replace after you have found correct registration. The operation sequence 
with mouse takes a little practice to become familiar with it. You are, of 
course, using paste as a dummy operation to combine sequential image frames 
to find alignment positions; not actually pasteing in the usual sense.

Some useful hints: 
note that you can use arrow keys instead of mouse for accurate movement of 
paste.
'undo' is useful, particularly when implemented as toggled single key macro 
to paste/undo/translate until movement flicker is minimised.
also make sure you understand "restoreRoi"

For EM which is monochrome, I see no advantage in Photoshop but 
Photoshop is more convenient for colour images.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


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Peter,
I had a similar problem and somebody from the 
group suggested a shareware called Platypus Animator to 
make avi movies. It is easy to use - you just load up 
individual tif files in the correct order and then tell it 
to make the avi file. I have then been able to play the 
movies in Powerpoint - as an option in ppt you can loop the 
movie to play continuously. I have tried this with upto 30 
768x512 pix frames. Paul.

On Mon, 22 Mar 1999 11:31:59 -0700 Peter Guthrie 
<Peter.Guthrie@hsc.utah.edu> wrote:

> I know aspects of this have been discussed, but I have not yet found a
> satisfactory solution to this porblem.
> 
> I have a variety of movies I have made in nih-image (generally calcium
> imaging) which I need to be able to play in PowerPoint on a Windows
> computer.  I can save the movies in quicktime from nih-image, flatten them
> with MoviePlayer (2.5.1), and play them on the Windows machine with Apple's
> Quicktime Player.  The problem comes with trying to import them into
> PowerPoint.  Some of the movies will import and play fine; others will not.
> >From !!long and repeated!! discussions with Microsoft, it is clear that if
> the movie will not play in their Media Player, then it will not play in
> PowerPoint.
> 
> I have tried to convert them to MPEG using Sparkle (2.4.5) with marginal
> success.  Sometimes the movie looks OK, sometimes, it will lock up the
> Windows Media Player.  I have tried converting to AVI movies using TRMOOV
> (which works sometimes) and using the Asymetrix Digital Video Producer
> (which sometimes works), but have not found any conversion system which
> will work with all Macintosh Quicktime movies.  The only thing I am fairly
> confident will always work is to convert the movies to individual frames,
> convert the frames to jpeg files, and reassemble the frames into an AVI
> movie using AVIConstructor on the Windows computer.
> 
> Does anyone have a better way (using freeware, shareware, or even
> commercial software)?  Does anyone know if using a different version of
> Quicktime, MoviePlayer, or Sparkle might be more successful?
> 
> Thanks
> 
> 
> Peter Guthrie
> Department of Neurobiology & Anatomy
> University of Utah School of Medicine
> 50 N Medical Drive
> Salt Lake City, UT  84132
> (801) 581-8336       (801) 581-4233 fax
> Peter.Guthrie@hsc.utah.edu
> 

----------------------
Paul Stoodley

Environmental         Tel: 01392 264348       
Microbiology          Fax: 01392 263700
Research              email: p.stoodley@exeter.ac.uk
Group
Exeter University

Biological Sciences
Hatherly Laboratories
Prince of Wales Road
Exeter EX4 4PS. UK.


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------------------------------

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nih-image-d Digest				Volume 99 : Issue 70

Today's Topics:
  unsubscribe                           [ Michael Clayton <clayton@bcm.tmc.ed ]
  registration of serial sections       [ "peter.shaw" <peter.shaw@bbsrc.ac.u ]
  Re: registration of serial sections   [ Joel Brody <jbrody@itsa.ucsf.edu> ]
  unsubscribe                           [ ebonino@physun.geo.ulg.ac.be ]
  overlapping image alignment           [ Ralf Kemkemer <ralf.kemkemer@physik ]
  NIH Animations to Windows Powerpoint  [ Peter Guthrie <Peter.Guthrie@hsc.ut ]
  Re: registration of serial sections   [ "Ken Baker" <kwb@bserv.com> ]
  registration of serial sections       [ GJOSS@rna.bio.mq.edu.au ]
  Re: NIH Animations to Windows Powerp  [ paul stoodley <P.Stoodley@exeter.ac ]

------------------------------

Date: Mon, 22 Mar 1999 08:16:18 -0600
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------------------------------

Date: Mon, 22 Mar 99 14:48:42 +0000
From: "peter.shaw" <peter.shaw@bbsrc.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: registration of serial sections
Message-Id: <990322144841.655@mserv.jic.bbsrc.ac.uk.0>
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Hi NIH-Imagers

I have a request for advice from NIH-Image experts. I am trying to use NIH-Image to analyse EM 
serial section stacks of nuclei. However, I do not have any true fiducial markers, and will need 
to register the sections as best I can by using structures such as nuclear outline, nucleolar 
outline, coiled bodies etc. I would like to do this by eye - flipping back and forth between each 
section and the next one  while moving the next to align it. I think only x-y translational 
alignment  is needed. Any ideas about how NIH-Image could do this? Thanks.

Peter Shaw  John Innes Centre, Norwich, UK. 01603-452571
peter.shaw@bbsrc.ac.uk

------------------------------

Date: Mon, 22 Mar 1999 09:02:05 -0800
From: Joel Brody <jbrody@itsa.ucsf.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: registration of serial sections
Message-Id: <v03130300b31c276e3eb9@[128.218.158.175]>
Content-Type: text/plain; charset="us-ascii"

Peter,

We have used the 'Paste Control' and/or the 'Live Paste' features in
NIH-Image with a lot of success.  We can superimpose the current image with
the previous image to line up the relvant features.

Joel


>Hi NIH-Imagers
>
>I have a request for advice from NIH-Image experts. I am trying to use
>NIH-Image to analyse EM
>serial section stacks of nuclei. However, I do not have any true fiducial
>markers, and will need
>to register the sections as best I can by using structures such as nuclear
>outline, nucleolar
>outline, coiled bodies etc. I would like to do this by eye - flipping back
>and forth between each
>section and the next one  while moving the next to align it. I think only
>x-y translational
>alignment  is needed. Any ideas about how NIH-Image could do this? Thanks.
>
>Peter Shaw  John Innes Centre, Norwich, UK. 01603-452571
>peter.shaw@bbsrc.ac.uk


****************************************************************************

CunhaLab, UCSF                          |
Mount Zion Cancer Center, Box 0540      |
2340 Sutter Street, Room S241	        | Tel:     (415) 476-6746
San Francisco, CA 94115    	        | Fax:     (415) 502-2270

------------------------------

Date: Mon, 22 Mar 1999 20:11:05 -0100
From: ebonino@physun.geo.ulg.ac.be
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
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unsubscribe

------------------------------

Date: Mon, 22 Mar 1999 19:23:45 +0100
From: Ralf Kemkemer <ralf.kemkemer@physik.uni-ulm.de>
To: nih-image@io.ece.drexel.edu
Subject: overlapping image alignment
Message-ID: <36F68AB1.401247CD@physik.uni-ulm.de>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi,
I take adjacent overlapping images and would like to align and add them
to a larger montage automatically.
Has anyone done something similar and can give me some hints?
Thank you for any help!

Ralf

------------------------------

Date: Mon, 22 Mar 1999 11:31:59 -0700
From: Peter Guthrie <Peter.Guthrie@hsc.utah.edu>
To: nih-image@io.ece.drexel.edu
Subject: NIH Animations to Windows Powerpoint
Message-id: <l03010d00b31c3aa4d25f@[155.100.251.108]>
Content-type: text/plain; charset="us-ascii"

I know aspects of this have been discussed, but I have not yet found a
satisfactory solution to this porblem.

I have a variety of movies I have made in nih-image (generally calcium
imaging) which I need to be able to play in PowerPoint on a Windows
computer.  I can save the movies in quicktime from nih-image, flatten them
with MoviePlayer (2.5.1), and play them on the Windows machine with Apple's
Quicktime Player.  The problem comes with trying to import them into
PowerPoint.  Some of the movies will import and play fine; others will not.
>From !!long and repeated!! discussions with Microsoft, it is clear that if
the movie will not play in their Media Player, then it will not play in
PowerPoint.

I have tried to convert them to MPEG using Sparkle (2.4.5) with marginal
success.  Sometimes the movie looks OK, sometimes, it will lock up the
Windows Media Player.  I have tried converting to AVI movies using TRMOOV
(which works sometimes) and using the Asymetrix Digital Video Producer
(which sometimes works), but have not found any conversion system which
will work with all Macintosh Quicktime movies.  The only thing I am fairly
confident will always work is to convert the movies to individual frames,
convert the frames to jpeg files, and reassemble the frames into an AVI
movie using AVIConstructor on the Windows computer.

Does anyone have a better way (using freeware, shareware, or even
commercial software)?  Does anyone know if using a different version of
Quicktime, MoviePlayer, or Sparkle might be more successful?

Thanks


Peter Guthrie
Department of Neurobiology & Anatomy
University of Utah School of Medicine
50 N Medical Drive
Salt Lake City, UT  84132
(801) 581-8336       (801) 581-4233 fax
Peter.Guthrie@hsc.utah.edu

------------------------------

Date: Mon, 22 Mar 1999 16:00:45 -0500
From: "Ken Baker" <kwb@bserv.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: registration of serial sections
Message-Id: <199903222058.PAA03951@bserv.com>
Content-type: text/plain; charset="US-ASCII"
Content-transfer-encoding: 7bit

Hello Peter,
As an alternative you can use Photoshop to cut and paste individual images
as "layers". The transparency of the image "layer" can be reduced to allow
rotational or X-Y alignment to underlying reference points in the image
"layer" below. The now aligned image can be cut and paste and used in NIH as
you please. Hope this helps.
--
Ken Baker M.Sc.
Microscopy, Imaging, Analysis
--
KWB@bserv.com
519-853-4787



----------
>From: "peter.shaw" <peter.shaw@bbsrc.ac.uk>
>To: nih-image@io.ece.drexel.edu
>Subject: registration of serial sections
>Date: Mon, Mar 22, 1999, 9:48 AM
>

> Hi NIH-Imagers
>
> I have a request for advice from NIH-Image experts. I am trying to use
> NIH-Image to analyse EM
> serial section stacks of nuclei. However, I do not have any true fiducial
> markers, and will need
> to register the sections as best I can by using structures such as nuclear
> outline, nucleolar
> outline, coiled bodies etc. I would like to do this by eye - flipping back
> and forth between each
> section and the next one  while moving the next to align it. I think only
> x-y translational
> alignment  is needed. Any ideas about how NIH-Image could do this? Thanks.
>
> Peter Shaw  John Innes Centre, Norwich, UK. 01603-452571
> peter.shaw@bbsrc.ac.uk
>
> 

------------------------------

Date:          Tue, 23 Mar 1999 9:26:55 +1100
From: GJOSS@rna.bio.mq.edu.au
To: peter.shaw@bbsrc.ac.uk, nih-image@io.ece.drexel.edu
Subject:       registration of serial sections
Message-ID: <2AA37D54F84@rna.bio.mq.edu.au>

>Subject: registration of serial sections
>To: nih-image@io.ece.drexel.edu
>Date: Mon, 22 Mar 99 14:48:42 +0000
>
>Hi NIH-Imagers
>
>I have a request for advice from NIH-Image experts. I am trying to use 
>NIH-Image to analyse EM 
>serial section stacks of nuclei. However, I do not have any true fiducial 
>markers, and will need 
>to register the sections as best I can by using structures such as nuclear 
>outline, nucleolar 
>outline, coiled bodies etc. I would like to do this by eye - flipping back 
>and forth between each 
>section and the next one  while moving the next to align it. I think only 
>x-y translational 
>alignment  is needed. Any ideas about how NIH-Image could do this? Thanks.
>
>Peter Shaw  John Innes Centre, Norwich, UK. 01603-452571
>peter.shaw@bbsrc.ac.uk
>
>
As Joel Brody stated the key to this is the use of 'Paste Control' which 
offers blend,replace and particularly XOR options. XOR will cause a paste 
of unregististed but identical scenes to turn all white (0) when 
registration is achieved. For similar scenes, the edge differences will be 
very clear when nearly registered. You can switch paste mode to copy or 
replace after you have found correct registration. The operation sequence 
with mouse takes a little practice to become familiar with it. You are, of 
course, using paste as a dummy operation to combine sequential image frames 
to find alignment positions; not actually pasteing in the usual sense.

Some useful hints: 
note that you can use arrow keys instead of mouse for accurate movement of 
paste.
'undo' is useful, particularly when implemented as toggled single key macro 
to paste/undo/translate until movement flicker is minimised.
also make sure you understand "restoreRoi"

For EM which is monochrome, I see no advantage in Photoshop but 
Photoshop is more convenient for colour images.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Tue, 23 Mar 1999 09:27:25 +0000 (GMT Standard Time)
From: paul stoodley <P.Stoodley@exeter.ac.uk>
To: nih-image@io.ece.drexel.edu
cc: nih-image@io.ece.drexel.edu
Subject: Re: NIH Animations to Windows Powerpoint
Message-ID: <SIMEON.9903230925.A@sn687.ex.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

Peter,
I had a similar problem and somebody from the 
group suggested a shareware called Platypus Animator to 
make avi movies. It is easy to use - you just load up 
individual tif files in the correct order and then tell it 
to make the avi file. I have then been able to play the 
movies in Powerpoint - as an option in ppt you can loop the 
movie to play continuously. I have tried this with upto 30 
768x512 pix frames. Paul.

On Mon, 22 Mar 1999 11:31:59 -0700 Peter Guthrie 
<Peter.Guthrie@hsc.utah.edu> wrote:

> I know aspects of this have been discussed, but I have not yet found a
> satisfactory solution to this porblem.
> 
> I have a variety of movies I have made in nih-image (generally calcium
> imaging) which I need to be able to play in PowerPoint on a Windows
> computer.  I can save the movies in quicktime from nih-image, flatten them
> with MoviePlayer (2.5.1), and play them on the Windows machine with Apple's
> Quicktime Player.  The problem comes with trying to import them into
> PowerPoint.  Some of the movies will import and play fine; others will not.
> >From !!long and repeated!! discussions with Microsoft, it is clear that if
> the movie will not play in their Media Player, then it will not play in
> PowerPoint.
> 
> I have tried to convert them to MPEG using Sparkle (2.4.5) with marginal
> success.  Sometimes the movie looks OK, sometimes, it will lock up the
> Windows Media Player.  I have tried converting to AVI movies using TRMOOV
> (which works sometimes) and using the Asymetrix Digital Video Producer
> (which sometimes works), but have not found any conversion system which
> will work with all Macintosh Quicktime movies.  The only thing I am fairly
> confident will always work is to convert the movies to individual frames,
> convert the frames to jpeg files, and reassemble the frames into an AVI
> movie using AVIConstructor on the Windows computer.
> 
> Does anyone have a better way (using freeware, shareware, or even
> commercial software)?  Does anyone know if using a different version of
> Quicktime, MoviePlayer, or Sparkle might be more successful?
> 
> Thanks
> 
> 
> Peter Guthrie
> Department of Neurobiology & Anatomy
> University of Utah School of Medicine
> 50 N Medical Drive
> Salt Lake City, UT  84132
> (801) 581-8336       (801) 581-4233 fax
> Peter.Guthrie@hsc.utah.edu
> 

----------------------
Paul Stoodley

Environmental         Tel: 01392 264348       
Microbiology          Fax: 01392 263700
Research              email: p.stoodley@exeter.ac.uk
Group
Exeter University

Biological Sciences
Hatherly Laboratories
Prince of Wales Road
Exeter EX4 4PS. UK.

--------------------------------
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From nih-image-request@io.ece.drexel.edu Tue Mar 23 05:23 EST 1999
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To: nih-image@io.ece.drexel.edu, Peter Shaw <peter.shaw@bbsrc.ac.uk>
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
Subject: Re: Registration of serial sections
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Peter Shaw wrote:

>...I am trying to use NIH-Image to analyse EM serial section stacks of
>nuclei. However, I do not have any true fiducial markers, and will need
>to register the sections as best I can by using structures such as nuclear
>outline, nucleolar outline, coiled bodies etc.
>...I think only x-y translational alignment is needed.

A spin-off of NIH Image, called Image SXM, has been written to handle
scanning microscopy images. In addition to various routines written with
SEM, SPM or SAM images in mind, there are also some routines of more
general interest.

One of the latest to be added is an 'Auto Register' routine that uses
cross-correlation of images to shift all slices of a stack into registry
with the current slice. It sounds like this might be of use to you.

The latest version of Image SXM is being beta-tested for release next
month. Anyone interested in this version with the 'Auto Register' feature
can email me for a copy.

For more information about Image SXM, see http://reg.ssci.liv.ac.uk

___________________________________________________________________
Dr Steve Barrett
Surface Science Research Centre
University of Liverpool
Liverpool L69 3BX
United Kingdom

Tel: 44-(0)151-794-3894 / 3874 / 3541
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk
___________________________________________________________________



From nih-image-request@io.ece.drexel.edu Tue Mar 23 06:39 EST 1999
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To: nih-image@io.ece.drexel.edu
From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: Re: Big Images, memory limits and what to do
Cc: GJOSS@rna.bio.mq.edu.au.Noel.Goldsmith@dsto.defence.gov.au
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>I have also found that I cannot 'import' images longer than about 20K even 
>if only 1 wide. 

the limit is 32K lines: this works:
macro 'open long file' var test:string;
begin setImport('custom'); setcustom(10,32767,0); import('test');end;

and this doesn't.
macro 'open long file' var test:string;
begin setImport('custom'); setcustom(10,32768,0); import('test');end;

For some silly reason, the file is available in the 'windows' menu, but it is not displayed on my screen.

Ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156



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>I have a request for advice from NIH-Image experts. I 
>am trying to use NIH-Image to analyse EM 
>serial section stacks of nuclei. However, I do not 
>have any true fiducial markers, and will need 
>to register the sections as best I can by using 
>structures such as nuclear outline, nucleolar 
>outline, coiled bodies etc. I would like to do this by 
>eye - flipping back and forth between each 
>section and the next one  while moving the next to 
>align it. I think only x-y translational 
>alignment  is needed. Any ideas about how NIH-Image 
>could do this? Thanks.

Use Object Image to put nondestructive markers on each image that is collected in a stack. If you got them all right, by shifting and flipping to and fro, apply the 'register' command. Use the nondestructive markers to enter the fiducials, ie. click on each nondestructive marker while actually entering the fiducials.

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156



From nih-image-request@io.ece.drexel.edu Tue Mar 23 07:20 EST 1999
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From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: NIH Animations to Windows Powerpoint
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>Does anyone have a better way (using freeware, shareware, or even
>commercial software)?  Does anyone know if using a different version of
>Quicktime, MoviePlayer, or Sparkle might be more successful?

You could consider a web browser for display, rather than PowerPoint. Web browsers have an unequalled platform independenness. If you install the quicktime plugin on either machine, you can present any graphic material on either machine.
To save PowerPoint stuff for this kind of presentation, print them to a pdf file (e.g. with the PDFWriter that is bundled from the first version of Adobe Acrobat) and link the presentation in HTML to the acrobat file. A plugin for acrobat exists too, circumventing any problem you are currently experiencing. We have our lectures in HTML presented from a FileMaker database this way.

Ard



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Can someone please tell me where I can find or download a document describing the validation or FDA approval of NIH Image 1.61?

Thank you

Tim Crowe
crowet@cesmtp.ccf.org


From nih-image-request@io.ece.drexel.edu Tue Mar 23 11:18 EST 1999
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Subject: Re: NIH Animations to Windows Powerpoint
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>...I have a variety of movies I have made in nih-image...The problem
> comes with trying to import them into PowerPoint.  Some of the movies
> will import and play fine; others will not...


   I had a similar problem last summer, and spent considerable time
tracking down various aspects of the solution.  What I found was:
   First, what codec are you using to compress the movies?  I have found
that only Cinepak (the native codec) and a couple of others (which
unfortunately I don't remember now) will work.
   Second, PowerPoint uses the ActiveMovie driver mciqtz.drv to play
QuickTime movies.  If you have removed Internet Explorer from your PC (as I
always do), you probably removed this driver (as I did), since MicroSoft at
some point made it part of Explorer (one origin of their claim that
Explorer can't be reomved without compromising the system).  The driver can
be restored by installing the latest version of MediaPlayer.
   Third, I found early on that I sometimes had to change the file
extension from .mov to .qt before PowerPoint would properly insert a movie.
(This is probably related to the next "fix," which, with the previous
three, finally resolved all of the problems.)
   Fourth, PowerPoint looks for the mciqtz driver through a pointer called
MPEGvideo in the system.ini file.  Certain installers, like those for
QuickTime and some DVD drivers, may change this pointer, and some other
pointers that associate file extensions with MPEGVideo.  The instructions
for restoring these pointers can be found in:

   http://support.microsoft.com/support/kb/articles/q178/2/91.asp

Hope this helps.



From nih-image-request@io.ece.drexel.edu Tue Mar 23 11:49 EST 1999
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Date: Tue, 23 Mar 1999 08:32:28 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re:registration of serial sections
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Open those images with common structures and make a small stack.  Then use
the "Register.." function found in the Stacks Menu.  This is explained in
the manual more fully, but you just click on two points common to each
image as you step through the stack.  The function performs the alignment.
You can then convert the aligned stack back into individual files with
"Stack to Windows".  close all but one of those files to use as the
aligment template for the next few images in your series.

Photoshop layers are convenient for alignment of small numbers of images.

Regards,
Glen



Glen MacDonald
   Research Scientist
Hearing Research Laboratories of the
Virginia Merrill Bloedel Hearing Research Center
Box 35-7923
University of Washington
Seattle, WA  98195-7923
(206) 616-4156
glenmac@u.washington.edu




From nih-image-request@io.ece.drexel.edu Tue Mar 23 14:41 EST 1999
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From: Christian Schaller <schaller@spuds.lpl.arizona.edu>
Subject: Max Macro Token Size Tweaking
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Hi there, folks. I've got a big ol' macro file I'm developing, and I
just hit a limit: The maximum number of tokens that Image can handle
is 20,000. What I'm writing is a bit bigger than that. I'm thinking of
tweaking the source code and recompiling Image with MaxMacroSize (in
Globals.p) set to something slightly larger: 25,000.

Is such a tweak likely to break something, or is that a variable that
I can safely modify?

(Keep in mind it's not the file size of the macro file that I'm hitting,
it's the actual number of tokens. The file size is still at about 90%
of the upper limit...)

Thanks a bunch,

Chris Schaller

-----------------------------------------------------------------------------

Christian J. Schaller                            Applications Systems Analyst
Lunar and Planetary Laboratory                 schaller@spuds.lpl.arizona.edu
The University of Arizona               http://www.lpl.arizona.edu/~schaller/
Tucson, AZ 85721-0077                                            520/621-7200



From nih-image-request@io.ece.drexel.edu Tue Mar 23 20:17 EST 1999
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Date: Wed, 24 Mar 1999 10:02:31 +0900
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Dear all,

 I am new to this nih-image site discussion.
I would like to know how I could implement 'wavelet transform' with this
nih-image program. Is there any possibility that the nih-image will add
this type of plug-in functions in the near future? Or, is there any site
I could get help with implementing this wavelet transform?

Thanks in advance,

Jong Kim


From nih-image-request@io.ece.drexel.edu Wed Mar 24 01:12 EST 1999
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From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: Video from Image to PP
Date: Wed, 24 Mar 1999 17:01:07 +1100
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Hi,
I have used the following app, VFW   (Video for Windows)
http://www.eskimo.com/~pristine/video.html#vfw

The restrictions are.
1. When you make the Quicktime movie do it without compression. And it
should be flat.
2. Convert it in VFW it makes an AVI.
3. Make sure the AVI is placed in Power point on the pc.
4. Make sure the movie is on the pc. (To do 3 it should have been).
Then it should work.
hth.

Noel Goldsmith


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------------------------------

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nih-image-d Digest				Volume 99 : Issue 71

Today's Topics:
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
  Re: Registration of serial sections   [ Steve Barrett <S.D.Barrett@liverpoo ]
  Re: Big Images, memory limits and wh  [ Ard Jonker <a.jonker@amc.uva.nl> ]
  Re: registration of serial sections   [ Ard Jonker <a.jonker@amc.uva.nl> ]
  NIH Animations to Windows Powerpoint  [ Ard Jonker <a.jonker@amc.uva.nl> ]
  validation                            [ "Tim Crowe" <crowet@ccf.org> ]
  Re: NIH Animations to Windows Powerp  [ jgilkey@u.arizona.edu (John C. Gilk ]
  Re:registration of serial sections    [ "G. Macdonald" <glenmac@u.washingto ]
  Max Macro Token Size Tweaking         [ Christian Schaller <schaller@spuds. ]
  Wavelet Plug-in Possibility           [ "J. Kim" <jongkim8@mail.shinbiro.co ]
  Video from Image to PP                [ "Goldsmith, Noel" <Noel.Goldsmith@d ]

------------------------------

Date: Tue, 23 Mar 1999 05:05:01 -0500 (EST)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199903231005.FAA09105@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
                   ---------------------------
     


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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

------------------------------

Date: Tue, 23 Mar 1999 10:09:59 +0000
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
To: nih-image@io.ece.drexel.edu, Peter Shaw <peter.shaw@bbsrc.ac.uk>
Subject: Re: Registration of serial sections
Message-Id: <l03130301b31d165367c1@[138.253.47.16]>
Content-Type: text/plain; charset="us-ascii"

Peter Shaw wrote:

>...I am trying to use NIH-Image to analyse EM serial section stacks of
>nuclei. However, I do not have any true fiducial markers, and will need
>to register the sections as best I can by using structures such as nuclear
>outline, nucleolar outline, coiled bodies etc.
>...I think only x-y translational alignment is needed.

A spin-off of NIH Image, called Image SXM, has been written to handle
scanning microscopy images. In addition to various routines written with
SEM, SPM or SAM images in mind, there are also some routines of more
general interest.

One of the latest to be added is an 'Auto Register' routine that uses
cross-correlation of images to shift all slices of a stack into registry
with the current slice. It sounds like this might be of use to you.

The latest version of Image SXM is being beta-tested for release next
month. Anyone interested in this version with the 'Auto Register' feature
can email me for a copy.

For more information about Image SXM, see http://reg.ssci.liv.ac.uk

___________________________________________________________________
Dr Steve Barrett
Surface Science Research Centre
University of Liverpool
Liverpool L69 3BX
United Kingdom

Tel: 44-(0)151-794-3894 / 3874 / 3541
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk
___________________________________________________________________

------------------------------

Date: Tue, 23 Mar 1999 12:25:16 +0100
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Cc: GJOSS@rna.bio.mq.edu.au.Noel.Goldsmith@dsto.defence.gov.au
Subject: Re: Big Images, memory limits and what to do
Message-Id: <l03130304b31d29f97717@[145.117.43.50]>
Content-Type: text/plain; charset="us-ascii"

>I have also found that I cannot 'import' images longer than about 20K even 
>if only 1 wide. 

the limit is 32K lines: this works:
macro 'open long file' var test:string;
begin setImport('custom'); setcustom(10,32767,0); import('test');end;

and this doesn't.
macro 'open long file' var test:string;
begin setImport('custom'); setcustom(10,32768,0); import('test');end;

For some silly reason, the file is available in the 'windows' menu, but it is not displayed on my screen.

Ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156

------------------------------

Date: Tue, 23 Mar 1999 12:59:24 +0100
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: registration of serial sections
Message-Id: <l03130306b31d322c6482@[145.117.43.50]>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 8bit

>I have a request for advice from NIH-Image experts. I 
>am trying to use NIH-Image to analyse EM 
>serial section stacks of nuclei. However, I do not 
>have any true fiducial markers, and will need 
>to register the sections as best I can by using 
>structures such as nuclear outline, nucleolar 
>outline, coiled bodies etc. I would like to do this by 
>eye - flipping back and forth between each 
>section and the next one  while moving the next to 
>align it. I think only x-y translational 
>alignment  is needed. Any ideas about how NIH-Image 
>could do this? Thanks.

Use Object Image to put nondestructive markers on each image that is collected in a stack. If you got them all right, by shifting and flipping to and fro, apply the 'register' command. Use the nondestructive markers to enter the fiducials, ie. click on each nondestructive marker while actually entering the fiducials.

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156

------------------------------

Date: Tue, 23 Mar 1999 13:04:20 +0100
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: NIH Animations to Windows Powerpoint
Message-Id: <l03130307b31d330b98f7@[145.117.43.50]>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 8bit

>Does anyone have a better way (using freeware, shareware, or even
>commercial software)?  Does anyone know if using a different version of
>Quicktime, MoviePlayer, or Sparkle might be more successful?

You could consider a web browser for display, rather than PowerPoint. Web browsers have an unequalled platform independenness. If you install the quicktime plugin on either machine, you can present any graphic material on either machine.
To save PowerPoint stuff for this kind of presentation, print them to a pdf file (e.g. with the PDFWriter that is bundled from the first version of Adobe Acrobat) and link the presentation in HTML to the acrobat file. A plugin for acrobat exists too, circumventing any problem you are currently experiencing. We have our lectures in HTML presented from a FileMaker database this way.

Ard

------------------------------

Date: Tue, 23 Mar 1999 09:36:50 -0500
From: "Tim Crowe" <crowet@ccf.org>
To: <nih-image@io.ece.drexel.edu>
Subject:  validation
Message-Id: <s6f76028.022@cesmtp.ccf.org>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline
Content-Transfer-Encoding: 8bit

Can someone please tell me where I can find or download a document describing the validation or FDA approval of NIH Image 1.61?

Thank you

Tim Crowe
crowet@cesmtp.ccf.org

------------------------------

Date: Tue, 23 Mar 1999 09:02:20 -0700
From: jgilkey@u.arizona.edu (John C. Gilkey)
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Animations to Windows Powerpoint
Message-Id: <v02140b00b31d637837d6@[128.196.140.81]>
Content-Type: text/plain; charset="us-ascii"

>...I have a variety of movies I have made in nih-image...The problem
> comes with trying to import them into PowerPoint.  Some of the movies
> will import and play fine; others will not...


   I had a similar problem last summer, and spent considerable time
tracking down various aspects of the solution.  What I found was:
   First, what codec are you using to compress the movies?  I have found
that only Cinepak (the native codec) and a couple of others (which
unfortunately I don't remember now) will work.
   Second, PowerPoint uses the ActiveMovie driver mciqtz.drv to play
QuickTime movies.  If you have removed Internet Explorer from your PC (as I
always do), you probably removed this driver (as I did), since MicroSoft at
some point made it part of Explorer (one origin of their claim that
Explorer can't be reomved without compromising the system).  The driver can
be restored by installing the latest version of MediaPlayer.
   Third, I found early on that I sometimes had to change the file
extension from .mov to .qt before PowerPoint would properly insert a movie.
(This is probably related to the next "fix," which, with the previous
three, finally resolved all of the problems.)
   Fourth, PowerPoint looks for the mciqtz driver through a pointer called
MPEGvideo in the system.ini file.  Certain installers, like those for
QuickTime and some DVD drivers, may change this pointer, and some other
pointers that associate file extensions with MPEGVideo.  The instructions
for restoring these pointers can be found in:

   http://support.microsoft.com/support/kb/articles/q178/2/91.asp

Hope this helps.

------------------------------

Date: Tue, 23 Mar 1999 08:32:28 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re:registration of serial sections
Message-ID: <Pine.A41.4.05.9903230823140.116802-100000@homer06.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Open those images with common structures and make a small stack.  Then use
the "Register.." function found in the Stacks Menu.  This is explained in
the manual more fully, but you just click on two points common to each
image as you step through the stack.  The function performs the alignment.
You can then convert the aligned stack back into individual files with
"Stack to Windows".  close all but one of those files to use as the
aligment template for the next few images in your series.

Photoshop layers are convenient for alignment of small numbers of images.

Regards,
Glen



Glen MacDonald
   Research Scientist
Hearing Research Laboratories of the
Virginia Merrill Bloedel Hearing Research Center
Box 35-7923
University of Washington
Seattle, WA  98195-7923
(206) 616-4156
glenmac@u.washington.edu

------------------------------

Date: Tue, 23 Mar 1999 12:27:06 -0700
From: Christian Schaller <schaller@spuds.lpl.arizona.edu>
To: nih-image@io.ece.drexel.edu
Subject: Max Macro Token Size Tweaking
Message-Id: <l03130302b31d9a227063@[128.196.88.104]>
Content-Type: text/plain; charset="us-ascii"

Hi there, folks. I've got a big ol' macro file I'm developing, and I
just hit a limit: The maximum number of tokens that Image can handle
is 20,000. What I'm writing is a bit bigger than that. I'm thinking of
tweaking the source code and recompiling Image with MaxMacroSize (in
Globals.p) set to something slightly larger: 25,000.

Is such a tweak likely to break something, or is that a variable that
I can safely modify?

(Keep in mind it's not the file size of the macro file that I'm hitting,
it's the actual number of tokens. The file size is still at about 90%
of the upper limit...)

Thanks a bunch,

Chris Schaller

-----------------------------------------------------------------------------

Christian J. Schaller                            Applications Systems Analyst
Lunar and Planetary Laboratory                 schaller@spuds.lpl.arizona.edu
The University of Arizona               http://www.lpl.arizona.edu/~schaller/
Tucson, AZ 85721-0077                                            520/621-7200

------------------------------

Date: Wed, 24 Mar 1999 10:02:31 +0900
From: "J. Kim" <jongkim8@mail.shinbiro.com>
To: nih-image@io.ece.drexel.edu
Subject: Wavelet Plug-in Possibility
Message-ID: <36F839A7.AE255B84@mail.shinbiro.com>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 8bit

Dear all,

 I am new to this nih-image site discussion.
I would like to know how I could implement 'wavelet transform' with this
nih-image program. Is there any possibility that the nih-image will add
this type of plug-in functions in the near future? Or, is there any site
I could get help with implementing this wavelet transform?

Thanks in advance,

Jong Kim

------------------------------

Date: Wed, 24 Mar 1999 17:01:07 +1100
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: Video from Image to PP
Message-Id: <F98649A5EE8ED11190160000F802756598D022@exchvic3.dsto.defence.gov.au>
Content-Type: text/plain;
	charset="windows-1252"

Hi,
I have used the following app, VFW   (Video for Windows)
http://www.eskimo.com/~pristine/video.html#vfw

The restrictions are.
1. When you make the Quicktime movie do it without compression. And it
should be flat.
2. Convert it in VFW it makes an AVI.
3. Make sure the AVI is placed in Power point on the pc.
4. Make sure the movie is on the pc. (To do 3 it should have been).
Then it should work.
hth.

Noel Goldsmith

--------------------------------
End of nih-image-d Digest V99 Issue #71
***************************************

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Message-ID: <002201be75f9$46a24a20$99efe18f@amendola.unina.it>
From: "Eugenio Amendola" <amendola@unina.it>
To: "NIH-Image mailing list" <nih-image@io.ece.drexel.edu>
Subject: reading ancient documents
Date: Wed, 24 Mar 1999 14:21:20 +0100
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Hello Imagers Friends.
I would like to ask some help on a topic involving imaging and reading =
old wood tablets from Ercolano archeological site.
The old roman city of Ercolano was covered by hot ashes erupted by =
Vesuvio in 69 A.D. The public archives were written on wood tablets, =
that were burnt to carbon by hot ashes . Also the ink in use at that =
time were burnt down.
The old script is still recognizable, but reding the tablet is quite =
difficult.
Does anyone can give me some advice about NOT DESTRUCTIVE tecniques for =
evidencing the burnt (organic) ink? Some kind of illumination tecnique =
would be quite convenient. The samples are of great value, and any =
permanent treatment is absolutely impossible.
Thank you in advance for any advice and help.
Eugenio Amendola
_________________________________________
_________________________________________

Dr. Eugenio Amendola
Italian National Council of Research
Institute of Composite Material Technology
P.le Tecchio 80, 80125 - Naples, ITALY
Tel.     39 (0) 81 7682511
fax      39 (0) 81 7682404
email   amendola@unina.it
URL    http:\\143.225.239.86

------=_NextPart_000_001D_01BE7601.96668AA0
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	charset="iso-8859-1"
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD W3 HTML//EN">
<HTML>
<HEAD>

<META content=3Dtext/html;charset=3Diso-8859-1 =
http-equiv=3DContent-Type>
<META content=3D'"MSHTML 4.72.3110.7"' name=3DGENERATOR>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT color=3D#000000 size=3D2>Hello Imagers Friends.</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT><FONT size=3D2>I would like =
to ask some=20
help on a topic involving imaging and reading old wood tablets from =
Ercolano=20
archeological site.</FONT></DIV>
<DIV><FONT size=3D2>The old roman city of Ercolano was covered by hot =
ashes=20
erupted by Vesuvio in 69 A.D. The public archives were written on wood =
tablets,=20
that were burnt to carbon by hot ashes . Also the ink in use at that =
time were=20
burnt down.</FONT></DIV>
<DIV><FONT size=3D2>The old script is still recognizable, but reding the =
tablet is=20
quite difficult.</FONT></DIV>
<DIV><FONT size=3D2>Does anyone can give me some advice about NOT =
DESTRUCTIVE=20
tecniques for evidencing the burnt (organic) ink? Some kind of =
illumination=20
tecnique would be quite convenient. The samples are of great value, and =
any=20
permanent treatment is absolutely impossible.</FONT></DIV>
<DIV><FONT size=3D2>Thank you in advance for any advice and =
help.</FONT></DIV>
<DIV><FONT size=3D2>Eugenio Amendola</FONT></DIV>
<DIV><FONT color=3D#000000=20
size=3D2>_________________________________________<BR>___________________=
______________________</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000000 size=3D2>Dr. Eugenio Amendola<BR>Italian =
National Council=20
of Research<BR>Institute of Composite Material Technology<BR>P.le =
Tecchio 80,=20
80125 - Naples, ITALY<BR>Tel.&nbsp;&nbsp;&nbsp;&nbsp; 39 (0) 81=20
7682511<BR>fax&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 39 (0) 81=20
7682404<BR>email&nbsp;&nbsp; <A=20
href=3D"mailto:amendola@unina.it">amendola@unina.it</A><BR>URL&nbsp;&nbsp=
;&nbsp;=20
http:\\143.225.239.86</FONT></DIV></BODY></HTML>

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From nih-image-request@io.ece.drexel.edu Thu Mar 25 01:17 EST 1999
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Hi image people,
Our department (Human Movement & Performance) is looking for hardware & 
software that can be used with a  laptop/notebook PC (not Apple).
We want to play movies from a PAL source at a preset screen location (eg top 
right of screen) and have a Labview application going around it displaying 
data in real time. 
We also want to be able to:
(1) Delay the movie by up to 5 sec relative to the incoming PAL signal;
(2) Be sure that the movie window (location & size) is saved when 
applications are shut down.
(3) Output combined video + labview as PAL (to a VCR)
The movie would want be >30 frames/sec.
Has anyone any suggestions as to hardware & software vendors?


Robert Stokes.


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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 72

Today's Topics:
  reading ancient documents             [ "Eugenio Amendola" <amendola@unina. ]
  Video into laptop                     [ "Robert Stokes" <RobertStokes@vu.ed ]

------------------------------

Date: Wed, 24 Mar 1999 14:21:20 +0100
From: "Eugenio Amendola" <amendola@unina.it>
To: "NIH-Image mailing list" <nih-image@io.ece.drexel.edu>
Subject: reading ancient documents
Message-ID: <002201be75f9$46a24a20$99efe18f@amendola.unina.it>
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Hello Imagers Friends.
I would like to ask some help on a topic involving imaging and reading =
old wood tablets from Ercolano archeological site.
The old roman city of Ercolano was covered by hot ashes erupted by =
Vesuvio in 69 A.D. The public archives were written on wood tablets, =
that were burnt to carbon by hot ashes . Also the ink in use at that =
time were burnt down.
The old script is still recognizable, but reding the tablet is quite =
difficult.
Does anyone can give me some advice about NOT DESTRUCTIVE tecniques for =
evidencing the burnt (organic) ink? Some kind of illumination tecnique =
would be quite convenient. The samples are of great value, and any =
permanent treatment is absolutely impossible.
Thank you in advance for any advice and help.
Eugenio Amendola
_________________________________________
_________________________________________

Dr. Eugenio Amendola
Italian National Council of Research
Institute of Composite Material Technology
P.le Tecchio 80, 80125 - Naples, ITALY
Tel.     39 (0) 81 7682511
fax      39 (0) 81 7682404
email   amendola@unina.it
URL    http:\\143.225.239.86

------=_NextPart_000_001D_01BE7601.96668AA0
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD W3 HTML//EN">
<HTML>
<HEAD>

<META content=3Dtext/html;charset=3Diso-8859-1 =
http-equiv=3DContent-Type>
<META content=3D'"MSHTML 4.72.3110.7"' name=3DGENERATOR>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT color=3D#000000 size=3D2>Hello Imagers Friends.</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT><FONT size=3D2>I would like =
to ask some=20
help on a topic involving imaging and reading old wood tablets from =
Ercolano=20
archeological site.</FONT></DIV>
<DIV><FONT size=3D2>The old roman city of Ercolano was covered by hot =
ashes=20
erupted by Vesuvio in 69 A.D. The public archives were written on wood =
tablets,=20
that were burnt to carbon by hot ashes . Also the ink in use at that =
time were=20
burnt down.</FONT></DIV>
<DIV><FONT size=3D2>The old script is still recognizable, but reding the =
tablet is=20
quite difficult.</FONT></DIV>
<DIV><FONT size=3D2>Does anyone can give me some advice about NOT =
DESTRUCTIVE=20
tecniques for evidencing the burnt (organic) ink? Some kind of =
illumination=20
tecnique would be quite convenient. The samples are of great value, and =
any=20
permanent treatment is absolutely impossible.</FONT></DIV>
<DIV><FONT size=3D2>Thank you in advance for any advice and =
help.</FONT></DIV>
<DIV><FONT size=3D2>Eugenio Amendola</FONT></DIV>
<DIV><FONT color=3D#000000=20
size=3D2>_________________________________________<BR>___________________=
______________________</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000000 size=3D2>Dr. Eugenio Amendola<BR>Italian =
National Council=20
of Research<BR>Institute of Composite Material Technology<BR>P.le =
Tecchio 80,=20
80125 - Naples, ITALY<BR>Tel.&nbsp;&nbsp;&nbsp;&nbsp; 39 (0) 81=20
7682511<BR>fax&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 39 (0) 81=20
7682404<BR>email&nbsp;&nbsp; <A=20
href=3D"mailto:amendola@unina.it">amendola@unina.it</A><BR>URL&nbsp;&nbsp=
;&nbsp;=20
http:\\143.225.239.86</FONT></DIV></BODY></HTML>

------=_NextPart_000_001D_01BE7601.96668AA0--

------------------------------

Date: Thu, 25 Mar 99 17:04:06 +1100
From: "Robert Stokes" <RobertStokes@vu.edu.au>
To: <nih-image@io.ece.drexel.edu>
Subject: Video into laptop
Message-ID: <vines.LnH8+tdRyqA@gnu1.vu.edu.au>
Content-type: text/plain; charset=us-ascii

Hi image people,
Our department (Human Movement & Performance) is looking for hardware & 
software that can be used with a  laptop/notebook PC (not Apple).
We want to play movies from a PAL source at a preset screen location (eg top 
right of screen) and have a Labview application going around it displaying 
data in real time. 
We also want to be able to:
(1) Delay the movie by up to 5 sec relative to the incoming PAL signal;
(2) Be sure that the movie window (location & size) is saved when 
applications are shut down.
(3) Output combined video + labview as PAL (to a VCR)
The movie would want be >30 frames/sec.
Has anyone any suggestions as to hardware & software vendors?


Robert Stokes.

--------------------------------
End of nih-image-d Digest V99 Issue #72
***************************************

From nih-image-request@io.ece.drexel.edu Thu Mar 25 12:55 EST 1999
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Subject: cell position
To: nih-image@io.ece.drexel.edu (NIH Image)
Date: Thu, 25 Mar 1999 12:37:22 -0500 (EST)
From: "DAVID W SCHMIDTKE" <dws@seas.upenn.edu>
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Dear Imagers,

Thanks for the recent help on tracing a image in a stack.  

I have another question for you.  As I wrote in an earlier macro I am 
trying to track the x-y coordinates of a particle through a stack of 
images.  Currently what I am doing is outlining the cell manually in each 
frame using the draw boundary function.  Once I have the cell outlined in 
each frame of the stack, I then have to go back through the stack and 
click inside the boundary with the wand tool to "select the ROI".  
Once I have clicked inside of the boundary and a ROI is selected the 
x-y center of the ROI is automatically calculated and recorded using a macro.  

The question I have is once I have outlined the boundary of the cell is 
it possible to have Scion Image automatically find this ROI (i.e the drawn 
boundary around the cell) in each frame and scroll through the stack.  I've 
tried to use the AnalyzeParticles command but have not had much luck.  Thanks 
for the help.

David Schmidtke
dws@seas.upenn.edu


From nih-image-request@io.ece.drexel.edu Thu Mar 25 13:35 EST 1999
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Date-warning: Date header was inserted by bodkin.nuigalway.ie
From: Catherine Carolan <Catherine.Carolan@NUIGALWAY.IE>
Subject: combining red /green stacks
To: nih-image@io.ece.drexel.edu
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Hi all,
I am using NIH Image to combine red and green TIFF images from a Leica
confocal using the "color it" macro.  If I try to color combine two stacks
the combined images look completely digitized and are of no use. I have
overcome this somewhat by combining two images only (selected from the two
stacks) but I always loose definition compared to the original red or green
image. Does anyone know how I could combine my images and still  maintain
the original detail.

Thanks
Catherine

Dr. Catherine Carolan
Dept of Physiology
National University of Ireland, Galway
University Road,
Galway
Ireland.

Phone : 	353 91 524411 ext. 3573
Fax : 	353 91 750544
Email : 	catherine.carolan@nuigalway.ie



From nih-image-request@io.ece.drexel.edu Thu Mar 25 15:07 EST 1999
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Date: Thu, 25 Mar 1999 14:37:33 -0800
To: nih-image@io.ece.drexel.edu
From: Michael Cammer <cammer@aecom.yu.edu>
Subject: Re: combining red /green stacks
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A few years ago we made merging macros that made each original 8 bit image
into a 4 bit image and then put the two four bit images together with a
custom look up table.  We have since abandoned this, but it works if you
don't mind only 16 gray values per image.  
********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************


From nih-image-request@io.ece.drexel.edu Thu Mar 25 15:28 EST 1999
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Date: Thu, 25 Mar 1999 12:04:34 -0800 (PST)
From: David Ehrhardt <ehrhardt@camelot.Stanford.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Re: combining red /green stacks
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On Thu, 25 Mar 1999, Catherine Carolan wrote:

> Hi all,
> I am using NIH Image to combine red and green TIFF images from a Leica
> confocal using the "color it" macro.  If I try to color combine two stacks
> the combined images look completely digitized and are of no use. I have
> overcome this somewhat by combining two images only (selected from the two
> stacks) but I always loose definition compared to the original red or green
> image. Does anyone know how I could combine my images and still  maintain
> the original detail.
> 
> Thanks
> Catherine

You want a 24 bit color merge rather than an 8 bit color merge.  The
easiest way I have found to merge stacks of images is to use a utility
called .picmerge available from:

http://rsb.info.nih.gov:80/NIH-IMAGE/Default.html

To use this utility, you need to create an intermediate image stack where
each frame consists of one channel (red) on the left and the other channel
(green) on the right.  i.e. the two channels are side by side in a
double-wide frame. NIH Image has a macro called "merge two stacks" in the
"confocal macros" to create this intermediate stack. Once created, this
stack is merged by .picmerge to create a PICT file for each frame.  These
frames can be recombined into a Quicktime movie with Graphic Converter for
playback at full bit depth on the Mac. 

Good luck!

David   

> 
> Dr. Catherine Carolan
> Dept of Physiology
> National University of Ireland, Galway
> University Road,
> Galway
> Ireland.
> 
> Phone : 	353 91 524411 ext. 3573
> Fax : 	353 91 750544
> Email : 	catherine.carolan@nuigalway.ie
> 
> 
> 

David Ehrhardt				
Carnegie Institution of Washington
Department of Plant Biology		Phone (650) 325-1521 x261
260 Panama St., Stanford, CA 94305	FAX (650) 325-6857



From nih-image-request@io.ece.drexel.edu Thu Mar 25 21:09 EST 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: dws@seas.upenn.edu, nih-image@io.ece.drexel.edu
Date:          Fri, 26 Mar 1999 8:48:34 +1100
Subject:       Re: cell position
Priority: normal
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>Subject: cell position
>To: nih-image@io.ece.drexel.edu (NIH Image)
>Date: Thu, 25 Mar 1999 12:37:22 -0500 (EST)
>From: "DAVID W SCHMIDTKE" <dws@seas.upenn.edu>
...............
>Thanks for the recent help on tracing a image in a stack.  
>
>I have another question for you.  As I wrote in an earlier macro I am 
>trying to track the x-y coordinates of a particle through a stack of 
>images.  Currently what I am doing is outlining the cell manually in each 
>frame using the draw boundary function.  Once I have the cell outlined in 
>each frame of the stack, I then have to go back through the stack and 
>click inside the boundary with the wand tool to "select the ROI".  
>Once I have clicked inside of the boundary and a ROI is selected the 
>x-y center of the ROI is automatically calculated and recorded using a 
>macro.  
>
>The question I have is once I have outlined the boundary of the cell is 
>it possible to have Scion Image automatically find this ROI (i.e the drawn 
>boundary around the cell) in each frame and scroll through the stack.  
>I've 
>tried to use the AnalyzeParticles command but have not had much luck.  
>Thanks 
>for the help.
>
>David Schmidtke
>dws@seas.upenn.edu

AnalyzeParticles('include'); (interior holes) options should locate a (list 
of ) centroids for you but be aware they will be spatially scaled unless 
you use SetScale(0,'pixel').

You might choose 'fill' rather than 'drawBoundary' but I too prefer the 
later.

Precede AnalyzeParticles with setThreshold(255); and an appropriate 
'setParticlesize' or if you want to use setDensitySlice, the foreGround for 
drawBoundary will need to be 1<>254 not default 255.

What specifically is your problem with AnalyzeParticles?


Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #73
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 73

Today's Topics:
  unsubscribe                           [ Legrand <legrand@naxos.unice.fr> ]
  cell position                         [ "DAVID W SCHMIDTKE" <dws@seas.upenn ]
  combining red /green stacks           [ Catherine Carolan <Catherine.Carola ]
  Re: combining red /green stacks       [ Michael Cammer <cammer@aecom.yu.edu ]
  Re: combining red /green stacks       [ David Ehrhardt <ehrhardt@camelot.St ]
  Re: cell position                     [ GJOSS@rna.bio.mq.edu.au ]

------------------------------

Date: Thu, 25 Mar 99 09:07:30 +0100
From: Legrand <legrand@naxos.unice.fr>
To: <nih-image-d@io.ece.drexel.edu>
Subject: unsubscribe
Message-Id: <199903250815.JAA09292@naxos.unice.fr>
Content-Type: text/plain; charset="US-ASCII"


------------------------------

Date: Thu, 25 Mar 1999 12:37:22 -0500 (EST)
From: "DAVID W SCHMIDTKE" <dws@seas.upenn.edu>
To: nih-image@io.ece.drexel.edu (NIH Image)
Subject: cell position
Message-Id: <199903251737.MAA16049@blue.seas.upenn.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit

Dear Imagers,

Thanks for the recent help on tracing a image in a stack.  

I have another question for you.  As I wrote in an earlier macro I am 
trying to track the x-y coordinates of a particle through a stack of 
images.  Currently what I am doing is outlining the cell manually in each 
frame using the draw boundary function.  Once I have the cell outlined in 
each frame of the stack, I then have to go back through the stack and 
click inside the boundary with the wand tool to "select the ROI".  
Once I have clicked inside of the boundary and a ROI is selected the 
x-y center of the ROI is automatically calculated and recorded using a macro.  

The question I have is once I have outlined the boundary of the cell is 
it possible to have Scion Image automatically find this ROI (i.e the drawn 
boundary around the cell) in each frame and scroll through the stack.  I've 
tried to use the AnalyzeParticles command but have not had much luck.  Thanks 
for the help.

David Schmidtke
dws@seas.upenn.edu

------------------------------

Date: Thu, 25 Mar 1999 18:19:16 +0000 (GMT)
From: Catherine Carolan <Catherine.Carolan@NUIGALWAY.IE>
To: nih-image@io.ece.drexel.edu
Subject: combining red /green stacks
Message-id: <l03102802b3202a12c3b6@[140.203.26.3]>
Content-type: text/plain; charset="us-ascii"

Hi all,
I am using NIH Image to combine red and green TIFF images from a Leica
confocal using the "color it" macro.  If I try to color combine two stacks
the combined images look completely digitized and are of no use. I have
overcome this somewhat by combining two images only (selected from the two
stacks) but I always loose definition compared to the original red or green
image. Does anyone know how I could combine my images and still  maintain
the original detail.

Thanks
Catherine

Dr. Catherine Carolan
Dept of Physiology
National University of Ireland, Galway
University Road,
Galway
Ireland.

Phone : 	353 91 524411 ext. 3573
Fax : 	353 91 750544
Email : 	catherine.carolan@nuigalway.ie

------------------------------

Date: Thu, 25 Mar 1999 14:37:33 -0800
From: Michael Cammer <cammer@aecom.yu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: combining red /green stacks
Message-Id: <3.0.5.32.19990325143733.009cd470@mailserver.aecom.yu.edu>
Content-Type: text/plain; charset="us-ascii"

A few years ago we made merging macros that made each original 8 bit image
into a 4 bit image and then put the two four bit images together with a
custom look up table.  We have since abandoned this, but it works if you
don't mind only 16 gray values per image.  
********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************

------------------------------

Date: Thu, 25 Mar 1999 12:04:34 -0800 (PST)
From: David Ehrhardt <ehrhardt@camelot.Stanford.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Re: combining red /green stacks
Message-ID: <Pine.GUL.3.95.990325114900.9173A-100000@camelot.Stanford.EDU>
Content-Type: TEXT/PLAIN; charset=US-ASCII

On Thu, 25 Mar 1999, Catherine Carolan wrote:

> Hi all,
> I am using NIH Image to combine red and green TIFF images from a Leica
> confocal using the "color it" macro.  If I try to color combine two stacks
> the combined images look completely digitized and are of no use. I have
> overcome this somewhat by combining two images only (selected from the two
> stacks) but I always loose definition compared to the original red or green
> image. Does anyone know how I could combine my images and still  maintain
> the original detail.
> 
> Thanks
> Catherine

You want a 24 bit color merge rather than an 8 bit color merge.  The
easiest way I have found to merge stacks of images is to use a utility
called .picmerge available from:

http://rsb.info.nih.gov:80/NIH-IMAGE/Default.html

To use this utility, you need to create an intermediate image stack where
each frame consists of one channel (red) on the left and the other channel
(green) on the right.  i.e. the two channels are side by side in a
double-wide frame. NIH Image has a macro called "merge two stacks" in the
"confocal macros" to create this intermediate stack. Once created, this
stack is merged by .picmerge to create a PICT file for each frame.  These
frames can be recombined into a Quicktime movie with Graphic Converter for
playback at full bit depth on the Mac. 

Good luck!

David   

> 
> Dr. Catherine Carolan
> Dept of Physiology
> National University of Ireland, Galway
> University Road,
> Galway
> Ireland.
> 
> Phone : 	353 91 524411 ext. 3573
> Fax : 	353 91 750544
> Email : 	catherine.carolan@nuigalway.ie
> 
> 
> 

David Ehrhardt				
Carnegie Institution of Washington
Department of Plant Biology		Phone (650) 325-1521 x261
260 Panama St., Stanford, CA 94305	FAX (650) 325-6857

------------------------------

Date:          Fri, 26 Mar 1999 8:48:34 +1100
From: GJOSS@rna.bio.mq.edu.au
To: dws@seas.upenn.edu, nih-image@io.ece.drexel.edu
Subject:       Re: cell position
Message-ID: <2F1996C474D@rna.bio.mq.edu.au>

>Subject: cell position
>To: nih-image@io.ece.drexel.edu (NIH Image)
>Date: Thu, 25 Mar 1999 12:37:22 -0500 (EST)
>From: "DAVID W SCHMIDTKE" <dws@seas.upenn.edu>
...............
>Thanks for the recent help on tracing a image in a stack.  
>
>I have another question for you.  As I wrote in an earlier macro I am 
>trying to track the x-y coordinates of a particle through a stack of 
>images.  Currently what I am doing is outlining the cell manually in each 
>frame using the draw boundary function.  Once I have the cell outlined in 
>each frame of the stack, I then have to go back through the stack and 
>click inside the boundary with the wand tool to "select the ROI".  
>Once I have clicked inside of the boundary and a ROI is selected the 
>x-y center of the ROI is automatically calculated and recorded using a 
>macro.  
>
>The question I have is once I have outlined the boundary of the cell is 
>it possible to have Scion Image automatically find this ROI (i.e the drawn 
>boundary around the cell) in each frame and scroll through the stack.  
>I've 
>tried to use the AnalyzeParticles command but have not had much luck.  
>Thanks 
>for the help.
>
>David Schmidtke
>dws@seas.upenn.edu

AnalyzeParticles('include'); (interior holes) options should locate a (list 
of ) centroids for you but be aware they will be spatially scaled unless 
you use SetScale(0,'pixel').

You might choose 'fill' rather than 'drawBoundary' but I too prefer the 
later.

Precede AnalyzeParticles with setThreshold(255); and an appropriate 
'setParticlesize' or if you want to use setDensitySlice, the foreGround for 
drawBoundary will need to be 1<>254 not default 255.

What specifically is your problem with AnalyzeParticles?


Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

--------------------------------
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nih-image-d Digest				Volume 99 : Issue 74

Today's Topics:
  unsubscribe                           [ "Bob Cormier" <cormierb@psychiatry1 ]

------------------------------

Date: Fri, 26 Mar 1999 09:08:43 -0600
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From nih-image-request@io.ece.drexel.edu Sat Mar 27 09:59 EST 1999
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From nih-image-request@io.ece.drexel.edu Sat Mar 27 12:58 EST 1999
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Date: Sat, 27 Mar 1999 08:11:34 +0100
To: nih-image@io.ece.drexel.edu
From: "Anneke M.Th. Harbers and Ard Jonker" <a_team@dds.nl>
Subject: Object Image promo (was: cell position)
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Sorry folks, I can't resist, and I Norbert owes me one. Sorry for the
lengthly posting, but I hope many of you can benefit. I visited Norbert
this week and he showed the new version of Object-Image. It is really worth
trying if you haven't tried a fresh version since 6 months. I think Norbert
really did a good job in flattening the learning curve by the newer
versions. Don't let the "1.62" fool you, as it fooled me, pay attention to
the nuber after the n (n7 public now).

>I have another question for you.  As I wrote in an earlier macro I am
>trying to track the x-y coordinates of a particle through a stack of
>images.  Currently what I am doing is outlining the cell manually in each
>frame using the draw boundary function.  Once I have the cell outlined in
>each frame of the stack, I then have to go back through the stack and
>click inside the boundary with the wand tool to "select the ROI".
>Once I have clicked inside of the boundary and a ROI is selected the
>x-y center of the ROI is automatically calculated and recorded using a
>macro.
>
>The question I have is once I have outlined the boundary of the cell is
>it possible to have Scion Image automatically find this ROI (i.e the drawn
>boundary around the cell) in each frame and scroll through the stack.  I've
>tried to use the AnalyzeParticles command but have not had much luck.  Thanks
>for the help.

If you mean 'automatically find this ROI', you might as well use
Object-Image. That program can remember ROI's (though the ROI in a stored
form is called an Object, hence the name Object Image) and can recreate a
ROI from an object and vice versa. Each top, left of an outline-bounding
box is available from macros.

Create a new object file. Object Image asks you if you want to define
objects. Say yes. Click the car, not the bus (single mode) in the dialog.
Drag an outline from the left panel to the centre of the window. Then close
dialog. Click on the object button in the tools window. Go to your stack
and select a ROI the way you usually do. Now move the mouse close to the
red object outline in the object tools window. The cursor should change to
a dotted rectangle with a leftward arrow. Click and see your ROI converted
to an object! You can do this for multiple outlines in one slice. If you
save the object file, all objects are saved. If you open the file, all
objects are still there, ready to be used. Non destructively marked.

If you are there, do try a macro in the build-in editor and click in the
magnifier on the top right hand of your macro window. Now isn't that handy?
(spoiler: you have all the macro names available in a popup, and can use
the popup for navigation). Another one: hold the command-key if you choose
a macro command. See the little bug cursor? That's debug (The-Bug:-) Trace,
stap, walk or breakpoint to test your macros.

I think that you actually want to have a ROI recreated in slice number n,
and test to see if the centre of the cell outline in slice n+1 is within
the ROI of slice number n, right? That should be simple with Object Image.
Object to ROI, copy ROI, choose other slice, restore ROI and now some extra
commands to check if your cell is within the ROI.

This program is available from the server of Norbert Vischer,
simon.bio.uva.nl, in the directory Object-Image. This is the URL:
ftp://simon.bio.uva.nl//pub/Object-Image1.62n7+.sea
While you are there, grab a copy of the manual:
ftp://simon.bio.uva.nl//pub/Object-ImageDoc.sea

Ard



From nih-image-d-request@io.ece.drexel.edu Sun Mar 28 06:12 EST 1999
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------------------------------

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nih-image-d Digest				Volume 99 : Issue 75

Today's Topics:
  unsubscribe                           [ Legrand <legrand@naxos.unice.fr> ]
  Object Image promo (was: cell positi  [ "Anneke M.Th. Harbers and Ard Jonke ]

------------------------------

Date: Sat, 27 Mar 99 15:47:54 +0100
From: Legrand <legrand@naxos.unice.fr>
To: <nih-image@io.ece.drexel.edu>
Subject: unsubscribe
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------------------------------

Date: Sat, 27 Mar 1999 08:11:34 +0100
From: "Anneke M.Th. Harbers and Ard Jonker" <a_team@dds.nl>
To: nih-image@io.ece.drexel.edu
Subject: Object Image promo (was: cell position)
Message-Id: <l03130300b3222e2a702a@[194.109.129.162]>
Content-Type: text/plain; charset="us-ascii"

Sorry folks, I can't resist, and I Norbert owes me one. Sorry for the
lengthly posting, but I hope many of you can benefit. I visited Norbert
this week and he showed the new version of Object-Image. It is really worth
trying if you haven't tried a fresh version since 6 months. I think Norbert
really did a good job in flattening the learning curve by the newer
versions. Don't let the "1.62" fool you, as it fooled me, pay attention to
the nuber after the n (n7 public now).

>I have another question for you.  As I wrote in an earlier macro I am
>trying to track the x-y coordinates of a particle through a stack of
>images.  Currently what I am doing is outlining the cell manually in each
>frame using the draw boundary function.  Once I have the cell outlined in
>each frame of the stack, I then have to go back through the stack and
>click inside the boundary with the wand tool to "select the ROI".
>Once I have clicked inside of the boundary and a ROI is selected the
>x-y center of the ROI is automatically calculated and recorded using a
>macro.
>
>The question I have is once I have outlined the boundary of the cell is
>it possible to have Scion Image automatically find this ROI (i.e the drawn
>boundary around the cell) in each frame and scroll through the stack.  I've
>tried to use the AnalyzeParticles command but have not had much luck.  Thanks
>for the help.

If you mean 'automatically find this ROI', you might as well use
Object-Image. That program can remember ROI's (though the ROI in a stored
form is called an Object, hence the name Object Image) and can recreate a
ROI from an object and vice versa. Each top, left of an outline-bounding
box is available from macros.

Create a new object file. Object Image asks you if you want to define
objects. Say yes. Click the car, not the bus (single mode) in the dialog.
Drag an outline from the left panel to the centre of the window. Then close
dialog. Click on the object button in the tools window. Go to your stack
and select a ROI the way you usually do. Now move the mouse close to the
red object outline in the object tools window. The cursor should change to
a dotted rectangle with a leftward arrow. Click and see your ROI converted
to an object! You can do this for multiple outlines in one slice. If you
save the object file, all objects are saved. If you open the file, all
objects are still there, ready to be used. Non destructively marked.

If you are there, do try a macro in the build-in editor and click in the
magnifier on the top right hand of your macro window. Now isn't that handy?
(spoiler: you have all the macro names available in a popup, and can use
the popup for navigation). Another one: hold the command-key if you choose
a macro command. See the little bug cursor? That's debug (The-Bug:-) Trace,
stap, walk or breakpoint to test your macros.

I think that you actually want to have a ROI recreated in slice number n,
and test to see if the centre of the cell outline in slice n+1 is within
the ROI of slice number n, right? That should be simple with Object Image.
Object to ROI, copy ROI, choose other slice, restore ROI and now some extra
commands to check if your cell is within the ROI.

This program is available from the server of Norbert Vischer,
simon.bio.uva.nl, in the directory Object-Image. This is the URL:
ftp://simon.bio.uva.nl//pub/Object-Image1.62n7+.sea
While you are there, grab a copy of the manual:
ftp://simon.bio.uva.nl//pub/Object-ImageDoc.sea

Ard

--------------------------------
End of nih-image-d Digest V99 Issue #75
***************************************

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Date: Sun, 28 Mar 1999 11:48:13 -0500 (EST)
From: Kanu P Singh <kanu@UDel.Edu>
To: nih-image@io.ece.drexel.edu
Subject: UNsubscibe
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I would like to unsubscribe.
Thanks,
Kanu

On Sat, 27 Mar 1999 nih-image-d-request@io.ece.drexel.edu wrote:


  [NON-Text Body part not included]


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nih-image-d Digest				Volume 99 : Issue 76

Today's Topics:
  UNsubscibe                            [ Kanu P Singh <kanu@UDel.Edu> ]

------------------------------

Date: Sun, 28 Mar 1999 11:48:13 -0500 (EST)
From: Kanu P Singh <kanu@UDel.Edu>
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I would like to unsubscribe.
Thanks,
Kanu

On Sat, 27 Mar 1999 nih-image-d-request@io.ece.drexel.edu wrote:


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From nih-image-request@io.ece.drexel.edu Mon Mar 29 14:07 EST 1999
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Date: Mon, 29 Mar 1999 10:43:16 -0800
To: nih-image@io.ece.drexel.edu
From: Carsten Bruckner <bruckner@u.washington.edu>
Subject:  Re: combining red /green stacks
Resent-Message-ID: <"Jofof1.0.N-1.iey_s"@io>
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If you want to combine two 8-bit images into another 8 bit image, you could
divide each image by two (for a max value of 127), and then add them (for a
max of 254).  In effect, you're converting the red and green channels to 7
bit images before adding into an 8 bit image.

-----------------------
Carsten Bruckner
U. of Washington
Dept. of Chemistry
Box 351700
Seattle, WA 98195-1700

Tel. 206-543-6144
-----------------------



From nih-image-request@io.ece.drexel.edu Tue Mar 30 03:50 EST 1999
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To: nih-image@io.ece.drexel.edu
From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: Re: Object Image promo (was: cell position)
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Earlier, I wrote
>Sorry folks, I can't resist, and I Norbert owes me one. Sorry for the

<OOPS> That should have been "and I owe Norbert one" of course...
Ard



From nih-image-d-request@io.ece.drexel.edu Tue Mar 30 06:19 EST 1999
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Subject: nih-image-d Digest V99 #77
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 77

Today's Topics:
  Re: combining red /green stacks       [ Carsten Bruckner <bruckner@u.washin ]
  Re: Object Image promo (was: cell po  [ Ard Jonker <a.jonker@amc.uva.nl> ]

------------------------------

Date: Mon, 29 Mar 1999 10:43:16 -0800
From: Carsten Bruckner <bruckner@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject:  Re: combining red /green stacks
Message-Id: <l03130301b3257693904d@[128.95.172.244]>
Content-Type: text/plain; charset="us-ascii"

If you want to combine two 8-bit images into another 8 bit image, you could
divide each image by two (for a max value of 127), and then add them (for a
max of 254).  In effect, you're converting the red and green channels to 7
bit images before adding into an 8 bit image.

-----------------------
Carsten Bruckner
U. of Washington
Dept. of Chemistry
Box 351700
Seattle, WA 98195-1700

Tel. 206-543-6144
-----------------------

------------------------------

Date: Tue, 30 Mar 1999 10:16:47 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Object Image promo (was: cell position)
Message-Id: <l03130302b32638497666@[145.117.43.50]>
Content-Type: text/plain; charset="us-ascii"

Earlier, I wrote
>Sorry folks, I can't resist, and I Norbert owes me one. Sorry for the

<OOPS> That should have been "and I owe Norbert one" of course...
Ard

--------------------------------
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***************************************

From nih-image-request@io.ece.drexel.edu Tue Mar 30 09:48 EST 1999
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Date: Tue, 30 Mar 1999 16:29:23 +0200
To: nih-image@io.ece.drexel.edu
From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: Re: nih-image-d Digest V99 #77
Resent-Message-ID: <"FgyPp.0.285.-yD0t"@io>
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>If you want to combine two 8-bit images into another 8 bit image, you could
>divide each image by two (for a max value of 127), and then add them (for a
>max of 254).  In effect, you're converting the red and green channels to 7
>bit images before adding into an 8 bit image.

How do you distinguish a nearly full-red from a nearly full-green pixel?
I'm afraid that a full-red pixel will show up (127 from red+0 from green=127) the same as a full-green pixel (0 from red+127 from green =127).

Ard



From nih-image-request@io.ece.drexel.edu Tue Mar 30 10:42 EST 1999
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Date: 30 Mar 99 10:22:53 EST
From: Charles.P.Daghlian@Dartmouth.EDU (Charles P. Daghlian)
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--- You wrote:
If you want to combine two 8-bit images into another 8 bit image, you could
divide each image by two (for a max value of 127), and then add them (for a
max of 254).  In effect, you're converting the red and green channels to 7
bit images before adding into an 8 bit image.
--- end of quote ---
Another way would be to take slice n of the red and green stacks, copy them and paste into a temp stack (macro command MakeNewStack - you will have to set the newSize)  as red and green, create a new blank slice in the temp stack, then use RGB to 8 bit command in Stacks menu. Copy the new 8 bit image and paste into a new stack (makeNewStack again). Dispose of the 8 bit image and repeate with slice n+1. At the end you will have a stack of the combined red and green stacks.

Chuck


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nih-image-d Digest				Volume 99 : Issue 78

Today's Topics:
  Re: nih-image-d Digest V99 #77        [ Ard Jonker <a.jonker@amc.uva.nl> ]
  Re: combining red /green stacks       [ Charles.P.Daghlian@Dartmouth.EDU (C ]
  unsubscibe                            [ DGregart@aol.com ]
  subscribe                             [ Neuroart@aol.com ]

------------------------------

Date: Tue, 30 Mar 1999 16:29:23 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #77
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>If you want to combine two 8-bit images into another 8 bit image, you could
>divide each image by two (for a max value of 127), and then add them (for a
>max of 254).  In effect, you're converting the red and green channels to 7
>bit images before adding into an 8 bit image.

How do you distinguish a nearly full-red from a nearly full-green pixel?
I'm afraid that a full-red pixel will show up (127 from red+0 from green=127) the same as a full-green pixel (0 from red+127 from green =127).

Ard

------------------------------

Date: 30 Mar 99 10:22:53 EST
From: Charles.P.Daghlian@Dartmouth.EDU (Charles P. Daghlian)
To: nih-image@io.ece.drexel.edu
Subject: Re: combining red /green stacks 
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--- You wrote:
If you want to combine two 8-bit images into another 8 bit image, you could
divide each image by two (for a max value of 127), and then add them (for a
max of 254).  In effect, you're converting the red and green channels to 7
bit images before adding into an 8 bit image.
--- end of quote ---
Another way would be to take slice n of the red and green stacks, copy them and paste into a temp stack (macro command MakeNewStack - you will have to set the newSize)  as red and green, create a new blank slice in the temp stack, then use RGB to 8 bit command in Stacks menu. Copy the new 8 bit image and paste into a new stack (makeNewStack again). Dispose of the 8 bit image and repeate with slice n+1. At the end you will have a stack of the combined red and green stacks.

Chuck

------------------------------

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------------------------------

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--------------------------------
End of nih-image-d Digest V99 Issue #78
***************************************

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Date: Thu, 01 Apr 1999 10:40:34 +0200
From: "U.Marti" <ulrich.marti@dkf2.unibe.ch>
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Hi there,

I am looking for a makro to calculate all possible distances between
pairs of pixels in a binary image.

Thanks for any help

U. Marti


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Could you be a little more specific and describe your problem?. How will
you recognize the pair of pixels for measuring? 
Maybe this is of modest help, but the following macro could be a
start...


var x,y1,x2,y2:integer;

macro 'DistanceBetweenPixels';

begin
  FindFirstPixelCoord;   
  FindSecPixelCoord;
  MakelineRoi(x1,y1,x2,y2); 
  measure;       
end;   


Gary.


>-----Original Message-----
>From:	U.Marti [SMTP:ulrich.marti@dkf2.unibe.ch]
>Sent:	1. april 1999 10:41
>To:	NIH List
>Subject:	Makro
>
>Hi there,
>
>I am looking for a makro to calculate all possible distances between
>pairs of pixels in a binary image.
>
>Thanks for any help
>
>U. Marti
>


From nih-image-request@io.ece.drexel.edu Thu Apr  1 07:19 EST 1999
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From: "U.Marti" <ulrich.marti@dkf2.unibe.ch>
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Hi there

It looks like my question was not clear. I am looking for a macro to
calculate all distances between pair of pixels. That means: I will make
a binary picture of a tissue section. Then I will reduce the number of
pixels to lets say 32x32. Then I need all possible distances between the
pixels. After that I will classify the distances in groups and determine
the number of group members. I hope this makes it more clear.

Thank for any help

Ulrich Marti


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Date: Thu, 01 Apr 1999 14:58:31 +0100
From: Stamatis Pagakis <spagaki@nimr.mrc.ac.uk>
Subject: Watershed algorithm
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Hi


does anyone know where we can find an inplemented GRAYSCALE watershed
algorithm?

Thanks



*-----------------*------------------*----------------------*---------------*
>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <
>Confocal and Image Analysis Laboratory             Tel: +44 (0)181 913 8675 <
>Membrane Biology                                Mobile: 0370 654288         <
>National Institute for Medical Research    Switchboard: 0181 9593666 x2621  <
>The Ridgeway                                   Message: x2219, x2622        <
>Mill Hill, London NW7 1AA                          FAX: +44 (0)181 906 4477 <


From nih-image-request@io.ece.drexel.edu Thu Apr  1 14:46 EST 1999
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Subject: Western Blot protein band quantification
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     Dear NIH-image subscribers,
     
     Please pardon me if this question has been asked previously, I could 
     not find a specific answer among the old questions that have been 
     posted.  
     
     How do I quantify protein bands on a Western blot using NIH-image and 
     a frame grabber?
     
     I am using BCIP/NBT to stain the protein bands blue during western 
     blotting.  I have been able to digitize the blot using a frame grabber 
     and the Scion image program.  That is as far as I have gotten. I would 
     like to be able to quantify the protein bands and therefore need to be 
     able to determine the density and area of the bands and be able to 
     subtract background.  If anyone has any information or a methodology 
     they would like to share regarding my question please let me know.  
     Thank you very much for your help. 
     
     Julie Russell
     Biological Science Laboratory Technician (APL Corp.)
     at USGS-Patuxent Wildlife Research Center
     Laurel, Maryland
     301-497-5678
     Julie_Russell@usgs.gov


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From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: Western Blot protein band quantification
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>     Dear NIH-image subscribers,
>
>     Please pardon me if this question has been asked previously, I could
>     not find a specific answer among the old questions that have been
>     posted.
>
>     How do I quantify protein bands on a Western blot using NIH-image and
>     a frame grabber?
>
>     I am using BCIP/NBT to stain the protein bands blue during western
>     blotting.  I have been able to digitize the blot using a frame grabber
>     and the Scion image program.  That is as far as I have gotten. I would
>     like to be able to quantify the protein bands and therefore need to be
>     able to determine the density and area of the bands and be able to
>     subtract background.  If anyone has any information or a methodology
>     they would like to share regarding my question please let me know.
>     Thank you very much for your help.

There is an online NIH Image gel analysis tutorial at

       http://scrc.dcrt.nih.gov/imaging/tutorials/gel_density/short/index.html

-wayne



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Date: Thu, 01 Apr 1999 15:26:02 +0000
From: Marcia Goldfarb <anatekep@maine.rr.com>
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Julie

What you want to do is not an inconsequential project. You need an
understanding of thresholding for one thing. I suggest John Russ' book
"The Image Processing Handbook", but that is not a simple read. There is
a macro from Thomas Seebacher (an NIH-Image plug in) which measures area
and density of bands in gels. I have had a paper accepted for
publication in the journal "Electrophoresis" on measurement of spots in
2-D gels. It should be coming out very soon and you may be able to get
an idea of how to proceed from it. If this is a major project for you, I
recommend taking John Russ' course at  North Carolina State.

Marcia Goldfarb
Anatek-EP
17 Bishop St
Portland, ME 04103

email: anatekep@maine.rr.com




From nih-image-request@io.ece.drexel.edu Thu Apr  1 20:40 EST 1999
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Dear Imagers,

I am trying to set up a Sony XC-77 CCD camera, but have problems. The XC-77
is properly attached to a microscope, and I have a Scion LG-3 capture card
in a PowerMac 7200/90 running Sys 8.1 and NIH-Image 1.60. For the XC-77 I
am using a small 12V DC power supply.

Although I get some sort of a live image with Start Capturing, the image is
very poor. It is strongly shadowed, with additional vertical and horizontal
tripes. The image flicks from one presentation to another about every 1
second, and displays horizontal bands ~30-50 pixels wide that sometimes
move up the image. Aggh!

Is it likely that the power supply to the XC-77 is the problem?

Any assistance will be greatly appreciated.







Doug Mason

Mason Geoscience Pty Ltd
Petrological Services for the Exploration and Mining Industry
email   : drmason@interconnect.com.au
post    : PO Box 78, Glenside  SA  5065, Australia
phone   : +61-8-83901507
fax     : +61-8-83901194



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nih-image-d Digest				Volume 99 : Issue 79

Today's Topics:
  Makro                                 [ "U.Marti" <ulrich.marti@dkf2.unibe. ]
  RE: Makro                             [ Gary Chinga <gary.chinga@pfi.no> ]
  Makro                                 [ "U.Marti" <ulrich.marti@dkf2.unibe. ]
  Watershed algorithm                   [ Stamatis Pagakis <spagaki@nimr.mrc. ]
  Western Blot protein band quantifica  [ Julie_Russell@usgs.gov (Julie Russe ]
  Re: Western Blot protein band quanti  [ Wayne Rasband <wayne@codon.nih.gov> ]
  Re: Western Blot protein band quanti  [ Marcia Goldfarb <anatekep@maine.rr. ]
  Camera setup problem                  [ Doug Mason <drmason@interconnect.co ]

------------------------------

Date: Thu, 01 Apr 1999 10:40:34 +0200
From: "U.Marti" <ulrich.marti@dkf2.unibe.ch>
To: NIH List <nih-image@io.ece.drexel.edu>
Subject: Makro
Message-id: <370330FF.2A102CEA@dkf2.unibe.ch>
Content-type: text/plain; charset=us-ascii; x-mac-type="54455854"; 
              x-mac-creator="4D4F5353"
Content-transfer-encoding: 7bit

Hi there,

I am looking for a makro to calculate all possible distances between
pairs of pixels in a binary image.

Thanks for any help

U. Marti

------------------------------

Date: Thu, 1 Apr 1999 11:11:36 +0200
From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Makro
Message-ID: <c=NO%a=_%p=pfi%l=PFINT1-990401091136Z-4032@pfint1.pfi.no>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

Could you be a little more specific and describe your problem?. How will
you recognize the pair of pixels for measuring? 
Maybe this is of modest help, but the following macro could be a
start...


var x,y1,x2,y2:integer;

macro 'DistanceBetweenPixels';

begin
  FindFirstPixelCoord;   
  FindSecPixelCoord;
  MakelineRoi(x1,y1,x2,y2); 
  measure;       
end;   


Gary.


>-----Original Message-----
>From:	U.Marti [SMTP:ulrich.marti@dkf2.unibe.ch]
>Sent:	1. april 1999 10:41
>To:	NIH List
>Subject:	Makro
>
>Hi there,
>
>I am looking for a makro to calculate all possible distances between
>pairs of pixels in a binary image.
>
>Thanks for any help
>
>U. Marti
>

------------------------------

Date: Thu, 01 Apr 1999 13:59:29 +0200
From: "U.Marti" <ulrich.marti@dkf2.unibe.ch>
To: NIH List <nih-image@io.ece.drexel.edu>
Subject: Makro
Message-id: <37035F9A.B72D0838@dkf2.unibe.ch>
Content-type: text/plain; charset=us-ascii; x-mac-type="54455854"; 
              x-mac-creator="4D4F5353"
Content-transfer-encoding: 7bit

Hi there

It looks like my question was not clear. I am looking for a macro to
calculate all distances between pair of pixels. That means: I will make
a binary picture of a tissue section. Then I will reduce the number of
pixels to lets say 32x32. Then I need all possible distances between the
pixels. After that I will classify the distances in groups and determine
the number of group members. I hope this makes it more clear.

Thank for any help

Ulrich Marti

------------------------------

Date: Thu, 01 Apr 1999 14:58:31 +0100
From: Stamatis Pagakis <spagaki@nimr.mrc.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Watershed algorithm
Message-id: <Pine.SGI.4.10.9904011456550.3326-100000@membo2.nimr.mrc.ac.uk>
Content-type: TEXT/PLAIN; charset=US-ASCII

Hi


does anyone know where we can find an inplemented GRAYSCALE watershed
algorithm?

Thanks



*-----------------*------------------*----------------------*---------------*
>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <
>Confocal and Image Analysis Laboratory             Tel: +44 (0)181 913 8675 <
>Membrane Biology                                Mobile: 0370 654288         <
>National Institute for Medical Research    Switchboard: 0181 9593666 x2621  <
>The Ridgeway                                   Message: x2219, x2622        <
>Mill Hill, London NW7 1AA                          FAX: +44 (0)181 906 4477 <

------------------------------

Date: Thu, 1 Apr 1999 14:21:42 -0700
From: Julie_Russell@usgs.gov (Julie Russell)
To: nih-image@io.ece.drexel.edu
Subject: Western Blot protein band quantification
Message-ID: <00048684.@usgs.gov>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Description: cc:Mail note part

     Dear NIH-image subscribers,
     
     Please pardon me if this question has been asked previously, I could 
     not find a specific answer among the old questions that have been 
     posted.  
     
     How do I quantify protein bands on a Western blot using NIH-image and 
     a frame grabber?
     
     I am using BCIP/NBT to stain the protein bands blue during western 
     blotting.  I have been able to digitize the blot using a frame grabber 
     and the Scion image program.  That is as far as I have gotten. I would 
     like to be able to quantify the protein bands and therefore need to be 
     able to determine the density and area of the bands and be able to 
     subtract background.  If anyone has any information or a methodology 
     they would like to share regarding my question please let me know.  
     Thank you very much for your help. 
     
     Julie Russell
     Biological Science Laboratory Technician (APL Corp.)
     at USGS-Patuxent Wildlife Research Center
     Laurel, Maryland
     301-497-5678
     Julie_Russell@usgs.gov

------------------------------

Date: Thu, 1 Apr 1999 16:31:51 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Western Blot protein band quantification
Message-Id: <v03007803b32985ffbadd@[128.231.99.220]>
Content-Type: text/plain; charset="us-ascii"

>     Dear NIH-image subscribers,
>
>     Please pardon me if this question has been asked previously, I could
>     not find a specific answer among the old questions that have been
>     posted.
>
>     How do I quantify protein bands on a Western blot using NIH-image and
>     a frame grabber?
>
>     I am using BCIP/NBT to stain the protein bands blue during western
>     blotting.  I have been able to digitize the blot using a frame grabber
>     and the Scion image program.  That is as far as I have gotten. I would
>     like to be able to quantify the protein bands and therefore need to be
>     able to determine the density and area of the bands and be able to
>     subtract background.  If anyone has any information or a methodology
>     they would like to share regarding my question please let me know.
>     Thank you very much for your help.

There is an online NIH Image gel analysis tutorial at

       http://scrc.dcrt.nih.gov/imaging/tutorials/gel_density/short/index.html

-wayne

------------------------------

Date: Thu, 01 Apr 1999 15:26:02 +0000
From: Marcia Goldfarb <anatekep@maine.rr.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Western Blot protein band quantification
Message-ID: <37039008.7B599ED9@maine.rr.com>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Julie

What you want to do is not an inconsequential project. You need an
understanding of thresholding for one thing. I suggest John Russ' book
"The Image Processing Handbook", but that is not a simple read. There is
a macro from Thomas Seebacher (an NIH-Image plug in) which measures area
and density of bands in gels. I have had a paper accepted for
publication in the journal "Electrophoresis" on measurement of spots in
2-D gels. It should be coming out very soon and you may be able to get
an idea of how to proceed from it. If this is a major project for you, I
recommend taking John Russ' course at  North Carolina State.

Marcia Goldfarb
Anatek-EP
17 Bishop St
Portland, ME 04103

email: anatekep@maine.rr.com

------------------------------

Date: Fri, 2 Apr 1999 10:51:20 +1030
From: Doug Mason <drmason@interconnect.com.au>
To: nih-image@io.ece.drexel.edu
Subject: Camera setup problem
Message-Id: <l03110700b329bb94ee5a@[210.8.6.190]>
Content-Type: text/plain; charset="us-ascii"

Dear Imagers,

I am trying to set up a Sony XC-77 CCD camera, but have problems. The XC-77
is properly attached to a microscope, and I have a Scion LG-3 capture card
in a PowerMac 7200/90 running Sys 8.1 and NIH-Image 1.60. For the XC-77 I
am using a small 12V DC power supply.

Although I get some sort of a live image with Start Capturing, the image is
very poor. It is strongly shadowed, with additional vertical and horizontal
tripes. The image flicks from one presentation to another about every 1
second, and displays horizontal bands ~30-50 pixels wide that sometimes
move up the image. Aggh!

Is it likely that the power supply to the XC-77 is the problem?

Any assistance will be greatly appreciated.







Doug Mason

Mason Geoscience Pty Ltd
Petrological Services for the Exploration and Mining Industry
email   : drmason@interconnect.com.au
post    : PO Box 78, Glenside  SA  5065, Australia
phone   : +61-8-83901507
fax     : +61-8-83901194

--------------------------------
End of nih-image-d Digest V99 Issue #79
***************************************

From nih-image-request@io.ece.drexel.edu Fri Apr  2 06:22 EST 1999
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Date: Fri, 2 Apr 1999 13:17:27 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Makro
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>
>Hi there
>
>It looks like my question was not clear. I am looking for a macro to
>calculate all distances between pair of pixels. That means: I will make
>a binary picture of a tissue section. Then I will reduce the number of
>pixels to lets say 32x32. Then I need all possible distances between the
>pixels. After that I will classify the distances in groups and determine
>the number of group members. I hope this makes it more clear.
>
>Thank for any help
>
>Ulrich Marti


Instead of calculating *all* distances, you can use a statistical approach:
Repeat to choose a random point within the bounding rectangle of the object
until 'GetPixel' indicates that the the point is inside the object. Then,
choose the second point in the same way, and you have a random pair.
Calculate the point distance.
You may prefer to immediately classify the distance and increment a bin
counter (e.g. rUser1[thisbin]), instead of storing the the distance itself.
You can then collect as many samples as you want without overflow. The
amount of samples does not depend on the object size, so there is no need
to reduce it to 32 * 32.


Norbert Vischer                  University of Amsterdam
Scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



From nih-image-request@io.ece.drexel.edu Fri Apr  2 18:37 EST 1999
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Date: Fri, 02 Apr 1999 15:50:23 -0600
From: Duncan Young <dyoung@post.cis.smu.edu>
Organization: Student at SMU
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Hi there,
  I have been using a 16-bit planetary topographic dataset along with
Image. I have made a macro to calibrate the resulting 8-bit data to
elevations - however I have to use some Unix tools on a Sun to get the
highest data number for the conversion. I was wonder if there was a way
to directly get this number through Image (I dont really trust the
inbuilt autoscaling - it seems to do funny things to this dataset).

Cheers,
   Duncan Young
   Department of Geological Sciences
   Southern Methodist University


From nih-image-d-request@io.ece.drexel.edu Sat Apr  3 05:15 EST 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 80

Today's Topics:
  Re: Makro                             [ Norbert Vischer <vischer@bio.uva.nl ]
  Getting 16-bit values                 [ Duncan Young <dyoung@post.cis.smu.e ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]

------------------------------

Date: Fri, 2 Apr 1999 13:17:27 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Makro
Message-Id: <l03010d00b32a574c1404@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

>
>Hi there
>
>It looks like my question was not clear. I am looking for a macro to
>calculate all distances between pair of pixels. That means: I will make
>a binary picture of a tissue section. Then I will reduce the number of
>pixels to lets say 32x32. Then I need all possible distances between the
>pixels. After that I will classify the distances in groups and determine
>the number of group members. I hope this makes it more clear.
>
>Thank for any help
>
>Ulrich Marti


Instead of calculating *all* distances, you can use a statistical approach:
Repeat to choose a random point within the bounding rectangle of the object
until 'GetPixel' indicates that the the point is inside the object. Then,
choose the second point in the same way, and you have a random pair.
Calculate the point distance.
You may prefer to immediately classify the distance and increment a bin
counter (e.g. rUser1[thisbin]), instead of storing the the distance itself.
You can then collect as many samples as you want without overflow. The
amount of samples does not depend on the object size, so there is no need
to reduce it to 32 * 32.


Norbert Vischer                  University of Amsterdam
Scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: Fri, 02 Apr 1999 15:50:23 -0600
From: Duncan Young <dyoung@post.cis.smu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Getting 16-bit values
Message-ID: <37053B9F.154D@mail.smu.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi there,
  I have been using a 16-bit planetary topographic dataset along with
Image. I have made a macro to calibrate the resulting 8-bit data to
elevations - however I have to use some Unix tools on a Sun to get the
highest data number for the conversion. I was wonder if there was a way
to directly get this number through Image (I dont really trust the
inbuilt autoscaling - it seems to do funny things to this dataset).

Cheers,
   Duncan Young
   Department of Geological Sciences
   Southern Methodist University

------------------------------

Date: Sat, 3 Apr 1999 05:05:01 -0500 (EST)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199904031005.FAA26764@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
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         ls latest
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command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
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Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
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Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--


From nih-image-request@io.ece.drexel.edu Sat Apr  3 11:28 EST 1999
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From: Jon Vaughan <jvaughan@hamilton.edu>
Message-Id: <199904031614.LAA06229@hamilton.edu>
Subject: Saving measurements from every slice to a single file
To: nih-image@io.ece.drexel.edu
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Dear Imagers,

I've read the manual, but still can't solve what must be a simple and
frequently-encountered problem: for each image in a stack, I want to
measure some particles, then save the measurements to disk in a file. Some
manual intervention is required, so the macro operates on a slice-by-slice
basis.  Is there a way to have all the measurements in a single file,
appropriately labelled by slice number?  The Export function, in my hands,
seems to make a separate file for each slice (which must then be
separately named), as does SaveAs the results window. Not resetting the
measurement counter does concatenate the measurements, but it is confusing
not to have the measurements from each slice distinguished in some way
other than number since there are a different number in each slice.  If
someone has a simple solution to this task, I'd be grateful. 

Thanks!

 -- 
Jonathan Vaughan       Psychology, Hamilton College        jvaughan@hamilton.edu


From nih-image-request@io.ece.drexel.edu Sat Apr  3 16:05 EST 1999
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Date: Sat, 03 Apr 1999 12:54:50 -0800
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Saving measurements from every slice to a single file
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I have written some macros that do some things that sound similar. I want a
table with some measurements, and a slice number. There are three macros.
One sets up measurements, and two do some measurements and save the result
to the results. Finally, I save the results manually. They are listed
below. Hope this helps. Note that I end up with one line, with both sets of
measurements on the same line, and a slice number.

DTL

macro 'Set up measurements [M]';
begin
ResetCounter;
SetUser1Label('L');
SetUser2Label('Slice_No');
SetOptions('A, User1, User2');
CurWindow := WindowTitle;
end;

macro 'Measure L [L]';
begin
Measure;
rUser1[rCount] := rArea[rCount];
rUser2[rCount] := SliceNumber;
ShowResults;
SelectWindow(CurWindow);
end;

macro 'Measure MA [A]';
begin
Measure;
rArea[rCount-1] := rArea[rCount];
SetCounter(rCount-1);
ShowResults;
SelectWindow(CurWindow);
end;


--On Sat, Apr 3, 1999 11:14 AM -0500 Jon Vaughan <jvaughan@hamilton.edu>
wrote:

> Dear Imagers,
> 
> I've read the manual, but still can't solve what must be a simple and
> frequently-encountered problem: for each image in a stack, I want to
> measure some particles, then save the measurements to disk in a file. Some
> manual intervention is required, so the macro operates on a slice-by-slice
> basis.  Is there a way to have all the measurements in a single file,
> appropriately labelled by slice number?  The Export function, in my hands,
> seems to make a separate file for each slice (which must then be
> separately named), as does SaveAs the results window. Not resetting the
> measurement counter does concatenate the measurements, but it is confusing
> not to have the measurements from each slice distinguished in some way
> other than number since there are a different number in each slice.  If
> someone has a simple solution to this task, I'd be grateful. 
> 
> Thanks!
> 
>  -- 
> Jonathan Vaughan       Psychology, Hamilton College
> jvaughan@hamilton.edu
> 





From nih-image-request@io.ece.drexel.edu Sat Apr  3 16:38 EST 1999
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Date: Sat, 3 Apr 1999 23:31:54 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Saving measurements from every slice to a single file
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>Dear Imagers,
>
>I've read the manual, but still can't solve what must be a simple and
>frequently-encountered problem: for each image in a stack, I want to
>measure some particles, then save the measurements to disk in a file. Some
>manual intervention is required, so the macro operates on a slice-by-slice
>basis.  Is there a way to have all the measurements in a single file,
>appropriately labelled by slice number?  The Export function, in my hands,
>seems to make a separate file for each slice (which must then be
>separately named), as does SaveAs the results window. Not resetting the
>measurement counter does concatenate the measurements, but it is confusing
>not to have the measurements from each slice distinguished in some way
>other than number since there are a different number in each slice.  If
>someone has a simple solution to this task, I'd be grateful.
>

You can try Object-Image, which stores measurements with slice
identification across many images and stacks, using  non-destructive
marking and labelling, bidirectional linking between results and object
markers, double-clickable object files, manual interaction like
editing/deleting and more.
The Example "ParitcleAxes.sea" demonstrates the non-destructive marking of
particle axes. In Object-Image, there is less need to work with
intermediate text files (and then reconstructing the context in Excel)
because Object-Image cares for the house-keeping and allows you to evaluate
your data on macro level.

Norbert

Norbert Vischer                  University of Amsterdam
Scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



From nih-image-d-request@io.ece.drexel.edu Sun Apr  4 06:11 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #81
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 81

Today's Topics:
  Saving measurements from every slice  [ Jon Vaughan <jvaughan@hamilton.edu> ]
  Re: Saving measurements from every s  [ David Linker <dtlinker@u.washington ]
  Re: Saving measurements from every s  [ Norbert Vischer <vischer@bio.uva.nl ]

------------------------------

Date: Sat, 3 Apr 1999 11:14:15 -0500 (EST)
From: Jon Vaughan <jvaughan@hamilton.edu>
To: nih-image@io.ece.drexel.edu
Subject: Saving measurements from every slice to a single file
Message-Id: <199904031614.LAA06229@hamilton.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit

Dear Imagers,

I've read the manual, but still can't solve what must be a simple and
frequently-encountered problem: for each image in a stack, I want to
measure some particles, then save the measurements to disk in a file. Some
manual intervention is required, so the macro operates on a slice-by-slice
basis.  Is there a way to have all the measurements in a single file,
appropriately labelled by slice number?  The Export function, in my hands,
seems to make a separate file for each slice (which must then be
separately named), as does SaveAs the results window. Not resetting the
measurement counter does concatenate the measurements, but it is confusing
not to have the measurements from each slice distinguished in some way
other than number since there are a different number in each slice.  If
someone has a simple solution to this task, I'd be grateful. 

Thanks!

 -- 
Jonathan Vaughan       Psychology, Hamilton College        jvaughan@hamilton.edu

------------------------------

Date: Sat, 03 Apr 1999 12:54:50 -0800
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Saving measurements from every slice to a single file
Message-ID: <3467981.3132132890@huginn.medicine.washington.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

I have written some macros that do some things that sound similar. I want a
table with some measurements, and a slice number. There are three macros.
One sets up measurements, and two do some measurements and save the result
to the results. Finally, I save the results manually. They are listed
below. Hope this helps. Note that I end up with one line, with both sets of
measurements on the same line, and a slice number.

DTL

macro 'Set up measurements [M]';
begin
ResetCounter;
SetUser1Label('L');
SetUser2Label('Slice_No');
SetOptions('A, User1, User2');
CurWindow := WindowTitle;
end;

macro 'Measure L [L]';
begin
Measure;
rUser1[rCount] := rArea[rCount];
rUser2[rCount] := SliceNumber;
ShowResults;
SelectWindow(CurWindow);
end;

macro 'Measure MA [A]';
begin
Measure;
rArea[rCount-1] := rArea[rCount];
SetCounter(rCount-1);
ShowResults;
SelectWindow(CurWindow);
end;


--On Sat, Apr 3, 1999 11:14 AM -0500 Jon Vaughan <jvaughan@hamilton.edu>
wrote:

> Dear Imagers,
> 
> I've read the manual, but still can't solve what must be a simple and
> frequently-encountered problem: for each image in a stack, I want to
> measure some particles, then save the measurements to disk in a file. Some
> manual intervention is required, so the macro operates on a slice-by-slice
> basis.  Is there a way to have all the measurements in a single file,
> appropriately labelled by slice number?  The Export function, in my hands,
> seems to make a separate file for each slice (which must then be
> separately named), as does SaveAs the results window. Not resetting the
> measurement counter does concatenate the measurements, but it is confusing
> not to have the measurements from each slice distinguished in some way
> other than number since there are a different number in each slice.  If
> someone has a simple solution to this task, I'd be grateful. 
> 
> Thanks!
> 
>  -- 
> Jonathan Vaughan       Psychology, Hamilton College
> jvaughan@hamilton.edu
> 

------------------------------

Date: Sat, 3 Apr 1999 23:31:54 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Saving measurements from every slice to a single file
Message-Id: <l03010d01b32c360126b9@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

>Dear Imagers,
>
>I've read the manual, but still can't solve what must be a simple and
>frequently-encountered problem: for each image in a stack, I want to
>measure some particles, then save the measurements to disk in a file. Some
>manual intervention is required, so the macro operates on a slice-by-slice
>basis.  Is there a way to have all the measurements in a single file,
>appropriately labelled by slice number?  The Export function, in my hands,
>seems to make a separate file for each slice (which must then be
>separately named), as does SaveAs the results window. Not resetting the
>measurement counter does concatenate the measurements, but it is confusing
>not to have the measurements from each slice distinguished in some way
>other than number since there are a different number in each slice.  If
>someone has a simple solution to this task, I'd be grateful.
>

You can try Object-Image, which stores measurements with slice
identification across many images and stacks, using  non-destructive
marking and labelling, bidirectional linking between results and object
markers, double-clickable object files, manual interaction like
editing/deleting and more.
The Example "ParitcleAxes.sea" demonstrates the non-destructive marking of
particle axes. In Object-Image, there is less need to work with
intermediate text files (and then reconstructing the context in Excel)
because Object-Image cares for the house-keeping and allows you to evaluate
your data on macro level.

Norbert

Norbert Vischer                  University of Amsterdam
Scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

--------------------------------
End of nih-image-d Digest V99 Issue #81
***************************************

From nih-image-request@io.ece.drexel.edu Mon Apr  5 14:23 EDT 1999
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Date: Mon, 05 Apr 1999 14:05:44 -0400
Subject: Monitor for stage position?
From: "Ken Baker" <kwb@bserv.com>
To: nih-image@io.ece.drexel.edu
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Hello Imagers,
Is anybody aware of any device that will monitor and report x-y stage
position as the stage is being manually moved.
For example, an operator examines a series of 24 wells by manually moving
from well 1 through 24 and enters intensity data for each well. Rather than
visually monitoring and recording the well being evaluated we would like
this information to correlate with some kind of position output.
We're assuming that if such a thing exists,  simple stage tracking might be
less expensive and possibly less complicated than a full blown motorized
stage setup.
Thanks in advance.
Regards,
        Ken
                --
KWB@bserv.com
519-853-4787



From nih-image-request@io.ece.drexel.edu Mon Apr  5 14:52 EDT 1999
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Date: Mon, 05 Apr 1999 14:35:44 -0400
To: nih-image@io.ece.drexel.edu
From: Bill Miller <microbill@mohawk.net>
Subject: Re: Monitor for stage position?
In-Reply-To: <199904051753.NAA04381@bserv.com>
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check with Flexbar - Lance Larkin - 203-230-9487 - they make both manual
and motorived x-y tables.  For a x-y stage I'd check eith Prior ot Ludl.

Bill Miller


At 02:05 PM 4/5/99 -0400, you wrote:
>Hello Imagers,
>Is anybody aware of any device that will monitor and report x-y stage
>position as the stage is being manually moved.
>For example, an operator examines a series of 24 wells by manually moving
>from well 1 through 24 and enters intensity data for each well. Rather than
>visually monitoring and recording the well being evaluated we would like
>this information to correlate with some kind of position output.
>We're assuming that if such a thing exists,  simple stage tracking might be
>less expensive and possibly less complicated than a full blown motorized
>stage setup.
>Thanks in advance.
>Regards,
>        Ken
>                --
>KWB@bserv.com
>519-853-4787
>
>
>
>


From nih-image-request@io.ece.drexel.edu Mon Apr  5 15:05 EDT 1999
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Resent-Date: Mon, 5 Apr 1999 15:05:22 -0400 (EDT)
From: "Herbert M. Geller" <geller@UMDNJ.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Re: Monitor for stage position?
In-Reply-To: <199904051753.NAA04381@bserv.com>
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A simple way to do this is with digital indicators which 
are normally used in the machine tool industry to track 
position of lathes, etc.  You attach them to your stage and 
get a digital readout of movement, which can also be 
recorded onto a computer.  


On Mon, 05 Apr 1999 14:05:44 -0400 Ken Baker 
<kwb@bserv.com> wrote:

> Hello Imagers,
> Is anybody aware of any device that will monitor and report x-y stage
> position as the stage is being manually moved.
> For example, an operator examines a series of 24 wells by manually moving
> from well 1 through 24 and enters intensity data for each well. Rather than
> visually monitoring and recording the well being evaluated we would like
> this information to correlate with some kind of position output.
> We're assuming that if such a thing exists,  simple stage tracking might be
> less expensive and possibly less complicated than a full blown motorized
> stage setup.
> Thanks in advance.
> Regards,
>         Ken
>                 --
> KWB@bserv.com
> 519-853-4787
> 

----------------------------------------------------------
Herbert M. Geller, Ph.D.
Professor
Department of Pharmacology           voice -  732-235-4084
Robert Wood Johnson Medical School     fax -  732-235-4073
Piscataway, New Jersey 08854   Internet - geller@umdnj.edu
www: http://www2.umdnj.edu/~geller/lab/


From nih-image-d-request@io.ece.drexel.edu Tue Apr  6 06:12 EDT 1999
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Subject: nih-image-d Digest V99 #82
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 82

Today's Topics:
  Monitor for stage position?           [ "Ken Baker" <kwb@bserv.com> ]
  Re: Monitor for stage position?       [ Bill Miller <microbill@mohawk.net> ]
  Re: Monitor for stage position?       [ "Herbert M. Geller" <geller@UMDNJ.E ]

------------------------------

Date: Mon, 05 Apr 1999 14:05:44 -0400
From: "Ken Baker" <kwb@bserv.com>
To: nih-image@io.ece.drexel.edu
Subject: Monitor for stage position?
Message-Id: <199904051753.NAA04381@bserv.com>
Content-type: text/plain; charset="US-ASCII"
Content-transfer-encoding: 7bit

Hello Imagers,
Is anybody aware of any device that will monitor and report x-y stage
position as the stage is being manually moved.
For example, an operator examines a series of 24 wells by manually moving
from well 1 through 24 and enters intensity data for each well. Rather than
visually monitoring and recording the well being evaluated we would like
this information to correlate with some kind of position output.
We're assuming that if such a thing exists,  simple stage tracking might be
less expensive and possibly less complicated than a full blown motorized
stage setup.
Thanks in advance.
Regards,
        Ken
                --
KWB@bserv.com
519-853-4787

------------------------------

Date: Mon, 05 Apr 1999 14:35:44 -0400
From: Bill Miller <microbill@mohawk.net>
To: nih-image@io.ece.drexel.edu
Subject: Re: Monitor for stage position?
Message-Id: <3.0.5.32.19990405143544.007d9100@mohawk.net>
Content-Type: text/plain; charset="us-ascii"

check with Flexbar - Lance Larkin - 203-230-9487 - they make both manual
and motorived x-y tables.  For a x-y stage I'd check eith Prior ot Ludl.

Bill Miller


At 02:05 PM 4/5/99 -0400, you wrote:
>Hello Imagers,
>Is anybody aware of any device that will monitor and report x-y stage
>position as the stage is being manually moved.
>For example, an operator examines a series of 24 wells by manually moving
>from well 1 through 24 and enters intensity data for each well. Rather than
>visually monitoring and recording the well being evaluated we would like
>this information to correlate with some kind of position output.
>We're assuming that if such a thing exists,  simple stage tracking might be
>less expensive and possibly less complicated than a full blown motorized
>stage setup.
>Thanks in advance.
>Regards,
>        Ken
>                --
>KWB@bserv.com
>519-853-4787
>
>
>
>

------------------------------

Date: Mon, 5 Apr 1999 14:51:07 -0400 (Eastern Daylight Time)
From: "Herbert M. Geller" <geller@UMDNJ.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Re: Monitor for stage position?
Message-ID: <SIMEON.9904051407.E@hmgpc.umdnj.edu>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

A simple way to do this is with digital indicators which 
are normally used in the machine tool industry to track 
position of lathes, etc.  You attach them to your stage and 
get a digital readout of movement, which can also be 
recorded onto a computer.  


On Mon, 05 Apr 1999 14:05:44 -0400 Ken Baker 
<kwb@bserv.com> wrote:

> Hello Imagers,
> Is anybody aware of any device that will monitor and report x-y stage
> position as the stage is being manually moved.
> For example, an operator examines a series of 24 wells by manually moving
> from well 1 through 24 and enters intensity data for each well. Rather than
> visually monitoring and recording the well being evaluated we would like
> this information to correlate with some kind of position output.
> We're assuming that if such a thing exists,  simple stage tracking might be
> less expensive and possibly less complicated than a full blown motorized
> stage setup.
> Thanks in advance.
> Regards,
>         Ken
>                 --
> KWB@bserv.com
> 519-853-4787
> 

----------------------------------------------------------
Herbert M. Geller, Ph.D.
Professor
Department of Pharmacology           voice -  732-235-4084
Robert Wood Johnson Medical School     fax -  732-235-4073
Piscataway, New Jersey 08854   Internet - geller@umdnj.edu
www: http://www2.umdnj.edu/~geller/lab/

--------------------------------
End of nih-image-d Digest V99 Issue #82
***************************************

From nih-image-request@io.ece.drexel.edu Tue Apr  6 08:58 EDT 1999
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>Date: Thu, 01 Apr 1999 13:59:29 +0200
>From: "U.Marti" <ulrich.marti@dkf2.unibe.ch>
>To: NIH List <nih-image@io.ece.drexel.edu>
>Subject: Makro
>Message-id: <37035F9A.B72D0838@dkf2.unibe.ch>
>Content-type: text/plain; charset=us-ascii; x-mac-type="54455854";
>              x-mac-creator="4D4F5353"
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>
>Hi there
>
>It looks like my question was not clear. I am looking for a macro to
>calculate all distances between pair of pixels. That means: I will make
>a binary picture of a tissue section. Then I will reduce the number of
>pixels to lets say 32x32. Then I need all possible distances between the
>pixels. After that I will classify the distances in groups and determine
>the number of group members. I hope this makes it more clear.
>
>Thank for any help
>
>Ulrich Marti
75 <

If you want to do "autocorrelation" - or cross-correlation
i.e. looking for regularity of inter-cell-distances in a cell
mosaic="pixel" = x/y-coordinates
you might consider the approach of Bob Rodieck:

The density recovery profile: A method for the analysis of points in the
plane applicable to retinal studies.
Visual Neurosci.6: 95-111

or
Kouyama, N.
Marshak, D.W.
The topographical relationship between two neuronal mosaics in the short
wavelength-sensitive system of the primate retina.
Vis. Neurosc.14: 159-167.

(Dr.E.Fernandez and we are working on another implementation of this approach).

P.Ahnelt

  _    _    _
 / \  / \  / \   e-mail: peter.ahnelt@univie.ac.at
 |R|  |G|  |B|   Adress: Peter Ahnelt
 '|  '|  '|           Dept. Gen. & Compar. Physiology
 []  []  []           University of Vienna, Medical School
 ()  ()  ()           Schwarzspanierstr. 17,  A-1090 Vienna
  |    |    |       Tel. 43 1 4277/ 62330,62301  FAX 43 1 4277/ 9623
 __  __   _   http://www.univie.ac.at/Vergl-Physiologie/www/gphy_morph.html
                  



From nih-image-request@io.ece.drexel.edu Tue Apr  6 11:02 EDT 1999
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Subject: NAND macro?
Date: Tue, 6 Apr 99 10:51:30 -0400
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I'm using Scion Image to track and record position data from video tapes 
of people moving through spaces.  I'm trying to set Scion up to do this 
automaticaly, and would like to subtract out the stationary background.  
Unfortunatly, scion doesn't have a NAND function included with its image 
processesing tools.  Has anyone writen a NAND macro or plugin? Or 
suggestions on the best way to do this?
        thanks,
          -skye

                                  -000-
Skye Bender-deMoll 
  | Bennington College
  | Bennington VT 05201
  | 802.440.4626 
  |---------------------- skyebend@bennington.edu
  | 38755 Reed Road
  | Nehalem OR 97131
  | 503.368.6294


From nih-image-request@io.ece.drexel.edu Tue Apr  6 11:24 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: Jen-Wei Lin <jenwelin@bio.bu.edu>
Subject: NuBus card
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Hi all:
	I am looking for a LG-3 frame grabber, NuBus version that is.  If
anyone has it, I am interested in buying it.
Thanks!
Jen-Wei


Jen-Wei Lin, Ph.D.
Biology
Boston University
5 Cummington St.
Boston, MA 02215

TEL:617-353-3443 or -3444
FAX: 617-353-6340



From nih-image-request@io.ece.drexel.edu Tue Apr  6 12:32 EDT 1999
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Date: Tue, 6 Apr 1999 09:19:28 -0700 (PDT)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #82
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Boechler makes digital stage encoders with LED readout and optional serial
output to a computer.  Heidenhain has a series of machine tool products,
i've set up
their Metro digital length gauge and VRZ 405 readout unit to deliver focus
motion of the stage to the Mac serial port.  Image macros allow users to
write depth stamp on images, measure depth, or to obtain an audible alert
when a given depth of
focus has been reached.

Regards,
Glen


Glen MacDonald
   Research Scientist
Hearing Research Laboratories of the
Virginia Merrill Bloedel Hearing Research Center
Box 35-7923
University of Washington
Seattle, WA  98195-7923
(206) 616-4156
glenmac@u.washington.edu



From nih-image-request@io.ece.drexel.edu Tue Apr  6 20:03 EDT 1999
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Date: Tue, 6 Apr 1999 16:52:37 -0700 (PDT)
From: Lesley Weston <lesley@interchange.ubc.ca>
To: Skye Bender-deMoll <skyebend@bennington.edu>
cc: nih-image@io.ece.drexel.edu
Subject: Re: NAND macro?
In-Reply-To: <199904061441.KAA15268@barid.bennington.edu>
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If all else fails, you could try subtracting the first image from all subsequent
images. I have a macro to do this (written with a lot of help from people on
this list), and would be happy to send it to you if you like.

Lesley Weston.



On Tue, 6 Apr 1999, Skye Bender-deMoll wrote:

> I'm using Scion Image to track and record position data from video tapes 
> of people moving through spaces.  I'm trying to set Scion up to do this 
> automaticaly, and would like to subtract out the stationary background.  
> Unfortunatly, scion doesn't have a NAND function included with its image 
> processesing tools.  Has anyone writen a NAND macro or plugin? Or 
> suggestions on the best way to do this?
>         thanks,
>           -skye
> 
>                                   -000-
> Skye Bender-deMoll 
>   | Bennington College
>   | Bennington VT 05201
>   | 802.440.4626 
>   |---------------------- skyebend@bennington.edu
>   | 38755 Reed Road
>   | Nehalem OR 97131
>   | 503.368.6294
> 
> 


From nih-image-request@io.ece.drexel.edu Tue Apr  6 21:34 EDT 1999
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From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: Getting 16-bit values
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At 03:50 PM 4/2/99 -0600, you wrote:
>Hi there,
>  I have been using a 16-bit planetary topographic dataset along with
>Image. I have made a macro to calibrate the resulting 8-bit data to
>elevations - however I have to use some Unix tools on a Sun to get the
>highest data number for the conversion. I was wonder if there was a way
>to directly get this number through Image (I dont really trust the
>inbuilt autoscaling - it seems to do funny things to this dataset).

When importing a 16-bit images, NIH Image displays the minimum and maximum pixel value in the Info window. My new ImageJ program (http://rsb.info.nih.gov/ij/) works directly with 16-bit images (no scaling required), but it currently lacks density calibration.

-wayne


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From nih-image-d-request@io.ece.drexel.edu Wed Apr  7 06:16 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 83

Today's Topics:
  Re: nih-image-d Digest V99 #79        [ Peter Ahnelt <peter.ahnelt@univie.a ]
  NAND macro?                           [ Skye Bender-deMoll <skyebend@bennin ]
  NuBus card                            [ Jen-Wei Lin <jenwelin@bio.bu.edu> ]
  Re: nih-image-d Digest V99 #82        [ "G. Macdonald" <glenmac@u.washingto ]
  Re: NAND macro?                       [ Lesley Weston <lesley@interchange.u ]
  Re: Getting 16-bit values             [ Wayne Rasband <wayne@codon.nih.gov> ]
  unsubscribe                           [ "Robert Cormier" <cormierb@psychiat ]

------------------------------

Date: Tue, 6 Apr 1999 14:47:26 +0200
From: Peter Ahnelt <peter.ahnelt@univie.ac.at>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #79
Message-Id: <l03130305b32fb109a1ec@[131.130.51.13]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

>Date: Thu, 01 Apr 1999 13:59:29 +0200
>From: "U.Marti" <ulrich.marti@dkf2.unibe.ch>
>To: NIH List <nih-image@io.ece.drexel.edu>
>Subject: Makro
>Message-id: <37035F9A.B72D0838@dkf2.unibe.ch>
>Content-type: text/plain; charset=us-ascii; x-mac-type="54455854";
>              x-mac-creator="4D4F5353"
>Content-transfer-encoding: 7bit
>
>Hi there
>
>It looks like my question was not clear. I am looking for a macro to
>calculate all distances between pair of pixels. That means: I will make
>a binary picture of a tissue section. Then I will reduce the number of
>pixels to lets say 32x32. Then I need all possible distances between the
>pixels. After that I will classify the distances in groups and determine
>the number of group members. I hope this makes it more clear.
>
>Thank for any help
>
>Ulrich Marti
75 <

If you want to do "autocorrelation" - or cross-correlation
i.e. looking for regularity of inter-cell-distances in a cell
mosaic="pixel" = x/y-coordinates
you might consider the approach of Bob Rodieck:

The density recovery profile: A method for the analysis of points in the
plane applicable to retinal studies.
Visual Neurosci.6: 95-111

or
Kouyama, N.
Marshak, D.W.
The topographical relationship between two neuronal mosaics in the short
wavelength-sensitive system of the primate retina.
Vis. Neurosc.14: 159-167.

(Dr.E.Fernandez and we are working on another implementation of this approach).

P.Ahnelt

  _    _    _
 / \  / \  / \   e-mail: peter.ahnelt@univie.ac.at
 |R|  |G|  |B|   Adress: Peter Ahnelt
 '|  '|  '|           Dept. Gen. & Compar. Physiology
 []  []  []           University of Vienna, Medical School
 ()  ()  ()           Schwarzspanierstr. 17,  A-1090 Vienna
  |    |    |       Tel. 43 1 4277/ 62330,62301  FAX 43 1 4277/ 9623
 __  __   _   http://www.univie.ac.at/Vergl-Physiologie/www/gphy_morph.html
                  

------------------------------

Date: Tue, 6 Apr 99 10:51:30 -0400
From: Skye Bender-deMoll <skyebend@bennington.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: NAND macro?
Message-Id: <199904061441.KAA15268@barid.bennington.edu>
Content-Type: text/plain; charset="US-ASCII"

I'm using Scion Image to track and record position data from video tapes 
of people moving through spaces.  I'm trying to set Scion up to do this 
automaticaly, and would like to subtract out the stationary background.  
Unfortunatly, scion doesn't have a NAND function included with its image 
processesing tools.  Has anyone writen a NAND macro or plugin? Or 
suggestions on the best way to do this?
        thanks,
          -skye

                                  -000-
Skye Bender-deMoll 
  | Bennington College
  | Bennington VT 05201
  | 802.440.4626 
  |---------------------- skyebend@bennington.edu
  | 38755 Reed Road
  | Nehalem OR 97131
  | 503.368.6294

------------------------------

Date: Tue, 6 Apr 1999 11:10:16 -0400
From: Jen-Wei Lin <jenwelin@bio.bu.edu>
To: nih-image@io.ece.drexel.edu
Subject: NuBus card
Message-Id: <l03130306b32fd3c223f0@[128.197.80.179]>
Content-Type: text/plain; charset="us-ascii"

Hi all:
	I am looking for a LG-3 frame grabber, NuBus version that is.  If
anyone has it, I am interested in buying it.
Thanks!
Jen-Wei


Jen-Wei Lin, Ph.D.
Biology
Boston University
5 Cummington St.
Boston, MA 02215

TEL:617-353-3443 or -3444
FAX: 617-353-6340

------------------------------

Date: Tue, 6 Apr 1999 09:19:28 -0700 (PDT)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #82
Message-ID: <Pine.A41.4.10.9904060913090.123704-100000@homer39.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Boechler makes digital stage encoders with LED readout and optional serial
output to a computer.  Heidenhain has a series of machine tool products,
i've set up
their Metro digital length gauge and VRZ 405 readout unit to deliver focus
motion of the stage to the Mac serial port.  Image macros allow users to
write depth stamp on images, measure depth, or to obtain an audible alert
when a given depth of
focus has been reached.

Regards,
Glen


Glen MacDonald
   Research Scientist
Hearing Research Laboratories of the
Virginia Merrill Bloedel Hearing Research Center
Box 35-7923
University of Washington
Seattle, WA  98195-7923
(206) 616-4156
glenmac@u.washington.edu

------------------------------

Date: Tue, 6 Apr 1999 16:52:37 -0700 (PDT)
From: Lesley Weston <lesley@interchange.ubc.ca>
To: Skye Bender-deMoll <skyebend@bennington.edu>
cc: nih-image@io.ece.drexel.edu
Subject: Re: NAND macro?
Message-ID: <Pine.GSO.3.95q.990406165007.26278F-100000@interchange.ubc.ca>
Content-Type: TEXT/PLAIN; charset=US-ASCII

If all else fails, you could try subtracting the first image from all subsequent
images. I have a macro to do this (written with a lot of help from people on
this list), and would be happy to send it to you if you like.

Lesley Weston.



On Tue, 6 Apr 1999, Skye Bender-deMoll wrote:

> I'm using Scion Image to track and record position data from video tapes 
> of people moving through spaces.  I'm trying to set Scion up to do this 
> automaticaly, and would like to subtract out the stationary background.  
> Unfortunatly, scion doesn't have a NAND function included with its image 
> processesing tools.  Has anyone writen a NAND macro or plugin? Or 
> suggestions on the best way to do this?
>         thanks,
>           -skye
> 
>                                   -000-
> Skye Bender-deMoll 
>   | Bennington College
>   | Bennington VT 05201
>   | 802.440.4626 
>   |---------------------- skyebend@bennington.edu
>   | 38755 Reed Road
>   | Nehalem OR 97131
>   | 503.368.6294
> 
> 

------------------------------

Date: Tue, 06 Apr 1999 21:27:55 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Getting 16-bit values
Message-Id: <3.0.5.32.19990406212755.00793b10@codon.nih.gov>
Content-Type: text/plain; charset="us-ascii"

At 03:50 PM 4/2/99 -0600, you wrote:
>Hi there,
>  I have been using a 16-bit planetary topographic dataset along with
>Image. I have made a macro to calibrate the resulting 8-bit data to
>elevations - however I have to use some Unix tools on a Sun to get the
>highest data number for the conversion. I was wonder if there was a way
>to directly get this number through Image (I dont really trust the
>inbuilt autoscaling - it seems to do funny things to this dataset).

When importing a 16-bit images, NIH Image displays the minimum and maximum pixel value in the Info window. My new ImageJ program (http://rsb.info.nih.gov/ij/) works directly with 16-bit images (no scaling required), but it currently lacks density calibration.

-wayne

------------------------------

Date: Tue, 6 Apr 1999 21:04:06 -0500
From: "Robert Cormier" <cormierb@psychiatry1.wustl.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: unsubscribe
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	charset="iso-8859-1"
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--------------------------------
End of nih-image-d Digest V99 Issue #83
***************************************

From nih-image-request@io.ece.drexel.edu Wed Apr  7 08:21 EDT 1999
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From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Newer = Slower with Codewarrior and NIH versions?
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To Wayne and others:

I get speed variations up to factor 20 using different versions of
CodeWarrior and NIH Image/ppc versions on the same computer. I am using a
test macro which I received from Greg Joss (see below); other macros show
less extreme variations. The elapsed time appears in the Info message
window in ticks.

It appears to me that new versions run slower.

In my experiments, I downloaded the sources from zippy, I put the
Codewarrior CD (either CW2 or CW4) into the computer, and dragged the
project file onto the icon of "CodeWarrior IDE x.x" on the CD, using the
unpatched compiler version of that CD. When the compiler asked to convert,
I clicked yes, compiled the ppc version and ran the macro. I have a
G3/266Mhz tower Mac with OS 8.1.

I've got astonishing results:

#1. NIH Image 1.62b21 fat compiled from zippy:         9 ticks
#2. NIH Image 1.62b30 fat compiled from zippy:        92 ticks

#3. source 1.62b20 compiled with CW2                  11 ticks
#4. source 1.62b20 compiled with CW4                 185 ticks

#5. source 1.62b30 compiled with CW2                  92 ticks
#6. source 1.62b30 compiled with CW2, profiler trick  11 ticks

#7. source 1.62b30 compiled with CW4,                 185 ticks
#8. source 1.62b30 compiled with CW4, profiler trick  185 ticks

I cannot explain these variations with optimization settings. Also, if I
use the converted project file  from #8 and recompile it with CW2, I still
get the good value of 11 ticks (as in #6), which indicates that the
conversion has not spoiled the settings. Using Metroworks patches didn't
change much. I discovered the profiler trick by accident, when I wanted to
analyze speed statistics.
This is the profiler trick with its speedy side effect:
- Include the statement
  if ProfilerInit(collectDetailed, bestTimeBase, 50, 25) = noErr then
ProfilerTerm;
- add ProfilerPPC.Lib to the project
- uncomment "uses {Profiler,}"
- leave "Generating Profiler Info" unchecked



My questions are:

- Can other people (partly) reproduce what I measured?
- Has anyone an explanation for the profiler trick?



Here follows Greg's macro which I used:

macro 'test/0';
var i,count,ppv,min,max,et:integer;
begin
  et:=tickCount;
  setNewSize(256, 256);
  makeNewWindow('test');
  selectAll;
  for i:=1 to 25 do
    GetPlotData(count,ppv,min,max);
  showMessage(tickCount-et);
end



Norbert Vischer                  University of Amsterdam
Scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



From nih-image-request@io.ece.drexel.edu Wed Apr  7 08:29 EDT 1999
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Date: Wed, 7 Apr 1999 08:17:20 -0400
To: nih-image@io.ece.drexel.edu
From: francus@geo.umass.edu (Pierre Francus)
Subject: assembling images 
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Dear Imagers,

I want to assemble several images to build a large mosaic picture. Images
have a 20 % overlapping area.
I guess somebody has already written a macro for doing that (maybe using
the "register" function ???), but I cannot find it.

Thanks in advance

Pierre

*****************************************
Pierre FRANCUS, Ph.D.
PostDoctoral Research Associate
University of Massachusetts
Department of Geosciences
Morrill Sciences Center
Amherst - MA 01003-5820

Phone: 1-413-545-0659
fax: 1-413-545-1200
E-mail: francus@geo.umass.edu
http://www.geo.umass.edu/climate/francus/
*****************************************



From nih-image-request@io.ece.drexel.edu Wed Apr  7 13:26 EDT 1999
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Resent-Date: Wed, 7 Apr 1999 13:26:17 -0400 (EDT)
Message-Id: <199904071713.NAA26214@newman.concentric.net>
Subject: Image Archival Program
Date: Wed, 7 Apr 99 09:20:43 -0800
From: Your Name <wtdenet@concentric.net>
To: <nih-image@io.ece.drexel.edu>
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Hello Imagers,

I want to purchase a good image archival software program to organize my 
images and video clips. I primarily use a G3 for my imaging work. I do 
not want to spend a great deal of money for this software and am 
wondering if people out there have any favorites. This information may be 
of general interest to other people also finding their growing image 
collection difficult to manage. 

Thank you,

Wilfred Denetclaw Jr., Ph.D.
Department of Anatomy
UCSF


From nih-image-request@io.ece.drexel.edu Wed Apr  7 15:58 EDT 1999
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From: "Purdy, Sam" <SPurdy@nationalsteel.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Image Archival Program
Date: Wed, 7 Apr 1999 14:52:03 -0500
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We use Adobe Photoshop for our image archiving of stills and to adjust
contrast, brightness, etc. We find it quite satisfactory. Usual
disclaimers of interest. Just a satisfied customer.

Best regards, 
Sam Purdy

>----------
>From: 	Your Name
>Sent: 	Wednesday, April 7, 1999 1:20 PM
>To: 	nih-image@io.ece.drexel.edu
>Subject: 	Image Archival Program
>
>Hello Imagers,
>
>I want to purchase a good image archival software program to organize my 
>images and video clips. I primarily use a G3 for my imaging work. I do 
>not want to spend a great deal of money for this software and am 
>wondering if people out there have any favorites. This information may be 
>of general interest to other people also finding their growing image 
>collection difficult to manage. 
>
>Thank you,
>
>Wilfred Denetclaw Jr., Ph.D.
>Department of Anatomy
>UCSF
>
>


From nih-image-d-request@io.ece.drexel.edu Thu Apr  8 06:15 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #84
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 84

Today's Topics:
  Newer = Slower with Codewarrior and   [ Norbert Vischer <vischer@bio.uva.nl ]
  assembling images                     [ francus@geo.umass.edu (Pierre Franc ]
  Image Archival Program                [ Your Name <wtdenet@concentric.net> ]
  RE: Image Archival Program            [ "Purdy, Sam" <SPurdy@nationalsteel. ]

------------------------------

Date: Wed, 7 Apr 1999 14:13:17 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Newer = Slower with Codewarrior and NIH versions?
Message-Id: <l03110702b330e8ae3db9@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

To Wayne and others:

I get speed variations up to factor 20 using different versions of
CodeWarrior and NIH Image/ppc versions on the same computer. I am using a
test macro which I received from Greg Joss (see below); other macros show
less extreme variations. The elapsed time appears in the Info message
window in ticks.

It appears to me that new versions run slower.

In my experiments, I downloaded the sources from zippy, I put the
Codewarrior CD (either CW2 or CW4) into the computer, and dragged the
project file onto the icon of "CodeWarrior IDE x.x" on the CD, using the
unpatched compiler version of that CD. When the compiler asked to convert,
I clicked yes, compiled the ppc version and ran the macro. I have a
G3/266Mhz tower Mac with OS 8.1.

I've got astonishing results:

#1. NIH Image 1.62b21 fat compiled from zippy:         9 ticks
#2. NIH Image 1.62b30 fat compiled from zippy:        92 ticks

#3. source 1.62b20 compiled with CW2                  11 ticks
#4. source 1.62b20 compiled with CW4                 185 ticks

#5. source 1.62b30 compiled with CW2                  92 ticks
#6. source 1.62b30 compiled with CW2, profiler trick  11 ticks

#7. source 1.62b30 compiled with CW4,                 185 ticks
#8. source 1.62b30 compiled with CW4, profiler trick  185 ticks

I cannot explain these variations with optimization settings. Also, if I
use the converted project file  from #8 and recompile it with CW2, I still
get the good value of 11 ticks (as in #6), which indicates that the
conversion has not spoiled the settings. Using Metroworks patches didn't
change much. I discovered the profiler trick by accident, when I wanted to
analyze speed statistics.
This is the profiler trick with its speedy side effect:
- Include the statement
  if ProfilerInit(collectDetailed, bestTimeBase, 50, 25) = noErr then
ProfilerTerm;
- add ProfilerPPC.Lib to the project
- uncomment "uses {Profiler,}"
- leave "Generating Profiler Info" unchecked



My questions are:

- Can other people (partly) reproduce what I measured?
- Has anyone an explanation for the profiler trick?



Here follows Greg's macro which I used:

macro 'test/0';
var i,count,ppv,min,max,et:integer;
begin
  et:=tickCount;
  setNewSize(256, 256);
  makeNewWindow('test');
  selectAll;
  for i:=1 to 25 do
    GetPlotData(count,ppv,min,max);
  showMessage(tickCount-et);
end



Norbert Vischer                  University of Amsterdam
Scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: Wed, 7 Apr 1999 08:17:20 -0400
From: francus@geo.umass.edu (Pierre Francus)
To: nih-image@io.ece.drexel.edu
Subject: assembling images 
Message-Id: <v01530500b330fa9e4a62@[128.119.67.41]>
Content-Type: text/plain; charset="us-ascii"

Dear Imagers,

I want to assemble several images to build a large mosaic picture. Images
have a 20 % overlapping area.
I guess somebody has already written a macro for doing that (maybe using
the "register" function ???), but I cannot find it.

Thanks in advance

Pierre

*****************************************
Pierre FRANCUS, Ph.D.
PostDoctoral Research Associate
University of Massachusetts
Department of Geosciences
Morrill Sciences Center
Amherst - MA 01003-5820

Phone: 1-413-545-0659
fax: 1-413-545-1200
E-mail: francus@geo.umass.edu
http://www.geo.umass.edu/climate/francus/
*****************************************

------------------------------

Date: Wed, 7 Apr 99 09:20:43 -0800
From: Your Name <wtdenet@concentric.net>
To: <nih-image@io.ece.drexel.edu>
Subject: Image Archival Program
Message-Id: <199904071713.NAA26214@newman.concentric.net>
Content-Type: text/plain; charset="US-ASCII"

Hello Imagers,

I want to purchase a good image archival software program to organize my 
images and video clips. I primarily use a G3 for my imaging work. I do 
not want to spend a great deal of money for this software and am 
wondering if people out there have any favorites. This information may be 
of general interest to other people also finding their growing image 
collection difficult to manage. 

Thank you,

Wilfred Denetclaw Jr., Ph.D.
Department of Anatomy
UCSF

------------------------------

Date: Wed, 7 Apr 1999 14:52:03 -0500
From: "Purdy, Sam" <SPurdy@nationalsteel.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Image Archival Program
Message-ID: <c=US%a=_%p=NATIONAL_STEEL%l=NSCGLDNT03-990407195203Z-2340@nschqdnt09.nationalsteel.com>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

We use Adobe Photoshop for our image archiving of stills and to adjust
contrast, brightness, etc. We find it quite satisfactory. Usual
disclaimers of interest. Just a satisfied customer.

Best regards, 
Sam Purdy

>----------
>From: 	Your Name
>Sent: 	Wednesday, April 7, 1999 1:20 PM
>To: 	nih-image@io.ece.drexel.edu
>Subject: 	Image Archival Program
>
>Hello Imagers,
>
>I want to purchase a good image archival software program to organize my 
>images and video clips. I primarily use a G3 for my imaging work. I do 
>not want to spend a great deal of money for this software and am 
>wondering if people out there have any favorites. This information may be 
>of general interest to other people also finding their growing image 
>collection difficult to manage. 
>
>Thank you,
>
>Wilfred Denetclaw Jr., Ph.D.
>Department of Anatomy
>UCSF
>
>

--------------------------------
End of nih-image-d Digest V99 Issue #84
***************************************

From nih-image-request@io.ece.drexel.edu Thu Apr  8 06:58 EDT 1999
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Date: Thu, 08 Apr 1999 12:44:30 +0200
From: Lucas Bickel <lukas.bickel@zmk.unibe.ch>
Subject: Re: nih-image-d Digest V99 #84
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>I want to purchase a good image archival software program to organize my
>images and video clips. I primarily use a G3 for my imaging work. I do
>not want to spend a great deal of money for this software and am
>wondering if people out there have any favorites. This information may be
>of general interest to other people also finding their growing image
>collection difficult to manage.

I would have a look at Grafic Converter. Thats a small shareware app that
has an function called 'open Browser' it will let you look at your HD with
a list of previews. If you sort your pics logical in the Finder then this
tool schould do a very good job.


-----------------------------------
    Lucas Bickel
    Freiburgstrasse 7
    3010 Bern
-----------------------------------
Voice  +41 31 632 86 18
Pager  +41 74 490 30 02
-----------------------------------



From nih-image-request@io.ece.drexel.edu Thu Apr  8 07:17 EDT 1999
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Date: Thu, 8 Apr 1999 12:06:28 +0100
To: nih-image@io.ece.drexel.edu
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
Subject: Re: Newer = Slower with Codewarrior...?
Cc: Norbert Vischer <vischer@bio.uva.nl>
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Norbert Vischer wrote:

>I get speed variations up to factor 20 using different versions of
>CodeWarrior and NIH Image/ppc versions on the same computer...
>It appears to me that new versions run slower.

CodeWarrior Pro 4 has a problem. Metrowerks are aware of it - I informed
them some months ago about the slow compilation speeds and execution speeds
of the compiled applications. I went back to using CodeWarrior Pro 3 and am
awaiting the release of v5 before upgrading again. As far the Pascal
compiler is concerned, v4 has no significant advantage over v3.

___________________________________________________________________
Dr Steve Barrett
Surface Science Research Centre
University of Liverpool
Liverpool L69 3BX
United Kingdom

Tel: 44-(0)151-794-3894 / 3874 / 3541
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk
___________________________________________________________________



From nih-image-request@io.ece.drexel.edu Thu Apr  8 07:26 EDT 1999
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> >I want to purchase a good image archival software program to organize my
> >images and video clips. I primarily use a G3 for my imaging work. I do
> >not want to spend a great deal of money for this software and am
> >wondering if people out there have any favorites. This information may be
> >of general interest to other people also finding their growing image
> >collection difficult to manage.

I don't know about Mac applications, but Jasc Media center is a good 
shareware app for the PC. Organizes thumbnails of most types of multimedia 
files. I've mostly used it for batch conversion of image files.  It's 
available from www.download.com or www.jasc.com


------------------------------------
Jenny Gregory
Department of Orthopaedics
University of Aberdeen
Aberdeen
AB25 2ZD
Scotland

j.gregory@abdn.ac.uk





From nih-image-request@io.ece.drexel.edu Thu Apr  8 07:50 EDT 1999
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Date: Thu, 08 Apr 1999 06:38:40 -0500
From: Michael Herron <herro001@maroon.tc.umn.edu>
Reply-To: Michael J Herron <herro001@maroon.tc.umn.edu>
Organization: U of MN, Medicine, Infectious Diseases
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QuickNailer is another very useful program.  It prepare thumbnail sheets
that are clickable, AND it will save them as HTML pages if you like.

You can drag a whole folder (or zip disk) onto the icon and it will
catalog the whole thing.

Lucas Bickel wrote:
> 
> >I want to purchase a good image archival software program to organize my
> >images and video clips. I primarily use a G3 for my imaging work. I do
> >not want to spend a great deal of money for this software and am
> >wondering if people out there have any favorites. This information may be
> >of general interest to other people also finding their growing image
> >collection difficult to manage.
> 
> I would have a look at Grafic Converter. Thats a small shareware app that
> has an function called 'open Browser' it will let you look at your HD with
> a list of previews. If you sort your pics logical in the Finder then this
> tool schould do a very good job.
> 
> -----------------------------------
>     Lucas Bickel
>     Freiburgstrasse 7
>     3010 Bern
> -----------------------------------
> Voice  +41 31 632 86 18
> Pager  +41 74 490 30 02
> -----------------------------------

-- 

   _________________________________________________
     /  Michael J. Herron                          /
    /     U of MN,Medicine/Infectious Diseases    /
   /        herro001@maroon.tc.umn.edu           /
  /           http://128.101.243.213            /
 /_____________________________________________/


From nih-image-request@io.ece.drexel.edu Thu Apr  8 09:37 EDT 1999
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From: Jeff Reidler <Jreidler@scioncorp.com>
Subject: Re: Image Archival Program
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>Date: Wed, 7 Apr 99 09:20:43 -0800
>From:  Wilfred Denetclaw <wtdenet@concentric.net>
>To: <nih-image@io.ece.drexel.edu>
>Digest V99 #84
>I want to purchase a good image archival software program to organize my
>images and video clips. I primarily use a G3 for my imaging work. I do
>not want to spend a great deal of money for this software and am
>wondering if people out there have any favorites.

You might try Thumbs Plus at http://www.cerious.com
30-day free trial, under $100, also Network version available for under
$300 (I think)

Jeff Reidler, Scion Corp



From nih-image-request@io.ece.drexel.edu Thu Apr  8 15:13 EDT 1999
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Date: Thu, 08 Apr 1999 11:55:59 -0700
From: "Harvey J. Karten" <hjkarten@ucsd.edu>
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Organization: UCSD
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I strongly recommend Thumbsplus from Cerious Software (http://www.cerious.com). It
is the excellent and very cheap ($75.00). It is also the only software that
provides input filters for BioRAD and Olympus confocal native files, including 12
bit stacks. The PC version 4.0 was recently released and is more advanced than the
older Mac version 3.2. But the owner, Phillip Crews, is an excellent and highly
responsive person. He also seems to be an outstanding graphics software person.

We found this much better than Portfolio. Photoshop does not provide archiving.
Canto Cumulus is very expensive, and also doesn't support BioRAD or Olympus files.
Search from Multi-Ad has not been updated in a number of years. Unlike the other
three programs, it is only available for Mac.

A more detailed summary is presented in a chapter I recently posted on our web
site, http://www-cajal.ucsd.edu
Follow the leads until to get to the chapter on Image Databases.

regards, Harvey Karten


> Subject: RE: Image Archival Program
> Date: Wed, 7 Apr 1999 14:52:03 -0500
> From: "Purdy, Sam" <SPurdy@nationalsteel.com>
> To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
>
> We use Adobe Photoshop for our image archiving of stills and to adjust
> contrast, brightness, etc. We find it quite satisfactory. Usual
> disclaimers of interest. Just a satisfied customer.
>
> Best regards,
> Sam Purdy
>
> >----------
> >From:  Your Name
> >Sent:  Wednesday, April 7, 1999 1:20 PM
> >To:    nih-image@io.ece.drexel.edu
> >Subject:       Image Archival Program
> >
> >Hello Imagers,
> >
> >I want to purchase a good image archival software program to organize my
> >images and video clips. I primarily use a G3 for my imaging work. I do
> >not want to spend a great deal of money for this software and am
> >wondering if people out there have any favorites. This information may be
> >of general interest to other people also finding their growing image
> >collection difficult to manage.
> >
> >Thank you,
> >
> >Wilfred Denetclaw Jr., Ph.D.
> >Department of Anatomy
> >UCSF
> >
> >



--
Harvey J. Karten, M.D.
Dept. of Neurosciences
University of California at San Diego
La Jolla, CA 92093
Phone (Voice) 619-534-4938
FAX  619-534-6602
EMail: hjkarten@ucsd.edu
Retina Information Home Page
URL: http://www-cajal.ucsd.edu
Tayana Manual: ftp://cajal.ucsd.edu/pub/outgoing/Tayana/



From nih-image-d-request@io.ece.drexel.edu Fri Apr  9 06:18 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #85
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 85

Today's Topics:
  Re: nih-image-d Digest V99 #84        [ Lucas Bickel <lukas.bickel@zmk.unib ]
  Re: Newer = Slower with Codewarrior.  [ Steve Barrett <S.D.Barrett@liverpoo ]
  Re: nih-image-d Digest V99 #84        [ "j.gregory" <ort056@abdn.ac.uk> ]
  Re: nih-image-d Digest V99 #84        [ Michael Herron <herro001@maroon.tc. ]
  Re: Image Archival Program            [ Jeff Reidler <Jreidler@scioncorp.co ]
  Image ARchival Software               [ "Harvey J. Karten" <hjkarten@ucsd.e ]

------------------------------

Date: Thu, 08 Apr 1999 12:44:30 +0200
From: Lucas Bickel <lukas.bickel@zmk.unibe.ch>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #84
Message-id: <l03130300b332376ae8e5@[130.92.198.63]>
Content-type: text/plain; charset="us-ascii"

>I want to purchase a good image archival software program to organize my
>images and video clips. I primarily use a G3 for my imaging work. I do
>not want to spend a great deal of money for this software and am
>wondering if people out there have any favorites. This information may be
>of general interest to other people also finding their growing image
>collection difficult to manage.

I would have a look at Grafic Converter. Thats a small shareware app that
has an function called 'open Browser' it will let you look at your HD with
a list of previews. If you sort your pics logical in the Finder then this
tool schould do a very good job.


-----------------------------------
    Lucas Bickel
    Freiburgstrasse 7
    3010 Bern
-----------------------------------
Voice  +41 31 632 86 18
Pager  +41 74 490 30 02
-----------------------------------

------------------------------

Date: Thu, 8 Apr 1999 12:06:28 +0100
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
To: nih-image@io.ece.drexel.edu
Cc: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Newer = Slower with Codewarrior...?
Message-Id: <l03130302b3323ce2d848@[138.253.47.16]>
Content-Type: text/plain; charset="us-ascii"

Norbert Vischer wrote:

>I get speed variations up to factor 20 using different versions of
>CodeWarrior and NIH Image/ppc versions on the same computer...
>It appears to me that new versions run slower.

CodeWarrior Pro 4 has a problem. Metrowerks are aware of it - I informed
them some months ago about the slow compilation speeds and execution speeds
of the compiled applications. I went back to using CodeWarrior Pro 3 and am
awaiting the release of v5 before upgrading again. As far the Pascal
compiler is concerned, v4 has no significant advantage over v3.

___________________________________________________________________
Dr Steve Barrett
Surface Science Research Centre
University of Liverpool
Liverpool L69 3BX
United Kingdom

Tel: 44-(0)151-794-3894 / 3874 / 3541
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk
___________________________________________________________________

------------------------------

Date: Thu, 8 Apr 1999 12:14:34 +0100 (BST)
From: "j.gregory" <ort056@abdn.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #84
Message-ID: <SIMEON.9904081234.A@pc3.abdn.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

> >I want to purchase a good image archival software program to organize my
> >images and video clips. I primarily use a G3 for my imaging work. I do
> >not want to spend a great deal of money for this software and am
> >wondering if people out there have any favorites. This information may be
> >of general interest to other people also finding their growing image
> >collection difficult to manage.

I don't know about Mac applications, but Jasc Media center is a good 
shareware app for the PC. Organizes thumbnails of most types of multimedia 
files. I've mostly used it for batch conversion of image files.  It's 
available from www.download.com or www.jasc.com


------------------------------------
Jenny Gregory
Department of Orthopaedics
University of Aberdeen
Aberdeen
AB25 2ZD
Scotland

j.gregory@abdn.ac.uk

------------------------------

Date: Thu, 08 Apr 1999 06:38:40 -0500
From: Michael Herron <herro001@maroon.tc.umn.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #84
Message-Id: <370C9528.168EF669@maroon.tc.umn.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

QuickNailer is another very useful program.  It prepare thumbnail sheets
that are clickable, AND it will save them as HTML pages if you like.

You can drag a whole folder (or zip disk) onto the icon and it will
catalog the whole thing.

Lucas Bickel wrote:
> 
> >I want to purchase a good image archival software program to organize my
> >images and video clips. I primarily use a G3 for my imaging work. I do
> >not want to spend a great deal of money for this software and am
> >wondering if people out there have any favorites. This information may be
> >of general interest to other people also finding their growing image
> >collection difficult to manage.
> 
> I would have a look at Grafic Converter. Thats a small shareware app that
> has an function called 'open Browser' it will let you look at your HD with
> a list of previews. If you sort your pics logical in the Finder then this
> tool schould do a very good job.
> 
> -----------------------------------
>     Lucas Bickel
>     Freiburgstrasse 7
>     3010 Bern
> -----------------------------------
> Voice  +41 31 632 86 18
> Pager  +41 74 490 30 02
> -----------------------------------

-- 

   _________________________________________________
     /  Michael J. Herron                          /
    /     U of MN,Medicine/Infectious Diseases    /
   /        herro001@maroon.tc.umn.edu           /
  /           http://128.101.243.213            /
 /_____________________________________________/

------------------------------

Date: Thu, 8 Apr 1999 09:27:32 -0400
From: Jeff Reidler <Jreidler@scioncorp.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Image Archival Program
Message-Id: <l03102802b3325e8080b4@[10.0.0.248]>
Content-Type: text/plain; charset="us-ascii"

>Date: Wed, 7 Apr 99 09:20:43 -0800
>From:  Wilfred Denetclaw <wtdenet@concentric.net>
>To: <nih-image@io.ece.drexel.edu>
>Digest V99 #84
>I want to purchase a good image archival software program to organize my
>images and video clips. I primarily use a G3 for my imaging work. I do
>not want to spend a great deal of money for this software and am
>wondering if people out there have any favorites.

You might try Thumbs Plus at http://www.cerious.com
30-day free trial, under $100, also Network version available for under
$300 (I think)

Jeff Reidler, Scion Corp

------------------------------

Date: Thu, 08 Apr 1999 11:55:59 -0700
From: "Harvey J. Karten" <hjkarten@ucsd.edu>
To: nih-image@io.ece.drexel.edu
Subject: Image ARchival Software
Message-ID: <370CFBBF.F93EBC81@ucsd.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Transfer-Encoding: 7bit

I strongly recommend Thumbsplus from Cerious Software (http://www.cerious.com). It
is the excellent and very cheap ($75.00). It is also the only software that
provides input filters for BioRAD and Olympus confocal native files, including 12
bit stacks. The PC version 4.0 was recently released and is more advanced than the
older Mac version 3.2. But the owner, Phillip Crews, is an excellent and highly
responsive person. He also seems to be an outstanding graphics software person.

We found this much better than Portfolio. Photoshop does not provide archiving.
Canto Cumulus is very expensive, and also doesn't support BioRAD or Olympus files.
Search from Multi-Ad has not been updated in a number of years. Unlike the other
three programs, it is only available for Mac.

A more detailed summary is presented in a chapter I recently posted on our web
site, http://www-cajal.ucsd.edu
Follow the leads until to get to the chapter on Image Databases.

regards, Harvey Karten


> Subject: RE: Image Archival Program
> Date: Wed, 7 Apr 1999 14:52:03 -0500
> From: "Purdy, Sam" <SPurdy@nationalsteel.com>
> To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
>
> We use Adobe Photoshop for our image archiving of stills and to adjust
> contrast, brightness, etc. We find it quite satisfactory. Usual
> disclaimers of interest. Just a satisfied customer.
>
> Best regards,
> Sam Purdy
>
> >----------
> >From:  Your Name
> >Sent:  Wednesday, April 7, 1999 1:20 PM
> >To:    nih-image@io.ece.drexel.edu
> >Subject:       Image Archival Program
> >
> >Hello Imagers,
> >
> >I want to purchase a good image archival software program to organize my
> >images and video clips. I primarily use a G3 for my imaging work. I do
> >not want to spend a great deal of money for this software and am
> >wondering if people out there have any favorites. This information may be
> >of general interest to other people also finding their growing image
> >collection difficult to manage.
> >
> >Thank you,
> >
> >Wilfred Denetclaw Jr., Ph.D.
> >Department of Anatomy
> >UCSF
> >
> >



--
Harvey J. Karten, M.D.
Dept. of Neurosciences
University of California at San Diego
La Jolla, CA 92093
Phone (Voice) 619-534-4938
FAX  619-534-6602
EMail: hjkarten@ucsd.edu
Retina Information Home Page
URL: http://www-cajal.ucsd.edu
Tayana Manual: ftp://cajal.ucsd.edu/pub/outgoing/Tayana/

--------------------------------
End of nih-image-d Digest V99 Issue #85
***************************************

From nih-image-request@io.ece.drexel.edu Fri Apr  9 16:14 EDT 1999
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Date: Fri, 9 Apr 1999 08:21:51 +0200
To: nih-image@io.ece.drexel.edu
From: "Anneke M.Th. Harbers and Ard Jonker" <a_team@dds.nl>
Subject: Image Archival Program
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>I want to purchase a good image archival software program to organize my
>images and video clips. I primarily use a G3 for my imaging work. I do
>not want to spend a great deal of money for this software and am
>wondering if people out there have any favorites. This information may be
>of general interest to other people also finding their growing image
>collection difficult to manage.

iView (shareware; www.iview-multimedia..com) does what you want. Keeping
thumbnails of images and movies, this program is reasonable fast and has a
load of options. Current version 3.4 or better, has loads of importers
(ranging from PageMaker, Quark, EPS, Canvas using internal importers, to
all QT formats using QT) and is quite improved over the last few versions.
Ard



From nih-image-d-request@io.ece.drexel.edu Sun Apr 11 06:08 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #86
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 86

Today's Topics:
  Image Archival Program                [ "Anneke M.Th. Harbers and Ard Jonke ]

------------------------------

Date: Fri, 9 Apr 1999 08:21:51 +0200
From: "Anneke M.Th. Harbers and Ard Jonker" <a_team@dds.nl>
To: nih-image@io.ece.drexel.edu
Subject: Image Archival Program
Message-Id: <l03130301b3334b8f649e@[194.109.148.113]>
Content-Type: text/plain; charset="us-ascii"

>I want to purchase a good image archival software program to organize my
>images and video clips. I primarily use a G3 for my imaging work. I do
>not want to spend a great deal of money for this software and am
>wondering if people out there have any favorites. This information may be
>of general interest to other people also finding their growing image
>collection difficult to manage.

iView (shareware; www.iview-multimedia..com) does what you want. Keeping
thumbnails of images and movies, this program is reasonable fast and has a
load of options. Current version 3.4 or better, has loads of importers
(ranging from PageMaker, Quark, EPS, Canvas using internal importers, to
all QT formats using QT) and is quite improved over the last few versions.
Ard

--------------------------------
End of nih-image-d Digest V99 Issue #86
***************************************

From nih-image-request@io.ece.drexel.edu Mon Apr 12 04:36 EDT 1999
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Resent-Date: Mon, 12 Apr 1999 04:36:13 -0400 (EDT)
Date: Mon, 12 Apr 1999 10:23:18 +0200
From: Lucas Bickel <lukas.bickel@zmk.unibe.ch>
Subject: Re: nih-image-d Digest V99 #86
In-reply-to: <199904111000.GAA07009@io.ece.drexel.edu>
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Hi imagers

Can anybody help me contrast conrrect two images? I tried it with writing
to the LUT of one of the images, but it doesn't seem to work that way, now
i'm searching a way to change the Histogram.

I hope someone cam help

L. Bickel


-----------------------------------
    Lucas Bickel
    Freiburgstrasse 7
    3010 Bern
-----------------------------------
Voice  +41 31 632 86 18
Pager  +41 74 490 30 02
-----------------------------------



From nih-image-request@io.ece.drexel.edu Mon Apr 12 09:34 EDT 1999
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From: Anthony Ting <mcbaet@mcbsgs1.imcb.nus.edu.sg>
Subject: Need photo-quality printer: dye-sub or ink-jet or ???
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Hi there,

	I'd like to get some advice on the purchase of a photo-quality printer.
The input is primarily confocal images and I'd like to have the output look
like my slides.  Currently, we're using a Tektronix Phaser IID, but it's on
it's last legs and I wanted to get some opinion on what the latest
technology is out there.

Thanks,

Tony

-------------------------------------------------------------------
Anthony Ting, PhD		      		 phone: 65-874-7846
Institute of Molecular and Cell Biology          fax: 65-779-1117
30 Medical Drive
Singapore   117609


From nih-image-request@io.ece.drexel.edu Mon Apr 12 12:28 EDT 1999
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From: Joel Brody <jbrody@itsa.ucsf.edu>
Subject: Re: Need photo-quality printer: dye-sub or ink-jet or ???
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Ink-jet: I have an Epson 740 and it prints very-near photo quality with
hi-quality paper.  The Epson 900 is supposed to have an even smaller drop
size which should give even better quality.

Instead of dye sub you might want to check out the Fujix Pictrographic
printers.  Foe some odd reason Fujix does not push these although they blow
dye-subs out of the water in terms of quality.  Out department has had one
for several years and it has been very reliable and its consumables are in
the same price range as dye subs.


Joel

>Hi there,
>
>	I'd like to get some advice on the purchase of a photo-quality printer.
>The input is primarily confocal images and I'd like to have the output look
>like my slides.  Currently, we're using a Tektronix Phaser IID, but it's on
>it's last legs and I wanted to get some opinion on what the latest
>technology is out there.
>
>Thanks,
>
>Tony
>
>-------------------------------------------------------------------
>Anthony Ting, PhD		      		 phone: 65-874-7846
>Institute of Molecular and Cell Biology          fax: 65-779-1117
>30 Medical Drive
>Singapore   117609


****************************************************************************

CunhaLab, UCSF                          |
Mount Zion Cancer Center, Box 0540      |
2340 Sutter Street, Room S241	        | Tel:     (415) 476-6746
San Francisco, CA 94115    	        | Fax:     (415) 502-2270



From nih-image-request@io.ece.drexel.edu Mon Apr 12 13:04 EDT 1999
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Subject: Object Image
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We are having a memory problem when starting up Object Image.  We have 128
MB on board our computer.  In the info window we set Object Image to
require at least 64MB to run and to prefer 100MB.  Yet every time it runs,
it only is allocated 13090 bytes.  Any hints?
Thanks-

********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************


From nih-image-request@io.ece.drexel.edu Mon Apr 12 13:18 EDT 1999
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From: Peter Lombrozo <peter@di.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Need photo-quality printer: dye-sub or ink-jet or ???
Date: Mon, 12 Apr 1999 09:35:32 -0700
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About the newest thing in printers these days is the ridiculously low price on
the new color lasers like the Tek 740.  However, even though they do a good job
on presentation graphics, they still don't come close to the photographic
quality of any dye-sub.  They are faster and cheaper to run, but if you're
looking for slide quality, you'll either have to stick with the dye-sub
(Tektronix has pretty much gotten out of this), or the actually quite good
photo-realistic ink-jets.  Be aware that in pricing ink jets, even though the
paper is cheaper and they usually rate 0.20 to 0.50/page for consumables, this
is only for max 20% coverage.  If you do full photographic page, it could cost
$1.50/page or more, especially if you use the high-quality glossy at $1/page
(but worth it!).

Peter Lombrozo

<<             NANOSCOPES                >> Peter Lombrozo
<<   See More & More of Less & Less      >> peter@di.com 
<< until you see Everything of Nothing!  >> Software Engineer



> -----Original Message-----
> From:	Anthony Ting [SMTP:mcbaet@mcbsgs1.imcb.nus.edu.sg]
> Sent:	Monday, April 12, 1999 5:51 AM
> To:	nih-image@io.ece.drexel.edu
> Subject:	Need photo-quality printer: dye-sub or ink-jet or ???
> 
> Hi there,
> 
> 	I'd like to get some advice on the purchase of a photo-quality printer.
> The input is primarily confocal images and I'd like to have the output look
> like my slides.  Currently, we're using a Tektronix Phaser IID, but it's on
> it's last legs and I wanted to get some opinion on what the latest
> technology is out there.
> 
> Thanks,
> 
> Tony
> 
> -------------------------------------------------------------------
> Anthony Ting, PhD		      		 phone: 65-874-7846
> Institute of Molecular and Cell Biology          fax: 65-779-1117
> 30 Medical Drive
> Singapore   117609


From nih-image-request@io.ece.drexel.edu Mon Apr 12 14:25 EDT 1999
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Date: Mon, 12 Apr 1999 13:42:02 -0400
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From: David Knecht <knecht@uconnvm.uconn.edu>
Subject: RE: Need photo-quality printer: dye-sub or ink-jet or ???
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I just did a test printing a high resolution color image on my Epson 600
ink jet (about $200) and my Tektronics dye sub (about $6000).  They color
rendition was different, but I could not tell you which was which based
upon image quality.  The newer Epson 700 is apparently even better.  I
would not spend the extra money for a dye sub anymore.  Dave

>About the newest thing in printers these days is the ridiculously low price on
>the new color lasers like the Tek 740.  However, even though they do a
>good job
>on presentation graphics, they still don't come close to the photographic
>quality of any dye-sub.  They are faster and cheaper to run, but if you're
>looking for slide quality, you'll either have to stick with the dye-sub
>(Tektronix has pretty much gotten out of this), or the actually quite good
>photo-realistic ink-jets.  Be aware that in pricing ink jets, even though the
>paper is cheaper and they usually rate 0.20 to 0.50/page for consumables, this
>is only for max 20% coverage.  If you do full photographic page, it could cost
>$1.50/page or more, especially if you use the high-quality glossy at $1/page
>(but worth it!).
>
>Peter Lombrozo
>
><<             NANOSCOPES                >> Peter Lombrozo
><<   See More & More of Less & Less      >> peter@di.com
><< until you see Everything of Nothing!  >> Software Engineer
>
>
>
>> -----Original Message-----
>> From:	Anthony Ting [SMTP:mcbaet@mcbsgs1.imcb.nus.edu.sg]
>> Sent:	Monday, April 12, 1999 5:51 AM
>> To:	nih-image@io.ece.drexel.edu
>> Subject:	Need photo-quality printer: dye-sub or ink-jet or ???
>>
>> Hi there,
>>
>> 	I'd like to get some advice on the purchase of a photo-quality printer.
>> The input is primarily confocal images and I'd like to have the output look
>> like my slides.  Currently, we're using a Tektronix Phaser IID, but it's on
>> it's last legs and I wanted to get some opinion on what the latest
>> technology is out there.
>>
>> Thanks,
>>
>> Tony
>>
>> -------------------------------------------------------------------
>> Anthony Ting, PhD		      		 phone: 65-874-7846
>> Institute of Molecular and Cell Biology          fax: 65-779-1117
>> 30 Medical Drive
>> Singapore   117609


Dr. David Knecht
Department of Molecular and Cell Biology
University of Connecticut
75 N. Eagleville Rd.
U-125
Storrs, CT 06269
Knecht@uconnvm.uconn.edu
860-486-2200
860-486-4331 (fax)



From nih-image-request@io.ece.drexel.edu Mon Apr 12 14:33 EDT 1999
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Mime-Version: 1.0
Date: Mon, 12 Apr 1999 20:23:17 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Object Image
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>We are having a memory problem when starting up Object Image.  We have 128
>MB on board our computer.  In the info window we set Object Image to
>require at least 64MB to run and to prefer 100MB.  Yet every time it runs,
>it only is allocated 13090 bytes.  Any hints?
>Thanks-


I'll have a look if I can reproduce this. Could you meanwhile tell me which
version you use? (the newest version is 1.62n12). Do you mean 13090K
instead 13090 bytes?
Check out that you don't have several versions (NIH Image or Object-Image)
which you confuse. (Search for creator = Imag and file type = APPL). To
isolate this problem, be sure to double-click the same version that you
altered in the info window, rather than opening it via a document. If you
want to keep several versions, hide all except the one to be used with
AppHider (see my web site).

Norbert



From nih-image-request@io.ece.drexel.edu Mon Apr 12 15:18 EDT 1999
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Date: Mon, 12 Apr 1999 16:07:08 -0300
From: Ruy Jaeger <rgjaeger@fo.usp.br>
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Fuji Pictrography is definitely the best choice


Ruy




Anthony Ting wrote:
> 
> Hi there,
> 
>         I'd like to get some advice on the purchase of a photo-quality printer.
> The input is primarily confocal images and I'd like to have the output look
> like my slides.  Currently, we're using a Tektronix Phaser IID, but it's on
> it's last legs and I wanted to get some opinion on what the latest
> technology is out there.
> 
> Thanks,
> 
> Tony
> 
> -------------------------------------------------------------------
> Anthony Ting, PhD                                phone: 65-874-7846
> Institute of Molecular and Cell Biology          fax: 65-779-1117
> 30 Medical Drive
> Singapore   117609


From nih-image-request@io.ece.drexel.edu Mon Apr 12 22:15 EDT 1999
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Message-ID: <3713176D.C8E958C6@bme.ym.edu.tw>
Date: Tue, 13 Apr 1999 10:08:03 +0000
From: Woeichyn Chu <wchu@bme.ym.edu.tw>
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Organization: National Yang Ming University
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Couple of months ago I did some comparisons on high quality dye sub printers vs.
Fuji Pictrography model PG-3000. Conclusion: if budget allows, I would go for the
latter one (price is ~40% higher though).

woeichyn

Ruy Jaeger wrote:

> Fuji Pictrography is definitely the best choice
>
> Ruy
>
> Anthony Ting wrote:
> >
> > Hi there,
> >
> >         I'd like to get some advice on the purchase of a photo-quality printer.
> > The input is primarily confocal images and I'd like to have the output look
> > like my slides.  Currently, we're using a Tektronix Phaser IID, but it's on
> > it's last legs and I wanted to get some opinion on what the latest
> > technology is out there.
> >
> > Thanks,
> >
> > Tony
> >
> > -------------------------------------------------------------------
> > Anthony Ting, PhD                                phone: 65-874-7846
> > Institute of Molecular and Cell Biology          fax: 65-779-1117
> > 30 Medical Drive
> > Singapore   117609


--
Sincerely yours,

Woeichyn Chu, Ph.D.
Associate Professor
Institute of Biomedical Engineering
National Yang Ming University       '__|__     _  /__\__   -|=|-   /
Shih-Pai, Taipei, Taiwan 112       /___|___   | |'|__|__    |+| --'-.
Tel: 886.2.28267025(Office)          / | \    |_| |__|__    -+-  /  |
Tel: 886.2.28267170(Lab.)           /  |  \       |__|__    -+- /   /
Fax: 886.2.28210847                '  `|   `      |         ---'  _/
Email: wchu@bme.ym.edu.tw



From nih-image-d-request@io.ece.drexel.edu Mon Apr 12 22:18 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199904130218.WAA07817@io.ece.drexel.edu>
Subject: nih-image-d Digest V99 #87
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 87

Today's Topics:
  Re: nih-image-d Digest V99 #86        [ Lucas Bickel <lukas.bickel@zmk.unib ]
  Need photo-quality printer: dye-sub   [ Anthony Ting <mcbaet@mcbsgs1.imcb.n ]
  Object Image                          [ Michael Cammer <cammer@aecom.yu.edu ]
  Re: Need photo-quality printer: dye-  [ Joel Brody <jbrody@itsa.ucsf.edu> ]
  RE: Need photo-quality printer: dye-  [ Peter Lombrozo <peter@di.com> ]
  RE: Need photo-quality printer: dye-  [ David Knecht <knecht@uconnvm.uconn. ]
  Re: Object Image                      [ Norbert Vischer <vischer@bio.uva.nl ]
  Re: Need photo-quality printer: dye-  [ Ruy Jaeger <rgjaeger@fo.usp.br> ]
  Re: Need photo-quality printer: dye-  [ Woeichyn Chu <wchu@bme.ym.edu.tw> ]

------------------------------

Date: Mon, 12 Apr 1999 10:23:18 +0200
From: Lucas Bickel <lukas.bickel@zmk.unibe.ch>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #86
Message-id: <l03130300b3375d20daa7@[130.92.198.63]>
Content-type: text/plain; charset="us-ascii"

Hi imagers

Can anybody help me contrast conrrect two images? I tried it with writing
to the LUT of one of the images, but it doesn't seem to work that way, now
i'm searching a way to change the Histogram.

I hope someone cam help

L. Bickel


-----------------------------------
    Lucas Bickel
    Freiburgstrasse 7
    3010 Bern
-----------------------------------
Voice  +41 31 632 86 18
Pager  +41 74 490 30 02
-----------------------------------

------------------------------

Date: Mon, 12 Apr 1999 20:50:32 +0800
From: Anthony Ting <mcbaet@mcbsgs1.imcb.nus.edu.sg>
To: nih-image@io.ece.drexel.edu
Subject: Need photo-quality printer: dye-sub or ink-jet or ???
Message-Id: <3.0.1.32.19990412205032.007494d4@imcb.nus.edu.sg>
Content-Type: text/plain; charset="us-ascii"

Hi there,

	I'd like to get some advice on the purchase of a photo-quality printer.
The input is primarily confocal images and I'd like to have the output look
like my slides.  Currently, we're using a Tektronix Phaser IID, but it's on
it's last legs and I wanted to get some opinion on what the latest
technology is out there.

Thanks,

Tony

-------------------------------------------------------------------
Anthony Ting, PhD		      		 phone: 65-874-7846
Institute of Molecular and Cell Biology          fax: 65-779-1117
30 Medical Drive
Singapore   117609

------------------------------

Date: Mon, 12 Apr 1999 11:24:00 -0700
From: Michael Cammer <cammer@aecom.yu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Object Image
Message-Id: <3.0.5.32.19990412112400.009e8aa0@mailserver.aecom.yu.edu>
Content-Type: text/plain; charset="us-ascii"

We are having a memory problem when starting up Object Image.  We have 128
MB on board our computer.  In the info window we set Object Image to
require at least 64MB to run and to prefer 100MB.  Yet every time it runs,
it only is allocated 13090 bytes.  Any hints?
Thanks-

********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************

------------------------------

Date: Mon, 12 Apr 1999 08:56:22 -0700
From: Joel Brody <jbrody@itsa.ucsf.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Need photo-quality printer: dye-sub or ink-jet or ???
Message-Id: <v03130300b337c71f446b@[128.218.158.175]>
Content-Type: text/plain; charset="us-ascii"

Ink-jet: I have an Epson 740 and it prints very-near photo quality with
hi-quality paper.  The Epson 900 is supposed to have an even smaller drop
size which should give even better quality.

Instead of dye sub you might want to check out the Fujix Pictrographic
printers.  Foe some odd reason Fujix does not push these although they blow
dye-subs out of the water in terms of quality.  Out department has had one
for several years and it has been very reliable and its consumables are in
the same price range as dye subs.


Joel

>Hi there,
>
>	I'd like to get some advice on the purchase of a photo-quality printer.
>The input is primarily confocal images and I'd like to have the output look
>like my slides.  Currently, we're using a Tektronix Phaser IID, but it's on
>it's last legs and I wanted to get some opinion on what the latest
>technology is out there.
>
>Thanks,
>
>Tony
>
>-------------------------------------------------------------------
>Anthony Ting, PhD		      		 phone: 65-874-7846
>Institute of Molecular and Cell Biology          fax: 65-779-1117
>30 Medical Drive
>Singapore   117609


****************************************************************************

CunhaLab, UCSF                          |
Mount Zion Cancer Center, Box 0540      |
2340 Sutter Street, Room S241	        | Tel:     (415) 476-6746
San Francisco, CA 94115    	        | Fax:     (415) 502-2270

------------------------------

Date: Mon, 12 Apr 1999 09:35:32 -0700
From: Peter Lombrozo <peter@di.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Need photo-quality printer: dye-sub or ink-jet or ???
Message-ID: <B1AA3C851F6DD011BEEB0040333A8B54803559@exchange.di.com>
Content-Type: text/plain

About the newest thing in printers these days is the ridiculously low price on
the new color lasers like the Tek 740.  However, even though they do a good job
on presentation graphics, they still don't come close to the photographic
quality of any dye-sub.  They are faster and cheaper to run, but if you're
looking for slide quality, you'll either have to stick with the dye-sub
(Tektronix has pretty much gotten out of this), or the actually quite good
photo-realistic ink-jets.  Be aware that in pricing ink jets, even though the
paper is cheaper and they usually rate 0.20 to 0.50/page for consumables, this
is only for max 20% coverage.  If you do full photographic page, it could cost
$1.50/page or more, especially if you use the high-quality glossy at $1/page
(but worth it!).

Peter Lombrozo

<<             NANOSCOPES                >> Peter Lombrozo
<<   See More & More of Less & Less      >> peter@di.com 
<< until you see Everything of Nothing!  >> Software Engineer



> -----Original Message-----
> From:	Anthony Ting [SMTP:mcbaet@mcbsgs1.imcb.nus.edu.sg]
> Sent:	Monday, April 12, 1999 5:51 AM
> To:	nih-image@io.ece.drexel.edu
> Subject:	Need photo-quality printer: dye-sub or ink-jet or ???
> 
> Hi there,
> 
> 	I'd like to get some advice on the purchase of a photo-quality printer.
> The input is primarily confocal images and I'd like to have the output look
> like my slides.  Currently, we're using a Tektronix Phaser IID, but it's on
> it's last legs and I wanted to get some opinion on what the latest
> technology is out there.
> 
> Thanks,
> 
> Tony
> 
> -------------------------------------------------------------------
> Anthony Ting, PhD		      		 phone: 65-874-7846
> Institute of Molecular and Cell Biology          fax: 65-779-1117
> 30 Medical Drive
> Singapore   117609

------------------------------

Date: Mon, 12 Apr 1999 13:42:02 -0400
From: David Knecht <knecht@uconnvm.uconn.edu>
To: nih-image@io.ece.drexel.edu
Subject: RE: Need photo-quality printer: dye-sub or ink-jet or ???
Message-Id: <l03130308b337e07c64fa@[137.99.71.142]>
Content-Type: text/plain; charset="us-ascii"

I just did a test printing a high resolution color image on my Epson 600
ink jet (about $200) and my Tektronics dye sub (about $6000).  They color
rendition was different, but I could not tell you which was which based
upon image quality.  The newer Epson 700 is apparently even better.  I
would not spend the extra money for a dye sub anymore.  Dave

>About the newest thing in printers these days is the ridiculously low price on
>the new color lasers like the Tek 740.  However, even though they do a
>good job
>on presentation graphics, they still don't come close to the photographic
>quality of any dye-sub.  They are faster and cheaper to run, but if you're
>looking for slide quality, you'll either have to stick with the dye-sub
>(Tektronix has pretty much gotten out of this), or the actually quite good
>photo-realistic ink-jets.  Be aware that in pricing ink jets, even though the
>paper is cheaper and they usually rate 0.20 to 0.50/page for consumables, this
>is only for max 20% coverage.  If you do full photographic page, it could cost
>$1.50/page or more, especially if you use the high-quality glossy at $1/page
>(but worth it!).
>
>Peter Lombrozo
>
><<             NANOSCOPES                >> Peter Lombrozo
><<   See More & More of Less & Less      >> peter@di.com
><< until you see Everything of Nothing!  >> Software Engineer
>
>
>
>> -----Original Message-----
>> From:	Anthony Ting [SMTP:mcbaet@mcbsgs1.imcb.nus.edu.sg]
>> Sent:	Monday, April 12, 1999 5:51 AM
>> To:	nih-image@io.ece.drexel.edu
>> Subject:	Need photo-quality printer: dye-sub or ink-jet or ???
>>
>> Hi there,
>>
>> 	I'd like to get some advice on the purchase of a photo-quality printer.
>> The input is primarily confocal images and I'd like to have the output look
>> like my slides.  Currently, we're using a Tektronix Phaser IID, but it's on
>> it's last legs and I wanted to get some opinion on what the latest
>> technology is out there.
>>
>> Thanks,
>>
>> Tony
>>
>> -------------------------------------------------------------------
>> Anthony Ting, PhD		      		 phone: 65-874-7846
>> Institute of Molecular and Cell Biology          fax: 65-779-1117
>> 30 Medical Drive
>> Singapore   117609


Dr. David Knecht
Department of Molecular and Cell Biology
University of Connecticut
75 N. Eagleville Rd.
U-125
Storrs, CT 06269
Knecht@uconnvm.uconn.edu
860-486-2200
860-486-4331 (fax)

------------------------------

Date: Mon, 12 Apr 1999 20:23:17 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Object Image
Message-Id: <l03010d01b337e68b45e3@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

>We are having a memory problem when starting up Object Image.  We have 128
>MB on board our computer.  In the info window we set Object Image to
>require at least 64MB to run and to prefer 100MB.  Yet every time it runs,
>it only is allocated 13090 bytes.  Any hints?
>Thanks-


I'll have a look if I can reproduce this. Could you meanwhile tell me which
version you use? (the newest version is 1.62n12). Do you mean 13090K
instead 13090 bytes?
Check out that you don't have several versions (NIH Image or Object-Image)
which you confuse. (Search for creator = Imag and file type = APPL). To
isolate this problem, be sure to double-click the same version that you
altered in the info window, rather than opening it via a document. If you
want to keep several versions, hide all except the one to be used with
AppHider (see my web site).

Norbert

------------------------------

Date: Mon, 12 Apr 1999 16:07:08 -0300
From: Ruy Jaeger <rgjaeger@fo.usp.br>
To: nih-image@io.ece.drexel.edu
Subject: Re: Need photo-quality printer: dye-sub or ink-jet or ???
Message-ID: <3712445B.2079@siso.fo.usp.br>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Fuji Pictrography is definitely the best choice


Ruy




Anthony Ting wrote:
> 
> Hi there,
> 
>         I'd like to get some advice on the purchase of a photo-quality printer.
> The input is primarily confocal images and I'd like to have the output look
> like my slides.  Currently, we're using a Tektronix Phaser IID, but it's on
> it's last legs and I wanted to get some opinion on what the latest
> technology is out there.
> 
> Thanks,
> 
> Tony
> 
> -------------------------------------------------------------------
> Anthony Ting, PhD                                phone: 65-874-7846
> Institute of Molecular and Cell Biology          fax: 65-779-1117
> 30 Medical Drive
> Singapore   117609

------------------------------

Date: Tue, 13 Apr 1999 10:08:03 +0000
From: Woeichyn Chu <wchu@bme.ym.edu.tw>
To: nih-image@io.ece.drexel.edu
Subject: Re: Need photo-quality printer: dye-sub or ink-jet or ???
Message-ID: <3713176D.C8E958C6@bme.ym.edu.tw>
Content-Type: text/plain; charset=big5; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Couple of months ago I did some comparisons on high quality dye sub printers vs.
Fuji Pictrography model PG-3000. Conclusion: if budget allows, I would go for the
latter one (price is ~40% higher though).

woeichyn

Ruy Jaeger wrote:

> Fuji Pictrography is definitely the best choice
>
> Ruy
>
> Anthony Ting wrote:
> >
> > Hi there,
> >
> >         I'd like to get some advice on the purchase of a photo-quality printer.
> > The input is primarily confocal images and I'd like to have the output look
> > like my slides.  Currently, we're using a Tektronix Phaser IID, but it's on
> > it's last legs and I wanted to get some opinion on what the latest
> > technology is out there.
> >
> > Thanks,
> >
> > Tony
> >
> > -------------------------------------------------------------------
> > Anthony Ting, PhD                                phone: 65-874-7846
> > Institute of Molecular and Cell Biology          fax: 65-779-1117
> > 30 Medical Drive
> > Singapore   117609


--
Sincerely yours,

Woeichyn Chu, Ph.D.
Associate Professor
Institute of Biomedical Engineering
National Yang Ming University       '__|__     _  /__\__   -|=|-   /
Shih-Pai, Taipei, Taiwan 112       /___|___   | |'|__|__    |+| --'-.
Tel: 886.2.28267025(Office)          / | \    |_| |__|__    -+-  /  |
Tel: 886.2.28267170(Lab.)           /  |  \       |__|__    -+- /   /
Fax: 886.2.28210847                '  `|   `      |         ---'  _/
Email: wchu@bme.ym.edu.tw

--------------------------------
End of nih-image-d Digest V99 Issue #87
***************************************

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Date: Tue, 13 Apr 1999 12:56:51 +0800
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Does anyone using NIH image to do microarray analysis?  Are the intrinsic
array variables enough to hold all the data? Any information would be
appreciated.


Cha Ze Lee, MD, Ph. D.
National Taiwan University Hospital



From nih-image-request@io.ece.drexel.edu Tue Apr 13 01:22 EDT 1999
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Organization:  Dept. of Biological Sciences
To: lukas.bickel@zmk.unibe.ch, nih-image@io.ece.drexel.edu
Date:          Tue, 13 Apr 1999 15:19:03 +1000
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>Date: Mon, 12 Apr 1999 10:23:18 +0200
>From: Lucas Bickel <lukas.bickel@zmk.unibe.ch>
>Subject: Re: nih-image-d Digest V99 #86
>To: nih-image@io.ece.drexel.edu
>
>Can anybody help me contrast conrrect two images? I tried it with writing
>to the LUT of one of the images, but it doesn't seem to work that way, now
>i'm searching a way to change the Histogram.
>
>I hope someone cam help
>
Writing to the Lut of one or both images to procuce some "normalised" 
contrast sounds correct to me. 
It is also the way to change the Histogram; 
ie change the LUT 'appropriately' and then ApplyLUT.

What is it that "doesn't seem to work that way"?

eg have you looked at, say: 
macro 'Equalize';
in 
LUT Macros
supplied with NIH-Image?
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


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                   NIH-image Mailing List Help 
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From nih-image-request@io.ece.drexel.edu Tue Apr 13 08:02 EDT 1999
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From: Bill Miller <microbill@mohawk.net>
Subject: Re: Need photo-quality printer: dye-sub or ink-jet or ???
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I almost hate to get into this - but here goes - Dye sub printers make
PRETTY pictures. If what you need is pretty pictures they are great - and
the Fuji (a slightly different technology ) is superb. But the best of them
print at 300 to 400dpi. If you have scientific images from light or
electron microscopy (particularly electron microscopy) you may well have
information that will be lost at this relatively low resolution.  Yes, if
you print the pictures big enough that is not a problem - but who prints
everything at 8.5x11?  I know it's hard to believe that a printer that only
costs 5% -10% of the price of a dye sub can be any good but the new
generation of inkjets are great. They have a better color gamut (printing
from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub.  As
always the best advice is to get the same image printed on both and then
choose - print what you will normally be printing and at the size you would
normally use (you do want to compare apples to  apples don't you?) I know
buying an expensive dye sub makes you feel good and increases your prestige
among your peers ("OOOOOO, have you seen his new mega dollar
printer!!!???") but really, couldn't you use the money better for something
else? 

Good Luck  -

Bill Miller

At 10:08 AM 4/13/99 +0000, Woeichyn Chu wrote:
>Couple of months ago I did some comparisons on high quality dye sub
printers vs.
>Fuji Pictrography model PG-3000. Conclusion: if budget allows, I would go
for the
>latter one (price is ~40% higher though).
>
>woeichyn
>
>Ruy Jaeger wrote:
>
>> Fuji Pictrography is definitely the best choice
>>
>> Ruy
>>
>> Anthony Ting wrote:
>> >
>> > Hi there,
>> >
>> >         I'd like to get some advice on the purchase of a photo-quality
printer.
>> > The input is primarily confocal images and I'd like to have the output
look
>> > like my slides.  Currently, we're using a Tektronix Phaser IID, but
it's on
>> > it's last legs and I wanted to get some opinion on what the latest
>> > technology is out there.
>> >
>> > Thanks,
>> >
>> > Tony
>> >
>> > -------------------------------------------------------------------
>> > Anthony Ting, PhD                                phone: 65-874-7846
>> > Institute of Molecular and Cell Biology          fax: 65-779-1117
>> > 30 Medical Drive
>> > Singapore   117609
>
>
>--
>Sincerely yours,
>
>Woeichyn Chu, Ph.D.
>Associate Professor
>Institute of Biomedical Engineering
>National Yang Ming University       '__|__     _  /__\__   -|=|-   /
>Shih-Pai, Taipei, Taiwan 112       /___|___   | |'|__|__    |+| --'-.
>Tel: 886.2.28267025(Office)          / | \    |_| |__|__    -+-  /  |
>Tel: 886.2.28267170(Lab.)           /  |  \       |__|__    -+- /   /
>Fax: 886.2.28210847                '  `|   `      |         ---'  _/
>Email: wchu@bme.ym.edu.tw
>
>
>
>


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Date: Tue, 13 Apr 1999 09:46:10 -0700
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Actually, that isn't true.  The difference is the technology used.  Dye-sub is
continuous tone.  This means that every spot the printer puts down is capable of
256 shades, no dithering takes place except to interpolate to the correct size.
If you print one-to-one, a 1200 X 1200 pixel image on a 300 dpi dye-sub would
print 4"x4" WITHOUT any loss of data resolution from the original data.  This
defines photographic quality - film grains do the same thing.

In contrast, any ink-jet or laser color printer needs to dither in order to get
more colors and shades than are in the ink toners/cartridge.  These printers can
only put a spot down or not (although some expensive printers are able to adjust
the spot size) and need to use "supercells" of about 16 x 16 spots to get 256
shades of a color which reduces the spatial resolution.  The 6 process inks
really help because they reduce the supercell to 4 X 4.  Notice that even then,
you need the full 1200 dpi of an ink-jet to get the same color AND spatial
resolution as a dye-sub.  Also, special techniques are used to prevent the
dither pattern from showing as repeated structure on an image.  That being said,
the new process-ink jets are really awesome for the price, but they don't have
any better image resolution than dye-subs, even at 4X the dpi.

Peter Lombrozo

<<             NANOSCOPES                >> Peter Lombrozo
<<   See More & More of Less & Less      >> peter@di.com 
<< until you see Everything of Nothing!  >> Software Engineer



> -----Original Message-----
> From:	Bill Miller [SMTP:microbill@mohawk.net]
> Sent:	Tuesday, April 13, 1999 4:44 AM
> To:	wchu@bme.ym.edu.tw; nih-image@io.ece.drexel.edu
> Subject:	Re: Need photo-quality printer: dye-sub or ink-jet or ???
> 
> I almost hate to get into this - but here goes - Dye sub printers make
> PRETTY pictures. If what you need is pretty pictures they are great - and
> the Fuji (a slightly different technology ) is superb. But the best of them
> print at 300 to 400dpi. If you have scientific images from light or
> electron microscopy (particularly electron microscopy) you may well have
> information that will be lost at this relatively low resolution.  Yes, if
> you print the pictures big enough that is not a problem - but who prints
> everything at 8.5x11?  I know it's hard to believe that a printer that only
> costs 5% -10% of the price of a dye sub can be any good but the new
> generation of inkjets are great. They have a better color gamut (printing
> from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
> dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub. 


From nih-image-request@io.ece.drexel.edu Tue Apr 13 13:42 EDT 1999
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From: Joel Brody <jbrody@itsa.ucsf.edu>
Subject: Re: Need photo-quality printer: dye-sub or ink-jet or ???
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Bill,

You are confusing what is meant by resolution.  I really don't know enough
printer 'theory' to do an adequate explanation, but a Fujix Pictrographic
at 3-400 dpi is much better resolution than an Epson ink-jet.  Essentially
a Fujix 'dot' is the final color.  An Epson 'dot' is one of the colors of
the 6-7 inks that have to be put together into a psuedo-pixel.  I believe
the 'final' resolution of an Epson is more in the 150-200dpi range.  Fujix
prints are indistinguishable from photographs and do not fade particularly
quickly.  Epson prints are great 'for the price', but they are not in the
same league as the Fujix.

Joel


>I almost hate to get into this - but here goes - Dye sub printers make
>PRETTY pictures. If what you need is pretty pictures they are great - and
>the Fuji (a slightly different technology ) is superb. But the best of them
>print at 300 to 400dpi. If you have scientific images from light or
>electron microscopy (particularly electron microscopy) you may well have
>information that will be lost at this relatively low resolution.  Yes, if
>you print the pictures big enough that is not a problem - but who prints
>everything at 8.5x11?  I know it's hard to believe that a printer that only
>costs 5% -10% of the price of a dye sub can be any good but the new
>generation of inkjets are great. They have a better color gamut (printing
>from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
>dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub.  As
>always the best advice is to get the same image printed on both and then
>choose - print what you will normally be printing and at the size you would
>normally use (you do want to compare apples to  apples don't you?) I know
>buying an expensive dye sub makes you feel good and increases your prestige
>among your peers ("OOOOOO, have you seen his new mega dollar
>printer!!!???") but really, couldn't you use the money better for something
>else?
>
>Good Luck  -
>
>Bill Miller

****************************************************************************

CunhaLab, UCSF                          |
Mount Zion Cancer Center, Box 0540      |
2340 Sutter Street, Room S241	        | Tel:     (415) 476-6746
San Francisco, CA 94115    	        | Fax:     (415) 502-2270



From nih-image-request@io.ece.drexel.edu Tue Apr 13 14:36 EDT 1999
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From: Paul Lampe <plampe@fred.fhcrc.org>
Subject: Stacks to movies
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We create stacks on our microscope via Metamorph (Universal Imaging) and
would like to import the stacks to NIH Image to make movies.  If we use the
import command with TIFF checked we get the first image and it looks fine
but none of the subsequent images are imported.  Anyone have an easy fix?



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From: "Philippe GUILLAUD" <guillaud@ccr.jussieu.fr>
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In fact NIH Image can't read directly Metamorph stacks (a sort of multitiff
file format) you must import images one by one (with the open all option
checked). You can also make movies directly in metamorph (AVI format) and
import them on Macintosh to view them in QuickTime.

Philippe GUILLAUD
Service Imagerie
Universit Pierre et Marie Curie - Paris 6
France

----- Message d'origine -----
De : Paul Lampe <plampe@fred.fhcrc.org>
 : <nih-image@io.ece.drexel.edu>
Envoy : mardi 13 avril 1999 20:20
Objet : Stacks to movies


> We create stacks on our microscope via Metamorph (Universal Imaging) and
> would like to import the stacks to NIH Image to make movies.  If we use
the
> import command with TIFF checked we get the first image and it looks fine
> but none of the subsequent images are imported.  Anyone have an easy fix?
>
>


From nih-image-d-request@io.ece.drexel.edu Tue Apr 13 16:32 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #88
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 88

Today's Topics:
  microarray analysis                   [ czl@ccms.ntu.edu.tw ]
  Re:contrast correction (nih-image Di  [ GJOSS@rna.bio.mq.edu.au ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
  Re: Need photo-quality printer: dye-  [ Bill Miller <microbill@mohawk.net> ]
  RE: Need photo-quality printer: dye-  [ Peter Lombrozo <peter@di.com> ]
  Re: Need photo-quality printer: dye-  [ Joel Brody <jbrody@itsa.ucsf.edu> ]
  Stacks to movies                      [ Paul Lampe <plampe@fred.fhcrc.org> ]
  Re: Stacks to movies                  [ "Philippe GUILLAUD" <guillaud@ccr.j ]

------------------------------

Date: Tue, 13 Apr 1999 12:56:51 +0800
From: czl@ccms.ntu.edu.tw
To: nih-image@io.ece.drexel.edu
Subject: microarray analysis
Message-Id: <v04003a03b3387d31af23@[140.112.133.81]>
Content-Type: text/plain; charset="us-ascii"

Does anyone using NIH image to do microarray analysis?  Are the intrinsic
array variables enough to hold all the data? Any information would be
appreciated.


Cha Ze Lee, MD, Ph. D.
National Taiwan University Hospital

------------------------------

Date:          Tue, 13 Apr 1999 15:19:03 +1000
From: GJOSS@rna.bio.mq.edu.au
To: lukas.bickel@zmk.unibe.ch, nih-image@io.ece.drexel.edu
Subject:       Re:contrast correction (nih-image Digest V99 #86
Message-ID: <1914D6467A6@rna.bio.mq.edu.au>

>Date: Mon, 12 Apr 1999 10:23:18 +0200
>From: Lucas Bickel <lukas.bickel@zmk.unibe.ch>
>Subject: Re: nih-image-d Digest V99 #86
>To: nih-image@io.ece.drexel.edu
>
>Can anybody help me contrast conrrect two images? I tried it with writing
>to the LUT of one of the images, but it doesn't seem to work that way, now
>i'm searching a way to change the Histogram.
>
>I hope someone cam help
>
Writing to the Lut of one or both images to procuce some "normalised" 
contrast sounds correct to me. 
It is also the way to change the Histogram; 
ie change the LUT 'appropriately' and then ApplyLUT.

What is it that "doesn't seem to work that way"?

eg have you looked at, say: 
macro 'Equalize';
in 
LUT Macros
supplied with NIH-Image?
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Tue, 13 Apr 1999 05:05:01 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199904130905.FAA23474@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
                   ---------------------------
     


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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
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Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

------------------------------

Date: Tue, 13 Apr 1999 07:44:27 -0400
From: Bill Miller <microbill@mohawk.net>
To: wchu@bme.ym.edu.tw, nih-image@io.ece.drexel.edu
Subject: Re: Need photo-quality printer: dye-sub or ink-jet or ???
Message-Id: <3.0.5.32.19990413074427.007fa900@mohawk.net>
Content-Type: text/plain; charset="us-ascii"

I almost hate to get into this - but here goes - Dye sub printers make
PRETTY pictures. If what you need is pretty pictures they are great - and
the Fuji (a slightly different technology ) is superb. But the best of them
print at 300 to 400dpi. If you have scientific images from light or
electron microscopy (particularly electron microscopy) you may well have
information that will be lost at this relatively low resolution.  Yes, if
you print the pictures big enough that is not a problem - but who prints
everything at 8.5x11?  I know it's hard to believe that a printer that only
costs 5% -10% of the price of a dye sub can be any good but the new
generation of inkjets are great. They have a better color gamut (printing
from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub.  As
always the best advice is to get the same image printed on both and then
choose - print what you will normally be printing and at the size you would
normally use (you do want to compare apples to  apples don't you?) I know
buying an expensive dye sub makes you feel good and increases your prestige
among your peers ("OOOOOO, have you seen his new mega dollar
printer!!!???") but really, couldn't you use the money better for something
else? 

Good Luck  -

Bill Miller

At 10:08 AM 4/13/99 +0000, Woeichyn Chu wrote:
>Couple of months ago I did some comparisons on high quality dye sub
printers vs.
>Fuji Pictrography model PG-3000. Conclusion: if budget allows, I would go
for the
>latter one (price is ~40% higher though).
>
>woeichyn
>
>Ruy Jaeger wrote:
>
>> Fuji Pictrography is definitely the best choice
>>
>> Ruy
>>
>> Anthony Ting wrote:
>> >
>> > Hi there,
>> >
>> >         I'd like to get some advice on the purchase of a photo-quality
printer.
>> > The input is primarily confocal images and I'd like to have the output
look
>> > like my slides.  Currently, we're using a Tektronix Phaser IID, but
it's on
>> > it's last legs and I wanted to get some opinion on what the latest
>> > technology is out there.
>> >
>> > Thanks,
>> >
>> > Tony
>> >
>> > -------------------------------------------------------------------
>> > Anthony Ting, PhD                                phone: 65-874-7846
>> > Institute of Molecular and Cell Biology          fax: 65-779-1117
>> > 30 Medical Drive
>> > Singapore   117609
>
>
>--
>Sincerely yours,
>
>Woeichyn Chu, Ph.D.
>Associate Professor
>Institute of Biomedical Engineering
>National Yang Ming University       '__|__     _  /__\__   -|=|-   /
>Shih-Pai, Taipei, Taiwan 112       /___|___   | |'|__|__    |+| --'-.
>Tel: 886.2.28267025(Office)          / | \    |_| |__|__    -+-  /  |
>Tel: 886.2.28267170(Lab.)           /  |  \       |__|__    -+- /   /
>Fax: 886.2.28210847                '  `|   `      |         ---'  _/
>Email: wchu@bme.ym.edu.tw
>
>
>
>

------------------------------

Date: Tue, 13 Apr 1999 09:46:10 -0700
From: Peter Lombrozo <peter@di.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Need photo-quality printer: dye-sub or ink-jet or ???
Message-ID: <B1AA3C851F6DD011BEEB0040333A8B5480355F@exchange.di.com>
Content-Type: text/plain

Actually, that isn't true.  The difference is the technology used.  Dye-sub is
continuous tone.  This means that every spot the printer puts down is capable of
256 shades, no dithering takes place except to interpolate to the correct size.
If you print one-to-one, a 1200 X 1200 pixel image on a 300 dpi dye-sub would
print 4"x4" WITHOUT any loss of data resolution from the original data.  This
defines photographic quality - film grains do the same thing.

In contrast, any ink-jet or laser color printer needs to dither in order to get
more colors and shades than are in the ink toners/cartridge.  These printers can
only put a spot down or not (although some expensive printers are able to adjust
the spot size) and need to use "supercells" of about 16 x 16 spots to get 256
shades of a color which reduces the spatial resolution.  The 6 process inks
really help because they reduce the supercell to 4 X 4.  Notice that even then,
you need the full 1200 dpi of an ink-jet to get the same color AND spatial
resolution as a dye-sub.  Also, special techniques are used to prevent the
dither pattern from showing as repeated structure on an image.  That being said,
the new process-ink jets are really awesome for the price, but they don't have
any better image resolution than dye-subs, even at 4X the dpi.

Peter Lombrozo

<<             NANOSCOPES                >> Peter Lombrozo
<<   See More & More of Less & Less      >> peter@di.com 
<< until you see Everything of Nothing!  >> Software Engineer



> -----Original Message-----
> From:	Bill Miller [SMTP:microbill@mohawk.net]
> Sent:	Tuesday, April 13, 1999 4:44 AM
> To:	wchu@bme.ym.edu.tw; nih-image@io.ece.drexel.edu
> Subject:	Re: Need photo-quality printer: dye-sub or ink-jet or ???
> 
> I almost hate to get into this - but here goes - Dye sub printers make
> PRETTY pictures. If what you need is pretty pictures they are great - and
> the Fuji (a slightly different technology ) is superb. But the best of them
> print at 300 to 400dpi. If you have scientific images from light or
> electron microscopy (particularly electron microscopy) you may well have
> information that will be lost at this relatively low resolution.  Yes, if
> you print the pictures big enough that is not a problem - but who prints
> everything at 8.5x11?  I know it's hard to believe that a printer that only
> costs 5% -10% of the price of a dye sub can be any good but the new
> generation of inkjets are great. They have a better color gamut (printing
> from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
> dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub. 

------------------------------

Date: Tue, 13 Apr 1999 10:25:33 -0700
From: Joel Brody <jbrody@itsa.ucsf.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Need photo-quality printer: dye-sub or ink-jet or ???
Message-Id: <v03130304b3392c566747@[128.218.158.175]>
Content-Type: text/plain; charset="us-ascii"

Bill,

You are confusing what is meant by resolution.  I really don't know enough
printer 'theory' to do an adequate explanation, but a Fujix Pictrographic
at 3-400 dpi is much better resolution than an Epson ink-jet.  Essentially
a Fujix 'dot' is the final color.  An Epson 'dot' is one of the colors of
the 6-7 inks that have to be put together into a psuedo-pixel.  I believe
the 'final' resolution of an Epson is more in the 150-200dpi range.  Fujix
prints are indistinguishable from photographs and do not fade particularly
quickly.  Epson prints are great 'for the price', but they are not in the
same league as the Fujix.

Joel


>I almost hate to get into this - but here goes - Dye sub printers make
>PRETTY pictures. If what you need is pretty pictures they are great - and
>the Fuji (a slightly different technology ) is superb. But the best of them
>print at 300 to 400dpi. If you have scientific images from light or
>electron microscopy (particularly electron microscopy) you may well have
>information that will be lost at this relatively low resolution.  Yes, if
>you print the pictures big enough that is not a problem - but who prints
>everything at 8.5x11?  I know it's hard to believe that a printer that only
>costs 5% -10% of the price of a dye sub can be any good but the new
>generation of inkjets are great. They have a better color gamut (printing
>from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
>dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub.  As
>always the best advice is to get the same image printed on both and then
>choose - print what you will normally be printing and at the size you would
>normally use (you do want to compare apples to  apples don't you?) I know
>buying an expensive dye sub makes you feel good and increases your prestige
>among your peers ("OOOOOO, have you seen his new mega dollar
>printer!!!???") but really, couldn't you use the money better for something
>else?
>
>Good Luck  -
>
>Bill Miller

****************************************************************************

CunhaLab, UCSF                          |
Mount Zion Cancer Center, Box 0540      |
2340 Sutter Street, Room S241	        | Tel:     (415) 476-6746
San Francisco, CA 94115    	        | Fax:     (415) 502-2270

------------------------------

Date: Tue, 13 Apr 1999 11:20:38 -0700
From: Paul Lampe <plampe@fred.fhcrc.org>
To: nih-image@io.ece.drexel.edu
Subject: Stacks to movies
Message-Id: <l03010d04b338d91c5f45@[140.107.54.131]>
Content-Type: text/plain; charset="us-ascii"

We create stacks on our microscope via Metamorph (Universal Imaging) and
would like to import the stacks to NIH Image to make movies.  If we use the
import command with TIFF checked we get the first image and it looks fine
but none of the subsequent images are imported.  Anyone have an easy fix?

------------------------------

Date: Tue, 13 Apr 1999 22:16:22 +0200
From: "Philippe GUILLAUD" <guillaud@ccr.jussieu.fr>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: Stacks to movies
Message-ID: <001a01be85ea$806cad80$9f519d86@guillaud>
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

In fact NIH Image can't read directly Metamorph stacks (a sort of multitiff
file format) you must import images one by one (with the open all option
checked). You can also make movies directly in metamorph (AVI format) and
import them on Macintosh to view them in QuickTime.

Philippe GUILLAUD
Service Imagerie
Universit Pierre et Marie Curie - Paris 6
France

----- Message d'origine -----
De : Paul Lampe <plampe@fred.fhcrc.org>
 : <nih-image@io.ece.drexel.edu>
Envoy : mardi 13 avril 1999 20:20
Objet : Stacks to movies


> We create stacks on our microscope via Metamorph (Universal Imaging) and
> would like to import the stacks to NIH Image to make movies.  If we use
the
> import command with TIFF checked we get the first image and it looks fine
> but none of the subsequent images are imported.  Anyone have an easy fix?
>
>

--------------------------------
End of nih-image-d Digest V99 Issue #88
***************************************

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Just another voice in support of the Fuji. The ink-jets use pseudo-pixels, and give
resolution in the range of less than 150-200 dpi or maybe less. The advertizing
makes you think you're getting a genuine 1400 dpi. That is hokum. They also don't
have the outstanding black contrast of the Fuji. The Kodak 8250 series is close to
the Fuji, but still not as good.

If you want to see the difference between ink-jet and dye-sub technology at a more
affordable price range, get an Olympus P-300 dye-sub. The prints are only about 3.5
x 4.5 inches, but they are vastly better than any images obtainable with an ink-jet.
I think the P-300 has recently been replaced by the P-330. The printer is only about
$350. Each print is about $0.35 to $0.50. Color is outstanding. Resolution is about
305 dpi. Kodak makes a small dye-sub with the same small size paper, but it only
provides 149 dpi. Price per print is slightly less than the Olympus. Prints are not
as crisp. One very big problem with the Olympus is that they refuse to provide a
driver for Windows NT. But they do have drivers for Win 95, Win 98 and MacOS.

Harvey Karten

> Actually, that isn't true.  The difference is the technology used.  Dye-sub is
> continuous tone.  This means that every spot the printer puts down is capable of
> 256 shades, no dithering takes place except to interpolate to the correct size.
> If you print one-to-one, a 1200 X 1200 pixel image on a 300 dpi dye-sub would
> print 4"x4" WITHOUT any loss of data resolution from the original data.  This
> defines photographic quality - film grains do the same thing.
>
> In contrast, any ink-jet or laser color printer needs to dither in order to get
> more colors and shades than are in the ink toners/cartridge.  These printers can
> only put a spot down or not (although some expensive printers are able to adjust
> the spot size) and need to use "supercells" of about 16 x 16 spots to get 256
> shades of a color which reduces the spatial resolution.  The 6 process inks
> really help because they reduce the supercell to 4 X 4.  Notice that even then,
> you need the full 1200 dpi of an ink-jet to get the same color AND spatial
> resolution as a dye-sub.  Also, special techniques are used to prevent the
> dither pattern from showing as repeated structure on an image.  That being said,
> the new process-ink jets are really awesome for the price, but they don't have
> any better image resolution than dye-subs, even at 4X the dpi.
>
> Peter Lombrozo
>
> <<             NANOSCOPES                >> Peter Lombrozo
> <<   See More & More of Less & Less      >> peter@di.com
> << until you see Everything of Nothing!  >> Software Engineer
>
> > -----Original Message-----
> > From: Bill Miller [SMTP:microbill@mohawk.net]
> > Sent: Tuesday, April 13, 1999 4:44 AM
> > To:   wchu@bme.ym.edu.tw; nih-image@io.ece.drexel.edu
> > Subject:      Re: Need photo-quality printer: dye-sub or ink-jet or ???
> >
> > I almost hate to get into this - but here goes - Dye sub printers make
> > PRETTY pictures. If what you need is pretty pictures they are great - and
> > the Fuji (a slightly different technology ) is superb. But the best of them
> > print at 300 to 400dpi. If you have scientific images from light or
> > electron microscopy (particularly electron microscopy) you may well have
> > information that will be lost at this relatively low resolution.  Yes, if
> > you print the pictures big enough that is not a problem - but who prints
> > everything at 8.5x11?  I know it's hard to believe that a printer that only
> > costs 5% -10% of the price of a dye sub can be any good but the new
> > generation of inkjets are great. They have a better color gamut (printing
> > from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
> > dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub.
>
>   ------------------------------------------------------------------------
>
> Subject: Re: Need photo-quality printer: dye-sub or ink-jet or ???
> Date: Tue, 13 Apr 1999 10:25:33 -0700
> From: Joel Brody <jbrody@itsa.ucsf.edu>
> To: nih-image@io.ece.drexel.edu
>
> Bill,
>
> You are confusing what is meant by resolution.  I really don't know enough
> printer 'theory' to do an adequate explanation, but a Fujix Pictrographic
> at 3-400 dpi is much better resolution than an Epson ink-jet.  Essentially
> a Fujix 'dot' is the final color.  An Epson 'dot' is one of the colors of
> the 6-7 inks that have to be put together into a psuedo-pixel.  I believe
> the 'final' resolution of an Epson is more in the 150-200dpi range.  Fujix
> prints are indistinguishable from photographs and do not fade particularly
> quickly.  Epson prints are great 'for the price', but they are not in the
> same league as the Fujix.
>
> Joel
>
> >I almost hate to get into this - but here goes - Dye sub printers make
> >PRETTY pictures. If what you need is pretty pictures they are great - and
> >the Fuji (a slightly different technology ) is superb. But the best of them
> >print at 300 to 400dpi. If you have scientific images from light or
> >electron microscopy (particularly electron microscopy) you may well have
> >information that will be lost at this relatively low resolution.  Yes, if
> >you print the pictures big enough that is not a problem - but who prints
> >everything at 8.5x11?  I know it's hard to believe that a printer that only
> >costs 5% -10% of the price of a dye sub can be any good but the new
> >generation of inkjets are great. They have a better color gamut (printing
> >from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
> >dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub.  As
> >always the best advice is to get the same image printed on both and then
> >choose - print what you will normally be printing and at the size you would
> >normally use (you do want to compare apples to  apples don't you?) I know
> >buying an expensive dye sub makes you feel good and increases your prestige
> >among your peers ("OOOOOO, have you seen his new mega dollar
> >printer!!!???") but really, couldn't you use the money better for something
> >else?
> >
> >Good Luck  -
> >
> >Bill Miller
>
> ****************************************************************************
>




From nih-image-request@io.ece.drexel.edu Wed Apr 14 12:19 EDT 1999
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Date: 14 Apr 99 11:58:39 -0400
From: Jonathan WISCO <jjwisco@cajal-1.bu.edu>
Subject: RE: nih-image-d Digest V99 #88
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         Reply to:   RE: nih-image-d Digest V99 #88
I look at MR Images with NIH Image, but lately NIH Image has had problems assigning greyscale values to pixels.  These pixels end up as different colors or black, when they should be a shade of grey.  Any ideas on how to remedy this?

Jonathan J. Wisco


nih-image-d-request wrote:
>------------------------------
>
>Content-Type: text/plain
>
>nih-image-d Digest				Volume 99 : Issue 88
>
>Today's Topics:
>  microarray analysis                   [ czl@ccms.ntu.edu.tw ]
>  Re:contrast correction (nih-image Di  [ GJOSS@rna.bio.mq.edu.au ]
>  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
>  Re: Need photo-quality printer: dye-  [ Bill Miller <microbill@mohawk.net> ]
>  RE: Need photo-quality printer: dye-  [ Peter Lombrozo <peter@di.com> ]
>  Re: Need photo-quality printer: dye-  [ Joel Brody <jbrody@itsa.ucsf.edu> ]
>  Stacks to movies                      [ Paul Lampe <plampe@fred.fhcrc.org> ]
>  Re: Stacks to movies                  [ "Philippe GUILLAUD" <guillaud@ccr.j ]
>
>------------------------------
>
>Date: Tue, 13 Apr 1999 12:56:51 +0800
>From: czl@ccms.ntu.edu.tw
>To: nih-image@io.ece.drexel.edu
>Subject: microarray analysis
>Message-Id: <v04003a03b3387d31af23@[140.112.133.81]>
>Content-Type: text/plain; charset="us-ascii"
>
>Does anyone using NIH image to do microarray analysis?  Are the intrinsic
>array variables enough to hold all the data? Any information would be
>appreciated.
>
>
>Cha Ze Lee, MD, Ph. D.
>National Taiwan University Hospital
>
>------------------------------
>
>Date:          Tue, 13 Apr 1999 15:19:03 +1000
>From: GJOSS@rna.bio.mq.edu.au
>To: lukas.bickel@zmk.unibe.ch, nih-image@io.ece.drexel.edu
>Subject:       Re:contrast correction (nih-image Digest V99 #86
>Message-ID: <1914D6467A6@rna.bio.mq.edu.au>
>
>>Date: Mon, 12 Apr 1999 10:23:18 +0200
>>From: Lucas Bickel <lukas.bickel@zmk.unibe.ch>
>>Subject: Re: nih-image-d Digest V99 #86
>>To: nih-image@io.ece.drexel.edu
>>
>>Can anybody help me contrast conrrect two images? I tried it with writing
>>to the LUT of one of the images, but it doesn't seem to work that way, now
>>i'm searching a way to change the Histogram.
>>
>>I hope someone cam help
>>
>Writing to the Lut of one or both images to procuce some "normalised" >contrast sounds correct to me. >It is also the way to change the Histogram; >ie change the LUT 'appropriately' and then ApplyLUT.
>
>What is it that "doesn't seem to work that way"?
>
>eg have you looked at, say: >macro 'Equalize';
>in >LUT Macros
>supplied with NIH-Image?
>Greg Joss,
>School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
>Macquarie University,          Email gjoss@rna.bio.mq.edu.au
>North Ryde, (Sydney,) NSW 2109, Australia
>
>------------------------------
>
>Date: Tue, 13 Apr 1999 05:05:01 -0400 (EDT)
>From: nih-image-owner@io.ece.drexel.edu
>To: nih-image@io.ece.drexel.edu
>Subject: ADMIN: list commands
>Message-Id: <199904130905.FAA23474@io.ece.drexel.edu>
>
>                   NIH-image Mailing List Help >                   ---------------------------
>     >
>
>nih-image-d-request@biomed.drexel.edu  - Aministration for Digest
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>
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>         get latest/862         or whatever filenumber you need
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>         archive maxfiles 35    or however many you want
>then use Unix metacharacters to get more than one file. * matches any string.
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>--
>
>------------------------------
>
>Date: Tue, 13 Apr 1999 07:44:27 -0400
>From: Bill Miller <microbill@mohawk.net>
>To: wchu@bme.ym.edu.tw, nih-image@io.ece.drexel.edu
>Subject: Re: Need photo-quality printer: dye-sub or ink-jet or ???
>Message-Id: <3.0.5.32.19990413074427.007fa900@mohawk.net>
>Content-Type: text/plain; charset="us-ascii"
>
>I almost hate to get into this - but here goes - Dye sub printers make
>PRETTY pictures. If what you need is pretty pictures they are great - and
>the Fuji (a slightly different technology ) is superb. But the best of them
>print at 300 to 400dpi. If you have scientific images from light or
>electron microscopy (particularly electron microscopy) you may well have
>information that will be lost at this relatively low resolution.  Yes, if
>you print the pictures big enough that is not a problem - but who prints
>everything at 8.5x11?  I know it's hard to believe that a printer that only
>costs 5% -10% of the price of a dye sub can be any good but the new
>generation of inkjets are great. They have a better color gamut (printing
>from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
>dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub.  As
>always the best advice is to get the same image printed on both and then
>choose - print what you will normally be printing and at the size you would
>normally use (you do want to compare apples to  apples don't you?) I know
>buying an expensive dye sub makes you feel good and increases your prestige
>among your peers ("OOOOOO, have you seen his new mega dollar
>printer!!!???") but really, couldn't you use the money better for something
>else? >
>Good Luck  -
>
>Bill Miller
>
>At 10:08 AM 4/13/99 +0000, Woeichyn Chu wrote:
>>Couple of months ago I did some comparisons on high quality dye sub
>printers vs.
>>Fuji Pictrography model PG-3000. Conclusion: if budget allows, I would go
>for the
>>latter one (price is ~40% higher though).
>>
>>woeichyn
>>
>>Ruy Jaeger wrote:
>>
>>> Fuji Pictrography is definitely the best choice
>>>
>>> Ruy
>>>
>>> Anthony Ting wrote:
>>> >
>>> > Hi there,
>>> >
>>> >         I'd like to get some advice on the purchase of a photo-quality
>printer.
>>> > The input is primarily confocal images and I'd like to have the output
>look
>>> > like my slides.  Currently, we're using a Tektronix Phaser IID, but
>it's on
>>> > it's last legs and I wanted to get some opinion on what the latest
>>> > technology is out there.
>>> >
>>> > Thanks,
>>> >
>>> > Tony
>>> >
>>> > -------------------------------------------------------------------
>>> > Anthony Ting, PhD                                phone: 65-874-7846
>>> > Institute of Molecular and Cell Biology          fax: 65-779-1117
>>> > 30 Medical Drive
>>> > Singapore   117609
>>
>>
>>--
>>Sincerely yours,
>>
>>Woeichyn Chu, Ph.D.
>>Associate Professor
>>Institute of Biomedical Engineering
>>National Yang Ming University       '__|__     _  /__\__   -|=|-   /
>>Shih-Pai, Taipei, Taiwan 112       /___|___   | |'|__|__    |+| --'-.
>>Tel: 886.2.28267025(Office)          / | \    |_| |__|__    -+-  /  |
>>Tel: 886.2.28267170(Lab.)           /  |  \       |__|__    -+- /   /
>>Fax: 886.2.28210847                '  `|   `      |         ---'  _/
>>Email: wchu@bme.ym.edu.tw
>>
>>
>>
>>
>
>------------------------------
>
>Date: Tue, 13 Apr 1999 09:46:10 -0700
>From: Peter Lombrozo <peter@di.com>
>To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
>Subject: RE: Need photo-quality printer: dye-sub or ink-jet or ???
>Message-ID: <B1AA3C851F6DD011BEEB0040333A8B5480355F@exchange.di.com>
>Content-Type: text/plain
>
>Actually, that isn't true.  The difference is the technology used.  Dye-sub is
>continuous tone.  This means that every spot the printer puts down is capable of
>256 shades, no dithering takes place except to interpolate to the correct size.
>If you print one-to-one, a 1200 X 1200 pixel image on a 300 dpi dye-sub would
>print 4"x4" WITHOUT any loss of data resolution from the original data.  This
>defines photographic quality - film grains do the same thing.
>
>In contrast, any ink-jet or laser color printer needs to dither in order to get
>more colors and shades than are in the ink toners/cartridge.  These printers can
>only put a spot down or not (although some expensive printers are able to adjust
>the spot size) and need to use "supercells" of about 16 x 16 spots to get 256
>shades of a color which reduces the spatial resolution.  The 6 process inks
>really help because they reduce the supercell to 4 X 4.  Notice that even then,
>you need the full 1200 dpi of an ink-jet to get the same color AND spatial
>resolution as a dye-sub.  Also, special techniques are used to prevent the
>dither pattern from showing as repeated structure on an image.  That being said,
>the new process-ink jets are really awesome for the price, but they don't have
>any better image resolution than dye-subs, even at 4X the dpi.
>
>Peter Lombrozo
>
><<             NANOSCOPES                >> Peter Lombrozo
><<   See More & More of Less & Less      >> peter@di.com ><< until you see Everything of Nothing!  >> Software Engineer
>
>
>
>> -----Original Message-----
>> From:	Bill Miller [SMTP:microbill@mohawk.net]
>> Sent:	Tuesday, April 13, 1999 4:44 AM
>> To:	wchu@bme.ym.edu.tw; nih-image@io.ece.drexel.edu
>> Subject:	Re: Need photo-quality printer: dye-sub or ink-jet or ???
>> >> I almost hate to get into this - but here goes - Dye sub printers make
>> PRETTY pictures. If what you need is pretty pictures they are great - and
>> the Fuji (a slightly different technology ) is superb. But the best of them
>> print at 300 to 400dpi. If you have scientific images from light or
>> electron microscopy (particularly electron microscopy) you may well have
>> information that will be lost at this relatively low resolution.  Yes, if
>> you print the pictures big enough that is not a problem - but who prints
>> everything at 8.5x11?  I know it's hard to believe that a printer that only
>> costs 5% -10% of the price of a dye sub can be any good but the new
>> generation of inkjets are great. They have a better color gamut (printing
>> from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
>> dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub. >
>------------------------------
>
>Date: Tue, 13 Apr 1999 10:25:33 -0700
>From: Joel Brody <jbrody@itsa.ucsf.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Need photo-quality printer: dye-sub or ink-jet or ???
>Message-Id: <v03130304b3392c566747@[128.218.158.175]>
>Content-Type: text/plain; charset="us-ascii"
>
>Bill,
>
>You are confusing what is meant by resolution.  I really don't know enough
>printer 'theory' to do an adequate explanation, but a Fujix Pictrographic
>at 3-400 dpi is much better resolution than an Epson ink-jet.  Essentially
>a Fujix 'dot' is the final color.  An Epson 'dot' is one of the colors of
>the 6-7 inks that have to be put together into a psuedo-pixel.  I believe
>the 'final' resolution of an Epson is more in the 150-200dpi range.  Fujix
>prints are indistinguishable from photographs and do not fade particularly
>quickly.  Epson prints are great 'for the price', but they are not in the
>same league as the Fujix.
>
>Joel
>
>
>>I almost hate to get into this - but here goes - Dye sub printers make
>>PRETTY pictures. If what you need is pretty pictures they are great - and
>>the Fuji (a slightly different technology ) is superb. But the best of them
>>print at 300 to 400dpi. If you have scientific images from light or
>>electron microscopy (particularly electron microscopy) you may well have
>>information that will be lost at this relatively low resolution.  Yes, if
>>you print the pictures big enough that is not a problem - but who prints
>>everything at 8.5x11?  I know it's hard to believe that a printer that only
>>costs 5% -10% of the price of a dye sub can be any good but the new
>>generation of inkjets are great. They have a better color gamut (printing
>>from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
>>dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub.  As
>>always the best advice is to get the same image printed on both and then
>>choose - print what you will normally be printing and at the size you would
>>normally use (you do want to compare apples to  apples don't you?) I know
>>buying an expensive dye sub makes you feel good and increases your prestige
>>among your peers ("OOOOOO, have you seen his new mega dollar
>>printer!!!???") but really, couldn't you use the money better for something
>>else?
>>
>>Good Luck  -
>>
>>Bill Miller
>
>*****************************************************************
>***********
>
>CunhaLab, UCSF                          |
>Mount Zion Cancer Center, Box 0540      |
>2340 Sutter Street, Room S241	        | Tel:     (415) 476-6746
>San Francisco, CA 94115    	        | Fax:     (415) 502-2270
>
>------------------------------
>
>Date: Tue, 13 Apr 1999 11:20:38 -0700
>From: Paul Lampe <plampe@fred.fhcrc.org>
>To: nih-image@io.ece.drexel.edu
>Subject: Stacks to movies
>Message-Id: <l03010d04b338d91c5f45@[140.107.54.131]>
>Content-Type: text/plain; charset="us-ascii"
>
>We create stacks on our microscope via Metamorph (Universal Imaging) and
>would like to import the stacks to NIH Image to make movies.  If we use the
>import command with TIFF checked we get the first image and it looks fine
>but none of the subsequent images are imported.  Anyone have an easy fix?
>
>------------------------------
>
>Date: Tue, 13 Apr 1999 22:16:22 +0200
>From: "Philippe GUILLAUD" <guillaud@ccr.jussieu.fr>
>To: <nih-image@io.ece.drexel.edu>
>Subject: Re: Stacks to movies
>Message-ID: <001a01be85ea$806cad80$9f519d86@guillaud>
>Content-Type: text/plain;
>	charset="iso-8859-1"
>Content-Transfer-Encoding: 8bit
>
>In fact NIH Image can't read directly Metamorph stacks (a sort of multitiff
>file format) you must import images one by one (with the open all option
>checked). You can also make movies directly in metamorph (AVI format) and
>import them on Macintosh to view them in QuickTime.
>
>Philippe GUILLAUD
>Service Imagerie
>Universit Pierre et Marie Curie - Paris 6
>France
>
>----- Message d'origine -----
>De : Paul Lampe <plampe@fred.fhcrc.org>
> : <nih-image@io.ece.drexel.edu>
>Envoy : mardi 13 avril 1999 20:20
>Objet : Stacks to movies
>
>
>> We create stacks on our microscope via Metamorph (Universal Imaging) and
>> would like to import the stacks to NIH Image to make movies.  If we use
>the
>> import command with TIFF checked we get the first image and it looks fine
>> but none of the subsequent images are imported.  Anyone have an easy fix?
>>
>>
>
>--------------------------------
>End of nih-image-d Digest V99 Issue #88
>***************************************
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------------------------------

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nih-image-d Digest				Volume 99 : Issue 89

Today's Topics:
  RE: Need photo-quality printer: dye-  [ "Harvey J. Karten" <hjkarten@ucsd.e ]
  RE: nih-image-d Digest V99 #88        [ Jonathan WISCO <jjwisco@cajal-1.bu. ]

------------------------------

Date: Tue, 13 Apr 1999 17:52:22 -0700
From: "Harvey J. Karten" <hjkarten@ucsd.edu>
To: nih-image@io.ece.drexel.edu
Subject: RE: Need photo-quality printer: dye-sub or ink-jet or ???
Message-ID: <3713E6C6.240164AF@ucsd.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Just another voice in support of the Fuji. The ink-jets use pseudo-pixels, and give
resolution in the range of less than 150-200 dpi or maybe less. The advertizing
makes you think you're getting a genuine 1400 dpi. That is hokum. They also don't
have the outstanding black contrast of the Fuji. The Kodak 8250 series is close to
the Fuji, but still not as good.

If you want to see the difference between ink-jet and dye-sub technology at a more
affordable price range, get an Olympus P-300 dye-sub. The prints are only about 3.5
x 4.5 inches, but they are vastly better than any images obtainable with an ink-jet.
I think the P-300 has recently been replaced by the P-330. The printer is only about
$350. Each print is about $0.35 to $0.50. Color is outstanding. Resolution is about
305 dpi. Kodak makes a small dye-sub with the same small size paper, but it only
provides 149 dpi. Price per print is slightly less than the Olympus. Prints are not
as crisp. One very big problem with the Olympus is that they refuse to provide a
driver for Windows NT. But they do have drivers for Win 95, Win 98 and MacOS.

Harvey Karten

> Actually, that isn't true.  The difference is the technology used.  Dye-sub is
> continuous tone.  This means that every spot the printer puts down is capable of
> 256 shades, no dithering takes place except to interpolate to the correct size.
> If you print one-to-one, a 1200 X 1200 pixel image on a 300 dpi dye-sub would
> print 4"x4" WITHOUT any loss of data resolution from the original data.  This
> defines photographic quality - film grains do the same thing.
>
> In contrast, any ink-jet or laser color printer needs to dither in order to get
> more colors and shades than are in the ink toners/cartridge.  These printers can
> only put a spot down or not (although some expensive printers are able to adjust
> the spot size) and need to use "supercells" of about 16 x 16 spots to get 256
> shades of a color which reduces the spatial resolution.  The 6 process inks
> really help because they reduce the supercell to 4 X 4.  Notice that even then,
> you need the full 1200 dpi of an ink-jet to get the same color AND spatial
> resolution as a dye-sub.  Also, special techniques are used to prevent the
> dither pattern from showing as repeated structure on an image.  That being said,
> the new process-ink jets are really awesome for the price, but they don't have
> any better image resolution than dye-subs, even at 4X the dpi.
>
> Peter Lombrozo
>
> <<             NANOSCOPES                >> Peter Lombrozo
> <<   See More & More of Less & Less      >> peter@di.com
> << until you see Everything of Nothing!  >> Software Engineer
>
> > -----Original Message-----
> > From: Bill Miller [SMTP:microbill@mohawk.net]
> > Sent: Tuesday, April 13, 1999 4:44 AM
> > To:   wchu@bme.ym.edu.tw; nih-image@io.ece.drexel.edu
> > Subject:      Re: Need photo-quality printer: dye-sub or ink-jet or ???
> >
> > I almost hate to get into this - but here goes - Dye sub printers make
> > PRETTY pictures. If what you need is pretty pictures they are great - and
> > the Fuji (a slightly different technology ) is superb. But the best of them
> > print at 300 to 400dpi. If you have scientific images from light or
> > electron microscopy (particularly electron microscopy) you may well have
> > information that will be lost at this relatively low resolution.  Yes, if
> > you print the pictures big enough that is not a problem - but who prints
> > everything at 8.5x11?  I know it's hard to believe that a printer that only
> > costs 5% -10% of the price of a dye sub can be any good but the new
> > generation of inkjets are great. They have a better color gamut (printing
> > from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
> > dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub.
>
>   ------------------------------------------------------------------------
>
> Subject: Re: Need photo-quality printer: dye-sub or ink-jet or ???
> Date: Tue, 13 Apr 1999 10:25:33 -0700
> From: Joel Brody <jbrody@itsa.ucsf.edu>
> To: nih-image@io.ece.drexel.edu
>
> Bill,
>
> You are confusing what is meant by resolution.  I really don't know enough
> printer 'theory' to do an adequate explanation, but a Fujix Pictrographic
> at 3-400 dpi is much better resolution than an Epson ink-jet.  Essentially
> a Fujix 'dot' is the final color.  An Epson 'dot' is one of the colors of
> the 6-7 inks that have to be put together into a psuedo-pixel.  I believe
> the 'final' resolution of an Epson is more in the 150-200dpi range.  Fujix
> prints are indistinguishable from photographs and do not fade particularly
> quickly.  Epson prints are great 'for the price', but they are not in the
> same league as the Fujix.
>
> Joel
>
> >I almost hate to get into this - but here goes - Dye sub printers make
> >PRETTY pictures. If what you need is pretty pictures they are great - and
> >the Fuji (a slightly different technology ) is superb. But the best of them
> >print at 300 to 400dpi. If you have scientific images from light or
> >electron microscopy (particularly electron microscopy) you may well have
> >information that will be lost at this relatively low resolution.  Yes, if
> >you print the pictures big enough that is not a problem - but who prints
> >everything at 8.5x11?  I know it's hard to believe that a printer that only
> >costs 5% -10% of the price of a dye sub can be any good but the new
> >generation of inkjets are great. They have a better color gamut (printing
> >from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
> >dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub.  As
> >always the best advice is to get the same image printed on both and then
> >choose - print what you will normally be printing and at the size you would
> >normally use (you do want to compare apples to  apples don't you?) I know
> >buying an expensive dye sub makes you feel good and increases your prestige
> >among your peers ("OOOOOO, have you seen his new mega dollar
> >printer!!!???") but really, couldn't you use the money better for something
> >else?
> >
> >Good Luck  -
> >
> >Bill Miller
>
> ****************************************************************************
>

------------------------------

Date: 14 Apr 99 11:58:39 -0400
From: Jonathan WISCO <jjwisco@cajal-1.bu.edu>
To: "nih-image" <nih-image@io.ece.drexel.edu>
Subject: RE: nih-image-d Digest V99 #88
Message-Id: <199904141556.LAA22538@bu.edu>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

         Reply to:   RE: nih-image-d Digest V99 #88
I look at MR Images with NIH Image, but lately NIH Image has had problems assigning greyscale values to pixels.  These pixels end up as different colors or black, when they should be a shade of grey.  Any ideas on how to remedy this?

Jonathan J. Wisco


nih-image-d-request wrote:
>------------------------------
>
>Content-Type: text/plain
>
>nih-image-d Digest				Volume 99 : Issue 88
>
>Today's Topics:
>  microarray analysis                   [ czl@ccms.ntu.edu.tw ]
>  Re:contrast correction (nih-image Di  [ GJOSS@rna.bio.mq.edu.au ]
>  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
>  Re: Need photo-quality printer: dye-  [ Bill Miller <microbill@mohawk.net> ]
>  RE: Need photo-quality printer: dye-  [ Peter Lombrozo <peter@di.com> ]
>  Re: Need photo-quality printer: dye-  [ Joel Brody <jbrody@itsa.ucsf.edu> ]
>  Stacks to movies                      [ Paul Lampe <plampe@fred.fhcrc.org> ]
>  Re: Stacks to movies                  [ "Philippe GUILLAUD" <guillaud@ccr.j ]
>
>------------------------------
>
>Date: Tue, 13 Apr 1999 12:56:51 +0800
>From: czl@ccms.ntu.edu.tw
>To: nih-image@io.ece.drexel.edu
>Subject: microarray analysis
>Message-Id: <v04003a03b3387d31af23@[140.112.133.81]>
>Content-Type: text/plain; charset="us-ascii"
>
>Does anyone using NIH image to do microarray analysis?  Are the intrinsic
>array variables enough to hold all the data? Any information would be
>appreciated.
>
>
>Cha Ze Lee, MD, Ph. D.
>National Taiwan University Hospital
>
>------------------------------
>
>Date:          Tue, 13 Apr 1999 15:19:03 +1000
>From: GJOSS@rna.bio.mq.edu.au
>To: lukas.bickel@zmk.unibe.ch, nih-image@io.ece.drexel.edu
>Subject:       Re:contrast correction (nih-image Digest V99 #86
>Message-ID: <1914D6467A6@rna.bio.mq.edu.au>
>
>>Date: Mon, 12 Apr 1999 10:23:18 +0200
>>From: Lucas Bickel <lukas.bickel@zmk.unibe.ch>
>>Subject: Re: nih-image-d Digest V99 #86
>>To: nih-image@io.ece.drexel.edu
>>
>>Can anybody help me contrast conrrect two images? I tried it with writing
>>to the LUT of one of the images, but it doesn't seem to work that way, now
>>i'm searching a way to change the Histogram.
>>
>>I hope someone cam help
>>
>Writing to the Lut of one or both images to procuce some "normalised" >contrast sounds correct to me. >It is also the way to change the Histogram; >ie change the LUT 'appropriately' and then ApplyLUT.
>
>What is it that "doesn't seem to work that way"?
>
>eg have you looked at, say: >macro 'Equalize';
>in >LUT Macros
>supplied with NIH-Image?
>Greg Joss,
>School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
>Macquarie University,          Email gjoss@rna.bio.mq.edu.au
>North Ryde, (Sydney,) NSW 2109, Australia
>
>------------------------------
>
>Date: Tue, 13 Apr 1999 05:05:01 -0400 (EDT)
>From: nih-image-owner@io.ece.drexel.edu
>To: nih-image@io.ece.drexel.edu
>Subject: ADMIN: list commands
>Message-Id: <199904130905.FAA23474@io.ece.drexel.edu>
>
>                   NIH-image Mailing List Help >                   ---------------------------
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>--
>
>------------------------------
>
>Date: Tue, 13 Apr 1999 07:44:27 -0400
>From: Bill Miller <microbill@mohawk.net>
>To: wchu@bme.ym.edu.tw, nih-image@io.ece.drexel.edu
>Subject: Re: Need photo-quality printer: dye-sub or ink-jet or ???
>Message-Id: <3.0.5.32.19990413074427.007fa900@mohawk.net>
>Content-Type: text/plain; charset="us-ascii"
>
>I almost hate to get into this - but here goes - Dye sub printers make
>PRETTY pictures. If what you need is pretty pictures they are great - and
>the Fuji (a slightly different technology ) is superb. But the best of them
>print at 300 to 400dpi. If you have scientific images from light or
>electron microscopy (particularly electron microscopy) you may well have
>information that will be lost at this relatively low resolution.  Yes, if
>you print the pictures big enough that is not a problem - but who prints
>everything at 8.5x11?  I know it's hard to believe that a printer that only
>costs 5% -10% of the price of a dye sub can be any good but the new
>generation of inkjets are great. They have a better color gamut (printing
>from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
>dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub.  As
>always the best advice is to get the same image printed on both and then
>choose - print what you will normally be printing and at the size you would
>normally use (you do want to compare apples to  apples don't you?) I know
>buying an expensive dye sub makes you feel good and increases your prestige
>among your peers ("OOOOOO, have you seen his new mega dollar
>printer!!!???") but really, couldn't you use the money better for something
>else? >
>Good Luck  -
>
>Bill Miller
>
>At 10:08 AM 4/13/99 +0000, Woeichyn Chu wrote:
>>Couple of months ago I did some comparisons on high quality dye sub
>printers vs.
>>Fuji Pictrography model PG-3000. Conclusion: if budget allows, I would go
>for the
>>latter one (price is ~40% higher though).
>>
>>woeichyn
>>
>>Ruy Jaeger wrote:
>>
>>> Fuji Pictrography is definitely the best choice
>>>
>>> Ruy
>>>
>>> Anthony Ting wrote:
>>> >
>>> > Hi there,
>>> >
>>> >         I'd like to get some advice on the purchase of a photo-quality
>printer.
>>> > The input is primarily confocal images and I'd like to have the output
>look
>>> > like my slides.  Currently, we're using a Tektronix Phaser IID, but
>it's on
>>> > it's last legs and I wanted to get some opinion on what the latest
>>> > technology is out there.
>>> >
>>> > Thanks,
>>> >
>>> > Tony
>>> >
>>> > -------------------------------------------------------------------
>>> > Anthony Ting, PhD                                phone: 65-874-7846
>>> > Institute of Molecular and Cell Biology          fax: 65-779-1117
>>> > 30 Medical Drive
>>> > Singapore   117609
>>
>>
>>--
>>Sincerely yours,
>>
>>Woeichyn Chu, Ph.D.
>>Associate Professor
>>Institute of Biomedical Engineering
>>National Yang Ming University       '__|__     _  /__\__   -|=|-   /
>>Shih-Pai, Taipei, Taiwan 112       /___|___   | |'|__|__    |+| --'-.
>>Tel: 886.2.28267025(Office)          / | \    |_| |__|__    -+-  /  |
>>Tel: 886.2.28267170(Lab.)           /  |  \       |__|__    -+- /   /
>>Fax: 886.2.28210847                '  `|   `      |         ---'  _/
>>Email: wchu@bme.ym.edu.tw
>>
>>
>>
>>
>
>------------------------------
>
>Date: Tue, 13 Apr 1999 09:46:10 -0700
>From: Peter Lombrozo <peter@di.com>
>To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
>Subject: RE: Need photo-quality printer: dye-sub or ink-jet or ???
>Message-ID: <B1AA3C851F6DD011BEEB0040333A8B5480355F@exchange.di.com>
>Content-Type: text/plain
>
>Actually, that isn't true.  The difference is the technology used.  Dye-sub is
>continuous tone.  This means that every spot the printer puts down is capable of
>256 shades, no dithering takes place except to interpolate to the correct size.
>If you print one-to-one, a 1200 X 1200 pixel image on a 300 dpi dye-sub would
>print 4"x4" WITHOUT any loss of data resolution from the original data.  This
>defines photographic quality - film grains do the same thing.
>
>In contrast, any ink-jet or laser color printer needs to dither in order to get
>more colors and shades than are in the ink toners/cartridge.  These printers can
>only put a spot down or not (although some expensive printers are able to adjust
>the spot size) and need to use "supercells" of about 16 x 16 spots to get 256
>shades of a color which reduces the spatial resolution.  The 6 process inks
>really help because they reduce the supercell to 4 X 4.  Notice that even then,
>you need the full 1200 dpi of an ink-jet to get the same color AND spatial
>resolution as a dye-sub.  Also, special techniques are used to prevent the
>dither pattern from showing as repeated structure on an image.  That being said,
>the new process-ink jets are really awesome for the price, but they don't have
>any better image resolution than dye-subs, even at 4X the dpi.
>
>Peter Lombrozo
>
><<             NANOSCOPES                >> Peter Lombrozo
><<   See More & More of Less & Less      >> peter@di.com ><< until you see Everything of Nothing!  >> Software Engineer
>
>
>
>> -----Original Message-----
>> From:	Bill Miller [SMTP:microbill@mohawk.net]
>> Sent:	Tuesday, April 13, 1999 4:44 AM
>> To:	wchu@bme.ym.edu.tw; nih-image@io.ece.drexel.edu
>> Subject:	Re: Need photo-quality printer: dye-sub or ink-jet or ???
>> >> I almost hate to get into this - but here goes - Dye sub printers make
>> PRETTY pictures. If what you need is pretty pictures they are great - and
>> the Fuji (a slightly different technology ) is superb. But the best of them
>> print at 300 to 400dpi. If you have scientific images from light or
>> electron microscopy (particularly electron microscopy) you may well have
>> information that will be lost at this relatively low resolution.  Yes, if
>> you print the pictures big enough that is not a problem - but who prints
>> everything at 8.5x11?  I know it's hard to believe that a printer that only
>> costs 5% -10% of the price of a dye sub can be any good but the new
>> generation of inkjets are great. They have a better color gamut (printing
>> from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
>> dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub. >
>------------------------------
>
>Date: Tue, 13 Apr 1999 10:25:33 -0700
>From: Joel Brody <jbrody@itsa.ucsf.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Need photo-quality printer: dye-sub or ink-jet or ???
>Message-Id: <v03130304b3392c566747@[128.218.158.175]>
>Content-Type: text/plain; charset="us-ascii"
>
>Bill,
>
>You are confusing what is meant by resolution.  I really don't know enough
>printer 'theory' to do an adequate explanation, but a Fujix Pictrographic
>at 3-400 dpi is much better resolution than an Epson ink-jet.  Essentially
>a Fujix 'dot' is the final color.  An Epson 'dot' is one of the colors of
>the 6-7 inks that have to be put together into a psuedo-pixel.  I believe
>the 'final' resolution of an Epson is more in the 150-200dpi range.  Fujix
>prints are indistinguishable from photographs and do not fade particularly
>quickly.  Epson prints are great 'for the price', but they are not in the
>same league as the Fujix.
>
>Joel
>
>
>>I almost hate to get into this - but here goes - Dye sub printers make
>>PRETTY pictures. If what you need is pretty pictures they are great - and
>>the Fuji (a slightly different technology ) is superb. But the best of them
>>print at 300 to 400dpi. If you have scientific images from light or
>>electron microscopy (particularly electron microscopy) you may well have
>>information that will be lost at this relatively low resolution.  Yes, if
>>you print the pictures big enough that is not a problem - but who prints
>>everything at 8.5x11?  I know it's hard to believe that a printer that only
>>costs 5% -10% of the price of a dye sub can be any good but the new
>>generation of inkjets are great. They have a better color gamut (printing
>>from 6 or 7 different inks) as well as MUCH higher resolution (1200 to 1400
>>dpi) - your 4x5 print will have more detail than an 8.5x11 dye sub.  As
>>always the best advice is to get the same image printed on both and then
>>choose - print what you will normally be printing and at the size you would
>>normally use (you do want to compare apples to  apples don't you?) I know
>>buying an expensive dye sub makes you feel good and increases your prestige
>>among your peers ("OOOOOO, have you seen his new mega dollar
>>printer!!!???") but really, couldn't you use the money better for something
>>else?
>>
>>Good Luck  -
>>
>>Bill Miller
>
>*****************************************************************
>***********
>
>CunhaLab, UCSF                          |
>Mount Zion Cancer Center, Box 0540      |
>2340 Sutter Street, Room S241	        | Tel:     (415) 476-6746
>San Francisco, CA 94115    	        | Fax:     (415) 502-2270
>
>------------------------------
>
>Date: Tue, 13 Apr 1999 11:20:38 -0700
>From: Paul Lampe <plampe@fred.fhcrc.org>
>To: nih-image@io.ece.drexel.edu
>Subject: Stacks to movies
>Message-Id: <l03010d04b338d91c5f45@[140.107.54.131]>
>Content-Type: text/plain; charset="us-ascii"
>
>We create stacks on our microscope via Metamorph (Universal Imaging) and
>would like to import the stacks to NIH Image to make movies.  If we use the
>import command with TIFF checked we get the first image and it looks fine
>but none of the subsequent images are imported.  Anyone have an easy fix?
>
>------------------------------
>
>Date: Tue, 13 Apr 1999 22:16:22 +0200
>From: "Philippe GUILLAUD" <guillaud@ccr.jussieu.fr>
>To: <nih-image@io.ece.drexel.edu>
>Subject: Re: Stacks to movies
>Message-ID: <001a01be85ea$806cad80$9f519d86@guillaud>
>Content-Type: text/plain;
>	charset="iso-8859-1"
>Content-Transfer-Encoding: 8bit
>
>In fact NIH Image can't read directly Metamorph stacks (a sort of multitiff
>file format) you must import images one by one (with the open all option
>checked). You can also make movies directly in metamorph (AVI format) and
>import them on Macintosh to view them in QuickTime.
>
>Philippe GUILLAUD
>Service Imagerie
>Universit Pierre et Marie Curie - Paris 6
>France
>
>----- Message d'origine -----
>De : Paul Lampe <plampe@fred.fhcrc.org>
> : <nih-image@io.ece.drexel.edu>
>Envoy : mardi 13 avril 1999 20:20
>Objet : Stacks to movies
>
>
>> We create stacks on our microscope via Metamorph (Universal Imaging) and
>> would like to import the stacks to NIH Image to make movies.  If we use
>the
>> import command with TIFF checked we get the first image and it looks fine
>> but none of the subsequent images are imported.  Anyone have an easy fix?
>>
>>
>
>--------------------------------
>End of nih-image-d Digest V99 Issue #88
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nih-image-d Digest				Volume 99 : Issue 90

Today's Topics:
  subscribe                             [ "Robert M. Fecke" <fecke@mse.eng.oh ]
  Importing GE Signa MRI's using NIH I  [ Jonathan WISCO <jjwisco@cajal-1.bu. ]

------------------------------

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Date: 15 Apr 99 11:01:55 -0400
From: Jonathan WISCO <jjwisco@cajal-1.bu.edu>
To: NIH Image <nih-image@io.ece.drexel.edu>
Subject: Importing GE Signa MRI's using NIH Image 1.61
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I am trying to import GE Signa MRI's into NIH Image v.1.61.  When I do, many of the pixels are assigned a color instead of a greyscale shade.  Any ideas why this might be?  Is there a way to remedy this?  I started having these problems after updating my Mac G3 operating system to system 8.5.  Could it be an NIH Image version not compatible with OS 8.5?

Jonathan J. Wisco
Anatomy and Neurobiology
Boston University School of Medicine

--------------------------------
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From nih-image-request@io.ece.drexel.edu Thu Apr 15 11:16 EDT 1999
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I am trying to import GE Signa MRI's into NIH Image v.1.61.  When I do, many of the pixels are assigned a color instead of a greyscale shade.  Any ideas why this might be?  Is there a way to remedy this?  I started having these problems after updating my Mac G3 operating system to system 8.5.  Could it be an NIH Image version not compatible with OS 8.5?

Jonathan J. Wisco
Anatomy and Neurobiology
Boston University School of Medicine




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From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
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Jonathan,

I suspect you have several reserved LUT colors.

Options/LUT Options/
Make reserved entries to 0

Cengizhan


--------------------------------------------
Cengizhan Ozturk
cozturk@mri.jhu.edu
http://www.mri.jhu.edu/~cozturk

Medical Imaging Laboratory
Johns Hopkins University
Phone: 	(410)614 5292 / (410)502 6905
Fax: 	(410)-502 6915
--------------------------------------------

On 15 Apr 1999, Jonathan WISCO wrote:

> I am trying to import GE Signa MRI's into NIH Image v.1.61.  When I do, many of the pixels are assigned a color instead of a greyscale shade.  Any ideas why this might be?  Is there a way to remedy this?  I started having these problems after updating my Mac G3 operating system to system 8.5.  Could it be an NIH Image version not compatible with OS 8.5?
> 
> Jonathan J. Wisco
> Anatomy and Neurobiology
> Boston University School of Medicine
> 
> 
> 
> 


From nih-image-request@io.ece.drexel.edu Thu Apr 15 17:03 EDT 1999
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From: Daniel Twelker <twelker@uclink4.berkeley.edu>
Subject: automated measures
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Warning:  NIH Image Novice here.  I read in the NIH Image documentation
about the possibility of automated or semi-automated measures, but I
haven't been able to figure out how to do them.  On a tiff image of the
human eye I would like to be able to automatically find the center of the
pupil, for instance.  I would like another procedure to find the edge of a
lesion and then to automatically calculate the distance between the center
of the pupil and the nearest portion of the edge.  Have there been macros
or spin-off programs already written and if so, which ones and how to I
access them?  If someone is willing to discuss these issues and a few more
questions, please e-mail me directly.  Thanks in advance.

Dan



From nih-image-request@io.ece.drexel.edu Thu Apr 15 18:45 EDT 1999
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Date: Thu, 15 Apr 1999 15:33:54 -0800
From: "Mark N. Rand" <mnr@saul.u.washington.edu>
Reply-To: mnr@u.washington.edu
Subject: A new tool for analyzing ion-sensitive fluorescence data.
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Dear Imagers, 

This announcement is of potential interest to biologists doing ion-sensitive
fluorescence measurements in living cells. The analysis of such experiments
using Excel or even more expensive, dedicated software often leaves much to be
desired. A few months ago, with considerable help from Howard Rodstein at
WaveMetrics, I developed a set of Igor procedures to measure and analyze
ratiometric imaging experiments. The procedures also work with data from
single-wavelength dyes. They are currently available from the WaveMetrics web
site (http://www.wavemetrics.com/TechZone/User_ThirdParty/ratioImage.html) in
both Mac and Windows versions. The Igor Demo program may be used to give them a
test-drive.

Standard disclaimers: I have no financial interest in WaveMetrics, etc. Use at
your own risk, etc. The procedures are free and you can customize them for your
own purposes. If you develop useful extensions of the program I'd greatly
appreciate hearing about it.

Sincerely,


Mark N. Rand, Ph.D.
Assistant Research Professor
U.W. Dept. Neurology, School of Medicine
1959 NE Pacific St., Box 356465
Seattle WA 98195-6465

fax: (206) 616-8272
vox: (206) 616-5153

<_){{{{><    <_){{{{><    <_){{{{><    <_){{{{><    <_){{{{><    <_){{{{>< 


From nih-image-request@io.ece.drexel.edu Thu Apr 15 19:11 EDT 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
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Date:          Fri, 16 Apr 1999 9:02:50 +1000
Subject:       Re: automated measures
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>Date: Thu, 15 Apr 1999 13:51:13 -0700
>To: nih-image@io.ece.drexel.edu
>From: Daniel Twelker <twelker@uclink4.berkeley.edu>
>Subject: automated measures
>
>Warning:  NIH Image Novice here.  I read in the NIH Image documentation
>about the possibility of automated or semi-automated measures, but I
>haven't been able to figure out how to do them.  On a tiff image of the
>human eye I would like to be able to automatically find the center of the
>pupil, for instance.  I would like another procedure to find the edge of a
>lesion and then to automatically calculate the distance between the center
>of the pupil and the nearest portion of the edge.  Have there been macros
>or spin-off programs already written and if so, which ones and how to I
>access them?  If someone is willing to discuss these issues and a few more
>questions, please e-mail me directly.  Thanks in advance.
>
>Dan
>
There are Macros (see appendix in manual) in a folder so named that come 
with the NIH-Image package available at http://rsb.info.nih.gov/nih-image/
There is also a host of user-contributed macros on that site that will 
serve as examples for macro programming.

I would expect 
autothreshold;analyzeParticles; 
might be sufficient to segment the pupil from an image of the eye on the 
basis of 'darkness' and 
will return the centroid in rX[],rY[] arrays. 
The circumference/area ratio or major/minor axis available in 
rLength[],rArea[],rMajor[],rMinor[] 
will allow confirmation of pupil on the basis of its size and circularity.

The lesion may be more problematic but given segmentation, Image allows 
definition of the boundary of ROIs Region-of-Interest. EDM (Euclidean 
Distance Map) in Binary(Process menu invoked by "binary('edm')" will allow 
easy determination of "the distance between the center of the pupil and the 
nearest portion of the edge."

Send an sample image as a tiff file attachment (preferably binhex encoded 
by emailer) to aid any further detailed discussion.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


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From: "Mark N. Rand" <mnr@saul.u.washington.edu>
Reply-To: mnr@u.washington.edu
Subject: A new tool for analyzing ion-sensitive fluorescence data.
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(Also sent to the Confocal and Igor groups; my apologies if I've created
redundant messages in your mailbox!)

Dear Imagers, 

This announcement is of potential interest to biologists doing ion-sensitive
fluorescence measurements in living cells. The analysis of such experiments
using Excel or even more expensive, dedicated software often leaves much to be
desired. A few months ago, with considerable help from Howard Rodstein at
WaveMetrics, I developed a set of Igor procedures to measure and analyze
ratiometric imaging experiments. The procedures also work with data from
single-wavelength dyes. They are currently available from the WaveMetrics web
site (http://www.wavemetrics.com/TechZone/User_ThirdParty/ratioImage.html) in
both Mac and Windows versions. The Igor Demo program may be used to give them a
test-drive.

Standard disclaimers: I have no financial interest in WaveMetrics, etc. Use at
your own risk, etc. The procedures are free and you can customize them for your
own purposes. If you develop useful extensions of the program I'd greatly
appreciate hearing about it.

Sincerely,


Mark N. Rand, Ph.D.
Assistant Research Professor
U.W. Dept. Neurology, School of Medicine
1959 NE Pacific St., Box 356465
Seattle WA 98195-6465

fax: (206) 616-8272
vox: (206) 616-5153

<*){{{{><    <*){{{{><    <*){{{{><    <*){{{{><    <*){{{{><    <*){{{{>< 


From nih-image-d-request@io.ece.drexel.edu Fri Apr 16 06:16 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 91

Today's Topics:
  Re: Importing GE Signa MRI's using N  [ Cengizhan Ozturk <cozturk@mri.jhu.e ]
  automated measures                    [ Daniel Twelker <twelker@uclink4.ber ]
  A new tool for analyzing ion-sensiti  [ "Mark N. Rand" <mnr@saul.u.washingt ]
  Re: automated measures                [ GJOSS@rna.bio.mq.edu.au ]
  A new tool for analyzing ion-sensiti  [ "Mark N. Rand" <mnr@saul.u.washingt ]

------------------------------

Date: Thu, 15 Apr 1999 12:21:18 -0400 (EDT)
From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
To: Jonathan WISCO <jjwisco@cajal-1.bu.edu>
cc: NIH Image <nih-image@io.ece.drexel.edu>
Subject: Re: Importing GE Signa MRI's using NIH Image 1.61
Message-ID: <Pine.SGI.3.91.990415121905.19740C-100000@henryv>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Jonathan,

I suspect you have several reserved LUT colors.

Options/LUT Options/
Make reserved entries to 0

Cengizhan


--------------------------------------------
Cengizhan Ozturk
cozturk@mri.jhu.edu
http://www.mri.jhu.edu/~cozturk

Medical Imaging Laboratory
Johns Hopkins University
Phone: 	(410)614 5292 / (410)502 6905
Fax: 	(410)-502 6915
--------------------------------------------

On 15 Apr 1999, Jonathan WISCO wrote:

> I am trying to import GE Signa MRI's into NIH Image v.1.61.  When I do, many of the pixels are assigned a color instead of a greyscale shade.  Any ideas why this might be?  Is there a way to remedy this?  I started having these problems after updating my Mac G3 operating system to system 8.5.  Could it be an NIH Image version not compatible with OS 8.5?
> 
> Jonathan J. Wisco
> Anatomy and Neurobiology
> Boston University School of Medicine
> 
> 
> 
> 

------------------------------

Date: Thu, 15 Apr 1999 13:51:13 -0700
From: Daniel Twelker <twelker@uclink4.berkeley.edu>
To: nih-image@io.ece.drexel.edu
Subject: automated measures
Message-Id: <v03020900b33bfce69d78@[128.32.232.125]>
Content-Type: text/plain; charset="us-ascii"

Warning:  NIH Image Novice here.  I read in the NIH Image documentation
about the possibility of automated or semi-automated measures, but I
haven't been able to figure out how to do them.  On a tiff image of the
human eye I would like to be able to automatically find the center of the
pupil, for instance.  I would like another procedure to find the edge of a
lesion and then to automatically calculate the distance between the center
of the pupil and the nearest portion of the edge.  Have there been macros
or spin-off programs already written and if so, which ones and how to I
access them?  If someone is willing to discuss these issues and a few more
questions, please e-mail me directly.  Thanks in advance.

Dan

------------------------------

Date: Thu, 15 Apr 1999 15:33:54 -0800
From: "Mark N. Rand" <mnr@saul.u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: A new tool for analyzing ion-sensitive fluorescence data.
Message-ID: <MailDrop1.2d7j-PPC.990415153354@[128.95.211.127]>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

Dear Imagers, 

This announcement is of potential interest to biologists doing ion-sensitive
fluorescence measurements in living cells. The analysis of such experiments
using Excel or even more expensive, dedicated software often leaves much to be
desired. A few months ago, with considerable help from Howard Rodstein at
WaveMetrics, I developed a set of Igor procedures to measure and analyze
ratiometric imaging experiments. The procedures also work with data from
single-wavelength dyes. They are currently available from the WaveMetrics web
site (http://www.wavemetrics.com/TechZone/User_ThirdParty/ratioImage.html) in
both Mac and Windows versions. The Igor Demo program may be used to give them a
test-drive.

Standard disclaimers: I have no financial interest in WaveMetrics, etc. Use at
your own risk, etc. The procedures are free and you can customize them for your
own purposes. If you develop useful extensions of the program I'd greatly
appreciate hearing about it.

Sincerely,


Mark N. Rand, Ph.D.
Assistant Research Professor
U.W. Dept. Neurology, School of Medicine
1959 NE Pacific St., Box 356465
Seattle WA 98195-6465

fax: (206) 616-8272
vox: (206) 616-5153

<_){{{{><    <_){{{{><    <_){{{{><    <_){{{{><    <_){{{{><    <_){{{{>< 

------------------------------

Date:          Fri, 16 Apr 1999 9:02:50 +1000
From: GJOSS@rna.bio.mq.edu.au
To: twelker@uclink4.berkeley.edu, nih-image@io.ece.drexel.edu
Subject:       Re: automated measures
Message-ID: <1D30D49349E@rna.bio.mq.edu.au>

>Date: Thu, 15 Apr 1999 13:51:13 -0700
>To: nih-image@io.ece.drexel.edu
>From: Daniel Twelker <twelker@uclink4.berkeley.edu>
>Subject: automated measures
>
>Warning:  NIH Image Novice here.  I read in the NIH Image documentation
>about the possibility of automated or semi-automated measures, but I
>haven't been able to figure out how to do them.  On a tiff image of the
>human eye I would like to be able to automatically find the center of the
>pupil, for instance.  I would like another procedure to find the edge of a
>lesion and then to automatically calculate the distance between the center
>of the pupil and the nearest portion of the edge.  Have there been macros
>or spin-off programs already written and if so, which ones and how to I
>access them?  If someone is willing to discuss these issues and a few more
>questions, please e-mail me directly.  Thanks in advance.
>
>Dan
>
There are Macros (see appendix in manual) in a folder so named that come 
with the NIH-Image package available at http://rsb.info.nih.gov/nih-image/
There is also a host of user-contributed macros on that site that will 
serve as examples for macro programming.

I would expect 
autothreshold;analyzeParticles; 
might be sufficient to segment the pupil from an image of the eye on the 
basis of 'darkness' and 
will return the centroid in rX[],rY[] arrays. 
The circumference/area ratio or major/minor axis available in 
rLength[],rArea[],rMajor[],rMinor[] 
will allow confirmation of pupil on the basis of its size and circularity.

The lesion may be more problematic but given segmentation, Image allows 
definition of the boundary of ROIs Region-of-Interest. EDM (Euclidean 
Distance Map) in Binary(Process menu invoked by "binary('edm')" will allow 
easy determination of "the distance between the center of the pupil and the 
nearest portion of the edge."

Send an sample image as a tiff file attachment (preferably binhex encoded 
by emailer) to aid any further detailed discussion.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Thu, 15 Apr 1999 16:29:27 -0800
From: "Mark N. Rand" <mnr@saul.u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: A new tool for analyzing ion-sensitive fluorescence data.
Message-ID: <MailDrop1.2d7j-PPC.990415162927@[128.95.211.127]>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

(Also sent to the Confocal and Igor groups; my apologies if I've created
redundant messages in your mailbox!)

Dear Imagers, 

This announcement is of potential interest to biologists doing ion-sensitive
fluorescence measurements in living cells. The analysis of such experiments
using Excel or even more expensive, dedicated software often leaves much to be
desired. A few months ago, with considerable help from Howard Rodstein at
WaveMetrics, I developed a set of Igor procedures to measure and analyze
ratiometric imaging experiments. The procedures also work with data from
single-wavelength dyes. They are currently available from the WaveMetrics web
site (http://www.wavemetrics.com/TechZone/User_ThirdParty/ratioImage.html) in
both Mac and Windows versions. The Igor Demo program may be used to give them a
test-drive.

Standard disclaimers: I have no financial interest in WaveMetrics, etc. Use at
your own risk, etc. The procedures are free and you can customize them for your
own purposes. If you develop useful extensions of the program I'd greatly
appreciate hearing about it.

Sincerely,


Mark N. Rand, Ph.D.
Assistant Research Professor
U.W. Dept. Neurology, School of Medicine
1959 NE Pacific St., Box 356465
Seattle WA 98195-6465

fax: (206) 616-8272
vox: (206) 616-5153

<*){{{{><    <*){{{{><    <*){{{{><    <*){{{{><    <*){{{{><    <*){{{{>< 

--------------------------------
End of nih-image-d Digest V99 Issue #91
***************************************

From nih-image-request@io.ece.drexel.edu Fri Apr 16 09:11 EDT 1999
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Date: Fri, 16 Apr 1999 13:57:39 +0100
From: Jeremy Brown <brownj@netmatters.co.uk>
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Does anyone have a good reference for NOT using DAB or streptavidin-biotin
amplification for densitometery based measurements.

Cheers,
Jeremy Brown


From nih-image-d-request@io.ece.drexel.edu Sat Apr 17 06:08 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 92

Today's Topics:
  Densitometery                         [ Jeremy Brown <brownj@netmatters.co. ]

------------------------------

Date: Fri, 16 Apr 1999 13:57:39 +0100
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Densitometery
Message-ID: <371733A3.8B3EA54B@netmatters.co.uk>
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Does anyone have a good reference for NOT using DAB or streptavidin-biotin
amplification for densitometery based measurements.

Cheers,
Jeremy Brown

--------------------------------
End of nih-image-d Digest V99 Issue #92
***************************************

From nih-image-request@io.ece.drexel.edu Mon Apr 19 13:32 EDT 1999
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Subject: Re: nih-image-d Digest V99 #91
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Dear Imagers,

We are currently working on a calcium imaging project that looks at the
uptake in
dorsal cells of the lamprey spinal cord. We have been successful measuring
the intensity of
the responses of multiple ROIs in a single frame and have looked at a
single ROI across
many frames. Ultimately, what we would like to do is a combination of the
two and measure
the responses of multiple ROIs across numerous frames in a movie. Has
anyone used NIH
image to do this before or have any ideas on how this may be done? We have
tried pulling
up various macros to adjust but have yet to be successful. Thank you in
advance for any
ideas or suggestions.

Sincerely,

Kari Scantlebury
Undergraduate Research
State Univ. of NY at Geneseo
KQS99@uno.cc.geneseo.edu


>------------------------------
>Date: Thu, 15 Apr 1999 15:33:54 -0800
>From: "Mark N. Rand" <mnr@saul.u.washington.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: A new tool for analyzing ion-sensitive fluorescence data.
>Message-ID: <MailDrop1.2d7j-PPC.990415153354@[128.95.211.127]>
>Content-Type: TEXT/PLAIN; CHARSET=US-ASCII
>
>Dear Imagers,
>
>This announcement is of potential interest to biologists doing ion-sensitive
>fluorescence measurements in living cells. The analysis of such experiments
>using Excel or even more expensive, dedicated software often leaves much to be
>desired. A few months ago, with considerable help from Howard Rodstein at
>WaveMetrics, I developed a set of Igor procedures to measure and analyze
>ratiometric imaging experiments. The procedures also work with data from
>single-wavelength dyes. They are currently available from the WaveMetrics web
>site (http://www.wavemetrics.com/TechZone/User_ThirdParty/ratioImage.html) in
>both Mac and Windows versions. The Igor Demo program may be used to give
>them a
>test-drive.
>
>Standard disclaimers: I have no financial interest in WaveMetrics, etc. Use at
>your own risk, etc. The procedures are free and you can customize them for
>your
>own purposes. If you develop useful extensions of the program I'd greatly
>appreciate hearing about it.
>
>Sincerely,
>
>
>Mark N. Rand, Ph.D.
>Assistant Research Professor
>U.W. Dept. Neurology, School of Medicine
>1959 NE Pacific St., Box 356465
>Seattle WA 98195-6465
>
>fax: (206) 616-8272
>vox: (206) 616-5153
>
>



From nih-image-request@io.ece.drexel.edu Mon Apr 19 16:44 EDT 1999
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Date: Mon, 19 Apr 1999 13:33:43 -0700 (PDT)
From: steve spencer <stephen_spencer@yahoo.com>
Subject: Re: automated measures
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Hi, I am using a histogram method for analysis of
various brain structures and up till not have been
using the paintbrush to outline them. I would like to
switch to using the pencil but when I set a threshold
the 1 pixel line width of the pecil does not keep
diagonal pixels from being measured. Is there a way to
foce NIH image to consider diaginal lines as closed
rather then letting any touching pixel become
activated?
Thanks =)
steve spencer
western Psyche
_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-request@io.ece.drexel.edu Mon Apr 19 19:17 EDT 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: stephen_spencer@yahoo.com, nih-image@io.ece.drexel.edu
Date:          Tue, 20 Apr 1999 9:12:47 +1000
Subject:       Re: automated measures
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>Date: Mon, 19 Apr 1999 13:33:43 -0700 (PDT)
>From: steve spencer <stephen_spencer@yahoo.com>
>Subject: Re: automated measures
>To: nih-image@io.ece.drexel.edu
>
>Hi, I am using a histogram method for analysis of
>various brain structures and up till not have been
>using the paintbrush to outline them. I would like to
>switch to using the pencil but when I set a threshold
>the 1 pixel line width of the pecil does not keep
>diagonal pixels from being measured. Is there a way to
>foce NIH image to consider diaginal lines as closed
>rather then letting any touching pixel become
>activated?
>Thanks =)
>steve spencer
>western Psyche

I suggest that you are using the wrong tools for outlining.
Use one/more of the ROI selection tools.
You have available
straight, segmented and freehand line tools
polygon, oval and rectangular area selection tools

control/option keys which allow modification of 
existing selections by add/subtract.

With all, when you have selection, you can simply measure or
if you prefer, drawboundary 
(with linewidth set to 2 to avoid problem with diagonal pixels
on later selections)

In practice, the polygon is the most frexible as it allows 
point by point extension and then area review/correction by
control/option addition/subtraction.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Mon Apr 19 19:39 EDT 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: McPherso@uno.cc.geneseo.edu, nih-image@io.ece.drexel.edu
Date:          Tue, 20 Apr 1999 9:35:04 +1000
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>Date: Mon, 19 Apr 1999 12:14:26 -0400
>From: Duane McPherson <McPherso@uno.cc.geneseo.edu>
>
>We are currently working on a calcium imaging project that looks at the
>uptake in
>dorsal cells of the lamprey spinal cord. We have been successful measuring
>the intensity of
>the responses of multiple ROIs in a single frame and have looked at a
>single ROI across
>many frames. Ultimately, what we would like to do is a combination of the
>two and measure
>the responses of multiple ROIs across numerous frames in a movie. Has
>anyone used NIH
>image to do this before or have any ideas on how this may be done? We have
>tried pulling
>up various macros to adjust but have yet to be successful. Thank you in
>advance for any
>ideas or suggestions.
>
>Sincerely,
>
>Kari Scantlebury
>Undergraduate Research
>State Univ. of NY at Geneseo
>KQS99@uno.cc.geneseo.edu
>
You will get the most elegant solution by using Object-Image, an extention 
of NIH-Image by Norbert Vischer available via 
http://simon.bio.uva.nl/object-image.html. 
This will allow recording of ROIs as objects and also supports useful 3D 
displays/analysis.

Within NIH-Image as supplied, you can transfer ROI's accross images using 
restoreRoi; {Restore Selection(Analyze}  
This is a little tricky to use as you need to 
"selectPic(fromId);selectPic(toId);restoreRoi;"    successively, but works 
excellently.
You can store multiple ROIs by transfer to separate images or save/open 
them as 'outline' files but I tend to use a binary or color map image of 
ROIs and reinstate them successively using autoOutline(x,y); 
This allows you to define ROI set then process movie for each ROI or else 
process each frame for each ROI in turn, whatever you choose.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-d-request@io.ece.drexel.edu Tue Apr 20 06:11 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #93
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 93

Today's Topics:
  Re: nih-image-d Digest V99 #91        [ Duane McPherson <McPherso@uno.cc.ge ]
  Re: automated measures                [ steve spencer <stephen_spencer@yaho ]
  Re: automated measures                [ GJOSS@rna.bio.mq.edu.au ]
  Re: multiple ROIs (was nih-image-d D  [ GJOSS@rna.bio.mq.edu.au ]

------------------------------

Date: Mon, 19 Apr 1999 12:14:26 -0400
From: Duane McPherson <McPherso@uno.cc.geneseo.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #91
Message-id: <l03130300b340ff314452@[137.238.67.133]>
Content-type: text/plain; charset="us-ascii"

Dear Imagers,

We are currently working on a calcium imaging project that looks at the
uptake in
dorsal cells of the lamprey spinal cord. We have been successful measuring
the intensity of
the responses of multiple ROIs in a single frame and have looked at a
single ROI across
many frames. Ultimately, what we would like to do is a combination of the
two and measure
the responses of multiple ROIs across numerous frames in a movie. Has
anyone used NIH
image to do this before or have any ideas on how this may be done? We have
tried pulling
up various macros to adjust but have yet to be successful. Thank you in
advance for any
ideas or suggestions.

Sincerely,

Kari Scantlebury
Undergraduate Research
State Univ. of NY at Geneseo
KQS99@uno.cc.geneseo.edu


>------------------------------
>Date: Thu, 15 Apr 1999 15:33:54 -0800
>From: "Mark N. Rand" <mnr@saul.u.washington.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: A new tool for analyzing ion-sensitive fluorescence data.
>Message-ID: <MailDrop1.2d7j-PPC.990415153354@[128.95.211.127]>
>Content-Type: TEXT/PLAIN; CHARSET=US-ASCII
>
>Dear Imagers,
>
>This announcement is of potential interest to biologists doing ion-sensitive
>fluorescence measurements in living cells. The analysis of such experiments
>using Excel or even more expensive, dedicated software often leaves much to be
>desired. A few months ago, with considerable help from Howard Rodstein at
>WaveMetrics, I developed a set of Igor procedures to measure and analyze
>ratiometric imaging experiments. The procedures also work with data from
>single-wavelength dyes. They are currently available from the WaveMetrics web
>site (http://www.wavemetrics.com/TechZone/User_ThirdParty/ratioImage.html) in
>both Mac and Windows versions. The Igor Demo program may be used to give
>them a
>test-drive.
>
>Standard disclaimers: I have no financial interest in WaveMetrics, etc. Use at
>your own risk, etc. The procedures are free and you can customize them for
>your
>own purposes. If you develop useful extensions of the program I'd greatly
>appreciate hearing about it.
>
>Sincerely,
>
>
>Mark N. Rand, Ph.D.
>Assistant Research Professor
>U.W. Dept. Neurology, School of Medicine
>1959 NE Pacific St., Box 356465
>Seattle WA 98195-6465
>
>fax: (206) 616-8272
>vox: (206) 616-5153
>
>

------------------------------

Date: Mon, 19 Apr 1999 13:33:43 -0700 (PDT)
From: steve spencer <stephen_spencer@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: automated measures
Message-ID: <19990419203343.23255.rocketmail@web107.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

Hi, I am using a histogram method for analysis of
various brain structures and up till not have been
using the paintbrush to outline them. I would like to
switch to using the pencil but when I set a threshold
the 1 pixel line width of the pecil does not keep
diagonal pixels from being measured. Is there a way to
foce NIH image to consider diaginal lines as closed
rather then letting any touching pixel become
activated?
Thanks =)
steve spencer
western Psyche
_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com

------------------------------

Date:          Tue, 20 Apr 1999 9:12:47 +1000
From: GJOSS@rna.bio.mq.edu.au
To: stephen_spencer@yahoo.com, nih-image@io.ece.drexel.edu
Subject:       Re: automated measures
Message-ID: <2333EEC5774@rna.bio.mq.edu.au>

>Date: Mon, 19 Apr 1999 13:33:43 -0700 (PDT)
>From: steve spencer <stephen_spencer@yahoo.com>
>Subject: Re: automated measures
>To: nih-image@io.ece.drexel.edu
>
>Hi, I am using a histogram method for analysis of
>various brain structures and up till not have been
>using the paintbrush to outline them. I would like to
>switch to using the pencil but when I set a threshold
>the 1 pixel line width of the pecil does not keep
>diagonal pixels from being measured. Is there a way to
>foce NIH image to consider diaginal lines as closed
>rather then letting any touching pixel become
>activated?
>Thanks =)
>steve spencer
>western Psyche

I suggest that you are using the wrong tools for outlining.
Use one/more of the ROI selection tools.
You have available
straight, segmented and freehand line tools
polygon, oval and rectangular area selection tools

control/option keys which allow modification of 
existing selections by add/subtract.

With all, when you have selection, you can simply measure or
if you prefer, drawboundary 
(with linewidth set to 2 to avoid problem with diagonal pixels
on later selections)

In practice, the polygon is the most frexible as it allows 
point by point extension and then area review/correction by
control/option addition/subtraction.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date:          Tue, 20 Apr 1999 9:35:04 +1000
From: GJOSS@rna.bio.mq.edu.au
To: McPherso@uno.cc.geneseo.edu, nih-image@io.ece.drexel.edu
Subject:       Re: multiple ROIs (was nih-image-d Digest V99 #91
Message-ID: <2339E5A4C5F@rna.bio.mq.edu.au>

>Date: Mon, 19 Apr 1999 12:14:26 -0400
>From: Duane McPherson <McPherso@uno.cc.geneseo.edu>
>
>We are currently working on a calcium imaging project that looks at the
>uptake in
>dorsal cells of the lamprey spinal cord. We have been successful measuring
>the intensity of
>the responses of multiple ROIs in a single frame and have looked at a
>single ROI across
>many frames. Ultimately, what we would like to do is a combination of the
>two and measure
>the responses of multiple ROIs across numerous frames in a movie. Has
>anyone used NIH
>image to do this before or have any ideas on how this may be done? We have
>tried pulling
>up various macros to adjust but have yet to be successful. Thank you in
>advance for any
>ideas or suggestions.
>
>Sincerely,
>
>Kari Scantlebury
>Undergraduate Research
>State Univ. of NY at Geneseo
>KQS99@uno.cc.geneseo.edu
>
You will get the most elegant solution by using Object-Image, an extention 
of NIH-Image by Norbert Vischer available via 
http://simon.bio.uva.nl/object-image.html. 
This will allow recording of ROIs as objects and also supports useful 3D 
displays/analysis.

Within NIH-Image as supplied, you can transfer ROI's accross images using 
restoreRoi; {Restore Selection(Analyze}  
This is a little tricky to use as you need to 
"selectPic(fromId);selectPic(toId);restoreRoi;"    successively, but works 
excellently.
You can store multiple ROIs by transfer to separate images or save/open 
them as 'outline' files but I tend to use a binary or color map image of 
ROIs and reinstate them successively using autoOutline(x,y); 
This allows you to define ROI set then process movie for each ROI or else 
process each frame for each ROI in turn, whatever you choose.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

--------------------------------
End of nih-image-d Digest V99 Issue #93
***************************************

From nih-image-request@io.ece.drexel.edu Tue Apr 20 10:29 EDT 1999
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Resent-Date: Tue, 20 Apr 1999 10:29:17 -0400 (EDT)
From: DrJohnRuss@aol.com
Message-ID: <2bb3b58c.244de3fb@aol.com>
Date: Tue, 20 Apr 1999 10:06:51 EDT
Subject: 16 bit grey and 48 bit color images
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This is a request for input, opinions and comments. It has definite 
commercial overtones, for which I apologize to anyone offended, but there are 
also some technical issues that directly affect this particular group of 
people and I don't know any more straightforward way to address them. The 
basic question is "Who is using images - or plans to use them - with more 
than 8 bits per channel, and what are they trying to do with them?"

Some of the members of this group are already familiar with the Image 
Processing Tool Kit, a set of plug-ins for Photoshop-compatible programs 
(including NIH-Image). We've nearly completed work on version 3 of the Tool 
Kit (which will be announced separately in a few weeks) and the next thing on 
our agenda is dealing with images with more than 8 bits of depth. Several of 
you have asked me about plug-ins with this capability in the past. There are 
relatively few options for processing and measurement of these images. A few 
rather expensive commercial packages such as IPLab and Image Pro Plus can 
handle them, there is the still incomplete Image/J, and Photoshop itself can 
acquire them from the increasing number of cameras and scanners that offer 
more grey-scale and color resolution. But we think that there may be a need 
(opportunity) for a set of plug-ins like the Tool Kit (which runs on both Mac 
and Windows computers) that offer similar capabilities for images with up to 
16 bits of grey or 48 bits of RGB info (that is actually more than realistic 
devices can deliver, but many scanners have 10-12 bits per channel range and 
some cooled cameras are 12-14 bit, and these images are usually stored as 
16/48 bit images just as video camera images with a real grey scale 
resolution of 6-7 bits are usually stored as 8 bits). For electron microscope 
images (especially diffraction patterns), medical X-rays, astronomical 
pictures, fluorescence microscopy, scanned photographic negatives, and some 
other applications the extra depth is really important. These images are not 
fully displayed on a computer monitor (but can be manipulated there, enhanced 
and measured), and can't be printed with all of their depth (but can be 
reduced in various nonlinear ways to produce good prints).

We (my son writes the programs and I write the accompanying tutorials) have 
some questions about the real needs in this area, and would greatly 
appreciate any serious input. The Tool Kit (which deals with 8 bit grey and 
24 bit RGB images) contains an exhaustive set of processing and measurement 
options - much more detailed than NIH-Image. Is it worthwhile to adapt all of 
these to 16/48 bit, or is a minimal set of processing tools enough, after 
which reduction to 8 bit would be reasonable if slightly less convenient? 
Densitometric and colorimetric measurements would be included but what kinds 
of manual and automatic tools are needed to define the regions for 
measurement? Are there some additional kinds of processing and measurement 
tools that are needed that should be included in this package (for example, 
we already have a good FFT package but are people seriously interested in 
wavelets for reconstruction)?

There are really two categories of people that we deal with - those that are 
trying to measure images and content, and those that are trying to process 
their images for better viewing. Both use many of the same tools (sharpening, 
noise removal, color correction, etc.). This is why Photoshop is used so much 
by scientists even though it was not really designed for such applications. 
It also helps that practically every scanner and camera sold comes with a 
Photoshop acquisition plug-in. What we've been adding are functions that make 
Photoshop a useful tool for scientists, but leaves the burden of the basic 
image editing and handling to Adobe. Certainly that is a task that has placed 
an expensive development load on other programs, ranging from NIH-Image to 
expensive high-end commercial packages. So, what's missing?

And finally the big question- what would people be willing to pay for a 
package structured like the Tool Kit that handles these deep images. The Tool 
Kit price ($250 list, $50 less with the coupon in the third edition of The 
Image Processing Handbook) seems to have been accepted as a reasonable 
low-cost add-on by a lot of people, many of whom have spent about $600 for 
Photoshop anyway. We certainly haven't gotten rich from the Tool Kit, but it 
has sold enough copies to justify the extensive and ongoing development 
effort we've invested. The market for a 16/48 bit package (which would also 
handle 8/24 bit images) is probably smaller, which means the cost has to be 
higher. But how much? We want people to use it, and not resent or resist the 
higher price. Would you spend $500? $750? For what combination of 
capabilities?

We've tried to ask questions like this on the Photoshop news group but the 
discussion keeps getting hijacked by an argument over whether Photoshop's 
internal format for deep images adds noise and whether gamma correction is 
proper, etc. Please, if you have been following that (pointless) argument 
don't bring it here. If you want to post your answers for everyone to comment 
on, that's great. If you would prefer to answer privately, send email to me 
(DrJohnRuss@AOL.com) or Chris (JCR6@AOL.com). If you want to bite my head off 
for raising a question with commercial overtones on this group, well, that's 
OK too.

Thanks,

John Russ


From nih-image-d-request@io.ece.drexel.edu Wed Apr 21 06:16 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #94
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 94

Today's Topics:
  16 bit grey and 48 bit color images   [ DrJohnRuss@aol.com ]

------------------------------

Date: Tue, 20 Apr 1999 10:06:51 EDT
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Subject: 16 bit grey and 48 bit color images
Message-ID: <2bb3b58c.244de3fb@aol.com>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

This is a request for input, opinions and comments. It has definite 
commercial overtones, for which I apologize to anyone offended, but there are 
also some technical issues that directly affect this particular group of 
people and I don't know any more straightforward way to address them. The 
basic question is "Who is using images - or plans to use them - with more 
than 8 bits per channel, and what are they trying to do with them?"

Some of the members of this group are already familiar with the Image 
Processing Tool Kit, a set of plug-ins for Photoshop-compatible programs 
(including NIH-Image). We've nearly completed work on version 3 of the Tool 
Kit (which will be announced separately in a few weeks) and the next thing on 
our agenda is dealing with images with more than 8 bits of depth. Several of 
you have asked me about plug-ins with this capability in the past. There are 
relatively few options for processing and measurement of these images. A few 
rather expensive commercial packages such as IPLab and Image Pro Plus can 
handle them, there is the still incomplete Image/J, and Photoshop itself can 
acquire them from the increasing number of cameras and scanners that offer 
more grey-scale and color resolution. But we think that there may be a need 
(opportunity) for a set of plug-ins like the Tool Kit (which runs on both Mac 
and Windows computers) that offer similar capabilities for images with up to 
16 bits of grey or 48 bits of RGB info (that is actually more than realistic 
devices can deliver, but many scanners have 10-12 bits per channel range and 
some cooled cameras are 12-14 bit, and these images are usually stored as 
16/48 bit images just as video camera images with a real grey scale 
resolution of 6-7 bits are usually stored as 8 bits). For electron microscope 
images (especially diffraction patterns), medical X-rays, astronomical 
pictures, fluorescence microscopy, scanned photographic negatives, and some 
other applications the extra depth is really important. These images are not 
fully displayed on a computer monitor (but can be manipulated there, enhanced 
and measured), and can't be printed with all of their depth (but can be 
reduced in various nonlinear ways to produce good prints).

We (my son writes the programs and I write the accompanying tutorials) have 
some questions about the real needs in this area, and would greatly 
appreciate any serious input. The Tool Kit (which deals with 8 bit grey and 
24 bit RGB images) contains an exhaustive set of processing and measurement 
options - much more detailed than NIH-Image. Is it worthwhile to adapt all of 
these to 16/48 bit, or is a minimal set of processing tools enough, after 
which reduction to 8 bit would be reasonable if slightly less convenient? 
Densitometric and colorimetric measurements would be included but what kinds 
of manual and automatic tools are needed to define the regions for 
measurement? Are there some additional kinds of processing and measurement 
tools that are needed that should be included in this package (for example, 
we already have a good FFT package but are people seriously interested in 
wavelets for reconstruction)?

There are really two categories of people that we deal with - those that are 
trying to measure images and content, and those that are trying to process 
their images for better viewing. Both use many of the same tools (sharpening, 
noise removal, color correction, etc.). This is why Photoshop is used so much 
by scientists even though it was not really designed for such applications. 
It also helps that practically every scanner and camera sold comes with a 
Photoshop acquisition plug-in. What we've been adding are functions that make 
Photoshop a useful tool for scientists, but leaves the burden of the basic 
image editing and handling to Adobe. Certainly that is a task that has placed 
an expensive development load on other programs, ranging from NIH-Image to 
expensive high-end commercial packages. So, what's missing?

And finally the big question- what would people be willing to pay for a 
package structured like the Tool Kit that handles these deep images. The Tool 
Kit price ($250 list, $50 less with the coupon in the third edition of The 
Image Processing Handbook) seems to have been accepted as a reasonable 
low-cost add-on by a lot of people, many of whom have spent about $600 for 
Photoshop anyway. We certainly haven't gotten rich from the Tool Kit, but it 
has sold enough copies to justify the extensive and ongoing development 
effort we've invested. The market for a 16/48 bit package (which would also 
handle 8/24 bit images) is probably smaller, which means the cost has to be 
higher. But how much? We want people to use it, and not resent or resist the 
higher price. Would you spend $500? $750? For what combination of 
capabilities?

We've tried to ask questions like this on the Photoshop news group but the 
discussion keeps getting hijacked by an argument over whether Photoshop's 
internal format for deep images adds noise and whether gamma correction is 
proper, etc. Please, if you have been following that (pointless) argument 
don't bring it here. If you want to post your answers for everyone to comment 
on, that's great. If you would prefer to answer privately, send email to me 
(DrJohnRuss@AOL.com) or Chris (JCR6@AOL.com). If you want to bite my head off 
for raising a question with commercial overtones on this group, well, that's 
OK too.

Thanks,

John Russ

--------------------------------
End of nih-image-d Digest V99 Issue #94
***************************************

From nih-image-request@io.ece.drexel.edu Wed Apr 21 14:11 EDT 1999
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Date: Wed, 21 Apr 1999 10:46:34 -0700
To: nih-image@io.ece.drexel.edu
From: Daniel Twelker <twelker@uclink4.berkeley.edu>
Subject: Portable NIH Image
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I am trying to come up with a high quality image acquisition and analysis
system that is portable.  This will be for a monochrome industrial camera,
8-bit, NIH Image system.  Any recommendations?
Thanks in advance,
Dan



From nih-image-request@io.ece.drexel.edu Wed Apr 21 15:55 EDT 1999
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Date: Wed, 21 Apr 1999 15:41:42 -0400
To: nih-image@io.ece.drexel.edu
From: g jones <gj15n@nih.gov>
Subject: Dr. Russ-48 bits
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I only dabble in image processing but i love all the technology and try to
follow it...
so my contribution is only philosophical/pedantic. If you build it they
will come.
Film is going the way of the dinosaur for many applications, and image
acquisition
is becoming higher and higher tech. Competition will make cameras better,faster
before we know it. It's refreshing to see somebody cares about reasonable
prices too.
I imagine the lower the price the more poeple will use it...who knows but
your package
could become a defacto standard because "everyone's using it". Astronomical
software
prices nowdays certainly dissuades many from even considering products.
Just my humble
opinion as a gov't employee with no commercial interests.



From nih-image-request@io.ece.drexel.edu Wed Apr 21 22:58 EDT 1999
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From: Anthony Boxshall <boxshall@biology.ucsc.edu>
Subject: Digital Camera and Otoliths
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I have just recently resubscribed so I have missed recent traffic.  I tried
the recent archive but I was unsuccessful.  In the past I have seen hints
and discussion on brands of digital cameras and would like to tap into
those with knowledge.

We will be reading otoliths (fish ear bones) using a Nikon inverted scope
and/or Leica dissecting scope.  We want to get a digital camera to do this
and are casting around for suggestions of brands to buy.  We have heard
good reports of the Real 14 but at $9000 we would like to pay less.

Does anyone have a suggestion list of good brands to look at?
OR better still, bought one recently and got any comments?

Thanks
anthony

________________________________________________________
Dr Anthony Boxshall		Ph:	(831) 459-4098 (Office)
Biology @ EMS,			(831) 459-5460 (Marine Lab)
UCSC, 1156 High St.		Fax: 	(intl:1)-(831) 459-4882
Santa Cruz, CA		Office Room No: EMS A421
USA  95064		Email: Boxshall@darwin.ucsc.edu
________________________________________________________
If you're interested in furniture for a sustainable
future with an Australian twist see:
http://www.users.bigpond.com/endemica/
**********************************************************


From nih-image-request@io.ece.drexel.edu Thu Apr 22 02:05 EDT 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: boxshall@biology.ucsc.edu, nih-image@io.ece.drexel.edu
Date:          Thu, 22 Apr 1999 15:57:20 +1000
Subject:       Re: Digital Camera and Otoliths
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>Date: Wed, 21 Apr 1999 19:47:18 -0700
>To: nih-image@io.ece.drexel.edu
>From: Anthony Boxshall <boxshall@biology.ucsc.edu>
>Subject: Digital Camera and Otoliths
>
>I have just recently resubscribed so I have missed recent traffic.  I 
>tried
>the recent archive but I was unsuccessful.  In the past I have seen hints
>and discussion on brands of digital cameras and would like to tap into
>those with knowledge.
>
>We will be reading otoliths (fish ear bones) using a Nikon inverted scope
>and/or Leica dissecting scope.  We want to get a digital camera to do this
>and are casting around for suggestions of brands to buy.  We have heard
>good reports of the Real 14 but at $9000 we would like to pay less.
>
>Does anyone have a suggestion list of good brands to look at?
>OR better still, bought one recently and got any comments?
>
>Thanks
>anthony
>
>________________________________________________________
>Dr Anthony Boxshall		Ph:	(831) 459-4098 (Office)
>Biology @ EMS,			(831) 459-5460 (Marine Lab)
>UCSC, 1156 High St.		Fax: 	(intl:1)-(831) 459-4882
>Santa Cruz, CA		Office Room No: EMS A421
>USA  95064		Email: Boxshall@darwin.ucsc.edu


$9000!? 
I wonder what resolution you are looking for and why?

Are you intending to image whole otoliths for shape or 
polished surface transects for growth rings or
both?

If anyone can recommend a digital camera that will give better control of 
contrast range than a reasonable monochrome PAL (768x512) video camera with 
a framegrabber supported by NIH-Image capture software (eg Scion LG3),
I would be interested to know.

My impression of digital cameras has been that software interface to 
actively control capture contrast via histogram of ROI is lacking. Consumer 
level cameras with colour losses resolution and colour is generally not of 
use for scientific measurement.

It would certainly make sense for a good quality, good resolution, 
monochrome digital camera with useful software control of capture at a 
reasonable price (ie comparable to US$800 PAL video camera + $895 LG3 ) to 
be available but I dont know of one.

Any suggestions?

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-d-request@io.ece.drexel.edu Thu Apr 22 06:20 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #95
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------------------------------

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nih-image-d Digest				Volume 99 : Issue 95

Today's Topics:
  NIH Text File import/conversion       [ "Mark C. Olm" <olm1@ix.netcom.com> ]
  Portable NIH Image                    [ Daniel Twelker <twelker@uclink4.ber ]
  Dr. Russ-48 bits                      [ g jones <gj15n@nih.gov> ]
  DV video capture                      [ "Hillman, Paul" <hillman@plk.af.mil ]
  Digital Camera and Otoliths           [ Anthony Boxshall <boxshall@biology. ]
  Re: Digital Camera and Otoliths       [ GJOSS@rna.bio.mq.edu.au ]

------------------------------

Date: Wed, 21 Apr 1999 09:26:03 -0700
From: "Mark C. Olm" <olm1@ix.netcom.com>
To: nih-image-d@io.ece.drexel.edu
Subject: NIH Text File import/conversion
Message-ID: <371DFC1B.3EB0289A@ix.netcom.com>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

 I need to convert variable format text files either to directly load or
to the
"accepted" ASCI text import format for NIH.  I have row data in variable
number
of fields (column) per line so that each row of the grid (image) is
contained on multiple lines (variable number of lines due to the size of
the numbers but each row would have the same total number of readings).
Due to the output from the other grid program, each line of the ASCII
file has a hard return so that NIH interprets each line as a row.  I
actually have over 256 rows in the grid so that a
spreadsheet/spreadsheet macro solution breaks down.  Any help for a
macro or even how to go about this problem would be greatly appreciated.

Many Thanks in advance.  - Mark






I need to read in a large grid from a different format than that
required by the "TEXT" import in NIH.  Is there no other way to write
(or obtain) a macro that would read a varied number of text file formats
and write a compatible text file for import to NIH ???

------------------------------

Date: Wed, 21 Apr 1999 10:46:34 -0700
From: Daniel Twelker <twelker@uclink4.berkeley.edu>
To: nih-image@io.ece.drexel.edu
Subject: Portable NIH Image
Message-Id: <v03020901b343bd4db0ec@[128.32.232.125]>
Content-Type: text/plain; charset="us-ascii"

I am trying to come up with a high quality image acquisition and analysis
system that is portable.  This will be for a monochrome industrial camera,
8-bit, NIH Image system.  Any recommendations?
Thanks in advance,
Dan

------------------------------

Date: Wed, 21 Apr 1999 15:41:42 -0400
From: g jones <gj15n@nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Dr. Russ-48 bits
Message-Id: <v04003a00b3439a9efb50@[165.112.72.45]>
Content-Type: text/plain; charset="us-ascii"

I only dabble in image processing but i love all the technology and try to
follow it...
so my contribution is only philosophical/pedantic. If you build it they
will come.
Film is going the way of the dinosaur for many applications, and image
acquisition
is becoming higher and higher tech. Competition will make cameras better,faster
before we know it. It's refreshing to see somebody cares about reasonable
prices too.
I imagine the lower the price the more poeple will use it...who knows but
your package
could become a defacto standard because "everyone's using it". Astronomical
software
prices nowdays certainly dissuades many from even considering products.
Just my humble
opinion as a gov't employee with no commercial interests.

------------------------------

Date: Wed, 21 Apr 1999 18:44:25 -0600
From: "Hillman, Paul" <hillman@plk.af.mil>
To: nih-image-d@io.ece.drexel.edu
Subject: DV video capture
Message-ID: <178F01F1C3BBD2118DF30008C733107107A6E8@de-x3.plk.af.mil>
Content-Type: text/plain;
	charset="windows-1252"
Content-Transfer-Encoding: 8bit

I have a BW G3 with firewire/DV/iLink input.  Is there an acquire plug-in
for NIH-IMAGE to capture frames from this input?

I can always capture in Adobe Priemier and transfer to Image, but having
Image directly capture would be nice.

Can anyone directly me to source code for writing my own.  I think I have
seen the source code for image capture for other video boards, but nothing
for the firewire/DV port.

I am using Sony's media converter to capture analog video with this Mac, I
don't have a digital camcorder.  This device takes s-video/composite and
converts them to DV, which is then feed to the firewire port on the G3.
This is a cheap but high quality way of getting video/audio into a BW G3.
Apple's video player sees the DV but will not capture it.

________________________________________________________________
"640K ought to be good enough for anybody."  Bill Gates

Paul Hillman         \____ ...,. ____/    hillman@plk.af.mil
StarFire Optical Range    ( o o )     P_D_Hillman@compuserve.com
AFRL/DES                   \   /         CIM: 71773,643 
3550 Aberdeen Ave SE        (_)          real time (505)846-5032
Kirtland AFB NM  87117                   FAX:(505)846-2213 
________________________________________________________________

------------------------------

Date: Wed, 21 Apr 1999 19:47:18 -0700
From: Anthony Boxshall <boxshall@biology.ucsc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Digital Camera and Otoliths
Message-Id: <3.0.1.32.19990421194718.007aaad0@darwin.ucsc.edu>
Content-Type: text/plain; charset="us-ascii"

I have just recently resubscribed so I have missed recent traffic.  I tried
the recent archive but I was unsuccessful.  In the past I have seen hints
and discussion on brands of digital cameras and would like to tap into
those with knowledge.

We will be reading otoliths (fish ear bones) using a Nikon inverted scope
and/or Leica dissecting scope.  We want to get a digital camera to do this
and are casting around for suggestions of brands to buy.  We have heard
good reports of the Real 14 but at $9000 we would like to pay less.

Does anyone have a suggestion list of good brands to look at?
OR better still, bought one recently and got any comments?

Thanks
anthony

________________________________________________________
Dr Anthony Boxshall		Ph:	(831) 459-4098 (Office)
Biology @ EMS,			(831) 459-5460 (Marine Lab)
UCSC, 1156 High St.		Fax: 	(intl:1)-(831) 459-4882
Santa Cruz, CA		Office Room No: EMS A421
USA  95064		Email: Boxshall@darwin.ucsc.edu
________________________________________________________
If you're interested in furniture for a sustainable
future with an Australian twist see:
http://www.users.bigpond.com/endemica/
**********************************************************

------------------------------

Date:          Thu, 22 Apr 1999 15:57:20 +1000
From: GJOSS@rna.bio.mq.edu.au
To: boxshall@biology.ucsc.edu, nih-image@io.ece.drexel.edu
Subject:       Re: Digital Camera and Otoliths
Message-ID: <26A018E0B1B@rna.bio.mq.edu.au>

>Date: Wed, 21 Apr 1999 19:47:18 -0700
>To: nih-image@io.ece.drexel.edu
>From: Anthony Boxshall <boxshall@biology.ucsc.edu>
>Subject: Digital Camera and Otoliths
>
>I have just recently resubscribed so I have missed recent traffic.  I 
>tried
>the recent archive but I was unsuccessful.  In the past I have seen hints
>and discussion on brands of digital cameras and would like to tap into
>those with knowledge.
>
>We will be reading otoliths (fish ear bones) using a Nikon inverted scope
>and/or Leica dissecting scope.  We want to get a digital camera to do this
>and are casting around for suggestions of brands to buy.  We have heard
>good reports of the Real 14 but at $9000 we would like to pay less.
>
>Does anyone have a suggestion list of good brands to look at?
>OR better still, bought one recently and got any comments?
>
>Thanks
>anthony
>
>________________________________________________________
>Dr Anthony Boxshall		Ph:	(831) 459-4098 (Office)
>Biology @ EMS,			(831) 459-5460 (Marine Lab)
>UCSC, 1156 High St.		Fax: 	(intl:1)-(831) 459-4882
>Santa Cruz, CA		Office Room No: EMS A421
>USA  95064		Email: Boxshall@darwin.ucsc.edu


$9000!? 
I wonder what resolution you are looking for and why?

Are you intending to image whole otoliths for shape or 
polished surface transects for growth rings or
both?

If anyone can recommend a digital camera that will give better control of 
contrast range than a reasonable monochrome PAL (768x512) video camera with 
a framegrabber supported by NIH-Image capture software (eg Scion LG3),
I would be interested to know.

My impression of digital cameras has been that software interface to 
actively control capture contrast via histogram of ROI is lacking. Consumer 
level cameras with colour losses resolution and colour is generally not of 
use for scientific measurement.

It would certainly make sense for a good quality, good resolution, 
monochrome digital camera with useful software control of capture at a 
reasonable price (ie comparable to US$800 PAL video camera + $895 LG3 ) to 
be available but I dont know of one.

Any suggestions?

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

--------------------------------
End of nih-image-d Digest V99 Issue #95
***************************************

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                   NIH-image Mailing List Help 
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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
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From nih-image-request@io.ece.drexel.edu Fri Apr 23 12:37 EDT 1999
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To: DrJohnRuss@aol.com, nih-image@io.ece.drexel.edu
From: Michael Cammer <cammer@aecom.yu.edu>
Subject: Re: 16 bit grey and 48 bit color images
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We routinely analyze images from 12 to 15 bit cooled CCD cameras.  Also,
the gel scanner (another facility) is 12 or 16 bits.
This analysis usually is change in fluorescence in cells over time or
fluorescence in different cell lines (e.g. knock outs, under-expressors, WT
and over expression) or fluorescence at specific locations in the cells.  
For these applications we use IP Lab spectrum because NIH-Image does not
have sufficient dynamic range.
********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************


From nih-image-request@io.ece.drexel.edu Fri Apr 23 15:07 EDT 1999
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Date: Fri, 23 Apr 1999 14:54:58 -0400
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
Subject: QT4beta weirding out list archives ??
To: nih-image@io.ece.drexel.edu
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Ever since I loaded up the new Quicktime 4 beta, the digests show up as
some kind of QuickTime items instead of having the envelope icons when I
view them in Eudora. This is annoying and leaves me unable to read them.
Evidently QT4 is overriding the Eudora internal mapping of mime types.

Has anyone else encountered this problem, and can you suggest how I fix this?

Please email me directly since this chicken and egg problem means I can't
read your suggestions via the list digest ;/ I'll post any solutions I get
to the list.

Thanks.

Bill Christens-Barry
-------------------------
Bill Christens-Barry, PhD
Johns Hopkins University Applied Physics Laboratory
wacb@aplcomm.jhuapl.edu
-------------------------


From nih-image-request@io.ece.drexel.edu Fri Apr 23 18:05 EDT 1999
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Date: Fri, 23 Apr 1999 14:54:14 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: FYI:Experiences with B/W G3 and Aurora Fuse
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I thought I would summarize my experience with the Aurora Fuse and the new
G3's and NIH Image for those interested on this list.

I wrote for a G3 Mac in a grant, and by the time I got the money, the model
I had specified was not sold, and the replacement was the B/W G3's. I had
planned on using an Apple AV digitizer card, but they stopped making these.
I was using NIH Image to control a VCR through a RS-422 serial line, and
now the G3's didn't have RS-422.

I got one of the B/W G3's and looked for a video digitizing board. I
finally settled on the Aurora Fuse. Iomega Buz was reported to not work
with the B/W G3's, and the Scion was too expensive for my budget. For the
serial interface, I ended up with a Keyspan USB-Serial adapter.

The Fuse works well with NIH Image. It is possible to capture images using
the "Capture" command. The only problem is changing the digitizer settings,
which requires using the plug-in digitizer.

Getting serial output to work was more of a hassel. I was using macros to
send the messages. This sends the messages to the modem port. The Keyspan
software maps only the printer port to one of the two serial lines. I had
to re-compile NIH Image to send the messages to the printer port. (change
references in Macros1.p from ".AOut" to ".BOut", and ".AIn" to ".BIn").

Then, I had a problem with handshake. I called Keyspan and found that there
was a problem with the 1.5 drivers, and that the most recent version
(1.7b3) would solve it. It did.

Now everything is up and running, with the macros controlling the VCR, and
capture through the Fuse. I should mention that my main application is
measuring dimensions from gray images.

DTL



From nih-image-request@io.ece.drexel.edu Fri Apr 23 18:10 EDT 1999
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Date: Fri, 23 Apr 1999 14:58:31 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: FYI:Compiling 1.62 under CW4
Message-ID: <258719.3133868311@huginn.medicine.washington.edu>
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I recently had to recompile version 1.62 under CW4 for running on a G3. I
had some interesting problems, which I thought might be informative to
others.

Everything seemed to compile just fine until I started to increase
optimization for speed. I found that if I went higher than level 2, the
application crashed. Then, when I went down to no optimization, I noted
that the toolbar was lacking any icons. On a hunch, I shut off "Schedule
Instructions" on the PPC Processor Options, and the icons came back! I then
increased optimizations all the way up to 4, and everything still ran just
fine!

Apparenetly there is a bug related to "Schedule Instructions".

DTL



From nih-image-request@io.ece.drexel.edu Fri Apr 23 19:28 EDT 1999
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Date: Fri, 23 Apr 1999 19:19:20 -0400
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From: Deric Wisleder <dxw32@psu.edu>
Subject: Header information
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I am using Scion release beta 3b which I think is up to date.  My images
are MRI data converted to .acr (DICOM 2) format (DICOM 3 .dcm will not
import).  

I can view a few header fields, but there is much more information that I
can not view.  OSIRIS (another software) will display extensive header
information, but it will not print it.  Can someone help me to view and
print image header information?  Thank you very much.

Sincerly,

Deric Wisleder


From nih-image-d-request@io.ece.drexel.edu Sat Apr 24 06:10 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #96
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 96

Today's Topics:
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
  Re: 16 bit grey and 48 bit color ima  [ Michael Cammer <cammer@aecom.yu.edu ]
  QT4beta weirding out list archives ?  [ Bill Christens-Barry <wacb@aplcomm. ]
  FYI:Experiences with B/W G3 and Auro  [ David Linker <dtlinker@u.washington ]
  FYI:Compiling 1.62 under CW4          [ David Linker <dtlinker@u.washington ]
  Header information                    [ Deric Wisleder <dxw32@psu.edu> ]

------------------------------

Date: Fri, 23 Apr 1999 05:05:01 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199904230905.FAA17290@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
                   ---------------------------
     


nih-image-d-request@biomed.drexel.edu  - Aministration for Digest
nih-image-request@biomed.drexel.edu   - Administation for List


     *********************************************************
     *    DO NOT SEND ADMINISTRATIVE COMMANDS TO THE LIST    *
     *********************************************************
nih-image@biomed.drexel.edu   - Sends mail to everyone on the list 


Subscribe
---------
To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu.
The Subject of the message should contain "Subscribe".

As in:		To: nih-image-request@biomed.drexel.edu
		Subject: subscribe


Subscribe to Digest
-------------------
To subscribe to a digested version of the list, send E-mail to 
nih-image-d-request@biomed.drexel.edu.

The Subject of the message should contain "Subscribe".

As in:		To: nih-image-d-request@biomed.drexel.edu
		Subject: subscribe


Unsubscribe
-----------
To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu.
The Subject of the message should contain "unsubscribe".

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		Subject: unsubscribe


Unsubscribe to Digest
--------------------
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nih-image-d-request@biomed.drexel.edu.
The Subject of the message should contain "unsubscribe".

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		Subject: unsubscribe


Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

------------------------------

Date: Fri, 23 Apr 1999 12:23:58 -0700
From: Michael Cammer <cammer@aecom.yu.edu>
To: DrJohnRuss@aol.com, nih-image@io.ece.drexel.edu
Subject: Re: 16 bit grey and 48 bit color images
Message-Id: <3.0.5.32.19990423122358.009f3e40@mailserver.aecom.yu.edu>
Content-Type: text/plain; charset="us-ascii"

We routinely analyze images from 12 to 15 bit cooled CCD cameras.  Also,
the gel scanner (another facility) is 12 or 16 bits.
This analysis usually is change in fluorescence in cells over time or
fluorescence in different cell lines (e.g. knock outs, under-expressors, WT
and over expression) or fluorescence at specific locations in the cells.  
For these applications we use IP Lab spectrum because NIH-Image does not
have sufficient dynamic range.
********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************

------------------------------

Date: Fri, 23 Apr 1999 14:54:58 -0400
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
To: nih-image@io.ece.drexel.edu
Subject: QT4beta weirding out list archives ??
Message-id: <v04011701b34671614aea@[128.244.128.7]>
Content-type: text/plain; charset=us-ascii
Content-transfer-encoding: 7BIT

Ever since I loaded up the new Quicktime 4 beta, the digests show up as
some kind of QuickTime items instead of having the envelope icons when I
view them in Eudora. This is annoying and leaves me unable to read them.
Evidently QT4 is overriding the Eudora internal mapping of mime types.

Has anyone else encountered this problem, and can you suggest how I fix this?

Please email me directly since this chicken and egg problem means I can't
read your suggestions via the list digest ;/ I'll post any solutions I get
to the list.

Thanks.

Bill Christens-Barry
-------------------------
Bill Christens-Barry, PhD
Johns Hopkins University Applied Physics Laboratory
wacb@aplcomm.jhuapl.edu
-------------------------

------------------------------

Date: Fri, 23 Apr 1999 14:54:14 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: FYI:Experiences with B/W G3 and Aurora Fuse
Message-ID: <243296.3133868054@huginn.medicine.washington.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

I thought I would summarize my experience with the Aurora Fuse and the new
G3's and NIH Image for those interested on this list.

I wrote for a G3 Mac in a grant, and by the time I got the money, the model
I had specified was not sold, and the replacement was the B/W G3's. I had
planned on using an Apple AV digitizer card, but they stopped making these.
I was using NIH Image to control a VCR through a RS-422 serial line, and
now the G3's didn't have RS-422.

I got one of the B/W G3's and looked for a video digitizing board. I
finally settled on the Aurora Fuse. Iomega Buz was reported to not work
with the B/W G3's, and the Scion was too expensive for my budget. For the
serial interface, I ended up with a Keyspan USB-Serial adapter.

The Fuse works well with NIH Image. It is possible to capture images using
the "Capture" command. The only problem is changing the digitizer settings,
which requires using the plug-in digitizer.

Getting serial output to work was more of a hassel. I was using macros to
send the messages. This sends the messages to the modem port. The Keyspan
software maps only the printer port to one of the two serial lines. I had
to re-compile NIH Image to send the messages to the printer port. (change
references in Macros1.p from ".AOut" to ".BOut", and ".AIn" to ".BIn").

Then, I had a problem with handshake. I called Keyspan and found that there
was a problem with the 1.5 drivers, and that the most recent version
(1.7b3) would solve it. It did.

Now everything is up and running, with the macros controlling the VCR, and
capture through the Fuse. I should mention that my main application is
measuring dimensions from gray images.

DTL

------------------------------

Date: Fri, 23 Apr 1999 14:58:31 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: FYI:Compiling 1.62 under CW4
Message-ID: <258719.3133868311@huginn.medicine.washington.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

I recently had to recompile version 1.62 under CW4 for running on a G3. I
had some interesting problems, which I thought might be informative to
others.

Everything seemed to compile just fine until I started to increase
optimization for speed. I found that if I went higher than level 2, the
application crashed. Then, when I went down to no optimization, I noted
that the toolbar was lacking any icons. On a hunch, I shut off "Schedule
Instructions" on the PPC Processor Options, and the icons came back! I then
increased optimizations all the way up to 4, and everything still ran just
fine!

Apparenetly there is a bug related to "Schedule Instructions".

DTL

------------------------------

Date: Fri, 23 Apr 1999 19:19:20 -0400
From: Deric Wisleder <dxw32@psu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Header information
Message-Id: <4.1.19990423191149.009776c0@mail.psu.edu>
Content-Type: text/plain; charset="us-ascii"

I am using Scion release beta 3b which I think is up to date.  My images
are MRI data converted to .acr (DICOM 2) format (DICOM 3 .dcm will not
import).  

I can view a few header fields, but there is much more information that I
can not view.  OSIRIS (another software) will display extensive header
information, but it will not print it.  Can someone help me to view and
print image header information?  Thank you very much.

Sincerly,

Deric Wisleder

--------------------------------
End of nih-image-d Digest V99 Issue #96
***************************************

From nih-image-request@io.ece.drexel.edu Mon Apr 26 03:57 EDT 1999
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Date: Mon, 26 Apr 1999 09:44:55 +0200
To: nih-image@io.ece.drexel.edu
From: Ben Elkin <elk@igb.fhg.de>
Subject: Re: Digital Camera and Otoliths
Cc: gray@matcogroup.com
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Anthony Boxshall wrote:
>
>We will be reading otoliths (fish ear bones) using a Nikon inverted scope
>and/or Leica dissecting scope.  We want to get a digital camera to do this
>and are casting around for suggestions of brands to buy.  We have heard
>good reports of the Real 14 but at $9000 we would like to pay less.
>
>Does anyone have a suggestion list of good brands to look at?
>OR better still, bought one recently and got any comments?
>

I have sent a short description of a digital camera from Sound Vision (
http://www.cmospro.com/ ) to this list a while ago. Since then we din't use
the camera too often (optical microscopy is an ancillary technique for us),
and the use was for relatively routine tasks only - but we were *fully*
satisfied with the camera. In the next couple of days we are going to test
it for fluorescence.

-------------------------------------------
>* This is a camera for still images only *
>
>The first impressions are good. The camera is a digital one, which means
>that the signal from the light detector is converted *once* into the
>digital form and transferred digitally to the computer via SCSI interface.
>This means:
>
>1. No pixel jitter
>2. You don't need any frame grabber.
>3. You can use it with Mac or Wintel.
>4. From 2. and 3. follows that you don't need a dedicated computer. You
>can use one which happens to stand where you take your pictures.
>
>The software (plugin for Photoshop) is OK, but (on a Mac) you have to
>allocate at least 20 MB to Photoshop. I haven't yet tested the plugin it
>with NIH-Image.
>
>Camera uses an internal rotating RGB filter wheel with a monochrome sensor
>(and trades off the aquisition speed for the image quality).
>
>The resolution (non-interpolated) is 800*960 (RGB). The camera captures
>with 10 bit per pixel and color channel, but normally saves as 24 bit RGB.
>
>It provides "live" (a couple of frames/sec) video for image ajustment.
>
>On a microscopy image produced with this camera I could actually see more
>details as compared to looking through the microscope ocular.
>
>The camera has C-mount and comes with reasonable accessory if you want.
>The camera price in USA is below $2000.
>
>The user manual is published on the company web site (
>http://www.cmospro.com/images/Cp.pdf ).




Ben Elkin

=======================================
elk@igb.fhg.de

http://www.igb.fhg.de/GVT/

Fraunhofer Institute for Interfacial Technology and Bioengineering
                    (fuer Grenzflaechen und Bioverfahrenstechnik)

Nobelstr. 12    D-70569 Stuttgart    Germany

Tel. +49 - 711 - 970-4144, -4161
Fax                 -4200




From nih-image-request@io.ece.drexel.edu Mon Apr 26 04:22 EDT 1999
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Date: Mon, 26 Apr 1999 10:06:20 +0200
To: nih-image@io.ece.drexel.edu
From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: Re: nih-image-d Digest V99 #95
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> I need to convert variable format text files either to directly load or
>to the
>"accepted" ASCI text import format for NIH.  I have row data in variable
>number
>of fields (column) per line so that each row of the grid (image) is
>contained on multiple lines (variable number of lines due to the size of
>the numbers but each row would have the same total number of readings).
>Due to the output from the other grid program, each line of the ASCII
>file has a hard return so that NIH interprets each line as a row.  I
>actually have over 256 rows in the grid so that a
>spreadsheet/spreadsheet macro solution breaks down.  Any help for a
>macro or even how to go about this problem would be greatly appreciated.

I wrote macros that generate (not read) files for virtual reality. You could see how I have solved particular matters and maybe benefit from it. Given its goal, 90% may be trendy waste, but 10% may be useful to you.

There are 3 limitations to the use of these macros: rights remain with me, you cannot directly distribute any of the source, only via a request to me, I cannot be held responsible for any malfuncitoning of the macros (though I'd like to hear from them, to improve the macros).

Regards, Ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156



From nih-image-request@io.ece.drexel.edu Mon Apr 26 10:58 EDT 1999
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Resent-Date: Mon, 26 Apr 1999 10:58:48 -0400 (EDT)
Message-Id: <199904261433.KAA19650@barid.bennington.edu>
Subject: transforming pixels into real coordinates
Date: Mon, 26 Apr 99 10:44:18 -0400
x-sender: skyebend@pop.bennington.edu
x-mailer: Claris Emailer 1.1
From: Skye Bender-deMoll <skyebend@bennington.edu>
To: <nih-image@io.ece.drexel.edu>
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I'm using Scion image to extract the paths of people's motion from video 
clips.  I have writen a macro (with the help of some people on this list- 
thanks) which allows me to get the XY of the pixel location of each 
person in each frame as they move.  However, many of the clips are not 
shot from directly overhead.  Because there is a fair ammount of 
perspective in each image, the regular measurement commands won't give me 
the real distances across the entire frame.  I would like to be able to 
transform the XY data I have from the plane of the image to the actual 
plane which the people are moving in.  Has anyone done this?  I would 
greatly appriciate suggestions and/or sources for macros or equations 
related to perspective transformation.   
        Thanks,
            -Skye

P.S.  Does anyone know of any freeware for Macintosh with X-Y-Z plotting 
capabilites?  Most programs seem to do 3D histograms, but won't do real 
plotting.  

                                  -000-
Skye Bender-deMoll 
  | Bennington College
  | Bennington VT 05201
  | 802.440.4626 
  |---------------------- skyebend@bennington.edu
  | 38755 Reed Road
  | Nehalem OR 97131
  | 503.368.6294


From nih-image-request@io.ece.drexel.edu Mon Apr 26 11:32 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: "=?iso-8859-1?Q?=22Dr._Luis_F._Hern=E1ndez=22?="  <lhernan@criba.edu.ar>
Subject: Convert Color negs
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Imagers:
We want to convert scanned 35 mm color negatives (obtained with an UMAX
1200S plus its Transparency Unit) into positive color images. How can we do
this?
Is Photoshop the only alternative?. Is there any plug-in for Image or
Photoshop that can easily perform this operation? Is there any other source
of information (web site) to go through?
Many thanks for your help.
Kind regards,



_______________________________________________________
Dr. Luis F. Hernandez, Ph.D.
Laboratorio de Botanica
Departamento de Agronomia
U N I V E R S I D A D  N A C I O N A L  D E L  S U R
8000. Bahia Blanca - ARGENTINA

<mailto: lhernan@criba.edu.ar>
Telefonos (0291) 453-4775/453-0024
FAX: 54 - 0291 - 452-1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.



From nih-image-request@io.ece.drexel.edu Mon Apr 26 11:56 EDT 1999
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Date: Mon, 26 Apr 1999 11:48:33 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: Convert Color negs
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>Imagers:
>We want to convert scanned 35 mm color negatives (obtained with an UMAX
>1200S plus its Transparency Unit) into positive color images. How can we do
>this?
>Is Photoshop the only alternative?. Is there any plug-in for Image or
>Photoshop that can easily perform this operation? Is there any other source
>of information (web site) to go through?
>Many thanks for your help.
>Kind regards,

The "Invert" command in ImageJ (http://rsb.info.nih.gov/ij/) will do this.
Compared to NIH Image, ImageJ has much better support for RGB images.

-wayne



From nih-image-request@io.ece.drexel.edu Mon Apr 26 12:04 EDT 1999
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Subject: Re: FYI:Experiences with B/W G3 and Aurora Fuse
Date: Mon, 26 Apr 99 11:47:03 -0400
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i too have been updated/outcarded/out'buz'ed by apple trying to do better 
and losing something in the translation.
my research also involves time/space analysis of microscopic objects.
i would appreciate any information on this aurora fuze card (specs, url, 
price, resolution, resolution, resolution etc.)


From nih-image-request@io.ece.drexel.edu Mon Apr 26 12:45 EDT 1999
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Date: Mon, 26 Apr 1999 18:18:49 +0200 (MET DST)
From: Szalay Ferenc <fszalay@ns.univet.hu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Convert Color negs
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To > Dr. Luis F. Hernandez, Ph.D.

> Imagers:
> We want to convert scanned 35 mm color negatives (obtained with an UMAX
> 1200S plus its Transparency Unit) into positive color images. How can we do
> this?
> Is Photoshop the only alternative?. Is there any plug-in for Image or
> Photoshop that can easily perform this operation? Is there any other source
> of information (web site) to go through?

Inversion of colors is included in almost any graphic program.
If your problem is the serial conversion of many image files then you 
need e.g. GraphicConverter by Thorsten Lemke on Mac (www.download.com). 
For this operation it has to be registered.
On PC I am using IrfanView (Win95, freeware) - oops it does not support 
inversion during batch conversions! - but still great and Xnview  
(http://perso.wanadoo.fr/pierre.g) wich really does it. It is also freeware.

F. Szalay


From nih-image-request@io.ece.drexel.edu Mon Apr 26 15:27 EDT 1999
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Date: Mon, 26 Apr 1999 12:15:01 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
cc: "Jared L. Rifkin" <jared_rifkin@qc.edu>
Subject: Re: FYI:Experiences with B/W G3 and Aurora Fuse
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URL:
http://www.auroradsgn.com/

Specs - see web pages

Regular price was $499, they have a lower educational price. 

DTL

--On Mon, Apr 26, 1999 11:47 AM -0400 "Jared L. Rifkin"
<jared_rifkin@qc.edu> wrote:

> i too have been updated/outcarded/out'buz'ed by apple trying to do better 
> and losing something in the translation.
> my research also involves time/space analysis of microscopic objects.
> i would appreciate any information on this aurora fuze card (specs, url, 
> price, resolution, resolution, resolution etc.)
> 





From nih-image-request@io.ece.drexel.edu Tue Apr 27 05:25 EDT 1999
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From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Thresholding
Date: Tue, 27 Apr 1999 09:50:19 +0200
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hi!

I understand that the  threshold of an image is based on the analysis of
the histogram, but I am wondering how thresholding is performed in the
NIH Image program. Which algorithm is used in order to automatically
find the threshold value??? 

Thanks.

Gary.


From nih-image-d-request@io.ece.drexel.edu Tue Apr 27 05:42 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #97
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 97

Today's Topics:
  Re: Digital Camera and Otoliths       [ Ben Elkin <elk@igb.fhg.de> ]
  Re: nih-image-d Digest V99 #95        [ Ard Jonker <a.jonker@amc.uva.nl> ]
  transforming pixels into real coordi  [ Skye Bender-deMoll <skyebend@bennin ]
  Convert Color negs                    [ "=?iso-8859-1?Q?=22Dr._Luis_F._Hern ]
  Re: Convert Color negs                [ Wayne Rasband <wayne@codon.nih.gov> ]
  Re: FYI:Experiences with B/W G3 and   [ "Jared L. Rifkin" <jared_rifkin@qc. ]
  Re: Convert Color negs                [ Szalay Ferenc <fszalay@ns.univet.hu ]
  Re: FYI:Experiences with B/W G3 and   [ David Linker <dtlinker@u.washington ]
  Thresholding                          [ Gary Chinga <gary.chinga@pfi.no> ]

------------------------------

Date: Mon, 26 Apr 1999 09:44:55 +0200
From: Ben Elkin <elk@igb.fhg.de>
To: nih-image@io.ece.drexel.edu
Cc: gray@matcogroup.com
Subject: Re: Digital Camera and Otoliths
Message-Id: <l03130300b349c3c4a989@[129.233.21.143]>
Content-Type: text/plain; charset="us-ascii"

Anthony Boxshall wrote:
>
>We will be reading otoliths (fish ear bones) using a Nikon inverted scope
>and/or Leica dissecting scope.  We want to get a digital camera to do this
>and are casting around for suggestions of brands to buy.  We have heard
>good reports of the Real 14 but at $9000 we would like to pay less.
>
>Does anyone have a suggestion list of good brands to look at?
>OR better still, bought one recently and got any comments?
>

I have sent a short description of a digital camera from Sound Vision (
http://www.cmospro.com/ ) to this list a while ago. Since then we din't use
the camera too often (optical microscopy is an ancillary technique for us),
and the use was for relatively routine tasks only - but we were *fully*
satisfied with the camera. In the next couple of days we are going to test
it for fluorescence.

-------------------------------------------
>* This is a camera for still images only *
>
>The first impressions are good. The camera is a digital one, which means
>that the signal from the light detector is converted *once* into the
>digital form and transferred digitally to the computer via SCSI interface.
>This means:
>
>1. No pixel jitter
>2. You don't need any frame grabber.
>3. You can use it with Mac or Wintel.
>4. From 2. and 3. follows that you don't need a dedicated computer. You
>can use one which happens to stand where you take your pictures.
>
>The software (plugin for Photoshop) is OK, but (on a Mac) you have to
>allocate at least 20 MB to Photoshop. I haven't yet tested the plugin it
>with NIH-Image.
>
>Camera uses an internal rotating RGB filter wheel with a monochrome sensor
>(and trades off the aquisition speed for the image quality).
>
>The resolution (non-interpolated) is 800*960 (RGB). The camera captures
>with 10 bit per pixel and color channel, but normally saves as 24 bit RGB.
>
>It provides "live" (a couple of frames/sec) video for image ajustment.
>
>On a microscopy image produced with this camera I could actually see more
>details as compared to looking through the microscope ocular.
>
>The camera has C-mount and comes with reasonable accessory if you want.
>The camera price in USA is below $2000.
>
>The user manual is published on the company web site (
>http://www.cmospro.com/images/Cp.pdf ).




Ben Elkin

=======================================
elk@igb.fhg.de

http://www.igb.fhg.de/GVT/

Fraunhofer Institute for Interfacial Technology and Bioengineering
                    (fuer Grenzflaechen und Bioverfahrenstechnik)

Nobelstr. 12    D-70569 Stuttgart    Germany

Tel. +49 - 711 - 970-4144, -4161
Fax                 -4200

------------------------------

Date: Mon, 26 Apr 1999 10:06:20 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #95
Message-Id: <l03130304b349cdbf9bc0@[145.117.43.50]>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 8bit

> I need to convert variable format text files either to directly load or
>to the
>"accepted" ASCI text import format for NIH.  I have row data in variable
>number
>of fields (column) per line so that each row of the grid (image) is
>contained on multiple lines (variable number of lines due to the size of
>the numbers but each row would have the same total number of readings).
>Due to the output from the other grid program, each line of the ASCII
>file has a hard return so that NIH interprets each line as a row.  I
>actually have over 256 rows in the grid so that a
>spreadsheet/spreadsheet macro solution breaks down.  Any help for a
>macro or even how to go about this problem would be greatly appreciated.

I wrote macros that generate (not read) files for virtual reality. You could see how I have solved particular matters and maybe benefit from it. Given its goal, 90% may be trendy waste, but 10% may be useful to you.

There are 3 limitations to the use of these macros: rights remain with me, you cannot directly distribute any of the source, only via a request to me, I cannot be held responsible for any malfuncitoning of the macros (though I'd like to hear from them, to improve the macros).

Regards, Ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156

------------------------------

Date: Mon, 26 Apr 99 10:44:18 -0400
From: Skye Bender-deMoll <skyebend@bennington.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: transforming pixels into real coordinates
Message-Id: <199904261433.KAA19650@barid.bennington.edu>
Content-Type: text/plain; charset="US-ASCII"

I'm using Scion image to extract the paths of people's motion from video 
clips.  I have writen a macro (with the help of some people on this list- 
thanks) which allows me to get the XY of the pixel location of each 
person in each frame as they move.  However, many of the clips are not 
shot from directly overhead.  Because there is a fair ammount of 
perspective in each image, the regular measurement commands won't give me 
the real distances across the entire frame.  I would like to be able to 
transform the XY data I have from the plane of the image to the actual 
plane which the people are moving in.  Has anyone done this?  I would 
greatly appriciate suggestions and/or sources for macros or equations 
related to perspective transformation.   
        Thanks,
            -Skye

P.S.  Does anyone know of any freeware for Macintosh with X-Y-Z plotting 
capabilites?  Most programs seem to do 3D histograms, but won't do real 
plotting.  

                                  -000-
Skye Bender-deMoll 
  | Bennington College
  | Bennington VT 05201
  | 802.440.4626 
  |---------------------- skyebend@bennington.edu
  | 38755 Reed Road
  | Nehalem OR 97131
  | 503.368.6294

------------------------------

Date: Mon, 26 Apr 1999 12:21:09 -0300
From: "=?iso-8859-1?Q?=22Dr._Luis_F._Hern=E1ndez=22?="  <lhernan@criba.edu.ar>
To: nih-image@io.ece.drexel.edu
Subject: Convert Color negs
Message-Id: <v03130300b34a3340edc5@[170.210.187.214]>
Content-Type: text/plain; charset="us-ascii"

Imagers:
We want to convert scanned 35 mm color negatives (obtained with an UMAX
1200S plus its Transparency Unit) into positive color images. How can we do
this?
Is Photoshop the only alternative?. Is there any plug-in for Image or
Photoshop that can easily perform this operation? Is there any other source
of information (web site) to go through?
Many thanks for your help.
Kind regards,



_______________________________________________________
Dr. Luis F. Hernandez, Ph.D.
Laboratorio de Botanica
Departamento de Agronomia
U N I V E R S I D A D  N A C I O N A L  D E L  S U R
8000. Bahia Blanca - ARGENTINA

<mailto: lhernan@criba.edu.ar>
Telefonos (0291) 453-4775/453-0024
FAX: 54 - 0291 - 452-1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.

------------------------------

Date: Mon, 26 Apr 1999 11:48:33 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Convert Color negs
Message-Id: <v03007803b34a3a56849f@[128.231.99.206]>
Content-Type: text/plain; charset="us-ascii"

>Imagers:
>We want to convert scanned 35 mm color negatives (obtained with an UMAX
>1200S plus its Transparency Unit) into positive color images. How can we do
>this?
>Is Photoshop the only alternative?. Is there any plug-in for Image or
>Photoshop that can easily perform this operation? Is there any other source
>of information (web site) to go through?
>Many thanks for your help.
>Kind regards,

The "Invert" command in ImageJ (http://rsb.info.nih.gov/ij/) will do this.
Compared to NIH Image, ImageJ has much better support for RGB images.

-wayne

------------------------------

Date: Mon, 26 Apr 99 11:47:03 -0400
From: "Jared L. Rifkin" <jared_rifkin@qc.edu>
To: <nih-image@io.ece.drexel.edu>, <nih-image@io.ece.drexel.edu>
Subject: Re: FYI:Experiences with B/W G3 and Aurora Fuse
Message-ID: <E891CF190F@qc1.qc.edu>
Content-Type: text/plain; charset="US-ASCII"

i too have been updated/outcarded/out'buz'ed by apple trying to do better 
and losing something in the translation.
my research also involves time/space analysis of microscopic objects.
i would appreciate any information on this aurora fuze card (specs, url, 
price, resolution, resolution, resolution etc.)

------------------------------

Date: Mon, 26 Apr 1999 18:18:49 +0200 (MET DST)
From: Szalay Ferenc <fszalay@ns.univet.hu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Convert Color negs
Message-ID: <Pine.SUN.3.91.990426175859.17526A-100000@ns.univet.hu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

To > Dr. Luis F. Hernandez, Ph.D.

> Imagers:
> We want to convert scanned 35 mm color negatives (obtained with an UMAX
> 1200S plus its Transparency Unit) into positive color images. How can we do
> this?
> Is Photoshop the only alternative?. Is there any plug-in for Image or
> Photoshop that can easily perform this operation? Is there any other source
> of information (web site) to go through?

Inversion of colors is included in almost any graphic program.
If your problem is the serial conversion of many image files then you 
need e.g. GraphicConverter by Thorsten Lemke on Mac (www.download.com). 
For this operation it has to be registered.
On PC I am using IrfanView (Win95, freeware) - oops it does not support 
inversion during batch conversions! - but still great and Xnview  
(http://perso.wanadoo.fr/pierre.g) wich really does it. It is also freeware.

F. Szalay

------------------------------

Date: Mon, 26 Apr 1999 12:15:01 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
cc: "Jared L. Rifkin" <jared_rifkin@qc.edu>
Subject: Re: FYI:Experiences with B/W G3 and Aurora Fuse
Message-ID: <221799.3134117701@huginn.medicine.washington.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

URL:
http://www.auroradsgn.com/

Specs - see web pages

Regular price was $499, they have a lower educational price. 

DTL

--On Mon, Apr 26, 1999 11:47 AM -0400 "Jared L. Rifkin"
<jared_rifkin@qc.edu> wrote:

> i too have been updated/outcarded/out'buz'ed by apple trying to do better 
> and losing something in the translation.
> my research also involves time/space analysis of microscopic objects.
> i would appreciate any information on this aurora fuze card (specs, url, 
> price, resolution, resolution, resolution etc.)
> 

------------------------------

Date: Tue, 27 Apr 1999 09:50:19 +0200
From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Thresholding
Message-ID: <c=NO%a=_%p=pfi%l=PFINT1-990427075019Z-985@pfint1.pfi.no>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

hi!

I understand that the  threshold of an image is based on the analysis of
the histogram, but I am wondering how thresholding is performed in the
NIH Image program. Which algorithm is used in order to automatically
find the threshold value??? 

Thanks.

Gary.

--------------------------------
End of nih-image-d Digest V99 Issue #97
***************************************

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Date: Tue, 27 Apr 1999 08:47:17 +0000
From: Marcia Goldfarb <anatekep@maine.rr.com>
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Gary:

My understanding is the threshold value is what the user considers
valid. I threshold at 2std from the mean using the histogram numbers.
This is based on the supposition of statistics that data points greater
than 2stds may be considered background.

Marcia Goldfarb
Anatek-EP
17 Bishop St
Portland, ME 04103

email: anatekep@maine.rr.com


From nih-image-request@io.ece.drexel.edu Tue Apr 27 10:04 EDT 1999
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From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
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>Gary:
>
>My understanding is the threshold value is what the user considers
>valid. I threshold at 2std from the mean using the histogram numbers.
>This is based on the supposition of statistics that data points greater
>than 2stds may be considered background.
>
>Marcia Goldfarb
>Anatek-EP
>17 Bishop St
>Portland, ME 04103
>
>email: anatekep@maine.rr.com

This very legitimate question is coming back at regular intervals. The
basic procedure is described in  Ridler and Calvard,IEEE Trans. Systems,
Man, Cybernetics Vol SMC8, No8, August 1978. Basically, the algorithm
defines the threshold in the middel between the average foreground value
and the average background value, using an iterative procedure. This
results in the optimal threshold, assuming that the probability of
misclassification of pixels in foreground and background is the same, and
assuming that the partition of foreground and background is the same. (As
this is almost never true, the algorithm has a slight bias in favor of the
smallest area. If you are interested I can post a small macro that takes
care of this, and also can shift the threshold value according to a preset
p value for the foreground, making the thresholding more or less critical
than 50-50).

Arnout



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>>>> Arnout Ruifrok <arnout@odin.mdacc.tmc.edu> 04/27 10:04 AM >>>
>>Gary:
>>
>>My understanding is the threshold value is what the user considers
>>valid. I threshold at 2std from the mean using the histogram
numbers.
>>This is based on the supposition of statistics that data points
greater
>>than 2stds may be considered background.
>>
>>Marcia Goldfarb
>>Anatek-EP
>>17 Bishop St
>>Portland, ME 04103
>>
>>email: anatekep@maine.rr.com 
>
>This very legitimate question is coming back at regular intervals.
The
>basic procedure is described in  Ridler and Calvard,IEEE Trans.
Systems,
>Man, Cybernetics Vol SMC8, No8, August 1978. Basically, the algorithm
>defines the threshold in the middel between the average foreground
value
>and the average background value, using an iterative procedure. This
>results in the optimal threshold, assuming that the probability of
>misclassification of pixels in foreground and background is the same,
and
>assuming that the partition of foreground and background is the same.
(As
>this is almost never true, the algorithm has a slight bias in favor of
the
>smallest area. If you are interested I can post a small macro that
takes
>are of this, and also can shift the threshold value according to a
preset
> value for the foreground, making the thresholding more or less
critical
>than 50-50).
>
>Arnout

    I think that formal risk-analysis would actually include the
selection of 
a threshold as one of the optimal statistical outcomes of analyzing
what
the costs are of making mistakes in each direction (too high vs too
low).
All that is quite complex and the assumptions one uses are often 
hidden.  Besides people disaagree on how to do it.

    On a practical basis,  for things that really matter, what I'd 
suggest is writing a macro to automate the reading of images,
and to redo the analysis for a range of thresholds sufficient to 
cover what are 'surely' the range from too-low to too-high.

Then,  determine whatever your hypothesis is at each 
threshold, and maybe plot the results versus threshold.

If the conclusion is TRUE at all thresholds,  then it's 
pretty safe to go ahead and assert it.

If the conclusion CHANGES from True to False 
depending on threshold,  then be extremely 
cautious about what you want to assert, based
on this.

For example,  you may find that variable Y1 and 
Y2 both increase as threshold X increases, but
Y2 increases faster than Y1 and is always 
higher than Y1.   It would be SAFE to assert
that Y2 > Y1.   it would be risky to assert that
the RATIO of Y2 to Y1 is some particular
number, as that is sensitive to threshold. 

In fact, if at low thresholds Y1 is less than y2,
and at high thresholds Y1 is greater than Y2, 
it is unclear you can assert anything at all, 
unless you can demonstrate convincingly
that the threshold has to be on one or the
other sides of the point at which y1 and Y2
cross. 

You can wrap this in fancy statistical jargon and 
equations, but the logic of basic sensitivity 
analysis should be apparent to common sense,
and it's not a bad thing to check before 
publishing or otherwise placing a lot of 
reliance on threshold-sensitive conclusions.

Wade 


    
    




R. Wade Schuette
MCIT CDR Team
phone:  734 763-4486
alpha pager: 734 797-6622
Arbor Lakes, Bldg 3, Suite 1300
4251 Plymouth Rd.
Ann Arbor, MI 48105-2785


From nih-image-request@io.ece.drexel.edu Tue Apr 27 10:55 EDT 1999
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From: Michael Cammer <cammer@aecom.yu.edu>
Subject: Re: image cataloguing
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We have looked at two systems being marketed by Electroimage.
http://www.electroimage.com/  Due to the huge volume of our facility, we
are looking into their enterprise system.  The demo looks impressive and if
it works for us, we'll certainly let you know.  
********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************


From nih-image-request@io.ece.drexel.edu Tue Apr 27 17:09 EDT 1999
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Date: Tue, 27 Apr 1999 16:48:53 -0400
Subject: Re: Thresholding
From: "Ken Baker" <kwb@bserv.com>
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Dear Arnouk,
I would appreciate it if you would post the macro you mention.
Thanks in advance.
Regards,
        Ken
                --
KWB@bserv.com
519-853-4787


----------
>From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Thresholding
>Date: Tue, Apr 27, 1999, 9:52 AM
>

>>Gary:
>>
>>My understanding is the threshold value is what the user considers
>>valid. I threshold at 2std from the mean using the histogram numbers.
>>This is based on the supposition of statistics that data points greater
>>than 2stds may be considered background.
>>
>>Marcia Goldfarb
>>Anatek-EP
>>17 Bishop St
>>Portland, ME 04103
>>
>>email: anatekep@maine.rr.com
>
> This very legitimate question is coming back at regular intervals. The
> basic procedure is described in  Ridler and Calvard,IEEE Trans. Systems,
> Man, Cybernetics Vol SMC8, No8, August 1978. Basically, the algorithm
> defines the threshold in the middel between the average foreground value
> and the average background value, using an iterative procedure. This
> results in the optimal threshold, assuming that the probability of
> misclassification of pixels in foreground and background is the same, and
> assuming that the partition of foreground and background is the same. (As
> this is almost never true, the algorithm has a slight bias in favor of the
> smallest area. If you are interested I can post a small macro that takes
> care of this, and also can shift the threshold value according to a preset
> p value for the foreground, making the thresholding more or less critical
> than 50-50).
>
> Arnout
>
>
> 


From nih-image-d-request@io.ece.drexel.edu Wed Apr 28 06:20 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 98

Today's Topics:
  Re: Thresholding                      [ Marcia Goldfarb <anatekep@maine.rr. ]
  Re: Thresholding                      [ Arnout Ruifrok <arnout@odin.mdacc.t ]
  Re: Thresholding                      [ "Wade Schuette" <schuette@umich.edu ]
  Re: image cataloguing                 [ Michael Cammer <cammer@aecom.yu.edu ]
  Re: Thresholding                      [ "Ken Baker" <kwb@bserv.com> ]

------------------------------

Date: Tue, 27 Apr 1999 08:47:17 +0000
From: Marcia Goldfarb <anatekep@maine.rr.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Thresholding
Message-ID: <37257994.6A486F4F@maine.rr.com>
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Gary:

My understanding is the threshold value is what the user considers
valid. I threshold at 2std from the mean using the histogram numbers.
This is based on the supposition of statistics that data points greater
than 2stds may be considered background.

Marcia Goldfarb
Anatek-EP
17 Bishop St
Portland, ME 04103

email: anatekep@maine.rr.com

------------------------------

Date: Tue, 27 Apr 1999 08:52:01 -0500 (CDT)
From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Thresholding
Message-Id: <v03102800b34b28ba6d6e@[143.111.62.105]>
Content-Type: text/plain; charset="us-ascii"

>Gary:
>
>My understanding is the threshold value is what the user considers
>valid. I threshold at 2std from the mean using the histogram numbers.
>This is based on the supposition of statistics that data points greater
>than 2stds may be considered background.
>
>Marcia Goldfarb
>Anatek-EP
>17 Bishop St
>Portland, ME 04103
>
>email: anatekep@maine.rr.com

This very legitimate question is coming back at regular intervals. The
basic procedure is described in  Ridler and Calvard,IEEE Trans. Systems,
Man, Cybernetics Vol SMC8, No8, August 1978. Basically, the algorithm
defines the threshold in the middel between the average foreground value
and the average background value, using an iterative procedure. This
results in the optimal threshold, assuming that the probability of
misclassification of pixels in foreground and background is the same, and
assuming that the partition of foreground and background is the same. (As
this is almost never true, the algorithm has a slight bias in favor of the
smallest area. If you are interested I can post a small macro that takes
care of this, and also can shift the threshold value according to a preset
p value for the foreground, making the thresholding more or less critical
than 50-50).

Arnout

------------------------------

Date: Tue, 27 Apr 1999 10:33:52 -0400
From: "Wade Schuette" <schuette@umich.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Thresholding
Message-Id: <s7259298.004@umich.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline

>>>> Arnout Ruifrok <arnout@odin.mdacc.tmc.edu> 04/27 10:04 AM >>>
>>Gary:
>>
>>My understanding is the threshold value is what the user considers
>>valid. I threshold at 2std from the mean using the histogram
numbers.
>>This is based on the supposition of statistics that data points
greater
>>than 2stds may be considered background.
>>
>>Marcia Goldfarb
>>Anatek-EP
>>17 Bishop St
>>Portland, ME 04103
>>
>>email: anatekep@maine.rr.com 
>
>This very legitimate question is coming back at regular intervals.
The
>basic procedure is described in  Ridler and Calvard,IEEE Trans.
Systems,
>Man, Cybernetics Vol SMC8, No8, August 1978. Basically, the algorithm
>defines the threshold in the middel between the average foreground
value
>and the average background value, using an iterative procedure. This
>results in the optimal threshold, assuming that the probability of
>misclassification of pixels in foreground and background is the same,
and
>assuming that the partition of foreground and background is the same.
(As
>this is almost never true, the algorithm has a slight bias in favor of
the
>smallest area. If you are interested I can post a small macro that
takes
>are of this, and also can shift the threshold value according to a
preset
> value for the foreground, making the thresholding more or less
critical
>than 50-50).
>
>Arnout

    I think that formal risk-analysis would actually include the
selection of 
a threshold as one of the optimal statistical outcomes of analyzing
what
the costs are of making mistakes in each direction (too high vs too
low).
All that is quite complex and the assumptions one uses are often 
hidden.  Besides people disaagree on how to do it.

    On a practical basis,  for things that really matter, what I'd 
suggest is writing a macro to automate the reading of images,
and to redo the analysis for a range of thresholds sufficient to 
cover what are 'surely' the range from too-low to too-high.

Then,  determine whatever your hypothesis is at each 
threshold, and maybe plot the results versus threshold.

If the conclusion is TRUE at all thresholds,  then it's 
pretty safe to go ahead and assert it.

If the conclusion CHANGES from True to False 
depending on threshold,  then be extremely 
cautious about what you want to assert, based
on this.

For example,  you may find that variable Y1 and 
Y2 both increase as threshold X increases, but
Y2 increases faster than Y1 and is always 
higher than Y1.   It would be SAFE to assert
that Y2 > Y1.   it would be risky to assert that
the RATIO of Y2 to Y1 is some particular
number, as that is sensitive to threshold. 

In fact, if at low thresholds Y1 is less than y2,
and at high thresholds Y1 is greater than Y2, 
it is unclear you can assert anything at all, 
unless you can demonstrate convincingly
that the threshold has to be on one or the
other sides of the point at which y1 and Y2
cross. 

You can wrap this in fancy statistical jargon and 
equations, but the logic of basic sensitivity 
analysis should be apparent to common sense,
and it's not a bad thing to check before 
publishing or otherwise placing a lot of 
reliance on threshold-sensitive conclusions.

Wade 


    
    




R. Wade Schuette
MCIT CDR Team
phone:  734 763-4486
alpha pager: 734 797-6622
Arbor Lakes, Bldg 3, Suite 1300
4251 Plymouth Rd.
Ann Arbor, MI 48105-2785

------------------------------

Date: Tue, 27 Apr 1999 10:43:54 -0700
From: Michael Cammer <cammer@aecom.yu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: image cataloguing
Message-Id: <3.0.5.32.19990427104354.00a0eec0@mailserver.aecom.yu.edu>
Content-Type: text/plain; charset="us-ascii"

We have looked at two systems being marketed by Electroimage.
http://www.electroimage.com/  Due to the huge volume of our facility, we
are looking into their enterprise system.  The demo looks impressive and if
it works for us, we'll certainly let you know.  
********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************

------------------------------

Date: Tue, 27 Apr 1999 16:48:53 -0400
From: "Ken Baker" <kwb@bserv.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Thresholding
Message-Id: <199904272042.QAA27253@bserv.com>
Content-type: text/plain; charset="US-ASCII"
Content-transfer-encoding: 7bit

Dear Arnouk,
I would appreciate it if you would post the macro you mention.
Thanks in advance.
Regards,
        Ken
                --
KWB@bserv.com
519-853-4787


----------
>From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Thresholding
>Date: Tue, Apr 27, 1999, 9:52 AM
>

>>Gary:
>>
>>My understanding is the threshold value is what the user considers
>>valid. I threshold at 2std from the mean using the histogram numbers.
>>This is based on the supposition of statistics that data points greater
>>than 2stds may be considered background.
>>
>>Marcia Goldfarb
>>Anatek-EP
>>17 Bishop St
>>Portland, ME 04103
>>
>>email: anatekep@maine.rr.com
>
> This very legitimate question is coming back at regular intervals. The
> basic procedure is described in  Ridler and Calvard,IEEE Trans. Systems,
> Man, Cybernetics Vol SMC8, No8, August 1978. Basically, the algorithm
> defines the threshold in the middel between the average foreground value
> and the average background value, using an iterative procedure. This
> results in the optimal threshold, assuming that the probability of
> misclassification of pixels in foreground and background is the same, and
> assuming that the partition of foreground and background is the same. (As
> this is almost never true, the algorithm has a slight bias in favor of the
> smallest area. If you are interested I can post a small macro that takes
> care of this, and also can shift the threshold value according to a preset
> p value for the foreground, making the thresholding more or less critical
> than 50-50).
>
> Arnout
>
>
> 

--------------------------------
End of nih-image-d Digest V99 Issue #98
***************************************

From nih-image-request@io.ece.drexel.edu Wed Apr 28 09:32 EDT 1999
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From: Eric Bittman <elb@bio.umass.edu>
Subject: Re: Thresholding
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In my experience, 2SD is too lax a criterion even though by definition it
sets the 95% confidence interval. We typically use 3 or 3.5 SD's above the
mean, taken from some area we know (for biological reasons) contains no
specific staining. But before each major experiment we count cells in
several sections the old fashioned way (by eye), and then run a linear
regression vs. the count given by NIH Image using 2.5, 3, or 3.5 SD's. This
is advisable because both the intensity of background and foreground is
likely to vary from run to run, even if you use the same tissue and
antibody. We use whichever criterion number of SD's matches best to the eye
count.


Eric L. Bittman
Professor of Biology
University of Massachusetts
Amherst, MA 01003
(413)545-4344 (FAX: -3243)
http://www.umass.edu/neuro/faculty/bittman.html
http://www.umass.edu/cns/



From nih-image-request@io.ece.drexel.edu Wed Apr 28 09:47 EDT 1999
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Date: Wed, 28 Apr 1999 08:32:44 -0500 (CDT)
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To: nih-image@io.ece.drexel.edu
From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
Subject: Re: Thresholding
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>Dear Arnouk,
>I would appreciate it if you would post the macro you mention.
>Thanks in advance.
>Regards,
>        Ken
>                --
>KWB@bserv.com
>519-853-4787
>
>

With lots of disclaimers, and Wade Schuette's statement that basically no
method is a good method, I hope to give a workable method, that maybe gives
satisfactory results in most of the cases, and maybe not in some of the
cases, depending on the question and the answer you are looking for and
certainly not in the discontinuous y1 and y2 spaces, but hopefully will
suffice for splitting a gayscale image in a foreground (dark) and a
background (light), except when used on an inverted image, and vice versa,
using a method that includes consideration of the partitioning of the
pixels in foreground and background, with the possibility of selecting the
probability of maybe misclassifying a preset percentage of all
misclassified pixels as foreground, and assuming more or less Gaussian
distribution of the grayscale values in the background as well as the
foreground, which may or may not be actually true and should be tested
before drawing any conclusion.
Of course I am not responsible for any of the misclassifications, which
will with 100% certainty occur at an a priory unknown frequency.

Good luck,
Arnout



--------------------------------------------------------------
Macro 'threshold [T]';
var
p,a,b,c,q1,q2:real;
pic,mask,T1,T2,i:integer;

begin
ResetCounter;
pic:=pidnumber;
p:=getnumber('foreground p value (0<p<1):',0.5);
duplicate('mask');
mask:=pidnumber;
autothreshold;
makebinary;
selectall;
copy;
setoptions('area,mean,std.dev.');

for i:=1 to 2 do begin
repeat
 T2:=T1;
 ResetCounter;
 choosepic(pic);
 duplicate('temp');
 paste;
 Doand;
 setthreshold(1);
 measure;
 dispose;
 choosepic(mask);
 invert;
 selectall;
 copy;
 choosepic(pic);
 duplicate('temp');
 paste;
 Doand;
 setthreshold(1);
 measure;
 dispose;
  q1:=rarea[2]/(rarea[1]+rarea[2]);
  q2:=rarea[1]/(rarea[1]+rarea[2]);
  a:=sqr(rstddev[2])-sqr(rstddev[1]);
  b:=2*(rMean[2]*sqr(rstddev[1])-rMean[1]*sqr(rstddev[2]));
  c:=sqr(rstddev[2])*sqr(rMean[1])-sqr(rstddev[1])*sqr(rmean[2])
+2*sqr(rstddev[2])*sqr(rstddev[1])*ln(rstddev[1]/rstddev[2]*(q1*(1-p))/(q2*(p)))
;
T1:=(-b-sqrt(sqr(b)-4*a*c))/(2*a);
showmessage(a,'\',b,'\',c,'\',t1);
showmessage(rarea[1],'\',rmean[1],'\',rstddev[1],'\',rarea[2],'\',rmean[2],'\',r
stddev[2]);
 ChoosePic(pic);
 selectall;
 copy;
 choosepic(mask);
 setthreshold(T1);
 makebinary;
 invert;
 selectall;
 copy;
 killroi;
 showmessage('threshhold:',T1);
 until round(T1)=round(T2);
 end;
choosepic(mask);
dispose;
selectpic(pic);
setthreshold(T1);
killroi;
end;



From nih-image-request@io.ece.drexel.edu Wed Apr 28 10:29 EDT 1999
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From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Thresholding
Date: Wed, 28 Apr 1999 16:14:31 +0200
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Thanks for the macro and the reference, it is of great help.

Gary.
------------------------------------------------------------------
Gary Chinga
PhD student
The Norwegian University of Science and Technology
Dept. of Chem. Engineering
Sem Saelandsv. 4
Trondheim
N7034 Norway




>-----Original Message-----
>From:	Arnout Ruifrok [SMTP:arnout@odin.mdacc.tmc.edu]
>Sent:	28. april 1999 15:33
>To:	nih-image@io.ece.drexel.edu
>Subject:	Re: Thresholding
>
>>Dear Arnouk,
>>I would appreciate it if you would post the macro you mention.
>>Thanks in advance.
>>Regards,
>>        Ken
>>                --
>>KWB@bserv.com
>>519-853-4787
>>
>>
>
>With lots of disclaimers, and Wade Schuette's statement that basically no
>method is a good method, I hope to give a workable method, that maybe gives
>satisfactory results in most of the cases, and maybe not in some of the
>cases, depending on the question and the answer you are looking for and
>certainly not in the discontinuous y1 and y2 spaces, but hopefully will
>suffice for splitting a gayscale image in a foreground (dark) and a
>background (light), except when used on an inverted image, and vice versa,
>using a method that includes consideration of the partitioning of the
>pixels in foreground and background, with the possibility of selecting the
>probability of maybe misclassifying a preset percentage of all
>misclassified pixels as foreground, and assuming more or less Gaussian
>distribution of the grayscale values in the background as well as the
>foreground, which may or may not be actually true and should be tested
>before drawing any conclusion.
>Of course I am not responsible for any of the misclassifications, which
>will with 100% certainty occur at an a priory unknown frequency.
>
>Good luck,
>Arnout
>
>
>
>--------------------------------------------------------------
>Macro 'threshold [T]';
>var
>p,a,b,c,q1,q2:real;
>pic,mask,T1,T2,i:integer;
>
>begin
>ResetCounter;
>pic:=pidnumber;
>p:=getnumber('foreground p value (0<p<1):',0.5);
>duplicate('mask');
>mask:=pidnumber;
>autothreshold;
>makebinary;
>selectall;
>copy;
>setoptions('area,mean,std.dev.');
>
>for i:=1 to 2 do begin
>repeat
> T2:=T1;
> ResetCounter;
> choosepic(pic);
> duplicate('temp');
> paste;
> Doand;
> setthreshold(1);
> measure;
> dispose;
> choosepic(mask);
> invert;
> selectall;
> copy;
> choosepic(pic);
> duplicate('temp');
> paste;
> Doand;
> setthreshold(1);
> measure;
> dispose;
>  q1:=rarea[2]/(rarea[1]+rarea[2]);
>  q2:=rarea[1]/(rarea[1]+rarea[2]);
>  a:=sqr(rstddev[2])-sqr(rstddev[1]);
>  b:=2*(rMean[2]*sqr(rstddev[1])-rMean[1]*sqr(rstddev[2]));
>  c:=sqr(rstddev[2])*sqr(rMean[1])-sqr(rstddev[1])*sqr(rmean[2])
>+2*sqr(rstddev[2])*sqr(rstddev[1])*ln(rstddev[1]/rstddev[2]*(q1*(1-p))/(q2*(p
>)))
>;
>T1:=(-b-sqrt(sqr(b)-4*a*c))/(2*a);
>showmessage(a,'\',b,'\',c,'\',t1);
>showmessage(rarea[1],'\',rmean[1],'\',rstddev[1],'\',rarea[2],'\',rmean[2],'\
>',r
>stddev[2]);
> ChoosePic(pic);
> selectall;
> copy;
> choosepic(mask);
> setthreshold(T1);
> makebinary;
> invert;
> selectall;
> copy;
> killroi;
> showmessage('threshhold:',T1);
> until round(T1)=round(T2);
> end;
>choosepic(mask);
>dispose;
>selectpic(pic);
>setthreshold(T1);
>killroi;
>end;
>
>


From nih-image-request@io.ece.drexel.edu Wed Apr 28 15:34 EDT 1999
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Date: Wed, 28 Apr 1999 15:19:56 -0400 (EDT)
From: Vikas Prabhakar <vp@duke.edu>
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To: nih-image@io.ece.drexel.edu
Subject: Overlay Images in Color
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	I understand that Image can convert my tiff images 
	in grayscale to color using different colortables. 
	I want to produce an image that is an overlay of 5 
	images in different colors. Is there a built-in 
	macro to do this, or can it be done otherwise 
	simply? Thanks, Vikas


From nih-image-request@io.ece.drexel.edu Wed Apr 28 15:42 EDT 1999
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	for cshtest@io.ece.drexel.edu; Wed, 28 Apr 1999 15:42:07 -0400 (EDT)
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Date: Wed, 28 Apr 1999 15:30:16 -0400
To: nih-image@io.ece.drexel.edu
From: Deric Wisleder <dxw32@psu.edu>
Subject: Print header information ?
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--=====================_82087306==_.ALT
Content-Type: text/plain; charset="us-ascii"

Hello again,

I thought it would be simple to view and print all the dicom header fields from
MR images, but I have not yet found an accomodating software.  I downloaded
"Windows Hexadecimal Editor for Windows 95 (WHexEd95) version 1.2".  It
presents the information in a jumbled column down the right hand side.  


My question again.

I am using Scion release beta 3b which I think is up to date.  My images are
MRI data converted to .acr (DICOM 2) format (DICOM 3 .dcm will not import).  

I can view a few header fields, but there is much more information that I can
not view.  OSIRIS (another software) will display extensive header information,
but it will not print it.  Can someone help me to view and print image header
information?  Thank you very much.

Sincerly,

Deric Wisleder 

--=====================_82087306==_.ALT
Content-Type: text/html; charset="us-ascii"

<html>
<font size=3>Hello again,<br>
<br>
I thought it would be simple to view and print all the dicom header
fields from MR images, but I have not yet found an accomodating
software.&nbsp; I downloaded &quot;Windows Hexadecimal Editor for Windows
95 (WHexEd95) version 1.2&quot;.&nbsp; It presents the information in a
jumbled column down the right hand side.&nbsp; <br>
<br>
<br>
My question again.<br>
<br>
I am using Scion release beta 3b which I think is up to date.&nbsp; My
images are MRI data converted to .acr (DICOM 2) format (DICOM 3 .dcm will
not import).&nbsp; <br>
<br>
I can view a few header fields, but there is much more information that I
can not view.&nbsp; OSIRIS (another software) will display extensive
header information, but it will not print it.&nbsp; Can someone help me
to view and print image header information?&nbsp; Thank you very
much.<br>
<br>
Sincerly,<br>
<br>
Deric Wisleder </font><br>
</html>

--=====================_82087306==_.ALT--


From nih-image-d-request@io.ece.drexel.edu Thu Apr 29 06:19 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #99
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 99

Today's Topics:
  Re: Thresholding                      [ Eric Bittman <elb@bio.umass.edu> ]
  Re: Thresholding                      [ Arnout Ruifrok <arnout@odin.mdacc.t ]
  RE: Thresholding                      [ Gary Chinga <gary.chinga@pfi.no> ]
  Overlay Images in Color               [ Vikas Prabhakar <vp@duke.edu> ]
  Print header information ?            [ Deric Wisleder <dxw32@psu.edu> ]

------------------------------

Date: Wed, 28 Apr 1999 09:15:26 -0400
From: Eric Bittman <elb@bio.umass.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Thresholding
Message-Id: <l03102805b34cb9988b0b@[128.119.55.182]>
Content-Type: text/plain; charset="us-ascii"

In my experience, 2SD is too lax a criterion even though by definition it
sets the 95% confidence interval. We typically use 3 or 3.5 SD's above the
mean, taken from some area we know (for biological reasons) contains no
specific staining. But before each major experiment we count cells in
several sections the old fashioned way (by eye), and then run a linear
regression vs. the count given by NIH Image using 2.5, 3, or 3.5 SD's. This
is advisable because both the intensity of background and foreground is
likely to vary from run to run, even if you use the same tissue and
antibody. We use whichever criterion number of SD's matches best to the eye
count.


Eric L. Bittman
Professor of Biology
University of Massachusetts
Amherst, MA 01003
(413)545-4344 (FAX: -3243)
http://www.umass.edu/neuro/faculty/bittman.html
http://www.umass.edu/cns/

------------------------------

Date: Wed, 28 Apr 1999 08:32:44 -0500 (CDT)
From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Thresholding
Message-Id: <v03102800b34c781a2ec6@[143.111.62.105]>
Content-Type: text/plain; charset="us-ascii"

>Dear Arnouk,
>I would appreciate it if you would post the macro you mention.
>Thanks in advance.
>Regards,
>        Ken
>                --
>KWB@bserv.com
>519-853-4787
>
>

With lots of disclaimers, and Wade Schuette's statement that basically no
method is a good method, I hope to give a workable method, that maybe gives
satisfactory results in most of the cases, and maybe not in some of the
cases, depending on the question and the answer you are looking for and
certainly not in the discontinuous y1 and y2 spaces, but hopefully will
suffice for splitting a gayscale image in a foreground (dark) and a
background (light), except when used on an inverted image, and vice versa,
using a method that includes consideration of the partitioning of the
pixels in foreground and background, with the possibility of selecting the
probability of maybe misclassifying a preset percentage of all
misclassified pixels as foreground, and assuming more or less Gaussian
distribution of the grayscale values in the background as well as the
foreground, which may or may not be actually true and should be tested
before drawing any conclusion.
Of course I am not responsible for any of the misclassifications, which
will with 100% certainty occur at an a priory unknown frequency.

Good luck,
Arnout



--------------------------------------------------------------
Macro 'threshold [T]';
var
p,a,b,c,q1,q2:real;
pic,mask,T1,T2,i:integer;

begin
ResetCounter;
pic:=pidnumber;
p:=getnumber('foreground p value (0<p<1):',0.5);
duplicate('mask');
mask:=pidnumber;
autothreshold;
makebinary;
selectall;
copy;
setoptions('area,mean,std.dev.');

for i:=1 to 2 do begin
repeat
 T2:=T1;
 ResetCounter;
 choosepic(pic);
 duplicate('temp');
 paste;
 Doand;
 setthreshold(1);
 measure;
 dispose;
 choosepic(mask);
 invert;
 selectall;
 copy;
 choosepic(pic);
 duplicate('temp');
 paste;
 Doand;
 setthreshold(1);
 measure;
 dispose;
  q1:=rarea[2]/(rarea[1]+rarea[2]);
  q2:=rarea[1]/(rarea[1]+rarea[2]);
  a:=sqr(rstddev[2])-sqr(rstddev[1]);
  b:=2*(rMean[2]*sqr(rstddev[1])-rMean[1]*sqr(rstddev[2]));
  c:=sqr(rstddev[2])*sqr(rMean[1])-sqr(rstddev[1])*sqr(rmean[2])
+2*sqr(rstddev[2])*sqr(rstddev[1])*ln(rstddev[1]/rstddev[2]*(q1*(1-p))/(q2*(p)))
;
T1:=(-b-sqrt(sqr(b)-4*a*c))/(2*a);
showmessage(a,'\',b,'\',c,'\',t1);
showmessage(rarea[1],'\',rmean[1],'\',rstddev[1],'\',rarea[2],'\',rmean[2],'\',r
stddev[2]);
 ChoosePic(pic);
 selectall;
 copy;
 choosepic(mask);
 setthreshold(T1);
 makebinary;
 invert;
 selectall;
 copy;
 killroi;
 showmessage('threshhold:',T1);
 until round(T1)=round(T2);
 end;
choosepic(mask);
dispose;
selectpic(pic);
setthreshold(T1);
killroi;
end;

------------------------------

Date: Wed, 28 Apr 1999 16:14:31 +0200
From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Thresholding
Message-ID: <c=NO%a=_%p=pfi%l=PFINT1-990428141431Z-1343@pfint1.pfi.no>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

Thanks for the macro and the reference, it is of great help.

Gary.
------------------------------------------------------------------
Gary Chinga
PhD student
The Norwegian University of Science and Technology
Dept. of Chem. Engineering
Sem Saelandsv. 4
Trondheim
N7034 Norway




>-----Original Message-----
>From:	Arnout Ruifrok [SMTP:arnout@odin.mdacc.tmc.edu]
>Sent:	28. april 1999 15:33
>To:	nih-image@io.ece.drexel.edu
>Subject:	Re: Thresholding
>
>>Dear Arnouk,
>>I would appreciate it if you would post the macro you mention.
>>Thanks in advance.
>>Regards,
>>        Ken
>>                --
>>KWB@bserv.com
>>519-853-4787
>>
>>
>
>With lots of disclaimers, and Wade Schuette's statement that basically no
>method is a good method, I hope to give a workable method, that maybe gives
>satisfactory results in most of the cases, and maybe not in some of the
>cases, depending on the question and the answer you are looking for and
>certainly not in the discontinuous y1 and y2 spaces, but hopefully will
>suffice for splitting a gayscale image in a foreground (dark) and a
>background (light), except when used on an inverted image, and vice versa,
>using a method that includes consideration of the partitioning of the
>pixels in foreground and background, with the possibility of selecting the
>probability of maybe misclassifying a preset percentage of all
>misclassified pixels as foreground, and assuming more or less Gaussian
>distribution of the grayscale values in the background as well as the
>foreground, which may or may not be actually true and should be tested
>before drawing any conclusion.
>Of course I am not responsible for any of the misclassifications, which
>will with 100% certainty occur at an a priory unknown frequency.
>
>Good luck,
>Arnout
>
>
>
>--------------------------------------------------------------
>Macro 'threshold [T]';
>var
>p,a,b,c,q1,q2:real;
>pic,mask,T1,T2,i:integer;
>
>begin
>ResetCounter;
>pic:=pidnumber;
>p:=getnumber('foreground p value (0<p<1):',0.5);
>duplicate('mask');
>mask:=pidnumber;
>autothreshold;
>makebinary;
>selectall;
>copy;
>setoptions('area,mean,std.dev.');
>
>for i:=1 to 2 do begin
>repeat
> T2:=T1;
> ResetCounter;
> choosepic(pic);
> duplicate('temp');
> paste;
> Doand;
> setthreshold(1);
> measure;
> dispose;
> choosepic(mask);
> invert;
> selectall;
> copy;
> choosepic(pic);
> duplicate('temp');
> paste;
> Doand;
> setthreshold(1);
> measure;
> dispose;
>  q1:=rarea[2]/(rarea[1]+rarea[2]);
>  q2:=rarea[1]/(rarea[1]+rarea[2]);
>  a:=sqr(rstddev[2])-sqr(rstddev[1]);
>  b:=2*(rMean[2]*sqr(rstddev[1])-rMean[1]*sqr(rstddev[2]));
>  c:=sqr(rstddev[2])*sqr(rMean[1])-sqr(rstddev[1])*sqr(rmean[2])
>+2*sqr(rstddev[2])*sqr(rstddev[1])*ln(rstddev[1]/rstddev[2]*(q1*(1-p))/(q2*(p
>)))
>;
>T1:=(-b-sqrt(sqr(b)-4*a*c))/(2*a);
>showmessage(a,'\',b,'\',c,'\',t1);
>showmessage(rarea[1],'\',rmean[1],'\',rstddev[1],'\',rarea[2],'\',rmean[2],'\
>',r
>stddev[2]);
> ChoosePic(pic);
> selectall;
> copy;
> choosepic(mask);
> setthreshold(T1);
> makebinary;
> invert;
> selectall;
> copy;
> killroi;
> showmessage('threshhold:',T1);
> until round(T1)=round(T2);
> end;
>choosepic(mask);
>dispose;
>selectpic(pic);
>setthreshold(T1);
>killroi;
>end;
>
>

------------------------------

Date: Wed, 28 Apr 1999 15:19:56 -0400 (EDT)
From: Vikas Prabhakar <vp@duke.edu>
To: nih-image@io.ece.drexel.edu
Subject: Overlay Images in Color
Message-ID: <Pine.SOL.3.91.990428151044.1869A-100000@godzilla1.acpub.duke.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

	I understand that Image can convert my tiff images 
	in grayscale to color using different colortables. 
	I want to produce an image that is an overlay of 5 
	images in different colors. Is there a built-in 
	macro to do this, or can it be done otherwise 
	simply? Thanks, Vikas

------------------------------

Date: Wed, 28 Apr 1999 15:30:16 -0400
From: Deric Wisleder <dxw32@psu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Print header information ?
Message-Id: <4.1.19990428151519.00956f10@mail.psu.edu>
Content-Type: multipart/alternative;
	boundary="=====================_82087306==_.ALT"

--=====================_82087306==_.ALT
Content-Type: text/plain; charset="us-ascii"

Hello again,

I thought it would be simple to view and print all the dicom header fields from
MR images, but I have not yet found an accomodating software.  I downloaded
"Windows Hexadecimal Editor for Windows 95 (WHexEd95) version 1.2".  It
presents the information in a jumbled column down the right hand side.  


My question again.

I am using Scion release beta 3b which I think is up to date.  My images are
MRI data converted to .acr (DICOM 2) format (DICOM 3 .dcm will not import).  

I can view a few header fields, but there is much more information that I can
not view.  OSIRIS (another software) will display extensive header information,
but it will not print it.  Can someone help me to view and print image header
information?  Thank you very much.

Sincerly,

Deric Wisleder 

--=====================_82087306==_.ALT
Content-Type: text/html; charset="us-ascii"

<html>
<font size=3>Hello again,<br>
<br>
I thought it would be simple to view and print all the dicom header
fields from MR images, but I have not yet found an accomodating
software.&nbsp; I downloaded &quot;Windows Hexadecimal Editor for Windows
95 (WHexEd95) version 1.2&quot;.&nbsp; It presents the information in a
jumbled column down the right hand side.&nbsp; <br>
<br>
<br>
My question again.<br>
<br>
I am using Scion release beta 3b which I think is up to date.&nbsp; My
images are MRI data converted to .acr (DICOM 2) format (DICOM 3 .dcm will
not import).&nbsp; <br>
<br>
I can view a few header fields, but there is much more information that I
can not view.&nbsp; OSIRIS (another software) will display extensive
header information, but it will not print it.&nbsp; Can someone help me
to view and print image header information?&nbsp; Thank you very
much.<br>
<br>
Sincerly,<br>
<br>
Deric Wisleder </font><br>
</html>

--=====================_82087306==_.ALT--

--------------------------------
End of nih-image-d Digest V99 Issue #99
***************************************

From nih-image-request@io.ece.drexel.edu Thu Apr 29 14:49 EDT 1999
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Date: Thu, 29 Apr 1999 20:33:45 +0200
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From: "J.P. Poindessault" <jpp@campus.univ-poitiers.fr>
Subject: how to create a new 32bit real stack ?
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Hello,

I use Scion Image 1.62a.
I probably missed something but I do not find how to create a new stack of
32 bit real data in a macro.
 1- ImageMath(copy real,pid,pid,1,0,pid) where pid is for a 8bit image
outputs an error saying that the destination image is not real
 2- I did not found how to make a new stack from a real image in the macro
language, is there a WindowtoStack macro ?.

If someone can help, thanks.

Jean-Pierre


----------------------------------
Jean Pierre Poindessault
Laboratoire des Biomembranes et Signalisation Cellulaire
UMR 6558, Dpt Informatique - 86022 Poitiers Cedex - FRANCE
Phone:  33 (0) 5 49 45 36 3 8 - Fax: 33 (0) 5 49 45 40 14
------------------------------------



From nih-image-d-request@io.ece.drexel.edu Fri Apr 30 06:12 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #100
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 100

Today's Topics:
  how to create a new 32bit real stack  [ "J.P. Poindessault" <jpp@campus.uni ]
  averaging several images              [ "Hillman, Paul" <hillman@plk.af.mil ]

------------------------------

Date: Thu, 29 Apr 1999 20:33:45 +0200
From: "J.P. Poindessault" <jpp@campus.univ-poitiers.fr>
To: nih-image@io.ece.drexel.edu
Subject: how to create a new 32bit real stack ?
Message-Id: <l03102800b34e54e9f8a3@[193.51.68.110]>
Content-Type: text/plain; charset="us-ascii"

Hello,

I use Scion Image 1.62a.
I probably missed something but I do not find how to create a new stack of
32 bit real data in a macro.
 1- ImageMath(copy real,pid,pid,1,0,pid) where pid is for a 8bit image
outputs an error saying that the destination image is not real
 2- I did not found how to make a new stack from a real image in the macro
language, is there a WindowtoStack macro ?.

If someone can help, thanks.

Jean-Pierre


----------------------------------
Jean Pierre Poindessault
Laboratoire des Biomembranes et Signalisation Cellulaire
UMR 6558, Dpt Informatique - 86022 Poitiers Cedex - FRANCE
Phone:  33 (0) 5 49 45 36 3 8 - Fax: 33 (0) 5 49 45 40 14
------------------------------------

------------------------------

Date: Thu, 29 Apr 1999 15:02:39 -0600
From: "Hillman, Paul" <hillman@plk.af.mil>
To: "'nih-image-d@io.ece.drexel.edu'" <nih-image-d@io.ece.drexel.edu>
Subject: averaging several images
Message-ID: <178F01F1C3BBD2118DF30008C7331071018F87@de-x3.plk.af.mil>
Content-Type: text/plain;
	charset="windows-1252"
Content-Transfer-Encoding: 8bit

In image I saw image math where you can add, subtract, multiply, divide, two
images, then multiply by a constant and add or subtract a constant.

I would like to average several images. Although  this might be a good
"starter" macro, why reinvent the wheel. Is there a macro already to do
this?  Maybe average all the images in one folder?

Thanks all!

________________________________________________________________
"640K ought to be good enough for anybody."  Bill Gates

Paul Hillman         \____ ...,. ____/    hillman@plk.af.mil
StarFire Optical Range    ( o o )     P_D_Hillman@compuserve.com
AFRL/DES                   \   /         CIM: 71773,643 
3550 Aberdeen Ave SE        (_)          real time (505)846-5032
Kirtland AFB NM  87117                   FAX:(505)846-2213 
________________________________________________________________

--------------------------------
End of nih-image-d Digest V99 Issue #100
****************************************

From nih-image-request@io.ece.drexel.edu Fri Apr 30 15:33 EDT 1999
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Date: Fri, 30 Apr 1999 15:18:17 -0400 (EDT)
From: Elizabeth Esther Stillwell <estillw@emory.edu>
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To: nih-image@io.ece.drexel.edu
Subject: Pixel analysis
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I am looking at the aggregation of one protein (centrosomal), in Hela
cells  stained immunocytochemically in red, in response
the overexpression of another protein (also centrosomal) with a GFP- tag.
Because the GFP fluorescence  is stable under my fixation conditions, I
can look at both signals in each cell. 

The proteins co-localize, and I would to try to quantitate this phenomenon
using some some sort of pixel analysis. Can anyone suggest the best  way
to do this using NIH Image?

Thanks,
Elizabeth 



Elizabeth Stillwell
Department of Cell Biology
Emory University
1648 Pierce Drive
Atlanta, GA 30322


404-727-0445 phone
404-727-6256 fax



From nih-image-request@io.ece.drexel.edu Fri Apr 30 16:57 EDT 1999
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Resent-Date: Fri, 30 Apr 1999 16:57:34 -0400 (EDT)
Date: Fri, 30 Apr 1999 16:47:52 -0400
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
Subject: framegrabber for G3 powerbooks?
To: nih-image@io.ece.drexel.edu
Message-id: <v04011703b34f8e455673@[128.244.128.218]>
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I'll be getting a G3 PowerBook in the next several months and would like to
use it for b/w and color imaging applications, including quantitative
microscopy. I'm trying to understand what options I have for interfacing a
framegrabber and camera to these models. This will likely influence the
model of PowerBook I purchase.

Several things I'm confused about:

Are there any internal framegrabbers that can be used in PowerBooks? This
would be the best solution for me, because I could then use CCDs that I
currently have or could buy a scientific grade CCD camera.

Among the choices of ports on these machines are SCSI, PCIMIA, and Firewire
(IEEE1394). Are there external framegrabbers can be used with these ports,
and what other external hardware is needed to support or house these? Is
portability, noise, power, or assembly an issue with any of these? I
currently use framegrabbers that use PCI or NuBus internal slots in desktop
Macs, and have no experience with external boards. Are there other issues
re: external boards?

There are consumer and professional video cameras that can be connected to
Firewire ports. Can any of these these yield good quantitative data? Do any
of these have cmounts allowing use with a microscope? What about other
(forthcoming) cameras supporting FireWire?

Thanks.

Bill Christens-Barry

-------------------------
Bill Christens-Barry, PhD
Johns Hopkins University Applied Physics Laboratory
wacb@aplcomm.jhuapl.edu
-------------------------


From nih-image-request@io.ece.drexel.edu Fri Apr 30 20:29 EDT 1999
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Date: Fri, 30 Apr 1999 20:19:05 -0400 (EDT)
From: Elizabeth Esther Stillwell <estillw@emory.edu>
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Subject: Pixel analysis 
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I am looking at the aggregation of one protein (centrosomal), in Hela
cells  stained immunocytochemically in red, in response
the overexpression of another protein (also centrosomal) with a GFP- tag.
Because the GFP fluorescence  is stable under my fixation conditions, I
can look at both signals in each cell. 

The proteins co-localize, and I would to try to quantitate this phenomenon
using some some sort of pixel analysis. Can anyone suggest the best  way
to do this using NIH Image?

Thanks,
Elizabeth 



Elizabeth Stillwell
Department of Cell Biology
Emory University
1648 Pierce Drive
Atlanta, GA 30322


404-727-0445 phone
404-727-6256 fax




From nih-image-d-request@io.ece.drexel.edu Sat May  1 10:56 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #101
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 101

Today's Topics:
  Pixel analysis                        [ Elizabeth Esther Stillwell <estillw ]
  framegrabber for G3 powerbooks?       [ Bill Christens-Barry <wacb@aplcomm. ]
  Pixel analysis                        [ Elizabeth Esther Stillwell <estillw ]
  Re: framegrabber for G3 powerbooks?/  [ Jeremy Brown <brownj@netmatters.co. ]

------------------------------

Date: Fri, 30 Apr 1999 15:18:17 -0400 (EDT)
From: Elizabeth Esther Stillwell <estillw@emory.edu>
To: nih-image@io.ece.drexel.edu
Subject: Pixel analysis
Message-ID: <Pine.GSO.4.05.9904301455440.24120-100000@paladin.cc.emory.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I am looking at the aggregation of one protein (centrosomal), in Hela
cells  stained immunocytochemically in red, in response
the overexpression of another protein (also centrosomal) with a GFP- tag.
Because the GFP fluorescence  is stable under my fixation conditions, I
can look at both signals in each cell. 

The proteins co-localize, and I would to try to quantitate this phenomenon
using some some sort of pixel analysis. Can anyone suggest the best  way
to do this using NIH Image?

Thanks,
Elizabeth 



Elizabeth Stillwell
Department of Cell Biology
Emory University
1648 Pierce Drive
Atlanta, GA 30322


404-727-0445 phone
404-727-6256 fax

------------------------------

Date: Fri, 30 Apr 1999 16:47:52 -0400
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
To: nih-image@io.ece.drexel.edu
Subject: framegrabber for G3 powerbooks?
Message-id: <v04011703b34f8e455673@[128.244.128.218]>
Content-type: text/plain; charset=us-ascii
Content-transfer-encoding: 7BIT

I'll be getting a G3 PowerBook in the next several months and would like to
use it for b/w and color imaging applications, including quantitative
microscopy. I'm trying to understand what options I have for interfacing a
framegrabber and camera to these models. This will likely influence the
model of PowerBook I purchase.

Several things I'm confused about:

Are there any internal framegrabbers that can be used in PowerBooks? This
would be the best solution for me, because I could then use CCDs that I
currently have or could buy a scientific grade CCD camera.

Among the choices of ports on these machines are SCSI, PCIMIA, and Firewire
(IEEE1394). Are there external framegrabbers can be used with these ports,
and what other external hardware is needed to support or house these? Is
portability, noise, power, or assembly an issue with any of these? I
currently use framegrabbers that use PCI or NuBus internal slots in desktop
Macs, and have no experience with external boards. Are there other issues
re: external boards?

There are consumer and professional video cameras that can be connected to
Firewire ports. Can any of these these yield good quantitative data? Do any
of these have cmounts allowing use with a microscope? What about other
(forthcoming) cameras supporting FireWire?

Thanks.

Bill Christens-Barry

-------------------------
Bill Christens-Barry, PhD
Johns Hopkins University Applied Physics Laboratory
wacb@aplcomm.jhuapl.edu
-------------------------

------------------------------

Date: Fri, 30 Apr 1999 20:19:05 -0400 (EDT)
From: Elizabeth Esther Stillwell <estillw@emory.edu>
To: nih-image@io.ece.drexel.edu
Subject: Pixel analysis 
Message-ID: <Pine.GSO.4.05.9904302018440.1731-100000@paladin.cc.emory.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I am looking at the aggregation of one protein (centrosomal), in Hela
cells  stained immunocytochemically in red, in response
the overexpression of another protein (also centrosomal) with a GFP- tag.
Because the GFP fluorescence  is stable under my fixation conditions, I
can look at both signals in each cell. 

The proteins co-localize, and I would to try to quantitate this phenomenon
using some some sort of pixel analysis. Can anyone suggest the best  way
to do this using NIH Image?

Thanks,
Elizabeth 



Elizabeth Stillwell
Department of Cell Biology
Emory University
1648 Pierce Drive
Atlanta, GA 30322


404-727-0445 phone
404-727-6256 fax

------------------------------

Date: Sat, 01 May 1999 15:47:57 +0100
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: framegrabber for G3 powerbooks?/firewire is here!
Message-ID: <372B140D.3A213B3E@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Details of the first firewire C-mount cameras that I've come across can be
obtained from Aegis:

http://www.aegis-elec.com/v300.html


DFW-V300

640x480 non compressed 24 bit YUV digital output, 30 fps at this resolution
(uncompressed) and no additional power supply required.

There is also some hint of a DFW-V500, but I have been unable to get any
details on this out of sony's web sites.

Anyone out there with a Blue and White G3 tried the
DFW-V300 yet?

I don't have a price quote but I would assume that it is significantly cheaper
than most of the SCSI based options.

Lack of power supply makes it attractive for use with G3 PowerBooks, assuming
they do include fire wire?

Jeremy Brown


Bill Christens-Barry wrote:

> I'll be getting a G3 PowerBook in the next several months and would like to
> use it for b/w and color imaging applications, including quantitative
> microscopy. I'm trying to understand what options I have for interfacing a
> framegrabber and camera to these models. This will likely influence the
> model of PowerBook I purchase.
>
> Several things I'm confused about:
>
> Are there any internal framegrabbers that can be used in PowerBooks? This
> would be the best solution for me, because I could then use CCDs that I
> currently have or could buy a scientific grade CCD camera.
>
> Among the choices of ports on these machines are SCSI, PCIMIA, and Firewire
> (IEEE1394). Are there external framegrabbers can be used with these ports,
> and what other external hardware is needed to support or house these? Is
> portability, noise, power, or assembly an issue with any of these? I
> currently use framegrabbers that use PCI or NuBus internal slots in desktop
> Macs, and have no experience with external boards. Are there other issues
> re: external boards?
>
> There are consumer and professional video cameras that can be connected to
> Firewire ports. Can any of these these yield good quantitative data? Do any
> of these have cmounts allowing use with a microscope? What about other
> (forthcoming) cameras supporting FireWire?
>
> Thanks.
>
> Bill Christens-Barry
>
> -------------------------
> Bill Christens-Barry, PhD
> Johns Hopkins University Applied Physics Laboratory
> wacb@aplcomm.jhuapl.edu
> -------------------------

--------------------------------
End of nih-image-d Digest V99 Issue #101
****************************************

From nih-image-request@io.ece.drexel.edu Sat May  1 11:01 EDT 1999
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Date: Sat, 01 May 1999 15:47:57 +0100
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References: <v04011703b34f8e455673@[128.244.128.218]>
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Details of the first firewire C-mount cameras that I've come across can be
obtained from Aegis:

http://www.aegis-elec.com/v300.html


DFW-V300

640x480 non compressed 24 bit YUV digital output, 30 fps at this resolution
(uncompressed) and no additional power supply required.

There is also some hint of a DFW-V500, but I have been unable to get any
details on this out of sony's web sites.

Anyone out there with a Blue and White G3 tried the
DFW-V300 yet?

I don't have a price quote but I would assume that it is significantly cheaper
than most of the SCSI based options.

Lack of power supply makes it attractive for use with G3 PowerBooks, assuming
they do include fire wire?

Jeremy Brown


Bill Christens-Barry wrote:

> I'll be getting a G3 PowerBook in the next several months and would like to
> use it for b/w and color imaging applications, including quantitative
> microscopy. I'm trying to understand what options I have for interfacing a
> framegrabber and camera to these models. This will likely influence the
> model of PowerBook I purchase.
>
> Several things I'm confused about:
>
> Are there any internal framegrabbers that can be used in PowerBooks? This
> would be the best solution for me, because I could then use CCDs that I
> currently have or could buy a scientific grade CCD camera.
>
> Among the choices of ports on these machines are SCSI, PCIMIA, and Firewire
> (IEEE1394). Are there external framegrabbers can be used with these ports,
> and what other external hardware is needed to support or house these? Is
> portability, noise, power, or assembly an issue with any of these? I
> currently use framegrabbers that use PCI or NuBus internal slots in desktop
> Macs, and have no experience with external boards. Are there other issues
> re: external boards?
>
> There are consumer and professional video cameras that can be connected to
> Firewire ports. Can any of these these yield good quantitative data? Do any
> of these have cmounts allowing use with a microscope? What about other
> (forthcoming) cameras supporting FireWire?
>
> Thanks.
>
> Bill Christens-Barry
>
> -------------------------
> Bill Christens-Barry, PhD
> Johns Hopkins University Applied Physics Laboratory
> wacb@aplcomm.jhuapl.edu
> -------------------------


From nih-image-request@io.ece.drexel.edu Sat May  1 11:43 EDT 1999
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From: Mansoor@nso1.uchc.edu (Mansoor,George)
To: estillw@emory.edu (Elizabeth Esther Stillwell),
        nih-image@io.ece.drexel.edu
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is there a macro that will automatically measure bewteen two lines draw on a 
image? I wouldlike to trace a vessel and have a macro tat will give me the 
diameter automatically rather than having to manually measure it.


Thanks for the help
 ----------
From: Elizabeth Esther Stillwell
To: nih-image@io.ece.drexel.edu
Subject: Pixel analysis
Date: Friday, April 30, 1999 8:19PM





I am looking at the aggregation of one protein (centrosomal), in Hela
cells  stained immunocytochemically in red, in response
the overexpression of another protein (also centrosomal) with a GFP- tag.
Because the GFP fluorescence  is stable under my fixation conditions, I
can look at both signals in each cell.

The proteins co-localize, and I would to try to quantitate this phenomenon
using some some sort of pixel analysis. Can anyone suggest the best  way
to do this using NIH Image?

Thanks,
Elizabeth



Elizabeth Stillwell
Department of Cell Biology
Emory University
1648 Pierce Drive
Atlanta, GA 30322


404-727-0445 phone
404-727-6256 fax




From nih-image-request@io.ece.drexel.edu Sat May  1 14:57 EDT 1999
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Dear Elizabeth,

I was doing pretty much the same kind of work with two-color colocalization.
With advice from NIH Image group, I've developed a set of macros to do just 
that. I can post them here or send directly to you.

In short, once I (1) get "green" and "red" images, I (2) threshold them, and
then
merge them back (3) into color image and calculate the amount of overlap, 
this step also allows to visually compare the overlay to the original and
make sure
the overlap is close to what was there. A numerical output is printed into a
text file.

Colocalization study is much better to perform with confocal microscope, as you 
surely know, because you don't have false "colocalization" of signals from
different 
focal planes. Recent discussion in this list on dangers of thresholding will
be very 
helpful in interpretation of data, and making sure it's independent of the
selected
threshold level. 

BTW, I am very interested what are your fixation conditions:  in my experiments 
natural (e)GFP signal was way too weak in fixed cells, and I had to use
anti-GFP Abs 
+ FITC-coupled secondary for colocalization. I would appreciate it if you
email this 
information directly to me.

Alex Gimelbrant


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------------------------------

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nih-image-d Digest				Volume 99 : Issue 102

Today's Topics:
  RE: Pixel analysis                    [ Mansoor@nso1.uchc.edu (Mansoor,Geor ]
  Re: Pixel analysis                    [ alex gimelbrant <aagime0@pop.uky.ed ]

------------------------------

Date: Sat, 01 May 1999 11:22:54 -0400
From: Mansoor@nso1.uchc.edu (Mansoor,George)
To: estillw@emory.edu (Elizabeth Esther Stillwell),
        nih-image@io.ece.drexel.edu
Subject: RE: Pixel analysis
Message-ID: <1999May01.112700.1274.1784551@msgate.uchc.edu>
Content-Type: text/plain; charset="US-ASCII"

is there a macro that will automatically measure bewteen two lines draw on a 
image? I wouldlike to trace a vessel and have a macro tat will give me the 
diameter automatically rather than having to manually measure it.


Thanks for the help
 ----------
From: Elizabeth Esther Stillwell
To: nih-image@io.ece.drexel.edu
Subject: Pixel analysis
Date: Friday, April 30, 1999 8:19PM





I am looking at the aggregation of one protein (centrosomal), in Hela
cells  stained immunocytochemically in red, in response
the overexpression of another protein (also centrosomal) with a GFP- tag.
Because the GFP fluorescence  is stable under my fixation conditions, I
can look at both signals in each cell.

The proteins co-localize, and I would to try to quantitate this phenomenon
using some some sort of pixel analysis. Can anyone suggest the best  way
to do this using NIH Image?

Thanks,
Elizabeth



Elizabeth Stillwell
Department of Cell Biology
Emory University
1648 Pierce Drive
Atlanta, GA 30322


404-727-0445 phone
404-727-6256 fax

------------------------------

Date: Sat, 1 May 1999 14:46:07 -0400 (EDT)
From: alex gimelbrant <aagime0@pop.uky.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re:  Pixel analysis
Message-Id: <199905011846.OAA13222@pop.uky.edu>
Content-Type: text/plain; charset="us-ascii"

Dear Elizabeth,

I was doing pretty much the same kind of work with two-color colocalization.
With advice from NIH Image group, I've developed a set of macros to do just 
that. I can post them here or send directly to you.

In short, once I (1) get "green" and "red" images, I (2) threshold them, and
then
merge them back (3) into color image and calculate the amount of overlap, 
this step also allows to visually compare the overlay to the original and
make sure
the overlap is close to what was there. A numerical output is printed into a
text file.

Colocalization study is much better to perform with confocal microscope, as you 
surely know, because you don't have false "colocalization" of signals from
different 
focal planes. Recent discussion in this list on dangers of thresholding will
be very 
helpful in interpretation of data, and making sure it's independent of the
selected
threshold level. 

BTW, I am very interested what are your fixation conditions:  in my experiments 
natural (e)GFP signal was way too weak in fixed cells, and I had to use
anti-GFP Abs 
+ FITC-coupled secondary for colocalization. I would appreciate it if you
email this 
information directly to me.

Alex Gimelbrant

--------------------------------
End of nih-image-d Digest V99 Issue #102
****************************************

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From nih-image-request@io.ece.drexel.edu Mon May  3 11:05 EDT 1999
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Date: Mon, 03 May 1999 09:41:35 -0500 (CDT)
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From: David Morilak <morilak@uthscsa.edu>
Subject: Pixel analysis
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Elizabeth:

This might do what you want:

Capture the first image (eg red). Switch filters and capture your green
image without moving the specimen. Now open the images (one at a time) and
Threshold or Density Slice each one to get rid of background and maintain
signal (this is of course the most difficult part, but is really the
subject of another discussion). Then Make Binary (or Save as Binary - I
don't remember the exact command but the idea is to end up with two black &
white images, with signal being black). Analyze-Measure to get the area, in
sq pixels, represented by each signal independently. Now Select All on your
first image and Copy, then switch to your second image and Paste, then open
the Paste Control window and choose "And". Now if you Analyze-Measure you
will get the area, in sq pixels, of the overlap between the two images
which should represent the region of co-expression. You can express this as
a percentage of the area from each of the individual signals to get an
estimate of the degree of co-localization of the two signals.

In theory this should work as planned, but in practice I suspect the most
difficulty will arise when you try to isolate the signal in your
fluoresecnt images. Our eyes are great filters, and we easily ignore all
those irrelevant distractions when we look down the micrsocope that will
nonetheless be detected by your camera and may well fall within your
density slice. Also, this could be much more difficult if the intensity of
your signal shows a lot of variation across the specimen, or your
signal-to-noise is variable. But these aren't really issues of image
analysis, but rather of immunocytochemistry....

Good Luck!

-David Morilak



David Morilak, Ph.D.
Dept of Pharmacology
Univ Texas Health Science Center
7703 Floyd Curl Drive
San Antonio, TX 78284-7764

ph: 210-567-4174
FAX: 210-567-4303
E-mail: morilak@uthscsa.edu



From nih-image-request@io.ece.drexel.edu Mon May  3 16:16 EDT 1999
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From: "Hillman, Paul" <hillman@plk.af.mil>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: firewire and video
Date: Mon, 3 May 1999 13:54:11 -0600 
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Bill Christens recently asked about firewire and powerbooks for inputing
video.

The recent consumer DV camcorders use firewire.  There are two pin outs,
4pin and 6pin.  The B&W G3 macs use 6 pin, Apple and many computer cable
places have converter cables.  The other two pins are power.

The DV port runs at 10Mbps. I purchased a Sony media converter.  It does a
DV <-> video or S-video conversion.  I have used it to input video and audio
to my G3.

I am not too familiar, but I think 640x480x24bits x ~30frames is above this
bandwidth.  I don't know how to tell the Sony to just send 8bit grayscale.
I am not sure DV is specified for greyscale.

Just some items to look into.



________________________________________________________________
"640K ought to be good enough for anybody."  Bill Gates

Paul Hillman         \____ ...,. ____/    hillman@plk.af.mil
StarFire Optical Range    ( o o )     P_D_Hillman@compuserve.com
AFRL/DES                   \   /         CIM: 71773,643 
3550 Aberdeen Ave SE        (_)          real time (505)846-5032
Kirtland AFB NM  87117                   FAX:(505)846-2213 
________________________________________________________________


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Date: Mon, 03 May 1999 23:31:34 +0100
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The DFW-V300 apparently runs at 20 Megabytes /s which still does not quite add
up to 640x480x24bits x ~30frames/s, but there you go.

In theory 40 megabytes /s is possible with firewire (marginally slower than the
fastest SCSI standard currently available) but still very attractive. I imagine
that higher resolution cameras will make an appearance pretty soon to compete
with the existing SCSI based solutions.

Jeremy

"Hillman, Paul" wrote:

> Bill Christens recently asked about firewire and powerbooks for inputing
> video.
>
> The recent consumer DV camcorders use firewire.  There are two pin outs,
> 4pin and 6pin.  The B&W G3 macs use 6 pin, Apple and many computer cable
> places have converter cables.  The other two pins are power.
>
> The DV port runs at 10Mbps. I purchased a Sony media converter.  It does a
> DV <-> video or S-video conversion.  I have used it to input video and audio
> to my G3.
>
> I am not too familiar, but I think 640x480x24bits x ~30frames is above this
> bandwidth.  I don't know how to tell the Sony to just send 8bit grayscale.
> I am not sure DV is specified for greyscale.
>
> Just some items to look into.
>
> ________________________________________________________________
> "640K ought to be good enough for anybody."  Bill Gates
>
> Paul Hillman         \____ ...,. ____/    hillman@plk.af.mil
> StarFire Optical Range    ( o o )     P_D_Hillman@compuserve.com
> AFRL/DES                   \   /         CIM: 71773,643
> 3550 Aberdeen Ave SE        (_)          real time (505)846-5032
> Kirtland AFB NM  87117                   FAX:(505)846-2213
> ________________________________________________________________


From nih-image-request@io.ece.drexel.edu Mon May  3 20:14 EDT 1999
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hello... i am a new user of NIH-image (PC version)...
i want to interpolate between several 2D images to
construct one 3D volume... your help is most
appreciated.

_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com


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nih-image-d Digest				Volume 99 : Issue 103

Today's Topics:
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
  Pixel analysis                        [ David Morilak <morilak@uthscsa.edu> ]
  firewire and video                    [ "Hillman, Paul" <hillman@plk.af.mil ]
  Re: firewire and video                [ Jeremy Brown <brownj@netmatters.co. ]
  info                                  [ Mounir Zok <mouniros@yahoo.com> ]

------------------------------

Date: Mon, 3 May 1999 05:05:01 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199905030905.FAA06930@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
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Archive
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Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

------------------------------

Date: Mon, 03 May 1999 09:41:35 -0500 (CDT)
From: David Morilak <morilak@uthscsa.edu>
To: estillw@emory.edu
Cc: nih-image@io.ece.drexel.edu
Subject: Pixel analysis
Message-id: <l03130300b3531d8074e3@[129.111.17.122]>
Content-type: text/plain; charset=us-ascii
Content-transfer-encoding: 7BIT

Elizabeth:

This might do what you want:

Capture the first image (eg red). Switch filters and capture your green
image without moving the specimen. Now open the images (one at a time) and
Threshold or Density Slice each one to get rid of background and maintain
signal (this is of course the most difficult part, but is really the
subject of another discussion). Then Make Binary (or Save as Binary - I
don't remember the exact command but the idea is to end up with two black &
white images, with signal being black). Analyze-Measure to get the area, in
sq pixels, represented by each signal independently. Now Select All on your
first image and Copy, then switch to your second image and Paste, then open
the Paste Control window and choose "And". Now if you Analyze-Measure you
will get the area, in sq pixels, of the overlap between the two images
which should represent the region of co-expression. You can express this as
a percentage of the area from each of the individual signals to get an
estimate of the degree of co-localization of the two signals.

In theory this should work as planned, but in practice I suspect the most
difficulty will arise when you try to isolate the signal in your
fluoresecnt images. Our eyes are great filters, and we easily ignore all
those irrelevant distractions when we look down the micrsocope that will
nonetheless be detected by your camera and may well fall within your
density slice. Also, this could be much more difficult if the intensity of
your signal shows a lot of variation across the specimen, or your
signal-to-noise is variable. But these aren't really issues of image
analysis, but rather of immunocytochemistry....

Good Luck!

-David Morilak



David Morilak, Ph.D.
Dept of Pharmacology
Univ Texas Health Science Center
7703 Floyd Curl Drive
San Antonio, TX 78284-7764

ph: 210-567-4174
FAX: 210-567-4303
E-mail: morilak@uthscsa.edu

------------------------------

Date: Mon, 3 May 1999 13:54:11 -0600 
From: "Hillman, Paul" <hillman@plk.af.mil>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: firewire and video
Message-ID: <178F01F1C3BBD2118DF30008C7331071018F97@de-x3.plk.af.mil>
Content-Type: text/plain;
	charset="windows-1252"
Content-Transfer-Encoding: 8bit

Bill Christens recently asked about firewire and powerbooks for inputing
video.

The recent consumer DV camcorders use firewire.  There are two pin outs,
4pin and 6pin.  The B&W G3 macs use 6 pin, Apple and many computer cable
places have converter cables.  The other two pins are power.

The DV port runs at 10Mbps. I purchased a Sony media converter.  It does a
DV <-> video or S-video conversion.  I have used it to input video and audio
to my G3.

I am not too familiar, but I think 640x480x24bits x ~30frames is above this
bandwidth.  I don't know how to tell the Sony to just send 8bit grayscale.
I am not sure DV is specified for greyscale.

Just some items to look into.



________________________________________________________________
"640K ought to be good enough for anybody."  Bill Gates

Paul Hillman         \____ ...,. ____/    hillman@plk.af.mil
StarFire Optical Range    ( o o )     P_D_Hillman@compuserve.com
AFRL/DES                   \   /         CIM: 71773,643 
3550 Aberdeen Ave SE        (_)          real time (505)846-5032
Kirtland AFB NM  87117                   FAX:(505)846-2213 
________________________________________________________________

------------------------------

Date: Mon, 03 May 1999 23:31:34 +0100
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: firewire and video
Message-ID: <372E2393.165B4710@netmatters.co.uk>
Content-Type: text/plain; charset=iso-8859-1; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 8bit

The DFW-V300 apparently runs at 20 Megabytes /s which still does not quite add
up to 640x480x24bits x ~30frames/s, but there you go.

In theory 40 megabytes /s is possible with firewire (marginally slower than the
fastest SCSI standard currently available) but still very attractive. I imagine
that higher resolution cameras will make an appearance pretty soon to compete
with the existing SCSI based solutions.

Jeremy

"Hillman, Paul" wrote:

> Bill Christens recently asked about firewire and powerbooks for inputing
> video.
>
> The recent consumer DV camcorders use firewire.  There are two pin outs,
> 4pin and 6pin.  The B&W G3 macs use 6 pin, Apple and many computer cable
> places have converter cables.  The other two pins are power.
>
> The DV port runs at 10Mbps. I purchased a Sony media converter.  It does a
> DV <-> video or S-video conversion.  I have used it to input video and audio
> to my G3.
>
> I am not too familiar, but I think 640x480x24bits x ~30frames is above this
> bandwidth.  I don't know how to tell the Sony to just send 8bit grayscale.
> I am not sure DV is specified for greyscale.
>
> Just some items to look into.
>
> ________________________________________________________________
> "640K ought to be good enough for anybody."  Bill Gates
>
> Paul Hillman         \____ ...,. ____/    hillman@plk.af.mil
> StarFire Optical Range    ( o o )     P_D_Hillman@compuserve.com
> AFRL/DES                   \   /         CIM: 71773,643
> 3550 Aberdeen Ave SE        (_)          real time (505)846-5032
> Kirtland AFB NM  87117                   FAX:(505)846-2213
> ________________________________________________________________

------------------------------

Date: Mon, 3 May 1999 17:06:37 -0700 (PDT)
From: Mounir Zok <mouniros@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: info
Message-ID: <19990504000637.19312.rocketmail@web601.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

hello... i am a new user of NIH-image (PC version)...
i want to interpolate between several 2D images to
construct one 3D volume... your help is most
appreciated.

_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com

--------------------------------
End of nih-image-d Digest V99 Issue #103
****************************************

From nih-image-request@io.ece.drexel.edu Tue May  4 09:41 EDT 1999
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	for cshtest@io.ece.drexel.edu; Tue, 4 May 1999 09:41:06 -0400 (EDT)
Resent-Date: Tue, 4 May 1999 09:41:06 -0400 (EDT)
Message-ID: <19990504132322.26607.rocketmail@web125.yahoomail.com>
Date: Tue, 4 May 1999 06:23:22 -0700 (PDT)
From: Mounir Zok <mouniros@yahoo.com>
Subject: help with nih-imagej
To: nih-image@io.ece.drexel.edu
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i am working on a project where i have to interpolate
between ten two-dimensional graphic files (brain
sections) to produce one three-dimensional volume
(i.e. a brain volume). i am very new to imagej and can
use all help offered. thank you in advance.

_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-request@io.ece.drexel.edu Tue May  4 16:09 EDT 1999
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Resent-Date: Tue, 4 May 1999 16:09:13 -0400 (EDT)
Date: Tue, 04 May 1999 12:37:07 -0700
From: "Kevin E. Cooper" <kevin.cooper@asu.edu>
Subject: information on 3-d imaging
To: nih-image@io.ece.drexel.edu
Message-id: <003d01be9665$7eed5960$f524db81@enpc2294.eas.asu.edu>
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This is a multi-part message in MIME format.

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Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

I am also new to this news group and am interested in a similar concept =
as Mounir Zok. I would like to be able to take a top and side image of =
an object and convert that to a three dimensional image. I am not =
interested in displaying the 3-d image only obtaining a matrix in 3-d =
space that tells me the x,y,z coordinates of the bounded object. Any =
help on software that exists or coding that has been written for similar =
purposes would be greatly appreciated.
__________________________

Kevin Cooper
Arizona State University
College of Engineering And Applied Sciences
Department of Chemical, Bio and Materials Engineering
P O Box 876006
Tempe AZ 85287-6006
Phone: 602-965-1061
Fax: 602-965-0037

------=_NextPart_000_003A_01BE962A.D2423620
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD W3 HTML//EN">
<HTML>
<HEAD>

<META content=3Dtext/html;charset=3Diso-8859-1 =
http-equiv=3DContent-Type>
<META content=3D'"MSHTML 4.72.3110.7"' name=3DGENERATOR>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT color=3D#000000 face=3D"Times New Roman">I am also new to =
this news group=20
and am interested in a similar concept as Mounir Zok. I would like to be =
able to=20
take a top and side image of an object and convert that to a three =
dimensional=20
image. I am not interested in displaying the 3-d image only obtaining a =
matrix=20
in 3-d space that tells me the x,y,z coordinates of the bounded object. =
Any help=20
on software that exists or coding that has been written for similar =
purposes=20
would be greatly appreciated.</FONT></DIV>
<DIV><FONT color=3D#000000=20
face=3D"Times New Roman">__________________________</FONT></DIV>
<DIV><FONT color=3D#000000 face=3D"Times New Roman"></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000000 face=3D"Times New Roman">Kevin =
Cooper<BR>Arizona State=20
University<BR>College of Engineering And Applied Sciences<BR>Department =
of=20
Chemical, Bio and Materials Engineering<BR>P O Box 876006<BR>Tempe AZ=20
85287-6006<BR>Phone: 602-965-1061<BR>Fax:=20
602-965-0037</FONT></DIV></BODY></HTML>

------=_NextPart_000_003A_01BE962A.D2423620--


From nih-image-d-request@io.ece.drexel.edu Wed May  5 06:19 EDT 1999
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Date: Wed, 5 May 1999 06:19:42 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199905051019.GAA07253@io.ece.drexel.edu>
Subject: nih-image-d Digest V99 #104
X-Loop: nih-image-d@biomed.drexel.edu
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To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 104

Today's Topics:
  help with nih-imagej                  [ Mounir Zok <mouniros@yahoo.com> ]
  information on 3-d imaging            [ "Kevin E. Cooper" <kevin.cooper@asu ]

------------------------------

Date: Tue, 4 May 1999 06:23:22 -0700 (PDT)
From: Mounir Zok <mouniros@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: help with nih-imagej
Message-ID: <19990504132322.26607.rocketmail@web125.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

i am working on a project where i have to interpolate
between ten two-dimensional graphic files (brain
sections) to produce one three-dimensional volume
(i.e. a brain volume). i am very new to imagej and can
use all help offered. thank you in advance.

_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com

------------------------------

Date: Tue, 04 May 1999 12:37:07 -0700
From: "Kevin E. Cooper" <kevin.cooper@asu.edu>
To: nih-image@io.ece.drexel.edu
Subject: information on 3-d imaging
Message-id: <003d01be9665$7eed5960$f524db81@enpc2294.eas.asu.edu>
Content-type: multipart/alternative;
	boundary="----=_NextPart_000_003A_01BE962A.D2423620"

This is a multi-part message in MIME format.

------=_NextPart_000_003A_01BE962A.D2423620
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

I am also new to this news group and am interested in a similar concept =
as Mounir Zok. I would like to be able to take a top and side image of =
an object and convert that to a three dimensional image. I am not =
interested in displaying the 3-d image only obtaining a matrix in 3-d =
space that tells me the x,y,z coordinates of the bounded object. Any =
help on software that exists or coding that has been written for similar =
purposes would be greatly appreciated.
__________________________

Kevin Cooper
Arizona State University
College of Engineering And Applied Sciences
Department of Chemical, Bio and Materials Engineering
P O Box 876006
Tempe AZ 85287-6006
Phone: 602-965-1061
Fax: 602-965-0037

------=_NextPart_000_003A_01BE962A.D2423620
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD W3 HTML//EN">
<HTML>
<HEAD>

<META content=3Dtext/html;charset=3Diso-8859-1 =
http-equiv=3DContent-Type>
<META content=3D'"MSHTML 4.72.3110.7"' name=3DGENERATOR>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT color=3D#000000 face=3D"Times New Roman">I am also new to =
this news group=20
and am interested in a similar concept as Mounir Zok. I would like to be =
able to=20
take a top and side image of an object and convert that to a three =
dimensional=20
image. I am not interested in displaying the 3-d image only obtaining a =
matrix=20
in 3-d space that tells me the x,y,z coordinates of the bounded object. =
Any help=20
on software that exists or coding that has been written for similar =
purposes=20
would be greatly appreciated.</FONT></DIV>
<DIV><FONT color=3D#000000=20
face=3D"Times New Roman">__________________________</FONT></DIV>
<DIV><FONT color=3D#000000 face=3D"Times New Roman"></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000000 face=3D"Times New Roman">Kevin =
Cooper<BR>Arizona State=20
University<BR>College of Engineering And Applied Sciences<BR>Department =
of=20
Chemical, Bio and Materials Engineering<BR>P O Box 876006<BR>Tempe AZ=20
85287-6006<BR>Phone: 602-965-1061<BR>Fax:=20
602-965-0037</FONT></DIV></BODY></HTML>

------=_NextPart_000_003A_01BE962A.D2423620--

--------------------------------
End of nih-image-d Digest V99 Issue #104
****************************************

From nih-image-request@io.ece.drexel.edu Wed May  5 07:16 EDT 1999
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>     I am also new to this news group  and am interested in a similar concept as Mounir Zok. I would like to be able to  take a top and side image of an object and convert that to a three dimensional  image. I am not interested in displaying the 3-d image only obtaining a matrix  in 3-d space that tells me the x,y,z coordinates of the bounded object. Any help  on software that exists or coding that has been written for similar purposes  would be greatly appreciated. 

If you can segment the image based on the density of the brain vs. the density of the surrounding 'space', you can use the magic wand tool to catch the outline. With the help of Object-Image, you can turn the marching ants outline into an object of type ROI. Do this for all slices, then export the object xyz coordinates to a rotater file and look at the result. You cannot measure in rotator, but you can view the object and rotate it in realtime. The rotator input file is a series of (x,y,z) coordinates, probably exactly what you need as 'coordinates of the bounded object'.

Regards, Ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156



From nih-image-d-request@io.ece.drexel.edu Thu May  6 06:13 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 105

Today's Topics:
  Re: nih-image-d Digest V99 #104       [ Ard Jonker <a.jonker@amc.uva.nl> ]

------------------------------

Date: Wed, 5 May 1999 12:58:14 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #104
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>     I am also new to this news group  and am interested in a similar concept as Mounir Zok. I would like to be able to  take a top and side image of an object and convert that to a three dimensional  image. I am not interested in displaying the 3-d image only obtaining a matrix  in 3-d space that tells me the x,y,z coordinates of the bounded object. Any help  on software that exists or coding that has been written for similar purposes  would be greatly appreciated. 

If you can segment the image based on the density of the brain vs. the density of the surrounding 'space', you can use the magic wand tool to catch the outline. With the help of Object-Image, you can turn the marching ants outline into an object of type ROI. Do this for all slices, then export the object xyz coordinates to a rotater file and look at the result. You cannot measure in rotator, but you can view the object and rotate it in realtime. The rotator input file is a series of (x,y,z) coordinates, probably exactly what you need as 'coordinates of the bounded object'.

Regards, Ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156

--------------------------------
End of nih-image-d Digest V99 Issue #105
****************************************

From nih-image-request@io.ece.drexel.edu Thu May  6 08:40 EDT 1999
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From: Mark Vivino <mvivino@yahoo.com>
Subject: Project engineer
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PROJECT ENGINEERING
Onsite in Dade, Broward, Palm Beach areas of Florida. By remote or as
consultant elsewhere and anywhere in the world.

BIOMEDICAL ENGINEERING
Research and development for scientists, physicians and researchers,
Densitometry, Quantitative measurements, Systems Design, Medical systems,
Ophthalmic, cardiovascular and neurological systems and instrumentation

LABVIEW PROGRAMMER
VI, Data acquisition, Instrumentation, Test, Testing, Measurement, Imaging,
Control

VIDEO AND IMAGING
NIH Image, Framegrabbers, Video, Imaging, Cameras, CCD's, Tape recorders 

ELECTRICAL ENGINEERING
Computer automation, Computer control, Microprocessors, Systems Design

COMPUTER ENGINEERING
LabView, Fortran, Assembly, Pascal, C, Macintosh, Windows, DOS, VAX/VMS, MS
Office, Adobe

TELECOMMUNICATIONS
Data communications, Telecommunications Systems, Telephony


Contact:
Mark Vivino
mvivino@yahoo.com
305-324-6902

===
Mark A. Vivino
Biomedical Engineer
mvivino@yahoo.com
http://www.mindspring.com/~mvivino/
_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-request@io.ece.drexel.edu Thu May  6 08:50 EDT 1999
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Subject: ROI in object image
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I know I'm going to feel pretty stupid when someone points out how to do
this but I just blew an afternoon trying to figure it out and failed.

I'm trying to do a 3D wireframe reconstruction of serial sections through a
skull. I already have created wireframes by tracing the objects of interest
in every slice in the stack, and converted the outlines to a binary image
that makes a nice reconstruction when using the Project function in Image.

Now what I want to do is use Object Image to create an object file for
export to Rotater. It seems like I should be able to select the outlines
I've already created and make those the ROI object in each cell. But how do
I do that? I don't want to have to retrace every single outline in every
slice.

Gary Radice		804-289-8107
Department of Biology	804-289-8233 (FAX)
University of Richmond 	gradice@richmond.edu
Richmond VA 23173	



From nih-image-request@io.ece.drexel.edu Thu May  6 10:14 EDT 1999
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Hello Mark,
	My name is Diego Azcurra and I am an Electronic Engineer that work
in
 design and development of HW and SW in Siemens SA. 
 
		I want to receive more information about your email, if it
is possible. Because of my background, I think that I can apply to more than
one of the items, although I think that more information is necessary to
take a good decision.

		Looking for a soon answer, I greet you sincerely
 			
 							Diego Azcurra
 							

> -----Original Message-----
> From:	Mark Vivino [SMTP:mvivino@yahoo.com]
> Sent:	Thursday, May 06, 1999 9:26 AM
> To:	nih-image@io.ece.drexel.edu
> Subject:	Project engineer
> 
> PROJECT ENGINEERING
> Onsite in Dade, Broward, Palm Beach areas of Florida. By remote or as
> consultant elsewhere and anywhere in the world.
> 
> BIOMEDICAL ENGINEERING
> Research and development for scientists, physicians and researchers,
> Densitometry, Quantitative measurements, Systems Design, Medical systems,
> Ophthalmic, cardiovascular and neurological systems and instrumentation
> 
> LABVIEW PROGRAMMER
> VI, Data acquisition, Instrumentation, Test, Testing, Measurement,
> Imaging,
> Control
> 
> VIDEO AND IMAGING
> NIH Image, Framegrabbers, Video, Imaging, Cameras, CCD's, Tape recorders 
> 
> ELECTRICAL ENGINEERING
> Computer automation, Computer control, Microprocessors, Systems Design
> 
> COMPUTER ENGINEERING
> LabView, Fortran, Assembly, Pascal, C, Macintosh, Windows, DOS, VAX/VMS,
> MS
> Office, Adobe
> 
> TELECOMMUNICATIONS
> Data communications, Telecommunications Systems, Telephony
> 
> 
> Contact:
> Mark Vivino
> mvivino@yahoo.com
> 305-324-6902
> 
> ===
> Mark A. Vivino
> Biomedical Engineer
> mvivino@yahoo.com
> http://www.mindspring.com/~mvivino/
> _________________________________________________________
> Do You Yahoo!?
> Get your free @yahoo.com address at http://mail.yahoo.com

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5.5.2448.0">
<TITLE>RE: Project engineer</TITLE>
</HEAD>
<BODY>

<P><FONT FACE=3D"Arial">Hello Mark,</FONT>
<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <FONT FACE=3D"Arial">My =
name is Diego Azcurra and I am an Electronic Engineer that work =
in</FONT>
<BR><FONT FACE=3D"Arial">&nbsp;design and development of HW and SW in =
Siemens SA. </FONT>
<BR><FONT FACE=3D"Arial">&nbsp;</FONT>
<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <FONT FACE=3D"Arial">I want =
to receive more information about your email, if it is possible. =
Because of my background, I think that I can apply to more than one of =
the items, although I think that more information is necessary to take =
a good decision.</FONT></P>

<P>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <FONT FACE=3D"Arial">Looking =
for a soon answer, I greet you sincerely</FONT>
<BR><FONT FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </FONT>
<BR><FONT FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Diego Azcurra</FONT>
<BR><FONT FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </FONT>
</P>
<UL>
<P><FONT SIZE=3D1 FACE=3D"Arial">-----Original Message-----</FONT>
<BR><B><FONT SIZE=3D1 FACE=3D"Arial">From:&nbsp;&nbsp;</FONT></B> <FONT =
SIZE=3D1 FACE=3D"Arial">Mark Vivino [SMTP:mvivino@yahoo.com]</FONT>
<BR><B><FONT SIZE=3D1 FACE=3D"Arial">Sent:&nbsp;&nbsp;</FONT></B> <FONT =
SIZE=3D1 FACE=3D"Arial">Thursday, May 06, 1999 9:26 AM</FONT>
<BR><B><FONT SIZE=3D1 =
FACE=3D"Arial">To:&nbsp;&nbsp;&nbsp;&nbsp;</FONT></B> <FONT SIZE=3D1 =
FACE=3D"Arial">nih-image@io.ece.drexel.edu</FONT>
<BR><B><FONT SIZE=3D1 =
FACE=3D"Arial">Subject:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT>=
</B> <FONT SIZE=3D1 FACE=3D"Arial">Project engineer</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">PROJECT ENGINEERING</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Onsite in Dade, Broward, Palm Beach =
areas of Florida. By remote or as</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">consultant elsewhere and anywhere in =
the world.</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">BIOMEDICAL ENGINEERING</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Research and development for =
scientists, physicians and researchers,</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Densitometry, Quantitative =
measurements, Systems Design, Medical systems,</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Ophthalmic, cardiovascular and =
neurological systems and instrumentation</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">LABVIEW PROGRAMMER</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">VI, Data acquisition, =
Instrumentation, Test, Testing, Measurement, Imaging,</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Control</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">VIDEO AND IMAGING</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">NIH Image, Framegrabbers, Video, =
Imaging, Cameras, CCD's, Tape recorders </FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">ELECTRICAL ENGINEERING</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Computer automation, Computer =
control, Microprocessors, Systems Design</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">COMPUTER ENGINEERING</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">LabView, Fortran, Assembly, Pascal, =
C, Macintosh, Windows, DOS, VAX/VMS, MS</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Office, Adobe</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">TELECOMMUNICATIONS</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Data communications, =
Telecommunications Systems, Telephony</FONT>
</P>
<BR>

<P><FONT SIZE=3D2 FACE=3D"Arial">Contact:</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Mark Vivino</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">mvivino@yahoo.com</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">305-324-6902</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">=3D=3D=3D</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Mark A. Vivino</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Biomedical Engineer</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">mvivino@yahoo.com</FONT>
<BR><U><FONT COLOR=3D"#0000FF" SIZE=3D2 FACE=3D"Arial"><A =
HREF=3D"http://www.mindspring.com/~mvivino/" =
TARGET=3D"_blank">http://www.mindspring.com/~mvivino/</A></FONT></U>
<BR><FONT SIZE=3D2 =
FACE=3D"Arial">_________________________________________________________=
</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Do You Yahoo!?</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Get your free @yahoo.com address =
at</FONT><U> <FONT COLOR=3D"#0000FF" SIZE=3D2 FACE=3D"Arial"><A =
HREF=3D"http://mail.yahoo.com" =
TARGET=3D"_blank">http://mail.yahoo.com</A></FONT></U>
</P>
</UL>
</BODY>
</HTML>
------_=_NextPart_001_01BE97C8.24BD54D6--


From nih-image-request@io.ece.drexel.edu Thu May  6 10:32 EDT 1999
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Date: Thu, 6 May 1999 09:12:44 -0600
To: nih-image@io.ece.drexel.edu
From: "Randy M. Wadkins" <rwadkins@saci.org>
Subject: Metrowerks drops Pascal
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Hi All:
It was pointed out today on MacInTouch that Metrowerks will not be
supporting Mac Pascal after the current release.  This probably means no
compiler for OS X or anything from here on out.  All those concerned might
want to write Metrowerks and voice your concerns.

--Randy
******************************************************************
"To me, it's a good idea to always carry two sacks of something
when you walk around.  That way, if anybody says, 'Hey, can you
give me a hand?' You can say, 'Sorry, got these sacks.'"
--Jack Handy, _Deep_Thoughts_


Randy M. Wadkins, Ph.D.
Cancer Therapy & Research Center
Institute for Drug Development
14960 Omicron Drive
San Antonio, TX 78245
phone: (210)-677-3835
fax: (210)-677-0058
E-mail:  rwadkins@saci.org
CTRC Homepage: http://www.ctrc.saci.org
******************************************************************


From nih-image-request@io.ece.drexel.edu Thu May  6 11:35 EDT 1999
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Date: Thu, 06 May 1999 11:10:37 -0400
From: "Wade Schuette" <schuette@umich.edu>
To: nih-image@io.ece.drexel.edu, rwadkins@saci.org
Subject: Re: Metrowerks drops Pascal
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 Yeh, but cynical comment, it will probably be about as effective
as all the protests when Apple decided to drop support for Lisp,
as, you know, too small a market to matter anymore to them.

   On a purely pragmatic basis, I'd say EITHER find or create
a vendor that would be interested in supporting the product separately
(in which case a threat to abandon Metrowerks might have some clout),
OR pull out those Java books and start helping Wayne complete 
ImageJ's functionality.

   (Getting Apple involved in the protest might have more clout
anyway)

   Of those two choices, I'd go with Java.  Wayne's got the kernel
done
and it's just waiting on manpower to complete the same functionality
we
have now, including things like a retroactive macro
interpreter/complier
for all the existing code and expertise base in writing macros that,
one
would think, should qualify for SOME government biomedical grant. 

   Wade


>>> "Randy M. Wadkins" <rwadkins@saci.org> 05/06 10:31 AM >>>
Hi All:
It was pointed out today on MacInTouch that Metrowerks will not be
supporting Mac Pascal after the current release.  This probably means
no
compiler for OS X or anything from here on out.  All those concerned
might
want to write Metrowerks and voice your concerns.

--Randy
******************************************************************
"To me, it's a good idea to always carry two sacks of something
when you walk around.  That way, if anybody says, 'Hey, can you
give me a hand?' You can say, 'Sorry, got these sacks.'"
--Jack Handy, _Deep_Thoughts_


Randy M. Wadkins, Ph.D.
Cancer Therapy & Research Center
Institute for Drug Development
14960 Omicron Drive
San Antonio, TX 78245
phone: (210)-677-3835
fax: (210)-677-0058
E-mail:  rwadkins@saci.org 
CTRC Homepage: http://www.ctrc.saci.org 
******************************************************************


From nih-image-request@io.ece.drexel.edu Thu May  6 19:57 EDT 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: nih-image@io.ece.drexel.edu
Date:          Fri, 7 May 1999 9:50:06 +1000
Subject:       Re: ROI in object image
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>Date: Thu, 6 May 1999 08:29:46 -0400
>To: nih-image@io.ece.drexel.edu
>From: Gary Radice <gradice@richmond.edu>
>Subject: ROI in object image
>
>I know I'm going to feel pretty stupid when someone points out how to do
>this but I just blew an afternoon trying to figure it out and failed.
>
>I'm trying to do a 3D wireframe reconstruction of serial sections through 
>a
>skull. I already have created wireframes by tracing the objects of 
>interest
>in every slice in the stack, and converted the outlines to a binary image
>that makes a nice reconstruction when using the Project function in Image.
>
>Now what I want to do is use Object Image to create an object file for
>export to Rotater. It seems like I should be able to select the outlines
>I've already created and make those the ROI object in each cell. But how 
>do
>I do that? I don't want to have to retrace every single outline in every
>slice.
>
>Gary Radice		804-289-8107
>Department of Biology	804-289-8233 (FAX)
>University of Richmond 	gradice@richmond.edu
>Richmond VA 23173	

Reads like you had missed the point of how useful Object-Image is! :-)

Back at the tracing of the objects of interest to produce your binary 
image, you could have used Object-Image to record the tracing as 
Objects(polygon or ROI) which would have been non-destructive color 
overlays recorded as coordinate lists by Object-Image and exported direct 
to Rotator.

All is not lost however :-), you can now belatedly convert your binary 
outline stack to roi objects simply by wand'ing (or autoOutline) to obtain 
a roi on eack slice in turn and then roiToObject (by sequence menu or 
macro). That is all that is necessary to allow you to export wireframe to 
Rotator for active 3D display.

ie click on object tool, you will be lead by dialog through
new object file (object menu
define a roi object (by dragging to sequence window)

select wand tool
wand binary outline
move tool to sequence window (tool will change automatically to left arrow 
connected to a rect roi ) and click on roiObject.
next slice with '.' or pagedown key and repeat for stack.

exportXYZdata(object menu

fini
(Would have been much nicer at start with grayscale stack :-)

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-d-request@io.ece.drexel.edu Fri May  7 06:20 EDT 1999
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Subject: nih-image-d Digest V99 #106
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nih-image-d Digest				Volume 99 : Issue 106

Today's Topics:
  Project engineer                      [ Mark Vivino <mvivino@yahoo.com> ]
  ROI in object image                   [ Gary Radice <gradice@richmond.edu> ]
  RE: Project engineer                  [ =?iso-8859-1?Q?=22Azcurra=2C_Diego_ ]
  Metrowerks drops Pascal               [ "Randy M. Wadkins" <rwadkins@saci.o ]
  Re: Metrowerks drops Pascal           [ "Wade Schuette" <schuette@umich.edu ]
  Re: ROI in object image               [ GJOSS@rna.bio.mq.edu.au ]

------------------------------

Date: Thu, 6 May 1999 05:26:25 -0700 (PDT)
From: Mark Vivino <mvivino@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: Project engineer
Message-ID: <19990506122625.11633.rocketmail@send501.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

PROJECT ENGINEERING
Onsite in Dade, Broward, Palm Beach areas of Florida. By remote or as
consultant elsewhere and anywhere in the world.

BIOMEDICAL ENGINEERING
Research and development for scientists, physicians and researchers,
Densitometry, Quantitative measurements, Systems Design, Medical systems,
Ophthalmic, cardiovascular and neurological systems and instrumentation

LABVIEW PROGRAMMER
VI, Data acquisition, Instrumentation, Test, Testing, Measurement, Imaging,
Control

VIDEO AND IMAGING
NIH Image, Framegrabbers, Video, Imaging, Cameras, CCD's, Tape recorders 

ELECTRICAL ENGINEERING
Computer automation, Computer control, Microprocessors, Systems Design

COMPUTER ENGINEERING
LabView, Fortran, Assembly, Pascal, C, Macintosh, Windows, DOS, VAX/VMS, MS
Office, Adobe

TELECOMMUNICATIONS
Data communications, Telecommunications Systems, Telephony


Contact:
Mark Vivino
mvivino@yahoo.com
305-324-6902

===
Mark A. Vivino
Biomedical Engineer
mvivino@yahoo.com
http://www.mindspring.com/~mvivino/
_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com

------------------------------

Date: Thu, 6 May 1999 08:29:46 -0400
From: Gary Radice <gradice@richmond.edu>
To: nih-image@io.ece.drexel.edu
Subject: ROI in object image
Message-Id: <l03130300b357398dd7ec@[141.166.55.15]>
Content-Type: text/plain; charset="us-ascii"

I know I'm going to feel pretty stupid when someone points out how to do
this but I just blew an afternoon trying to figure it out and failed.

I'm trying to do a 3D wireframe reconstruction of serial sections through a
skull. I already have created wireframes by tracing the objects of interest
in every slice in the stack, and converted the outlines to a binary image
that makes a nice reconstruction when using the Project function in Image.

Now what I want to do is use Object Image to create an object file for
export to Rotater. It seems like I should be able to select the outlines
I've already created and make those the ROI object in each cell. But how do
I do that? I don't want to have to retrace every single outline in every
slice.

Gary Radice		804-289-8107
Department of Biology	804-289-8233 (FAX)
University of Richmond 	gradice@richmond.edu
Richmond VA 23173	

------------------------------

Date: Thu, 6 May 1999 10:55:15 -0300 
From: =?iso-8859-1?Q?=22Azcurra=2C_Diego_Andr=E9s=22?=
	 <Diego.Azcurra@siemens.com.ar>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Project engineer
Message-ID: <5286B576E0F1D1118B1C0000F6163D0409CBA6@buer104e.siemens.com.ar>
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Hello Mark,
	My name is Diego Azcurra and I am an Electronic Engineer that work
in
 design and development of HW and SW in Siemens SA. 
 
		I want to receive more information about your email, if it
is possible. Because of my background, I think that I can apply to more than
one of the items, although I think that more information is necessary to
take a good decision.

		Looking for a soon answer, I greet you sincerely
 			
 							Diego Azcurra
 							

> -----Original Message-----
> From:	Mark Vivino [SMTP:mvivino@yahoo.com]
> Sent:	Thursday, May 06, 1999 9:26 AM
> To:	nih-image@io.ece.drexel.edu
> Subject:	Project engineer
> 
> PROJECT ENGINEERING
> Onsite in Dade, Broward, Palm Beach areas of Florida. By remote or as
> consultant elsewhere and anywhere in the world.
> 
> BIOMEDICAL ENGINEERING
> Research and development for scientists, physicians and researchers,
> Densitometry, Quantitative measurements, Systems Design, Medical systems,
> Ophthalmic, cardiovascular and neurological systems and instrumentation
> 
> LABVIEW PROGRAMMER
> VI, Data acquisition, Instrumentation, Test, Testing, Measurement,
> Imaging,
> Control
> 
> VIDEO AND IMAGING
> NIH Image, Framegrabbers, Video, Imaging, Cameras, CCD's, Tape recorders 
> 
> ELECTRICAL ENGINEERING
> Computer automation, Computer control, Microprocessors, Systems Design
> 
> COMPUTER ENGINEERING
> LabView, Fortran, Assembly, Pascal, C, Macintosh, Windows, DOS, VAX/VMS,
> MS
> Office, Adobe
> 
> TELECOMMUNICATIONS
> Data communications, Telecommunications Systems, Telephony
> 
> 
> Contact:
> Mark Vivino
> mvivino@yahoo.com
> 305-324-6902
> 
> ===
> Mark A. Vivino
> Biomedical Engineer
> mvivino@yahoo.com
> http://www.mindspring.com/~mvivino/
> _________________________________________________________
> Do You Yahoo!?
> Get your free @yahoo.com address at http://mail.yahoo.com

------_=_NextPart_001_01BE97C8.24BD54D6
Content-Type: text/html
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
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<META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; =
charset=3Dus-ascii">
<META NAME=3D"Generator" CONTENT=3D"MS Exchange Server version =
5.5.2448.0">
<TITLE>RE: Project engineer</TITLE>
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<BODY>

<P><FONT FACE=3D"Arial">Hello Mark,</FONT>
<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <FONT FACE=3D"Arial">My =
name is Diego Azcurra and I am an Electronic Engineer that work =
in</FONT>
<BR><FONT FACE=3D"Arial">&nbsp;design and development of HW and SW in =
Siemens SA. </FONT>
<BR><FONT FACE=3D"Arial">&nbsp;</FONT>
<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <FONT FACE=3D"Arial">I want =
to receive more information about your email, if it is possible. =
Because of my background, I think that I can apply to more than one of =
the items, although I think that more information is necessary to take =
a good decision.</FONT></P>

<P>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <FONT FACE=3D"Arial">Looking =
for a soon answer, I greet you sincerely</FONT>
<BR><FONT FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </FONT>
<BR><FONT FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Diego Azcurra</FONT>
<BR><FONT FACE=3D"Arial">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </FONT>
</P>
<UL>
<P><FONT SIZE=3D1 FACE=3D"Arial">-----Original Message-----</FONT>
<BR><B><FONT SIZE=3D1 FACE=3D"Arial">From:&nbsp;&nbsp;</FONT></B> <FONT =
SIZE=3D1 FACE=3D"Arial">Mark Vivino [SMTP:mvivino@yahoo.com]</FONT>
<BR><B><FONT SIZE=3D1 FACE=3D"Arial">Sent:&nbsp;&nbsp;</FONT></B> <FONT =
SIZE=3D1 FACE=3D"Arial">Thursday, May 06, 1999 9:26 AM</FONT>
<BR><B><FONT SIZE=3D1 =
FACE=3D"Arial">To:&nbsp;&nbsp;&nbsp;&nbsp;</FONT></B> <FONT SIZE=3D1 =
FACE=3D"Arial">nih-image@io.ece.drexel.edu</FONT>
<BR><B><FONT SIZE=3D1 =
FACE=3D"Arial">Subject:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT>=
</B> <FONT SIZE=3D1 FACE=3D"Arial">Project engineer</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">PROJECT ENGINEERING</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Onsite in Dade, Broward, Palm Beach =
areas of Florida. By remote or as</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">consultant elsewhere and anywhere in =
the world.</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">BIOMEDICAL ENGINEERING</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Research and development for =
scientists, physicians and researchers,</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Densitometry, Quantitative =
measurements, Systems Design, Medical systems,</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Ophthalmic, cardiovascular and =
neurological systems and instrumentation</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">LABVIEW PROGRAMMER</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">VI, Data acquisition, =
Instrumentation, Test, Testing, Measurement, Imaging,</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Control</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">VIDEO AND IMAGING</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">NIH Image, Framegrabbers, Video, =
Imaging, Cameras, CCD's, Tape recorders </FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">ELECTRICAL ENGINEERING</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Computer automation, Computer =
control, Microprocessors, Systems Design</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">COMPUTER ENGINEERING</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">LabView, Fortran, Assembly, Pascal, =
C, Macintosh, Windows, DOS, VAX/VMS, MS</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Office, Adobe</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">TELECOMMUNICATIONS</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Data communications, =
Telecommunications Systems, Telephony</FONT>
</P>
<BR>

<P><FONT SIZE=3D2 FACE=3D"Arial">Contact:</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Mark Vivino</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">mvivino@yahoo.com</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">305-324-6902</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">=3D=3D=3D</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Mark A. Vivino</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Biomedical Engineer</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">mvivino@yahoo.com</FONT>
<BR><U><FONT COLOR=3D"#0000FF" SIZE=3D2 FACE=3D"Arial"><A =
HREF=3D"http://www.mindspring.com/~mvivino/" =
TARGET=3D"_blank">http://www.mindspring.com/~mvivino/</A></FONT></U>
<BR><FONT SIZE=3D2 =
FACE=3D"Arial">_________________________________________________________=
</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Do You Yahoo!?</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">Get your free @yahoo.com address =
at</FONT><U> <FONT COLOR=3D"#0000FF" SIZE=3D2 FACE=3D"Arial"><A =
HREF=3D"http://mail.yahoo.com" =
TARGET=3D"_blank">http://mail.yahoo.com</A></FONT></U>
</P>
</UL>
</BODY>
</HTML>
------_=_NextPart_001_01BE97C8.24BD54D6--

------------------------------

Date: Thu, 6 May 1999 09:12:44 -0600
From: "Randy M. Wadkins" <rwadkins@saci.org>
To: nih-image@io.ece.drexel.edu
Subject: Metrowerks drops Pascal
Message-Id: <v04020a01b357614dba71@[192.238.18.184]>
Content-Type: text/plain; charset="us-ascii"

Hi All:
It was pointed out today on MacInTouch that Metrowerks will not be
supporting Mac Pascal after the current release.  This probably means no
compiler for OS X or anything from here on out.  All those concerned might
want to write Metrowerks and voice your concerns.

--Randy
******************************************************************
"To me, it's a good idea to always carry two sacks of something
when you walk around.  That way, if anybody says, 'Hey, can you
give me a hand?' You can say, 'Sorry, got these sacks.'"
--Jack Handy, _Deep_Thoughts_


Randy M. Wadkins, Ph.D.
Cancer Therapy & Research Center
Institute for Drug Development
14960 Omicron Drive
San Antonio, TX 78245
phone: (210)-677-3835
fax: (210)-677-0058
E-mail:  rwadkins@saci.org
CTRC Homepage: http://www.ctrc.saci.org
******************************************************************

------------------------------

Date: Thu, 06 May 1999 11:10:37 -0400
From: "Wade Schuette" <schuette@umich.edu>
To: nih-image@io.ece.drexel.edu, rwadkins@saci.org
Subject: Re: Metrowerks drops Pascal
Message-Id: <s73178cf.039@umich.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline

 Yeh, but cynical comment, it will probably be about as effective
as all the protests when Apple decided to drop support for Lisp,
as, you know, too small a market to matter anymore to them.

   On a purely pragmatic basis, I'd say EITHER find or create
a vendor that would be interested in supporting the product separately
(in which case a threat to abandon Metrowerks might have some clout),
OR pull out those Java books and start helping Wayne complete 
ImageJ's functionality.

   (Getting Apple involved in the protest might have more clout
anyway)

   Of those two choices, I'd go with Java.  Wayne's got the kernel
done
and it's just waiting on manpower to complete the same functionality
we
have now, including things like a retroactive macro
interpreter/complier
for all the existing code and expertise base in writing macros that,
one
would think, should qualify for SOME government biomedical grant. 

   Wade


>>> "Randy M. Wadkins" <rwadkins@saci.org> 05/06 10:31 AM >>>
Hi All:
It was pointed out today on MacInTouch that Metrowerks will not be
supporting Mac Pascal after the current release.  This probably means
no
compiler for OS X or anything from here on out.  All those concerned
might
want to write Metrowerks and voice your concerns.

--Randy
******************************************************************
"To me, it's a good idea to always carry two sacks of something
when you walk around.  That way, if anybody says, 'Hey, can you
give me a hand?' You can say, 'Sorry, got these sacks.'"
--Jack Handy, _Deep_Thoughts_


Randy M. Wadkins, Ph.D.
Cancer Therapy & Research Center
Institute for Drug Development
14960 Omicron Drive
San Antonio, TX 78245
phone: (210)-677-3835
fax: (210)-677-0058
E-mail:  rwadkins@saci.org 
CTRC Homepage: http://www.ctrc.saci.org 
******************************************************************

------------------------------

Date:          Fri, 7 May 1999 9:50:06 +1000
From: GJOSS@rna.bio.mq.edu.au
To: nih-image@io.ece.drexel.edu
Subject:       Re: ROI in object image
Message-ID: <3CBFE8144BC@rna.bio.mq.edu.au>

>Date: Thu, 6 May 1999 08:29:46 -0400
>To: nih-image@io.ece.drexel.edu
>From: Gary Radice <gradice@richmond.edu>
>Subject: ROI in object image
>
>I know I'm going to feel pretty stupid when someone points out how to do
>this but I just blew an afternoon trying to figure it out and failed.
>
>I'm trying to do a 3D wireframe reconstruction of serial sections through 
>a
>skull. I already have created wireframes by tracing the objects of 
>interest
>in every slice in the stack, and converted the outlines to a binary image
>that makes a nice reconstruction when using the Project function in Image.
>
>Now what I want to do is use Object Image to create an object file for
>export to Rotater. It seems like I should be able to select the outlines
>I've already created and make those the ROI object in each cell. But how 
>do
>I do that? I don't want to have to retrace every single outline in every
>slice.
>
>Gary Radice		804-289-8107
>Department of Biology	804-289-8233 (FAX)
>University of Richmond 	gradice@richmond.edu
>Richmond VA 23173	

Reads like you had missed the point of how useful Object-Image is! :-)

Back at the tracing of the objects of interest to produce your binary 
image, you could have used Object-Image to record the tracing as 
Objects(polygon or ROI) which would have been non-destructive color 
overlays recorded as coordinate lists by Object-Image and exported direct 
to Rotator.

All is not lost however :-), you can now belatedly convert your binary 
outline stack to roi objects simply by wand'ing (or autoOutline) to obtain 
a roi on eack slice in turn and then roiToObject (by sequence menu or 
macro). That is all that is necessary to allow you to export wireframe to 
Rotator for active 3D display.

ie click on object tool, you will be lead by dialog through
new object file (object menu
define a roi object (by dragging to sequence window)

select wand tool
wand binary outline
move tool to sequence window (tool will change automatically to left arrow 
connected to a rect roi ) and click on roiObject.
next slice with '.' or pagedown key and repeat for stack.

exportXYZdata(object menu

fini
(Would have been much nicer at start with grayscale stack :-)

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

--------------------------------
End of nih-image-d Digest V99 Issue #106
****************************************

From nih-image-request@io.ece.drexel.edu Fri May  7 07:29 EDT 1999
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From: "Keith Norman" <k.norman@sheffield.ac.uk>
To: <nih-image@io.ece.drexel.edu>
Subject: Opening stacks
Date: Fri, 7 May 1999 12:14:53 -0700
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I'm using image to analyse movement of particles (cells or beads) in blood
vessels. Experiments are stored on video cassettes, digitized using a
Miromotion video compression card and saved as movie files.

Image opens these files as TIFF stacks and with the amount of RAM alocated
to Image I can open 500 frames.

Is there any way to instruct Image to open only selected frames (eg. first
frame only, frames 1-10, or frames 500-600) of the movie?

thanks in advance for any help.

Keith Norman
University of Sheffield
Clinical Sciences Centre
Northern General Hospital
Sheffield S5 7AU
UK

Tel +44 114 271 4665
Fax +44 114 261 9587
email k.norman@sheffield.ac.uk


From nih-image-request@io.ece.drexel.edu Fri May  7 10:03 EDT 1999
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Date: Fri, 23 Apr 1999 06:42:57 -0700
From: "Harvey J. Karten" <hjkarten@ucsd.edu>
Reply-To: hjkarten@ucsd.edu
Organization: UCSD
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I agree with the suggestion that we move on to ImageJ. It is cross
platform compatible, and is getting ever closer to NIH-Image in
functionality. Pat Kelly in my lab has been writing plug-ins, as have a
few others. But Wayne's efforts will best be appreciated and extended if
more of us join the action. ImageJ has many potential advantages, in
addition to being cross platform compatible. It is able to handle 16 bit
images, true 24 bit RGB, possibly 48/64 bit RGB (16 bit per channel of
RGB/Alpha). It needs some of the tools of NIH-Image, but these can
largely be handled via plug-ins, such as the Projection routines, etc.

Come on, guys and gals, we're about to enter the 21st century.8 bit
indexed color is not where it is at.

--
Harvey J. Karten, M.D.
Dept. of Neurosciences
University of California at San Diego
La Jolla, CA 92093-0608
Phone (Voice): 619-534-4938
FAX:  619-534-6602
EMail: HJKarten@ucsd.edu
Alternate Email: kartenh@sdsc.edu
Retina Information System: http://www-cajal.ucsd.edu
Tayana Manual: ftp://cajal.ucsd.edu/pub/outgoing/Tayana/



From nih-image-d-request@io.ece.drexel.edu Sat May  8 06:08 EDT 1999
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------------------------------

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nih-image-d Digest				Volume 99 : Issue 107

Today's Topics:
  Opening stacks                        [ "Keith Norman" <k.norman@sheffield. ]
  Pascal, and jumping on ImageJ         [ "Harvey J. Karten" <hjkarten@ucsd.e ]

------------------------------

Date: Fri, 7 May 1999 12:14:53 -0700
From: "Keith Norman" <k.norman@sheffield.ac.uk>
To: <nih-image@io.ece.drexel.edu>
Subject: Opening stacks
Message-ID: <000f01be98bd$e2a11140$a16ca78f@shef.ac.uk>
Content-Type: text/plain;
	charset="iso-8859-1"
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I'm using image to analyse movement of particles (cells or beads) in blood
vessels. Experiments are stored on video cassettes, digitized using a
Miromotion video compression card and saved as movie files.

Image opens these files as TIFF stacks and with the amount of RAM alocated
to Image I can open 500 frames.

Is there any way to instruct Image to open only selected frames (eg. first
frame only, frames 1-10, or frames 500-600) of the movie?

thanks in advance for any help.

Keith Norman
University of Sheffield
Clinical Sciences Centre
Northern General Hospital
Sheffield S5 7AU
UK

Tel +44 114 271 4665
Fax +44 114 261 9587
email k.norman@sheffield.ac.uk

------------------------------

Date: Fri, 23 Apr 1999 06:42:57 -0700
From: "Harvey J. Karten" <hjkarten@ucsd.edu>
To: nih-image@io.ece.drexel.edu
Subject: Pascal, and jumping on ImageJ
Message-ID: <372078E0.FD537915@ucsd.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

I agree with the suggestion that we move on to ImageJ. It is cross
platform compatible, and is getting ever closer to NIH-Image in
functionality. Pat Kelly in my lab has been writing plug-ins, as have a
few others. But Wayne's efforts will best be appreciated and extended if
more of us join the action. ImageJ has many potential advantages, in
addition to being cross platform compatible. It is able to handle 16 bit
images, true 24 bit RGB, possibly 48/64 bit RGB (16 bit per channel of
RGB/Alpha). It needs some of the tools of NIH-Image, but these can
largely be handled via plug-ins, such as the Projection routines, etc.

Come on, guys and gals, we're about to enter the 21st century.8 bit
indexed color is not where it is at.

--
Harvey J. Karten, M.D.
Dept. of Neurosciences
University of California at San Diego
La Jolla, CA 92093-0608
Phone (Voice): 619-534-4938
FAX:  619-534-6602
EMail: HJKarten@ucsd.edu
Alternate Email: kartenh@sdsc.edu
Retina Information System: http://www-cajal.ucsd.edu
Tayana Manual: ftp://cajal.ucsd.edu/pub/outgoing/Tayana/

--------------------------------
End of nih-image-d Digest V99 Issue #107
****************************************

From nih-image-request@io.ece.drexel.edu Sun May  9 20:04 EDT 1999
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From: Mansoor@nso1.uchc.edu (Mansoor,George)
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Date: Sun, 09 May 1999 19:43:02 -0400
Subject: RE: Pixel analysis
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I am posting this brief request for assistance again. Very simply I am 
trying to automatically measure the diameter of a small vesel segment 
obtained by ultrasound inaging. I would like to be able to trace the eadge 
of the vessel on the upper border and the lower border and have a macro give 
me multiple shortest distance readings between the two lines. Any help from 
the officianados or anyone doing similar work.

This must be dead easy for someone who knows NIH image well.

Thanks for your help.
 ----------
From: Elizabeth Esther Stillwell
To: nih-image@io.ece.drexel.edu
Subject: Pixel analysis
Date: Friday, April 30, 1999 3:18PM



I am looking at the aggregation of one protein (centrosomal), in Hela
cells  stained immunocytochemically in red, in response
the overexpression of another protein (also centrosomal) with a GFP- tag.
Because the GFP fluorescence  is stable under my fixation conditions, I
can look at both signals in each cell.

The proteins co-localize, and I would to try to quantitate this phenomenon
using some some sort of pixel analysis. Can anyone suggest the best  way
to do this using NIH Image?

Thanks,
Elizabeth



Elizabeth Stillwell
Department of Cell Biology
Emory University
1648 Pierce Drive
Atlanta, GA 30322


404-727-0445 phone
404-727-6256 fax



From nih-image-request@io.ece.drexel.edu Sun May  9 20:14 EDT 1999
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Date: Mon, 10 May 1999 10:05:13 +1000
To: nih-image@io.ece.drexel.edu
From: Cathy Gorrie <C.Gorrie@unsw.edu.au>
Subject: Re: ROI in object image
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>I know I'm going to feel pretty stupid when someone points out how to do
>this but I just blew an afternoon trying to figure it out and failed.
>
>I'm trying to do a 3D wireframe reconstruction of serial sections through a
>skull. I already have created wireframes by tracing the objects of interest
>in every slice in the stack, and converted the outlines to a binary image
>that makes a nice reconstruction when using the Project function in Image.
>
>Now what I want to do is use Object Image to create an object file for
>export to Rotater. It seems like I should be able to select the outlines
>I've already created and make those the ROI object in each cell. But how do
>I do that? I don't want to have to retrace every single outline in every
>slice.
>


Gary,

I don't know if this will help but there is a NIH macro in 'Plotting 
Macro's' called 'record XY [X]'. This will give you a list of the XY 
coordinates of an ROI when highlighted by marching ants. You can 
import them into Excel and remove the serial numbers and commas 
between XY coordinates during the transfer. You will have to add Z 
coordinates and a colour signifier for Rotator.
I do this in NIH rather than Object Image but the macro should work in both.

Cath

---------------------------------------------------------------------- 
----------
Cathy Gorrie
Scientific Officer

School of Anatomy
UNSW, Kensington
Sydney 2052
Australia

ph   	9385 2462
fax 	9313 6252


From nih-image-request@io.ece.drexel.edu Mon May 10 01:04 EDT 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: Mansoor@nso1.uchc.edu, nih-image@io.ece.drexel.edu
Date:          Mon, 10 May 1999 14:57:50 +1000
Subject:       RE: Pixel analysis?
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>From: Mansoor@nso1.uchc.edu (Mansoor,George)
>To: nih-image@io.ece.drexel.edu
>Organization: UConn Health Center, 263 Farmington Ave, Farmington CT, USA
>Date: Sun, 09 May 1999 19:43:02 -0400
>Subject: RE: Pixel analysis
>
>I am posting this brief request for assistance again. Very simply I am 
>trying to automatically measure the diameter of a small vesel segment 
>obtained by ultrasound inaging. I would like to be able to trace the eadge 
>of the vessel on the upper border and the lower border and have a macro 
>give me multiple shortest distance readings between the two lines. Any 
help >from the officianados or anyone doing similar work.
>
>This must be dead easy for someone who knows NIH image well.
>
>Thanks for your help.
> ----------
{ Euclidean Distance Map
prototype NIH-Image macro written by
Greg Joss,             1999-05-10
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia
in response to Mansoor@nso1.uchc.edu (Mansoor,George)

A number of issues are glossed over to keep illustration uncluttered but 
hopefully the method is apparent. It is not essential to fill image as 
opposed to line trace of edge, but it simplifies viewing.
}
macro'[F1]make test image';begin 
  {variable channel width through black backround}
  setBackGround(0);setForeGround(255);
  setNewSize(256,128);makeNewWindow('test Distance Map');
  makeOvalRoi(-5,-32,320,84);fill;
  makeOvalRoi(90,24,150,80);clear;
  makeOvalRoi(-10,90,360,80);fill;
  killroi;
  end

macro'[F2] measure channel diameter';
  var n,mean,mode,min,max,x,y,i,j:integer;
  begin 
  selectWindow('test Distance Map');invertY(false);
  selectAll;duplicate('Distance Map');invert;binary('edm');
  enhanceContrast;
  measure;GetResults(n,mean,mode,min,max);
  duplicate('centerLine');tileWindows;
  setDensitySlice(22,254);makeBinary;skeletonize;
  selectWindow('Distance Map');selectAll;copy;
  selectWindow('centerLine');paste;setOption;doAnd;
  selectAll;copy;
  showHistogram;
  selectWindow('test Distance Map');paste;setOption;doReplace;
  {channel width can be read as pixel intensity on centerLine}

  {graph channel width in 128 color on test image by
   reading pixel intensity on centerLine}
  setForeGround(128);moveTo(12,127-39);y:=70;
  for x:=12 to 255 do begin 
    i:=getPixel(x,y);
    j:=1;while (i=0) and (j<2) do begin 
      i:= getPixel(x,y-j);
      if i>0 then y:=y-j else begin
        i:= getPixel(x,y+j);if i>0 then y:=y+j;end;
        j:=j+1;end;
    lineTo(x,127-i);
    end;
  invertY(true);
  end

macro'[F12]disposeAll';begin disposeAll;end
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Mon May 10 01:09 EDT 1999
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>From: "Keith Norman" <k.norman@sheffield.ac.uk>
>To: <nih-image@io.ece.drexel.edu>
>Subject: Opening stacks
>Date: Fri, 7 May 1999 12:14:53 -0700
>
>I'm using image to analyse movement of particles (cells or beads) in blood
>vessels. Experiments are stored on video cassettes, digitized using a
>Miromotion video compression card and saved as movie files.
>
>Image opens these files as TIFF stacks and with the amount of RAM alocated
>to Image I can open 500 frames.
>
>Is there any way to instruct Image to open only selected frames (eg. first
>frame only, frames 1-10, or frames 500-600) of the movie?
>
>thanks in advance for any help.
>
>Keith Norman
>University of Sheffield
>Clinical Sciences Centre
>Northern General Hospital
>Sheffield S5 7AU
>UK
>
>Tel +44 114 271 4665
>Fax +44 114 261 9587
>email k.norman@sheffield.ac.uk
>
I'll attach to direct email a macro I wrote in '97 which does sampling of 
tiff movie stacks by using "import".
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Mon May 10 02:33 EDT 1999
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Date: Mon, 10 May 1999 08:11:33 +0200 (MET DST)
From: Szalay Ferenc <fszalay@ns.univet.hu>
To: nih-image@io.ece.drexel.edu
Subject: Adaptive thresholding
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Dear Imagers,

Could anyone send information on adaptive thresholding ready-made macros 
or any Image related material on it.

Thanks in advance

F. Szalay


From nih-image-request@io.ece.drexel.edu Mon May 10 03:25 EDT 1999
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From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: Re: nih-image-d Digest V99 #106
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>Now what I want to do is use Object Image to create an object file for
>export to Rotater.

Yes, you could load the outlines one by one in the original stack and
convert them to objects. Next time, create objects directly without first
exporting them as Outlines. ObjectImage does all administration for you.

A walkthrough given the outlines: open the stack of images. Set the slice
distance in the 'stack info' dialog box of the 'stack' menu. Make a new
object file and drag one object of type ROI to the centre of the dialog
box. Use single (the car, not the bus, radio button). Close the dialog box.
Click on the 'obj' button in the tool box once. The Object toolbox should
be visible on the left of your screen. Click on its menu bar tab to have
only a tiny part visible, in which a red outline should appear.

Load the first outline. When the ants march, move your cursor over the red
outline in the object window. You will see your cursor change to a dashed
rectangle with a tiny arrow. While your cursor looks like that, click on
the ROI in the object window (NOT in your stack). See how your outline in
the stack changes to a red outline. Proceed to the next slice (this is
needed as it provides depth information to the object), load its outline
and repeat the procedure above. When all outlines are processed, choose
'exportXYZ'.

Ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156



From nih-image-request@io.ece.drexel.edu Mon May 10 09:57 EDT 1999
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From: "Wade Schuette" <schuette@umich.edu>
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Subject: Re: RE: Pixel analysis
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Well, actually, edge location and vessel measuring,
judging from the number of papers monthly on the 
subject in the imaging journals, is a hard, open question.

Let's assume that you are going to take responsibility for
manually tracing each edge by hand, to simplify that task.

If you take one edge, and build a Euclidean distance Map
from that, it will assign most other pixels in that working image
a greyscale value that defines shortest distance from that 
pixel to all possible points on the edge. 

If you then write a macro to walk along the other edge  (ie, 
for all y, for all x, if this pixel is edge-colored in image A, go
to same location in image B and get-pixel-value of the Euclidean
Distance Map at that point, and save it/file it/compute something.)

That would probably work for many cases, and only give conceptually
difficult readings where vessels branch or are convoluted. If your 
vessel segments are fairly straight, not branching over the region of 
interest, it would probably work for you.

Wade Schuette
schuette@umich.edu


>>> Mansoor,George <Mansoor@nso1.uchc.edu> 05/09 8:04 PM >>>

I am posting this brief request for assistance again. Very simply I am

trying to automatically measure the diameter of a small vesel segment 
obtained by ultrasound inaging. I would like to be able to trace the
eadge 
of the vessel on the upper border and the lower border and have a macro
give 
me multiple shortest distance readings between the two lines. Any help
from 
the officianados or anyone doing similar work.

This must be dead easy for someone who knows NIH image well.

Thanks for your help.
 ----------
From: Elizabeth Esther Stillwell
To: nih-image@io.ece.drexel.edu 
Subject: Pixel analysis
Date: Friday, April 30, 1999 3:18PM



I am looking at the aggregation of one protein (centrosomal), in Hela
cells  stained immunocytochemically in red, in response
the overexpression of another protein (also centrosomal) with a GFP-
tag.
Because the GFP fluorescence  is stable under my fixation conditions,
I
can look at both signals in each cell.

The proteins co-localize, and I would to try to quantitate this
phenomenon
using some some sort of pixel analysis. Can anyone suggest the best 
way
to do this using NIH Image?

Thanks,
Elizabeth



Elizabeth Stillwell
Department of Cell Biology
Emory University
1648 Pierce Drive
Atlanta, GA 30322


404-727-0445 phone
404-727-6256 fax



From nih-image-request@io.ece.drexel.edu Mon May 10 10:17 EDT 1999
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From: DrJohnRuss@aol.com
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Date: Mon, 10 May 1999 09:58:09 EDT
Subject: Re: RE: Pixel analysis
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In a message dated 5/10/99 9:53:15 AM, schuette@umich.edu writes:

>If you take one edge, and build a Euclidean distance Map
>from that, it will assign most other pixels in that working image
>a greyscale value that defines shortest distance from that 
>pixel to all possible points on the edge. 
>
>If you then write a macro to walk along the other edge  (ie, 
>for all y, for all x, if this pixel is edge-colored in image A, go
>to same location in image B and get-pixel-value of the Euclidean
>Distance Map at that point, and save it/file it/compute something.)
>
>That would probably work for many cases, and only give conceptually
>difficult readings where vessels branch or are convoluted. If your 
>vessel segments are fairly straight, not branching over the region of 
>interest, it would probably work for you.
>
Actually, there is an even simpler way using the Euclidean distance map. 
Threshold the feature (vessel in this case). Make two copies of the image. 
Convert one to the EDM, so that every pixel has a value equal to the distance 
from the edge. Skeletonize the other, which selects the pixels midway between 
the edges. Combine the two images, keeping whichever pixel is lighter. This 
erases all pixels except those along the skeleton, but those have the value 
from the EDM. The histogram of these pixels (just do the whole image and 
ignore all of the white pixels) gives you everything you want to know about 
the feature - the average width (and other statistical properties), min, max, 
etc.

John Russ


From nih-image-request@io.ece.drexel.edu Mon May 10 16:02 EDT 1999
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Hello:
We have recently upgraded one of our G3-266 from 2 Mb to 6 Mb SGRAM. How is
the way to check out that the new DIMMS are really working? System Profile,
TechTool Pro and Nortor Syetm Info seem to be blind about the VRAM
configuration.
Regards,

_______________________________________________________
Dr. Luis F. Hernandez, Ph.D.
Laboratorio de Botanica
Departamento de Agronomia
U N I V E R S I D A D  N A C I O N A L  D E L  S U R
8000. Bahia Blanca - ARGENTINA

<mailto: lhernan@criba.edu.ar>
Telefonos (0291) 453-4775/453-0024
FAX: 54 - 0291 - 452-1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.



From nih-image-d-request@io.ece.drexel.edu Mon May 10 16:16 EDT 1999
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------------------------------

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nih-image-d Digest				Volume 99 : Issue 108

Today's Topics:
  RE: Pixel analysis                    [ Mansoor@nso1.uchc.edu (Mansoor,Geor ]
  Re: ROI in object image               [ Cathy Gorrie <C.Gorrie@unsw.edu.au> ]
  RE: Pixel analysis?                   [ GJOSS@rna.bio.mq.edu.au ]
  Re: Opening stacks                    [ GJOSS@rna.bio.mq.edu.au ]
  Adaptive thresholding                 [ Szalay Ferenc <fszalay@ns.univet.hu ]
  Re: nih-image-d Digest V99 #106       [ Ard Jonker <a.jonker@amc.uva.nl> ]
  Re: RE: Pixel analysis                [ "Wade Schuette" <schuette@umich.edu ]
  Re: RE: Pixel analysis                [ DrJohnRuss@aol.com ]
  VideoRAM (SGRAM)                      [ "=?iso-8859-1?Q?=22Dr._Luis_F._Hern ]

------------------------------

Date: Sun, 09 May 1999 19:43:02 -0400
From: Mansoor@nso1.uchc.edu (Mansoor,George)
To: nih-image@io.ece.drexel.edu
Subject: RE: Pixel analysis
Message-ID: <1999May09.193937.1274.1790657@msgate.uchc.edu>
Content-Type: text/plain; charset="US-ASCII"

I am posting this brief request for assistance again. Very simply I am 
trying to automatically measure the diameter of a small vesel segment 
obtained by ultrasound inaging. I would like to be able to trace the eadge 
of the vessel on the upper border and the lower border and have a macro give 
me multiple shortest distance readings between the two lines. Any help from 
the officianados or anyone doing similar work.

This must be dead easy for someone who knows NIH image well.

Thanks for your help.
 ----------
From: Elizabeth Esther Stillwell
To: nih-image@io.ece.drexel.edu
Subject: Pixel analysis
Date: Friday, April 30, 1999 3:18PM



I am looking at the aggregation of one protein (centrosomal), in Hela
cells  stained immunocytochemically in red, in response
the overexpression of another protein (also centrosomal) with a GFP- tag.
Because the GFP fluorescence  is stable under my fixation conditions, I
can look at both signals in each cell.

The proteins co-localize, and I would to try to quantitate this phenomenon
using some some sort of pixel analysis. Can anyone suggest the best  way
to do this using NIH Image?

Thanks,
Elizabeth



Elizabeth Stillwell
Department of Cell Biology
Emory University
1648 Pierce Drive
Atlanta, GA 30322


404-727-0445 phone
404-727-6256 fax

------------------------------

Date: Mon, 10 May 1999 10:05:13 +1000
From: Cathy Gorrie <C.Gorrie@unsw.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Re: ROI in object image
Message-Id: <v04204e09b35bd1a95b8a@[129.94.31.4]>
Content-Type: text/plain; charset="us-ascii" ; format="flowed"

>I know I'm going to feel pretty stupid when someone points out how to do
>this but I just blew an afternoon trying to figure it out and failed.
>
>I'm trying to do a 3D wireframe reconstruction of serial sections through a
>skull. I already have created wireframes by tracing the objects of interest
>in every slice in the stack, and converted the outlines to a binary image
>that makes a nice reconstruction when using the Project function in Image.
>
>Now what I want to do is use Object Image to create an object file for
>export to Rotater. It seems like I should be able to select the outlines
>I've already created and make those the ROI object in each cell. But how do
>I do that? I don't want to have to retrace every single outline in every
>slice.
>


Gary,

I don't know if this will help but there is a NIH macro in 'Plotting 
Macro's' called 'record XY [X]'. This will give you a list of the XY 
coordinates of an ROI when highlighted by marching ants. You can 
import them into Excel and remove the serial numbers and commas 
between XY coordinates during the transfer. You will have to add Z 
coordinates and a colour signifier for Rotator.
I do this in NIH rather than Object Image but the macro should work in both.

Cath

---------------------------------------------------------------------- 
----------
Cathy Gorrie
Scientific Officer

School of Anatomy
UNSW, Kensington
Sydney 2052
Australia

ph   	9385 2462
fax 	9313 6252

------------------------------

Date:          Mon, 10 May 1999 14:57:50 +1000
From: GJOSS@rna.bio.mq.edu.au
To: Mansoor@nso1.uchc.edu, nih-image@io.ece.drexel.edu
Subject:       RE: Pixel analysis?
Message-ID: <419251A59A6@rna.bio.mq.edu.au>

>From: Mansoor@nso1.uchc.edu (Mansoor,George)
>To: nih-image@io.ece.drexel.edu
>Organization: UConn Health Center, 263 Farmington Ave, Farmington CT, USA
>Date: Sun, 09 May 1999 19:43:02 -0400
>Subject: RE: Pixel analysis
>
>I am posting this brief request for assistance again. Very simply I am 
>trying to automatically measure the diameter of a small vesel segment 
>obtained by ultrasound inaging. I would like to be able to trace the eadge 
>of the vessel on the upper border and the lower border and have a macro 
>give me multiple shortest distance readings between the two lines. Any 
help >from the officianados or anyone doing similar work.
>
>This must be dead easy for someone who knows NIH image well.
>
>Thanks for your help.
> ----------
{ Euclidean Distance Map
prototype NIH-Image macro written by
Greg Joss,             1999-05-10
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia
in response to Mansoor@nso1.uchc.edu (Mansoor,George)

A number of issues are glossed over to keep illustration uncluttered but 
hopefully the method is apparent. It is not essential to fill image as 
opposed to line trace of edge, but it simplifies viewing.
}
macro'[F1]make test image';begin 
  {variable channel width through black backround}
  setBackGround(0);setForeGround(255);
  setNewSize(256,128);makeNewWindow('test Distance Map');
  makeOvalRoi(-5,-32,320,84);fill;
  makeOvalRoi(90,24,150,80);clear;
  makeOvalRoi(-10,90,360,80);fill;
  killroi;
  end

macro'[F2] measure channel diameter';
  var n,mean,mode,min,max,x,y,i,j:integer;
  begin 
  selectWindow('test Distance Map');invertY(false);
  selectAll;duplicate('Distance Map');invert;binary('edm');
  enhanceContrast;
  measure;GetResults(n,mean,mode,min,max);
  duplicate('centerLine');tileWindows;
  setDensitySlice(22,254);makeBinary;skeletonize;
  selectWindow('Distance Map');selectAll;copy;
  selectWindow('centerLine');paste;setOption;doAnd;
  selectAll;copy;
  showHistogram;
  selectWindow('test Distance Map');paste;setOption;doReplace;
  {channel width can be read as pixel intensity on centerLine}

  {graph channel width in 128 color on test image by
   reading pixel intensity on centerLine}
  setForeGround(128);moveTo(12,127-39);y:=70;
  for x:=12 to 255 do begin 
    i:=getPixel(x,y);
    j:=1;while (i=0) and (j<2) do begin 
      i:= getPixel(x,y-j);
      if i>0 then y:=y-j else begin
        i:= getPixel(x,y+j);if i>0 then y:=y+j;end;
        j:=j+1;end;
    lineTo(x,127-i);
    end;
  invertY(true);
  end

macro'[F12]disposeAll';begin disposeAll;end
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date:          Mon, 10 May 1999 15:06:52 +1000
From: GJOSS@rna.bio.mq.edu.au
To: nih-image@io.ece.drexel.edu
Subject:       Re: Opening stacks
Message-ID: <4194B832B97@rna.bio.mq.edu.au>

>From: "Keith Norman" <k.norman@sheffield.ac.uk>
>To: <nih-image@io.ece.drexel.edu>
>Subject: Opening stacks
>Date: Fri, 7 May 1999 12:14:53 -0700
>
>I'm using image to analyse movement of particles (cells or beads) in blood
>vessels. Experiments are stored on video cassettes, digitized using a
>Miromotion video compression card and saved as movie files.
>
>Image opens these files as TIFF stacks and with the amount of RAM alocated
>to Image I can open 500 frames.
>
>Is there any way to instruct Image to open only selected frames (eg. first
>frame only, frames 1-10, or frames 500-600) of the movie?
>
>thanks in advance for any help.
>
>Keith Norman
>University of Sheffield
>Clinical Sciences Centre
>Northern General Hospital
>Sheffield S5 7AU
>UK
>
>Tel +44 114 271 4665
>Fax +44 114 261 9587
>email k.norman@sheffield.ac.uk
>
I'll attach to direct email a macro I wrote in '97 which does sampling of 
tiff movie stacks by using "import".
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Mon, 10 May 1999 08:11:33 +0200 (MET DST)
From: Szalay Ferenc <fszalay@ns.univet.hu>
To: nih-image@io.ece.drexel.edu
Subject: Adaptive thresholding
Message-ID: <Pine.SUN.3.91.990510080626.12915A-100000@ns.univet.hu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear Imagers,

Could anyone send information on adaptive thresholding ready-made macros 
or any Image related material on it.

Thanks in advance

F. Szalay

------------------------------

Date: Mon, 10 May 1999 09:12:43 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #106
Message-Id: <l03130301b35c3367ee66@[145.117.43.50]>
Content-Type: text/plain; charset="us-ascii"

>Now what I want to do is use Object Image to create an object file for
>export to Rotater.

Yes, you could load the outlines one by one in the original stack and
convert them to objects. Next time, create objects directly without first
exporting them as Outlines. ObjectImage does all administration for you.

A walkthrough given the outlines: open the stack of images. Set the slice
distance in the 'stack info' dialog box of the 'stack' menu. Make a new
object file and drag one object of type ROI to the centre of the dialog
box. Use single (the car, not the bus, radio button). Close the dialog box.
Click on the 'obj' button in the tool box once. The Object toolbox should
be visible on the left of your screen. Click on its menu bar tab to have
only a tiny part visible, in which a red outline should appear.

Load the first outline. When the ants march, move your cursor over the red
outline in the object window. You will see your cursor change to a dashed
rectangle with a tiny arrow. While your cursor looks like that, click on
the ROI in the object window (NOT in your stack). See how your outline in
the stack changes to a red outline. Proceed to the next slice (this is
needed as it provides depth information to the object), load its outline
and repeat the procedure above. When all outlines are processed, choose
'exportXYZ'.

Ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156

------------------------------

Date: Mon, 10 May 1999 09:44:12 -0400
From: "Wade Schuette" <schuette@umich.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: RE: Pixel analysis
Message-Id: <s736aa82.002@umich.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline

Well, actually, edge location and vessel measuring,
judging from the number of papers monthly on the 
subject in the imaging journals, is a hard, open question.

Let's assume that you are going to take responsibility for
manually tracing each edge by hand, to simplify that task.

If you take one edge, and build a Euclidean distance Map
from that, it will assign most other pixels in that working image
a greyscale value that defines shortest distance from that 
pixel to all possible points on the edge. 

If you then write a macro to walk along the other edge  (ie, 
for all y, for all x, if this pixel is edge-colored in image A, go
to same location in image B and get-pixel-value of the Euclidean
Distance Map at that point, and save it/file it/compute something.)

That would probably work for many cases, and only give conceptually
difficult readings where vessels branch or are convoluted. If your 
vessel segments are fairly straight, not branching over the region of 
interest, it would probably work for you.

Wade Schuette
schuette@umich.edu


>>> Mansoor,George <Mansoor@nso1.uchc.edu> 05/09 8:04 PM >>>

I am posting this brief request for assistance again. Very simply I am

trying to automatically measure the diameter of a small vesel segment 
obtained by ultrasound inaging. I would like to be able to trace the
eadge 
of the vessel on the upper border and the lower border and have a macro
give 
me multiple shortest distance readings between the two lines. Any help
from 
the officianados or anyone doing similar work.

This must be dead easy for someone who knows NIH image well.

Thanks for your help.
 ----------
From: Elizabeth Esther Stillwell
To: nih-image@io.ece.drexel.edu 
Subject: Pixel analysis
Date: Friday, April 30, 1999 3:18PM



I am looking at the aggregation of one protein (centrosomal), in Hela
cells  stained immunocytochemically in red, in response
the overexpression of another protein (also centrosomal) with a GFP-
tag.
Because the GFP fluorescence  is stable under my fixation conditions,
I
can look at both signals in each cell.

The proteins co-localize, and I would to try to quantitate this
phenomenon
using some some sort of pixel analysis. Can anyone suggest the best 
way
to do this using NIH Image?

Thanks,
Elizabeth



Elizabeth Stillwell
Department of Cell Biology
Emory University
1648 Pierce Drive
Atlanta, GA 30322


404-727-0445 phone
404-727-6256 fax

------------------------------

Date: Mon, 10 May 1999 09:58:09 EDT
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re: RE: Pixel analysis
Message-ID: <b66a4a59.24683ff1@aol.com>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

In a message dated 5/10/99 9:53:15 AM, schuette@umich.edu writes:

>If you take one edge, and build a Euclidean distance Map
>from that, it will assign most other pixels in that working image
>a greyscale value that defines shortest distance from that 
>pixel to all possible points on the edge. 
>
>If you then write a macro to walk along the other edge  (ie, 
>for all y, for all x, if this pixel is edge-colored in image A, go
>to same location in image B and get-pixel-value of the Euclidean
>Distance Map at that point, and save it/file it/compute something.)
>
>That would probably work for many cases, and only give conceptually
>difficult readings where vessels branch or are convoluted. If your 
>vessel segments are fairly straight, not branching over the region of 
>interest, it would probably work for you.
>
Actually, there is an even simpler way using the Euclidean distance map. 
Threshold the feature (vessel in this case). Make two copies of the image. 
Convert one to the EDM, so that every pixel has a value equal to the distance 
from the edge. Skeletonize the other, which selects the pixels midway between 
the edges. Combine the two images, keeping whichever pixel is lighter. This 
erases all pixels except those along the skeleton, but those have the value 
from the EDM. The histogram of these pixels (just do the whole image and 
ignore all of the white pixels) gives you everything you want to know about 
the feature - the average width (and other statistical properties), min, max, 
etc.

John Russ

------------------------------

Date: Mon, 10 May 1999 16:51:36 -0300
From: "=?iso-8859-1?Q?=22Dr._Luis_F._Hern=E1ndez=22?="  <lhernan@criba.edu.ar>
To: nih-image@io.ece.drexel.edu
Subject: VideoRAM (SGRAM)
Message-Id: <v03130300b35ce76280d6@[170.210.187.214]>
Content-Type: text/plain; charset="us-ascii"

Hello:
We have recently upgraded one of our G3-266 from 2 Mb to 6 Mb SGRAM. How is
the way to check out that the new DIMMS are really working? System Profile,
TechTool Pro and Nortor Syetm Info seem to be blind about the VRAM
configuration.
Regards,

_______________________________________________________
Dr. Luis F. Hernandez, Ph.D.
Laboratorio de Botanica
Departamento de Agronomia
U N I V E R S I D A D  N A C I O N A L  D E L  S U R
8000. Bahia Blanca - ARGENTINA

<mailto: lhernan@criba.edu.ar>
Telefonos (0291) 453-4775/453-0024
FAX: 54 - 0291 - 452-1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.

--------------------------------
End of nih-image-d Digest V99 Issue #108
****************************************

From nih-image-request@io.ece.drexel.edu Mon May 10 19:26 EDT 1999
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From: "James Holman" <J.holman@mailbox.gu.edu.au>
To: <nih-image@io.ece.drexel.edu>
Subject: Outlining particles.
Date: Tue, 11 May 1999 09:15:49 +1000
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Hi All,

I am working with leaves that have been eaten by insects.  This means =
that the parameters derived from the program would be different to an =
intact / uneaten leaves (which I am actually after).  Can you tell me =
how to get the program to automatically outline the leaves whilst =
ignoring the bites on the edges i.e. outlining the presumed leaf edge.

Cheers
James

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<STYLE></STYLE>
</HEAD>
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<DIV><FONT size=3D2>Hi All,</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>I am working with leaves that have been eaten by=20
insects.&nbsp; This means that the parameters derived from the program =
would be=20
different to an&nbsp;intact / uneaten leaves (which I am actually =
after).&nbsp;=20
Can you tell me how to get the program to automatically outline the =
leaves=20
whilst ignoring the bites on the edges i.e. outlining the presumed leaf=20
edge.</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>Cheers</FONT></DIV>
<DIV><FONT size=3D2>James</FONT></DIV></BODY></HTML>

------=_NextPart_000_0041_01BE9B8E.DC19EB20--


From nih-image-request@io.ece.drexel.edu Tue May 11 00:08 EDT 1999
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Date: Mon, 10 May 1999 23:56:41 -0400
Subject: Color merge functions for LC tunable filter
From: "Ross Nakatsuji" <pp002736@mindspring.com>
To: nih-image@io.ece.drexel.edu
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Hi all,

Has anyone written any color merge macros for use with a CRI Micro*Color LC
tunable filter? We've written a standalone Windows program and an IPP
plug-in. Anyone interested in a TWAIN driver for the filter and popular
cameras? Mac? Windows? 95/98? NT?

I'm a Mac-guy in a Windows-only company. Enough feedback and maybe we can
get some Mac support for something in addition to IPLab.
=========================
Ross Nakatsuji, Technical Sales Support
Cambridge Research & Instrumentation, Inc.
80 Ashford Street
Boston, MA 02134
TEL: 617.787.5700 FAX: 617.787.4488
website: http://www.cri-inc.com
e-mail (CRI): techsupport@cri-inc.com
e-mail (home): pp002736@mindspring.com


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From: Ciprian Almonte <calmonte+@pitt.edu>
Subject: Re: VideoRAM (SGRAM)
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Luis System Profiler is able to check VRAM.  Launch System Profiler and
click on Memory overview.  It shows the size of all the memory you have
installed in your computer.
Suerte,

>Hello:
>We have recently upgraded one of our G3-266 from 2 Mb to 6 Mb SGRAM. How is
>the way to check out that the new DIMMS are really working? System Profile,
>TechTool Pro and Nortor Syetm Info seem to be blind about the VRAM
>configuration.
>Regards,
>_______________________________________________________
>Dr. Luis F. Hernandez, Ph.D.
>Laboratorio de Botanica
>Departamento de Agronomia
>U N I V E R S I D A D  N A C I O N A L  D E L  S U R
>8000. Bahia Blanca - ARGENTINA
>
><mailto: lhernan@criba.edu.ar>
>Telefonos (0291) 453-4775/453-0024
>FAX: 54 - 0291 - 452-1942
>_______________________________________________________
>The box said: "Requires Windows 98 or better".....
>So I bought a Macintosh.

--Ciprian

_____________________________________________________________
Ciprian A. Almonte			Phone:  (412) 648-9796
University of Pittsburgh		FAX: (412) 648-8330
Center for Biologic Imaging		http://sbic6.sbic.pitt.edu
Pittsburgh, PA 15261 USA		mailto:calmonte@pitt.edu
_____________________________________________________________


From nih-image-request@io.ece.drexel.edu Tue May 11 04:16 EDT 1999
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Date: Tue, 11 May 1999 11:06:32 +0300 (EET DST)
From: Najeeb Halabi <nmh08@aub.edu.lb>
To: nih-image@io.ece.drexel.edu
Subject: Problems with electrophoretic gels
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	Hi!  We've been trying to use Image for the PC (from Scioncorp) to
analyze electrophoretic gels.  We've read all the online manuals but don't
trust any of the numbers.

	1.  What's the best way to compare the total amount of protein in
one lane compared to that in another lane on the same gel?  We are not
interested in particular values but only in the ratios between one lane
and the next.  What we tried to do is get a mean value from a rectangle
drawn through the bands of one lane, move that rectangle to the next lane,
and get a second mean value.  However, the ratio of mean values we get
from adding know amounts of proteins are not equal.

	2.  Is it possible to compare these ratios between one gel and
another without using optical density step tablets?

	3.  Any other advice would be really appreciated.  Thanks in
advance!  





From nih-image-request@io.ece.drexel.edu Tue May 11 05:40 EDT 1999
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From: crespi marco <crespi2.marco@hsr.it>
Subject: winview
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I have a problem to transfer series of image aquired using a ccd-camera
controlled by Winview (the file format is .spe).
Do someone know if there is a macro in NIH (scion coporation) to recognize
this kind of format? 
Thanks,
Marco
Dr. Crespi Marco
Neurobiology of the Learning Unit
Dibit-San Raffaele Institute
via Olgettina 58
20132 MILANO, Italy
phone 	+39.02.2643-4823
fax	   	+39.02.2643-4813
E-mail:crespi2.marco@hsr.it



From nih-image-request@io.ece.drexel.edu Tue May 11 08:52 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: "=?iso-8859-1?Q?=22Dr._Luis_F._Hern=E1ndez=22?="  <lhernan@criba.edu.ar>
Subject: Re: VideoRAM (SGRAM)
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Dear Ciprian:
>Luis System Profiler is able to check VRAM.  Launch System Profiler and
>click on Memory overview.  It shows the size of all the memory you have
>installed in your computer.

Unfortunately my System Profiler Vers 1.3.2. does not have the Memory
Overview option. All the Memory (DRAM) info comes in the same window of
System Overview. Any suggestion?
Muchas Gracias,

_______________________________________________________
Dr. Luis F. Hernandez, Ph.D.
Laboratorio de Botanica
Departamento de Agronomia
U N I V E R S I D A D  N A C I O N A L  D E L  S U R
8000. Bahia Blanca - ARGENTINA

<mailto: lhernan@criba.edu.ar>
Telefonos (0291) 453-4775/453-0024
FAX: 54 - 0291 - 452-1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.



From nih-image-request@io.ece.drexel.edu Tue May 11 09:33 EDT 1999
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Date: Tue, 11 May 1999 09:19:04 +0000
From: Marcia Goldfarb <anatekep@maine.rr.com>
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Najeeb

I can not answer the first question, as the description is too vague. I
use a macro from Thomas Seebacher ( email:
Thomas.Seebacher@uni-konstanz.de) which has worked well for me. The
answer to question 2 is no.

Marcia Goldfarb
Anatek-EP
17 Bishop St
Portland, ME 04103

email: anatekep@maine.rr.com


From nih-image-request@io.ece.drexel.edu Tue May 11 17:46 EDT 1999
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Date: Tue, 11 May 1999 14:40:38 -0700
To: nih-image@io.ece.drexel.edu
From: "Patrick S. Page-McCaw" <mccaw@phy.ucsf.EDU>
Subject: particle tracking help, quicktime help
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I am using NIH Image to track the motion of fish during startle behavior.
The fish move very rapidly when they are startled, but are pretty much
stationary otherwise.  I observe when they move and, roughly, how much they
move in each frame.  I capture 630 frame movies off a DV camera, Sony
DCR-TRV9 (NTSC so interlaced), over firewire to Radius MotoDV and store the
movies as quicktime movies on a G3 (beige 192 MB RAM, need 600 MB memory
given to Image to run).  This is not optimal, but it was, relatively,
inexpensive. I capture 25 or so movies to the HD, then process these
overnight. The movies are in color as with MotoDV I cant change the codec.

I am writing a macro that determines xy coordinates of all fish (up to 25)
in each frame, their areas (fast fish are bigger due to interlacing), and
also looks for fish that have moved between frame(i) and frame(i-1) by
subtracting the two frames and looking for objects that have not
'disappeared' in the difference image.  Eventually, I would like to track
the fish using their xy coordinates, but that can be done outside NIH
Image, with coordinates supplied by NIH iMage.

What I've written works pretty well, but it is very slow.  My questions are:

1.  Import from the quicktime file is very slow; it is the single slowest
step and requires at least a third of the total processing time.  Up to
frame 250 or so, importing is fairly fast, but then slows down alot, I
believe it is imported to VM.  Is there a way to import, in a loop, a
fraction of the movie, say 2 to 100 frames, and process those rather than
import the whole movie?

2.  I would like to write the data to a file.  Currently, I can take data
from only a few frames, before the 32K limit in text files is reached (20
fish X 630 frames X at least 20 characters >> 32K).  I have considered
writing the data to an image window with each pixel acting as a character,
then reading the file as text (somehow), but this seems less than elegant
(ie., more complicated than I want to deal with).  Is there a more elegant
solution?  If this is necessary, how do I read the image as text?

3.   How much faster would this macro be if it ran compiled?  This is the
first programming I have done since Jr High School, where I println'd my
name ten times, so I have no idea how complicated/time-consuming this will
be.

4.  I would like to save the processed movie as a quicktime movie, but when
I do this in the macro I get the qt window settings so I cant run
overnight; is there a way to set the qt settings within a macro?

5.  To get rid of background prior to thresholding and particles, I
subtract from each movie frame a frame that has no fish in the dish, then I
continue with the processing as outlined above.  This works well, but if I
could do the subtraction during recording, I could save the movie as a much
smaller file. I am told that SGIs can do this kind of real-time
subtraction, can a mac?

Thank you in advance for your help,

Patrick



___________________________________________________________________________
Patrick S. Page-McCaw
University of California, San Francisco
Department of Physiology, Box 0444
513 Parnassus Avenue, Room S-864
San Francisco, California 94143-0444

phone:  415 476-8367
fax:    415 476-4929 attn P. Page-McCaw
email:  mccaw@phy.ucsf.edu



From nih-image-d-request@io.ece.drexel.edu Tue May 11 17:48 EDT 1999
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Date: Tue, 11 May 1999 17:48:26 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199905112148.RAA16105@io.ece.drexel.edu>
Subject: nih-image-d Digest V99 #109
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 109

Today's Topics:
  Outlining particles.                  [ "James Holman" <J.holman@mailbox.gu ]
  Color merge functions for LC tunable  [ "Ross Nakatsuji" <pp002736@mindspri ]
  Re: VideoRAM (SGRAM)                  [ Ciprian Almonte <calmonte+@pitt.edu ]
  Problems with electrophoretic gels    [ Najeeb Halabi <nmh08@aub.edu.lb> ]
  Measuring radiating lines             [ "MAX PUAUD" <scxmax@szn1.agric.nott ]
  winview                               [ crespi marco <crespi2.marco@hsr.it> ]
  Re: VideoRAM (SGRAM)                  [ "=?iso-8859-1?Q?=22Dr._Luis_F._Hern ]
  Re: Problems with electrophoretic ge  [ Marcia Goldfarb <anatekep@maine.rr. ]
  particle tracking help, quicktime he  [ "Patrick S. Page-McCaw" <mccaw@phy. ]

------------------------------

Date: Tue, 11 May 1999 09:15:49 +1000
From: "James Holman" <J.holman@mailbox.gu.edu.au>
To: <nih-image@io.ece.drexel.edu>
Subject: Outlining particles.
Message-ID: <004401be9b3b$0b4687e0$02000003@jimmy>
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_0041_01BE9B8E.DC19EB20"

This is a multi-part message in MIME format.

------=_NextPart_000_0041_01BE9B8E.DC19EB20
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Hi All,

I am working with leaves that have been eaten by insects.  This means =
that the parameters derived from the program would be different to an =
intact / uneaten leaves (which I am actually after).  Can you tell me =
how to get the program to automatically outline the leaves whilst =
ignoring the bites on the edges i.e. outlining the presumed leaf edge.

Cheers
James

------=_NextPart_000_0041_01BE9B8E.DC19EB20
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content=3D"text/html; charset=3Diso-8859-1" =
http-equiv=3DContent-Type>
<META content=3D"MSHTML 5.00.2314.1000" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT size=3D2>Hi All,</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>I am working with leaves that have been eaten by=20
insects.&nbsp; This means that the parameters derived from the program =
would be=20
different to an&nbsp;intact / uneaten leaves (which I am actually =
after).&nbsp;=20
Can you tell me how to get the program to automatically outline the =
leaves=20
whilst ignoring the bites on the edges i.e. outlining the presumed leaf=20
edge.</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>Cheers</FONT></DIV>
<DIV><FONT size=3D2>James</FONT></DIV></BODY></HTML>

------=_NextPart_000_0041_01BE9B8E.DC19EB20--

------------------------------

Date: Mon, 10 May 1999 23:56:41 -0400
From: "Ross Nakatsuji" <pp002736@mindspring.com>
To: nih-image@io.ece.drexel.edu
Subject: Color merge functions for LC tunable filter
Message-Id: <199905110355.XAA26665@smtp2.mindspring.com>
Content-type: text/plain; charset="US-ASCII"
Content-transfer-encoding: 7bit

Hi all,

Has anyone written any color merge macros for use with a CRI Micro*Color LC
tunable filter? We've written a standalone Windows program and an IPP
plug-in. Anyone interested in a TWAIN driver for the filter and popular
cameras? Mac? Windows? 95/98? NT?

I'm a Mac-guy in a Windows-only company. Enough feedback and maybe we can
get some Mac support for something in addition to IPLab.
=========================
Ross Nakatsuji, Technical Sales Support
Cambridge Research & Instrumentation, Inc.
80 Ashford Street
Boston, MA 02134
TEL: 617.787.5700 FAX: 617.787.4488
website: http://www.cri-inc.com
e-mail (CRI): techsupport@cri-inc.com
e-mail (home): pp002736@mindspring.com

------------------------------

Date: Tue, 11 May 1999 01:14:28 -0400
From: Ciprian Almonte <calmonte+@pitt.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: VideoRAM (SGRAM)
Message-Id: <v04020a01b35d6c7b996a@[136.142.22.214]>
Content-Type: text/plain; charset="us-ascii"

Luis System Profiler is able to check VRAM.  Launch System Profiler and
click on Memory overview.  It shows the size of all the memory you have
installed in your computer.
Suerte,

>Hello:
>We have recently upgraded one of our G3-266 from 2 Mb to 6 Mb SGRAM. How is
>the way to check out that the new DIMMS are really working? System Profile,
>TechTool Pro and Nortor Syetm Info seem to be blind about the VRAM
>configuration.
>Regards,
>_______________________________________________________
>Dr. Luis F. Hernandez, Ph.D.
>Laboratorio de Botanica
>Departamento de Agronomia
>U N I V E R S I D A D  N A C I O N A L  D E L  S U R
>8000. Bahia Blanca - ARGENTINA
>
><mailto: lhernan@criba.edu.ar>
>Telefonos (0291) 453-4775/453-0024
>FAX: 54 - 0291 - 452-1942
>_______________________________________________________
>The box said: "Requires Windows 98 or better".....
>So I bought a Macintosh.

--Ciprian

_____________________________________________________________
Ciprian A. Almonte			Phone:  (412) 648-9796
University of Pittsburgh		FAX: (412) 648-8330
Center for Biologic Imaging		http://sbic6.sbic.pitt.edu
Pittsburgh, PA 15261 USA		mailto:calmonte@pitt.edu
_____________________________________________________________

------------------------------

Date: Tue, 11 May 1999 11:06:32 +0300 (EET DST)
From: Najeeb Halabi <nmh08@aub.edu.lb>
To: nih-image@io.ece.drexel.edu
Subject: Problems with electrophoretic gels
Message-ID: <Pine.GSO.4.02.9905071311410.20575-100000@layla.aub.edu.lb>
Content-Type: TEXT/PLAIN; charset=US-ASCII

	Hi!  We've been trying to use Image for the PC (from Scioncorp) to
analyze electrophoretic gels.  We've read all the online manuals but don't
trust any of the numbers.

	1.  What's the best way to compare the total amount of protein in
one lane compared to that in another lane on the same gel?  We are not
interested in particular values but only in the ratios between one lane
and the next.  What we tried to do is get a mean value from a rectangle
drawn through the bands of one lane, move that rectangle to the next lane,
and get a second mean value.  However, the ratio of mean values we get
from adding know amounts of proteins are not equal.

	2.  Is it possible to compare these ratios between one gel and
another without using optical density step tablets?

	3.  Any other advice would be really appreciated.  Thanks in
advance!  

------------------------------

Date: Tue, 11 May 1999 09:24:21 +0100
From: "MAX PUAUD" <scxmax@szn1.agric.nottingham.ac.uk>
To: nih-image-d@io.ece.drexel.edu
Subject: Measuring radiating lines
Message-Id: <E10h7q8-0003ab-00@nottingham.ac.uk>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7BIT

Hello

I am new on this seving list.
I have looked into the archive but did not find the answer to my 
problems. Sorry if I missed it.

I have images obtained after puncture into a film. The images are 
basically lines radiating from the center. I am interested in 
measuring the length of each of these lines.

I have tried the object recognition procedure but the lines are too 
blurry to be seen properly. I was thinking of using a circular profile 
and increase the radius. I am not aware of any tools to do so.

If anyone has any idea.

Thank you very much for your help.

Max.

------------------------------     
Max Puaud
Applied Biochemistry and Food Science
Sutton Bonington Campus
Nottingham University
Loughborough LE12 5RD
(44) (0)115 951 6198

scxmax@szn1.agric.nottingham.ac.uk

------------------------------

Date: Tue, 11 May 1999 11:24:27 +0200
From: crespi marco <crespi2.marco@hsr.it>
To: nih-image@io.ece.drexel.edu
Subject: winview
Message-ID: <772719659CE.AAA3762@www.hsr.it>
Content-Type: text/plain; charset="us-ascii"

I have a problem to transfer series of image aquired using a ccd-camera
controlled by Winview (the file format is .spe).
Do someone know if there is a macro in NIH (scion coporation) to recognize
this kind of format? 
Thanks,
Marco
Dr. Crespi Marco
Neurobiology of the Learning Unit
Dibit-San Raffaele Institute
via Olgettina 58
20132 MILANO, Italy
phone 	+39.02.2643-4823
fax	   	+39.02.2643-4813
E-mail:crespi2.marco@hsr.it

------------------------------

Date: Tue, 11 May 1999 09:43:17 -0300
From: "=?iso-8859-1?Q?=22Dr._Luis_F._Hern=E1ndez=22?="  <lhernan@criba.edu.ar>
To: nih-image@io.ece.drexel.edu
Subject: Re: VideoRAM (SGRAM)
Message-Id: <v03130300b35dd5bbd085@[170.210.187.214]>
Content-Type: text/plain; charset="us-ascii"

Dear Ciprian:
>Luis System Profiler is able to check VRAM.  Launch System Profiler and
>click on Memory overview.  It shows the size of all the memory you have
>installed in your computer.

Unfortunately my System Profiler Vers 1.3.2. does not have the Memory
Overview option. All the Memory (DRAM) info comes in the same window of
System Overview. Any suggestion?
Muchas Gracias,

_______________________________________________________
Dr. Luis F. Hernandez, Ph.D.
Laboratorio de Botanica
Departamento de Agronomia
U N I V E R S I D A D  N A C I O N A L  D E L  S U R
8000. Bahia Blanca - ARGENTINA

<mailto: lhernan@criba.edu.ar>
Telefonos (0291) 453-4775/453-0024
FAX: 54 - 0291 - 452-1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.

------------------------------

Date: Tue, 11 May 1999 09:19:04 +0000
From: Marcia Goldfarb <anatekep@maine.rr.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Problems with electrophoretic gels
Message-ID: <3737F604.545EBEB7@maine.rr.com>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Najeeb

I can not answer the first question, as the description is too vague. I
use a macro from Thomas Seebacher ( email:
Thomas.Seebacher@uni-konstanz.de) which has worked well for me. The
answer to question 2 is no.

Marcia Goldfarb
Anatek-EP
17 Bishop St
Portland, ME 04103

email: anatekep@maine.rr.com

------------------------------

Date: Tue, 11 May 1999 14:40:38 -0700
From: "Patrick S. Page-McCaw" <mccaw@phy.ucsf.EDU>
To: nih-image@io.ece.drexel.edu
Subject: particle tracking help, quicktime help
Message-Id: <v03102801b35d431d9fc3@[128.218.190.207]>
Content-Type: text/plain; charset="us-ascii"

I am using NIH Image to track the motion of fish during startle behavior.
The fish move very rapidly when they are startled, but are pretty much
stationary otherwise.  I observe when they move and, roughly, how much they
move in each frame.  I capture 630 frame movies off a DV camera, Sony
DCR-TRV9 (NTSC so interlaced), over firewire to Radius MotoDV and store the
movies as quicktime movies on a G3 (beige 192 MB RAM, need 600 MB memory
given to Image to run).  This is not optimal, but it was, relatively,
inexpensive. I capture 25 or so movies to the HD, then process these
overnight. The movies are in color as with MotoDV I cant change the codec.

I am writing a macro that determines xy coordinates of all fish (up to 25)
in each frame, their areas (fast fish are bigger due to interlacing), and
also looks for fish that have moved between frame(i) and frame(i-1) by
subtracting the two frames and looking for objects that have not
'disappeared' in the difference image.  Eventually, I would like to track
the fish using their xy coordinates, but that can be done outside NIH
Image, with coordinates supplied by NIH iMage.

What I've written works pretty well, but it is very slow.  My questions are:

1.  Import from the quicktime file is very slow; it is the single slowest
step and requires at least a third of the total processing time.  Up to
frame 250 or so, importing is fairly fast, but then slows down alot, I
believe it is imported to VM.  Is there a way to import, in a loop, a
fraction of the movie, say 2 to 100 frames, and process those rather than
import the whole movie?

2.  I would like to write the data to a file.  Currently, I can take data
from only a few frames, before the 32K limit in text files is reached (20
fish X 630 frames X at least 20 characters >> 32K).  I have considered
writing the data to an image window with each pixel acting as a character,
then reading the file as text (somehow), but this seems less than elegant
(ie., more complicated than I want to deal with).  Is there a more elegant
solution?  If this is necessary, how do I read the image as text?

3.   How much faster would this macro be if it ran compiled?  This is the
first programming I have done since Jr High School, where I println'd my
name ten times, so I have no idea how complicated/time-consuming this will
be.

4.  I would like to save the processed movie as a quicktime movie, but when
I do this in the macro I get the qt window settings so I cant run
overnight; is there a way to set the qt settings within a macro?

5.  To get rid of background prior to thresholding and particles, I
subtract from each movie frame a frame that has no fish in the dish, then I
continue with the processing as outlined above.  This works well, but if I
could do the subtraction during recording, I could save the movie as a much
smaller file. I am told that SGIs can do this kind of real-time
subtraction, can a mac?

Thank you in advance for your help,

Patrick



___________________________________________________________________________
Patrick S. Page-McCaw
University of California, San Francisco
Department of Physiology, Box 0444
513 Parnassus Avenue, Room S-864
San Francisco, California 94143-0444

phone:  415 476-8367
fax:    415 476-4929 attn P. Page-McCaw
email:  mccaw@phy.ucsf.edu

--------------------------------
End of nih-image-d Digest V99 Issue #109
****************************************

From nih-image-request@io.ece.drexel.edu Tue May 11 18:06 EDT 1999
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What colour cameras would the listmembers recommend for use with NIH?
Unfortunately, I've got a limited budget so cost is a major factor.

Nick

_______________________________________________________________
Dr. Nicholas Welham             Applied Mathematics
tel +61-2-6249-0520               Research School of Physical Sciences and
Engineering
fax +61-2-6249-0511              Australian National University 
http://rsphysse.anu.edu.au     ACT 0200, Australia

The opinions expressed here are not those of the University or Department -
if they were I'd be paid considerably more than I am.


From nih-image-request@io.ece.drexel.edu Tue May 11 22:03 EDT 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: mccaw@phy.ucsf.EDU, nih-image@io.ece.drexel.edu
Date:          Wed, 12 May 1999 11:57:14 +1000
Subject:       Re: particle tracking help, quicktime help
Priority: normal
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>Date: Tue, 11 May 1999 14:40:38 -0700
>To: nih-image@io.ece.drexel.edu
>From: "Patrick S. Page-McCaw" <mccaw@phy.ucsf.EDU>
>Subject: particle tracking help, quicktime help
>
>I am using NIH Image to track the motion of fish during startle behavior.
>The fish move very rapidly when they are startled, but are pretty much
>stationary otherwise.  I observe when they move and, roughly, how much 
>they
>move in each frame.  I capture 630 frame movies off a DV camera, Sony
>DCR-TRV9 (NTSC so interlaced), over firewire to Radius MotoDV and store 
>the 
>movies as quicktime movies on a G3 (beige 192 MB RAM, need 600 MB memory
>given to Image to run).  This is not optimal, but it was, relatively,
>inexpensive. I capture 25 or so movies to the HD, then process these
>overnight. The movies are in color as with MotoDV I cant change the codec.
>
>I am writing a macro that determines xy coordinates of all fish (up to 25)
>in each frame, their areas (fast fish are bigger due to interlacing), and
>also looks for fish that have moved between frame(i) and frame(i-1) by
>subtracting the two frames and looking for objects that have not
>'disappeared' in the difference image.  Eventually, I would like to track
>the fish using their xy coordinates, but that can be done outside NIH
>Image, with coordinates supplied by NIH iMage.
>
>What I've written works pretty well, but it is very slow.  My questions 
>are:
>
>1.  Import from the quicktime file is very slow; it is the single slowest
>step and requires at least a third of the total processing time.  Up to
>frame 250 or so, importing is fairly fast, but then slows down alot, I
>believe it is imported to VM.  Is there a way to import, in a loop, a
>fraction of the movie, say 2 to 100 frames, and process those rather than
>import the whole movie?

I will attach a macro to a direct email which does that for uncompressed 
QTime  and tiff movie files.
>
>2.  I would like to write the data to a file.  Currently, I can take data
>from only a few frames, before the 32K limit in text files is reached (20
>fish X 630 frames X at least 20 characters >> 32K).  I have considered
>writing the data to an image window with each pixel acting as a character,
>then reading the file as text (somehow), but this seems less than elegant
>(ie., more complicated than I want to deal with).  Is there a more elegant
>solution?  If this is necessary, how do I read the image as text?

There are a number of approachs you can take to this aspect including write 
text to an image window, write/save multiple 32K text files to be combined 
later in say XCel or bblite. By far the simplest in this case would be to 
write to NIH-Image Results tables. Standard version allows 8000 rows, you 
can use all columns ( rArea, rMean, rStdDev, rX, rY, rMin, rMax, 
rLength, rMajor, rMinor, rAngle as well as rUser1,2)
ie 13x8000 real numbers
and save as tab delimited text.
eg use rUser1,2 for frame, fish and any of the other columns for output 
numbers; setCounter(rCount+1) to increment row; 
Start macro with showResults;dispose; so that Results window is not 
displayed during operation or else window update will slow down with a 
large number of rows.
>
>3.   How much faster would this macro be if it ran compiled?  This is the
>first programming I have done since Jr High School, where I println'd my
>name ten times, so I have no idea how complicated/time-consuming this will
>be.

On the G3, it is definitely not worth the candle unless you wanted to do 
some peculiar pixel by pixel operations not implemented as commands. Even 
these should be implemented as "user"code which can be invoked by macro 
command. The macro interpreter is quite fast and each command can invoke a 
large set of precompiled machine operations so that the interpreter 
overhead for a well designed process should be quite low. 

>
>4.  I would like to save the processed movie as a quicktime movie, but 
>when
>I do this in the macro I get the qt window settings so I cant run
>overnight; is there a way to set the qt settings within a macro?

Haven't looked at this but a big advantage of NIH-Image over commercial 
programs is that you look up source code to see exactly whats done and 
what's available. If you dont want to do that, or as is quite likely, you 
cant avoid QT dialogue, why not save output as tiff during o'nite run. 
(convert later if desired, not so slow if just open/save)
>
>5.  To get rid of background prior to thresholding and particles, I
>subtract from each movie frame a frame that has no fish in the dish, then 
>I
>continue with the processing as outlined above.  This works well, but if I
>could do the subtraction during recording, I could save the movie as a 
>much
>smaller file. I am told that SGIs can do this kind of real-time
>subtraction, can a mac?

Your problem here is firewire to Radius MotoDV frontend?
If you can talk direct to camera from NIH-Image, you can do subtraction in 
NIH-Image. I have done this for timelapse activity recording / motion 
tracking for weeks with only active>theshold minimum movement (as judged by 
area of differences) frames being stored ex background.

macro '[f1]test';var s,i,p1,p2:integer;begin 
p1:=nPics-1;p2:=nPics;
s:=TickCount;
for i:=1 to 100 do begin
choosePic(p1);selectAll;copy;
choosePic(p2);paste;setOption;Subtract;
end;
showMessage((TickCount-s)/60);
end

Takes just under 14 seconds on a G3 (7 640x480 frames a second).
So you are not going to get video rates on a G3 in NIH-Image macros but 
this may well be fast enough depending on activity and overlap between 
frames. 

>Thank you in advance for your help,
>
>Patrick

>__________________________________________________________________________
>_
>Patrick S. Page-McCaw
>University of California, San Francisco
>Department of Physiology, Box 0444
>513 Parnassus Avenue, Room S-864
>San Francisco, California 94143-0444
>
>phone:  415 476-8367
>fax:    415 476-4929 attn P. Page-McCaw
>email:  mccaw@phy.ucsf.edu
>
>
>
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Wed May 12 09:39 EDT 1999
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Date: Wed, 12 May 1999 09:18:57 -0400
From: "Wade Schuette" <schuette@umich.edu>
To: nih-image@io.ece.drexel.edu, mccaw@phy.ucsf.EDU
Subject: Re: particle tracking help, quicktime help
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>From: "Patrick S. Page-McCaw" <mccaw@phy.ucsf.EDU>
>Subject: particle tracking help, quicktime help
>
>I am using NIH Image to track the motion of fish during startle
behavior.
...

One thing you might want to explore is finding an optimal value of 
the shutter speed.   For some purposes, I found that using a long
exposure let me capture, essentially, both the position and the
velocity of 
each moving object.   (You say faster is larger in interlace, but I'm
talking,
say, quadrupling the exposure time to see what you get.)

Of course, you lose sharpness of image (without complex deconvolution)
but it all depends on what you need to measure easily.

Wade Schuette
schuette@umich.edu



From nih-image-d-request@io.ece.drexel.edu Wed May 12 09:41 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #110
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 110

Today's Topics:
  Colour camera recommendations         [ Nicholas.Welham@anu.edu.au (Dr. Nic ]
  Re: particle tracking help, quicktim  [ GJOSS@rna.bio.mq.edu.au ]
  Re: particle tracking help, quicktim  [ "Wade Schuette" <schuette@umich.edu ]

------------------------------

Date: Wed, 12 May 1999 07:54:16 +1000 (EST)
From: Nicholas.Welham@anu.edu.au (Dr. Nicholas J. Welham)
To: nih-image@io.ece.drexel.edu
Subject: Colour camera recommendations
Message-Id: <199905112154.HAA24834@rsphysse.anu.edu.au>
Content-Type: text/plain; charset="us-ascii"

What colour cameras would the listmembers recommend for use with NIH?
Unfortunately, I've got a limited budget so cost is a major factor.

Nick

_______________________________________________________________
Dr. Nicholas Welham             Applied Mathematics
tel +61-2-6249-0520               Research School of Physical Sciences and
Engineering
fax +61-2-6249-0511              Australian National University 
http://rsphysse.anu.edu.au     ACT 0200, Australia

The opinions expressed here are not those of the University or Department -
if they were I'd be paid considerably more than I am.

------------------------------

Date:          Wed, 12 May 1999 11:57:14 +1000
From: GJOSS@rna.bio.mq.edu.au
To: mccaw@phy.ucsf.EDU, nih-image@io.ece.drexel.edu
Subject:       Re: particle tracking help, quicktime help
Message-ID: <446264E4837@rna.bio.mq.edu.au>

>Date: Tue, 11 May 1999 14:40:38 -0700
>To: nih-image@io.ece.drexel.edu
>From: "Patrick S. Page-McCaw" <mccaw@phy.ucsf.EDU>
>Subject: particle tracking help, quicktime help
>
>I am using NIH Image to track the motion of fish during startle behavior.
>The fish move very rapidly when they are startled, but are pretty much
>stationary otherwise.  I observe when they move and, roughly, how much 
>they
>move in each frame.  I capture 630 frame movies off a DV camera, Sony
>DCR-TRV9 (NTSC so interlaced), over firewire to Radius MotoDV and store 
>the 
>movies as quicktime movies on a G3 (beige 192 MB RAM, need 600 MB memory
>given to Image to run).  This is not optimal, but it was, relatively,
>inexpensive. I capture 25 or so movies to the HD, then process these
>overnight. The movies are in color as with MotoDV I cant change the codec.
>
>I am writing a macro that determines xy coordinates of all fish (up to 25)
>in each frame, their areas (fast fish are bigger due to interlacing), and
>also looks for fish that have moved between frame(i) and frame(i-1) by
>subtracting the two frames and looking for objects that have not
>'disappeared' in the difference image.  Eventually, I would like to track
>the fish using their xy coordinates, but that can be done outside NIH
>Image, with coordinates supplied by NIH iMage.
>
>What I've written works pretty well, but it is very slow.  My questions 
>are:
>
>1.  Import from the quicktime file is very slow; it is the single slowest
>step and requires at least a third of the total processing time.  Up to
>frame 250 or so, importing is fairly fast, but then slows down alot, I
>believe it is imported to VM.  Is there a way to import, in a loop, a
>fraction of the movie, say 2 to 100 frames, and process those rather than
>import the whole movie?

I will attach a macro to a direct email which does that for uncompressed 
QTime  and tiff movie files.
>
>2.  I would like to write the data to a file.  Currently, I can take data
>from only a few frames, before the 32K limit in text files is reached (20
>fish X 630 frames X at least 20 characters >> 32K).  I have considered
>writing the data to an image window with each pixel acting as a character,
>then reading the file as text (somehow), but this seems less than elegant
>(ie., more complicated than I want to deal with).  Is there a more elegant
>solution?  If this is necessary, how do I read the image as text?

There are a number of approachs you can take to this aspect including write 
text to an image window, write/save multiple 32K text files to be combined 
later in say XCel or bblite. By far the simplest in this case would be to 
write to NIH-Image Results tables. Standard version allows 8000 rows, you 
can use all columns ( rArea, rMean, rStdDev, rX, rY, rMin, rMax, 
rLength, rMajor, rMinor, rAngle as well as rUser1,2)
ie 13x8000 real numbers
and save as tab delimited text.
eg use rUser1,2 for frame, fish and any of the other columns for output 
numbers; setCounter(rCount+1) to increment row; 
Start macro with showResults;dispose; so that Results window is not 
displayed during operation or else window update will slow down with a 
large number of rows.
>
>3.   How much faster would this macro be if it ran compiled?  This is the
>first programming I have done since Jr High School, where I println'd my
>name ten times, so I have no idea how complicated/time-consuming this will
>be.

On the G3, it is definitely not worth the candle unless you wanted to do 
some peculiar pixel by pixel operations not implemented as commands. Even 
these should be implemented as "user"code which can be invoked by macro 
command. The macro interpreter is quite fast and each command can invoke a 
large set of precompiled machine operations so that the interpreter 
overhead for a well designed process should be quite low. 

>
>4.  I would like to save the processed movie as a quicktime movie, but 
>when
>I do this in the macro I get the qt window settings so I cant run
>overnight; is there a way to set the qt settings within a macro?

Haven't looked at this but a big advantage of NIH-Image over commercial 
programs is that you look up source code to see exactly whats done and 
what's available. If you dont want to do that, or as is quite likely, you 
cant avoid QT dialogue, why not save output as tiff during o'nite run. 
(convert later if desired, not so slow if just open/save)
>
>5.  To get rid of background prior to thresholding and particles, I
>subtract from each movie frame a frame that has no fish in the dish, then 
>I
>continue with the processing as outlined above.  This works well, but if I
>could do the subtraction during recording, I could save the movie as a 
>much
>smaller file. I am told that SGIs can do this kind of real-time
>subtraction, can a mac?

Your problem here is firewire to Radius MotoDV frontend?
If you can talk direct to camera from NIH-Image, you can do subtraction in 
NIH-Image. I have done this for timelapse activity recording / motion 
tracking for weeks with only active>theshold minimum movement (as judged by 
area of differences) frames being stored ex background.

macro '[f1]test';var s,i,p1,p2:integer;begin 
p1:=nPics-1;p2:=nPics;
s:=TickCount;
for i:=1 to 100 do begin
choosePic(p1);selectAll;copy;
choosePic(p2);paste;setOption;Subtract;
end;
showMessage((TickCount-s)/60);
end

Takes just under 14 seconds on a G3 (7 640x480 frames a second).
So you are not going to get video rates on a G3 in NIH-Image macros but 
this may well be fast enough depending on activity and overlap between 
frames. 

>Thank you in advance for your help,
>
>Patrick

>__________________________________________________________________________
>_
>Patrick S. Page-McCaw
>University of California, San Francisco
>Department of Physiology, Box 0444
>513 Parnassus Avenue, Room S-864
>San Francisco, California 94143-0444
>
>phone:  415 476-8367
>fax:    415 476-4929 attn P. Page-McCaw
>email:  mccaw@phy.ucsf.edu
>
>
>
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Wed, 12 May 1999 09:18:57 -0400
From: "Wade Schuette" <schuette@umich.edu>
To: nih-image@io.ece.drexel.edu, mccaw@phy.ucsf.EDU
Subject: Re: particle tracking help, quicktime help
Message-Id: <s7394794.094@umich.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline

>From: "Patrick S. Page-McCaw" <mccaw@phy.ucsf.EDU>
>Subject: particle tracking help, quicktime help
>
>I am using NIH Image to track the motion of fish during startle
behavior.
...

One thing you might want to explore is finding an optimal value of 
the shutter speed.   For some purposes, I found that using a long
exposure let me capture, essentially, both the position and the
velocity of 
each moving object.   (You say faster is larger in interlace, but I'm
talking,
say, quadrupling the exposure time to see what you get.)

Of course, you lose sharpness of image (without complex deconvolution)
but it all depends on what you need to measure easily.

Wade Schuette
schuette@umich.edu

--------------------------------
End of nih-image-d Digest V99 Issue #110
****************************************

From nih-image-request@io.ece.drexel.edu Wed May 12 19:37 EDT 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id TAA16873
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Resent-Date: Wed, 12 May 1999 19:37:56 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: schuette@umich.edu, nih-image@io.ece.drexel.edu
Date:          Thu, 13 May 1999 9:28:32 +1000
Subject:       Re: particle tracking help, quicktime help
Priority: normal
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>Date: Wed, 12 May 1999 09:18:57 -0400
>From: "Wade Schuette" <schuette@umich.edu>
>To: nih-image@io.ece.drexel.edu, mccaw@phy.ucsf.EDU
>Subject: Re: particle tracking help, quicktime help
>
>>From: "Patrick S. Page-McCaw" <mccaw@phy.ucsf.EDU>
>>Subject: particle tracking help, quicktime help
>>
>>I am using NIH Image to track the motion of fish during startle
>behavior.
>...
>
>One thing you might want to explore is finding an optimal value of 
>the shutter speed.   For some purposes, I found that using a long
>exposure let me capture, essentially, both the position and the
>velocity of 
>each moving object.   (You say faster is larger in interlace, but I'm
>talking, say, quadrupling the exposure time to see what you get.)
>
>Of course, you lose sharpness of image (without complex deconvolution)
>but it all depends on what you need to measure easily.
>
>Wade Schuette
>schuette@umich.edu

Wade,

Your comment is interesting. If using a standard video to capture motion, I 
would think that one has little access to long exposure times.
I can appreciate that, in the days of film recording, the streaked images 
obtained using extended (but 'optimal') exposure could be made good use of 
to measure average speed. In a similar vein, deliberate blurring of images 
by out-of-focus has been suggested on this maillist as a means of image 
smoothing.
 
It would be my approach that all these effects and more can be better 
achieved by the capture of multiple images to be combined in a controled 
way by image processing techniques. I suppose I try to have it both ways in 
that with timelapse of cell movement for example, I always use an 'optimal' 
average composite image to reduce camera noise; ie I might average 4-8 
frames at maximum speed to obtain 'crisp' images for processing done on a 
longer cycle of 15 to 60 seconds. Overlaying of images or coded map 
projections can then be done using a number of different operations eg or, 
add, average etc.

For more high speed imageing, the effect you suggest can be simultated and 
enhanced by using a balance between AverageFrames('str',frames) during 
capture and AverageSlices as post capture processing.

I prefer to throw away excess data as a post capture process (but I have to 
confess to being a bowerbird and usually hang onto original data :-)
The dramatic increase in capacity/performance vs decrease in costs in  
recent years makes this even more practical.

What aspect of your suggested technique am I failing to appreciate?

Greg.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Thu May 13 05:16 EDT 1999
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                   NIH-image Mailing List Help 
                   ---------------------------
     


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From nih-image-request@io.ece.drexel.edu Thu May 13 09:31 EDT 1999
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Hello,

I am new to macro language in nih-image and am having difficulty creating
a triangular ROI (90, 45, 45 degrees) where the coordinates of each of the
three points of the triangle are known prior to defining the ROI.

MakeRoi is defined for a rectangular ROI and does not seem to be
applicable. I can create the trianlge using the polygon tool, but I have
many images to process and a macro would be of great help.

I am using Sciom Image Beta 3b Thanks in advance listers.

____________________________________________________________________
Greg Kawchuk D.C., M.Sc.
Clinician, University Health Services 
Ph.D. Candidate, McCaig Centre for Joint Injury and Arthritis Research
University of Calgary
http://www.ucalgary.ca/~gkawchuk


From nih-image-request@io.ece.drexel.edu Thu May 13 11:05 EDT 1999
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Date: Thu, 13 May 1999 09:55:11 -0700
From: scidi <scidi@cwix.com>
Subject: Used Mistusbishi P-90U (W) pritner???
To: nih-image@io.ece.drexel.edu
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To all imagers:

I am in need of a used Mitsubishi P-90U (W) black and white thermal printer.
Any users out there with an outdated imaging system looking to sell this
printer???  Any help is most appreciated.  thanks


Mark Molenda
Scientific Digital Imaging
1407 S 59th St.
Milwaukee, WI  53214-5122

phone/fax  (414)476-2694
e-mail:  sicdi@cwix.com


From nih-image-d-request@io.ece.drexel.edu Thu May 13 11:06 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 111

Today's Topics:
  Re: particle tracking help, quicktim  [ GJOSS@rna.bio.mq.edu.au ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
  Create a triangular ROI macro?        [ Greg Kawchuk <kawchuk@mccaig.ucalga ]
  Used Mistusbishi P-90U (W) pritner??  [ scidi <scidi@cwix.com> ]

------------------------------

Date:          Thu, 13 May 1999 9:28:32 +1000
From: GJOSS@rna.bio.mq.edu.au
To: schuette@umich.edu, nih-image@io.ece.drexel.edu
Subject:       Re: particle tracking help, quicktime help
Message-ID: <45BAD983018@rna.bio.mq.edu.au>

>Date: Wed, 12 May 1999 09:18:57 -0400
>From: "Wade Schuette" <schuette@umich.edu>
>To: nih-image@io.ece.drexel.edu, mccaw@phy.ucsf.EDU
>Subject: Re: particle tracking help, quicktime help
>
>>From: "Patrick S. Page-McCaw" <mccaw@phy.ucsf.EDU>
>>Subject: particle tracking help, quicktime help
>>
>>I am using NIH Image to track the motion of fish during startle
>behavior.
>...
>
>One thing you might want to explore is finding an optimal value of 
>the shutter speed.   For some purposes, I found that using a long
>exposure let me capture, essentially, both the position and the
>velocity of 
>each moving object.   (You say faster is larger in interlace, but I'm
>talking, say, quadrupling the exposure time to see what you get.)
>
>Of course, you lose sharpness of image (without complex deconvolution)
>but it all depends on what you need to measure easily.
>
>Wade Schuette
>schuette@umich.edu

Wade,

Your comment is interesting. If using a standard video to capture motion, I 
would think that one has little access to long exposure times.
I can appreciate that, in the days of film recording, the streaked images 
obtained using extended (but 'optimal') exposure could be made good use of 
to measure average speed. In a similar vein, deliberate blurring of images 
by out-of-focus has been suggested on this maillist as a means of image 
smoothing.
 
It would be my approach that all these effects and more can be better 
achieved by the capture of multiple images to be combined in a controled 
way by image processing techniques. I suppose I try to have it both ways in 
that with timelapse of cell movement for example, I always use an 'optimal' 
average composite image to reduce camera noise; ie I might average 4-8 
frames at maximum speed to obtain 'crisp' images for processing done on a 
longer cycle of 15 to 60 seconds. Overlaying of images or coded map 
projections can then be done using a number of different operations eg or, 
add, average etc.

For more high speed imageing, the effect you suggest can be simultated and 
enhanced by using a balance between AverageFrames('str',frames) during 
capture and AverageSlices as post capture processing.

I prefer to throw away excess data as a post capture process (but I have to 
confess to being a bowerbird and usually hang onto original data :-)
The dramatic increase in capacity/performance vs decrease in costs in  
recent years makes this even more practical.

What aspect of your suggested technique am I failing to appreciate?

Greg.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Thu, 13 May 1999 05:05:01 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199905130905.FAA26915@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
                   ---------------------------
     


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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

------------------------------

Date: Thu, 13 May 1999 07:14:00 -0600 (MDT)
From: Greg Kawchuk <kawchuk@mccaig.ucalgary.ca>
To: nih-image@io.ece.drexel.edu
Subject: Create a triangular ROI macro?
Message-Id: <Pine.SUN.3.95.990513070835.15268E-100000@epicenter>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hello,

I am new to macro language in nih-image and am having difficulty creating
a triangular ROI (90, 45, 45 degrees) where the coordinates of each of the
three points of the triangle are known prior to defining the ROI.

MakeRoi is defined for a rectangular ROI and does not seem to be
applicable. I can create the trianlge using the polygon tool, but I have
many images to process and a macro would be of great help.

I am using Sciom Image Beta 3b Thanks in advance listers.

____________________________________________________________________
Greg Kawchuk D.C., M.Sc.
Clinician, University Health Services 
Ph.D. Candidate, McCaig Centre for Joint Injury and Arthritis Research
University of Calgary
http://www.ucalgary.ca/~gkawchuk

------------------------------

Date: Thu, 13 May 1999 09:55:11 -0700
From: scidi <scidi@cwix.com>
To: nih-image@io.ece.drexel.edu
Subject: Used Mistusbishi P-90U (W) pritner???
Message-id: <001301be9d61$5edec980$e9a73ea6@pavilion>
Content-type: text/plain;	charset="iso-8859-1"
Content-transfer-encoding: 7bit

To all imagers:

I am in need of a used Mitsubishi P-90U (W) black and white thermal printer.
Any users out there with an outdated imaging system looking to sell this
printer???  Any help is most appreciated.  thanks


Mark Molenda
Scientific Digital Imaging
1407 S 59th St.
Milwaukee, WI  53214-5122

phone/fax  (414)476-2694
e-mail:  sicdi@cwix.com

--------------------------------
End of nih-image-d Digest V99 Issue #111
****************************************

From nih-image-request@io.ece.drexel.edu Thu May 13 11:09 EDT 1999
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	for cshtest@io.ece.drexel.edu; Thu, 13 May 1999 11:09:55 -0400 (EDT)
Resent-Date: Thu, 13 May 1999 11:09:55 -0400 (EDT)
Message-Id: <199905131457.KAA12696@io.ece.drexel.edu>
X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410)
Date: Fri, 14 May 1999 01:03:58 +1000
Subject: original Think Pascal code of NIH image
From: "Chih-L Han" <jessehcl@cardiologist.org>
To: nih-image@io.ece.drexel.edu
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Dear NIH imagers,

Can anyone advice me where I can download the original Think Pascal source
of NIH image?

Thank you very much for your assistance in advance.



          _____
           |_|*     Chih-L Han MD
         {~._.~}    http://come.to/macbiomed
          ( Y )     mailto:jessehcl@cardiologist.org
         ()~*~U)    ICQ:7281420
         (_)-(_)    efax://+1 707 929 0531
         AGCTACGTAAATAATCCTACGGGCACATTGGCAATTGCGTAACG

 


From nih-image-request@io.ece.drexel.edu Thu May 13 12:27 EDT 1999
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Resent-Date: Thu, 13 May 1999 12:27:06 -0400 (EDT)
From: S Keenan <s.keenan@Queens-Belfast.AC.UK>
Sender: S.Keenan@Queens-Belfast.AC.UK
To: nih-image@io.ece.drexel.edu
Subject: measuring areas by freehand selection
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Date: Thu, 13 May 1999 17:12:51 +0100 (GMT Daylight Time)
Priority: NORMAL
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We are attempting to measure callus areas on colour micrograph 
tif images employing Scion Image. This may be obvious, but how 
does one measure the area by freehand selection in Pixels2. 
We have tried multiple methods however with no success. An area 
can be calculated by rectangle selection but freehand selection 
is failing to give any result. Cheers

                 
Stephen




From nih-image-request@io.ece.drexel.edu Thu May 13 13:40 EDT 1999
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From: Angela Klaus <avklaus@amnh.org>
Subject: Re: measuring areas by freehand selection
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Stephen...

I've just started using Scion Image recently, so I'm not sure what
"Pixels2" refers to - but I've been having similar problems.  Actually, I
get meaningful results, but when I use the freehand line tool, the line of
interest disappears from the image.  The measurement comes out correct.  If
I use the straight line tool, the line I've drawn remains visible until I
draw the next line.

Best,

Angela


At 05:12 PM 5/13/99 +0100, you wrote:
>We are attempting to measure callus areas on colour micrograph 
>tif images employing Scion Image. This may be obvious, but how 
>does one measure the area by freehand selection in Pixels2. 
>We have tried multiple methods however with no success. An area 
>can be calculated by rectangle selection but freehand selection 
>is failing to give any result. Cheers
>
>                 
>Stephen
>
>
>
>
>
---------------------------------------------
Angela V. Klaus

Manager, Core Microscopy Facility
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024-5192 USA

Email:  avklaus@amnh.org
Voice: (212)769-5977, 5469
Fax: (212)769-5495
---------------------------------------------


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>>>I am using NIH Image to track the motion of fish during startle
>>>behavior.
>>>...  Patrick
>>
>>One thing you might want to explore is finding an optimal value of
>>the shutter speed.   For some purposes, I found that using a long
>>exposure let me capture, essentially, both the position and the
>>velocity of each moving object.
>>
>>Wade Schuette
>>schuette@umich.edu
>
>Wade,
>
>Your comment is interesting. If using a standard video to capture motion, I
>would think that one has little access to long exposure times.
>I can appreciate that, in the days of film recording, the streaked images
>obtained using extended (but 'optimal') exposure could be made good use of
>to measure average speed. In a similar vein, deliberate blurring of images
>by out-of-focus has been suggested on this maillist as a means of image
>smoothing.
>
>It would be my approach that all these effects and more can be better
>achieved by the capture of multiple images to be combined in a controled
>way by image processing techniques. ...
>
>For more high speed imageing, the effect you suggest can be simultated and
>enhanced by using a balance between AverageFrames('str',frames) during
>capture and AverageSlices as post capture processing.
>
...
>
>What aspect of your suggested technique am I failing to appreciate?
>
>Greg.
>Greg Joss,


I have taken an approach close to Greg's to make fish spaghetti (tracks of
the fish over 8 to 10 frames) and my macro does this.  This is very useful
for qualitative measurements of the fish behavior, but has been difficult
to make quantitative.  It was originally my plan to take the approach that
Wade has suggested, but with my commercial video camera (Sony DCR-TRV9)
this is not possible.  We are currently looking in to cameras which would
give more flexibility.

Patrick



___________________________________________________________________________
Patrick S. Page-McCaw
University of California, San Francisco
Department of Physiology, Box 0444
513 Parnassus Avenue, Room S-864
San Francisco, California 94143-0444

phone:  415 476-8367
fax:    415 476-4929 attn P. Page-McCaw
email:  mccaw@phy.ucsf.edu



From nih-image-request@io.ece.drexel.edu Thu May 13 19:16 EDT 1999
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To: s.keenan@Queens-Belfast.AC.UK, nih-image@io.ece.drexel.edu
Date:          Fri, 14 May 1999 9:08:17 +1000
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>From: S Keenan <s.keenan@Queens-Belfast.AC.UK>
>To: nih-image@io.ece.drexel.edu
>Subject: measuring areas by freehand selection
>Date: Thu, 13 May 1999 17:12:51 +0100 (GMT Daylight Time)
>
>We are attempting to measure callus areas on colour micrograph 
>tif images employing Scion Image. This may be obvious, but how 
>does one measure the area by freehand selection in Pixels2. 
>We have tried multiple methods however with no success. An area 
>can be calculated by rectangle selection but freehand selection 
>is failing to give any result. Cheers
>
Stephen,

To measure areas, it is not sufficient to 'outline' an 'area' with a 
freehand LINE selection (which is what I suspect you are doing).
It is necessary to make a closed AREA selection.

You can do this in many ways including:
Use rect,oval,polygon, freehand area(4th tool from top right) tools
or threshold/densitySlice and wand.

Area selections can be successively modified using control/option keys(Mac) 
or ctrl/alt?(PC,see manual) + - will be displayed alongside cursor.

A selection can be restored using "restore selection(analyse menu") or 
saved as an outline or recorded on the image with drawboundary.
If you drawboundary with an exclusive color, selections can be maped on 
image and selectively restored with setdensitySlice and wand.


Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Thu May 13 19:37 EDT 1999
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From: Steve Martin <s.martin@physio.unimelb.EDU.AU>
Subject: Re: Create a triangular ROI macro?
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Greg,

I have not done much Image macroing lately, but I believe you could create
and save the ROI once (manually), and read in this ROI for use with your
sequence of images.

HTH

Steve

At 11:14 PM +1000 on 13/5/99, Greg Kawchuk wrote:

> Hello,
>
> I am new to macro language in nih-image and am having difficulty creating
> a triangular ROI (90, 45, 45 degrees) where the coordinates of each of the
> three points of the triangle are known prior to defining the ROI.
>
> MakeRoi is defined for a rectangular ROI and does not seem to be
> applicable. I can create the trianlge using the polygon tool, but I have
> many images to process and a macro would be of great help.
>
> I am using Sciom Image Beta 3b Thanks in advance listers.
>
> ____________________________________________________________________
> Greg Kawchuk D.C., M.Sc.
> Clinician, University Health Services
> Ph.D. Candidate, McCaig Centre for Joint Injury and Arthritis Research
> University of Calgary
> http://www.ucalgary.ca/~gkawchuk


From nih-image-request@io.ece.drexel.edu Thu May 13 21:25 EDT 1999
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From: ad1054@worldpath.net (Dr. Christopher Coulon)
Subject: Re: Create a triangular ROI macro?
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Greg,

I can't really tell from your message what your situation is, but here is a
work-around that will give you a triangular ROI on any given image.  You
have to type in the three x,y coordinates of your triangle at the prompts.
This is simply to demonstrate the feasibility of creating your triangular
ROI.  You can have a macro take the coordinates from the image in some
cases, but it really depends on what you are trying to do.  Please email me
off list if you want a more detailed response.

Chris

********** triangle ROI macro **********

macro '[F15] draw triangle';
var
  x1,x2,x3,y1,y2,y3,origIm:integer;

begin
  origIm:=pidnumber;duplicate('test image');
  selectAll;clear;killROI;
  x1:=GetNumber('enter first X coordinate ',0,0);
  y1:=GetNumber('enter first Y coordinate ',0,0);
  x2:=GetNumber('enter second X coordinate ',0,0);
  y2:=GetNumber('enter second Y coordinate ',0,0);
  x3:=GetNumber('enter third X coordinate ',0,0);
  y3:=GetNumber('enter third Y coordinate ',0,0);
  moveTo(x1,y1);lineTo(x2,y2);lineTo(x3,y3);lineTo(x1,y1);
  setThreshold(1);autoOutline(x1,y1);dispose;
  selectPic(origIm);restoreROI;
end;

>Hello,
>
>I am new to macro language in nih-image and am having difficulty creating
>a triangular ROI (90, 45, 45 degrees) where the coordinates of each of the
>three points of the triangle are known prior to defining the ROI.
>
>MakeRoi is defined for a rectangular ROI and does not seem to be
>applicable. I can create the trianlge using the polygon tool, but I have
>many images to process and a macro would be of great help.

* * * * * * * * * * * * * * * * * *
* Dr. Christopher Hunt Coulon     *
* The GAIA Group                  *
* 40 Chick Road                   *
* Wolfeboro, New Hampshire 03894  *
* 603 569-0028                    *
* www.worldpath.net/~ad1054       *
* * * * * * * * * * * * * * * * * *



From nih-image-request@io.ece.drexel.edu Thu May 13 22:32 EDT 1999
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To: nih-image@io.ece.drexel.edu
Date:          Fri, 14 May 1999 12:24:43 +1000
Subject:       Re: original Think Pascal code of NIH image
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>Date: Fri, 14 May 1999 01:03:58 +1000
>Subject: original Think Pascal code of NIH image
>From: "Chih-L Han" <jessehcl@cardiologist.org>
>To: nih-image@io.ece.drexel.edu
>Dear NIH imagers,
>
>Can anyone advice me where I can download the original Think Pascal source
>of NIH image?
>
>Thank you very much for your assistance in advance.
>
I will attach v1.55 source(last Think Pascal version) by direct email.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Fri May 14 03:53 EDT 1999
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From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: Image J? Should I or Shouldn't I.
Date: Fri, 14 May 1999 17:39:44 +1000
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Hi, 
I agree that moving to Image J with its enhanced pixel depth etc and colour
capability would be a good idea, and am prepared to pick up Java (he says
lightly).

BUT
I see some  problems with the move to Image J, and I hope that the wise
heads on the list can tell me where and how I am wrong.

My main use of Image is with Kodak Megaplus cameras, the 1.4 and the 1.6i
both being in use. I rely on the Image macros to control sequential
acquisitions and move the stage between each frame, so I can cover a large
area or capture a series of images through a defined focus range. I need
serial port access to do this.

I am using these with the PDI digital boards for the PCI bus.
These allow the camera to have the shutter speed changed and the gain and
offset changed (for the i series). And also controls image size, transfer
size and etc. An immediate advantage of Image J would be the ability to use
the 10 bits available from the 1.6i camera.

To get these to work from Image J, I would have to do the following things.
I think?

1. Make an interface into Image J to support the camera functions.?

2. Or Make a plug-in for Image J which did the above.?

3. Understand how to write the driver for the card to work with Image J?

4. Or maybe I should make the card talk to Quicktime?

I await responses to my questions.
I do have the code for the PDI boards, so I am well placed to have a go, but
my programming skills are not terrific, but I can do things, it just takes
me longer.

If anyone can provide me with some cogent arguments I will listen and act.

On a slightly different point, what tools do i need for Java, I have CW4.
And are any books recommended?
TIA

Noel Goldsmith
AMRL
DSTO
Melbourne Australia


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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #112
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 112

Today's Topics:
  original Think Pascal code of NIH im  [ "Chih-L Han" <jessehcl@cardiologist ]
  measuring areas by freehand selectio  [ S Keenan <s.keenan@Queens-Belfast.A ]
  Re: measuring areas by freehand sele  [ Angela Klaus <avklaus@amnh.org> ]
  Re: particle tracking help, quicktim  [ "Patrick S. Page-McCaw" <mccaw@phy. ]
  Re: measuring areas by freehand sele  [ GJOSS@rna.bio.mq.edu.au ]
  Re: Create a triangular ROI macro?    [ Steve Martin <s.martin@physio.unime ]
  Re: Create a triangular ROI macro?    [ ad1054@worldpath.net (Dr. Christoph ]
  Re: original Think Pascal code of NI  [ GJOSS@rna.bio.mq.edu.au ]
  Image J? Should I or Shouldn't I.     [ "Goldsmith, Noel" <Noel.Goldsmith@d ]

------------------------------

Date: Fri, 14 May 1999 01:03:58 +1000
From: "Chih-L Han" <jessehcl@cardiologist.org>
To: nih-image@io.ece.drexel.edu
Subject: original Think Pascal code of NIH image
Message-Id: <199905131457.KAA12696@io.ece.drexel.edu>
Content-type: text/plain; charset="Big5"
Content-transfer-encoding: 7bit

Dear NIH imagers,

Can anyone advice me where I can download the original Think Pascal source
of NIH image?

Thank you very much for your assistance in advance.



          _____
           |_|*     Chih-L Han MD
         {~._.~}    http://come.to/macbiomed
          ( Y )     mailto:jessehcl@cardiologist.org
         ()~*~U)    ICQ:7281420
         (_)-(_)    efax://+1 707 929 0531
         AGCTACGTAAATAATCCTACGGGCACATTGGCAATTGCGTAACG

 

------------------------------

Date: Thu, 13 May 1999 17:12:51 +0100 (GMT Daylight Time)
From: S Keenan <s.keenan@Queens-Belfast.AC.UK>
To: nih-image@io.ece.drexel.edu
Subject: measuring areas by freehand selection
Message-ID: <SIMEON.9905131751.A@sk.fujin.qub.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

We are attempting to measure callus areas on colour micrograph 
tif images employing Scion Image. This may be obvious, but how 
does one measure the area by freehand selection in Pixels2. 
We have tried multiple methods however with no success. An area 
can be calculated by rectangle selection but freehand selection 
is failing to give any result. Cheers

                 
Stephen

------------------------------

Date: Thu, 13 May 1999 13:26:54 -0400
From: Angela Klaus <avklaus@amnh.org>
To: nih-image@io.ece.drexel.edu
Subject: Re: measuring areas by freehand selection
Message-Id: <3.0.5.32.19990513132654.00939790@amnh.org>
Content-Type: text/plain; charset="us-ascii"

Stephen...

I've just started using Scion Image recently, so I'm not sure what
"Pixels2" refers to - but I've been having similar problems.  Actually, I
get meaningful results, but when I use the freehand line tool, the line of
interest disappears from the image.  The measurement comes out correct.  If
I use the straight line tool, the line I've drawn remains visible until I
draw the next line.

Best,

Angela


At 05:12 PM 5/13/99 +0100, you wrote:
>We are attempting to measure callus areas on colour micrograph 
>tif images employing Scion Image. This may be obvious, but how 
>does one measure the area by freehand selection in Pixels2. 
>We have tried multiple methods however with no success. An area 
>can be calculated by rectangle selection but freehand selection 
>is failing to give any result. Cheers
>
>                 
>Stephen
>
>
>
>
>
---------------------------------------------
Angela V. Klaus

Manager, Core Microscopy Facility
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024-5192 USA

Email:  avklaus@amnh.org
Voice: (212)769-5977, 5469
Fax: (212)769-5495
---------------------------------------------

------------------------------

Date: Thu, 13 May 1999 12:42:54 -0700
From: "Patrick S. Page-McCaw" <mccaw@phy.ucsf.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Re: particle tracking help, quicktime help
Message-Id: <v03102804b360d823fa54@[128.218.190.207]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

>>>I am using NIH Image to track the motion of fish during startle
>>>behavior.
>>>...  Patrick
>>
>>One thing you might want to explore is finding an optimal value of
>>the shutter speed.   For some purposes, I found that using a long
>>exposure let me capture, essentially, both the position and the
>>velocity of each moving object.
>>
>>Wade Schuette
>>schuette@umich.edu
>
>Wade,
>
>Your comment is interesting. If using a standard video to capture motion, I
>would think that one has little access to long exposure times.
>I can appreciate that, in the days of film recording, the streaked images
>obtained using extended (but 'optimal') exposure could be made good use of
>to measure average speed. In a similar vein, deliberate blurring of images
>by out-of-focus has been suggested on this maillist as a means of image
>smoothing.
>
>It would be my approach that all these effects and more can be better
>achieved by the capture of multiple images to be combined in a controled
>way by image processing techniques. ...
>
>For more high speed imageing, the effect you suggest can be simultated and
>enhanced by using a balance between AverageFrames('str',frames) during
>capture and AverageSlices as post capture processing.
>
...
>
>What aspect of your suggested technique am I failing to appreciate?
>
>Greg.
>Greg Joss,


I have taken an approach close to Greg's to make fish spaghetti (tracks of
the fish over 8 to 10 frames) and my macro does this.  This is very useful
for qualitative measurements of the fish behavior, but has been difficult
to make quantitative.  It was originally my plan to take the approach that
Wade has suggested, but with my commercial video camera (Sony DCR-TRV9)
this is not possible.  We are currently looking in to cameras which would
give more flexibility.

Patrick



___________________________________________________________________________
Patrick S. Page-McCaw
University of California, San Francisco
Department of Physiology, Box 0444
513 Parnassus Avenue, Room S-864
San Francisco, California 94143-0444

phone:  415 476-8367
fax:    415 476-4929 attn P. Page-McCaw
email:  mccaw@phy.ucsf.edu

------------------------------

Date:          Fri, 14 May 1999 9:08:17 +1000
From: GJOSS@rna.bio.mq.edu.au
To: s.keenan@Queens-Belfast.AC.UK, nih-image@io.ece.drexel.edu
CC: avklaus@amnh.org
Subject:       Re: measuring areas by freehand selection
Message-ID: <13F0206C80@rna.bio.mq.edu.au>

>From: S Keenan <s.keenan@Queens-Belfast.AC.UK>
>To: nih-image@io.ece.drexel.edu
>Subject: measuring areas by freehand selection
>Date: Thu, 13 May 1999 17:12:51 +0100 (GMT Daylight Time)
>
>We are attempting to measure callus areas on colour micrograph 
>tif images employing Scion Image. This may be obvious, but how 
>does one measure the area by freehand selection in Pixels2. 
>We have tried multiple methods however with no success. An area 
>can be calculated by rectangle selection but freehand selection 
>is failing to give any result. Cheers
>
Stephen,

To measure areas, it is not sufficient to 'outline' an 'area' with a 
freehand LINE selection (which is what I suspect you are doing).
It is necessary to make a closed AREA selection.

You can do this in many ways including:
Use rect,oval,polygon, freehand area(4th tool from top right) tools
or threshold/densitySlice and wand.

Area selections can be successively modified using control/option keys(Mac) 
or ctrl/alt?(PC,see manual) + - will be displayed alongside cursor.

A selection can be restored using "restore selection(analyse menu") or 
saved as an outline or recorded on the image with drawboundary.
If you drawboundary with an exclusive color, selections can be maped on 
image and selectively restored with setdensitySlice and wand.


Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Fri, 14 May 1999 09:26:43 +1000
From: Steve Martin <s.martin@physio.unimelb.EDU.AU>
To: nih-image@io.ece.drexel.edu
Subject: Re: Create a triangular ROI macro?
Message-Id: <v04011701b3610ea53936@[128.250.109.214]>
Content-Type: text/plain; charset="us-ascii"

Greg,

I have not done much Image macroing lately, but I believe you could create
and save the ROI once (manually), and read in this ROI for use with your
sequence of images.

HTH

Steve

At 11:14 PM +1000 on 13/5/99, Greg Kawchuk wrote:

> Hello,
>
> I am new to macro language in nih-image and am having difficulty creating
> a triangular ROI (90, 45, 45 degrees) where the coordinates of each of the
> three points of the triangle are known prior to defining the ROI.
>
> MakeRoi is defined for a rectangular ROI and does not seem to be
> applicable. I can create the trianlge using the polygon tool, but I have
> many images to process and a macro would be of great help.
>
> I am using Sciom Image Beta 3b Thanks in advance listers.
>
> ____________________________________________________________________
> Greg Kawchuk D.C., M.Sc.
> Clinician, University Health Services
> Ph.D. Candidate, McCaig Centre for Joint Injury and Arthritis Research
> University of Calgary
> http://www.ucalgary.ca/~gkawchuk

------------------------------

Date: Thu, 13 May 1999 21:16:14 -0400
From: ad1054@worldpath.net (Dr. Christopher Coulon)
To: nih-image@io.ece.drexel.edu
Subject: Re: Create a triangular ROI macro?
Message-Id: <v01520d01b36126fddc56@[208.133.217.54]>
Content-Type: text/plain; charset="us-ascii"

Greg,

I can't really tell from your message what your situation is, but here is a
work-around that will give you a triangular ROI on any given image.  You
have to type in the three x,y coordinates of your triangle at the prompts.
This is simply to demonstrate the feasibility of creating your triangular
ROI.  You can have a macro take the coordinates from the image in some
cases, but it really depends on what you are trying to do.  Please email me
off list if you want a more detailed response.

Chris

********** triangle ROI macro **********

macro '[F15] draw triangle';
var
  x1,x2,x3,y1,y2,y3,origIm:integer;

begin
  origIm:=pidnumber;duplicate('test image');
  selectAll;clear;killROI;
  x1:=GetNumber('enter first X coordinate ',0,0);
  y1:=GetNumber('enter first Y coordinate ',0,0);
  x2:=GetNumber('enter second X coordinate ',0,0);
  y2:=GetNumber('enter second Y coordinate ',0,0);
  x3:=GetNumber('enter third X coordinate ',0,0);
  y3:=GetNumber('enter third Y coordinate ',0,0);
  moveTo(x1,y1);lineTo(x2,y2);lineTo(x3,y3);lineTo(x1,y1);
  setThreshold(1);autoOutline(x1,y1);dispose;
  selectPic(origIm);restoreROI;
end;

>Hello,
>
>I am new to macro language in nih-image and am having difficulty creating
>a triangular ROI (90, 45, 45 degrees) where the coordinates of each of the
>three points of the triangle are known prior to defining the ROI.
>
>MakeRoi is defined for a rectangular ROI and does not seem to be
>applicable. I can create the trianlge using the polygon tool, but I have
>many images to process and a macro would be of great help.

* * * * * * * * * * * * * * * * * *
* Dr. Christopher Hunt Coulon     *
* The GAIA Group                  *
* 40 Chick Road                   *
* Wolfeboro, New Hampshire 03894  *
* 603 569-0028                    *
* www.worldpath.net/~ad1054       *
* * * * * * * * * * * * * * * * * *

------------------------------

Date:          Fri, 14 May 1999 12:24:43 +1000
From: GJOSS@rna.bio.mq.edu.au
To: nih-image@io.ece.drexel.edu
Subject:       Re: original Think Pascal code of NIH image
Message-ID: <17364C05E2@rna.bio.mq.edu.au>

>Date: Fri, 14 May 1999 01:03:58 +1000
>Subject: original Think Pascal code of NIH image
>From: "Chih-L Han" <jessehcl@cardiologist.org>
>To: nih-image@io.ece.drexel.edu
>Dear NIH imagers,
>
>Can anyone advice me where I can download the original Think Pascal source
>of NIH image?
>
>Thank you very much for your assistance in advance.
>
I will attach v1.55 source(last Think Pascal version) by direct email.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Fri, 14 May 1999 17:39:44 +1000
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: Image J? Should I or Shouldn't I.
Message-Id: <F98649A5EE8ED11190160000F802756598D071@exchvic3.dsto.defence.gov.au>
Content-Type: text/plain;
	charset="windows-1252"

Hi, 
I agree that moving to Image J with its enhanced pixel depth etc and colour
capability would be a good idea, and am prepared to pick up Java (he says
lightly).

BUT
I see some  problems with the move to Image J, and I hope that the wise
heads on the list can tell me where and how I am wrong.

My main use of Image is with Kodak Megaplus cameras, the 1.4 and the 1.6i
both being in use. I rely on the Image macros to control sequential
acquisitions and move the stage between each frame, so I can cover a large
area or capture a series of images through a defined focus range. I need
serial port access to do this.

I am using these with the PDI digital boards for the PCI bus.
These allow the camera to have the shutter speed changed and the gain and
offset changed (for the i series). And also controls image size, transfer
size and etc. An immediate advantage of Image J would be the ability to use
the 10 bits available from the 1.6i camera.

To get these to work from Image J, I would have to do the following things.
I think?

1. Make an interface into Image J to support the camera functions.?

2. Or Make a plug-in for Image J which did the above.?

3. Understand how to write the driver for the card to work with Image J?

4. Or maybe I should make the card talk to Quicktime?

I await responses to my questions.
I do have the code for the PDI boards, so I am well placed to have a go, but
my programming skills are not terrific, but I can do things, it just takes
me longer.

If anyone can provide me with some cogent arguments I will listen and act.

On a slightly different point, what tools do i need for Java, I have CW4.
And are any books recommended?
TIA

Noel Goldsmith
AMRL
DSTO
Melbourne Australia

--------------------------------
End of nih-image-d Digest V99 Issue #112
****************************************

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Date: Fri, 14 May 1999 17:16:00 +0000
From: "Swidbert R. Ott" <sro21@hermes.cam.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: AutoMatch --- general update
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Dear all,

this might be of interest to all who use, or want to use, AutoMatch (the
automatic image mosaicking package for NIH Image).

This info originated as a reply to Dr. Fernandez's questions, and he
kindly agreed to me sending this to the list.  His original message to me
is included at the bottom of this posting.

Comments or suggestions welcome as always.

Regards,

Swidbert R. Ott,

_________________________________________________________________________

Dear Dr. Fernandez,

This turns out to be a lenghty reply.  Would you mind If I also post this
to the NIH mail list, as a kind of general update on AutoMatch?

It is good to hear that you find AutoMatch useful.  I have completely lost
track of who is using it.  There was a storm of interest when I first
released it, and I tried to keep track of who uses it, but you cannot
really.  I recently did a citation search for my paper on the method and
the software, and I got only one citation, and this was in a
review article on chemical microscopy!  I reckon many people who have the
software don't even know about the paper, because it came out only after
the software was released.

What I'm saying is please do cite the paper in your method section :)

Now my thoughts on your questions:

1) AutoMatch will not run on a PC.  Although ScionImage has the "same"
macro programming language as the Mac version, there are several commands
that are platform specific, and AutoMatch uses them a lot, so one would
have to modify the code.  I tried to bring the thing to the PC, but last
time I looked at ScionImage, there were some commands actually missing
rather than just having equivalents  (no functions, e.g.) so I gave up for
now.

So getting a new PC compatible is not an option if you want to speed up
your mosaicking.  But I don't really see what the advantage of buying the
PC would be in regard of your frame grabber.  You say you cannot use your
Nubus grabber with the new G3's, but you wouldn't be able to use it with a
PC either, so new fast hardware means new grabber;  I'm sure you could
find some good use for the old Mac + grabber (spare setup, teaching,
whatever)

2) There is no newer version yet.  I thought I'd rewrite the whole thing
as a stand-alone application program, to get rid of some glitches in the
design that are a consequence of restrictions in the macro language, see
below).  But in what?  Java (for portability)?  Forth (because I'm
reasonably familiar with it)?  C++?

I cannot, and don't want to, program under Windows, programming the Mac is
challenge enough for an amateur like me, so a standalone version would
mean Mac-only forever (yeah, people ought to buy Macs anyway ;) unless
Java is a way out of the dilemma.

3) Getting a new G3 for assembling the images, and continuing to grab them
on the old machine, is definitely an option, although I reckon that in the
long run you will still want a grabber card for the G3.

Getting the images over to the G3 for processing is quite
straight-forward, although you need to know what you are doing.  Why?
Well in retrospect, I must admit that I made some problematic design
decisions when writing the software, to make it work "nicely."  One thing,
and many have found this a problem, is that you cannot work with images
that were acquired outside AutoMatch.  This is because AutoMatch needs
additional information that it writes to internal log files during
acquisition.  This information is stored in files in the AutoMatch
preferences folder within the System Folder, together with the individual
frames.

While you cannot process images that were captured outside AutoMatch, you
*can* process images captured within AM on another machine.  You need to
transfer the AM preferences folder from the acquisition Mac to the
processing Mac, since it contains the frames (one stack per composite
image) and the log files (essential!).  I.e. the AM prefs folder on the
processing Mac needs to be replaced with the one from the acquisition Mac.
(Maybe it is enough to replace the "framestacks" folder, or whatever I
called it, *within* the AM preferences folder, I cannot remember whether
the log files are within the framestacks folder or one folder level
upwards;  I will check this out.)

So in short, the recommendation would be to get a decent G3 (oh god, the
G4's will be out this summer!) and capture on the old Mac for the time
being, and eventually get a PCI framegrabber card lateron.

I hope this  helps you a bit; let me know if there is anything else I can
do (apart from re-writing a better version ;).

Best regards, Swidbert

______________________
Swidbert R. Ott
Dept. Zoology, Univ. Cambridge
Downing Street, Cambridge CB2 3EJ, UK


 On Wed, 12 May 1999, Eduardo Fernandez wrote:

> Dear Dr. Ott:
> 
> First of all my congratulations for your very nice and helpful 
> software for image mosaicking. We have been using AutoMatch 3.0b for
> making retinal mosaics. The problem is that we are using an old 6100
> PowerMacintosh, with 40 MB of RAM and it is  is very, very slow. We
> are thinking on upgrading to a new Mac, but our Frame Grabber Card is
> a Nubus VG-5 and the new Macintosh, as you know,  don't have any Nubus
> slot. We are thinking on two possibilities:
> 
> - Using our 6100 to capture the images and the new Mac to process
> them. Is it possible?? - Using a PC compatible (with Scion Image) to
> make everything. (????)
> 
> Any other suggestion? What do you recomend? 
> Do you have any new version of AutoMatch?
> 
> Thanks in advance for all your help and congratulations again.
> 
> Best regards,
> Eduardo Fernandez
> 
> ***********************************************************
>              Eduardo Fernandez, MD and PhD.    
>   ***        EMail:   E.FERNANDEZ@UMH.ES
> *     *      Dept. Histology and
> *  0  *      Institute of Bioengineering
> *     *      Facultad de Medicina
>   ***        Universidad Miguel Hernandez
>              Alicante 03550         TEL: (9) 6591 9439
>              Spain, EUROPE          FAX: (9) 6591 9434
> 
> Do you want to know more about the Organization of the Vertebrate
> Retina?  Then open our book on the WWW
>            in USA:  http://insight.med.utah.edu/Webvision
>            in Europe: http://retina.umh.es/webvision/
> *******************************************************************
> 




Swidbert R OTT
Department of Zoology
University of Cambridge
Downing Street
Cambridge CB2 3EJ
ENGLAND

"C makes you think that it is the best programming language in the world. 

Forth makes you think that you are the best programmer in the world."



From nih-image-request@io.ece.drexel.edu Fri May 14 20:06 EDT 1999
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Date: Fri, 14 May 1999 17:55:35 -0600 (MDT)
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Can anyone tell me if Scion Image is able to IMPORT a *.bmp image? I'd
like to import vs. open so I can bring up many images at one time
rahter than clicking them open one at a time.

Thanks in advance.

____________________________________________________________________
Greg Kawchuk D.C., M.Sc.
Clinician, University Health Services 
Ph.D. Candidate, McCaig Centre for Joint Injury and Arthritis Research
University of Calgary
http://www.ucalgary.ca/~gkawchuk


From nih-image-request@io.ece.drexel.edu Fri May 14 22:41 EDT 1999
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At 05:55 PM 5/14/99 -0600, you wrote:
>
>
>Can anyone tell me if Scion Image is able to IMPORT a *.bmp image? I'd
>like to import vs. open so I can bring up many images at one time
>rahter than clicking them open one at a time.

Check "Open All" in the Open dialog to open a folder of of bmp (or tiff) files. You can also use ImageJ to open a folder of bmp, tiff or gif files as a stack, save it as a tiff stack, then open it in NIH Image or Scion Image.

-wayne


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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 113

Today's Topics:
  AutoMatch --- general update          [ "Swidbert R. Ott" <sro21@hermes.cam ]
  BMP Import in Scion Image             [ Greg Kawchuk <kawchuk@mccaig.ucalga ]
  Re: BMP Import in Scion Image         [ Wayne Rasband <wayne@codon.nih.gov> ]

------------------------------

Date: Fri, 14 May 1999 17:16:00 +0000
From: "Swidbert R. Ott" <sro21@hermes.cam.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: AutoMatch --- general update
Message-ID: <1833732.3135690960@neuron05.zoo.cam.ac.uk>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Dear all,

this might be of interest to all who use, or want to use, AutoMatch (the
automatic image mosaicking package for NIH Image).

This info originated as a reply to Dr. Fernandez's questions, and he
kindly agreed to me sending this to the list.  His original message to me
is included at the bottom of this posting.

Comments or suggestions welcome as always.

Regards,

Swidbert R. Ott,

_________________________________________________________________________

Dear Dr. Fernandez,

This turns out to be a lenghty reply.  Would you mind If I also post this
to the NIH mail list, as a kind of general update on AutoMatch?

It is good to hear that you find AutoMatch useful.  I have completely lost
track of who is using it.  There was a storm of interest when I first
released it, and I tried to keep track of who uses it, but you cannot
really.  I recently did a citation search for my paper on the method and
the software, and I got only one citation, and this was in a
review article on chemical microscopy!  I reckon many people who have the
software don't even know about the paper, because it came out only after
the software was released.

What I'm saying is please do cite the paper in your method section :)

Now my thoughts on your questions:

1) AutoMatch will not run on a PC.  Although ScionImage has the "same"
macro programming language as the Mac version, there are several commands
that are platform specific, and AutoMatch uses them a lot, so one would
have to modify the code.  I tried to bring the thing to the PC, but last
time I looked at ScionImage, there were some commands actually missing
rather than just having equivalents  (no functions, e.g.) so I gave up for
now.

So getting a new PC compatible is not an option if you want to speed up
your mosaicking.  But I don't really see what the advantage of buying the
PC would be in regard of your frame grabber.  You say you cannot use your
Nubus grabber with the new G3's, but you wouldn't be able to use it with a
PC either, so new fast hardware means new grabber;  I'm sure you could
find some good use for the old Mac + grabber (spare setup, teaching,
whatever)

2) There is no newer version yet.  I thought I'd rewrite the whole thing
as a stand-alone application program, to get rid of some glitches in the
design that are a consequence of restrictions in the macro language, see
below).  But in what?  Java (for portability)?  Forth (because I'm
reasonably familiar with it)?  C++?

I cannot, and don't want to, program under Windows, programming the Mac is
challenge enough for an amateur like me, so a standalone version would
mean Mac-only forever (yeah, people ought to buy Macs anyway ;) unless
Java is a way out of the dilemma.

3) Getting a new G3 for assembling the images, and continuing to grab them
on the old machine, is definitely an option, although I reckon that in the
long run you will still want a grabber card for the G3.

Getting the images over to the G3 for processing is quite
straight-forward, although you need to know what you are doing.  Why?
Well in retrospect, I must admit that I made some problematic design
decisions when writing the software, to make it work "nicely."  One thing,
and many have found this a problem, is that you cannot work with images
that were acquired outside AutoMatch.  This is because AutoMatch needs
additional information that it writes to internal log files during
acquisition.  This information is stored in files in the AutoMatch
preferences folder within the System Folder, together with the individual
frames.

While you cannot process images that were captured outside AutoMatch, you
*can* process images captured within AM on another machine.  You need to
transfer the AM preferences folder from the acquisition Mac to the
processing Mac, since it contains the frames (one stack per composite
image) and the log files (essential!).  I.e. the AM prefs folder on the
processing Mac needs to be replaced with the one from the acquisition Mac.
(Maybe it is enough to replace the "framestacks" folder, or whatever I
called it, *within* the AM preferences folder, I cannot remember whether
the log files are within the framestacks folder or one folder level
upwards;  I will check this out.)

So in short, the recommendation would be to get a decent G3 (oh god, the
G4's will be out this summer!) and capture on the old Mac for the time
being, and eventually get a PCI framegrabber card lateron.

I hope this  helps you a bit; let me know if there is anything else I can
do (apart from re-writing a better version ;).

Best regards, Swidbert

______________________
Swidbert R. Ott
Dept. Zoology, Univ. Cambridge
Downing Street, Cambridge CB2 3EJ, UK


 On Wed, 12 May 1999, Eduardo Fernandez wrote:

> Dear Dr. Ott:
> 
> First of all my congratulations for your very nice and helpful 
> software for image mosaicking. We have been using AutoMatch 3.0b for
> making retinal mosaics. The problem is that we are using an old 6100
> PowerMacintosh, with 40 MB of RAM and it is  is very, very slow. We
> are thinking on upgrading to a new Mac, but our Frame Grabber Card is
> a Nubus VG-5 and the new Macintosh, as you know,  don't have any Nubus
> slot. We are thinking on two possibilities:
> 
> - Using our 6100 to capture the images and the new Mac to process
> them. Is it possible?? - Using a PC compatible (with Scion Image) to
> make everything. (????)
> 
> Any other suggestion? What do you recomend? 
> Do you have any new version of AutoMatch?
> 
> Thanks in advance for all your help and congratulations again.
> 
> Best regards,
> Eduardo Fernandez
> 
> ***********************************************************
>              Eduardo Fernandez, MD and PhD.    
>   ***        EMail:   E.FERNANDEZ@UMH.ES
> *     *      Dept. Histology and
> *  0  *      Institute of Bioengineering
> *     *      Facultad de Medicina
>   ***        Universidad Miguel Hernandez
>              Alicante 03550         TEL: (9) 6591 9439
>              Spain, EUROPE          FAX: (9) 6591 9434
> 
> Do you want to know more about the Organization of the Vertebrate
> Retina?  Then open our book on the WWW
>            in USA:  http://insight.med.utah.edu/Webvision
>            in Europe: http://retina.umh.es/webvision/
> *******************************************************************
> 




Swidbert R OTT
Department of Zoology
University of Cambridge
Downing Street
Cambridge CB2 3EJ
ENGLAND

"C makes you think that it is the best programming language in the world. 

Forth makes you think that you are the best programmer in the world."

------------------------------

Date: Fri, 14 May 1999 17:55:35 -0600 (MDT)
From: Greg Kawchuk <kawchuk@mccaig.ucalgary.ca>
To: nih-image@io.ece.drexel.edu
Subject: BMP Import in Scion Image
Message-Id: <Pine.SUN.3.95.990514175337.18557A-100000@epicenter>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Can anyone tell me if Scion Image is able to IMPORT a *.bmp image? I'd
like to import vs. open so I can bring up many images at one time
rahter than clicking them open one at a time.

Thanks in advance.

____________________________________________________________________
Greg Kawchuk D.C., M.Sc.
Clinician, University Health Services 
Ph.D. Candidate, McCaig Centre for Joint Injury and Arthritis Research
University of Calgary
http://www.ucalgary.ca/~gkawchuk

------------------------------

Date: Fri, 14 May 1999 22:33:28 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: BMP Import in Scion Image
Message-Id: <3.0.5.32.19990514223328.007b78d0@codon.nih.gov>
Content-Type: text/plain; charset="us-ascii"

At 05:55 PM 5/14/99 -0600, you wrote:
>
>
>Can anyone tell me if Scion Image is able to IMPORT a *.bmp image? I'd
>like to import vs. open so I can bring up many images at one time
>rahter than clicking them open one at a time.

Check "Open All" in the Open dialog to open a folder of of bmp (or tiff) files. You can also use ImageJ to open a folder of bmp, tiff or gif files as a stack, save it as a tiff stack, then open it in NIH Image or Scion Image.

-wayne

--------------------------------
End of nih-image-d Digest V99 Issue #113
****************************************

From nih-image-request@io.ece.drexel.edu Mon May 17 09:23 EDT 1999
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Date: Mon, 17 May 1999 15:04:28 +0200
From: Lucas Bickel <lukas.bickel@zmk.unibe.ch>
Subject: pidNumber /w Text windows
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Hi

I've got some problem with PidNumbers. I'm using a text window called
debugger to log everything in a macro of mine. So I have to reselect the
debugger-window after opening other windows. Now my problem is that the
following code:

	procedure SetupDebugger;
	begin
		NewTextWindow ('Debugger');
		writeln('creating Debugger window');
		DebuggerPid := PidNumber;
		writeln('saving DebuggerPid  ---> ', DebuggerPid);
	end;

returns the following Output:

	creating Debugger window
	saving DebuggerPid  --->    0

I don't now why but the script just doesn't want to return a valid pid
number for the text window. I hope somone nows how I can solve my problem

Thanks

Lucas

-----------------------------------
    Lucas Bickel
    Freiburgstrasse 7
    3010 Bern
-----------------------------------
Voice  +41 31 632 86 18
Pager  +41 74 490 30 02
-----------------------------------



From nih-image-request@io.ece.drexel.edu Mon May 17 09:57 EDT 1999
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Date: Mon, 17 May 1999 09:40:42 -0400
To: nih-image@io.ece.drexel.edu
From: ad1054@worldpath.net (Dr. Christopher Coulon)
Subject: Re: pidNumber /w Text windows
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Lucas,

pidnumbers only work with image windows.  If you want to call your text
window in a macro, use selectWindow('Debugger');

Chris

>Hi
>
>I've got some problem with PidNumbers. I'm using a text window called
>debugger to log everything in a macro of mine. So I have to reselect the
>debugger-window after opening other windows. Now my problem is that the
>following code:
>
>        procedure SetupDebugger;
>        begin
>                NewTextWindow ('Debugger');
>                writeln('creating Debugger window');
>                DebuggerPid := PidNumber;
>                writeln('saving DebuggerPid  ---> ', DebuggerPid);
>        end;
>
>returns the following Output:
>
>        creating Debugger window
>        saving DebuggerPid  --->    0
>
>I don't now why but the script just doesn't want to return a valid pid
>number for the text window. I hope somone nows how I can solve my problem
>
>Thanks
>
>Lucas

* * * * * * * * * * * * * * * * * *
* Dr. Christopher Hunt Coulon     *
* The GAIA Group                  *
* 40 Chick Road                   *
* Wolfeboro, New Hampshire 03894  *
* 603 569-0028                    *
* www.worldpath.net/~ad1054       *
* * * * * * * * * * * * * * * * * *



From nih-image-request@io.ece.drexel.edu Mon May 17 14:02 EDT 1999
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Date: Mon, 17 May 1999 13:45:45 -0400 (EDT)
From: Tim Quagliaroli <tmq4s@rayleigh.mech.virginia.edu>
To: nih-image@io.ece.drexel.edu
Subject: Geometric Correction Macro?
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I've been hunting about for pre-existing programs available for Scion
Image that handle the correction of geometric distortion. Looking through
the NIH-Image archives, I saw that there had been some written by a Bill
Gandler. However, the programs do not seem to exist in
codon.nih.gov/pub/nih-image/contrib/. Is there some other place where
these programs might reside? 

	Tim Q



From nih-image-request@io.ece.drexel.edu Mon May 17 16:13 EDT 1999
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Date: Mon, 17 May 1999 12:57:05 -0700 (PDT)
From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: Setting "1/2 size video"/video control in macro
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Hello,

I have an application where I need to switch from full size to half size
video (normally done under video control) mid-stream during a macro. I
can't seem to set this (I tried various things using SetVideo but this
doesn't seem to be an option).

My problem is I need to capture about 3 minutes of full screen at 1 Hz
then 10 sec at 10 Hz (at half size), then 2 min at 1 Hz (full screen).
The problem is that the video capture card I have doesn't work perfectly
with image and won't get over 4 Hz at full screen (it gets 15 Hz at 1/2
screen).

Is it possible to set the video size in a Macro?

Thanks all!
Stephan
 

------------------------------
Stephan G. Anagnostaras, Ph.D. 
UCLA Dept. of Neurobiology         
stephan@lifesci.ucla.edu    
------------------------------
Work, Gonda: (310) 267-2522
      Psych: (310) 794-5339
        Fax: (310) 206-5895
       Home: (310) 306-0294
------------------------------


From nih-image-request@io.ece.drexel.edu Mon May 17 19:49 EDT 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: stephan@protos.lifesci.ucla.edu, nih-image@io.ece.drexel.edu
Date:          Tue, 18 May 1999 9:39:03 +1000
Subject:       Re: Setting "1/2 size video"/video control in macro
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>Date: Mon, 17 May 1999 12:57:05 -0700 (PDT)
>From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Setting "1/2 size video"/video control in macro
>
>Hello,
>
>I have an application where I need to switch from full size to half size
>video (normally done under video control) mid-stream during a macro. I
>can't seem to set this (I tried various things using SetVideo but this
>doesn't seem to be an option).
>
>My problem is I need to capture about 3 minutes of full screen at 1 Hz
>then 10 sec at 10 Hz (at half size), then 2 min at 1 Hz (full screen).
>The problem is that the video capture card I have doesn't work perfectly
>with image and won't get over 4 Hz at full screen (it gets 15 Hz at 1/2
>screen).
>
>Is it possible to set the video size in a Macro?
>
>Thanks all!
>Stephan
> 
>
>------------------------------
>Stephan G. Anagnostaras, Ph.D. 
>UCLA Dept. of Neurobiology         
>stephan@lifesci.ucla.edu    
>------------------------------
>Work, Gonda: (310) 267-2522
>      Psych: (310) 794-5339
>        Fax: (310) 206-5895
>       Home: (310) 306-0294
>------------------------------

The following macro illustrates a method to achieve that result.

The preliminary "'makeNewStack('halfvideo');" 
is to allow illustration of use of 'existing' which looks for 'Movie'.
'blind' is to allow faster capture.

For the timelapse portion, I would normally use 
AverageFrames('integrate'{or average},frames);
selectAll;copy;selectPic(stack);paste;
rather than the convenient MakeMovie to allow improved image quality and 
other functions between frames.

macro'[f1]capture';var p:integer;begin
StartCapturing;
setNewSize(384,256);
makeNewStack('halfvideo');for p:=1 to 9 do addslice;
p:=pidNumber;

StartCapturing;
makeRoi(0,0,768,512);
MakeMovie( 'time stamp',5,1);
SetPicName('Movie0');
StopCapturing;
selectPic(p);SetPicName('Movie');
StartCapturing;
makeRoi(0,0,384,256);
MakeMovie('existing blind time stamp',10,.1);
SetPicName('Movie1');
StopCapturing;
StartCapturing;
makeRoi(0,0,768,512);
MakeMovie('time stamp',5,1);
SetPicName('Movie2');
StopCapturing;
end
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Mon May 17 20:26 EDT 1999
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Date: Tue, 18 May 1999 01:53:54 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: pidNumber /w Text windows
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>Hi
>
>I've got some problem with PidNumbers. I'm using a text window called
>debugger to log everything in a macro of mine.

Because your window name is Debugger, you may find it useful to know that
Object-Image has a built-in macro debugger.
While single-stepping through a macro, you can simultaneously observe your
source text, the active image, the current roi and all variables. Variables
are highlighted when their value changes; they also can be changed on the
fly by double-clicking on them.  A window with all variables is also
optionally visible after a macro  error (together with the error message),
while the offending macro line is highlighted.
You can set permanent breakpoints with "break;", conditional breakpoints
like break('capslock'), loop breakpoints (option-downArrow) and temporary
breakpoints with the 'RunTo' cursor.

You can enter the single-step debugger by holding the command key down
while selecting a macro via menu.

The macro debugger is useful for writing and debugging complex macros, but
also for beginners, who want to study the behaviour of existing macros.


See the "Help" or "?" menu for more features.

Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



From nih-image-request@io.ece.drexel.edu Tue May 18 04:46 EDT 1999
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Date: Tue, 18 May 1999 10:32:53 +0200 (MET DST)
From: Patrick Doyle <Patrick.Doyle@curie.fr>
To: nih-image@io.ece.drexel.edu
Subject: RAM on board or computer
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1) I am considering buying a Scion LG3 or AG5 capture
baord which will be used with a Pentium PC and
don`t know whether I should invest in memory directly
on the board or if I can just use the RAM on my 
computer for capturing sequences of images ?

2) Also, does anyone know what I can really expect
   for a capture rate on a PC (at least 350 MHz) ?
   Scion doesn`t quote the capture rate for PC`s.


thanks in advance,
Patrick Doyle



_/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/  
(=\         Dr. Patrick S. Doyle
 \=)     Laboratoire Physico- Chimie
  /         Institut Curie PCC 
 /=)  11 rue Pierre et Marie Curie
(=/            75005 Paris
 /               France
(=/
	    tel 01.42.34.64.68
_/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/    



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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 114

Today's Topics:
  pidNumber /w Text windows             [ Lucas Bickel <lukas.bickel@zmk.unib ]
  Re: pidNumber /w Text windows         [ ad1054@worldpath.net (Dr. Christoph ]
  Geometric Correction Macro?           [ Tim Quagliaroli <tmq4s@rayleigh.mec ]
  Setting "1/2 size video"/video contr  [ Stephan Anagnostaras <stephan@proto ]
  Re: Setting "1/2 size video"/video c  [ GJOSS@rna.bio.mq.edu.au ]
  Re: pidNumber /w Text windows         [ Norbert Vischer <vischer@bio.uva.nl ]
  RAM on board or computer              [ Patrick Doyle <Patrick.Doyle@curie. ]

------------------------------

Date: Mon, 17 May 1999 15:04:28 +0200
From: Lucas Bickel <lukas.bickel@zmk.unibe.ch>
To: nih-image@io.ece.drexel.edu
Subject: pidNumber /w Text windows
Message-id: <l03130301b365c264095f@[130.92.198.63]>
Content-type: text/plain; charset=us-ascii
Content-transfer-encoding: 7BIT

Hi

I've got some problem with PidNumbers. I'm using a text window called
debugger to log everything in a macro of mine. So I have to reselect the
debugger-window after opening other windows. Now my problem is that the
following code:

	procedure SetupDebugger;
	begin
		NewTextWindow ('Debugger');
		writeln('creating Debugger window');
		DebuggerPid := PidNumber;
		writeln('saving DebuggerPid  ---> ', DebuggerPid);
	end;

returns the following Output:

	creating Debugger window
	saving DebuggerPid  --->    0

I don't now why but the script just doesn't want to return a valid pid
number for the text window. I hope somone nows how I can solve my problem

Thanks

Lucas

-----------------------------------
    Lucas Bickel
    Freiburgstrasse 7
    3010 Bern
-----------------------------------
Voice  +41 31 632 86 18
Pager  +41 74 490 30 02
-----------------------------------

------------------------------

Date: Mon, 17 May 1999 09:40:42 -0400
From: ad1054@worldpath.net (Dr. Christopher Coulon)
To: nih-image@io.ece.drexel.edu
Subject: Re: pidNumber /w Text windows
Message-Id: <v01520d00b365cbdbb635@[208.133.217.192]>
Content-Type: text/plain; charset="us-ascii"

Lucas,

pidnumbers only work with image windows.  If you want to call your text
window in a macro, use selectWindow('Debugger');

Chris

>Hi
>
>I've got some problem with PidNumbers. I'm using a text window called
>debugger to log everything in a macro of mine. So I have to reselect the
>debugger-window after opening other windows. Now my problem is that the
>following code:
>
>        procedure SetupDebugger;
>        begin
>                NewTextWindow ('Debugger');
>                writeln('creating Debugger window');
>                DebuggerPid := PidNumber;
>                writeln('saving DebuggerPid  ---> ', DebuggerPid);
>        end;
>
>returns the following Output:
>
>        creating Debugger window
>        saving DebuggerPid  --->    0
>
>I don't now why but the script just doesn't want to return a valid pid
>number for the text window. I hope somone nows how I can solve my problem
>
>Thanks
>
>Lucas

* * * * * * * * * * * * * * * * * *
* Dr. Christopher Hunt Coulon     *
* The GAIA Group                  *
* 40 Chick Road                   *
* Wolfeboro, New Hampshire 03894  *
* 603 569-0028                    *
* www.worldpath.net/~ad1054       *
* * * * * * * * * * * * * * * * * *

------------------------------

Date: Mon, 17 May 1999 13:45:45 -0400 (EDT)
From: Tim Quagliaroli <tmq4s@rayleigh.mech.virginia.edu>
To: nih-image@io.ece.drexel.edu
Subject: Geometric Correction Macro?
Message-ID: <Pine.A41.4.05.9905171339220.14296-100000@rayleigh.mech.Virginia.EDU>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I've been hunting about for pre-existing programs available for Scion
Image that handle the correction of geometric distortion. Looking through
the NIH-Image archives, I saw that there had been some written by a Bill
Gandler. However, the programs do not seem to exist in
codon.nih.gov/pub/nih-image/contrib/. Is there some other place where
these programs might reside? 

	Tim Q

------------------------------

Date: Mon, 17 May 1999 12:57:05 -0700 (PDT)
From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: Setting "1/2 size video"/video control in macro
Message-ID: <Pine.GSO.4.10.9905171252320.17220-100000@protos.lifesci.ucla.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hello,

I have an application where I need to switch from full size to half size
video (normally done under video control) mid-stream during a macro. I
can't seem to set this (I tried various things using SetVideo but this
doesn't seem to be an option).

My problem is I need to capture about 3 minutes of full screen at 1 Hz
then 10 sec at 10 Hz (at half size), then 2 min at 1 Hz (full screen).
The problem is that the video capture card I have doesn't work perfectly
with image and won't get over 4 Hz at full screen (it gets 15 Hz at 1/2
screen).

Is it possible to set the video size in a Macro?

Thanks all!
Stephan
 

- ----------------------------
Stephan G. Anagnostaras, Ph.D. 
UCLA Dept. of Neurobiology         
stephan@lifesci.ucla.edu    
- ----------------------------
Work, Gonda: (310) 267-2522
      Psych: (310) 794-5339
        Fax: (310) 206-5895
       Home: (310) 306-0294
- ----------------------------

------------------------------

Date:          Tue, 18 May 1999 9:39:03 +1000
From: GJOSS@rna.bio.mq.edu.au
To: stephan@protos.lifesci.ucla.edu, nih-image@io.ece.drexel.edu
Subject:       Re: Setting "1/2 size video"/video control in macro
Message-ID: <747AE76B58@rna.bio.mq.edu.au>

>Date: Mon, 17 May 1999 12:57:05 -0700 (PDT)
>From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Setting "1/2 size video"/video control in macro
>
>Hello,
>
>I have an application where I need to switch from full size to half size
>video (normally done under video control) mid-stream during a macro. I
>can't seem to set this (I tried various things using SetVideo but this
>doesn't seem to be an option).
>
>My problem is I need to capture about 3 minutes of full screen at 1 Hz
>then 10 sec at 10 Hz (at half size), then 2 min at 1 Hz (full screen).
>The problem is that the video capture card I have doesn't work perfectly
>with image and won't get over 4 Hz at full screen (it gets 15 Hz at 1/2
>screen).
>
>Is it possible to set the video size in a Macro?
>
>Thanks all!
>Stephan
> 
>
>------------------------------
>Stephan G. Anagnostaras, Ph.D. 
>UCLA Dept. of Neurobiology         
>stephan@lifesci.ucla.edu    
>------------------------------
>Work, Gonda: (310) 267-2522
>      Psych: (310) 794-5339
>        Fax: (310) 206-5895
>       Home: (310) 306-0294
>------------------------------

The following macro illustrates a method to achieve that result.

The preliminary "'makeNewStack('halfvideo');" 
is to allow illustration of use of 'existing' which looks for 'Movie'.
'blind' is to allow faster capture.

For the timelapse portion, I would normally use 
AverageFrames('integrate'{or average},frames);
selectAll;copy;selectPic(stack);paste;
rather than the convenient MakeMovie to allow improved image quality and 
other functions between frames.

macro'[f1]capture';var p:integer;begin
StartCapturing;
setNewSize(384,256);
makeNewStack('halfvideo');for p:=1 to 9 do addslice;
p:=pidNumber;

StartCapturing;
makeRoi(0,0,768,512);
MakeMovie( 'time stamp',5,1);
SetPicName('Movie0');
StopCapturing;
selectPic(p);SetPicName('Movie');
StartCapturing;
makeRoi(0,0,384,256);
MakeMovie('existing blind time stamp',10,.1);
SetPicName('Movie1');
StopCapturing;
StartCapturing;
makeRoi(0,0,768,512);
MakeMovie('time stamp',5,1);
SetPicName('Movie2');
StopCapturing;
end
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Tue, 18 May 1999 01:53:54 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: pidNumber /w Text windows
Message-Id: <l03010d02b366515ec2b7@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

>Hi
>
>I've got some problem with PidNumbers. I'm using a text window called
>debugger to log everything in a macro of mine.

Because your window name is Debugger, you may find it useful to know that
Object-Image has a built-in macro debugger.
While single-stepping through a macro, you can simultaneously observe your
source text, the active image, the current roi and all variables. Variables
are highlighted when their value changes; they also can be changed on the
fly by double-clicking on them.  A window with all variables is also
optionally visible after a macro  error (together with the error message),
while the offending macro line is highlighted.
You can set permanent breakpoints with "break;", conditional breakpoints
like break('capslock'), loop breakpoints (option-downArrow) and temporary
breakpoints with the 'RunTo' cursor.

You can enter the single-step debugger by holding the command key down
while selecting a macro via menu.

The macro debugger is useful for writing and debugging complex macros, but
also for beginners, who want to study the behaviour of existing macros.


See the "Help" or "?" menu for more features.

Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: Tue, 18 May 1999 10:32:53 +0200 (MET DST)
From: Patrick Doyle <Patrick.Doyle@curie.fr>
To: nih-image@io.ece.drexel.edu
Subject: RAM on board or computer
Message-ID: <Pine.GSO.3.96.990518102728.27686A-100000@burton.curie.fr>
Content-Type: TEXT/PLAIN; charset=US-ASCII

1) I am considering buying a Scion LG3 or AG5 capture
baord which will be used with a Pentium PC and
don`t know whether I should invest in memory directly
on the board or if I can just use the RAM on my 
computer for capturing sequences of images ?

2) Also, does anyone know what I can really expect
   for a capture rate on a PC (at least 350 MHz) ?
   Scion doesn`t quote the capture rate for PC`s.


thanks in advance,
Patrick Doyle



_/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/  
(=\         Dr. Patrick S. Doyle
 \=)     Laboratoire Physico- Chimie
  /         Institut Curie PCC 
 /=)  11 rue Pierre et Marie Curie
(=/            75005 Paris
 /               France
(=/
	    tel 01.42.34.64.68
_/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/    

--------------------------------
End of nih-image-d Digest V99 Issue #114
****************************************

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To: nih-image@io.ece.drexel.edu
From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: Re: nih-image-d Digest V99 #109
Cc: lhernan@criba.edu.ar
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>>Luis System Profiler is able to check VRAM.
<...>
>Unfortunately my System Profiler Vers 1.3.2. does not have the Memory
>Overview option.
system profiler 2.1.2:
http://asu.info.apple.com/swupdates.nsf/artnum/n10098

ard



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Date: Tue, 18 May 1999 08:39:49 -0700 (PDT)
From: "T. Hickson" <hickson@pangea.Stanford.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Radial distortion correction for NIH-Image
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I am looking for an NIH-Image macro or plug-in that will handle geometric
distortions (radial distortion and alignment, mostly) of images.  I'm
trying to remove a radial distortion caused by my camera lens.  

I have looked at the archives of this list and have found that some
plug-ins existed in the past, but they do not appear to be available on
the ftp site anymore (the postings were in 1994).  Is there anything out
there??  

Cheers,

Tom

**************************************************************

Thomas A. Hickson
St. Anthony Falls Laboratory
2-3rd Ave. SE,  Room 381
University of Minnesota
Minneapolis, MN  55414

Phone:  612-627-4594
Fax:	612-627-4609
e-mail:	hickson@pangea.stanford.edu

**************************************************************

	To doubt everything or to believe everything are
	two equally convenient solutions; both dispense
	with the necessity of reflection.
						H. Poincare


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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 115

Today's Topics:
  Re: nih-image-d Digest V99 #109       [ Ard Jonker <a.jonker@amc.uva.nl> ]
  Radial distortion correction for NIH  [ "T. Hickson" <hickson@pangea.Stanfo ]

------------------------------

Date: Tue, 18 May 1999 12:38:02 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Cc: lhernan@criba.edu.ar
Subject: Re: nih-image-d Digest V99 #109
Message-Id: <l03130302b366f322fb84@[145.117.43.50]>
Content-Type: text/plain; charset="us-ascii"

>>Luis System Profiler is able to check VRAM.
<...>
>Unfortunately my System Profiler Vers 1.3.2. does not have the Memory
>Overview option.
system profiler 2.1.2:
http://asu.info.apple.com/swupdates.nsf/artnum/n10098

ard

------------------------------

Date: Tue, 18 May 1999 08:39:49 -0700 (PDT)
From: "T. Hickson" <hickson@pangea.Stanford.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Radial distortion correction for NIH-Image
Message-ID: <Pine.OSF.3.93.990518083717.25866C-100000@pangea.Stanford.EDU>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I am looking for an NIH-Image macro or plug-in that will handle geometric
distortions (radial distortion and alignment, mostly) of images.  I'm
trying to remove a radial distortion caused by my camera lens.  

I have looked at the archives of this list and have found that some
plug-ins existed in the past, but they do not appear to be available on
the ftp site anymore (the postings were in 1994).  Is there anything out
there??  

Cheers,

Tom

**************************************************************

Thomas A. Hickson
St. Anthony Falls Laboratory
2-3rd Ave. SE,  Room 381
University of Minnesota
Minneapolis, MN  55414

Phone:  612-627-4594
Fax:	612-627-4609
e-mail:	hickson@pangea.stanford.edu

**************************************************************

	To doubt everything or to believe everything are
	two equally convenient solutions; both dispense
	with the necessity of reflection.
						H. Poincare

--------------------------------
End of nih-image-d Digest V99 Issue #115
****************************************

From nih-image-request@io.ece.drexel.edu Wed May 19 08:48 EDT 1999
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Subject: Stereo reconstructions
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Dear Imagers

I want to determine the x,y,z coordinates of particles from a stereo pair. (Actually gold 
particles located within the depth of an EM section). Does anyone know of software, macro or 
similar to do this? Thanks for your help.

Peter Shaw. John Innes Centre, Norwich, UK. (peter.shaw@bbsrc.ac.uk)


From nih-image-request@io.ece.drexel.edu Wed May 19 09:36 EDT 1999
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Date: Wed, 19 May 1999 06:19:38 -0700 (PDT)
From: steve spencer <stephen_spencer@yahoo.com>
Subject: xy coordinate mapping
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Hello, I was wondering if someone knew of a macro that
would give me the coordinates and intensitie values of
each pixel aquired from a specific slice in an
anatomical tiff file.
Thanking yopu in advance
steve spencer
western psyche
_____________________________________________________________
Do You Yahoo!?
Free instant messaging and more at http://messenger.yahoo.com


From nih-image-request@io.ece.drexel.edu Wed May 19 10:32 EDT 1999
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Date: Wed, 19 May 1999 09:31:44 +0100
To: nih-image@io.ece.drexel.edu
From: "Malinda E.C. Fitzgerald" <malinda@cbu.edu>
Subject: use of intrensic digital on G3's
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Hi I am in the process of setting up a new video system.  I want to order a
new blue G3.  It has a intrensic firewire system that processes the digital
signal.  Has anyone used the product by sony that is an A/D converter that
takes the video image information and then goes to the video card in the
Mac?  I understand Newer Tech is coming out with a new box called firestorm
in July.  Any information would be appreciated.  Malinda

Malinda E.C. Fitzgerald, Ph.D.
Associate Professor
Department of Biology
650 E Parkway So.
Christian Brothers University
Memphis, TN   38104
901-321-3262 office
901-321-4433 fax



From nih-image-request@io.ece.drexel.edu Wed May 19 11:13 EDT 1999
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From: Kevin Pedley <Kevin.Pedley@kcl.ac.uk>
Subject: Deconvolution software 
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Peter,

I spoke to you about three years ago and you offered to provide us with
youur deconvolution software but we were and remain Unix-box free,
operating entirely on high end Pentiums and Macs.

I was therfore very interested when I was asked some time ago by Andrew
Dixon if I wanted to beta test their upcomming deconvolution software,
SharpVu.  I said yes please but heard nothing further despite several
inquiries.  I met Nick White a couple of weeks ago in Oxford and he told me
that the release had been shelved and also that it was a port of your Unix
software to OS/2.

I have been using OpenLab's deconvolution module but would really prefer to
use an algorithm that is better tested and less of a black box.  I was
wondering whether your software will run under Linux and if so, it is it
still possible for us to use it?

Regards,
Kevin Pedley.



 _____________________________________________________________________
 Dr. Kevin Pedley,                           e-mail:Kevin.Pedley@KCL.AC.UK
 Physiology Division,                           Phone: (+44)-171-333-4599
 King's College London.                      Fax:   (+44)-171-937-7783
 Campden Hill Road,
 London W8 7AH.
 U.K. 
 http://life.kcl.ac.uk/ImageLab.htm
_____________________________________________________________________
 



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Subject: Stochastic Screening
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Hello:
Any suggestion where to get a plug-in for Image or Photoshop to perform
Stochastic Screening on color and gray-scale images?
Regards,

_______________________________________________________
Dr. Luis F. Hernandez, Ph.D.
Laboratorio de Botanica
Departamento de Agronomia
U N I V E R S I D A D  N A C I O N A L  D E L  S U R
8000. Bahia Blanca - ARGENTINA

<mailto: lhernan@criba.edu.ar>
Telefonos (0291) 453-4775/453-0024
FAX: 54 - 0291 - 452-1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.



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From: Kevin Pedley <Kevin.Pedley@kcl.ac.uk>
Subject: Deconvolution software 
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Apologies for my lastmessage which should not have been sent to the list.


 _____________________________________________________________________
 Dr. Kevin Pedley,                           e-mail:Kevin.Pedley@KCL.AC.UK
 Physiology Division,                           Phone: (+44)-171-333-4599
 King's College London.                      Fax:   (+44)-171-937-7783
 Campden Hill Road,
 London W8 7AH.
 U.K. 
 http://life.kcl.ac.uk/ImageLab.htm
_____________________________________________________________________
 



From nih-image-request@io.ece.drexel.edu Wed May 19 12:46 EDT 1999
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I need a macro that simply overlays a black box on to the center of another
image.  We have been using an overhead transparency previously to accomplish
the task, but I'm not sure how to create a line drawing of a rectangle
without covering up the image behind it.  Any suggestions?

------------------------------------
       Jason Tangen
       University of Lethbridge
       Psychology and Neuroscience
       tangj0@uleth.ca
------------------------------------


From nih-image-request@io.ece.drexel.edu Wed May 19 13:31 EDT 1999
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Subject: Re: use of intrensic digital on G3's
Date: Wed, 19 May 99 13:15:55 -0400
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i am also interested in solutions to this problem without going to a 
digital camera (which would be in the five digits to satisfy my 
resolution requirements). i already have a blue g3.
please pass on to me any answers/updates you have on this problem.
what is this sony product that you mention.
many thanks.


From nih-image-request@io.ece.drexel.edu Wed May 19 13:55 EDT 1999
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Date: Wed, 19 May 1999 10:40:53 -0700 (PDT)
From: steve spencer <stephen_spencer@yahoo.com>
Subject: max measurements
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Hello, does anyone know how to take scion image above
8000 for maximum amount of measurements?
Thanks
steve spencer

_____________________________________________________________
Do You Yahoo!?
Free instant messaging and more at http://messenger.yahoo.com


From nih-image-request@io.ece.drexel.edu Wed May 19 14:24 EDT 1999
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Date: Wed, 19 May 1999 14:16:26 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: Image J? Should I or Shouldn't I.
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>Hi,
>I agree that moving to Image J with its enhanced pixel depth etc and colour
>capability would be a good idea, and am prepared to pick up Java (he says
>lightly).
>
>BUT
>I see some  problems with the move to Image J, and I hope that the wise
>heads on the list can tell me where and how I am wrong.
>
>My main use of Image is with Kodak Megaplus cameras, the 1.4 and the 1.6i
>both being in use. I rely on the Image macros to control sequential
>acquisitions and move the stage between each frame, so I can cover a large
>area or capture a series of images through a defined focus range. I need
>serial port access to do this.
>
>I am using these with the PDI digital boards for the PCI bus.
>These allow the camera to have the shutter speed changed and the gain and
>offset changed (for the i series). And also controls image size, transfer
>size and etc. An immediate advantage of Image J would be the ability to use
>the 10 bits available from the 1.6i camera.
>
>To get these to work from Image J, I would have to do the following things.
>I think?
>
>1. Make an interface into Image J to support the camera functions.?
>
>2. Or Make a plug-in for Image J which did the above.?
>
>3. Understand how to write the driver for the card to work with Image J?
>
>4. Or maybe I should make the card talk to Quicktime?
>
>I await responses to my questions.
>I do have the code for the PDI boards, so I am well placed to have a go, but
>my programming skills are not terrific, but I can do things, it just takes
>me longer.
>
>If anyone can provide me with some cogent arguments I will listen and act.

ImageJ plugins, which are written in Java, cannot directly access hardware
so the driver for the PDI card would need to be written in C. You could
write a QuickTime driver but that would also need to be written in C and
QuickTime capture support is limited to 8-bit grayscale and RGB. Java
programs can access the serial ports using Sun's Java Communications API.
An implementation of this API for the Mac is available from
http://www.vmeng.com/beard/javax.comm.MRJ/index.html. As you can see,
getting the PDI card to work with ImageJ is not a task for the faint
hearted. I suspect you will decide to continue using NIH Image.

>
>On a slightly different point, what tools do i need for Java, I have CW4.
>And are any books recommended?

CW4 is the only tool you need. There are some recommended books on the
ImageJ home page (http://rsb.info.nih.gov/ij/) under "Links".

-wayne




From nih-image-d-request@io.ece.drexel.edu Thu May 20 01:10 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #116
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 116

Today's Topics:
  Stereo reconstructions                [ "peter.shaw" <peter.shaw@bbsrc.ac.u ]
  xy coordinate mapping                 [ steve spencer <stephen_spencer@yaho ]
  use of intrensic digital on G3's      [ "Malinda E.C. Fitzgerald" <malinda@ ]
  Deconvolution software                [ Kevin Pedley <Kevin.Pedley@kcl.ac.u ]
  Stochastic Screening                  [ "=?iso-8859-1?Q?=22Dr._Luis_F._Hern ]
  Deconvolution software                [ Kevin Pedley <Kevin.Pedley@kcl.ac.u ]
  simple macro?                         [ "Jason Tangen" <tangj0@uleth.ca> ]
  Re: use of intrensic digital on G3's  [ jared rifkin <jared_rifkin@qc.edu> ]
  max measurements                      [ steve spencer <stephen_spencer@yaho ]
  Re: Image J? Should I or Shouldn't I  [ Wayne Rasband <wayne@codon.nih.gov> ]
  Re: simple macro?                     [ GJOSS@rna.bio.mq.edu.au ]

------------------------------

Date: Wed, 19 May 1999 12:17:47 +0100
From: "peter.shaw" <peter.shaw@bbsrc.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Stereo reconstructions
Message-Id: <990519121746.781@mserv.jic.bbsrc.ac.uk.0>
Content-Return: allowed
Content-Type: text/plain; charset="ISO-8859-1"; Type="Text"; name="Cover_Memo.TXT"; x-dmw-oid="2A864886F70F0301"; x-dmw-btname="PlainText"

Dear Imagers

I want to determine the x,y,z coordinates of particles from a stereo pair. (Actually gold 
particles located within the depth of an EM section). Does anyone know of software, macro or 
similar to do this? Thanks for your help.

Peter Shaw. John Innes Centre, Norwich, UK. (peter.shaw@bbsrc.ac.uk)

------------------------------

Date: Wed, 19 May 1999 06:19:38 -0700 (PDT)
From: steve spencer <stephen_spencer@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: xy coordinate mapping
Message-ID: <19990519131938.27274.rocketmail@web108.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

Hello, I was wondering if someone knew of a macro that
would give me the coordinates and intensitie values of
each pixel aquired from a specific slice in an
anatomical tiff file.
Thanking yopu in advance
steve spencer
western psyche
_____________________________________________________________
Do You Yahoo!?
Free instant messaging and more at http://messenger.yahoo.com

------------------------------

Date: Wed, 19 May 1999 09:31:44 +0100
From: "Malinda E.C. Fitzgerald" <malinda@cbu.edu>
To: nih-image@io.ece.drexel.edu
Subject: use of intrensic digital on G3's
Message-Id: <v03007804b368269da688@[205.129.119.164]>
Content-Type: text/plain; charset="us-ascii"

Hi I am in the process of setting up a new video system.  I want to order a
new blue G3.  It has a intrensic firewire system that processes the digital
signal.  Has anyone used the product by sony that is an A/D converter that
takes the video image information and then goes to the video card in the
Mac?  I understand Newer Tech is coming out with a new box called firestorm
in July.  Any information would be appreciated.  Malinda

Malinda E.C. Fitzgerald, Ph.D.
Associate Professor
Department of Biology
650 E Parkway So.
Christian Brothers University
Memphis, TN   38104
901-321-3262 office
901-321-4433 fax

------------------------------

Date: Wed, 19 May 1999 15:47:58 +0100
From: Kevin Pedley <Kevin.Pedley@kcl.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Deconvolution software 
Message-Id: <4.1.19990519150404.00a03190@mail.kcl.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Peter,

I spoke to you about three years ago and you offered to provide us with
youur deconvolution software but we were and remain Unix-box free,
operating entirely on high end Pentiums and Macs.

I was therfore very interested when I was asked some time ago by Andrew
Dixon if I wanted to beta test their upcomming deconvolution software,
SharpVu.  I said yes please but heard nothing further despite several
inquiries.  I met Nick White a couple of weeks ago in Oxford and he told me
that the release had been shelved and also that it was a port of your Unix
software to OS/2.

I have been using OpenLab's deconvolution module but would really prefer to
use an algorithm that is better tested and less of a black box.  I was
wondering whether your software will run under Linux and if so, it is it
still possible for us to use it?

Regards,
Kevin Pedley.



 _____________________________________________________________________
 Dr. Kevin Pedley,                           e-mail:Kevin.Pedley@KCL.AC.UK
 Physiology Division,                           Phone: (+44)-171-333-4599
 King's College London.                      Fax:   (+44)-171-937-7783
 Campden Hill Road,
 London W8 7AH.
 U.K. 
 http://life.kcl.ac.uk/ImageLab.htm
_____________________________________________________________________
 

------------------------------

Date: Wed, 19 May 1999 12:43:51 -0300
From: "=?iso-8859-1?Q?=22Dr._Luis_F._Hern=E1ndez=22?="  <lhernan@criba.edu.ar>
To: nih-image@io.ece.drexel.edu
Subject: Stochastic Screening
Message-Id: <v03130300b3688c0d8d6a@[170.210.187.214]>
Content-Type: text/plain; charset="us-ascii"

Hello:
Any suggestion where to get a plug-in for Image or Photoshop to perform
Stochastic Screening on color and gray-scale images?
Regards,

_______________________________________________________
Dr. Luis F. Hernandez, Ph.D.
Laboratorio de Botanica
Departamento de Agronomia
U N I V E R S I D A D  N A C I O N A L  D E L  S U R
8000. Bahia Blanca - ARGENTINA

<mailto: lhernan@criba.edu.ar>
Telefonos (0291) 453-4775/453-0024
FAX: 54 - 0291 - 452-1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.

------------------------------

Date: Wed, 19 May 1999 17:13:15 +0100
From: Kevin Pedley <Kevin.Pedley@kcl.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Deconvolution software 
Message-Id: <4.1.19990519171237.009eee70@mail.kcl.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Apologies for my lastmessage which should not have been sent to the list.


 _____________________________________________________________________
 Dr. Kevin Pedley,                           e-mail:Kevin.Pedley@KCL.AC.UK
 Physiology Division,                           Phone: (+44)-171-333-4599
 King's College London.                      Fax:   (+44)-171-937-7783
 Campden Hill Road,
 London W8 7AH.
 U.K. 
 http://life.kcl.ac.uk/ImageLab.htm
_____________________________________________________________________
 

------------------------------

Date: Wed, 19 May 1999 10:33:27 -0600
From: "Jason Tangen" <tangj0@uleth.ca>
To: nih-image@io.ece.drexel.edu
Subject: simple macro?
Message-ID: <77271C8CC53.AAA3C69@mercury.online.uleth.ca>
Content-type: text/plain; charset="US-ASCII"
Content-transfer-encoding: 7bit

I need a macro that simply overlays a black box on to the center of another
image.  We have been using an overhead transparency previously to accomplish
the task, but I'm not sure how to create a line drawing of a rectangle
without covering up the image behind it.  Any suggestions?

------------------------------------
       Jason Tangen
       University of Lethbridge
       Psychology and Neuroscience
       tangj0@uleth.ca
------------------------------------

------------------------------

Date: Wed, 19 May 99 13:15:55 -0400
From: jared rifkin <jared_rifkin@qc.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: use of intrensic digital on G3's
Message-ID: <3121E0B4B8F@qc1.qc.edu>
Content-Type: text/plain; charset="US-ASCII"

i am also interested in solutions to this problem without going to a 
digital camera (which would be in the five digits to satisfy my 
resolution requirements). i already have a blue g3.
please pass on to me any answers/updates you have on this problem.
what is this sony product that you mention.
many thanks.

------------------------------

Date: Wed, 19 May 1999 10:40:53 -0700 (PDT)
From: steve spencer <stephen_spencer@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: max measurements
Message-ID: <19990519174053.20881.rocketmail@web123.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

Hello, does anyone know how to take scion image above
8000 for maximum amount of measurements?
Thanks
steve spencer

_____________________________________________________________
Do You Yahoo!?
Free instant messaging and more at http://messenger.yahoo.com

------------------------------

Date: Wed, 19 May 1999 14:16:26 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Image J? Should I or Shouldn't I.
Message-Id: <v03007801b368aa16e2c0@[128.231.99.206]>
Content-Type: text/plain; charset="us-ascii"

>Hi,
>I agree that moving to Image J with its enhanced pixel depth etc and colour
>capability would be a good idea, and am prepared to pick up Java (he says
>lightly).
>
>BUT
>I see some  problems with the move to Image J, and I hope that the wise
>heads on the list can tell me where and how I am wrong.
>
>My main use of Image is with Kodak Megaplus cameras, the 1.4 and the 1.6i
>both being in use. I rely on the Image macros to control sequential
>acquisitions and move the stage between each frame, so I can cover a large
>area or capture a series of images through a defined focus range. I need
>serial port access to do this.
>
>I am using these with the PDI digital boards for the PCI bus.
>These allow the camera to have the shutter speed changed and the gain and
>offset changed (for the i series). And also controls image size, transfer
>size and etc. An immediate advantage of Image J would be the ability to use
>the 10 bits available from the 1.6i camera.
>
>To get these to work from Image J, I would have to do the following things.
>I think?
>
>1. Make an interface into Image J to support the camera functions.?
>
>2. Or Make a plug-in for Image J which did the above.?
>
>3. Understand how to write the driver for the card to work with Image J?
>
>4. Or maybe I should make the card talk to Quicktime?
>
>I await responses to my questions.
>I do have the code for the PDI boards, so I am well placed to have a go, but
>my programming skills are not terrific, but I can do things, it just takes
>me longer.
>
>If anyone can provide me with some cogent arguments I will listen and act.

ImageJ plugins, which are written in Java, cannot directly access hardware
so the driver for the PDI card would need to be written in C. You could
write a QuickTime driver but that would also need to be written in C and
QuickTime capture support is limited to 8-bit grayscale and RGB. Java
programs can access the serial ports using Sun's Java Communications API.
An implementation of this API for the Mac is available from
http://www.vmeng.com/beard/javax.comm.MRJ/index.html. As you can see,
getting the PDI card to work with ImageJ is not a task for the faint
hearted. I suspect you will decide to continue using NIH Image.

>
>On a slightly different point, what tools do i need for Java, I have CW4.
>And are any books recommended?

CW4 is the only tool you need. There are some recommended books on the
ImageJ home page (http://rsb.info.nih.gov/ij/) under "Links".

-wayne

------------------------------

Date:          Thu, 20 May 1999 15:04:02 +1000
From: GJOSS@rna.bio.mq.edu.au
To: tangj0@uleth.ca, nih-image@io.ece.drexel.edu
Subject:       Re: simple macro?
Message-ID: <4F7010384@rna.bio.mq.edu.au>

>Date: Wed, 19 May 1999 10:33:27 -0600
>Subject: simple macro?
>From: "Jason Tangen" <tangj0@uleth.ca>
>To: nih-image@io.ece.drexel.edu
>
>I need a macro that simply overlays a black box on to the center of 
>another
>image.  We have been using an overhead transparency previously to 
>accomplish
>the task, but I'm not sure how to create a line drawing of a rectangle
>without covering up the image behind it.  Any suggestions?
>
>------------------------------------
>       Jason Tangen
>       University of Lethbridge
>       Psychology and Neuroscience
>       tangj0@uleth.ca
>------------------------------------
If you want non-destructive marking, you should get:
Object-Image, an extention of NIH-Image by Norbert Vischer is 
available via http://simon.bio.uva.nl/object-image.html.


If you intend writeing macros, I cannot recommend it highly enough.

Either way, the following should get you started.

macro'/0Black Box';var w,h:integer;begin
getPicSize(w,h);
makeRoi(w/4,h/4,w/2,h/2);
setForeGround(255);
setLineWidth(3);
drawBoundary;
killroi;
end 

Leave out the 
"setForeGround(255);
setLineWidth(3);
drawBoundary;
killroi;
"
if the marching ants are enough.

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

--------------------------------
End of nih-image-d Digest V99 Issue #116
****************************************

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Organization:  Dept. of Biological Sciences
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>Date: Wed, 19 May 1999 10:33:27 -0600
>Subject: simple macro?
>From: "Jason Tangen" <tangj0@uleth.ca>
>To: nih-image@io.ece.drexel.edu
>
>I need a macro that simply overlays a black box on to the center of 
>another
>image.  We have been using an overhead transparency previously to 
>accomplish
>the task, but I'm not sure how to create a line drawing of a rectangle
>without covering up the image behind it.  Any suggestions?
>
>------------------------------------
>       Jason Tangen
>       University of Lethbridge
>       Psychology and Neuroscience
>       tangj0@uleth.ca
>------------------------------------
If you want non-destructive marking, you should get:
Object-Image, an extention of NIH-Image by Norbert Vischer is 
available via http://simon.bio.uva.nl/object-image.html.


If you intend writeing macros, I cannot recommend it highly enough.

Either way, the following should get you started.

macro'/0Black Box';var w,h:integer;begin
getPicSize(w,h);
makeRoi(w/4,h/4,w/2,h/2);
setForeGround(255);
setLineWidth(3);
drawBoundary;
killroi;
end 

Leave out the 
"setForeGround(255);
setLineWidth(3);
drawBoundary;
killroi;
"
if the marching ants are enough.

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


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Subject: overlay a rectangle
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Jason:

Try drawing your black rectangle in one image, Select All, Copy, then go to
the second image, open the Paste Control window, Paste, and select "OR".
This should give you the black rectangle superimposed on the second image.

-David Morilak


David Morilak, Ph.D.
Dept of Pharmacology
Univ Texas Health Science Center
7703 Floyd Curl Drive
San Antonio, TX 78284-7764

ph: 210-567-4174
FAX: 210-567-4303
E-mail: morilak@uthscsa.edu



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Date:          Fri, 21 May 1999 9:12:37 +1000
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>Date: Thu, 20 May 1999 10:24:23 -0500 (CDT)
>From: David Morilak <morilak@uthscsa.edu>
>Subject: overlay a rectangle
>To: tangj0@uleth.ca
>Cc: nih-image@io.ece.drexel.edu

>Jason:
>
>Try drawing your black rectangle in one image, Select All, Copy, then go 
>to
>the second image, open the Paste Control window, Paste, and select "OR".
>This should give you the black rectangle superimposed on the second image.
>
>-David Morilak
>

David's post reminded me of a useful technique 
for non-destructive marking which is sometimes useful.

The following macro is an extention of reply to "a simple macro".
As prompted by David but not the same, it uses an "XOR" paste.

The advantage is that the first application is clearly visible against ANY 
background (black,white,gray or coloured) but, if repeated, the second 
operation restores the image to the original values.
It can be extended to use as a non-destructive cursor or window.

macro'/0Black Box';var w,h,p:integer;begin
p:=pidNumber;
getPicSize(w,h);
setNewSize(w,h);
setBackGround(0);
makeNewWindow('temp');
makeRoi(w/4,h/4,w/2,h/2);
setForeGround(255);
setLineWidth(3);
drawBoundary;
selectAll;
copy;
dispose;
selectPic(p);
paste;setOption;doXor;
end 

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


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nrew  e mail address jcmain@pacbell.net  thank you
-----Original Message-----
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<nih-image-d-request@io.ece.drexel.edu>
To: nih-image-d@io.ece.drexel.edu <nih-image-d@io.ece.drexel.edu>
Date: Wednesday, April 28, 1999 3:13 AM
Subject: nih-image-d Digest V99 #98



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nih-image-d Digest				Volume 99 : Issue 98

Today's Topics:
  Re: Thresholding                      [ Marcia Goldfarb <anatekep@maine.rr. ]
  Re: Thresholding                      [ Arnout Ruifrok <arnout@odin.mdacc.t ]
  Re: Thresholding                      [ "Wade Schuette" <schuette@umich.edu ]
  Re: image cataloguing                 [ Michael Cammer <cammer@aecom.yu.edu ]
  Re: Thresholding                      [ "Ken Baker" <kwb@bserv.com> ]

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Date: Tue, 27 Apr 1999 08:47:17 +0000
From: Marcia Goldfarb <anatekep@maine.rr.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Thresholding
Message-ID: <37257994.6A486F4F@maine.rr.com>
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Gary:

My understanding is the threshold value is what the user considers
valid. I threshold at 2std from the mean using the histogram numbers.
This is based on the supposition of statistics that data points greater
than 2stds may be considered background.

Marcia Goldfarb
Anatek-EP
17 Bishop St
Portland, ME 04103

email: anatekep@maine.rr.com

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Date: Tue, 27 Apr 1999 08:52:01 -0500 (CDT)
From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Thresholding
Message-Id: <v03102800b34b28ba6d6e@[143.111.62.105]>
Content-Type: text/plain; charset="us-ascii"

>Gary:
>
>My understanding is the threshold value is what the user considers
>valid. I threshold at 2std from the mean using the histogram numbers.
>This is based on the supposition of statistics that data points greater
>than 2stds may be considered background.
>
>Marcia Goldfarb
>Anatek-EP
>17 Bishop St
>Portland, ME 04103
>
>email: anatekep@maine.rr.com

This very legitimate question is coming back at regular intervals. The
basic procedure is described in  Ridler and Calvard,IEEE Trans. Systems,
Man, Cybernetics Vol SMC8, No8, August 1978. Basically, the algorithm
defines the threshold in the middel between the average foreground value
and the average background value, using an iterative procedure. This
results in the optimal threshold, assuming that the probability of
misclassification of pixels in foreground and background is the same, and
assuming that the partition of foreground and background is the same. (As
this is almost never true, the algorithm has a slight bias in favor of the
smallest area. If you are interested I can post a small macro that takes
care of this, and also can shift the threshold value according to a preset
p value for the foreground, making the thresholding more or less critical
than 50-50).

Arnout

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Date: Tue, 27 Apr 1999 10:33:52 -0400
From: "Wade Schuette" <schuette@umich.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Thresholding
Message-Id: <s7259298.004@umich.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline

>>>> Arnout Ruifrok <arnout@odin.mdacc.tmc.edu> 04/27 10:04 AM >>>
>>Gary:
>>
>>My understanding is the threshold value is what the user considers
>>valid. I threshold at 2std from the mean using the histogram
numbers.
>>This is based on the supposition of statistics that data points
greater
>>than 2stds may be considered background.
>>
>>Marcia Goldfarb
>>Anatek-EP
>>17 Bishop St
>>Portland, ME 04103
>>
>>email: anatekep@maine.rr.com 
>
>This very legitimate question is coming back at regular intervals.
The
>basic procedure is described in  Ridler and Calvard,IEEE Trans.
Systems,
>Man, Cybernetics Vol SMC8, No8, August 1978. Basically, the algorithm
>defines the threshold in the middel between the average foreground
value
>and the average background value, using an iterative procedure. This
>results in the optimal threshold, assuming that the probability of
>misclassification of pixels in foreground and background is the same,
and
>assuming that the partition of foreground and background is the same.
(As
>this is almost never true, the algorithm has a slight bias in favor of
the
>smallest area. If you are interested I can post a small macro that
takes
>are of this, and also can shift the threshold value according to a
preset
> value for the foreground, making the thresholding more or less
critical
>than 50-50).
>
>Arnout

    I think that formal risk-analysis would actually include the
selection of 
a threshold as one of the optimal statistical outcomes of analyzing
what
the costs are of making mistakes in each direction (too high vs too
low).
All that is quite complex and the assumptions one uses are often 
hidden.  Besides people disaagree on how to do it.

    On a practical basis,  for things that really matter, what I'd 
suggest is writing a macro to automate the reading of images,
and to redo the analysis for a range of thresholds sufficient to 
cover what are 'surely' the range from too-low to too-high.

Then,  determine whatever your hypothesis is at each 
threshold, and maybe plot the results versus threshold.

If the conclusion is TRUE at all thresholds,  then it's 
pretty safe to go ahead and assert it.

If the conclusion CHANGES from True to False 
depending on threshold,  then be extremely 
cautious about what you want to assert, based
on this.

For example,  you may find that variable Y1 and 
Y2 both increase as threshold X increases, but
Y2 increases faster than Y1 and is always 
higher than Y1.   It would be SAFE to assert
that Y2 > Y1.   it would be risky to assert that
the RATIO of Y2 to Y1 is some particular
number, as that is sensitive to threshold. 

In fact, if at low thresholds Y1 is less than y2,
and at high thresholds Y1 is greater than Y2, 
it is unclear you can assert anything at all, 
unless you can demonstrate convincingly
that the threshold has to be on one or the
other sides of the point at which y1 and Y2
cross. 

You can wrap this in fancy statistical jargon and 
equations, but the logic of basic sensitivity 
analysis should be apparent to common sense,
and it's not a bad thing to check before 
publishing or otherwise placing a lot of 
reliance on threshold-sensitive conclusions.

Wade 


    
    




R. Wade Schuette
MCIT CDR Team
phone:  734 763-4486
alpha pager: 734 797-6622
Arbor Lakes, Bldg 3, Suite 1300
4251 Plymouth Rd.
Ann Arbor, MI 48105-2785

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Date: Tue, 27 Apr 1999 10:43:54 -0700
From: Michael Cammer <cammer@aecom.yu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: image cataloguing
Message-Id: <3.0.5.32.19990427104354.00a0eec0@mailserver.aecom.yu.edu>
Content-Type: text/plain; charset="us-ascii"

We have looked at two systems being marketed by Electroimage.
http://www.electroimage.com/  Due to the huge volume of our facility, we
are looking into their enterprise system.  The demo looks impressive and if
it works for us, we'll certainly let you know.  
********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************

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Date: Tue, 27 Apr 1999 16:48:53 -0400
From: "Ken Baker" <kwb@bserv.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Thresholding
Message-Id: <199904272042.QAA27253@bserv.com>
Content-type: text/plain; charset="US-ASCII"
Content-transfer-encoding: 7bit

Dear Arnouk,
I would appreciate it if you would post the macro you mention.
Thanks in advance.
Regards,
        Ken
                --
KWB@bserv.com
519-853-4787


----------
>From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Thresholding
>Date: Tue, Apr 27, 1999, 9:52 AM
>

>>Gary:
>>
>>My understanding is the threshold value is what the user considers
>>valid. I threshold at 2std from the mean using the histogram numbers.
>>This is based on the supposition of statistics that data points greater
>>than 2stds may be considered background.
>>
>>Marcia Goldfarb
>>Anatek-EP
>>17 Bishop St
>>Portland, ME 04103
>>
>>email: anatekep@maine.rr.com
>
> This very legitimate question is coming back at regular intervals. The
> basic procedure is described in  Ridler and Calvard,IEEE Trans. Systems,
> Man, Cybernetics Vol SMC8, No8, August 1978. Basically, the algorithm
> defines the threshold in the middel between the average foreground value
> and the average background value, using an iterative procedure. This
> results in the optimal threshold, assuming that the probability of
> misclassification of pixels in foreground and background is the same, and
> assuming that the partition of foreground and background is the same. (As
> this is almost never true, the algorithm has a slight bias in favor of the
> smallest area. If you are interested I can post a small macro that takes
> care of this, and also can shift the threshold value according to a preset
> p value for the foreground, making the thresholding more or less critical
> than 50-50).
>
> Arnout
>
>
> 

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------------------------------

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nih-image-d Digest				Volume 99 : Issue 117

Today's Topics:
  overlay a rectangle                   [ David Morilak <morilak@uthscsa.edu> ]
  Re: overlay a rectangle               [ GJOSS@rna.bio.mq.edu.au ]
  Fw: nih-image-d Digest V99 #98        [ "Joan C. Main" <jcmain@pacbell.net> ]
  subscribe                             [ Karl Jenkinson <K.Jenkinson@Anatomy ]

------------------------------

Date: Thu, 20 May 1999 10:24:23 -0500 (CDT)
From: David Morilak <morilak@uthscsa.edu>
To: tangj0@uleth.ca
Cc: nih-image@io.ece.drexel.edu
Subject: overlay a rectangle
Message-id: <l03130300b3699367e76b@[129.111.17.122]>
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Jason:

Try drawing your black rectangle in one image, Select All, Copy, then go to
the second image, open the Paste Control window, Paste, and select "OR".
This should give you the black rectangle superimposed on the second image.

-David Morilak


David Morilak, Ph.D.
Dept of Pharmacology
Univ Texas Health Science Center
7703 Floyd Curl Drive
San Antonio, TX 78284-7764

ph: 210-567-4174
FAX: 210-567-4303
E-mail: morilak@uthscsa.edu

------------------------------

Date:          Fri, 21 May 1999 9:12:37 +1000
From: GJOSS@rna.bio.mq.edu.au
To: morilak@uthscsa.edu, nih-image@io.ece.drexel.edu, tangj0@uleth.ca
Subject:       Re: overlay a rectangle
Message-ID: <171D0E7680@rna.bio.mq.edu.au>

>Date: Thu, 20 May 1999 10:24:23 -0500 (CDT)
>From: David Morilak <morilak@uthscsa.edu>
>Subject: overlay a rectangle
>To: tangj0@uleth.ca
>Cc: nih-image@io.ece.drexel.edu

>Jason:
>
>Try drawing your black rectangle in one image, Select All, Copy, then go 
>to
>the second image, open the Paste Control window, Paste, and select "OR".
>This should give you the black rectangle superimposed on the second image.
>
>-David Morilak
>

David's post reminded me of a useful technique 
for non-destructive marking which is sometimes useful.

The following macro is an extention of reply to "a simple macro".
As prompted by David but not the same, it uses an "XOR" paste.

The advantage is that the first application is clearly visible against ANY 
background (black,white,gray or coloured) but, if repeated, the second 
operation restores the image to the original values.
It can be extended to use as a non-destructive cursor or window.

macro'/0Black Box';var w,h,p:integer;begin
p:=pidNumber;
getPicSize(w,h);
setNewSize(w,h);
setBackGround(0);
makeNewWindow('temp');
makeRoi(w/4,h/4,w/2,h/2);
setForeGround(255);
setLineWidth(3);
drawBoundary;
selectAll;
copy;
dispose;
selectPic(p);
paste;setOption;doXor;
end 

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Fri, 28 May 1999 19:54:12 -0700
From: "Joan C. Main" <jcmain@pacbell.net>
To: "scion image" <nih-image@io.ece.drexel.edu>
Subject: Fw: nih-image-d Digest V99 #98
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nrew  e mail address jcmain@pacbell.net  thank you
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Subject: nih-image-d Digest V99 #98



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nih-image-d Digest				Volume 99 : Issue 98

Today's Topics:
  Re: Thresholding                      [ Marcia Goldfarb <anatekep@maine.rr. ]
  Re: Thresholding                      [ Arnout Ruifrok <arnout@odin.mdacc.t ]
  Re: Thresholding                      [ "Wade Schuette" <schuette@umich.edu ]
  Re: image cataloguing                 [ Michael Cammer <cammer@aecom.yu.edu ]
  Re: Thresholding                      [ "Ken Baker" <kwb@bserv.com> ]

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Date: Tue, 27 Apr 1999 08:47:17 +0000
From: Marcia Goldfarb <anatekep@maine.rr.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Thresholding
Message-ID: <37257994.6A486F4F@maine.rr.com>
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Gary:

My understanding is the threshold value is what the user considers
valid. I threshold at 2std from the mean using the histogram numbers.
This is based on the supposition of statistics that data points greater
than 2stds may be considered background.

Marcia Goldfarb
Anatek-EP
17 Bishop St
Portland, ME 04103

email: anatekep@maine.rr.com

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Date: Tue, 27 Apr 1999 08:52:01 -0500 (CDT)
From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Thresholding
Message-Id: <v03102800b34b28ba6d6e@[143.111.62.105]>
Content-Type: text/plain; charset="us-ascii"

>Gary:
>
>My understanding is the threshold value is what the user considers
>valid. I threshold at 2std from the mean using the histogram numbers.
>This is based on the supposition of statistics that data points greater
>than 2stds may be considered background.
>
>Marcia Goldfarb
>Anatek-EP
>17 Bishop St
>Portland, ME 04103
>
>email: anatekep@maine.rr.com

This very legitimate question is coming back at regular intervals. The
basic procedure is described in  Ridler and Calvard,IEEE Trans. Systems,
Man, Cybernetics Vol SMC8, No8, August 1978. Basically, the algorithm
defines the threshold in the middel between the average foreground value
and the average background value, using an iterative procedure. This
results in the optimal threshold, assuming that the probability of
misclassification of pixels in foreground and background is the same, and
assuming that the partition of foreground and background is the same. (As
this is almost never true, the algorithm has a slight bias in favor of the
smallest area. If you are interested I can post a small macro that takes
care of this, and also can shift the threshold value according to a preset
p value for the foreground, making the thresholding more or less critical
than 50-50).

Arnout

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Date: Tue, 27 Apr 1999 10:33:52 -0400
From: "Wade Schuette" <schuette@umich.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Thresholding
Message-Id: <s7259298.004@umich.edu>
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>>>> Arnout Ruifrok <arnout@odin.mdacc.tmc.edu> 04/27 10:04 AM >>>
>>Gary:
>>
>>My understanding is the threshold value is what the user considers
>>valid. I threshold at 2std from the mean using the histogram
numbers.
>>This is based on the supposition of statistics that data points
greater
>>than 2stds may be considered background.
>>
>>Marcia Goldfarb
>>Anatek-EP
>>17 Bishop St
>>Portland, ME 04103
>>
>>email: anatekep@maine.rr.com 
>
>This very legitimate question is coming back at regular intervals.
The
>basic procedure is described in  Ridler and Calvard,IEEE Trans.
Systems,
>Man, Cybernetics Vol SMC8, No8, August 1978. Basically, the algorithm
>defines the threshold in the middel between the average foreground
value
>and the average background value, using an iterative procedure. This
>results in the optimal threshold, assuming that the probability of
>misclassification of pixels in foreground and background is the same,
and
>assuming that the partition of foreground and background is the same.
(As
>this is almost never true, the algorithm has a slight bias in favor of
the
>smallest area. If you are interested I can post a small macro that
takes
>are of this, and also can shift the threshold value according to a
preset
> value for the foreground, making the thresholding more or less
critical
>than 50-50).
>
>Arnout

    I think that formal risk-analysis would actually include the
selection of 
a threshold as one of the optimal statistical outcomes of analyzing
what
the costs are of making mistakes in each direction (too high vs too
low).
All that is quite complex and the assumptions one uses are often 
hidden.  Besides people disaagree on how to do it.

    On a practical basis,  for things that really matter, what I'd 
suggest is writing a macro to automate the reading of images,
and to redo the analysis for a range of thresholds sufficient to 
cover what are 'surely' the range from too-low to too-high.

Then,  determine whatever your hypothesis is at each 
threshold, and maybe plot the results versus threshold.

If the conclusion is TRUE at all thresholds,  then it's 
pretty safe to go ahead and assert it.

If the conclusion CHANGES from True to False 
depending on threshold,  then be extremely 
cautious about what you want to assert, based
on this.

For example,  you may find that variable Y1 and 
Y2 both increase as threshold X increases, but
Y2 increases faster than Y1 and is always 
higher than Y1.   It would be SAFE to assert
that Y2 > Y1.   it would be risky to assert that
the RATIO of Y2 to Y1 is some particular
number, as that is sensitive to threshold. 

In fact, if at low thresholds Y1 is less than y2,
and at high thresholds Y1 is greater than Y2, 
it is unclear you can assert anything at all, 
unless you can demonstrate convincingly
that the threshold has to be on one or the
other sides of the point at which y1 and Y2
cross. 

You can wrap this in fancy statistical jargon and 
equations, but the logic of basic sensitivity 
analysis should be apparent to common sense,
and it's not a bad thing to check before 
publishing or otherwise placing a lot of 
reliance on threshold-sensitive conclusions.

Wade 


    
    




R. Wade Schuette
MCIT CDR Team
phone:  734 763-4486
alpha pager: 734 797-6622
Arbor Lakes, Bldg 3, Suite 1300
4251 Plymouth Rd.
Ann Arbor, MI 48105-2785

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Date: Tue, 27 Apr 1999 10:43:54 -0700
From: Michael Cammer <cammer@aecom.yu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: image cataloguing
Message-Id: <3.0.5.32.19990427104354.00a0eec0@mailserver.aecom.yu.edu>
Content-Type: text/plain; charset="us-ascii"

We have looked at two systems being marketed by Electroimage.
http://www.electroimage.com/  Due to the huge volume of our facility, we
are looking into their enterprise system.  The demo looks impressive and if
it works for us, we'll certainly let you know.  
********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************

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Date: Tue, 27 Apr 1999 16:48:53 -0400
From: "Ken Baker" <kwb@bserv.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Thresholding
Message-Id: <199904272042.QAA27253@bserv.com>
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Dear Arnouk,
I would appreciate it if you would post the macro you mention.
Thanks in advance.
Regards,
        Ken
                --
KWB@bserv.com
519-853-4787


----------
>From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Thresholding
>Date: Tue, Apr 27, 1999, 9:52 AM
>

>>Gary:
>>
>>My understanding is the threshold value is what the user considers
>>valid. I threshold at 2std from the mean using the histogram numbers.
>>This is based on the supposition of statistics that data points greater
>>than 2stds may be considered background.
>>
>>Marcia Goldfarb
>>Anatek-EP
>>17 Bishop St
>>Portland, ME 04103
>>
>>email: anatekep@maine.rr.com
>
> This very legitimate question is coming back at regular intervals. The
> basic procedure is described in  Ridler and Calvard,IEEE Trans. Systems,
> Man, Cybernetics Vol SMC8, No8, August 1978. Basically, the algorithm
> defines the threshold in the middel between the average foreground value
> and the average background value, using an iterative procedure. This
> results in the optimal threshold, assuming that the probability of
> misclassification of pixels in foreground and background is the same, and
> assuming that the partition of foreground and background is the same. (As
> this is almost never true, the algorithm has a slight bias in favor of the
> smallest area. If you are interested I can post a small macro that takes
> care of this, and also can shift the threshold value according to a preset
> p value for the foreground, making the thresholding more or less critical
> than 50-50).
>
> Arnout
>
>
> 

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------------------------------

Date: Fri, 21 May 1999 15:14:03 +1000
From: Karl Jenkinson <K.Jenkinson@Anatomy.Unimelb.EDU.AU>
To: nih-image@io.ece.drexel.edu
Subject: subscribe
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subscribe

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End of nih-image-d Digest V99 Issue #117
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Subject: Executor...?
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Hi!

I do have a simple question, is there somebody that actually use
Executor to run NIH Image/Object Image in windows or NT? Does it work?.

I know that it would be easier to run Scion Image, but I also want to
use Object Image in my PC. Is that possible?

Thanks.

Gary.


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> ----------
> From: 	Hillman, Paul
> Sent: 	Friday, 21  May 1999 11:41 AM
> To: 	'Malinda E.C. Fitzgerald'; ',nih-image@io.ece.drexel.edu'
> Subject: 	RE: use of intrensic digital on G3's
> 
> Milinda,
> 
> I have the said Sony device, DVMC-DA1 (or something very similar).
> 
> The Sony's device converts Analog video to DV video, one of the protocals
> that can be carried on firewire.
> 
> I only have Adobe Preimere 4.2 LE.  I can record video and audio, but
> video at only 320x240.  The device manual says the data rate is 100mbps,
> which I am not sure will support 640x480 at 30 frames/sec.  (note: I can
> capture 640x480 but its very pixelated, the device is still sending
> 320x240).
> 
> I think if you have the full drivers for DV video, you might be able to
> change the resolution of the capture.  Someone sent me the drivers they
> recieved with Apple's firewire card (one is labeled DV control), I could
> not get them to work with Preimere 4.2 LE.  I feel you will probably need
> some drivers with what ever capture software you use.  I asked on this
> list for drivers for NIH and did not see any replies.  The sony device
> does not come with any drivers or software.
> 
> ProMax sells DV video/firewire drivers, but only with versions of Priemere
> 5.1.
> 
> I would appreciate any info you find.
> 
> ________________________________________________________________
> "640K ought to be good enough for anybody."  Bill Gates
> 
> Paul Hillman         \____ ...,. ____/    hillman@plk.af.mil
> StarFire Optical Range    ( o o )     P_D_Hillman@compuserve.com
> AFRL/DES                   \   /         CIM: 71773,643 
> 3550 Aberdeen Ave SE        (_)          real time (505)846-5032
> Kirtland AFB NM  87117                   FAX:(505)846-2213 
> ________________________________________________________________
> 
> ----------
> From: 	Malinda E.C. Fitzgerald
> Sent: 	Wednesday, 19  May 1999 2:31 AM
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	use of intrensic digital on G3's
> 
> Hi I am in the process of setting up a new video system.  I want to order
> a
> new blue G3.  It has a intrensic firewire system that processes the
> digital
> signal.  Has anyone used the product by sony that is an A/D converter that
> takes the video image information and then goes to the video card in the
> Mac?  I understand Newer Tech is coming out with a new box called
> firestorm
> in July.  Any information would be appreciated.  Malinda
> 
> Malinda E.C. Fitzgerald, Ph.D.
> Associate Professor
> Department of Biology
> 650 E Parkway So.
> Christian Brothers University
> Memphis, TN   38104
> 901-321-3262 office
> 901-321-4433 fax
> 
> 


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From:          Gary Chinga <gary.chinga@pfi.no>
To:            "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject:       Executor...?
Date:          Fri, 21 May 1999 18:56:32 +0200
Reply-to:      nih-image@io.ece.drexel.edu

Hi!

I do have a simple question, is there somebody that actually use
Executor to run NIH Image/Object Image in windows or NT? Does it work?.

I know that it would be easier to run Scion Image, but I also want to
use Object Image in my PC. Is that possible?

Thanks.

Gary.

I have run Image 1.5something in Executor in Win 95--no real problems 
---
Paul Busse
Math & Science Center
Richmond, VA


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Hi Gary,

NIH Image runs great under executor under WinNT/95 to the extend that it
even outperforms Scion Image in terms of displaying large images. They
load faster and moving with the "hand"tool is smoother and faster.
Biggest setback I found is that it is impossible (if someone knows
differently please let me know) to use the installed (Scion)
framegrabber boards. NIH Image just doesn't "see them".

Cheers, Gerrit

paul-busse.com@mb.mailbank.com wrote:
> 
> From:          Gary Chinga <gary.chinga@pfi.no>
> To:            "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
> Subject:       Executor...?
> Date:          Fri, 21 May 1999 18:56:32 +0200
> Reply-to:      nih-image@io.ece.drexel.edu
> 
> Hi!
> 
> I do have a simple question, is there somebody that actually use
> Executor to run NIH Image/Object Image in windows or NT? Does it work?.
> 
> I know that it would be easier to run Scion Image, but I also want to
> use Object Image in my PC. Is that possible?
> 
> Thanks.
> 
> Gary.
> 
> I have run Image 1.5something in Executor in Win 95--no real problems
> ---
> Paul Busse
> Math & Science Center
> Richmond, VA

-- 
==================================================================
Gerrit Beemster 
DEPARTMENT OF GENETICS                         Fax:32 (0)9 2645349
UNIVERSITY OF GENT, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
Vlaams Instituut voor Biotechnologie                           VIB
mailto:gebee@gengenp.rug.ac.be    	   http://www.plantgenetics.rug.ac.be
==================================================================


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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 118

Today's Topics:
  Executor...?                          [ Gary Chinga <gary.chinga@pfi.no> ]
  FW: use of intrensic digital on G3's  [ "Hillman, Paul" <hillman@plk.af.mil ]
  Re: Executor...?                      [ paul-busse.com@mb.mailbank.com ]
  Re: Executor...?                      [ Gerrit Beemster <gebee@gengenp.rug. ]

------------------------------

Date: Fri, 21 May 1999 18:56:32 +0200
From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Executor...?
Message-ID: <c=NO%a=_%p=pfi%l=PFINT1-990521165632Z-4925@pfint1.pfi.no>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

Hi!

I do have a simple question, is there somebody that actually use
Executor to run NIH Image/Object Image in windows or NT? Does it work?.

I know that it would be easier to run Scion Image, but I also want to
use Object Image in my PC. Is that possible?

Thanks.

Gary.

------------------------------

Date: Fri, 21 May 1999 12:00:46 -0600
From: "Hillman, Paul" <hillman@plk.af.mil>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: FW: use of intrensic digital on G3's
Message-ID: <178F01F1C3BBD2118DF30008C7331071018FE6@DE-X3>
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	charset="windows-1252"
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> ----------
> From: 	Hillman, Paul
> Sent: 	Friday, 21  May 1999 11:41 AM
> To: 	'Malinda E.C. Fitzgerald'; ',nih-image@io.ece.drexel.edu'
> Subject: 	RE: use of intrensic digital on G3's
> 
> Milinda,
> 
> I have the said Sony device, DVMC-DA1 (or something very similar).
> 
> The Sony's device converts Analog video to DV video, one of the protocals
> that can be carried on firewire.
> 
> I only have Adobe Preimere 4.2 LE.  I can record video and audio, but
> video at only 320x240.  The device manual says the data rate is 100mbps,
> which I am not sure will support 640x480 at 30 frames/sec.  (note: I can
> capture 640x480 but its very pixelated, the device is still sending
> 320x240).
> 
> I think if you have the full drivers for DV video, you might be able to
> change the resolution of the capture.  Someone sent me the drivers they
> recieved with Apple's firewire card (one is labeled DV control), I could
> not get them to work with Preimere 4.2 LE.  I feel you will probably need
> some drivers with what ever capture software you use.  I asked on this
> list for drivers for NIH and did not see any replies.  The sony device
> does not come with any drivers or software.
> 
> ProMax sells DV video/firewire drivers, but only with versions of Priemere
> 5.1.
> 
> I would appreciate any info you find.
> 
> ________________________________________________________________
> "640K ought to be good enough for anybody."  Bill Gates
> 
> Paul Hillman         \____ ...,. ____/    hillman@plk.af.mil
> StarFire Optical Range    ( o o )     P_D_Hillman@compuserve.com
> AFRL/DES                   \   /         CIM: 71773,643 
> 3550 Aberdeen Ave SE        (_)          real time (505)846-5032
> Kirtland AFB NM  87117                   FAX:(505)846-2213 
> ________________________________________________________________
> 
> ----------
> From: 	Malinda E.C. Fitzgerald
> Sent: 	Wednesday, 19  May 1999 2:31 AM
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	use of intrensic digital on G3's
> 
> Hi I am in the process of setting up a new video system.  I want to order
> a
> new blue G3.  It has a intrensic firewire system that processes the
> digital
> signal.  Has anyone used the product by sony that is an A/D converter that
> takes the video image information and then goes to the video card in the
> Mac?  I understand Newer Tech is coming out with a new box called
> firestorm
> in July.  Any information would be appreciated.  Malinda
> 
> Malinda E.C. Fitzgerald, Ph.D.
> Associate Professor
> Department of Biology
> 650 E Parkway So.
> Christian Brothers University
> Memphis, TN   38104
> 901-321-3262 office
> 901-321-4433 fax
> 
> 

------------------------------

Date: Fri, 21 May 1999 16:08:00 +0000
From: paul-busse.com@mb.mailbank.com
To: nih-image@io.ece.drexel.edu
Subject: Re: Executor...?
Message-Id: <199905212008.NAA11779@mb3.mailbank.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7BIT

From:          Gary Chinga <gary.chinga@pfi.no>
To:            "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject:       Executor...?
Date:          Fri, 21 May 1999 18:56:32 +0200
Reply-to:      nih-image@io.ece.drexel.edu

Hi!

I do have a simple question, is there somebody that actually use
Executor to run NIH Image/Object Image in windows or NT? Does it work?.

I know that it would be easier to run Scion Image, but I also want to
use Object Image in my PC. Is that possible?

Thanks.

Gary.

I have run Image 1.5something in Executor in Win 95--no real problems 
---
Paul Busse
Math & Science Center
Richmond, VA

------------------------------

Date: Sat, 22 May 1999 09:01:28 +0200
From: Gerrit Beemster <gebee@gengenp.rug.ac.be>
To: nih-image@io.ece.drexel.edu
Subject: Re: Executor...?
Message-ID: <37465648.23AEAA03@gengenp.rug.ac.be>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi Gary,

NIH Image runs great under executor under WinNT/95 to the extend that it
even outperforms Scion Image in terms of displaying large images. They
load faster and moving with the "hand"tool is smoother and faster.
Biggest setback I found is that it is impossible (if someone knows
differently please let me know) to use the installed (Scion)
framegrabber boards. NIH Image just doesn't "see them".

Cheers, Gerrit

paul-busse.com@mb.mailbank.com wrote:
> 
> From:          Gary Chinga <gary.chinga@pfi.no>
> To:            "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
> Subject:       Executor...?
> Date:          Fri, 21 May 1999 18:56:32 +0200
> Reply-to:      nih-image@io.ece.drexel.edu
> 
> Hi!
> 
> I do have a simple question, is there somebody that actually use
> Executor to run NIH Image/Object Image in windows or NT? Does it work?.
> 
> I know that it would be easier to run Scion Image, but I also want to
> use Object Image in my PC. Is that possible?
> 
> Thanks.
> 
> Gary.
> 
> I have run Image 1.5something in Executor in Win 95--no real problems
> ---
> Paul Busse
> Math & Science Center
> Richmond, VA

-- 
==================================================================
Gerrit Beemster 
DEPARTMENT OF GENETICS                         Fax:32 (0)9 2645349
UNIVERSITY OF GENT, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
Vlaams Instituut voor Biotechnologie                           VIB
mailto:gebee@gengenp.rug.ac.be    	   http://www.plantgenetics.rug.ac.be
==================================================================

--------------------------------
End of nih-image-d Digest V99 Issue #118
****************************************

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                   NIH-image Mailing List Help 
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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
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2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
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Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
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--


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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 119

Today's Topics:
  unsubscribe                           [ "joanna everett" <joanna_everett@ho ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]

------------------------------

Date: Sat, 22 May 1999 15:34:38 PDT
From: "joanna everett" <joanna_everett@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-ID: <19990522223439.31754.qmail@hotmail.com>
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>Subject: nih-image-d Digest V99 #118
>Date: Sat, 22 May 1999 06:02:28 -0400 (EDT)
>
><< message2.txt >>
><< message4.txt >>
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><< message10.txt >>


______________________________________________________
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------------------------------

Date: Sun, 23 May 1999 05:05:01 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199905230905.FAA16418@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
                   ---------------------------
     


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--------------------
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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

--------------------------------
End of nih-image-d Digest V99 Issue #119
****************************************

From nih-image-request@io.ece.drexel.edu Mon May 24 11:38 EDT 1999
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egrep OneScanner /*



From nih-image-request@io.ece.drexel.edu Mon May 24 14:51 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: Carol Sheppard <sheppc@mail.wsu.edu>
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Greetings,

Can anyone out there tell me if there are NIH image macros (acquisition and
analysis) for fura-2 imaging using a Mac?

Thanks very much.

Carol
Carol A. Sheppard
Assistant Professor
Department of Entomology
Washington State University
(509) 335-1432
sheppc@mail.wsu.edu


From nih-image-request@io.ece.drexel.edu Mon May 24 16:20 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: Carol Sheppard <sheppc@mail.wsu.edu>
Subject: Calcium imaging 
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Can anyone tell me if NIH image is being used to acquire and analyze images
of fura-2 loaded cells (which require  ratioing)?

Thanks very much.

Carol Sheppard
Carol A. Sheppard
Assistant Professor
Department of Entomology
Washington State University
(509) 335-1432
sheppc@mail.wsu.edu


From nih-image-d-request@io.ece.drexel.edu Tue May 25 06:13 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #120
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 120

Today's Topics:
  archive                               [ Juliann Seebauer <jzzz@uiuc.edu> ]
  Unidentified subject!                 [ Carol Sheppard <sheppc@mail.wsu.edu ]
  Calcium imaging                       [ Carol Sheppard <sheppc@mail.wsu.edu ]

------------------------------

Date: Mon, 24 May 1999 10:23:48 -0500
From: Juliann Seebauer <jzzz@uiuc.edu>
To: nih-image@io.ece.drexel.edu
Subject: archive
Message-Id: <v03102801b36f1ed1ede0@[128.174.55.43]>
Content-Type: text/plain; charset="us-ascii"

egrep OneScanner /*

------------------------------

Date: Mon, 24 May 1999 11:31:00 -0700
From: Carol Sheppard <sheppc@mail.wsu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <v04011706b36f4b2ae476@[134.121.87.43]>
Content-Type: text/plain; charset="us-ascii"

Greetings,

Can anyone out there tell me if there are NIH image macros (acquisition and
analysis) for fura-2 imaging using a Mac?

Thanks very much.

Carol
Carol A. Sheppard
Assistant Professor
Department of Entomology
Washington State University
(509) 335-1432
sheppc@mail.wsu.edu

------------------------------

Date: Mon, 24 May 1999 13:00:49 -0700
From: Carol Sheppard <sheppc@mail.wsu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Calcium imaging 
Message-Id: <v04011718b36f6021d1ee@[134.121.87.43]>
Content-Type: text/plain; charset="us-ascii"

Can anyone tell me if NIH image is being used to acquire and analyze images
of fura-2 loaded cells (which require  ratioing)?

Thanks very much.

Carol Sheppard
Carol A. Sheppard
Assistant Professor
Department of Entomology
Washington State University
(509) 335-1432
sheppc@mail.wsu.edu

--------------------------------
End of nih-image-d Digest V99 Issue #120
****************************************

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Please cancel my subscription.
Thanks,

Prof. Gershon Golomb,
Head, Dept. of Pharmaceutics
School of Pharmacy, The Hebrew University of Jerusalem
POBOX 12065, Jerusalem 91120, Israel
FAX - 972-2-6436246
Phone - 972-2-6757014
e-mail - golomb@cc.huji.ac.il



From nih-image-request@io.ece.drexel.edu Tue May 25 10:14 EDT 1999
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Once before, in the past, we had a macro that checked rCount and when it
approached 8000 we had it save the measurments and reset to 0.  Not
elegant, but it worked.

At 10:40 AM 5/19/99 -0700, you wrote:
>Hello, does anyone know how to take scion image above
>8000 for maximum amount of measurements?
>Thanks
>steve spencer

********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************


From nih-image-request@io.ece.drexel.edu Tue May 25 10:39 EDT 1999
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Hello all-
This is somewhat off-topic, but I thought that some of you might work in
institutions that might be able to provide me with a lead...
I am working on a field project with Cliff Swallows which involves
inspecting their nests, which are built sort of like an upside down mud
igloo.  The nest is enclosed, with a 5-10 cm long tunnel leading to the
nest, which has an opening of about 5-8 cm.  I'm wondering if there are
any old, used fiber optics systems out there which are small enough to
run on a car battery (with a converter), and most importantly,
inexpensive (this is somewhat of a shoestring project).

Since this doesn't really pertain to image processing, if you have any
info, please respond directly to me at kokopellis@att.net.

thanks for the bandwidth--
Chris Cline
Salt Lake City, UT


From nih-image-request@io.ece.drexel.edu Tue May 25 12:34 EDT 1999
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From: SolamereTG@aol.com
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Date: Tue, 25 May 1999 12:12:48 EDT
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In a message dated 5/24/99 2:10:54 PM, sheppc@mail.wsu.edu writes:

<<Can anyone tell me if NIH image is being used to acquire and analyze images
of fura-2 loaded cells (which require  ratioing)?
>>

Yes we use it to generate a ratio stack from images acquired at 30 fps. This 
is done post acquisition at this speed.  If you are doing time lapse capture 
of paired frames the ratio can be done in between acquiring the ratio pairs. 
For Fura -2 imaging at video rates or faster you will need a frame transfer 
(progressive scan camera). Our macro lets you select the roi from the 
original stack and then ratios the odd frames/even frames to produce a stack.

George A. Peeters
Solamere Technology Group


From nih-image-d-request@io.ece.drexel.edu Wed May 26 06:16 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 121

Today's Topics:
  subscription                          [ golomb@cc.huji.ac.il (Gershon Golom ]
  Re: max measurements                  [ Michael Cammer <cammer@aecom.yu.edu ]
  Looking for inexpensive, used, small  [ kW <kokopellis@att.net> ]
  Re: Calcium imaging                   [ SolamereTG@aol.com ]

------------------------------

Date: Tue, 25 May 1999 13:27:05 +0300
From: golomb@cc.huji.ac.il (Gershon Golomb)
To: nih-image@io.ece.drexel.edu
Subject: subscription
Message-Id: <v02130505b3702b4b62d7@[132.64.165.8]>
Content-Type: text/plain; charset="us-ascii"

Please cancel my subscription.
Thanks,

Prof. Gershon Golomb,
Head, Dept. of Pharmaceutics
School of Pharmacy, The Hebrew University of Jerusalem
POBOX 12065, Jerusalem 91120, Israel
FAX - 972-2-6436246
Phone - 972-2-6757014
e-mail - golomb@cc.huji.ac.il

------------------------------

Date: Tue, 25 May 1999 10:05:16 -0700
From: Michael Cammer <cammer@aecom.yu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: max measurements
Message-Id: <3.0.5.32.19990525100516.00a38eb0@mailserver.aecom.yu.edu>
Content-Type: text/plain; charset="us-ascii"

Once before, in the past, we had a macro that checked rCount and when it
approached 8000 we had it save the measurments and reset to 0.  Not
elegant, but it worked.

At 10:40 AM 5/19/99 -0700, you wrote:
>Hello, does anyone know how to take scion image above
>8000 for maximum amount of measurements?
>Thanks
>steve spencer

********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************

------------------------------

Date: Tue, 25 May 1999 08:29:25 -0700
From: kW <kokopellis@att.net>
To: nih-image@io.ece.drexel.edu
Subject: Looking for inexpensive, used, small fiber optics
Message-ID: <374AC1D5.50266536@att.net>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hello all-
This is somewhat off-topic, but I thought that some of you might work in
institutions that might be able to provide me with a lead...
I am working on a field project with Cliff Swallows which involves
inspecting their nests, which are built sort of like an upside down mud
igloo.  The nest is enclosed, with a 5-10 cm long tunnel leading to the
nest, which has an opening of about 5-8 cm.  I'm wondering if there are
any old, used fiber optics systems out there which are small enough to
run on a car battery (with a converter), and most importantly,
inexpensive (this is somewhat of a shoestring project).

Since this doesn't really pertain to image processing, if you have any
info, please respond directly to me at kokopellis@att.net.

thanks for the bandwidth--
Chris Cline
Salt Lake City, UT

------------------------------

Date: Tue, 25 May 1999 12:12:48 EDT
From: SolamereTG@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re: Calcium imaging
Message-ID: <392c37df.247c2600@aol.com>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

In a message dated 5/24/99 2:10:54 PM, sheppc@mail.wsu.edu writes:

<<Can anyone tell me if NIH image is being used to acquire and analyze images
of fura-2 loaded cells (which require  ratioing)?
>>

Yes we use it to generate a ratio stack from images acquired at 30 fps. This 
is done post acquisition at this speed.  If you are doing time lapse capture 
of paired frames the ratio can be done in between acquiring the ratio pairs. 
For Fura -2 imaging at video rates or faster you will need a frame transfer 
(progressive scan camera). Our macro lets you select the roi from the 
original stack and then ratios the odd frames/even frames to produce a stack.

George A. Peeters
Solamere Technology Group

--------------------------------
End of nih-image-d Digest V99 Issue #121
****************************************

From nih-image-request@io.ece.drexel.edu Thu May 27 11:18 EDT 1999
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From: David Keeble <D.R.T.Keeble@Bradford.ac.uk>
Subject: Timing Question
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Hi,
I have a question about synchronization of the display of images in IMAGE
to the frame rate. I have access to a bunch of macros which diplay stimuli
for psychophysical experiments, which it would be very convenient to use.
In such experiments it is important to control the duration that the
stimulus is on the screen very precisely, which effectively means
synchronizing the display to screen retrace. Unfortunately there is nothing
in these macros or, it seems, in IMAGE that allows anything like this. I
have searched the archive and found a previous brief discussion of this
issue, the upshot of which was that IMAGE was non-optimal for such
psychophysical experiments, owing to this timing problem. However, for
various reasons that aren't important, I do wish to use these macros for
these kinds of experiments. I want to know whether the following way of
getting around the timing problem is viable:

I have code in C, written under Think C but no doubt portable to
Codewarrior, which will accomplish the task of waiting for the retrace
interval. If I could interface this code to an IMAGE Macro, this would
allow me to synchronise the "Paste" and "Clear" macro commands to the
retrace interval. From all I have read in the IMAGE manual and in the
archives, it appears that the only way of doing this is to write a plug-in,
and access it through a macro command. Is that correct, or is there some
other way? I need to know some very basic things about writing plug-ins: ie
how do you do it? Does Codewarrior have the facility to write a plug-in
that will work with IMAGE? Apparently the plug-in has to be compatible with
adobe photoshop, but it's not clear to me what that would mean.

Thanks in advance for any help.

davidk

--
David Keeble                  D.R.T.Keeble@Bradford.ac.uk
Department of Optometry,        University of Bradford
Richmond Rd, Bradford BD7 1DP,    United Kingdom
(Phone)+44 1274 236252      (Fax) +44 1274 235570
http://www.brad.ac.uk/acad/optom/DRTKeebleProfile.html



From nih-image-d-request@io.ece.drexel.edu Fri May 28 06:21 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #122
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 122

Today's Topics:
  Timing Question                       [ David Keeble <D.R.T.Keeble@Bradford ]

------------------------------

Date: Thu, 27 May 1999 16:01:02 +0000
From: David Keeble <D.R.T.Keeble@Bradford.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Timing Question
Message-Id: <l03130307b338dc1312c4@[143.53.224.81]>
Content-Type: text/plain; charset="us-ascii"

Hi,
I have a question about synchronization of the display of images in IMAGE
to the frame rate. I have access to a bunch of macros which diplay stimuli
for psychophysical experiments, which it would be very convenient to use.
In such experiments it is important to control the duration that the
stimulus is on the screen very precisely, which effectively means
synchronizing the display to screen retrace. Unfortunately there is nothing
in these macros or, it seems, in IMAGE that allows anything like this. I
have searched the archive and found a previous brief discussion of this
issue, the upshot of which was that IMAGE was non-optimal for such
psychophysical experiments, owing to this timing problem. However, for
various reasons that aren't important, I do wish to use these macros for
these kinds of experiments. I want to know whether the following way of
getting around the timing problem is viable:

I have code in C, written under Think C but no doubt portable to
Codewarrior, which will accomplish the task of waiting for the retrace
interval. If I could interface this code to an IMAGE Macro, this would
allow me to synchronise the "Paste" and "Clear" macro commands to the
retrace interval. From all I have read in the IMAGE manual and in the
archives, it appears that the only way of doing this is to write a plug-in,
and access it through a macro command. Is that correct, or is there some
other way? I need to know some very basic things about writing plug-ins: ie
how do you do it? Does Codewarrior have the facility to write a plug-in
that will work with IMAGE? Apparently the plug-in has to be compatible with
adobe photoshop, but it's not clear to me what that would mean.

Thanks in advance for any help.

davidk

--
David Keeble                  D.R.T.Keeble@Bradford.ac.uk
Department of Optometry,        University of Bradford
Richmond Rd, Bradford BD7 1DP,    United Kingdom
(Phone)+44 1274 236252      (Fax) +44 1274 235570
http://www.brad.ac.uk/acad/optom/DRTKeebleProfile.html

--------------------------------
End of nih-image-d Digest V99 Issue #122
****************************************

From nih-image-request@io.ece.drexel.edu Fri May 28 18:40 EDT 1999
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Date: Fri, 28 May 1999 15:25:38 -0700
To: nih-image@io.ece.drexel.edu
From: Daniel Twelker <twelker@uclink4.berkeley.edu>
Subject: color measurement with monochrome camera
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I would like to measure the amount of redness in a close up image of a
person's eye. I have ordered a Scion LG-3, B/W G3, and a monochrome video
camera that will be attached to an anterior segment camera (basically a
microscope with illumination system mounted sideways to image the eye). Can
anyone suggest a procedure and/or a good reference to do this? Thanks in
advance.
Dan Twelker



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From: nih-image-d-request@io.ece.drexel.edu
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 123

Today's Topics:
  color measurement with monochrome ca  [ Daniel Twelker <twelker@uclink4.ber ]
  Object Image and system conflict?     [ Kris Jorgensen <kris@purdue.edu> ]

------------------------------

Date: Fri, 28 May 1999 15:25:38 -0700
From: Daniel Twelker <twelker@uclink4.berkeley.edu>
To: nih-image@io.ece.drexel.edu
Subject: color measurement with monochrome camera
Message-Id: <v03020903b374c6600800@[128.32.232.125]>
Content-Type: text/plain; charset="us-ascii"

I would like to measure the amount of redness in a close up image of a
person's eye. I have ordered a Scion LG-3, B/W G3, and a monochrome video
camera that will be attached to an anterior segment camera (basically a
microscope with illumination system mounted sideways to image the eye). Can
anyone suggest a procedure and/or a good reference to do this? Thanks in
advance.
Dan Twelker

------------------------------

Date: Sat, 29 May 1999 12:06:53 -0500
From: Kris Jorgensen <kris@purdue.edu>
To: nih-image@io.ece.drexel.edu
Subject: Object Image and system conflict?
Message-Id: <37501EAD.A06D25A9@purdue.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi,
I have noticed that Object Image runs fine on one machine but on my
machine at home there is a long pause after a click and when the menu
drops down. Does anyone know which system extension may be causing this?

Kris


-- 
Kris L. Jorgensen
Office:     ME 183
Phone:      (765) 494-8585
Lab:        (765) 484-8757
Email:      kris@purdue.edu
WWW:        http://www.ecn.purdue.edu/~kris

--------------------------------
End of nih-image-d Digest V99 Issue #123
****************************************

From nih-image-request@io.ece.drexel.edu Sat May 29 13:20 EDT 1999
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Date: Sat, 29 May 1999 12:06:53 -0500
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Hi,
I have noticed that Object Image runs fine on one machine but on my
machine at home there is a long pause after a click and when the menu
drops down. Does anyone know which system extension may be causing this?

Kris


-- 
Kris L. Jorgensen
Office:     ME 183
Phone:      (765) 494-8585
Lab:        (765) 484-8757
Email:      kris@purdue.edu
WWW:        http://www.ecn.purdue.edu/~kris


From nih-image-request@io.ece.drexel.edu Sat May 29 16:30 EDT 1999
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Hi,
I have requested several times to unsunscribe me.
Please take care.
Thanks,

Prof. Gershon Golomb,
Head, Dept. of Pharmaceutics
School of Pharmacy, The Hebrew University of Jerusalem
POBOX 12065, Jerusalem 91120, Israel
FAX - 972-2-6436246
Phone - 972-2-6757014
e-mail - golomb@cc.huji.ac.il



From nih-image-d-request@io.ece.drexel.edu Sun May 30 18:53 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #124
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------------------------------

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nih-image-d Digest				Volume 99 : Issue 124

Today's Topics:
  Re: nih-image-d Digest V99 #122       [ golomb@cc.huji.ac.il (Gershon Golom ]
  lens distortion correction?           [ HertzbJB@utrc.utc.com ]

------------------------------

Date: Sat, 29 May 1999 23:18:42 +0300
From: golomb@cc.huji.ac.il (Gershon Golomb)
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #122
Message-Id: <v02130500b375fbfb9c25@[128.139.5.90]>
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Hi,
I have requested several times to unsunscribe me.
Please take care.
Thanks,

Prof. Gershon Golomb,
Head, Dept. of Pharmaceutics
School of Pharmacy, The Hebrew University of Jerusalem
POBOX 12065, Jerusalem 91120, Israel
FAX - 972-2-6436246
Phone - 972-2-6757014
e-mail - golomb@cc.huji.ac.il

------------------------------

Date: Sun, 30 May 1999 18:37:41 -0400
From: HertzbJB@utrc.utc.com
To: nih-image@io.ece.drexel.edu
Subject: lens distortion correction?
Message-ID: <62835D8790DBD111981100805FA7E4C475DE34@EXPRESS1>
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I would like to find a plug-in or algorithm which can correct for "barrel"
or "pincushion" distortions in images obtained with short-focal-length
lenses. Has anyone written a plug-in for NIH-Image to accomplish this?
Barring that, does anyone know of any other software which can do it?

I believe someone posted to the list a few weeks ago with a similar request,
but I didn't see a reply posted to the list.

Thanks

-Jared Hertzberg

------_=_NextPart_001_01BEAAED.674CA580
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; =
charset=3Diso-8859-1">
<META NAME=3D"Generator" CONTENT=3D"MS Exchange Server version =
5.5.2448.0">
<TITLE>lens distortion correction?</TITLE>
</HEAD>
<BODY>
<BR>

<P><FONT SIZE=3D2 FACE=3D"Arial">I would like to find a plug-in or =
algorithm which can correct for "barrel" or "pincushion" distortions in =
images obtained with short-focal-length lenses. Has anyone written a =
plug-in for NIH-Image to accomplish this? Barring that, does anyone =
know of any other software which can do it?</FONT></P>

<P><FONT SIZE=3D2 FACE=3D"Arial">I believe someone posted to the list a =
few weeks ago with a similar request, but I didn't see a reply posted =
to the list.</FONT></P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Thanks</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">-Jared Hertzberg</FONT>
</P>

</BODY>
</HTML>
------_=_NextPart_001_01BEAAED.674CA580--

--------------------------------
End of nih-image-d Digest V99 Issue #124
****************************************

From nih-image-request@io.ece.drexel.edu Sun May 30 18:59 EDT 1999
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To: nih-image@io.ece.drexel.edu
Subject: lens distortion correction?
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I would like to find a plug-in or algorithm which can correct for "barrel"
or "pincushion" distortions in images obtained with short-focal-length
lenses. Has anyone written a plug-in for NIH-Image to accomplish this?
Barring that, does anyone know of any other software which can do it?

I believe someone posted to the list a few weeks ago with a similar request,
but I didn't see a reply posted to the list.

Thanks

-Jared Hertzberg

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	charset="iso-8859-1"
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<META NAME=3D"Generator" CONTENT=3D"MS Exchange Server version =
5.5.2448.0">
<TITLE>lens distortion correction?</TITLE>
</HEAD>
<BODY>
<BR>

<P><FONT SIZE=3D2 FACE=3D"Arial">I would like to find a plug-in or =
algorithm which can correct for "barrel" or "pincushion" distortions in =
images obtained with short-focal-length lenses. Has anyone written a =
plug-in for NIH-Image to accomplish this? Barring that, does anyone =
know of any other software which can do it?</FONT></P>

<P><FONT SIZE=3D2 FACE=3D"Arial">I believe someone posted to the list a =
few weeks ago with a similar request, but I didn't see a reply posted =
to the list.</FONT></P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Thanks</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">-Jared Hertzberg</FONT>
</P>

</BODY>
</HTML>
------_=_NextPart_001_01BEAAED.674CA580--


From nih-image-request@io.ece.drexel.edu Tue Jun  1 08:55 EDT 1999
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Date: Tue, 01 Jun 1999 14:37:59 +0200
From: Lucas Bickel <lukas.bickel@zmk.unibe.ch>
Subject: Perimeter?
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I am trying to write a macro wich lets the user define a Roi and save it as
a roi file. I then found a macro for triangle Rois in the archive (
latest/1331). I copied it and made my changes. When I run the macro I get
an error message saying

	***************************************************
	*		Perimater too long.
	*		(10000 coordinates)	*
	*					*
	*       ( OK )				*
	***************************************************

I would now like to now if there is an other way to achieve what I want and
what the error message wants to say.

macro'Perimeter error[F5]';
var
 	i, corners		: integer;
  	x, y 		: integer;
  	ReferencePid	: integer;
begin
 	ReferencePid := PidNumber;
 	duplicate('test image');
 	corners := GetNumber('How many points should your Roi have?', 3, 0);
  	for i:=0 to corners do
  		begin
  			if Button then
  				begin
  					GetMouse(x, y);
  					rUser1[i] := x;
  					rUser2[i] := y;
  					wait(0.2);
  					beep;
  				end;
  		end;
  	moveTo(rUser1[1], rUser2[1]);
  	for i:=1 to corners  do
  		begin
  			lineTo(rUser1[i], rUser2[i]);
  		end;
 	setThreshold(1);
	autoOutline(rUser1[1],rUser2[1]);
	dispose;
	selectPic(ReferencePid);
	 restoreROI;
end;

Thanks in advance

Lucas


-----------------------------------
    Lucas Bickel
    Freiburgstrasse 7
    3010 Bern
-----------------------------------
Voice  +41 31 632 86 18
Pager  +41 74 490 30 02
-----------------------------------



From nih-image-request@io.ece.drexel.edu Tue Jun  1 09:28 EDT 1999
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From: "Bill Clerici, Ph.D." <bcler1@pop.uky.edu>
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Many people seem to have problems with this. Put the word "unsubscribe" in
the subject line, and you should be removed from the list.


At 11:18 PM 5/29/99 +0300, you wrote:
>Hi,
>I have requested several times to unsunscribe me.
>Please take care.
>Thanks,
>
>Prof. Gershon Golomb,
>Head, Dept. of Pharmaceutics
>School of Pharmacy, The Hebrew University of Jerusalem
>POBOX 12065, Jerusalem 91120, Israel
>FAX - 972-2-6436246
>Phone - 972-2-6757014
>e-mail - golomb@cc.huji.ac.il
>
>
>

--------------------------------------------
William J. Clerici, Ph.D.
Associate Professor
Rm. C-236, Department of Surgery
Division of Otolaryngology-HNS
University of Kentucky Chandler Medical Center
800 Rose Street
Lexington, KY 40536-0084
           ------------------
Telephone: (606) 257-5097
      (lab): (606) 257-6020
      FAX: (606) 257-5096
      e-mail: bcler1@pop.uky.edu
--------------------------------------------


From nih-image-request@io.ece.drexel.edu Tue Jun  1 09:41 EDT 1999
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Date: Tue, 1 Jun 1999 15:33:09 +0200
To: nih-image@io.ece.drexel.edu
From: Ben Elkin <elk@igb.fhg.de>
Subject: Re: nih-image-d Digest V99 #122
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>
>At 11:18 PM 5/29/99 +0300, you wrote:
>>Hi,
>>I have requested several times to unsunscribe me.
>>Please take care.
>>Thanks,
>>
>>Prof. Gershon Golomb,
>>Head, Dept. of Pharmaceutics

Dear Prof. Golomb,

even though there might be a person who administrates the list and would
take care to unsubscribe you from the list, it is always better to use the
standard mechanism:


Unsubscribe
-----------
To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu.
the Subject of the message should contain "unsubscribe".

As in:		To: nih-image-request@biomed.drexel.edu
		Subject: unsubscribe

Please send the mail to the address above, not to the list itself.

Regards


Ben Elkin

=======================================
elk@igb.fhg.de

http://www.igb.fhg.de/GVT/

Fraunhofer Institute for Interfacial Technology and Bioengineering
                    (fuer Grenzflaechen und Bioverfahrenstechnik)

Nobelstr. 12    D-70569 Stuttgart    Germany

Tel. +49 - 711 - 970-4144, -4161
Fax                 -4200




From nih-image-request@io.ece.drexel.edu Tue Jun  1 10:04 EDT 1999
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From: "Ryan, Fiona - Technician Mechanical Engineering"
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> Regards,
> Fiona 
> 
> Fiona Ryan
> Mechanical Engineering Technician,
> I.T.Tallaght
> Tallaght,
> Dublin 24.
> Tel *:- 	+353 1 4042567
> Fax :-	+353 1 4042504
> E-Mail* :- Fiona.Ryan@it-tallaght.ie
> 
> 
> 



From nih-image-request@io.ece.drexel.edu Tue Jun  1 11:06 EDT 1999
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Date: Tue, 1 Jun 1999 09:42:15 -0500
To: nih-image@io.ece.drexel.edu
From: Thomas Hickson <hicks007@tc.umn.edu>
Subject: Re: lens distortion correction?
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--============_-1283874358==_ma============
Content-Type: text/plain; charset="us-ascii"

I was the one that posted the message about lens distortion correction.  I
did not get anything for NIH-Image, but there are plug-ins for Photoshop
and GraphicConverter that work very nicely.  Here's the web site:

http://www.fh-furtwangen.de/~dersch/

You can download straight from there.

Cheers,

Tom

>I would like to find a plug-in or algorithm which can correct for "barrel"
>or "pincushion" distortions in images obtained with short-focal-length
>lenses. Has anyone written a plug-in for NIH-Image to accomplish this?
>Barring that, does anyone know of any other software which can do it?
>
>I believe someone posted to the list a few weeks ago with a similar
>request, but I didn't see a reply posted to the list.
>
>Thanks
>
>-Jared Hertzberg

************************************************************

Thomas A. Hickson
St. Anthony Falls Laboratory
2-3rd Ave. SE,  Room 381
University of Minnesota
Minneapolis, MN  55414

Phone:  612-627-4594
Fax:	612-627-4609
e-mail:	hickson@pangea.stanford.edu

************************************************************

	To doubt everything or to believe everything are
	two equally convenient solutions; both dispense
	with the necessity of reflection.
						H. Poincare
--============_-1283874358==_ma============
Content-Type: text/enriched; charset="us-ascii"

<fontfamily><param>Arial</param><smaller>I was the one that posted the
message about lens distortion correction.  I did not get anything for
NIH-Image, but there are plug-ins for Photoshop and GraphicConverter
that work very nicely.  Here's the web site:


http://www.fh-furtwangen.de/~dersch/


You can download straight from there.  


Cheers,


Tom


<excerpt>I would like to find a plug-in or algorithm which can correct
for "barrel" or "pincushion" distortions in images obtained with
short-focal-length lenses. Has anyone written a plug-in for NIH-Image
to accomplish this? Barring that, does anyone know of any other
software which can do it?


I believe someone posted to the list a few weeks ago with a similar
request, but I didn't see a reply posted to the list.


Thanks


-Jared Hertzberg

</excerpt></smaller></fontfamily>

<fontfamily><param>Geneva</param>************************************************************


Thomas A. Hickson

St. Anthony Falls Laboratory

2-3rd Ave. SE,  Room 381

University of Minnesota

Minneapolis, MN  55414


Phone:  612-627-4594

Fax:	612-627-4609

e-mail:	hickson@pangea.stanford.edu


************************************************************


	To doubt everything or to believe everything are

	two equally convenient solutions; both dispense

	with the necessity of reflection.

						H. Poincare</fontfamily>

--============_-1283874358==_ma============--


From nih-image-request@io.ece.drexel.edu Tue Jun  1 15:31 EDT 1999
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Date: Tue, 01 Jun 1999 16:29:31 -0300
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Dear Friends:
How  can I download executor?.
Thanks


From nih-image-request@io.ece.drexel.edu Wed Jun  2 04:27 EDT 1999
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Use this site for a free demo:

http://www.ardi.com/

Gary.



>-----Original Message-----
>From:	Ruben Iacono [SMTP:rubeniac@huemul.ffyb.uba.ar]
>Sent:	1. juni 1999 21:30
>To:	nih-image@io.ece.drexel.edu
>Subject:	Re: Executor...?
>
>Dear Friends:
>How  can I download executor?.
>Thanks
>


From nih-image-d-request@io.ece.drexel.edu Wed Jun  2 04:30 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #125
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 125

Today's Topics:
  Perimeter?                            [ Lucas Bickel <lukas.bickel@zmk.unib ]
  Re: nih-image-d Digest V99 #122       [ "Bill Clerici, Ph.D." <bcler1@pop.u ]
  Re: nih-image-d Digest V99 #122       [ Ben Elkin <elk@igb.fhg.de> ]
  unsubscribe                           [ "Ryan, Fiona - Technician Mechanica ]
  Re: lens distortion correction?       [ Thomas Hickson <hicks007@tc.umn.edu ]
  Re: Executor...?                      [ Ruben Iacono <rubeniac@huemul.ffyb. ]
  RE: Executor...?                      [ Gary Chinga <gary.chinga@pfi.no> ]

------------------------------

Date: Tue, 01 Jun 1999 14:37:59 +0200
From: Lucas Bickel <lukas.bickel@zmk.unibe.ch>
To: nih-image@io.ece.drexel.edu
Subject: Perimeter?
Message-id: <l03130302b37980f23f1d@[130.92.198.63]>
Content-type: text/plain; charset=us-ascii
Content-transfer-encoding: 7BIT

I am trying to write a macro wich lets the user define a Roi and save it as
a roi file. I then found a macro for triangle Rois in the archive (
latest/1331). I copied it and made my changes. When I run the macro I get
an error message saying

	***************************************************
	*		Perimater too long.
	*		(10000 coordinates)	*
	*					*
	*       ( OK )				*
	***************************************************

I would now like to now if there is an other way to achieve what I want and
what the error message wants to say.

macro'Perimeter error[F5]';
var
 	i, corners		: integer;
  	x, y 		: integer;
  	ReferencePid	: integer;
begin
 	ReferencePid := PidNumber;
 	duplicate('test image');
 	corners := GetNumber('How many points should your Roi have?', 3, 0);
  	for i:=0 to corners do
  		begin
  			if Button then
  				begin
  					GetMouse(x, y);
  					rUser1[i] := x;
  					rUser2[i] := y;
  					wait(0.2);
  					beep;
  				end;
  		end;
  	moveTo(rUser1[1], rUser2[1]);
  	for i:=1 to corners  do
  		begin
  			lineTo(rUser1[i], rUser2[i]);
  		end;
 	setThreshold(1);
	autoOutline(rUser1[1],rUser2[1]);
	dispose;
	selectPic(ReferencePid);
	 restoreROI;
end;

Thanks in advance

Lucas


-----------------------------------
    Lucas Bickel
    Freiburgstrasse 7
    3010 Bern
-----------------------------------
Voice  +41 31 632 86 18
Pager  +41 74 490 30 02
-----------------------------------

------------------------------

Date: Tue, 01 Jun 1999 09:16:49 -0400
From: "Bill Clerici, Ph.D." <bcler1@pop.uky.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #122
Message-Id: <3.0.5.32.19990601091649.009cc700@pop.uky.edu>
Content-Type: text/plain; charset="us-ascii"

Many people seem to have problems with this. Put the word "unsubscribe" in
the subject line, and you should be removed from the list.


At 11:18 PM 5/29/99 +0300, you wrote:
>Hi,
>I have requested several times to unsunscribe me.
>Please take care.
>Thanks,
>
>Prof. Gershon Golomb,
>Head, Dept. of Pharmaceutics
>School of Pharmacy, The Hebrew University of Jerusalem
>POBOX 12065, Jerusalem 91120, Israel
>FAX - 972-2-6436246
>Phone - 972-2-6757014
>e-mail - golomb@cc.huji.ac.il
>
>
>

--------------------------------------------
William J. Clerici, Ph.D.
Associate Professor
Rm. C-236, Department of Surgery
Division of Otolaryngology-HNS
University of Kentucky Chandler Medical Center
800 Rose Street
Lexington, KY 40536-0084
           ------------------
Telephone: (606) 257-5097
      (lab): (606) 257-6020
      FAX: (606) 257-5096
      e-mail: bcler1@pop.uky.edu
--------------------------------------------

------------------------------

Date: Tue, 1 Jun 1999 15:33:09 +0200
From: Ben Elkin <elk@igb.fhg.de>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #122
Message-Id: <l03130300b37990217d8e@[129.233.21.143]>
Content-Type: text/plain; charset="us-ascii"

>
>At 11:18 PM 5/29/99 +0300, you wrote:
>>Hi,
>>I have requested several times to unsunscribe me.
>>Please take care.
>>Thanks,
>>
>>Prof. Gershon Golomb,
>>Head, Dept. of Pharmaceutics

Dear Prof. Golomb,

even though there might be a person who administrates the list and would
take care to unsubscribe you from the list, it is always better to use the
standard mechanism:


Unsubscribe
-----------
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		Subject: unsubscribe

Please send the mail to the address above, not to the list itself.

Regards


Ben Elkin

=======================================
elk@igb.fhg.de

http://www.igb.fhg.de/GVT/

Fraunhofer Institute for Interfacial Technology and Bioengineering
                    (fuer Grenzflaechen und Bioverfahrenstechnik)

Nobelstr. 12    D-70569 Stuttgart    Germany

Tel. +49 - 711 - 970-4144, -4161
Fax                 -4200

------------------------------

Date: Tue, 1 Jun 1999 14:39:44 +0100 
From: "Ryan, Fiona - Technician Mechanical Engineering"
	 <Fiona.Ryan@IT-Tallaght.ie>
To: NIH-Queries <nih-image@io.ece.drexel.edu>
Subject: unsubscribe
Message-ID: <D7FFC2BFF870D211A89600A0C9DD656C4A3377@gpo.it-tallaght.ie>
Content-Type: multipart/mixed;
	boundary="----_=_NextPart_000_01BEAC34.351D5346"

This message is in MIME format. Since your mail reader does not understand
this format, some or all of this message may not be legible.

------_=_NextPart_000_01BEAC34.351D5346
Content-Type: text/plain



> Regards,
> Fiona 
> 
> Fiona Ryan
> Mechanical Engineering Technician,
> I.T.Tallaght
> Tallaght,
> Dublin 24.
> Tel *:- 	+353 1 4042567
> Fax :-	+353 1 4042504
> E-Mail* :- Fiona.Ryan@it-tallaght.ie
> 
> 
> 

------------------------------

Date: Tue, 1 Jun 1999 09:42:15 -0500
From: Thomas Hickson <hicks007@tc.umn.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: lens distortion correction?
Message-Id: <v04011700b379a15337af@[128.101.165.11]>
Content-Type: multipart/alternative; boundary="============_-1283874358==_ma============"

--============_-1283874358==_ma============
Content-Type: text/plain; charset="us-ascii"

I was the one that posted the message about lens distortion correction.  I
did not get anything for NIH-Image, but there are plug-ins for Photoshop
and GraphicConverter that work very nicely.  Here's the web site:

http://www.fh-furtwangen.de/~dersch/

You can download straight from there.

Cheers,

Tom

>I would like to find a plug-in or algorithm which can correct for "barrel"
>or "pincushion" distortions in images obtained with short-focal-length
>lenses. Has anyone written a plug-in for NIH-Image to accomplish this?
>Barring that, does anyone know of any other software which can do it?
>
>I believe someone posted to the list a few weeks ago with a similar
>request, but I didn't see a reply posted to the list.
>
>Thanks
>
>-Jared Hertzberg

************************************************************

Thomas A. Hickson
St. Anthony Falls Laboratory
2-3rd Ave. SE,  Room 381
University of Minnesota
Minneapolis, MN  55414

Phone:  612-627-4594
Fax:	612-627-4609
e-mail:	hickson@pangea.stanford.edu

************************************************************

	To doubt everything or to believe everything are
	two equally convenient solutions; both dispense
	with the necessity of reflection.
						H. Poincare
--============_-1283874358==_ma============
Content-Type: text/enriched; charset="us-ascii"

<fontfamily><param>Arial</param><smaller>I was the one that posted the
message about lens distortion correction.  I did not get anything for
NIH-Image, but there are plug-ins for Photoshop and GraphicConverter
that work very nicely.  Here's the web site:


http://www.fh-furtwangen.de/~dersch/


You can download straight from there.  


Cheers,


Tom


<excerpt>I would like to find a plug-in or algorithm which can correct
for "barrel" or "pincushion" distortions in images obtained with
short-focal-length lenses. Has anyone written a plug-in for NIH-Image
to accomplish this? Barring that, does anyone know of any other
software which can do it?


I believe someone posted to the list a few weeks ago with a similar
request, but I didn't see a reply posted to the list.


Thanks


-Jared Hertzberg

</excerpt></smaller></fontfamily>

<fontfamily><param>Geneva</param>************************************************************


Thomas A. Hickson

St. Anthony Falls Laboratory

2-3rd Ave. SE,  Room 381

University of Minnesota

Minneapolis, MN  55414


Phone:  612-627-4594

Fax:	612-627-4609

e-mail:	hickson@pangea.stanford.edu


************************************************************


	To doubt everything or to believe everything are

	two equally convenient solutions; both dispense

	with the necessity of reflection.

						H. Poincare</fontfamily>

--============_-1283874358==_ma============--

------------------------------

Date: Tue, 01 Jun 1999 16:29:31 -0300
From: Ruben Iacono <rubeniac@huemul.ffyb.uba.ar>
To: nih-image@io.ece.drexel.edu
Subject: Re: Executor...?
Message-ID: <37543499.75B7@huemul.ffyb.uba.ar>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Dear Friends:
How  can I download executor?.
Thanks

------------------------------

Date: Wed, 2 Jun 1999 10:10:44 +0200
From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Executor...?
Message-ID: <c=NO%a=_%p=pfi%l=PFINT1-990602081044Z-378@pfint1.pfi.no>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

Use this site for a free demo:

http://www.ardi.com/

Gary.



>-----Original Message-----
>From:	Ruben Iacono [SMTP:rubeniac@huemul.ffyb.uba.ar]
>Sent:	1. juni 1999 21:30
>To:	nih-image@io.ece.drexel.edu
>Subject:	Re: Executor...?
>
>Dear Friends:
>How  can I download executor?.
>Thanks
>

--------------------------------
End of nih-image-d Digest V99 Issue #125
****************************************

From nih-image-request@io.ece.drexel.edu Thu Jun  3 04:02 EDT 1999
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Dear Listmembers,

I am interested in buying a framgrabber card for my G3. What it should
primarily do, is to capture a grayscale video signal 640x480 at a rate of
30 frames per second. Over a 20 min time this would accumulate into the gb
range. Not possible to manage this.

I would like the board to compress every forth of the complete 640x480
frame in y-dimension (sum up every pixel in a column, but no computing in
X-dimension). The upper forth will result in a line, 4 out of 4 will give 4
single lines. Keep these 640x1 lines in memory and discard the rest. The
data to be saved should be around 92.1 MB in size.

Is this possible ? I have the AG-5 card in mind, when writing this, but
don't know if it can do the job.

Thanks in advance for your help.

Best Regards, Peter




----------------------------------------------------
Peter Bramlage
Kardiologisches Labor der 1.Medizinischen Klinik der Charit
Universittsklinikum der Humboldt - Universitt zu Berlin
Ziegelstrae 5-9
D-10117 Berlin
Germany

Tel.:  ++49/30/2802 6373
Fax:   ++49/30/2802-6509
e-mail: Peter.Bramlage@rz.hu-berlin.de
---------------------------------------------------- 



From nih-image-request@io.ece.drexel.edu Thu Jun  3 05:23 EDT 1999
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                   NIH-image Mailing List Help 
                   ---------------------------
     


nih-image-d-request@biomed.drexel.edu  - Aministration for Digest
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     *********************************************************
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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
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         get latest/*           all 50
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8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
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egrep case_insensitive_regular_expression filename ...
maxfiles nnn
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Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
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--


From nih-image-request@io.ece.drexel.edu Thu Jun  3 08:31 EDT 1999
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From: Stein Roervik <steinr@chembio.ntnu.no>
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>Hi,
>I have a question about synchronization of the display of images in IMAGE
>to the frame rate. I have access to a bunch of macros which diplay stimuli
>for psychophysical experiments, which it would be very convenient to use.
>In such experiments it is important to control the duration that the
>stimulus is on the screen very precisely, which effectively means
>synchronizing the display to screen retrace. Unfortunately there is nothing
..
>
>I have code in C, written under Think C but no doubt portable to
>Codewarrior, which will accomplish the task of waiting for the retrace
>interval. If I could interface this code to an IMAGE Macro, this would
>allow me to synchronise the "Paste" and "Clear" macro commands to the
>retrace interval. From all I have read in the IMAGE manual and in the
>archives, it appears that the only way of doing this is to write a plug-in,
>and access it through a macro command. Is that correct, or is there some
>other way? I need to know some very basic things about writing plug-ins: ie

The simplest and fastest way to do this is to modify the image source code.
You need the CodeWarrior Pascal compiler. You have to translate your C code
to Pascal. There are tips in the User.p file and the "Inside NIH image"
manual that will help you getting started.

>how do you do it? Does Codewarrior have the facility to write a plug-in
>that will work with IMAGE? Apparently the plug-in has to be compatible with
>adobe photoshop, but it's not clear to me what that would mean.
>
CodeWarrior comes with simple example plug-ins using the PhotoShop calling
conventions. These work fine with NIH image as long as they are compiled
for 68k or PPC as separate files. Look for files in folders on the example
CD named something like "code fragment examples". You can also download the
complete plug-in SDK from Adobe, but that is a huge package so I recommend
you try with the simple examples on the CW disks first.

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+



From nih-image-request@io.ece.drexel.edu Thu Jun  3 10:55 EDT 1999
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Resent-Date: Thu, 3 Jun 1999 10:55:46 -0400 (EDT)
Date: Thu, 03 Jun 1999 16:30:57 +0200
From: Guus Zijlstra <gzijlstra@rulsfb.leidenuniv.nl>
Subject: setting standard frame size
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Dear Image friends,

I can't seem to create a standard sized frame. After I've set the scale,
which usually is in millimetres, creating a frame for particle analysis and
subsequenytly doing the analsysis gives different calculations for the area
of the frame size I've created. Even if I save the standard sized frame,
the program calculates different values for the area of this frame each
time I import it in different images. What am I doing wrong here? I make
sure the scale has been set properly!I assume it is possible for this
program to compute the area of a self made frame size after the scale has
been set. I'm looking forward to receiving an answer soon.

Many thanks,

Guus Zijlstra
G.G.O. Zijlstra
Behaviourial Biology
Institute of Ecological and Evolutionary Sciences
Leiden University
Kaiserstraat 63
P.O. Box 9516
2300 RA Leiden
+31-71-5275018/5121824


From nih-image-d-request@io.ece.drexel.edu Fri Jun  4 06:15 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #126
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 126

Today's Topics:
  Framegrabber                          [ Peter Bramlage <Peter.Bramlage@rz.h ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
  Re: Timing Question                   [ Stein Roervik <steinr@chembio.ntnu. ]
  setting standard frame size           [ Guus Zijlstra <gzijlstra@rulsfb.lei ]

------------------------------

Date: Thu, 3 Jun 1999 09:32:49 +0200
From: Peter Bramlage <Peter.Bramlage@rz.hu-berlin.de>
To: nih-image@io.ece.drexel.edu
Subject: Framegrabber
Message-Id: <l03130300b37bdbe128f8@[141.42.23.131]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Dear Listmembers,

I am interested in buying a framgrabber card for my G3. What it should
primarily do, is to capture a grayscale video signal 640x480 at a rate of
30 frames per second. Over a 20 min time this would accumulate into the gb
range. Not possible to manage this.

I would like the board to compress every forth of the complete 640x480
frame in y-dimension (sum up every pixel in a column, but no computing in
X-dimension). The upper forth will result in a line, 4 out of 4 will give 4
single lines. Keep these 640x1 lines in memory and discard the rest. The
data to be saved should be around 92.1 MB in size.

Is this possible ? I have the AG-5 card in mind, when writing this, but
don't know if it can do the job.

Thanks in advance for your help.

Best Regards, Peter




----------------------------------------------------
Peter Bramlage
Kardiologisches Labor der 1.Medizinischen Klinik der Charit
Universittsklinikum der Humboldt - Universitt zu Berlin
Ziegelstrae 5-9
D-10117 Berlin
Germany

Tel.:  ++49/30/2802 6373
Fax:   ++49/30/2802-6509
e-mail: Peter.Bramlage@rz.hu-berlin.de
---------------------------------------------------- 

------------------------------

Date: Thu, 3 Jun 1999 05:05:01 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199906030905.FAA29122@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
                   ---------------------------
     


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Subscribe
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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

------------------------------

Date: Thu, 3 Jun 1999 14:16:44 +0200
From: Stein Roervik <steinr@chembio.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Re: Timing Question
Message-Id: <v03102801b37c1f767841@[129.241.83.55]>
Content-Type: text/plain; charset="us-ascii"

>Hi,
>I have a question about synchronization of the display of images in IMAGE
>to the frame rate. I have access to a bunch of macros which diplay stimuli
>for psychophysical experiments, which it would be very convenient to use.
>In such experiments it is important to control the duration that the
>stimulus is on the screen very precisely, which effectively means
>synchronizing the display to screen retrace. Unfortunately there is nothing
..
>
>I have code in C, written under Think C but no doubt portable to
>Codewarrior, which will accomplish the task of waiting for the retrace
>interval. If I could interface this code to an IMAGE Macro, this would
>allow me to synchronise the "Paste" and "Clear" macro commands to the
>retrace interval. From all I have read in the IMAGE manual and in the
>archives, it appears that the only way of doing this is to write a plug-in,
>and access it through a macro command. Is that correct, or is there some
>other way? I need to know some very basic things about writing plug-ins: ie

The simplest and fastest way to do this is to modify the image source code.
You need the CodeWarrior Pascal compiler. You have to translate your C code
to Pascal. There are tips in the User.p file and the "Inside NIH image"
manual that will help you getting started.

>how do you do it? Does Codewarrior have the facility to write a plug-in
>that will work with IMAGE? Apparently the plug-in has to be compatible with
>adobe photoshop, but it's not clear to me what that would mean.
>
CodeWarrior comes with simple example plug-ins using the PhotoShop calling
conventions. These work fine with NIH image as long as they are compiled
for 68k or PPC as separate files. Look for files in folders on the example
CD named something like "code fragment examples". You can also download the
complete plug-in SDK from Adobe, but that is a huge package so I recommend
you try with the simple examples on the CW disks first.

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+

------------------------------

Date: Thu, 03 Jun 1999 16:30:57 +0200
From: Guus Zijlstra <gzijlstra@rulsfb.leidenuniv.nl>
To: nih-image@io.ece.drexel.edu
Cc: bolhuis@rulsfb.leidenuniv.nl
Subject: setting standard frame size
Message-id: <3.0.5.32.19990603163057.0090ccd0@rulsfb.leidenuniv.nl>
Content-type: text/plain; charset="us-ascii"

Dear Image friends,

I can't seem to create a standard sized frame. After I've set the scale,
which usually is in millimetres, creating a frame for particle analysis and
subsequenytly doing the analsysis gives different calculations for the area
of the frame size I've created. Even if I save the standard sized frame,
the program calculates different values for the area of this frame each
time I import it in different images. What am I doing wrong here? I make
sure the scale has been set properly!I assume it is possible for this
program to compute the area of a self made frame size after the scale has
been set. I'm looking forward to receiving an answer soon.

Many thanks,

Guus Zijlstra
G.G.O. Zijlstra
Behaviourial Biology
Institute of Ecological and Evolutionary Sciences
Leiden University
Kaiserstraat 63
P.O. Box 9516
2300 RA Leiden
+31-71-5275018/5121824

--------------------------------
End of nih-image-d Digest V99 Issue #126
****************************************

From nih-image-request@io.ece.drexel.edu Fri Jun  4 08:28 EDT 1999
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	for cshtest@io.ece.drexel.edu; Fri, 4 Jun 1999 08:28:13 -0400 (EDT)
Resent-Date: Fri, 4 Jun 1999 08:28:13 -0400 (EDT)
Date: Fri, 04 Jun 1999 14:14:50 +0200
From: Lucas Bickel <bickel@geocities.com>
Subject: polygonal Roi
X-Sender: bickel@mail.geocities.com
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Hi
Is there a way to to define  a polygonal Roi from a macro? I searched the
old archive but only found a article on triangular Rois.

Thanks in advance

Lucas

-----------------------------------
    Lucas Bickel
    Freiburgstrasse 7
    3010 Bern
-----------------------------------
Voice  +41 31 632 86 18
Pager  +41 74 490 30 02
-----------------------------------



From nih-image-request@io.ece.drexel.edu Fri Jun  4 08:47 EDT 1999
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Date: Fri, 4 Jun 1999 08:37:06 -0400
To: nih-image@io.ece.drexel.edu
From: ad1054@worldpath.net (Dr. Christopher Coulon)
Subject: Re: polygonal Roi
Resent-Message-ID: <"iDa5w1.0.xZ1.jXyLt"@io>
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Lucas,

It should be just an extension of the triangular ROI, which is just the
simplest case (i.e., three points).  Please get back to me offline if you
need some help.

Chris

>Hi
>Is there a way to to define  a polygonal Roi from a macro? I searched the
>old archive but only found a article on triangular Rois.
>
>Thanks in advance
>
>Lucas
>
>-----------------------------------
>    Lucas Bickel
>    Freiburgstrasse 7
>    3010 Bern
>-----------------------------------
>Voice  +41 31 632 86 18
>Pager  +41 74 490 30 02
>-----------------------------------

* * * * * * * * * * * * * * * * * *
* Dr. Christopher Hunt Coulon     *
* The GAIA Group                  *
* 40 Chick Road                   *
* Wolfeboro, New Hampshire 03894  *
* 603 569-0028                    *
* * * * * * * * * * * * * * * * * *



From nih-image-request@io.ece.drexel.edu Fri Jun  4 17:58 EDT 1999
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Date: Fri, 4 Jun 1999 17:33:15 -0400
To: nih-image@io.ece.drexel.edu
From: David Knecht <knecht@uconnvm.uconn.edu>
Subject: local contrast enhance
Resent-Message-ID: <"zh8xR3.0.Qr.Jb4Mt"@io>
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Has anyone written a stack macro that will do enhance contrast within a
selected region throughout a stack instead of for the entire image?  Dave

Home of the 1999 NCAA Basketball National Champion HUSKIES !!!
************************************************************

Dr. David Knecht
Department of Molecular and Cell Biology
University of Connecticut
75 N. Eagleville Rd.   U-125
Storrs, CT 06269
Knecht@uconnvm.uconn.edu
860-486-2200      860-486-4331 (fax)

************************************************************



From nih-image-d-request@io.ece.drexel.edu Sat Jun  5 06:10 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #127
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 127

Today's Topics:
  polygonal Roi                         [ Lucas Bickel <bickel@geocities.com> ]
  Re: polygonal Roi                     [ ad1054@worldpath.net (Dr. Christoph ]
  local contrast enhance                [ David Knecht <knecht@uconnvm.uconn. ]

------------------------------

Date: Fri, 04 Jun 1999 14:14:50 +0200
From: Lucas Bickel <bickel@geocities.com>
To: nih-image@io.ece.drexel.edu
Subject: polygonal Roi
Message-id: <l03130300b37d734f69c8@[130.92.198.63]>
Content-type: text/plain; charset=us-ascii
Content-transfer-encoding: 7BIT

Hi
Is there a way to to define  a polygonal Roi from a macro? I searched the
old archive but only found a article on triangular Rois.

Thanks in advance

Lucas

-----------------------------------
    Lucas Bickel
    Freiburgstrasse 7
    3010 Bern
-----------------------------------
Voice  +41 31 632 86 18
Pager  +41 74 490 30 02
-----------------------------------

------------------------------

Date: Fri, 4 Jun 1999 08:37:06 -0400
From: ad1054@worldpath.net (Dr. Christopher Coulon)
To: nih-image@io.ece.drexel.edu
Subject: Re: polygonal Roi
Message-Id: <v01520d01b37d78834192@[208.133.217.173]>
Content-Type: text/plain; charset="us-ascii"

Lucas,

It should be just an extension of the triangular ROI, which is just the
simplest case (i.e., three points).  Please get back to me offline if you
need some help.

Chris

>Hi
>Is there a way to to define  a polygonal Roi from a macro? I searched the
>old archive but only found a article on triangular Rois.
>
>Thanks in advance
>
>Lucas
>
>-----------------------------------
>    Lucas Bickel
>    Freiburgstrasse 7
>    3010 Bern
>-----------------------------------
>Voice  +41 31 632 86 18
>Pager  +41 74 490 30 02
>-----------------------------------

* * * * * * * * * * * * * * * * * *
* Dr. Christopher Hunt Coulon     *
* The GAIA Group                  *
* 40 Chick Road                   *
* Wolfeboro, New Hampshire 03894  *
* 603 569-0028                    *
* * * * * * * * * * * * * * * * * *

------------------------------

Date: Fri, 4 Jun 1999 17:33:15 -0400
From: David Knecht <knecht@uconnvm.uconn.edu>
To: nih-image@io.ece.drexel.edu
Subject: local contrast enhance
Message-Id: <l03130300b37df6583479@[137.99.71.142]>
Content-Type: text/plain; charset="us-ascii"

Has anyone written a stack macro that will do enhance contrast within a
selected region throughout a stack instead of for the entire image?  Dave

Home of the 1999 NCAA Basketball National Champion HUSKIES !!!
************************************************************

Dr. David Knecht
Department of Molecular and Cell Biology
University of Connecticut
75 N. Eagleville Rd.   U-125
Storrs, CT 06269
Knecht@uconnvm.uconn.edu
860-486-2200      860-486-4331 (fax)

************************************************************

--------------------------------
End of nih-image-d Digest V99 Issue #127
****************************************

From nih-image-request@io.ece.drexel.edu Sun Jun  6 09:58 EDT 1999
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Resent-Date: Sun, 6 Jun 1999 09:58:31 -0400 (EDT)
From: toukol@mindspring.com
Message-Id: <199906061343.JAA14864@io.ece.drexel.edu>
Subject: Homeworkers Needed!
Date: Sun, 6 Jun 1999 03:12:51
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From nih-image-d-request@io.ece.drexel.edu Mon Jun  7 06:18 EDT 1999
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Date: Mon, 7 Jun 1999 06:18:04 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199906071018.GAA27478@io.ece.drexel.edu>
Subject: nih-image-d Digest V99 #128
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------------------------------

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nih-image-d Digest				Volume 99 : Issue 128

Today's Topics:
  Homeworkers Needed!                   [ toukol@mindspring.com ]

------------------------------

Date: Sun, 6 Jun 1999 03:12:51
From: toukol@mindspring.com
To: nih-image@io.ece.drexel.edu
Subject: Homeworkers Needed!
Message-Id: <199906061343.JAA14864@io.ece.drexel.edu>

Dear Future Associate,

You Can Work At Home & Set Your Own Hours.  Start earning Big 
Money in a short time
       
                                    NO Newspaper Advertising!

Your job will be to stuff and mail envelopes for our company. You 
will receive $.25 for each and every envelope you stuff and mail 
out.

Just follow our simple instructions and you will be making money 
as easy as
1 2 3

For example stuff and mail 200 envelopes and you will receive 
$50.00. Stuff and mail 1000 and you will receive $250.00. Stuff 
and mail 2000 and you will receive $500.00 and more 

Never before has there been an easier way to make money from 
home!

Our Company's Home Mailing Program is designed for people with 
little or no experience and provides simple, step by step 
instructions.  

There is no prior experience or special skills necessary on your 
part, Just stuffing envelopes.

We need the help of honest and reliable home workers like you.  
Because we are overloaded with work and have more than our staff 
can handle. We have now expanded our mailing program and are 
expecting to reach millions more with our offers throughout the 
US and Canada.

Our system of stuffing and mailing envelopes is very simple and 
easy to do!
You will not be required to buy envelopes or postage stamps.

We will gladly furnish all circulars at no cost to you. We assure 
you that as a participant in our program you will never have to 
mail anything objective or offensive. 

There are no quotas to meet, and there no contracts to sign. You 
can work as much, or as little as you want. Payment for each 
envelope you send out is Guaranteed!

Here is what you will receive when you get your first Package.  
Inside you will find 100 envelopes, 100 labels and 100 sales 
letters ready to stuff and mail

As soon as you are done with stuffing and mailing these first 
letters, your payment will arrive shortly, thereafter. All you 
have to do is to order more free supplies and stuff and mail more 
envelopes to make more money.

Our sales literature which you will be stuffing and mailing will 
contain
information outlining our highly informative manuals that we are
advertising nationwide.  As a free gift you will receive a 
special manual valued at  $24.95, absolutely free, just for 
joining our Home Mailers Program.

Plus you will get your own special code number, so that we will 
know how much you are to get paid.  And to make re-ordering of 
more envelopes, that our company supplies very simple for you.

We are giving you this free bonus because we want you to be 
confident in our company and to ensure that we will be doing 
business with you for a long time.

Benefits Of This Job:

1. You do not have to quit your present job, to earn more money 
at home
2. You can make between $2,500 to $4,500 a month depending on the 
amount of time you are willing to spend stuffing and mailing 
envelopes
3. This is a great opportunity for the students, mothers, 
disabled persons or those who are home bodies.

To secure your position and to show us that you are serious about 
earning extra income at home we require a one-time registration 
fee of $35.00.
This fee covers the cost of your initial start up package,  which 
includes 100 envelopes, 100 labels and 100 sales letters and a 
manual, your registration fee will be refunded back to you 
shortly thereafter.

Money Back Guarantee!

We guarantee that as soon as you stuff and mail your first 300 
envelopes You will be paid $75.00 and your registration fee will 
be refunded.

Many of you wonder why it is necessary to pay a deposit to get a 
job. It is because we are looking for people that seriously want 
to work from home.  

*  If 3.000 people told us they wanted to start working from home 
and we sent out 3.000 packages free to every one.  And then half 
of the people decided not to work, this would be a potential loss 
of more than $60,000 in supply's and shipping that we have sent 
out to people that don't want to work

We have instituted this policy to make sure that you really want 
to work and at least finish your first package.

To Get Started Today Please Enclose Your Registration Fee of $35
Check,Cash Or Money Order and fill out the application below and 
mail to:

AHWA CO
425 S Fairfax Blvd., STE 306
Los Angeles, CA 90036

Name_____________________________________________________

Address___________________________________________________

City____________________________________ State______________

Zip Code________________

Telephone Number(s)_________________________________________

E-mail Address______________________________________________



For all orders, please allow seven (7) days for delivery and up 
to 10 days. Cash and Money Orders will result in faster shipping 
of your package.
 
 
 
 
 
 
 
 

--------------------------------
End of nih-image-d Digest V99 Issue #128
****************************************

From nih-image-request@io.ece.drexel.edu Mon Jun  7 09:18 EDT 1999
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	for cshtest@io.ece.drexel.edu; Mon, 7 Jun 1999 09:18:13 -0400 (EDT)
Resent-Date: Mon, 7 Jun 1999 09:18:13 -0400 (EDT)
Message-ID: <01BEB0C4.8DE471F0.tea@neuro.duke.edu>
From: tea@neuro.duke.edu (Cerkvenik, Tea)
Reply-To: "tea@neuro.duke.edu" <tea@neuro.duke.edu>
To: "nih-image@io.ece.drexel.edu" <nih-image@io.ece.drexel.edu>
Subject: RE:Homeworkers Needed!
Date: Mon, 7 Jun 1999 09:03:04 -0000
Organization: Neurobiology Department - Duke
X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211
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FYI, several weeks ago, a message similar to this one was sent from the 
same email account (toukol@mindspring.com) and has been reported as a SCAM 
on American Home Workers Web Site and AOL.

Tea C.

-----Original Message-----
From:	toukol@mindspring.com [SMTP:toukol@mindspring.com]
Sent:	Sunday, June 06, 1999 3:13 AM
To:	nih-image@io.ece.drexel.edu
Subject:	Homeworkers Needed!

Dear Future Associate,

You Can Work At Home & Set Your Own Hours.  Start earning Big
Money in a short time

                                    NO Newspaper Advertising!

Your job will be to stuff and mail envelopes for our company. You
will receive $.25 for each and every envelope you stuff and mail
out.

Just follow our simple instructions and you will be making money
as easy as
1? 2? 3

For example stuff and mail 200 envelopes and you will receive
$50.00. Stuff and mail 1000 and you will receive $250.00. Stuff
and mail 2000 and you will receive $500.00 and more

Never before has there been an easier way to make money from
home!

Our Company's Home Mailing Program is designed for people with
little or no experience and provides simple, step by step
instructions.

There is no prior experience or special skills necessary on your
part, Just stuffing envelopes.

We need the help of honest and reliable home workers like you.
Because we are overloaded with work and have more than our staff
can handle. We have now expanded our mailing program and are
expecting to reach millions more with our offers throughout the
US and Canada.

Our system of stuffing and mailing envelopes is very simple and
easy to do!
You will not be required to buy envelopes or postage stamps.

We will gladly furnish all circulars at no cost to you. We assure
you that as a participant in our program you will never have to
mail anything objective or offensive.

There are no quotas to meet, and there no contracts to sign. You
can work as much, or as little as you want. Payment for each
envelope you send out is Guaranteed!

Here is what you will receive when you get your first Package.
Inside you will find 100 envelopes, 100 labels and 100 sales
letters ready to stuff and mail

As soon as you are done with stuffing and mailing these first
letters, your payment will arrive shortly, thereafter. All you
have to do is to order more free supplies and stuff and mail more
envelopes to make more money.

Our sales literature which you will be stuffing and mailing will
contain
information outlining our highly informative manuals that we are
advertising nationwide.  As a free gift you will receive a
special manual valued at  $24.95, absolutely free, just for
joining our Home Mailers Program.

Plus you will get your own special code number, so that we will
know how much you are to get paid.  And to make re-ordering of
more envelopes, that our company supplies very simple for you.

We are giving you this free bonus because we want you to be
confident in our company and to ensure that we will be doing
business with you for a long time.

Benefits Of This Job:

1. You do not have to quit your present job, to earn more money
at home
2. You can make between $2,500 to $4,500 a month depending on the
amount of time you are willing to spend stuffing and mailing
envelopes
3. This is a great opportunity for the students, mothers,
disabled persons or those who are home bodies.

To secure your position and to show us that you are serious about
earning extra income at home we require a one-time registration
fee of $35.00.
This fee covers the cost of your initial start up package,  which
includes 100 envelopes, 100 labels and 100 sales letters and a
manual, your registration fee will be refunded back to you
shortly thereafter.

Money Back Guarantee!

We guarantee that as soon as you stuff and mail your first 300
envelopes You will be paid $75.00 and your registration fee will
be refunded.

Many of you wonder why it is necessary to pay a deposit to get a
job. It is because we are looking for people that seriously want
to work from home.

*  If 3.000 people told us they wanted to start working from home
and we sent out 3.000 packages free to every one.  And then half
of the people decided not to work, this would be a potential loss
of more than $60,000 in supply's and shipping that we have sent
out to people that don't want to work

We have instituted this policy to make sure that you really want
to work and at least finish your first package.

To Get Started Today Please Enclose Your Registration Fee of $35
Check,Cash Or Money Order and fill out the application below and
mail to:

AHWA CO
425 S Fairfax Blvd., STE 306
Los Angeles, CA 90036

Name_____________________________________________________

Address___________________________________________________

City____________________________________ State______________

Zip Code________________

Telephone Number(s)_________________________________________

E-mail Address______________________________________________



For all orders, please allow seven (7) days for delivery and up
to 10 days. Cash and Money Orders will result in faster shipping
of your package.


From nih-image-request@io.ece.drexel.edu Mon Jun  7 10:50 EDT 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA20080
	for cshtest@io.ece.drexel.edu; Mon, 7 Jun 1999 10:50:40 -0400 (EDT)
Resent-Date: Mon, 7 Jun 1999 10:50:40 -0400 (EDT)
Message-Id: <3.0.5.32.19990607103412.00843520@pop.uky.edu>
X-Sender: bcler1@pop.uky.edu
X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32)
Date: Mon, 07 Jun 1999 10:34:12 -0400
To: nih-image@io.ece.drexel.edu
From: "Bill Clerici, Ph.D." <bcler1@pop.uky.edu>
Subject: Re: Homeworkers Needed!
In-Reply-To: <199906061343.JAA14864@io.ece.drexel.edu>
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Please do not send me any more of your disgusting, unethical tripe. For
taking advantage of people who do not know better, I hope that you are
caught, sent to prison and made the Lucky Pierre provider for your cell
block. Hopefully, your greed will make you susceptible to the same form of
scam that you are perpetrating, and, you will lose even more than you steal.






At 03:12 AM 6/6/99, you wrote:
>Dear Future Associate,
>
>You Can Work At Home & Set Your Own Hours.  Start earning Big 
>Money in a short time
>       
>                                    NO Newspaper Advertising!
>
>Your job will be to stuff and mail envelopes for our company. You 
>will receive $.25 for each and every envelope you stuff and mail 
>out.
>
>Just follow our simple instructions and you will be making money 
>as easy as
>1 2 3
>
>For example stuff and mail 200 envelopes and you will receive 
>$50.00. Stuff and mail 1000 and you will receive $250.00. Stuff 
>and mail 2000 and you will receive $500.00 and more 
>
>Never before has there been an easier way to make money from 
>home!
>
>Our Company's Home Mailing Program is designed for people with 
>little or no experience and provides simple, step by step 
>instructions.  
>
>There is no prior experience or special skills necessary on your 
>part, Just stuffing envelopes.
>
>We need the help of honest and reliable home workers like you.  
>Because we are overloaded with work and have more than our staff 
>can handle. We have now expanded our mailing program and are 
>expecting to reach millions more with our offers throughout the 
>US and Canada.
>
>Our system of stuffing and mailing envelopes is very simple and 
>easy to do!
>You will not be required to buy envelopes or postage stamps.
>
>We will gladly furnish all circulars at no cost to you. We assure 
>you that as a participant in our program you will never have to 
>mail anything objective or offensive. 
>
>There are no quotas to meet, and there no contracts to sign. You 
>can work as much, or as little as you want. Payment for each 
>envelope you send out is Guaranteed!
>
>Here is what you will receive when you get your first Package.  
>Inside you will find 100 envelopes, 100 labels and 100 sales 
>letters ready to stuff and mail
>
>As soon as you are done with stuffing and mailing these first 
>letters, your payment will arrive shortly, thereafter. All you 
>have to do is to order more free supplies and stuff and mail more 
>envelopes to make more money.
>
>Our sales literature which you will be stuffing and mailing will 
>contain
>information outlining our highly informative manuals that we are
>advertising nationwide.  As a free gift you will receive a 
>special manual valued at  $24.95, absolutely free, just for 
>joining our Home Mailers Program.
>
>Plus you will get your own special code number, so that we will 
>know how much you are to get paid.  And to make re-ordering of 
>more envelopes, that our company supplies very simple for you.
>
>We are giving you this free bonus because we want you to be 
>confident in our company and to ensure that we will be doing 
>business with you for a long time.
>
>Benefits Of This Job:
>
>1. You do not have to quit your present job, to earn more money 
>at home
>2. You can make between $2,500 to $4,500 a month depending on the 
>amount of time you are willing to spend stuffing and mailing 
>envelopes
>3. This is a great opportunity for the students, mothers, 
>disabled persons or those who are home bodies.
>
>To secure your position and to show us that you are serious about 
>earning extra income at home we require a one-time registration 
>fee of $35.00.
>This fee covers the cost of your initial start up package,  which 
>includes 100 envelopes, 100 labels and 100 sales letters and a 
>manual, your registration fee will be refunded back to you 
>shortly thereafter.
>
>Money Back Guarantee!
>
>We guarantee that as soon as you stuff and mail your first 300 
>envelopes You will be paid $75.00 and your registration fee will 
>be refunded.
>
>Many of you wonder why it is necessary to pay a deposit to get a 
>job. It is because we are looking for people that seriously want 
>to work from home.  
>
>*  If 3.000 people told us they wanted to start working from home 
>and we sent out 3.000 packages free to every one.  And then half 
>of the people decided not to work, this would be a potential loss 
>of more than $60,000 in supply's and shipping that we have sent 
>out to people that don't want to work
>
>We have instituted this policy to make sure that you really want 
>to work and at least finish your first package.
>
>To Get Started Today Please Enclose Your Registration Fee of $35
>Check,Cash Or Money Order and fill out the application below and 
>mail to:
>
>AHWA CO
>425 S Fairfax Blvd., STE 306
>Los Angeles, CA 90036
>
>Name_____________________________________________________
>
>Address___________________________________________________
>
>City____________________________________ State______________
>
>Zip Code________________
>
>Telephone Number(s)_________________________________________
>
>E-mail Address______________________________________________
>
>
>
>For all orders, please allow seven (7) days for delivery and up 
>to 10 days. Cash and Money Orders will result in faster shipping 
>of your package.
> 
> 
> 
> 
> 
> 
> 
> 
>
>

--------------------------------------------
William J. Clerici, Ph.D.
Associate Professor
Rm. C-236, Department of Surgery
Division of Otolaryngology-HNS
University of Kentucky Chandler Medical Center
800 Rose Street
Lexington, KY 40536-0084
           ------------------
Telephone: (606) 257-5097
      (lab): (606) 257-6020
      FAX: (606) 257-5096
      e-mail: bcler1@pop.uky.edu
--------------------------------------------


From nih-image-request@io.ece.drexel.edu Mon Jun  7 13:44 EDT 1999
Received: (from lists@localhost)
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	for cshtest@io.ece.drexel.edu; Mon, 7 Jun 1999 13:44:10 -0400 (EDT)
Resent-Date: Mon, 7 Jun 1999 13:44:10 -0400 (EDT)
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Date: Mon, 07 Jun 1999 10:30:54 -0700
From: George Harvey <gwil@postoffice.worldnet.att.net>
Reply-To: gwil@worldnet.att.net
Organization: C. Yeung Consulting
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nih-image-d-request@io.ece.drexel.edu wrote:
> 
> Subject:
> 
> nih-image-d Digest                              Volume 99 : Issue 128
> 
> Today's Topics:
>   Homeworkers Needed!                   [ toukol@mindspring.com ]
> 
>   ------------------------------------------------------------------------
> 
> Subject: Homeworkers Needed!
> Date: Sun, 6 Jun 1999 03:12:51
> From: toukol@mindspring.com
> To: nih-image@io.ece.drexel.edu
> 
> Dear Future Associate,
> 
> You Can Work At Home & Set Your Own Hours.  Start earning Big
> Money in a short time
> 
>                                     NO Newspaper Advertising!
> 
> Your job will be to stuff and mail envelopes for our company. You
> will receive $.25 for each and every envelope you stuff and mail
> out.
> 
> Just follow our simple instructions and you will be making money
> as easy as
> 1 2 3
> 
> For example stuff and mail 200 envelopes and you will receive
> $50.00. Stuff and mail 1000 and you will receive $250.00. Stuff
> and mail 2000 and you will receive $500.00 and more
> 
> Never before has there been an easier way to make money from
> home!
> 
> Our Company's Home Mailing Program is designed for people with
> little or no experience and provides simple, step by step
> instructions.
> 
> There is no prior experience or special skills necessary on your
> part, Just stuffing envelopes.
> 
> We need the help of honest and reliable home workers like you.
> Because we are overloaded with work and have more than our staff
> can handle. We have now expanded our mailing program and are
> expecting to reach millions more with our offers throughout the
> US and Canada.
> 
> Our system of stuffing and mailing envelopes is very simple and
> easy to do!
> You will not be required to buy envelopes or postage stamps.
> 
> We will gladly furnish all circulars at no cost to you. We assure
> you that as a participant in our program you will never have to
> mail anything objective or offensive.
> 
> There are no quotas to meet, and there no contracts to sign. You
> can work as much, or as little as you want. Payment for each
> envelope you send out is Guaranteed!
> 
> Here is what you will receive when you get your first Package.
> Inside you will find 100 envelopes, 100 labels and 100 sales
> letters ready to stuff and mail
> 
> As soon as you are done with stuffing and mailing these first
> letters, your payment will arrive shortly, thereafter. All you
> have to do is to order more free supplies and stuff and mail more
> envelopes to make more money.
> 
> Our sales literature which you will be stuffing and mailing will
> contain
> information outlining our highly informative manuals that we are
> advertising nationwide.  As a free gift you will receive a
> special manual valued at  $24.95, absolutely free, just for
> joining our Home Mailers Program.
> 
> Plus you will get your own special code number, so that we will
> know how much you are to get paid.  And to make re-ordering of
> more envelopes, that our company supplies very simple for you.
> 
> We are giving you this free bonus because we want you to be
> confident in our company and to ensure that we will be doing
> business with you for a long time.
> 
> Benefits Of This Job:
> 
> 1. You do not have to quit your present job, to earn more money
> at home
> 2. You can make between $2,500 to $4,500 a month depending on the
> amount of time you are willing to spend stuffing and mailing
> envelopes
> 3. This is a great opportunity for the students, mothers,
> disabled persons or those who are home bodies.
> 
> To secure your position and to show us that you are serious about
> earning extra income at home we require a one-time registration
> fee of $35.00.
> This fee covers the cost of your initial start up package,  which
> includes 100 envelopes, 100 labels and 100 sales letters and a
> manual, your registration fee will be refunded back to you
> shortly thereafter.
> 
> Money Back Guarantee!
> 
> We guarantee that as soon as you stuff and mail your first 300
> envelopes You will be paid $75.00 and your registration fee will
> be refunded.
> 
> Many of you wonder why it is necessary to pay a deposit to get a
> job. It is because we are looking for people that seriously want
> to work from home.
> 
> *  If 3.000 people told us they wanted to start working from home
> and we sent out 3.000 packages free to every one.  And then half
> of the people decided not to work, this would be a potential loss
> of more than $60,000 in supply's and shipping that we have sent
> out to people that don't want to work
> 
> We have instituted this policy to make sure that you really want
> to work and at least finish your first package.
> 
> To Get Started Today Please Enclose Your Registration Fee of $35
> Check,Cash Or Money Order and fill out the application below and
> mail to:
> 
> AHWA CO
> 425 S Fairfax Blvd., STE 306
> Los Angeles, CA 90036
> 
> Name_____________________________________________________
> 
> Address___________________________________________________
> 
> City____________________________________ State______________
> 
> Zip Code________________
> 
> Telephone Number(s)_________________________________________
> 
> E-mail Address______________________________________________
> 
> For all orders, please allow seven (7) days for delivery and up
> to 10 days. Cash and Money Orders will result in faster shipping
> of your package.
> 
> 
> 
> 
> 
> 
> 
>


From nih-image-request@io.ece.drexel.edu Mon Jun  7 17:26 EDT 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA26510
	for cshtest@io.ece.drexel.edu; Mon, 7 Jun 1999 17:26:52 -0400 (EDT)
Resent-Date: Mon, 7 Jun 1999 17:26:52 -0400 (EDT)
Date: Mon, 7 Jun 1999 17:15:29 -0400 (EDT)
From: Glenn C Yiu <gcy3@columbia.edu>
Sender: gcy3@columbia.edu
To: nih-image@io.ece.drexel.edu
Subject: Quantitating GFP expression
In-Reply-To: <199906071016.GAA27290@io.ece.drexel.edu>
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Dear all,

Our molecular & cellular neurobiology lab in Rockefeller U. is trying to
study the effects of synapsin phosphorylation on morphology of neurons.
Is there an objective quantitative method in NIH-Image that can
differentiate between images of neurons that are GFP-positive and those
that are not?  Can something be implemented in the form of a macro to run
through a large number of images of neurons and differentiate between
GFP-positive and GFP-negative neurons?  Any help would be greatly
appreciated.

Thanks,
Glenn Yiu
Greengard Lab '99


From nih-image-request@io.ece.drexel.edu Tue Jun  8 05:22 EDT 1999
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Date: Tue, 8 Jun 1999 10:53:16 +0200 (MET DST)
Message-Id: <l03020903b382a7b5dbde@[193.145.218.132]>
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
From: Enric Saiz <enric@icm.csic.es>
Subject: 3-D tracks
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Dear colleagues,

I will appreciate very much any information you can provide me in order to
solve the following question.

I plan to film 3-D tracks of the swimming paths of little planktonic
crustaceans (copepods) confined in experimental aquaria. The purpose is to
obtain the 3-D coordinates of these bugs over a certain period of time
(let's say 5 min tracks). The temporal resolution of the data does not have
to be very high, 5 frames per second would be good enough.

My idea is to have 2 orthogonal B&W cameras and combine somehow both 2-D
pictures, so that I can identify the bug and then obtain x-y-z coordinates.

One possibility is to use a video screen splitter, so that I combine the
image of both cameras in one single monitor, having, per instance, half
screen allocated to each camera. Then I can record on tape, digitize with
any frame grabber (for instance the Mac AV-built frame grabber) and make
short movies with NIH Image. The problem with this possibility is that I
loose half the picture of each camera, what limits quite a lot my field of
view and consequently the length of the swimming path I try to track.

I have heard that one possibility would be to enter the signals of both B&W
cameras through a RGB card, so that in one single picture I would have both
full screen pictures of both cameras, in two different colors.

My question is:

Is this feasible? How can I do it? What hardware and/or software do I need?
Can I combine both pictures on tape with a VCR and then digitize sections
of the tape with my AV-built frame grabber?

Thanks for reading this.

Enric Saiz





******************************
Enric Saiz
Institut de Cincies del Mar, CSIC
Plaa del Mar s/n
08039 Barcelona
Catalonia, SPAIN

PLEASE NOTE NEW PHONE NUMBERS!!!

Phone: +34+93+2216416
Fax: +34+93+2217340

Visit our Web Page
http://www.icm.csic.es/bio/index_bio.html
******************************



From nih-image-d-request@io.ece.drexel.edu Tue Jun  8 05:26 EDT 1999
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Date: Tue, 8 Jun 1999 05:26:44 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199906080926.FAA27596@io.ece.drexel.edu>
Subject: nih-image-d Digest V99 #129
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 129

Today's Topics:
  RE:Homeworkers Needed!                [ tea@neuro.duke.edu (Cerkvenik, Tea) ]
  Re: Homeworkers Needed!               [ "Bill Clerici, Ph.D." <bcler1@pop.u ]
  Re: nih-image-d Digest V99 #128       [ George Harvey <gwil@postoffice.worl ]
  Quantitating GFP expression           [ Glenn C Yiu <gcy3@columbia.edu> ]
  3-D tracks                            [ Enric Saiz <enric@icm.csic.es> ]

------------------------------

Date: Mon, 7 Jun 1999 09:03:04 -0000
From: tea@neuro.duke.edu (Cerkvenik, Tea)
To: "nih-image@io.ece.drexel.edu" <nih-image@io.ece.drexel.edu>
Subject: RE:Homeworkers Needed!
Message-ID: <01BEB0C4.8DE471F0.tea@neuro.duke.edu>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

FYI, several weeks ago, a message similar to this one was sent from the 
same email account (toukol@mindspring.com) and has been reported as a SCAM 
on American Home Workers Web Site and AOL.

Tea C.

-----Original Message-----
From:	toukol@mindspring.com [SMTP:toukol@mindspring.com]
Sent:	Sunday, June 06, 1999 3:13 AM
To:	nih-image@io.ece.drexel.edu
Subject:	Homeworkers Needed!

Dear Future Associate,

You Can Work At Home & Set Your Own Hours.  Start earning Big
Money in a short time

                                    NO Newspaper Advertising!

Your job will be to stuff and mail envelopes for our company. You
will receive $.25 for each and every envelope you stuff and mail
out.

Just follow our simple instructions and you will be making money
as easy as
1? 2? 3

For example stuff and mail 200 envelopes and you will receive
$50.00. Stuff and mail 1000 and you will receive $250.00. Stuff
and mail 2000 and you will receive $500.00 and more

Never before has there been an easier way to make money from
home!

Our Company's Home Mailing Program is designed for people with
little or no experience and provides simple, step by step
instructions.

There is no prior experience or special skills necessary on your
part, Just stuffing envelopes.

We need the help of honest and reliable home workers like you.
Because we are overloaded with work and have more than our staff
can handle. We have now expanded our mailing program and are
expecting to reach millions more with our offers throughout the
US and Canada.

Our system of stuffing and mailing envelopes is very simple and
easy to do!
You will not be required to buy envelopes or postage stamps.

We will gladly furnish all circulars at no cost to you. We assure
you that as a participant in our program you will never have to
mail anything objective or offensive.

There are no quotas to meet, and there no contracts to sign. You
can work as much, or as little as you want. Payment for each
envelope you send out is Guaranteed!

Here is what you will receive when you get your first Package.
Inside you will find 100 envelopes, 100 labels and 100 sales
letters ready to stuff and mail

As soon as you are done with stuffing and mailing these first
letters, your payment will arrive shortly, thereafter. All you
have to do is to order more free supplies and stuff and mail more
envelopes to make more money.

Our sales literature which you will be stuffing and mailing will
contain
information outlining our highly informative manuals that we are
advertising nationwide.  As a free gift you will receive a
special manual valued at  $24.95, absolutely free, just for
joining our Home Mailers Program.

Plus you will get your own special code number, so that we will
know how much you are to get paid.  And to make re-ordering of
more envelopes, that our company supplies very simple for you.

We are giving you this free bonus because we want you to be
confident in our company and to ensure that we will be doing
business with you for a long time.

Benefits Of This Job:

1. You do not have to quit your present job, to earn more money
at home
2. You can make between $2,500 to $4,500 a month depending on the
amount of time you are willing to spend stuffing and mailing
envelopes
3. This is a great opportunity for the students, mothers,
disabled persons or those who are home bodies.

To secure your position and to show us that you are serious about
earning extra income at home we require a one-time registration
fee of $35.00.
This fee covers the cost of your initial start up package,  which
includes 100 envelopes, 100 labels and 100 sales letters and a
manual, your registration fee will be refunded back to you
shortly thereafter.

Money Back Guarantee!

We guarantee that as soon as you stuff and mail your first 300
envelopes You will be paid $75.00 and your registration fee will
be refunded.

Many of you wonder why it is necessary to pay a deposit to get a
job. It is because we are looking for people that seriously want
to work from home.

*  If 3.000 people told us they wanted to start working from home
and we sent out 3.000 packages free to every one.  And then half
of the people decided not to work, this would be a potential loss
of more than $60,000 in supply's and shipping that we have sent
out to people that don't want to work

We have instituted this policy to make sure that you really want
to work and at least finish your first package.

To Get Started Today Please Enclose Your Registration Fee of $35
Check,Cash Or Money Order and fill out the application below and
mail to:

AHWA CO
425 S Fairfax Blvd., STE 306
Los Angeles, CA 90036

Name_____________________________________________________

Address___________________________________________________

City____________________________________ State______________

Zip Code________________

Telephone Number(s)_________________________________________

E-mail Address______________________________________________



For all orders, please allow seven (7) days for delivery and up
to 10 days. Cash and Money Orders will result in faster shipping
of your package.

------------------------------

Date: Mon, 07 Jun 1999 10:34:12 -0400
From: "Bill Clerici, Ph.D." <bcler1@pop.uky.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Homeworkers Needed!
Message-Id: <3.0.5.32.19990607103412.00843520@pop.uky.edu>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Please do not send me any more of your disgusting, unethical tripe. For
taking advantage of people who do not know better, I hope that you are
caught, sent to prison and made the Lucky Pierre provider for your cell
block. Hopefully, your greed will make you susceptible to the same form of
scam that you are perpetrating, and, you will lose even more than you steal.






At 03:12 AM 6/6/99, you wrote:
>Dear Future Associate,
>
>You Can Work At Home & Set Your Own Hours.  Start earning Big 
>Money in a short time
>       
>                                    NO Newspaper Advertising!
>
>Your job will be to stuff and mail envelopes for our company. You 
>will receive $.25 for each and every envelope you stuff and mail 
>out.
>
>Just follow our simple instructions and you will be making money 
>as easy as
>1 2 3
>
>For example stuff and mail 200 envelopes and you will receive 
>$50.00. Stuff and mail 1000 and you will receive $250.00. Stuff 
>and mail 2000 and you will receive $500.00 and more 
>
>Never before has there been an easier way to make money from 
>home!
>
>Our Company's Home Mailing Program is designed for people with 
>little or no experience and provides simple, step by step 
>instructions.  
>
>There is no prior experience or special skills necessary on your 
>part, Just stuffing envelopes.
>
>We need the help of honest and reliable home workers like you.  
>Because we are overloaded with work and have more than our staff 
>can handle. We have now expanded our mailing program and are 
>expecting to reach millions more with our offers throughout the 
>US and Canada.
>
>Our system of stuffing and mailing envelopes is very simple and 
>easy to do!
>You will not be required to buy envelopes or postage stamps.
>
>We will gladly furnish all circulars at no cost to you. We assure 
>you that as a participant in our program you will never have to 
>mail anything objective or offensive. 
>
>There are no quotas to meet, and there no contracts to sign. You 
>can work as much, or as little as you want. Payment for each 
>envelope you send out is Guaranteed!
>
>Here is what you will receive when you get your first Package.  
>Inside you will find 100 envelopes, 100 labels and 100 sales 
>letters ready to stuff and mail
>
>As soon as you are done with stuffing and mailing these first 
>letters, your payment will arrive shortly, thereafter. All you 
>have to do is to order more free supplies and stuff and mail more 
>envelopes to make more money.
>
>Our sales literature which you will be stuffing and mailing will 
>contain
>information outlining our highly informative manuals that we are
>advertising nationwide.  As a free gift you will receive a 
>special manual valued at  $24.95, absolutely free, just for 
>joining our Home Mailers Program.
>
>Plus you will get your own special code number, so that we will 
>know how much you are to get paid.  And to make re-ordering of 
>more envelopes, that our company supplies very simple for you.
>
>We are giving you this free bonus because we want you to be 
>confident in our company and to ensure that we will be doing 
>business with you for a long time.
>
>Benefits Of This Job:
>
>1. You do not have to quit your present job, to earn more money 
>at home
>2. You can make between $2,500 to $4,500 a month depending on the 
>amount of time you are willing to spend stuffing and mailing 
>envelopes
>3. This is a great opportunity for the students, mothers, 
>disabled persons or those who are home bodies.
>
>To secure your position and to show us that you are serious about 
>earning extra income at home we require a one-time registration 
>fee of $35.00.
>This fee covers the cost of your initial start up package,  which 
>includes 100 envelopes, 100 labels and 100 sales letters and a 
>manual, your registration fee will be refunded back to you 
>shortly thereafter.
>
>Money Back Guarantee!
>
>We guarantee that as soon as you stuff and mail your first 300 
>envelopes You will be paid $75.00 and your registration fee will 
>be refunded.
>
>Many of you wonder why it is necessary to pay a deposit to get a 
>job. It is because we are looking for people that seriously want 
>to work from home.  
>
>*  If 3.000 people told us they wanted to start working from home 
>and we sent out 3.000 packages free to every one.  And then half 
>of the people decided not to work, this would be a potential loss 
>of more than $60,000 in supply's and shipping that we have sent 
>out to people that don't want to work
>
>We have instituted this policy to make sure that you really want 
>to work and at least finish your first package.
>
>To Get Started Today Please Enclose Your Registration Fee of $35
>Check,Cash Or Money Order and fill out the application below and 
>mail to:
>
>AHWA CO
>425 S Fairfax Blvd., STE 306
>Los Angeles, CA 90036
>
>Name_____________________________________________________
>
>Address___________________________________________________
>
>City____________________________________ State______________
>
>Zip Code________________
>
>Telephone Number(s)_________________________________________
>
>E-mail Address______________________________________________
>
>
>
>For all orders, please allow seven (7) days for delivery and up 
>to 10 days. Cash and Money Orders will result in faster shipping 
>of your package.
> 
> 
> 
> 
> 
> 
> 
> 
>
>

--------------------------------------------
William J. Clerici, Ph.D.
Associate Professor
Rm. C-236, Department of Surgery
Division of Otolaryngology-HNS
University of Kentucky Chandler Medical Center
800 Rose Street
Lexington, KY 40536-0084
           ------------------
Telephone: (606) 257-5097
      (lab): (606) 257-6020
      FAX: (606) 257-5096
      e-mail: bcler1@pop.uky.edu
--------------------------------------------

------------------------------

Date: Mon, 07 Jun 1999 10:30:54 -0700
From: George Harvey <gwil@postoffice.worldnet.att.net>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #128
Message-ID: <375C01CD.5D57B2@postoffice.worldnet.att.net>
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

nih-image-d-request@io.ece.drexel.edu wrote:
> 
> Subject:
> 
> nih-image-d Digest                              Volume 99 : Issue 128
> 
> Today's Topics:
>   Homeworkers Needed!                   [ toukol@mindspring.com ]
> 
>   ------------------------------------------------------------------------
> 
> Subject: Homeworkers Needed!
> Date: Sun, 6 Jun 1999 03:12:51
> From: toukol@mindspring.com
> To: nih-image@io.ece.drexel.edu
> 
> Dear Future Associate,
> 
> You Can Work At Home & Set Your Own Hours.  Start earning Big
> Money in a short time
> 
>                                     NO Newspaper Advertising!
> 
> Your job will be to stuff and mail envelopes for our company. You
> will receive $.25 for each and every envelope you stuff and mail
> out.
> 
> Just follow our simple instructions and you will be making money
> as easy as
> 1 2 3
> 
> For example stuff and mail 200 envelopes and you will receive
> $50.00. Stuff and mail 1000 and you will receive $250.00. Stuff
> and mail 2000 and you will receive $500.00 and more
> 
> Never before has there been an easier way to make money from
> home!
> 
> Our Company's Home Mailing Program is designed for people with
> little or no experience and provides simple, step by step
> instructions.
> 
> There is no prior experience or special skills necessary on your
> part, Just stuffing envelopes.
> 
> We need the help of honest and reliable home workers like you.
> Because we are overloaded with work and have more than our staff
> can handle. We have now expanded our mailing program and are
> expecting to reach millions more with our offers throughout the
> US and Canada.
> 
> Our system of stuffing and mailing envelopes is very simple and
> easy to do!
> You will not be required to buy envelopes or postage stamps.
> 
> We will gladly furnish all circulars at no cost to you. We assure
> you that as a participant in our program you will never have to
> mail anything objective or offensive.
> 
> There are no quotas to meet, and there no contracts to sign. You
> can work as much, or as little as you want. Payment for each
> envelope you send out is Guaranteed!
> 
> Here is what you will receive when you get your first Package.
> Inside you will find 100 envelopes, 100 labels and 100 sales
> letters ready to stuff and mail
> 
> As soon as you are done with stuffing and mailing these first
> letters, your payment will arrive shortly, thereafter. All you
> have to do is to order more free supplies and stuff and mail more
> envelopes to make more money.
> 
> Our sales literature which you will be stuffing and mailing will
> contain
> information outlining our highly informative manuals that we are
> advertising nationwide.  As a free gift you will receive a
> special manual valued at  $24.95, absolutely free, just for
> joining our Home Mailers Program.
> 
> Plus you will get your own special code number, so that we will
> know how much you are to get paid.  And to make re-ordering of
> more envelopes, that our company supplies very simple for you.
> 
> We are giving you this free bonus because we want you to be
> confident in our company and to ensure that we will be doing
> business with you for a long time.
> 
> Benefits Of This Job:
> 
> 1. You do not have to quit your present job, to earn more money
> at home
> 2. You can make between $2,500 to $4,500 a month depending on the
> amount of time you are willing to spend stuffing and mailing
> envelopes
> 3. This is a great opportunity for the students, mothers,
> disabled persons or those who are home bodies.
> 
> To secure your position and to show us that you are serious about
> earning extra income at home we require a one-time registration
> fee of $35.00.
> This fee covers the cost of your initial start up package,  which
> includes 100 envelopes, 100 labels and 100 sales letters and a
> manual, your registration fee will be refunded back to you
> shortly thereafter.
> 
> Money Back Guarantee!
> 
> We guarantee that as soon as you stuff and mail your first 300
> envelopes You will be paid $75.00 and your registration fee will
> be refunded.
> 
> Many of you wonder why it is necessary to pay a deposit to get a
> job. It is because we are looking for people that seriously want
> to work from home.
> 
> *  If 3.000 people told us they wanted to start working from home
> and we sent out 3.000 packages free to every one.  And then half
> of the people decided not to work, this would be a potential loss
> of more than $60,000 in supply's and shipping that we have sent
> out to people that don't want to work
> 
> We have instituted this policy to make sure that you really want
> to work and at least finish your first package.
> 
> To Get Started Today Please Enclose Your Registration Fee of $35
> Check,Cash Or Money Order and fill out the application below and
> mail to:
> 
> AHWA CO
> 425 S Fairfax Blvd., STE 306
> Los Angeles, CA 90036
> 
> Name_____________________________________________________
> 
> Address___________________________________________________
> 
> City____________________________________ State______________
> 
> Zip Code________________
> 
> Telephone Number(s)_________________________________________
> 
> E-mail Address______________________________________________
> 
> For all orders, please allow seven (7) days for delivery and up
> to 10 days. Cash and Money Orders will result in faster shipping
> of your package.
> 
> 
> 
> 
> 
> 
> 
>

------------------------------

Date: Mon, 7 Jun 1999 17:15:29 -0400 (EDT)
From: Glenn C Yiu <gcy3@columbia.edu>
To: nih-image@io.ece.drexel.edu
Subject: Quantitating GFP expression
Message-ID: <Pine.GSO.4.10.9906071709290.18766-100000@ciao.cc.columbia.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear all,

Our molecular & cellular neurobiology lab in Rockefeller U. is trying to
study the effects of synapsin phosphorylation on morphology of neurons.
Is there an objective quantitative method in NIH-Image that can
differentiate between images of neurons that are GFP-positive and those
that are not?  Can something be implemented in the form of a macro to run
through a large number of images of neurons and differentiate between
GFP-positive and GFP-negative neurons?  Any help would be greatly
appreciated.

Thanks,
Glenn Yiu
Greengard Lab '99

------------------------------

Date: Tue, 8 Jun 1999 10:53:16 +0200 (MET DST)
From: Enric Saiz <enric@icm.csic.es>
To: nih-image@io.ece.drexel.edu
Subject: 3-D tracks
Message-Id: <l03020903b382a7b5dbde@[193.145.218.132]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Dear colleagues,

I will appreciate very much any information you can provide me in order to
solve the following question.

I plan to film 3-D tracks of the swimming paths of little planktonic
crustaceans (copepods) confined in experimental aquaria. The purpose is to
obtain the 3-D coordinates of these bugs over a certain period of time
(let's say 5 min tracks). The temporal resolution of the data does not have
to be very high, 5 frames per second would be good enough.

My idea is to have 2 orthogonal B&W cameras and combine somehow both 2-D
pictures, so that I can identify the bug and then obtain x-y-z coordinates.

One possibility is to use a video screen splitter, so that I combine the
image of both cameras in one single monitor, having, per instance, half
screen allocated to each camera. Then I can record on tape, digitize with
any frame grabber (for instance the Mac AV-built frame grabber) and make
short movies with NIH Image. The problem with this possibility is that I
loose half the picture of each camera, what limits quite a lot my field of
view and consequently the length of the swimming path I try to track.

I have heard that one possibility would be to enter the signals of both B&W
cameras through a RGB card, so that in one single picture I would have both
full screen pictures of both cameras, in two different colors.

My question is:

Is this feasible? How can I do it? What hardware and/or software do I need?
Can I combine both pictures on tape with a VCR and then digitize sections
of the tape with my AV-built frame grabber?

Thanks for reading this.

Enric Saiz





******************************
Enric Saiz
Institut de Cincies del Mar, CSIC
Plaa del Mar s/n
08039 Barcelona
Catalonia, SPAIN

PLEASE NOTE NEW PHONE NUMBERS!!!

Phone: +34+93+2216416
Fax: +34+93+2217340

Visit our Web Page
http://www.icm.csic.es/bio/index_bio.html
******************************

--------------------------------
End of nih-image-d Digest V99 Issue #129
****************************************

From nih-image-request@io.ece.drexel.edu Tue Jun  8 12:20 EDT 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA03593
	for cshtest@io.ece.drexel.edu; Tue, 8 Jun 1999 12:20:27 -0400 (EDT)
Resent-Date: Tue, 8 Jun 1999 12:20:27 -0400 (EDT)
Message-ID: <8948DD9B2EDCD111B49500805FA783730223521A@1upmc-msx2.isdbu.upmc.edu>
From: "Harenski, Keith" <harenskik@msx.upmc.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Length Measurement
Date: Tue, 8 Jun 1999 11:56:33 -0400 
MIME-Version: 1.0
X-Mailer: Internet Mail Service (5.5.2448.0)
Resent-Message-ID: <"IB2LG3.0.BL.QrJNt"@io>
Resent-From: nih-image@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/1399
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 257

i was wondering if it was possible (eg. is there a macro available) to
objectively caculate the maximum width (length) of an irregular object.
additionally, i would like the program to draw a line connecting those two
points.  

thanks in advance... Keith


From nih-image-request@io.ece.drexel.edu Tue Jun  8 17:51 EDT 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA06605
	for cshtest@io.ece.drexel.edu; Tue, 8 Jun 1999 17:51:45 -0400 (EDT)
Resent-Date: Tue, 8 Jun 1999 17:51:45 -0400 (EDT)
Message-Id: <l03130300b3833ba3db80@[131.215.5.35]>
Mime-Version: 1.0
Date: Tue, 8 Jun 1999 14:40:42 -0700
To: nih-image@io.ece.drexel.edu
From: Steve Potter <spotter@gg.caltech.edu>
Subject: How to Average Frames,Pixera
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We are considering getting the Pixera Pro camera. There seems to
be conflicting info in the archive about the compatibility of this
camera with NIH Image.  Specifically, I would like to hear from
anyone who has been able to average frames acquired from the Pixera Pro
(not the 120es, which has its own software for doing that). Or if
you tried and failed, let me know.  Pixera says the TWAIN-compliant
Photoshop plugin ought to be compatible with NIH Image.  Is it?
If not, has anyone created a Photoshop 'action' that averages frames?
I would like to hear from anyone who has imaged fluorescence with this
camera, successes only.

As I have posted here in the past (see tutorial below), the improvement one
can get with dim fluorescence by properly setting Min and Max in the
Average Frames dialog is quite remarkable.  Cheap CCDs (not cooled) have
too much dark noise to average light on-chip, so averaging frames is the
way to go.  As far as I know, the macro I asked for in 1996 still has
not been written, has it? email me: spotter@gg.caltech.edu

Here is my tutorial on Frame Averaging, dug out of the NIH Image Archives
from 1996, and just as useful today:


Subject: How to improve contrast

Hi Imagers,
We all want to increase image quality and contrast, right? Using the
"Average Frames" utility (in Special menu) to reduce noise is
straightforward--just specify how many frames you want to average, and
click OK. Improving contrast is a little trickier, and I will describe how
below. If you already know how, and do not plan on reading the rest, one
question: Is there a macro that does all this automatically? Please email
me if so: spotter@gg.caltech.edu

I have figured out how to use the "Average Frames" utility to stretch the
max and min values of an image to 0 and 255. Why do this? In my case, I may
have a dim fluorescent neuron that, in a single frame, has grey values
ranging from 233-255. I can hardly see anything. If one just uses "Enhance
Contrast" on a such a single 8-bit image, the histogram is full of gaps.
This can cause lots of posterizing, and yucky stuff when you try to filter
the image. The "Average Frames" utility fixes this problem nicely, by
summing up to 128 frames into a 16-bit number. The v1.60 manual has this
arcane advice for us: "Check Integrate to sum the frames, rather than
averaging them. Integration increases image quality and contrast in low
light situations. Frames are summed using a 16-bit buffer and the resulting
16-bit pixel values are linearly scaled to a range of 0 to 255. . If Fix
Scale is checked, the values in Min and Max control how integrated images
are linearly scaled from 16-bits to 8-bits. If it is not checked, the
computed minimum and maximum values are used. The actual minimum and
maximum values are always displayed in the Info window." Great, what do you
do now? After lots of trial and error, I figured out what. Take a single
test image. Use Show Histogram to find out what the minimum and maximum
values are--as you slide the mouse left and right, watch the counts in the
Info window. In my case, I see nothing but zeros until I get to 233.
Alternatively, you can point to parts of the image that you think are the
dimmest and the brightest, and note the Values in the Info window. Select
the Integrate and Fix Scale boxes in the Average Frames window. Now set
Min, in the Average Frames window to _the product_ of the brightest pixel
value and the Number of Frames. (Because 0 is white, 255 is black). Set Max
to _the product_ of the darkest pixel value and Number of Frames. For
example for my dim neuron, if I want to average 10 frames, I set Min to
2330 and Max to 2550. Click OK, and watch the Info window to see frame
counter going while the computer adds up the grabbed images. Then it does
the math, converts it back to 8 bits, and the result is a nice bright
contrasty neuron, with a smooth, gap-free histogram! The manual says:
"Check Calibrate to set up a calibration function so that approximations of
the 16-bit values are displayed in the Info and Results windows." If you
had checked the Calibrate box, nothing extra happens except the actual Max
and Min values appear in the Info window, after the integrating process is
over. You may want to try again by typing those numbers into the Max and
Min boxes. Or you may not: You might rather choose to 'zoom in' on a
portion of the histogram, maxing out all pixels brighter or dimmer, to
highlight a set of greyscales. For example, suppose I had a fleck of
brightly stained debris next to my dim neuron. And suppose that the dimmest
parts of the dim neuron are actually somewhat brighter than the background.
Say, the debris is a value of 27, the neuron is from 210 to 236, and the
background is from 245-255. Then to enhance the contrast of just the
neuron, I would integrate 10 frames, and set Max and Min to 2360 and 2100,
respectively. The more frames you integrate, the smoother the histogram
will be. Very nice.

 Now, if someone would just write a macro that takes the max and min values
of a region of interest and uses them to set the Fix Scale parameters for
the desired Number of Frames--making the whole process automatic, I would
be delighted!

Thanks, Steve
spotter@gg.caltech.edu

_______________________________________________________________________________

Steve Potter, Doctor of Philosophy          | "Too much self-love can make
Senior Research Fellow                      | you jealous of the people
156-29 Division of Biology                  | who envy you."
California Institute of Technology          |
Pasadena, CA 91125                          |              -Unknown
spotter@gg.caltech.edu                      |
http://www.caltech.edu/~pinelab/steve.html  |



From nih-image-request@io.ece.drexel.edu Tue Jun  8 19:23 EDT 1999
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We are investigating cerebral microvasculature and require a method to
compare shape of vessel profiles.  Exploring the possibilities of Fourier
descriptors has been thwarted by repeated computer crashes when we attempt
to open ImageFFt128b6.hqx.  Can anyone suggest how we might be able to do
this?

________________________________________________________________________________
Patricia Waley
Centre for Education and Research on Ageing
Concord Hospital
Concord NSW 2139
Ph: (02) 9767 6586
Fax: (02) 9767 8315
Email: patw@pathology.usyd.edu.au
________________________________________________________________________________



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From: DrJohnRuss@aol.com
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In a message dated 6/8/99 7:18:11 PM, patw@med.usyd.edu.au writes:

>We are investigating cerebral microvasculature and require a method to
>compare shape of vessel profiles.  Exploring the possibilities of Fourier
>descriptors has been thwarted by repeated computer crashes when we attempt
>to open ImageFFt128b6.hqx.  Can anyone suggest how we might be able to
>do this?

There really is no reason to try to use the older program, as the current 
versions of the standard NIH-Image written for the PPC include all of the 
same Fourier processing capabilities. However, neither of these does what you 
want. They perform an 2D FFT on the entire grey scale image, whereas what I 
believe you are talking about is to use harmonic analysis on the shape of the 
vessels. NIH-Image doesn't provide that capability. There are a few programs 
that do (much more expensive) and I've been experimenting with a variant of 
the technique that may become part of the Image Processing Tool Kit in some 
future release. Your best bet at the moment is probably to use Image to write 
out a file of the coordinates of the boundary of the vessel and perform the 
harmonic analysis off-line.

John Russ


From nih-image-d-request@io.ece.drexel.edu Wed Jun  9 06:11 EDT 1999
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Subject: nih-image-d Digest V99 #130
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 130

Today's Topics:
  Length Measurement                    [ "Harenski, Keith" <harenskik@msx.up ]
  How to Average Frames,Pixera          [ Steve Potter <spotter@gg.caltech.ed ]
  Re: Fourier Descriptors               [ Patricia Waley <patw@med.usyd.edu.a ]
  Re: Fourier Descriptors               [ DrJohnRuss@aol.com ]

------------------------------

Date: Tue, 8 Jun 1999 11:56:33 -0400 
From: "Harenski, Keith" <harenskik@msx.upmc.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Length Measurement
Message-ID: <8948DD9B2EDCD111B49500805FA783730223521A@1upmc-msx2.isdbu.upmc.edu>
Content-Type: text/plain

i was wondering if it was possible (eg. is there a macro available) to
objectively caculate the maximum width (length) of an irregular object.
additionally, i would like the program to draw a line connecting those two
points.  

thanks in advance... Keith

------------------------------

Date: Tue, 8 Jun 1999 14:40:42 -0700
From: Steve Potter <spotter@gg.caltech.edu>
To: nih-image@io.ece.drexel.edu
Subject: How to Average Frames,Pixera
Message-Id: <l03130300b3833ba3db80@[131.215.5.35]>
Content-Type: text/plain; charset="us-ascii"

We are considering getting the Pixera Pro camera. There seems to
be conflicting info in the archive about the compatibility of this
camera with NIH Image.  Specifically, I would like to hear from
anyone who has been able to average frames acquired from the Pixera Pro
(not the 120es, which has its own software for doing that). Or if
you tried and failed, let me know.  Pixera says the TWAIN-compliant
Photoshop plugin ought to be compatible with NIH Image.  Is it?
If not, has anyone created a Photoshop 'action' that averages frames?
I would like to hear from anyone who has imaged fluorescence with this
camera, successes only.

As I have posted here in the past (see tutorial below), the improvement one
can get with dim fluorescence by properly setting Min and Max in the
Average Frames dialog is quite remarkable.  Cheap CCDs (not cooled) have
too much dark noise to average light on-chip, so averaging frames is the
way to go.  As far as I know, the macro I asked for in 1996 still has
not been written, has it? email me: spotter@gg.caltech.edu

Here is my tutorial on Frame Averaging, dug out of the NIH Image Archives
from 1996, and just as useful today:


Subject: How to improve contrast

Hi Imagers,
We all want to increase image quality and contrast, right? Using the
"Average Frames" utility (in Special menu) to reduce noise is
straightforward--just specify how many frames you want to average, and
click OK. Improving contrast is a little trickier, and I will describe how
below. If you already know how, and do not plan on reading the rest, one
question: Is there a macro that does all this automatically? Please email
me if so: spotter@gg.caltech.edu

I have figured out how to use the "Average Frames" utility to stretch the
max and min values of an image to 0 and 255. Why do this? In my case, I may
have a dim fluorescent neuron that, in a single frame, has grey values
ranging from 233-255. I can hardly see anything. If one just uses "Enhance
Contrast" on a such a single 8-bit image, the histogram is full of gaps.
This can cause lots of posterizing, and yucky stuff when you try to filter
the image. The "Average Frames" utility fixes this problem nicely, by
summing up to 128 frames into a 16-bit number. The v1.60 manual has this
arcane advice for us: "Check Integrate to sum the frames, rather than
averaging them. Integration increases image quality and contrast in low
light situations. Frames are summed using a 16-bit buffer and the resulting
16-bit pixel values are linearly scaled to a range of 0 to 255. . If Fix
Scale is checked, the values in Min and Max control how integrated images
are linearly scaled from 16-bits to 8-bits. If it is not checked, the
computed minimum and maximum values are used. The actual minimum and
maximum values are always displayed in the Info window." Great, what do you
do now? After lots of trial and error, I figured out what. Take a single
test image. Use Show Histogram to find out what the minimum and maximum
values are--as you slide the mouse left and right, watch the counts in the
Info window. In my case, I see nothing but zeros until I get to 233.
Alternatively, you can point to parts of the image that you think are the
dimmest and the brightest, and note the Values in the Info window. Select
the Integrate and Fix Scale boxes in the Average Frames window. Now set
Min, in the Average Frames window to _the product_ of the brightest pixel
value and the Number of Frames. (Because 0 is white, 255 is black). Set Max
to _the product_ of the darkest pixel value and Number of Frames. For
example for my dim neuron, if I want to average 10 frames, I set Min to
2330 and Max to 2550. Click OK, and watch the Info window to see frame
counter going while the computer adds up the grabbed images. Then it does
the math, converts it back to 8 bits, and the result is a nice bright
contrasty neuron, with a smooth, gap-free histogram! The manual says:
"Check Calibrate to set up a calibration function so that approximations of
the 16-bit values are displayed in the Info and Results windows." If you
had checked the Calibrate box, nothing extra happens except the actual Max
and Min values appear in the Info window, after the integrating process is
over. You may want to try again by typing those numbers into the Max and
Min boxes. Or you may not: You might rather choose to 'zoom in' on a
portion of the histogram, maxing out all pixels brighter or dimmer, to
highlight a set of greyscales. For example, suppose I had a fleck of
brightly stained debris next to my dim neuron. And suppose that the dimmest
parts of the dim neuron are actually somewhat brighter than the background.
Say, the debris is a value of 27, the neuron is from 210 to 236, and the
background is from 245-255. Then to enhance the contrast of just the
neuron, I would integrate 10 frames, and set Max and Min to 2360 and 2100,
respectively. The more frames you integrate, the smoother the histogram
will be. Very nice.

 Now, if someone would just write a macro that takes the max and min values
of a region of interest and uses them to set the Fix Scale parameters for
the desired Number of Frames--making the whole process automatic, I would
be delighted!

Thanks, Steve
spotter@gg.caltech.edu

_______________________________________________________________________________

Steve Potter, Doctor of Philosophy          | "Too much self-love can make
Senior Research Fellow                      | you jealous of the people
156-29 Division of Biology                  | who envy you."
California Institute of Technology          |
Pasadena, CA 91125                          |              -Unknown
spotter@gg.caltech.edu                      |
http://www.caltech.edu/~pinelab/steve.html  |

------------------------------

Date: Wed, 9 Jun 1999 09:14:54 +1000
From: Patricia Waley <patw@med.usyd.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Re: Fourier Descriptors
Message-Id: <v03110700b3835177f40f@[152.76.71.133]>
Content-Type: text/plain; charset="us-ascii"

We are investigating cerebral microvasculature and require a method to
compare shape of vessel profiles.  Exploring the possibilities of Fourier
descriptors has been thwarted by repeated computer crashes when we attempt
to open ImageFFt128b6.hqx.  Can anyone suggest how we might be able to do
this?

________________________________________________________________________________
Patricia Waley
Centre for Education and Research on Ageing
Concord Hospital
Concord NSW 2139
Ph: (02) 9767 6586
Fax: (02) 9767 8315
Email: patw@pathology.usyd.edu.au
________________________________________________________________________________

------------------------------

Date: Tue, 8 Jun 1999 19:50:09 EDT
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re: Fourier Descriptors
Message-ID: <146b056e.248f0631@aol.com>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

In a message dated 6/8/99 7:18:11 PM, patw@med.usyd.edu.au writes:

>We are investigating cerebral microvasculature and require a method to
>compare shape of vessel profiles.  Exploring the possibilities of Fourier
>descriptors has been thwarted by repeated computer crashes when we attempt
>to open ImageFFt128b6.hqx.  Can anyone suggest how we might be able to
>do this?

There really is no reason to try to use the older program, as the current 
versions of the standard NIH-Image written for the PPC include all of the 
same Fourier processing capabilities. However, neither of these does what you 
want. They perform an 2D FFT on the entire grey scale image, whereas what I 
believe you are talking about is to use harmonic analysis on the shape of the 
vessels. NIH-Image doesn't provide that capability. There are a few programs 
that do (much more expensive) and I've been experimenting with a variant of 
the technique that may become part of the Image Processing Tool Kit in some 
future release. Your best bet at the moment is probably to use Image to write 
out a file of the coordinates of the boundary of the vessel and perform the 
harmonic analysis off-line.

John Russ

--------------------------------
End of nih-image-d Digest V99 Issue #130
****************************************

From nih-image-request@io.ece.drexel.edu Wed Jun  9 07:34 EDT 1999
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From: Dafna Shashua <dshashua@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: rotation and digitation
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Hello!
I am looking for two macros:
1. a macro that requests input of two landmarks, and then rotates the image
so the line between the landmark is horizontal
2. a macro that "requests" the  manual digitation of a set of landmarks,
and then plots the coordinates (and a set of calculated angles between
landmarks, if possible)
any ideas?
Thanks,
Dafna


_______________________________________________________________
Get Free Email and Do More On The Web. Visit http://www.msn.com


From nih-image-request@io.ece.drexel.edu Wed Jun  9 07:34 EDT 1999
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From: Dafna Shashua <dshashua@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: rotation and digitation
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Hello!
I am looking for two macros:
1. a macro that requests input of two landmarks, and then rotates the image
so the line between the landmark is horizontal
2. a macro that "requests" the  manual digitation of a set of landmarks,
and then plots the coordinates (and a set of calculated angles between
landmarks, if possible)
any ideas?
Thanks,
Dafna


_______________________________________________________________
Get Free Email and Do More On The Web. Visit http://www.msn.com


From nih-image-request@io.ece.drexel.edu Wed Jun  9 12:44 EDT 1999
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Subject: Re: How to Average Frames,Pixera
Date: Wed, 9 Jun 99 12:31:20 -0400
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please post response to all re  answer to Potter's amazingly 
understandable discourse on image enhancement.

also- how can i combine trapping say 10 frames (for averaging) every 
minute for perhaps an hour or two. i'm tracking cell movements - they are 
slow and single frames are just too noisy to get good resolution -and- i 
don't have the memory to trap and store contnuous video of a couple of 
hours. 
don't shoot me but i primarily use Adobe Premiere, not nih image.  i 
know- i'm an alien but have pity.

-dr. j. rifkin
biology dept
queens college
new york, ny 11367
jared_rifkin@qc.edu


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>From: Steve Potter <spotter@gg.caltech.edu>
>Subject: How to Average Frames,Pixera
>We are considering getting the Pixera Pro camera.

We have good results with the Cohu 2200 series for use in brightfield and
fluorescence.  It gives live video and integration capabilities within NIH
Image.  We also have written some macros to simplify the integration, and
these are included in Scion Image.

Although the Cohu 2200 only integrates FIELDS, we have found that the
quality of the image is quite good.  We have direct image comparisons of
Field and Frame capture.

The Cohu 2200 is available as PAL or NTSC formats.
Reply directly to me if you want to receive image comparisons.
Jeff Reidler, Scion Corporation
http://www.scioncorp.com



From nih-image-request@io.ece.drexel.edu Wed Jun  9 13:28 EDT 1999
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From: "Cengizhan Ozturk" <cozturk@mri.jhu.edu>
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Subject: Re: Length Measurement
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Keith,

There are routines (and a special compiled version of NIH-image) which
calculates the convex hull of a binary object. Once you have the convex hull
the problem is much simpler.

Cengizhan


-----Original Message-----
From: Harenski, Keith <harenskik@msx.upmc.edu>
To: 'nih-image@io.ece.drexel.edu' <nih-image@io.ece.drexel.edu>
Date: Tuesday, June 08, 1999 12:31 PM
Subject: Length Measurement


>i was wondering if it was possible (eg. is there a macro available) to
>objectively caculate the maximum width (length) of an irregular object.
>additionally, i would like the program to draw a line connecting those two
>points.
>
>thanks in advance... Keith
>
>


From nih-image-request@io.ece.drexel.edu Wed Jun  9 13:53 EDT 1999
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From: Steve Potter <spotter@gg.caltech.edu>
Message-Id: <199906091743.KAA09891@druggist.gg.caltech.edu>
Subject: Field vs. Frame avg
To: nih-image@io.ece.drexel.edu
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Jeff, please explain what the difference between fields and frames
are.  The only two kinds of integration I know about are
"on-chip", used only in cooled CCDs, where the pixels are not scanned for
a while, and the chip collects light for some amount of time,
usually seconds.  The other kind is frame averaging, where the
detector collects light for some short time (less than a second, often
1/30 of a second), reads the data into some memory (either in chips
in the camera, in the interface board, or in the RAM of the host computer),
and collects another frame, and does math on the digitized frames to
average them.  "Fields" I have only heard about with respect to old
analog video cameras that output two interlaced fields of scan lines
per frame.  What is going on in the Cohu, and what am I missing here?
Thanks,

Steve Potter
spotter@gg.caltech.edu


> 
> >From: Steve Potter <spotter@gg.caltech.edu>
> >Subject: How to Average Frames,Pixera
> >We are considering getting the Pixera Pro camera.
> 
> We have good results with the Cohu 2200 series for use in brightfield and
> fluorescence.  It gives live video and integration capabilities within NIH
> Image.  We also have written some macros to simplify the integration, and
> these are included in Scion Image.
> 
> Although the Cohu 2200 only integrates FIELDS, we have found that the
> quality of the image is quite good.  We have direct image comparisons of
> Field and Frame capture.
> 
> The Cohu 2200 is available as PAL or NTSC formats.
> Reply directly to me if you want to receive image comparisons.
> Jeff Reidler, Scion Corporation
> http://www.scioncorp.com
> 
> 
> 


From nih-image-request@io.ece.drexel.edu Wed Jun  9 20:34 EDT 1999
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I am interested in making volumetric measures using stacked MRI images. Is
there a way this can be done in NIH Image 1.62.  The archives listed several
similar requests but I was unable to find a response to them.
--
Mike Torry, Ph.D.
Steadman Hawkins Sports Medicine Foundation
181 West Meadow Drive, Suite 1000
Vail, CO  81657
Work:    (970) 479-5793
Fax:     (970) 479-9753
--


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______________________________________________
James Holman
Australian School of Environmental Studies
Griffith University, Nathan Campus
Queensland, Australia 4111

Home: 07 3511 6736
Griffith Uni.: 07 3875 7483
Qld. Herbarium:  07 3896 9547

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From nih-image-request@io.ece.drexel.edu Thu Jun 10 02:51 EDT 1999
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From: Edgar Rivedal <edgar.rivedal@labmed.uio.no>
Subject: TIFF Mac/PC
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I use both Mac and PC to work on grey level tif files. When saving tif
files the question of Byte order, Mac or IBM PC, comes up. Is there more to
this then the attachment of .tif to the file name, and is there something
to be aware of with regard to preserving quality of the images when working
on the same tif files in both platforms? 

The print out is in our hands generally better when coming from the same
file and program (i.e.Photoshop or Image)on a Mac than on a PC. This seems
to be the case for both colour and grey tone printouts, from laser, dye
sublimation and ink jet. Is this something one just has to accept as a
fact, or is it a matter of adjustment and drivers?


Edgar 


_____________________________________

Edgar Rivedal (edgarr@labmed.uio.no)
Institute for Cancer Research     
Oslo, Norway 
_____________________________________


From nih-image-d-request@io.ece.drexel.edu Thu Jun 10 02:55 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #131
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 131

Today's Topics:
  rotation and digitation               [ Dafna Shashua <dshashua@hotmail.com ]
  rotation and digitation               [ Dafna Shashua <dshashua@hotmail.com ]
  Re: How to Average Frames,Pixera      [ jared rifkin <jared_rifkin@qc.edu> ]
  Re: nih-image-d Digest V99 #130       [ Jeff Reidler <Jreidler@scioncorp.co ]
  Re: Length Measurement                [ "Cengizhan Ozturk" <cozturk@mri.jhu ]
  Field vs. Frame avg                   [ Steve Potter <spotter@gg.caltech.ed ]
  <no subject>                          [ "Michael R. Torry, Ph.D." <mike.tor ]
  unsubsrcribe                          [ "James Holman" <J.holman@mailbox.gu ]
  TIFF Mac/PC                           [ Edgar Rivedal <edgar.rivedal@labmed ]

------------------------------

Date: Wed, 09 Jun 1999 04:21:04 PDT
From: Dafna Shashua <dshashua@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: rotation and digitation
Message-ID: <19990609112115.61848.qmail@hotmail.com>
Content-Type: text/plain; format=flowed

Hello!
I am looking for two macros:
1. a macro that requests input of two landmarks, and then rotates the image
so the line between the landmark is horizontal
2. a macro that "requests" the  manual digitation of a set of landmarks,
and then plots the coordinates (and a set of calculated angles between
landmarks, if possible)
any ideas?
Thanks,
Dafna


_______________________________________________________________
Get Free Email and Do More On The Web. Visit http://www.msn.com

------------------------------

Date: Wed, 09 Jun 1999 04:20:07 PDT
From: Dafna Shashua <dshashua@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: rotation and digitation
Message-ID: <19990609112144.632.qmail@hotmail.com>
Content-Type: text/plain; format=flowed

Hello!
I am looking for two macros:
1. a macro that requests input of two landmarks, and then rotates the image
so the line between the landmark is horizontal
2. a macro that "requests" the  manual digitation of a set of landmarks,
and then plots the coordinates (and a set of calculated angles between
landmarks, if possible)
any ideas?
Thanks,
Dafna


_______________________________________________________________
Get Free Email and Do More On The Web. Visit http://www.msn.com

------------------------------

Date: Wed, 9 Jun 99 12:31:20 -0400
From: jared rifkin <jared_rifkin@qc.edu>
To: <nih-image@io.ece.drexel.edu>, <nih-image@io.ece.drexel.edu>
Subject: Re: How to Average Frames,Pixera
Message-ID: <2900AC114A@qc1.qc.edu>
Content-Type: text/plain; charset="US-ASCII"

please post response to all re  answer to Potter's amazingly 
understandable discourse on image enhancement.

also- how can i combine trapping say 10 frames (for averaging) every 
minute for perhaps an hour or two. i'm tracking cell movements - they are 
slow and single frames are just too noisy to get good resolution -and- i 
don't have the memory to trap and store contnuous video of a couple of 
hours. 
don't shoot me but i primarily use Adobe Premiere, not nih image.  i 
know- i'm an alien but have pity.

-dr. j. rifkin
biology dept
queens college
new york, ny 11367
jared_rifkin@qc.edu

------------------------------

Date: Wed, 9 Jun 1999 12:52:32 -0400
From: Jeff Reidler <Jreidler@scioncorp.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #130
Message-Id: <l03102809b3844ac53804@[10.0.0.248]>
Content-Type: text/plain; charset="us-ascii"

>From: Steve Potter <spotter@gg.caltech.edu>
>Subject: How to Average Frames,Pixera
>We are considering getting the Pixera Pro camera.

We have good results with the Cohu 2200 series for use in brightfield and
fluorescence.  It gives live video and integration capabilities within NIH
Image.  We also have written some macros to simplify the integration, and
these are included in Scion Image.

Although the Cohu 2200 only integrates FIELDS, we have found that the
quality of the image is quite good.  We have direct image comparisons of
Field and Frame capture.

The Cohu 2200 is available as PAL or NTSC formats.
Reply directly to me if you want to receive image comparisons.
Jeff Reidler, Scion Corporation
http://www.scioncorp.com

------------------------------

Date: Wed, 9 Jun 1999 13:18:08 -0400
From: "Cengizhan Ozturk" <cozturk@mri.jhu.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: Length Measurement
Message-ID: <008901beb29c$0b74d140$32a0dc80@alonso.bme-mri.jhu.edu>
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 7bit

Keith,

There are routines (and a special compiled version of NIH-image) which
calculates the convex hull of a binary object. Once you have the convex hull
the problem is much simpler.

Cengizhan


-----Original Message-----
From: Harenski, Keith <harenskik@msx.upmc.edu>
To: 'nih-image@io.ece.drexel.edu' <nih-image@io.ece.drexel.edu>
Date: Tuesday, June 08, 1999 12:31 PM
Subject: Length Measurement


>i was wondering if it was possible (eg. is there a macro available) to
>objectively caculate the maximum width (length) of an irregular object.
>additionally, i would like the program to draw a line connecting those two
>points.
>
>thanks in advance... Keith
>
>

------------------------------

Date: Wed, 09 Jun 1999 10:43:11 PDT
From: Steve Potter <spotter@gg.caltech.edu>
To: nih-image@io.ece.drexel.edu
Subject: Field vs. Frame avg
Message-Id: <199906091743.KAA09891@druggist.gg.caltech.edu>

Jeff, please explain what the difference between fields and frames
are.  The only two kinds of integration I know about are
"on-chip", used only in cooled CCDs, where the pixels are not scanned for
a while, and the chip collects light for some amount of time,
usually seconds.  The other kind is frame averaging, where the
detector collects light for some short time (less than a second, often
1/30 of a second), reads the data into some memory (either in chips
in the camera, in the interface board, or in the RAM of the host computer),
and collects another frame, and does math on the digitized frames to
average them.  "Fields" I have only heard about with respect to old
analog video cameras that output two interlaced fields of scan lines
per frame.  What is going on in the Cohu, and what am I missing here?
Thanks,

Steve Potter
spotter@gg.caltech.edu


> 
> >From: Steve Potter <spotter@gg.caltech.edu>
> >Subject: How to Average Frames,Pixera
> >We are considering getting the Pixera Pro camera.
> 
> We have good results with the Cohu 2200 series for use in brightfield and
> fluorescence.  It gives live video and integration capabilities within NIH
> Image.  We also have written some macros to simplify the integration, and
> these are included in Scion Image.
> 
> Although the Cohu 2200 only integrates FIELDS, we have found that the
> quality of the image is quite good.  We have direct image comparisons of
> Field and Frame capture.
> 
> The Cohu 2200 is available as PAL or NTSC formats.
> Reply directly to me if you want to receive image comparisons.
> Jeff Reidler, Scion Corporation
> http://www.scioncorp.com
> 
> 
> 

------------------------------

Date: Wed, 09 Jun 1999 18:29:56 -0600
From: "Michael R. Torry, Ph.D." <mike.torry@shsmf.org>
To: nih-image@io.ece.drexel.edu
Subject: <no subject>
Message-ID: <1283144108-26382056@ns1.ortho-con.com>
Content-type: text/plain; charset="US-ASCII"
Content-transfer-encoding: 7bit

I am interested in making volumetric measures using stacked MRI images. Is
there a way this can be done in NIH Image 1.62.  The archives listed several
similar requests but I was unable to find a response to them.
--
Mike Torry, Ph.D.
Steadman Hawkins Sports Medicine Foundation
181 West Meadow Drive, Suite 1000
Vail, CO  81657
Work:    (970) 479-5793
Fax:     (970) 479-9753
--

------------------------------

Date: Thu, 10 Jun 1999 10:43:55 +1000
From: "James Holman" <J.holman@mailbox.gu.edu.au>
To: "image" <nih-image@io.ece.drexel.edu>
Subject: unsubsrcribe
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______________________________________________
James Holman
Australian School of Environmental Studies
Griffith University, Nathan Campus
Queensland, Australia 4111

Home: 07 3511 6736
Griffith Uni.: 07 3875 7483
Qld. Herbarium:  07 3896 9547

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University,=20
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<DIV>&nbsp;</DIV>
<DIV>Home: 07 3511 6736<BR>Griffith Uni.: 07 3875 7483<BR>Qld. =
Herbarium:&nbsp;=20
07 3896 9547</DIV></BODY></HTML>

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------------------------------

Date: Thu, 10 Jun 1999 08:37:28 +0200
From: Edgar Rivedal <edgar.rivedal@labmed.uio.no>
To: nih-image@io.ece.drexel.edu
Subject: TIFF Mac/PC
Message-Id: <3.0.3.32.19990610083728.00930420@uio-pop.uio.no>
Content-Type: text/plain; charset="us-ascii"

I use both Mac and PC to work on grey level tif files. When saving tif
files the question of Byte order, Mac or IBM PC, comes up. Is there more to
this then the attachment of .tif to the file name, and is there something
to be aware of with regard to preserving quality of the images when working
on the same tif files in both platforms? 

The print out is in our hands generally better when coming from the same
file and program (i.e.Photoshop or Image)on a Mac than on a PC. This seems
to be the case for both colour and grey tone printouts, from laser, dye
sublimation and ink jet. Is this something one just has to accept as a
fact, or is it a matter of adjustment and drivers?


Edgar 


_____________________________________

Edgar Rivedal (edgarr@labmed.uio.no)
Institute for Cancer Research     
Oslo, Norway 
_____________________________________

--------------------------------
End of nih-image-d Digest V99 Issue #131
****************************************

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>1. a macro that requests input of two landmarks, and then rotates the image
>so the line between the landmark is horizontal

This should be simple using the answer on the following question:

>2. a macro that "requests" the  manual digitation of a set of landmarks,
>and then plots the coordinates (and a set of calculated angles between
>landmarks, if possible)

Try Object Image, that gives you a live spreadsheet. Road map: get ObjectImage 
ftp://simon.bio.uva.nl//pub/Object-Image1.62n18.sea.hqx
Then open an image you want to analyse. Choose 'Objects/new object file',name it, click OK. Click OK when you are asked to define new objects. In the next window, drag and drop an angle into the right side part of the window, you have defined an angle.
THEN when finished click OK. Click on the 'object' button in the tools window, you'll see AngleA in yellow, with a red angle icon. Move to your image. Click the first angle point, click the hinge and click the third point that defines the angle. From the 'Objects' menu, choose 'show Obj results'. There is your angle.

Now click a second triplet of points and there is another angle! Choose the lower tab in the tools window (under the card and object tools). A menu drops. Choose the open arrow and move one of the points of the angles you have defined. See how the spreadsheet window changes with it....

You want the points that make up the triangle? Close the object file, we'll make another one. Redo the things above, but stop at "THEN". First, ywith the help of the buttons in this window you define 'new result', at the next window, choose operation 'Xpos' and click OK. Repeat another 2 times, now choose as operation 'Ypos' and 'Zpos' respectively. Continue at "then" and see that in the results window also your endpoints are shown.

Maybe, if there is enough demand, Norbert one day might be inclided to program a registration interface based upon the point-objects you place in a stack of images. Define two or more corresponding point-objects in each slice and choose a register command (not (yet) available).

For your alignment question: use the angle you have defined above for an automated scaleandrotate macro command.
ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156



From nih-image-request@io.ece.drexel.edu Thu Jun 10 07:20 EDT 1999
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The Mac vs. PC byte order is just about the byte order (aha.. :) in the
file and does not affect the *quality* of the image; both are lossless
image formats.  It can affect the *readability* though; some PC programs
may refuse to open 'Mac' byte order tiffs (Photoshop deals with both of
course).

The 'Mac'and 'PC' byte order is a bit of a misnomer anyway.  The Tiff
format specifications allow both of the two possible byte orders, and any
serious software reading Tiffs should handle both.  It just happened that
one byte order became de-facto standard on the Mac and the opposite on the
PC.

---off topic starts here---

(Why is the standard pointer arrow in Windows white with a black
border?---exactly, because the Mac pointer was black with a white border.
Why is the default position for the Start button in Windows at the bottom
of the screen, with the menue 'dropping upwards'?  Because in western
culture, we start reading a page from the bottom upwards?  Because
things dropping upwards is such a familiar metaphor from our
physical world?---No, because the Mac menu bar is at the top of the
screen, with menus dropping down, as things normally do.)

Swidbert R. Ott
Dept Zoology, Cambridge UK




 On Thu, 10 Jun 1999, Edgar Rivedal wrote:

> I use both Mac and PC to work on grey level tif files. When saving tif
> files the question of Byte order, Mac or IBM PC, comes up. Is there more to
> this then the attachment of .tif to the file name, and is there something
> to be aware of with regard to preserving quality of the images when working
> on the same tif files in both platforms? 
> 
> The print out is in our hands generally better when coming from the same
> file and program (i.e.Photoshop or Image)on a Mac than on a PC. This seems
> to be the case for both colour and grey tone printouts, from laser, dye
> sublimation and ink jet. Is this something one just has to accept as a
> fact, or is it a matter of adjustment and drivers?
> 
> 
> Edgar 
> 
> 
> _____________________________________
> 
> Edgar Rivedal (edgarr@labmed.uio.no)
> Institute for Cancer Research     
> Oslo, Norway 
> _____________________________________
> 
> 


From nih-image-request@io.ece.drexel.edu Thu Jun 10 09:29 EDT 1999
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We do volumetric measurements in our lab by making
roi's on each of the 2d slices then just multiplying
by the slice thickness of the scan to give a volume.
If you are interrested in the tequnique please email
me and i can be more verbose.
stev spencer
spencersm@msx.upmc.edu

--- "Michael R. Torry, Ph.D." <mike.torry@shsmf.org>
wrote:
> I am interested in making volumetric measures using
> stacked MRI images. Is
> there a way this can be done in NIH Image 1.62.  The
> archives listed several
> similar requests but I was unable to find a response
> to them.
> --
> Mike Torry, Ph.D.
> Steadman Hawkins Sports Medicine Foundation
> 181 West Meadow Drive, Suite 1000
> Vail, CO  81657
> Work:    (970) 479-5793
> Fax:     (970) 479-9753
> --
> 
> 

_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-request@io.ece.drexel.edu Thu Jun 10 09:55 EDT 1999
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Date: Thu, 10 Jun 1999 08:41:55 -0500
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Organization: U of MN, Medicine, Infectious Diseases
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Also, I suspect that the byte order is much less of an issue than it was?
Versions of Quicktime newer than 3.0 seem to handle it seemlessly.

Could someone correct me on this?

Mike

"S.R. Ott" wrote:
> 
> The Mac vs. PC byte order is just about the byte order (aha.. :) in the
> file and does not affect the *quality* of the image; both are lossless
> image formats.  It can affect the *readability* though; some PC programs
> may refuse to open 'Mac' byte order tiffs (Photoshop deals with both of
> course).
> 
> The 'Mac'and 'PC' byte order is a bit of a misnomer anyway.  The Tiff
> format specifications allow both of the two possible byte orders, and any
> serious software reading Tiffs should handle both.  It just happened that
> one byte order became de-facto standard on the Mac and the opposite on the
> PC.
> 
> ---off topic starts here---
> 
> (Why is the standard pointer arrow in Windows white with a black
> border?---exactly, because the Mac pointer was black with a white border.
> Why is the default position for the Start button in Windows at the bottom
> of the screen, with the menue 'dropping upwards'?  Because in western
> culture, we start reading a page from the bottom upwards?  Because
> things dropping upwards is such a familiar metaphor from our
> physical world?---No, because the Mac menu bar is at the top of the
> screen, with menus dropping down, as things normally do.)
> 
> Swidbert R. Ott
> Dept Zoology, Cambridge UK
> 
>  On Thu, 10 Jun 1999, Edgar Rivedal wrote:
> 
> > I use both Mac and PC to work on grey level tif files. When saving tif
> > files the question of Byte order, Mac or IBM PC, comes up. Is there more to
> > this then the attachment of .tif to the file name, and is there something
> > to be aware of with regard to preserving quality of the images when working
> > on the same tif files in both platforms?
> >
> > The print out is in our hands generally better when coming from the same
> > file and program (i.e.Photoshop or Image)on a Mac than on a PC. This seems
> > to be the case for both colour and grey tone printouts, from laser, dye
> > sublimation and ink jet. Is this something one just has to accept as a
> > fact, or is it a matter of adjustment and drivers?
> >
> >
> > Edgar
> >
> >
> > _____________________________________
> >
> > Edgar Rivedal (edgarr@labmed.uio.no)
> > Institute for Cancer Research
> > Oslo, Norway
> > _____________________________________
> >
> >

-- 

   _________________________________________________
     /  Michael J. Herron                          /
    /     U of MN,Medicine/Infectious Diseases    /
   /        herro001@maroon.tc.umn.edu           /
  /           http://128.101.243.213            /
 /_____________________________________________/


From nih-image-request@io.ece.drexel.edu Thu Jun 10 10:13 EDT 1999
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From: "Mandish Rai" <raim@ccf.org>
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Subject: NIH Image Validation?
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Hello!
I need to show a third-party that NIH Image has been validated.  Does anyone know of any sources that can be used? If not, any suggestions?

Thanks,
Mandish

_____________________________________

Mandish Rai (raim@ccf.org)
The Cleveland Clinic Foundation     
Cleveland, Ohio   USA 
_____________________________________


From nih-image-request@io.ece.drexel.edu Thu Jun 10 11:41 EDT 1999
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Steve,
thanks for your reply to my volume question.
Lets say you have about 5 sequencial, axial image slices. do you multiply
each slice by the slice thickness then sum the results of this calculation
for all five slices?
Thanks for your help.
--
Mike Torry, Ph.D.
Steadman Hawkins Sports Medicine Foundation
181 West Meadow Drive, Suite 1000
Vail, CO  81657
Work:    (970) 479-5793
Fax:     (970) 479-9753
--


----------
>From: steve spencer <stephen_spencer@yahoo.com>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: <no subject>
>Date: Thu, Jun 10, 1999, 7:14 AM
>

> We do volumetric measurements in our lab by making
> roi's on each of the 2d slices then just multiplying
> by the slice thickness of the scan to give a volume.
> If you are interrested in the tequnique please email
> me and i can be more verbose.
> stev spencer
> spencersm@msx.upmc.edu
>
> --- "Michael R. Torry, Ph.D." <mike.torry@shsmf.org>
> wrote:
>> I am interested in making volumetric measures using
>> stacked MRI images. Is
>> there a way this can be done in NIH Image 1.62.  The
>> archives listed several
>> similar requests but I was unable to find a response
>> to them.
>> --
>> Mike Torry, Ph.D.
>> Steadman Hawkins Sports Medicine Foundation
>> 181 West Meadow Drive, Suite 1000
>> Vail, CO  81657
>> Work:    (970) 479-5793
>> Fax:     (970) 479-9753
>> --
>>
>>
>
> _________________________________________________________
> Do You Yahoo!?
> Get your free @yahoo.com address at http://mail.yahoo.com
> 


From nih-image-request@io.ece.drexel.edu Thu Jun 10 12:01 EDT 1999
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From: jgilkey@u.arizona.edu (John C. Gilkey)
Subject: Re: TIFF Mac/PC
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>The print out is in our hands generally better when coming from the same
>file and program (i.e.Photoshop or Image)on a Mac than on a PC. This seems
>to be the case for both colour and grey tone printouts, from laser, dye
>sublimation and ink jet. Is this something one just has to accept as a
>fact, or is it a matter of adjustment and drivers?

    All Macs have a "hardware lookup table" in the video circuitry that
allows for correction of gamma (the nonlinear response of a CRT monitor).
Macs by default provide some correction for gamma (just enough to match the
"gamma" - strictly speaking, only a CRT has gamma - of a laser printer), so
the printed image will look more like the image on the monitor. There are
many software packages available for Macs that permit full correction of
gamma from the scanner through the monitor to the printer.
   PCs do not by default correct for Gamma, and not all PC video cards have
the requisite hardware lookup tables for correction, so the printed image
is likely to look rather different from the image on the monitor.  The only
color correction software packages that I have been able to find for PCs
are made by Kodak (Colorflow ICC Monitor Profile Builder and Colorflow ICC
Profile Tools - the latter for scanners and printers).
   A number of hardware and software manufacturers (the International Color
Consortium, ICC) got together in 1993 to work out an operating-system-level
solution to the color correction problem.  This solution will use hardware
profiles provded by equipment mnufacutrers (or created by the user every
month or so for a monitor as the phosphors age) to automatically do color
correction, and while it will not be entirely invisible to the user, it is
better than the current situation.  Apple, working with Linotype-Hell, came
up with ColorSync, which was released in 1993. Microsoft, working with
Kodak, incorporated Image Color Matching in Windows 95, but this apparently
did not work out.  Microsoft is now working with Linotype-Hell on another
system to be incorporated in Windows 2000.  Photoshop 5, by the way,
recognizes ICC hardware profiles and can do its own correction on either
platform.

For a discussion of gamma, see
    Poynton, C.A.. 1993. "Gamma" and its disguises: the nonlinear mappings
of intensity in perception, CRTs, Film and Video. Soc. Motion Picture &
Television Engineers 102:1099 1108.  The paper is also available in Adobe
PDF format from http://198.53.144.31/ ~poynton/papers/SMPTE_93_Gamma.html.
An update is available from http://198.53.144.31/
~poynton/Poynton-T-I-Digital-Video.html

For information on International Color Consortium color correction, see:
    http://www.color.org



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Date: Thu, 10 Jun 1999 12:45:39 -0500
To: nih-image@io.ece.drexel.edu
From: "Scott D. Davilla" <davilla@4pi.com>
Subject: Re: TIFF Mac/PC
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>The 'Mac'and 'PC' byte order is a bit of a misnomer anyway.  The Tiff
>format specifications allow both of the two possible byte orders, and any
>serious software reading Tiffs should handle both.  It just happened that
>one byte order became de-facto standard on the Mac and the opposite on the
>PC.

	Actually not correct. Byte order refers to the order in which bytes
appear in memory. There are two flavors, big endian and little endian. The
term big/little endian comes from Gulliver's Travels and two factions
within Lilliputian society that argued about which end of the egg to open,
the big end or the little end.
	Intel processors use little endian order, Motorola processors use
big endian order. PC's developed using Intel processors, Mac's developed
using Motorola processors thus is why they still use their particular
flavor.
	Another interesting point is that byte images do not require byte
swaps. You only need to pay attention to byte order if you are dealing with
16-bit or greater. However, the byte order is still important with TIFF
based byte images because the header that describes the image uses 16-bit
or greater data fields.

	I will not go into it but you can find several interesting
discussions on the net about the big and little endian wars.

Scott
-----------------------------------------------------------------------
Scott D. Davilla                              Phone: 919 489-1757 (tel)
4pi Analysis, Inc.                            Fax:   919 489-1487 (fax)
3500 Westgate Drive, Suite 403                email: davilla@4pi.com
Durham, North Carolina  27707-2534            web: http://www.4pi.com


From nih-image-request@io.ece.drexel.edu Thu Jun 10 13:26 EDT 1999
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Date: Thu, 10 Jun 1999 10:15:48 -0700
From: David Linker <dtlinker@u.washington.edu>
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I don't know how to do this within Image, but I use a macro to store areas
on a results table, which I then transfer to Excel to calculate volumes.

DTL

--On Wed, Jun 9, 1999 6:29 PM -0600 "Michael R. Torry, Ph.D."
<mike.torry@shsmf.org> wrote:

> I am interested in making volumetric measures using stacked MRI images. Is
> there a way this can be done in NIH Image 1.62.  The archives listed
> several similar requests but I was unable to find a response to them.
> --
> Mike Torry, Ph.D.
> Steadman Hawkins Sports Medicine Foundation
> 181 West Meadow Drive, Suite 1000
> Vail, CO  81657
> Work:    (970) 479-5793
> Fax:     (970) 479-9753
> --
> 





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From: David Linker <dtlinker@u.washington.edu>
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        "Michael R. Torry, Ph.D." <mike.torry@shsmf.org>
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This is one way to do it. In fact, calculating the volume from a number of
slices can be thought of as a numerical integration problem, integrating a
graph of area versus depth. As such, this integration can be performed by a
number of techniques, including the rectangular rule, trapezoidal rule, and
parabolic rule (also called Simpson's rule). Each of these has advantages
and disadvantages. What you described is the simplest, and corresponds to
the rectangular rule. It is probably adequate for most situations.


DTL

--On Thu, Jun 10, 1999 9:28 AM -0600 "Michael R. Torry, Ph.D."
<mike.torry@shsmf.org> wrote:

> Steve,
> thanks for your reply to my volume question.
> Lets say you have about 5 sequencial, axial image slices. do you multiply
> each slice by the slice thickness then sum the results of this calculation
> for all five slices?
> Thanks for your help.
> --
> Mike Torry, Ph.D.
> Steadman Hawkins Sports Medicine Foundation
> 181 West Meadow Drive, Suite 1000
> Vail, CO  81657
> Work:    (970) 479-5793
> Fax:     (970) 479-9753
> --
> 
> 
> ----------
>> From: steve spencer <stephen_spencer@yahoo.com>
>> To: nih-image@io.ece.drexel.edu
>> Subject: Re: <no subject>
>> Date: Thu, Jun 10, 1999, 7:14 AM
>> 
> 
>> We do volumetric measurements in our lab by making
>> roi's on each of the 2d slices then just multiplying
>> by the slice thickness of the scan to give a volume.
>> If you are interrested in the tequnique please email
>> me and i can be more verbose.
>> stev spencer
>> spencersm@msx.upmc.edu
>> 
>> --- "Michael R. Torry, Ph.D." <mike.torry@shsmf.org>
>> wrote:
>>> I am interested in making volumetric measures using
>>> stacked MRI images. Is
>>> there a way this can be done in NIH Image 1.62.  The
>>> archives listed several
>>> similar requests but I was unable to find a response
>>> to them.
>>> --
>>> Mike Torry, Ph.D.
>>> Steadman Hawkins Sports Medicine Foundation
>>> 181 West Meadow Drive, Suite 1000
>>> Vail, CO  81657
>>> Work:    (970) 479-5793
>>> Fax:     (970) 479-9753
>>> --
>>> 
>>> 
>> 
>> _________________________________________________________
>> Do You Yahoo!?
>> Get your free @yahoo.com address at http://mail.yahoo.com
>> 
> 





From nih-image-request@io.ece.drexel.edu Thu Jun 10 13:38 EDT 1999
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From: steve spencer <stephen_spencer@yahoo.com>
Subject: Re: NIH Image Validation?
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There are definietly sources for that search for
articles by keshavan  he has done it for schizophrenia
research using phantom sheres and post mordem

--- Mandish Rai <raim@ccf.org> wrote:
> Hello!
> I need to show a third-party that NIH Image has been
> validated.  Does anyone know of any sources that can
> be used? If not, any suggestions?
> 
> Thanks,
> Mandish
> 
> _____________________________________
> 
> Mandish Rai (raim@ccf.org)
> The Cleveland Clinic Foundation     
> Cleveland, Ohio   USA 
> _____________________________________
> 
> 

_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-request@io.ece.drexel.edu Thu Jun 10 15:53 EDT 1999
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From: squeen@selway.umt.edu
Sender: "Sue Queen" <squeen@selway.umt.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: Tissue autoradiography
Date: Thu, 10 Jun 1999 13:24:23 -0600
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I am attempting to use NIH image for radioligand autoradiography in CNS
tissue. My previous experience has been using an image analysis system by
Southern Micro.  I would appreciate contact from someone who is using NIH
image for similar purposes. I have been taking measurements with a
calibrated standard curve, generally fit with the Rodbard equation. Is there
a macro for tissue autoradiography? Do most users ignore background gray
levels, or use background subtract? Is there a way to replicate the
measuring tool so that one consistently measures the same size area in each
region, and from section to section?
Thanks for the help.


From nih-image-request@io.ece.drexel.edu Fri Jun 11 04:01 EDT 1999
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From: Gary Chinga <gary.chinga@pfi.no>
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Hi!

To measure the volume of reconstructed cells I used the follolwing
equation.

Area (A) = Sx dy 				
Volume =Sz (Ai +  Ai Ai+1 + Ai+1)/3	

The relative volume of the objects was calculated using the area of each
profile and the thickness (z) of the sections used. 
For more details,  see 
Coombs, G.H., Tetley, L., Moss, V.A. and Vickerman, K. (1986).
Three-dimensional structure of the leishmania amastigote as revealed by
computer-aided reconstruction from serial sections. Parasitology 92:
13-23. 

Gary.
------------------------------------------------------------------
Gary Chinga
PhD student
The Norwegian University of Science and Technology
Dept. of Chem. Engineering
Sem Saelandsv. 4
Trondheim
N7034 Norway
Direct line : +47 73550537
email: gary.chinga@pfi.no








>-----Original Message-----
>From:	Michael R. Torry, Ph.D. [SMTP:mike.torry@shsmf.org]
>Sent:	10. juni 1999 17:29
>To:	nih-image@io.ece.drexel.edu
>Subject:	Re: <no subject>
>
>Steve,
>thanks for your reply to my volume question.
>Lets say you have about 5 sequencial, axial image slices. do you multiply
>each slice by the slice thickness then sum the results of this calculation
>for all five slices?
>Thanks for your help.
>--
>Mike Torry, Ph.D.
>Steadman Hawkins Sports Medicine Foundation
>181 West Meadow Drive, Suite 1000
>Vail, CO  81657
>Work:    (970) 479-5793
>Fax:     (970) 479-9753
>--
>
>
>----------
>>From: steve spencer <stephen_spencer@yahoo.com>
>>To: nih-image@io.ece.drexel.edu
>>Subject: Re: <no subject>
>>Date: Thu, Jun 10, 1999, 7:14 AM
>>
>
>> We do volumetric measurements in our lab by making
>> roi's on each of the 2d slices then just multiplying
>> by the slice thickness of the scan to give a volume.
>> If you are interrested in the tequnique please email
>> me and i can be more verbose.
>> stev spencer
>> spencersm@msx.upmc.edu
>>
>> --- "Michael R. Torry, Ph.D." <mike.torry@shsmf.org>
>> wrote:
>>> I am interested in making volumetric measures using
>>> stacked MRI images. Is
>>> there a way this can be done in NIH Image 1.62.  The
>>> archives listed several
>>> similar requests but I was unable to find a response
>>> to them.
>>> --
>>> Mike Torry, Ph.D.
>>> Steadman Hawkins Sports Medicine Foundation
>>> 181 West Meadow Drive, Suite 1000
>>> Vail, CO  81657
>>> Work:    (970) 479-5793
>>> Fax:     (970) 479-9753
>>> --
>>>
>>>
>>
>> _________________________________________________________
>> Do You Yahoo!?
>> Get your free @yahoo.com address at http://mail.yahoo.com
>> 
>


From nih-image-d-request@io.ece.drexel.edu Fri Jun 11 04:16 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #132
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 132

Today's Topics:
  Re: rotation and digitation           [ Ard Jonker <a.jonker@amc.uva.nl> ]
  Re: TIFF Mac/PC                       [ "S.R. Ott" <sro21@hermes.cam.ac.uk> ]
  Re: <no subject>                      [ steve spencer <stephen_spencer@yaho ]
  Re: TIFF Mac/PC                       [ Michael Herron <herro001@maroon.tc. ]
  NIH Image Validation?                 [ "Mandish Rai" <raim@ccf.org> ]
  Re: <no subject>                      [ "Michael R. Torry, Ph.D." <mike.tor ]
  Re: TIFF Mac/PC                       [ jgilkey@u.arizona.edu (John C. Gilk ]
  Re: TIFF Mac/PC                       [ "Scott D. Davilla" <davilla@4pi.com ]
  Re: <no subject>                      [ David Linker <dtlinker@u.washington ]
  Re: <no subject>                      [ David Linker <dtlinker@u.washington ]
  Re: NIH Image Validation?             [ steve spencer <stephen_spencer@yaho ]
  Tissue autoradiography                [ squeen@selway.umt.edu ]
  RE: <no subject>                      [ Gary Chinga <gary.chinga@pfi.no> ]

------------------------------

Date: Thu, 10 Jun 1999 12:38:30 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: rotation and digitation
Message-Id: <l03130300b38528948d44@[145.117.53.66]>
Content-Type: text/plain; charset="us-ascii"
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>1. a macro that requests input of two landmarks, and then rotates the image
>so the line between the landmark is horizontal

This should be simple using the answer on the following question:

>2. a macro that "requests" the  manual digitation of a set of landmarks,
>and then plots the coordinates (and a set of calculated angles between
>landmarks, if possible)

Try Object Image, that gives you a live spreadsheet. Road map: get ObjectImage 
ftp://simon.bio.uva.nl//pub/Object-Image1.62n18.sea.hqx
Then open an image you want to analyse. Choose 'Objects/new object file',name it, click OK. Click OK when you are asked to define new objects. In the next window, drag and drop an angle into the right side part of the window, you have defined an angle.
THEN when finished click OK. Click on the 'object' button in the tools window, you'll see AngleA in yellow, with a red angle icon. Move to your image. Click the first angle point, click the hinge and click the third point that defines the angle. From the 'Objects' menu, choose 'show Obj results'. There is your angle.

Now click a second triplet of points and there is another angle! Choose the lower tab in the tools window (under the card and object tools). A menu drops. Choose the open arrow and move one of the points of the angles you have defined. See how the spreadsheet window changes with it....

You want the points that make up the triangle? Close the object file, we'll make another one. Redo the things above, but stop at "THEN". First, ywith the help of the buttons in this window you define 'new result', at the next window, choose operation 'Xpos' and click OK. Repeat another 2 times, now choose as operation 'Ypos' and 'Zpos' respectively. Continue at "then" and see that in the results window also your endpoints are shown.

Maybe, if there is enough demand, Norbert one day might be inclided to program a registration interface based upon the point-objects you place in a stack of images. Define two or more corresponding point-objects in each slice and choose a register command (not (yet) available).

For your alignment question: use the angle you have defined above for an automated scaleandrotate macro command.
ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156

------------------------------

Date: Thu, 10 Jun 1999 12:05:29 +0100 (BST)
From: "S.R. Ott" <sro21@hermes.cam.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: TIFF Mac/PC
Message-ID: <Pine.SOL.3.95q.990610114753.20029A-100000@red.csi.cam.ac.uk>
Content-Type: TEXT/PLAIN; charset=US-ASCII

The Mac vs. PC byte order is just about the byte order (aha.. :) in the
file and does not affect the *quality* of the image; both are lossless
image formats.  It can affect the *readability* though; some PC programs
may refuse to open 'Mac' byte order tiffs (Photoshop deals with both of
course).

The 'Mac'and 'PC' byte order is a bit of a misnomer anyway.  The Tiff
format specifications allow both of the two possible byte orders, and any
serious software reading Tiffs should handle both.  It just happened that
one byte order became de-facto standard on the Mac and the opposite on the
PC.

---off topic starts here---

(Why is the standard pointer arrow in Windows white with a black
border?---exactly, because the Mac pointer was black with a white border.
Why is the default position for the Start button in Windows at the bottom
of the screen, with the menue 'dropping upwards'?  Because in western
culture, we start reading a page from the bottom upwards?  Because
things dropping upwards is such a familiar metaphor from our
physical world?---No, because the Mac menu bar is at the top of the
screen, with menus dropping down, as things normally do.)

Swidbert R. Ott
Dept Zoology, Cambridge UK




 On Thu, 10 Jun 1999, Edgar Rivedal wrote:

> I use both Mac and PC to work on grey level tif files. When saving tif
> files the question of Byte order, Mac or IBM PC, comes up. Is there more to
> this then the attachment of .tif to the file name, and is there something
> to be aware of with regard to preserving quality of the images when working
> on the same tif files in both platforms? 
> 
> The print out is in our hands generally better when coming from the same
> file and program (i.e.Photoshop or Image)on a Mac than on a PC. This seems
> to be the case for both colour and grey tone printouts, from laser, dye
> sublimation and ink jet. Is this something one just has to accept as a
> fact, or is it a matter of adjustment and drivers?
> 
> 
> Edgar 
> 
> 
> _____________________________________
> 
> Edgar Rivedal (edgarr@labmed.uio.no)
> Institute for Cancer Research     
> Oslo, Norway 
> _____________________________________
> 
> 

------------------------------

Date: Thu, 10 Jun 1999 06:14:34 -0700 (PDT)
From: steve spencer <stephen_spencer@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: <no subject>
Message-ID: <19990610131434.5945.rocketmail@web119.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

We do volumetric measurements in our lab by making
roi's on each of the 2d slices then just multiplying
by the slice thickness of the scan to give a volume.
If you are interrested in the tequnique please email
me and i can be more verbose.
stev spencer
spencersm@msx.upmc.edu

--- "Michael R. Torry, Ph.D." <mike.torry@shsmf.org>
wrote:
> I am interested in making volumetric measures using
> stacked MRI images. Is
> there a way this can be done in NIH Image 1.62.  The
> archives listed several
> similar requests but I was unable to find a response
> to them.
> --
> Mike Torry, Ph.D.
> Steadman Hawkins Sports Medicine Foundation
> 181 West Meadow Drive, Suite 1000
> Vail, CO  81657
> Work:    (970) 479-5793
> Fax:     (970) 479-9753
> --
> 
> 

_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com

------------------------------

Date: Thu, 10 Jun 1999 08:41:55 -0500
From: Michael Herron <herro001@maroon.tc.umn.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: TIFF Mac/PC
Message-Id: <375FC0A2.FEA79698@maroon.tc.umn.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Also, I suspect that the byte order is much less of an issue than it was?
Versions of Quicktime newer than 3.0 seem to handle it seemlessly.

Could someone correct me on this?

Mike

"S.R. Ott" wrote:
> 
> The Mac vs. PC byte order is just about the byte order (aha.. :) in the
> file and does not affect the *quality* of the image; both are lossless
> image formats.  It can affect the *readability* though; some PC programs
> may refuse to open 'Mac' byte order tiffs (Photoshop deals with both of
> course).
> 
> The 'Mac'and 'PC' byte order is a bit of a misnomer anyway.  The Tiff
> format specifications allow both of the two possible byte orders, and any
> serious software reading Tiffs should handle both.  It just happened that
> one byte order became de-facto standard on the Mac and the opposite on the
> PC.
> 
> ---off topic starts here---
> 
> (Why is the standard pointer arrow in Windows white with a black
> border?---exactly, because the Mac pointer was black with a white border.
> Why is the default position for the Start button in Windows at the bottom
> of the screen, with the menue 'dropping upwards'?  Because in western
> culture, we start reading a page from the bottom upwards?  Because
> things dropping upwards is such a familiar metaphor from our
> physical world?---No, because the Mac menu bar is at the top of the
> screen, with menus dropping down, as things normally do.)
> 
> Swidbert R. Ott
> Dept Zoology, Cambridge UK
> 
>  On Thu, 10 Jun 1999, Edgar Rivedal wrote:
> 
> > I use both Mac and PC to work on grey level tif files. When saving tif
> > files the question of Byte order, Mac or IBM PC, comes up. Is there more to
> > this then the attachment of .tif to the file name, and is there something
> > to be aware of with regard to preserving quality of the images when working
> > on the same tif files in both platforms?
> >
> > The print out is in our hands generally better when coming from the same
> > file and program (i.e.Photoshop or Image)on a Mac than on a PC. This seems
> > to be the case for both colour and grey tone printouts, from laser, dye
> > sublimation and ink jet. Is this something one just has to accept as a
> > fact, or is it a matter of adjustment and drivers?
> >
> >
> > Edgar
> >
> >
> > _____________________________________
> >
> > Edgar Rivedal (edgarr@labmed.uio.no)
> > Institute for Cancer Research
> > Oslo, Norway
> > _____________________________________
> >
> >

-- 

   _________________________________________________
     /  Michael J. Herron                          /
    /     U of MN,Medicine/Infectious Diseases    /
   /        herro001@maroon.tc.umn.edu           /
  /           http://128.101.243.213            /
 /_____________________________________________/

------------------------------

Date: Thu, 10 Jun 1999 10:00:02 -0400
From: "Mandish Rai" <raim@ccf.org>
To: <nih-image@io.ece.drexel.edu>
Subject: NIH Image Validation?
Message-Id: <s75f8c6d.015@cesmtp.ccf.org>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline
Content-Transfer-Encoding: 8bit

Hello!
I need to show a third-party that NIH Image has been validated.  Does anyone know of any sources that can be used? If not, any suggestions?

Thanks,
Mandish

_____________________________________

Mandish Rai (raim@ccf.org)
The Cleveland Clinic Foundation     
Cleveland, Ohio   USA 
_____________________________________

------------------------------

Date: Thu, 10 Jun 1999 09:28:31 -0600
From: "Michael R. Torry, Ph.D." <mike.torry@shsmf.org>
To: nih-image@io.ece.drexel.edu
Subject: Re: <no subject>
Message-ID: <1283090192-29625223@ns1.ortho-con.com>
Content-type: text/plain; charset="US-ASCII"
Content-transfer-encoding: 7bit

Steve,
thanks for your reply to my volume question.
Lets say you have about 5 sequencial, axial image slices. do you multiply
each slice by the slice thickness then sum the results of this calculation
for all five slices?
Thanks for your help.
--
Mike Torry, Ph.D.
Steadman Hawkins Sports Medicine Foundation
181 West Meadow Drive, Suite 1000
Vail, CO  81657
Work:    (970) 479-5793
Fax:     (970) 479-9753
--


----------
>From: steve spencer <stephen_spencer@yahoo.com>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: <no subject>
>Date: Thu, Jun 10, 1999, 7:14 AM
>

> We do volumetric measurements in our lab by making
> roi's on each of the 2d slices then just multiplying
> by the slice thickness of the scan to give a volume.
> If you are interrested in the tequnique please email
> me and i can be more verbose.
> stev spencer
> spencersm@msx.upmc.edu
>
> --- "Michael R. Torry, Ph.D." <mike.torry@shsmf.org>
> wrote:
>> I am interested in making volumetric measures using
>> stacked MRI images. Is
>> there a way this can be done in NIH Image 1.62.  The
>> archives listed several
>> similar requests but I was unable to find a response
>> to them.
>> --
>> Mike Torry, Ph.D.
>> Steadman Hawkins Sports Medicine Foundation
>> 181 West Meadow Drive, Suite 1000
>> Vail, CO  81657
>> Work:    (970) 479-5793
>> Fax:     (970) 479-9753
>> --
>>
>>
>
> _________________________________________________________
> Do You Yahoo!?
> Get your free @yahoo.com address at http://mail.yahoo.com
> 

------------------------------

Date: Thu, 10 Jun 1999 08:42:01 -0700
From: jgilkey@u.arizona.edu (John C. Gilkey)
To: nih-image@io.ece.drexel.edu
Subject: Re: TIFF Mac/PC
Message-Id: <v02140b00b385841f9cf2@[128.196.140.225]>
Content-Type: text/plain; charset="us-ascii"

>The print out is in our hands generally better when coming from the same
>file and program (i.e.Photoshop or Image)on a Mac than on a PC. This seems
>to be the case for both colour and grey tone printouts, from laser, dye
>sublimation and ink jet. Is this something one just has to accept as a
>fact, or is it a matter of adjustment and drivers?

    All Macs have a "hardware lookup table" in the video circuitry that
allows for correction of gamma (the nonlinear response of a CRT monitor).
Macs by default provide some correction for gamma (just enough to match the
"gamma" - strictly speaking, only a CRT has gamma - of a laser printer), so
the printed image will look more like the image on the monitor. There are
many software packages available for Macs that permit full correction of
gamma from the scanner through the monitor to the printer.
   PCs do not by default correct for Gamma, and not all PC video cards have
the requisite hardware lookup tables for correction, so the printed image
is likely to look rather different from the image on the monitor.  The only
color correction software packages that I have been able to find for PCs
are made by Kodak (Colorflow ICC Monitor Profile Builder and Colorflow ICC
Profile Tools - the latter for scanners and printers).
   A number of hardware and software manufacturers (the International Color
Consortium, ICC) got together in 1993 to work out an operating-system-level
solution to the color correction problem.  This solution will use hardware
profiles provded by equipment mnufacutrers (or created by the user every
month or so for a monitor as the phosphors age) to automatically do color
correction, and while it will not be entirely invisible to the user, it is
better than the current situation.  Apple, working with Linotype-Hell, came
up with ColorSync, which was released in 1993. Microsoft, working with
Kodak, incorporated Image Color Matching in Windows 95, but this apparently
did not work out.  Microsoft is now working with Linotype-Hell on another
system to be incorporated in Windows 2000.  Photoshop 5, by the way,
recognizes ICC hardware profiles and can do its own correction on either
platform.

For a discussion of gamma, see
    Poynton, C.A.. 1993. "Gamma" and its disguises: the nonlinear mappings
of intensity in perception, CRTs, Film and Video. Soc. Motion Picture &
Television Engineers 102:1099 1108.  The paper is also available in Adobe
PDF format from http://198.53.144.31/ ~poynton/papers/SMPTE_93_Gamma.html.
An update is available from http://198.53.144.31/
~poynton/Poynton-T-I-Digital-Video.html

For information on International Color Consortium color correction, see:
    http://www.color.org

------------------------------

Date: Thu, 10 Jun 1999 12:45:39 -0500
From: "Scott D. Davilla" <davilla@4pi.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: TIFF Mac/PC
Message-Id: <v04011700b385a5cbbc76@[206.6.156.3]>
Content-Type: text/plain; charset="us-ascii"

>The 'Mac'and 'PC' byte order is a bit of a misnomer anyway.  The Tiff
>format specifications allow both of the two possible byte orders, and any
>serious software reading Tiffs should handle both.  It just happened that
>one byte order became de-facto standard on the Mac and the opposite on the
>PC.

	Actually not correct. Byte order refers to the order in which bytes
appear in memory. There are two flavors, big endian and little endian. The
term big/little endian comes from Gulliver's Travels and two factions
within Lilliputian society that argued about which end of the egg to open,
the big end or the little end.
	Intel processors use little endian order, Motorola processors use
big endian order. PC's developed using Intel processors, Mac's developed
using Motorola processors thus is why they still use their particular
flavor.
	Another interesting point is that byte images do not require byte
swaps. You only need to pay attention to byte order if you are dealing with
16-bit or greater. However, the byte order is still important with TIFF
based byte images because the header that describes the image uses 16-bit
or greater data fields.

	I will not go into it but you can find several interesting
discussions on the net about the big and little endian wars.

Scott
-----------------------------------------------------------------------
Scott D. Davilla                              Phone: 919 489-1757 (tel)
4pi Analysis, Inc.                            Fax:   919 489-1487 (fax)
3500 Westgate Drive, Suite 403                email: davilla@4pi.com
Durham, North Carolina  27707-2534            web: http://www.4pi.com

------------------------------

Date: Thu, 10 Jun 1999 10:15:48 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
cc: "Michael R. Torry, Ph.D." <mike.torry@shsmf.org>
Subject: Re: <no subject>
Message-ID: <96127.3137998548@huginn.medicine.washington.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

I don't know how to do this within Image, but I use a macro to store areas
on a results table, which I then transfer to Excel to calculate volumes.

DTL

--On Wed, Jun 9, 1999 6:29 PM -0600 "Michael R. Torry, Ph.D."
<mike.torry@shsmf.org> wrote:

> I am interested in making volumetric measures using stacked MRI images. Is
> there a way this can be done in NIH Image 1.62.  The archives listed
> several similar requests but I was unable to find a response to them.
> --
> Mike Torry, Ph.D.
> Steadman Hawkins Sports Medicine Foundation
> 181 West Meadow Drive, Suite 1000
> Vail, CO  81657
> Work:    (970) 479-5793
> Fax:     (970) 479-9753
> --
> 

------------------------------

Date: Thu, 10 Jun 1999 10:23:20 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu,
        "Michael R. Torry, Ph.D." <mike.torry@shsmf.org>
Subject: Re: <no subject>
Message-ID: <123365.3137999000@huginn.medicine.washington.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

This is one way to do it. In fact, calculating the volume from a number of
slices can be thought of as a numerical integration problem, integrating a
graph of area versus depth. As such, this integration can be performed by a
number of techniques, including the rectangular rule, trapezoidal rule, and
parabolic rule (also called Simpson's rule). Each of these has advantages
and disadvantages. What you described is the simplest, and corresponds to
the rectangular rule. It is probably adequate for most situations.


DTL

--On Thu, Jun 10, 1999 9:28 AM -0600 "Michael R. Torry, Ph.D."
<mike.torry@shsmf.org> wrote:

> Steve,
> thanks for your reply to my volume question.
> Lets say you have about 5 sequencial, axial image slices. do you multiply
> each slice by the slice thickness then sum the results of this calculation
> for all five slices?
> Thanks for your help.
> --
> Mike Torry, Ph.D.
> Steadman Hawkins Sports Medicine Foundation
> 181 West Meadow Drive, Suite 1000
> Vail, CO  81657
> Work:    (970) 479-5793
> Fax:     (970) 479-9753
> --
> 
> 
> ----------
>> From: steve spencer <stephen_spencer@yahoo.com>
>> To: nih-image@io.ece.drexel.edu
>> Subject: Re: <no subject>
>> Date: Thu, Jun 10, 1999, 7:14 AM
>> 
> 
>> We do volumetric measurements in our lab by making
>> roi's on each of the 2d slices then just multiplying
>> by the slice thickness of the scan to give a volume.
>> If you are interrested in the tequnique please email
>> me and i can be more verbose.
>> stev spencer
>> spencersm@msx.upmc.edu
>> 
>> --- "Michael R. Torry, Ph.D." <mike.torry@shsmf.org>
>> wrote:
>>> I am interested in making volumetric measures using
>>> stacked MRI images. Is
>>> there a way this can be done in NIH Image 1.62.  The
>>> archives listed several
>>> similar requests but I was unable to find a response
>>> to them.
>>> --
>>> Mike Torry, Ph.D.
>>> Steadman Hawkins Sports Medicine Foundation
>>> 181 West Meadow Drive, Suite 1000
>>> Vail, CO  81657
>>> Work:    (970) 479-5793
>>> Fax:     (970) 479-9753
>>> --
>>> 
>>> 
>> 
>> _________________________________________________________
>> Do You Yahoo!?
>> Get your free @yahoo.com address at http://mail.yahoo.com
>> 
> 

------------------------------

Date: Thu, 10 Jun 1999 10:35:45 -0700 (PDT)
From: steve spencer <stephen_spencer@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Image Validation?
Message-ID: <19990610173545.18801.rocketmail@web121.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

There are definietly sources for that search for
articles by keshavan  he has done it for schizophrenia
research using phantom sheres and post mordem

--- Mandish Rai <raim@ccf.org> wrote:
> Hello!
> I need to show a third-party that NIH Image has been
> validated.  Does anyone know of any sources that can
> be used? If not, any suggestions?
> 
> Thanks,
> Mandish
> 
> _____________________________________
> 
> Mandish Rai (raim@ccf.org)
> The Cleveland Clinic Foundation     
> Cleveland, Ohio   USA 
> _____________________________________
> 
> 

_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com

------------------------------

Date: Thu, 10 Jun 1999 13:24:23 -0600
From: squeen@selway.umt.edu
To: <nih-image@io.ece.drexel.edu>
Subject: Tissue autoradiography
Message-ID: <011B80F4AEB0D211801E006008E89C7807C969@bigpharm.pharmacy.umt.edu>
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 7bit

I am attempting to use NIH image for radioligand autoradiography in CNS
tissue. My previous experience has been using an image analysis system by
Southern Micro.  I would appreciate contact from someone who is using NIH
image for similar purposes. I have been taking measurements with a
calibrated standard curve, generally fit with the Rodbard equation. Is there
a macro for tissue autoradiography? Do most users ignore background gray
levels, or use background subtract? Is there a way to replicate the
measuring tool so that one consistently measures the same size area in each
region, and from section to section?
Thanks for the help.

------------------------------

Date: Fri, 11 Jun 1999 09:43:57 +0200
From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: <no subject>
Message-ID: <c=NO%a=_%p=pfi%l=PFINT1-990611074357Z-1814@pfint1.pfi.no>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Hi!

To measure the volume of reconstructed cells I used the follolwing
equation.

Area (A) = Sx dy 				
Volume =Sz (Ai +  Ai Ai+1 + Ai+1)/3	

The relative volume of the objects was calculated using the area of each
profile and the thickness (z) of the sections used. 
For more details,  see 
Coombs, G.H., Tetley, L., Moss, V.A. and Vickerman, K. (1986).
Three-dimensional structure of the leishmania amastigote as revealed by
computer-aided reconstruction from serial sections. Parasitology 92:
13-23. 

Gary.
------------------------------------------------------------------
Gary Chinga
PhD student
The Norwegian University of Science and Technology
Dept. of Chem. Engineering
Sem Saelandsv. 4
Trondheim
N7034 Norway
Direct line : +47 73550537
email: gary.chinga@pfi.no








>-----Original Message-----
>From:	Michael R. Torry, Ph.D. [SMTP:mike.torry@shsmf.org]
>Sent:	10. juni 1999 17:29
>To:	nih-image@io.ece.drexel.edu
>Subject:	Re: <no subject>
>
>Steve,
>thanks for your reply to my volume question.
>Lets say you have about 5 sequencial, axial image slices. do you multiply
>each slice by the slice thickness then sum the results of this calculation
>for all five slices?
>Thanks for your help.
>--
>Mike Torry, Ph.D.
>Steadman Hawkins Sports Medicine Foundation
>181 West Meadow Drive, Suite 1000
>Vail, CO  81657
>Work:    (970) 479-5793
>Fax:     (970) 479-9753
>--
>
>
>----------
>>From: steve spencer <stephen_spencer@yahoo.com>
>>To: nih-image@io.ece.drexel.edu
>>Subject: Re: <no subject>
>>Date: Thu, Jun 10, 1999, 7:14 AM
>>
>
>> We do volumetric measurements in our lab by making
>> roi's on each of the 2d slices then just multiplying
>> by the slice thickness of the scan to give a volume.
>> If you are interrested in the tequnique please email
>> me and i can be more verbose.
>> stev spencer
>> spencersm@msx.upmc.edu
>>
>> --- "Michael R. Torry, Ph.D." <mike.torry@shsmf.org>
>> wrote:
>>> I am interested in making volumetric measures using
>>> stacked MRI images. Is
>>> there a way this can be done in NIH Image 1.62.  The
>>> archives listed several
>>> similar requests but I was unable to find a response
>>> to them.
>>> --
>>> Mike Torry, Ph.D.
>>> Steadman Hawkins Sports Medicine Foundation
>>> 181 West Meadow Drive, Suite 1000
>>> Vail, CO  81657
>>> Work:    (970) 479-5793
>>> Fax:     (970) 479-9753
>>> --
>>>
>>>
>>
>> _________________________________________________________
>> Do You Yahoo!?
>> Get your free @yahoo.com address at http://mail.yahoo.com
>> 
>

--------------------------------
End of nih-image-d Digest V99 Issue #132
****************************************

From nih-image-request@io.ece.drexel.edu Fri Jun 11 04:16 EDT 1999
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The URL 

http://198.53.144.31/ ~poynton/papers/SMPTE_93_Gamma.html.

is outdated. If possible, can you mail me the paper (in PDF).  

Thanks.

Gary.



>For a discussion of gamma, see
>    Poynton, C.A.. 1993. "Gamma" and its disguises: the nonlinear mappings
>of intensity in perception, CRTs, Film and Video. Soc. Motion Picture &
>Television Engineers 102:1099 1108.  The paper is also available in Adobe
>PDF format from http://198.53.144.31/ ~poynton/papers/SMPTE_93_Gamma.html.
>An update is available from http://198.53.144.31/
>~poynton/Poynton-T-I-Digital-Video.html
>
>For information on International Color Consortium color correction, see:
>    http://www.color.org
>
>


From nih-image-request@io.ece.drexel.edu Fri Jun 11 05:53 EDT 1999
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Date: Fri, 11 Jun 1999 11:42:14 +0200
To: nih-image@io.ece.drexel.edu
From: Stein Roervik <steinr@chembio.ntnu.no>
Subject: RE: TIFF Mac/PC
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>The URL
>
>http://198.53.144.31/ ~poynton/papers/SMPTE_93_Gamma.html.
>
>is outdated. If possible, can you mail me the paper (in PDF).
>

Du m fjerne spacen som ble satt inn av mailer programmet pga linjeskift:

http://198.53.144.31/~poynton/papers/SMPTE_93_Gamma.html
http://198.53.144.31/~poynton/Poynton-T-I-Digital-Video.html

Sjekket disse linkene nettopp, de virker.

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+



From nih-image-request@io.ece.drexel.edu Fri Jun 11 12:04 EDT 1999
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From: jgilkey@u.arizona.edu (John C. Gilkey)
Subject: RE: TIFF Mac/PC
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Gary,
   I guess Stein has already gotten back to you - there was an extra space
in the URLs I sent out.  Try:

   http://198.53.144.31/~poynton/papers/SMPTE_93_Gamma.html.

John



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Date: Fri, 11 Jun 1999 17:06:45  --633121
From: "Swidbert R OTT" <sro21@hermes.cam.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: TIFF Mac/PC
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--On Thu, Jun 10, 1999 12:45 pm "Scott D. Davilla" <davilla@4pi.com> wrote:


>> The 'Mac'and 'PC' byte order is a bit of a misnomer 
>> anyway.  The Tiff format specifications allow both of the 
>> two possible byte orders, and any serious software 
>> reading Tiffs should handle both.  It just happened that
>> one byte order became de-facto standard on the Mac and 
>> the opposite on the PC.


> 	Actually not correct.

I would really like somebody to point out to me why any of the points made
by Scott proves my original statement to be incorrect.

> Byte order refers to the order in which bytes appear in 
> memory.

If you are talking about machine architecture and processors, sure, you can
have it only one way or the other.  Here we talk about a *file_format*. 
Although it is more convenient to read a little-endian byte-order file
under a little-endian machine architecture, you can of course read
big-endian files on little-endian machines and vice versa.  The Tiff
specification explicitly allows both byte orders.  Any piece of software,
on whatever platform, that can read Tiff files of only one byte order
simply does not conform to the Tiff specifications.

> There are two flavors, big endian and little endian. The
> term big/little endian comes from Gulliver's Travels and 
> two factions within Lilliputian society that argued about 
> which end of the egg to open, the big end or the little 
> end.

Although correct, it seems that this is not the information that would
prove me wrong.

> Intel processors use little endian order, Motorola
> processors use big endian order. PC's developed using 
> Intel processors, Mac's developed using Motorola
> processors thus is why they still use their particular
> flavor.

First: May I draw your attention to my original statement:  "It just
happened that one byte order became de-facto standard on the Mac and the
opposite on the PC."
It happened for the reason you give, of course, plus the fact that the Tiff
standard allows you to use whatever byte-order is convenient under your
architecture.

Second: May I draw your attention to the fact that there are more than two
types of processor in this world, and more than two platforms.
   Apart from the fact that the byte-order in a standardized file format is
independent (though not independently convenient) of the byte-order in the
hardware architecture, this is the second reason why "Mac Tiff" and "PC
Tiff" are misnomers.  You might as well call them "Amiga Tiff", "SGI Tiff",
"Atari Tiff", "StrongArm Tiff", "6502 Tiff", "NeXT Cube Tiff" or whatever. 
*Big-endian Tiff* and *Little-endian Tiff* is what they are if you want to
be strict.  I don't want to be, which is why I said the usual "Mac" vs. "PC
Tiff" is *a_bit* of a misnomer.



-----------------------------------------------------------------------
> Scott D. Davilla                              Phone: 919 489-1757 (tel)
> 4pi Analysis, Inc.                            Fax:   919 489-1487 (fax)
> 3500 Westgate Drive, Suite 403                email: davilla@4pi.com
> Durham, North Carolina  27707-2534            web: http://www.4pi.com
> 



--------------------------------------------------
Swidbert R OTT
Department of Zoology
University of Cambridge
Downing Street
Cambridge CB2 3EJ
ENGLAND


From nih-image-request@io.ece.drexel.edu Fri Jun 11 14:25 EDT 1999
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Hi,

We have recently upgraded our computer to G3 and since then I have not been
able to use NIH for quantification of western blots.  We have changed all
the settings for the protgram to the recomended ones.  However, I am still
not able to use the program.  Here is the problem.  After scanning the blot
and loading the macros when I mark the first lane I get only that lane in
the temp window and cannot mark the 2nd and 3ed lane.  I would very much
appreciate any help regarding this problem.

Thanks,

Maryam


******************************************************************************


Maryam Rafie-Kolpin, Ph.D.
Harvard-MIT Division of Health Science and Technology
77 Mass Ave.
E25-537
Cambridge, MA  02139

Phone#  (617) 253-1446
Fax     (617) 253-3459

******************************************************************************

                        



From nih-image-d-request@io.ece.drexel.edu Sat Jun 12 06:12 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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nih-image-d Digest				Volume 99 : Issue 133

Today's Topics:
  RE: TIFF Mac/PC                       [ Gary Chinga <gary.chinga@pfi.no> ]
  RE: TIFF Mac/PC                       [ Stein Roervik <steinr@chembio.ntnu. ]
  RE: TIFF Mac/PC                       [ jgilkey@u.arizona.edu (John C. Gilk ]
  Re: TIFF Mac/PC                       [ "Swidbert R OTT" <sro21@hermes.cam. ]
  Unidentified subject!                 [ Maryam Rafie-Kolpin <mkolpin@MIT.ED ]

------------------------------

Date: Fri, 11 Jun 1999 09:58:57 +0200
From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: TIFF Mac/PC
Message-ID: <c=NO%a=_%p=pfi%l=PFINT1-990611075857Z-1817@pfint1.pfi.no>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

The URL 

http://198.53.144.31/ ~poynton/papers/SMPTE_93_Gamma.html.

is outdated. If possible, can you mail me the paper (in PDF).  

Thanks.

Gary.



>For a discussion of gamma, see
>    Poynton, C.A.. 1993. "Gamma" and its disguises: the nonlinear mappings
>of intensity in perception, CRTs, Film and Video. Soc. Motion Picture &
>Television Engineers 102:1099 1108.  The paper is also available in Adobe
>PDF format from http://198.53.144.31/ ~poynton/papers/SMPTE_93_Gamma.html.
>An update is available from http://198.53.144.31/
>~poynton/Poynton-T-I-Digital-Video.html
>
>For information on International Color Consortium color correction, see:
>    http://www.color.org
>
>

------------------------------

Date: Fri, 11 Jun 1999 11:42:14 +0200
From: Stein Roervik <steinr@chembio.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: RE: TIFF Mac/PC
Message-Id: <v03102800b38689e5de4c@[129.241.83.55]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

>The URL
>
>http://198.53.144.31/ ~poynton/papers/SMPTE_93_Gamma.html.
>
>is outdated. If possible, can you mail me the paper (in PDF).
>

Du m fjerne spacen som ble satt inn av mailer programmet pga linjeskift:

http://198.53.144.31/~poynton/papers/SMPTE_93_Gamma.html
http://198.53.144.31/~poynton/Poynton-T-I-Digital-Video.html

Sjekket disse linkene nettopp, de virker.

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+

------------------------------

Date: Fri, 11 Jun 1999 08:48:11 -0700
From: jgilkey@u.arizona.edu (John C. Gilkey)
To: nih-image@io.ece.drexel.edu
Subject: RE: TIFF Mac/PC
Message-Id: <v02140b00b386dfc0b92d@[128.196.140.225]>
Content-Type: text/plain; charset="us-ascii"

Gary,
   I guess Stein has already gotten back to you - there was an extra space
in the URLs I sent out.  Try:

   http://198.53.144.31/~poynton/papers/SMPTE_93_Gamma.html.

John

------------------------------

Date: Fri, 11 Jun 1999 17:06:45  --633121
From: "Swidbert R OTT" <sro21@hermes.cam.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: TIFF Mac/PC
Message-ID: <416400.3138109605@neuron06.zoo.cam.ac.uk>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

--On Thu, Jun 10, 1999 12:45 pm "Scott D. Davilla" <davilla@4pi.com> wrote:


>> The 'Mac'and 'PC' byte order is a bit of a misnomer 
>> anyway.  The Tiff format specifications allow both of the 
>> two possible byte orders, and any serious software 
>> reading Tiffs should handle both.  It just happened that
>> one byte order became de-facto standard on the Mac and 
>> the opposite on the PC.


> 	Actually not correct.

I would really like somebody to point out to me why any of the points made
by Scott proves my original statement to be incorrect.

> Byte order refers to the order in which bytes appear in 
> memory.

If you are talking about machine architecture and processors, sure, you can
have it only one way or the other.  Here we talk about a *file_format*. 
Although it is more convenient to read a little-endian byte-order file
under a little-endian machine architecture, you can of course read
big-endian files on little-endian machines and vice versa.  The Tiff
specification explicitly allows both byte orders.  Any piece of software,
on whatever platform, that can read Tiff files of only one byte order
simply does not conform to the Tiff specifications.

> There are two flavors, big endian and little endian. The
> term big/little endian comes from Gulliver's Travels and 
> two factions within Lilliputian society that argued about 
> which end of the egg to open, the big end or the little 
> end.

Although correct, it seems that this is not the information that would
prove me wrong.

> Intel processors use little endian order, Motorola
> processors use big endian order. PC's developed using 
> Intel processors, Mac's developed using Motorola
> processors thus is why they still use their particular
> flavor.

First: May I draw your attention to my original statement:  "It just
happened that one byte order became de-facto standard on the Mac and the
opposite on the PC."
It happened for the reason you give, of course, plus the fact that the Tiff
standard allows you to use whatever byte-order is convenient under your
architecture.

Second: May I draw your attention to the fact that there are more than two
types of processor in this world, and more than two platforms.
   Apart from the fact that the byte-order in a standardized file format is
independent (though not independently convenient) of the byte-order in the
hardware architecture, this is the second reason why "Mac Tiff" and "PC
Tiff" are misnomers.  You might as well call them "Amiga Tiff", "SGI Tiff",
"Atari Tiff", "StrongArm Tiff", "6502 Tiff", "NeXT Cube Tiff" or whatever. 
*Big-endian Tiff* and *Little-endian Tiff* is what they are if you want to
be strict.  I don't want to be, which is why I said the usual "Mac" vs. "PC
Tiff" is *a_bit* of a misnomer.



-----------------------------------------------------------------------
> Scott D. Davilla                              Phone: 919 489-1757 (tel)
> 4pi Analysis, Inc.                            Fax:   919 489-1487 (fax)
> 3500 Westgate Drive, Suite 403                email: davilla@4pi.com
> Durham, North Carolina  27707-2534            web: http://www.4pi.com
> 



--------------------------------------------------
Swidbert R OTT
Department of Zoology
University of Cambridge
Downing Street
Cambridge CB2 3EJ
ENGLAND

------------------------------

Date: Fri, 11 Jun 1999 02:25:26 -0500
From: Maryam Rafie-Kolpin <mkolpin@MIT.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <v03020900b38663e118f2@[18.42.1.75]>
Content-Type: text/plain; charset="us-ascii"

Hi,

We have recently upgraded our computer to G3 and since then I have not been
able to use NIH for quantification of western blots.  We have changed all
the settings for the protgram to the recomended ones.  However, I am still
not able to use the program.  Here is the problem.  After scanning the blot
and loading the macros when I mark the first lane I get only that lane in
the temp window and cannot mark the 2nd and 3ed lane.  I would very much
appreciate any help regarding this problem.

Thanks,

Maryam


******************************************************************************


Maryam Rafie-Kolpin, Ph.D.
Harvard-MIT Division of Health Science and Technology
77 Mass Ave.
E25-537
Cambridge, MA  02139

Phone#  (617) 253-1446
Fax     (617) 253-3459

******************************************************************************

                        

--------------------------------
End of nih-image-d Digest V99 Issue #133
****************************************

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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 134

Today's Topics:
  Unidentified subject!                 [ Patrick Kiser <pfk2@acpub.duke.edu> ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
  courtesy                              [ jared rifkin <jared_rifkin@qc.edu> ]

------------------------------

Date: Sat, 12 Jun 1999 15:53:01 -0400
From: Patrick Kiser <pfk2@acpub.duke.edu>
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Subject: Unidentified subject!
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unsubscribe

------------------------------

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                   NIH-image Mailing List Help 
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2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
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quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
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Lines starting with a '#' are ignored.
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ls latest
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--

------------------------------

Date: Sun, 13 Jun 99 12:44:17 -0400
From: jared rifkin <jared_rifkin@qc.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: courtesy
Message-ID: <893A3772C7@qc1.qc.edu>
Content-Type: text/plain; charset="US-ASCII"

please- as a matter of simple courtesy:

follow the administrative rules if you want to 'unsubscribe' - don't send 
that message to the entire list of sunscribers.

thank you.

--------------------------------
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please- as a matter of simple courtesy:

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thank you.


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>I want to determine the x,y,z coordinates of particles from a stereo pair.
>(Actually gold
>particles located within the depth of an EM section). Does anyone know of
>software, macro or
>similar to do this? Thanks for your help.
>
>Peter Shaw. John Innes Centre, Norwich, UK. (peter.shaw@bbsrc.ac.uk)

Hi,

I have added source code to do this for remote mapping of topographic
surfaces from a pair of photographs, which you may be able to use.  The
requirements are:

- a pair of photographs taken from accurately known XYZ  positions (for us
this is a GPS position),

- a minimum of two known positions or the vector to those positions which
act as references on each photograph (for us a theodolite vector measured
in the field, or a position known by theodolite triangulation or GPS).

You add common points that you can identify on the two photographs, the
routine then interpolates vectors from the reference positions, and
triangulates these vectors.  You add all the points with clicking and
they're marked with non-destructive overlain crosses.

Our use is for mapping the lava dome at Montserrat.  If you have suitable
input information (camera and reference positions) you should be able to
use it though.

Regards - Richard


Richard Herd
Montserrat Volcano Observatory
St Johns
Montserrat
West Indies
email : rahe@ua.nkw.ac.uk
phone : (1) 664 491 5647
FAX : (1) 664 491 2324



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he made a mistake - I assume the same one that you made




At 12:44 PM 6/13/99 -0400, you wrote:
>please- as a matter of simple courtesy:
>
>follow the administrative rules if you want to 'unsubscribe' - don't send 
>that message to the entire list of sunscribers.
>
>thank you.
>
>

--------------------------------------------
William J. Clerici, Ph.D.
Associate Professor
Rm. C-236, Department of Surgery
Division of Otolaryngology-HNS
University of Kentucky Chandler Medical Center
800 Rose Street
Lexington, KY 40536-0084
           ------------------
Telephone: (606) 257-5097
      (lab): (606) 257-6020
      FAX: (606) 257-5096
      e-mail: bcler1@pop.uky.edu
--------------------------------------------


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Russell L. McCally, Ph.D
The Johns Hopkins University Applied Physics Laboratory
Institute for Advanced Science and Technology in Medicine
Laurel, MD 20723

(443) 778-6201 / Baltimore
(240) 228-6201 / Washington
FAX  (443) 778-5889 or (240) 228-5889



From nih-image-request@io.ece.drexel.edu Mon Jun 14 14:26 EDT 1999
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i have a question regarding using NIH image for analyzing MRI's.
What i would like to do is be able to construct a plot of a line in an MRI.
It should be able to read average densities along the line of around 10-15
pixels, much like a surface plot, but also be able to do this for a stack
of around 80 images, giving a density plot for each image. I would rather
find a way to do this automatically, without having to measure each image
individually.  Any suggestions on how i may accomplish this?



From nih-image-request@io.ece.drexel.edu Mon Jun 14 15:03 EDT 1999
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when I used image to scan a TEM negative, I get garbage on my screen.
On the preview screen of the scanner plug-in, the picture looks fine and

then when I scan, I get gritty, very dark images.  what could be causing

this and how can I fix it?

Anu Gupta


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Subject: nih-image-d Digest V99 #135
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 135

Today's Topics:
  Re: Stereo reconstructions            [ Richard Herd <rahe@unixa.nerc-keywo ]
  Re: courtesy                          [ "Bill Clerici, Ph.D." <bcler1@pop.u ]
  unsuscribe                            [ rmccally@aplcomm.jhuapl.edu ]
  MRI question                          [ ankoor shah <ashah7@ix.netcom.com> ]
  garbage scans                         [ Anu Gupta <angst16+@pitt.edu> ]

------------------------------

Date: Mon, 14 Jun 1999 06:55:45 +0400 (GMT)
From: Richard Herd <rahe@unixa.nerc-keyworth.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Stereo reconstructions
Message-Id: <l03130300b38913291959@[205.160.233.169]>
Content-Type: text/plain; charset="us-ascii"

>I want to determine the x,y,z coordinates of particles from a stereo pair.
>(Actually gold
>particles located within the depth of an EM section). Does anyone know of
>software, macro or
>similar to do this? Thanks for your help.
>
>Peter Shaw. John Innes Centre, Norwich, UK. (peter.shaw@bbsrc.ac.uk)

Hi,

I have added source code to do this for remote mapping of topographic
surfaces from a pair of photographs, which you may be able to use.  The
requirements are:

- a pair of photographs taken from accurately known XYZ  positions (for us
this is a GPS position),

- a minimum of two known positions or the vector to those positions which
act as references on each photograph (for us a theodolite vector measured
in the field, or a position known by theodolite triangulation or GPS).

You add common points that you can identify on the two photographs, the
routine then interpolates vectors from the reference positions, and
triangulates these vectors.  You add all the points with clicking and
they're marked with non-destructive overlain crosses.

Our use is for mapping the lava dome at Montserrat.  If you have suitable
input information (camera and reference positions) you should be able to
use it though.

Regards - Richard


Richard Herd
Montserrat Volcano Observatory
St Johns
Montserrat
West Indies
email : rahe@ua.nkw.ac.uk
phone : (1) 664 491 5647
FAX : (1) 664 491 2324

------------------------------

Date: Mon, 14 Jun 1999 08:34:44 -0400
From: "Bill Clerici, Ph.D." <bcler1@pop.uky.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: courtesy
Message-Id: <3.0.5.32.19990614083444.0089d100@pop.uky.edu>
Content-Type: text/plain; charset="us-ascii"

he made a mistake - I assume the same one that you made




At 12:44 PM 6/13/99 -0400, you wrote:
>please- as a matter of simple courtesy:
>
>follow the administrative rules if you want to 'unsubscribe' - don't send 
>that message to the entire list of sunscribers.
>
>thank you.
>
>

--------------------------------------------
William J. Clerici, Ph.D.
Associate Professor
Rm. C-236, Department of Surgery
Division of Otolaryngology-HNS
University of Kentucky Chandler Medical Center
800 Rose Street
Lexington, KY 40536-0084
           ------------------
Telephone: (606) 257-5097
      (lab): (606) 257-6020
      FAX: (606) 257-5096
      e-mail: bcler1@pop.uky.edu
--------------------------------------------

------------------------------

Date: Mon, 14 Jun 1999 09:33:19 -0400
From: rmccally@aplcomm.jhuapl.edu
To: nih-image@io.ece.drexel.edu
Subject: unsuscribe
Message-id: <v03007801b38ab50f9e10@[128.244.56.142]>
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Russell L. McCally, Ph.D
The Johns Hopkins University Applied Physics Laboratory
Institute for Advanced Science and Technology in Medicine
Laurel, MD 20723

(443) 778-6201 / Baltimore
(240) 228-6201 / Washington
FAX  (443) 778-5889 or (240) 228-5889

------------------------------

Date: Mon, 14 Jun 1999 10:13:17 -0800
From: ankoor shah <ashah7@ix.netcom.com>
To: nih-image@io.ece.drexel.edu
Subject: MRI question
Message-Id: <l03130302b38af5aa8cf7@[128.125.35.193]>
Content-Type: text/plain; charset="us-ascii"

i have a question regarding using NIH image for analyzing MRI's.
What i would like to do is be able to construct a plot of a line in an MRI.
It should be able to read average densities along the line of around 10-15
pixels, much like a surface plot, but also be able to do this for a stack
of around 80 images, giving a density plot for each image. I would rather
find a way to do this automatically, without having to measure each image
individually.  Any suggestions on how i may accomplish this?

------------------------------

Date: Mon, 14 Jun 1999 14:47:39 -0400
From: Anu Gupta <angst16+@pitt.edu>
To: nih-image@io.ece.drexel.edu
Subject: garbage scans
Message-ID: <37654E4B.E7ADB71C@pitt.edu>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
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when I used image to scan a TEM negative, I get garbage on my screen.
On the preview screen of the scanner plug-in, the picture looks fine and

then when I scan, I get gritty, very dark images.  what could be causing

this and how can I fix it?

Anu Gupta

--------------------------------
End of nih-image-d Digest V99 Issue #135
****************************************

From nih-image-request@io.ece.drexel.edu Tue Jun 15 08:36 EDT 1999
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From: mdparadi@MIT.EDU (Marc d. Paradis)
Subject: Re: Unidentified subject!
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Hello,
        The NIH quantification macro requires that you selct a "strongly"
rectanglar ROI around your band, that is, you must include a lot of space
above and below the band which you are trying to scan.  If you drag the
selection box only around the band of interest, the macro doesn't know
which way the lane runs and therefore cannot quantitate it.  If this does
not fix the problem, then this problem is beyond my understanding of the
macro.


                                -Marc d. Paradis
                                Dept. of Brain & Cognitive Science
                                M.I.T.

>Hi,
>
>We have recently upgraded our computer to G3 and since then I have not been
>able to use NIH for quantification of western blots.  We have changed all
>the settings for the protgram to the recomended ones.  However, I am still
>not able to use the program.  Here is the problem.  After scanning the blot
>and loading the macros when I mark the first lane I get only that lane in
>the temp window and cannot mark the 2nd and 3ed lane.  I would very much
>appreciate any help regarding this problem.
>
>Thanks,
>
>Maryam
>
>
>******************************************************************************
>
>
>Maryam Rafie-Kolpin, Ph.D.
>Harvard-MIT Division of Health Science and Technology
>77 Mass Ave.
>E25-537
>Cambridge, MA  02139
>
>Phone#  (617) 253-1446
>Fax     (617) 253-3459
>
>******************************************************************************
>
>



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From nih-image-request@io.ece.drexel.edu Tue Jun 15 11:55 EDT 1999
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Date: Tue, 15 Jun 1999 11:27:24 -0400
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_______________________________________________
Kelly L. Davis,
	<kelly@drexel.edu>
Neuropsychology			215 895 2455
Drexel University	http://www.pages.drexel.edu/grad/kld22

Ask not what disease the person has, but rather what person the disease
has.   ---attributed to William Osler



From nih-image-request@io.ece.drexel.edu Tue Jun 15 11:56 EDT 1999
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Date: Tue, 15 Jun 1999 11:48:17 -0400 (EDT)
From: "Dr. Shugang Ge" <nssgg@neuro.hfh.edu>
Subject: Parameter is too long
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I use NIH image for particle analysis. After every 6 analysis, there is 
always a message reads "parameter is too long" appeared. This prevents me 
from further usage of particle analysis, unless I restart my computer. 
Simply close and re-open the NIHimage program does not work. 

Anybody please tell me what should I do to eleminate this problem. Thanks

Shugang Ge
Neurosurgery Research
Henry Ford Hospital 


From nih-image-request@io.ece.drexel.edu Tue Jun 15 14:41 EDT 1999
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Subject: stereo images
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Are there any macros available for taking Silicon Graphics IRIX 6.5 .mv or
.tif images and converting them into anaglyphs (stereo images)?


From nih-image-request@io.ece.drexel.edu Tue Jun 15 21:09 EDT 1999
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Message-ID: <3766F691.550A0B12@fsktm.um.edu.my>
Date: Wed, 16 Jun 1999 08:57:53 +0800
From: selva <selva@fsktm.um.edu.my>
Organization: FSKTM
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I have bought the Siemens CT/MR to ACR/NEMA conversion program from
Evergreen Tech.  to read MRI images from the MOD disks using the pioneer
SCSI drive, about three years ago. The siemen magneton scanner at the
University hospital is not connected to the network and could only store
the MRI images in the optical disks. The scanners previously used Siemen
magneton vision Numaris 3  V8 31 C. We did not have any problems reading
the images from the optical disks as the Evergreen software converts it
to ACR NEMA which then can be imported to nih-image.

Lately Siemen upgraded the software at the MRI scanner to Siemen
magnetom vision Numaris 3 V8 33 B. According to the radiologists this
upgrading is neccessary for Y2K compliance. Our problem is that the
Evergreen software is unable to read the images. The  software keeps
giving the following error message

        Error opening dataset : dataset value error

This error message only seems to appear on scans which were done
recently (from May 1999), but scans done before this date work fine.
What we are worried is that the Siemens scanner is saving the MR data in
a new format and the  software is unable to read and convert it.  We
have reported this problem to Evergreen but we have not received any
reply. Is there any alternative software which will be able to read the
siemen images stored in the  MOD in the new format. We are really in a
dilemma and our research is at a standstill. Any help or suggestion will
be much appreciated.

Thank you,

Selva









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nih-image-d Digest				Volume 99 : Issue 136

Today's Topics:
  Re: Unidentified subject!             [ mdparadi@MIT.EDU (Marc d. Paradis) ]
  unsubscribe                           [ Susanne <correcto@dragon.upc.qc.ca> ]
  unsubscribe                           [ "Kelly L. Davis" <kelly@drexel.edu> ]
  Parameter is too long                 [ "Dr. Shugang Ge" <nssgg@neuro.hfh.e ]
  stereo images                         [ Catherine Ripley <ripley@aecom.yu.e ]
  Siemens CT/MR to ACR/NEMA             [ selva <selva@fsktm.um.edu.my> ]
  scrolling image with drawing line to  [ MARIAC <mariac@ird.ne> ]

------------------------------

Date: Tue, 15 Jun 1999 08:23:17 -0400
From: mdparadi@MIT.EDU (Marc d. Paradis)
To: nih-image@io.ece.drexel.edu
Subject: Re: Unidentified subject!
Message-Id: <v02140b02b38bf4ce8528@[18.42.1.20]>
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Hello,
        The NIH quantification macro requires that you selct a "strongly"
rectanglar ROI around your band, that is, you must include a lot of space
above and below the band which you are trying to scan.  If you drag the
selection box only around the band of interest, the macro doesn't know
which way the lane runs and therefore cannot quantitate it.  If this does
not fix the problem, then this problem is beyond my understanding of the
macro.


                                -Marc d. Paradis
                                Dept. of Brain & Cognitive Science
                                M.I.T.

>Hi,
>
>We have recently upgraded our computer to G3 and since then I have not been
>able to use NIH for quantification of western blots.  We have changed all
>the settings for the protgram to the recomended ones.  However, I am still
>not able to use the program.  Here is the problem.  After scanning the blot
>and loading the macros when I mark the first lane I get only that lane in
>the temp window and cannot mark the 2nd and 3ed lane.  I would very much
>appreciate any help regarding this problem.
>
>Thanks,
>
>Maryam
>
>
>******************************************************************************
>
>
>Maryam Rafie-Kolpin, Ph.D.
>Harvard-MIT Division of Health Science and Technology
>77 Mass Ave.
>E25-537
>Cambridge, MA  02139
>
>Phone#  (617) 253-1446
>Fax     (617) 253-3459
>
>******************************************************************************
>
>

------------------------------

Date: Mon, 14 Jun 1999 22:18:53 -0400
From: Susanne <correcto@dragon.upc.qc.ca>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <v04003a03b38b68807939@[205.205.174.83]>
Content-Type: text/plain; charset="us-ascii"


------------------------------

Date: Tue, 15 Jun 1999 11:27:24 -0400
From: "Kelly L. Davis" <kelly@drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-id: <v03110700b38c21473255@[204.183.92.6]>
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_______________________________________________
Kelly L. Davis,
	<kelly@drexel.edu>
Neuropsychology			215 895 2455
Drexel University	http://www.pages.drexel.edu/grad/kld22

Ask not what disease the person has, but rather what person the disease
has.   ---attributed to William Osler

------------------------------

Date: Tue, 15 Jun 1999 11:48:17 -0400 (EDT)
From: "Dr. Shugang Ge" <nssgg@neuro.hfh.edu>
To: nih-image@io.ece.drexel.edu
Subject: Parameter is too long
Message-Id: <Pine.3.89.9906151132.C29112-0100000@neurk11.neuro.hfh.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I use NIH image for particle analysis. After every 6 analysis, there is 
always a message reads "parameter is too long" appeared. This prevents me 
from further usage of particle analysis, unless I restart my computer. 
Simply close and re-open the NIHimage program does not work. 

Anybody please tell me what should I do to eleminate this problem. Thanks

Shugang Ge
Neurosurgery Research
Henry Ford Hospital 

------------------------------

Date: Tue, 15 Jun 1999 14:13:13 -0400
From: Catherine Ripley <ripley@aecom.yu.edu>
To: nih-image@io.ece.drexel.edu
Subject: stereo images
Message-Id: <3.0.6.32.19990615141313.007a8100@mailserver.aecom.yu.edu>
Content-Type: text/plain; charset="us-ascii"

Are there any macros available for taking Silicon Graphics IRIX 6.5 .mv or
.tif images and converting them into anaglyphs (stereo images)?

------------------------------

Date: Wed, 16 Jun 1999 08:57:53 +0800
From: selva <selva@fsktm.um.edu.my>
To: nih-image@io.ece.drexel.edu
Subject: Siemens CT/MR to ACR/NEMA 
Message-ID: <3766F691.550A0B12@fsktm.um.edu.my>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

I have bought the Siemens CT/MR to ACR/NEMA conversion program from
Evergreen Tech.  to read MRI images from the MOD disks using the pioneer
SCSI drive, about three years ago. The siemen magneton scanner at the
University hospital is not connected to the network and could only store
the MRI images in the optical disks. The scanners previously used Siemen
magneton vision Numaris 3  V8 31 C. We did not have any problems reading
the images from the optical disks as the Evergreen software converts it
to ACR NEMA which then can be imported to nih-image.

Lately Siemen upgraded the software at the MRI scanner to Siemen
magnetom vision Numaris 3 V8 33 B. According to the radiologists this
upgrading is neccessary for Y2K compliance. Our problem is that the
Evergreen software is unable to read the images. The  software keeps
giving the following error message

        Error opening dataset : dataset value error

This error message only seems to appear on scans which were done
recently (from May 1999), but scans done before this date work fine.
What we are worried is that the Siemens scanner is saving the MR data in
a new format and the  software is unable to read and convert it.  We
have reported this problem to Evergreen but we have not received any
reply. Is there any alternative software which will be able to read the
siemen images stored in the  MOD in the new format. We are really in a
dilemma and our research is at a standstill. Any help or suggestion will
be much appreciated.

Thank you,

Selva

------------------------------

Date: Wed, 16 Jun 1999 10:13:54 +0200
From: MARIAC <mariac@ird.ne>
To: nih-image@io.ece.drexel.edu
Subject: scrolling image with drawing line tolls
Message-Id: <3.0.1.32.19990616101354.007d6a90@192.136.57.17>
Content-Type: text/enriched; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Hello,


I would like to know if its possible to make the image windows scroll when I=
 use tools like the line drawing tool. I'm working with scionimage/pc.

Thanks


C=E9dric.

<bold><italic><color><param>0000,8080,0000</param>=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

</color><color><param>0000,0000,ffff</param>

</color></italic></bold><italic><color><param>0000,0000,ffff</param>C=E9dric
<bold>Mariac

</bold></color></italic>Laboratoire de g=E9n=E9tique des plantes


IRD L'institut de recherche pour le d=E9veloppement=20

anciennement ORSTOM

BP 11416 Niamey=20

Republique du NIGER


<underline><color><param>0000,8080,0000</param>E-mail
:</color></underline><color><param>0000,8080,0000</param>
</color>mariac@ird.ne

<underline><color><param>0000,8080,0000</param>Tel :</color></underline>
(227) 75 31 15 / 75 26 10 / 75 38 27

<underline><color><param>0000,8080,0000</param>Fax :</color></underline>=
 (227) 75 28 04 / 75 20 54

<underline><color><param>0000,0000,fefe</param>

</color></underline><bold><italic><color><param>0000,8080,0000</param>=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D</color></ita=
lic></bold>=20

--------------------------------
End of nih-image-d Digest V99 Issue #136
****************************************

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From: MARIAC <mariac@ird.ne>
Subject: scrolling image with drawing line tolls
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Hello,


I would like to know if its possible to make the image windows scroll when I=
 use tools like the line drawing tool. I'm working with scionimage/pc.

Thanks


C=E9dric.

<bold><italic><color><param>0000,8080,0000</param>=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

</color><color><param>0000,0000,ffff</param>

</color></italic></bold><italic><color><param>0000,0000,ffff</param>C=E9dric
<bold>Mariac

</bold></color></italic>Laboratoire de g=E9n=E9tique des plantes


IRD L'institut de recherche pour le d=E9veloppement=20

anciennement ORSTOM

BP 11416 Niamey=20

Republique du NIGER


<underline><color><param>0000,8080,0000</param>E-mail
:</color></underline><color><param>0000,8080,0000</param>
</color>mariac@ird.ne

<underline><color><param>0000,8080,0000</param>Tel :</color></underline>
(227) 75 31 15 / 75 26 10 / 75 38 27

<underline><color><param>0000,8080,0000</param>Fax :</color></underline>=
 (227) 75 28 04 / 75 20 54

<underline><color><param>0000,0000,fefe</param>

</color></underline><bold><italic><color><param>0000,8080,0000</param>=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D</color></ita=
lic></bold>=20



From nih-image-request@io.ece.drexel.edu Wed Jun 16 14:08 EDT 1999
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Date: Wed, 16 Jun 1999 13:48:14 -0400
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The Siemens routine initiated by "System; External Data" from the Numaris pulldown allows you to 'Export' image files. The format of the files
created by this routine is Dicom 3 (it was Dicom 2, but the new Numaris is different, I think). I'm not sure how to archive these on the Pioneer: it
can be mounted, however, as a standard UNIX SCSI device.

Paul Hees
Cardiology Division
Johns Hopkins University School of Medicine
phees@jhmi.edu

>   ------------------------------------------------------------------------
>
> Subject: Siemens CT/MR to ACR/NEMA
> Date: Wed, 16 Jun 1999 08:57:53 +0800
> From: selva <selva@fsktm.um.edu.my>
> To: nih-image@io.ece.drexel.edu
>
> I have bought the Siemens CT/MR to ACR/NEMA conversion program from
> Evergreen Tech.  to read MRI images from the MOD disks using the pioneer
> SCSI drive, about three years ago. The siemen magneton scanner at the
> University hospital is not connected to the network and could only store
> the MRI images in the optical disks. The scanners previously used Siemen
> magneton vision Numaris 3  V8 31 C. We did not have any problems reading
> the images from the optical disks as the Evergreen software converts it
> to ACR NEMA which then can be imported to nih-image.
>
> Lately Siemen upgraded the software at the MRI scanner to Siemen
> magnetom vision Numaris 3 V8 33 B. According to the radiologists this
> upgrading is neccessary for Y2K compliance. Our problem is that the
> Evergreen software is unable to read the images. The  software keeps
> giving the following error message
>
>         Error opening dataset : dataset value error
>
> This error message only seems to appear on scans which were done
> recently (from May 1999), but scans done before this date work fine.
> What we are worried is that the Siemens scanner is saving the MR data in
> a new format and the  software is unable to read and convert it.  We
> have reported this problem to Evergreen but we have not received any
> reply. Is there any alternative software which will be able to read the
> siemen images stored in the  MOD in the new format. We are really in a
> dilemma and our research is at a standstill. Any help or suggestion will
> be much appreciated.
>
> Thank you,
>
> Selva
>


From nih-image-request@io.ece.drexel.edu Wed Jun 16 16:22 EDT 1999
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From: Greg Joss <gjoss@hotmail.com>
To: nih-image@io.ece.drexel.edu
Cc: patw@med.usyd.edu.au
Subject: Re: Fourier Descriptors
Date: Thu, 17 Jun 1999 06:05:35 EST
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>From: DrJohnRuss@aol.com
>Date: Tue, 8 Jun 1999 19:50:09 EDT
>Subject: Re: Fourier Descriptors
>To: nih-image@io.ece.drexel.edu
>
>In a message dated 6/8/99 7:18:11 PM, patw@med.usyd.edu.au writes:
>
> >We are investigating cerebral microvasculature and require a method to
> >compare shape of vessel profiles.  Exploring the possibilities of Fourier
> >descriptors has been thwarted by repeated computer crashes when we 
>attempt
> >to open ImageFFt128b6.hqx.  Can anyone suggest how we might be able to
> >do this?
>
>There really is no reason to try to use the older program, as the current
>versions of the standard NIH-Image written for the PPC include all of the
>same Fourier processing capabilities. However, neither of these does what 
>you
>want. They perform an 2D FFT on the entire grey scale image, whereas what I
>believe you are talking about is to use harmonic analysis on the shape of 
>the
>vessels. NIH-Image doesn't provide that capability. There are a few 
>programs
>that do (much more expensive) and I've been experimenting with a variant of
>the technique that may become part of the Image Processing Tool Kit in some
>future release. Your best bet at the moment is probably to use Image to 
>write
>out a file of the coordinates of the boundary of the vessel and perform the
>harmonic analysis off-line.
>
>John Russ
>

Pat,

I developed such a procedure to do harmonic analysis on the shape of objects 
in colaboration with Mick Howland (ex Southern Cross University, now 
Tasmania National Parks?) for the purpose of characterising fish otolith 
(earbone) shapes using NIH-Image. The procedure worked quite well and was 
easy to interface with. ie select a ROI (outline) and macro returned array 
of parameters. There are some tricks involved with xyCoordinates and whole 
would be better implemented now in Object-Image.

I am currently in transit (Berlin) but expect to be back in harness at 
Macquarie Uni about end July if you can wait till then. I would suggest 
that, if you need to develope routines from scratch yourself, it would be 
worthwhile waiting as you would spend some considerable time doing it 
yourself unless you are much more proficient than we were.

Greg Joss
gjoss@rna.bio.mq.edu.au



______________________________________________________
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From nih-image-request@io.ece.drexel.edu Wed Jun 16 16:56 EDT 1999
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From: Greg Joss <gjoss@hotmail.com>
To: nih-image@io.ece.drexel.edu
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Subject: Re: How to Average Frames,Pixera
Date: Thu, 17 Jun 1999 06:41:12 EST
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>Subject: Re: How to Average Frames,Pixera
>Date: Wed, 9 Jun 99 12:31:20 -0400
>From: jared rifkin <jared_rifkin@qc.edu>
>To: <nih-image@io.ece.drexel.edu>

>also- how can i combine trapping say 10 frames (for averaging) every
>minute for perhaps an hour or two. i'm tracking cell movements - they are
>slow and single frames are just too noisy to get good resolution -and- i
>don't have the memory to trap and store contnuous video of a couple of
>hours.
>don't shoot me but i primarily use Adobe Premiere, not nih image.  i
>know- i'm an alien but have pity.
>
>-dr. j. rifkin
>biology dept
>queens college
>new york, ny 11367
>jared_rifkin@qc.edu

Jared,
I dont know Pixera interface, but if you were doing video capture via 
NIH-Image or Object-Image, it is, in principle quite straight forward to do 
what you ask.

repeat begin
StartCapturing;{is needed to initiate video each time}
AverageFrames('Average',frames);
{Averages or integrates  video frames. integrate will fit histogram to 
1<>254 each captured frame; Average will maintain same intensity calibration 
}
saveAs(filename,n:4:0); {or copy;selectPic(stackP); paste;}
wait(delay);
end until keydown('control');

would in principle do it; but you would probably want considerable 
elaboration in practice.

I am not confident that this would help with Pixera as I presume you would 
be capturing an RGB stack which needs to be averaged in each R,G,B etc but I 
would have thought that Pixera would have considerable problems with 
tracking cells as frame capture speed is quite slow.

With video camera, you can capture 16 frames in <1 sec so that cell movement 
blurring is negligible. A inexpensive monochrome video camera can give 
excellent quality with Scion LG3 averaged frames even under very low light 
level noisey conditions.

Greg Joss
gjoss@rna.bio.mq.edu.au


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From nih-image-request@io.ece.drexel.edu Wed Jun 16 17:03 EDT 1999
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Date: Wed, 16 Jun 1999 13:47:06 -0700
From: "Kevin E. Cooper" <kevin.cooper@asu.edu>
Subject: Re: Fourier Descriptors
To: nih-image@io.ece.drexel.edu
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unsubscribe
-----Original Message-----
From: Greg Joss <gjoss@hotmail.com>
To: nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
Cc: patw@med.usyd.edu.au <patw@med.usyd.edu.au>
Date: Wednesday, June 16, 1999 1:25 PM
Subject: Re: Fourier Descriptors


>>From: DrJohnRuss@aol.com
>>Date: Tue, 8 Jun 1999 19:50:09 EDT
>>Subject: Re: Fourier Descriptors
>>To: nih-image@io.ece.drexel.edu
>>
>>In a message dated 6/8/99 7:18:11 PM, patw@med.usyd.edu.au writes:
>>
>> >We are investigating cerebral microvasculature and require a method to
>> >compare shape of vessel profiles.  Exploring the possibilities of
Fourier
>> >descriptors has been thwarted by repeated computer crashes when we
>>attempt
>> >to open ImageFFt128b6.hqx.  Can anyone suggest how we might be able to
>> >do this?
>>
>>There really is no reason to try to use the older program, as the current
>>versions of the standard NIH-Image written for the PPC include all of the
>>same Fourier processing capabilities. However, neither of these does what
>>you
>>want. They perform an 2D FFT on the entire grey scale image, whereas what
I
>>believe you are talking about is to use harmonic analysis on the shape of
>>the
>>vessels. NIH-Image doesn't provide that capability. There are a few
>>programs
>>that do (much more expensive) and I've been experimenting with a variant
of
>>the technique that may become part of the Image Processing Tool Kit in
some
>>future release. Your best bet at the moment is probably to use Image to
>>write
>>out a file of the coordinates of the boundary of the vessel and perform
the
>>harmonic analysis off-line.
>>
>>John Russ
>>
>
>Pat,
>
>I developed such a procedure to do harmonic analysis on the shape of
objects
>in colaboration with Mick Howland (ex Southern Cross University, now
>Tasmania National Parks?) for the purpose of characterising fish otolith
>(earbone) shapes using NIH-Image. The procedure worked quite well and was
>easy to interface with. ie select a ROI (outline) and macro returned array
>of parameters. There are some tricks involved with xyCoordinates and whole
>would be better implemented now in Object-Image.
>
>I am currently in transit (Berlin) but expect to be back in harness at
>Macquarie Uni about end July if you can wait till then. I would suggest
>that, if you need to develope routines from scratch yourself, it would be
>worthwhile waiting as you would spend some considerable time doing it
>yourself unless you are much more proficient than we were.
>
>Greg Joss
>gjoss@rna.bio.mq.edu.au
>
>
>
>______________________________________________________
>Get Your Private, Free Email at http://www.hotmail.com
>


From nih-image-request@io.ece.drexel.edu Wed Jun 16 17:09 EDT 1999
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-----Original Message-----
From: Ben Elkin <elk@igb.fhg.de>
To: nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
Date: Tuesday, June 01, 1999 6:45 AM
Subject: Re: nih-image-d Digest V99 #122


>>
>>At 11:18 PM 5/29/99 +0300, you wrote:
>>>Hi,
>>>I have requested several times to unsunscribe me.
>>>Please take care.
>>>Thanks,
>>>
>>>Prof. Gershon Golomb,
>>>Head, Dept. of Pharmaceutics
>
>Dear Prof. Golomb,
>
>even though there might be a person who administrates the list and would
>take care to unsubscribe you from the list, it is always better to use the
>standard mechanism:
>
>
>Unsubscribe
>-----------
>To unsubscribe to the list, send E-mail to
nih-image-request@biomed.drexel.edu.
>the Subject of the message should contain "unsubscribe".
>
>As in: To: nih-image-request@biomed.drexel.edu
> Subject: unsubscribe
>
>Please send the mail to the address above, not to the list itself.
>
>Regards
>
>
>Ben Elkin
>
>=======================================
>elk@igb.fhg.de
>
>http://www.igb.fhg.de/GVT/
>
>Fraunhofer Institute for Interfacial Technology and Bioengineering
>                    (fuer Grenzflaechen und Bioverfahrenstechnik)
>
>Nobelstr. 12    D-70569 Stuttgart    Germany
>
>Tel. +49 - 711 - 970-4144, -4161
>Fax                 -4200
>
>
>


From nih-image-request@io.ece.drexel.edu Thu Jun 17 03:11 EDT 1999
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From: Tim Fairchild <timf@cyllene.uwa.edu.au>
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Whilst capturing some images a couple of days ago, I came across an
ominous problem.  Whilst I was capturing the darker images, the exposure
time was correctly set, however when I was capturing the lighter images,
I was losing a lot of information, due to the exposure time not being
long enough during the capture.  To counteract this, I changed the
exposure time and captured the image (PAS stain) using the colour mode.
We are concurrently using a kodak scanner step tablet (ST-34) to convert
our measures into O.D. units.  My questions therefore are:

Should I convert my image into a greyscale before analysis?
Should I capture the step tablet in colour mode?
Should I just change the exposure time and capture the images in B&W?

The system we are using is a CMOS-PRO digital camera mounted on a Nikon
Eclipse microscope.

Thanks in advance
Tim.
-----------------------------------------------------------------
Timothy J. Fairchild B.Sc. (Hons)
PhD Candidate
Co-ordinator for Centre of Athletic Testing
Department of Human Movement and Exercise Science
Nedlands, Western Australia 6907
Telephone: (+61 8) 9380 2793
Facsimile:  (+61 8) 9380 1039
Email: timf@cyllene.uwa.edu.au
http://www.general.uwa.edu.au/~hmweb/index.htm




From nih-image-d-request@io.ece.drexel.edu Thu Jun 17 06:15 EDT 1999
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Subject: nih-image-d Digest V99 #137
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 137

Today's Topics:
  Re: nih-image-d Digest V99 #136       [ "Paul S. Hees" <phees@welch.jhu.edu ]
  Re: Fourier Descriptors               [ Greg Joss <gjoss@hotmail.com> ]
  Re: How to Average Frames,Pixera      [ Greg Joss <gjoss@hotmail.com> ]
  Re: Fourier Descriptors               [ "Kevin E. Cooper" <kevin.cooper@asu ]
  unsubscribe                           [ "Kevin E. Cooper" <kevin.cooper@asu ]
  Colour vs. Greyscale                  [ Tim Fairchild <timf@cyllene.uwa.edu ]

------------------------------

Date: Wed, 16 Jun 1999 13:48:14 -0400
From: "Paul S. Hees" <phees@welch.jhu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #136
Message-ID: <3767E35B.71770F5D@welch.jhu.edu>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

The Siemens routine initiated by "System; External Data" from the Numaris pulldown allows you to 'Export' image files. The format of the files
created by this routine is Dicom 3 (it was Dicom 2, but the new Numaris is different, I think). I'm not sure how to archive these on the Pioneer: it
can be mounted, however, as a standard UNIX SCSI device.

Paul Hees
Cardiology Division
Johns Hopkins University School of Medicine
phees@jhmi.edu

>   ------------------------------------------------------------------------
>
> Subject: Siemens CT/MR to ACR/NEMA
> Date: Wed, 16 Jun 1999 08:57:53 +0800
> From: selva <selva@fsktm.um.edu.my>
> To: nih-image@io.ece.drexel.edu
>
> I have bought the Siemens CT/MR to ACR/NEMA conversion program from
> Evergreen Tech.  to read MRI images from the MOD disks using the pioneer
> SCSI drive, about three years ago. The siemen magneton scanner at the
> University hospital is not connected to the network and could only store
> the MRI images in the optical disks. The scanners previously used Siemen
> magneton vision Numaris 3  V8 31 C. We did not have any problems reading
> the images from the optical disks as the Evergreen software converts it
> to ACR NEMA which then can be imported to nih-image.
>
> Lately Siemen upgraded the software at the MRI scanner to Siemen
> magnetom vision Numaris 3 V8 33 B. According to the radiologists this
> upgrading is neccessary for Y2K compliance. Our problem is that the
> Evergreen software is unable to read the images. The  software keeps
> giving the following error message
>
>         Error opening dataset : dataset value error
>
> This error message only seems to appear on scans which were done
> recently (from May 1999), but scans done before this date work fine.
> What we are worried is that the Siemens scanner is saving the MR data in
> a new format and the  software is unable to read and convert it.  We
> have reported this problem to Evergreen but we have not received any
> reply. Is there any alternative software which will be able to read the
> siemen images stored in the  MOD in the new format. We are really in a
> dilemma and our research is at a standstill. Any help or suggestion will
> be much appreciated.
>
> Thank you,
>
> Selva
>

------------------------------

Date: Thu, 17 Jun 1999 06:05:35 EST
From: Greg Joss <gjoss@hotmail.com>
To: nih-image@io.ece.drexel.edu
Cc: patw@med.usyd.edu.au
Subject: Re: Fourier Descriptors
Message-ID: <19990616200544.66677.qmail@hotmail.com>
Content-Type: text/plain; format=flowed

>From: DrJohnRuss@aol.com
>Date: Tue, 8 Jun 1999 19:50:09 EDT
>Subject: Re: Fourier Descriptors
>To: nih-image@io.ece.drexel.edu
>
>In a message dated 6/8/99 7:18:11 PM, patw@med.usyd.edu.au writes:
>
> >We are investigating cerebral microvasculature and require a method to
> >compare shape of vessel profiles.  Exploring the possibilities of Fourier
> >descriptors has been thwarted by repeated computer crashes when we 
>attempt
> >to open ImageFFt128b6.hqx.  Can anyone suggest how we might be able to
> >do this?
>
>There really is no reason to try to use the older program, as the current
>versions of the standard NIH-Image written for the PPC include all of the
>same Fourier processing capabilities. However, neither of these does what 
>you
>want. They perform an 2D FFT on the entire grey scale image, whereas what I
>believe you are talking about is to use harmonic analysis on the shape of 
>the
>vessels. NIH-Image doesn't provide that capability. There are a few 
>programs
>that do (much more expensive) and I've been experimenting with a variant of
>the technique that may become part of the Image Processing Tool Kit in some
>future release. Your best bet at the moment is probably to use Image to 
>write
>out a file of the coordinates of the boundary of the vessel and perform the
>harmonic analysis off-line.
>
>John Russ
>

Pat,

I developed such a procedure to do harmonic analysis on the shape of objects 
in colaboration with Mick Howland (ex Southern Cross University, now 
Tasmania National Parks?) for the purpose of characterising fish otolith 
(earbone) shapes using NIH-Image. The procedure worked quite well and was 
easy to interface with. ie select a ROI (outline) and macro returned array 
of parameters. There are some tricks involved with xyCoordinates and whole 
would be better implemented now in Object-Image.

I am currently in transit (Berlin) but expect to be back in harness at 
Macquarie Uni about end July if you can wait till then. I would suggest 
that, if you need to develope routines from scratch yourself, it would be 
worthwhile waiting as you would spend some considerable time doing it 
yourself unless you are much more proficient than we were.

Greg Joss
gjoss@rna.bio.mq.edu.au



______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com

------------------------------

Date: Thu, 17 Jun 1999 06:41:12 EST
From: Greg Joss <gjoss@hotmail.com>
To: nih-image@io.ece.drexel.edu
Cc: jared_rifkin@qc.edu
Subject: Re: How to Average Frames,Pixera
Message-ID: <19990616204117.13925.qmail@hotmail.com>
Content-Type: text/plain; format=flowed

>Subject: Re: How to Average Frames,Pixera
>Date: Wed, 9 Jun 99 12:31:20 -0400
>From: jared rifkin <jared_rifkin@qc.edu>
>To: <nih-image@io.ece.drexel.edu>

>also- how can i combine trapping say 10 frames (for averaging) every
>minute for perhaps an hour or two. i'm tracking cell movements - they are
>slow and single frames are just too noisy to get good resolution -and- i
>don't have the memory to trap and store contnuous video of a couple of
>hours.
>don't shoot me but i primarily use Adobe Premiere, not nih image.  i
>know- i'm an alien but have pity.
>
>-dr. j. rifkin
>biology dept
>queens college
>new york, ny 11367
>jared_rifkin@qc.edu

Jared,
I dont know Pixera interface, but if you were doing video capture via 
NIH-Image or Object-Image, it is, in principle quite straight forward to do 
what you ask.

repeat begin
StartCapturing;{is needed to initiate video each time}
AverageFrames('Average',frames);
{Averages or integrates  video frames. integrate will fit histogram to 
1<>254 each captured frame; Average will maintain same intensity calibration 
}
saveAs(filename,n:4:0); {or copy;selectPic(stackP); paste;}
wait(delay);
end until keydown('control');

would in principle do it; but you would probably want considerable 
elaboration in practice.

I am not confident that this would help with Pixera as I presume you would 
be capturing an RGB stack which needs to be averaged in each R,G,B etc but I 
would have thought that Pixera would have considerable problems with 
tracking cells as frame capture speed is quite slow.

With video camera, you can capture 16 frames in <1 sec so that cell movement 
blurring is negligible. A inexpensive monochrome video camera can give 
excellent quality with Scion LG3 averaged frames even under very low light 
level noisey conditions.

Greg Joss
gjoss@rna.bio.mq.edu.au


______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com

------------------------------

Date: Wed, 16 Jun 1999 13:47:06 -0700
From: "Kevin E. Cooper" <kevin.cooper@asu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Fourier Descriptors
Message-id: <000601beb839$65c04a60$f524db81@enpc2294.eas.asu.edu>
Content-type: text/plain;	charset="iso-8859-1"
Content-transfer-encoding: 7bit

unsubscribe
-----Original Message-----
From: Greg Joss <gjoss@hotmail.com>
To: nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
Cc: patw@med.usyd.edu.au <patw@med.usyd.edu.au>
Date: Wednesday, June 16, 1999 1:25 PM
Subject: Re: Fourier Descriptors


>>From: DrJohnRuss@aol.com
>>Date: Tue, 8 Jun 1999 19:50:09 EDT
>>Subject: Re: Fourier Descriptors
>>To: nih-image@io.ece.drexel.edu
>>
>>In a message dated 6/8/99 7:18:11 PM, patw@med.usyd.edu.au writes:
>>
>> >We are investigating cerebral microvasculature and require a method to
>> >compare shape of vessel profiles.  Exploring the possibilities of
Fourier
>> >descriptors has been thwarted by repeated computer crashes when we
>>attempt
>> >to open ImageFFt128b6.hqx.  Can anyone suggest how we might be able to
>> >do this?
>>
>>There really is no reason to try to use the older program, as the current
>>versions of the standard NIH-Image written for the PPC include all of the
>>same Fourier processing capabilities. However, neither of these does what
>>you
>>want. They perform an 2D FFT on the entire grey scale image, whereas what
I
>>believe you are talking about is to use harmonic analysis on the shape of
>>the
>>vessels. NIH-Image doesn't provide that capability. There are a few
>>programs
>>that do (much more expensive) and I've been experimenting with a variant
of
>>the technique that may become part of the Image Processing Tool Kit in
some
>>future release. Your best bet at the moment is probably to use Image to
>>write
>>out a file of the coordinates of the boundary of the vessel and perform
the
>>harmonic analysis off-line.
>>
>>John Russ
>>
>
>Pat,
>
>I developed such a procedure to do harmonic analysis on the shape of
objects
>in colaboration with Mick Howland (ex Southern Cross University, now
>Tasmania National Parks?) for the purpose of characterising fish otolith
>(earbone) shapes using NIH-Image. The procedure worked quite well and was
>easy to interface with. ie select a ROI (outline) and macro returned array
>of parameters. There are some tricks involved with xyCoordinates and whole
>would be better implemented now in Object-Image.
>
>I am currently in transit (Berlin) but expect to be back in harness at
>Macquarie Uni about end July if you can wait till then. I would suggest
>that, if you need to develope routines from scratch yourself, it would be
>worthwhile waiting as you would spend some considerable time doing it
>yourself unless you are much more proficient than we were.
>
>Greg Joss
>gjoss@rna.bio.mq.edu.au
>
>
>
>______________________________________________________
>Get Your Private, Free Email at http://www.hotmail.com
>

------------------------------

Date: Wed, 16 Jun 1999 13:52:51 -0700
From: "Kevin E. Cooper" <kevin.cooper@asu.edu>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-id: <012d01beb83a$331cec20$f524db81@enpc2294.eas.asu.edu>
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Content-transfer-encoding: 7bit

-----Original Message-----
From: Ben Elkin <elk@igb.fhg.de>
To: nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
Date: Tuesday, June 01, 1999 6:45 AM
Subject: Re: nih-image-d Digest V99 #122


>>
>>At 11:18 PM 5/29/99 +0300, you wrote:
>>>Hi,
>>>I have requested several times to unsunscribe me.
>>>Please take care.
>>>Thanks,
>>>
>>>Prof. Gershon Golomb,
>>>Head, Dept. of Pharmaceutics
>
>Dear Prof. Golomb,
>
>even though there might be a person who administrates the list and would
>take care to unsubscribe you from the list, it is always better to use the
>standard mechanism:
>
>
>Unsubscribe
>-----------
>To unsubscribe to the list, send E-mail to
nih-image-request@biomed.drexel.edu.
>the Subject of the message should contain "unsubscribe".
>
>As in: To: nih-image-request@biomed.drexel.edu
> Subject: unsubscribe
>
>Please send the mail to the address above, not to the list itself.
>
>Regards
>
>
>Ben Elkin
>
>=======================================
>elk@igb.fhg.de
>
>http://www.igb.fhg.de/GVT/
>
>Fraunhofer Institute for Interfacial Technology and Bioengineering
>                    (fuer Grenzflaechen und Bioverfahrenstechnik)
>
>Nobelstr. 12    D-70569 Stuttgart    Germany
>
>Tel. +49 - 711 - 970-4144, -4161
>Fax                 -4200
>
>
>

------------------------------

Date: Thu, 17 Jun 1999 15:03:30 +0800
From: Tim Fairchild <timf@cyllene.uwa.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Colour vs. Greyscale
Message-ID: <37689DA0.BB9E1FE6@cyllene.uwa.edu.au>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Whilst capturing some images a couple of days ago, I came across an
ominous problem.  Whilst I was capturing the darker images, the exposure
time was correctly set, however when I was capturing the lighter images,
I was losing a lot of information, due to the exposure time not being
long enough during the capture.  To counteract this, I changed the
exposure time and captured the image (PAS stain) using the colour mode.
We are concurrently using a kodak scanner step tablet (ST-34) to convert
our measures into O.D. units.  My questions therefore are:

Should I convert my image into a greyscale before analysis?
Should I capture the step tablet in colour mode?
Should I just change the exposure time and capture the images in B&W?

The system we are using is a CMOS-PRO digital camera mounted on a Nikon
Eclipse microscope.

Thanks in advance
Tim.
-----------------------------------------------------------------
Timothy J. Fairchild B.Sc. (Hons)
PhD Candidate
Co-ordinator for Centre of Athletic Testing
Department of Human Movement and Exercise Science
Nedlands, Western Australia 6907
Telephone: (+61 8) 9380 2793
Facsimile:  (+61 8) 9380 1039
Email: timf@cyllene.uwa.edu.au
http://www.general.uwa.edu.au/~hmweb/index.htm

--------------------------------
End of nih-image-d Digest V99 Issue #137
****************************************

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>------------------------------
>nih-image-d Digest				Volume 99 : Issue 137
>
>Today's Topics:
>  Re: nih-image-d Digest V99 #136       [ "Paul S. Hees"
><phees@welch.jhu.edu ]
>  Re: Fourier Descriptors               [ Greg Joss <gjoss@hotmail.com> ]
>  Re: How to Average Frames,Pixera      [ Greg Joss <gjoss@hotmail.com> ]
>  Re: Fourier Descriptors               [ "Kevin E. Cooper"
><kevin.cooper@asu ]
>  unsubscribe                           [ "Kevin E. Cooper"
><kevin.cooper@asu ]
>  Colour vs. Greyscale                  [ Tim Fairchild
><timf@cyllene.uwa.edu ]
>
>------------------------------
>Date: Wed, 16 Jun 1999 13:48:14 -0400
>From: "Paul S. Hees" <phees@welch.jhu.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: nih-image-d Digest V99 #136
>Message-ID: <3767E35B.71770F5D@welch.jhu.edu>
>Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854";
>x-mac-creator="4D4F5353"
>Content-Transfer-Encoding: 7bit
>
>The Siemens routine initiated by "System; External Data" from the Numaris
>pulldown allows you to 'Export' image files. The format of the files
>created by this routine is Dicom 3 (it was Dicom 2, but the new Numaris is
>different, I think). I'm not sure how to archive these on the Pioneer: it
>can be mounted, however, as a standard UNIX SCSI device.
>
>Paul Hees
>Cardiology Division
>Johns Hopkins University School of Medicine
>phees@jhmi.edu
>
>>   ------------------------------------------------------------------------
>>
>> Subject: Siemens CT/MR to ACR/NEMA
>> Date: Wed, 16 Jun 1999 08:57:53 +0800
>> From: selva <selva@fsktm.um.edu.my>
>> To: nih-image@io.ece.drexel.edu
>>
>> I have bought the Siemens CT/MR to ACR/NEMA conversion program from
>> Evergreen Tech.  to read MRI images from the MOD disks using the pioneer
>> SCSI drive, about three years ago. The siemen magneton scanner at the
>> University hospital is not connected to the network and could only store
>> the MRI images in the optical disks. The scanners previously used Siemen
>> magneton vision Numaris 3  V8 31 C. We did not have any problems reading
>> the images from the optical disks as the Evergreen software converts it
>> to ACR NEMA which then can be imported to nih-image.
>>
>> Lately Siemen upgraded the software at the MRI scanner to Siemen
>> magnetom vision Numaris 3 V8 33 B. According to the radiologists this
>> upgrading is neccessary for Y2K compliance. Our problem is that the
>> Evergreen software is unable to read the images. The  software keeps
>> giving the following error message
>>
>>         Error opening dataset : dataset value error
>>
>> This error message only seems to appear on scans which were done
>> recently (from May 1999), but scans done before this date work fine.
>> What we are worried is that the Siemens scanner is saving the MR data in
>> a new format and the  software is unable to read and convert it.  We
>> have reported this problem to Evergreen but we have not received any
>> reply. Is there any alternative software which will be able to read the
>> siemen images stored in the  MOD in the new format. We are really in a
>> dilemma and our research is at a standstill. Any help or suggestion will
>> be much appreciated.
>>
>> Thank you,
>>
>> Selva
>>
>
>------------------------------
>Date: Thu, 17 Jun 1999 06:05:35 EST
>From: Greg Joss <gjoss@hotmail.com>
>To: nih-image@io.ece.drexel.edu
>Cc: patw@med.usyd.edu.au
>Subject: Re: Fourier Descriptors
>Message-ID: <19990616200544.66677.qmail@hotmail.com>
>Content-Type: text/plain; format=flowed
>
>>From: DrJohnRuss@aol.com
>>Date: Tue, 8 Jun 1999 19:50:09 EDT
>>Subject: Re: Fourier Descriptors
>>To: nih-image@io.ece.drexel.edu
>>
>>In a message dated 6/8/99 7:18:11 PM, patw@med.usyd.edu.au writes:
>>
>> >We are investigating cerebral microvasculature and require a method to
>> >compare shape of vessel profiles.  Exploring the possibilities of Fourier
>> >descriptors has been thwarted by repeated computer crashes when we
>>attempt
>> >to open ImageFFt128b6.hqx.  Can anyone suggest how we might be able to
>> >do this?
>>
>>There really is no reason to try to use the older program, as the current
>>versions of the standard NIH-Image written for the PPC include all of the
>>same Fourier processing capabilities. However, neither of these does what
>>you
>>want. They perform an 2D FFT on the entire grey scale image, whereas what I
>>believe you are talking about is to use harmonic analysis on the shape of
>>the
>>vessels. NIH-Image doesn't provide that capability. There are a few
>>programs
>>that do (much more expensive) and I've been experimenting with a variant of
>>the technique that may become part of the Image Processing Tool Kit in some
>>future release. Your best bet at the moment is probably to use Image to
>>write
>>out a file of the coordinates of the boundary of the vessel and perform the
>>harmonic analysis off-line.
>>
>>John Russ
>>
>
>Pat,
>
>I developed such a procedure to do harmonic analysis on the shape of objects
>in colaboration with Mick Howland (ex Southern Cross University, now
>Tasmania National Parks?) for the purpose of characterising fish otolith
>(earbone) shapes using NIH-Image. The procedure worked quite well and was
>easy to interface with. ie select a ROI (outline) and macro returned array
>of parameters. There are some tricks involved with xyCoordinates and whole
>would be better implemented now in Object-Image.
>
>I am currently in transit (Berlin) but expect to be back in harness at
>Macquarie Uni about end July if you can wait till then. I would suggest
>that, if you need to develope routines from scratch yourself, it would be
>worthwhile waiting as you would spend some considerable time doing it
>yourself unless you are much more proficient than we were.
>
>Greg Joss
>gjoss@rna.bio.mq.edu.au
>
>
>
>______________________________________________________
>Get Your Private, Free Email at http://www.hotmail.com
>
>------------------------------
>Date: Thu, 17 Jun 1999 06:41:12 EST
>From: Greg Joss <gjoss@hotmail.com>
>To: nih-image@io.ece.drexel.edu
>Cc: jared_rifkin@qc.edu
>Subject: Re: How to Average Frames,Pixera
>Message-ID: <19990616204117.13925.qmail@hotmail.com>
>Content-Type: text/plain; format=flowed
>
>>Subject: Re: How to Average Frames,Pixera
>>Date: Wed, 9 Jun 99 12:31:20 -0400
>>From: jared rifkin <jared_rifkin@qc.edu>
>>To: <nih-image@io.ece.drexel.edu>
>
>>also- how can i combine trapping say 10 frames (for averaging) every
>>minute for perhaps an hour or two. i'm tracking cell movements - they are
>>slow and single frames are just too noisy to get good resolution -and- i
>>don't have the memory to trap and store contnuous video of a couple of
>>hours.
>>don't shoot me but i primarily use Adobe Premiere, not nih image.  i
>>know- i'm an alien but have pity.
>>
>>-dr. j. rifkin
>>biology dept
>>queens college
>>new york, ny 11367
>>jared_rifkin@qc.edu
>
>Jared,
>I dont know Pixera interface, but if you were doing video capture via
>NIH-Image or Object-Image, it is, in principle quite straight forward to do
>what you ask.
>
>repeat begin
>StartCapturing;{is needed to initiate video each time}
>AverageFrames('Average',frames);
>{Averages or integrates  video frames. integrate will fit histogram to
>1<>254 each captured frame; Average will maintain same intensity calibration
>}
>saveAs(filename,n:4:0); {or copy;selectPic(stackP); paste;}
>wait(delay);
>end until keydown('control');
>
>would in principle do it; but you would probably want considerable
>elaboration in practice.
>
>I am not confident that this would help with Pixera as I presume you would
>be capturing an RGB stack which needs to be averaged in each R,G,B etc but I
>would have thought that Pixera would have considerable problems with
>tracking cells as frame capture speed is quite slow.
>
>With video camera, you can capture 16 frames in <1 sec so that cell movement
>blurring is negligible. A inexpensive monochrome video camera can give
>excellent quality with Scion LG3 averaged frames even under very low light
>level noisey conditions.
>
>Greg Joss
>gjoss@rna.bio.mq.edu.au
>
>
>______________________________________________________
>Get Your Private, Free Email at http://www.hotmail.com
>
>------------------------------
>Date: Wed, 16 Jun 1999 13:47:06 -0700
>From: "Kevin E. Cooper" <kevin.cooper@asu.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Fourier Descriptors
>Message-id: <000601beb839$65c04a60$f524db81@enpc2294.eas.asu.edu>
>Content-type: text/plain
>Content-transfer-encoding: 7bit
>
>unsubscribe
>-----Original Message-----
>From: Greg Joss <gjoss@hotmail.com>
>To: nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
>Cc: patw@med.usyd.edu.au <patw@med.usyd.edu.au>
>Date: Wednesday, June 16, 1999 1:25 PM
>Subject: Re: Fourier Descriptors
>
>
>>>From: DrJohnRuss@aol.com
>>>Date: Tue, 8 Jun 1999 19:50:09 EDT
>>>Subject: Re: Fourier Descriptors
>>>To: nih-image@io.ece.drexel.edu
>>>
>>>In a message dated 6/8/99 7:18:11 PM, patw@med.usyd.edu.au writes:
>>>
>>> >We are investigating cerebral microvasculature and require a method to
>>> >compare shape of vessel profiles.  Exploring the possibilities of
>Fourier
>>> >descriptors has been thwarted by repeated computer crashes when we
>>>attempt
>>> >to open ImageFFt128b6.hqx.  Can anyone suggest how we might be able to
>>> >do this?
>>>
>>>There really is no reason to try to use the older program, as the current
>>>versions of the standard NIH-Image written for the PPC include all of the
>>>same Fourier processing capabilities. However, neither of these does what
>>>you
>>>want. They perform an 2D FFT on the entire grey scale image, whereas what
>I
>>>believe you are talking about is to use harmonic analysis on the shape of
>>>the
>>>vessels. NIH-Image doesn't provide that capability. There are a few
>>>programs
>>>that do (much more expensive) and I've been experimenting with a variant
>of
>>>the technique that may become part of the Image Processing Tool Kit in
>some
>>>future release. Your best bet at the moment is probably to use Image to
>>>write
>>>out a file of the coordinates of the boundary of the vessel and perform
>the
>>>harmonic analysis off-line.
>>>
>>>John Russ
>>>
>>
>>Pat,
>>
>>I developed such a procedure to do harmonic analysis on the shape of
>objects
>>in colaboration with Mick Howland (ex Southern Cross University, now
>>Tasmania National Parks?) for the purpose of characterising fish otolith
>>(earbone) shapes using NIH-Image. The procedure worked quite well and was
>>easy to interface with. ie select a ROI (outline) and macro returned array
>>of parameters. There are some tricks involved with xyCoordinates and whole
>>would be better implemented now in Object-Image.
>>
>>I am currently in transit (Berlin) but expect to be back in harness at
>>Macquarie Uni about end July if you can wait till then. I would suggest
>>that, if you need to develope routines from scratch yourself, it would be
>>worthwhile waiting as you would spend some considerable time doing it
>>yourself unless you are much more proficient than we were.
>>
>>Greg Joss
>>gjoss@rna.bio.mq.edu.au
>>
>>
>>
>>______________________________________________________
>>Get Your Private, Free Email at http://www.hotmail.com
>>
>
>------------------------------
>Date: Wed, 16 Jun 1999 13:52:51 -0700
>From: "Kevin E. Cooper" <kevin.cooper@asu.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: unsubscribe
>Message-id: <012d01beb83a$331cec20$f524db81@enpc2294.eas.asu.edu>
>Content-type: text/plain
>Content-transfer-encoding: 7bit
>
>-----Original Message-----
>From: Ben Elkin <elk@igb.fhg.de>
>To: nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
>Date: Tuesday, June 01, 1999 6:45 AM
>Subject: Re: nih-image-d Digest V99 #122
>
>
>>>
>>>At 11:18 PM 5/29/99 +0300, you wrote:
>>>>Hi,
>>>>I have requested several times to unsunscribe me.
>>>>Please take care.
>>>>Thanks,
>>>>
>>>>Prof. Gershon Golomb,
>>>>Head, Dept. of Pharmaceutics
>>
>>Dear Prof. Golomb,
>>
>>even though there might be a person who administrates the list and would
>>take care to unsubscribe you from the list, it is always better to use the
>>standard mechanism:
>>
>>
>>Unsubscribe
>>-----------
>>To unsubscribe to the list, send E-mail to
>nih-image-request@biomed.drexel.edu.
>>the Subject of the message should contain "unsubscribe".
>>
>>As in: To: nih-image-request@biomed.drexel.edu
>> Subject: unsubscribe
>>
>>Please send the mail to the address above, not to the list itself.
>>
>>Regards
>>
>>
>>Ben Elkin
>>
>>=======================================
>>elk@igb.fhg.de
>>
>>http://www.igb.fhg.de/GVT/
>>
>>Fraunhofer Institute for Interfacial Technology and Bioengineering
>>                    (fuer Grenzflaechen und Bioverfahrenstechnik)
>>
>>Nobelstr. 12    D-70569 Stuttgart    Germany
>>
>>Tel. +49 - 711 - 970-4144, -4161
>>Fax                 -4200
>>
>>
>>
>
>------------------------------
>Date: Thu, 17 Jun 1999 15:03:30 +0800
>From: Tim Fairchild <timf@cyllene.uwa.edu.au>
>To: nih-image@io.ece.drexel.edu
>Subject: Colour vs. Greyscale
>Message-ID: <37689DA0.BB9E1FE6@cyllene.uwa.edu.au>
>Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854";
>x-mac-creator="4D4F5353"
>Content-Transfer-Encoding: 7bit
>
>Whilst capturing some images a couple of days ago, I came across an
>ominous problem.  Whilst I was capturing the darker images, the exposure
>time was correctly set, however when I was capturing the lighter images,
>I was losing a lot of information, due to the exposure time not being
>long enough during the capture.  To counteract this, I changed the
>exposure time and captured the image (PAS stain) using the colour mode.
>We are concurrently using a kodak scanner step tablet (ST-34) to convert
>our measures into O.D. units.  My questions therefore are:
>
>Should I convert my image into a greyscale before analysis?
>Should I capture the step tablet in colour mode?
>Should I just change the exposure time and capture the images in B&W?
>
>The system we are using is a CMOS-PRO digital camera mounted on a Nikon
>Eclipse microscope.
>
>Thanks in advance
>Tim.
>-----------------------------------------------------------------
>Timothy J. Fairchild B.Sc. (Hons)
>PhD Candidate
>Co-ordinator for Centre of Athletic Testing
>Department of Human Movement and Exercise Science
>Nedlands, Western Australia 6907
>Telephone: (+61 8) 9380 2793
>Facsimile:  (+61 8) 9380 1039
>Email: timf@cyllene.uwa.edu.au
>http://www.general.uwa.edu.au/~hmweb/index.htm
>
>--------------------------------




From nih-image-request@io.ece.drexel.edu Thu Jun 17 13:23 EDT 1999
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Resent-Date: Thu, 17 Jun 1999 13:23:56 -0400 (EDT)
From: mbarish@smtplink.Coh.ORG
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Date: Thu, 17 Jun 1999 10:11:04 -0700
To: <nih-image@io.ece.drexel.edu>
Subject: OMDR for sale
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I would like to sell a Panasonic TQ2028F (high resolution monochrome) Optical
Memory Disk Recorder that is in perfect condition.  I also have a few disks for
the recorder.  If anyone is interested, please contact me directly.  Thank you.

Michael E. Barish, Ph.D.
Associate Research Scientist
Division of Neurosciences
Beckman Research Institute of the City of Hope
Duarte, CA 91010 
tel: +1 (626) 301-8188
fax: +1 (626) 301-8948
e-mail: mbarish@coh.org


From nih-image-request@io.ece.drexel.edu Thu Jun 17 13:53 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: Christer Ericsson <ericsson@acsu.buffalo.edu>
Subject: Anaglyphs from BioRad confocal stack
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How do I create red/green anaglyphs from a BioRad confocal microscope 
stack, on a Mac?
Christer Ericsson, DDS, PhD
State University of New York at Buffalo
Department of Biochemical Pharmacology
327 Hochstetter Hall-North Campus
Buffalo, NY 14260-1200

email:                  ericsson@acsu.buffalo.edu
phone:                  (716) 645-3926
fax:                    (716) 645-3850
WWW:                    http://tyr.cmb.ki.se
Videoconference:        CU-SeeMe IP# 128.205.183.71


From nih-image-request@io.ece.drexel.edu Fri Jun 18 04:23 EDT 1999
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Date: Fri, 18 Jun 1999 10:16:08 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Anaglyphs from BioRad confocal stack
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>How do I create red/green anaglyphs from a BioRad confocal microscope
>stack, on a Mac?
>Christer Ericsson, DDS, PhD

There are macros available to create animated stereo images in red/green,
red/blue or grayscale pairs:

<ftp://simon/pub/macros/StackMacros%201.0>

1. Adjust slice spacing (stacks menu),
2. enter the number of projections
   (e.g. 5 projections needed for 4 stereo images)
3. Choose "project for Stereo Sequence"
4. Choose "Red-green Stereo Sequence"
   or "Grayscale stereo sequence"




From nih-image-d-request@io.ece.drexel.edu Fri Jun 18 04:24 EDT 1999
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Subject: nih-image-d Digest V99 #138
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 138

Today's Topics:
  unsubscribe                           [ Patrick Kiser <pfk2@acpub.duke.edu> ]
  OMDR for sale                         [ mbarish@smtplink.Coh.ORG ]
  Anaglyphs from BioRad confocal stack  [ Christer Ericsson <ericsson@acsu.bu ]
  Re: Anaglyphs from BioRad confocal s  [ Norbert Vischer <vischer@bio.uva.nl ]

------------------------------

Date: Thu, 17 Jun 1999 07:54:04 -0400
From: Patrick Kiser <pfk2@acpub.duke.edu>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe 
Message-Id: <l03010d00b38e922526d0@[152.3.249.39]>
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>------------------------------
>nih-image-d Digest				Volume 99 : Issue 137
>
>Today's Topics:
>  Re: nih-image-d Digest V99 #136       [ "Paul S. Hees"
><phees@welch.jhu.edu ]
>  Re: Fourier Descriptors               [ Greg Joss <gjoss@hotmail.com> ]
>  Re: How to Average Frames,Pixera      [ Greg Joss <gjoss@hotmail.com> ]
>  Re: Fourier Descriptors               [ "Kevin E. Cooper"
><kevin.cooper@asu ]
>  unsubscribe                           [ "Kevin E. Cooper"
><kevin.cooper@asu ]
>  Colour vs. Greyscale                  [ Tim Fairchild
><timf@cyllene.uwa.edu ]
>
>------------------------------
>Date: Wed, 16 Jun 1999 13:48:14 -0400
>From: "Paul S. Hees" <phees@welch.jhu.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: nih-image-d Digest V99 #136
>Message-ID: <3767E35B.71770F5D@welch.jhu.edu>
>Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854";
>x-mac-creator="4D4F5353"
>Content-Transfer-Encoding: 7bit
>
>The Siemens routine initiated by "System; External Data" from the Numaris
>pulldown allows you to 'Export' image files. The format of the files
>created by this routine is Dicom 3 (it was Dicom 2, but the new Numaris is
>different, I think). I'm not sure how to archive these on the Pioneer: it
>can be mounted, however, as a standard UNIX SCSI device.
>
>Paul Hees
>Cardiology Division
>Johns Hopkins University School of Medicine
>phees@jhmi.edu
>
>>   ------------------------------------------------------------------------
>>
>> Subject: Siemens CT/MR to ACR/NEMA
>> Date: Wed, 16 Jun 1999 08:57:53 +0800
>> From: selva <selva@fsktm.um.edu.my>
>> To: nih-image@io.ece.drexel.edu
>>
>> I have bought the Siemens CT/MR to ACR/NEMA conversion program from
>> Evergreen Tech.  to read MRI images from the MOD disks using the pioneer
>> SCSI drive, about three years ago. The siemen magneton scanner at the
>> University hospital is not connected to the network and could only store
>> the MRI images in the optical disks. The scanners previously used Siemen
>> magneton vision Numaris 3  V8 31 C. We did not have any problems reading
>> the images from the optical disks as the Evergreen software converts it
>> to ACR NEMA which then can be imported to nih-image.
>>
>> Lately Siemen upgraded the software at the MRI scanner to Siemen
>> magnetom vision Numaris 3 V8 33 B. According to the radiologists this
>> upgrading is neccessary for Y2K compliance. Our problem is that the
>> Evergreen software is unable to read the images. The  software keeps
>> giving the following error message
>>
>>         Error opening dataset : dataset value error
>>
>> This error message only seems to appear on scans which were done
>> recently (from May 1999), but scans done before this date work fine.
>> What we are worried is that the Siemens scanner is saving the MR data in
>> a new format and the  software is unable to read and convert it.  We
>> have reported this problem to Evergreen but we have not received any
>> reply. Is there any alternative software which will be able to read the
>> siemen images stored in the  MOD in the new format. We are really in a
>> dilemma and our research is at a standstill. Any help or suggestion will
>> be much appreciated.
>>
>> Thank you,
>>
>> Selva
>>
>
>------------------------------
>Date: Thu, 17 Jun 1999 06:05:35 EST
>From: Greg Joss <gjoss@hotmail.com>
>To: nih-image@io.ece.drexel.edu
>Cc: patw@med.usyd.edu.au
>Subject: Re: Fourier Descriptors
>Message-ID: <19990616200544.66677.qmail@hotmail.com>
>Content-Type: text/plain; format=flowed
>
>>From: DrJohnRuss@aol.com
>>Date: Tue, 8 Jun 1999 19:50:09 EDT
>>Subject: Re: Fourier Descriptors
>>To: nih-image@io.ece.drexel.edu
>>
>>In a message dated 6/8/99 7:18:11 PM, patw@med.usyd.edu.au writes:
>>
>> >We are investigating cerebral microvasculature and require a method to
>> >compare shape of vessel profiles.  Exploring the possibilities of Fourier
>> >descriptors has been thwarted by repeated computer crashes when we
>>attempt
>> >to open ImageFFt128b6.hqx.  Can anyone suggest how we might be able to
>> >do this?
>>
>>There really is no reason to try to use the older program, as the current
>>versions of the standard NIH-Image written for the PPC include all of the
>>same Fourier processing capabilities. However, neither of these does what
>>you
>>want. They perform an 2D FFT on the entire grey scale image, whereas what I
>>believe you are talking about is to use harmonic analysis on the shape of
>>the
>>vessels. NIH-Image doesn't provide that capability. There are a few
>>programs
>>that do (much more expensive) and I've been experimenting with a variant of
>>the technique that may become part of the Image Processing Tool Kit in some
>>future release. Your best bet at the moment is probably to use Image to
>>write
>>out a file of the coordinates of the boundary of the vessel and perform the
>>harmonic analysis off-line.
>>
>>John Russ
>>
>
>Pat,
>
>I developed such a procedure to do harmonic analysis on the shape of objects
>in colaboration with Mick Howland (ex Southern Cross University, now
>Tasmania National Parks?) for the purpose of characterising fish otolith
>(earbone) shapes using NIH-Image. The procedure worked quite well and was
>easy to interface with. ie select a ROI (outline) and macro returned array
>of parameters. There are some tricks involved with xyCoordinates and whole
>would be better implemented now in Object-Image.
>
>I am currently in transit (Berlin) but expect to be back in harness at
>Macquarie Uni about end July if you can wait till then. I would suggest
>that, if you need to develope routines from scratch yourself, it would be
>worthwhile waiting as you would spend some considerable time doing it
>yourself unless you are much more proficient than we were.
>
>Greg Joss
>gjoss@rna.bio.mq.edu.au
>
>
>
>______________________________________________________
>Get Your Private, Free Email at http://www.hotmail.com
>
>------------------------------
>Date: Thu, 17 Jun 1999 06:41:12 EST
>From: Greg Joss <gjoss@hotmail.com>
>To: nih-image@io.ece.drexel.edu
>Cc: jared_rifkin@qc.edu
>Subject: Re: How to Average Frames,Pixera
>Message-ID: <19990616204117.13925.qmail@hotmail.com>
>Content-Type: text/plain; format=flowed
>
>>Subject: Re: How to Average Frames,Pixera
>>Date: Wed, 9 Jun 99 12:31:20 -0400
>>From: jared rifkin <jared_rifkin@qc.edu>
>>To: <nih-image@io.ece.drexel.edu>
>
>>also- how can i combine trapping say 10 frames (for averaging) every
>>minute for perhaps an hour or two. i'm tracking cell movements - they are
>>slow and single frames are just too noisy to get good resolution -and- i
>>don't have the memory to trap and store contnuous video of a couple of
>>hours.
>>don't shoot me but i primarily use Adobe Premiere, not nih image.  i
>>know- i'm an alien but have pity.
>>
>>-dr. j. rifkin
>>biology dept
>>queens college
>>new york, ny 11367
>>jared_rifkin@qc.edu
>
>Jared,
>I dont know Pixera interface, but if you were doing video capture via
>NIH-Image or Object-Image, it is, in principle quite straight forward to do
>what you ask.
>
>repeat begin
>StartCapturing;{is needed to initiate video each time}
>AverageFrames('Average',frames);
>{Averages or integrates  video frames. integrate will fit histogram to
>1<>254 each captured frame; Average will maintain same intensity calibration
>}
>saveAs(filename,n:4:0); {or copy;selectPic(stackP); paste;}
>wait(delay);
>end until keydown('control');
>
>would in principle do it; but you would probably want considerable
>elaboration in practice.
>
>I am not confident that this would help with Pixera as I presume you would
>be capturing an RGB stack which needs to be averaged in each R,G,B etc but I
>would have thought that Pixera would have considerable problems with
>tracking cells as frame capture speed is quite slow.
>
>With video camera, you can capture 16 frames in <1 sec so that cell movement
>blurring is negligible. A inexpensive monochrome video camera can give
>excellent quality with Scion LG3 averaged frames even under very low light
>level noisey conditions.
>
>Greg Joss
>gjoss@rna.bio.mq.edu.au
>
>
>______________________________________________________
>Get Your Private, Free Email at http://www.hotmail.com
>
>------------------------------
>Date: Wed, 16 Jun 1999 13:47:06 -0700
>From: "Kevin E. Cooper" <kevin.cooper@asu.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Fourier Descriptors
>Message-id: <000601beb839$65c04a60$f524db81@enpc2294.eas.asu.edu>
>Content-type: text/plain
>Content-transfer-encoding: 7bit
>
>unsubscribe
>-----Original Message-----
>From: Greg Joss <gjoss@hotmail.com>
>To: nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
>Cc: patw@med.usyd.edu.au <patw@med.usyd.edu.au>
>Date: Wednesday, June 16, 1999 1:25 PM
>Subject: Re: Fourier Descriptors
>
>
>>>From: DrJohnRuss@aol.com
>>>Date: Tue, 8 Jun 1999 19:50:09 EDT
>>>Subject: Re: Fourier Descriptors
>>>To: nih-image@io.ece.drexel.edu
>>>
>>>In a message dated 6/8/99 7:18:11 PM, patw@med.usyd.edu.au writes:
>>>
>>> >We are investigating cerebral microvasculature and require a method to
>>> >compare shape of vessel profiles.  Exploring the possibilities of
>Fourier
>>> >descriptors has been thwarted by repeated computer crashes when we
>>>attempt
>>> >to open ImageFFt128b6.hqx.  Can anyone suggest how we might be able to
>>> >do this?
>>>
>>>There really is no reason to try to use the older program, as the current
>>>versions of the standard NIH-Image written for the PPC include all of the
>>>same Fourier processing capabilities. However, neither of these does what
>>>you
>>>want. They perform an 2D FFT on the entire grey scale image, whereas what
>I
>>>believe you are talking about is to use harmonic analysis on the shape of
>>>the
>>>vessels. NIH-Image doesn't provide that capability. There are a few
>>>programs
>>>that do (much more expensive) and I've been experimenting with a variant
>of
>>>the technique that may become part of the Image Processing Tool Kit in
>some
>>>future release. Your best bet at the moment is probably to use Image to
>>>write
>>>out a file of the coordinates of the boundary of the vessel and perform
>the
>>>harmonic analysis off-line.
>>>
>>>John Russ
>>>
>>
>>Pat,
>>
>>I developed such a procedure to do harmonic analysis on the shape of
>objects
>>in colaboration with Mick Howland (ex Southern Cross University, now
>>Tasmania National Parks?) for the purpose of characterising fish otolith
>>(earbone) shapes using NIH-Image. The procedure worked quite well and was
>>easy to interface with. ie select a ROI (outline) and macro returned array
>>of parameters. There are some tricks involved with xyCoordinates and whole
>>would be better implemented now in Object-Image.
>>
>>I am currently in transit (Berlin) but expect to be back in harness at
>>Macquarie Uni about end July if you can wait till then. I would suggest
>>that, if you need to develope routines from scratch yourself, it would be
>>worthwhile waiting as you would spend some considerable time doing it
>>yourself unless you are much more proficient than we were.
>>
>>Greg Joss
>>gjoss@rna.bio.mq.edu.au
>>
>>
>>
>>______________________________________________________
>>Get Your Private, Free Email at http://www.hotmail.com
>>
>
>------------------------------
>Date: Wed, 16 Jun 1999 13:52:51 -0700
>From: "Kevin E. Cooper" <kevin.cooper@asu.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: unsubscribe
>Message-id: <012d01beb83a$331cec20$f524db81@enpc2294.eas.asu.edu>
>Content-type: text/plain
>Content-transfer-encoding: 7bit
>
>-----Original Message-----
>From: Ben Elkin <elk@igb.fhg.de>
>To: nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
>Date: Tuesday, June 01, 1999 6:45 AM
>Subject: Re: nih-image-d Digest V99 #122
>
>
>>>
>>>At 11:18 PM 5/29/99 +0300, you wrote:
>>>>Hi,
>>>>I have requested several times to unsunscribe me.
>>>>Please take care.
>>>>Thanks,
>>>>
>>>>Prof. Gershon Golomb,
>>>>Head, Dept. of Pharmaceutics
>>
>>Dear Prof. Golomb,
>>
>>even though there might be a person who administrates the list and would
>>take care to unsubscribe you from the list, it is always better to use the
>>standard mechanism:
>>
>>
>>Unsubscribe
>>-----------
>>To unsubscribe to the list, send E-mail to
>nih-image-request@biomed.drexel.edu.
>>the Subject of the message should contain "unsubscribe".
>>
>>As in: To: nih-image-request@biomed.drexel.edu
>> Subject: unsubscribe
>>
>>Please send the mail to the address above, not to the list itself.
>>
>>Regards
>>
>>
>>Ben Elkin
>>
>>=======================================
>>elk@igb.fhg.de
>>
>>http://www.igb.fhg.de/GVT/
>>
>>Fraunhofer Institute for Interfacial Technology and Bioengineering
>>                    (fuer Grenzflaechen und Bioverfahrenstechnik)
>>
>>Nobelstr. 12    D-70569 Stuttgart    Germany
>>
>>Tel. +49 - 711 - 970-4144, -4161
>>Fax                 -4200
>>
>>
>>
>
>------------------------------
>Date: Thu, 17 Jun 1999 15:03:30 +0800
>From: Tim Fairchild <timf@cyllene.uwa.edu.au>
>To: nih-image@io.ece.drexel.edu
>Subject: Colour vs. Greyscale
>Message-ID: <37689DA0.BB9E1FE6@cyllene.uwa.edu.au>
>Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854";
>x-mac-creator="4D4F5353"
>Content-Transfer-Encoding: 7bit
>
>Whilst capturing some images a couple of days ago, I came across an
>ominous problem.  Whilst I was capturing the darker images, the exposure
>time was correctly set, however when I was capturing the lighter images,
>I was losing a lot of information, due to the exposure time not being
>long enough during the capture.  To counteract this, I changed the
>exposure time and captured the image (PAS stain) using the colour mode.
>We are concurrently using a kodak scanner step tablet (ST-34) to convert
>our measures into O.D. units.  My questions therefore are:
>
>Should I convert my image into a greyscale before analysis?
>Should I capture the step tablet in colour mode?
>Should I just change the exposure time and capture the images in B&W?
>
>The system we are using is a CMOS-PRO digital camera mounted on a Nikon
>Eclipse microscope.
>
>Thanks in advance
>Tim.
>-----------------------------------------------------------------
>Timothy J. Fairchild B.Sc. (Hons)
>PhD Candidate
>Co-ordinator for Centre of Athletic Testing
>Department of Human Movement and Exercise Science
>Nedlands, Western Australia 6907
>Telephone: (+61 8) 9380 2793
>Facsimile:  (+61 8) 9380 1039
>Email: timf@cyllene.uwa.edu.au
>http://www.general.uwa.edu.au/~hmweb/index.htm
>
>--------------------------------

------------------------------

Date: Thu, 17 Jun 1999 10:11:04 -0700
From: mbarish@smtplink.Coh.ORG
To: <nih-image@io.ece.drexel.edu>
Subject: OMDR for sale
Message-Id: <9906179296.AA929639337@smtplink.coh.org>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Description: "cc:Mail Note Part"

I would like to sell a Panasonic TQ2028F (high resolution monochrome) Optical
Memory Disk Recorder that is in perfect condition.  I also have a few disks for
the recorder.  If anyone is interested, please contact me directly.  Thank you.

Michael E. Barish, Ph.D.
Associate Research Scientist
Division of Neurosciences
Beckman Research Institute of the City of Hope
Duarte, CA 91010 
tel: +1 (626) 301-8188
fax: +1 (626) 301-8948
e-mail: mbarish@coh.org

------------------------------

Date: Thu, 17 Jun 1999 13:47:15 -0400
From: Christer Ericsson <ericsson@acsu.buffalo.edu>
To: nih-image@io.ece.drexel.edu
Subject: Anaglyphs from BioRad confocal stack
Message-Id: <v04205102b38ee4a624f4@[128.205.183.71]>
Content-Type: text/plain; charset="us-ascii" ; format="flowed"

How do I create red/green anaglyphs from a BioRad confocal microscope 
stack, on a Mac?
Christer Ericsson, DDS, PhD
State University of New York at Buffalo
Department of Biochemical Pharmacology
327 Hochstetter Hall-North Campus
Buffalo, NY 14260-1200

email:                  ericsson@acsu.buffalo.edu
phone:                  (716) 645-3926
fax:                    (716) 645-3850
WWW:                    http://tyr.cmb.ki.se
Videoconference:        CU-SeeMe IP# 128.205.183.71

------------------------------

Date: Fri, 18 Jun 1999 10:16:08 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Anaglyphs from BioRad confocal stack
Message-Id: <l03110700b38faf460cd4@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

>How do I create red/green anaglyphs from a BioRad confocal microscope
>stack, on a Mac?
>Christer Ericsson, DDS, PhD

There are macros available to create animated stereo images in red/green,
red/blue or grayscale pairs:

<ftp://simon/pub/macros/StackMacros%201.0>

1. Adjust slice spacing (stacks menu),
2. enter the number of projections
   (e.g. 5 projections needed for 4 stereo images)
3. Choose "project for Stereo Sequence"
4. Choose "Red-green Stereo Sequence"
   or "Grayscale stereo sequence"

--------------------------------
End of nih-image-d Digest V99 Issue #138
****************************************

From nih-image-request@io.ece.drexel.edu Fri Jun 18 08:57 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: "Can't find application" error
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I get the error
"application NIH Image 1.62 cannot be found"
(unexpected error -2048)

when double-clicking an NIH TEXT file.

I can avoid this error and work as usual by selecting the control panel
"File exchange" and unchecking "Translate documents automatically"; still
I'd like to find out the reason for this.

The problem appears since I have upgraded my G3 Mac to OS 8.6. The error
comes up with or without NIH Image loaded, I can't even open the text file
from within NIH Image. However, a PICT file behaves normal. Removing all
other applications with creator 'Imag' and rebuilding the desktop doesn't
help.


I was first contacted by a user of Object-Image who couldn't double-click
object files, but as mentioned above, I can reproduce this also with text
files and standard NIH Image.
Another anomality I have noticed is that the small microscope icon appears
distorted when the application is active.

My questions is:
- Is there anyone who had loading problems, and was it in
  combination with or without Object-Image?

Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



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 <v04205102b38ee4a624f4@[128.205.183.71]>
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Date: Fri, 18 Jun 1999 10:01:18 -0400
To: nih-image@io.ece.drexel.edu
From: "Stephen J. Moorman" <sjm8@po.cwru.edu>
Subject: Re: "Can't find application" error
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I have a new 400 Mhz G3 and an old 266 Mhz G3.  I upgraded to OS 8.6 on
both.  I have not been able to reproduce this on either machine.  However,
I run Scion Image 1.62 on both.  I find it difficult to imagine that that
could solve your problem.

>I get the error
>"application NIH Image 1.62 cannot be found"
>(unexpected error -2048)
>
>when double-clicking an NIH TEXT file.


Stephen J. Moorman, Ph.D.
Assistant Professor of Anatomy
Case Western Reserve University
10900 Euclid Ave.
Cleveland, OH 44106-4930

Telephone: 216-368-2855
Fax: 216-368-8669
e-mail: sjm8@po.cwru.edu

http://mediswww.cwru.edu/dept/anatomy/moorman/



From nih-image-request@io.ece.drexel.edu Fri Jun 18 13:44 EDT 1999
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Date: Fri, 18 Jun 1999 12:00:52 -0400
To: nih-image@io.ece.drexel.edu
From: David Knecht <knecht@uconnvm.uconn.edu>
Subject: Re: Anaglyphs from BioRad confocal stack
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The ftp address does not seem to work for me.  Dave

>>How do I create red/green anaglyphs from a BioRad confocal microscope
>>stack, on a Mac?
>>Christer Ericsson, DDS, PhD
>
>There are macros available to create animated stereo images in red/green,
>red/blue or grayscale pairs:
>
><ftp://simon/pub/macros/StackMacros%201.0>
>
>1. Adjust slice spacing (stacks menu),
>2. enter the number of projections
>   (e.g. 5 projections needed for 4 stereo images)
>3. Choose "project for Stereo Sequence"
>4. Choose "Red-green Stereo Sequence"
>   or "Grayscale stereo sequence"


Home of the 1999 NCAA Basketball National Champion HUSKIES !!!
************************************************************

Dr. David Knecht
Department of Molecular and Cell Biology
University of Connecticut
75 N. Eagleville Rd.   U-125
Storrs, CT 06269
Knecht@uconnvm.uconn.edu
860-486-2200      860-486-4331 (fax)

************************************************************



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 <v04205102b38ee4a624f4@[128.205.183.71]>
Mime-Version: 1.0
Date: Fri, 18 Jun 1999 19:51:34 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Anaglyphs from BioRad confocal stack
Resent-Message-ID: <"E1CQ92.0.kI.uOeQt"@io>
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>The ftp address does not seem to work for me.  Dave
>
I simply copied the address from Fetch, which also translates blanks,
because the file name is "StackMacros 1.0".
Look at

ftp://simon/pub/macros/

or at the website given below.

The correct sequence should be:
>1. Adjust slice spacing (stacks menu),
>2. Choose "project for Stereo Sequence"
>3. enter the number of projections
>   (e.g. 5 projections are needed for 4 stereo images)
>4. Choose "Red-green Stereo Sequence"
>   or "Grayscale stereo sequence"

It works on fluorescence images with bright objects and dark background.

Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



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Date: Fri, 18 Jun 1999 21:30:39 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Anaglyphs from BioRad confocal stack
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Sorry, it was a local address;
look for StackMacros 1.0 at:

ftp://simon.bio.uva.nl/pub/macros/



Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



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nih-image-d Digest				Volume 99 : Issue 139

Today's Topics:
  "Can't find application" error        [ Norbert Vischer <vischer@bio.uva.nl ]
  Re: "Can't find application" error    [ "Stephen J. Moorman" <sjm8@po.cwru. ]
  Re: Anaglyphs from BioRad confocal s  [ David Knecht <knecht@uconnvm.uconn. ]
  Re: Anaglyphs from BioRad confocal s  [ Norbert Vischer <vischer@bio.uva.nl ]
  Re: Anaglyphs from BioRad confocal s  [ Norbert Vischer <vischer@bio.uva.nl ]
  frozen capture                        [ "B. Iyengar" <iyengabg@mcmail.cis.M ]

------------------------------

Date: Fri, 18 Jun 1999 14:52:55 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: "Can't find application" error
Message-Id: <l03110700b38fdfae8417@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

I get the error
"application NIH Image 1.62 cannot be found"
(unexpected error -2048)

when double-clicking an NIH TEXT file.

I can avoid this error and work as usual by selecting the control panel
"File exchange" and unchecking "Translate documents automatically"; still
I'd like to find out the reason for this.

The problem appears since I have upgraded my G3 Mac to OS 8.6. The error
comes up with or without NIH Image loaded, I can't even open the text file
from within NIH Image. However, a PICT file behaves normal. Removing all
other applications with creator 'Imag' and rebuilding the desktop doesn't
help.


I was first contacted by a user of Object-Image who couldn't double-click
object files, but as mentioned above, I can reproduce this also with text
files and standard NIH Image.
Another anomality I have noticed is that the small microscope icon appears
distorted when the application is active.

My questions is:
- Is there anyone who had loading problems, and was it in
  combination with or without Object-Image?

Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: Fri, 18 Jun 1999 10:01:18 -0400
From: "Stephen J. Moorman" <sjm8@po.cwru.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: "Can't find application" error
Message-Id: <l03130300b39000fbb0cd@[129.22.112.115]>
Content-Type: text/plain; charset="us-ascii"

I have a new 400 Mhz G3 and an old 266 Mhz G3.  I upgraded to OS 8.6 on
both.  I have not been able to reproduce this on either machine.  However,
I run Scion Image 1.62 on both.  I find it difficult to imagine that that
could solve your problem.

>I get the error
>"application NIH Image 1.62 cannot be found"
>(unexpected error -2048)
>
>when double-clicking an NIH TEXT file.


Stephen J. Moorman, Ph.D.
Assistant Professor of Anatomy
Case Western Reserve University
10900 Euclid Ave.
Cleveland, OH 44106-4930

Telephone: 216-368-2855
Fax: 216-368-8669
e-mail: sjm8@po.cwru.edu

http://mediswww.cwru.edu/dept/anatomy/moorman/

------------------------------

Date: Fri, 18 Jun 1999 12:00:52 -0400
From: David Knecht <knecht@uconnvm.uconn.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Anaglyphs from BioRad confocal stack
Message-Id: <l03130304b3901d9c17c7@[137.99.71.142]>
Content-Type: text/plain; charset="us-ascii"

The ftp address does not seem to work for me.  Dave

>>How do I create red/green anaglyphs from a BioRad confocal microscope
>>stack, on a Mac?
>>Christer Ericsson, DDS, PhD
>
>There are macros available to create animated stereo images in red/green,
>red/blue or grayscale pairs:
>
><ftp://simon/pub/macros/StackMacros%201.0>
>
>1. Adjust slice spacing (stacks menu),
>2. enter the number of projections
>   (e.g. 5 projections needed for 4 stereo images)
>3. Choose "project for Stereo Sequence"
>4. Choose "Red-green Stereo Sequence"
>   or "Grayscale stereo sequence"


Home of the 1999 NCAA Basketball National Champion HUSKIES !!!
************************************************************

Dr. David Knecht
Department of Molecular and Cell Biology
University of Connecticut
75 N. Eagleville Rd.   U-125
Storrs, CT 06269
Knecht@uconnvm.uconn.edu
860-486-2200      860-486-4331 (fax)

************************************************************

------------------------------

Date: Fri, 18 Jun 1999 19:51:34 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Anaglyphs from BioRad confocal stack
Message-Id: <l03010d00b390362a052a@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

>The ftp address does not seem to work for me.  Dave
>
I simply copied the address from Fetch, which also translates blanks,
because the file name is "StackMacros 1.0".
Look at

ftp://simon/pub/macros/

or at the website given below.

The correct sequence should be:
>1. Adjust slice spacing (stacks menu),
>2. Choose "project for Stereo Sequence"
>3. enter the number of projections
>   (e.g. 5 projections are needed for 4 stereo images)
>4. Choose "Red-green Stereo Sequence"
>   or "Grayscale stereo sequence"

It works on fluorescence images with bright objects and dark background.

Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: Fri, 18 Jun 1999 21:30:39 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Anaglyphs from BioRad confocal stack
Message-Id: <l03010d02b3904df2d35a@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

Sorry, it was a local address;
look for StackMacros 1.0 at:

ftp://simon.bio.uva.nl/pub/macros/



Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: Fri, 18 Jun 1999 16:42:19 -0400 (EDT)
From: "B. Iyengar" <iyengabg@mcmail.cis.McMaster.CA>
To: nih-image-d@io.ece.drexel.edu
cc: iyengabg@mcmaster.ca
Subject: frozen capture
Message-ID: <Pine.SOL.3.96.990618162901.1661B-100000@mcmail.cis.McMaster.CA>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hello all!
I put together this first macro that was to get me x-y coordinates of a
moving target with time, triggered by a mouse click. While I hacked this I
trouble shot my way thru using a normal blank window. I then took this
macro to a window that ran a live capture of a bug crawling around, now
when I click on the bug as I try to track it, the capture freezes. Is
there a way out of this? The macro I wrote is as follows: Thanks for any
help. I use an AG-5 card in a 9500 powermac, and Image 1.61 PPC. Please
also direct any answer to iyengabg@mcmaster.ca
------------------------------------------------------------------------
macro 'get(X,Y) and time [F1]';
{This macro will get X-Y Coordinates and a timepoint for each co-ordinate}
var
x,y:integer;
Counter,width, height:integer;
year,month,day,hour,minute,second,dayofweek:integer;
begin
  GetPicSize(width,height);
  NewTextWindow('Tracking Data',300,500);
  MoveWindow(250,520);
  Writeln('Count,   X,   Y,   mins, secs');
   
	for Counter:=1 to 100 do 

	begin
        SetCursor('cross');
        NextWindow;
        ShowMessage('To track aim on the moving specimen with the cursor
and then press the mouse button.');
        Repeat Until Button;
    	GetMouse(x,y);
    	GetTime(year,month,day,hour,minute,second,dayofweek);
        Beep;
        Wait(.5);
        SelectWindow('Tracking Data');
        Writeln(Counter:5:0,','x:5:0,',',(height-y):5:0, ',', minute:5:1,
',', second:5:1);
        end;
   Save;
end;
-----------------------------------------------------------------------
cheers,
Bala

--------------------------------
End of nih-image-d Digest V99 Issue #139
****************************************

From nih-image-request@io.ece.drexel.edu Sun Jun 20 07:54 EDT 1999
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Hi,
I have requested several times to unsunscribe me.
Please take care.
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Guus Zijlstra    

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Tel. +31-(0)71-5275018
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nih-image-d Digest				Volume 99 : Issue 140

Today's Topics:
  Unsubscribe!!!!!                      [ "Guus en Tessa" <gnt@worldonline.nl ]
  Re Can't find application error.      [ "Goldsmith, Noel" <Noel.Goldsmith@d ]

------------------------------

Date: Sun, 20 Jun 1999 13:46:48 +0200
From: "Guus en Tessa" <gnt@worldonline.nl>
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Hi,
I have requested several times to unsunscribe me.
Please take care.
Thanks,

Guus Zijlstra    

Behavioural Biology Group
Institute of Evolutionary and Ecological Sciences
Leiden University
Kaiserstraat 63
2300 RA Leiden
P.O.B. 9516

Tel. +31-(0)71-5275018
E-mail: gzijlstra@rulsfb.leidenuniv.nl

------------------------------

Date: Mon, 21 Jun 1999 15:35:18 +1000
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: Re Can't find application error.
Message-Id: <F98649A5EE8ED11190160000F802756598D0CD@exchvic3.dsto.defence.gov.au>
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Norbert Vischer reports trouble when he double clicks on a file from Image.
The only strange behaviour I see on a beige G3 300 is the launching of Image
SXM instead of standard Image 1.62 when a document is double clicked.
I suspect that Object Image may have something to do with this. When I get
some time I will get Object Image and try it out.
best wishes
Noel.

--------------------------------
End of nih-image-d Digest V99 Issue #140
****************************************

From nih-image-request@io.ece.drexel.edu Mon Jun 21 01:50 EDT 1999
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From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
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Norbert Vischer reports trouble when he double clicks on a file from Image.
The only strange behaviour I see on a beige G3 300 is the launching of Image
SXM instead of standard Image 1.62 when a document is double clicked.
I suspect that Object Image may have something to do with this. When I get
some time I will get Object Image and try it out.
best wishes
Noel.



From nih-image-request@io.ece.drexel.edu Mon Jun 21 03:14 EDT 1999
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From: Greg Joss <gjoss@hotmail.com>
To: nih-image@io.ece.drexel.edu, Noel.Goldsmith@dsto.defence.gov.au
Subject: Re Can't find application error.
Date: Mon, 21 Jun 1999 16:54:48 EST
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>From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
>Reply-To: nih-image@io.ece.drexel.edu
>To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
>Subject: Re Can't find application error.
>Date: Mon, 21 Jun 1999 15:35:18 +1000
>
>Norbert Vischer reports trouble when he double clicks on a file from Image.
>The only strange behaviour I see on a beige G3 300 is the launching of 
>Image
>SXM instead of standard Image 1.62 when a document is double clicked.

I would have thought that was simply a result of the most recently installed 
program catching 'Imag'

I recently (early last week) had the problem that Norbert refers to on a 
beige G3 running OS8.1 but at the time I was able to open via menu so I just 
went around it. Might have been Object-Image.p1 or n16; I am not sure.  I am 
now running Object-Image14.6.99-PPC and the problem doesn't occur. (about to 
install Object-Image1.62p2).

>I suspect that Object Image may have something to do with this. When I >get 
>some time I will get Object Image and try it out.
>best wishes
>Noel.

Noel,
I couldn't recommend Object-Image highly enough and suggest you make time to 
get it before doing any further macro programming as Object-Image help, 
debug and dialog facilities have taken macro programming a leap forward over 
recent months making it even easier and more efficient while fully being 
backwards compatable with NIH-Image

Regards,
Greg
gjoss@rna.bio.mq.edu.au



______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com


From nih-image-request@io.ece.drexel.edu Mon Jun 21 03:32 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Can't find application error.
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>Norbert Vischer reports trouble when he double clicks on a file from Image.
>The only strange behaviour I see on a beige G3 300 is the launching of Image
>SXM instead of standard Image 1.62 when a document is double clicked.
>I suspect that Object Image may have something to do with this. When I get
>some time I will get Object Image and try it out.
>best wishes
>Noel.

As stated before, the problem disappears when disabling the "File exchange"
control panel. It also disappears, when "File Exchange Preferences" is
removed.

In my example, I suspect that "File Exchange Preferences" is corrupted: it
contains two 'prat' resources with the names:

TEXTImaggfBr
TEXTImagImag

suggesting two different target applications  for text files created by
Image, one of which points to GifBuilder (gfBr), which doesn't make sense.

If anyone else has such problems, please let me know.



From nih-image-request@io.ece.drexel.edu Mon Jun 21 15:49 EDT 1999
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Date: Mon, 21 Jun 1999 15:30:24 -0400
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
Subject: Options for measurements ignored in exported measurements file?
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I've found that when I Export()  measurements from a macro using v1.62,
what results is a file with all of the possible measurements (there are
14). This occurs even if I have previously selected (via the check boxes in
the 'Analyze/Options...' menu or using the SetOptions() macro command) a
lesser number to be shown in the Results window.

I'd like to figure out how to alter this behavior to allow only the
displayed measurements to be exported. My naive look at the source code
suggests to me that what I want is what is supposed to happen, but I'm not
confident of this. The file.p module has a procedure ExportMeasurements()
that calls a utilities.p procedure CopyResultsToBuffer().
CopyResultsToBuffer() contains some code that identifies which of the
various measurement options the user wanted. This code consists of a series
of tests for the desired options, e.g. 'if MajorAxisM in measurements
then', where 'measurements' was evidently established by the check boxes or
SetOption() macro command via the analysis.p procedure
DoMeasurementOptions().

Also, I haven't figured out how to select the 'ShowHeadings' option from
within the macro language. Is this possible? On a related note, I would
like to gain macro language access to some of the measurement arrays (such
as the mode[] array) that hold measurements. How hard would it be to code
this?

Thanks.

Bill Christens-Barry
-------------------------
Bill Christens-Barry, PhD
Johns Hopkins University Applied Physics Laboratory
wacb@aplcomm.jhuapl.edu
-------------------------


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I have had some interest in my modifications to NIH-Image for handling
stereo photos for deriving XYZ points.  I have put a copy on our anonymous
ftp server - ftp.bgs.ac.uk in the directory /pubload/Montserrat.   The
files needed are:

NIHImage.hqx - software
Texts.hqx - test sample and reference points in text files + description of
how to use the routine
K8.hqx - demo photo 1 of the Montserrat lava dome
K9.hqx - demo photo 2 of the Montserrat lava dome

There are a number of other things available in this version of NIH-Image:

- Import of tab-delimited data files (including column headers and null
data).  Columns in order X,Y,Z1,Z2...Zn.
- Surface gridding routines for Z values of imported data to generate
surface maps.  Grid histogram with percentile choices.
- Spatial referencing for surface maps.  Easting and northing shown in Info
window, and preserved with the map.
- ROI operations.  Use a ROI on a map to extract a portion of data from a
data set.
- Stats routines on point source data based on position relative to ROI.
- Dynamic array sizes defined in options to minimise the memory overhead.

- Overlay and printing of linework on a spatially referenced map.  Printing
as hairlines and non destructive to image.
- Line following routines for digitising linework.

- Artificial particle distribution - (random, clustered and self-avoiding),
- nearest neighbour histogram calculations for particle distributions,

- Principal components routine for multiband images - correlation matrix
for a stack of images, eigensystem analysis and principal component images
- Bivariate scatter graph for a pair of images in a stack.
- More filtering routines.

Regards - Richard Herd



Richard Herd
Montserrat Volcano Observatory
St Johns
Montserrat
West Indies
email : rahe@ua.nkw.ac.uk
phone : (1) 664 491 5647
FAX : (1) 664 491 2324



From nih-image-request@io.ece.drexel.edu Mon Jun 21 17:15 EDT 1999
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Subject: Re: Options for measurements ignored in exported measurements
 file?
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There is a compiler bug which doesn't handle the extension from 8 to 16 bit
sets properly. The problem occurs at "MinorAxis", which is the 8th
measurement option, and faultly 'propagates sign' to all further
measurement options.

instead:
Measurements := Measurements + [MinorAxisM];
I could work around by:


var
 n_MinorAxis: SetOfMeasurements;
.....
  Measurements := Measurements + [MajorAxisM];
  n_MinorAxis := [MinorAxisM];
  if pos('minor', options) <> 0 then
  Measurements := Measurements + n_MinorAxis;




Norbert Vischer                  University of Amsterdam
Scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



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unsubscribe me please.  anthony.mollano@mc.rochester.edu

-----------------------------------------
Anthony V. Mollano
University of Rochester School of Medicine
Email: Anthony.Mollano@mc.rochester.edu
Home Phone: (716) 473-2163


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From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: Re: "Can't find application" error
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>I get the error "application NIH Image 1.62 cannot be found" 
>(unexpected error -2048) when double-clicking an NIH TEXT file.
>...
>The problem appears since I have upgraded my G3 Mac to OS 8.6. The error
>comes up with or without NIH Image loaded, I can't even open the text file
>from within NIH Image. However, a PICT file behaves normal. Removing all
>other applications with creator 'Imag' and rebuilding the desktop doesn't
>help.

I run 8.6 on a G3 (b/w) and run Object Image, can open any (NIH-Image) text file. No problem. Of course you checked file type and creator with ResEdit?

ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156
PGP fingerprint B263 BEAF 48E2 FE6E 2525  B8C3 EBF9 7685 9A1E 8A3A



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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 141

Today's Topics:
  Re Can't find application error.      [ Greg Joss <gjoss@hotmail.com> ]
  Re: Can't find application error.     [ Norbert Vischer <vischer@bio.uva.nl ]
  Options for measurements ignored in   [ Bill Christens-Barry <wacb@aplcomm. ]
  Stereo photos                         [ Richard Herd <rahe@unixa.nerc-keywo ]
  Re: Options for measurements ignored  [ Norbert Vischer <vischer@bio.uva.nl ]
  Re: nih-image-d Digest V99 #138       [ Anthony Mollano <Anthony.Mollano@mc ]
  Re: "Can't find application" error    [ Ard Jonker <a.jonker@amc.uva.nl> ]

------------------------------

Date: Mon, 21 Jun 1999 16:54:48 EST
From: Greg Joss <gjoss@hotmail.com>
To: nih-image@io.ece.drexel.edu, Noel.Goldsmith@dsto.defence.gov.au
Subject: Re Can't find application error.
Message-ID: <19990621065449.96162.qmail@hotmail.com>
Content-Type: text/plain; format=flowed

>From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
>Reply-To: nih-image@io.ece.drexel.edu
>To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
>Subject: Re Can't find application error.
>Date: Mon, 21 Jun 1999 15:35:18 +1000
>
>Norbert Vischer reports trouble when he double clicks on a file from Image.
>The only strange behaviour I see on a beige G3 300 is the launching of 
>Image
>SXM instead of standard Image 1.62 when a document is double clicked.

I would have thought that was simply a result of the most recently installed 
program catching 'Imag'

I recently (early last week) had the problem that Norbert refers to on a 
beige G3 running OS8.1 but at the time I was able to open via menu so I just 
went around it. Might have been Object-Image.p1 or n16; I am not sure.  I am 
now running Object-Image14.6.99-PPC and the problem doesn't occur. (about to 
install Object-Image1.62p2).

>I suspect that Object Image may have something to do with this. When I >get 
>some time I will get Object Image and try it out.
>best wishes
>Noel.

Noel,
I couldn't recommend Object-Image highly enough and suggest you make time to 
get it before doing any further macro programming as Object-Image help, 
debug and dialog facilities have taken macro programming a leap forward over 
recent months making it even easier and more efficient while fully being 
backwards compatable with NIH-Image

Regards,
Greg
gjoss@rna.bio.mq.edu.au



______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com

------------------------------

Date: Mon, 21 Jun 1999 09:20:44 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Can't find application error.
Message-Id: <l03110700b3938d4e6811@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

>Norbert Vischer reports trouble when he double clicks on a file from Image.
>The only strange behaviour I see on a beige G3 300 is the launching of Image
>SXM instead of standard Image 1.62 when a document is double clicked.
>I suspect that Object Image may have something to do with this. When I get
>some time I will get Object Image and try it out.
>best wishes
>Noel.

As stated before, the problem disappears when disabling the "File exchange"
control panel. It also disappears, when "File Exchange Preferences" is
removed.

In my example, I suspect that "File Exchange Preferences" is corrupted: it
contains two 'prat' resources with the names:

TEXTImaggfBr
TEXTImagImag

suggesting two different target applications  for text files created by
Image, one of which points to GifBuilder (gfBr), which doesn't make sense.

If anyone else has such problems, please let me know.

------------------------------

Date: Mon, 21 Jun 1999 15:30:24 -0400
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
To: nih-image@io.ece.drexel.edu
Subject: Options for measurements ignored in exported measurements file?
Message-id: <v04011700b393fe3b7d83@[128.244.128.182]>
Content-type: text/plain; charset=us-ascii
Content-transfer-encoding: 7BIT

I've found that when I Export()  measurements from a macro using v1.62,
what results is a file with all of the possible measurements (there are
14). This occurs even if I have previously selected (via the check boxes in
the 'Analyze/Options...' menu or using the SetOptions() macro command) a
lesser number to be shown in the Results window.

I'd like to figure out how to alter this behavior to allow only the
displayed measurements to be exported. My naive look at the source code
suggests to me that what I want is what is supposed to happen, but I'm not
confident of this. The file.p module has a procedure ExportMeasurements()
that calls a utilities.p procedure CopyResultsToBuffer().
CopyResultsToBuffer() contains some code that identifies which of the
various measurement options the user wanted. This code consists of a series
of tests for the desired options, e.g. 'if MajorAxisM in measurements
then', where 'measurements' was evidently established by the check boxes or
SetOption() macro command via the analysis.p procedure
DoMeasurementOptions().

Also, I haven't figured out how to select the 'ShowHeadings' option from
within the macro language. Is this possible? On a related note, I would
like to gain macro language access to some of the measurement arrays (such
as the mode[] array) that hold measurements. How hard would it be to code
this?

Thanks.

Bill Christens-Barry
-------------------------
Bill Christens-Barry, PhD
Johns Hopkins University Applied Physics Laboratory
wacb@aplcomm.jhuapl.edu
-------------------------

------------------------------

Date: Mon, 21 Jun 1999 16:25:51 +0400 (GMT)
From: Richard Herd <rahe@unixa.nerc-keyworth.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Stereo photos
Message-Id: <l03130300b39417f04f86@[205.160.233.211]>
Content-Type: text/plain; charset="us-ascii"

I have had some interest in my modifications to NIH-Image for handling
stereo photos for deriving XYZ points.  I have put a copy on our anonymous
ftp server - ftp.bgs.ac.uk in the directory /pubload/Montserrat.   The
files needed are:

NIHImage.hqx - software
Texts.hqx - test sample and reference points in text files + description of
how to use the routine
K8.hqx - demo photo 1 of the Montserrat lava dome
K9.hqx - demo photo 2 of the Montserrat lava dome

There are a number of other things available in this version of NIH-Image:

- Import of tab-delimited data files (including column headers and null
data).  Columns in order X,Y,Z1,Z2...Zn.
- Surface gridding routines for Z values of imported data to generate
surface maps.  Grid histogram with percentile choices.
- Spatial referencing for surface maps.  Easting and northing shown in Info
window, and preserved with the map.
- ROI operations.  Use a ROI on a map to extract a portion of data from a
data set.
- Stats routines on point source data based on position relative to ROI.
- Dynamic array sizes defined in options to minimise the memory overhead.

- Overlay and printing of linework on a spatially referenced map.  Printing
as hairlines and non destructive to image.
- Line following routines for digitising linework.

- Artificial particle distribution - (random, clustered and self-avoiding),
- nearest neighbour histogram calculations for particle distributions,

- Principal components routine for multiband images - correlation matrix
for a stack of images, eigensystem analysis and principal component images
- Bivariate scatter graph for a pair of images in a stack.
- More filtering routines.

Regards - Richard Herd



Richard Herd
Montserrat Volcano Observatory
St Johns
Montserrat
West Indies
email : rahe@ua.nkw.ac.uk
phone : (1) 664 491 5647
FAX : (1) 664 491 2324

------------------------------

Date: Mon, 21 Jun 1999 23:10:01 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Options for measurements ignored in exported measurements
 file?
Message-Id: <l03010d00b39458eb93fb@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

There is a compiler bug which doesn't handle the extension from 8 to 16 bit
sets properly. The problem occurs at "MinorAxis", which is the 8th
measurement option, and faultly 'propagates sign' to all further
measurement options.

instead:
Measurements := Measurements + [MinorAxisM];
I could work around by:


var
 n_MinorAxis: SetOfMeasurements;
.....
  Measurements := Measurements + [MajorAxisM];
  n_MinorAxis := [MinorAxisM];
  if pos('minor', options) <> 0 then
  Measurements := Measurements + n_MinorAxis;




Norbert Vischer                  University of Amsterdam
Scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: Mon, 21 Jun 1999 17:08:44 -0400
From: Anthony Mollano <Anthony.Mollano@mc.rochester.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #138
Message-ID: <SIMEON.9906211744.A@muahost.mc.rochester.edu>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

unsubscribe me please.  anthony.mollano@mc.rochester.edu

-----------------------------------------
Anthony V. Mollano
University of Rochester School of Medicine
Email: Anthony.Mollano@mc.rochester.edu
Home Phone: (716) 473-2163

------------------------------

Date: Tue, 22 Jun 1999 08:38:55 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: "Can't find application" error
Message-Id: <l03130300b394ddfb9c6c@[145.117.53.66]>
Content-Type: text/plain; charset="us-ascii"

>I get the error "application NIH Image 1.62 cannot be found" 
>(unexpected error -2048) when double-clicking an NIH TEXT file.
>...
>The problem appears since I have upgraded my G3 Mac to OS 8.6. The error
>comes up with or without NIH Image loaded, I can't even open the text file
>from within NIH Image. However, a PICT file behaves normal. Removing all
>other applications with creator 'Imag' and rebuilding the desktop doesn't
>help.

I run 8.6 on a G3 (b/w) and run Object Image, can open any (NIH-Image) text file. No problem. Of course you checked file type and creator with ResEdit?

ard

dr A.Jonker <a.jonker@amc.uva.nl>  |Academic Medical Centre
Dep of Cell Biology and Histology  |Meibergdreef 15
Faculty of Medicine                |1105 AZ Amsterdam
University of Amsterdam            |The Netherlands
tel +31 20 566 5304                |fax +31 20 697 4156
PGP fingerprint B263 BEAF 48E2 FE6E 2525  B8C3 EBF9 7685 9A1E 8A3A

--------------------------------
End of nih-image-d Digest V99 Issue #141
****************************************

From nih-image-request@io.ece.drexel.edu Tue Jun 22 15:53 EDT 1999
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From: "Jackie E. Kylander" <jek@med.unc.edu>
Subject: software FPU
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I'm using a DataTranslation capture board in a PowerMac 8100.
DataTranslation has abandoned the Macintosh and the ColorKit software that
made it easy to capture images. Software FPU had worked well with OS8.1,
but due to a crash, I installed OS 8.5.1. Software FPU now crashes my Mac
and the ColorKit app won't run without it. I found that this simple program
worked a bit better than Image for color capture. Does anyone know if
software FPU is still being supported or how I can convince ColorKit to run
on my PowerMac? TIA

Jackie E. Kylander <jek@med.unc.edu>
Administrator, Cystic Fibrosis Center Imaging Facility

People for Computational Freedom <http://www.unc.edu/campus/sigs/compfree>



From nih-image-request@io.ece.drexel.edu Tue Jun 22 18:06 EDT 1999
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Subject: Re: software FPU
Date: Tue, 22 Jun 99 16:12:31 -0400
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why do you need a FPU emulator with os8???


From nih-image-request@io.ece.drexel.edu Tue Jun 22 18:06 EDT 1999
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funny you should mention the Data Translation board!!!!!
i've got a G3 and arranged to get a DT-3152 board to evaluate.- Yes the 
G3 has PCI slots but Data Translation uses only a Windows driver.  sooo- 
i tried installing their driver via 'Virtual PC' which works fine on 
every Windows-based software i've tried. but I could not load their 
driver. After some back and forth with Data Translation- i got the 
following msg from their tech support:


***************************************************

Subject:     Mac 63 w/PCI slots
Sent:        6/23/19 4:43 PM
Received:    6/22/99 12:24 PM
From:        Larry Bell, LBell@datx.com
To:          Jared_Rifkin@QC.edu

Sorry but we have not ran into this situation and the Dt3152 is not
supported in a mac system using a 3rd party Emulation software.


Best Regards

Larry Bell

Data Translation Tech Support

 Note: Do not respond to this message directly it cannot be processed.
 
 All technical support questions must go to tsupport@datx.com for
 processing.
 Or contact the distributor near you, see,
 http://www.datx.com/buy/int/int.html

He is evaluating the board and has "an unusual system".  Mac G3 w/PCI
slots.  Using PC Emulation software.  Installed other win based software
and it works fine.  He installed the software for the DT3152 and he was
ok until the end of the installation where it asked if finished and he
clicked Yes. Then it was supposed to ask to restart computer and it
didn't so he can't move on to next step.  He will re-install PC Emulator
while waiting for Tech support.  he has a class until 2:30 so he asked
that you call back at 3 or close to it.  Otherwise, send email to :
Jared_Rifkin@QC.edu


**********************************************

i won't comment on DT's lack of internal communications between their 
sales and tech dept's!!!!
 BUT-
does anybody out there know of a comparable hi-res (4M pixel) capture 
board that can be used on a MAC?????


From nih-image-request@io.ece.drexel.edu Wed Jun 23 05:21 EDT 1999
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                   NIH-image Mailing List Help 
                   ---------------------------
     


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0)  Remember that Archive is case-sensitive.
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2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
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5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--


From nih-image-request@io.ece.drexel.edu Wed Jun 23 15:58 EDT 1999
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From: hard@acsu.buffalo.edu
Date: Wed, 23 Jun 1999 15:35:23 -0500
To: "NIH-Image list" <nih-image@io.ece.drexel.edu>
Subject: Course Announcement
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Course Announcement

Title: Optical Microscopy and Imaging in the Biomedical Sciences

When: October 6 - October 14, 1999

Where: Marine Biology Laboratory, Woods Hole, MA, USA

Tuition: $2050 (Includes room and board, text, handouts, supplies)

Application Deadline: August 3, 1999

Admission application and information:
     Carol Hamel, Admissions Coordinator
     Marine Biological Laboratory
     7 MBL Street
     Woods Hole, MA 02543-1015
     (508) 289-7401
     Internet: admissions@mbl.edu
     WWW: http://www.mbl.edu (Application forms available via Adobe Acrobat)

Course Director: Colin S. Izzard, State University of New York @ Albany
                 Phone: [518] 442 - 4367
                 EMail: csizzard@csc.albany.edu

Course Description:

For Whom:
      Designed primarily for research scientists, physicians, postdoctoral 
trainees and advanced graduate students in animal, plant, medical and 
material sciences. Non-biologists seeking a comprehensive introduction to 
microscopy and video-imaging will benefit greatly from this course as well. 
There are no specific prerequisites, but an understanding of the basic 
principles of optics is desirable. Limited to 24 students.

  The eight day course consists of lectures, laboratory demonstrations, 
exercises and discussions that will enable the participant to obtain and 
interpret microscope images of high quality, to perform quantitative optical

measurements, and to produce photographic and video records for
documentation 
and analysis.

Topics to be covered include:
      principles of microscope design and image formation
      bright field, dark field, phase contrast, polarized light,
differential
         interference contrast, interference reflection, and fluorescence
         microscopy
      confocal scanning microscopy, multiphoton excitation fluorescence
         microscopy and image deconvolution
      digital image restoration and 3-D reconstruction
      video imaging, recording, enhancement, and intensification
      analog and digital image processing and analysis
      fluorescent probes and ratiometric-imaging
      laser tweezers and laser scissors

  Applications to live cells will be emphasized; other specimens will be 
covered as well.

  Students will have direct hands-on experience with state-of-the-art 
microscopes, video cameras, recorders and image processing equipment
provided 
by major optical and electronics companies. Instruction will be provided by 
experienced staff from universities and industry.

  Students are encouraged to bring their own biological (primary 
cultures, cell lines, etc.) and material specimens and to discuss individual

research problems with the faculty.


From nih-image-d-request@io.ece.drexel.edu Wed Jun 23 16:00 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 142

Today's Topics:
  software FPU                          [ "Jackie E. Kylander" <jek@med.unc.e ]
  Re: software FPU                      [ jared rifkin <jared_rifkin@qc.edu> ]
  Re: software FPU                      [ jared rifkin <jared_rifkin@qc.edu> ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
  Course Announcement                   [ hard@acsu.buffalo.edu ]

------------------------------

Date: Tue, 22 Jun 1999 15:31:57 -0400
From: "Jackie E. Kylander" <jek@med.unc.edu>
To: nih-image@io.ece.drexel.edu
Subject: software FPU
Message-Id: <l03130304b395942cd2dd@[152.19.45.164]>
Content-Type: text/plain; charset="us-ascii"

I'm using a DataTranslation capture board in a PowerMac 8100.
DataTranslation has abandoned the Macintosh and the ColorKit software that
made it easy to capture images. Software FPU had worked well with OS8.1,
but due to a crash, I installed OS 8.5.1. Software FPU now crashes my Mac
and the ColorKit app won't run without it. I found that this simple program
worked a bit better than Image for color capture. Does anyone know if
software FPU is still being supported or how I can convince ColorKit to run
on my PowerMac? TIA

Jackie E. Kylander <jek@med.unc.edu>
Administrator, Cystic Fibrosis Center Imaging Facility

People for Computational Freedom <http://www.unc.edu/campus/sigs/compfree>

------------------------------

Date: Tue, 22 Jun 99 16:12:31 -0400
From: jared rifkin <jared_rifkin@qc.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: software FPU
Message-ID: <15117846F6@qc1.qc.edu>
Content-Type: text/plain; charset="US-ASCII"

why do you need a FPU emulator with os8???

------------------------------

Date: Tue, 22 Jun 99 16:11:31 -0400
From: jared rifkin <jared_rifkin@qc.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: software FPU
Message-ID: <150D277BB0@qc1.qc.edu>
Content-Type: text/plain; charset="US-ASCII"

funny you should mention the Data Translation board!!!!!
i've got a G3 and arranged to get a DT-3152 board to evaluate.- Yes the 
G3 has PCI slots but Data Translation uses only a Windows driver.  sooo- 
i tried installing their driver via 'Virtual PC' which works fine on 
every Windows-based software i've tried. but I could not load their 
driver. After some back and forth with Data Translation- i got the 
following msg from their tech support:


***************************************************

Subject:     Mac 63 w/PCI slots
Sent:        6/23/19 4:43 PM
Received:    6/22/99 12:24 PM
From:        Larry Bell, LBell@datx.com
To:          Jared_Rifkin@QC.edu

Sorry but we have not ran into this situation and the Dt3152 is not
supported in a mac system using a 3rd party Emulation software.


Best Regards

Larry Bell

Data Translation Tech Support

 Note: Do not respond to this message directly it cannot be processed.
 
 All technical support questions must go to tsupport@datx.com for
 processing.
 Or contact the distributor near you, see,
 http://www.datx.com/buy/int/int.html

He is evaluating the board and has "an unusual system".  Mac G3 w/PCI
slots.  Using PC Emulation software.  Installed other win based software
and it works fine.  He installed the software for the DT3152 and he was
ok until the end of the installation where it asked if finished and he
clicked Yes. Then it was supposed to ask to restart computer and it
didn't so he can't move on to next step.  He will re-install PC Emulator
while waiting for Tech support.  he has a class until 2:30 so he asked
that you call back at 3 or close to it.  Otherwise, send email to :
Jared_Rifkin@QC.edu


**********************************************

i won't comment on DT's lack of internal communications between their 
sales and tech dept's!!!!
 BUT-
does anybody out there know of a comparable hi-res (4M pixel) capture 
board that can be used on a MAC?????

------------------------------

Date: Wed, 23 Jun 1999 05:05:02 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199906230905.FAA23510@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
                   ---------------------------
     


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     *********************************************************
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     *********************************************************
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Subscribe
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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

------------------------------

Date: Wed, 23 Jun 1999 15:35:23 -0500
From: hard@acsu.buffalo.edu
To: "NIH-Image list" <nih-image@io.ece.drexel.edu>
Subject: Course Announcement
Message-ID: <1607719.3139140923@cilly3.cds.buffalo.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Course Announcement

Title: Optical Microscopy and Imaging in the Biomedical Sciences

When: October 6 - October 14, 1999

Where: Marine Biology Laboratory, Woods Hole, MA, USA

Tuition: $2050 (Includes room and board, text, handouts, supplies)

Application Deadline: August 3, 1999

Admission application and information:
     Carol Hamel, Admissions Coordinator
     Marine Biological Laboratory
     7 MBL Street
     Woods Hole, MA 02543-1015
     (508) 289-7401
     Internet: admissions@mbl.edu
     WWW: http://www.mbl.edu (Application forms available via Adobe Acrobat)

Course Director: Colin S. Izzard, State University of New York @ Albany
                 Phone: [518] 442 - 4367
                 EMail: csizzard@csc.albany.edu

Course Description:

For Whom:
      Designed primarily for research scientists, physicians, postdoctoral 
trainees and advanced graduate students in animal, plant, medical and 
material sciences. Non-biologists seeking a comprehensive introduction to 
microscopy and video-imaging will benefit greatly from this course as well. 
There are no specific prerequisites, but an understanding of the basic 
principles of optics is desirable. Limited to 24 students.

  The eight day course consists of lectures, laboratory demonstrations, 
exercises and discussions that will enable the participant to obtain and 
interpret microscope images of high quality, to perform quantitative optical

measurements, and to produce photographic and video records for
documentation 
and analysis.

Topics to be covered include:
      principles of microscope design and image formation
      bright field, dark field, phase contrast, polarized light,
differential
         interference contrast, interference reflection, and fluorescence
         microscopy
      confocal scanning microscopy, multiphoton excitation fluorescence
         microscopy and image deconvolution
      digital image restoration and 3-D reconstruction
      video imaging, recording, enhancement, and intensification
      analog and digital image processing and analysis
      fluorescent probes and ratiometric-imaging
      laser tweezers and laser scissors

  Applications to live cells will be emphasized; other specimens will be 
covered as well.

  Students will have direct hands-on experience with state-of-the-art 
microscopes, video cameras, recorders and image processing equipment
provided 
by major optical and electronics companies. Instruction will be provided by 
experienced staff from universities and industry.

  Students are encouraged to bring their own biological (primary 
cultures, cell lines, etc.) and material specimens and to discuss individual

research problems with the faculty.

--------------------------------
End of nih-image-d Digest V99 Issue #142
****************************************

From nih-image-request@io.ece.drexel.edu Wed Jun 23 19:42 EDT 1999
Received: (from lists@localhost)
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Resent-Date: Wed, 23 Jun 1999 19:42:32 -0400 (EDT)
From: mfb5@cornell.edu
Date: Wed, 23 Jun 1999 19:32:21 -0400 (EDT)
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To: nih-image@io.ece.drexel.edu
Subject: Image aquisition problem
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Our lab has just begun to gather data using NIH image.  While the program 
works great for measurements on images that we have, we haven't been able 
to actually aquire new images with the program.  It seems to be a problem 
with the plug-ins.  We have a Mac G3, os 8.6.  None of the downloaded 
plug-ins have been able to work with the NIH image program.  If anyone 
could give us some advice, we'd greatly appreciate it. 

Best,

Mike Benard

*************************************
Michael F. Benard
Section of Ecology and Systematics
Cornell University
Ithaca, NY 14850
(607) 254 - 4293
*************************************


From nih-image-request@io.ece.drexel.edu Wed Jun 23 20:36 EDT 1999
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Resent-Date: Wed, 23 Jun 1999 20:36:42 -0400 (EDT)
Date: Wed, 23 Jun 1999 17:26:39 -0700
From: David Linker <dtlinker@u.washington.edu>
To: mfb5@cornell.edu
cc: nih-image@io.ece.drexel.edu
Subject: Re: Image aquisition problem
Message-ID: <520784.3139147599@huginn.medicine.washington.edu>
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I use the plug-in routinely to acquire images using a B/W G3, with no
problem. What digitizing hardware are you using? My experience is that
hardware either comes with its own plug-in, or it works with the plug-in
digitizer.

DTL

--On Wed, Jun 23, 1999 7:32 PM -0400 mfb5@cornell.edu wrote:

> Our lab has just begun to gather data using NIH image.  While the program 
> works great for measurements on images that we have, we haven't been able 
> to actually aquire new images with the program.  It seems to be a problem 
> with the plug-ins.  We have a Mac G3, os 8.6.  None of the downloaded 
> plug-ins have been able to work with the NIH image program.  If anyone 
> could give us some advice, we'd greatly appreciate it. 
> 
> Best,
> 
> Mike Benard
> 
> *************************************
> Michael F. Benard
> Section of Ecology and Systematics
> Cornell University
> Ithaca, NY 14850
> (607) 254 - 4293
> *************************************
> 





From nih-image-d-request@io.ece.drexel.edu Thu Jun 24 15:54 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #143
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 143

Today's Topics:
  Image aquisition problem              [ mfb5@cornell.edu ]
  Re: Image aquisition problem          [ David Linker <dtlinker@u.washington ]
  Object-Image Manual                   [ "Giles, Bill" <William.Giles@TIMET. ]

------------------------------

Date: Wed, 23 Jun 1999 19:32:21 -0400 (EDT)
From: mfb5@cornell.edu
To: nih-image@io.ece.drexel.edu
Subject: Image aquisition problem
Message-ID: <Pine.SOL.3.91.990623192750.22519A-100000@travelers.mail.cornell.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Our lab has just begun to gather data using NIH image.  While the program 
works great for measurements on images that we have, we haven't been able 
to actually aquire new images with the program.  It seems to be a problem 
with the plug-ins.  We have a Mac G3, os 8.6.  None of the downloaded 
plug-ins have been able to work with the NIH image program.  If anyone 
could give us some advice, we'd greatly appreciate it. 

Best,

Mike Benard

*************************************
Michael F. Benard
Section of Ecology and Systematics
Cornell University
Ithaca, NY 14850
(607) 254 - 4293
*************************************

------------------------------

Date: Wed, 23 Jun 1999 17:26:39 -0700
From: David Linker <dtlinker@u.washington.edu>
To: mfb5@cornell.edu
cc: nih-image@io.ece.drexel.edu
Subject: Re: Image aquisition problem
Message-ID: <520784.3139147599@huginn.medicine.washington.edu>
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I use the plug-in routinely to acquire images using a B/W G3, with no
problem. What digitizing hardware are you using? My experience is that
hardware either comes with its own plug-in, or it works with the plug-in
digitizer.

DTL

--On Wed, Jun 23, 1999 7:32 PM -0400 mfb5@cornell.edu wrote:

> Our lab has just begun to gather data using NIH image.  While the program 
> works great for measurements on images that we have, we haven't been able 
> to actually aquire new images with the program.  It seems to be a problem 
> with the plug-ins.  We have a Mac G3, os 8.6.  None of the downloaded 
> plug-ins have been able to work with the NIH image program.  If anyone 
> could give us some advice, we'd greatly appreciate it. 
> 
> Best,
> 
> Mike Benard
> 
> *************************************
> Michael F. Benard
> Section of Ecology and Systematics
> Cornell University
> Ithaca, NY 14850
> (607) 254 - 4293
> *************************************
> 

------------------------------

Date: Thu, 24 Jun 1999 13:37:22 -0600
From: "Giles, Bill" <William.Giles@TIMET.com>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Object-Image Manual
Message-ID: <C395B6F570ADD11199F300A0C9A94BA303BF2E@henexc1.timet.com>
Content-Type: text/plain

Hi list,

Ive just d/led Object-Image and Executor to run on my PC.(WOW,Executor
really works!).

I'm hopefully using Object-Image for the overlay function. More questions to
follow once I have it running.

I was able to decompress Object-Image and Rotator, but the documentation
files wouldn't decompress, so I'm out in the dark as to how the overlay
functions operate.

Any ideas on the decompression? 


Bill


TIMET
William.Giles@TIMET.com

--------------------------------
End of nih-image-d Digest V99 Issue #143
****************************************

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Hi list,

Ive just d/led Object-Image and Executor to run on my PC.(WOW,Executor
really works!).

I'm hopefully using Object-Image for the overlay function. More questions to
follow once I have it running.

I was able to decompress Object-Image and Rotator, but the documentation
files wouldn't decompress, so I'm out in the dark as to how the overlay
functions operate.

Any ideas on the decompression? 


Bill


TIMET
William.Giles@TIMET.com






From nih-image-request@io.ece.drexel.edu Thu Jun 24 16:58 EDT 1999
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Subject: Re: Image aquisition problem
Date: Thu, 24 Jun 99 16:42:11 -0400
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1) pls post all replies re:blue G3 and appropriate digitizers and 
compatibility issues with NIH Image and to other imaging software to 
entire newsgroup.

2)????? has anyone tried the sony digital/analog converter to send images 
from an analog video camera thru the firewire port directly into the mac 
hard drive??  are there impedance mismatch problems that haven't been 
addressed?? i've tried this combo and the ported images are distorted in 
color, horizontal registration, and an overall distortion of the image. 
(old performa with the cheap old apple digitizer card gave reasonably 
good images.) ?????


From nih-image-request@io.ece.drexel.edu Thu Jun 24 19:20 EDT 1999
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From: John Gripp <mrgripper@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: 16-bit image formatting
Date: Thu, 24 Jun 1999 16:09:19 PDT
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We are exporting images acquired via laser scanner in 16-bit, unsigned
TIFF image formats to the NIH Image software package.  However, the
data doesn't appear to be consistent with the data viewed with the scanner 
software and the scanner vendor claims that the NIH IMAGE software is 
scaling 16 bit image data to an 8 bit representation of that  data.

I have attempted to evaluate the NIH IMAGE web site for further information 
regarding current versions of the software and their ability to accept 16 
bit TIFF File formats, but the info I have found seems quite dated...I have 
heard that the current versions of the software do accept the 16-bit files 
unaltered from current scanning
instruments.  Is this true???  If not, is our laser scanner vendor
correct about this discrepancy???  If so, what can we do to make
the data consistant from acquisition to analysis???

Thanks,

John G.


_______________________________________________________________
Get Free Email and Do More On The Web. Visit http://www.msn.com


From nih-image-request@io.ece.drexel.edu Thu Jun 24 21:55 EDT 1999
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Message-ID: <3772DF1C.22E0786@cyllene.uwa.edu.au>
Date: Fri, 25 Jun 1999 09:45:12 +0800
From: Tim Fairchild <timf@cyllene.uwa.edu.au>
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Subject: "Count and Tag"
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Does Image allow you to conduct a "count and tag"?  I have tried using
the image wand for this, but since I have to chose either threshold or
density slice for this function, it dosn't give me the desired response,
since some of the cells I am counting bleed into each other (and
therefore makes it all a bit messy).  So I guess what I am looking for
is a tool that allows me to mark the cell (preferably just with a mouse
click) and conduct an automatic count.

In today's 'day and age', I don't want to revert to pen and paper,

please help!!!

Thanks
Tim.
-----------------------------------------------------------------
Timothy J. Fairchild B.Sc. (Hons)
PhD Candidate
Co-ordinator for Centre of Athletic Testing
Department of Human Movement and Exercise Science
Nedlands, Western Australia 6907
Telephone: (+61 8) 9380 2793
Facsimile:  (+61 8) 9380 1039
Email: timf@cyllene.uwa.edu.au
http://www.general.uwa.edu.au/~hmweb/index.htm




From nih-image-request@io.ece.drexel.edu Thu Jun 24 21:55 EDT 1999
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Date: Thu, 24 Jun 1999 21:51:31 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: 16-bit image formatting
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At 04:09 PM 6/24/99 PDT, you wrote:
>We are exporting images acquired via laser scanner in 16-bit, unsigned
>TIFF image formats to the NIH Image software package.  However, the
>data doesn't appear to be consistent with the data viewed with the scanner 
>software and the scanner vendor claims that the NIH IMAGE software is 
>scaling 16 bit image data to an 8 bit representation of that  data.
>
>I have attempted to evaluate the NIH IMAGE web site for further information 
>regarding current versions of the software and their ability to accept 16 
>bit TIFF File formats, but the info I have found seems quite dated...I have 
>heard that the current versions of the software do accept the 16-bit files 
>unaltered from current scanning
>instruments.  Is this true???  If not, is our laser scanner vendor
>correct about this discrepancy???  If so, what can we do to make
>the data consistant from acquisition to analysis???

NIH Image scales imported 16-bit images to 8-bits. My new ImageJ program, on the other hand, provides full 16-bit support. The ImageJ Web site is at http://rsb.info.nih.gov/ij/.

-wayne


From nih-image-request@io.ece.drexel.edu Fri Jun 25 04:00 EDT 1999
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Message-ID: <001601bebedf$457c21a0$99efe18f@unina.it>
From: "Eugenio Amendola" <amendola@unina.it>
To: "NIH-Image mailing list" <nih-image@io.ece.drexel.edu>
Subject: executor
Date: Fri, 25 Jun 1999 09:49:35 +0200
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This is a multi-part message in MIME format.

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Hi chaps,
in the last days I've read some messages dealing with executor. I really =
would like to run Object Image (and some other little application) on my =
PC, and some time ago started puzzling about Mac emulator. I landed on =
executor too. Downloaded the demo, but it didn't work much. Recently I =
tried again, and found noticeable improvement. But my understanding is =
that Executor doesn't run PowerMacintosh application. Am I write, or am =
I wrong? Should I resigne and run Object-Image (does exist non-Power-Mac =
release?)?
Sincerely
Eugenio

----------------------------
----------------------------
Dr. Eugenio Amendola
Italian National Council of Research
Institute of Composite Materials Technology
P.le Tecchio 80, 80125 Naples
ITALY
Tel:       (+) 39 081 7682511
fax:       (+) 39 081 7682404
email:    amendola@unina.it
url:        143.225.239.86

------=_NextPart_000_0013_01BEBEF0.0887D260
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	charset="iso-8859-1"
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content=3D"text/html; charset=3Diso-8859-1" =
http-equiv=3DContent-Type>
<META content=3D"MSHTML 5.00.2014.210" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#c8e0d8>
<DIV><FONT face=3DArial size=3D2>Hi chaps,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>in the last days I've read some =
messages dealing=20
with executor. I really would like to run Object Image (and some other =
little=20
application) on my PC, and some time ago started puzzling about Mac =
emulator. I=20
landed on executor too. Downloaded the demo, but it didn't work much. =
Recently I=20
tried again, and found noticeable improvement. But my understanding is =
that=20
Executor doesn't run PowerMacintosh application. Am I write, or am I =
wrong?=20
Should I resigne and run Object-Image (does exist non-Power-Mac=20
release?)?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Sincerely</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Eugenio</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial=20
size=3D2>----------------------------<BR>----------------------------<BR>=
Dr.=20
Eugenio Amendola<BR>Italian National Council of Research<BR>Institute of =

Composite Materials Technology<BR>P.le Tecchio 80, 80125=20
Naples<BR>ITALY<BR>Tel:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (+) 39 081=20
7682511<BR>fax:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (+) 39 081=20
7682404<BR>email:&nbsp;&nbsp;&nbsp; <A=20
href=3D"mailto:amendola@unina.it">amendola@unina.it</A><BR>url:&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
143.225.239.86</FONT></DIV></BODY></HTML>

------=_NextPart_000_0013_01BEBEF0.0887D260--


From nih-image-request@io.ece.drexel.edu Fri Jun 25 06:27 EDT 1999
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Date: Fri, 25 Jun 1999 12:21:18 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Object-Image and Executor on the PC
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At the moment, there a number of people who try out Object-Image in
combination with the Mac emulator "Executor" on a PC. I haven't invested
much time in that subject yet, but there are already some positive
experiences.

Object-Image is only distributed as fat binary, which means that Executor
should be able to execute the 68k part of it. Probably some features are
not supported like framegrabber access, serial port, help balloons, help
menu, AppleScript. In a future version I'll try to design the pictorial
help (help menu) so that it is accessible also within Executor.
Documentation and tutorial sofar is distributed in Microsoft Word 5 format
for the Macintosh. Until there is a better solution, I have now put
additionally a html version onto my server (obtained by automatic
conversion). An Acrobat verison (thanks to Stephen Martin) is available on
request.

I appreciate any feedback on this subject, especially from those who can
tell about different behaviour on Mac and PC.



Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



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From: nih-image-d-request@io.ece.drexel.edu
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 144

Today's Topics:
  Re: Image aquisition problem          [ jared rifkin <jared_rifkin@qc.edu> ]
  Serial port control                   [ "B. Iyengar" <iyengabg@mcmail.cis.M ]
  16-bit image formatting               [ John Gripp <mrgripper@hotmail.com> ]
  "Count and Tag"                       [ Tim Fairchild <timf@cyllene.uwa.edu ]
  Re: 16-bit image formatting           [ Wayne Rasband <wayne@codon.nih.gov> ]
  executor                              [ "Eugenio Amendola" <amendola@unina. ]
  Object-Image and Executor on the PC   [ Norbert Vischer <vischer@bio.uva.nl ]
  scrolling image with drawing line to  [ MARIAC <mariac@ird.ne> ]

------------------------------

Date: Thu, 24 Jun 99 16:42:11 -0400
From: jared rifkin <jared_rifkin@qc.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: Image aquisition problem
Message-ID: <1687356340@qc1.qc.edu>
Content-Type: text/plain; charset="US-ASCII"

1) pls post all replies re:blue G3 and appropriate digitizers and 
compatibility issues with NIH Image and to other imaging software to 
entire newsgroup.

2)????? has anyone tried the sony digital/analog converter to send images 
from an analog video camera thru the firewire port directly into the mac 
hard drive??  are there impedance mismatch problems that haven't been 
addressed?? i've tried this combo and the ported images are distorted in 
color, horizontal registration, and an overall distortion of the image. 
(old performa with the cheap old apple digitizer card gave reasonably 
good images.) ?????

------------------------------

Date: Thu, 24 Jun 1999 17:52:47 -0400 (EDT)
From: "B. Iyengar" <iyengabg@mcmail.cis.McMaster.CA>
To: nih-image-d@io.ece.drexel.edu
Subject: Serial port control
Message-ID: <Pine.SOL.3.96.990624173952.12489C-100000@mcmail.cis.McMaster.CA>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hello all!
I would like to control a flourescent lamp (lights ON/Off in a timed (10s) 
and cyclical manner) using NIH-Image. First, I would like to know if there
exists a hardware interface of the shelf that takes mac serial port signal
and controls the powersupply of the lamp. Any information on this is most
welcome! 
regds,
Bala

------------------------------

Date: Thu, 24 Jun 1999 16:09:19 PDT
From: John Gripp <mrgripper@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: 16-bit image formatting
Message-ID: <19990624230922.8133.qmail@hotmail.com>
Content-Type: text/plain; format=flowed

We are exporting images acquired via laser scanner in 16-bit, unsigned
TIFF image formats to the NIH Image software package.  However, the
data doesn't appear to be consistent with the data viewed with the scanner 
software and the scanner vendor claims that the NIH IMAGE software is 
scaling 16 bit image data to an 8 bit representation of that  data.

I have attempted to evaluate the NIH IMAGE web site for further information 
regarding current versions of the software and their ability to accept 16 
bit TIFF File formats, but the info I have found seems quite dated...I have 
heard that the current versions of the software do accept the 16-bit files 
unaltered from current scanning
instruments.  Is this true???  If not, is our laser scanner vendor
correct about this discrepancy???  If so, what can we do to make
the data consistant from acquisition to analysis???

Thanks,

John G.


_______________________________________________________________
Get Free Email and Do More On The Web. Visit http://www.msn.com

------------------------------

Date: Fri, 25 Jun 1999 09:45:12 +0800
From: Tim Fairchild <timf@cyllene.uwa.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: "Count and Tag"
Message-ID: <3772DF1C.22E0786@cyllene.uwa.edu.au>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Does Image allow you to conduct a "count and tag"?  I have tried using
the image wand for this, but since I have to chose either threshold or
density slice for this function, it dosn't give me the desired response,
since some of the cells I am counting bleed into each other (and
therefore makes it all a bit messy).  So I guess what I am looking for
is a tool that allows me to mark the cell (preferably just with a mouse
click) and conduct an automatic count.

In today's 'day and age', I don't want to revert to pen and paper,

please help!!!

Thanks
Tim.
-----------------------------------------------------------------
Timothy J. Fairchild B.Sc. (Hons)
PhD Candidate
Co-ordinator for Centre of Athletic Testing
Department of Human Movement and Exercise Science
Nedlands, Western Australia 6907
Telephone: (+61 8) 9380 2793
Facsimile:  (+61 8) 9380 1039
Email: timf@cyllene.uwa.edu.au
http://www.general.uwa.edu.au/~hmweb/index.htm

------------------------------

Date: Thu, 24 Jun 1999 21:51:31 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: 16-bit image formatting
Message-Id: <3.0.5.32.19990624215131.009aa460@codon.nih.gov>
Content-Type: text/plain; charset="us-ascii"

At 04:09 PM 6/24/99 PDT, you wrote:
>We are exporting images acquired via laser scanner in 16-bit, unsigned
>TIFF image formats to the NIH Image software package.  However, the
>data doesn't appear to be consistent with the data viewed with the scanner 
>software and the scanner vendor claims that the NIH IMAGE software is 
>scaling 16 bit image data to an 8 bit representation of that  data.
>
>I have attempted to evaluate the NIH IMAGE web site for further information 
>regarding current versions of the software and their ability to accept 16 
>bit TIFF File formats, but the info I have found seems quite dated...I have 
>heard that the current versions of the software do accept the 16-bit files 
>unaltered from current scanning
>instruments.  Is this true???  If not, is our laser scanner vendor
>correct about this discrepancy???  If so, what can we do to make
>the data consistant from acquisition to analysis???

NIH Image scales imported 16-bit images to 8-bits. My new ImageJ program, on the other hand, provides full 16-bit support. The ImageJ Web site is at http://rsb.info.nih.gov/ij/.

-wayne

------------------------------

Date: Fri, 25 Jun 1999 09:49:35 +0200
From: "Eugenio Amendola" <amendola@unina.it>
To: "NIH-Image mailing list" <nih-image@io.ece.drexel.edu>
Subject: executor
Message-ID: <001601bebedf$457c21a0$99efe18f@unina.it>
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_0013_01BEBEF0.0887D260"

This is a multi-part message in MIME format.

------=_NextPart_000_0013_01BEBEF0.0887D260
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Hi chaps,
in the last days I've read some messages dealing with executor. I really =
would like to run Object Image (and some other little application) on my =
PC, and some time ago started puzzling about Mac emulator. I landed on =
executor too. Downloaded the demo, but it didn't work much. Recently I =
tried again, and found noticeable improvement. But my understanding is =
that Executor doesn't run PowerMacintosh application. Am I write, or am =
I wrong? Should I resigne and run Object-Image (does exist non-Power-Mac =
release?)?
Sincerely
Eugenio

----------------------------
----------------------------
Dr. Eugenio Amendola
Italian National Council of Research
Institute of Composite Materials Technology
P.le Tecchio 80, 80125 Naples
ITALY
Tel:       (+) 39 081 7682511
fax:       (+) 39 081 7682404
email:    amendola@unina.it
url:        143.225.239.86

------=_NextPart_000_0013_01BEBEF0.0887D260
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content=3D"text/html; charset=3Diso-8859-1" =
http-equiv=3DContent-Type>
<META content=3D"MSHTML 5.00.2014.210" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#c8e0d8>
<DIV><FONT face=3DArial size=3D2>Hi chaps,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>in the last days I've read some =
messages dealing=20
with executor. I really would like to run Object Image (and some other =
little=20
application) on my PC, and some time ago started puzzling about Mac =
emulator. I=20
landed on executor too. Downloaded the demo, but it didn't work much. =
Recently I=20
tried again, and found noticeable improvement. But my understanding is =
that=20
Executor doesn't run PowerMacintosh application. Am I write, or am I =
wrong?=20
Should I resigne and run Object-Image (does exist non-Power-Mac=20
release?)?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Sincerely</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Eugenio</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial=20
size=3D2>----------------------------<BR>----------------------------<BR>=
Dr.=20
Eugenio Amendola<BR>Italian National Council of Research<BR>Institute of =

Composite Materials Technology<BR>P.le Tecchio 80, 80125=20
Naples<BR>ITALY<BR>Tel:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (+) 39 081=20
7682511<BR>fax:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (+) 39 081=20
7682404<BR>email:&nbsp;&nbsp;&nbsp; <A=20
href=3D"mailto:amendola@unina.it">amendola@unina.it</A><BR>url:&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
143.225.239.86</FONT></DIV></BODY></HTML>

------=_NextPart_000_0013_01BEBEF0.0887D260--

------------------------------

Date: Fri, 25 Jun 1999 12:21:18 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Object-Image and Executor on the PC
Message-Id: <l03110700b398eb39f7bb@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

At the moment, there a number of people who try out Object-Image in
combination with the Mac emulator "Executor" on a PC. I haven't invested
much time in that subject yet, but there are already some positive
experiences.

Object-Image is only distributed as fat binary, which means that Executor
should be able to execute the 68k part of it. Probably some features are
not supported like framegrabber access, serial port, help balloons, help
menu, AppleScript. In a future version I'll try to design the pictorial
help (help menu) so that it is accessible also within Executor.
Documentation and tutorial sofar is distributed in Microsoft Word 5 format
for the Macintosh. Until there is a better solution, I have now put
additionally a html version onto my server (obtained by automatic
conversion). An Acrobat verison (thanks to Stephen Martin) is available on
request.

I appreciate any feedback on this subject, especially from those who can
tell about different behaviour on Mac and PC.



Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: Fri, 25 Jun 1999 15:24:26 +0200
From: MARIAC <mariac@ird.ne>
To: nih-image@io.ece.drexel.edu
Subject: scrolling image with drawing line tolls
Message-Id: <3.0.1.32.19990625152426.007ac100@192.136.57.17>
Content-Type: text/enriched; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Hi,


I would like to know if its possible to make the image  scroll in the=
 windows with tools like the line drawing tool. I'm working with=
 scionimage/pc.

Thanks,


C=E9dric.

<bold><italic><color><param>0000,8080,0000</param>=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

</color><color><param>0000,0000,ffff</param>

</color></italic></bold><italic><color><param>0000,0000,ffff</param>C=E9dric
<bold>Mariac

</bold></color></italic>Laboratoire de g=E9n=E9tique des plantes


IRD L'institut de recherche pour le d=E9veloppement=20

anciennement ORSTOM

BP 11416 Niamey=20

Republique du NIGER


<underline><color><param>0000,8080,0000</param>E-mail
:</color></underline><color><param>0000,8080,0000</param>
</color>mariac@ird.ne

<underline><color><param>0000,8080,0000</param>Tel :</color></underline>
(227) 75 31 15 / 75 26 10 / 75 38 27

<underline><color><param>0000,8080,0000</param>Fax :</color></underline>=
 (227) 75 28 04 / 75 20 54

<underline><color><param>0000,0000,fefe</param>

</color></underline><bold><italic><color><param>0000,8080,0000</param>=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D</color></ita=
lic></bold>=20

--------------------------------
End of nih-image-d Digest V99 Issue #144
****************************************

From nih-image-request@io.ece.drexel.edu Fri Jun 25 10:41 EDT 1999
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Resent-Date: Fri, 25 Jun 1999 10:41:32 -0400 (EDT)
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X-Sender: mariac@192.136.57.17
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Date: Fri, 25 Jun 1999 15:24:26 +0200
To: nih-image@io.ece.drexel.edu
From: MARIAC <mariac@ird.ne>
Subject: scrolling image with drawing line tolls
Mime-Version: 1.0
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Hi,


I would like to know if its possible to make the image  scroll in the=
 windows with tools like the line drawing tool. I'm working with=
 scionimage/pc.

Thanks,


C=E9dric.

<bold><italic><color><param>0000,8080,0000</param>=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

</color><color><param>0000,0000,ffff</param>

</color></italic></bold><italic><color><param>0000,0000,ffff</param>C=E9dric
<bold>Mariac

</bold></color></italic>Laboratoire de g=E9n=E9tique des plantes


IRD L'institut de recherche pour le d=E9veloppement=20

anciennement ORSTOM

BP 11416 Niamey=20

Republique du NIGER


<underline><color><param>0000,8080,0000</param>E-mail
:</color></underline><color><param>0000,8080,0000</param>
</color>mariac@ird.ne

<underline><color><param>0000,8080,0000</param>Tel :</color></underline>
(227) 75 31 15 / 75 26 10 / 75 38 27

<underline><color><param>0000,8080,0000</param>Fax :</color></underline>=
 (227) 75 28 04 / 75 20 54

<underline><color><param>0000,0000,fefe</param>

</color></underline><bold><italic><color><param>0000,8080,0000</param>=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D</color></ita=
lic></bold>=20



From nih-image-request@io.ece.drexel.edu Fri Jun 25 11:43 EDT 1999
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Resent-Date: Fri, 25 Jun 1999 11:43:46 -0400 (EDT)
Message-ID: <3773A127.9D305D89@emory.edu>
Date: Fri, 25 Jun 1999 11:32:55 -0400
From: "Tom Noga, MD" <jnoga@emory.edu>
X-Mailer: Mozilla 4.5 [en] (Win98; I)
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To: nih-image@io.ece.drexel.edu
Subject: Re: best scanner for lab work
References: <3.0.5.32.19990624215131.009aa460@codon.nih.gov>
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can anybody recommend the best quality scanner at a reasonable price (ie, best buy)  for scientific work (mostly transparency scanning of autoradiograms; also gels, blots, etc)?  i
have been using a UMax 1200 for over 5 years and wonder if i need an upgrade to get the best fidelity possible. i understand an OD of 3 or greater is desirable, but my UMax 1200
doesn't seem to have an OD rating (at least this info is not readily available).
thank you.

tom noga, md
emory university


From nih-image-request@io.ece.drexel.edu Fri Jun 25 12:13 EDT 1999
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Date: Fri, 25 Jun 1999 11:55:57 -0400
To: nih-image@io.ece.drexel.edu
From: "Gloria.Hoffman" <gehoffma@umaryland.edu>
Subject: Re: best scanner for lab work
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I find the Epson Expression 636 or  very good with great fidelity - it is
very much better than the UMax was. It's a flat bed scanner with a
transparency adapter. Reasonable price  -has transparency adaptor. For
slide scanning the Nikon Coolscan is wonderful.



>can anybody recommend the best quality scanner at a reasonable price (ie,
>best buy)  for scientific work (mostly transparency scanning of
>autoradiograms; also gels, blots, etc)?  i
>have been using a UMax 1200 for over 5 years and wonder if i need an
>upgrade to get the best fidelity possible. i understand an OD of 3 or
>greater is desirable, but my UMax 1200
>doesn't seem to have an OD rating (at least this info is not readily
>available).
>thank you.
>
>tom noga, md
>emory university

**************************************************
"Scientists are half B.F. Skinner,
and half P.T. Barnum..."  [Homer Simpson]
**************************************************
Gloria E. Hoffman, Ph.D.
Department of Anatomy and Neurobiology
685 W Baltimore St
Baltimore MD 21201
Phone 410 706-2438
Lab: 410 706-2440
Fax 410 706-2512
email gehoffma@umaryland.edu


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To: "'Tim Fairchild'" <timf@cyllene.uwa.edu.au>
Cc: "nih-image@io.ece.drexel.edu" <nih-image@io.ece.drexel.edu>
Subject: RE: "Count and Tag"
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-----Original Message-----
From:	Tim Fairchild [SMTP:timf@cyllene.uwa.edu.au]
Sent:	25 June 1999 02:45
To:	nih-image@io.ece.drexel.edu
Subject:	"Count and Tag"

Does Image allow you to conduct a "count and tag"?  I have tried using
the image wand for this, but since I have to chose either threshold or
density slice for this function, it dosn't give me the desired response,
since some of the cells I am counting bleed into each other (and
therefore makes it all a bit messy).  So I guess what I am looking for
is a tool that allows me to mark the cell (preferably just with a mouse
click) and conduct an automatic count.

In today's 'day and age', I don't want to revert to pen and paper,

please help!!!

Thanks
Tim.
-----------------------------------------------------------------
Timothy J. Fairchild B.Sc. (Hons)
PhD Candidate
Co-ordinator for Centre of Athletic Testing
Department of Human Movement and Exercise Science
Nedlands, Western Australia 6907
Telephone: (+61 8) 9380 2793
Facsimile:  (+61 8) 9380 1039
Email: timf@cyllene.uwa.edu.au
http://www.general.uwa.edu.au/~hmweb/index.htm



From nih-image-request@io.ece.drexel.edu Fri Jun 25 12:22 EDT 1999
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Date: Fri, 25 Jun 1999 11:06:59 -0500
From: Michail A Esterman <ESTERMAN_MICHAIL_A@Lilly.com>
Subject: Re: best scanner for lab work
To: nih-image@io.ece.drexel.edu
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I just purchased a Microtek ScanMaker 9600XL which comes with a transparency
adaptor and is one of the few scanners remaining on the market with a
transparency adapter.  You can order these from PC Warehouse or PC Connection
for reasonable price.

Mike Esterman
Scientific Imaging Center
Lilly Research Labs




"Tom Noga, MD" <jnoga@emory.edu> on 06/25/99 10:32:55 AM

Please respond to nih-image@io.ece.drexel.edu


To:   nih-image@io.ece.drexel.edu
cc:
Subject:  Re: best scanner for lab work






can anybody recommend the best quality scanner at a reasonable price (ie, best
buy)  for scientific work (mostly transparency scanning of autoradiograms;
also gels, blots, etc)?  i
have been using a UMax 1200 for over 5 years and wonder if i need an upgrade
to get the best fidelity possible. i understand an OD of 3 or greater is
desirable, but my UMax 1200
doesn't seem to have an OD rating (at least this info is not readily
available).
thank you.

tom noga, md
emory university








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Cc: "nih-image@io.ece.drexel.edu" <nih-image@io.ece.drexel.edu>
Subject: RE: "Count and Tag"
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The x-y tool will do this for you. You can increase the size of the marker 
by increasing the line size. Using this option not only gives you a count 
of the cells you identify but also records where they are.


-----Original Message-----
From:	Tim Fairchild [SMTP:timf@cyllene.uwa.edu.au]
Sent:	25 June 1999 02:45
To:	nih-image@io.ece.drexel.edu
Subject:	"Count and Tag"

Does Image allow you to conduct a "count and tag"?  I have tried using
the image wand for this, but since I have to chose either threshold or
density slice for this function, it dosn't give me the desired response,
since some of the cells I am counting bleed into each other (and
therefore makes it all a bit messy).  So I guess what I am looking for
is a tool that allows me to mark the cell (preferably just with a mouse
click) and conduct an automatic count.

In today's 'day and age', I don't want to revert to pen and paper,

please help!!!

Thanks
Tim.
-----------------------------------------------------------------
Timothy J. Fairchild B.Sc. (Hons)
PhD Candidate
Co-ordinator for Centre of Athletic Testing
Department of Human Movement and Exercise Science
Nedlands, Western Australia 6907
Telephone: (+61 8) 9380 2793
Facsimile:  (+61 8) 9380 1039
Email: timf@cyllene.uwa.edu.au
http://www.general.uwa.edu.au/~hmweb/index.htm



From nih-image-request@io.ece.drexel.edu Fri Jun 25 12:41 EDT 1999
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 <3.0.5.32.19990624215131.009aa460@codon.nih.gov>
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I'll side with Dr. Hoffman in recommending the Epson 636.  We have had a
great experience with ours which we run off of a G3 Power Mac.  We scan
everything from color photos to blots and the quality of scans is excellent.





>I find the Epson Expression 636 or  very good with great fidelity - it is
>very much better than the UMax was. It's a flat bed scanner with a
>transparency adapter. Reasonable price  -has transparency adaptor. For
>slide scanning the Nikon Coolscan is wonderful.
>
>
>
>>can anybody recommend the best quality scanner at a reasonable price (ie,
>>best buy)  for scientific work (mostly transparency scanning of
>>autoradiograms; also gels, blots, etc)?  i
>>have been using a UMax 1200 for over 5 years and wonder if i need an
>>upgrade to get the best fidelity possible. i understand an OD of 3 or
>>greater is desirable, but my UMax 1200
>>doesn't seem to have an OD rating (at least this info is not readily
>>available).
>>thank you.
>>
>>tom noga, md
>>emory university
>
>**************************************************
>"Scientists are half B.F. Skinner,
>and half P.T. Barnum..."  [Homer Simpson]
>**************************************************
>Gloria E. Hoffman, Ph.D.
>Department of Anatomy and Neurobiology
>685 W Baltimore St
>Baltimore MD 21201
>Phone 410 706-2438
>Lab: 410 706-2440
>Fax 410 706-2512
>email gehoffma@umaryland.edu


Jason Sigel
Staff Research Supervisor
UCLA School of Medicine
San Fernando Valley Program
16111 Plummer Street, Mail Code 151
Sepulveda, CA 91343
phone: 818-891-7711 x2372
fax: 818-895-5835



From nih-image-request@io.ece.drexel.edu Fri Jun 25 16:20 EDT 1999
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dr. hoffman,
i thank you & others (esterman and hoffman) for quick response. i really
appreciate it. i am unclear about a few things. . i see the Epson Expression
800 series ($699-999) and the Expression 836XL ($2998 w/ transp adapter), but
the 636U is a Perfection series Epson ($199-299) in my ClubMac catalogue. can
you clarify which model you have and do you know what the OD (optical density)
or dynamic range is? and the price range you paid?
thanks once again.
tom noga

"Gloria.Hoffman" wrote:

> I find the Epson Expression 636 or  very good with great fidelity - it is
> very much better than the UMax was. It's a flat bed scanner with a
> transparency adapter. Reasonable price  -has transparency adaptor. For
> slide scanning the Nikon Coolscan is wonderful.
>
> >can anybody recommend the best quality scanner at a reasonable price (ie,
> >best buy)  for scientific work (mostly transparency scanning of
> >autoradiograms; also gels, blots, etc)?  i
> >have been using a UMax 1200 for over 5 years and wonder if i need an
> >upgrade to get the best fidelity possible. i understand an OD of 3 or
> >greater is desirable, but my UMax 1200
> >doesn't seem to have an OD rating (at least this info is not readily
> >available).
> >thank you.
> >
> >tom noga, md
> >emory university
>
> **************************************************
> "Scientists are half B.F. Skinner,
> and half P.T. Barnum..."  [Homer Simpson]
> **************************************************
> Gloria E. Hoffman, Ph.D.
> Department of Anatomy and Neurobiology
> 685 W Baltimore St
> Baltimore MD 21201
> Phone 410 706-2438
> Lab: 410 706-2440
> Fax 410 706-2512
> email gehoffma@umaryland.edu


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From: "Marc A. Steed" <steedma@email.uc.edu>
Subject: Re: best scanner for lab work
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 <3773A127.9D305D89@emory.edu>
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I also recommend the Epson 636.  We have scanned MRI films and 35 mm slides
(transparency adapter available for $129) with great results.  We have run
the SCSI cable to a switch box and can scan from either a PowerMac 8600 or
a Wintel machine. 

It's a great investment for the money...
-Marc

In our lab we use it to scan MRI films and 35 mm slidesAt 12:30 PM 6/25/99
, you wrote:
>I'll side with Dr. Hoffman in recommending the Epson 636.  We have had a
>great experience with ours which we run off of a G3 Power Mac.  We scan
>everything from color photos to blots and the quality of scans is excellent.
>
>
>
>
>
>>I find the Epson Expression 636 or  very good with great fidelity - it is
>>very much better than the UMax was. It's a flat bed scanner with a
>>transparency adapter. Reasonable price  -has transparency adaptor. For
>>slide scanning the Nikon Coolscan is wonderful.
>>
>>
>>
>>>can anybody recommend the best quality scanner at a reasonable price (ie,
>>>best buy)  for scientific work (mostly transparency scanning of
>>>autoradiograms; also gels, blots, etc)?  i
>>>have been using a UMax 1200 for over 5 years and wonder if i need an
>>>upgrade to get the best fidelity possible. i understand an OD of 3 or
>>>greater is desirable, but my UMax 1200
>>>doesn't seem to have an OD rating (at least this info is not readily
>>>available).
>>>thank you.
>>>
>>>tom noga, md
>>>emory university
>>
>>**************************************************
>>"Scientists are half B.F. Skinner,
>>and half P.T. Barnum..."  [Homer Simpson]
>>**************************************************
>>Gloria E. Hoffman, Ph.D.
>>Department of Anatomy and Neurobiology
>>685 W Baltimore St
>>Baltimore MD 21201
>>Phone 410 706-2438
>>Lab: 410 706-2440
>>Fax 410 706-2512
>>email gehoffma@umaryland.edu
>
>
>Jason Sigel
>Staff Research Supervisor
>UCLA School of Medicine
>San Fernando Valley Program
>16111 Plummer Street, Mail Code 151
>Sepulveda, CA 91343
>phone: 818-891-7711 x2372
>fax: 818-895-5835
>

===============
Marc A. Steed, MS               
429 Dyer Hall
Department of Psychology
University of Cincinnati
Cincinnati, OH  45221
(513) 556-1615 (Dyer Hall)
(513) 558-5113 (Med. Sci. Blg.)
(513) 556-1904 (fax)
===============


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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 145

Today's Topics:
  Re: best scanner for lab work         [ "Tom Noga, MD" <jnoga@emory.edu> ]
  Re: best scanner for lab work         [ "Gloria.Hoffman" <gehoffma@umarylan ]
  RE: "Count and Tag"                   [ Keith Norman <k.norman@sheffield.ac ]
  RE: "Count and Tag"                   [ Keith Norman <k.norman@sheffield.ac ]
  Re: best scanner for lab work         [ Michail A Esterman <ESTERMAN_MICHAI ]
  Re: best scanner for lab work         [ jsigel@ucla.edu ]
  Re: best scanner for lab work         [ "Tom Noga, MD" <jnoga@emory.edu> ]
  Re: best scanner for lab work         [ "Marc A. Steed" <steedma@email.uc.e ]

------------------------------

Date: Fri, 25 Jun 1999 11:32:55 -0400
From: "Tom Noga, MD" <jnoga@emory.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: best scanner for lab work
Message-ID: <3773A127.9D305D89@emory.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

can anybody recommend the best quality scanner at a reasonable price (ie, best buy)  for scientific work (mostly transparency scanning of autoradiograms; also gels, blots, etc)?  i
have been using a UMax 1200 for over 5 years and wonder if i need an upgrade to get the best fidelity possible. i understand an OD of 3 or greater is desirable, but my UMax 1200
doesn't seem to have an OD rating (at least this info is not readily available).
thank you.

tom noga, md
emory university

------------------------------

Date: Fri, 25 Jun 1999 11:55:57 -0400
From: "Gloria.Hoffman" <gehoffma@umaryland.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: best scanner for lab work
Message-Id: <v040117a0b3995492c44e@[134.192.131.169]>
Content-Type: text/plain; charset="us-ascii"

I find the Epson Expression 636 or  very good with great fidelity - it is
very much better than the UMax was. It's a flat bed scanner with a
transparency adapter. Reasonable price  -has transparency adaptor. For
slide scanning the Nikon Coolscan is wonderful.



>can anybody recommend the best quality scanner at a reasonable price (ie,
>best buy)  for scientific work (mostly transparency scanning of
>autoradiograms; also gels, blots, etc)?  i
>have been using a UMax 1200 for over 5 years and wonder if i need an
>upgrade to get the best fidelity possible. i understand an OD of 3 or
>greater is desirable, but my UMax 1200
>doesn't seem to have an OD rating (at least this info is not readily
>available).
>thank you.
>
>tom noga, md
>emory university

**************************************************
"Scientists are half B.F. Skinner,
and half P.T. Barnum..."  [Homer Simpson]
**************************************************
Gloria E. Hoffman, Ph.D.
Department of Anatomy and Neurobiology
685 W Baltimore St
Baltimore MD 21201
Phone 410 706-2438
Lab: 410 706-2440
Fax 410 706-2512
email gehoffma@umaryland.edu

------------------------------

Date: Fri, 25 Jun 1999 17:04:05 +0100
From: Keith Norman <k.norman@sheffield.ac.uk>
To: "'Tim Fairchild'" <timf@cyllene.uwa.edu.au>
Cc: "nih-image@io.ece.drexel.edu" <nih-image@io.ece.drexel.edu>
Subject: RE: "Count and Tag"
Message-ID: <01BEBF2C.BBF340A0.k.norman@sheffield.ac.uk>

-----Original Message-----
From:	Tim Fairchild [SMTP:timf@cyllene.uwa.edu.au]
Sent:	25 June 1999 02:45
To:	nih-image@io.ece.drexel.edu
Subject:	"Count and Tag"

Does Image allow you to conduct a "count and tag"?  I have tried using
the image wand for this, but since I have to chose either threshold or
density slice for this function, it dosn't give me the desired response,
since some of the cells I am counting bleed into each other (and
therefore makes it all a bit messy).  So I guess what I am looking for
is a tool that allows me to mark the cell (preferably just with a mouse
click) and conduct an automatic count.

In today's 'day and age', I don't want to revert to pen and paper,

please help!!!

Thanks
Tim.
-----------------------------------------------------------------
Timothy J. Fairchild B.Sc. (Hons)
PhD Candidate
Co-ordinator for Centre of Athletic Testing
Department of Human Movement and Exercise Science
Nedlands, Western Australia 6907
Telephone: (+61 8) 9380 2793
Facsimile:  (+61 8) 9380 1039
Email: timf@cyllene.uwa.edu.au
http://www.general.uwa.edu.au/~hmweb/index.htm

------------------------------

Date: Fri, 25 Jun 1999 17:06:12 +0100
From: Keith Norman <k.norman@sheffield.ac.uk>
To: "'Tim Fairchild'" <timf@cyllene.uwa.edu.au>
Cc: "nih-image@io.ece.drexel.edu" <nih-image@io.ece.drexel.edu>
Subject: RE: "Count and Tag"
Message-ID: <01BEBF2D.07EF2820.k.norman@sheffield.ac.uk>

The x-y tool will do this for you. You can increase the size of the marker 
by increasing the line size. Using this option not only gives you a count 
of the cells you identify but also records where they are.


-----Original Message-----
From:	Tim Fairchild [SMTP:timf@cyllene.uwa.edu.au]
Sent:	25 June 1999 02:45
To:	nih-image@io.ece.drexel.edu
Subject:	"Count and Tag"

Does Image allow you to conduct a "count and tag"?  I have tried using
the image wand for this, but since I have to chose either threshold or
density slice for this function, it dosn't give me the desired response,
since some of the cells I am counting bleed into each other (and
therefore makes it all a bit messy).  So I guess what I am looking for
is a tool that allows me to mark the cell (preferably just with a mouse
click) and conduct an automatic count.

In today's 'day and age', I don't want to revert to pen and paper,

please help!!!

Thanks
Tim.
-----------------------------------------------------------------
Timothy J. Fairchild B.Sc. (Hons)
PhD Candidate
Co-ordinator for Centre of Athletic Testing
Department of Human Movement and Exercise Science
Nedlands, Western Australia 6907
Telephone: (+61 8) 9380 2793
Facsimile:  (+61 8) 9380 1039
Email: timf@cyllene.uwa.edu.au
http://www.general.uwa.edu.au/~hmweb/index.htm

------------------------------

Date: Fri, 25 Jun 1999 11:06:59 -0500
From: Michail A Esterman <ESTERMAN_MICHAIL_A@Lilly.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: best scanner for lab work
Message-id: <0525679B.00588914.00@aammta1.d51.lilly.com>
Content-type: text/plain; charset=us-ascii
Content-disposition: inline

I just purchased a Microtek ScanMaker 9600XL which comes with a transparency
adaptor and is one of the few scanners remaining on the market with a
transparency adapter.  You can order these from PC Warehouse or PC Connection
for reasonable price.

Mike Esterman
Scientific Imaging Center
Lilly Research Labs




"Tom Noga, MD" <jnoga@emory.edu> on 06/25/99 10:32:55 AM

Please respond to nih-image@io.ece.drexel.edu


To:   nih-image@io.ece.drexel.edu
cc:
Subject:  Re: best scanner for lab work






can anybody recommend the best quality scanner at a reasonable price (ie, best
buy)  for scientific work (mostly transparency scanning of autoradiograms;
also gels, blots, etc)?  i
have been using a UMax 1200 for over 5 years and wonder if i need an upgrade
to get the best fidelity possible. i understand an OD of 3 or greater is
desirable, but my UMax 1200
doesn't seem to have an OD rating (at least this info is not readily
available).
thank you.

tom noga, md
emory university

------------------------------

Date: Fri, 25 Jun 1999 09:30:32 -0700
From: jsigel@ucla.edu
To: nih-image@io.ece.drexel.edu
Subject: Re: best scanner for lab work
Message-Id: <v03102802b3995eb0dcc8@[207.217.13.16]>
Content-Type: text/plain; charset="us-ascii"

I'll side with Dr. Hoffman in recommending the Epson 636.  We have had a
great experience with ours which we run off of a G3 Power Mac.  We scan
everything from color photos to blots and the quality of scans is excellent.





>I find the Epson Expression 636 or  very good with great fidelity - it is
>very much better than the UMax was. It's a flat bed scanner with a
>transparency adapter. Reasonable price  -has transparency adaptor. For
>slide scanning the Nikon Coolscan is wonderful.
>
>
>
>>can anybody recommend the best quality scanner at a reasonable price (ie,
>>best buy)  for scientific work (mostly transparency scanning of
>>autoradiograms; also gels, blots, etc)?  i
>>have been using a UMax 1200 for over 5 years and wonder if i need an
>>upgrade to get the best fidelity possible. i understand an OD of 3 or
>>greater is desirable, but my UMax 1200
>>doesn't seem to have an OD rating (at least this info is not readily
>>available).
>>thank you.
>>
>>tom noga, md
>>emory university
>
>**************************************************
>"Scientists are half B.F. Skinner,
>and half P.T. Barnum..."  [Homer Simpson]
>**************************************************
>Gloria E. Hoffman, Ph.D.
>Department of Anatomy and Neurobiology
>685 W Baltimore St
>Baltimore MD 21201
>Phone 410 706-2438
>Lab: 410 706-2440
>Fax 410 706-2512
>email gehoffma@umaryland.edu


Jason Sigel
Staff Research Supervisor
UCLA School of Medicine
San Fernando Valley Program
16111 Plummer Street, Mail Code 151
Sepulveda, CA 91343
phone: 818-891-7711 x2372
fax: 818-895-5835

------------------------------

Date: Fri, 25 Jun 1999 16:10:24 -0400
From: "Tom Noga, MD" <jnoga@emory.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: best scanner for lab work
Message-ID: <3773E230.20CAE84F@emory.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

dr. hoffman,
i thank you & others (esterman and hoffman) for quick response. i really
appreciate it. i am unclear about a few things. . i see the Epson Expression
800 series ($699-999) and the Expression 836XL ($2998 w/ transp adapter), but
the 636U is a Perfection series Epson ($199-299) in my ClubMac catalogue. can
you clarify which model you have and do you know what the OD (optical density)
or dynamic range is? and the price range you paid?
thanks once again.
tom noga

"Gloria.Hoffman" wrote:

> I find the Epson Expression 636 or  very good with great fidelity - it is
> very much better than the UMax was. It's a flat bed scanner with a
> transparency adapter. Reasonable price  -has transparency adaptor. For
> slide scanning the Nikon Coolscan is wonderful.
>
> >can anybody recommend the best quality scanner at a reasonable price (ie,
> >best buy)  for scientific work (mostly transparency scanning of
> >autoradiograms; also gels, blots, etc)?  i
> >have been using a UMax 1200 for over 5 years and wonder if i need an
> >upgrade to get the best fidelity possible. i understand an OD of 3 or
> >greater is desirable, but my UMax 1200
> >doesn't seem to have an OD rating (at least this info is not readily
> >available).
> >thank you.
> >
> >tom noga, md
> >emory university
>
> **************************************************
> "Scientists are half B.F. Skinner,
> and half P.T. Barnum..."  [Homer Simpson]
> **************************************************
> Gloria E. Hoffman, Ph.D.
> Department of Anatomy and Neurobiology
> 685 W Baltimore St
> Baltimore MD 21201
> Phone 410 706-2438
> Lab: 410 706-2440
> Fax 410 706-2512
> email gehoffma@umaryland.edu

------------------------------

Date: Fri, 25 Jun 1999 22:44:05 -0400
From: "Marc A. Steed" <steedma@email.uc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: best scanner for lab work
Message-Id: <4.1.19990625223820.0095d6c0@email.uc.edu>
Content-Type: text/plain; charset="us-ascii"

I also recommend the Epson 636.  We have scanned MRI films and 35 mm slides
(transparency adapter available for $129) with great results.  We have run
the SCSI cable to a switch box and can scan from either a PowerMac 8600 or
a Wintel machine. 

It's a great investment for the money...
-Marc

In our lab we use it to scan MRI films and 35 mm slidesAt 12:30 PM 6/25/99
, you wrote:
>I'll side with Dr. Hoffman in recommending the Epson 636.  We have had a
>great experience with ours which we run off of a G3 Power Mac.  We scan
>everything from color photos to blots and the quality of scans is excellent.
>
>
>
>
>
>>I find the Epson Expression 636 or  very good with great fidelity - it is
>>very much better than the UMax was. It's a flat bed scanner with a
>>transparency adapter. Reasonable price  -has transparency adaptor. For
>>slide scanning the Nikon Coolscan is wonderful.
>>
>>
>>
>>>can anybody recommend the best quality scanner at a reasonable price (ie,
>>>best buy)  for scientific work (mostly transparency scanning of
>>>autoradiograms; also gels, blots, etc)?  i
>>>have been using a UMax 1200 for over 5 years and wonder if i need an
>>>upgrade to get the best fidelity possible. i understand an OD of 3 or
>>>greater is desirable, but my UMax 1200
>>>doesn't seem to have an OD rating (at least this info is not readily
>>>available).
>>>thank you.
>>>
>>>tom noga, md
>>>emory university
>>
>>**************************************************
>>"Scientists are half B.F. Skinner,
>>and half P.T. Barnum..."  [Homer Simpson]
>>**************************************************
>>Gloria E. Hoffman, Ph.D.
>>Department of Anatomy and Neurobiology
>>685 W Baltimore St
>>Baltimore MD 21201
>>Phone 410 706-2438
>>Lab: 410 706-2440
>>Fax 410 706-2512
>>email gehoffma@umaryland.edu
>
>
>Jason Sigel
>Staff Research Supervisor
>UCLA School of Medicine
>San Fernando Valley Program
>16111 Plummer Street, Mail Code 151
>Sepulveda, CA 91343
>phone: 818-891-7711 x2372
>fax: 818-895-5835
>

===============
Marc A. Steed, MS               
429 Dyer Hall
Department of Psychology
University of Cincinnati
Cincinnati, OH  45221
(513) 556-1615 (Dyer Hall)
(513) 558-5113 (Med. Sci. Blg.)
(513) 556-1904 (fax)
===============

--------------------------------
End of nih-image-d Digest V99 Issue #145
****************************************

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Date: Sat, 26 Jun 1999 09:47:45 -0700 (PDT)
From: Mark Vivino <mvivino@yahoo.com>
Subject: Re: best scanner for lab work
To: nih-image@io.ece.drexel.edu
Cc: "Tom Noga, MD" <jnoga@emory.edu>
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> i understand an OD of 3 or
> greater is desirable, but my UMax 1200
> doesn't seem to have an OD rating (at least this info is not readily

Whoa nelly! Those kind of specs are given by varying gain on these scanners.
You are lucky to get 0.5 to 1.0 OD in any one scene on a scanner. That is, an
OD of 1.0 range imaged properly in one image would be pretty good for a
simple scanner. Pretty good means NIH Image can fit the curve easily.

If you had a scanner with 3.0 OD on one scene it might cost you several
hundred thousand. Like a scanning densitometer.

Just be careful on these ratings.

Mark
===
Mark A. Vivino
Biomedical Engineer
mvivino@yahoo.com
http://www.mindspring.com/~mvivino/
_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-request@io.ece.drexel.edu Sat Jun 26 13:01 EDT 1999
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thank you, marc. have you used it to scan autoradiographic films or Nissl-stained
tissue sections?
tom noga

"Marc A. Steed" wrote:

> I also recommend the Epson 636.  We have scanned MRI films and 35 mm slides
> (transparency adapter available for $129) with great results.  We have run
> the SCSI cable to a switch box and can scan from either a PowerMac 8600 or
> a Wintel machine.
>
> It's a great investment for the money...
> -Marc
>
> In our lab we use it to scan MRI films and 35 mm slidesAt 12:30 PM 6/25/99
> , you wrote:
> >I'll side with Dr. Hoffman in recommending the Epson 636.  We have had a
> >great experience with ours which we run off of a G3 Power Mac.  We scan
> >everything from color photos to blots and the quality of scans is excellent.
> >
> >
> >
> >
> >
> >>I find the Epson Expression 636 or  very good with great fidelity - it is
> >>very much better than the UMax was. It's a flat bed scanner with a
> >>transparency adapter. Reasonable price  -has transparency adaptor. For
> >>slide scanning the Nikon Coolscan is wonderful.
> >>
> >>
> >>
> >>>can anybody recommend the best quality scanner at a reasonable price (ie,
> >>>best buy)  for scientific work (mostly transparency scanning of
> >>>autoradiograms; also gels, blots, etc)?  i
> >>>have been using a UMax 1200 for over 5 years and wonder if i need an
> >>>upgrade to get the best fidelity possible. i understand an OD of 3 or
> >>>greater is desirable, but my UMax 1200
> >>>doesn't seem to have an OD rating (at least this info is not readily
> >>>available).
> >>>thank you.
> >>>
> >>>tom noga, md
> >>>emory university
> >>
> >>**************************************************
> >>"Scientists are half B.F. Skinner,
> >>and half P.T. Barnum..."  [Homer Simpson]
> >>**************************************************
> >>Gloria E. Hoffman, Ph.D.
> >>Department of Anatomy and Neurobiology
> >>685 W Baltimore St
> >>Baltimore MD 21201
> >>Phone 410 706-2438
> >>Lab: 410 706-2440
> >>Fax 410 706-2512
> >>email gehoffma@umaryland.edu
> >
> >
> >Jason Sigel
> >Staff Research Supervisor
> >UCLA School of Medicine
> >San Fernando Valley Program
> >16111 Plummer Street, Mail Code 151
> >Sepulveda, CA 91343
> >phone: 818-891-7711 x2372
> >fax: 818-895-5835
> >
>
> ===============
> Marc A. Steed, MS
> 429 Dyer Hall
> Department of Psychology
> University of Cincinnati
> Cincinnati, OH  45221
> (513) 556-1615 (Dyer Hall)
> (513) 558-5113 (Med. Sci. Blg.)
> (513) 556-1904 (fax)
> ===============

--
J. Thomas Noga, MD
Assistant Professor of Psychiatry
Emory University Department of Psychiatry
Medical Director, Geropsychiatric Partial Hospitalization
Wesley Woods Geriatric Hospital at Emory University
ph 404-728-6690
fax 404-728-4963
jnoga@emory.edu



From nih-image-request@io.ece.drexel.edu Sat Jun 26 15:45 EDT 1999
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From: Mark Vivino <mvivino@yahoo.com>
Subject: Re: best scanner for lab work
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Just wanted to answer your question on scanners and OD range a little more.
Obviously the scanner to select will have an OD range greater than any of
your autorads. It should also be able to disable autogain and allow you to
adjust gain and contrast (and pedastal if you use a TV camera) as desired
through software or HW control.

I would recomend going down to the store with a ND step tablet and a few
floppies. Try asking if you can scan the step tablet. Save the image to disk
and have a look for yourself within NIH Image. 

Also try to find out the range of your autorads and see if you are doing
better with the scanner. I don't know how to tell you how to do this. You
have a better feel for the concentration range you are using.

You might be able to get some info on the single line CCD array in any given
scanner and look it up in a CCD design spec. You might be able to figure out
range capabilities.

But in short, most people don't buy scanners for incredible OD range so
makers of scanners don't care to satisfy scientists too much. You are a
limited market and if you are working on the fine details of a gel with 2.0
OD range between bands you need a very expensive imager.

Mark

===
Mark A. Vivino
Biomedical Engineer
mvivino@yahoo.com
http://www.mindspring.com/~mvivino/
_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com


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From: "Tom Noga, MD" <jnoga@emory.edu>
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What's an ND step tablet?

Tom
jnoga@emory.edu

Mark Vivino wrote:

> Just wanted to answer your question on scanners and OD range a little more.
> Obviously the scanner to select will have an OD range greater than any of
> your autorads. It should also be able to disable autogain and allow you to
> adjust gain and contrast (and pedastal if you use a TV camera) as desired
> through software or HW control.
>
> I would recomend going down to the store with a ND step tablet and a few
> floppies. Try asking if you can scan the step tablet. Save the image to disk
> and have a look for yourself within NIH Image.
>
> Also try to find out the range of your autorads and see if you are doing
> better with the scanner. I don't know how to tell you how to do this. You
> have a better feel for the concentration range you are using.
>
> You might be able to get some info on the single line CCD array in any given
> scanner and look it up in a CCD design spec. You might be able to figure out
> range capabilities.
>
> But in short, most people don't buy scanners for incredible OD range so
> makers of scanners don't care to satisfy scientists too much. You are a
> limited market and if you are working on the fine details of a gel with 2.0
> OD range between bands you need a very expensive imager.
>
> Mark
>
> ===
> Mark A. Vivino
> Biomedical Engineer
> mvivino@yahoo.com
> http://www.mindspring.com/~mvivino/
> _________________________________________________________
> Do You Yahoo!?
> Get your free @yahoo.com address at http://mail.yahoo.com






From nih-image-d-request@io.ece.drexel.edu Sun Jun 27 06:12 EDT 1999
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Subject: nih-image-d Digest V99 #146
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 146

Today's Topics:
  Re: best scanner for lab work         [ Mark Vivino <mvivino@yahoo.com> ]
  Re: best scanner for lab work         [ "Tom Noga, MD" <jnoga@emory.edu> ]
  Re: best scanner for lab work         [ Mark Vivino <mvivino@yahoo.com> ]
  Re: best scanner for lab work         [ "Tom Noga, MD" <jnoga@emory.edu> ]

------------------------------

Date: Sat, 26 Jun 1999 09:47:45 -0700 (PDT)
From: Mark Vivino <mvivino@yahoo.com>
To: nih-image@io.ece.drexel.edu
Cc: "Tom Noga, MD" <jnoga@emory.edu>
Subject: Re: best scanner for lab work
Message-ID: <19990626164745.12736.rocketmail@web505.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

> i understand an OD of 3 or
> greater is desirable, but my UMax 1200
> doesn't seem to have an OD rating (at least this info is not readily

Whoa nelly! Those kind of specs are given by varying gain on these scanners.
You are lucky to get 0.5 to 1.0 OD in any one scene on a scanner. That is, an
OD of 1.0 range imaged properly in one image would be pretty good for a
simple scanner. Pretty good means NIH Image can fit the curve easily.

If you had a scanner with 3.0 OD on one scene it might cost you several
hundred thousand. Like a scanning densitometer.

Just be careful on these ratings.

Mark
===
Mark A. Vivino
Biomedical Engineer
mvivino@yahoo.com
http://www.mindspring.com/~mvivino/
_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com

------------------------------

Date: Sat, 26 Jun 1999 12:51:07 -0400
From: "Tom Noga, MD" <jnoga@emory.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: best scanner for lab work
Message-ID: <377504FB.6859A061@emory.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

thank you, marc. have you used it to scan autoradiographic films or Nissl-stained
tissue sections?
tom noga

"Marc A. Steed" wrote:

> I also recommend the Epson 636.  We have scanned MRI films and 35 mm slides
> (transparency adapter available for $129) with great results.  We have run
> the SCSI cable to a switch box and can scan from either a PowerMac 8600 or
> a Wintel machine.
>
> It's a great investment for the money...
> -Marc
>
> In our lab we use it to scan MRI films and 35 mm slidesAt 12:30 PM 6/25/99
> , you wrote:
> >I'll side with Dr. Hoffman in recommending the Epson 636.  We have had a
> >great experience with ours which we run off of a G3 Power Mac.  We scan
> >everything from color photos to blots and the quality of scans is excellent.
> >
> >
> >
> >
> >
> >>I find the Epson Expression 636 or  very good with great fidelity - it is
> >>very much better than the UMax was. It's a flat bed scanner with a
> >>transparency adapter. Reasonable price  -has transparency adaptor. For
> >>slide scanning the Nikon Coolscan is wonderful.
> >>
> >>
> >>
> >>>can anybody recommend the best quality scanner at a reasonable price (ie,
> >>>best buy)  for scientific work (mostly transparency scanning of
> >>>autoradiograms; also gels, blots, etc)?  i
> >>>have been using a UMax 1200 for over 5 years and wonder if i need an
> >>>upgrade to get the best fidelity possible. i understand an OD of 3 or
> >>>greater is desirable, but my UMax 1200
> >>>doesn't seem to have an OD rating (at least this info is not readily
> >>>available).
> >>>thank you.
> >>>
> >>>tom noga, md
> >>>emory university
> >>
> >>**************************************************
> >>"Scientists are half B.F. Skinner,
> >>and half P.T. Barnum..."  [Homer Simpson]
> >>**************************************************
> >>Gloria E. Hoffman, Ph.D.
> >>Department of Anatomy and Neurobiology
> >>685 W Baltimore St
> >>Baltimore MD 21201
> >>Phone 410 706-2438
> >>Lab: 410 706-2440
> >>Fax 410 706-2512
> >>email gehoffma@umaryland.edu
> >
> >
> >Jason Sigel
> >Staff Research Supervisor
> >UCLA School of Medicine
> >San Fernando Valley Program
> >16111 Plummer Street, Mail Code 151
> >Sepulveda, CA 91343
> >phone: 818-891-7711 x2372
> >fax: 818-895-5835
> >
>
> ===============
> Marc A. Steed, MS
> 429 Dyer Hall
> Department of Psychology
> University of Cincinnati
> Cincinnati, OH  45221
> (513) 556-1615 (Dyer Hall)
> (513) 558-5113 (Med. Sci. Blg.)
> (513) 556-1904 (fax)
> ===============

--
J. Thomas Noga, MD
Assistant Professor of Psychiatry
Emory University Department of Psychiatry
Medical Director, Geropsychiatric Partial Hospitalization
Wesley Woods Geriatric Hospital at Emory University
ph 404-728-6690
fax 404-728-4963
jnoga@emory.edu

------------------------------

Date: Sat, 26 Jun 1999 12:35:32 -0700 (PDT)
From: Mark Vivino <mvivino@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: best scanner for lab work
Message-ID: <19990626193532.18506.rocketmail@web502.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

Just wanted to answer your question on scanners and OD range a little more.
Obviously the scanner to select will have an OD range greater than any of
your autorads. It should also be able to disable autogain and allow you to
adjust gain and contrast (and pedastal if you use a TV camera) as desired
through software or HW control.

I would recomend going down to the store with a ND step tablet and a few
floppies. Try asking if you can scan the step tablet. Save the image to disk
and have a look for yourself within NIH Image. 

Also try to find out the range of your autorads and see if you are doing
better with the scanner. I don't know how to tell you how to do this. You
have a better feel for the concentration range you are using.

You might be able to get some info on the single line CCD array in any given
scanner and look it up in a CCD design spec. You might be able to figure out
range capabilities.

But in short, most people don't buy scanners for incredible OD range so
makers of scanners don't care to satisfy scientists too much. You are a
limited market and if you are working on the fine details of a gel with 2.0
OD range between bands you need a very expensive imager.

Mark

===
Mark A. Vivino
Biomedical Engineer
mvivino@yahoo.com
http://www.mindspring.com/~mvivino/
_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com

------------------------------

Date: Sat, 26 Jun 1999 21:35:54 -0400
From: "Tom Noga, MD" <jnoga@emory.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: best scanner for lab work
Message-ID: <37757FFA.23C6D785@emory.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

What's an ND step tablet?

Tom
jnoga@emory.edu

Mark Vivino wrote:

> Just wanted to answer your question on scanners and OD range a little more.
> Obviously the scanner to select will have an OD range greater than any of
> your autorads. It should also be able to disable autogain and allow you to
> adjust gain and contrast (and pedastal if you use a TV camera) as desired
> through software or HW control.
>
> I would recomend going down to the store with a ND step tablet and a few
> floppies. Try asking if you can scan the step tablet. Save the image to disk
> and have a look for yourself within NIH Image.
>
> Also try to find out the range of your autorads and see if you are doing
> better with the scanner. I don't know how to tell you how to do this. You
> have a better feel for the concentration range you are using.
>
> You might be able to get some info on the single line CCD array in any given
> scanner and look it up in a CCD design spec. You might be able to figure out
> range capabilities.
>
> But in short, most people don't buy scanners for incredible OD range so
> makers of scanners don't care to satisfy scientists too much. You are a
> limited market and if you are working on the fine details of a gel with 2.0
> OD range between bands you need a very expensive imager.
>
> Mark
>
> ===
> Mark A. Vivino
> Biomedical Engineer
> mvivino@yahoo.com
> http://www.mindspring.com/~mvivino/
> _________________________________________________________
> Do You Yahoo!?
> Get your free @yahoo.com address at http://mail.yahoo.com

--------------------------------
End of nih-image-d Digest V99 Issue #146
****************************************

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Date: Sun, 27 Jun 1999 11:43:24 -0700 (PDT)
From: Mark Vivino <mvivino@yahoo.com>
Subject: Re: best scanner for lab work
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--- "Tom Noga, MD" <jnoga@emory.edu> wrote:

> What's an ND step tablet?

A neutral density step tablet, or a spectrally flat (close to it) tablet with
density steps increasing incrementally along the length usually by 0.1
density (Example 0.02, 0.1, 0.21, 0.3....2.0 and some up to 3.0 depending on
$$ you want to spend). Available at your photo store. Best are Kodak
calibrated kind but also very expensive. There are others.

Mark
===
Mark A. Vivino
Biomedical Engineer
mvivino@yahoo.com
http://www.mindspring.com/~mvivino/
_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-d-request@io.ece.drexel.edu Mon Jun 28 06:18 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 147

Today's Topics:
  Re: best scanner for lab work         [ Mark Vivino <mvivino@yahoo.com> ]

------------------------------

Date: Sun, 27 Jun 1999 11:43:24 -0700 (PDT)
From: Mark Vivino <mvivino@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: best scanner for lab work
Message-ID: <19990627184324.7115.rocketmail@send501.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

--- "Tom Noga, MD" <jnoga@emory.edu> wrote:

> What's an ND step tablet?

A neutral density step tablet, or a spectrally flat (close to it) tablet with
density steps increasing incrementally along the length usually by 0.1
density (Example 0.02, 0.1, 0.21, 0.3....2.0 and some up to 3.0 depending on
$$ you want to spend). Available at your photo store. Best are Kodak
calibrated kind but also very expensive. There are others.

Mark
===
Mark A. Vivino
Biomedical Engineer
mvivino@yahoo.com
http://www.mindspring.com/~mvivino/
_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com

--------------------------------
End of nih-image-d Digest V99 Issue #147
****************************************

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From: ankoor shah <ashah7@ix.netcom.com>
Subject: plotting macro
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hello all,
   I was hoping that someone fluent in the image/macro programming language
could aid me in solving a problem.  I've been trying to modify the plotting
profile macro to  plot profiles with values for each image through a stack
automatically.  I have tried to combine the codes for the "plot profile and
display values" and "plot z-axis profile" macros, but i've hit a point
where I can get it to go through the stack and plot profiles, but it can't
take measurements and display the values. All i need in terms of
measurements is the pixel number and mean density. If anyone knows how to
program this, or knows of a program that does this, I would appreciate it.



From nih-image-request@io.ece.drexel.edu Mon Jun 28 20:40 EDT 1999
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Date: 28 Jun 99 18:33:01 MDT
From: CHRIS TULLY <cptully@usa.net>
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Subject: Re: [plotting macro]
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Ankoor-

I'm not positive that I understand what you want.  Do you want a listing of
numeric values (x,y,i), where i is intensity for each profile?  Or do you want
a profile plot with the mean density listed on the plot (I am unsure what you
mean by pixel number)?

I have some ideas for what to do but wanted to clarify the above points before
I start making suggestions.

Chris Tully
Owner
Tully Imaging Specialists

ankoor shah <ashah7@ix.netcom.com> wrote:
hello all,
   I was hoping that someone fluent in the image/macro programming language
could aid me in solving a problem.  I've been trying to modify the plotting
profile macro to  plot profiles with values for each image through a stack
automatically.  I have tried to combine the codes for the "plot profile and
display values" and "plot z-axis profile" macros, but i've hit a point
where I can get it to go through the stack and plot profiles, but it can't
take measurements and display the values. All i need in terms of
measurements is the pixel number and mean density. If anyone knows how to
program this, or knows of a program that does this, I would appreciate it.



From nih-image-request@io.ece.drexel.edu Tue Jun 29 00:44 EDT 1999
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Date: Mon, 28 Jun 1999 21:39:55 -0700
To: nih-image@io.ece.drexel.edu
From: cabbage@uclink4.berkeley.edu (ankoor)
Subject: Re: [plotting macro]
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Specifically, i have been looking at stacks of MRI images for tumor
analysis. I have been drawing a line of about 10 pixel, which is my region
of interest.  The plot profile macro then measures the mean intensity of
the image at each pixel along the length of the line. The plot then shows
the intensity contrast in the line of ten pixels. This works well for one
image. However, I use stacks of about 80 images, and i would like to do a
more dynamic analysis of the ROI for the entire stack.  What i meant by
"pixel number" is that when i do a "plot profile and display values" it
gives me a pixel number (1-10) and the mean intensity at each pixel.  I
hope this is a bit more clear, and again, any suggestions would be
appreciated.

At 6:33 PM 6/28/99, CHRIS TULLY wrote:
>Ankoor-
>
>I'm not positive that I understand what you want.  Do you want a listing of
>numeric values (x,y,i), where i is intensity for each profile?  Or do you want
>a profile plot with the mean density listed on the plot (I am unsure what you
>mean by pixel number)?
>
>I have some ideas for what to do but wanted to clarify the above points before
>I start making suggestions.
>
>



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------------------------------

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nih-image-d Digest				Volume 99 : Issue 148

Today's Topics:
  plotting macro                        [ ankoor shah <ashah7@ix.netcom.com> ]
  Re: [plotting macro]                  [ CHRIS TULLY <cptully@usa.net> ]
  Re: [plotting macro]                  [ cabbage@uclink4.berkeley.edu (ankoo ]

------------------------------

Date: Mon, 28 Jun 1999 11:47:29 -0700
From: ankoor shah <ashah7@ix.netcom.com>
To: nih-image@io.ece.drexel.edu
Subject: plotting macro
Message-Id: <l03130304b39d72650a3d@[128.125.35.193]>
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hello all,
   I was hoping that someone fluent in the image/macro programming language
could aid me in solving a problem.  I've been trying to modify the plotting
profile macro to  plot profiles with values for each image through a stack
automatically.  I have tried to combine the codes for the "plot profile and
display values" and "plot z-axis profile" macros, but i've hit a point
where I can get it to go through the stack and plot profiles, but it can't
take measurements and display the values. All i need in terms of
measurements is the pixel number and mean density. If anyone knows how to
program this, or knows of a program that does this, I would appreciate it.

------------------------------

Date: 28 Jun 99 18:33:01 MDT
From: CHRIS TULLY <cptully@usa.net>
To: nih-image@io.ece.drexel.edu
Subject: Re: [plotting macro]
Message-ID: <19990629003301.28968.qmail@nwcst287.netaddress.usa.net>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 8bit

Ankoor-

I'm not positive that I understand what you want.  Do you want a listing of
numeric values (x,y,i), where i is intensity for each profile?  Or do you want
a profile plot with the mean density listed on the plot (I am unsure what you
mean by pixel number)?

I have some ideas for what to do but wanted to clarify the above points before
I start making suggestions.

Chris Tully
Owner
Tully Imaging Specialists

ankoor shah <ashah7@ix.netcom.com> wrote:
hello all,
   I was hoping that someone fluent in the image/macro programming language
could aid me in solving a problem.  I've been trying to modify the plotting
profile macro to  plot profiles with values for each image through a stack
automatically.  I have tried to combine the codes for the "plot profile and
display values" and "plot z-axis profile" macros, but i've hit a point
where I can get it to go through the stack and plot profiles, but it can't
take measurements and display the values. All i need in terms of
measurements is the pixel number and mean density. If anyone knows how to
program this, or knows of a program that does this, I would appreciate it.

------------------------------

Date: Mon, 28 Jun 1999 21:39:55 -0700
From: cabbage@uclink4.berkeley.edu (ankoor)
To: nih-image@io.ece.drexel.edu
Subject: Re: [plotting macro]
Message-Id: <v02140b00b39dfc3193a9@[209.110.245.61]>
Content-Type: text/plain; charset="us-ascii"

Specifically, i have been looking at stacks of MRI images for tumor
analysis. I have been drawing a line of about 10 pixel, which is my region
of interest.  The plot profile macro then measures the mean intensity of
the image at each pixel along the length of the line. The plot then shows
the intensity contrast in the line of ten pixels. This works well for one
image. However, I use stacks of about 80 images, and i would like to do a
more dynamic analysis of the ROI for the entire stack.  What i meant by
"pixel number" is that when i do a "plot profile and display values" it
gives me a pixel number (1-10) and the mean intensity at each pixel.  I
hope this is a bit more clear, and again, any suggestions would be
appreciated.

At 6:33 PM 6/28/99, CHRIS TULLY wrote:
>Ankoor-
>
>I'm not positive that I understand what you want.  Do you want a listing of
>numeric values (x,y,i), where i is intensity for each profile?  Or do you want
>a profile plot with the mean density listed on the plot (I am unsure what you
>mean by pixel number)?
>
>I have some ideas for what to do but wanted to clarify the above points before
>I start making suggestions.
>
>

--------------------------------
End of nih-image-d Digest V99 Issue #148
****************************************

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         Reply to:   RE: nih-image-d Digest V99 #148
Does anyone know of an MRI segmenting macro for NIH Image?

Jonathan J. Wisco
Department of Anatomy and Neurobiology
Boston University School of Medicine



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------------------------------

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nih-image-d Digest				Volume 99 : Issue 149

Today's Topics:
  RE: nih-image-d Digest V99 #148       [ Jonathan WISCO <jjwisco@cajal-1.bu. ]
  unsubscribe                           [ "Kevin E. Cooper" <kevin.cooper@asu ]

------------------------------

Date: 29 Jun 99 12:11:16 -0400
From: Jonathan WISCO <jjwisco@cajal-1.bu.edu>
To: "nih-image" <nih-image@io.ece.drexel.edu>
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         Reply to:   RE: nih-image-d Digest V99 #148
Does anyone know of an MRI segmenting macro for NIH Image?

Jonathan J. Wisco
Department of Anatomy and Neurobiology
Boston University School of Medicine

------------------------------

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__________________________

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Arizona State University
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P O Box 876006
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Phone: 602-965-1061
Fax: 602-965-0037

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From nih-image-request@io.ece.drexel.edu Wed Jun 30 11:03 EDT 1999
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I am a new NIH Image user, about to get set up. I would like to use the
Iomega Buz PCI card to capture video images, but I don't know NIH Image can
use this card to capture images. Is there a plug-in available that can do
this?

John Bixby


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I would like to use Clontech's Microarrays (atlas). They offer a analysis
Software which I cannot afford.
So I would like to analyze the blots using NIH image.
We use a phosho - imager which gives you a grayscale TIFF image ot the
filter.
The task would be to automatically find the dots and integrate their
intensity.
The dots are arranged in a regular order, so maybe one could use a static
raster to find the dots.
Thanks for any help!
 
Ralf
 
 

Ralf Sigmund 
Max-Planck-Institut Hannover 
Feodor-Lynen-Str. 7 
30625 Hannover 
T: 0511-5359-233 Fax: 0511-5359-203 



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From nih-image-request@io.ece.drexel.edu Wed Jun 30 13:03 EDT 1999
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From: francus@geo.umass.edu (Pierre Francus)
Subject: lighting geological samples
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Dear imagers,

I would like to build some light box to take digital picture of muddy sediment
cores having the following specifications:

1- In order to avoid dessication of the sample, I intend to use fluorescent
bulbs.
2- It seems necessary to have high frequency light (at least 20 KhZ ?) to
avoid light intensity fluctuation while digital camera is running.
3- I would like to use a "daylight" bulb to fake a natural lighting.
4- Indirect lighting is necessary to avoid reflections of the wet surface
of the sample.

Does somebody know parts that meets those specifications and where I can
purchase them in the States ?

Advices dealing with the building of this kind of light boxes are also welcome.

Thanks in advance

Pierre


*****************************************
Pierre FRANCUS, Ph.D.
PostDoctoral Research Associate
University of Massachusetts
Department of Geosciences
Morrill Sciences Center
Amherst - MA 01003-5820

Phone: 1-413-545-0659
fax: 1-413-545-1200
E-mail: francus@geo.umass.edu
http://www.geo.umass.edu/climate/francus/
*****************************************



From nih-image-request@io.ece.drexel.edu Wed Jun 30 13:48 EDT 1999
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Date: Wed, 30 Jun 1999 12:33:21 -0500
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Ralf ,

I want to do the same thing.  I don't know what you mean by a "static raster",
but it should be fairly simple to measure the dot intensity.  I will
play with
some of clontech's images and see what works.

By the way, I would like to use Chemiluminesence instead of P32 or P33
do you have any info 
on using Chemiluminesence with the Atlas system?

Mike

"Sigmund, Ralf" wrote:
> 
> I would like to use Clontech's Microarrays (atlas). They offer a analysis
> Software which I cannot afford.
> So I would like to analyze the blots using NIH image.
> We use a phosho - imager which gives you a grayscale TIFF image ot the
> filter.
> The task would be to automatically find the dots and integrate their
> intensity.
> The dots are arranged in a regular order, so maybe one could use a static
> raster to find the dots.
> Thanks for any help!
> 
> Ralf
> 
> 
> 
> Ralf Sigmund
> Max-Planck-Institut Hannover
> Feodor-Lynen-Str. 7
> 30625 Hannover
> T: 0511-5359-233 Fax: 0511-5359-203

-- 

   _________________________________________________
     /  Michael J. Herron                          /
    /     U of MN,Medicine/Infectious Diseases    /
   /        herro001@maroon.tc.umn.edu           /
  /           http://128.101.243.213            /
 /_____________________________________________/


From nih-image-request@io.ece.drexel.edu Wed Jun 30 14:55 EDT 1999
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Date: Wed, 30 Jun 1999 14:35:22 -0400
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
Subject: conflict between QuickTime 4.0 and Object Image 1.62p2?
To: nih-image@io.ece.drexel.edu
Cc: vischer@bio.uva.nl
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On computers at home and in my lab, I've found that Object-Image 
1.62p2 is unable to open its own object files while QuickTime 4.0 is 
running under MacOS 8.6. The dialog that comes up offers the bizarre 
explanation that the Object Image application can't be found, even 
when I try to open the file from within the application while it's 
running or if I drag the file onto the app's icon. Mind you, I've 
verified the problem with Norbert's example files. When I turn QT4 
off, everything works cleanly.

Has anyone else observed this, or know how to overcome it? I've tried 
turning off some of the QT-related extensions, but the problem 
persists. Object Image is such a valuable tool that I'm willing to 
disable QT4, but I'd like to find another way. Can anyone suggest 
diagnostics that would help discover the cause of this conflict?

Thanks.

Bill Christens-Barry
-------------------------
Bill Christens-Barry, PhD
Johns Hopkins University Applied Physics Laboratory
wacb@aplcomm.jhuapl.edu
-------------------------


From nih-image-request@io.ece.drexel.edu Wed Jun 30 15:32 EDT 1999
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Date: Wed, 30 Jun 1999 21:16:01 +0200
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From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: conflict between QuickTime 4.0 and Object Image 1.62p2?
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I had a similar problem which disappeared when disabling the "File exchange"
control panel. It also disappears, when "File Exchange Preferences" is
removed.

I wonder whether this is a problem of Object-Image, or if it occurs also
with NIH Image in combination of other spin-offs (feedback is welcome)


Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



From nih-image-d-request@io.ece.drexel.edu Thu Jul  1 06:16 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #150
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 150

Today's Topics:
  frame grabber                         [ "John L. Bixby" <jbixby@chroma.med. ]
  analyze Clontech Microarray scans     [ "Sigmund, Ralf" <Ralf.Sigmund@MPIHA ]
  lighting geological samples           [ francus@geo.umass.edu (Pierre Franc ]
  Re: analyze Clontech Microarray scan  [ Michael Herron <herro001@maroon.tc. ]
  conflict between QuickTime 4.0 and O  [ Bill Christens-Barry <wacb@aplcomm. ]
  Re: conflict between QuickTime 4.0 a  [ Norbert Vischer <vischer@bio.uva.nl ]

------------------------------

Date: Wed, 30 Jun 1999 10:46:57 -0400
From: "John L. Bixby" <jbixby@chroma.med.miami.edu>
To: NIH Image <nih-image@io.ece.drexel.edu>
Subject: frame grabber
Message-Id: <199906301445.KAA09635@io.ece.drexel.edu>
Content-type: text/plain; charset="US-ASCII"
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I am a new NIH Image user, about to get set up. I would like to use the
Iomega Buz PCI card to capture video images, but I don't know NIH Image can
use this card to capture images. Is there a plug-in available that can do
this?

John Bixby

------------------------------

Date: Wed, 30 Jun 1999 17:05:56 +0200
From: "Sigmund, Ralf" <Ralf.Sigmund@MPIHAN.MPG.de>
To: "NIH Image List (E-Mail)" <nih-image@io.ece.drexel.edu>
Subject: analyze Clontech Microarray scans
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I would like to use Clontech's Microarrays (atlas). They offer a analysis
Software which I cannot afford.
So I would like to analyze the blots using NIH image.
We use a phosho - imager which gives you a grayscale TIFF image ot the
filter.
The task would be to automatically find the dots and integrate their
intensity.
The dots are arranged in a regular order, so maybe one could use a static
raster to find the dots.
Thanks for any help!
 
Ralf
 
 

Ralf Sigmund 
Max-Planck-Institut Hannover 
Feodor-Lynen-Str. 7 
30625 Hannover 
T: 0511-5359-233 Fax: 0511-5359-203 



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TEL;HOME;VOICE:49 511 2107506
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------------------------------

Date: Wed, 30 Jun 1999 12:48:24 -0400
From: francus@geo.umass.edu (Pierre Francus)
To: nih-image@io.ece.drexel.edu
Subject: lighting geological samples
Message-Id: <v01530504b39ff3b9cfa5@[128.119.67.41]>
Content-Type: text/plain; charset="us-ascii"

Dear imagers,

I would like to build some light box to take digital picture of muddy sediment
cores having the following specifications:

1- In order to avoid dessication of the sample, I intend to use fluorescent
bulbs.
2- It seems necessary to have high frequency light (at least 20 KhZ ?) to
avoid light intensity fluctuation while digital camera is running.
3- I would like to use a "daylight" bulb to fake a natural lighting.
4- Indirect lighting is necessary to avoid reflections of the wet surface
of the sample.

Does somebody know parts that meets those specifications and where I can
purchase them in the States ?

Advices dealing with the building of this kind of light boxes are also welcome.

Thanks in advance

Pierre


*****************************************
Pierre FRANCUS, Ph.D.
PostDoctoral Research Associate
University of Massachusetts
Department of Geosciences
Morrill Sciences Center
Amherst - MA 01003-5820

Phone: 1-413-545-0659
fax: 1-413-545-1200
E-mail: francus@geo.umass.edu
http://www.geo.umass.edu/climate/francus/
*****************************************

------------------------------

Date: Wed, 30 Jun 1999 12:33:21 -0500
From: Michael Herron <herro001@maroon.tc.umn.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: analyze Clontech Microarray scans
Message-Id: <377A5414.CF53FC36@tc.umn.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Ralf ,

I want to do the same thing.  I don't know what you mean by a "static raster",
but it should be fairly simple to measure the dot intensity.  I will
play with
some of clontech's images and see what works.

By the way, I would like to use Chemiluminesence instead of P32 or P33
do you have any info 
on using Chemiluminesence with the Atlas system?

Mike

"Sigmund, Ralf" wrote:
> 
> I would like to use Clontech's Microarrays (atlas). They offer a analysis
> Software which I cannot afford.
> So I would like to analyze the blots using NIH image.
> We use a phosho - imager which gives you a grayscale TIFF image ot the
> filter.
> The task would be to automatically find the dots and integrate their
> intensity.
> The dots are arranged in a regular order, so maybe one could use a static
> raster to find the dots.
> Thanks for any help!
> 
> Ralf
> 
> 
> 
> Ralf Sigmund
> Max-Planck-Institut Hannover
> Feodor-Lynen-Str. 7
> 30625 Hannover
> T: 0511-5359-233 Fax: 0511-5359-203

-- 

   _________________________________________________
     /  Michael J. Herron                          /
    /     U of MN,Medicine/Infectious Diseases    /
   /        herro001@maroon.tc.umn.edu           /
  /           http://128.101.243.213            /
 /_____________________________________________/

------------------------------

Date: Wed, 30 Jun 1999 14:35:22 -0400
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
To: nih-image@io.ece.drexel.edu
Cc: vischer@bio.uva.nl
Subject: conflict between QuickTime 4.0 and Object Image 1.62p2?
Message-id: <v04205503b3a0101bb828@[128.244.128.182]>
Content-type: text/plain; format=flowed; charset=us-ascii
Content-transfer-encoding: 7BIT

On computers at home and in my lab, I've found that Object-Image 
1.62p2 is unable to open its own object files while QuickTime 4.0 is 
running under MacOS 8.6. The dialog that comes up offers the bizarre 
explanation that the Object Image application can't be found, even 
when I try to open the file from within the application while it's 
running or if I drag the file onto the app's icon. Mind you, I've 
verified the problem with Norbert's example files. When I turn QT4 
off, everything works cleanly.

Has anyone else observed this, or know how to overcome it? I've tried 
turning off some of the QT-related extensions, but the problem 
persists. Object Image is such a valuable tool that I'm willing to 
disable QT4, but I'd like to find another way. Can anyone suggest 
diagnostics that would help discover the cause of this conflict?

Thanks.

Bill Christens-Barry
-------------------------
Bill Christens-Barry, PhD
Johns Hopkins University Applied Physics Laboratory
wacb@aplcomm.jhuapl.edu
-------------------------

------------------------------

Date: Wed, 30 Jun 1999 21:16:01 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: conflict between QuickTime 4.0 and Object Image 1.62p2?
Message-Id: <l03010d00b3a01b4864b8@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

I had a similar problem which disappeared when disabling the "File exchange"
control panel. It also disappears, when "File Exchange Preferences" is
removed.

I wonder whether this is a problem of Object-Image, or if it occurs also
with NIH Image in combination of other spin-offs (feedback is welcome)


Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

--------------------------------
End of nih-image-d Digest V99 Issue #150
****************************************

From nih-image-request@io.ece.drexel.edu Thu Jul  1 11:07 EDT 1999
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Date: Thu, 01 Jul 1999 10:46:55 -0400
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
Subject: Re:conflict between QuickTime 4.0 and Object Image 1.62p2: workaround
In-reply-to: <199907011016.GAA04906@io.ece.drexel.edu>
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>In response to my posting:
>
>Date: Wed, 30 Jun 1999 14:35:22 -0400
>From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
>Subject: conflict between QuickTime 4.0 and Object Image 1.62p2?
>
>On computers at home and in my lab, I've found that Object-Image 
>1.62p2 is unable to open its own object files while QuickTime 4.0 is 
>running under MacOS 8.6. The dialog that comes up offers the bizarre 
>explanation that the Object Image application can't be found, even 
>when I try to open the file from within the application while it's 
>running or if I drag the file onto the app's icon. Mind you, I've 
>verified the problem with Norbert's example files. When I turn QT4 
>off, everything works cleanly.
>
>Has anyone else observed this, or know how to overcome it? I've 
>tried turning off some of the QT-related extensions, but the problem 
>persists. Object Image is such a valuable tool that I'm willing to 
>disable QT4, but I'd like to find another way. Can anyone suggest 
>diagnostics that would help discover the cause of this conflict?
>
>Norbert Vischer responded:

>Date: Wed, 30 Jun 1999 21:16:01 +0200
>From: Norbert Vischer <vischer@bio.uva.nl>
>Subject: Re: conflict between QuickTime 4.0 and Object Image 1.62p2?
>
>I had a similar problem which disappeared when disabling the "File exchange"
>control panel. It also disappears, when "File Exchange Preferences" is
>removed.
>
>I wonder whether this is a problem of Object-Image, or if it occurs also
>with NIH Image in combination of other spin-offs (feedback is welcome)
>
>Norbert Vischer                  University of Amsterdam
>scientific engineer              Molecular Cell Biology
>                                 Kruislaan 316
>tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
>e-mail: vischer@bio.uva.nl       The Netherlands
>http://simon.bio.uva.nl/object-image.html
>

I tried Norbert's suggestion to remove "File Exchange Preferences" 
and was happy to find that this allowed Object Image 1.62p2 to open 
its object files fine even with QT4 on. I haven't tried using File 
Exchange since removing the preferences, so I don't know whether its 
use will cause the problem to recur. If so, I might write an 
AppleScript that moves the File Exchange preferences before launching 
Object Image. In any case, I'm much happier without File Exchange 
than without QT4.

I haven't seen this problem in the few adaptations of NIH Image that 
I've created, or in other versions that I've used.

Thanks.

Bill Christens-Barry

-------------------------
Bill Christens-Barry, PhD
Johns Hopkins University Applied Physics Laboratory
wacb@aplcomm.jhuapl.edu
-------------------------


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I don't know about the Buz, but I have used the Aurora Fuse without
difficulty. using the "plug-in digitizer". It should work for any hardware
that supports a "vdig" component.

DTL

--On Wed, Jun 30, 1999 10:46 AM -0400 "John L. Bixby"
<jbixby@chroma.med.miami.edu> wrote:

> I am a new NIH Image user, about to get set up. I would like to use the
> Iomega Buz PCI card to capture video images, but I don't know NIH Image
> can use this card to capture images. Is there a plug-in available that
> can do this?
> 
> John Bixby
> 





From nih-image-request@io.ece.drexel.edu Thu Jul  1 19:41 EDT 1999
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Appologies for sending this to the list. I have lost my unsubscribe 
instructions.

Please could someone remove me from the list or send 
instructions to enable me to do so.

Many thanks,
Dr IAN OLIVER
Centre for Biodiversity and Bioresources
School of Biological Sciences
Macquarie University
SYDNEY 2109 AUSTRALIA

Ph. (02) 9850 7248
Fax (02) 9850 9237

Email ioliver@rna.bio.mq.edu.au


From nih-image-request@io.ece.drexel.edu Thu Jul  1 23:00 EDT 1999
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At 09:29 AM 7/2/99 +1000, you wrote:
>Appologies for sending this to the list. I have lost my unsubscribe 
>instructions.
>
>Please could someone remove me from the list or send 
>instructions to enable me to do so.

Instructions can be found at http://rsb.info.nih.gov/nih-image/ under "FAQs".

-wayne


From nih-image-d-request@io.ece.drexel.edu Fri Jul  2 06:20 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 151

Today's Topics:
  Re:conflict between QuickTime 4.0 an  [ Bill Christens-Barry <wacb@aplcomm. ]
  Re: frame grabber                     [ David Linker <dtlinker@u.washington ]
  unsubscribe                           [ "Ian Oliver" <ioliver@rna.bio.mq.ed ]
  Re: unsubscribe                       [ Wayne Rasband <wayne@codon.nih.gov> ]

------------------------------

Date: Thu, 01 Jul 1999 10:46:55 -0400
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
To: nih-image@io.ece.drexel.edu
Cc: vischer@bio.uva.nl
Subject: Re:conflict between QuickTime 4.0 and Object Image 1.62p2: workaround
Message-id: <v04205501b3a12cb24e8d@[128.244.128.182]>
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>In response to my posting:
>
>Date: Wed, 30 Jun 1999 14:35:22 -0400
>From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
>Subject: conflict between QuickTime 4.0 and Object Image 1.62p2?
>
>On computers at home and in my lab, I've found that Object-Image 
>1.62p2 is unable to open its own object files while QuickTime 4.0 is 
>running under MacOS 8.6. The dialog that comes up offers the bizarre 
>explanation that the Object Image application can't be found, even 
>when I try to open the file from within the application while it's 
>running or if I drag the file onto the app's icon. Mind you, I've 
>verified the problem with Norbert's example files. When I turn QT4 
>off, everything works cleanly.
>
>Has anyone else observed this, or know how to overcome it? I've 
>tried turning off some of the QT-related extensions, but the problem 
>persists. Object Image is such a valuable tool that I'm willing to 
>disable QT4, but I'd like to find another way. Can anyone suggest 
>diagnostics that would help discover the cause of this conflict?
>
>Norbert Vischer responded:

>Date: Wed, 30 Jun 1999 21:16:01 +0200
>From: Norbert Vischer <vischer@bio.uva.nl>
>Subject: Re: conflict between QuickTime 4.0 and Object Image 1.62p2?
>
>I had a similar problem which disappeared when disabling the "File exchange"
>control panel. It also disappears, when "File Exchange Preferences" is
>removed.
>
>I wonder whether this is a problem of Object-Image, or if it occurs also
>with NIH Image in combination of other spin-offs (feedback is welcome)
>
>Norbert Vischer                  University of Amsterdam
>scientific engineer              Molecular Cell Biology
>                                 Kruislaan 316
>tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
>e-mail: vischer@bio.uva.nl       The Netherlands
>http://simon.bio.uva.nl/object-image.html
>

I tried Norbert's suggestion to remove "File Exchange Preferences" 
and was happy to find that this allowed Object Image 1.62p2 to open 
its object files fine even with QT4 on. I haven't tried using File 
Exchange since removing the preferences, so I don't know whether its 
use will cause the problem to recur. If so, I might write an 
AppleScript that moves the File Exchange preferences before launching 
Object Image. In any case, I'm much happier without File Exchange 
than without QT4.

I haven't seen this problem in the few adaptations of NIH Image that 
I've created, or in other versions that I've used.

Thanks.

Bill Christens-Barry

-------------------------
Bill Christens-Barry, PhD
Johns Hopkins University Applied Physics Laboratory
wacb@aplcomm.jhuapl.edu
-------------------------

------------------------------

Date: Thu, 01 Jul 1999 11:01:32 -0700
From: David Linker <dtlinker@u.washington.edu>
To: "John L. Bixby" <jbixby@chroma.med.miami.edu>
cc: nih-image@io.ece.drexel.edu
Subject: Re: frame grabber
Message-ID: <496805.3139815692@huginn.medicine.washington.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

I don't know about the Buz, but I have used the Aurora Fuse without
difficulty. using the "plug-in digitizer". It should work for any hardware
that supports a "vdig" component.

DTL

--On Wed, Jun 30, 1999 10:46 AM -0400 "John L. Bixby"
<jbixby@chroma.med.miami.edu> wrote:

> I am a new NIH Image user, about to get set up. I would like to use the
> Iomega Buz PCI card to capture video images, but I don't know NIH Image
> can use this card to capture images. Is there a plug-in available that
> can do this?
> 
> John Bixby
> 

------------------------------

Date: Fri, 2 Jul 1999 09:29:36 +1000
From: "Ian Oliver" <ioliver@rna.bio.mq.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <199907012329.JAA14427@llymarch.bio.mq.edu.au>

Appologies for sending this to the list. I have lost my unsubscribe 
instructions.

Please could someone remove me from the list or send 
instructions to enable me to do so.

Many thanks,
Dr IAN OLIVER
Centre for Biodiversity and Bioresources
School of Biological Sciences
Macquarie University
SYDNEY 2109 AUSTRALIA

Ph. (02) 9850 7248
Fax (02) 9850 9237

Email ioliver@rna.bio.mq.edu.au

------------------------------

Date: Thu, 01 Jul 1999 22:55:02 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: unsubscribe
Message-Id: <3.0.5.32.19990701225502.009b0100@codon.nih.gov>
Content-Type: text/plain; charset="us-ascii"

At 09:29 AM 7/2/99 +1000, you wrote:
>Appologies for sending this to the list. I have lost my unsubscribe 
>instructions.
>
>Please could someone remove me from the list or send 
>instructions to enable me to do so.

Instructions can be found at http://rsb.info.nih.gov/nih-image/ under "FAQs".

-wayne

--------------------------------
End of nih-image-d Digest V99 Issue #151
****************************************

From nih-image-request@io.ece.drexel.edu Fri Jul  2 06:57 EDT 1999
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Date: Fri, 2 Jul 1999 03:45:50 -0700 (PDT)
From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: Iomega Buz
In-Reply-To: <199907021017.GAA02298@io.ece.drexel.edu>
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The iomega buz works fine with Image, without a plug in (as a quicktime
digitizer). 

------------------------------
Stephan G. Anagnostaras, Ph.D. 
UCLA Dept. of Neurobiology         
stephan@lifesci.ucla.edu    
------------------------------
Work, Gonda: (310) 267-2522
      Psych: (310) 794-5339
        Fax: (310) 206-5895
       Home: (310) 306-0294
------------------------------


From nih-image-request@io.ece.drexel.edu Fri Jul  2 09:34 EDT 1999
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Date: Fri, 2 Jul 1999 09:19:12 -0400
To: nih-image@io.ece.drexel.edu
From: Louie Kerr <lkerr@mbl.edu>
Subject: Re: lighting geological samples
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There are several companies that produce light sources and boxes to meet
these requirements.

One that we have dealt with and are very happy with is:
Fostec, Inc.
62 Columbus Street
Auburn, MY  13021
315-255-2791

Hope that helps,
Louie


At 12:48 PM -0400 6/30/99, Pierre Francus wrote:
>Dear imagers,
>
>I would like to build some light box to take digital picture of muddy sediment
>cores having the following specifications:
>
>1- In order to avoid dessication of the sample, I intend to use fluorescent
>bulbs.
>2- It seems necessary to have high frequency light (at least 20 KhZ ?) to
>avoid light intensity fluctuation while digital camera is running.
>3- I would like to use a "daylight" bulb to fake a natural lighting.
>4- Indirect lighting is necessary to avoid reflections of the wet surface
>of the sample.
>
>Does somebody know parts that meets those specifications and where I can
>purchase them in the States ?
>
>Advices dealing with the building of this kind of light boxes are also
>welcome.
>
>Thanks in advance
>
>Pierre
>
>
>*****************************************
>Pierre FRANCUS, Ph.D.
>PostDoctoral Research Associate
>University of Massachusetts
>Department of Geosciences
>Morrill Sciences Center
>Amherst - MA 01003-5820
>
>Phone: 1-413-545-0659
>fax: 1-413-545-1200
>E-mail: francus@geo.umass.edu
>http://www.geo.umass.edu/climate/francus/
>*****************************************


Louie Kerr
Research and Education Support Coordinator
Marine Biological Laboratory
7 MBL Street
Woods Hole, MA  02543
508-289-7273
508-540-6902 (FAX)
508-292-0289 (Cell phone)

VISIT OUR WEB SITE:
http://www.mbl.edu



From nih-image-request@io.ece.drexel.edu Fri Jul  2 17:23 EDT 1999
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Date: Fri, 02 Jul 1999 16:06:30 -0500 (CDT)
From: lcunningham@macalester.edu
Subject: Mac G3 interfacing
To: nih-image@io.ece.drexel.edu
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I would like to take time lapse photos of mussels moving over a one month
period and then measure distance moved using NIH Image to analyze the
photos.  In order to do this I'm trying to hook up 2 CCD cameras to a Data
Translation framegrabber card to simultaneously photograph two separate
experimental set-ups. Has anyone attempted a similar task?  Do you know if
it is possible to connect 2 cameras to one frame grabber card?  Can I put
a frame grabber card directly into the G3 or do I have to buy an RGB
converter?   


From nih-image-d-request@io.ece.drexel.edu Sat Jul  3 05:14 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #152
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 152

Today's Topics:
  Iomega Buz                            [ Stephan Anagnostaras <stephan@proto ]
  Re: lighting geological samples       [ Louie Kerr <lkerr@mbl.edu> ]
  Mac G3 interfacing                    [ lcunningham@macalester.edu ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]

------------------------------

Date: Fri, 2 Jul 1999 03:45:50 -0700 (PDT)
From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: Iomega Buz
Message-ID: <Pine.GSO.4.10.9907020344440.12824-100000@protos.lifesci.ucla.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

The iomega buz works fine with Image, without a plug in (as a quicktime
digitizer). 

- ----------------------------
Stephan G. Anagnostaras, Ph.D. 
UCLA Dept. of Neurobiology         
stephan@lifesci.ucla.edu    
- ----------------------------
Work, Gonda: (310) 267-2522
      Psych: (310) 794-5339
        Fax: (310) 206-5895
       Home: (310) 306-0294
- ----------------------------

------------------------------

Date: Fri, 2 Jul 1999 09:19:12 -0400
From: Louie Kerr <lkerr@mbl.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: lighting geological samples
Message-Id: <l03010d01b3a2695f84a6@[128.128.172.184]>
Content-Type: text/plain; charset="us-ascii"

There are several companies that produce light sources and boxes to meet
these requirements.

One that we have dealt with and are very happy with is:
Fostec, Inc.
62 Columbus Street
Auburn, MY  13021
315-255-2791

Hope that helps,
Louie


At 12:48 PM -0400 6/30/99, Pierre Francus wrote:
>Dear imagers,
>
>I would like to build some light box to take digital picture of muddy sediment
>cores having the following specifications:
>
>1- In order to avoid dessication of the sample, I intend to use fluorescent
>bulbs.
>2- It seems necessary to have high frequency light (at least 20 KhZ ?) to
>avoid light intensity fluctuation while digital camera is running.
>3- I would like to use a "daylight" bulb to fake a natural lighting.
>4- Indirect lighting is necessary to avoid reflections of the wet surface
>of the sample.
>
>Does somebody know parts that meets those specifications and where I can
>purchase them in the States ?
>
>Advices dealing with the building of this kind of light boxes are also
>welcome.
>
>Thanks in advance
>
>Pierre
>
>
>*****************************************
>Pierre FRANCUS, Ph.D.
>PostDoctoral Research Associate
>University of Massachusetts
>Department of Geosciences
>Morrill Sciences Center
>Amherst - MA 01003-5820
>
>Phone: 1-413-545-0659
>fax: 1-413-545-1200
>E-mail: francus@geo.umass.edu
>http://www.geo.umass.edu/climate/francus/
>*****************************************


Louie Kerr
Research and Education Support Coordinator
Marine Biological Laboratory
7 MBL Street
Woods Hole, MA  02543
508-289-7273
508-540-6902 (FAX)
508-292-0289 (Cell phone)

VISIT OUR WEB SITE:
http://www.mbl.edu

------------------------------

Date: Fri, 02 Jul 1999 16:06:30 -0500 (CDT)
From: lcunningham@macalester.edu
To: nih-image@io.ece.drexel.edu
Subject: Mac G3 interfacing
Message-id: <Pine.PMDF.3.96.990702155533.556158B-100000@macalester.edu>
Content-type: TEXT/PLAIN; charset=US-ASCII

I would like to take time lapse photos of mussels moving over a one month
period and then measure distance moved using NIH Image to analyze the
photos.  In order to do this I'm trying to hook up 2 CCD cameras to a Data
Translation framegrabber card to simultaneously photograph two separate
experimental set-ups. Has anyone attempted a similar task?  Do you know if
it is possible to connect 2 cameras to one frame grabber card?  Can I put
a frame grabber card directly into the G3 or do I have to buy an RGB
converter?   

------------------------------

Date: Sat, 3 Jul 1999 05:05:02 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199907030905.FAA12296@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
                   ---------------------------
     


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         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

--------------------------------
End of nih-image-d Digest V99 Issue #152
****************************************

From nih-image-request@io.ece.drexel.edu Sat Jul  3 05:20 EDT 1999
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0)  Remember that Archive is case-sensitive.
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(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
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then use Unix metacharacters to get more than one file. * matches any string.
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         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--


From nih-image-request@io.ece.drexel.edu Sat Jul  3 06:50 EDT 1999
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Resent-Date: Sat, 3 Jul 1999 06:50:57 -0400 (EDT)
Message-ID: <377DE86D.54BE@bluewin.ch>
Date: Sat, 03 Jul 1999 12:39:44 +0200
From: Guy Mayor <guy.mayor@bluewin.ch>
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If you can process the image information in Black and white (which is
nearly always possible, playing with light), the easiest would be to use
a color frame grabber card and hook to it two B&W cameras  on two
different channels (you might even use three channels for 3 separate
experimental set ups).
You will get one RGB stacks with 3 images for each frame you make (every
hour?)
You may reconstruct a stack for each separate experimental setting on
the fly, but I would advice to save the stacks one by one and to build
the separate stacks after data acquisition.
As you need a period of troublefree framegrabing of ONE MONTH, day and
night! I suppose, I strongly recommand to consider the (cheap) buy of
AUTOBOOT and KEEP IT UP sharewares (<http://www.vl-brabant.be/mac/>).
Those two very usefull utilities will help you to warrant a near 100%
success for frame grabbing, even in case of application/system freeze or
power failure.
With this setting, you will also need a task automator to restart the
frame grabbing from within NIH image after i.e a power failure. I
strongly recommand for it OneClic
from <www.westcodesoft.com>, which allow you to perform easily simple to
very complex task automations.

If you don't need a "big enlargement", i.e if a close up (2-3 cm) is
enough to gather the necessary information, you have an even cheaper
alternative:
You may try an USB quickcam Pro (150 $?) camera giving you a color PAL
resolution on a field of 2-4 square cm (closest). You are in principle
able to run several of them (in theory, several dozen) simultaneoulsy if
your time lapse is long enough.
You will thus run several time lapse quicktime sequences in paralel and
import them later in NIH image for image processing. Secure data
acquisition is warranted as described above.

Depending on how you want to record/compute the moves of one/several
mussels, you may also consider to use software with an embedded move
tracking mechanism. Feel free to contact me if needed

Hopes that helps

Guy Mayor
 
----lcunningham@macalester.edu wrote-----

>I would like to take time lapse photos of mussels moving over a one month
>period and then measure distance moved using NIH Image to analyze the
>photos.  In order to do this I'm trying to hook up 2 CCD cameras to a Data
>Translation framegrabber card to simultaneously photograph two >separate
>experimental set-ups. Has anyone attempted a similar task?  Do you know if
>it is possible to connect 2 cameras to one frame grabber card?  Can I put
>a frame grabber card directly into the G3 or do I have to buy an RGB
>converter?


From nih-image-request@io.ece.drexel.edu Sat Jul  3 11:04 EDT 1999
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Resent-Date: Sat, 3 Jul 1999 11:04:39 -0400 (EDT)
Date: Sat, 03 Jul 1999 09:57:10 -0700
From: scidi <scidi@cwix.com>
Subject: Date/Time Stamp
To: nih-image@io.ece.drexel.edu
Reply-to: scidi <scidi@cwix.com>
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	charset="iso-8859-1"
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To All Imagers:

Does anyone have a macro that date/time stamps gels??  I have someone =
who wants one so that they don't have to keep typing it in.  Thanks!!!!



Mark Molenda
Scientific Digital Imaging
1407 S 59th St.
Milwaukee, WI  53214-5122

phone/fax  (414)476-2694
e-mail:  sicdi@cwix.com

------=_NextPart_000_0036_01BEC53A.6AE7BE20
Content-Type: text/html;
	charset="iso-8859-1"
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD W3 HTML//EN">
<HTML>
<HEAD>

<META content=3Dtext/html;charset=3Diso-8859-1 =
http-equiv=3DContent-Type>
<META content=3D'"MSHTML 4.72.3110.7"' name=3DGENERATOR>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT color=3D#000000 size=3D2>To All Imagers:</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT size=3D2>Does anyone have a macro that date/time stamps =
gels??&nbsp; I=20
have someone who wants one so that they don't have to keep typing it =
in.&nbsp;=20
Thanks!!!!</FONT></DIV>
<DIV><FONT size=3D2></FONT>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT color=3D#000000 size=3D2>Mark Molenda<BR>Scientific Digital=20
Imaging<BR>1407 S 59th St.<BR>Milwaukee, WI&nbsp; =
53214-5122</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000000 size=3D2>phone/fax&nbsp; =
(414)476-2694<BR>e-mail:&nbsp;=20
<A =
href=3D"mailto:sicdi@cwix.co">sicdi@cwix.co</A>m</FONT></DIV></BODY></HTM=
L>

------=_NextPart_000_0036_01BEC53A.6AE7BE20--


From nih-image-request@io.ece.drexel.edu Sat Jul  3 15:17 EDT 1999
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Date: Sat, 3 Jul 1999 20:09:16 +0200
To: nih-image@io.ece.drexel.edu
From: "Anneke M.Th. Harbers and Ard Jonker" <a_team@dds.nl>
Subject: Re: Mac G3 interfacing
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>I would like to take time lapse photos of mussels moving over a one month
>period and then measure distance moved using NIH Image to analyze the
>photos.  In order to do this I'm trying to hook up 2 CCD cameras to a Data
>Translation framegrabber card to simultaneously photograph two separate
>experimental set-ups. Has anyone attempted a similar task?  Do you know if
>it is possible to connect 2 cameras to one frame grabber card?  Can I put
>a frame grabber card directly into the G3 or do I have to buy an RGB
>converter?  

As a first remark: I think you record the scene with two cameras at an angle to be able to do 3D measurement by stereo imaging? Or do you need a special setup with two color cameras to analyse photographs (wet developed film, prints made on photo paper) that you took from the mussels? The former seems the more logical choise.
Ask yourself if it is really necessary to record the scene with color cameras. Monochrome cameras give you higher resolution than 1-chip color cameras and are way cheaper than 3-chip color cameras that can match the resolution of 1-chip monochrome video cameras. If you can do with grayscale imaging (ie. you haven't painted the mussels, and mussels normally happen to be gray in our country), you can use two of the 4 channels of a scion LG-3 frame grabber to record images from two cameras. AFAIK, the G3 takes an LG-3 without problems. I'll check shortly.

You can manually, or with the help of a macro, switch between channels and record one image in each channel, ie. take an image with each camera. As mussels aren't that fast in  moving, it wouldn't mind that you don't have instant access to both frames, you can do with consecutive recording.
If you have 3D points as measurements, you could visualise the tracks using ObjectImage and/or Rotater.

Regards, Ard



From nih-image-request@io.ece.drexel.edu Sat Jul  3 16:45 EDT 1999
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Date: Sat, 03 Jul 1999 16:35:31 -0400
To: nih-image@io.ece.drexel.edu
From: Dylan Bulseco <bulseco@os.com>
Subject: image registration
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>From looking at the online manual, I gather that the registration procedure
corrects only for translation and rotation, but not any type of warping?  I
this is correct, has anyone implemented any warping/hypergeometric
correction procedures for NIH Image?

Thanks,

Dylan


Dylan Bulseco, Ph.D.		bulseco@os.com
UMASS Medical Center	dbulseco@ummed.edu
Biotech IV, Room 321		http://hmsbeagle.com
377 Plantation St.		ph: 508.856.8683
Worcester, MA 01605		FAX: 508.856.8774


From nih-image-d-request@io.ece.drexel.edu Sun Jul  4 00:26 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 153

Today's Topics:
  Mac G3 interfacing                    [ Guy Mayor <guy.mayor@bluewin.ch> ]
  Date/Time Stamp                       [ scidi <scidi@cwix.com> ]
  Re: Mac G3 interfacing                [ "Anneke M.Th. Harbers and Ard Jonke ]
  image registration                    [ Dylan Bulseco <bulseco@os.com> ]
  Directional Thresholding              [ Greg Kawchuk <kawchuk@mccaig.ucalga ]

------------------------------

Date: Sat, 03 Jul 1999 12:39:44 +0200
From: Guy Mayor <guy.mayor@bluewin.ch>
To: nih-image@io.ece.drexel.edu
Subject: Mac G3 interfacing
Message-ID: <377DE86D.54BE@bluewin.ch>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

If you can process the image information in Black and white (which is
nearly always possible, playing with light), the easiest would be to use
a color frame grabber card and hook to it two B&W cameras  on two
different channels (you might even use three channels for 3 separate
experimental set ups).
You will get one RGB stacks with 3 images for each frame you make (every
hour?)
You may reconstruct a stack for each separate experimental setting on
the fly, but I would advice to save the stacks one by one and to build
the separate stacks after data acquisition.
As you need a period of troublefree framegrabing of ONE MONTH, day and
night! I suppose, I strongly recommand to consider the (cheap) buy of
AUTOBOOT and KEEP IT UP sharewares (<http://www.vl-brabant.be/mac/>).
Those two very usefull utilities will help you to warrant a near 100%
success for frame grabbing, even in case of application/system freeze or
power failure.
With this setting, you will also need a task automator to restart the
frame grabbing from within NIH image after i.e a power failure. I
strongly recommand for it OneClic
from <www.westcodesoft.com>, which allow you to perform easily simple to
very complex task automations.

If you don't need a "big enlargement", i.e if a close up (2-3 cm) is
enough to gather the necessary information, you have an even cheaper
alternative:
You may try an USB quickcam Pro (150 $?) camera giving you a color PAL
resolution on a field of 2-4 square cm (closest). You are in principle
able to run several of them (in theory, several dozen) simultaneoulsy if
your time lapse is long enough.
You will thus run several time lapse quicktime sequences in paralel and
import them later in NIH image for image processing. Secure data
acquisition is warranted as described above.

Depending on how you want to record/compute the moves of one/several
mussels, you may also consider to use software with an embedded move
tracking mechanism. Feel free to contact me if needed

Hopes that helps

Guy Mayor
 
----lcunningham@macalester.edu wrote-----

>I would like to take time lapse photos of mussels moving over a one month
>period and then measure distance moved using NIH Image to analyze the
>photos.  In order to do this I'm trying to hook up 2 CCD cameras to a Data
>Translation framegrabber card to simultaneously photograph two >separate
>experimental set-ups. Has anyone attempted a similar task?  Do you know if
>it is possible to connect 2 cameras to one frame grabber card?  Can I put
>a frame grabber card directly into the G3 or do I have to buy an RGB
>converter?

------------------------------

Date: Sat, 03 Jul 1999 09:57:10 -0700
From: scidi <scidi@cwix.com>
To: nih-image@io.ece.drexel.edu
Subject: Date/Time Stamp
Message-id: <003901bec575$17f61000$02a83ea6@pavilion>
Content-type: multipart/alternative;
	boundary="----=_NextPart_000_0036_01BEC53A.6AE7BE20"

This is a multi-part message in MIME format.

------=_NextPart_000_0036_01BEC53A.6AE7BE20
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

To All Imagers:

Does anyone have a macro that date/time stamps gels??  I have someone =
who wants one so that they don't have to keep typing it in.  Thanks!!!!



Mark Molenda
Scientific Digital Imaging
1407 S 59th St.
Milwaukee, WI  53214-5122

phone/fax  (414)476-2694
e-mail:  sicdi@cwix.com

------=_NextPart_000_0036_01BEC53A.6AE7BE20
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD W3 HTML//EN">
<HTML>
<HEAD>

<META content=3Dtext/html;charset=3Diso-8859-1 =
http-equiv=3DContent-Type>
<META content=3D'"MSHTML 4.72.3110.7"' name=3DGENERATOR>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT color=3D#000000 size=3D2>To All Imagers:</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT size=3D2>Does anyone have a macro that date/time stamps =
gels??&nbsp; I=20
have someone who wants one so that they don't have to keep typing it =
in.&nbsp;=20
Thanks!!!!</FONT></DIV>
<DIV><FONT size=3D2></FONT>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT color=3D#000000 size=3D2>Mark Molenda<BR>Scientific Digital=20
Imaging<BR>1407 S 59th St.<BR>Milwaukee, WI&nbsp; =
53214-5122</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000000 size=3D2>phone/fax&nbsp; =
(414)476-2694<BR>e-mail:&nbsp;=20
<A =
href=3D"mailto:sicdi@cwix.co">sicdi@cwix.co</A>m</FONT></DIV></BODY></HTM=
L>

------=_NextPart_000_0036_01BEC53A.6AE7BE20--

------------------------------

Date: Sat, 3 Jul 1999 20:09:16 +0200
From: "Anneke M.Th. Harbers and Ard Jonker" <a_team@dds.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Mac G3 interfacing
Message-Id: <l03130302b3a3ffd794bd@[192.0.1.2]>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 8bit

>I would like to take time lapse photos of mussels moving over a one month
>period and then measure distance moved using NIH Image to analyze the
>photos.  In order to do this I'm trying to hook up 2 CCD cameras to a Data
>Translation framegrabber card to simultaneously photograph two separate
>experimental set-ups. Has anyone attempted a similar task?  Do you know if
>it is possible to connect 2 cameras to one frame grabber card?  Can I put
>a frame grabber card directly into the G3 or do I have to buy an RGB
>converter?  

As a first remark: I think you record the scene with two cameras at an angle to be able to do 3D measurement by stereo imaging? Or do you need a special setup with two color cameras to analyse photographs (wet developed film, prints made on photo paper) that you took from the mussels? The former seems the more logical choise.
Ask yourself if it is really necessary to record the scene with color cameras. Monochrome cameras give you higher resolution than 1-chip color cameras and are way cheaper than 3-chip color cameras that can match the resolution of 1-chip monochrome video cameras. If you can do with grayscale imaging (ie. you haven't painted the mussels, and mussels normally happen to be gray in our country), you can use two of the 4 channels of a scion LG-3 frame grabber to record images from two cameras. AFAIK, the G3 takes an LG-3 without problems. I'll check shortly.

You can manually, or with the help of a macro, switch between channels and record one image in each channel, ie. take an image with each camera. As mussels aren't that fast in  moving, it wouldn't mind that you don't have instant access to both frames, you can do with consecutive recording.
If you have 3D points as measurements, you could visualise the tracks using ObjectImage and/or Rotater.

Regards, Ard

------------------------------

Date: Sat, 03 Jul 1999 16:35:31 -0400
From: Dylan Bulseco <bulseco@os.com>
To: nih-image@io.ece.drexel.edu
Subject: image registration
Message-Id: <4.1.19990703163401.009a16f0@os.com>
Content-Type: text/plain; charset="us-ascii"

>From looking at the online manual, I gather that the registration procedure
corrects only for translation and rotation, but not any type of warping?  I
this is correct, has anyone implemented any warping/hypergeometric
correction procedures for NIH Image?

Thanks,

Dylan


Dylan Bulseco, Ph.D.		bulseco@os.com
UMASS Medical Center	dbulseco@ummed.edu
Biotech IV, Room 321		http://hmsbeagle.com
377 Plantation St.		ph: 508.856.8683
Worcester, MA 01605		FAX: 508.856.8774

------------------------------

Date: Sat, 3 Jul 1999 22:18:37 -0600 (MDT)
From: Greg Kawchuk <kawchuk@mccaig.ucalgary.ca>
To: nih-image@io.ece.drexel.edu
Subject: Directional Thresholding
Message-Id: <Pine.SUN.3.95.990703220844.2067A-100000@epicenter>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I am looking for a way to threshold pixels around the circumference of an
object, but not within the object itself. Does anyone know how it might be
possible to threshold from the borders of the image and work toward the
centre of the image where if the threshold value was reached, the
thresholding would stop? This process would allow thresholding around the
edges of an object but it would not influence pixels inside the object. 


Greg Kawchuk D.C., M.Sc.
Clinician, University Health Services 
Ph.D. Candidate, McCaig Centre for Joint Injury and Arthritis Research
University of Calgary
http://www.ucalgary.ca/~gkawchuk

--------------------------------
End of nih-image-d Digest V99 Issue #153
****************************************

From nih-image-request@io.ece.drexel.edu Sun Jul  4 00:34 EDT 1999
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I am looking for a way to threshold pixels around the circumference of an
object, but not within the object itself. Does anyone know how it might be
possible to threshold from the borders of the image and work toward the
centre of the image where if the threshold value was reached, the
thresholding would stop? This process would allow thresholding around the
edges of an object but it would not influence pixels inside the object. 


Greg Kawchuk D.C., M.Sc.
Clinician, University Health Services 
Ph.D. Candidate, McCaig Centre for Joint Injury and Arthritis Research
University of Calgary
http://www.ucalgary.ca/~gkawchuk


From nih-image-request@io.ece.drexel.edu Sun Jul  4 21:09 EDT 1999
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Date: Sun, 4 Jul 1999 19:53:24 -0500 (CDT)
From: Ken Johnson <kenjohn@pathbox.wustl.edu>
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Subject: rgb vs indexed colour
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I'm opening a number of TIF files in NIH Image which automatically 
converts these files to an Indexed Colour Image. Is it  possible though to
make NIH Image to open these files as RGB files - or even to convert the
Indexed Colour file to RGB???

Any help with this would be much appreciated. Thanks.

Ken Johnson


From nih-image-request@io.ece.drexel.edu Mon Jul  5 00:01 EDT 1999
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At 07:53 PM 7/4/99 -0500, you wrote:
>I'm opening a number of TIF files in NIH Image which automatically 
>converts these files to an Indexed Colour Image. Is it  possible though to
>make NIH Image to open these files as RGB files - or even to convert the
>Indexed Colour file to RGB???

NIH Image opens an RGB TIFF file as a 3 slice (red, green and blue) stack and then automatically calls the "RGB to 8-bit Color" command to create an indexed color version. For better RGB support, try my new ImageJ program at http://rsb.info.nih.gov/ij/.


From nih-image-request@io.ece.drexel.edu Mon Jul  5 08:51 EDT 1999
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From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: Re: Date/Time Stamp
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>     To All Imagers:   Does anyone have a macro that date/time stamps
>gels??  I
>have someone who wants one so that they don't have to keep typing it in. 

Two solutions possible: you write in the datum and time in the first pixels
(coded, so it is invisible on the image; I have sampel macros) or you use
the date and time in an associated object file (use Object Image).
Benefit of the second solution is that in the same object file, you can
store outlines of the areas you have measured non-destructively, and the
outcome of these measurements and calculations you have performed with the
built-in spreadsheet.

Ard



From nih-image-request@io.ece.drexel.edu Mon Jul  5 08:52 EDT 1999
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From: Greg Joss <gjoss@hotmail.com>
To: cabbage@uclink4.berkeley.edu, nih-image@io.ece.drexel.edu
Subject: Re: [plotting macro]
Date: Mon, 05 Jul 1999 22:37:57 EST
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Ankoor,
As I didnt see any followup on the following posts, I thought I would add my 
two cents worth.
The following macro does a reSlice(Stack menu through a (MRI) stack but uses 
plotProfile data for each row.

macro'[M]RI lineRoi slice';{prototype only}
var pPid,sPid,i,x,x1,y1,x2,y2,width,count,ppv,min,max:integer;
begin
pPid:=pidNumber;

{prototype only}
{the following 3 lines of commands would normally be done via menu}
{
x1:=0;y1:=0;x2:=10;y2:=10;width:=8;
SetLineWidth(width);{macros allow larger widths than menu}
MakeLineRoi(x1,y1,x2,y2);
}
getRoi(x1,y1,x2,y2);
if x2=0 then exit('no Roi selection');
if get('roitype')<>6 then exit('not line Roi');
for i:= 1 to nSlices do begin
  selectSlice(i);
  GetPlotData(count,ppv,min,max);
  if i=1 then begin setNewSize(count,nSlices);
    makeNewWindow(windowTitle,'(',x1,y1,x2,y2,width,')');
    sPid:=pidNumber;
    end
  else selectPic(sPid);
  for x:=0 to count-1 do lineBuffer[x]:=round(PlotData[x]);
  putRow(0,i,count);
  selectPic(pPid);{faster as choosePic}
  end;
selectPic(sPid);enhanceContrast;
{SurfacePlot;}
end

Hope this helps.

Greg Joss.
gjoss@rna.bio.mq.edu.au
________________________________________________________________
>From: cabbage@uclink4.berkeley.edu (ankoor) Reply-To: 
>nih-image@io.ece.drexel.edu
>To: nih-image@io.ece.drexel.edu
>Subject: Re: [plotting macro]
>Date: Mon, 28 Jun 1999 21:39:55 -0700
>
>Specifically, i have been looking at stacks of MRI images for tumor 
> >analysis. I have been drawing a line of about 10 pixel, which is my 
> >region of interest. The plot profile macro then measures the mean 
> >intensity of the image at each pixel along the length of the line. The 
> >plot then shows the intensity contrast in the line of ten pixels. This 
> >works well for on image. However, I use stacks of about 80 images, and >i 
>would like to do a more dynamic analysis of the ROI for the entire >stack. 
>What i meant by "pixel number" is that when i do a "plot >profile and 
>display values" it gives me a pixel number (1-10) and the >mean intensity 
>at each pixel. I hope this is a bit more clear, and >again, any 
>suggestions would be appreciated.
>
>At 6:33 PM 6/28/99, CHRIS TULLY wrote:
>>Ankoor-
>>
>>I'm not positive that I understand what you want. Do you want a >>listing 
>>of numeric values (x,y,i), where i is intensity for each >>profile? Or do 
>>you want a profile plot with the mean density listed >>on the plot (I am 
>>unsure >>what you mean by pixel number)?
>>
>>I have some ideas for what to do but wanted to clarify the above >>points 
>>before I start making suggestions.
_________________________________________________________________
>From: ankoor shah <ashah7@ix.netcom.com>  SaveAddressBlockSender
>Reply-To: nih-image@io.ece.drexel.edu
>To: nih-image@io.ece.drexel.edu
>Subject: plotting macro
>Date: Mon, 28 Jun 1999 11:47:29 -0700
>
>hello all,
> I was hoping that someone fluent in the image/macro programming 
> >language could aid me in solving a problem. I've been trying to modify 
> >the plotting profile macro to plot profiles with values for each image 
> >through a stack automatically. I have tried to combine the codes for 
> >the "plot profile and display values" and "plot z-axis profile" macros, 
> >but i've hit a point where I can get it to go through the stack and >plot 
>profiles, but it can't take measurements and display the values. >All i 
>need in terms of measurements is the pixel number and mean >density. If 
>anyone knows how to program this, or knows of a program >that does this, I 
>would appreciate it.
_________________________________________________________________
Hope this helps.

Greg Joss.
gjoss@rna.bio.mq.edu.au



______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com


From nih-image-request@io.ece.drexel.edu Mon Jul  5 08:56 EDT 1999
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Subject: Re: Directional Thresholding
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>I am looking for a way to threshold pixels around the circumference of an
>object, but not within the object itself. Does anyone know how it might be
>possible to threshold from the borders of the image and work toward the
>centre of the image where if the threshold value was reached, the
>thresholding would stop? This process would allow thresholding around the
>edges of an object but it would not influence pixels inside the object.

If you have an outline ROI, copy the ROI, make a new image, restore the
ROI, choose 255 as foreground color, draw boundary, select all, copy the
selection, dispose of the copy image, paste doing AND in the original image
and you are left with the ROI pixels in their original grey values. now you
can threshold on the outline only. Maybe this is what you want, maybe I
misunderstood you.

ard



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Another way which I use and would certainly use for this.  In the PicHeader
record there are 512 bytes which are used to store various details about an
image (check in globals.p).  In the normal version of Image there are 200
unused bytes.  You can put in whatever you like here - a string array, real
numbers, a date record and so on - just make sure that the total bytes
comes to 512.  There is a bit of dancing around you have to do in other
source files to make sure it is written correctly into the PicHeader record
when you save a file, and read when you open that file.  If you want to be
able to access it in a number of routines, transfer it into the PicInfo
record.

Cheers - Richard

>>     Does anyone have a macro that date/time stamps
>>gels??

>Two solutions possible: you write in the datum and time in the first pixels
>(coded, so it is invisible on the image; I have sampel macros) or you use
>the date and time in an associated object file (use Object Image).
>Benefit of the second solution is that in the same object file, you can
>store outlines of the areas you have measured non-destructively, and the
>outcome of these measurements and calculations you have performed with the
>built-in spreadsheet.



Richard Herd
Montserrat Volcano Observatory
St Johns
Montserrat
West Indies
email : rahe@ua.nkw.ac.uk
phone : (1) 664 491 5647
FAX : (1) 664 491 2324



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Date: Mon, 5 Jul 1999 09:31:44 -0700
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From: Carsten Bruckner <bruckner@u.washington.edu>
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Canon looking for info for possible Mac product
by Dennis Sellers, dsellers@maccentral.com
July 5, 1999, 7:00 am ET

Kevin Fogarty, Product Planning, Visual Communications, Canon USA, Inc.,
wants to find out the extent of Mac use in the medical markets, and needs
your help.

"We are considering developing software for one of our products for the Mac
in the area of medical applications," Fogarty says. "It is a USB digital
camera that captures 900x1424 images. We have found some success in the PC
side but we need some information to justify a Macintosh version of the
software and driver. Any help or info is greatly appreciated."

Anyone at Apple, in Mac-related firms, or in medical firms who can supply
Fogarty with this info should email it to kfogarty@cusa.canon.com.



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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 154

Today's Topics:
  rgb vs indexed colour                 [ Ken Johnson <kenjohn@pathbox.wustl. ]
  Re: rgb vs indexed colour             [ Wayne Rasband <wayne@codon.nih.gov> ]
  Re: Date/Time Stamp                   [ Ard Jonker <a.jonker@amc.uva.nl> ]
  Re: [plotting macro]                  [ Greg Joss <gjoss@hotmail.com> ]
  Re: Directional Thresholding          [ Ard Jonker <a.jonker@amc.uva.nl> ]
  Re: Date/Time Stamp                   [ Richard Herd <rahe@unixa.nerc-keywo ]
  Canon USB camera needs?               [ Carsten Bruckner <bruckner@u.washin ]

------------------------------

Date: Sun, 4 Jul 1999 19:53:24 -0500 (CDT)
From: Ken Johnson <kenjohn@pathbox.wustl.edu>
To: nih-image@io.ece.drexel.edu
Subject: rgb vs indexed colour
Message-ID: <Pine.GSO.3.96.990704194947.7960A-100000@pathbox.wustl.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I'm opening a number of TIF files in NIH Image which automatically 
converts these files to an Indexed Colour Image. Is it  possible though to
make NIH Image to open these files as RGB files - or even to convert the
Indexed Colour file to RGB???

Any help with this would be much appreciated. Thanks.

Ken Johnson

------------------------------

Date: Sun, 04 Jul 1999 23:50:16 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: rgb vs indexed colour
Message-Id: <3.0.5.32.19990704235016.009ba280@codon.nih.gov>
Content-Type: text/plain; charset="us-ascii"

At 07:53 PM 7/4/99 -0500, you wrote:
>I'm opening a number of TIF files in NIH Image which automatically 
>converts these files to an Indexed Colour Image. Is it  possible though to
>make NIH Image to open these files as RGB files - or even to convert the
>Indexed Colour file to RGB???

NIH Image opens an RGB TIFF file as a 3 slice (red, green and blue) stack and then automatically calls the "RGB to 8-bit Color" command to create an indexed color version. For better RGB support, try my new ImageJ program at http://rsb.info.nih.gov/ij/.

------------------------------

Date: Mon, 5 Jul 1999 14:29:39 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Date/Time Stamp
Message-Id: <l03130301b3a6550230f9@[145.117.53.66]>
Content-Type: text/plain; charset="us-ascii"

>     To All Imagers:   Does anyone have a macro that date/time stamps
>gels??  I
>have someone who wants one so that they don't have to keep typing it in. 

Two solutions possible: you write in the datum and time in the first pixels
(coded, so it is invisible on the image; I have sampel macros) or you use
the date and time in an associated object file (use Object Image).
Benefit of the second solution is that in the same object file, you can
store outlines of the areas you have measured non-destructively, and the
outcome of these measurements and calculations you have performed with the
built-in spreadsheet.

Ard

------------------------------

Date: Mon, 05 Jul 1999 22:37:57 EST
From: Greg Joss <gjoss@hotmail.com>
To: cabbage@uclink4.berkeley.edu, nih-image@io.ece.drexel.edu
Subject: Re: [plotting macro]
Message-ID: <19990705123759.96012.qmail@hotmail.com>
Content-Type: text/plain; format=flowed

Ankoor,
As I didnt see any followup on the following posts, I thought I would add my 
two cents worth.
The following macro does a reSlice(Stack menu through a (MRI) stack but uses 
plotProfile data for each row.

macro'[M]RI lineRoi slice';{prototype only}
var pPid,sPid,i,x,x1,y1,x2,y2,width,count,ppv,min,max:integer;
begin
pPid:=pidNumber;

{prototype only}
{the following 3 lines of commands would normally be done via menu}
{
x1:=0;y1:=0;x2:=10;y2:=10;width:=8;
SetLineWidth(width);{macros allow larger widths than menu}
MakeLineRoi(x1,y1,x2,y2);
}
getRoi(x1,y1,x2,y2);
if x2=0 then exit('no Roi selection');
if get('roitype')<>6 then exit('not line Roi');
for i:= 1 to nSlices do begin
  selectSlice(i);
  GetPlotData(count,ppv,min,max);
  if i=1 then begin setNewSize(count,nSlices);
    makeNewWindow(windowTitle,'(',x1,y1,x2,y2,width,')');
    sPid:=pidNumber;
    end
  else selectPic(sPid);
  for x:=0 to count-1 do lineBuffer[x]:=round(PlotData[x]);
  putRow(0,i,count);
  selectPic(pPid);{faster as choosePic}
  end;
selectPic(sPid);enhanceContrast;
{SurfacePlot;}
end

Hope this helps.

Greg Joss.
gjoss@rna.bio.mq.edu.au
________________________________________________________________
>From: cabbage@uclink4.berkeley.edu (ankoor) Reply-To: 
>nih-image@io.ece.drexel.edu
>To: nih-image@io.ece.drexel.edu
>Subject: Re: [plotting macro]
>Date: Mon, 28 Jun 1999 21:39:55 -0700
>
>Specifically, i have been looking at stacks of MRI images for tumor 
> >analysis. I have been drawing a line of about 10 pixel, which is my 
> >region of interest. The plot profile macro then measures the mean 
> >intensity of the image at each pixel along the length of the line. The 
> >plot then shows the intensity contrast in the line of ten pixels. This 
> >works well for on image. However, I use stacks of about 80 images, and >i 
>would like to do a more dynamic analysis of the ROI for the entire >stack. 
>What i meant by "pixel number" is that when i do a "plot >profile and 
>display values" it gives me a pixel number (1-10) and the >mean intensity 
>at each pixel. I hope this is a bit more clear, and >again, any 
>suggestions would be appreciated.
>
>At 6:33 PM 6/28/99, CHRIS TULLY wrote:
>>Ankoor-
>>
>>I'm not positive that I understand what you want. Do you want a >>listing 
>>of numeric values (x,y,i), where i is intensity for each >>profile? Or do 
>>you want a profile plot with the mean density listed >>on the plot (I am 
>>unsure >>what you mean by pixel number)?
>>
>>I have some ideas for what to do but wanted to clarify the above >>points 
>>before I start making suggestions.
_________________________________________________________________
>From: ankoor shah <ashah7@ix.netcom.com>  SaveAddressBlockSender
>Reply-To: nih-image@io.ece.drexel.edu
>To: nih-image@io.ece.drexel.edu
>Subject: plotting macro
>Date: Mon, 28 Jun 1999 11:47:29 -0700
>
>hello all,
> I was hoping that someone fluent in the image/macro programming 
> >language could aid me in solving a problem. I've been trying to modify 
> >the plotting profile macro to plot profiles with values for each image 
> >through a stack automatically. I have tried to combine the codes for 
> >the "plot profile and display values" and "plot z-axis profile" macros, 
> >but i've hit a point where I can get it to go through the stack and >plot 
>profiles, but it can't take measurements and display the values. >All i 
>need in terms of measurements is the pixel number and mean >density. If 
>anyone knows how to program this, or knows of a program >that does this, I 
>would appreciate it.
_________________________________________________________________
Hope this helps.

Greg Joss.
gjoss@rna.bio.mq.edu.au



______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com

------------------------------

Date: Mon, 5 Jul 1999 14:37:20 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Directional Thresholding
Message-Id: <l03130302b3a656107055@[145.117.53.66]>
Content-Type: text/plain; charset="us-ascii"

>I am looking for a way to threshold pixels around the circumference of an
>object, but not within the object itself. Does anyone know how it might be
>possible to threshold from the borders of the image and work toward the
>centre of the image where if the threshold value was reached, the
>thresholding would stop? This process would allow thresholding around the
>edges of an object but it would not influence pixels inside the object.

If you have an outline ROI, copy the ROI, make a new image, restore the
ROI, choose 255 as foreground color, draw boundary, select all, copy the
selection, dispose of the copy image, paste doing AND in the original image
and you are left with the ROI pixels in their original grey values. now you
can threshold on the outline only. Maybe this is what you want, maybe I
misunderstood you.

ard

------------------------------

Date: Mon, 5 Jul 1999 11:02:32 +0400 (GMT)
From: Richard Herd <rahe@unixa.nerc-keyworth.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Date/Time Stamp
Message-Id: <l03130300b3a63e35fae6@[205.160.233.204]>
Content-Type: text/plain; charset="us-ascii"

Another way which I use and would certainly use for this.  In the PicHeader
record there are 512 bytes which are used to store various details about an
image (check in globals.p).  In the normal version of Image there are 200
unused bytes.  You can put in whatever you like here - a string array, real
numbers, a date record and so on - just make sure that the total bytes
comes to 512.  There is a bit of dancing around you have to do in other
source files to make sure it is written correctly into the PicHeader record
when you save a file, and read when you open that file.  If you want to be
able to access it in a number of routines, transfer it into the PicInfo
record.

Cheers - Richard

>>     Does anyone have a macro that date/time stamps
>>gels??

>Two solutions possible: you write in the datum and time in the first pixels
>(coded, so it is invisible on the image; I have sampel macros) or you use
>the date and time in an associated object file (use Object Image).
>Benefit of the second solution is that in the same object file, you can
>store outlines of the areas you have measured non-destructively, and the
>outcome of these measurements and calculations you have performed with the
>built-in spreadsheet.



Richard Herd
Montserrat Volcano Observatory
St Johns
Montserrat
West Indies
email : rahe@ua.nkw.ac.uk
phone : (1) 664 491 5647
FAX : (1) 664 491 2324

------------------------------

Date: Mon, 5 Jul 1999 09:31:44 -0700
From: Carsten Bruckner <bruckner@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Canon USB camera needs?
Message-Id: <l03130300b3a68e1316a1@[140.142.181.40]>
Content-Type: text/plain; charset="us-ascii"

Canon looking for info for possible Mac product
by Dennis Sellers, dsellers@maccentral.com
July 5, 1999, 7:00 am ET

Kevin Fogarty, Product Planning, Visual Communications, Canon USA, Inc.,
wants to find out the extent of Mac use in the medical markets, and needs
your help.

"We are considering developing software for one of our products for the Mac
in the area of medical applications," Fogarty says. "It is a USB digital
camera that captures 900x1424 images. We have found some success in the PC
side but we need some information to justify a Macintosh version of the
software and driver. Any help or info is greatly appreciated."

Anyone at Apple, in Mac-related firms, or in medical firms who can supply
Fogarty with this info should email it to kfogarty@cusa.canon.com.

--------------------------------
End of nih-image-d Digest V99 Issue #154
****************************************

From nih-image-request@io.ece.drexel.edu Tue Jul  6 10:30 EDT 1999
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Date: Tue, 6 Jul 1999 10:11:10 -0400
To: nih-image@io.ece.drexel.edu
From: "Gloria.Hoffman" <gehoffma@umaryland.edu>
Subject: Re: Canon USB camera needs?
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I think if the price is low, it would have appeal in the Mac side. (my lab
is totally Mac based). I personally like a bit higher resolution, but some
of my colleagues could benefit from such a device.

>Canon looking for info for possible Mac product
>by Dennis Sellers, dsellers@maccentral.com
>July 5, 1999, 7:00 am ET
>
>Kevin Fogarty, Product Planning, Visual Communications, Canon USA, Inc.,
>wants to find out the extent of Mac use in the medical markets, and needs
>your help.
>
>"We are considering developing software for one of our products for the Mac
>in the area of medical applications," Fogarty says. "It is a USB digital
>camera that captures 900x1424 images. We have found some success in the PC
>side but we need some information to justify a Macintosh version of the
>software and driver. Any help or info is greatly appreciated."
>
>Anyone at Apple, in Mac-related firms, or in medical firms who can supply
>Fogarty with this info should email it to kfogarty@cusa.canon.com.

**************************************************
"Scientists are half B.F. Skinner,
and half P.T. Barnum..."  [Homer Simpson]
**************************************************
Gloria E. Hoffman, Ph.D.
Department of Anatomy and Neurobiology
685 W Baltimore St
Baltimore MD 21201
Phone 410 706-2438
Lab: 410 706-2440
Fax 410 706-2512
email gehoffma@umaryland.edu


From nih-image-request@io.ece.drexel.edu Tue Jul  6 16:37 EDT 1999
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Date: Tue, 06 Jul 1999 16:19:35 -0400
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
Subject: Can I build microscope->CCD  -(FireWire)-> storage -> G3 laptop?
To: nih-image@io.ece.drexel.edu
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Here's my dream for a portable scientific-grade image acquisition 
system: use a high quality consumer color video camera / 3-CCD that 
allows use (via a c-mount) with a microscope to acquire a video 
stream that uses FireWire to send a stream of images (30 fps 
preferably) directly to (undoubtedly huge) storage and that could be 
accessed either directly or indirectly (from storage) by a host G3 
laptop. And the camera should be controllable via AppleScript using 
the NIH Image macro language.

How close to reality is this picture? What pieces are missing?  Here 
are some  existing items that may be part of the equation:
#1 cameras  that suppport FireWire (IEEE-1394)
       - many (http://www.digitalorigin.com/products/compat/dvqualifiedcam.html)
#2 consumer digital cameras with microscope (C-mount) adaptors
       - I'm not sure where I heard about these, but somewhere in the 
last few days a site streamed by
#3 adaptors  to connect a FireWire device toa  G3 laptop
       - Newertech FireWire 2Go 
(http://www.newertech.com/products/firewire/index.html)
       - Ratoc (http://www.rexpccard.co.jp/english/products/cbfw2.html)
#4 FireWire hard drives
       - Firepower (http://www.firepower.com/products/FireDrivespecs.html)
#5  NIH Image variants that have varying levels of AppleScript support:
       - Object Image 1.62p2 (http://simon.bio.uva.nl/object-image.html)
       - Image AE (ftp://codon.nih.gov/pub/nih-image/contrib/ImageAEv05.sea.bin)

Can anyone point to a FireWire camera that has uses c-mount (i.e. 
combines #1 and #2)? Best if it has square pixels, too.

Are there contradictions in what I'm trying to define here? I have a 
vague sense that some digital video formats use a pixel aspect ratio 
of 16:9.

How about software to stitch these things together - what else would I need?
Is there software (e.g. framegrabber for analog camera) that is 
missing? Hardware?

Has anyone put together something like this?

Thanks.

Bill Christens-Barry
-------------------------
Bill Christens-Barry, PhD
Johns Hopkins University Applied Physics Laboratory
wacb@aplcomm.jhuapl.edu
-------------------------


From nih-image-d-request@io.ece.drexel.edu Wed Jul  7 06:16 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 155

Today's Topics:
  Re: Canon USB camera needs?           [ "Gloria.Hoffman" <gehoffma@umarylan ]
  Can I build microscope->CCD -(FireWi  [ Bill Christens-Barry <wacb@aplcomm. ]

------------------------------

Date: Tue, 6 Jul 1999 10:11:10 -0400
From: "Gloria.Hoffman" <gehoffma@umaryland.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Canon USB camera needs?
Message-Id: <v04011707b3a7bdac1206@[134.192.131.169]>
Content-Type: text/plain; charset="us-ascii"

I think if the price is low, it would have appeal in the Mac side. (my lab
is totally Mac based). I personally like a bit higher resolution, but some
of my colleagues could benefit from such a device.

>Canon looking for info for possible Mac product
>by Dennis Sellers, dsellers@maccentral.com
>July 5, 1999, 7:00 am ET
>
>Kevin Fogarty, Product Planning, Visual Communications, Canon USA, Inc.,
>wants to find out the extent of Mac use in the medical markets, and needs
>your help.
>
>"We are considering developing software for one of our products for the Mac
>in the area of medical applications," Fogarty says. "It is a USB digital
>camera that captures 900x1424 images. We have found some success in the PC
>side but we need some information to justify a Macintosh version of the
>software and driver. Any help or info is greatly appreciated."
>
>Anyone at Apple, in Mac-related firms, or in medical firms who can supply
>Fogarty with this info should email it to kfogarty@cusa.canon.com.

**************************************************
"Scientists are half B.F. Skinner,
and half P.T. Barnum..."  [Homer Simpson]
**************************************************
Gloria E. Hoffman, Ph.D.
Department of Anatomy and Neurobiology
685 W Baltimore St
Baltimore MD 21201
Phone 410 706-2438
Lab: 410 706-2440
Fax 410 706-2512
email gehoffma@umaryland.edu

------------------------------

Date: Tue, 06 Jul 1999 16:19:35 -0400
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
To: nih-image@io.ece.drexel.edu
Subject: Can I build microscope->CCD  -(FireWire)-> storage -> G3 laptop?
Message-id: <v04205504b3a7dc88917b@[128.244.128.182]>
Content-type: text/plain; format=flowed; charset=us-ascii
Content-transfer-encoding: 7BIT

Here's my dream for a portable scientific-grade image acquisition 
system: use a high quality consumer color video camera / 3-CCD that 
allows use (via a c-mount) with a microscope to acquire a video 
stream that uses FireWire to send a stream of images (30 fps 
preferably) directly to (undoubtedly huge) storage and that could be 
accessed either directly or indirectly (from storage) by a host G3 
laptop. And the camera should be controllable via AppleScript using 
the NIH Image macro language.

How close to reality is this picture? What pieces are missing?  Here 
are some  existing items that may be part of the equation:
#1 cameras  that suppport FireWire (IEEE-1394)
       - many (http://www.digitalorigin.com/products/compat/dvqualifiedcam.html)
#2 consumer digital cameras with microscope (C-mount) adaptors
       - I'm not sure where I heard about these, but somewhere in the 
last few days a site streamed by
#3 adaptors  to connect a FireWire device toa  G3 laptop
       - Newertech FireWire 2Go 
(http://www.newertech.com/products/firewire/index.html)
       - Ratoc (http://www.rexpccard.co.jp/english/products/cbfw2.html)
#4 FireWire hard drives
       - Firepower (http://www.firepower.com/products/FireDrivespecs.html)
#5  NIH Image variants that have varying levels of AppleScript support:
       - Object Image 1.62p2 (http://simon.bio.uva.nl/object-image.html)
       - Image AE (ftp://codon.nih.gov/pub/nih-image/contrib/ImageAEv05.sea.bin)

Can anyone point to a FireWire camera that has uses c-mount (i.e. 
combines #1 and #2)? Best if it has square pixels, too.

Are there contradictions in what I'm trying to define here? I have a 
vague sense that some digital video formats use a pixel aspect ratio 
of 16:9.

How about software to stitch these things together - what else would I need?
Is there software (e.g. framegrabber for analog camera) that is 
missing? Hardware?

Has anyone put together something like this?

Thanks.

Bill Christens-Barry
-------------------------
Bill Christens-Barry, PhD
Johns Hopkins University Applied Physics Laboratory
wacb@aplcomm.jhuapl.edu
-------------------------

--------------------------------
End of nih-image-d Digest V99 Issue #155
****************************************

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Subject: Re: nih-image-d Digest V99 #155
Cc: kfogarty@cusa.canon.com, dsellers@maccentral.com
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>I think if the price is low, it would have appeal in the Mac side. (my lab
>is totally Mac based). I personally like a bit higher resolution, but some
>of my colleagues could benefit from such a device.
...
>>camera that captures 900x1424 images. We have found some success in the PC
>>side but we need some information to justify a Macintosh version of the
>>software and driver. Any help or info is greatly appreciated."

It should be considered that with this resolution with 8-bit monochrome
pixels and with the 12 Mbit/s rate of the USB bus, this camera will top at
about 1 image a second if it can get the bus for itself. This would maybe
be an argument to put it in the low-price regions, which would allow higher
volumes sold. What are the other specs? C-mount adapter? electronic
shutter? Time itegration?

It is not an alternative to video rate recording,  but it could be a good
alternative for the 'digital film' (www.imagek.com) and for 'wet film'
photograpy.

Ard



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To: nih-image@io.ece.drexel.edu
From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: Re: nih-image-d Digest V99 #155
Resent-Message-ID: <"N4SUq.0.731.cCpWt"@io>
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>Can anyone point to a FireWire camera that has uses c-mount (i.e. 
>combines #1 and #2)? Best if it has square pixels, too.

http://bpgprod.sel.sony.com/model.bpg?cat=Cameras+%26+Camcorders&subcat=Industrial&model=DFWVL500

no 3 chip color though.

ard



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To: nih-image@io.ece.drexel.edu
From: Doug Laidlaw <Douglass.Laidlaw@Colorado.EDU>
Subject: T2
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We have been using T2 to assess the extent of muscle activation following
various exercise protocols and, because of the 8-bit conversion of 16-bit
images in NIH Image, have chosen to use Matlab to calculate pixel-by-pixel
T2 values.  With the impressive development of ImageJ, has anyone written a
macro to calculate T1 or T2 relaxation times? Is there a reason not to?

**************************************************************************
Doug Laidlaw
Research Engineer
Neural Control of Movement Laboratory
Dept. Kinesiology and Applied Physiology
Campus Box 354
University of Colorado
Boulder, CO  80309-0354
ph. 303-492-4965
fax. 303-492-6778



From nih-image-request@io.ece.drexel.edu Wed Jul  7 10:23 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: Jeff Hardin <jdhardin@facstaff.wisc.edu>
Subject: NIH Image solution for Hamamatsu Orca 
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Hi folks-

Does anyone know of a NON plug-in solution for acquiring images from a
Hamamatsu Orca camera? I want something that has "faceless" acquisition to
a stack or single image, once suitable parameters have been set. At the
moment, the name of the I/O board we use escapes me. Currently we use the
QED Imaging plug-in, but the plug-in is such that can't operate in a
"faceless" mode.

Thanks!

Jeff

-------------------------------------------------------------
             Jeff Hardin, Associate Professor
       Dept. of Zoology, Univ. of Wisconsin-Madison
           1117 W. Johnson St., Madison, WI 53706
              voice: (608) 262-9634/265-2520
                   fax: (608) 262-7319
            email: jdhardin@facstaff.wisc.edu
           WWW: http://worms.zoology.wisc.edu/
-------------------------------------------------------------



From nih-image-request@io.ece.drexel.edu Wed Jul  7 12:57 EDT 1999
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Resent-Date: Wed, 7 Jul 1999 12:57:44 -0400 (EDT)
From: Johannes Spengler <SpenglerJ@cardiff.ac.uk>
Organization: Cardiff University
To: nih-image@io.ece.drexel.edu
Date: Wed, 7 Jul 1999 17:37:31 GMT0BST
Subject: Particle movement and velocity analysis
Reply-to: SpenglerJ@cardiff.ac.uk
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Dear colleagues,

Does anybody know about a maybe free or shareware or reasonably 
priced PIV processing software?

Our research interest is the behaviour and movement of cells 
and particles in ultrasonic standing waves. We have already got 
consecutive frames with good contrast, so we could work out the data 
manually. Because of the lack of lab monkeys, we are now 
looking for a way to process the velocity vectors out of the images
automatically. At the moment all commercial offers are unfortunately 
much to sophisticated and expensive for us.

Thanks in advance!

Best regards,

Johannes
-------
Cardiff University of Wales
School of Biosciences
PO Box 915

Cardiff CF10 3TL

T: +44-1222-876665
F: +44-1222-874305

http://www.cf.ac.uk/ultrasonics/


From nih-image-d-request@io.ece.drexel.edu Thu Jul  8 06:19 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #156
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 156

Today's Topics:
  Re: nih-image-d Digest V99 #155       [ Ard Jonker <a.jonker@amc.uva.nl> ]
  Re: nih-image-d Digest V99 #155       [ Ard Jonker <a.jonker@amc.uva.nl> ]
  T2                                    [ Doug Laidlaw <Douglass.Laidlaw@Colo ]
  NIH Image solution for Hamamatsu Orc  [ Jeff Hardin <jdhardin@facstaff.wisc ]
  Particle movement and velocity analy  [ Johannes Spengler <SpenglerJ@cardif ]

------------------------------

Date: Wed, 7 Jul 1999 12:40:05 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Cc: kfogarty@cusa.canon.com, dsellers@maccentral.com
Subject: Re: nih-image-d Digest V99 #155
Message-Id: <l03130302b3a8dd475468@[145.117.53.66]>
Content-Type: text/plain; charset="us-ascii"

>I think if the price is low, it would have appeal in the Mac side. (my lab
>is totally Mac based). I personally like a bit higher resolution, but some
>of my colleagues could benefit from such a device.
...
>>camera that captures 900x1424 images. We have found some success in the PC
>>side but we need some information to justify a Macintosh version of the
>>software and driver. Any help or info is greatly appreciated."

It should be considered that with this resolution with 8-bit monochrome
pixels and with the 12 Mbit/s rate of the USB bus, this camera will top at
about 1 image a second if it can get the bus for itself. This would maybe
be an argument to put it in the low-price regions, which would allow higher
volumes sold. What are the other specs? C-mount adapter? electronic
shutter? Time itegration?

It is not an alternative to video rate recording,  but it could be a good
alternative for the 'digital film' (www.imagek.com) and for 'wet film'
photograpy.

Ard

------------------------------

Date: Wed, 7 Jul 1999 12:56:35 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #155
Message-Id: <l03130303b3a8e2ae996a@[145.117.53.66]>
Content-Type: text/plain; charset="us-ascii"

>Can anyone point to a FireWire camera that has uses c-mount (i.e. 
>combines #1 and #2)? Best if it has square pixels, too.

http://bpgprod.sel.sony.com/model.bpg?cat=Cameras+%26+Camcorders&subcat=Industrial&model=DFWVL500

no 3 chip color though.

ard

------------------------------

Date: Wed, 7 Jul 1999 07:16:28 -0600
From: Doug Laidlaw <Douglass.Laidlaw@Colorado.EDU>
To: nih-image@io.ece.drexel.edu
Subject: T2
Message-Id: <v03007800b3a901ded5c7@[128.138.125.236]>
Content-Type: text/plain; charset="us-ascii"

We have been using T2 to assess the extent of muscle activation following
various exercise protocols and, because of the 8-bit conversion of 16-bit
images in NIH Image, have chosen to use Matlab to calculate pixel-by-pixel
T2 values.  With the impressive development of ImageJ, has anyone written a
macro to calculate T1 or T2 relaxation times? Is there a reason not to?

**************************************************************************
Doug Laidlaw
Research Engineer
Neural Control of Movement Laboratory
Dept. Kinesiology and Applied Physiology
Campus Box 354
University of Colorado
Boulder, CO  80309-0354
ph. 303-492-4965
fax. 303-492-6778

------------------------------

Date: Wed, 7 Jul 1999 08:54:34 -0500
From: Jeff Hardin <jdhardin@facstaff.wisc.edu>
To: nih-image@io.ece.drexel.edu
Subject: NIH Image solution for Hamamatsu Orca 
Message-Id: <v03007803b3a90be59155@[144.92.211.61]>
Content-Type: text/plain; charset="us-ascii"

Hi folks-

Does anyone know of a NON plug-in solution for acquiring images from a
Hamamatsu Orca camera? I want something that has "faceless" acquisition to
a stack or single image, once suitable parameters have been set. At the
moment, the name of the I/O board we use escapes me. Currently we use the
QED Imaging plug-in, but the plug-in is such that can't operate in a
"faceless" mode.

Thanks!

Jeff

-------------------------------------------------------------
             Jeff Hardin, Associate Professor
       Dept. of Zoology, Univ. of Wisconsin-Madison
           1117 W. Johnson St., Madison, WI 53706
              voice: (608) 262-9634/265-2520
                   fax: (608) 262-7319
            email: jdhardin@facstaff.wisc.edu
           WWW: http://worms.zoology.wisc.edu/
-------------------------------------------------------------

------------------------------

Date: Wed, 7 Jul 1999 17:37:31 GMT0BST
From: Johannes Spengler <SpenglerJ@cardiff.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Particle movement and velocity analysis
Message-ID: <41121B40B1C@RNCHCF1S.CF.AC.UK>

Dear colleagues,

Does anybody know about a maybe free or shareware or reasonably 
priced PIV processing software?

Our research interest is the behaviour and movement of cells 
and particles in ultrasonic standing waves. We have already got 
consecutive frames with good contrast, so we could work out the data 
manually. Because of the lack of lab monkeys, we are now 
looking for a way to process the velocity vectors out of the images
automatically. At the moment all commercial offers are unfortunately 
much to sophisticated and expensive for us.

Thanks in advance!

Best regards,

Johannes
-------
Cardiff University of Wales
School of Biosciences
PO Box 915

Cardiff CF10 3TL

T: +44-1222-876665
F: +44-1222-874305

http://www.cf.ac.uk/ultrasonics/

--------------------------------
End of nih-image-d Digest V99 Issue #156
****************************************

From nih-image-request@io.ece.drexel.edu Thu Jul  8 11:11 EDT 1999
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Date: Thu, 8 Jul 1999 09:50:38 -0500 (CDT)
From: Ken Johnson <kenjohn@pathbox.wustl.edu>
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To: nih-image@io.ece.drexel.edu
Subject: 24 bit colour merge
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Hi Image Users

Thanks for the help I've been getting.

I am still struggling though do get a good indexed colour image. I have
three channels saved from a Zeiss confocal image. These files open fine as
RGB stack  in Image which then converts this to an 8-bit indexed colour.
I want a 24 bit indexed colour though, which I can do with the RGB to 24
bit command (Thanks Jeff!). This image though is greyscale, so is it
possible to get the colour on this 24 bit image to create a composite?
The LUT options seems to be unavailable when a 24-bit window is open.

Thank again

Ken Johnson. 


From nih-image-d-request@io.ece.drexel.edu Fri Jul  9 06:13 EDT 1999
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Subject: nih-image-d Digest V99 #157
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 157

Today's Topics:
  24 bit colour merge                   [ Ken Johnson <kenjohn@pathbox.wustl. ]

------------------------------

Date: Thu, 8 Jul 1999 09:50:38 -0500 (CDT)
From: Ken Johnson <kenjohn@pathbox.wustl.edu>
To: nih-image@io.ece.drexel.edu
Subject: 24 bit colour merge
Message-ID: <Pine.GSO.3.96.990708094239.21944A-100000@pathbox.wustl.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi Image Users

Thanks for the help I've been getting.

I am still struggling though do get a good indexed colour image. I have
three channels saved from a Zeiss confocal image. These files open fine as
RGB stack  in Image which then converts this to an 8-bit indexed colour.
I want a 24 bit indexed colour though, which I can do with the RGB to 24
bit command (Thanks Jeff!). This image though is greyscale, so is it
possible to get the colour on this 24 bit image to create a composite?
The LUT options seems to be unavailable when a 24-bit window is open.

Thank again

Ken Johnson. 

--------------------------------
End of nih-image-d Digest V99 Issue #157
****************************************

From nih-image-request@io.ece.drexel.edu Fri Jul  9 09:30 EDT 1999
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From: Tom Morton <support@scioncorp.com>
Subject: 24 bit colour merge
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Ken,

If you hace your color depth set to 256 colors then your 24-bit image will
be greyscale.  The program will not try to translate those colors.  So,
make sure that you have color depth set to thousands or millions of colors.
This can be set in the Monitors and Sounds control panel.

Hope that helps.

Tom Morton



>Date: Thu, 8 Jul 1999 09:50:38 -0500 (CDT)
>From: Ken Johnson <kenjohn@pathbox.wustl.edu>
>To: nih-image@io.ece.drexel.edu
>Subject:
>Message-ID: <Pine.GSO.3.96.990708094239.21944A-100000@pathbox.wustl.edu>
>Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>Hi Image Users
>
>Thanks for the help I've been getting.
>
>I am still struggling though do get a good indexed colour image. I have
>three channels saved from a Zeiss confocal image. These files open fine as
>RGB stack  in Image which then converts this to an 8-bit indexed colour.
>I want a 24 bit indexed colour though, which I can do with the RGB to 24
>bit command (Thanks Jeff!). This image though is greyscale, so is it
>possible to get the colour on this 24 bit image to create a composite?
>The LUT options seems to be unavailable when a 24-bit window is open.
>
>Thank again
>
>Ken Johnson.
>
>--------------------------------



-----------------------------------------------------------------------
Tom Morton                                     support@scioncorp.com
Technical Services                             http://www.scioncorp.com
Scion Corporation                              ftp://scioncorp.com
82 Wormans Mill Rd., Suite H                   Phone: (301) 695-7870
Frederick, MD 21701                            Fax:   (301) 695-0035
-----------------------------------------------------------------------



From nih-image-d-request@io.ece.drexel.edu Sat Jul 10 06:12 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #158
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 158

Today's Topics:
  24 bit colour merge                   [ Tom Morton <support@scioncorp.com> ]

------------------------------

Date: Fri, 9 Jul 1999 08:47:59 -0400
From: Tom Morton <support@scioncorp.com>
To: nih-image@io.ece.drexel.edu
Subject: 24 bit colour merge
Message-Id: <l03130300b3ab9f7c63fd@[10.0.0.239]>
Content-Type: text/plain; charset="us-ascii"

Ken,

If you hace your color depth set to 256 colors then your 24-bit image will
be greyscale.  The program will not try to translate those colors.  So,
make sure that you have color depth set to thousands or millions of colors.
This can be set in the Monitors and Sounds control panel.

Hope that helps.

Tom Morton



>Date: Thu, 8 Jul 1999 09:50:38 -0500 (CDT)
>From: Ken Johnson <kenjohn@pathbox.wustl.edu>
>To: nih-image@io.ece.drexel.edu
>Subject:
>Message-ID: <Pine.GSO.3.96.990708094239.21944A-100000@pathbox.wustl.edu>
>Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>Hi Image Users
>
>Thanks for the help I've been getting.
>
>I am still struggling though do get a good indexed colour image. I have
>three channels saved from a Zeiss confocal image. These files open fine as
>RGB stack  in Image which then converts this to an 8-bit indexed colour.
>I want a 24 bit indexed colour though, which I can do with the RGB to 24
>bit command (Thanks Jeff!). This image though is greyscale, so is it
>possible to get the colour on this 24 bit image to create a composite?
>The LUT options seems to be unavailable when a 24-bit window is open.
>
>Thank again
>
>Ken Johnson.
>
>--------------------------------



-----------------------------------------------------------------------
Tom Morton                                     support@scioncorp.com
Technical Services                             http://www.scioncorp.com
Scion Corporation                              ftp://scioncorp.com
82 Wormans Mill Rd., Suite H                   Phone: (301) 695-7870
Frederick, MD 21701                            Fax:   (301) 695-0035
-----------------------------------------------------------------------

--------------------------------
End of nih-image-d Digest V99 Issue #158
****************************************

From nih-image-request@io.ece.drexel.edu Sun Jul 11 01:15 EDT 1999
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Date: Sun, 11 Jul 1999 20:01:32 +0200
To: nih-image@io.ece.drexel.edu
From: szeev@bgumail.bgu.ac.il (ze'ev silverman)
Subject: Scion LG-3 for sale
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I have a Scion LG-3 digitizing card to sell for anyone interested. It can
be shipped out in 24 hours....  Ze'ev Silverman

Ze'ev Silverman, Ph.D.
Zlotowski Center for Neuroscience
Faculty of Health Sciences
Ben-Gurion University of the Negev
Beer Sheva 84 103 Israel

Phone: (7) 647-7307/4 (lab)
Fax: (7) 647-7627
e-mail: szeev@bgumail.bgu.ac.il
http://medic.bgu.ac.il/homes/zeev/Zeev.html



From nih-image-d-request@io.ece.drexel.edu Mon Jul 12 01:30 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #159
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 159

Today's Topics:
  Scion LG-3 for sale                   [ szeev@bgumail.bgu.ac.il (ze'ev silv ]
  Re: Scion LG-3 for sale               [ Henrik Kaker <Henrik.Kaker@guest.ar ]

------------------------------

Date: Sun, 11 Jul 1999 20:01:32 +0200
From: szeev@bgumail.bgu.ac.il (ze'ev silverman)
To: nih-image@io.ece.drexel.edu
Subject: Scion LG-3 for sale
Message-Id: <v01540b01b3ae8bd343ca@[132.72.75.14]>
Content-Type: text/plain; charset="us-ascii"

I have a Scion LG-3 digitizing card to sell for anyone interested. It can
be shipped out in 24 hours....  Ze'ev Silverman

Ze'ev Silverman, Ph.D.
Zlotowski Center for Neuroscience
Faculty of Health Sciences
Ben-Gurion University of the Negev
Beer Sheva 84 103 Israel

Phone: (7) 647-7307/4 (lab)
Fax: (7) 647-7627
e-mail: szeev@bgumail.bgu.ac.il
http://medic.bgu.ac.il/homes/zeev/Zeev.html

------------------------------

Date: Mon, 12 Jul 1999 06:24:03 +0200
From: Henrik Kaker <Henrik.Kaker@guest.arnes.si>
To: nih-image@io.ece.drexel.edu
Subject: Re: Scion LG-3 for sale
Message-ID: <37896DE2.92C18501@guest.arnes.si>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Ze'ev Silverman, Ph.D.,

What is the price for this card.

Henrik

ze'ev silverman wrote:

> I have a Scion LG-3 digitizing card to sell for anyone interested. It can
> be shipped out in 24 hours....  Ze'ev Silverman
>
> Ze'ev Silverman, Ph.D.
> Zlotowski Center for Neuroscience
> Faculty of Health Sciences
> Ben-Gurion University of the Negev
> Beer Sheva 84 103 Israel
>
> Phone: (7) 647-7307/4 (lab)
> Fax: (7) 647-7627
> e-mail: szeev@bgumail.bgu.ac.il
> http://medic.bgu.ac.il/homes/zeev/Zeev.html

--
Henrik Kaker, Ph.D.
SEM-EDS Laboratory
Metal Ravne, Koroska cesta 14
Ravne, Slovenia, Phone: +386 602 21 131
Fax: +386 602 20 436
Mailto:Henrik.Kaker@guest.arnes.si
http://www2.arnes.si/guest/sgszmera1/index.html

--------------------------------
End of nih-image-d Digest V99 Issue #159
****************************************

From nih-image-request@io.ece.drexel.edu Mon Jul 12 01:34 EDT 1999
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Ze'ev Silverman, Ph.D.,

What is the price for this card.

Henrik

ze'ev silverman wrote:

> I have a Scion LG-3 digitizing card to sell for anyone interested. It can
> be shipped out in 24 hours....  Ze'ev Silverman
>
> Ze'ev Silverman, Ph.D.
> Zlotowski Center for Neuroscience
> Faculty of Health Sciences
> Ben-Gurion University of the Negev
> Beer Sheva 84 103 Israel
>
> Phone: (7) 647-7307/4 (lab)
> Fax: (7) 647-7627
> e-mail: szeev@bgumail.bgu.ac.il
> http://medic.bgu.ac.il/homes/zeev/Zeev.html

--
Henrik Kaker, Ph.D.
SEM-EDS Laboratory
Metal Ravne, Koroska cesta 14
Ravne, Slovenia, Phone: +386 602 21 131
Fax: +386 602 20 436
Mailto:Henrik.Kaker@guest.arnes.si
http://www2.arnes.si/guest/sgszmera1/index.html



From nih-image-request@io.ece.drexel.edu Mon Jul 12 11:48 EDT 1999
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Date: Mon, 12 Jul 1999 10:22:32 -0500
From: Lian Loo <lianloo@utmmg.med.uth.tmc.edu>
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I am a dermatologist from the University of Texas Medical School at
Houston.  We have a set of black and white photos from patients which
were taken using a Neutral density and UV filter.  Is there a way to
analyze the histogram to determine the two grayscale values where 50% of
the pixels are distributed?

--
Lian Loo, D.V.M.
University of Texas Medical School
Department of Dermatology
6431 Fannin St., MSB 1.008
Houston, TX  77030
----------------------------------
voice: (713)500-7156
fax:   (713)500-7168



From nih-image-request@io.ece.drexel.edu Mon Jul 12 11:56 EDT 1999
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From: "Bogdan Smolka" <BSmolka@peach.ia.polsl.gliwice.pl>
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Subject: Odp: Scion Image
Date: Mon, 12 Jul 1999 17:45:09 +0200
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Hi,
this is a very simple task.
What is the purpose of your research?
Do you want to binarize the images ?

Regards

Bogdan Smolka

-----Wiadomo oryginalna-----
Od: Lian Loo <lianloo@utmmg.med.uth.tmc.edu>
Do: nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
Data: 12 lipca 1999 19:41
Temat: Scion Image


>I am a dermatologist from the University of Texas Medical School at
>Houston.  We have a set of black and white photos from patients which
>were taken using a Neutral density and UV filter.  Is there a way to
>analyze the histogram to determine the two grayscale values where 50% of
>the pixels are distributed?
>
>--
>Lian Loo, D.V.M.
>University of Texas Medical School
>Department of Dermatology
>6431 Fannin St., MSB 1.008
>Houston, TX  77030
>----------------------------------
>voice: (713)500-7156
>fax:   (713)500-7168
>
>


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From: zhengjian li <zli4@umbc.edu>
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Subject: marco
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Hi, imagers

I attached an image I intend to analyze. I would like to count the
areas of bright part and dark part respectively with a macro. Any comment
will be appreciated.

Thank you very much!

Zhengjian Li




From nih-image-request@io.ece.drexel.edu Mon Jul 12 15:46 EDT 1999
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From: pro@umich.edu (Pravin Patil)
Subject: Color Image Processing
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Hey All!

        I want to quantify the amount of blue (% of pixels or something) in
an indexed color image.  Actually, the entire image is grey except for
some blue spots.   I have tried looking at the separate RGB channels that
NIH used to generate the indexed color image and threshold the sepearate
channels but none of them show any promise in resolving the grey/black and
the blue.

thanks for all of your help in advance as this is probably a simple
procedure for an experienced imager!


............................................................................
.............
Pravin V. Patil
E-mail: pro@umich.edu
University of Michigan
Research Associate
Orthopaedic Research Laboratories
Phone:  (313) 763-9674
Fax:  (313) 647-0003
............................................................................
.............



From nih-image-request@io.ece.drexel.edu Mon Jul 12 19:05 EDT 1999
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Subject: Re: Color Image Processing
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Pravin,

The gray-appearing pixels in your indexed color image will have a balance
in the RGB images, whereas the blue-appearing pixels will have more blue
(i.e., higher numbers in the blue image than the others).  There are
several ways to isolate the blue objects.  Sometimes you can simply
subtract (or divide) the red from the blue image, or you can average the
red and green and subtract/divide the resulting image from the blue.  The
resulting image can be thresholded and you can analyze particles to get the
necessary information (e.g., percentage of image, areas, positions, etc.).
If this doesn't help, get back to me offline and I will get into more
detail.

Chris

>Hey All!
>
>        I want to quantify the amount of blue (% of pixels or something) in
>an indexed color image.  Actually, the entire image is grey except for
>some blue spots.   I have tried looking at the separate RGB channels that
>NIH used to generate the indexed color image and threshold the sepearate
>channels but none of them show any promise in resolving the grey/black and
>the blue.

* * * * * * * * * * * * * * * * * *
* Dr. Christopher Hunt Coulon     *
* The GAIA Group                  *
* 40 Chick Road                   *
* Wolfeboro, New Hampshire 03894  *
* 603 569-0028                    *
* * * * * * * * * * * * * * * * * *



From nih-image-request@io.ece.drexel.edu Mon Jul 12 19:48 EDT 1999
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Date: Mon, 12 Jul 1999 16:37:26 -0700
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Pravin V. Patil asked
" I want to quantify the amount of blue (% of pixels or something) in
an indexed color image.  "

Response
I have been doing this for quite a while using indexed color photomicrographic
images. In these photomicrographs, the area of interest is red. I acquired a few
representative images, magnified them and took note of the specific color index
numbers of the red areas of interest. (Do this by moving a crosshair around the
color of interest and read out the number in the info box in the corner. Once
you know the colors you are interested in write a macro that converts all the
various shades of blue to color 35. I picked 35 because it is so easy to see.
Then set density slice at 35 and then measure.
.
------------
This is an example macro. If you want to use this macro, of course, you will
have to change it to pick blue not red...

{this first part initializes the various parts of the program}

macro 'setup for aec image analysis [s]';
{sets a number of the variables that need to be set for the image analysis to
work properly}
begin
setoptions('area');
setpalette('system palette');
setvideo('8-bit color','full','ntsc');
startcapturing;
setscale(27.713,'%',1);
end;

{This macro actually does the measuring}
macro 'AEC Stain %Area [0]';
begin
capture;
{this part sets the scale...totally dependant on your setup}
setscale(27.713,'%',1);

{changes all the reds in the image to color 35}
changevalues(16,19,35);
changevalues(22,34,35);
changevalues(54,54,35);
changevalues(59,71,35);
changevalues(94,106,35);
changevalues(130,130,35);
changevalues(136,136,35);
changevalues(141,143,35);
changevalues(172,173,35);
changevalues(179,179,35);
changevalues(216,221,35);

{this does the measuring}
  SetDensitySlice(35,35);
wait(.1);
measure;
disposeall;
startcapturing;
end;





--
Paul C. Grimm
Associate Professor
Pediatric Nephrology
University of California at San Diego

Email pgrimm@ucsd.edu
Phone 619-543-5218
Fax   619-543-3575
Snail mail
UCSD Pediatrics
Mail Stop 0831
9500 Gilman Drive,
La Jolla California
92093-0831

"Growing old is mandatory. Growing wise is optional."



From nih-image-request@io.ece.drexel.edu Tue Jul 13 04:51 EDT 1999
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Subject: Digital Video input (firewire): how?
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Dear List members,

Today there was an opportunity to record some date via Firewire from a
digital video recorder. Saving with EditDV demo and using a grayscale LUT
in (object) Image allows the opening of successive frames of the movie in
monochrome. This looks quite good, but I'd rather capture one single color
image (three frames in a stack) directly by a plugin.
Does NIH support this somehow? I haven't found a way yet...

Ard



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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #160
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 160

Today's Topics:
  Scion Image                           [ Lian Loo <lianloo@utmmg.med.uth.tmc ]
  Odp: Scion Image                      [ "Bogdan Smolka" <BSmolka@peach.ia.p ]
  marco                                 [ zhengjian li <zli4@umbc.edu> ]
  Color Image Processing                [ pro@umich.edu (Pravin Patil) ]
  Re: Color Image Processing            [ ad1054@worldpath.net (Dr. Christoph ]
  color image processing                [ Paul Grimm <pgrimm@ucsd.edu> ]
  Digital Video input (firewire): how?  [ Ard Jonker <a.jonker@amc.uva.nl> ]

------------------------------

Date: Mon, 12 Jul 1999 10:22:32 -0500
From: Lian Loo <lianloo@utmmg.med.uth.tmc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Scion Image
Message-ID: <378A0838.BB6F1DC7@utmmg.med.uth.tmc.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

I am a dermatologist from the University of Texas Medical School at
Houston.  We have a set of black and white photos from patients which
were taken using a Neutral density and UV filter.  Is there a way to
analyze the histogram to determine the two grayscale values where 50% of
the pixels are distributed?

--
Lian Loo, D.V.M.
University of Texas Medical School
Department of Dermatology
6431 Fannin St., MSB 1.008
Houston, TX  77030
----------------------------------
voice: (713)500-7156
fax:   (713)500-7168

------------------------------

Date: Mon, 12 Jul 1999 17:45:09 +0200
From: "Bogdan Smolka" <BSmolka@peach.ia.polsl.gliwice.pl>
To: <nih-image@io.ece.drexel.edu>
Subject: Odp: Scion Image
Message-ID: <003401becc7d$85beb9c0$1e0e9e9d@ZTSBSpc.ia.polsl.gliwice.pl>
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Hi,
this is a very simple task.
What is the purpose of your research?
Do you want to binarize the images ?

Regards

Bogdan Smolka

-----Wiadomo oryginalna-----
Od: Lian Loo <lianloo@utmmg.med.uth.tmc.edu>
Do: nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
Data: 12 lipca 1999 19:41
Temat: Scion Image


>I am a dermatologist from the University of Texas Medical School at
>Houston.  We have a set of black and white photos from patients which
>were taken using a Neutral density and UV filter.  Is there a way to
>analyze the histogram to determine the two grayscale values where 50% of
>the pixels are distributed?
>
>--
>Lian Loo, D.V.M.
>University of Texas Medical School
>Department of Dermatology
>6431 Fannin St., MSB 1.008
>Houston, TX  77030
>----------------------------------
>voice: (713)500-7156
>fax:   (713)500-7168
>
>

------------------------------

Date: Mon, 12 Jul 1999 13:31:17 -0400 (EDT)
From: zhengjian li <zli4@umbc.edu>
To: nih-image@io.ece.drexel.edu
Subject: marco
Message-ID: <Pine.SGI.3.96A.990712132532.3679157A-100001@umbc7.umbc.edu>
Content-Type: MULTIPART/MIXED; BOUNDARY="-2108357113-1837801624-931800677=:3679157"

  This message is in MIME format.  The first part should be readable text,
  while the remaining parts are likely unreadable without MIME-aware tools.
  Send mail to mime@docserver.cac.washington.edu for more info.

---2108357113-1837801624-931800677=:3679157
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi, imagers

I attached an image I intend to analyze. I would like to count the
areas of bright part and dark part respectively with a macro. Any comment
will be appreciated.

Thank you very much!

Zhengjian Li



------------------------------

Date: Mon, 12 Jul 1999 15:29:48 -0500
From: pro@umich.edu (Pravin Patil)
To: nih-image@io.ece.drexel.edu
Subject: Color Image Processing
Message-Id: <v02140b03b3affdf78fc6@[141.214.180.247]>
Content-Type: text/plain; charset="us-ascii"

Hey All!

        I want to quantify the amount of blue (% of pixels or something) in
an indexed color image.  Actually, the entire image is grey except for
some blue spots.   I have tried looking at the separate RGB channels that
NIH used to generate the indexed color image and threshold the sepearate
channels but none of them show any promise in resolving the grey/black and
the blue.

thanks for all of your help in advance as this is probably a simple
procedure for an experienced imager!


............................................................................
.............
Pravin V. Patil
E-mail: pro@umich.edu
University of Michigan
Research Associate
Orthopaedic Research Laboratories
Phone:  (313) 763-9674
Fax:  (313) 647-0003
............................................................................
.............

------------------------------

Date: Mon, 12 Jul 1999 18:50:51 -0400
From: ad1054@worldpath.net (Dr. Christopher Coulon)
To: nih-image@io.ece.drexel.edu
Subject: Re: Color Image Processing
Message-Id: <v01520d00b3b0217cd9df@[208.133.217.111]>
Content-Type: text/plain; charset="us-ascii"

Pravin,

The gray-appearing pixels in your indexed color image will have a balance
in the RGB images, whereas the blue-appearing pixels will have more blue
(i.e., higher numbers in the blue image than the others).  There are
several ways to isolate the blue objects.  Sometimes you can simply
subtract (or divide) the red from the blue image, or you can average the
red and green and subtract/divide the resulting image from the blue.  The
resulting image can be thresholded and you can analyze particles to get the
necessary information (e.g., percentage of image, areas, positions, etc.).
If this doesn't help, get back to me offline and I will get into more
detail.

Chris

>Hey All!
>
>        I want to quantify the amount of blue (% of pixels or something) in
>an indexed color image.  Actually, the entire image is grey except for
>some blue spots.   I have tried looking at the separate RGB channels that
>NIH used to generate the indexed color image and threshold the sepearate
>channels but none of them show any promise in resolving the grey/black and
>the blue.

* * * * * * * * * * * * * * * * * *
* Dr. Christopher Hunt Coulon     *
* The GAIA Group                  *
* 40 Chick Road                   *
* Wolfeboro, New Hampshire 03894  *
* 603 569-0028                    *
* * * * * * * * * * * * * * * * * *

------------------------------

Date: Mon, 12 Jul 1999 16:37:26 -0700
From: Paul Grimm <pgrimm@ucsd.edu>
To: NIH-image list <nih-image@io.ece.drexel.edu>
Subject: color image processing
Message-ID: <378A7C31.7AABB917@ucsd.edu>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Pravin V. Patil asked
" I want to quantify the amount of blue (% of pixels or something) in
an indexed color image.  "

Response
I have been doing this for quite a while using indexed color photomicrographic
images. In these photomicrographs, the area of interest is red. I acquired a few
representative images, magnified them and took note of the specific color index
numbers of the red areas of interest. (Do this by moving a crosshair around the
color of interest and read out the number in the info box in the corner. Once
you know the colors you are interested in write a macro that converts all the
various shades of blue to color 35. I picked 35 because it is so easy to see.
Then set density slice at 35 and then measure.
 .------------
This is an example macro. If you want to use this macro, of course, you will
have to change it to pick blue not red...

{this first part initializes the various parts of the program}

macro 'setup for aec image analysis [s]';
{sets a number of the variables that need to be set for the image analysis to
work properly}
begin
setoptions('area');
setpalette('system palette');
setvideo('8-bit color','full','ntsc');
startcapturing;
setscale(27.713,'%',1);
end;

{This macro actually does the measuring}
macro 'AEC Stain %Area [0]';
begin
capture;
{this part sets the scale...totally dependant on your setup}
setscale(27.713,'%',1);

{changes all the reds in the image to color 35}
changevalues(16,19,35);
changevalues(22,34,35);
changevalues(54,54,35);
changevalues(59,71,35);
changevalues(94,106,35);
changevalues(130,130,35);
changevalues(136,136,35);
changevalues(141,143,35);
changevalues(172,173,35);
changevalues(179,179,35);
changevalues(216,221,35);

{this does the measuring}
  SetDensitySlice(35,35);
wait(.1);
measure;
disposeall;
startcapturing;
end;





--
Paul C. Grimm
Associate Professor
Pediatric Nephrology
University of California at San Diego

Email pgrimm@ucsd.edu
Phone 619-543-5218
Fax   619-543-3575
Snail mail
UCSD Pediatrics
Mail Stop 0831
9500 Gilman Drive,
La Jolla California
92093-0831

"Growing old is mandatory. Growing wise is optional."

------------------------------

Date: Tue, 13 Jul 1999 10:30:02 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Digital Video input (firewire): how?
Message-Id: <l03130300b3b0a80ffc7a@[145.117.53.66]>
Content-Type: text/plain; charset="us-ascii"

Dear List members,

Today there was an opportunity to record some date via Firewire from a
digital video recorder. Saving with EditDV demo and using a grayscale LUT
in (object) Image allows the opening of successive frames of the movie in
monochrome. This looks quite good, but I'd rather capture one single color
image (three frames in a stack) directly by a plugin.
Does NIH support this somehow? I haven't found a way yet...

Ard

--------------------------------
End of nih-image-d Digest V99 Issue #160
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Archive
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Every submission sent to this list is archived.	 Following are the commands
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Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
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then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
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8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
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then use get to get the files you want.
This archive server knows the following commands:

get filename ...
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Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
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--


From nih-image-request@io.ece.drexel.edu Tue Jul 13 05:25 EDT 1999
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Date: Tue, 13 Jul 1999 11:09:49 +0000
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Dear imagers,
I am collecting optical slices at a series of focal depths through a 
small object in order to obtain a three-D coordinate reconstruction 
of the surface from light microscopic images. 

The idea is to find the regions of highest sharpness in a given slice,
outline it, calculate the x,y coordinates, and assign them to a 
z-value that can be obtained from the z-control of the microscope 
stage.
If repeating these operations at a series of focal heights a 3-D 
coordinate representation of the surface can (theoretically) be 
obtained.

The problem is to define the regions of highest sharpness in the 
images at each z-level. I try to do this with gradient operators (for 
example a sobel operator). Sharp regions appear specled areas, where 
the average grey value is higher than in an areas that are out of 
focus (eventually one should use the second derivative of the image 
??).

Questions:
Is this the right procedure for extracting regions of high focus ?
Is there any other procedure to characterize regions of highest 
sharpness in an image ? 
Is there eventually already a macro available in Nih-image for 3-D 
coordinate extraction by a similar microscopic focal slicing method 
through small objects ?

Any comment on this or similar techniques are greatly acknowledged.
Sincerely, Michael.

-- 
Dr. M. Knappertsbusch
Natural History Museum
Augustinergasse 2
4001-Basel, Switzerland

Tel. +41-61-266 55 64
Fax. +41-61-266 55 46
Email: Knappertsbus@ubaclu.unibas.ch


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Subject: sorry
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  This message is in MIME format.  The first part should be readable text,
  while the remaining parts are likely unreadable without MIME-aware tools.
  Send mail to mime@docserver.cac.washington.edu for more info.

---2108357113-1837801624-931800677=:3679157
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Hi, 

I just realized that sending out an image by attachment to a mailing list 
is totally inappropriate. I am very sorry for any inconveniences due to my
being ignorant.

Zhengjian Li 


---2108357113-1837801624-931800677=:3679157--


From nih-image-request@io.ece.drexel.edu Tue Jul 13 11:20 EDT 1999
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From: "Keshen Mathura" <keshen.mathura@student.uva.nl>
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Hello everyone,

I would like to archive my images on a CD-ROM, but I am
wondering if it is possible to put the images in somekind of
database which I can burn onto CD-ROM. I want to include
time, date, experiment and patient information with the
picture and I want to be able to look it up later so I can
find what I need fast.

Thanks in advance!

Regards,

Keshen


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Subject: text files to graphics?
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I thought I had done this a few years ago, but now I cannot remember how.  

We have a text file with three columns of real numbers corresponding to X,
Y and Z. 
We want to write a simple macro to import these columns, convert to integer
and to plot the numbers into a stack.

The last two steps are simple.  But we would love suggestions for getting
the text into the graphics.

Thanks.
********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
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Date: Tue, 13 Jul 1999 15:10:04 -0400 (EDT)
From: Keng-hui Lin <khlin@student.physics.upenn.edu>
To: nih-image@io.ece.drexel.edu
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Hi, all,
     In our lab we have been using NIH image to digitize vedio
tape. A postdoc in our lab wrote a Macro to do vedio control
through the serial port from NIH image.  Everything runs 
well on the Power Mac. Recently I got a G3 Mac and I tried 
to set up everything to run like the old Mac.  
However, I had problems with doing
vedio control from NIH image.  I was wondering whether
NIH image can talk to USB port as talk to seriel port.
Mr. Wayne Rasband told me some of the converters should work.
If people have similar problems and got it solved, please
let me know how you do it. I will really appreciate your
help.
    Thanks. 

     Keng-hui Lin
http://www.physics.upenn.edu/~khlin
Dept.  of Physics and Astronomy, 
University of Pennsylvania
209 S., 33rd Street, Philadelphia, PA 19104
Office: (215)898-5148 [Office]
Home:(215)988-0107






From nih-image-request@io.ece.drexel.edu Tue Jul 13 16:17 EDT 1999
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Date: Tue, 13 Jul 1999 16:10:47 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: text files to graphics?
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>I thought I had done this a few years ago, but now I cannot remember how.
>
>We have a text file with three columns of real numbers corresponding to X,
>Y and Z.
>We want to write a simple macro to import these columns, convert to integer
>and to plot the numbers into a stack.
>
>The last two steps are simple.  But we would love suggestions for getting
>the text into the graphics.

The  "Plot XYZ" macro in the "Plotting Macros" macro file may be what you
used before. It plots XY coordinate points with an optional intensity (Z)
on a single image. Values are read from a 2 or 3 column tab-delimited text
file. The data must be scaled as follows: 0<=X<width; 0<=Y<height;
0<=Z<=255, where width and height are the dimensions of the image.

-wayne



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From: hard@acsu.buffalo.edu
Date: Tue, 13 Jul 1999 16:19:25 -0500
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Subject: Course Announcement 2
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Course Announcement

Title: Optical Microscopy and Imaging in the Biomedical Sciences

When: October 6 - October 14, 1999

Where: Marine Biology Laboratory, Woods Hole, MA, USA

Tuition: $2050 (Includes room and board, text, handouts, supplies)

Application Deadline: August 3, 1999

Admission application and information:
     Carol Hamel, Admissions Coordinator
     Marine Biological Laboratory
     7 MBL Street
     Woods Hole, MA 02543-1015
     (508) 289-7401
     Internet: admissions@mbl.edu
     WWW: http://www.mbl.edu (Application forms available via Adobe Acrobat)

Course Director: Colin S. Izzard, State University of New York @ Albany
                 Phone: [518] 442 - 4367
                 EMail: csizzard@csc.albany.edu

Course Description:

For Whom:
      Designed primarily for research scientists, physicians, postdoctoral 
trainees and advanced graduate students in animal, plant, medical and 
material sciences. Non-biologists seeking a comprehensive introduction to 
microscopy and video-imaging will benefit greatly from this course as well. 
There are no specific prerequisites, but an understanding of the basic 
principles of optics is desirable. Limited to 24 students.

  The eight day course consists of lectures, laboratory demonstrations, 
exercises and discussions that will enable the participant to obtain and 
interpret microscope images of high quality, to perform quantitative optical
measurements, and to produce photographic and video records for
documentation 
and analysis.

Topics to be covered include:
      principles of microscope design and image formation
      bright field, dark field, phase contrast, polarized light,
differential
         interference contrast, interference reflection, and fluorescence
         microscopy
      confocal scanning microscopy, multiphoton excitation fluorescence
         microscopy and image deconvolution
      digital image restoration and 3-D reconstruction
      video imaging, recording, enhancement, and intensification
      analog and digital image processing and analysis
      fluorescent probes and ratiometric-imaging
      laser tweezers and laser scissors

  Applications to live cells will be emphasized; other specimens will be 
covered as well.

  Students will have direct hands-on experience with state-of-the-art 
microscopes, video cameras, recorders and image processing equipment
provided by major optical and electronics companies. Instruction will be
provided by experienced staff from universities and industry.

  Students are encouraged to bring their own biological (primary 
cultures, cell lines, etc.) and material specimens and to discuss individual
research problems with the faculty.


From nih-image-request@io.ece.drexel.edu Tue Jul 13 18:09 EDT 1999
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	for cshtest@io.ece.drexel.edu; Tue, 13 Jul 1999 18:09:14 -0400 (EDT)
Resent-Date: Tue, 13 Jul 1999 18:09:14 -0400 (EDT)
Date: Tue, 13 Jul 1999 14:06:50 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH and G3 USB port 
Message-ID: <1062269.3140863610@huginn.medicine.washington.edu>
In-Reply-To: <Pine.A32.3.93.990713150850.44696I-100000@student.physics.upenn.edu>
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I did this for my research as well. I used a USB-serial adapter from
Keyspan, but had to modify Image to work. The problem is that the macro
writes to the "modem" port, while the keyspan software only converts the
printer port automatically. I had to recompile NIH Image with the macro
output directed to the "printer" port. I also had trouble with the software
that came with the keyspan, and had to download an newer version, which
worked fine.

DTL

--On Tue, Jul 13, 1999 3:10 PM -0400 Keng-hui Lin
<khlin@student.physics.upenn.edu> wrote:

> Hi, all,
>      In our lab we have been using NIH image to digitize vedio
> tape. A postdoc in our lab wrote a Macro to do vedio control
> through the serial port from NIH image.  Everything runs 
> well on the Power Mac. Recently I got a G3 Mac and I tried 
> to set up everything to run like the old Mac.  
> However, I had problems with doing
> vedio control from NIH image.  I was wondering whether
> NIH image can talk to USB port as talk to seriel port.
> Mr. Wayne Rasband told me some of the converters should work.
> If people have similar problems and got it solved, please
> let me know how you do it. I will really appreciate your
> help.
>     Thanks. 
> 
>      Keng-hui Lin
> http://www.physics.upenn.edu/~khlin
> Dept.  of Physics and Astronomy, 
> University of Pennsylvania
> 209 S., 33rd Street, Philadelphia, PA 19104
> Office: (215)898-5148 [Office]
> Home:(215)988-0107
> 
> 
> 
> 
> 





From nih-image-request@io.ece.drexel.edu Tue Jul 13 19:20 EDT 1999
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unsubscribe

_________________________________________________________________________
Megan Lim-Fraser
Metabolism Program
Garvan Institute of Medical Research
384 Victoria St                                  Tel:  (02) 9295 8224
Darlinghurst NSW 2010                            Fax:  (02) 9295 8201
Australia                      email: m.lim-fraser@garvan.unsw.edu.au
_________________________________________________________________________



From nih-image-d-request@io.ece.drexel.edu Wed Jul 14 06:16 EDT 1999
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	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA17526;
	Wed, 14 Jul 1999 06:16:14 -0400 (EDT)
Date: Wed, 14 Jul 1999 06:16:14 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199907141016.GAA17526@io.ece.drexel.edu>
Subject: nih-image-d Digest V99 #161
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 161

Today's Topics:
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
  3-D coordinates from focal slices ?   [ Knappertsbusch <Knappertsbus@ubaclu ]
  sorry                                 [ zhengjian li <zli4@umbc.edu> ]
  Image Archive                         [ "Keshen Mathura" <keshen.mathura@st ]
  text files to graphics?               [ Michael Cammer <cammer@aecom.yu.edu ]
  NIH and G3 USB port                   [ Keng-hui Lin <khlin@student.physics ]
  Re: text files to graphics?           [ Wayne Rasband <wayne@codon.nih.gov> ]
  Course Announcement 2                 [ hard@acsu.buffalo.edu ]
  Re: NIH and G3 USB port               [ David Linker <dtlinker@u.washington ]
  Unidentified subject!                 [ m.lim-fraser@garvan.unsw.edu.au (Me ]

------------------------------

Date: Tue, 13 Jul 1999 05:05:01 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199907130905.FAA20924@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
                   ---------------------------
     


nih-image-d-request@biomed.drexel.edu  - Aministration for Digest
nih-image-request@biomed.drexel.edu   - Administation for List


     *********************************************************
     *    DO NOT SEND ADMINISTRATIVE COMMANDS TO THE LIST    *
     *********************************************************
nih-image@biomed.drexel.edu   - Sends mail to everyone on the list 


Subscribe
---------
To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu.
The Subject of the message should contain "Subscribe".

As in:		To: nih-image-request@biomed.drexel.edu
		Subject: subscribe


Subscribe to Digest
-------------------
To subscribe to a digested version of the list, send E-mail to 
nih-image-d-request@biomed.drexel.edu.

The Subject of the message should contain "Subscribe".

As in:		To: nih-image-d-request@biomed.drexel.edu
		Subject: subscribe


Unsubscribe
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Unsubscribe to Digest
--------------------
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The Subject of the message should contain "unsubscribe".

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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

------------------------------

Date: Tue, 13 Jul 1999 11:09:49 +0000
From: Knappertsbusch <Knappertsbus@ubaclu.unibas.ch>
To: nih-image@io.ece.drexel.edu
Subject: 3-D coordinates from focal slices ?
Message-ID: <378B1E7D.7480@ubaclu.unibas.ch>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Dear imagers,
I am collecting optical slices at a series of focal depths through a 
small object in order to obtain a three-D coordinate reconstruction 
of the surface from light microscopic images. 

The idea is to find the regions of highest sharpness in a given slice,
outline it, calculate the x,y coordinates, and assign them to a 
z-value that can be obtained from the z-control of the microscope 
stage.
If repeating these operations at a series of focal heights a 3-D 
coordinate representation of the surface can (theoretically) be 
obtained.

The problem is to define the regions of highest sharpness in the 
images at each z-level. I try to do this with gradient operators (for 
example a sobel operator). Sharp regions appear specled areas, where 
the average grey value is higher than in an areas that are out of 
focus (eventually one should use the second derivative of the image 
??).

Questions:
Is this the right procedure for extracting regions of high focus ?
Is there any other procedure to characterize regions of highest 
sharpness in an image ? 
Is there eventually already a macro available in Nih-image for 3-D 
coordinate extraction by a similar microscopic focal slicing method 
through small objects ?

Any comment on this or similar techniques are greatly acknowledged.
Sincerely, Michael.

-- 
Dr. M. Knappertsbusch
Natural History Museum
Augustinergasse 2
4001-Basel, Switzerland

Tel. +41-61-266 55 64
Fax. +41-61-266 55 46
Email: Knappertsbus@ubaclu.unibas.ch

------------------------------

Date: Tue, 13 Jul 1999 10:02:06 -0400 (EDT)
From: zhengjian li <zli4@umbc.edu>
To: nih-image@io.ece.drexel.edu
Subject: sorry
Message-ID: <Pine.SGI.3.96A.990713095735.4237987B-100000@umbc7.umbc.edu>
Content-Type: MULTIPART/MIXED; BOUNDARY="-2108357113-1837801624-931800677=:3679157"
Content-ID: <Pine.SGI.3.96A.990713095735.4237987C@umbc7.umbc.edu>

  This message is in MIME format.  The first part should be readable text,
  while the remaining parts are likely unreadable without MIME-aware tools.
  Send mail to mime@docserver.cac.washington.edu for more info.

---2108357113-1837801624-931800677=:3679157
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII
Content-ID: <Pine.SGI.3.96A.990713095735.4237987D@umbc7.umbc.edu>

Hi, 

I just realized that sending out an image by attachment to a mailing list 
is totally inappropriate. I am very sorry for any inconveniences due to my
being ignorant.

Zhengjian Li 


---2108357113-1837801624-931800677=:3679157--

------------------------------

Date: Tue, 13 Jul 1999 16:56:06 +0200
From: "Keshen Mathura" <keshen.mathura@student.uva.nl>
To: <nih-image@io.ece.drexel.edu>
Subject: Image Archive
Message-ID: <003f01becd3f$d85f23a0$40347591@amc.uva.nl>
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 7bit

Hello everyone,

I would like to archive my images on a CD-ROM, but I am
wondering if it is possible to put the images in somekind of
database which I can burn onto CD-ROM. I want to include
time, date, experiment and patient information with the
picture and I want to be able to look it up later so I can
find what I need fast.

Thanks in advance!

Regards,

Keshen

------------------------------

Date: Tue, 13 Jul 1999 15:00:47 -0700
From: Michael Cammer <cammer@aecom.yu.edu>
To: nih-image@io.ece.drexel.edu
Subject: text files to graphics?
Message-Id: <3.0.5.32.19990713150047.0092a640@mailserver.aecom.yu.edu>
Content-Type: text/plain; charset="us-ascii"

I thought I had done this a few years ago, but now I cannot remember how.  

We have a text file with three columns of real numbers corresponding to X,
Y and Z. 
We want to write a simple macro to import these columns, convert to integer
and to plot the numbers into a stack.

The last two steps are simple.  But we would love suggestions for getting
the text into the graphics.

Thanks.
********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************

------------------------------

Date: Tue, 13 Jul 1999 15:10:04 -0400 (EDT)
From: Keng-hui Lin <khlin@student.physics.upenn.edu>
To: nih-image@io.ece.drexel.edu
Subject: NIH and G3 USB port 
Message-ID: <Pine.A32.3.93.990713150850.44696I-100000@student.physics.upenn.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi, all,
     In our lab we have been using NIH image to digitize vedio
tape. A postdoc in our lab wrote a Macro to do vedio control
through the serial port from NIH image.  Everything runs 
well on the Power Mac. Recently I got a G3 Mac and I tried 
to set up everything to run like the old Mac.  
However, I had problems with doing
vedio control from NIH image.  I was wondering whether
NIH image can talk to USB port as talk to seriel port.
Mr. Wayne Rasband told me some of the converters should work.
If people have similar problems and got it solved, please
let me know how you do it. I will really appreciate your
help.
    Thanks. 

     Keng-hui Lin
http://www.physics.upenn.edu/~khlin
Dept.  of Physics and Astronomy, 
University of Pennsylvania
209 S., 33rd Street, Philadelphia, PA 19104
Office: (215)898-5148 [Office]
Home:(215)988-0107

------------------------------

Date: Tue, 13 Jul 1999 16:10:47 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: text files to graphics?
Message-Id: <v03007802b3b14b9877b3@[128.231.99.206]>
Content-Type: text/plain; charset="us-ascii"

>I thought I had done this a few years ago, but now I cannot remember how.
>
>We have a text file with three columns of real numbers corresponding to X,
>Y and Z.
>We want to write a simple macro to import these columns, convert to integer
>and to plot the numbers into a stack.
>
>The last two steps are simple.  But we would love suggestions for getting
>the text into the graphics.

The  "Plot XYZ" macro in the "Plotting Macros" macro file may be what you
used before. It plots XY coordinate points with an optional intensity (Z)
on a single image. Values are read from a 2 or 3 column tab-delimited text
file. The data must be scaled as follows: 0<=X<width; 0<=Y<height;
0<=Z<=255, where width and height are the dimensions of the image.

-wayne

------------------------------

Date: Tue, 13 Jul 1999 16:19:25 -0500
From: hard@acsu.buffalo.edu
To: "NIH-Image list" <nih-image@io.ece.drexel.edu>
Subject: Course Announcement 2
Message-ID: <1666948.3140871565@cilly3.cds.buffalo.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Course Announcement

Title: Optical Microscopy and Imaging in the Biomedical Sciences

When: October 6 - October 14, 1999

Where: Marine Biology Laboratory, Woods Hole, MA, USA

Tuition: $2050 (Includes room and board, text, handouts, supplies)

Application Deadline: August 3, 1999

Admission application and information:
     Carol Hamel, Admissions Coordinator
     Marine Biological Laboratory
     7 MBL Street
     Woods Hole, MA 02543-1015
     (508) 289-7401
     Internet: admissions@mbl.edu
     WWW: http://www.mbl.edu (Application forms available via Adobe Acrobat)

Course Director: Colin S. Izzard, State University of New York @ Albany
                 Phone: [518] 442 - 4367
                 EMail: csizzard@csc.albany.edu

Course Description:

For Whom:
      Designed primarily for research scientists, physicians, postdoctoral 
trainees and advanced graduate students in animal, plant, medical and 
material sciences. Non-biologists seeking a comprehensive introduction to 
microscopy and video-imaging will benefit greatly from this course as well. 
There are no specific prerequisites, but an understanding of the basic 
principles of optics is desirable. Limited to 24 students.

  The eight day course consists of lectures, laboratory demonstrations, 
exercises and discussions that will enable the participant to obtain and 
interpret microscope images of high quality, to perform quantitative optical
measurements, and to produce photographic and video records for
documentation 
and analysis.

Topics to be covered include:
      principles of microscope design and image formation
      bright field, dark field, phase contrast, polarized light,
differential
         interference contrast, interference reflection, and fluorescence
         microscopy
      confocal scanning microscopy, multiphoton excitation fluorescence
         microscopy and image deconvolution
      digital image restoration and 3-D reconstruction
      video imaging, recording, enhancement, and intensification
      analog and digital image processing and analysis
      fluorescent probes and ratiometric-imaging
      laser tweezers and laser scissors

  Applications to live cells will be emphasized; other specimens will be 
covered as well.

  Students will have direct hands-on experience with state-of-the-art 
microscopes, video cameras, recorders and image processing equipment
provided by major optical and electronics companies. Instruction will be
provided by experienced staff from universities and industry.

  Students are encouraged to bring their own biological (primary 
cultures, cell lines, etc.) and material specimens and to discuss individual
research problems with the faculty.

------------------------------

Date: Tue, 13 Jul 1999 14:06:50 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH and G3 USB port 
Message-ID: <1062269.3140863610@huginn.medicine.washington.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

I did this for my research as well. I used a USB-serial adapter from
Keyspan, but had to modify Image to work. The problem is that the macro
writes to the "modem" port, while the keyspan software only converts the
printer port automatically. I had to recompile NIH Image with the macro
output directed to the "printer" port. I also had trouble with the software
that came with the keyspan, and had to download an newer version, which
worked fine.

DTL

--On Tue, Jul 13, 1999 3:10 PM -0400 Keng-hui Lin
<khlin@student.physics.upenn.edu> wrote:

> Hi, all,
>      In our lab we have been using NIH image to digitize vedio
> tape. A postdoc in our lab wrote a Macro to do vedio control
> through the serial port from NIH image.  Everything runs 
> well on the Power Mac. Recently I got a G3 Mac and I tried 
> to set up everything to run like the old Mac.  
> However, I had problems with doing
> vedio control from NIH image.  I was wondering whether
> NIH image can talk to USB port as talk to seriel port.
> Mr. Wayne Rasband told me some of the converters should work.
> If people have similar problems and got it solved, please
> let me know how you do it. I will really appreciate your
> help.
>     Thanks. 
> 
>      Keng-hui Lin
> http://www.physics.upenn.edu/~khlin
> Dept.  of Physics and Astronomy, 
> University of Pennsylvania
> 209 S., 33rd Street, Philadelphia, PA 19104
> Office: (215)898-5148 [Office]
> Home:(215)988-0107
> 
> 
> 
> 
> 

------------------------------

Date: Wed, 14 Jul 1999 09:08:07 +1000 (EST)
From: m.lim-fraser@garvan.unsw.edu.au (Megan Lim Fraser)
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <199907132308.JAA19023@gimr.garvan.unsw.edu.au>
Content-Type: text/plain; charset="us-ascii"

unsubscribe

_________________________________________________________________________
Megan Lim-Fraser
Metabolism Program
Garvan Institute of Medical Research
384 Victoria St                                  Tel:  (02) 9295 8224
Darlinghurst NSW 2010                            Fax:  (02) 9295 8201
Australia                      email: m.lim-fraser@garvan.unsw.edu.au
_________________________________________________________________________

--------------------------------
End of nih-image-d Digest V99 Issue #161
****************************************

From nih-image-request@io.ece.drexel.edu Wed Jul 14 07:25 EDT 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id HAA25116
	for cshtest@io.ece.drexel.edu; Wed, 14 Jul 1999 07:25:52 -0400 (EDT)
Resent-Date: Wed, 14 Jul 1999 07:25:52 -0400 (EDT)
X-Authentication-Warning: bilayer.fki.dtu.dk: lars owned process doing -bs
Date: Wed, 14 Jul 1999 13:01:51 +0200 (MET DST)
From: Lars Kildemark <lars@fki.dtu.dk>
To: nih-image@io.ece.drexel.edu
Subject: Combined thresholding and edges.
In-Reply-To: <199907141000.GAA15625@io.ece.drexel.edu>
Message-ID: <Pine.LNX.3.95.990714125437.13785A-100000@bilayer.fki.dtu.dk>
MIME-Version: 1.0
Resent-Message-ID: <"DEdAR1.0.xa5.ty6Zt"@io>
Resent-From: nih-image@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/1556
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: TEXT/PLAIN; charset=US-ASCII
Content-Length: 977

I have a series of images which I would like to make binary. My problem is
that due to the origin of the images (AFM) a normal thresholding procedure
misclassifies too many pixels because of an uneven baseline. The edges
between the two levels that I want to distinguish are very clear and are
clearly marked by using 'find edges'. My question is then if there is
any method to combine the edge information and the thresholding such that
the number of misclassified pixels drops. Alternatively if it is possible
to elliminate the uneven background this would also help.

Thank you in advance!
Lars
__________________________________________________________
Lars Kildemark Nielsen          | e-mail: lars@kemi.dtu.dk                
Department of Chemistry         | phone : +45 45252363       
Technical University of Denmark | fax   : +45 45934808
Building 206                    |
DK-2800 Lyngby, Denmark         |
__________________________________________________________


From nih-image-request@io.ece.drexel.edu Wed Jul 14 08:03 EDT 1999
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From: Lance Davidson <lad4x@virginia.edu>
Subject: Re: text files to graphics?
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Michael,

PlotXYZ will only work on a single image not on a stack. It won't work if
you want to draw something on one slice, advance a slice, draw another
thing... An alternative is to use a macro file to input your text data.

For this sort of problem I generally take a multi-step approach: 

1. Write a procedure that will handle a single line or object of your data.
2. Use Perl or some other scripting language to parse/filter your text file
into a series of procedure calls where the text has been converted into
arguments in the procedure call.
3. Embed the formatted procedure calls into a macro and your procedure into
a macro file. Don't forget the macro file size limit!
4. Run the macro. 

If your text file is a product of another set of macros then you can
instead write the formatted procedure calls directly into a text file...
Eg. running one macro automatically builds the next macro file. Load the
new macro file and run that next.

This kludge works around the lack of a "readln" function in the NIH-Image
subset of pascal... But then again perl makes writting text_to_text filters
oh so easy. You can easily learn Perl in a day and next to NIH-Image is the
best freeware ever produced for the mac/pc/unix world.

Lance
________________________________________________________

Lance Davidson
Research Associate (Postdoctoral Fellow)
Gilmer Hall, Dept. of Biology
University of Virginia
Charlottesville, VA 22903

804-243-2596 lab phone
804-982-5626 fax

http://www.people.virginia.edu/~lad4x/


From nih-image-request@io.ece.drexel.edu Wed Jul 14 09:50 EDT 1999
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Date: Wed, 14 Jul 1999 09:33:48 -0400
From: Phil Allen <pallen@calvin.bwh.harvard.edu>
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To: nih-image@io.ece.drexel.edu
Subject: Re: Combined thresholding and edges.
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Lars-

How big is the noise in your baseline in pixels?  Single pixel noise could
probably be removed with the median filter.    If the noise is bigger than
that, an approach I used to extract bright fibers against a changing
background was to run a high pass filter on the image, and separately run a
median filter on the image, and then divide the high pass image by the median
filtered image.  The resulting image is almost completely uniform in pixel
intesity, with a slight but real increase in signal for the fibers.  This
signal can then be thresholded and made binary to extract the area.  If you
need more info, feel free to contact me directly.

Phil Allen, Ph.D.
Scientific Director, Confocal Core and
Hematology Division
Brigham and Women's Hospital

Lars Kildemark wrote:

> I have a series of images which I would like to make binary. My problem is
> that due to the origin of the images (AFM) a normal thresholding procedure
> misclassifies too many pixels because of an uneven baseline. The edges
> between the two levels that I want to distinguish are very clear and are
> clearly marked by using 'find edges'. My question is then if there is
> any method to combine the edge information and the thresholding such that
> the number of misclassified pixels drops. Alternatively if it is possible
> to elliminate the uneven background this would also help.
>
> Thank you in advance!
> Lars
> __________________________________________________________
> Lars Kildemark Nielsen          | e-mail: lars@kemi.dtu.dk
> Department of Chemistry         | phone : +45 45252363
> Technical University of Denmark | fax   : +45 45934808
> Building 206                    |
> DK-2800 Lyngby, Denmark         |
> __________________________________________________________


From nih-image-request@io.ece.drexel.edu Wed Jul 14 14:22 EDT 1999
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Subject: more text files to graphics?
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 <003f01becd3f$d85f23a0$40347591@amc.uva.nl>
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Thanks for pointing us to the XYZ plotting macros, but this isn't really
what we want to do.
Basically, we have a series of text files numbered 000 to 0??.  The
filename is our Z coordinate.
The format is as follows:

1	45	34
2	22	98
3	12	87
1	88	88
2	23	99

So the points 1..3 belong to one object and the points 1..2 belong to a
second object.  We want to draw each object at a specific pixel intensity
into a stack.  

>>We have a text file with three columns of real numbers corresponding to X,
>>Y and Z.
>>We want to write a simple macro to import these columns, convert to integer
>>and to plot the numbers into a stack.

********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************


From nih-image-request@io.ece.drexel.edu Wed Jul 14 18:11 EDT 1999
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From: ad1054@worldpath.net (Dr. Christopher Coulon)
Subject: re: marco
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Zhengjian,

This macro works on the image you posted.  You can adjust the variables to
tighten up the density slices.  Please get back to me offline if you need
further assistance (e.g., automating for variations in background and other
factors).

Chris

****** macro ******

procedure setVariables;
begin
  minL:=1;
  minU:=70;
  maxL:=170;
  maxU:=255;
  min:=5;
  max:=10000;
end;

procedure TextWindow;
begin
  DataTitle:=concat(winTitle,' data');
  newTextWindow(DataTitle,150,50);moveWindow(88+w,40);
  writeln('Areas in pixels');
end;

procedure measureFilaments;
var
  j,area,testCount,testIm:integer;

begin
  selectPic(origIm);duplicate('testImage');testIm:=pidNumber;
  if counter=0 then setDensitySlice(minL,minU)
  else setDensitySlice(maxL,maxU);
  analyzeParticles('reset');testCount:=rCount;
  area:=0;
    for j:=1 to rCount do begin
      area:=area+rArea[j];
    end;dispose;
  selectWindow(DataTitle);
    if counter=0 then writeLn('light filaments',chr(9),area)
    else writeLn('dark filaments',chr(9),area);
end;

macro '[F1] auto measure';
var
  origIm,minL,minU,maxL,maxU,counter,min,max,w,h:integer;
  winTitle,tab,DataTitle:string;

begin
  setScale(0,'pixel');
  origIm:=pidNumber;winTitle:=windowTitle;tab:=chr(9);counter:=0;
  getPicSize(w,h);
  setVariables;SetParticleSize(min,max);setOptions('area');
  TextWindow;selectPic(origIm);
  measureFilaments;
  counter:=1;
  measureFilaments;
end;

>Hi, imagers
>
>I attached an image I intend to analyze. I would like to count the
>areas of bright part and dark part respectively with a macro. Any comment
>will be appreciated.
>
>Thank you very much!
>
>Zhengjian Li

* * * * * * * * * * * * * * * * * *
* Dr. Christopher Hunt Coulon     *
* The GAIA Group                  *
* 40 Chick Road                   *
* Wolfeboro, New Hampshire 03894  *
* 603 569-0028                    *
* * * * * * * * * * * * * * * * * *



From nih-image-request@io.ece.drexel.edu Wed Jul 14 19:17 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 162

Today's Topics:
  Combined thresholding and edges.      [ Lars Kildemark <lars@fki.dtu.dk> ]
  Re: text files to graphics?           [ Lance Davidson <lad4x@virginia.edu> ]
  Re: Combined thresholding and edges.  [ Phil Allen <pallen@calvin.bwh.harva ]
  more text files to graphics?          [ Michael Cammer <cammer@aecom.yu.edu ]
  re: marco                             [ ad1054@worldpath.net (Dr. Christoph ]
  unsubscribe                           [ correcto@dragon.upc.qc.ca ]
  Re: Image Archive                     [ Ard Jonker <a.jonker@amc.uva.nl> ]

------------------------------

Date: Wed, 14 Jul 1999 13:01:51 +0200 (MET DST)
From: Lars Kildemark <lars@fki.dtu.dk>
To: nih-image@io.ece.drexel.edu
Subject: Combined thresholding and edges.
Message-ID: <Pine.LNX.3.95.990714125437.13785A-100000@bilayer.fki.dtu.dk>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I have a series of images which I would like to make binary. My problem is
that due to the origin of the images (AFM) a normal thresholding procedure
misclassifies too many pixels because of an uneven baseline. The edges
between the two levels that I want to distinguish are very clear and are
clearly marked by using 'find edges'. My question is then if there is
any method to combine the edge information and the thresholding such that
the number of misclassified pixels drops. Alternatively if it is possible
to elliminate the uneven background this would also help.

Thank you in advance!
Lars
__________________________________________________________
Lars Kildemark Nielsen          | e-mail: lars@kemi.dtu.dk                
Department of Chemistry         | phone : +45 45252363       
Technical University of Denmark | fax   : +45 45934808
Building 206                    |
DK-2800 Lyngby, Denmark         |
__________________________________________________________

------------------------------

Date: Wed, 14 Jul 1999 07:48:15 -0400
From: Lance Davidson <lad4x@virginia.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: text files to graphics?
Message-Id: <3.0.32.19990714074814.0070b124@unix.mail.virginia.edu>
Content-Type: text/plain; charset="us-ascii"

Michael,

PlotXYZ will only work on a single image not on a stack. It won't work if
you want to draw something on one slice, advance a slice, draw another
thing... An alternative is to use a macro file to input your text data.

For this sort of problem I generally take a multi-step approach: 

1. Write a procedure that will handle a single line or object of your data.
2. Use Perl or some other scripting language to parse/filter your text file
into a series of procedure calls where the text has been converted into
arguments in the procedure call.
3. Embed the formatted procedure calls into a macro and your procedure into
a macro file. Don't forget the macro file size limit!
4. Run the macro. 

If your text file is a product of another set of macros then you can
instead write the formatted procedure calls directly into a text file...
Eg. running one macro automatically builds the next macro file. Load the
new macro file and run that next.

This kludge works around the lack of a "readln" function in the NIH-Image
subset of pascal... But then again perl makes writting text_to_text filters
oh so easy. You can easily learn Perl in a day and next to NIH-Image is the
best freeware ever produced for the mac/pc/unix world.

Lance
________________________________________________________

Lance Davidson
Research Associate (Postdoctoral Fellow)
Gilmer Hall, Dept. of Biology
University of Virginia
Charlottesville, VA 22903

804-243-2596 lab phone
804-982-5626 fax

http://www.people.virginia.edu/~lad4x/

------------------------------

Date: Wed, 14 Jul 1999 09:33:48 -0400
From: Phil Allen <pallen@calvin.bwh.harvard.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Combined thresholding and edges.
Message-ID: <378C91BB.CB992C96@calvin.bwh.harvard.edu>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Lars-

How big is the noise in your baseline in pixels?  Single pixel noise could
probably be removed with the median filter.    If the noise is bigger than
that, an approach I used to extract bright fibers against a changing
background was to run a high pass filter on the image, and separately run a
median filter on the image, and then divide the high pass image by the median
filtered image.  The resulting image is almost completely uniform in pixel
intesity, with a slight but real increase in signal for the fibers.  This
signal can then be thresholded and made binary to extract the area.  If you
need more info, feel free to contact me directly.

Phil Allen, Ph.D.
Scientific Director, Confocal Core and
Hematology Division
Brigham and Women's Hospital

Lars Kildemark wrote:

> I have a series of images which I would like to make binary. My problem is
> that due to the origin of the images (AFM) a normal thresholding procedure
> misclassifies too many pixels because of an uneven baseline. The edges
> between the two levels that I want to distinguish are very clear and are
> clearly marked by using 'find edges'. My question is then if there is
> any method to combine the edge information and the thresholding such that
> the number of misclassified pixels drops. Alternatively if it is possible
> to elliminate the uneven background this would also help.
>
> Thank you in advance!
> Lars
> __________________________________________________________
> Lars Kildemark Nielsen          | e-mail: lars@kemi.dtu.dk
> Department of Chemistry         | phone : +45 45252363
> Technical University of Denmark | fax   : +45 45934808
> Building 206                    |
> DK-2800 Lyngby, Denmark         |
> __________________________________________________________

------------------------------

Date: Wed, 14 Jul 1999 14:10:47 -0700
From: Michael Cammer <cammer@aecom.yu.edu>
To: nih-image@io.ece.drexel.edu
Subject: more text files to graphics?
Message-Id: <3.0.5.32.19990714141047.0096b380@mailserver.aecom.yu.edu>
Content-Type: text/plain; charset="us-ascii"

Thanks for pointing us to the XYZ plotting macros, but this isn't really
what we want to do.
Basically, we have a series of text files numbered 000 to 0??.  The
filename is our Z coordinate.
The format is as follows:

1	45	34
2	22	98
3	12	87
1	88	88
2	23	99

So the points 1..3 belong to one object and the points 1..2 belong to a
second object.  We want to draw each object at a specific pixel intensity
into a stack.  

>>We have a text file with three columns of real numbers corresponding to X,
>>Y and Z.
>>We want to write a simple macro to import these columns, convert to integer
>>and to plot the numbers into a stack.

********************************************************************
*  Michael Cammer * Analytical Imaging Facility * Albert Einstein  *
*  College of Medicine * 1300 Morris Park Ave. * Bronx, NY  10461  *
*  (718) 430-2890 * work URL:  http://www.ca.aecom.yu.edu/aif/     *      
*  personal URL:  http://cammer.home.mindspring.com/               *
********************************************************************

------------------------------

Date: Wed, 14 Jul 1999 17:46:15 -0400
From: ad1054@worldpath.net (Dr. Christopher Coulon)
To: nih-image@io.ece.drexel.edu
Subject: re: marco
Message-Id: <v01520d00b3b2b41b5cc0@[208.133.221.222]>
Content-Type: text/plain; charset="us-ascii"

Zhengjian,

This macro works on the image you posted.  You can adjust the variables to
tighten up the density slices.  Please get back to me offline if you need
further assistance (e.g., automating for variations in background and other
factors).

Chris

****** macro ******

procedure setVariables;
begin
  minL:=1;
  minU:=70;
  maxL:=170;
  maxU:=255;
  min:=5;
  max:=10000;
end;

procedure TextWindow;
begin
  DataTitle:=concat(winTitle,' data');
  newTextWindow(DataTitle,150,50);moveWindow(88+w,40);
  writeln('Areas in pixels');
end;

procedure measureFilaments;
var
  j,area,testCount,testIm:integer;

begin
  selectPic(origIm);duplicate('testImage');testIm:=pidNumber;
  if counter=0 then setDensitySlice(minL,minU)
  else setDensitySlice(maxL,maxU);
  analyzeParticles('reset');testCount:=rCount;
  area:=0;
    for j:=1 to rCount do begin
      area:=area+rArea[j];
    end;dispose;
  selectWindow(DataTitle);
    if counter=0 then writeLn('light filaments',chr(9),area)
    else writeLn('dark filaments',chr(9),area);
end;

macro '[F1] auto measure';
var
  origIm,minL,minU,maxL,maxU,counter,min,max,w,h:integer;
  winTitle,tab,DataTitle:string;

begin
  setScale(0,'pixel');
  origIm:=pidNumber;winTitle:=windowTitle;tab:=chr(9);counter:=0;
  getPicSize(w,h);
  setVariables;SetParticleSize(min,max);setOptions('area');
  TextWindow;selectPic(origIm);
  measureFilaments;
  counter:=1;
  measureFilaments;
end;

>Hi, imagers
>
>I attached an image I intend to analyze. I would like to count the
>areas of bright part and dark part respectively with a macro. Any comment
>will be appreciated.
>
>Thank you very much!
>
>Zhengjian Li

* * * * * * * * * * * * * * * * * *
* Dr. Christopher Hunt Coulon     *
* The GAIA Group                  *
* 40 Chick Road                   *
* Wolfeboro, New Hampshire 03894  *
* 603 569-0028                    *
* * * * * * * * * * * * * * * * * *

------------------------------

Date: Fri, 25 Jun 1999 18:51:27 -0400
From: correcto@dragon.upc.qc.ca
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <v04020a01b399b8585693@[132.203.188.102]>
Content-Type: text/plain; charset="us-ascii"

Unsubscribe Please

------------------------------

Date: Thu, 15 Jul 1999 09:29:29 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Image Archive
Message-Id: <l03130300b3b33d070915@[145.117.53.66]>
Content-Type: text/plain; charset="us-ascii"

>I would like to archive my images on a CD-ROM, but I am
>wondering if it is possible to put the images in somekind of
>database which I can burn onto CD-ROM. I want to include
>time, date, experiment and patient information with the
>picture and I want to be able to look it up later so I can
>find what I need fast.

iView Multimedia will allow you to make a thumbnail index file and put
comments to the images in the index file (in various forms) that are
searchable. If you make a disk image of the size of a CD-ROM, you will be
able to fill it gradually with images and keep the index file with it on
the same image. Once the image fills, you write the image to disk and all
your references remain intact. By keeping the index files together on a
separate CD-ROM, searching can be done without having to put in all the
disks every time you want to search. Depending on the size of your
thumbnail (icon, small, medium, large or huge) and on the compression you
set, the index file may grow to 10% of the actual images.

A utility for quickly searching files by name or by comments is
DiskTracker. This program cannot make thumbnails, but it can search a
mulit-thousand files in an eyeblink.

Ard

--------------------------------
End of nih-image-d Digest V99 Issue #162
****************************************

From nih-image-request@io.ece.drexel.edu Thu Jul 15 03:54 EDT 1999
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Date: Thu, 15 Jul 1999 09:29:29 +0200
To: nih-image@io.ece.drexel.edu
From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: Re: Image Archive
Resent-Message-ID: <"TKgta1.0.OU6.gzOZt"@io>
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>I would like to archive my images on a CD-ROM, but I am
>wondering if it is possible to put the images in somekind of
>database which I can burn onto CD-ROM. I want to include
>time, date, experiment and patient information with the
>picture and I want to be able to look it up later so I can
>find what I need fast.

iView Multimedia will allow you to make a thumbnail index file and put
comments to the images in the index file (in various forms) that are
searchable. If you make a disk image of the size of a CD-ROM, you will be
able to fill it gradually with images and keep the index file with it on
the same image. Once the image fills, you write the image to disk and all
your references remain intact. By keeping the index files together on a
separate CD-ROM, searching can be done without having to put in all the
disks every time you want to search. Depending on the size of your
thumbnail (icon, small, medium, large or huge) and on the compression you
set, the index file may grow to 10% of the actual images.

A utility for quickly searching files by name or by comments is
DiskTracker. This program cannot make thumbnails, but it can search a
mulit-thousand files in an eyeblink.

Ard



From nih-image-request@io.ece.drexel.edu Thu Jul 15 05:30 EDT 1999
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Date: Thu, 15 Jul 1999 10:07:27 +0100
To: nih-image@io.ece.drexel.edu
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
Subject: Re: 3-D coordinates from focal slices ?
Cc: Knappertsbusch <Knappertsbus@ubaclu.unibas.ch>
Resent-Message-ID: <"zKhFD.0.Jo1.JJQZt"@io>
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Michael Knappertsbusch asked...

>Is this the right procedure for extracting regions of high focus ?
>Is there any other procedure to characterize regions of highest
>sharpness in an image ?

I have found that one way to extract the region of best focus is to
calculate the contrast at each pixel (the standard deviation of the
intensitites of neighbouring pixels). High contrast means well focused. Low
contrast means out of focus (usually).

I have used this in an algorithm in 'Image SXM' (an NIH Image spin-off) to
take a stack of images taken at different focal planes and to create a
single composite image that is in focus at all points in the image. It
works well for many images, and I am trying to improve it for images having
very high 'focus gradient' (ie, z change of focus per xy pixel).

Information on Image SXM can be found at http://reg.ssci.liv.ac.uk.

Steve

___________________________________________________________________
Dr Steve Barrett
Surface Science Research Centre
University of Liverpool
Liverpool L69 3BX
United Kingdom

Tel: 44-(0)151-794-3894 / 3874 / 3541
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk
___________________________________________________________________



From nih-image-request@io.ece.drexel.edu Thu Jul 15 06:11 EDT 1999
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Date: Thu, 15 Jul 1999 11:45:50 +0200
To: nih-image@io.ece.drexel.edu
From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: want to import a tiff as raw image
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Hello List,

obviously I'm overlooking something: When trying to import a file with
custom settings, NIH is determined to read it as a tiff file. I set size to
512x512, offset 8 (the size of the tiff header) and import the file.
Suddenly, there is the tiff file, with the tiff lut and the overexposed
pixels in a silly color. When I use HexEdit to remove the first 8 bytes
from the file, import done as described above works as expected: grayscale
image with the overexposed pixels as 255, as I want them.
The problem is that once this file is loaded as a tiff, the overexposed
pixels keep the silly value (25), even when the gray scale LUT is used,
rendering the file useless.

Is there an alternative way short from going through all 120 files with
hexedit?

Ard



From nih-image-request@io.ece.drexel.edu Thu Jul 15 11:57 EDT 1999
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References: <199907150740.DAA27107@io.ece.drexel.edu>
Mime-Version: 1.0
Date: Thu, 15 Jul 1999 09:09:56 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: want to import a tiff as raw image
Resent-Message-ID: <"eFPmn3.0.hS.84WZt"@io>
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>Hello List,
>
>obviously I'm overlooking something: When trying to import a file with
>custom settings, NIH is determined to read it as a tiff file. I set size to
>512x512, offset 8 (the size of the tiff header) and import the file.
>Suddenly, there is the tiff file, with the tiff lut and the overexposed
>pixels in a silly color. When I use HexEdit to remove the first 8 bytes
>from the file, import done as described above works as expected: grayscale
>image with the overexposed pixels as 255, as I want them.
>The problem is that once this file is loaded as a tiff, the overexposed
>pixels keep the silly value (25), even when the gray scale LUT is used,
>rendering the file useless.
>
>Is there an alternative way short from going through all 120 files with
>hexedit?

Holding the option key down when selecting the Import command disibles TIFF
detection, or use a  macro to open the files.

-wayne



From nih-image-request@io.ece.drexel.edu Thu Jul 15 12:48 EDT 1999
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Message-ID: <378E0A63.E6A64A51@utmmg.med.uth.tmc.edu>
Date: Thu, 15 Jul 1999 11:20:51 -0500
From: Lian Loo <lianloo@utmmg.med.uth.tmc.edu>
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I am a dermatologist at the University of Texas Medical School at
Houston.  We are trying to analyze skin photographs taken with a neutral
density filter and ultraviolet (UV) filter.  Our photographs are not
well illuminated.  We have the following questions:

1)  Can the Scion program do granulometry or texture calculations?  If
so, how?
2)  Can the Scion program do an adaptive threshold method? How?
3)  What is the best way to do contrast enhancement?
4)  What is the best way to analyze differences in photographs both
quantitatively and qualitatively?

--
Lian Loo, D.V.M.
University of Texas Medical School
Department of Dermatology
6431 Fannin St., MSB 1.008
Houston, TX  77030
----------------------------------
voice: (713)500-7156
fax:   (713)500-7168



From nih-image-request@io.ece.drexel.edu Thu Jul 15 19:08 EDT 1999
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Date: Thu, 15 Jul 1999 18:56:51 -0400 (EDT)
From: Rajat K Chakraborti <rkc@acsu.buffalo.edu>
To: nih-image@io.ece.drexel.edu
Subject: fitted ellipse
Message-ID: <Pine.GSO.4.05.9907151851090.14137-100000@hercules.acsu.buffalo.edu>
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Hi,

I am working with NIH-image software to measure suspended particles for my
research. While working with size measurements, I found that the software
measures directly area and perimeter. The long and short axis of the
object is just calculated as a best fitted ellipse. My question is how
that is fitted. What is the algorithm to get different long and short
sides of the object. 

I will be glad to know this answer.

*******************************************************************
Rajat Kanti Chakraborti
State University of New York at Buffalo
207 Jarvis Hall
Department of Civil, Structural and Environmental Engineering
Buffalo, NY 14260
Ph. (716) 645-2114 ext. 2336		Fax: (716) 645-3667

rkc@acsu.buffalo.edu
********************************************************************


From nih-image-request@io.ece.drexel.edu Thu Jul 15 19:57 EDT 1999
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Date: Thu, 15 Jul 1999 18:45:12 -0500
To: nih-image@io.ece.drexel.edu
From: Thomas Hickson <hicks007@tc.umn.edu>
Subject: Help, i want to unsubscribe from this list
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I have been trying to unsubscribe from this list for about a month and all
of my 'unsubscribe' messages get returned with an error.  I have never sent
an 'unsubscribe' to this list because I know that it doesn't work.  I have
followed all of the directions on the posting that comes out every other
week or so, but for naught.  Apparently, when I send the 'unsubscribe,' the
majordomo of the list doesn't recognize my e-mail address and bounces an
error back to me.  Could someone out there help me out?

Cheers,

Tom

************************************************************

Thomas A. Hickson
St. Anthony Falls Laboratory
2-3rd Ave. SE,  Room 381
University of Minnesota
Minneapolis, MN  55414

Phone:  612-627-4594
Fax:	612-627-4609
e-mail:	hicks007@tc.umn.edu

************************************************************

	To doubt everything or to believe everything are
	two equally convenient solutions; both dispense
	with the necessity of reflection.
						H. Poincare


From nih-image-d-request@io.ece.drexel.edu Fri Jul 16 06:10 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 163

Today's Topics:
  Re: 3-D coordinates from focal slice  [ Steve Barrett <S.D.Barrett@liverpoo ]
  want to import a tiff as raw image    [ Ard Jonker <a.jonker@amc.uva.nl> ]
  NIH Image Validation                  [ "Mandish Rai" <raim@ccf.org> ]
  Re: want to import a tiff as raw ima  [ Wayne Rasband <wayne@codon.nih.gov> ]
  Granulometry                          [ Lian Loo <lianloo@utmmg.med.uth.tmc ]
  fitted ellipse                        [ Rajat K Chakraborti <rkc@acsu.buffa ]
  Help, i want to unsubscribe from thi  [ Thomas Hickson <hicks007@tc.umn.edu ]

------------------------------

Date: Thu, 15 Jul 1999 10:07:27 +0100
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
To: nih-image@io.ece.drexel.edu
Cc: Knappertsbusch <Knappertsbus@ubaclu.unibas.ch>
Subject: Re: 3-D coordinates from focal slices ?
Message-Id: <l03130302b3b3509a2870@[138.253.47.16]>
Content-Type: text/plain; charset="us-ascii"

Michael Knappertsbusch asked...

>Is this the right procedure for extracting regions of high focus ?
>Is there any other procedure to characterize regions of highest
>sharpness in an image ?

I have found that one way to extract the region of best focus is to
calculate the contrast at each pixel (the standard deviation of the
intensitites of neighbouring pixels). High contrast means well focused. Low
contrast means out of focus (usually).

I have used this in an algorithm in 'Image SXM' (an NIH Image spin-off) to
take a stack of images taken at different focal planes and to create a
single composite image that is in focus at all points in the image. It
works well for many images, and I am trying to improve it for images having
very high 'focus gradient' (ie, z change of focus per xy pixel).

Information on Image SXM can be found at http://reg.ssci.liv.ac.uk.

Steve

___________________________________________________________________
Dr Steve Barrett
Surface Science Research Centre
University of Liverpool
Liverpool L69 3BX
United Kingdom

Tel: 44-(0)151-794-3894 / 3874 / 3541
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk
___________________________________________________________________

------------------------------

Date: Thu, 15 Jul 1999 11:45:50 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: want to import a tiff as raw image
Message-Id: <l03130303b3b35ce532cd@[145.117.53.66]>
Content-Type: text/plain; charset="us-ascii"

Hello List,

obviously I'm overlooking something: When trying to import a file with
custom settings, NIH is determined to read it as a tiff file. I set size to
512x512, offset 8 (the size of the tiff header) and import the file.
Suddenly, there is the tiff file, with the tiff lut and the overexposed
pixels in a silly color. When I use HexEdit to remove the first 8 bytes
from the file, import done as described above works as expected: grayscale
image with the overexposed pixels as 255, as I want them.
The problem is that once this file is loaded as a tiff, the overexposed
pixels keep the silly value (25), even when the gray scale LUT is used,
rendering the file useless.

Is there an alternative way short from going through all 120 files with
hexedit?

Ard

------------------------------

Date: Thu, 15 Jul 1999 08:39:57 -0400
From: "Mandish Rai" <raim@ccf.org>
To: <nih-image@io.ece.drexel.edu>
Subject: NIH Image Validation
Message-Id: <s78d9dd8.025@cesmtp.ccf.org>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline
Content-Transfer-Encoding: 8bit

Has anyone validated NIH Image?  If so, can you provide me with the reference information.

Thank you,

Mandish Rai

------------------------------

Date: Thu, 15 Jul 1999 09:09:56 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: want to import a tiff as raw image
Message-Id: <v03007800b3b38d817f58@[128.231.99.206]>
Content-Type: text/plain; charset="us-ascii"

>Hello List,
>
>obviously I'm overlooking something: When trying to import a file with
>custom settings, NIH is determined to read it as a tiff file. I set size to
>512x512, offset 8 (the size of the tiff header) and import the file.
>Suddenly, there is the tiff file, with the tiff lut and the overexposed
>pixels in a silly color. When I use HexEdit to remove the first 8 bytes
>from the file, import done as described above works as expected: grayscale
>image with the overexposed pixels as 255, as I want them.
>The problem is that once this file is loaded as a tiff, the overexposed
>pixels keep the silly value (25), even when the gray scale LUT is used,
>rendering the file useless.
>
>Is there an alternative way short from going through all 120 files with
>hexedit?

Holding the option key down when selecting the Import command disibles TIFF
detection, or use a  macro to open the files.

-wayne

------------------------------

Date: Thu, 15 Jul 1999 11:20:51 -0500
From: Lian Loo <lianloo@utmmg.med.uth.tmc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Granulometry
Message-ID: <378E0A63.E6A64A51@utmmg.med.uth.tmc.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

I am a dermatologist at the University of Texas Medical School at
Houston.  We are trying to analyze skin photographs taken with a neutral
density filter and ultraviolet (UV) filter.  Our photographs are not
well illuminated.  We have the following questions:

1)  Can the Scion program do granulometry or texture calculations?  If
so, how?
2)  Can the Scion program do an adaptive threshold method? How?
3)  What is the best way to do contrast enhancement?
4)  What is the best way to analyze differences in photographs both
quantitatively and qualitatively?

--
Lian Loo, D.V.M.
University of Texas Medical School
Department of Dermatology
6431 Fannin St., MSB 1.008
Houston, TX  77030
----------------------------------
voice: (713)500-7156
fax:   (713)500-7168

------------------------------

Date: Thu, 15 Jul 1999 18:56:51 -0400 (EDT)
From: Rajat K Chakraborti <rkc@acsu.buffalo.edu>
To: nih-image@io.ece.drexel.edu
Subject: fitted ellipse
Message-ID: <Pine.GSO.4.05.9907151851090.14137-100000@hercules.acsu.buffalo.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi,

I am working with NIH-image software to measure suspended particles for my
research. While working with size measurements, I found that the software
measures directly area and perimeter. The long and short axis of the
object is just calculated as a best fitted ellipse. My question is how
that is fitted. What is the algorithm to get different long and short
sides of the object. 

I will be glad to know this answer.

*******************************************************************
Rajat Kanti Chakraborti
State University of New York at Buffalo
207 Jarvis Hall
Department of Civil, Structural and Environmental Engineering
Buffalo, NY 14260
Ph. (716) 645-2114 ext. 2336		Fax: (716) 645-3667

rkc@acsu.buffalo.edu
********************************************************************

------------------------------

Date: Thu, 15 Jul 1999 18:45:12 -0500
From: Thomas Hickson <hicks007@tc.umn.edu>
To: nih-image@io.ece.drexel.edu
Subject: Help, i want to unsubscribe from this list
Message-Id: <v04011700b3b42267c9e3@[128.101.165.11]>
Content-Type: text/plain; charset="us-ascii"

I have been trying to unsubscribe from this list for about a month and all
of my 'unsubscribe' messages get returned with an error.  I have never sent
an 'unsubscribe' to this list because I know that it doesn't work.  I have
followed all of the directions on the posting that comes out every other
week or so, but for naught.  Apparently, when I send the 'unsubscribe,' the
majordomo of the list doesn't recognize my e-mail address and bounces an
error back to me.  Could someone out there help me out?

Cheers,

Tom

************************************************************

Thomas A. Hickson
St. Anthony Falls Laboratory
2-3rd Ave. SE,  Room 381
University of Minnesota
Minneapolis, MN  55414

Phone:  612-627-4594
Fax:	612-627-4609
e-mail:	hicks007@tc.umn.edu

************************************************************

	To doubt everything or to believe everything are
	two equally convenient solutions; both dispense
	with the necessity of reflection.
						H. Poincare

--------------------------------
End of nih-image-d Digest V99 Issue #163
****************************************

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Date: Fri, 16 Jul 1999 17:42:30 +0200
From: Gerrit Beemster <gebee@gengenp.rug.ac.be>
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Dear all,

After manually tracking particles in time lapse observations for years it
finally occurred to me it should be possible to do that sort of thing
automatically in a stack. There is a routine "autotrack" among the
usermacro's on zippy, but that is designed for filament growth rather than
particles it seems. Are there any routines like that around that I can
modify? Alternatively, if I start to program this myself what is the best
way to track a particle? 1. Use analyse particles to get X,Y coordinates +
size and density of all particles and then find one that matches in adjacent
images? 2. Find particles with the analyse particles, but then select an
area of pixels, say 5x5 and find a similar area in the proximity? 3. Another
way which I haven't come up with yet, but should work better?

I'd appriciate any help!

Cheers,

--
=====================================================================
Gerrit Beemster
Department of Genetics
K.L. Ledeganckstraat 35
B-9000 Gent
Belgium

phone: (32)9/2645010
fax:   (32)9/2645349
www: http://spider.rug.ac.be
=====================================================================



From nih-image-request@io.ece.drexel.edu Fri Jul 16 13:38 EDT 1999
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From: "Greg Joss" <gjoss@hotmail.com>
To: nih-image@io.ece.drexel.edu, gebee@gengenp.rug.ac.be
Subject: Re: Particle tracking
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>From: Gerrit Beemster <gebee@gengenp.rug.ac.be>
>Reply-To: nih-image@io.ece.drexel.edu
>To: nih-image@io.ece.drexel.edu
>Subject: Particle tracking
>Date: Fri, 16 Jul 1999 17:42:30 +0200
>
>Dear all,
>
>After manually tracking particles in time lapse observations for years it
>finally occurred to me it should be possible to do that sort of thing
>automatically in a stack. There is a routine "autotrack" among the
>usermacro's on zippy, but that is designed for filament growth rather than
>particles it seems. Are there any routines like that around that I can
>modify? Alternatively, if I start to program this myself what is the best
>way to track a particle? 1. Use analyse particles to get X,Y coordinates +
>size and density of all particles and then find one that matches in 
>adjacent
>images? 2. Find particles with the analyse particles, but then select an
>area of pixels, say 5x5 and find a similar area in the proximity? 3. 
>Another
>way which I haven't come up with yet, but should work better?
>
>I'd appriciate any help!
>
>Cheers,
>
>--
>=====================================================================
>Gerrit Beemster
>Department of Genetics
>K.L. Ledeganckstraat 35
>B-9000 Gent
>Belgium
>
>phone: (32)9/2645010
>fax:   (32)9/2645349
>www: http://spider.rug.ac.be
>=====================================================================

Gerrit,
A method which works well for cell tracking provided frames are sufficiently 
close so that successive images of particles overlap by some degree ( or 
will if you dilate the projections):

convert stack to binary images of particle projections;
analyzeParticles first frame to locate particle & centroids;
use autoOutline(x,y); to run through particle list to arbitarily assign a 
color id to each particle using setForeGround(rCount);fill;
(ie color by position in list);
This step is much more "watertight" if you use Object-Image as in addition 
to (rX,rY0, Object-Image returns (rLeft,rTop) for each analyzeParticles 
result which is gauranteed to work with autoOutline whereas centroid can 
sometimes fail to locate correct particle.

copy,paste color maped particles from current frame onto next frame using 
SetOption;doAND;
The result is a set of particles with color and Black where there is overlap 
or extention.
The next round of analyzeParticles will then give a rMin value which is the 
color id of the overlaping particle from the previous frame;
The color ID is propagated to the whole particle by autoOutline.
This process can then be propagated through the stack.

If more than 254 particles or particles leave/(re)enter the scene, then 
things get more complex, but the above should be sufficient to convey the 
general idea.

The result is that all particles are id'ed and located through time.
NIH-Image (or easier with Object-Image) can then be used to output a 
color-id'ed 3D track of each particle which can be viewed via projection 
tools or else output to Rotator.
Progressive cell boundarys can be displayed in place or displayed fixed 
(pinned) to centroid so that shape changes during motion are emphasised and 
measureable. Binary outlines can be used to reconstitute original grayscale 
images of individual cells in tracks or 'pinned' images

Works very well in practice and can be fully automated or just 
computer-assist'ed via macros.
Come back if you would like further comment.

Greg Joss,
gjoss@rna.bio.mq.edu.au


______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com


From nih-image-request@io.ece.drexel.edu Fri Jul 16 14:47 EDT 1999
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From: "Harenski, Keith" <harenskik@msx.upmc.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: AC-PC alignment
Date: Fri, 16 Jul 1999 14:23:20 -0400
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I am currently trying to find a way within NIH Image to align 124 coronal
stack images along the AC-PC line to put all the brains in a "standard
position" before structural measurement.  If anyone has any ideas as to how
to do this or has a macro that does AC-PC alignment (or something similar)
please let me know.

thanks in advance... Keith


From nih-image-d-request@io.ece.drexel.edu Sat Jul 17 06:17 EDT 1999
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------------------------------

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nih-image-d Digest				Volume 99 : Issue 164

Today's Topics:
  Particle tracking                     [ Gerrit Beemster <gebee@gengenp.rug. ]
  Re: Particle tracking                 [ "Greg Joss" <gjoss@hotmail.com> ]
  AC-PC alignment                       [ "Harenski, Keith" <harenskik@msx.up ]

------------------------------

Date: Fri, 16 Jul 1999 17:42:30 +0200
From: Gerrit Beemster <gebee@gengenp.rug.ac.be>
To: nih-image@io.ece.drexel.edu
Subject: Particle tracking
Message-ID: <378F52E6.EB6A4295@gengenp.rug.ac.be>
Content-Type: text/plain; charset=us-ascii
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Dear all,

After manually tracking particles in time lapse observations for years it
finally occurred to me it should be possible to do that sort of thing
automatically in a stack. There is a routine "autotrack" among the
usermacro's on zippy, but that is designed for filament growth rather than
particles it seems. Are there any routines like that around that I can
modify? Alternatively, if I start to program this myself what is the best
way to track a particle? 1. Use analyse particles to get X,Y coordinates +
size and density of all particles and then find one that matches in adjacent
images? 2. Find particles with the analyse particles, but then select an
area of pixels, say 5x5 and find a similar area in the proximity? 3. Another
way which I haven't come up with yet, but should work better?

I'd appriciate any help!

Cheers,

--
=====================================================================
Gerrit Beemster
Department of Genetics
K.L. Ledeganckstraat 35
B-9000 Gent
Belgium

phone: (32)9/2645010
fax:   (32)9/2645349
www: http://spider.rug.ac.be
=====================================================================

------------------------------

Date: Sat, 17 Jul 1999 03:13:58 EST
From: "Greg Joss" <gjoss@hotmail.com>
To: nih-image@io.ece.drexel.edu, gebee@gengenp.rug.ac.be
Subject: Re: Particle tracking
Message-ID: <19990716171358.18459.qmail@hotmail.com>
Content-Type: text/plain; format=flowed

>From: Gerrit Beemster <gebee@gengenp.rug.ac.be>
>Reply-To: nih-image@io.ece.drexel.edu
>To: nih-image@io.ece.drexel.edu
>Subject: Particle tracking
>Date: Fri, 16 Jul 1999 17:42:30 +0200
>
>Dear all,
>
>After manually tracking particles in time lapse observations for years it
>finally occurred to me it should be possible to do that sort of thing
>automatically in a stack. There is a routine "autotrack" among the
>usermacro's on zippy, but that is designed for filament growth rather than
>particles it seems. Are there any routines like that around that I can
>modify? Alternatively, if I start to program this myself what is the best
>way to track a particle? 1. Use analyse particles to get X,Y coordinates +
>size and density of all particles and then find one that matches in 
>adjacent
>images? 2. Find particles with the analyse particles, but then select an
>area of pixels, say 5x5 and find a similar area in the proximity? 3. 
>Another
>way which I haven't come up with yet, but should work better?
>
>I'd appriciate any help!
>
>Cheers,
>
>--
>=====================================================================
>Gerrit Beemster
>Department of Genetics
>K.L. Ledeganckstraat 35
>B-9000 Gent
>Belgium
>
>phone: (32)9/2645010
>fax:   (32)9/2645349
>www: http://spider.rug.ac.be
>=====================================================================

Gerrit,
A method which works well for cell tracking provided frames are sufficiently 
close so that successive images of particles overlap by some degree ( or 
will if you dilate the projections):

convert stack to binary images of particle projections;
analyzeParticles first frame to locate particle & centroids;
use autoOutline(x,y); to run through particle list to arbitarily assign a 
color id to each particle using setForeGround(rCount);fill;
(ie color by position in list);
This step is much more "watertight" if you use Object-Image as in addition 
to (rX,rY0, Object-Image returns (rLeft,rTop) for each analyzeParticles 
result which is gauranteed to work with autoOutline whereas centroid can 
sometimes fail to locate correct particle.

copy,paste color maped particles from current frame onto next frame using 
SetOption;doAND;
The result is a set of particles with color and Black where there is overlap 
or extention.
The next round of analyzeParticles will then give a rMin value which is the 
color id of the overlaping particle from the previous frame;
The color ID is propagated to the whole particle by autoOutline.
This process can then be propagated through the stack.

If more than 254 particles or particles leave/(re)enter the scene, then 
things get more complex, but the above should be sufficient to convey the 
general idea.

The result is that all particles are id'ed and located through time.
NIH-Image (or easier with Object-Image) can then be used to output a 
color-id'ed 3D track of each particle which can be viewed via projection 
tools or else output to Rotator.
Progressive cell boundarys can be displayed in place or displayed fixed 
(pinned) to centroid so that shape changes during motion are emphasised and 
measureable. Binary outlines can be used to reconstitute original grayscale 
images of individual cells in tracks or 'pinned' images

Works very well in practice and can be fully automated or just 
computer-assist'ed via macros.
Come back if you would like further comment.

Greg Joss,
gjoss@rna.bio.mq.edu.au


______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com

------------------------------

Date: Fri, 16 Jul 1999 14:23:20 -0400
From: "Harenski, Keith" <harenskik@msx.upmc.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: AC-PC alignment
Message-ID: <8948DD9B2EDCD111B49500805FA783730223521F@1upmc-msx2.isdbu.upmc.edu>
Content-Type: text/plain

I am currently trying to find a way within NIH Image to align 124 coronal
stack images along the AC-PC line to put all the brains in a "standard
position" before structural measurement.  If anyone has any ideas as to how
to do this or has a macro that does AC-PC alignment (or something similar)
please let me know.

thanks in advance... Keith

--------------------------------
End of nih-image-d Digest V99 Issue #164
****************************************

From nih-image-request@io.ece.drexel.edu Sun Jul 18 17:29 EDT 1999
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_________________________
Eric S. Corp
Research Associate Professor
Neuroscience and Behavior Program and
Center for Neuroendocrine Studies
518 Tobin Hall, Box 37710
University of Massachusetts
Amherst, MA 01003-7710, USA
(413) 545-4295  -0996 (FAX)
NSB program http://www.umass.edu/neuro/faculty/corp.html



      



From nih-image-request@io.ece.drexel.edu Mon Jul 19 08:06 EDT 1999
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Date: Mon, 19 Jul 1999 07:45:25 -0400
From: "Norris O'Dell" <nodell@mail.mcg.edu>
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Subject: Re: Course Announcement 2
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Thanks Mike, norris

>>> <hard@acsu.buffalo.edu> 07/13 6:05 PM >>>
Course Announcement

Title: Optical Microscopy and Imaging in the Biomedical Sciences

When: October 6 - October 14, 1999

Where: Marine Biology Laboratory, Woods Hole, MA, USA

Tuition: $2050 (Includes room and board, text, handouts, supplies)

Application Deadline: August 3, 1999

Admission application and information:
     Carol Hamel, Admissions Coordinator
     Marine Biological Laboratory
     7 MBL Street
     Woods Hole, MA 02543-1015
     (508) 289-7401
     Internet: admissions@mbl.edu 
     WWW: http://www.mbl.edu (Application forms available via Adobe Acrobat)

Course Director: Colin S. Izzard, State University of New York @ Albany
                 Phone: [518] 442 - 4367
                 EMail: csizzard@csc.albany.edu 

Course Description:

For Whom:
      Designed primarily for research scientists, physicians, postdoctoral 
trainees and advanced graduate students in animal, plant, medical and 
material sciences. Non-biologists seeking a comprehensive introduction to 
microscopy and video-imaging will benefit greatly from this course as well. 
There are no specific prerequisites, but an understanding of the basic 
principles of optics is desirable. Limited to 24 students.

  The eight day course consists of lectures, laboratory demonstrations, 
exercises and discussions that will enable the participant to obtain and 
interpret microscope images of high quality, to perform quantitative optical
measurements, and to produce photographic and video records for
documentation 
and analysis.

Topics to be covered include:
      principles of microscope design and image formation
      bright field, dark field, phase contrast, polarized light,
differential
         interference contrast, interference reflection, and fluorescence
         microscopy
      confocal scanning microscopy, multiphoton excitation fluorescence
         microscopy and image deconvolution
      digital image restoration and 3-D reconstruction
      video imaging, recording, enhancement, and intensification
      analog and digital image processing and analysis
      fluorescent probes and ratiometric-imaging
      laser tweezers and laser scissors

  Applications to live cells will be emphasized; other specimens will be 
covered as well.

  Students will have direct hands-on experience with state-of-the-art 
microscopes, video cameras, recorders and image processing equipment
provided by major optical and electronics companies. Instruction will be
provided by experienced staff from universities and industry.

  Students are encouraged to bring their own biological (primary 
cultures, cell lines, etc.) and material specimens and to discuss individual
research problems with the faculty.



From nih-image-d-request@io.ece.drexel.edu Tue Jul 20 06:15 EDT 1999
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------------------------------

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nih-image-d Digest				Volume 99 : Issue 165

Today's Topics:
  Unidentified subject!                 [ "Eric S. Corp" <escorp@psych.umass. ]
  Re: Course Announcement 2             [ "Norris O'Dell" <nodell@mail.mcg.ed ]

------------------------------

Date: Sun, 18 Jul 1999 17:12:25 -0400
From: "Eric S. Corp" <escorp@psych.umass.edu>
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_________________________
Eric S. Corp
Research Associate Professor
Neuroscience and Behavior Program and
Center for Neuroendocrine Studies
518 Tobin Hall, Box 37710
University of Massachusetts
Amherst, MA 01003-7710, USA
(413) 545-4295  -0996 (FAX)
NSB program http://www.umass.edu/neuro/faculty/corp.html



      

------------------------------

Date: Mon, 19 Jul 1999 07:45:25 -0400
From: "Norris O'Dell" <nodell@mail.mcg.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: Course Announcement 2
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Thanks Mike, norris

>>> <hard@acsu.buffalo.edu> 07/13 6:05 PM >>>
Course Announcement

Title: Optical Microscopy and Imaging in the Biomedical Sciences

When: October 6 - October 14, 1999

Where: Marine Biology Laboratory, Woods Hole, MA, USA

Tuition: $2050 (Includes room and board, text, handouts, supplies)

Application Deadline: August 3, 1999

Admission application and information:
     Carol Hamel, Admissions Coordinator
     Marine Biological Laboratory
     7 MBL Street
     Woods Hole, MA 02543-1015
     (508) 289-7401
     Internet: admissions@mbl.edu 
     WWW: http://www.mbl.edu (Application forms available via Adobe Acrobat)

Course Director: Colin S. Izzard, State University of New York @ Albany
                 Phone: [518] 442 - 4367
                 EMail: csizzard@csc.albany.edu 

Course Description:

For Whom:
      Designed primarily for research scientists, physicians, postdoctoral 
trainees and advanced graduate students in animal, plant, medical and 
material sciences. Non-biologists seeking a comprehensive introduction to 
microscopy and video-imaging will benefit greatly from this course as well. 
There are no specific prerequisites, but an understanding of the basic 
principles of optics is desirable. Limited to 24 students.

  The eight day course consists of lectures, laboratory demonstrations, 
exercises and discussions that will enable the participant to obtain and 
interpret microscope images of high quality, to perform quantitative optical
measurements, and to produce photographic and video records for
documentation 
and analysis.

Topics to be covered include:
      principles of microscope design and image formation
      bright field, dark field, phase contrast, polarized light,
differential
         interference contrast, interference reflection, and fluorescence
         microscopy
      confocal scanning microscopy, multiphoton excitation fluorescence
         microscopy and image deconvolution
      digital image restoration and 3-D reconstruction
      video imaging, recording, enhancement, and intensification
      analog and digital image processing and analysis
      fluorescent probes and ratiometric-imaging
      laser tweezers and laser scissors

  Applications to live cells will be emphasized; other specimens will be 
covered as well.

  Students will have direct hands-on experience with state-of-the-art 
microscopes, video cameras, recorders and image processing equipment
provided by major optical and electronics companies. Instruction will be
provided by experienced staff from universities and industry.

  Students are encouraged to bring their own biological (primary 
cultures, cell lines, etc.) and material specimens and to discuss individual
research problems with the faculty.

--------------------------------
End of nih-image-d Digest V99 Issue #165
****************************************

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To: nih-image@io.ece.drexel.edu
From: Nora Doegnitz <Nora.Doegnitz@epfl.ch>
Subject: align images
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I want to align images in a stack by using the register function with the
text file. But I do not understand the description of this function in the
nih-image manual.

All my images have only pixel coordinates. I do not use a microscope stage.
Let's say, I have 400x300 pixel images. The center point of the image is

cx=200, cy =150.

All my distances are in pixel dimensions, therefore I write the same in
line 2 and 3.

sx1=1	sy1=1	sx2=200	sy2=200
sx1=1	sy1=1	sx2=200	sy2=200

I measure the coordinates of three regions which I can find in all images.
I write these coordinates Px1,Py1,Px2,Py2,Px3,Py3 of the fist image  to the
4th line of the text file. In the next line I write the coordinates of the
second image and so on.

But what is the meaning of x? and y? in the text file? The center point of
all my images is always x=200, y=150. (That does not work, I tried.)


TEXT FILE:
cx	cy
sx1	sy1	sx2	sy2
sx1	sy1	sx2	sy2
x?	y?	Px1	Py1	Px2	Py2	Px3	Py3
x?	y?	Px1	Py1	Px2	Py2	Px3	Py3
...

Could you explain, how REGISTER with a text file works?
Or do you know a better way to align images?


I would be very happy about some help.

Thanks, Nora.




From nih-image-request@io.ece.drexel.edu Tue Jul 20 10:41 EDT 1999
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Date: Tue, 20 Jul 1999 09:22:37 -0500 (CDT)
From: Saveez <saveez@hbar.wustl.edu>
To: nih-image@io.ece.drexel.edu
Subject: Filament Tracking
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Hi,

 I am trying to write a filament tracking macro for scion and luckily 
enough I got this message from one of our collaborators, do you know 
where can I find this macro autotrack on zippy?

Thank you in advance.

saveez

PS attached you can find the email I got.

Saveez saffarian

Physics Department Washington University


From nih-image-request@io.ece.drexel.edu Tue Jul 20 10:51 EDT 1999
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Date: Tue, 20 Jul 1999 10:35:49 +0400 (GMT)
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From: Richard Herd <rahe@unixa.nerc-keyworth.ac.uk>
Subject: Re: more text files to graphics?
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Hi,

XYZ data import / manipulations / writing things to stacks and so on are
easily handled at source code level.  You have much much more freedom in
what you do working with source code rather than macros.  You can read in
data from a tab-delimited text file using:
  InitTextInput(MyFile, RefNum);
and
  GetLineFromText(rLine, nValues);
there are examples of how to use these in File2.p

Writing things at certain points on a specific slice can be done with
  PutPixel(x,y,value);
and
  SelectSlice(slice);

Cheers - Richard


>Thanks for pointing us to the XYZ plotting macros, but this isn't really
>what we want to do.
>Basically, we have a series of text files numbered 000 to 0??.  The
>filename is our Z coordinate.
>The format is as follows:
>
>1	45	34
>2	22	98
>3	12	87
>1	88	88
>2	23	99
>
>So the points 1..3 belong to one object and the points 1..2 belong to a
>second object.  We want to draw each object at a specific pixel intensity
>into a stack.
>
>>>We have a text file with three columns of real numbers corresponding to X,
>>>Y and Z.
>>>We want to write a simple macro to import these columns, convert to integer
>>>and to plot the numbers into a stack.



Richard Herd
Montserrat Volcano Observatory
St Johns
Montserrat
West Indies
email : rahe@ua.nkw.ac.uk
phone : (1) 664 491 5647
FAX : (1) 664 491 2324



From nih-image-d-request@io.ece.drexel.edu Tue Jul 20 22:08 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #166
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 166

Today's Topics:
  align images                          [ Nora Doegnitz <Nora.Doegnitz@epfl.c ]
  Filament Tracking                     [ Saveez <saveez@hbar.wustl.edu> ]
  Re: more text files to graphics?      [ Richard Herd <rahe@unixa.nerc-keywo ]
  losing hair on length problem         [ Bala Iyengar <iyengabg@mcmail.cis.m ]

------------------------------

Date: Tue, 20 Jul 1999 12:07:23 +0200
From: Nora Doegnitz <Nora.Doegnitz@epfl.ch>
To: nih-image@io.ece.drexel.edu
Subject: align images
Message-Id: <v03007801b3b9eec6dc58@[128.178.41.59]>
Content-Type: text/plain; charset="us-ascii"

I want to align images in a stack by using the register function with the
text file. But I do not understand the description of this function in the
nih-image manual.

All my images have only pixel coordinates. I do not use a microscope stage.
Let's say, I have 400x300 pixel images. The center point of the image is

cx=200, cy =150.

All my distances are in pixel dimensions, therefore I write the same in
line 2 and 3.

sx1=1	sy1=1	sx2=200	sy2=200
sx1=1	sy1=1	sx2=200	sy2=200

I measure the coordinates of three regions which I can find in all images.
I write these coordinates Px1,Py1,Px2,Py2,Px3,Py3 of the fist image  to the
4th line of the text file. In the next line I write the coordinates of the
second image and so on.

But what is the meaning of x? and y? in the text file? The center point of
all my images is always x=200, y=150. (That does not work, I tried.)


TEXT FILE:
cx	cy
sx1	sy1	sx2	sy2
sx1	sy1	sx2	sy2
x?	y?	Px1	Py1	Px2	Py2	Px3	Py3
x?	y?	Px1	Py1	Px2	Py2	Px3	Py3
...

Could you explain, how REGISTER with a text file works?
Or do you know a better way to align images?


I would be very happy about some help.

Thanks, Nora.

------------------------------

Date: Tue, 20 Jul 1999 09:22:37 -0500 (CDT)
From: Saveez <saveez@hbar.wustl.edu>
To: nih-image@io.ece.drexel.edu
Subject: Filament Tracking
Message-Id: <Pine.OSF.3.91.990720091352.22839B-200000@hbar.wustl.edu>
Content-Type: MULTIPART/MIXED; BOUNDARY="0-1295691872-932480538=:22839"
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  This message is in MIME format.  The first part should be readable text,
  while the remaining parts are likely unreadable without MIME-aware tools.
  Send mail to mime@docserver.cac.washington.edu for more info.

--0-1295691872-932480538=:22839
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII
Content-ID: <Pine.OSF.3.91.990720092229.22839E@hbar.wustl.edu>


Hi,

 I am trying to write a filament tracking macro for scion and luckily 
enough I got this message from one of our collaborators, do you know 
where can I find this macro autotrack on zippy?

Thank you in advance.

saveez

PS attached you can find the email I got.

Saveez saffarian

Physics Department Washington University

------------------------------

Date: Tue, 20 Jul 1999 10:35:49 +0400 (GMT)
From: Richard Herd <rahe@unixa.nerc-keyworth.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: more text files to graphics?
Message-Id: <l03130300b3b8a8deae72@[209.88.239.67]>
Content-Type: text/plain; charset="us-ascii"

Hi,

XYZ data import / manipulations / writing things to stacks and so on are
easily handled at source code level.  You have much much more freedom in
what you do working with source code rather than macros.  You can read in
data from a tab-delimited text file using:
  InitTextInput(MyFile, RefNum);
and
  GetLineFromText(rLine, nValues);
there are examples of how to use these in File2.p

Writing things at certain points on a specific slice can be done with
  PutPixel(x,y,value);
and
  SelectSlice(slice);

Cheers - Richard


>Thanks for pointing us to the XYZ plotting macros, but this isn't really
>what we want to do.
>Basically, we have a series of text files numbered 000 to 0??.  The
>filename is our Z coordinate.
>The format is as follows:
>
>1	45	34
>2	22	98
>3	12	87
>1	88	88
>2	23	99
>
>So the points 1..3 belong to one object and the points 1..2 belong to a
>second object.  We want to draw each object at a specific pixel intensity
>into a stack.
>
>>>We have a text file with three columns of real numbers corresponding to X,
>>>Y and Z.
>>>We want to write a simple macro to import these columns, convert to integer
>>>and to plot the numbers into a stack.



Richard Herd
Montserrat Volcano Observatory
St Johns
Montserrat
West Indies
email : rahe@ua.nkw.ac.uk
phone : (1) 664 491 5647
FAX : (1) 664 491 2324

------------------------------

Date: Tue, 20 Jul 1999 22:02:35 -0400 (EDT)
From: Bala Iyengar <iyengabg@mcmail.cis.mcmaster.ca>
To: nih-image@io.ece.drexel.edu
Subject: losing hair on length problem 
Message-Id: <l03130300b3ba9ddce420@[130.113.126.207]>
Content-Type: text/plain; charset="us-ascii"

Hello all,
I'm using a macro to dynamically (real time through an AG5 board and a CCD)
track a moving object using mouse movement. I use a BNC T-adapter in the
CCD that allows me to record the expt in a VCR simultaneously. The track
data (distance travelled in pixel units) generated in real time does not
seem to agree with the manual tracking (done offline) where I use an
acetate sheet placed on the TV monitor and track manually using a pen, I
then scan this track and measure the distance travelled once again in NIH
Image.The discrepancy is for eg; 210 pixels in offline mode Vs 300 pixels
in realtime mode.  I have caliberated (set scale) using known distances in
both methods, I get 60 pixels=1cm in the realtime situation and 75
pixels=1cm in the offline mode (adjusted pixel aspect ratio which = 0.926).
I write this with some desparation, I have scratched my head very hard and
I have very little hair left now. Any help will be greatly appreciated.
TIA,
Bala

--------------------------------
End of nih-image-d Digest V99 Issue #166
****************************************

From nih-image-request@io.ece.drexel.edu Tue Jul 20 22:14 EDT 1999
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Hello all,
I'm using a macro to dynamically (real time through an AG5 board and a CCD)
track a moving object using mouse movement. I use a BNC T-adapter in the
CCD that allows me to record the expt in a VCR simultaneously. The track
data (distance travelled in pixel units) generated in real time does not
seem to agree with the manual tracking (done offline) where I use an
acetate sheet placed on the TV monitor and track manually using a pen, I
then scan this track and measure the distance travelled once again in NIH
Image.The discrepancy is for eg; 210 pixels in offline mode Vs 300 pixels
in realtime mode.  I have caliberated (set scale) using known distances in
both methods, I get 60 pixels=1cm in the realtime situation and 75
pixels=1cm in the offline mode (adjusted pixel aspect ratio which = 0.926).
I write this with some desparation, I have scratched my head very hard and
I have very little hair left now. Any help will be greatly appreciated.
TIA,
Bala



From nih-image-request@io.ece.drexel.edu Wed Jul 21 04:03 EDT 1999
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Date: Wed, 21 Jul 1999 09:40:32 +0200
To: nih-image@io.ece.drexel.edu
From: "Claire.Mauduit" <mauduit@lsgrisn1.univ-lyon1.fr>
Subject: underestimated of bands
Resent-Message-ID: <"-mrt4.0.NX.GfNbt"@io>
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I begin to use the soft NIH image, and I have some questions.

For transparent gel image capture and quantification I use a duoscan T1200
Agfa, that contain a transparency plate. Are those conditions good or
comparable to the use of a transparent media adapter?

I began to scan and to quantify transparent gel images following the
instructions from " NIH image 1.60 tutorial, using image for densitometric
analysis of 1D gels." When I calibrate with the calibration tablet from
Kodak, (reflective tablet), I managed the calibration, with Rodbard
technic, only with the first five bands (on eleven existing on the tablet).
Is it suffisant, normal for  the calibration?


For the quantification of transparent gels, I used the macros gel plotting
2.1 ("european"). It seems that the software underestimated the bands. Is
there a tool for decrease the threshold?

I would be very happy about some help.

Thanks,

Claire



From nih-image-d-request@io.ece.drexel.edu Thu Jul 22 06:18 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #167
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 167

Today's Topics:
  underestimated of bands               [ "Claire.Mauduit" <mauduit@lsgrisn1. ]

------------------------------

Date: Wed, 21 Jul 1999 09:40:32 +0200
From: "Claire.Mauduit" <mauduit@lsgrisn1.univ-lyon1.fr>
To: nih-image@io.ece.drexel.edu
Subject: underestimated of bands
Message-Id: <l03130300b3bb292b4773@[134.214.8.121]>
Content-Type: text/plain; charset="us-ascii"

I begin to use the soft NIH image, and I have some questions.

For transparent gel image capture and quantification I use a duoscan T1200
Agfa, that contain a transparency plate. Are those conditions good or
comparable to the use of a transparent media adapter?

I began to scan and to quantify transparent gel images following the
instructions from " NIH image 1.60 tutorial, using image for densitometric
analysis of 1D gels." When I calibrate with the calibration tablet from
Kodak, (reflective tablet), I managed the calibration, with Rodbard
technic, only with the first five bands (on eleven existing on the tablet).
Is it suffisant, normal for  the calibration?


For the quantification of transparent gels, I used the macros gel plotting
2.1 ("european"). It seems that the software underestimated the bands. Is
there a tool for decrease the threshold?

I would be very happy about some help.

Thanks,

Claire

--------------------------------
End of nih-image-d Digest V99 Issue #167
****************************************

From nih-image-request@io.ece.drexel.edu Thu Jul 22 13:09 EDT 1999
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Resent-Date: Thu, 22 Jul 1999 13:09:14 -0400 (EDT)
Date: Thu, 22 Jul 1999 17:50:17 +0100
From: Stamatis Pagakis <spagaki@nimr.mrc.ac.uk>
Subject: Re: Object Image rotater files
In-reply-to: <l03130300b3b33d070915@[145.117.53.66]>
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Hi

We do cell tracking in Object image and then we want to see the paths in
Rotater.  However, the image we get is not very informative unless in
rotater we can see a box outlining the extend of our data.  Can we do this
easily, either in rotater or in Object image?

Thank you

Stamatis

*-----------------*------------------*----------------------*---------------*

>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <
>Confocal and Image Analysis Laboratory             Tel: +44 (0)181 913 8675 <
>Membrane Biology                                Mobile: 0370 654288         <
>National Institute for Medical Research    Switchboard: 0181 9593666 x2621  <
>The Ridgeway                                   Message: x2219, x2622        <
>Mill Hill, London NW7 1AA                          FAX: +44 (0)181 906 4477 <


From nih-image-request@io.ece.drexel.edu Thu Jul 22 17:41 EDT 1999
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From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Object Image rotater files
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>We do cell tracking in Object image and then we want to see the paths in
>Rotater.  However, the image we get is not very informative unless in
>rotater we can see a box outlining the extend of our data.  Can we do this
>>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <

You can do this by using the macro command SetMarker(x, y, z).
Here is an example macro:

{Macro to create a 3D bounding frame
in a stack using objects:

- stack should be in the front
- slice spacing should be > 0
- 3D flag must be set in "Define Objects"
- active object type in 'Sequence
  window' should be
  "Segmented line" (if necessary
  insert SwitchToObject commands)
- if slice spacing is large, the frame is only
  visible in 'Slice 2D' mode.

Remark:
a stack slice extends to +/-0.5 of its
nominal value. Example: if slice spacing is 10um,
the first slice extends between
5um <= z < 15um.}


macro 'Make 3D Bounding Box';
var x, y, xmax, ymax, z, n, margin: real;
begin
  GetPicSize (xmax, ymax);
  margin := 1; {inset by 1 pixel for better visibility}
  xmax := xmax - margin;
  ymax := ymax - margin;
  CloseCell; {optional}
  z := 0.5; {rounding up for home slice}
  for n := 1 to 2 do begin
    Setmarker(margin, margin, z);
    Setmarker(xmax, margin, z);
    Setmarker(xmax, ymax, z);
    Setmarker(margin, ymax, z);
    Setmarker(margin, margin, z);
    CloseCell;
    z := nslices + 0.4999; {rounding down for home slice}
    end;

  for n := 1 to 4 do begin
    if (n=1) or (n=4) then
      x := margin
    else
      x := xmax;
    if (n=1) or (n=2) then
      y := margin
    else
      y := ymax;
    SetMarker(x, y, 0.5);
    SetMarker(x, y, nslices + 0.4999);
    CloseCell;
    end;
end;

Norbert Vischer                  University of Amsterdam
Scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



From nih-image-request@io.ece.drexel.edu Thu Jul 22 22:14 EDT 1999
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	for cshtest@io.ece.drexel.edu; Thu, 22 Jul 1999 22:14:31 -0400 (EDT)
Resent-Date: Thu, 22 Jul 1999 22:14:31 -0400 (EDT)
Date: 	Thu, 22 Jul 1999 21:59:28 -0400
From: Xudong Cao <xudong@chem-eng.toronto.edu>
X-Sender: xudong@chem-eng.utoronto.ca
To: nih-image@io.ece.drexel.edu
Subject: coordinate
In-Reply-To: <l03010d00b3bd2d98a26a@[212.238.25.42]>
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Dear netters,
Does anybody know a simple way to record the positions of objects of 
interest under a microscope? A set of coordinate (x,y) in relative to a 
reference will do.   

Thanks.
_______________________________
Xudong CAO
Center for Biomaterials
University of Toronto             	
Phone: (416) 978 0343		 
Fax: (416) 978 1462               

In science one tries to tell people, in such a way as to be 
understood by everyone, something that no one ever knew 
before. But in poetry, it's the exact opposite. 
- Paul Dirac               
                                 


From nih-image-request@io.ece.drexel.edu Thu Jul 22 22:43 EDT 1999
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Resent-Date: Thu, 22 Jul 1999 22:43:20 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: xudong@chem-eng.toronto.edu, nih-image@io.ece.drexel.edu
Date:          Fri, 23 Jul 1999 12:38:52 +1000
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>Date: 	Thu, 22 Jul 1999 21:59:28 -0400
>From: Xudong Cao <xudong@chem-eng.toronto.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: coordinate
>
>Dear netters,
>Does anybody know a simple way to record the positions of objects of 
>interest under a microscope? A set of coordinate (x,y) in relative to a 
>reference will do.   
>
>Thanks.
>_______________________________
>Xudong CAO
>Center for Biomaterials
>University of Toronto             	
>Phone: (416) 978 0343		 
>Fax: (416) 978 1462               
>
In NIH-Image, 
the cursor tool (10th down on right hand side of tool window)
does just that when mouse positioned and clicked. 
The x,y values are stored in the Results table ShowResults(Analyze menu
Reserved colors and lineWidth settings can be used to change color/dot size 
used to mark objects.
Object-Image will allow non-destructive overlay of marked objects to be 
stored.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-request@io.ece.drexel.edu Fri Jul 23 03:39 EDT 1999
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From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: USB to Serial converter
Date: Fri, 23 Jul 1999 17:23:01 +1000
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Hi,
I have just tried a USB to serial converter on a 400 MHz G3 Powerbook.
Steps required
1. plug in usb to serial converter into running powerbook.
The alert then told me I needed to install the software, so I did.
I restarted the mac and selected the ports (there are two and you can assign
them to the modem port the printer port and some other port) using the
mini-iDock control panel.

2. I ran NIH-image 1.62 using a macro which does some stuff using the modem
port, and having already plugged the device into the port selected on the
miin-iDock as that port, and started doing things, just as I would if the
power book had a modem port in it.

The serial device in question is a little box we made here which reads three
BCD lines of data from 3 digital micrometers and pumps these digits out the
serial port, 3 strings of 7 digits with a sign.
No dramas, no problems no crashes and no errors.


Device
mini-iDock   made by NewMotion Co Ltd

try www.newmotion.com.tw
I would recommend this device for such purposes.
I have no interest in the manufacture or sales of this device.

Noel goldsmith



From nih-image-d-request@io.ece.drexel.edu Fri Jul 23 05:16 EDT 1999
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Date: Fri, 23 Jul 1999 05:16:24 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #168
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 168

Today's Topics:
  Re: Object Image rotater files        [ Stamatis Pagakis <spagaki@nimr.mrc. ]
  Re: Object Image rotater files        [ Norbert Vischer <vischer@bio.uva.nl ]
  coordinate                            [ Xudong Cao <xudong@chem-eng.toronto ]
  Re: coordinate                        [ GJOSS@rna.bio.mq.edu.au ]
  USB to Serial converter               [ "Goldsmith, Noel" <Noel.Goldsmith@d ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]

------------------------------

Date: Thu, 22 Jul 1999 17:50:17 +0100
From: Stamatis Pagakis <spagaki@nimr.mrc.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Object Image rotater files
Message-id: <Pine.SGI.4.10.9907221743580.13182-100000@membo2>
Content-type: TEXT/PLAIN; charset=US-ASCII

Hi

We do cell tracking in Object image and then we want to see the paths in
Rotater.  However, the image we get is not very informative unless in
rotater we can see a box outlining the extend of our data.  Can we do this
easily, either in rotater or in Object image?

Thank you

Stamatis

*-----------------*------------------*----------------------*---------------*

>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <
>Confocal and Image Analysis Laboratory             Tel: +44 (0)181 913 8675 <
>Membrane Biology                                Mobile: 0370 654288         <
>National Institute for Medical Research    Switchboard: 0181 9593666 x2621  <
>The Ridgeway                                   Message: x2219, x2622        <
>Mill Hill, London NW7 1AA                          FAX: +44 (0)181 906 4477 <

------------------------------

Date: Thu, 22 Jul 1999 23:38:23 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Object Image rotater files
Message-Id: <l03010d00b3bd2d98a26a@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

>We do cell tracking in Object image and then we want to see the paths in
>Rotater.  However, the image we get is not very informative unless in
>rotater we can see a box outlining the extend of our data.  Can we do this
>>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <

You can do this by using the macro command SetMarker(x, y, z).
Here is an example macro:

{Macro to create a 3D bounding frame
in a stack using objects:

- stack should be in the front
- slice spacing should be > 0
- 3D flag must be set in "Define Objects"
- active object type in 'Sequence
  window' should be
  "Segmented line" (if necessary
  insert SwitchToObject commands)
- if slice spacing is large, the frame is only
  visible in 'Slice 2D' mode.

Remark:
a stack slice extends to +/-0.5 of its
nominal value. Example: if slice spacing is 10um,
the first slice extends between
5um <= z < 15um.}


macro 'Make 3D Bounding Box';
var x, y, xmax, ymax, z, n, margin: real;
begin
  GetPicSize (xmax, ymax);
  margin := 1; {inset by 1 pixel for better visibility}
  xmax := xmax - margin;
  ymax := ymax - margin;
  CloseCell; {optional}
  z := 0.5; {rounding up for home slice}
  for n := 1 to 2 do begin
    Setmarker(margin, margin, z);
    Setmarker(xmax, margin, z);
    Setmarker(xmax, ymax, z);
    Setmarker(margin, ymax, z);
    Setmarker(margin, margin, z);
    CloseCell;
    z := nslices + 0.4999; {rounding down for home slice}
    end;

  for n := 1 to 4 do begin
    if (n=1) or (n=4) then
      x := margin
    else
      x := xmax;
    if (n=1) or (n=2) then
      y := margin
    else
      y := ymax;
    SetMarker(x, y, 0.5);
    SetMarker(x, y, nslices + 0.4999);
    CloseCell;
    end;
end;

Norbert Vischer                  University of Amsterdam
Scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: 	Thu, 22 Jul 1999 21:59:28 -0400
From: Xudong Cao <xudong@chem-eng.toronto.edu>
To: nih-image@io.ece.drexel.edu
Subject: coordinate
Message-ID: <Pine.SGI.3.91.990722215222.15655A-100000@chem-eng.utoronto.ca>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear netters,
Does anybody know a simple way to record the positions of objects of 
interest under a microscope? A set of coordinate (x,y) in relative to a 
reference will do.   

Thanks.
_______________________________
Xudong CAO
Center for Biomaterials
University of Toronto             	
Phone: (416) 978 0343		 
Fax: (416) 978 1462               

In science one tries to tell people, in such a way as to be 
understood by everyone, something that no one ever knew 
before. But in poetry, it's the exact opposite. 
- Paul Dirac               
                                 

------------------------------

Date:          Fri, 23 Jul 1999 12:38:52 +1000
From: GJOSS@rna.bio.mq.edu.au
To: xudong@chem-eng.toronto.edu, nih-image@io.ece.drexel.edu
Subject:       Re: coordinate
Message-ID: <25BF62C37@rna.bio.mq.edu.au>

>Date: 	Thu, 22 Jul 1999 21:59:28 -0400
>From: Xudong Cao <xudong@chem-eng.toronto.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: coordinate
>
>Dear netters,
>Does anybody know a simple way to record the positions of objects of 
>interest under a microscope? A set of coordinate (x,y) in relative to a 
>reference will do.   
>
>Thanks.
>_______________________________
>Xudong CAO
>Center for Biomaterials
>University of Toronto             	
>Phone: (416) 978 0343		 
>Fax: (416) 978 1462               
>
In NIH-Image, 
the cursor tool (10th down on right hand side of tool window)
does just that when mouse positioned and clicked. 
The x,y values are stored in the Results table ShowResults(Analyze menu
Reserved colors and lineWidth settings can be used to change color/dot size 
used to mark objects.
Object-Image will allow non-destructive overlay of marked objects to be 
stored.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

------------------------------

Date: Fri, 23 Jul 1999 17:23:01 +1000
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: USB to Serial converter
Message-Id: <F98649A5EE8ED11190160000F802756598D107@exchvic3.dsto.defence.gov.au>
Content-Type: text/plain;
	charset="windows-1252"

Hi,
I have just tried a USB to serial converter on a 400 MHz G3 Powerbook.
Steps required
1. plug in usb to serial converter into running powerbook.
The alert then told me I needed to install the software, so I did.
I restarted the mac and selected the ports (there are two and you can assign
them to the modem port the printer port and some other port) using the
mini-iDock control panel.

2. I ran NIH-image 1.62 using a macro which does some stuff using the modem
port, and having already plugged the device into the port selected on the
miin-iDock as that port, and started doing things, just as I would if the
power book had a modem port in it.

The serial device in question is a little box we made here which reads three
BCD lines of data from 3 digital micrometers and pumps these digits out the
serial port, 3 strings of 7 digits with a sign.
No dramas, no problems no crashes and no errors.


Device
mini-iDock   made by NewMotion Co Ltd

try www.newmotion.com.tw
I would recommend this device for such purposes.
I have no interest in the manufacture or sales of this device.

Noel goldsmith

------------------------------

Date: Fri, 23 Jul 1999 05:05:00 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199907230905.FAA00948@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
                   ---------------------------
     


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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

--------------------------------
End of nih-image-d Digest V99 Issue #168
****************************************

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                   NIH-image Mailing List Help 
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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--


From nih-image-request@io.ece.drexel.edu Fri Jul 23 10:51 EDT 1999
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From: "Abby K. Van-Den-Berg" <avan@zoo.uvm.edu>
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I'm analyzing color images with nih-image.  Is there an way to creat a
bitmask to eliminate the background pixels in the original color image?
Thanks,

-Abby



Abby van den Berg
Department of Forestry
University of Vermont
avan@zoo.uvm.edu


From nih-image-request@io.ece.drexel.edu Fri Jul 23 15:01 EDT 1999
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Resent-Date: Fri, 23 Jul 1999 15:01:34 -0400 (EDT)
Date: Fri, 23 Jul 1999 14:48:15 +0000
From: Sarah Emery <emery_s@cc.denison.edu>
Subject: numbering objects in stack
To: nih-image@io.ece.drexel.edu
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Dear NIH Imagers,
    I am using NIH Image to track the growth of individual plants in a
plot over time using color slides that I've put into stacks.  So far, I
have outlined and filled all of the plants with a single color and tried
to used density slice and then analyze particles to get the individual
plants numbered and then record area, perimeter, distance from each
other, etc. to then put in a spreadsheet and analyze.  The problem is
that the plants move slightly in relationship to each other over time
(yes-plants can move), so a single plant will get assigned a different
number at each slice in the stack because the spacing of the plants
change slightly (also, the slides were taken over a year's time, and the
photos aren't in perfect focus or scale with each other- about 25 slides
total).  I want to be able to assign a single number to each plant
(around 30 plants total) that it will keep throughout the whole time
sequence.  Does anyone know of a way of either hand-numbering
individuals through a stack, or of editing what individuals are numbered
as once NIH Image has done an "Analyze Particles"?  Any help would be
greatly appreciated.

Sarah Emery
emery_s@denison.edu


From nih-image-d-request@io.ece.drexel.edu Sat Jul 24 06:08 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #169
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 169

Today's Topics:
  masks                                 [ "Abby K. Van-Den-Berg" <avan@zoo.uv ]
  numbering objects in stack            [ Sarah Emery <emery_s@cc.denison.edu ]

------------------------------

Date: Fri, 23 Jul 1999 10:31:43 -0400 (EDT)
From: "Abby K. Van-Den-Berg" <avan@zoo.uvm.edu>
To: nih-image@io.ece.drexel.edu
Subject: masks
Message-ID: <Pine.A41.3.96.990723102945.56438A-100000@elk.uvm.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I'm analyzing color images with nih-image.  Is there an way to creat a
bitmask to eliminate the background pixels in the original color image?
Thanks,

-Abby



Abby van den Berg
Department of Forestry
University of Vermont
avan@zoo.uvm.edu

------------------------------

Date: Fri, 23 Jul 1999 14:48:15 +0000
From: Sarah Emery <emery_s@cc.denison.edu>
To: nih-image@io.ece.drexel.edu
Subject: numbering objects in stack
Message-id: <379880A9.B3A5C151@cc.denison.edu>
Content-type: text/plain; charset=us-ascii; x-mac-type="54455854";
 x-mac-creator="4D4F5353"
Content-transfer-encoding: 7bit

Dear NIH Imagers,
    I am using NIH Image to track the growth of individual plants in a
plot over time using color slides that I've put into stacks.  So far, I
have outlined and filled all of the plants with a single color and tried
to used density slice and then analyze particles to get the individual
plants numbered and then record area, perimeter, distance from each
other, etc. to then put in a spreadsheet and analyze.  The problem is
that the plants move slightly in relationship to each other over time
(yes-plants can move), so a single plant will get assigned a different
number at each slice in the stack because the spacing of the plants
change slightly (also, the slides were taken over a year's time, and the
photos aren't in perfect focus or scale with each other- about 25 slides
total).  I want to be able to assign a single number to each plant
(around 30 plants total) that it will keep throughout the whole time
sequence.  Does anyone know of a way of either hand-numbering
individuals through a stack, or of editing what individuals are numbered
as once NIH Image has done an "Analyze Particles"?  Any help would be
greatly appreciated.

Sarah Emery
emery_s@denison.edu

--------------------------------
End of nih-image-d Digest V99 Issue #169
****************************************

From nih-image-request@io.ece.drexel.edu Sun Jul 25 22:21 EDT 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: emery_s@cc.denison.edu, nih-image@io.ece.drexel.edu
Date:          Mon, 26 Jul 1999 12:09:52 +1000
Subject:       Re: numbering objects in stack
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>Date: Fri, 23 Jul 1999 14:48:15 +0000
>From: Sarah Emery <emery_s@cc.denison.edu>
>Subject: numbering objects in stack
>To: nih-image@io.ece.drexel.edu
>
>Dear NIH Imagers,
>    I am using NIH Image to track the growth of individual plants in a
>plot over time using color slides that I've put into stacks.  So far, I
>have outlined and filled all of the plants with a single color and tried
>to used density slice and then analyze particles to get the individual
>plants numbered and then record area, perimeter, distance from each
>other, etc. to then put in a spreadsheet and analyze.  The problem is
>that the plants move slightly in relationship to each other over time
>(yes-plants can move), so a single plant will get assigned a different
>number at each slice in the stack because the spacing of the plants
>change slightly (also, the slides were taken over a year's time, and the
>photos aren't in perfect focus or scale with each other- about 25 slides
>total).  I want to be able to assign a single number to each plant
>(around 30 plants total) that it will keep throughout the whole time
>sequence.  Does anyone know of a way of either hand-numbering
>individuals through a stack, or of editing what individuals are numbered
>as once NIH Image has done an "Analyze Particles"?  Any help would be
>greatly appreciated.
>
>Sarah Emery
>emery_s@denison.edu

Sarah,
If you simply want to manually identify rows of the result table so that 
the spreadsheet rows can be sorted etc, then a simple macro such as:
_________________________
var row,ident:integer;
macro'[F1]identify result row';begin 
SetUser1Label('Ident');
if (row>rcount) or (row<=0) then row:=1;
row:=getNumber('row:',row);
ident:=getNumber('ident:',ident);
rUser1[row]:=ident;
end
_________________________
will allow you to assign an ident to the rUser1[] column after the  
"Analyze Particles". 
{cut and paste to a text window and then "Load Macros from Window"}

As you "have outlined and filled all of the plants with a single color and 
tried to used density slice and then analyze particles"; an alternative 
would have been to make each plant self-identifying by filling each plant 
with a unique color (or index value);
Use a density slice to cover the range assigned, so that analyze particles 
would then return rMean[](also rMin,rMax) as the plant id.
If you set density slice to the single color, then 
_________________________
var x,y,ident:integer;
macro'[F2]identify autoOutlined Object';begin 
getMouse(x,y);autoOutLine(x,y);
setForeGround(getNumber('ident:',ident+1));
fill;
end
_________________________
would allow you to simply id each plant by color using the Wand or 
autoOutLine.

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-d-request@io.ece.drexel.edu Tue Jul 27 06:10 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #170
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 170

Today's Topics:
  Re: numbering objects in stack        [ GJOSS@rna.bio.mq.edu.au ]

------------------------------

Date:          Mon, 26 Jul 1999 12:09:52 +1000
From: GJOSS@rna.bio.mq.edu.au
To: emery_s@cc.denison.edu, nih-image@io.ece.drexel.edu
Subject:       Re: numbering objects in stack
Message-ID: <2A60C6190B@rna.bio.mq.edu.au>

>Date: Fri, 23 Jul 1999 14:48:15 +0000
>From: Sarah Emery <emery_s@cc.denison.edu>
>Subject: numbering objects in stack
>To: nih-image@io.ece.drexel.edu
>
>Dear NIH Imagers,
>    I am using NIH Image to track the growth of individual plants in a
>plot over time using color slides that I've put into stacks.  So far, I
>have outlined and filled all of the plants with a single color and tried
>to used density slice and then analyze particles to get the individual
>plants numbered and then record area, perimeter, distance from each
>other, etc. to then put in a spreadsheet and analyze.  The problem is
>that the plants move slightly in relationship to each other over time
>(yes-plants can move), so a single plant will get assigned a different
>number at each slice in the stack because the spacing of the plants
>change slightly (also, the slides were taken over a year's time, and the
>photos aren't in perfect focus or scale with each other- about 25 slides
>total).  I want to be able to assign a single number to each plant
>(around 30 plants total) that it will keep throughout the whole time
>sequence.  Does anyone know of a way of either hand-numbering
>individuals through a stack, or of editing what individuals are numbered
>as once NIH Image has done an "Analyze Particles"?  Any help would be
>greatly appreciated.
>
>Sarah Emery
>emery_s@denison.edu

Sarah,
If you simply want to manually identify rows of the result table so that 
the spreadsheet rows can be sorted etc, then a simple macro such as:
_________________________
var row,ident:integer;
macro'[F1]identify result row';begin 
SetUser1Label('Ident');
if (row>rcount) or (row<=0) then row:=1;
row:=getNumber('row:',row);
ident:=getNumber('ident:',ident);
rUser1[row]:=ident;
end
_________________________
will allow you to assign an ident to the rUser1[] column after the  
"Analyze Particles". 
{cut and paste to a text window and then "Load Macros from Window"}

As you "have outlined and filled all of the plants with a single color and 
tried to used density slice and then analyze particles"; an alternative 
would have been to make each plant self-identifying by filling each plant 
with a unique color (or index value);
Use a density slice to cover the range assigned, so that analyze particles 
would then return rMean[](also rMin,rMax) as the plant id.
If you set density slice to the single color, then 
_________________________
var x,y,ident:integer;
macro'[F2]identify autoOutlined Object';begin 
getMouse(x,y);autoOutLine(x,y);
setForeGround(getNumber('ident:',ident+1));
fill;
end
_________________________
would allow you to simply id each plant by color using the Wand or 
autoOutLine.

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

--------------------------------
End of nih-image-d Digest V99 Issue #170
****************************************

From nih-image-request@io.ece.drexel.edu Tue Jul 27 11:54 EDT 1999
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From: "Bogdan Smolka" <BSmolka@peach.ia.polsl.gliwice.pl>
To: <nih-image@io.ece.drexel.edu>
Subject: CALL FOR PAPERS ,  GKPO CONFERENCE, Poland
Date: Tue, 27 Jul 1999 17:33:18 +0200
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Content-Type: text/plain;
	charset="iso-8859-2"
Content-Transfer-Encoding: quoted-printable

Dear Friends,
I would like to inform you about  the GKPO'2000: 6th International =
Conference on Computer Graphics and Image Processing Conference, which =
will be held in Poland next year.=20

Looking forward to seeing you in Poland,

Yours sincerely,
dr Bogdan Smolka
Silesian Technical University
Gliwice, Poland

-------------------------------------------------------------------------=
--
CALL FOR PAPERS  *  CALL FOR PAPERS  *  CALL FOR PAPERS  *  CALL FOR =
PAPERS
-------------------------------------------------------------------------=
--
           =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =
GKPO'2000 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
                GKPO'2000: 6th International Conference on
                 Computer Graphics and Image Processing
           =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

The 6th GKPO'2000 intends to group the best researchers active in the =
field
of pictorial information exchange between computer and its environment.
The reviewing process and strict acceptance criteria assure high quality
of the accepted papers.

The Conference is planned as one track (oral and poster) presentations =
and
the number of participants is limited to max 80 persons.

The conference will be a forum for presentation of theoretical
aspects, methods, applications and systems of image processing. =
Unpublished
research papers are solicited, particulary concerning the following =
topics:
-- Image analysis and scene understanding
-- Multimodal and multisensor models of image formation
-- Pattern recognition in image processing
-- Motion analysis, visual navigation and active vision
-- Geometrical and structural models of objects and scenes
-- Fractal and chaos theory in image analysis
-- Modeling of human visual perception and mental imagery
-- Structure reconstruction, 3D imaging and image synthesis
-- Infrared, laser etc. imaging
-- Visualization and graphical data presentation
-- Virtual reality and pictorial interaction
-- Pictorial data bases and archivisation
-- Computational geometry
-- Computer-aided graphic design, arts and animation
-- Industrial, medical and other applications

The programme will include: invited papers by leading researchers, =
selected
contributions in oral and poster sessions, open session, presentations
of systems and social events.

DATE: 15-19 of May, 2000.

SUBMISSIONS: Authors are requested to submit four copies of manuscript =
in
English (max. 6 pages). Upon acceptance by the reviewers and Programme
Committee
(selection criteria include originality of ideas, accuracy and clarity =
of
explanation), authors will be asked to submit a PC diskette (in DOS
format),containing the text of the paper, prepared with LaTex with =
pictures
in POSTSCRIPT.

PROCEEDINGS of the Conference will be published as a special issue (vol. =
9(1//2))
of the Machine GRAPHICS & VISION Journal.

                   The best paper will be rewarded.

Declaration form expected by 31.07.1999.

DEADLINES:
Papers                                   --  30.10.1999.
Notification for acceptance              --  30.01.2000.
Submission of final version of papers    --  29.02.2000.

CHAIR of the Conference: W. MOKRZYCKI (PL)

V-CE CHAIR - Chair of the Programme Committee:  J.L. KULIKOWSKI (PL)

PROGRAMME COMMITTEE:
S. Ablameyko (BY)  P. Bhattacharya (US)  T. Belikova (RU)     E. =
Bengtsson (SE)
A. Borkowski (PL)  D. Chetverikov (HU)   L. Chmielewski (PL)  J. Chocjan =
(PL)
R. Choras (PL)     S. Dellepiane (IT)    U. Eckhardt (DE)     M. =
Flasinski (PL)
A. Gagalowicz (FR) D. Gillies (UK)       J. Goutsias (US)     E. Grabska =
(PL)
H. Heijmans (NL)   J.-M. Jolion (FR)     A. Kasinski (PL)     R. Klette =
(NZ)
W. Klonowski (PL)  E. Kolodzinski(PL)    R. Kozera (AU)       H. =
Kreowski (DE)
Z. Kulpa (PL)      M. Kurzynski (PL)     W. Kwiatkowski(PL)   G. Levina =
(RU)
L. Luchowski (PL)  V. Lukin (UA)         W. Malina (PL)       A. Materka =
(PL)
H. Niemann (DE)    M. Nieniewski (PL)    M. Paprzycki (US)    J. =
Roerdink (NL)
B. Sadykhov (BY)   B. Sankur (TR)        R. Sara (CZ)         V. Skala =
(CZ)
G. Sommer (DE)     J. Soldek (PL)        L. Szirmay-Kalos(HU) V. Valev =
(BG)
L. Vincent (US)    T. Vintsiuk (UA)      R. Vorobel (UA)      J. =
Zabrodzki (PL)
A. Zilinskas (LT)

V-CE CHAIR - Chair of the Organizing Committee:K .WOJCIECHOWSKI (PL)

ORGANIZING COMMITTEE:
D. Bereska, K. Fujarewicz, M. Grzegorek, K. Moscinska (PL)
Secretary: -- H. PALUS (PL)
tel./fax.: ++48-32 23-72-744,
e-mail: hpalus@ia.gliwice.edu.pl


Contact address:
GKPO'2000, ICS PAS,
Ordona 21, 01--237 Warsaw, Poland
fax.: ++48-22 37-65-64

GKPO'2000 on World Wide Web:
http://www.ippt.gov.pl/~zkulpa/MGV/GKPO2000.html

DECLARATION FORM: Prospective participants are kindly asked
to fill the Declaration Form below and send it by ordinary mail
or by fax to the Conference Contact Addrees given above.

See you at the Conference.

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
                                GKPO'2000

                            DECLARATION FORM

     I intend to participate in the GKPO'2000 Conference*

       Signature: ............          Date: .........

Name and title: .................................................

Affiliation: ....................................................

Address: ........................................................
.................................................................
................................................................



I plan:

  # to take part in the conference only
  # to submit a paper on oral session
  # to submit a paper on poster session


title of the paper
..................................................................
..................................................................
..................................................................

* - number of participants is limited to 80 persons

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

=20

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	charset="iso-8859-2"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD W3 HTML//EN">
<HTML>
<HEAD>

<META content=3Dtext/html;charset=3Diso-8859-2 =
http-equiv=3DContent-Type>
<META content=3D'"MSHTML 4.72.3612.1700"' name=3DGENERATOR>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT color=3D#000000><FONT size=3D3>Dear =
Friends,</FONT></FONT><FONT=20
size=3D3></FONT></DIV>
<DIV><FONT size=3D3>I would like to inform you about&nbsp; the =
</FONT><FONT=20
size=3D3>GKPO'2000: 6th International Conference on Computer Graphics =
and Image=20
Processing <FONT color=3D#000000>Conference, which will be held in =
Poland next=20
year. </FONT></FONT></DIV>
<DIV><FONT size=3D3><FONT color=3D#000000></FONT></FONT>&nbsp;</DIV>
<DIV><FONT size=3D3><FONT color=3D#000000>Looking forward to seeing you =
in=20
Poland,</FONT></FONT></DIV>
<DIV><FONT size=3D3><FONT color=3D#000000></FONT></FONT>&nbsp;</DIV>
<DIV>
<DIV><FONT size=3D2><FONT size=3D3>Yours sincerely,</FONT></DIV></DIV>
<DIV>
<DIV><FONT size=3D3>dr Bogdan Smolka</FONT></DIV>
<DIV><FONT size=3D3>Silesian Technical University</FONT></DIV>
<DIV><FONT size=3D3>Gliwice, Poland</FONT></DIV>
<DIV><FONT size=3D3></FONT>&nbsp;</DIV>
<DIV><FONT=20
size=3D3>----------------------------------------------------------------=
-----------<BR>CALL=20
FOR PAPERS&nbsp; *&nbsp; CALL FOR PAPERS&nbsp; *&nbsp; CALL FOR =
PAPERS&nbsp;=20
*&nbsp; CALL FOR=20
PAPERS<BR>---------------------------------------------------------------=
------------<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;=20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D GKPO'2000=20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<BR>&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;=20
GKPO'2000: 6th International Conference=20
on<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
Computer Graphics and Image=20
Processing<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;=20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
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BR><BR>The 6th GKPO'2000=20
intends to group the best researchers active in the field<BR>of =
pictorial=20
information exchange between computer and its environment.<BR>The =
reviewing=20
process and strict acceptance criteria assure high quality<BR>of the =
accepted=20
papers.<BR><BR>The Conference is planned as one track (oral and poster)=20
presentations and<BR>the number of participants is limited to max 80=20
persons.<BR><BR>The conference will be a forum for presentation of=20
theoretical<BR>aspects, methods, applications and systems of image =
processing.=20
Unpublished<BR>research papers are solicited, particulary concerning the =

following topics:<BR>-- Image analysis and scene understanding<BR>-- =
Multimodal=20
and multisensor models of image formation<BR>-- Pattern recognition in =
image=20
processing<BR>-- Motion analysis, visual navigation and active =
vision<BR>--=20
Geometrical and structural models of objects and scenes<BR>-- Fractal =
and chaos=20
theory in image analysis<BR>-- Modeling of human visual perception and =
mental=20
imagery<BR>-- Structure reconstruction, 3D imaging and image =
synthesis<BR>--=20
Infrared, laser etc. imaging<BR>-- Visualization and graphical data=20
presentation<BR>-- Virtual reality and pictorial interaction<BR>-- =
Pictorial=20
data bases and archivisation<BR>-- Computational geometry<BR>-- =
Computer-aided=20
graphic design, arts and animation<BR>-- Industrial, medical and other=20
applications<BR><BR>The programme will include: invited papers by =
leading=20
researchers, selected<BR>contributions in oral and poster sessions, open =

session, presentations<BR>of systems and social events.<BR><BR>DATE: =
15-19 of=20
May, 2000.<BR><BR>SUBMISSIONS: Authors are requested to submit four =
copies of=20
manuscript in<BR>English (max. 6 pages). Upon acceptance by the =
reviewers and=20
Programme<BR>Committee<BR>(selection criteria include originality of =
ideas,=20
accuracy and clarity of<BR>explanation), authors will be asked to submit =
a PC=20
diskette (in DOS<BR>format),containing the text of the paper, prepared =
with=20
LaTex with pictures<BR>in POSTSCRIPT.<BR><BR>PROCEEDINGS of the =
Conference will=20
be published as a special issue (vol. 9(1//2))<BR>of the Machine =
GRAPHICS &amp;=20
VISION=20
Journal.<BR><BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
The best paper will be rewarded.<BR><BR>Declaration form expected by=20
31.07.1999.<BR><BR>DEADLINES:<BR>Papers&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;=20
--&nbsp; 30.10.1999.<BR>Notification for=20
acceptance&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;=20
--&nbsp; 30.01.2000.<BR>Submission of final version of =
papers&nbsp;&nbsp;&nbsp;=20
--&nbsp; 29.02.2000.<BR><BR>CHAIR of the Conference: W. MOKRZYCKI=20
(PL)<BR><BR>V-CE CHAIR - Chair of the Programme Committee:&nbsp; J.L. =
KULIKOWSKI=20
(PL)<BR><BR>PROGRAMME COMMITTEE:<BR>S. Ablameyko (BY)&nbsp; P. =
Bhattacharya=20
(US)&nbsp; T. Belikova (RU)&nbsp;&nbsp;&nbsp;&nbsp; E. Bengtsson =
(SE)<BR>A.=20
Borkowski (PL)&nbsp; D. Chetverikov (HU)&nbsp;&nbsp; L. Chmielewski =
(PL)&nbsp;=20
J. Chocjan (PL)<BR>R. Choras (PL)&nbsp;&nbsp;&nbsp;&nbsp; S. Dellepiane=20
(IT)&nbsp;&nbsp;&nbsp; U. Eckhardt (DE)&nbsp;&nbsp;&nbsp;&nbsp; M. =
Flasinski=20
(PL)<BR>A. Gagalowicz (FR) D. Gillies =
(UK)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
J. Goutsias (US)&nbsp;&nbsp;&nbsp;&nbsp; E. Grabska (PL)<BR>H. Heijmans=20
(NL)&nbsp;&nbsp; J.-M. Jolion (FR)&nbsp;&nbsp;&nbsp;&nbsp; A. Kasinski=20
(PL)&nbsp;&nbsp;&nbsp;&nbsp; R. Klette (NZ)<BR>W. Klonowski (PL)&nbsp; =
E.=20
Kolodzinski(PL)&nbsp;&nbsp;&nbsp; R. Kozera=20
(AU)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; H. Kreowski (DE)<BR>Z. Kulpa=20
(PL)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; M. Kurzynski =
(PL)&nbsp;&nbsp;&nbsp;&nbsp; W.=20
Kwiatkowski(PL)&nbsp;&nbsp; G. Levina (RU)<BR>L. Luchowski (PL)&nbsp; V. =
Lukin=20
(UA)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; W. Malina=20
(PL)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A. Materka (PL)<BR>H. Niemann=20
(DE)&nbsp;&nbsp;&nbsp; M. Nieniewski (PL)&nbsp;&nbsp;&nbsp; M. Paprzycki =

(US)&nbsp;&nbsp;&nbsp; J. Roerdink (NL)<BR>B. Sadykhov (BY)&nbsp;&nbsp; =
B.=20
Sankur (TR)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; R. Sara=20
(CZ)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; V. Skala (CZ)<BR>G. =
Sommer=20
(DE)&nbsp;&nbsp;&nbsp;&nbsp; J. Soldek=20
(PL)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; L. Szirmay-Kalos(HU) V. =
Valev=20
(BG)<BR>L. Vincent (US)&nbsp;&nbsp;&nbsp; T. Vintsiuk=20
(UA)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; R. Vorobel =
(UA)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
J. Zabrodzki (PL)<BR>A. Zilinskas (LT)<BR><BR>V-CE CHAIR - Chair of the=20
Organizing Committee:K .WOJCIECHOWSKI (PL)<BR><BR>ORGANIZING =
COMMITTEE:<BR>D.=20
Bereska, K. Fujarewicz, M. Grzegorek, K. Moscinska (PL)<BR>Secretary: -- =
H.=20
PALUS (PL)<BR>tel./fax.: ++48-32 23-72-744,<BR>e-mail: <A=20
href=3D"mailto:hpalus@ia.gliwice.edu.pl">hpalus@ia.gliwice.edu.pl</A><BR>=
<BR><BR>Contact=20
address:<BR>GKPO'2000, ICS PAS,<BR>Ordona 21, 01--237 Warsaw, =
Poland<BR>fax.:=20
++48-22 37-65-64<BR><BR>GKPO'2000 on World Wide Web:<BR><A=20
href=3D"http://www.ippt.gov.pl/~zkulpa/MGV/GKPO2000.html">http://www.ippt=
.gov.pl/~zkulpa/MGV/GKPO2000.html</A><BR><BR>DECLARATION=20
FORM: Prospective participants are kindly asked<BR>to fill the =
Declaration Form=20
below and send it by ordinary mail<BR>or by fax to the Conference =
Contact=20
Addrees given above.<BR><BR>See you at the=20
Conference.<BR><BR>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
GKPO'2000<BR><BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
DECLARATION FORM<BR><BR>&nbsp;&nbsp;&nbsp;&nbsp; I intend to participate =
in the=20
GKPO'2000 Conference*<BR><BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
Signature:=20
............&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Date: =

.........<BR><BR>Name and title:=20
.................................................<BR><BR>Affiliation:=20
....................................................<BR><BR>Address:=20
........................................................<BR>.............=
....................................................<BR>.................=
...............................................<BR><BR><BR><BR>I=20
plan:<BR><BR>&nbsp; # to take part in the conference only<BR>&nbsp; # to =
submit=20
a paper on oral session<BR>&nbsp; # to submit a paper on poster=20
session<BR><BR><BR>title of the=20
paper<BR>................................................................=
..<BR>..................................................................<=
BR>..................................................................<BR>=
<BR>*=20
- number of participants is limited to 80=20
persons<BR><BR>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
<BR></FONT></DIV>
<DIV><FONT color=3D#000000><FONT size=3D3></FONT></FONT><FONT=20
size=3D3>&nbsp;</FONT></DIV></DIV></FONT></BODY></HTML>

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From nih-image-d-request@io.ece.drexel.edu Wed Jul 28 06:14 EDT 1999
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Date: Wed, 28 Jul 1999 06:14:35 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #171
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nih-image-d Digest				Volume 99 : Issue 171

Today's Topics:
  CALL FOR PAPERS , GKPO CONFERENCE, P  [ "Bogdan Smolka" <BSmolka@peach.ia.p ]

------------------------------

Date: Tue, 27 Jul 1999 17:33:18 +0200
From: "Bogdan Smolka" <BSmolka@peach.ia.polsl.gliwice.pl>
To: <nih-image@io.ece.drexel.edu>
Subject: CALL FOR PAPERS ,  GKPO CONFERENCE, Poland
Message-ID: <007801bed845$59f31b00$1e0e9e9d@ZTSBSpc.ia.polsl.gliwice.pl>
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Dear Friends,
I would like to inform you about  the GKPO'2000: 6th International =
Conference on Computer Graphics and Image Processing Conference, which =
will be held in Poland next year.=20

Looking forward to seeing you in Poland,

Yours sincerely,
dr Bogdan Smolka
Silesian Technical University
Gliwice, Poland

-------------------------------------------------------------------------=
--
CALL FOR PAPERS  *  CALL FOR PAPERS  *  CALL FOR PAPERS  *  CALL FOR =
PAPERS
-------------------------------------------------------------------------=
--
           =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =
GKPO'2000 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
                GKPO'2000: 6th International Conference on
                 Computer Graphics and Image Processing
           =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

The 6th GKPO'2000 intends to group the best researchers active in the =
field
of pictorial information exchange between computer and its environment.
The reviewing process and strict acceptance criteria assure high quality
of the accepted papers.

The Conference is planned as one track (oral and poster) presentations =
and
the number of participants is limited to max 80 persons.

The conference will be a forum for presentation of theoretical
aspects, methods, applications and systems of image processing. =
Unpublished
research papers are solicited, particulary concerning the following =
topics:
-- Image analysis and scene understanding
-- Multimodal and multisensor models of image formation
-- Pattern recognition in image processing
-- Motion analysis, visual navigation and active vision
-- Geometrical and structural models of objects and scenes
-- Fractal and chaos theory in image analysis
-- Modeling of human visual perception and mental imagery
-- Structure reconstruction, 3D imaging and image synthesis
-- Infrared, laser etc. imaging
-- Visualization and graphical data presentation
-- Virtual reality and pictorial interaction
-- Pictorial data bases and archivisation
-- Computational geometry
-- Computer-aided graphic design, arts and animation
-- Industrial, medical and other applications

The programme will include: invited papers by leading researchers, =
selected
contributions in oral and poster sessions, open session, presentations
of systems and social events.

DATE: 15-19 of May, 2000.

SUBMISSIONS: Authors are requested to submit four copies of manuscript =
in
English (max. 6 pages). Upon acceptance by the reviewers and Programme
Committee
(selection criteria include originality of ideas, accuracy and clarity =
of
explanation), authors will be asked to submit a PC diskette (in DOS
format),containing the text of the paper, prepared with LaTex with =
pictures
in POSTSCRIPT.

PROCEEDINGS of the Conference will be published as a special issue (vol. =
9(1//2))
of the Machine GRAPHICS & VISION Journal.

                   The best paper will be rewarded.

Declaration form expected by 31.07.1999.

DEADLINES:
Papers                                   --  30.10.1999.
Notification for acceptance              --  30.01.2000.
Submission of final version of papers    --  29.02.2000.

CHAIR of the Conference: W. MOKRZYCKI (PL)

V-CE CHAIR - Chair of the Programme Committee:  J.L. KULIKOWSKI (PL)

PROGRAMME COMMITTEE:
S. Ablameyko (BY)  P. Bhattacharya (US)  T. Belikova (RU)     E. =
Bengtsson (SE)
A. Borkowski (PL)  D. Chetverikov (HU)   L. Chmielewski (PL)  J. Chocjan =
(PL)
R. Choras (PL)     S. Dellepiane (IT)    U. Eckhardt (DE)     M. =
Flasinski (PL)
A. Gagalowicz (FR) D. Gillies (UK)       J. Goutsias (US)     E. Grabska =
(PL)
H. Heijmans (NL)   J.-M. Jolion (FR)     A. Kasinski (PL)     R. Klette =
(NZ)
W. Klonowski (PL)  E. Kolodzinski(PL)    R. Kozera (AU)       H. =
Kreowski (DE)
Z. Kulpa (PL)      M. Kurzynski (PL)     W. Kwiatkowski(PL)   G. Levina =
(RU)
L. Luchowski (PL)  V. Lukin (UA)         W. Malina (PL)       A. Materka =
(PL)
H. Niemann (DE)    M. Nieniewski (PL)    M. Paprzycki (US)    J. =
Roerdink (NL)
B. Sadykhov (BY)   B. Sankur (TR)        R. Sara (CZ)         V. Skala =
(CZ)
G. Sommer (DE)     J. Soldek (PL)        L. Szirmay-Kalos(HU) V. Valev =
(BG)
L. Vincent (US)    T. Vintsiuk (UA)      R. Vorobel (UA)      J. =
Zabrodzki (PL)
A. Zilinskas (LT)

V-CE CHAIR - Chair of the Organizing Committee:K .WOJCIECHOWSKI (PL)

ORGANIZING COMMITTEE:
D. Bereska, K. Fujarewicz, M. Grzegorek, K. Moscinska (PL)
Secretary: -- H. PALUS (PL)
tel./fax.: ++48-32 23-72-744,
e-mail: hpalus@ia.gliwice.edu.pl


Contact address:
GKPO'2000, ICS PAS,
Ordona 21, 01--237 Warsaw, Poland
fax.: ++48-22 37-65-64

GKPO'2000 on World Wide Web:
http://www.ippt.gov.pl/~zkulpa/MGV/GKPO2000.html

DECLARATION FORM: Prospective participants are kindly asked
to fill the Declaration Form below and send it by ordinary mail
or by fax to the Conference Contact Addrees given above.

See you at the Conference.

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
                                GKPO'2000

                            DECLARATION FORM

     I intend to participate in the GKPO'2000 Conference*

       Signature: ............          Date: .........

Name and title: .................................................

Affiliation: ....................................................

Address: ........................................................
.................................................................
................................................................



I plan:

  # to take part in the conference only
  # to submit a paper on oral session
  # to submit a paper on poster session


title of the paper
..................................................................
..................................................................
..................................................................

* - number of participants is limited to 80 persons

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

=20

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<!DOCTYPE HTML PUBLIC "-//W3C//DTD W3 HTML//EN">
<HTML>
<HEAD>

<META content=3Dtext/html;charset=3Diso-8859-2 =
http-equiv=3DContent-Type>
<META content=3D'"MSHTML 4.72.3612.1700"' name=3DGENERATOR>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT color=3D#000000><FONT size=3D3>Dear =
Friends,</FONT></FONT><FONT=20
size=3D3></FONT></DIV>
<DIV><FONT size=3D3>I would like to inform you about&nbsp; the =
</FONT><FONT=20
size=3D3>GKPO'2000: 6th International Conference on Computer Graphics =
and Image=20
Processing <FONT color=3D#000000>Conference, which will be held in =
Poland next=20
year. </FONT></FONT></DIV>
<DIV><FONT size=3D3><FONT color=3D#000000></FONT></FONT>&nbsp;</DIV>
<DIV><FONT size=3D3><FONT color=3D#000000>Looking forward to seeing you =
in=20
Poland,</FONT></FONT></DIV>
<DIV><FONT size=3D3><FONT color=3D#000000></FONT></FONT>&nbsp;</DIV>
<DIV>
<DIV><FONT size=3D2><FONT size=3D3>Yours sincerely,</FONT></DIV></DIV>
<DIV>
<DIV><FONT size=3D3>dr Bogdan Smolka</FONT></DIV>
<DIV><FONT size=3D3>Silesian Technical University</FONT></DIV>
<DIV><FONT size=3D3>Gliwice, Poland</FONT></DIV>
<DIV><FONT size=3D3></FONT>&nbsp;</DIV>
<DIV><FONT=20
size=3D3>----------------------------------------------------------------=
-----------<BR>CALL=20
FOR PAPERS&nbsp; *&nbsp; CALL FOR PAPERS&nbsp; *&nbsp; CALL FOR =
PAPERS&nbsp;=20
*&nbsp; CALL FOR=20
PAPERS<BR>---------------------------------------------------------------=
------------<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D GKPO'2000=20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<BR>&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;=20
GKPO'2000: 6th International Conference=20
on<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
Computer Graphics and Image=20
Processing<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;=20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
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BR><BR>The 6th GKPO'2000=20
intends to group the best researchers active in the field<BR>of =
pictorial=20
information exchange between computer and its environment.<BR>The =
reviewing=20
process and strict acceptance criteria assure high quality<BR>of the =
accepted=20
papers.<BR><BR>The Conference is planned as one track (oral and poster)=20
presentations and<BR>the number of participants is limited to max 80=20
persons.<BR><BR>The conference will be a forum for presentation of=20
theoretical<BR>aspects, methods, applications and systems of image =
processing.=20
Unpublished<BR>research papers are solicited, particulary concerning the =

following topics:<BR>-- Image analysis and scene understanding<BR>-- =
Multimodal=20
and multisensor models of image formation<BR>-- Pattern recognition in =
image=20
processing<BR>-- Motion analysis, visual navigation and active =
vision<BR>--=20
Geometrical and structural models of objects and scenes<BR>-- Fractal =
and chaos=20
theory in image analysis<BR>-- Modeling of human visual perception and =
mental=20
imagery<BR>-- Structure reconstruction, 3D imaging and image =
synthesis<BR>--=20
Infrared, laser etc. imaging<BR>-- Visualization and graphical data=20
presentation<BR>-- Virtual reality and pictorial interaction<BR>-- =
Pictorial=20
data bases and archivisation<BR>-- Computational geometry<BR>-- =
Computer-aided=20
graphic design, arts and animation<BR>-- Industrial, medical and other=20
applications<BR><BR>The programme will include: invited papers by =
leading=20
researchers, selected<BR>contributions in oral and poster sessions, open =

session, presentations<BR>of systems and social events.<BR><BR>DATE: =
15-19 of=20
May, 2000.<BR><BR>SUBMISSIONS: Authors are requested to submit four =
copies of=20
manuscript in<BR>English (max. 6 pages). Upon acceptance by the =
reviewers and=20
Programme<BR>Committee<BR>(selection criteria include originality of =
ideas,=20
accuracy and clarity of<BR>explanation), authors will be asked to submit =
a PC=20
diskette (in DOS<BR>format),containing the text of the paper, prepared =
with=20
LaTex with pictures<BR>in POSTSCRIPT.<BR><BR>PROCEEDINGS of the =
Conference will=20
be published as a special issue (vol. 9(1//2))<BR>of the Machine =
GRAPHICS &amp;=20
VISION=20
Journal.<BR><BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
The best paper will be rewarded.<BR><BR>Declaration form expected by=20
31.07.1999.<BR><BR>DEADLINES:<BR>Papers&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;=20
--&nbsp; 30.10.1999.<BR>Notification for=20
acceptance&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;=20
--&nbsp; 30.01.2000.<BR>Submission of final version of =
papers&nbsp;&nbsp;&nbsp;=20
--&nbsp; 29.02.2000.<BR><BR>CHAIR of the Conference: W. MOKRZYCKI=20
(PL)<BR><BR>V-CE CHAIR - Chair of the Programme Committee:&nbsp; J.L. =
KULIKOWSKI=20
(PL)<BR><BR>PROGRAMME COMMITTEE:<BR>S. Ablameyko (BY)&nbsp; P. =
Bhattacharya=20
(US)&nbsp; T. Belikova (RU)&nbsp;&nbsp;&nbsp;&nbsp; E. Bengtsson =
(SE)<BR>A.=20
Borkowski (PL)&nbsp; D. Chetverikov (HU)&nbsp;&nbsp; L. Chmielewski =
(PL)&nbsp;=20
J. Chocjan (PL)<BR>R. Choras (PL)&nbsp;&nbsp;&nbsp;&nbsp; S. Dellepiane=20
(IT)&nbsp;&nbsp;&nbsp; U. Eckhardt (DE)&nbsp;&nbsp;&nbsp;&nbsp; M. =
Flasinski=20
(PL)<BR>A. Gagalowicz (FR) D. Gillies =
(UK)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
J. Goutsias (US)&nbsp;&nbsp;&nbsp;&nbsp; E. Grabska (PL)<BR>H. Heijmans=20
(NL)&nbsp;&nbsp; J.-M. Jolion (FR)&nbsp;&nbsp;&nbsp;&nbsp; A. Kasinski=20
(PL)&nbsp;&nbsp;&nbsp;&nbsp; R. Klette (NZ)<BR>W. Klonowski (PL)&nbsp; =
E.=20
Kolodzinski(PL)&nbsp;&nbsp;&nbsp; R. Kozera=20
(AU)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; H. Kreowski (DE)<BR>Z. Kulpa=20
(PL)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; M. Kurzynski =
(PL)&nbsp;&nbsp;&nbsp;&nbsp; W.=20
Kwiatkowski(PL)&nbsp;&nbsp; G. Levina (RU)<BR>L. Luchowski (PL)&nbsp; V. =
Lukin=20
(UA)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; W. Malina=20
(PL)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; A. Materka (PL)<BR>H. Niemann=20
(DE)&nbsp;&nbsp;&nbsp; M. Nieniewski (PL)&nbsp;&nbsp;&nbsp; M. Paprzycki =

(US)&nbsp;&nbsp;&nbsp; J. Roerdink (NL)<BR>B. Sadykhov (BY)&nbsp;&nbsp; =
B.=20
Sankur (TR)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; R. Sara=20
(CZ)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; V. Skala (CZ)<BR>G. =
Sommer=20
(DE)&nbsp;&nbsp;&nbsp;&nbsp; J. Soldek=20
(PL)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; L. Szirmay-Kalos(HU) V. =
Valev=20
(BG)<BR>L. Vincent (US)&nbsp;&nbsp;&nbsp; T. Vintsiuk=20
(UA)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; R. Vorobel =
(UA)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
J. Zabrodzki (PL)<BR>A. Zilinskas (LT)<BR><BR>V-CE CHAIR - Chair of the=20
Organizing Committee:K .WOJCIECHOWSKI (PL)<BR><BR>ORGANIZING =
COMMITTEE:<BR>D.=20
Bereska, K. Fujarewicz, M. Grzegorek, K. Moscinska (PL)<BR>Secretary: -- =
H.=20
PALUS (PL)<BR>tel./fax.: ++48-32 23-72-744,<BR>e-mail: <A=20
href=3D"mailto:hpalus@ia.gliwice.edu.pl">hpalus@ia.gliwice.edu.pl</A><BR>=
<BR><BR>Contact=20
address:<BR>GKPO'2000, ICS PAS,<BR>Ordona 21, 01--237 Warsaw, =
Poland<BR>fax.:=20
++48-22 37-65-64<BR><BR>GKPO'2000 on World Wide Web:<BR><A=20
href=3D"http://www.ippt.gov.pl/~zkulpa/MGV/GKPO2000.html">http://www.ippt=
.gov.pl/~zkulpa/MGV/GKPO2000.html</A><BR><BR>DECLARATION=20
FORM: Prospective participants are kindly asked<BR>to fill the =
Declaration Form=20
below and send it by ordinary mail<BR>or by fax to the Conference =
Contact=20
Addrees given above.<BR><BR>See you at the=20
Conference.<BR><BR>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
GKPO'2000<BR><BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
DECLARATION FORM<BR><BR>&nbsp;&nbsp;&nbsp;&nbsp; I intend to participate =
in the=20
GKPO'2000 Conference*<BR><BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
Signature:=20
............&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Date: =

.........<BR><BR>Name and title:=20
.................................................<BR><BR>Affiliation:=20
....................................................<BR><BR>Address:=20
........................................................<BR>.............=
....................................................<BR>.................=
...............................................<BR><BR><BR><BR>I=20
plan:<BR><BR>&nbsp; # to take part in the conference only<BR>&nbsp; # to =
submit=20
a paper on oral session<BR>&nbsp; # to submit a paper on poster=20
session<BR><BR><BR>title of the=20
paper<BR>................................................................=
..<BR>..................................................................<=
BR>..................................................................<BR>=
<BR>*=20
- number of participants is limited to 80=20
persons<BR><BR>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
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<BR></FONT></DIV>
<DIV><FONT color=3D#000000><FONT size=3D3></FONT></FONT><FONT=20
size=3D3>&nbsp;</FONT></DIV></DIV></FONT></BODY></HTML>

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From nih-image-request@io.ece.drexel.edu Wed Jul 28 09:36 EDT 1999
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Date: Wed, 28 Jul 1999 09:23:03 -0400
Subject: IXMicro IXTV card with NIH Image?
From: "Peter, Jan" <JPeter@NRCan.gc.ca>
To: NIH Image message post <nih-image@io.ece.drexel.edu>
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I am trying to get Image 1.62 to work (i.e., capture an image) with my IXTV
card (sony ccd color camera on my microscope outputting a composite video
signal) on my Powertowerpro mac clone. The image appears well enough, but
there is a central portion that has lines and is "rough". Any ideas?

thanks in advance, Jan


From nih-image-request@io.ece.drexel.edu Wed Jul 28 16:28 EDT 1999
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From: Beth Fisher <bfisher@usc.edu>
Subject: algorithm
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To whom it may concern,

	I am writing my dissertation and want to be able to BRIEFLY describe the
algorithm that Scion image uses to capture the image (with the wand tool).
Is there documentation I could refer to in order to obtain that information?
I would be very grateful for your help.

Beth Fisher


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From: nih-image-d-request@io.ece.drexel.edu
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 172

Today's Topics:
  IXMicro IXTV card with NIH Image?     [ "Peter, Jan" <JPeter@NRCan.gc.ca> ]
  algorithm                             [ Beth Fisher <bfisher@usc.edu> ]

------------------------------

Date: Wed, 28 Jul 1999 09:23:03 -0400
From: "Peter, Jan" <JPeter@NRCan.gc.ca>
To: NIH Image message post <nih-image@io.ece.drexel.edu>
Subject: IXMicro IXTV card with NIH Image?
Message-Id: <199907281323.JAA19697@nrn1.NRCan.gc.ca>
Content-type: text/plain; charset="US-ASCII"
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I am trying to get Image 1.62 to work (i.e., capture an image) with my IXTV
card (sony ccd color camera on my microscope outputting a composite video
signal) on my Powertowerpro mac clone. The image appears well enough, but
there is a central portion that has lines and is "rough". Any ideas?

thanks in advance, Jan

------------------------------

Date: Wed, 28 Jul 1999 13:14:09 -0700
From: Beth Fisher <bfisher@usc.edu>
To: nih-image@io.ece.drexel.edu
Subject: algorithm
Message-Id: <3.0.5.32.19990728131409.007fb600@hsc.usc.edu>
Content-Type: text/plain; charset="us-ascii"

To whom it may concern,

	I am writing my dissertation and want to be able to BRIEFLY describe the
algorithm that Scion image uses to capture the image (with the wand tool).
Is there documentation I could refer to in order to obtain that information?
I would be very grateful for your help.

Beth Fisher

--------------------------------
End of nih-image-d Digest V99 Issue #172
****************************************

From nih-image-request@io.ece.drexel.edu Thu Jul 29 12:02 EDT 1999
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Date: Thu, 29 Jul 1999 11:47:40 -0400 (EDT)
From: "B. Iyengar" <iyengabg@mcmail.cis.McMaster.CA>
To: nih-image@io.ece.drexel.edu
Subject: trace and getmouse
In-Reply-To: <199907171000.GAA17472@io.ece.drexel.edu>
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Hello all,
Can someone answer me these two  questions? 

(1) How does one get a new image window (640x480) transparent so I could
see a live video (moving object) run by another app beneath it? 

(2). How can I get a pencil trace to also act as "getmouse(x,y)"? I would
like to trace (track) the moving object on the transparent window thereby
getting the trace on the image window as well as x,y data on a text
window. 
I am already using a macro that does the job of getting x, y
coords by moving the mouse on the object in the live capture window, would
like to get a pencil trace as well at the sametime that could be saved. Is
this possible, any macro example out there? Thanks a million for any
input.
Bala


From nih-image-request@io.ece.drexel.edu Thu Jul 29 21:58 EDT 1999
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Resent-Date: Thu, 29 Jul 1999 21:58:46 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: iyengabg@mcmail.cis.McMaster.CA, nih-image@io.ece.drexel.edu
Date:          Fri, 30 Jul 1999 11:53:49 +1000
Subject:       Re: trace and getmouse
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>Date: Thu, 29 Jul 1999 11:47:40 -0400 (EDT)
>From: "B. Iyengar" <iyengabg@mcmail.cis.McMaster.CA>
>To: nih-image@io.ece.drexel.edu
>Subject: trace and getmouse
>
>Hello all,
>Can someone answer me these two  questions? 
>
>(1) How does one get a new image window (640x480) transparent so I could
>see a live video (moving object) run by another app beneath it? 
>
>(2). How can I get a pencil trace to also act as "getmouse(x,y)"? I would
>like to trace (track) the moving object on the transparent window thereby
>getting the trace on the image window as well as x,y data on a text
>window. 
>I am already using a macro that does the job of getting x, y
>coords by moving the mouse on the object in the live capture window, would
>like to get a pencil trace as well at the sametime that could be saved. Is
>this possible, any macro example out there? Thanks a million for any
>input.

>Bala

It is not necessary know how to make an image window transparent ( I dont).
 
getmouse(x,y) will report coordinates relative to the top-left of the image 
window regardless of the window size or position, even to the extent of -ve 
coords. Thus you can either make a minimum size window (say 8x8) and move 
it so that it dos not obsure the live capture in the background application 
or else you can make a large (640x480 or larger) window but drag the bottom 
right corner to top left so that the window display is minimised (you can 
even use 'movewindow()' to move it offscreen but to a known x,y).

A simple macro such as

macro'[F1]mouse';var x,y:integer;begin 
while not button do begin
getMouse(x,y);
showMessage(x,y);
end;
end

will allow you to see your tracking of the object in the backkground image.

Simply adding a 'lineTo(x,y)' will do the pencil trace if the 'Image' image 
and the background image corners are coincident. You will need to add the 
appropriate displacement if you moved the 'Image' image offscreen.

It would make sense to record (x,y) values in the results array for later 
processing.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 173

Today's Topics:
  trace and getmouse                    [ "B. Iyengar" <iyengabg@mcmail.cis.M ]
  Re: trace and getmouse                [ GJOSS@rna.bio.mq.edu.au ]

------------------------------

Date: Thu, 29 Jul 1999 11:47:40 -0400 (EDT)
From: "B. Iyengar" <iyengabg@mcmail.cis.McMaster.CA>
To: nih-image@io.ece.drexel.edu
Subject: trace and getmouse
Message-ID: <Pine.SOL.3.96.990729112741.18771A-100000@mcmail.cis.McMaster.CA>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hello all,
Can someone answer me these two  questions? 

(1) How does one get a new image window (640x480) transparent so I could
see a live video (moving object) run by another app beneath it? 

(2). How can I get a pencil trace to also act as "getmouse(x,y)"? I would
like to trace (track) the moving object on the transparent window thereby
getting the trace on the image window as well as x,y data on a text
window. 
I am already using a macro that does the job of getting x, y
coords by moving the mouse on the object in the live capture window, would
like to get a pencil trace as well at the sametime that could be saved. Is
this possible, any macro example out there? Thanks a million for any
input.
Bala

------------------------------

Date:          Fri, 30 Jul 1999 11:53:49 +1000
From: GJOSS@rna.bio.mq.edu.au
To: iyengabg@mcmail.cis.McMaster.CA, nih-image@io.ece.drexel.edu
Subject:       Re: trace and getmouse
Message-ID: <149F13687@rna.bio.mq.edu.au>

>Date: Thu, 29 Jul 1999 11:47:40 -0400 (EDT)
>From: "B. Iyengar" <iyengabg@mcmail.cis.McMaster.CA>
>To: nih-image@io.ece.drexel.edu
>Subject: trace and getmouse
>
>Hello all,
>Can someone answer me these two  questions? 
>
>(1) How does one get a new image window (640x480) transparent so I could
>see a live video (moving object) run by another app beneath it? 
>
>(2). How can I get a pencil trace to also act as "getmouse(x,y)"? I would
>like to trace (track) the moving object on the transparent window thereby
>getting the trace on the image window as well as x,y data on a text
>window. 
>I am already using a macro that does the job of getting x, y
>coords by moving the mouse on the object in the live capture window, would
>like to get a pencil trace as well at the sametime that could be saved. Is
>this possible, any macro example out there? Thanks a million for any
>input.

>Bala

It is not necessary know how to make an image window transparent ( I dont).
 
getmouse(x,y) will report coordinates relative to the top-left of the image 
window regardless of the window size or position, even to the extent of -ve 
coords. Thus you can either make a minimum size window (say 8x8) and move 
it so that it dos not obsure the live capture in the background application 
or else you can make a large (640x480 or larger) window but drag the bottom 
right corner to top left so that the window display is minimised (you can 
even use 'movewindow()' to move it offscreen but to a known x,y).

A simple macro such as

macro'[F1]mouse';var x,y:integer;begin 
while not button do begin
getMouse(x,y);
showMessage(x,y);
end;
end

will allow you to see your tracking of the object in the backkground image.

Simply adding a 'lineTo(x,y)' will do the pencil trace if the 'Image' image 
and the background image corners are coincident. You will need to add the 
appropriate displacement if you moved the 'Image' image offscreen.

It would make sense to record (x,y) values in the results array for later 
processing.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

--------------------------------
End of nih-image-d Digest V99 Issue #173
****************************************

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Subject: RGB filters
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Imagers,

I want to grab red, green and blue greyscale microscope images in order to
create indexed colour derivative images. So I need to obtain Red, Green and
Blue filters for my microscope. But which ones?! When I talk to people in
camera stores, they say they have these red ones, these green ones, and "a
blue one will be dificult to identify". Does anyone have some
specifications for the R, G and B filters commonly used in photography? I
presume a wavelength or wavelength range is required to identify each
filter.


Doug Mason

Mason Geoscience Pty Ltd
Petrological Services for the Exploration and Mining Industry
email   : drmason@interconnect.com.au
post    : PO Box 78, Glenside  SA  5065, Australia
phone   : +61-8-83901507
fax     : +61-8-83901194



From nih-image-request@io.ece.drexel.edu Fri Jul 30 11:39 EDT 1999
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From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Scripting CoolSnap color camera
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I am setting up a microscope with CoolSnap, which is a color CCD camera
(1393 * 1040 pixels, cooled to 5 deg below ambient) and comes with a piece
of stand-alone acquisition software for Macintosh and PC, as well as with a
Photoshop acquisition plugin.

I am now trying to automate the acquisition with some script or macro. The
software is scriptable with AppleScript.
I wrote a script which can take images and change settings such as exposure
time etc.  However, the script is not able to save the images on disk.
Before I start to fiddle with some work-around like KeyQuencer, I'd like to
ask some questions:

1. Has anyone tried to script CoolSnap, or are there some sample scripts?

2. What about the Photoshop internal scripting language (I don't have
experience with that)


Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



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@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html


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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 174

Today's Topics:
  RGB filters                           [ Doug Mason <drmason@interconnect.co ]
  Scripting CoolSnap color camera       [ Norbert Vischer <vischer@bio.uva.nl ]
  Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
  Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
  Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
  Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
  Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]

------------------------------

Date: Fri, 30 Jul 1999 20:31:34 +1030
From: Doug Mason <drmason@interconnect.com.au>
To: nih-image@io.ece.drexel.edu
Subject: RGB filters
Message-Id: <l03110701b3c7267f9afd@[210.8.6.165]>
Content-Type: text/plain; charset="us-ascii"

Imagers,

I want to grab red, green and blue greyscale microscope images in order to
create indexed colour derivative images. So I need to obtain Red, Green and
Blue filters for my microscope. But which ones?! When I talk to people in
camera stores, they say they have these red ones, these green ones, and "a
blue one will be dificult to identify". Does anyone have some
specifications for the R, G and B filters commonly used in photography? I
presume a wavelength or wavelength range is required to identify each
filter.


Doug Mason

Mason Geoscience Pty Ltd
Petrological Services for the Exploration and Mining Industry
email   : drmason@interconnect.com.au
post    : PO Box 78, Glenside  SA  5065, Australia
phone   : +61-8-83901507
fax     : +61-8-83901194

------------------------------

Date: Fri, 30 Jul 1999 17:30:29 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Scripting CoolSnap color camera
Message-Id: <l03110700b3c76ec460a8@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

I am setting up a microscope with CoolSnap, which is a color CCD camera
(1393 * 1040 pixels, cooled to 5 deg below ambient) and comes with a piece
of stand-alone acquisition software for Macintosh and PC, as well as with a
Photoshop acquisition plugin.

I am now trying to automate the acquisition with some script or macro. The
software is scriptable with AppleScript.
I wrote a script which can take images and change settings such as exposure
time etc.  However, the script is not able to save the images on disk.
Before I start to fiddle with some work-around like KeyQuencer, I'd like to
ask some questions:

1. Has anyone tried to script CoolSnap, or are there some sample scripts?

2. What about the Photoshop internal scripting language (I don't have
experience with that)


Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: Fri, 30 Jul 1999 12:49:46 -0400 (EDT)
From: nih-image-request@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <199907301649.MAA04690@io.ece.drexel.edu>


------------------------------

Date: Fri, 30 Jul 1999 12:49:57 -0400 (EDT)
From: nih-image-request@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <199907301649.MAA04761@io.ece.drexel.edu>


------------------------------

Date: Fri, 30 Jul 1999 12:49:59 -0400 (EDT)
From: nih-image-request@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <199907301649.MAA04778@io.ece.drexel.edu>


------------------------------

Date: Fri, 30 Jul 1999 12:50:03 -0400 (EDT)
From: nih-image-request@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <199907301650.MAA04850@io.ece.drexel.edu>

@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: Fri, 30 Jul 1999 12:50:12 -0400 (EDT)
From: nih-image-request@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <199907301650.MAA04936@io.ece.drexel.edu>


--------------------------------
End of nih-image-d Digest V99 Issue #174
****************************************

From nih-image-request@io.ece.drexel.edu Sun Aug  1 00:55 EDT 1999
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Subject: Re: Scripting CoolSnap color camera
From: Tim Bates <tbates@bunyip.bhs.mq.edu.au>
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on Sat, Jul 31, 1999 1:30 AM, Norbert Vischer at vischer@bio.uva.nl wrote:

> I am setting up a microscope with CoolSnap, which is a color CCD camera
> (1393 * 1040 pixels, cooled to 5 deg below ambient) and comes with a piece
> of stand-alone acquisition software for Macintosh and PC, as well as with a
> Photoshop acquisition plugin.

Hi Norbert, what is the URL for CoolSnap?


From nih-image-request@io.ece.drexel.edu Sun Aug  1 15:21 EDT 1999
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Date: Sun, 1 Aug 1999 15:05:05 -0400 (EDT)
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Hi,

	I am attempting to use the NIH image program to measure the
surface area of corals from pictures taken with a digital camera.  The
camera only saves the pictures in jpg.  "Saving As" the pictues in bmp is
ok for "Paint" but the NIH program shuts down with the "illegal operation"
warning when I open the new bmp image.  Is there a way to convert these
images so that the NIH  program will accept them?  Are there any other
pitfalls that I should know about ahead of time to save me a headache or
two?  I realize from the disscussion archives that most of you are using
Mac's.  I do not have access to one and am stuck with a PC.  I am hoping
that some of you have had experience with this in the inferior format.

	I appreciate any help in this endevour.

Sincerely,
Lill

Lill Becker
Department of Biology
Florida International University
Miami, FL  33199   USA

	*******************************************
	*Are science and magic mutually exclusive?*
	*******************************************



From nih-image-request@io.ece.drexel.edu Sun Aug  1 22:41 EDT 1999
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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: drmason@interconnect.com.au, nih-image@io.ece.drexel.edu
Date:          Mon, 2 Aug 1999 12:28:50 +1000
Subject:       Re: RGB filters (Filters KODAK WRATTEN
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>Date: Fri, 30 Jul 1999 20:31:34 +1030
>To: nih-image@io.ece.drexel.edu
>From: Doug Mason <drmason@interconnect.com.au>
>Subject: RGB filters
>Imagers,
>
>I want to grab red, green and blue greyscale microscope images in order to
>create indexed colour derivative images. So I need to obtain Red, Green 
>and
>Blue filters for my microscope. But which ones?! When I talk to people in
>camera stores, they say they have these red ones, these green ones, and "a
>blue one will be dificult to identify". Does anyone have some
>specifications for the R, G and B filters commonly used in photography? I
>presume a wavelength or wavelength range is required to identify each
>filter.
>
>
>Doug Mason
>
>Mason Geoscience Pty Ltd
>Petrological Services for the Exploration and Mining Industry
>email   : drmason@interconnect.com.au
>post    : PO Box 78, Glenside  SA  5065, Australia
>phone   : +61-8-83901507
>fax     : +61-8-83901194
>
>
A previous post to maillist:
____________________________
From: GJOSS@rna.bio.mq.edu.au
To: SPurdy@nationalsteel.com, nih-image@io.ece.drexel.edu,
        e_bonino@hotmail.com
Date:          Thu, 25 Feb 1999 9:42:39 +1100
Subject:       RE: Filters KODAK WRATTEN

Following previous enquires of my own, I have recent Web reference
KSIS: Kodak Wratten Gelatin Filters, ( May 28 1998 )
http://www.kodak.com:80/country/US/en/digital/sis/wratten.shtml

and access to Kodak Data Book of applied photography vol1 
sheet FT-6 which gives spectrophotometric absorption curves for
25,47B,58 and 
29,47b,61.

I will email separately an attachment image of the curves to e_bonino and 
have copied Kodak support requesting that 
they extend their website to include such data.
______________________________
>From: "Purdy, Sam" <SPurdy@nationalsteel.com>
>To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
>Subject: RE: Filters KODAK WRATTEN
>Date: Wed, 24 Feb 1999 08:47:45 -0500
>
>Kodak publication B-3, Kodak Filters for Scientific and Technical Uses,
>contains transmittance curves for all Kodak filters. The particular
>filters:
>filter 25 transmits at wavelengths above 600 nanometers, 47B transmits
>at 430 nanometers, and  58 at 525 nonometers. Hope this helps.
>Sam Purdy
>National Steel Corp. 
>Trenton, MI, USA
______________________________

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-d-request@io.ece.drexel.edu Sun Aug  1 22:43 EDT 1999
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------------------------------

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nih-image-d Digest				Volume 99 : Issue 175

Today's Topics:
  Re: Scripting CoolSnap color camera   [ Tim Bates <tbates@bunyip.bhs.mq.edu ]
  New User Seeks Advice                 [ lillian c becker <lbecke01@fiu.edu> ]
  Re: RGB filters (Filters KODAK WRATT  [ GJOSS@rna.bio.mq.edu.au ]

------------------------------

Date: Sun, 01 Aug 1999 14:42:16 +1000
From: Tim Bates <tbates@bunyip.bhs.mq.edu.au>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: Scripting CoolSnap color camera
Message-ID: <B3CA0D48.488%tbates@bunyip.bhs.mq.edu.au>
Content-type: text/plain; charset="US-ASCII"
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on Sat, Jul 31, 1999 1:30 AM, Norbert Vischer at vischer@bio.uva.nl wrote:

> I am setting up a microscope with CoolSnap, which is a color CCD camera
> (1393 * 1040 pixels, cooled to 5 deg below ambient) and comes with a piece
> of stand-alone acquisition software for Macintosh and PC, as well as with a
> Photoshop acquisition plugin.

Hi Norbert, what is the URL for CoolSnap?

------------------------------

Date: Sun, 1 Aug 1999 15:05:05 -0400 (EDT)
From: lillian c becker <lbecke01@fiu.edu>
To: nih-image@io.ece.drexel.edu
Subject: New User Seeks Advice
Message-ID: <Pine.SOL.3.96.990801111018.27734A-100000@solix4-64>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi,

	I am attempting to use the NIH image program to measure the
surface area of corals from pictures taken with a digital camera.  The
camera only saves the pictures in jpg.  "Saving As" the pictues in bmp is
ok for "Paint" but the NIH program shuts down with the "illegal operation"
warning when I open the new bmp image.  Is there a way to convert these
images so that the NIH  program will accept them?  Are there any other
pitfalls that I should know about ahead of time to save me a headache or
two?  I realize from the disscussion archives that most of you are using
Mac's.  I do not have access to one and am stuck with a PC.  I am hoping
that some of you have had experience with this in the inferior format.

	I appreciate any help in this endevour.

Sincerely,
Lill

Lill Becker
Department of Biology
Florida International University
Miami, FL  33199   USA

	*******************************************
	*Are science and magic mutually exclusive?*
	*******************************************

------------------------------

Date:          Mon, 2 Aug 1999 12:28:50 +1000
From: GJOSS@rna.bio.mq.edu.au
To: drmason@interconnect.com.au, nih-image@io.ece.drexel.edu
Subject:       Re: RGB filters (Filters KODAK WRATTEN
Message-ID: <49E5024AA7@rna.bio.mq.edu.au>

>Date: Fri, 30 Jul 1999 20:31:34 +1030
>To: nih-image@io.ece.drexel.edu
>From: Doug Mason <drmason@interconnect.com.au>
>Subject: RGB filters
>Imagers,
>
>I want to grab red, green and blue greyscale microscope images in order to
>create indexed colour derivative images. So I need to obtain Red, Green 
>and
>Blue filters for my microscope. But which ones?! When I talk to people in
>camera stores, they say they have these red ones, these green ones, and "a
>blue one will be dificult to identify". Does anyone have some
>specifications for the R, G and B filters commonly used in photography? I
>presume a wavelength or wavelength range is required to identify each
>filter.
>
>
>Doug Mason
>
>Mason Geoscience Pty Ltd
>Petrological Services for the Exploration and Mining Industry
>email   : drmason@interconnect.com.au
>post    : PO Box 78, Glenside  SA  5065, Australia
>phone   : +61-8-83901507
>fax     : +61-8-83901194
>
>
A previous post to maillist:
____________________________
From: GJOSS@rna.bio.mq.edu.au
To: SPurdy@nationalsteel.com, nih-image@io.ece.drexel.edu,
        e_bonino@hotmail.com
Date:          Thu, 25 Feb 1999 9:42:39 +1100
Subject:       RE: Filters KODAK WRATTEN

Following previous enquires of my own, I have recent Web reference
KSIS: Kodak Wratten Gelatin Filters, ( May 28 1998 )
http://www.kodak.com:80/country/US/en/digital/sis/wratten.shtml

and access to Kodak Data Book of applied photography vol1 
sheet FT-6 which gives spectrophotometric absorption curves for
25,47B,58 and 
29,47b,61.

I will email separately an attachment image of the curves to e_bonino and 
have copied Kodak support requesting that 
they extend their website to include such data.
______________________________
>From: "Purdy, Sam" <SPurdy@nationalsteel.com>
>To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
>Subject: RE: Filters KODAK WRATTEN
>Date: Wed, 24 Feb 1999 08:47:45 -0500
>
>Kodak publication B-3, Kodak Filters for Scientific and Technical Uses,
>contains transmittance curves for all Kodak filters. The particular
>filters:
>filter 25 transmits at wavelengths above 600 nanometers, 47B transmits
>at 430 nanometers, and  58 at 525 nonometers. Hope this helps.
>Sam Purdy
>National Steel Corp. 
>Trenton, MI, USA
______________________________

Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

--------------------------------
End of nih-image-d Digest V99 Issue #175
****************************************

From nih-image-request@io.ece.drexel.edu Mon Aug  2 08:25 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: Ludger Offerhaus <ljo@gfz-potsdam.de>
Subject: grain area measurements
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dear imagers!

On a skeletonized binary image of grain boundaries in a ceramic aggregate
I'd like to measure grain areas as well as the grain length and width
(ellipse minor/major axes in NIH Image 1.62). using the wand tool, Image
(1) recognizes separate grains and (2) calculates ellipse minor and major
axes.

NIH Image seems unable to come up with realistic *area* measurements. After
setting the scale to about 18 pixels per micrometer, almost all grains
measured have an area of zero (even if ellipse m/m axes are e.g. 2 and 5
Microns, which should result in an area of a few square micrometers).

Any guesses as to what I could do about his?!
Thanks in advance!

cheers,
Ludger


--
Ludger Offerhaus
GeoForschungsZentrum Potsdam
Telegrafenberg, 14473 Potsdam, Duitsland
Tel: +49 (0)331 288 1326 / 1390
of (ook awap): 030 32 60 55 68
---
... aan een boom *zo* volgeladen / mist men n, twee pruimpjes niet ...
---



From nih-image-request@io.ece.drexel.edu Mon Aug  2 09:06 EDT 1999
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Date: Mon, 2 Aug 1999 15:02:38 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: grain area measurements
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>On a skeletonized binary image of grain boundaries in a ceramic aggregate
>I'd like to measure grain areas as well as the grain length and width
>(ellipse minor/major axes in NIH Image 1.62). using the wand tool, Image
>(1) recognizes separate grains and (2) calculates ellipse minor and major
>axes.
>
>NIH Image seems unable to come up with realistic *area* measurements. After
>setting the scale to about 18 pixels per micrometer, almost all grains
>measured have an area of zero (even if ellipse m/m axes are e.g. 2 and 5
>Microns, which should result in an area of a few square micrometers).
>Ludger Offerhaus
>GeoForschungsZentrum Potsdam


Just click the option "include interior holes".
The ellipse parameters are always calculated from 'filled objects',
independent of this setting. However, area measurements do listen to the
setting, so in your case you probably only got the area of the boundary.





From nih-image-request@io.ece.drexel.edu Mon Aug  2 09:18 EDT 1999
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Date: 02 Aug 99 09:11:10 -0500
From: Jonathan WISCO <jjwisco@cajal-1.bu.edu>
Subject: RE:nih-image-d Digest V99 #175
To: "nih-image" <nih-image@io.ece.drexel.edu>
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Lill,
   With a PC, I presume you are using Scion Image instead of NIH Image. 
Nevertheless, you might have better luck if you convert the jpg files to tif format
instead of bmp format.  A program like Photoshop will do the trick nicely.

Jonathan J. Wisco
Department of Anatomy and Neurobiology
Boston University School of Medicine

>Date: Sun, 1 Aug 1999 15:05:05 -0400 (EDT)
>From: lillian c becker <lbecke01@fiu.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: New User Seeks Advice
>Message-ID: <Pine.SOL.3.96.990801111018.27734A-100000@solix4-
>64>
>Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>Hi,
>
>	I am attempting to use the NIH image program to measure the
>surface area of corals from pictures taken with a digital camera.  The
>camera only saves the pictures in jpg.  "Saving As" the pictues in bmp 
>is
>ok for "Paint" but the NIH program shuts down with the "illegal 
>operation"
>warning when I open the new bmp image.  Is there a way to convert 
>these
>images so that the NIH  program will accept them?  Are there any other
>pitfalls that I should know about ahead of time to save me a headache 
>or
>two?  I realize from the disscussion archives that most of you are using
>Mac's.  I do not have access to one and am stuck with a PC.  I am 
>hoping
>that some of you have had experience with this in the inferior format.
>
>	I appreciate any help in this endevour.
>
>Sincerely,
>Lill
>
>Lill Becker
>Department of Biology
>Florida International University
>Miami, FL  33199   USA
>
>	*******************************************
>	*Are science and magic mutually exclusive?*
>	*******************************************
>
>------------------------------
>



From nih-image-request@io.ece.drexel.edu Mon Aug  2 09:35 EDT 1999
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Date: Mon, 02 Aug 1999 14:22:00 +0100
From: Stamatis Pagakis <spagaki@nimr.mrc.ac.uk>
Subject: Object Image:  Measuring average intensity over cells;
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Hi

We are using the nice outlining capabilities of object image to select
ROIs, but then we want to measure the average intensity over these ROIs.

We have seen in the manual that OI is not supposed to do this, but
that it is possible.  Has someone done it or could we receive some
pointers please on how we can implement it ourselves?

Thanks in advance

Stamatis


*-----------------*------------------*----------------------*---------------*
>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <
>Confocal and Image Analysis Laboratory             Tel: +44 (0)181 913 8675 <
>Membrane Biology                                Mobile: 0370 654288         <
>National Institute for Medical Research    Switchboard: 0181 9593666 x2621  <
>The Ridgeway                                   Message: x2219, x2622        <
>Mill Hill, London NW7 1AA                          FAX: +44 (0)181 906 4477 <


From nih-image-request@io.ece.drexel.edu Mon Aug  2 11:15 EDT 1999
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Date: Mon, 2 Aug 1999 17:08:46 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Object Image:  Measuring average intensity over cells;
Resent-Message-ID: <"V1fup1.0.aK5.XARft"@io>
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>Hi
>
>We are using the nice outlining capabilities of object image to select
>ROIs, but then we want to measure the average intensity over these ROIs.
>
>We have seen in the manual that OI is not supposed to do this, but
>that it is possible.  Has someone done it or could we receive some
>pointers please on how we can implement it ourselves?
>
>Thanks in advance
>
>Stamatis
>>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <



Stamatis, you can use the macro below which measures the
mean of all cells and puts the result in a new column called
'MyDensity'. Only the first "clone" of 'thisRoi' is measured.


macro 'Calc Densities';

{first closes all images, then opens
related images, creates rois and
measures densities.
Replace 'thisRoi' by the name of your
roi object as shown in the sequence
window}

var cell, im: integer;
theMean: real;
begin
  while nPics > 0 do begin
    SelectPic(1);
    Close;
    end;
  InitColumn('MyDensity');
  for im := 1 to nImages do begin
    ResetCounter;
    for cell := firstCell(im) to LastCell(im) do begin
      ShowCell(cell);
      if nClones('thisRoi') > 0 then begin
        SelectObject('thisRoi', 1);
        ObjectToRoi;
        Measure;
        theMean := rMean[rCount];
        SetValue('MyDensity', cell, theMean);
        end;
      end;
    if im <> nImages then
      Dispose;
  end;
  killroi;
end;



Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



From nih-image-request@io.ece.drexel.edu Mon Aug  2 11:48 EDT 1999
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Date: Mon, 2 Aug 1999 17:41:34 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Scripting CoolSnap color camera
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>on Sat, Jul 31, 1999 1:30 AM, Norbert Vischer at vischer@bio.uva.nl wrote:
>
>> I am setting up a microscope with CoolSnap, which is a color CCD camera
>> (1393 * 1040 pixels, cooled to 5 deg below ambient) and comes with a piece
>> of stand-alone acquisition software for Macintosh and PC, as well as with a
>> Photoshop acquisition plugin.
>
>Hi Norbert, what is the URL for CoolSnap?

here is an address:


http://www.photometrics.de/coolsnap.html


Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



From nih-image-request@io.ece.drexel.edu Mon Aug  2 11:57 EDT 1999
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From: Jochen Hoffmann <Jochen.Hoffmann@uni-konstanz.de>
Subject: Capture Frames
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Dear imagers!

I have a problem with the capture frames modus. It appears a message as
follows: <Capture Frames not supported when grabbing to screen.>
I posses version 1.62 and a PowerMac 8500.
Can anybody help me ?
Thanks, Jochen Hoffmann.

------------------------------------------------------------------------------
Adresse:

Privat:					Uni:

Jochen Hoffmann				Jochen Hoffmann
					c/o Prof. K. Mendgen
Blarerstrasse 35/37			Universitt Konstanz
78462 Konstanz				Fakultt fr Biologie
Tel.: 07531/189974			Phytopathologie
					Fach M 658
					D-78457 Konstanz

E-Mail: Jochen.Hoffmann@uni-konstanz.de
Fax:	(0049) 07531/88-3035
Tel.:	(0049) 07531/88-2107
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Date: Mon, 2 Aug 1999 16:24:17 -0700 (PDT)
From: Maria Arreola <micaela_qoya@yahoo.com>
Subject: Re: nih-image-d Digest V99 #175
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Hello Image users!
   Two things. First, to answer Lill Becker's question about saving
coral images, I am currently doing almost the same thing with some
coral images scanned into the computer and what I found has worked best
is to use Adobe Photoshop to open the images under Image.   Also I 
think a Tiff or a Pict File should also work.  Now my question to
everyone is a pretty simple one..how do I cite NIH Image in my
reference section of a research paper I am currently working on? Any
help would be appreciated.
                                  Thanks,
                            Maria Arreola-Espinoza
                       University of Colorado, Boulder


--- nih-image-d-request@io.ece.drexel.edu wrote:


> ATTACHMENT part 1 message/rfc822 
> 
> nih-image-d Digest				Volume 99 : Issue 175
> 
> Today's Topics:
>   Re: Scripting CoolSnap color camera   [ Tim Bates
> <tbates@bunyip.bhs.mq.edu ]
>   New User Seeks Advice                 [ lillian c
> becker <lbecke01@fiu.edu> ]
>   Re: RGB filters (Filters KODAK WRATT  [
> GJOSS@rna.bio.mq.edu.au ]
> 

> ATTACHMENT part 2 message/rfc822 
> Date: Sun, 01 Aug 1999 14:42:16 +1000
> From: Tim Bates <tbates@bunyip.bhs.mq.edu.au>
> To: <nih-image@io.ece.drexel.edu>
> Subject: Re: Scripting CoolSnap color camera
> 
> on Sat, Jul 31, 1999 1:30 AM, Norbert Vischer at
> vischer@bio.uva.nl wrote:
> 
> > I am setting up a microscope with CoolSnap, which
> is a color CCD camera
> > (1393 * 1040 pixels, cooled to 5 deg below
> ambient) and comes with a piece
> > of stand-alone acquisition software for Macintosh
> and PC, as well as with a
> > Photoshop acquisition plugin.
> 
> Hi Norbert, what is the URL for CoolSnap?
> 

> ATTACHMENT part 3 message/rfc822 
> Date: Sun, 1 Aug 1999 15:05:05 -0400 (EDT)
> From: lillian c becker <lbecke01@fiu.edu>
> To: nih-image@io.ece.drexel.edu
> Subject: New User Seeks Advice
> 
> Hi,
> 
> 	I am attempting to use the NIH image program to
> measure the
> surface area of corals from pictures taken with a
> digital camera.  The
> camera only saves the pictures in jpg.  "Saving As"
> the pictues in bmp is
> ok for "Paint" but the NIH program shuts down with
> the "illegal operation"
> warning when I open the new bmp image.  Is there a
> way to convert these
> images so that the NIH  program will accept them? 
> Are there any other
> pitfalls that I should know about ahead of time to
> save me a headache or
> two?  I realize from the disscussion archives that
> most of you are using
> Mac's.  I do not have access to one and am stuck
> with a PC.  I am hoping
> that some of you have had experience with this in
> the inferior format.
> 
> 	I appreciate any help in this endevour.
> 
> Sincerely,
> Lill
> 
> Lill Becker
> Department of Biology
> Florida International University
> Miami, FL  33199   USA
> 
> 	*******************************************
> 	*Are science and magic mutually exclusive?*
> 	*******************************************
> 

> ATTACHMENT part 4 message/rfc822 
> Date:          Mon, 2 Aug 1999 12:28:50 +1000
> From: GJOSS@rna.bio.mq.edu.au
> To: drmason@interconnect.com.au,
> nih-image@io.ece.drexel.edu
> Subject:       Re: RGB filters (Filters KODAK
> WRATTEN
> 
> >Date: Fri, 30 Jul 1999 20:31:34 +1030
> >To: nih-image@io.ece.drexel.edu
> >From: Doug Mason <drmason@interconnect.com.au>
> >Subject: RGB filters
> >Imagers,
> >
> >I want to grab red, green and blue greyscale
> microscope images in order to
> >create indexed colour derivative images. So I need
> to obtain Red, Green 
> >and
> >Blue filters for my microscope. But which ones?!
> When I talk to people in
> >camera stores, they say they have these red ones,
> these green ones, and "a
> >blue one will be dificult to identify". Does anyone
> have some
> >specifications for the R, G and B filters commonly
> used in photography? I
> >presume a wavelength or wavelength range is
> required to identify each
> >filter.
> >
> >
> >Doug Mason
> >
> >Mason Geoscience Pty Ltd
> >Petrological Services for the Exploration and
> Mining Industry
> >email   : drmason@interconnect.com.au
> >post    : PO Box 78, Glenside  SA  5065, Australia
> >phone   : +61-8-83901507
> >fax     : +61-8-83901194
> >
> >
> A previous post to maillist:
> ____________________________
> From: GJOSS@rna.bio.mq.edu.au
> To: SPurdy@nationalsteel.com,
> nih-image@io.ece.drexel.edu,
>         e_bonino@hotmail.com
> Date:          Thu, 25 Feb 1999 9:42:39 +1100
> Subject:       RE: Filters KODAK WRATTEN
> 
> Following previous enquires of my own, I have recent
> Web reference
> KSIS: Kodak Wratten Gelatin Filters, ( May 28 1998 )
> http://www.kodak.com:80/country/US/en/digital/sis/wratten.shtml
> 
> and access to Kodak Data Book of applied photography
> vol1 
> sheet FT-6 which gives spectrophotometric absorption
> curves for
> 25,47B,58 and 
> 29,47b,61.
> 
> I will email separately an attachment image of the
> curves to e_bonino and 
> have copied Kodak support requesting that 
> they extend their website to include such data.
> ______________________________
> >From: "Purdy, Sam" <SPurdy@nationalsteel.com>
> >To: "'nih-image@io.ece.drexel.edu'"
> <nih-image@io.ece.drexel.edu>
> >Subject: RE: Filters KODAK WRATTEN
> >Date: Wed, 24 Feb 1999 08:47:45 -0500
> >
> >Kodak publication B-3, Kodak Filters for Scientific
> and Technical Uses,
> >contains transmittance curves for all Kodak
> filters. The particular
> >filters:
> >filter 25 transmits at wavelengths above 600
> nanometers, 47B transmits
> >at 430 nanometers, and  58 at 525 nonometers. Hope
> this helps.
> >Sam Purdy
> >National Steel Corp. 
> >Trenton, MI, USA
> ______________________________
> 
> Greg Joss,
> School of Biological Sciences, Phone:(61)(2) 9850
> 8212 Fax: 9850 8174
> Macquarie University,          Email
> gjoss@rna.bio.mq.edu.au
> North Ryde, (Sydney,) NSW 2109, Australia
> 

_____________________________________________________________
Do You Yahoo!?
Free instant messaging and more at http://messenger.yahoo.com


From nih-image-d-request@io.ece.drexel.edu Tue Aug  3 05:18 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #176
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 176

Today's Topics:
  grain area measurements               [ Ludger Offerhaus <ljo@gfz-potsdam.d ]
  Re: grain area measurements           [ Norbert Vischer <vischer@bio.uva.nl ]
  RE:nih-image-d Digest V99 #175        [ Jonathan WISCO <jjwisco@cajal-1.bu. ]
  Object Image: Measuring average inte  [ Stamatis Pagakis <spagaki@nimr.mrc. ]
  Re: Object Image: Measuring average   [ Norbert Vischer <vischer@bio.uva.nl ]
  Re: Scripting CoolSnap color camera   [ Norbert Vischer <vischer@bio.uva.nl ]
  Capture Frames                        [ Jochen Hoffmann <Jochen.Hoffmann@un ]
  Re: nih-image-d Digest V99 #175       [ Maria Arreola <micaela_qoya@yahoo.c ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]

------------------------------

Date: Mon, 2 Aug 1999 14:11:56 +0200
From: Ludger Offerhaus <ljo@gfz-potsdam.de>
To: nih-image@io.ece.drexel.edu
Subject: grain area measurements
Message-Id: <l03130301b3cb38fdb16d@[139.17.139.125]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

dear imagers!

On a skeletonized binary image of grain boundaries in a ceramic aggregate
I'd like to measure grain areas as well as the grain length and width
(ellipse minor/major axes in NIH Image 1.62). using the wand tool, Image
(1) recognizes separate grains and (2) calculates ellipse minor and major
axes.

NIH Image seems unable to come up with realistic *area* measurements. After
setting the scale to about 18 pixels per micrometer, almost all grains
measured have an area of zero (even if ellipse m/m axes are e.g. 2 and 5
Microns, which should result in an area of a few square micrometers).

Any guesses as to what I could do about his?!
Thanks in advance!

cheers,
Ludger


--
Ludger Offerhaus
GeoForschungsZentrum Potsdam
Telegrafenberg, 14473 Potsdam, Duitsland
Tel: +49 (0)331 288 1326 / 1390
of (ook awap): 030 32 60 55 68
---
... aan een boom *zo* volgeladen / mist men n, twee pruimpjes niet ...
---

------------------------------

Date: Mon, 2 Aug 1999 15:02:38 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: grain area measurements
Message-Id: <l03110701b3cb44fd1d2e@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

>On a skeletonized binary image of grain boundaries in a ceramic aggregate
>I'd like to measure grain areas as well as the grain length and width
>(ellipse minor/major axes in NIH Image 1.62). using the wand tool, Image
>(1) recognizes separate grains and (2) calculates ellipse minor and major
>axes.
>
>NIH Image seems unable to come up with realistic *area* measurements. After
>setting the scale to about 18 pixels per micrometer, almost all grains
>measured have an area of zero (even if ellipse m/m axes are e.g. 2 and 5
>Microns, which should result in an area of a few square micrometers).
>Ludger Offerhaus
>GeoForschungsZentrum Potsdam


Just click the option "include interior holes".
The ellipse parameters are always calculated from 'filled objects',
independent of this setting. However, area measurements do listen to the
setting, so in your case you probably only got the area of the boundary.

------------------------------

Date: 02 Aug 99 09:11:10 -0500
From: Jonathan WISCO <jjwisco@cajal-1.bu.edu>
To: "nih-image" <nih-image@io.ece.drexel.edu>
Subject: RE:nih-image-d Digest V99 #175
Message-Id: <199908021303.JAA19796@bu.edu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset="US-Ascii"

Lill,
   With a PC, I presume you are using Scion Image instead of NIH Image. 
Nevertheless, you might have better luck if you convert the jpg files to tif format
instead of bmp format.  A program like Photoshop will do the trick nicely.

Jonathan J. Wisco
Department of Anatomy and Neurobiology
Boston University School of Medicine

>Date: Sun, 1 Aug 1999 15:05:05 -0400 (EDT)
>From: lillian c becker <lbecke01@fiu.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: New User Seeks Advice
>Message-ID: <Pine.SOL.3.96.990801111018.27734A-100000@solix4-
>64>
>Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>Hi,
>
>	I am attempting to use the NIH image program to measure the
>surface area of corals from pictures taken with a digital camera.  The
>camera only saves the pictures in jpg.  "Saving As" the pictues in bmp 
>is
>ok for "Paint" but the NIH program shuts down with the "illegal 
>operation"
>warning when I open the new bmp image.  Is there a way to convert 
>these
>images so that the NIH  program will accept them?  Are there any other
>pitfalls that I should know about ahead of time to save me a headache 
>or
>two?  I realize from the disscussion archives that most of you are using
>Mac's.  I do not have access to one and am stuck with a PC.  I am 
>hoping
>that some of you have had experience with this in the inferior format.
>
>	I appreciate any help in this endevour.
>
>Sincerely,
>Lill
>
>Lill Becker
>Department of Biology
>Florida International University
>Miami, FL  33199   USA
>
>	*******************************************
>	*Are science and magic mutually exclusive?*
>	*******************************************
>
>------------------------------
>

------------------------------

Date: Mon, 02 Aug 1999 14:22:00 +0100
From: Stamatis Pagakis <spagaki@nimr.mrc.ac.uk>
To: List <nih-image@io.ece.drexel.edu>
Subject: Object Image:  Measuring average intensity over cells;
Message-id: <Pine.SGI.4.10.9908021415420.15067-100000@membo2>
Content-type: TEXT/PLAIN; charset=US-ASCII

Hi

We are using the nice outlining capabilities of object image to select
ROIs, but then we want to measure the average intensity over these ROIs.

We have seen in the manual that OI is not supposed to do this, but
that it is possible.  Has someone done it or could we receive some
pointers please on how we can implement it ourselves?

Thanks in advance

Stamatis


*-----------------*------------------*----------------------*---------------*
>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <
>Confocal and Image Analysis Laboratory             Tel: +44 (0)181 913 8675 <
>Membrane Biology                                Mobile: 0370 654288         <
>National Institute for Medical Research    Switchboard: 0181 9593666 x2621  <
>The Ridgeway                                   Message: x2219, x2622        <
>Mill Hill, London NW7 1AA                          FAX: +44 (0)181 906 4477 <

------------------------------

Date: Mon, 2 Aug 1999 17:08:46 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Object Image:  Measuring average intensity over cells;
Message-Id: <l03110705b3cb63563f2b@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

>Hi
>
>We are using the nice outlining capabilities of object image to select
>ROIs, but then we want to measure the average intensity over these ROIs.
>
>We have seen in the manual that OI is not supposed to do this, but
>that it is possible.  Has someone done it or could we receive some
>pointers please on how we can implement it ourselves?
>
>Thanks in advance
>
>Stamatis
>>Dr Stamatis Pagakis				    spagaki@nimr.mrc.ac.uk   <



Stamatis, you can use the macro below which measures the
mean of all cells and puts the result in a new column called
'MyDensity'. Only the first "clone" of 'thisRoi' is measured.


macro 'Calc Densities';

{first closes all images, then opens
related images, creates rois and
measures densities.
Replace 'thisRoi' by the name of your
roi object as shown in the sequence
window}

var cell, im: integer;
theMean: real;
begin
  while nPics > 0 do begin
    SelectPic(1);
    Close;
    end;
  InitColumn('MyDensity');
  for im := 1 to nImages do begin
    ResetCounter;
    for cell := firstCell(im) to LastCell(im) do begin
      ShowCell(cell);
      if nClones('thisRoi') > 0 then begin
        SelectObject('thisRoi', 1);
        ObjectToRoi;
        Measure;
        theMean := rMean[rCount];
        SetValue('MyDensity', cell, theMean);
        end;
      end;
    if im <> nImages then
      Dispose;
  end;
  killroi;
end;



Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: Mon, 2 Aug 1999 17:41:34 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Scripting CoolSnap color camera
Message-Id: <l03110707b3cb6c946b86@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

>on Sat, Jul 31, 1999 1:30 AM, Norbert Vischer at vischer@bio.uva.nl wrote:
>
>> I am setting up a microscope with CoolSnap, which is a color CCD camera
>> (1393 * 1040 pixels, cooled to 5 deg below ambient) and comes with a piece
>> of stand-alone acquisition software for Macintosh and PC, as well as with a
>> Photoshop acquisition plugin.
>
>Hi Norbert, what is the URL for CoolSnap?

here is an address:


http://www.photometrics.de/coolsnap.html


Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: Mon, 2 Aug 1999 17:44:42 +0200
From: Jochen Hoffmann <Jochen.Hoffmann@uni-konstanz.de>
To: nih-image@io.ece.drexel.edu
Subject: Capture Frames
Message-Id: <l03102800b3cb6cff17b2@[134.34.124.55]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Dear imagers!

I have a problem with the capture frames modus. It appears a message as
follows: <Capture Frames not supported when grabbing to screen.>
I posses version 1.62 and a PowerMac 8500.
Can anybody help me ?
Thanks, Jochen Hoffmann.

------------------------------------------------------------------------------
Adresse:

Privat:					Uni:

Jochen Hoffmann				Jochen Hoffmann
					c/o Prof. K. Mendgen
Blarerstrasse 35/37			Universitt Konstanz
78462 Konstanz				Fakultt fr Biologie
Tel.: 07531/189974			Phytopathologie
					Fach M 658
					D-78457 Konstanz

E-Mail: Jochen.Hoffmann@uni-konstanz.de
Fax:	(0049) 07531/88-3035
Tel.:	(0049) 07531/88-2107
------------------------------------------------------------------------------

------------------------------

Date: Mon, 2 Aug 1999 16:24:17 -0700 (PDT)
From: Maria Arreola <micaela_qoya@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #175
Message-ID: <19990802232417.15545.rocketmail@web305.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

Hello Image users!
   Two things. First, to answer Lill Becker's question about saving
coral images, I am currently doing almost the same thing with some
coral images scanned into the computer and what I found has worked best
is to use Adobe Photoshop to open the images under Image.   Also I 
think a Tiff or a Pict File should also work.  Now my question to
everyone is a pretty simple one..how do I cite NIH Image in my
reference section of a research paper I am currently working on? Any
help would be appreciated.
                                  Thanks,
                            Maria Arreola-Espinoza
                       University of Colorado, Boulder


--- nih-image-d-request@io.ece.drexel.edu wrote:


> ATTACHMENT part 1 message/rfc822 
> 
> nih-image-d Digest				Volume 99 : Issue 175
> 
> Today's Topics:
>   Re: Scripting CoolSnap color camera   [ Tim Bates
> <tbates@bunyip.bhs.mq.edu ]
>   New User Seeks Advice                 [ lillian c
> becker <lbecke01@fiu.edu> ]
>   Re: RGB filters (Filters KODAK WRATT  [
> GJOSS@rna.bio.mq.edu.au ]
> 

> ATTACHMENT part 2 message/rfc822 
> Date: Sun, 01 Aug 1999 14:42:16 +1000
> From: Tim Bates <tbates@bunyip.bhs.mq.edu.au>
> To: <nih-image@io.ece.drexel.edu>
> Subject: Re: Scripting CoolSnap color camera
> 
> on Sat, Jul 31, 1999 1:30 AM, Norbert Vischer at
> vischer@bio.uva.nl wrote:
> 
> > I am setting up a microscope with CoolSnap, which
> is a color CCD camera
> > (1393 * 1040 pixels, cooled to 5 deg below
> ambient) and comes with a piece
> > of stand-alone acquisition software for Macintosh
> and PC, as well as with a
> > Photoshop acquisition plugin.
> 
> Hi Norbert, what is the URL for CoolSnap?
> 

> ATTACHMENT part 3 message/rfc822 
> Date: Sun, 1 Aug 1999 15:05:05 -0400 (EDT)
> From: lillian c becker <lbecke01@fiu.edu>
> To: nih-image@io.ece.drexel.edu
> Subject: New User Seeks Advice
> 
> Hi,
> 
> 	I am attempting to use the NIH image program to
> measure the
> surface area of corals from pictures taken with a
> digital camera.  The
> camera only saves the pictures in jpg.  "Saving As"
> the pictues in bmp is
> ok for "Paint" but the NIH program shuts down with
> the "illegal operation"
> warning when I open the new bmp image.  Is there a
> way to convert these
> images so that the NIH  program will accept them? 
> Are there any other
> pitfalls that I should know about ahead of time to
> save me a headache or
> two?  I realize from the disscussion archives that
> most of you are using
> Mac's.  I do not have access to one and am stuck
> with a PC.  I am hoping
> that some of you have had experience with this in
> the inferior format.
> 
> 	I appreciate any help in this endevour.
> 
> Sincerely,
> Lill
> 
> Lill Becker
> Department of Biology
> Florida International University
> Miami, FL  33199   USA
> 
> 	*******************************************
> 	*Are science and magic mutually exclusive?*
> 	*******************************************
> 

> ATTACHMENT part 4 message/rfc822 
> Date:          Mon, 2 Aug 1999 12:28:50 +1000
> From: GJOSS@rna.bio.mq.edu.au
> To: drmason@interconnect.com.au,
> nih-image@io.ece.drexel.edu
> Subject:       Re: RGB filters (Filters KODAK
> WRATTEN
> 
> >Date: Fri, 30 Jul 1999 20:31:34 +1030
> >To: nih-image@io.ece.drexel.edu
> >From: Doug Mason <drmason@interconnect.com.au>
> >Subject: RGB filters
> >Imagers,
> >
> >I want to grab red, green and blue greyscale
> microscope images in order to
> >create indexed colour derivative images. So I need
> to obtain Red, Green 
> >and
> >Blue filters for my microscope. But which ones?!
> When I talk to people in
> >camera stores, they say they have these red ones,
> these green ones, and "a
> >blue one will be dificult to identify". Does anyone
> have some
> >specifications for the R, G and B filters commonly
> used in photography? I
> >presume a wavelength or wavelength range is
> required to identify each
> >filter.
> >
> >
> >Doug Mason
> >
> >Mason Geoscience Pty Ltd
> >Petrological Services for the Exploration and
> Mining Industry
> >email   : drmason@interconnect.com.au
> >post    : PO Box 78, Glenside  SA  5065, Australia
> >phone   : +61-8-83901507
> >fax     : +61-8-83901194
> >
> >
> A previous post to maillist:
> ____________________________
> From: GJOSS@rna.bio.mq.edu.au
> To: SPurdy@nationalsteel.com,
> nih-image@io.ece.drexel.edu,
>         e_bonino@hotmail.com
> Date:          Thu, 25 Feb 1999 9:42:39 +1100
> Subject:       RE: Filters KODAK WRATTEN
> 
> Following previous enquires of my own, I have recent
> Web reference
> KSIS: Kodak Wratten Gelatin Filters, ( May 28 1998 )
> http://www.kodak.com:80/country/US/en/digital/sis/wratten.shtml
> 
> and access to Kodak Data Book of applied photography
> vol1 
> sheet FT-6 which gives spectrophotometric absorption
> curves for
> 25,47B,58 and 
> 29,47b,61.
> 
> I will email separately an attachment image of the
> curves to e_bonino and 
> have copied Kodak support requesting that 
> they extend their website to include such data.
> ______________________________
> >From: "Purdy, Sam" <SPurdy@nationalsteel.com>
> >To: "'nih-image@io.ece.drexel.edu'"
> <nih-image@io.ece.drexel.edu>
> >Subject: RE: Filters KODAK WRATTEN
> >Date: Wed, 24 Feb 1999 08:47:45 -0500
> >
> >Kodak publication B-3, Kodak Filters for Scientific
> and Technical Uses,
> >contains transmittance curves for all Kodak
> filters. The particular
> >filters:
> >filter 25 transmits at wavelengths above 600
> nanometers, 47B transmits
> >at 430 nanometers, and  58 at 525 nonometers. Hope
> this helps.
> >Sam Purdy
> >National Steel Corp. 
> >Trenton, MI, USA
> ______________________________
> 
> Greg Joss,
> School of Biological Sciences, Phone:(61)(2) 9850
> 8212 Fax: 9850 8174
> Macquarie University,          Email
> gjoss@rna.bio.mq.edu.au
> North Ryde, (Sydney,) NSW 2109, Australia
> 

_____________________________________________________________
Do You Yahoo!?
Free instant messaging and more at http://messenger.yahoo.com

------------------------------

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? matches any single character. []'s matches any single character shown in
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This archive server knows the following commands:

get filename ...
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From nih-image-request@io.ece.drexel.edu Tue Aug  3 11:50 EDT 1999
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Date: Tue, 03 Aug 1999 11:33:24 -0500
From: "Richard A. Fluck" <R_fluck@ACAD.FANDM.EDU>
Subject: scanner
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One of my colleagues here would like to digitize 4" by 5" electron
micrographs.  We have a Hewlett-Packard ScanJet 4c, but it has no adapter
for scanning such large negatives.  Any suggestions?


Richard A. Fluck, Dept. of Biology, Franklin and Marshall College, P.O. Box
3003, Lancaster, PA 17604-3003 USA; voice, (717)291-4152; fax, (717)
399-4548



From nih-image-request@io.ece.drexel.edu Tue Aug  3 20:07 EDT 1999
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From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: FW: grain area measurements
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> ----------
> From: 	Goldsmith, Noel
> Sent: 	Wednesday, 4 August 1999 9:48 AM
> To: 	'Ludger Offerhaus'
> Subject: 	RE: grain area measurements
> 
> Ludger,
> You need to increase the number of decimal points in the display of
> results. On the analyze menu select options and in the dialog that comes
> up increase the number of decimal points for the results display.
> I bet that your spatial scale is such that the area of the grains is
> smaller than 1 and if the default 2 decimals is on then the areas are all
> smaller than 0.01 and you can only see zeros. If you change to 4 or 6
> places then the numbers will appear in the results window.
> Best wishes Noel
> 
> ----------
> From: 	Ludger Offerhaus
> Sent: 	Monday, 2 August 1999 10:11 PM
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	grain area measurements
> 
> dear imagers!
> 
> On a skeletonized binary image of grain boundaries in a ceramic aggregate
> I'd like to measure grain areas as well as the grain length and width
> (ellipse minor/major axes in NIH Image 1.62). using the wand tool, Image
> (1) recognizes separate grains and (2) calculates ellipse minor and major
> axes.
> 
> NIH Image seems unable to come up with realistic *area* measurements.
> After
> setting the scale to about 18 pixels per micrometer, almost all grains
> measured have an area of zero (even if ellipse m/m axes are e.g. 2 and 5
> Microns, which should result in an area of a few square micrometers).
> 
> Any guesses as to what I could do about his?!
> Thanks in advance!
> 
> cheers,
> Ludger
> 
> 
> --
> Ludger Offerhaus
> GeoForschungsZentrum Potsdam
> Telegrafenberg, 14473 Potsdam, Duitsland
> Tel: +49 (0)331 288 1326 / 1390
> of (ook awap): 030 32 60 55 68
> ---
> ... aan een boom *zo* volgeladen / mist men n, twee pruimpjes niet ...
> ---
> 
> 


From nih-image-request@io.ece.drexel.edu Wed Aug  4 00:06 EDT 1999
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From: "Katsukuni FUJIMOTO, M.D." <katukuni@med.kawasaki-m.ac.jp>
To: <nih-image@io.ece.drexel.edu>
References: <F98649A5EE8ED11190160000F802756598D11E@exchvic3.dsto.defence.gov.au>
Subject: Re: grain area measurements
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----- Original Message -----
From: Goldsmith, Noel <Noel.Goldsmith@dsto.defence.gov.au>
To: 'Image Mailing List' <nih-image@io.ece.drexel.edu>
Sent: Wednesday, August 04, 1999 8:49 AM
Subject: FW: grain area measurements


>
>
> > ----------
> > From: Goldsmith, Noel
> > Sent: Wednesday, 4 August 1999 9:48 AM
> > To: 'Ludger Offerhaus'
> > Subject: RE: grain area measurements
> >
> > Ludger,
> > You need to increase the number of decimal points in the display of
> > results. On the analyze menu select options and in the dialog that comes
> > up increase the number of decimal points for the results display.
> > I bet that your spatial scale is such that the area of the grains is
> > smaller than 1 and if the default 2 decimals is on then the areas are
all
> > smaller than 0.01 and you can only see zeros. If you change to 4 or 6
> > places then the numbers will appear in the results window.
> > Best wishes Noel
> >
> > ----------
> > From: Ludger Offerhaus
> > Sent: Monday, 2 August 1999 10:11 PM
> > To: nih-image@io.ece.drexel.edu
> > Subject: grain area measurements
> >
> > dear imagers!
> >
> > On a skeletonized binary image of grain boundaries in a ceramic
aggregate
> > I'd like to measure grain areas as well as the grain length and width
> > (ellipse minor/major axes in NIH Image 1.62). using the wand tool, Image
> > (1) recognizes separate grains and (2) calculates ellipse minor and
major
> > axes.
> >
> > NIH Image seems unable to come up with realistic *area* measurements.
> > After
> > setting the scale to about 18 pixels per micrometer, almost all grains
> > measured have an area of zero (even if ellipse m/m axes are e.g. 2 and 5
> > Microns, which should result in an area of a few square micrometers).
> >
> > Any guesses as to what I could do about his?!
> > Thanks in advance!
> >
> > cheers,
> > Ludger
> >
> >
> > --
> > Ludger Offerhaus
> > GeoForschungsZentrum Potsdam
> > Telegrafenberg, 14473 Potsdam, Duitsland
> > Tel: +49 (0)331 288 1326 / 1390
> > of (ook awap): 030 32 60 55 68
> > ---
> > ... aan een boom *zo* volgeladen / mist men n, twee pruimpjes niet ...
> > ---
> >
> >
>
>


From nih-image-request@io.ece.drexel.edu Wed Aug  4 02:24 EDT 1999
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Message-ID: <01BEDE50.CFCB9C10@kahoolawe.geo.vu.nl>
From: "E.H.van den Berg" <berg@geo.vu.nl>
To: "nih-image@io.ece.drexel.edu" <nih-image@io.ece.drexel.edu>
Subject: 2D/3D-stereology
Date: Wed, 4 Aug 1999 08:10:26 +0200
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Dear all,
 
The size distribution of sand grains in an aeolian sediment constructed from 10 images of one thin section seems not to fit with lab measurement. Despite the fact that both methods measure different diameters, I would like to know what the effect of sectioning is on the size distribution obtained from thin sections.

I have applied a method presented bij Underwood in 1970 to correct for sectioning and create a 3D distribution of sizes. It has some effect (the distribution shifts to the coarser part, distribution is more narrow and seeper in the finer part) but I would like to check these calculations.

To avoid programming for the next couple of months, does someone have any suggestions for subroutines or macro's to convert 2D distributions to 3D ones?

Thanks in advance,


sincerely,

Elmer 


Elmer van den berg
Vrije Universiteit Amsterdam
Faculty of Earth Sciences


From nih-image-d-request@io.ece.drexel.edu Wed Aug  4 04:14 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 177

Today's Topics:
  scanner                               [ "Richard A. Fluck" <R_fluck@ACAD.FA ]
  FW: grain area measurements           [ "Goldsmith, Noel" <Noel.Goldsmith@d ]
  Re: grain area measurements           [ "Katsukuni FUJIMOTO, M.D." <katukun ]
  2D/3D-stereology                      [ "E.H.van den Berg" <berg@geo.vu.nl> ]
  Re: 2D/3D-stereology                  [ Jan Kreft <Kreft@cardiff.ac.uk> ]

------------------------------

Date: Tue, 03 Aug 1999 11:33:24 -0500
From: "Richard A. Fluck" <R_fluck@ACAD.FANDM.EDU>
To: nih-image@io.ece.drexel.edu
Subject: scanner
Message-id: <l03130308b3ccc9ebf9e1@[155.68.64.140]>
Content-type: text/plain; charset="us-ascii"

One of my colleagues here would like to digitize 4" by 5" electron
micrographs.  We have a Hewlett-Packard ScanJet 4c, but it has no adapter
for scanning such large negatives.  Any suggestions?


Richard A. Fluck, Dept. of Biology, Franklin and Marshall College, P.O. Box
3003, Lancaster, PA 17604-3003 USA; voice, (717)291-4152; fax, (717)
399-4548

------------------------------

Date: Wed, 4 Aug 1999 09:49:08 +1000 
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: FW: grain area measurements
Message-Id: <F98649A5EE8ED11190160000F802756598D11E@exchvic3.dsto.defence.gov.au>
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	charset="windows-1252"
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> ----------
> From: 	Goldsmith, Noel
> Sent: 	Wednesday, 4 August 1999 9:48 AM
> To: 	'Ludger Offerhaus'
> Subject: 	RE: grain area measurements
> 
> Ludger,
> You need to increase the number of decimal points in the display of
> results. On the analyze menu select options and in the dialog that comes
> up increase the number of decimal points for the results display.
> I bet that your spatial scale is such that the area of the grains is
> smaller than 1 and if the default 2 decimals is on then the areas are all
> smaller than 0.01 and you can only see zeros. If you change to 4 or 6
> places then the numbers will appear in the results window.
> Best wishes Noel
> 
> ----------
> From: 	Ludger Offerhaus
> Sent: 	Monday, 2 August 1999 10:11 PM
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	grain area measurements
> 
> dear imagers!
> 
> On a skeletonized binary image of grain boundaries in a ceramic aggregate
> I'd like to measure grain areas as well as the grain length and width
> (ellipse minor/major axes in NIH Image 1.62). using the wand tool, Image
> (1) recognizes separate grains and (2) calculates ellipse minor and major
> axes.
> 
> NIH Image seems unable to come up with realistic *area* measurements.
> After
> setting the scale to about 18 pixels per micrometer, almost all grains
> measured have an area of zero (even if ellipse m/m axes are e.g. 2 and 5
> Microns, which should result in an area of a few square micrometers).
> 
> Any guesses as to what I could do about his?!
> Thanks in advance!
> 
> cheers,
> Ludger
> 
> 
> --
> Ludger Offerhaus
> GeoForschungsZentrum Potsdam
> Telegrafenberg, 14473 Potsdam, Duitsland
> Tel: +49 (0)331 288 1326 / 1390
> of (ook awap): 030 32 60 55 68
> ---
> ... aan een boom *zo* volgeladen / mist men n, twee pruimpjes niet ...
> ---
> 
> 

------------------------------

Date: Wed, 4 Aug 1999 10:16:36 +0900
From: "Katsukuni FUJIMOTO, M.D." <katukuni@med.kawasaki-m.ac.jp>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: grain area measurements
Message-ID: <002c01bede18$708db8b0$6d370cac@med.kawasakim.ac.jp>
Content-Type: text/plain;
	charset="windows-1252"
Content-Transfer-Encoding: 8bit

----- Original Message -----
From: Goldsmith, Noel <Noel.Goldsmith@dsto.defence.gov.au>
To: 'Image Mailing List' <nih-image@io.ece.drexel.edu>
Sent: Wednesday, August 04, 1999 8:49 AM
Subject: FW: grain area measurements


>
>
> > ----------
> > From: Goldsmith, Noel
> > Sent: Wednesday, 4 August 1999 9:48 AM
> > To: 'Ludger Offerhaus'
> > Subject: RE: grain area measurements
> >
> > Ludger,
> > You need to increase the number of decimal points in the display of
> > results. On the analyze menu select options and in the dialog that comes
> > up increase the number of decimal points for the results display.
> > I bet that your spatial scale is such that the area of the grains is
> > smaller than 1 and if the default 2 decimals is on then the areas are
all
> > smaller than 0.01 and you can only see zeros. If you change to 4 or 6
> > places then the numbers will appear in the results window.
> > Best wishes Noel
> >
> > ----------
> > From: Ludger Offerhaus
> > Sent: Monday, 2 August 1999 10:11 PM
> > To: nih-image@io.ece.drexel.edu
> > Subject: grain area measurements
> >
> > dear imagers!
> >
> > On a skeletonized binary image of grain boundaries in a ceramic
aggregate
> > I'd like to measure grain areas as well as the grain length and width
> > (ellipse minor/major axes in NIH Image 1.62). using the wand tool, Image
> > (1) recognizes separate grains and (2) calculates ellipse minor and
major
> > axes.
> >
> > NIH Image seems unable to come up with realistic *area* measurements.
> > After
> > setting the scale to about 18 pixels per micrometer, almost all grains
> > measured have an area of zero (even if ellipse m/m axes are e.g. 2 and 5
> > Microns, which should result in an area of a few square micrometers).
> >
> > Any guesses as to what I could do about his?!
> > Thanks in advance!
> >
> > cheers,
> > Ludger
> >
> >
> > --
> > Ludger Offerhaus
> > GeoForschungsZentrum Potsdam
> > Telegrafenberg, 14473 Potsdam, Duitsland
> > Tel: +49 (0)331 288 1326 / 1390
> > of (ook awap): 030 32 60 55 68
> > ---
> > ... aan een boom *zo* volgeladen / mist men n, twee pruimpjes niet ...
> > ---
> >
> >
>
>

------------------------------

Date: Wed, 4 Aug 1999 08:10:26 +0200
From: "E.H.van den Berg" <berg@geo.vu.nl>
To: "nih-image@io.ece.drexel.edu" <nih-image@io.ece.drexel.edu>
Subject: 2D/3D-stereology
Message-ID: <01BEDE50.CFCB9C10@kahoolawe.geo.vu.nl>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 8bit

Dear all,
 
The size distribution of sand grains in an aeolian sediment constructed from 10 images of one thin section seems not to fit with lab measurement. Despite the fact that both methods measure different diameters, I would like to know what the effect of sectioning is on the size distribution obtained from thin sections.

I have applied a method presented bij Underwood in 1970 to correct for sectioning and create a 3D distribution of sizes. It has some effect (the distribution shifts to the coarser part, distribution is more narrow and seeper in the finer part) but I would like to check these calculations.

To avoid programming for the next couple of months, does someone have any suggestions for subroutines or macro's to convert 2D distributions to 3D ones?

Thanks in advance,


sincerely,

Elmer 


Elmer van den berg
Vrije Universiteit Amsterdam
Faculty of Earth Sciences

------------------------------

Date: Wed, 4 Aug 1999 09:02:49 +0100 (BST)
From: Jan Kreft <Kreft@cardiff.ac.uk>
To: "nih-image@io.ece.drexel.edu" <nih-image@io.ece.drexel.edu>
Subject: Re: 2D/3D-stereology
Message-ID: <Pine.OSF.3.95q.990804090113.8773A-100000@thor>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear Elmer,

I would like to learn something about methods to correct for sectioning
too. Could you give a reference for the Underwood method please?

Thanks, Jan.

Jan Kreft				Phone +44 (0)1222 875278
Cardiff School of Biosciences		Fax   +44 (0)1222 874305
Cardiff	University 			E-mail Kreft@cardiff.ac.uk
PO Box 915, Cardiff CF10 3TL, UK

On Wed, 4 Aug 1999, E.H.van den Berg wrote:

> Dear all,
>  
> The size distribution of sand grains in an aeolian sediment constructed from 10 images of one thin section seems not to fit with lab measurement. Despite the fact that both methods measure different diameters, I would like to know what the effect of sectioning is on the size distribution obtained from thin sections.
> 
> I have applied a method presented bij Underwood in 1970 to correct for sectioning and create a 3D distribution of sizes. It has some effect (the distribution shifts to the coarser part, distribution is more narrow and seeper in the finer part) but I would like to check these calculations.
> 
> To avoid programming for the next couple of months, does someone have any suggestions for subroutines or macro's to convert 2D distributions to 3D ones?
> 
> Thanks in advance,
> 
> 
> sincerely,
> 
> Elmer 
> 
> 
> Elmer van den berg
> Vrije Universiteit Amsterdam
> Faculty of Earth Sciences
> 
> 

--------------------------------
End of nih-image-d Digest V99 Issue #177
****************************************

From nih-image-request@io.ece.drexel.edu Wed Aug  4 04:17 EDT 1999
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Dear Elmer,

I would like to learn something about methods to correct for sectioning
too. Could you give a reference for the Underwood method please?

Thanks, Jan.

Jan Kreft				Phone +44 (0)1222 875278
Cardiff School of Biosciences		Fax   +44 (0)1222 874305
Cardiff	University 			E-mail Kreft@cardiff.ac.uk
PO Box 915, Cardiff CF10 3TL, UK

On Wed, 4 Aug 1999, E.H.van den Berg wrote:

> Dear all,
>  
> The size distribution of sand grains in an aeolian sediment constructed from 10 images of one thin section seems not to fit with lab measurement. Despite the fact that both methods measure different diameters, I would like to know what the effect of sectioning is on the size distribution obtained from thin sections.
> 
> I have applied a method presented bij Underwood in 1970 to correct for sectioning and create a 3D distribution of sizes. It has some effect (the distribution shifts to the coarser part, distribution is more narrow and seeper in the finer part) but I would like to check these calculations.
> 
> To avoid programming for the next couple of months, does someone have any suggestions for subroutines or macro's to convert 2D distributions to 3D ones?
> 
> Thanks in advance,
> 
> 
> sincerely,
> 
> Elmer 
> 
> 
> Elmer van den berg
> Vrije Universiteit Amsterdam
> Faculty of Earth Sciences
> 
> 


From nih-image-request@io.ece.drexel.edu Wed Aug  4 04:25 EDT 1999
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Date: Wed, 4 Aug 1999 10:11:19 +0200
To: nih-image@io.ece.drexel.edu
From: Ludger Offerhaus <ljo@gfz-potsdam.de>
Subject: Re: 2D/3D-stereology => Underwood 1970
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Underwood, E.E., Quantitative Stereology, Addison-Wesley, Reading (Mass), 1970
still is the standard textbook on stereology.

cheers,
Ludger

>Dear Elmer,
>
>I would like to learn something about methods to correct for sectioning
>too. Could you give a reference for the Underwood method please?
>
>Thanks, Jan.
>
>Jan Kreft				Phone +44 (0)1222 875278
>Cardiff School of Biosciences		Fax   +44 (0)1222 874305
>Cardiff	University 			E-mail Kreft@cardiff.ac.uk
>PO Box 915, Cardiff CF10 3TL, UK
>
>On Wed, 4 Aug 1999, E.H.van den Berg wrote:
>
>> Dear all,
>>
>> The size distribution of sand grains in an aeolian sediment constructed
>>from 10 images of one thin section seems not to fit with lab measurement.
>>Despite the fact that both methods measure different diameters, I would
>>like to know what the effect of sectioning is on the size distribution
>>obtained from thin sections.
>>
>> I have applied a method presented bij Underwood in 1970 to correct for
>>sectioning and create a 3D distribution of sizes. It has some effect (the
>>distribution shifts to the coarser part, distribution is more narrow and
>>seeper in the finer part) but I would like to check these calculations.
>>
>> To avoid programming for the next couple of months, does someone have
>>any suggestions for subroutines or macro's to convert 2D distributions to
>>3D ones?
>>
>> Thanks in advance,
>>
>>
>> sincerely,
>>
>> Elmer
>>
>>
>> Elmer van den berg
>> Vrije Universiteit Amsterdam
>> Faculty of Earth Sciences
>>
>>
>


--
Ludger Offerhaus
GeoForschungsZentrum Potsdam
Telegrafenberg, 14473 Potsdam, Duitsland
Tel: +49 (0)331 288 1326 / 1390
of (ook awap): 030 32 60 55 68
---
... aan een boom *zo* volgeladen / mist men n, twee pruimpjes niet ...
---



From nih-image-request@io.ece.drexel.edu Wed Aug  4 04:49 EDT 1999
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Message-ID: <01BEDE64.7B1DF7D0@kahoolawe.geo.vu.nl>
From: "E.H.van den Berg" <berg@geo.vu.nl>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: 2D/3D-stereology
Date: Wed, 4 Aug 1999 10:31:14 +0200
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Dear Mr Kreft,

I have to tell you that there is no method of Underwood, but in his =
reference work on stereology a number of methods for correcting thin =
section distribution are presented. He describes several methods that =
apply to specific measurements made in the thin sections, like area, =
diameter or chords.

Theoretical background information and practical examples can be found =
in:

Underwood, E.E., 1970. Quantitative Stereology. Addison-Wesley =
Publishing Company, Reading, Massachusetts.

Sorry for the misunderstanding and please ask,

sincerely,

elmer


From nih-image-request@io.ece.drexel.edu Wed Aug  4 06:32 EDT 1999
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X-Originating-IP: [134.157.132.99]
From: "Dagmar Iber" <iber_dagmar@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: problems with the import of textfiles into pictures
Date: Wed, 04 Aug 1999 12:18:45 CEST
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Hello,

I have saved the x-y-coordinates of an object in a picture and would now 
like to import the line described by the coordinates into this old picture 
in order to control whether the coordinates are describing that line 
correctly. How can I do that?

Thanks, dagmar


______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com


From nih-image-d-request@io.ece.drexel.edu Thu Aug  5 06:14 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 178

Today's Topics:
  Re: 2D/3D-stereology => Underwood 19  [ Ludger Offerhaus <ljo@gfz-potsdam.d ]
  RE: 2D/3D-stereology                  [ "E.H.van den Berg" <berg@geo.vu.nl> ]
  problems with the import of textfile  [ "Dagmar Iber" <iber_dagmar@hotmail. ]

------------------------------

Date: Wed, 4 Aug 1999 10:11:19 +0200
From: Ludger Offerhaus <ljo@gfz-potsdam.de>
To: nih-image@io.ece.drexel.edu
Subject: Re: 2D/3D-stereology => Underwood 1970
Message-Id: <l03130300b3cda58aa92f@[139.17.139.125]>
Content-Type: text/plain; charset="iso-8859-1"
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Underwood, E.E., Quantitative Stereology, Addison-Wesley, Reading (Mass), 1970
still is the standard textbook on stereology.

cheers,
Ludger

>Dear Elmer,
>
>I would like to learn something about methods to correct for sectioning
>too. Could you give a reference for the Underwood method please?
>
>Thanks, Jan.
>
>Jan Kreft				Phone +44 (0)1222 875278
>Cardiff School of Biosciences		Fax   +44 (0)1222 874305
>Cardiff	University 			E-mail Kreft@cardiff.ac.uk
>PO Box 915, Cardiff CF10 3TL, UK
>
>On Wed, 4 Aug 1999, E.H.van den Berg wrote:
>
>> Dear all,
>>
>> The size distribution of sand grains in an aeolian sediment constructed
>>from 10 images of one thin section seems not to fit with lab measurement.
>>Despite the fact that both methods measure different diameters, I would
>>like to know what the effect of sectioning is on the size distribution
>>obtained from thin sections.
>>
>> I have applied a method presented bij Underwood in 1970 to correct for
>>sectioning and create a 3D distribution of sizes. It has some effect (the
>>distribution shifts to the coarser part, distribution is more narrow and
>>seeper in the finer part) but I would like to check these calculations.
>>
>> To avoid programming for the next couple of months, does someone have
>>any suggestions for subroutines or macro's to convert 2D distributions to
>>3D ones?
>>
>> Thanks in advance,
>>
>>
>> sincerely,
>>
>> Elmer
>>
>>
>> Elmer van den berg
>> Vrije Universiteit Amsterdam
>> Faculty of Earth Sciences
>>
>>
>


--
Ludger Offerhaus
GeoForschungsZentrum Potsdam
Telegrafenberg, 14473 Potsdam, Duitsland
Tel: +49 (0)331 288 1326 / 1390
of (ook awap): 030 32 60 55 68
---
... aan een boom *zo* volgeladen / mist men n, twee pruimpjes niet ...
---

------------------------------

Date: Wed, 4 Aug 1999 10:31:14 +0200
From: "E.H.van den Berg" <berg@geo.vu.nl>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: 2D/3D-stereology
Message-ID: <01BEDE64.7B1DF7D0@kahoolawe.geo.vu.nl>
Content-Type: multipart/mixed; boundary="---- =_NextPart_000_01BEDE64.7B1F7E70"

------ =_NextPart_000_01BEDE64.7B1F7E70
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

Dear Mr Kreft,

I have to tell you that there is no method of Underwood, but in his =
reference work on stereology a number of methods for correcting thin =
section distribution are presented. He describes several methods that =
apply to specific measurements made in the thin sections, like area, =
diameter or chords.

Theoretical background information and practical examples can be found =
in:

Underwood, E.E., 1970. Quantitative Stereology. Addison-Wesley =
Publishing Company, Reading, Massachusetts.

Sorry for the misunderstanding and please ask,

sincerely,

elmer
------------------------------

Date: Wed, 04 Aug 1999 12:18:45 CEST
From: "Dagmar Iber" <iber_dagmar@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: problems with the import of textfiles into pictures
Message-ID: <19990804101846.94773.qmail@hotmail.com>
Content-Type: text/plain; charset=iso-8859-1; format=flowed

Hello,

I have saved the x-y-coordinates of an object in a picture and would now 
like to import the line described by the coordinates into this old picture 
in order to control whether the coordinates are describing that line 
correctly. How can I do that?

Thanks, dagmar


______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com

--------------------------------
End of nih-image-d Digest V99 Issue #178
****************************************

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>Attachment converted: Correct-o-Text:nih-image-d Digest V99 # 11
>(TEXT/CSOm) (00028CF1)




From nih-image-request@io.ece.drexel.edu Thu Aug  5 16:14 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: "=?iso-8859-1?Q?=22Dr._Luis_F._Hern=E1ndez=22?="  <lhernan@criba.edu.ar>
Subject: RGB percentages
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Dear Imagers:
We are working with RGB pictures of soybean leaves taken with a digital
camera over time.
Each picture is saved as JPG and converted with Photoshop in TIFF.
We want to measure on the images the percentage of green and red, in order
to obtain a ratio of change in the leaf colour as the soybean leaves age
and relate it with iths phenology. Can we use NIH to select in different
pictures known areas (say 2 cm x 2 cm) and get the information we want?. To
ensure that the final colour has only R and G without any B in it, how can
we substract beforehand all the BLUE info the image contains?
We have already worked with Photoshp and its eyedropper command but
(perhaps we do not know how) it only give us information for a single pixel.
Suggestions and comments will be appreciated.

_______________________________________________________
Dr. Luis F. Hernandez, Ph.D.
Laboratorio de Botanica
Departamento de Agronomia
U N I V E R S I D A D  N A C I O N A L  D E L  S U R
8000. Bahia Blanca - ARGENTINA

<mailto: lhernan@criba.edu.ar>
Telefonos (0291) 453-4775/453-0024
FAX: 54 - 0291 - 452-1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.



From nih-image-request@io.ece.drexel.edu Thu Aug  5 20:37 EDT 1999
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1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.


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1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.


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From: GJOSS@rna.bio.mq.edu.au
Organization:  Dept. of Biological Sciences
To: lhernan@criba.edu.ar, nih-image@io.ece.drexel.edu
Date:          Fri, 6 Aug 1999 14:30:47 +1000
Subject:       Re: RGB percentages
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>Date: Thu, 5 Aug 1999 16:53:27 -0300
>To: nih-image@io.ece.drexel.edu
>From: "=?iso-8859-1?Q?=22Dr._Luis_F._Hern=E1ndez=22?="  
><lhernan@criba.edu.ar>
>Subject: RGB percentages
>
>Dear Imagers:
>We are working with RGB pictures of soybean leaves taken with a digital
>camera over time.
>Each picture is saved as JPG and converted with Photoshop in TIFF.
>We want to measure on the images the percentage of green and red, in order
>to obtain a ratio of change in the leaf colour as the soybean leaves age
>and relate it with iths phenology. Can we use NIH to select in different
>pictures known areas (say 2 cm x 2 cm) and get the information we want?. 
>To
>ensure that the final colour has only R and G without any B in it, how can
>we substract beforehand all the BLUE info the image contains?
>We have already worked with Photoshp and its eyedropper command but
>(perhaps we do not know how) it only give us information for a single 
>pixel.
>Suggestions and comments will be appreciated.
>
>_______________________________________________________
>Dr. Luis F. Hernandez, Ph.D.
>Laboratorio de Botanica
>Departamento de Agronomia
>U N I V E R S I D A D  N A C I O N A L  D E L  S U R
>8000. Bahia Blanca - ARGENTINA
>
><mailto: lhernan@criba.edu.ar>
>Telefonos (0291) 453-4775/453-0024
>FAX: 54 - 0291 - 452-1942
>_______________________________________________________

Luis, 
To do what you ask will be straightforward in NIH-Image.
To achieve the desired results might be another matter.
 
When you open the TIFF image (converted from JPG with Photoshop),
it will open as a three slice stack (R,G,B) and also generate an 8 bit 
indexed color image. 
You can ignore the 8 bit indexed color version(only used for visual 
inspection).
You then have a three slice (R,G,B) stack. I gather you wish to ignore the 
Blue component. You can ratio the Red to Green by using ImageMath(Process 
menu {see manual} or simply by :
show paste control{windows menu}
select Green Slice;
selectAll;
copy;{edit menu}
select Red Slice;
paste;
setOption;Divide;
you would also want to check 'scaleMath' in the paste control window.
The result will be a scaled(1:254) ratio of red/green.
To ensure all images are scaled the same you can introduce 2 small patches 
into say the top/left of R&G slices to result in max and min value ratios 
(this is not related to calibration patches refered to below);
otherwise you can control scaling directly with imageMath.

So the ratio measurement with NIH-Image is relatively straightforward.

However there seem to me to be two major problems with the process:

One is how to ensure standardisation or calibration of the camera/lighting 
etc from shot to shot over time. I would try introducing standard red, 
green and white patches or strips to be included in the field captured each 
time to allow color calibration/checking.

The other is that I would not be at all confident that JPG compression 
didn't seriously interfere with colour ratios at a pixel level. I would in 
fact expect it to do something roughly equivalent to the dithering 
associated with the RGB to 8-bit indexed colour. See RGB to 8bit(stacks 
menu and use magnify tool to inspect detail of pixels. JPG is aimed at 
human perception, not at preservation of original data. It is aimed at 
preserving appearance at an image level, not the local pixel values. 
This may well invalidate the whole process and may not be so easy to 
investigate and impossible to compensate for. 
Amongst others, John Russ has given strong warnings about attempting to use 
(consumer) JPG cameras for scientific work.

Someone knowledgeable re JPG internals might like to make a more informed 
comment than mine.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-d-request@io.ece.drexel.edu Fri Aug  6 06:14 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #179
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 179

Today's Topics:
  unsubscibe                            [ Susanne <correcto@dragon.upc.qc.ca> ]
  RGB percentages                       [ "=?iso-8859-1?Q?=22Dr._Luis_F._Hern ]
  Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
  Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
  Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
  Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
  Re: RGB percentages                   [ GJOSS@rna.bio.mq.edu.au ]

------------------------------

Date: Wed, 4 Aug 1999 10:45:17 -0400
From: Susanne <correcto@dragon.upc.qc.ca>
To: nih-image@io.ece.drexel.edu
Subject: unsubscibe
Message-Id: <v04003a02b3ce0267d224@[205.205.174.64]>
Content-Type: text/plain; charset="us-ascii"

>Attachment converted: Correct-o-Text:nih-image-d Digest V99 # 11
>(TEXT/CSOm) (00028CF1)

------------------------------

Date: Thu, 5 Aug 1999 16:53:27 -0300
From: "=?iso-8859-1?Q?=22Dr._Luis_F._Hern=E1ndez=22?="  <lhernan@criba.edu.ar>
To: nih-image@io.ece.drexel.edu
Subject: RGB percentages
Message-Id: <v03130300b3cf97d218a4@[170.210.187.214]>
Content-Type: text/plain; charset="us-ascii"

Dear Imagers:
We are working with RGB pictures of soybean leaves taken with a digital
camera over time.
Each picture is saved as JPG and converted with Photoshop in TIFF.
We want to measure on the images the percentage of green and red, in order
to obtain a ratio of change in the leaf colour as the soybean leaves age
and relate it with iths phenology. Can we use NIH to select in different
pictures known areas (say 2 cm x 2 cm) and get the information we want?. To
ensure that the final colour has only R and G without any B in it, how can
we substract beforehand all the BLUE info the image contains?
We have already worked with Photoshp and its eyedropper command but
(perhaps we do not know how) it only give us information for a single pixel.
Suggestions and comments will be appreciated.

_______________________________________________________
Dr. Luis F. Hernandez, Ph.D.
Laboratorio de Botanica
Departamento de Agronomia
U N I V E R S I D A D  N A C I O N A L  D E L  S U R
8000. Bahia Blanca - ARGENTINA

<mailto: lhernan@criba.edu.ar>
Telefonos (0291) 453-4775/453-0024
FAX: 54 - 0291 - 452-1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.

------------------------------

Date: Thu, 5 Aug 1999 20:20:06 -0400 (EDT)
From: nih-image-request@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <199908060020.UAA28038@io.ece.drexel.edu>

1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.

------------------------------

Date: Thu, 5 Aug 1999 20:20:06 -0400 (EDT)
From: nih-image-request@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <199908060020.UAA28037@io.ece.drexel.edu>


------------------------------

Date: Thu, 5 Aug 1999 21:53:27 -0400 (EDT)
From: nih-image-request@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <199908060153.VAA13071@io.ece.drexel.edu>


------------------------------

Date: Thu, 5 Aug 1999 21:53:35 -0400 (EDT)
From: nih-image-request@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <199908060153.VAA13098@io.ece.drexel.edu>

1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.

------------------------------

Date:          Fri, 6 Aug 1999 14:30:47 +1000
From: GJOSS@rna.bio.mq.edu.au
To: lhernan@criba.edu.ar, nih-image@io.ece.drexel.edu
Subject:       Re: RGB percentages
Message-ID: <359804F4C@rna.bio.mq.edu.au>

>Date: Thu, 5 Aug 1999 16:53:27 -0300
>To: nih-image@io.ece.drexel.edu
>From: "=?iso-8859-1?Q?=22Dr._Luis_F._Hern=E1ndez=22?="  
><lhernan@criba.edu.ar>
>Subject: RGB percentages
>
>Dear Imagers:
>We are working with RGB pictures of soybean leaves taken with a digital
>camera over time.
>Each picture is saved as JPG and converted with Photoshop in TIFF.
>We want to measure on the images the percentage of green and red, in order
>to obtain a ratio of change in the leaf colour as the soybean leaves age
>and relate it with iths phenology. Can we use NIH to select in different
>pictures known areas (say 2 cm x 2 cm) and get the information we want?. 
>To
>ensure that the final colour has only R and G without any B in it, how can
>we substract beforehand all the BLUE info the image contains?
>We have already worked with Photoshp and its eyedropper command but
>(perhaps we do not know how) it only give us information for a single 
>pixel.
>Suggestions and comments will be appreciated.
>
>_______________________________________________________
>Dr. Luis F. Hernandez, Ph.D.
>Laboratorio de Botanica
>Departamento de Agronomia
>U N I V E R S I D A D  N A C I O N A L  D E L  S U R
>8000. Bahia Blanca - ARGENTINA
>
><mailto: lhernan@criba.edu.ar>
>Telefonos (0291) 453-4775/453-0024
>FAX: 54 - 0291 - 452-1942
>_______________________________________________________

Luis, 
To do what you ask will be straightforward in NIH-Image.
To achieve the desired results might be another matter.
 
When you open the TIFF image (converted from JPG with Photoshop),
it will open as a three slice stack (R,G,B) and also generate an 8 bit 
indexed color image. 
You can ignore the 8 bit indexed color version(only used for visual 
inspection).
You then have a three slice (R,G,B) stack. I gather you wish to ignore the 
Blue component. You can ratio the Red to Green by using ImageMath(Process 
menu {see manual} or simply by :
show paste control{windows menu}
select Green Slice;
selectAll;
copy;{edit menu}
select Red Slice;
paste;
setOption;Divide;
you would also want to check 'scaleMath' in the paste control window.
The result will be a scaled(1:254) ratio of red/green.
To ensure all images are scaled the same you can introduce 2 small patches 
into say the top/left of R&G slices to result in max and min value ratios 
(this is not related to calibration patches refered to below);
otherwise you can control scaling directly with imageMath.

So the ratio measurement with NIH-Image is relatively straightforward.

However there seem to me to be two major problems with the process:

One is how to ensure standardisation or calibration of the camera/lighting 
etc from shot to shot over time. I would try introducing standard red, 
green and white patches or strips to be included in the field captured each 
time to allow color calibration/checking.

The other is that I would not be at all confident that JPG compression 
didn't seriously interfere with colour ratios at a pixel level. I would in 
fact expect it to do something roughly equivalent to the dithering 
associated with the RGB to 8-bit indexed colour. See RGB to 8bit(stacks 
menu and use magnify tool to inspect detail of pixels. JPG is aimed at 
human perception, not at preservation of original data. It is aimed at 
preserving appearance at an image level, not the local pixel values. 
This may well invalidate the whole process and may not be so easy to 
investigate and impossible to compensate for. 
Amongst others, John Russ has given strong warnings about attempting to use 
(consumer) JPG cameras for scientific work.

Someone knowledgeable re JPG internals might like to make a more informed 
comment than mine.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

--------------------------------
End of nih-image-d Digest V99 Issue #179
****************************************

From nih-image-request@io.ece.drexel.edu Fri Aug  6 11:56 EDT 1999
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Date: Fri, 6 Aug 1999 08:41:08 -0700 (PDT)
From: Pauline Seta Yaralian <yaralian@almaak.usc.edu>
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From nih-image-request@io.ece.drexel.edu Fri Aug  6 15:27 EDT 1999
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From: HertzbJB@utrc.utc.com
Message-ID: <62835D8790DBD111981100805FA7E4C475DEFC@EXPRESS1>
To: nih-image@io.ece.drexel.edu
Subject: real-time capture?
Date: Fri, 6 Aug 1999 15:06:44 -0400 
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Hi. A question for all you image-capture gurus out there . . . 

I'd like to know whether I will be able capture full-frame video in
real-time with a Scion LG-3 installed in a 400 MHz PC. Or can I do only part
of the frame? How much of the frame will I be able to capture in real time? 

Do I really have to buy scores of MB of on-board memory so that the Scion
can capture just a few seconds of video to its internal memory, or can I
capture it all to my PC if I've got a fast enough PC?



Thanks

-Jared Hertzberg
 United Technologies Research Center

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charset=3Diso-8859-1">
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</HEAD>
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<P><FONT SIZE=3D2 FACE=3D"Arial">Hi. A question for all you =
image-capture gurus out there . . . </FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">I'd like to know whether I will be =
able capture full-frame video in real-time with a Scion LG-3 installed =
in a 400 MHz PC. Or can I do only part of the frame? How much of the =
frame will I be able to capture in real time? </FONT></P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Do I really have to buy scores of MB =
of on-board memory so that the Scion can capture just a few seconds of =
video to its internal memory, or can I capture it all to my PC if I've =
got a fast enough PC?</FONT></P>
<BR>
<BR>

<P><FONT SIZE=3D2 FACE=3D"Arial">Thanks</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">-Jared Hertzberg</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">&nbsp;United Technologies Research =
Center</FONT>
</P>

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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 180

Today's Topics:
  unsubscribe                           [ Pauline Seta Yaralian <yaralian@alm ]
  real-time capture?                    [ HertzbJB@utrc.utc.com ]

------------------------------

Date: Fri, 6 Aug 1999 08:41:08 -0700 (PDT)
From: Pauline Seta Yaralian <yaralian@almaak.usc.edu>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
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unsubscribe yaralian@almaak.usc.edu.

------------------------------

Date: Fri, 6 Aug 1999 15:06:44 -0400 
From: HertzbJB@utrc.utc.com
To: nih-image@io.ece.drexel.edu
Subject: real-time capture?
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Hi. A question for all you image-capture gurus out there . . . 

I'd like to know whether I will be able capture full-frame video in
real-time with a Scion LG-3 installed in a 400 MHz PC. Or can I do only part
of the frame? How much of the frame will I be able to capture in real time? 

Do I really have to buy scores of MB of on-board memory so that the Scion
can capture just a few seconds of video to its internal memory, or can I
capture it all to my PC if I've got a fast enough PC?



Thanks

-Jared Hertzberg
 United Technologies Research Center

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5.5.2448.0">
<TITLE>real-time capture?</TITLE>
</HEAD>
<BODY>

<P><FONT SIZE=3D2 FACE=3D"Arial">Hi. A question for all you =
image-capture gurus out there . . . </FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">I'd like to know whether I will be =
able capture full-frame video in real-time with a Scion LG-3 installed =
in a 400 MHz PC. Or can I do only part of the frame? How much of the =
frame will I be able to capture in real time? </FONT></P>

<P><FONT SIZE=3D2 FACE=3D"Arial">Do I really have to buy scores of MB =
of on-board memory so that the Scion can capture just a few seconds of =
video to its internal memory, or can I capture it all to my PC if I've =
got a fast enough PC?</FONT></P>
<BR>
<BR>

<P><FONT SIZE=3D2 FACE=3D"Arial">Thanks</FONT>
</P>

<P><FONT SIZE=3D2 FACE=3D"Arial">-Jared Hertzberg</FONT>
<BR><FONT SIZE=3D2 FACE=3D"Arial">&nbsp;United Technologies Research =
Center</FONT>
</P>

</BODY>
</HTML>
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End of nih-image-d Digest V99 Issue #180
****************************************

From nih-image-request@io.ece.drexel.edu Mon Aug  9 04:11 EDT 1999
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$)C
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nih-image-d-request@io.ece.drexel.edu wrote:

> Subject:
>
> nih-image-d Digest                              Volume 99 : Issue 179
>
> Today's Topics:
>   unsubscibe                            [ Susanne <correcto@dragon.upc.qc.ca> ]
>   RGB percentages                       [ "=?iso-8859-1?Q?=22Dr._Luis_F._Hern ]
>   Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
>   Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
>   Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
>   Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
>   Re: RGB percentages                   [ GJOSS@rna.bio.mq.edu.au ]
>
>   ------------------------------------------------------------------------
>
> Subject: unsubscibe
> Date: Wed, 4 Aug 1999 10:45:17 -0400
> From: Susanne <correcto@dragon.upc.qc.ca>
> To: nih-image@io.ece.drexel.edu
>
> >Attachment converted: Correct-o-Text:nih-image-d Digest V99 # 11
> >(TEXT/CSOm) (00028CF1)
>
>   ------------------------------------------------------------------------
>
> Subject: RGB percentages
> Date: Thu, 5 Aug 1999 16:53:27 -0300
> From: ""Dr. Luis F. Hernandez"" <lhernan@criba.edu.ar>
> To: nih-image@io.ece.drexel.edu
>
> Dear Imagers:
> We are working with RGB pictures of soybean leaves taken with a digital
> camera over time.
> Each picture is saved as JPG and converted with Photoshop in TIFF.
> We want to measure on the images the percentage of green and red, in order
> to obtain a ratio of change in the leaf colour as the soybean leaves age
> and relate it with iths phenology. Can we use NIH to select in different
> pictures known areas (say 2 cm x 2 cm) and get the information we want?. To
> ensure that the final colour has only R and G without any B in it, how can
> we substract beforehand all the BLUE info the image contains?
> We have already worked with Photoshp and its eyedropper command but
> (perhaps we do not know how) it only give us information for a single pixel.
> Suggestions and comments will be appreciated.
>
> _______________________________________________________
> Dr. Luis F. Hernandez, Ph.D.
> Laboratorio de Botanica
> Departamento de Agronomia
> U N I V E R S I D A D  N A C I O N A L  D E L  S U R
> 8000. Bahia Blanca - ARGENTINA
>
> <mailto: lhernan@criba.edu.ar>
> Telefonos (0291) 453-4775/453-0024
> FAX: 54 - 0291 - 452-1942
> _______________________________________________________
> The box said: "Requires Windows 98 or better".....
> So I bought a Macintosh.
>
>   ------------------------------------------------------------------------
>
> Subject: Unidentified subject!
> Date: Thu, 5 Aug 1999 20:20:06 -0400 (EDT)
> From: nih-image-request@io.ece.drexel.edu
> To: nih-image@io.ece.drexel.edu
>
> 1942
> _______________________________________________________
> The box said: "Requires Windows 98 or better".....
> So I bought a Macintosh.
>
>   ------------------------------------------------------------------------
>
> Subject: Unidentified subject!
> Date: Thu, 5 Aug 1999 20:20:06 -0400 (EDT)
> From: nih-image-request@io.ece.drexel.edu
> To: nih-image@io.ece.drexel.edu
>
> Subject: Unidentified subject!
> Date: Thu, 5 Aug 1999 21:53:27 -0400 (EDT)
> From: nih-image-request@io.ece.drexel.edu
> To: nih-image@io.ece.drexel.edu
>
> Subject: Unidentified subject!
> Date: Thu, 5 Aug 1999 21:53:35 -0400 (EDT)
> From: nih-image-request@io.ece.drexel.edu
> To: nih-image@io.ece.drexel.edu
>
> 1942
> _______________________________________________________
> The box said: "Requires Windows 98 or better".....
> So I bought a Macintosh.
>
>   ------------------------------------------------------------------------
>
> Subject: Re: RGB percentages
> Date: Fri, 6 Aug 1999 14:30:47 +1000
> From: GJOSS@rna.bio.mq.edu.au
> To: lhernan@criba.edu.ar, nih-image@io.ece.drexel.edu
>
> >Date: Thu, 5 Aug 1999 16:53:27 -0300
> >To: nih-image@io.ece.drexel.edu
> >From: "=?iso-8859-1?Q?=22Dr._Luis_F._Hern=E1ndez=22?="
> ><lhernan@criba.edu.ar>
> >Subject: RGB percentages
> >
> >Dear Imagers:
> >We are working with RGB pictures of soybean leaves taken with a digital
> >camera over time.
> >Each picture is saved as JPG and converted with Photoshop in TIFF.
> >We want to measure on the images the percentage of green and red, in order
> >to obtain a ratio of change in the leaf colour as the soybean leaves age
> >and relate it with iths phenology. Can we use NIH to select in different
> >pictures known areas (say 2 cm x 2 cm) and get the information we want?.
> >To
> >ensure that the final colour has only R and G without any B in it, how can
> >we substract beforehand all the BLUE info the image contains?
> >We have already worked with Photoshp and its eyedropper command but
> >(perhaps we do not know how) it only give us information for a single
> >pixel.
> >Suggestions and comments will be appreciated.
> >
> >_______________________________________________________
> >Dr. Luis F. Hernandez, Ph.D.
> >Laboratorio de Botanica
> >Departamento de Agronomia
> >U N I V E R S I D A D  N A C I O N A L  D E L  S U R
> >8000. Bahia Blanca - ARGENTINA
> >
> ><mailto: lhernan@criba.edu.ar>
> >Telefonos (0291) 453-4775/453-0024
> >FAX: 54 - 0291 - 452-1942
> >_______________________________________________________
>
> Luis,
> To do what you ask will be straightforward in NIH-Image.
> To achieve the desired results might be another matter.
>
> When you open the TIFF image (converted from JPG with Photoshop),
> it will open as a three slice stack (R,G,B) and also generate an 8 bit
> indexed color image.
> You can ignore the 8 bit indexed color version(only used for visual
> inspection).
> You then have a three slice (R,G,B) stack. I gather you wish to ignore the
> Blue component. You can ratio the Red to Green by using ImageMath(Process
> menu {see manual} or simply by :
> show paste control{windows menu}
> select Green Slice;
> selectAll;
> copy;{edit menu}
> select Red Slice;
> paste;
> setOption;Divide;
> you would also want to check 'scaleMath' in the paste control window.
> The result will be a scaled(1:254) ratio of red/green.
> To ensure all images are scaled the same you can introduce 2 small patches
> into say the top/left of R&G slices to result in max and min value ratios
> (this is not related to calibration patches refered to below);
> otherwise you can control scaling directly with imageMath.
>
> So the ratio measurement with NIH-Image is relatively straightforward.
>
> However there seem to me to be two major problems with the process:
>
> One is how to ensure standardisation or calibration of the camera/lighting
> etc from shot to shot over time. I would try introducing standard red,
> green and white patches or strips to be included in the field captured each
> time to allow color calibration/checking.
>
> The other is that I would not be at all confident that JPG compression
> didn't seriously interfere with colour ratios at a pixel level. I would in
> fact expect it to do something roughly equivalent to the dithering
> associated with the RGB to 8-bit indexed colour. See RGB to 8bit(stacks
> menu and use magnify tool to inspect detail of pixels. JPG is aimed at
> human perception, not at preservation of original data. It is aimed at
> preserving appearance at an image level, not the local pixel values.
> This may well invalidate the whole process and may not be so easy to
> investigate and impossible to compensate for.
> Amongst others, John Russ has given strong warnings about attempting to use
> (consumer) JPG cameras for scientific work.
>
> Someone knowledgeable re JPG internals might like to make a more informed
> comment than mine.
> Greg Joss,
> School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
> Macquarie University,          Email gjoss@rna.bio.mq.edu.au
> North Ryde, (Sydney,) NSW 2109, Australia



--
Sung-Oh Huh, Ph.D.
Assistant Professor
Hallym University College of Medicine
Dept. Pharmacology
Institute of Natural Medicine
1 Okchon-dong, Chunchon
Kangwon-do, 200-702
South Korea

e.mail: sohuh@sun.hallym.ac.kr
phone: +82-361-240-1655
fax: +82-361-240-1652



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From nih-image-request@io.ece.drexel.edu Mon Aug  9 04:34 EDT 1999
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Subject: Re: real-time capture?
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>Hi. A question for all you image-capture gurus out there . . .
>
>
>I'd like to know whether I will be able capture full-frame video in
>real-time with a Scion LG-3 installed in a 400 MHz PC. Or can I do only
>part of the frame? How much of the frame will I be able to capture in real
>time?
>
>
>Do I really have to buy scores of MB of on-board memory so that the Scion
>can capture just a few seconds of video to its internal memory, or can I
>capture it all to my PC if I've got a fast enough PC?

I would like to extend this question.

Capturing a 640*480 frame (NTSC 30 frames per second) over time would
result in 10 MB data / second. Using a Riad Level 0 formatted Diskarray,
consisting of an UltraWide SCSI Adapter and two UW-SCSI disks should result
in an increase in transfer to 20-35 MB/sec depending on disk speed.
Accumulating data would be 600 MB/minute or 6 GB every 10 minutes.

Does one of you out there have experience if this theoretical composition
would work in real life ?

The other question is, do you really need real time capture over a longer
time period, or would a smart algorithm (just recording differences between
successive images) prevent you from accumulating that much GB ? You don't
only have to save the data, you also will have to compute them properly.

Best Regards, Peter




----------------------------------------------------
Peter Bramlage
Kardiologisches Labor der 1.Medizinischen Klinik der Charit
Universittsklinikum der Humboldt - Universitt zu Berlin
Ziegelstrae 5-9
D-10117 Berlin
Germany

Tel.:  ++49/30/2802 6373
Fax:   ++49/30/2802-6509
e-mail: Peter.Bramlage@rz.hu-berlin.de
---------------------------------------------------- 



From nih-image-request@io.ece.drexel.edu Mon Aug  9 05:45 EDT 1999
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Date: Mon, 9 Aug 1999 11:31:54 +0200
To: nih-image@io.ece.drexel.edu
From: Beat Ludin <ludin@fmi.ch>
Subject: Re: real-time capture?
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>The other question is, do you really need real time capture over a longer
>time period, or would a smart algorithm (just recording differences between
>successive images) prevent you from accumulating that much GB ? You don't
>only have to save the data, you also will have to compute them properly.

FWIW, I just wanted to mention that there are inexpensive video 
capture cards out there, e.g. from FAST or Pinnacle Systems, which 
work fine for full-frame real-time recording with current IDE or SCSI 
drives. They usually come with software (e.g. Premiere lite) that 
allows export of TIFF sequences. Of course, the quality will be 
slightly worse compared to an LG-3, but if you use Y/C (S-Video) 
input, you should still get good b/w quality.

Cheers,

       Beat


LIFE IMAGING SERVICES
               - visit our new web site at www.lis.ch
+-----------------------------------------------------------
| Dr. B. Ludin
| Life Imaging Services     fon ++41 (0)79 235 7154
| Muehletalweg 22           fax ++41 (0)86 062 296 3160 NEW!
| CH-4600 Olten             beat.ludin@lis.ch
| Switzerland               http://www.lis.ch


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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 181

Today's Topics:
  unsubscribe                           [ Sung-Oh Huh <sohuh@sun.hallym.ac.kr ]
  unsubscribe                           [ Sung-Oh Huh <sohuh@sun.hallym.ac.kr ]
  Re: real-time capture?                [ Peter Bramlage <Peter.Bramlage@rz.h ]
  Re: real-time capture?                [ Beat Ludin <ludin@fmi.ch> ]
  Re: unsubscribe                       [ "Yoni" <yoni@cbis.ece.drexel.edu> ]
  Capture with LG3                      [ "Keith Norman" <k.norman@sheffield. ]

------------------------------

Date: Mon, 09 Aug 1999 16:50:40 +0900
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$)C
unsubscribe

nih-image-d-request@io.ece.drexel.edu wrote:

> Subject:
>
> nih-image-d Digest                              Volume 99 : Issue 179
>
> Today's Topics:
>   unsubscibe                            [ Susanne <correcto@dragon.upc.qc.ca> ]
>   RGB percentages                       [ "=?iso-8859-1?Q?=22Dr._Luis_F._Hern ]
>   Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
>   Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
>   Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
>   Unidentified subject!                 [ nih-image-request@io.ece.drexel.edu ]
>   Re: RGB percentages                   [ GJOSS@rna.bio.mq.edu.au ]
>
>   ------------------------------------------------------------------------
>
> Subject: unsubscibe
> Date: Wed, 4 Aug 1999 10:45:17 -0400
> From: Susanne <correcto@dragon.upc.qc.ca>
> To: nih-image@io.ece.drexel.edu
>
> >Attachment converted: Correct-o-Text:nih-image-d Digest V99 # 11
> >(TEXT/CSOm) (00028CF1)
>
>   ------------------------------------------------------------------------
>
> Subject: RGB percentages
> Date: Thu, 5 Aug 1999 16:53:27 -0300
> From: ""Dr. Luis F. Hernandez"" <lhernan@criba.edu.ar>
> To: nih-image@io.ece.drexel.edu
>
> Dear Imagers:
> We are working with RGB pictures of soybean leaves taken with a digital
> camera over time.
> Each picture is saved as JPG and converted with Photoshop in TIFF.
> We want to measure on the images the percentage of green and red, in order
> to obtain a ratio of change in the leaf colour as the soybean leaves age
> and relate it with iths phenology. Can we use NIH to select in different
> pictures known areas (say 2 cm x 2 cm) and get the information we want?. To
> ensure that the final colour has only R and G without any B in it, how can
> we substract beforehand all the BLUE info the image contains?
> We have already worked with Photoshp and its eyedropper command but
> (perhaps we do not know how) it only give us information for a single pixel.
> Suggestions and comments will be appreciated.
>
> _______________________________________________________
> Dr. Luis F. Hernandez, Ph.D.
> Laboratorio de Botanica
> Departamento de Agronomia
> U N I V E R S I D A D  N A C I O N A L  D E L  S U R
> 8000. Bahia Blanca - ARGENTINA
>
> <mailto: lhernan@criba.edu.ar>
> Telefonos (0291) 453-4775/453-0024
> FAX: 54 - 0291 - 452-1942
> _______________________________________________________
> The box said: "Requires Windows 98 or better".....
> So I bought a Macintosh.
>
>   ------------------------------------------------------------------------
>
> Subject: Unidentified subject!
> Date: Thu, 5 Aug 1999 20:20:06 -0400 (EDT)
> From: nih-image-request@io.ece.drexel.edu
> To: nih-image@io.ece.drexel.edu
>
> 1942
> _______________________________________________________
> The box said: "Requires Windows 98 or better".....
> So I bought a Macintosh.
>
>   ------------------------------------------------------------------------
>
> Subject: Unidentified subject!
> Date: Thu, 5 Aug 1999 20:20:06 -0400 (EDT)
> From: nih-image-request@io.ece.drexel.edu
> To: nih-image@io.ece.drexel.edu
>
> Subject: Unidentified subject!
> Date: Thu, 5 Aug 1999 21:53:27 -0400 (EDT)
> From: nih-image-request@io.ece.drexel.edu
> To: nih-image@io.ece.drexel.edu
>
> Subject: Unidentified subject!
> Date: Thu, 5 Aug 1999 21:53:35 -0400 (EDT)
> From: nih-image-request@io.ece.drexel.edu
> To: nih-image@io.ece.drexel.edu
>
> 1942
> _______________________________________________________
> The box said: "Requires Windows 98 or better".....
> So I bought a Macintosh.
>
>   ------------------------------------------------------------------------
>
> Subject: Re: RGB percentages
> Date: Fri, 6 Aug 1999 14:30:47 +1000
> From: GJOSS@rna.bio.mq.edu.au
> To: lhernan@criba.edu.ar, nih-image@io.ece.drexel.edu
>
> >Date: Thu, 5 Aug 1999 16:53:27 -0300
> >To: nih-image@io.ece.drexel.edu
> >From: "=?iso-8859-1?Q?=22Dr._Luis_F._Hern=E1ndez=22?="
> ><lhernan@criba.edu.ar>
> >Subject: RGB percentages
> >
> >Dear Imagers:
> >We are working with RGB pictures of soybean leaves taken with a digital
> >camera over time.
> >Each picture is saved as JPG and converted with Photoshop in TIFF.
> >We want to measure on the images the percentage of green and red, in order
> >to obtain a ratio of change in the leaf colour as the soybean leaves age
> >and relate it with iths phenology. Can we use NIH to select in different
> >pictures known areas (say 2 cm x 2 cm) and get the information we want?.
> >To
> >ensure that the final colour has only R and G without any B in it, how can
> >we substract beforehand all the BLUE info the image contains?
> >We have already worked with Photoshp and its eyedropper command but
> >(perhaps we do not know how) it only give us information for a single
> >pixel.
> >Suggestions and comments will be appreciated.
> >
> >_______________________________________________________
> >Dr. Luis F. Hernandez, Ph.D.
> >Laboratorio de Botanica
> >Departamento de Agronomia
> >U N I V E R S I D A D  N A C I O N A L  D E L  S U R
> >8000. Bahia Blanca - ARGENTINA
> >
> ><mailto: lhernan@criba.edu.ar>
> >Telefonos (0291) 453-4775/453-0024
> >FAX: 54 - 0291 - 452-1942
> >_______________________________________________________
>
> Luis,
> To do what you ask will be straightforward in NIH-Image.
> To achieve the desired results might be another matter.
>
> When you open the TIFF image (converted from JPG with Photoshop),
> it will open as a three slice stack (R,G,B) and also generate an 8 bit
> indexed color image.
> You can ignore the 8 bit indexed color version(only used for visual
> inspection).
> You then have a three slice (R,G,B) stack. I gather you wish to ignore the
> Blue component. You can ratio the Red to Green by using ImageMath(Process
> menu {see manual} or simply by :
> show paste control{windows menu}
> select Green Slice;
> selectAll;
> copy;{edit menu}
> select Red Slice;
> paste;
> setOption;Divide;
> you would also want to check 'scaleMath' in the paste control window.
> The result will be a scaled(1:254) ratio of red/green.
> To ensure all images are scaled the same you can introduce 2 small patches
> into say the top/left of R&G slices to result in max and min value ratios
> (this is not related to calibration patches refered to below);
> otherwise you can control scaling directly with imageMath.
>
> So the ratio measurement with NIH-Image is relatively straightforward.
>
> However there seem to me to be two major problems with the process:
>
> One is how to ensure standardisation or calibration of the camera/lighting
> etc from shot to shot over time. I would try introducing standard red,
> green and white patches or strips to be included in the field captured each
> time to allow color calibration/checking.
>
> The other is that I would not be at all confident that JPG compression
> didn't seriously interfere with colour ratios at a pixel level. I would in
> fact expect it to do something roughly equivalent to the dithering
> associated with the RGB to 8-bit indexed colour. See RGB to 8bit(stacks
> menu and use magnify tool to inspect detail of pixels. JPG is aimed at
> human perception, not at preservation of original data. It is aimed at
> preserving appearance at an image level, not the local pixel values.
> This may well invalidate the whole process and may not be so easy to
> investigate and impossible to compensate for.
> Amongst others, John Russ has given strong warnings about attempting to use
> (consumer) JPG cameras for scientific work.
>
> Someone knowledgeable re JPG internals might like to make a more informed
> comment than mine.
> Greg Joss,
> School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
> Macquarie University,          Email gjoss@rna.bio.mq.edu.au
> North Ryde, (Sydney,) NSW 2109, Australia



--
Sung-Oh Huh, Ph.D.
Assistant Professor
Hallym University College of Medicine
Dept. Pharmacology
Institute of Natural Medicine
1 Okchon-dong, Chunchon
Kangwon-do, 200-702
South Korea

e.mail: sohuh@sun.hallym.ac.kr
phone: +82-361-240-1655
fax: +82-361-240-1652

------------------------------

Date: Mon, 09 Aug 1999 16:52:49 +0900
From: Sung-Oh Huh <sohuh@sun.hallym.ac.kr>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-ID: <37AE88D1.F865A410@sun.hallym.ac.kr>
Content-Type: text/plain; charset=iso-2022-kr
Content-Transfer-Encoding: 7bit

unsubscribe

------------------------------

Date: Mon, 9 Aug 1999 10:22:07 +0200
From: Peter Bramlage <Peter.Bramlage@rz.hu-berlin.de>
To: nih-image@io.ece.drexel.edu
Subject: Re: real-time capture?
Message-Id: <l03130301b3d43d02ca2f@[141.42.23.131]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

>Hi. A question for all you image-capture gurus out there . . .
>
>
>I'd like to know whether I will be able capture full-frame video in
>real-time with a Scion LG-3 installed in a 400 MHz PC. Or can I do only
>part of the frame? How much of the frame will I be able to capture in real
>time?
>
>
>Do I really have to buy scores of MB of on-board memory so that the Scion
>can capture just a few seconds of video to its internal memory, or can I
>capture it all to my PC if I've got a fast enough PC?

I would like to extend this question.

Capturing a 640*480 frame (NTSC 30 frames per second) over time would
result in 10 MB data / second. Using a Riad Level 0 formatted Diskarray,
consisting of an UltraWide SCSI Adapter and two UW-SCSI disks should result
in an increase in transfer to 20-35 MB/sec depending on disk speed.
Accumulating data would be 600 MB/minute or 6 GB every 10 minutes.

Does one of you out there have experience if this theoretical composition
would work in real life ?

The other question is, do you really need real time capture over a longer
time period, or would a smart algorithm (just recording differences between
successive images) prevent you from accumulating that much GB ? You don't
only have to save the data, you also will have to compute them properly.

Best Regards, Peter




----------------------------------------------------
Peter Bramlage
Kardiologisches Labor der 1.Medizinischen Klinik der Charit
Universittsklinikum der Humboldt - Universitt zu Berlin
Ziegelstrae 5-9
D-10117 Berlin
Germany

Tel.:  ++49/30/2802 6373
Fax:   ++49/30/2802-6509
e-mail: Peter.Bramlage@rz.hu-berlin.de
---------------------------------------------------- 

------------------------------

Date: Mon, 9 Aug 1999 11:31:54 +0200
From: Beat Ludin <ludin@fmi.ch>
To: nih-image@io.ece.drexel.edu
Subject: Re: real-time capture?
Message-Id: <v04205502b3d44cf4441d@[195.24.87.241]>
Content-Type: text/plain; charset="us-ascii" ; format="flowed"

>The other question is, do you really need real time capture over a longer
>time period, or would a smart algorithm (just recording differences between
>successive images) prevent you from accumulating that much GB ? You don't
>only have to save the data, you also will have to compute them properly.

FWIW, I just wanted to mention that there are inexpensive video 
capture cards out there, e.g. from FAST or Pinnacle Systems, which 
work fine for full-frame real-time recording with current IDE or SCSI 
drives. They usually come with software (e.g. Premiere lite) that 
allows export of TIFF sequences. Of course, the quality will be 
slightly worse compared to an LG-3, but if you use Y/C (S-Video) 
input, you should still get good b/w quality.

Cheers,

       Beat


LIFE IMAGING SERVICES
               - visit our new web site at www.lis.ch
+-----------------------------------------------------------
| Dr. B. Ludin
| Life Imaging Services     fon ++41 (0)79 235 7154
| Muehletalweg 22           fax ++41 (0)86 062 296 3160 NEW!
| CH-4600 Olten             beat.ludin@lis.ch
| Switzerland               http://www.lis.ch

------------------------------

Date: Mon, 09 Aug 1999 08:22:05 -0800
From: "Yoni" <yoni@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: unsubscribe
Message-Id: <199908091221.IAA27619@cbis.ece.drexel.edu>
Content-type: text/plain; charset="ISO-2022-KR"
Content-transfer-encoding: 7bit

> unsubscribe
> 
> 


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------------------------------

Date: Tue, 10 Aug 1999 09:47:12 +0100
From: "Keith Norman" <k.norman@sheffield.ac.uk>
To: HertzbJB@utrc.utc.com, nih-image@io.ece.drexel.edu
Subject: Capture with LG3
Message-ID: <60B5E4560C@midhope.shef.ac.uk>
Content-type: text/plain; charset="US-ASCII"
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Jared,

Best capture rate I could achieve on a Pentium 500 for a full sized image
was 12fps. I never tried it but I assume if you halve the image size you can
achieve double the frame rate. In my experience Macs (even a fairly old ones
e.g. 100 MHz)  give you full frame rate for a full sized image. The more RAM
you have the more frames you can capture/keep open in image. The good news
is, as far as I could tell, installing the RAM on the motherboard is quick
enough, and gives you the flexibility of using it for other applications as
well.

Have you considered any of the commercial video compression cards that are
available? I'm having pretty good experience with a Miromotion DC30
compression card which is bundled with Adobe Premiere. You can capture as
much full motion video as your hard drive will allow, and can open as many
frames in Image as your RAM will allow. As far as I know, the Iomega Buzz
should do pretty much the same thing and comes in a little cheaper than the
Miromotion.

Hope this helps.

Keith Norman
Vascular Biology
University of Sheffield

--------------------------------
End of nih-image-d Digest V99 Issue #181
****************************************

From nih-image-request@io.ece.drexel.edu Tue Aug 10 05:02 EDT 1999
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Date: Tue, 10 Aug 1999 09:47:12 +0100
Subject: Capture with LG3
From: "Keith Norman" <k.norman@sheffield.ac.uk>
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Jared,

Best capture rate I could achieve on a Pentium 500 for a full sized image
was 12fps. I never tried it but I assume if you halve the image size you can
achieve double the frame rate. In my experience Macs (even a fairly old ones
e.g. 100 MHz)  give you full frame rate for a full sized image. The more RAM
you have the more frames you can capture/keep open in image. The good news
is, as far as I could tell, installing the RAM on the motherboard is quick
enough, and gives you the flexibility of using it for other applications as
well.

Have you considered any of the commercial video compression cards that are
available? I'm having pretty good experience with a Miromotion DC30
compression card which is bundled with Adobe Premiere. You can capture as
much full motion video as your hard drive will allow, and can open as many
frames in Image as your RAM will allow. As far as I know, the Iomega Buzz
should do pretty much the same thing and comes in a little cheaper than the
Miromotion.

Hope this helps.

Keith Norman
Vascular Biology
University of Sheffield


From nih-image-request@io.ece.drexel.edu Tue Aug 10 05:32 EDT 1999
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From: Peter Bramlage <Peter.Bramlage@rz.hu-berlin.de>
Subject: Re: Capture with LG3
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Keith, Jared,

>Best capture rate I could achieve on a Pentium 500 for a full sized image
>was 12fps. I never tried it but I assume if you halve the image size you can
>achieve double the frame rate. In my experience Macs (even a fairly old ones
>e.g. 100 MHz)  give you full frame rate for a full sized image. The more RAM
>you have the more frames you can capture/keep open in image. The good news
>is, as far as I could tell, installing the RAM on the motherboard is quick
>enough, and gives you the flexibility of using it for other applications as
>well.
>
>Have you considered any of the commercial video compression cards that are
>available? I'm having pretty good experience with a Miromotion DC30
>compression card which is bundled with Adobe Premiere. You can capture as
>much full motion video as your hard drive will allow, and can open as many
>frames in Image as your RAM will allow. As far as I know, the Iomega Buzz
>should do pretty much the same thing and comes in a little cheaper than the
>Miromotion.

I do live Capturing (30 fps) with a LG3 / G3 266 288 MB RAM. Capturing so
far is only limited by available RAM. What I would like to know is, if
writing the incoming data to the disk at that speed is possible (if the
UW-SCSI/disk configuration allows a sufficient transfer rate).

Best Regards, Peter






From nih-image-request@io.ece.drexel.edu Tue Aug 10 12:43 EDT 1999
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Hi

I'm new for this group. I have a question. The question is: Does anyone know 
an image program that I can quantify the fluorescence of microbeads or cells 
with a fluorophore? Is there any program that I can measure the fluorescence 
of an individual microbead or cell(+fluorophore)?

Thanks

Dincer


_______________________________________________________________
Get Free Email and Do More On The Web. Visit http://www.msn.com


From nih-image-request@io.ece.drexel.edu Tue Aug 10 20:16 EDT 1999
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From: Jason Ehrlich <jehrlich@leland.Stanford.EDU>
Message-Id: <199908110002.RAA29669@tree0.Stanford.EDU>
Subject: Video Output from NIH Image on PC
To: nih-image@io.ece.drexel.edu
Date: Tue, 10 Aug 1999 17:02:27 -0700 (PDT)
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greetings, net,

This is probably a FAQ so I apologize in advance.

I would like to output animated stacks (~50-100 frames, TIF files) to
videotape. Of course, I can take the individual TIFFs, dump them into
Adobe Premiere, generate an AVI file, and then output this onto video
using a Matrox card or similar. However, I find this solution clunky, slow
(even on a fast computer, compressing for output to the card is not fast),
and the quality of the image suffers. Moreover, the files are very large, 
and if I want to change the animation speed, I have to render the files
in Premiere again.

So my question is - does anyone have a solution for delivering the
animation directly from the screen to videotape, in real time, without
saving as a Quicktime or AVI file first?

I'm probably missing an easy way to do this.

I'm using Scion Image on a PC, but either a PC or Mac solution would be
great.

thanks,
jason

--------
jason ehrlich  -  jehrlich@stanford.edu
dept of molecular & cellular physiology
beckman center, stanford medical school
stanford, ca 94305


From nih-image-d-request@io.ece.drexel.edu Tue Aug 10 23:21 EDT 1999
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------------------------------

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nih-image-d Digest				Volume 99 : Issue 182

Today's Topics:
  Re: Capture with LG3                  [ Peter Bramlage <Peter.Bramlage@rz.h ]
  Question about nih-image              [ "Mehmet Bilgin" <mdbilgin@hotmail.c ]
  Video Output from NIH Image on PC     [ Jason Ehrlich <jehrlich@leland.Stan ]
  firewire image capture                [ Kathleen Annikki Moore <moorekat@ha ]

------------------------------

Date: Tue, 10 Aug 1999 11:17:07 +0200
From: Peter Bramlage <Peter.Bramlage@rz.hu-berlin.de>
To: nih-image@io.ece.drexel.edu
Subject: Re: Capture with LG3
Message-Id: <l03130301b3d59dbd02be@[141.42.23.131]>
Content-Type: text/plain; charset="us-ascii"

Keith, Jared,

>Best capture rate I could achieve on a Pentium 500 for a full sized image
>was 12fps. I never tried it but I assume if you halve the image size you can
>achieve double the frame rate. In my experience Macs (even a fairly old ones
>e.g. 100 MHz)  give you full frame rate for a full sized image. The more RAM
>you have the more frames you can capture/keep open in image. The good news
>is, as far as I could tell, installing the RAM on the motherboard is quick
>enough, and gives you the flexibility of using it for other applications as
>well.
>
>Have you considered any of the commercial video compression cards that are
>available? I'm having pretty good experience with a Miromotion DC30
>compression card which is bundled with Adobe Premiere. You can capture as
>much full motion video as your hard drive will allow, and can open as many
>frames in Image as your RAM will allow. As far as I know, the Iomega Buzz
>should do pretty much the same thing and comes in a little cheaper than the
>Miromotion.

I do live Capturing (30 fps) with a LG3 / G3 266 288 MB RAM. Capturing so
far is only limited by available RAM. What I would like to know is, if
writing the incoming data to the disk at that speed is possible (if the
UW-SCSI/disk configuration allows a sufficient transfer rate).

Best Regards, Peter

------------------------------

Date: Tue, 10 Aug 1999 11:26:16 CDT
From: "Mehmet Bilgin" <mdbilgin@hotmail.com>
To: nih-image@io.ece.drexel.edu
Cc: mdbilgin@hotmail.com
Subject: Question about nih-image
Message-ID: <19990810162616.35639.qmail@hotmail.com>
Content-Type: text/plain; format=flowed

Hi

I'm new for this group. I have a question. The question is: Does anyone know 
an image program that I can quantify the fluorescence of microbeads or cells 
with a fluorophore? Is there any program that I can measure the fluorescence 
of an individual microbead or cell(+fluorophore)?

Thanks

Dincer


_______________________________________________________________
Get Free Email and Do More On The Web. Visit http://www.msn.com

------------------------------

Date: Tue, 10 Aug 1999 17:02:27 -0700 (PDT)
From: Jason Ehrlich <jehrlich@leland.Stanford.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Video Output from NIH Image on PC
Message-Id: <199908110002.RAA29669@tree0.Stanford.EDU>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit

greetings, net,

This is probably a FAQ so I apologize in advance.

I would like to output animated stacks (~50-100 frames, TIF files) to
videotape. Of course, I can take the individual TIFFs, dump them into
Adobe Premiere, generate an AVI file, and then output this onto video
using a Matrox card or similar. However, I find this solution clunky, slow
(even on a fast computer, compressing for output to the card is not fast),
and the quality of the image suffers. Moreover, the files are very large, 
and if I want to change the animation speed, I have to render the files
in Premiere again.

So my question is - does anyone have a solution for delivering the
animation directly from the screen to videotape, in real time, without
saving as a Quicktime or AVI file first?

I'm probably missing an easy way to do this.

I'm using Scion Image on a PC, but either a PC or Mac solution would be
great.

thanks,
jason

--------
jason ehrlich  -  jehrlich@stanford.edu
dept of molecular & cellular physiology
beckman center, stanford medical school
stanford, ca 94305

------------------------------

Date: 	Tue, 10 Aug 1999 17:09:16 -1000
From: Kathleen Annikki Moore <moorekat@hawaii.edu>
To: nih-image@io.ece.drexel.edu
Subject: firewire image capture
Message-ID: <Pine.GSO.4.10.9908101658140.14266-100000@uhunix4>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Are still images captured with  mac laptop  firewire card connected to
Sony DFW-V500 digital camera (Wfine CCD, Primary Color Filter, Progressive
Scan, SquarePixels VGA (640 x 480), Non-Compressed YUV(4:2:2) Digital
Output) adequate for image processing?   Is Quicktime 4 adequate for
capturing? Is there some compression that occurs in process lowering image
quality? 
Thank you for any help.
Kathleen Moore

--------------------------------
End of nih-image-d Digest V99 Issue #182
****************************************

From nih-image-request@io.ece.drexel.edu Tue Aug 10 23:24 EDT 1999
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Are still images captured with  mac laptop  firewire card connected to
Sony DFW-V500 digital camera (Wfine CCD, Primary Color Filter, Progressive
Scan, SquarePixels VGA (640 x 480), Non-Compressed YUV(4:2:2) Digital
Output) adequate for image processing?   Is Quicktime 4 adequate for
capturing? Is there some compression that occurs in process lowering image
quality? 
Thank you for any help.
Kathleen Moore


From nih-image-request@io.ece.drexel.edu Wed Aug 11 05:35 EDT 1999
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Date: Wed, 11 Aug 1999 10:22:11 +0100
Subject: Re: firewire image capture
From: "Jeremy Brown" <jeremy.brown2@ed.ac.uk>
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My apologies, I did not realise how big the attachment was.

Sorry


****************************************
Jeremy Brown
Research Fellow
Department of Veterinary Clinical Studies
Royal (Dick) School of Veterinary Studies
Easter Bush Veterinary Centre
Easter Bush
Roslin
Midlothian
EH25 9RG
Scotland
UK
****************************************


From nih-image-request@io.ece.drexel.edu Wed Aug 11 05:42 EDT 1999
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Date: Wed, 11 Aug 1999 10:20:58 +0100
Subject: Re: firewire image capture
From: "Jeremy Brown" <jeremy.brown2@ed.ac.uk>
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--MS_Mac_OE_3017211658_3627115_MIME_Part
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Hello all,

I've did some extensive research into the possibility of using a Sony
DFW-V300/500 several months ago. To cut a long story short I was effectivel=
y
warned off purchasing one by Sony's own Technical people after making
enquires with several UK suppliers.

Although the DFW-V300 and 500 have been on the market for over a year now
Sony have made no attempt to develop software drives (PC or Mac). The idea
being that third parties would do this (Which to my knowledge they have
not). Adaptec were (over a year ago now) developing drivers for the cameras
but have since drop it, as I believe have Texas Instruments. The result is =
a
camera with no drivers (PC or Mac).

I would steer clear of these camera if I were you, at least for the moment
anyway. I may be wrong but I'll bet that nobody on the list has seen one
working, Sony UK will not even let me see the camera.


On the bright side there will shortly be a high resolution (megapixel)
Firewire camera from a small US company called Optronics.

http://www.optronics.com/

I've attached a more favourable response from them to this email. Members o=
f
the list may wish to inundate them with mail to the effect that a plugin fo=
r
NIH/Scion image would be most welcome. Especially by B&W Mac owners.

NB* I think that the latest firmware update for the B&W G3s does support 40
Megabytes/s, but I could be wrong.

Jeremy



**********************************************

Hello Jeremy and greetings from San Diego;
Thanks for your message regarding Firewire.  Your less than satisfactory
response from Sony and the world at large is not surprising.   Firewire is
much talked about but just not available new technology=85=85..yet.
It has taken our engineering group the last year and a half to create our
own Firewire interface for our digital camera.  When we started there were
no development tools so we had to create our own.  The result is that today
we are out on the "bleeding edge" with a  true 400 mega bit per second
Firewire interface digital camera that  is  ready for sale with delivery in
September.   A spec sheet on the camera is enclosed.

Now to respond to your comments.

True, Sony has had   Firewire video cameras on the market for the last year
or so.  They are not   realistic scientific cameras that offer an interface
for image analysis programs.    They were made more for the video
conferencing, broadcast  and consumer camcorder markets.  For example their
current Firewire is only 200mb per second.  It compresses the video
information through their proprietary CODEC scheme.  The result is about 3
million pixels per second.  Our MagnaFire digital camera by comparison send=
s
a non-compressed 10 bit signal at a rate of 16.9 million pixels per second.
We have discovered that Sony's VAIO desk top and laptop computers only
support 200mb Firewire.  They are working madly to increase the speed to
400.  Macintosh also only supports 200mb per second with the G3.  This will
increase in the future.
 Our goal now is to finish a software developers  kit for a PC interface (
you can buy a 400mb per second Firewire card from Texas Instruments that
really works).  We are collaborating with Media Cybernetics so that their
Image Pro Plus program will have the drivers to run our MagnaFire camera.
When we finish this project we will tackle a Mac interface.  This will
probably take several more months.  As for a PhotoShop plug-in, this is a
low priority as the camera has so many features that it needs a strong
control program.  For example, to control a time lapse experiment that can
utilize its six position filter wheel and wide exposure range.
Currently our MagnaFire camera has its own control program, however it does
not support any analysis.

Cheers,
Dave

**********************************************


****************************************
Jeremy Brown
Research Fellow
Department of Veterinary Clinical Studies
Royal (Dick) School of Veterinary Studies
Easter Bush Veterinary Centre
Easter Bush
Roslin
Midlothian
EH25 9RG
Scotland
UK
****************************************



----------
>From: Kathleen Annikki Moore <moorekat@hawaii.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: firewire image capture
>Date: Wed, Aug 11, 1999, 4:09 am
>

> Are still images captured with  mac laptop  firewire card connected to
> Sony DFW-V500 digital camera (Wfine CCD, Primary Color Filter, Progressiv=
e
> Scan, SquarePixels VGA (640 x 480), Non-Compressed YUV(4:2:2) Digital
> Output) adequate for image processing?   Is Quicktime 4 adequate for
> capturing? Is there some compression that occurs in process lowering imag=
e
> quality?
> Thank you for any help.
> Kathleen Moore
> 



From nih-image-d-request@io.ece.drexel.edu Wed Aug 11 05:48 EDT 1999
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Subject: nih-image-d Digest V99 #183
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 183

Today's Topics:
  Re: firewire image capture            [ "Jeremy Brown" <jeremy.brown2@ed.ac ]

------------------------------

Date: Wed, 11 Aug 1999 10:20:58 +0100
From: "Jeremy Brown" <jeremy.brown2@ed.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: firewire image capture
Message-Id: <199908110921.KAA16169@holyrood.ed.ac.uk>
Content-type: multipart/mixed;
   boundary="MS_Mac_OE_3017211658_3627115_MIME_Part"

> THIS MESSAGE IS IN MIME FORMAT. Since your mail reader does not understand
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--MS_Mac_OE_3017211658_3627115_MIME_Part
Content-type: text/plain; charset="ISO-8859-1"
Content-transfer-encoding: quoted-printable

Hello all,

I've did some extensive research into the possibility of using a Sony
DFW-V300/500 several months ago. To cut a long story short I was effectivel=
y
warned off purchasing one by Sony's own Technical people after making
enquires with several UK suppliers.

Although the DFW-V300 and 500 have been on the market for over a year now
Sony have made no attempt to develop software drives (PC or Mac). The idea
being that third parties would do this (Which to my knowledge they have
not). Adaptec were (over a year ago now) developing drivers for the cameras
but have since drop it, as I believe have Texas Instruments. The result is =
a
camera with no drivers (PC or Mac).

I would steer clear of these camera if I were you, at least for the moment
anyway. I may be wrong but I'll bet that nobody on the list has seen one
working, Sony UK will not even let me see the camera.


On the bright side there will shortly be a high resolution (megapixel)
Firewire camera from a small US company called Optronics.

http://www.optronics.com/

I've attached a more favourable response from them to this email. Members o=
f
the list may wish to inundate them with mail to the effect that a plugin fo=
r
NIH/Scion image would be most welcome. Especially by B&W Mac owners.

NB* I think that the latest firmware update for the B&W G3s does support 40
Megabytes/s, but I could be wrong.

Jeremy



**********************************************

Hello Jeremy and greetings from San Diego;
Thanks for your message regarding Firewire.  Your less than satisfactory
response from Sony and the world at large is not surprising.   Firewire is
much talked about but just not available new technology=85=85..yet.
It has taken our engineering group the last year and a half to create our
own Firewire interface for our digital camera.  When we started there were
no development tools so we had to create our own.  The result is that today
we are out on the "bleeding edge" with a  true 400 mega bit per second
Firewire interface digital camera that  is  ready for sale with delivery in
September.   A spec sheet on the camera is enclosed.

Now to respond to your comments.

True, Sony has had   Firewire video cameras on the market for the last year
or so.  They are not   realistic scientific cameras that offer an interface
for image analysis programs.    They were made more for the video
conferencing, broadcast  and consumer camcorder markets.  For example their
current Firewire is only 200mb per second.  It compresses the video
information through their proprietary CODEC scheme.  The result is about 3
million pixels per second.  Our MagnaFire digital camera by comparison send=
s
a non-compressed 10 bit signal at a rate of 16.9 million pixels per second.
We have discovered that Sony's VAIO desk top and laptop computers only
support 200mb Firewire.  They are working madly to increase the speed to
400.  Macintosh also only supports 200mb per second with the G3.  This will
increase in the future.
 Our goal now is to finish a software developers  kit for a PC interface (
you can buy a 400mb per second Firewire card from Texas Instruments that
really works).  We are collaborating with Media Cybernetics so that their
Image Pro Plus program will have the drivers to run our MagnaFire camera.
When we finish this project we will tackle a Mac interface.  This will
probably take several more months.  As for a PhotoShop plug-in, this is a
low priority as the camera has so many features that it needs a strong
control program.  For example, to control a time lapse experiment that can
utilize its six position filter wheel and wide exposure range.
Currently our MagnaFire camera has its own control program, however it does
not support any analysis.

Cheers,
Dave

**********************************************


****************************************
Jeremy Brown
Research Fellow
Department of Veterinary Clinical Studies
Royal (Dick) School of Veterinary Studies
Easter Bush Veterinary Centre
Easter Bush
Roslin
Midlothian
EH25 9RG
Scotland
UK
****************************************



----------
>From: Kathleen Annikki Moore <moorekat@hawaii.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: firewire image capture
>Date: Wed, Aug 11, 1999, 4:09 am
>

> Are still images captured with  mac laptop  firewire card connected to
> Sony DFW-V500 digital camera (Wfine CCD, Primary Color Filter, Progressiv=
e
> Scan, SquarePixels VGA (640 x 480), Non-Compressed YUV(4:2:2) Digital
> Output) adequate for image processing?   Is Quicktime 4 adequate for
> capturing? Is there some compression that occurs in process lowering imag=
e
> quality?
> Thank you for any help.
> Kathleen Moore
> 

--------------------------------
End of nih-image-d Digest V99 Issue #183
****************************************

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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 184

Today's Topics:
  Re: firewire image capture            [ "Jeremy Brown" <jeremy.brown2@ed.ac ]

------------------------------

Date: Wed, 11 Aug 1999 10:22:11 +0100
From: "Jeremy Brown" <jeremy.brown2@ed.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: firewire image capture
Message-Id: <199908110922.KAA16357@holyrood.ed.ac.uk>
Content-type: text/plain; charset="US-ASCII"
Content-transfer-encoding: 7bit

My apologies, I did not realise how big the attachment was.

Sorry


****************************************
Jeremy Brown
Research Fellow
Department of Veterinary Clinical Studies
Royal (Dick) School of Veterinary Studies
Easter Bush Veterinary Centre
Easter Bush
Roslin
Midlothian
EH25 9RG
Scotland
UK
****************************************

--------------------------------
End of nih-image-d Digest V99 Issue #184
****************************************

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Archive
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Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
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2)  title the Subject line of your email    archive
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then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
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8)   To search for text (e.g. the word color) in all the files in the


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then use get to get the files you want.
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get filename ...
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Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--


From nih-image-request@io.ece.drexel.edu Fri Aug 13 05:44 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: "Dr G. R. Coulton [bs_mp]" <g.coulton@ic.ac.uk>
Subject: 11th International Congress of Histochemistry and
  Cytochemistry (ICHC 2000)
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Dear All,

11th International Congress of Histochemistry and Cytochemistry (ICHC 2000)

I think that many on this list will find this meeting of interest to them.
Please take a minute to have a look at our web-site at
http://www.med.ic.ac.uk/external/ichc_2000

Best wishes

Gary
Dr. Gary Coulton
Molecular Pathology
Division of Biomedical Sciences
Imperial College School of Medicine
The Sir Alexander Fleming Building
South Kensington
London SW7 2AZ

tel 0044 (0)171 594 3190
fax 0044 (0)171 594 3022

e-mail g.coulton@ic.ac.uk

-------------------------------------
Announcing the 11th International Congress of Histochemistry and
Cytochemistry (ICHC 2000)

"Understanding Biocomplexity: The Post-Genome Challenge"

September 3-8, 2000, York, United Kingdom

ICHC 2000 will comprise 27 symposia addressing the latest developments and
applications of histochemistry and cytochemistry in the life sciences
including medicine.

SPEAKERS CONFIRMED (so far)
Lance Liotta (Bethesda)
Roger Tsien (La Jolla)
Dennis Noble (Oxford)
Paul Nakane (Mountain View)
Fre Bosman (Lausanne)
Margaret Buckingham (Paris)
John Couchman (Alabama)
Jim Coull (Boston)
Roel van Driel (Amsterdam)
David Eppel (Pacific Grove)
Reinhart Gossrau (Berlin)
Martin Green (Bebington)
Tom Just (Copenhagen)
Jeff Lichtman (St. Louis)
Joseph Mazurkiewicz (Albany)
Peter Nielsen (Copenhagen)
John O'Leary (Dublin)
Dennis Baskin (Washington)
Ralf Paus (Berlin)
Francesco Ramirez (New York)
Jim Smith (London)
John Stegeman (Woods Hole)
Hans Tanke (Leiden)
Anthony Thody (Bradford)
David Vaux (Oxford)
Lars-Inge Larsson (Frederiksberg) 
Keith Miller (London)
Mike Grant (Manchester)
Martin Humphries (Manchester)
Paul Martin (London)
Peter Mathiessen (Burnham on Crouch)
David Hinton (Davis) 

For further details of the meeting and how to pre-register please visit our
web-site at http://www.med.ic.ac.uk/external/ichc_2000

Hope to see you there.


From nih-image-request@io.ece.drexel.edu Fri Aug 13 08:56 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: "Dr G. R. Coulton [bs_mp]" <g.coulton@ic.ac.uk>
Subject: 11th International Congress of Histochemistry and
  Cytochemistry (ICHC 2000)
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Dear All,

11th International Congress of Histochemistry and Cytochemistry (ICHC 2000)

As many of you have noticed we are having local difficulties with our Web
server. Please wait a couple of days before trying again, I promise it will
be worth the wait.

Don't these things happen always at the most embarrassing time?

Bye

Gary


From nih-image-request@io.ece.drexel.edu Fri Aug 13 16:56 EDT 1999
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Date: Fri, 13 Aug 1999 15:47:37 -0500
Subject: Generation of rotational power spectra in NIH Image
From: "Karl E. Garsha" <keg@csd.uwm.edu>
To: nih-image@io.ece.drexel.edu
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Greetings,
I am attempting to objectively assess the number of individual subunits in a
radially symmetrical protein molecule.  I have produced quality TEM
micrographs of the protein which allow relatively convincing subjective
assesment of the quarternary conformation of this molecule through visual
inspection, however I would like to produce a rotational power spectrum of
the molecule to add more  weight to this data.  Crowther and Amos (J. Mol.
Biol. 60 (1971) 123) introduced rotational power spectrum analysis of
individual particles.  This technique has since been productively used in
many studies.  In this method,based on the Fourier Transform, a line graph
is produced which plots the rotational frequency against the log of power.  
The rotational frequency value which corresponds to the highest power is
taken to be the correct number of subunits composing radially symmetrical
particle.
    I have a rather limited background in mathematics, signal processing and
programming although I am trying to familiarize myself with the more general
concepts of these areas as they apply to this problem.  To date I am able to
generate the frequency transform of an isolated image in NIH Image using the
FFT macro, and I'm pretty much stuck not knowing where to go from this
point.  
    Comments from others more knowledgeable than I in the area of image
analysis would be greatly appreciated.  Thank you.
Sincerely, 
Karl Garsha-Lowly Graduate Student
University of Wisconsin-Milwaukee
Department of Biological Sciences
     


From nih-image-d-request@io.ece.drexel.edu Sat Aug 14 06:06 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #185
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 185

Today's Topics:
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
  11th International Congress of Histo  [ "Dr G. R. Coulton [bs_mp]" <g.coult ]
  11th International Congress of Histo  [ "Dr G. R. Coulton [bs_mp]" <g.coult ]
  Generation of rotational power spect  [ "Karl E. Garsha" <keg@csd.uwm.edu> ]

------------------------------

Date: Fri, 13 Aug 1999 05:05:01 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199908130905.FAA00753@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
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Archive
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Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

------------------------------

Date: Fri, 13 Aug 1999 10:32:03 +0100
From: "Dr G. R. Coulton [bs_mp]" <g.coulton@ic.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: 11th International Congress of Histochemistry and
  Cytochemistry (ICHC 2000)
Message-Id: <3.0.3.32.19990813103203.00eff680@icex4.cc.ic.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Dear All,

11th International Congress of Histochemistry and Cytochemistry (ICHC 2000)

I think that many on this list will find this meeting of interest to them.
Please take a minute to have a look at our web-site at
http://www.med.ic.ac.uk/external/ichc_2000

Best wishes

Gary
Dr. Gary Coulton
Molecular Pathology
Division of Biomedical Sciences
Imperial College School of Medicine
The Sir Alexander Fleming Building
South Kensington
London SW7 2AZ

tel 0044 (0)171 594 3190
fax 0044 (0)171 594 3022

e-mail g.coulton@ic.ac.uk

-------------------------------------
Announcing the 11th International Congress of Histochemistry and
Cytochemistry (ICHC 2000)

"Understanding Biocomplexity: The Post-Genome Challenge"

September 3-8, 2000, York, United Kingdom

ICHC 2000 will comprise 27 symposia addressing the latest developments and
applications of histochemistry and cytochemistry in the life sciences
including medicine.

SPEAKERS CONFIRMED (so far)
Lance Liotta (Bethesda)
Roger Tsien (La Jolla)
Dennis Noble (Oxford)
Paul Nakane (Mountain View)
Fre Bosman (Lausanne)
Margaret Buckingham (Paris)
John Couchman (Alabama)
Jim Coull (Boston)
Roel van Driel (Amsterdam)
David Eppel (Pacific Grove)
Reinhart Gossrau (Berlin)
Martin Green (Bebington)
Tom Just (Copenhagen)
Jeff Lichtman (St. Louis)
Joseph Mazurkiewicz (Albany)
Peter Nielsen (Copenhagen)
John O'Leary (Dublin)
Dennis Baskin (Washington)
Ralf Paus (Berlin)
Francesco Ramirez (New York)
Jim Smith (London)
John Stegeman (Woods Hole)
Hans Tanke (Leiden)
Anthony Thody (Bradford)
David Vaux (Oxford)
Lars-Inge Larsson (Frederiksberg) 
Keith Miller (London)
Mike Grant (Manchester)
Martin Humphries (Manchester)
Paul Martin (London)
Peter Mathiessen (Burnham on Crouch)
David Hinton (Davis) 

For further details of the meeting and how to pre-register please visit our
web-site at http://www.med.ic.ac.uk/external/ichc_2000

Hope to see you there.

------------------------------

Date: Fri, 13 Aug 1999 13:39:25 +0100
From: "Dr G. R. Coulton [bs_mp]" <g.coulton@ic.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: 11th International Congress of Histochemistry and
  Cytochemistry (ICHC 2000)
Message-Id: <3.0.3.32.19990813133925.009c7b40@icex4.cc.ic.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Dear All,

11th International Congress of Histochemistry and Cytochemistry (ICHC 2000)

As many of you have noticed we are having local difficulties with our Web
server. Please wait a couple of days before trying again, I promise it will
be worth the wait.

Don't these things happen always at the most embarrassing time?

Bye

Gary

------------------------------

Date: Fri, 13 Aug 1999 15:47:37 -0500
From: "Karl E. Garsha" <keg@csd.uwm.edu>
To: nih-image@io.ece.drexel.edu
Subject: Generation of rotational power spectra in NIH Image
Message-Id: <199908132038.PAA26100@batch1.csd.uwm.edu>
Content-type: text/plain; charset="US-ASCII"
Content-transfer-encoding: 7bit

Greetings,
I am attempting to objectively assess the number of individual subunits in a
radially symmetrical protein molecule.  I have produced quality TEM
micrographs of the protein which allow relatively convincing subjective
assesment of the quarternary conformation of this molecule through visual
inspection, however I would like to produce a rotational power spectrum of
the molecule to add more  weight to this data.  Crowther and Amos (J. Mol.
Biol. 60 (1971) 123) introduced rotational power spectrum analysis of
individual particles.  This technique has since been productively used in
many studies.  In this method,based on the Fourier Transform, a line graph
is produced which plots the rotational frequency against the log of power.  
The rotational frequency value which corresponds to the highest power is
taken to be the correct number of subunits composing radially symmetrical
particle.
    I have a rather limited background in mathematics, signal processing and
programming although I am trying to familiarize myself with the more general
concepts of these areas as they apply to this problem.  To date I am able to
generate the frequency transform of an isolated image in NIH Image using the
FFT macro, and I'm pretty much stuck not knowing where to go from this
point.  
    Comments from others more knowledgeable than I in the area of image
analysis would be greatly appreciated.  Thank you.
Sincerely, 
Karl Garsha-Lowly Graduate Student
University of Wisconsin-Milwaukee
Department of Biological Sciences
     

--------------------------------
End of nih-image-d Digest V99 Issue #185
****************************************

From nih-image-request@io.ece.drexel.edu Sat Aug 14 15:00 EDT 1999
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Resent-Date: Sat, 14 Aug 1999 15:00:02 -0400 (EDT)
Date: Sat, 14 Aug 1999 13:47:56 -0500 (CDT)
From: Ken Johnson <kenjohn@pathbox.wustl.edu>
X-Sender: kenjohn@pathbox.wustl.edu
To: nih-image@io.ece.drexel.edu
Subject: 24 bit colour movies
Message-ID: <Pine.GSO.3.96.990814134027.17038A-100000@pathbox.wustl.edu>
MIME-Version: 1.0
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Hello Image Users

I have been using NIH Image to create movies of live cells. This is fine
for creating 8-bit movies of either the R, G or B channels. These 3
channels can, of course, be combined to create an 8 bit indexed colour
sequence, which I can save as quicktime files. The prolem with this is the
loss of resolution when combining three 8-bit RGB images to one  8-bit
indexed
colour.

Using Scion mMage I can create a 24-bit Indexed colour Image, but am not
able to do further manipulations to this image - ie cropping, cutting
pasteing, stacking, let alone make movies. Does anyone have any
suggestions how I can make a 24-bit colour movie?

Thanks for your help on this one. 

Ken Johnson, Wash U Med School, MO.


From nih-image-d-request@io.ece.drexel.edu Sun Aug 15 06:05 EDT 1999
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Date: Sun, 15 Aug 1999 06:05:40 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #186
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 186

Today's Topics:
  24 bit colour movies                  [ Ken Johnson <kenjohn@pathbox.wustl. ]

------------------------------

Date: Sat, 14 Aug 1999 13:47:56 -0500 (CDT)
From: Ken Johnson <kenjohn@pathbox.wustl.edu>
To: nih-image@io.ece.drexel.edu
Subject: 24 bit colour movies
Message-ID: <Pine.GSO.3.96.990814134027.17038A-100000@pathbox.wustl.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hello Image Users

I have been using NIH Image to create movies of live cells. This is fine
for creating 8-bit movies of either the R, G or B channels. These 3
channels can, of course, be combined to create an 8 bit indexed colour
sequence, which I can save as quicktime files. The prolem with this is the
loss of resolution when combining three 8-bit RGB images to one  8-bit
indexed
colour.

Using Scion mMage I can create a 24-bit Indexed colour Image, but am not
able to do further manipulations to this image - ie cropping, cutting
pasteing, stacking, let alone make movies. Does anyone have any
suggestions how I can make a 24-bit colour movie?

Thanks for your help on this one. 

Ken Johnson, Wash U Med School, MO.

--------------------------------
End of nih-image-d Digest V99 Issue #186
****************************************

From nih-image-request@io.ece.drexel.edu Sun Aug 15 09:54 EDT 1999
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	Sun, 15 Aug 1999 09:54:17 -0400 (EDT)
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From: JLinn24538@aol.com
Message-ID: <efba902b.24e81d79@aol.com>
Date: Sun, 15 Aug 1999 09:41:13 EDT
Subject: Re:  24 bit colour movies
To: nih-image@io.ece.drexel.edu
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I've made 24 bit color movies using the following technique:
1) Create a series of RGB images in NIH _image and number them sequentially.
2) Use Graphic Converter to convert them to a set of 24 bit PICTs
3) Use PICT to Movie to create a movie from the sequentially numbered PICTs.

Both Graphic Converter and PICT to Movie are available at the NIH Image ftp 
site in the 'programs' directory.  Good Luck!

Jeff Linn


From nih-image-request@io.ece.drexel.edu Sun Aug 15 12:36 EDT 1999
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Date: Sun, 15 Aug 1999 09:26:05 -0700
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Subject: 24 bit color movies
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Ken,
    The fundamental problem is that NIH-Image can't deal with 24 bit
images. Scion provides a screen display that generates single frames,
but the ability to then handle large stacks of 24 bit images doesn't
seem to be built in to NIH-Image. Thus, I was never able to produce a
stack of 24 bit images.

However, the new program by Wayne Rasband, ImageJ, provides exactly the
sort of utility you are looking for. ImageJ is quickly developing all
those many complex routines previously available in Wayne's earlier
NIH-Image, but works on Macs, PCs, Unix boxes, and  Linux. We routinely
use ImageJ to view stacks of color images made up of three channels. The
actual display on the screen is as a 24 bit image. We can easily run
these stacks as "movies" for 3D animation of rotation series from
Confocal data sets. In our case, we rae actually using three channels of
12/16 bit images for each channel (i.e. 48 bit images), and retain the
original data in that high resolution format. We view them on the screen
as 24/32 bit images due to limitations in display hardware, and the
basic design of current generation of software.

Try ImageJ. It is the future.


Harvey

--
Harvey J. Karten, M.D.
Dept. of Neurosciences
University of California @ San Diego
La Jolla, CA 92093-0608
EMail: hjkarten@ucsd.edu
Phone (Lab): 619-534-4938
FAX (Lab): 619-534-6602
Home Phone: 619-755-8573
Retina Information System: http://www-cajal.ucsd.edu



From nih-image-d-request@io.ece.drexel.edu Mon Aug 16 01:13 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #187
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 187

Today's Topics:
  Re: 24 bit colour movies              [ JLinn24538@aol.com ]
  24 bit color movies                   [ "Harvey J. Karten" <hjkarten@ucsd.e ]
  Re: nih-image-d Digest V99 #186       [ "G. Macdonald" <glenmac@u.washingto ]

------------------------------

Date: Sun, 15 Aug 1999 09:41:13 EDT
From: JLinn24538@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re:  24 bit colour movies
Message-ID: <efba902b.24e81d79@aol.com>
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I've made 24 bit color movies using the following technique:
1) Create a series of RGB images in NIH _image and number them sequentially.
2) Use Graphic Converter to convert them to a set of 24 bit PICTs
3) Use PICT to Movie to create a movie from the sequentially numbered PICTs.

Both Graphic Converter and PICT to Movie are available at the NIH Image ftp 
site in the 'programs' directory.  Good Luck!

Jeff Linn

------------------------------

Date: Sun, 15 Aug 1999 09:26:05 -0700
From: "Harvey J. Karten" <hjkarten@ucsd.edu>
To: nih-image@io.ece.drexel.edu
Subject: 24 bit color movies
Message-ID: <37B6EA19.3D27C533@ucsd.edu>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
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Ken,
    The fundamental problem is that NIH-Image can't deal with 24 bit
images. Scion provides a screen display that generates single frames,
but the ability to then handle large stacks of 24 bit images doesn't
seem to be built in to NIH-Image. Thus, I was never able to produce a
stack of 24 bit images.

However, the new program by Wayne Rasband, ImageJ, provides exactly the
sort of utility you are looking for. ImageJ is quickly developing all
those many complex routines previously available in Wayne's earlier
NIH-Image, but works on Macs, PCs, Unix boxes, and  Linux. We routinely
use ImageJ to view stacks of color images made up of three channels. The
actual display on the screen is as a 24 bit image. We can easily run
these stacks as "movies" for 3D animation of rotation series from
Confocal data sets. In our case, we rae actually using three channels of
12/16 bit images for each channel (i.e. 48 bit images), and retain the
original data in that high resolution format. We view them on the screen
as 24/32 bit images due to limitations in display hardware, and the
basic design of current generation of software.

Try ImageJ. It is the future.


Harvey

--
Harvey J. Karten, M.D.
Dept. of Neurosciences
University of California @ San Diego
La Jolla, CA 92093-0608
EMail: hjkarten@ucsd.edu
Phone (Lab): 619-534-4938
FAX (Lab): 619-534-6602
Home Phone: 619-755-8573
Retina Information System: http://www-cajal.ucsd.edu

------------------------------

Date: Sun, 15 Aug 1999 21:51:22 -0700 (PDT)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #186
Message-ID: <Pine.A41.4.10.9908152140570.158812-100000@homer36.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Ken, 
the macro below will allow you to crop all the stacks for any sample to
the same roi.  YOu would need a macro to step
through the cropped stacks, grab the
images for each plane, assemble them into an RGB file and save.
Quicktime or GraphicConverter can take a folder of RGB Tiffs and convert
them to a movie.  I cut this out of a very largemacro file, so I hope all
the variables are here.  


Regards,
Glen


Glen MacDonald
   Research Scientist
Hearing Research Laboratories of the
Virginia Merrill Bloedel Hearing Research Center
Box 35-7923
University of Washington
Seattle, WA  98195-7923
(206) 616-4156
glenmac@u.washington.edu

----------
procedure CheckForSelection;
var 
  x1,y1,x2,y2,LineWidth:integer;
begin
  GetRoi(RoiLeft,RoiTop,RoiWidth,RoiHeight);
  GetLine(x1,y1,x2,y2,LineWidth);
  if (RoiWidth=0) or (x1>=0) then begin
    PutMessage('Please make a rectangular selection.');
    exit;
  end;
end;

procedure CropStacks;
var
  i,j,OldStack,NewStack:integer;
  RoiLeft,RoiTop,RoiWidth,RoiHeight:integer;
  N,NStacks:integer;
  OldStackName,NewStackName:string;
begin
 { CheckForStack;}
  CheckForSelection;
  NStacks:=npics;
  SaveState;
for j:=1 to NStacks do begin
  OldStack:=PicNumber;
  OldStackName:=WindowTitle;
  N:=nSlices;
  NewStackName:=concat(WindowTitle,' cropped');
 SetNewSize(RoiWidth,RoiHeight);
  MakeNewStack(NewStackName);
  NewStack:=PidNumber;  
  SelectPic(OldStack);
  MakeRoi(RoiLeft,RoiTop,RoiWidth,RoiHeight);
  for i:= 1 to N do begin
    SelectSlice(1);   
    Copy;
    SelectPic(NewStack);
    if i<>1 then AddSlice;
    Paste;
    SelectPic(OldStack);
    DeleteSlice;
  end;
  Dispose; {OldStack}
  SelectPic(NewStack);
  Save;
  Dispose; {NewStack}
  end; 
  RestoreState;
end;

macro 'Crop Stacks, No Scaling';  begin CropStacks; end; 
{The 'Crop Stacks, No Scaling' macro differs from the 2 above in that it
will operate on as many stacks as there is memory to hold open.  If memory
is limited, then modify it to either Open or Import files from the File
menu, with the Open All checked.  To use, draw a rectangular selection on
any slice of any of the stacks, then select this macro.  The selection
will be copied to a new stack entitled 'stackname cropped'.  Each stack
will be closed as it is operated on.  Each new stack will be closed after
saving.}

--------------------------------
End of nih-image-d Digest V99 Issue #187
****************************************

From nih-image-request@io.ece.drexel.edu Mon Aug 16 01:21 EDT 1999
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Date: Sun, 15 Aug 1999 21:51:22 -0700 (PDT)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #186
In-Reply-To: <199908151006.GAA07638@io.ece.drexel.edu>
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Ken, 
the macro below will allow you to crop all the stacks for any sample to
the same roi.  YOu would need a macro to step
through the cropped stacks, grab the
images for each plane, assemble them into an RGB file and save.
Quicktime or GraphicConverter can take a folder of RGB Tiffs and convert
them to a movie.  I cut this out of a very largemacro file, so I hope all
the variables are here.  


Regards,
Glen


Glen MacDonald
   Research Scientist
Hearing Research Laboratories of the
Virginia Merrill Bloedel Hearing Research Center
Box 35-7923
University of Washington
Seattle, WA  98195-7923
(206) 616-4156
glenmac@u.washington.edu

----------
procedure CheckForSelection;
var 
  x1,y1,x2,y2,LineWidth:integer;
begin
  GetRoi(RoiLeft,RoiTop,RoiWidth,RoiHeight);
  GetLine(x1,y1,x2,y2,LineWidth);
  if (RoiWidth=0) or (x1>=0) then begin
    PutMessage('Please make a rectangular selection.');
    exit;
  end;
end;

procedure CropStacks;
var
  i,j,OldStack,NewStack:integer;
  RoiLeft,RoiTop,RoiWidth,RoiHeight:integer;
  N,NStacks:integer;
  OldStackName,NewStackName:string;
begin
 { CheckForStack;}
  CheckForSelection;
  NStacks:=npics;
  SaveState;
for j:=1 to NStacks do begin
  OldStack:=PicNumber;
  OldStackName:=WindowTitle;
  N:=nSlices;
  NewStackName:=concat(WindowTitle,' cropped');
 SetNewSize(RoiWidth,RoiHeight);
  MakeNewStack(NewStackName);
  NewStack:=PidNumber;  
  SelectPic(OldStack);
  MakeRoi(RoiLeft,RoiTop,RoiWidth,RoiHeight);
  for i:= 1 to N do begin
    SelectSlice(1);   
    Copy;
    SelectPic(NewStack);
    if i<>1 then AddSlice;
    Paste;
    SelectPic(OldStack);
    DeleteSlice;
  end;
  Dispose; {OldStack}
  SelectPic(NewStack);
  Save;
  Dispose; {NewStack}
  end; 
  RestoreState;
end;

macro 'Crop Stacks, No Scaling';  begin CropStacks; end; 
{The 'Crop Stacks, No Scaling' macro differs from the 2 above in that it
will operate on as many stacks as there is memory to hold open.  If memory
is limited, then modify it to either Open or Import files from the File
menu, with the Open All checked.  To use, draw a rectangular selection on
any slice of any of the stacks, then select this macro.  The selection
will be copied to a new stack entitled 'stackname cropped'.  Each stack
will be closed as it is operated on.  Each new stack will be closed after
saving.}




From nih-image-request@io.ece.drexel.edu Tue Aug 17 14:04 EDT 1999
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Date: Tue, 17 Aug 1999 19:48:04 +0200
From: Ralf Kemkemer <ralf.kemkemer@physik.uni-ulm.de>
Organization: Biophysics - Uni Ulm
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Subject: G3 and Scion LG-3
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Hi!
We would like to buy a new Mac ("blue" G3).
Is there any problem using our old LG-3 Frame Grabber (PCI, Rev B) with
this G3?
Thanks for any information!
Ralf



From nih-image-request@io.ece.drexel.edu Tue Aug 17 18:16 EDT 1999
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From: "Megan Ferguson" <megan_ferguson@hotmail.com>
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Subject: scaling question
Date: Tue, 17 Aug 1999 15:01:34 PDT
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Hello,

I am using Image 1.62 to find the area of a black-and-white image of a leaf 
that I digitized using a flatbed scanner and Photoshop software.  When I set 
the scale in Image using a horizontal scale bar, the calculated area is 
148.62 cm2.  When I use a vertical scale bar on the same image to set the 
scale, however, the calculated area is 116.09 cm2.  I have tried the same 
procedure on several different images and there is always a discrepancy 
between the calculated areas.  Does anyone have any ideas of why I come up 
with two very different areas depending on which axis I set the scale?

Thanks for your help.

Megan










.


_______________________________________________________________
Get Free Email and Do More On The Web. Visit http://www.msn.com


From nih-image-d-request@io.ece.drexel.edu Wed Aug 18 06:12 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 188

Today's Topics:
  G3 and Scion LG-3                     [ Ralf Kemkemer <ralf.kemkemer@physik ]
  scaling question                      [ "Megan Ferguson" <megan_ferguson@ho ]
  crop and save under extended name?    [ Ludger Offerhaus <ljo@gfz-potsdam.d ]

------------------------------

Date: Tue, 17 Aug 1999 19:48:04 +0200
From: Ralf Kemkemer <ralf.kemkemer@physik.uni-ulm.de>
To: nih-image@io.ece.drexel.edu
Subject: G3 and Scion LG-3
Message-ID: <37B9A054.BE8D6A66@physik.uni-ulm.de>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi!
We would like to buy a new Mac ("blue" G3).
Is there any problem using our old LG-3 Frame Grabber (PCI, Rev B) with
this G3?
Thanks for any information!
Ralf

------------------------------

Date: Tue, 17 Aug 1999 15:01:34 PDT
From: "Megan Ferguson" <megan_ferguson@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: scaling question
Message-ID: <19990817220134.26710.qmail@hotmail.com>
Content-Type: text/plain; format=flowed

Hello,

I am using Image 1.62 to find the area of a black-and-white image of a leaf 
that I digitized using a flatbed scanner and Photoshop software.  When I set 
the scale in Image using a horizontal scale bar, the calculated area is 
148.62 cm2.  When I use a vertical scale bar on the same image to set the 
scale, however, the calculated area is 116.09 cm2.  I have tried the same 
procedure on several different images and there is always a discrepancy 
between the calculated areas.  Does anyone have any ideas of why I come up 
with two very different areas depending on which axis I set the scale?

Thanks for your help.

Megan










 .

_______________________________________________________________
Get Free Email and Do More On The Web. Visit http://www.msn.com

------------------------------

Date: Wed, 18 Aug 1999 11:59:39 +0200
From: Ludger Offerhaus <ljo@gfz-potsdam.de>
To: nih-image@io.ece.drexel.edu
Subject: crop and save under extended name?
Message-Id: <l03130309b3e033ce114e@[139.17.139.125]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Dear imagers!

The questions sounds simple to me, but I seem unable to find the answer in
my manuals.

How do I crop a single image and save it under a modified version of the
old file name?
So e.g. file <monster01.tif> would become <small monster01.tif>

If I use Duplicate ('window Title') all I seem to be able to do is enter a
completely new name, which is a bit of a nuisance, as I want to process
tens of files.

Thanks in advance!
best regards
Ludger


--
Ludger Offerhaus
GeoForschungsZentrum Potsdam
Telegrafenberg, 14473 Potsdam, Duitsland
Tel: +49 (0)331 288 1326 / 1390
of (ook awap): 030 32 60 55 68
---
... aan een boom *zo* volgeladen / mist men n, twee pruimpjes niet ...
---

--------------------------------
End of nih-image-d Digest V99 Issue #188
****************************************

From nih-image-request@io.ece.drexel.edu Wed Aug 18 06:15 EDT 1999
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From: Ludger Offerhaus <ljo@gfz-potsdam.de>
Subject: crop and save under extended name?
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Dear imagers!

The questions sounds simple to me, but I seem unable to find the answer in
my manuals.

How do I crop a single image and save it under a modified version of the
old file name?
So e.g. file <monster01.tif> would become <small monster01.tif>

If I use Duplicate ('window Title') all I seem to be able to do is enter a
completely new name, which is a bit of a nuisance, as I want to process
tens of files.

Thanks in advance!
best regards
Ludger


--
Ludger Offerhaus
GeoForschungsZentrum Potsdam
Telegrafenberg, 14473 Potsdam, Duitsland
Tel: +49 (0)331 288 1326 / 1390
of (ook awap): 030 32 60 55 68
---
... aan een boom *zo* volgeladen / mist men n, twee pruimpjes niet ...
---



From nih-image-request@io.ece.drexel.edu Wed Aug 18 07:42 EDT 1999
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Date: Wed, 18 Aug 1999 12:24:29 +0100
Subject: Re: crop and save under extended name?
From: "Jeremy Brown" <jeremy.brown2@ed.ac.uk>
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Try the following,


will save as BlahBlah.blah.small

Macro '[C] Crop and Save'
Var
Name,wPath,FullPath:string;
left,top,width,height:Integer;
begin
GetRoi(left,top,width,height);
wPath:= GetPath('window'); name:= WindowTitle;
FullPath:= concat(wPath, name,);
SaveAs(FullPath,'.Small');
Dispose;
repeat;
Open('any');
MakeROI(left,top,width,height);
wPath:= GetPath('window'); name:= WindowTitle;
FullPath:= concat(wPath, name,);
SaveAs(FullPath,'.Small');
Dispose;
until button;
end;

Jeremy

****************************************
Jeremy Brown
Research Fellow
Department of Veterinary Clinical Studies
Royal (Dick) School of Veterinary Studies
Easter Bush Veterinary Centre
Easter Bush
Roslin
Midlothian
EH25 9RG
Scotland
UK
****************************************



----------
>From: Ludger Offerhaus <ljo@gfz-potsdam.de>
>To: nih-image@io.ece.drexel.edu
>Subject: crop and save under extended name?
>Date: Wed, Aug 18, 1999, 10:59 am
>

> Dear imagers!
>
> The questions sounds simple to me, but I seem unable to find the answer in
> my manuals.
>
> How do I crop a single image and save it under a modified version of the
> old file name?
> So e.g. file <monster01.tif> would become <small monster01.tif>
>
> If I use Duplicate ('window Title') all I seem to be able to do is enter a
> completely new name, which is a bit of a nuisance, as I want to process
> tens of files.
>
> Thanks in advance!
> best regards
> Ludger
>
>
> --
> Ludger Offerhaus
> GeoForschungsZentrum Potsdam
> Telegrafenberg, 14473 Potsdam, Duitsland
> Tel: +49 (0)331 288 1326 / 1390
> of (ook awap): 030 32 60 55 68
> ---
> ... aan een boom *zo* volgeladen / mist men n, twee pruimpjes niet ...
> ---
>
> 


From nih-image-request@io.ece.drexel.edu Wed Aug 18 11:39 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: Jen-Wei Lin <jenwelin@bio.bu.edu>
Subject: Will LG-3 card work with 7100/80 upgraded to G3?
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Such is the pain with upgrades.  So we have this old LG-3 card in a
7100/80.  Has anyone tried to upgrade the computer w/ G3 card and get the
card to work?  If you do, please also provie info on the Mac OS and NIH
imaging versions you are using w/ it.
Thanks in advance.

Jen-Wei

Jen-Wei Lin, Ph.D.
Biology
Boston University
5 Cummington St.
Boston, MA 02215

TEL:617-353-3443 or -3444
FAX: 617-353-6340



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From: Ben Elkin <elk@igb.fhg.de>
Subject: Re: Will LG-3 card work with 7100/80 upgraded to G3?
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>Such is the pain with upgrades.  So we have this old LG-3 card in a
>7100/80.  Has anyone tried to upgrade the computer w/ G3 card and get the
>card to work?  If you do, please also provie info on the Mac OS and NIH
>imaging versions you are using w/ it.
>Thanks in advance.
>
>Jen-Wei

Yes, it works - no problems at all. Currently we have Mac OS 8.6 and NIH
Image 1.61.

Ben Elkin

=======================================
elk@igb.fhg.de

http://www.igb.fhg.de/GVT/

Fraunhofer Institute for Interfacial Engineering and Biotechnology
                    (fuer Grenzflaechen und Bioverfahrenstechnik)

Nobelstr. 12    D-70569 Stuttgart    Germany

Tel. +49 - 711 - 970-4144, -4161
Fax                 -4200




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From: Kathleen Annikki Moore <moorekat@hawaii.edu>
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Subject: zoom video optic lens/digital camera?
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Is a zoom video optic lens ( such as used for industrial inspections) with
magnification range at the monitor of 3.5X to 1350X mounted directly to
digital camera (with copy stand/optical lights and lower stage area
accessories etc) adequate for image processing(macro and microscopic).
Also, I looked in archive at Pixera cameras mixed reviews.  Is there a
digital camera $1000-$2000 that tethers to powerbook, macs that could be
used for microscopic image processing yet.  Thank you for any help.

Kathleen Moore



From nih-image-request@io.ece.drexel.edu Wed Aug 18 18:46 EDT 1999
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Hi,

	Thanks to all of you who sent suggestions about image conversion.
You were very helpful and kind.

	The new user has another problem.

	I took the advice of several of you and am using Photoshop to
convert jpeg images to tiff so that I can use the Scion program.  The
images appear fine.  When I open the converted file in Scion the window
takes up all of my screen but only shows the upper left one quarter or
less of my image.  Is there a way to scroll the picture or to reduce the
size?  The "maginifying glass" only enlarges it.  Anything else I have
tried changes the color/hues and not the size.  

	Thank you for your suggestions.

TTFN,
Lill

Lill Becker
Department of Biology
Florida International University
Miami, FL  33199   USA

	*******************************************
	*Are science and magic mutually exclusive?*
	*******************************************


From nih-image-d-request@io.ece.drexel.edu Thu Aug 19 04:47 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #189
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 189

Today's Topics:
  Re: crop and save under extended nam  [ "Jeremy Brown" <jeremy.brown2@ed.ac ]
  Will LG-3 card work with 7100/80 upg  [ Jen-Wei Lin <jenwelin@bio.bu.edu> ]
  Re: Will LG-3 card work with 7100/80  [ Ben Elkin <elk@igb.fhg.de> ]
  zoom video optic lens/digital camera  [ Kathleen Annikki Moore <moorekat@ha ]
  jpeg images                           [ lillian c becker <lbecke01@fiu.edu> ]
  Re: jpeg images + scaling in Scion    [ "j.gregory" <ort056@abdn.ac.uk> ]

------------------------------

Date: Wed, 18 Aug 1999 12:24:29 +0100
From: "Jeremy Brown" <jeremy.brown2@ed.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: crop and save under extended name?
Message-Id: <199908181124.MAA19221@holyrood.ed.ac.uk>
Content-type: text/plain; charset="ISO-8859-1"
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Try the following,


will save as BlahBlah.blah.small

Macro '[C] Crop and Save'
Var
Name,wPath,FullPath:string;
left,top,width,height:Integer;
begin
GetRoi(left,top,width,height);
wPath:= GetPath('window'); name:= WindowTitle;
FullPath:= concat(wPath, name,);
SaveAs(FullPath,'.Small');
Dispose;
repeat;
Open('any');
MakeROI(left,top,width,height);
wPath:= GetPath('window'); name:= WindowTitle;
FullPath:= concat(wPath, name,);
SaveAs(FullPath,'.Small');
Dispose;
until button;
end;

Jeremy

****************************************
Jeremy Brown
Research Fellow
Department of Veterinary Clinical Studies
Royal (Dick) School of Veterinary Studies
Easter Bush Veterinary Centre
Easter Bush
Roslin
Midlothian
EH25 9RG
Scotland
UK
****************************************



----------
>From: Ludger Offerhaus <ljo@gfz-potsdam.de>
>To: nih-image@io.ece.drexel.edu
>Subject: crop and save under extended name?
>Date: Wed, Aug 18, 1999, 10:59 am
>

> Dear imagers!
>
> The questions sounds simple to me, but I seem unable to find the answer in
> my manuals.
>
> How do I crop a single image and save it under a modified version of the
> old file name?
> So e.g. file <monster01.tif> would become <small monster01.tif>
>
> If I use Duplicate ('window Title') all I seem to be able to do is enter a
> completely new name, which is a bit of a nuisance, as I want to process
> tens of files.
>
> Thanks in advance!
> best regards
> Ludger
>
>
> --
> Ludger Offerhaus
> GeoForschungsZentrum Potsdam
> Telegrafenberg, 14473 Potsdam, Duitsland
> Tel: +49 (0)331 288 1326 / 1390
> of (ook awap): 030 32 60 55 68
> ---
> ... aan een boom *zo* volgeladen / mist men n, twee pruimpjes niet ...
> ---
>
> 

------------------------------

Date: Wed, 18 Aug 1999 11:22:45 -0400
From: Jen-Wei Lin <jenwelin@bio.bu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Will LG-3 card work with 7100/80 upgraded to G3?
Message-Id: <l03130303b3e07e99aed9@[128.197.80.179]>
Content-Type: text/plain; charset="us-ascii"

Such is the pain with upgrades.  So we have this old LG-3 card in a
7100/80.  Has anyone tried to upgrade the computer w/ G3 card and get the
card to work?  If you do, please also provie info on the Mac OS and NIH
imaging versions you are using w/ it.
Thanks in advance.

Jen-Wei

Jen-Wei Lin, Ph.D.
Biology
Boston University
5 Cummington St.
Boston, MA 02215

TEL:617-353-3443 or -3444
FAX: 617-353-6340

------------------------------

Date: Wed, 18 Aug 1999 17:49:17 +0200
From: Ben Elkin <elk@igb.fhg.de>
To: nih-image@io.ece.drexel.edu
Subject: Re: Will LG-3 card work with 7100/80 upgraded to G3?
Message-Id: <l03130300b3e0860775d6@[129.233.21.143]>
Content-Type: text/plain; charset="us-ascii"

>Such is the pain with upgrades.  So we have this old LG-3 card in a
>7100/80.  Has anyone tried to upgrade the computer w/ G3 card and get the
>card to work?  If you do, please also provie info on the Mac OS and NIH
>imaging versions you are using w/ it.
>Thanks in advance.
>
>Jen-Wei

Yes, it works - no problems at all. Currently we have Mac OS 8.6 and NIH
Image 1.61.

Ben Elkin

=======================================
elk@igb.fhg.de

http://www.igb.fhg.de/GVT/

Fraunhofer Institute for Interfacial Engineering and Biotechnology
                    (fuer Grenzflaechen und Bioverfahrenstechnik)

Nobelstr. 12    D-70569 Stuttgart    Germany

Tel. +49 - 711 - 970-4144, -4161
Fax                 -4200

------------------------------

Date: 	Wed, 18 Aug 1999 12:18:20 -1000
From: Kathleen Annikki Moore <moorekat@hawaii.edu>
To: nih-image@io.ece.drexel.edu
Subject: zoom video optic lens/digital camera?
Message-ID: <Pine.GSO.4.10.9908181210470.27529-100000@uhunix5>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Is a zoom video optic lens ( such as used for industrial inspections) with
magnification range at the monitor of 3.5X to 1350X mounted directly to
digital camera (with copy stand/optical lights and lower stage area
accessories etc) adequate for image processing(macro and microscopic).
Also, I looked in archive at Pixera cameras mixed reviews.  Is there a
digital camera $1000-$2000 that tethers to powerbook, macs that could be
used for microscopic image processing yet.  Thank you for any help.

Kathleen Moore

------------------------------

Date: Wed, 18 Aug 1999 18:30:50 -0400 (EDT)
From: lillian c becker <lbecke01@fiu.edu>
To: Jonathan WISCO <jjwisco@cajal-1.bu.edu>
cc: nih-image <nih-image@io.ece.drexel.edu>
Subject: jpeg images
Message-ID: <Pine.SOL.3.96.990818182450.23046B-100000@solix4-64>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi,

	Thanks to all of you who sent suggestions about image conversion.
You were very helpful and kind.

	The new user has another problem.

	I took the advice of several of you and am using Photoshop to
convert jpeg images to tiff so that I can use the Scion program.  The
images appear fine.  When I open the converted file in Scion the window
takes up all of my screen but only shows the upper left one quarter or
less of my image.  Is there a way to scroll the picture or to reduce the
size?  The "maginifying glass" only enlarges it.  Anything else I have
tried changes the color/hues and not the size.  

	Thank you for your suggestions.

TTFN,
Lill

Lill Becker
Department of Biology
Florida International University
Miami, FL  33199   USA

	*******************************************
	*Are science and magic mutually exclusive?*
	*******************************************

------------------------------

Date: Thu, 19 Aug 1999 09:36:53 +0100 (BST)
From: "j.gregory" <ort056@abdn.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: jpeg images + scaling in Scion
Message-ID: <SIMEON.9908190953.A@pc10.surg.abdn.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

Hi Lil,

I hope this helps...

Resize your window to the size you want and then from the options menu choose 
'scale to fit window'.   The image doesn't always look too good on the 
screen, but at least you can see the whole image.

Jenny Gregory


> Hi,
> 
> 	Thanks to all of you who sent suggestions about image conversion.
> You were very helpful and kind.
> 
> 	The new user has another problem.
> 
> 	I took the advice of several of you and am using Photoshop to
> convert jpeg images to tiff so that I can use the Scion program.  The
> images appear fine.  When I open the converted file in Scion the window
> takes up all of my screen but only shows the upper left one quarter or
> less of my image.  Is there a way to scroll the picture or to reduce the
> size?  The "maginifying glass" only enlarges it.  Anything else I have
> tried changes the color/hues and not the size.  
> 
> 	Thank you for your suggestions.
> 
> TTFN,
> Lill
> 
> Lill Becker
> Department of Biology
> Florida International University
> Miami, FL  33199   USA
> 
> 	*******************************************
> 	*Are science and magic mutually exclusive?*
> 	*******************************************
> 

--------------------------------
End of nih-image-d Digest V99 Issue #189
****************************************

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From: "j.gregory" <ort056@abdn.ac.uk>
Sender: ort056@abdn.ac.uk
To: nih-image@io.ece.drexel.edu
Subject: Re: jpeg images + scaling in Scion
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Date: Thu, 19 Aug 1999 09:36:53 +0100 (BST)
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Hi Lil,

I hope this helps...

Resize your window to the size you want and then from the options menu choose 
'scale to fit window'.   The image doesn't always look too good on the 
screen, but at least you can see the whole image.

Jenny Gregory


> Hi,
> 
> 	Thanks to all of you who sent suggestions about image conversion.
> You were very helpful and kind.
> 
> 	The new user has another problem.
> 
> 	I took the advice of several of you and am using Photoshop to
> convert jpeg images to tiff so that I can use the Scion program.  The
> images appear fine.  When I open the converted file in Scion the window
> takes up all of my screen but only shows the upper left one quarter or
> less of my image.  Is there a way to scroll the picture or to reduce the
> size?  The "maginifying glass" only enlarges it.  Anything else I have
> tried changes the color/hues and not the size.  
> 
> 	Thank you for your suggestions.
> 
> TTFN,
> Lill
> 
> Lill Becker
> Department of Biology
> Florida International University
> Miami, FL  33199   USA
> 
> 	*******************************************
> 	*Are science and magic mutually exclusive?*
> 	*******************************************
> 




From nih-image-request@io.ece.drexel.edu Thu Aug 19 05:44 EDT 1999
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From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: jpeg images + scaling in Scion
Date: Thu, 19 Aug 1999 11:31:53 +0200
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 I wrote a macro that let you see the whole image in a small 'overview'
window and then choose the region you want to see in the original image.
When using the macro open the original image, then use 'Overview [O]'
and move the ROI in the new OverView-window to the position you want to
see and choose 'Show Selection [S]'. If you dissable the ROI, use
'Restore Roi' to make a new selection, otherwise you will get an error
message.

The macro is slow, maybe someone in the list could take a look and
improve it.

Anyway, I hope this macro will be useful for you.

Gary.
------------------------------------------------------------------
Gary Chinga
PhD student
The Norwegian University of Science and Technology
Dept. of Chem. Engineering
Sem Saelandsv. 4
Trondheim
N7034 Norway
Direct line : +47 73550537
Fax: +47 73594080
email: gary.chinga@pfi.no


{----------------------------------------MACRO
-------------------------------------------}

var factor:real;
      OverviewStack,OverViewWindow,
      left,top,width,height,
      widthOverview,heightOverview
      widthRP,heightRP:integer;

Procedure Info;
begin
  widthOverview:=120;
end;  


Procedure PicSize;
Begin
   GetPicSize(width,height);
   factor:=250/width;
end;


Procedure MakeStack;
begin
  SelectAll;Copy; Dispose;
  SetNewSize(width,height);
  MakeNewStack('OverviewStack');Paste;
  AddSlice; Paste;
  OverViewStack:=PidNumber;
end;

procedure ScaleWindow;


begin
   if PidExists(OverviewWindow) then begin
      selectwindow('OverView');dispose;
   end;
   SetScaling('New Window,bilinear');
   ScaleandRotate(factor,factor,0);
   GetpicSize(widthRP,heightRP);
   SelectAll;Copy;Dispose;
   setNewSize(widthRP,heightRP);
   MakeNewWindow('OverView');Paste;
  
   OverviewWindow:=Pidnumber;
   heightOverview:=height/width*widthOverview;
   MakeRoi(0,0,widthOverview,heightOverview);
   GetRoi( left,top,width,height);
end;

macro 'Overview[O]'
Begin
  info;
  PicSize;
  MakeStack;
  ScaleWindow;

end;

macro 'Show Selection[S]'
var widthR,heightR:integer;

begin

  GetRoi(left,top,widthR,heightR);

  left:=left/widthRp;
  top:=top/heightRp;

  Choosepic(OverViewStack);
  chooseSlice(1);SelectAll;copy;ChooseSlice(2);paste;
  GetPicSize(width,height);

  widthR:=widthR/widthRp*width;
  heightR:=heightR/heightRp*height;

  left:=width*left;
  top:=height*top;

  MakeRoi(left,top,widthR,heightR);
  Duplicate('Temp'); 
  factor:=width/widthR;
  ScaleandRotate(factor,factor,0);
  SelectAll;copy;dispose;SelectWindow('Temp');dispose;
  Choosepic(OverViewStack);Paste;KillROi;
  selectPic(OverviewWindow);
end;

Macro 'Restore Roi [R]';
begin restoreRoi; end;

Macro 'Dispose[D]';
begin dispose;end;

{----------------------------------------------- MACRO
----------------------------------------------}


>-----Original Message-----
>From:	j.gregory [SMTP:ort056@abdn.ac.uk]
>Sent:	19. august 1999 10:37
>To:	nih-image@io.ece.drexel.edu
>Subject:	Re: jpeg images + scaling in Scion
>
>Hi Lil,
>
>I hope this helps...
>
>Resize your window to the size you want and then from the options menu choose
>'scale to fit window'.   The image doesn't always look too good on the 
>screen, but at least you can see the whole image.
>
>Jenny Gregory
>
>
>> Hi,
>> 
>> 	Thanks to all of you who sent suggestions about image conversion.
>> You were very helpful and kind.
>> 
>> 	The new user has another problem.
>> 
>> 	I took the advice of several of you and am using Photoshop to
>> convert jpeg images to tiff so that I can use the Scion program.  The
>> images appear fine.  When I open the converted file in Scion the window
>> takes up all of my screen but only shows the upper left one quarter or
>> less of my image.  Is there a way to scroll the picture or to reduce the
>> size?  The "maginifying glass" only enlarges it.  Anything else I have
>> tried changes the color/hues and not the size.  
>> 
>> 	Thank you for your suggestions.
>> 
>> TTFN,
>> Lill
>> 
>> Lill Becker
>> Department of Biology
>> Florida International University
>> Miami, FL  33199   USA
>> 
>> 	*******************************************
>> 	*Are science and magic mutually exclusive?*
>> 	*******************************************
>> 
>
>
>


From nih-image-request@io.ece.drexel.edu Thu Aug 19 12:57 EDT 1999
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Unsubscribe please



nih-image@io.ece.drexel.edu writes:
>------------------------------
>
>Content-Type: text/plain
>
>nih-image-d Digest				Volume 99 : Issue 189
>
>Today's Topics:
>  Re: crop and save under extended nam  [ "Jeremy Brown"
><jeremy.brown2@ed.ac ]
>  Will LG-3 card work with 7100/80 upg  [ Jen-Wei Lin
><jenwelin@bio.bu.edu> ]
>  Re: Will LG-3 card work with 7100/80  [ Ben Elkin <elk@igb.fhg.de> ]
>  zoom video optic lens/digital camera  [ Kathleen Annikki Moore
><moorekat@ha ]
>  jpeg images                           [ lillian c becker
><lbecke01@fiu.edu> ]
>  Re: jpeg images + scaling in Scion    [ "j.gregory" <ort056@abdn.ac.uk>
>]
>
>------------------------------
>
>Date: Wed, 18 Aug 1999 12:24:29 +0100
>From: "Jeremy Brown" <jeremy.brown2@ed.ac.uk>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: crop and save under extended name?
>Message-Id: <199908181124.MAA19221@holyrood.ed.ac.uk>
>Content-type: text/plain; charset="ISO-8859-1"
>Content-Transfer-Encoding: 8bit
>
>Try the following,
>
>
>will save as BlahBlah.blah.small
>
>Macro '[C] Crop and Save'
>Var
>Name,wPath,FullPath:string;
>left,top,width,height:Integer;
>begin
>GetRoi(left,top,width,height);
>wPath:= GetPath('window'); name:= WindowTitle;
>FullPath:= concat(wPath, name,);
>SaveAs(FullPath,'.Small');
>Dispose;
>repeat;
>Open('any');
>MakeROI(left,top,width,height);
>wPath:= GetPath('window'); name:= WindowTitle;
>FullPath:= concat(wPath, name,);
>SaveAs(FullPath,'.Small');
>Dispose;
>until button;
>end;
>
>Jeremy
>
>****************************************
>Jeremy Brown
>Research Fellow
>Department of Veterinary Clinical Studies
>Royal (Dick) School of Veterinary Studies
>Easter Bush Veterinary Centre
>Easter Bush
>Roslin
>Midlothian
>EH25 9RG
>Scotland
>UK
>****************************************
>
>
>
>----------
>>From: Ludger Offerhaus <ljo@gfz-potsdam.de>
>>To: nih-image@io.ece.drexel.edu
>>Subject: crop and save under extended name?
>>Date: Wed, Aug 18, 1999, 10:59 am
>>
>
>> Dear imagers!
>>
>> The questions sounds simple to me, but I seem unable to find the answer
>in
>> my manuals.
>>
>> How do I crop a single image and save it under a modified version of the
>> old file name?
>> So e.g. file <monster01.tif> would become <small monster01.tif>
>>
>> If I use Duplicate ('window Title') all I seem to be able to do is
>enter a
>> completely new name, which is a bit of a nuisance, as I want to process
>> tens of files.
>>
>> Thanks in advance!
>> best regards
>> Ludger
>>
>>
>> --
>> Ludger Offerhaus
>> GeoForschungsZentrum Potsdam
>> Telegrafenberg, 14473 Potsdam, Duitsland
>> Tel: +49 (0)331 288 1326 / 1390
>> of (ook awap): 030 32 60 55 68
>> ---
>> ... aan een boom *zo* volgeladen / mist men n, twee pruimpjes niet ...
>> ---
>>
>> 
>
>------------------------------
>
>Date: Wed, 18 Aug 1999 11:22:45 -0400
>From: Jen-Wei Lin <jenwelin@bio.bu.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Will LG-3 card work with 7100/80 upgraded to G3?
>Message-Id: <l03130303b3e07e99aed9@[128.197.80.179]>
>Content-Type: text/plain; charset="us-ascii"
>
>Such is the pain with upgrades.  So we have this old LG-3 card in a
>7100/80.  Has anyone tried to upgrade the computer w/ G3 card and get the
>card to work?  If you do, please also provie info on the Mac OS and NIH
>imaging versions you are using w/ it.
>Thanks in advance.
>
>Jen-Wei
>
>Jen-Wei Lin, Ph.D.
>Biology
>Boston University
>5 Cummington St.
>Boston, MA 02215
>
>TEL:617-353-3443 or -3444
>FAX: 617-353-6340
>
>------------------------------
>
>Date: Wed, 18 Aug 1999 17:49:17 +0200
>From: Ben Elkin <elk@igb.fhg.de>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Will LG-3 card work with 7100/80 upgraded to G3?
>Message-Id: <l03130300b3e0860775d6@[129.233.21.143]>
>Content-Type: text/plain; charset="us-ascii"
>
>>Such is the pain with upgrades.  So we have this old LG-3 card in a
>>7100/80.  Has anyone tried to upgrade the computer w/ G3 card and get the
>>card to work?  If you do, please also provie info on the Mac OS and NIH
>>imaging versions you are using w/ it.
>>Thanks in advance.
>>
>>Jen-Wei
>
>Yes, it works - no problems at all. Currently we have Mac OS 8.6 and NIH
>Image 1.61.
>
>Ben Elkin
>
>=======================================
>elk@igb.fhg.de
>
>http://www.igb.fhg.de/GVT/
>
>Fraunhofer Institute for Interfacial Engineering and Biotechnology
>                    (fuer Grenzflaechen und Bioverfahrenstechnik)
>
>Nobelstr. 12    D-70569 Stuttgart    Germany
>
>Tel. +49 - 711 - 970-4144, -4161
>Fax                 -4200
>
>------------------------------
>
>Date: 	Wed, 18 Aug 1999 12:18:20 -1000
>From: Kathleen Annikki Moore <moorekat@hawaii.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: zoom video optic lens/digital camera?
>Message-ID: <Pine.GSO.4.10.9908181210470.27529-100000@uhunix5>
>Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>Is a zoom video optic lens ( such as used for industrial inspections) with
>magnification range at the monitor of 3.5X to 1350X mounted directly to
>digital camera (with copy stand/optical lights and lower stage area
>accessories etc) adequate for image processing(macro and microscopic).
>Also, I looked in archive at Pixera cameras mixed reviews.  Is there a
>digital camera $1000-$2000 that tethers to powerbook, macs that could be
>used for microscopic image processing yet.  Thank you for any help.
>
>Kathleen Moore
>
>------------------------------
>
>Date: Wed, 18 Aug 1999 18:30:50 -0400 (EDT)
>From: lillian c becker <lbecke01@fiu.edu>
>To: Jonathan WISCO <jjwisco@cajal-1.bu.edu>
>cc: nih-image <nih-image@io.ece.drexel.edu>
>Subject: jpeg images
>Message-ID: <Pine.SOL.3.96.990818182450.23046B-100000@solix4-64>
>Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>Hi,
>
>	Thanks to all of you who sent suggestions about image conversion.
>You were very helpful and kind.
>
>	The new user has another problem.
>
>	I took the advice of several of you and am using Photoshop to
>convert jpeg images to tiff so that I can use the Scion program.  The
>images appear fine.  When I open the converted file in Scion the window
>takes up all of my screen but only shows the upper left one quarter or
>less of my image.  Is there a way to scroll the picture or to reduce the
>size?  The "maginifying glass" only enlarges it.  Anything else I have
>tried changes the color/hues and not the size.  
>
>	Thank you for your suggestions.
>
>TTFN,
>Lill
>
>Lill Becker
>Department of Biology
>Florida International University
>Miami, FL  33199   USA
>
>	*******************************************
>	*Are science and magic mutually exclusive?*
>	*******************************************
>
>------------------------------
>
>Date: Thu, 19 Aug 1999 09:36:53 +0100 (BST)
>From: "j.gregory" <ort056@abdn.ac.uk>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: jpeg images + scaling in Scion
>Message-ID: <SIMEON.9908190953.A@pc10.surg.abdn.ac.uk>
>Content-Type: TEXT/PLAIN; CHARSET=US-ASCII
>
>Hi Lil,
>
>I hope this helps...
>
>Resize your window to the size you want and then from the options menu
>choose 
>'scale to fit window'.   The image doesn't always look too good on the 
>screen, but at least you can see the whole image.
>
>Jenny Gregory
>
>
>> Hi,
>> 
>> 	Thanks to all of you who sent suggestions about image conversion.
>> You were very helpful and kind.
>> 
>> 	The new user has another problem.
>> 
>> 	I took the advice of several of you and am using Photoshop to
>> convert jpeg images to tiff so that I can use the Scion program.  The
>> images appear fine.  When I open the converted file in Scion the window
>> takes up all of my screen but only shows the upper left one quarter or
>> less of my image.  Is there a way to scroll the picture or to reduce the
>> size?  The "maginifying glass" only enlarges it.  Anything else I have
>> tried changes the color/hues and not the size.  
>> 
>> 	Thank you for your suggestions.
>> 
>> TTFN,
>> Lill
>> 
>> Lill Becker
>> Department of Biology
>> Florida International University
>> Miami, FL  33199   USA
>> 
>> 	*******************************************
>> 	*Are science and magic mutually exclusive?*
>> 	*******************************************
>> 
>
>--------------------------------
>End of nih-image-d Digest V99 Issue #189
>****************************************



Elizabeth Stillwell
Department of Cell Biology
1648 Pierce Drive
Emory University
Atlanta, GA 30030

email: estillw@emory.edu
           estillw@learnlink.emory.edu
  
phone:404-727-0445
FAX:   404-727-6256


From nih-image-d-request@io.ece.drexel.edu Thu Aug 19 20:50 EDT 1999
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	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA23977;
	Thu, 19 Aug 1999 20:50:16 -0400 (EDT)
Date: Thu, 19 Aug 1999 20:50:16 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #190
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 190

Today's Topics:
  RE: jpeg images + scaling in Scion    [ Gary Chinga <gary.chinga@pfi.no> ]
  unsubscribe                           [ estillw@learnlink.emory.edu (Elizab ]
  Unidentified subject!                 [ tmcmanus@zeiss.com ]

------------------------------

Date: Thu, 19 Aug 1999 11:31:53 +0200
From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: jpeg images + scaling in Scion
Message-ID: <c=NO%a=_%p=pfi%l=PFINT1-990819093153Z-1245@pfint1.pfi.no>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

 I wrote a macro that let you see the whole image in a small 'overview'
window and then choose the region you want to see in the original image.
When using the macro open the original image, then use 'Overview [O]'
and move the ROI in the new OverView-window to the position you want to
see and choose 'Show Selection [S]'. If you dissable the ROI, use
'Restore Roi' to make a new selection, otherwise you will get an error
message.

The macro is slow, maybe someone in the list could take a look and
improve it.

Anyway, I hope this macro will be useful for you.

Gary.
------------------------------------------------------------------
Gary Chinga
PhD student
The Norwegian University of Science and Technology
Dept. of Chem. Engineering
Sem Saelandsv. 4
Trondheim
N7034 Norway
Direct line : +47 73550537
Fax: +47 73594080
email: gary.chinga@pfi.no


{----------------------------------------MACRO
-------------------------------------------}

var factor:real;
      OverviewStack,OverViewWindow,
      left,top,width,height,
      widthOverview,heightOverview
      widthRP,heightRP:integer;

Procedure Info;
begin
  widthOverview:=120;
end;  


Procedure PicSize;
Begin
   GetPicSize(width,height);
   factor:=250/width;
end;


Procedure MakeStack;
begin
  SelectAll;Copy; Dispose;
  SetNewSize(width,height);
  MakeNewStack('OverviewStack');Paste;
  AddSlice; Paste;
  OverViewStack:=PidNumber;
end;

procedure ScaleWindow;


begin
   if PidExists(OverviewWindow) then begin
      selectwindow('OverView');dispose;
   end;
   SetScaling('New Window,bilinear');
   ScaleandRotate(factor,factor,0);
   GetpicSize(widthRP,heightRP);
   SelectAll;Copy;Dispose;
   setNewSize(widthRP,heightRP);
   MakeNewWindow('OverView');Paste;
  
   OverviewWindow:=Pidnumber;
   heightOverview:=height/width*widthOverview;
   MakeRoi(0,0,widthOverview,heightOverview);
   GetRoi( left,top,width,height);
end;

macro 'Overview[O]'
Begin
  info;
  PicSize;
  MakeStack;
  ScaleWindow;

end;

macro 'Show Selection[S]'
var widthR,heightR:integer;

begin

  GetRoi(left,top,widthR,heightR);

  left:=left/widthRp;
  top:=top/heightRp;

  Choosepic(OverViewStack);
  chooseSlice(1);SelectAll;copy;ChooseSlice(2);paste;
  GetPicSize(width,height);

  widthR:=widthR/widthRp*width;
  heightR:=heightR/heightRp*height;

  left:=width*left;
  top:=height*top;

  MakeRoi(left,top,widthR,heightR);
  Duplicate('Temp'); 
  factor:=width/widthR;
  ScaleandRotate(factor,factor,0);
  SelectAll;copy;dispose;SelectWindow('Temp');dispose;
  Choosepic(OverViewStack);Paste;KillROi;
  selectPic(OverviewWindow);
end;

Macro 'Restore Roi [R]';
begin restoreRoi; end;

Macro 'Dispose[D]';
begin dispose;end;

{----------------------------------------------- MACRO
----------------------------------------------}


>-----Original Message-----
>From:	j.gregory [SMTP:ort056@abdn.ac.uk]
>Sent:	19. august 1999 10:37
>To:	nih-image@io.ece.drexel.edu
>Subject:	Re: jpeg images + scaling in Scion
>
>Hi Lil,
>
>I hope this helps...
>
>Resize your window to the size you want and then from the options menu choose
>'scale to fit window'.   The image doesn't always look too good on the 
>screen, but at least you can see the whole image.
>
>Jenny Gregory
>
>
>> Hi,
>> 
>> 	Thanks to all of you who sent suggestions about image conversion.
>> You were very helpful and kind.
>> 
>> 	The new user has another problem.
>> 
>> 	I took the advice of several of you and am using Photoshop to
>> convert jpeg images to tiff so that I can use the Scion program.  The
>> images appear fine.  When I open the converted file in Scion the window
>> takes up all of my screen but only shows the upper left one quarter or
>> less of my image.  Is there a way to scroll the picture or to reduce the
>> size?  The "maginifying glass" only enlarges it.  Anything else I have
>> tried changes the color/hues and not the size.  
>> 
>> 	Thank you for your suggestions.
>> 
>> TTFN,
>> Lill
>> 
>> Lill Becker
>> Department of Biology
>> Florida International University
>> Miami, FL  33199   USA
>> 
>> 	*******************************************
>> 	*Are science and magic mutually exclusive?*
>> 	*******************************************
>> 
>
>
>

------------------------------

Date: Thu, 19 Aug 1999 12:31:50 -0400
From: estillw@learnlink.emory.edu (Elizabeth E. Stillwell)
To: nih-image@io.ece.drexel.edu
Cc: nih-image-d@io.ece.drexel.edu
Subject: unsubscribe
Message-id: <fc.00249f0f050659a13b9aca005b850a17.5065c28@learnlink.emory.edu>
Content-type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 8bit

Unsubscribe please



nih-image@io.ece.drexel.edu writes:
>------------------------------
>
>Content-Type: text/plain
>
>nih-image-d Digest				Volume 99 : Issue 189
>
>Today's Topics:
>  Re: crop and save under extended nam  [ "Jeremy Brown"
><jeremy.brown2@ed.ac ]
>  Will LG-3 card work with 7100/80 upg  [ Jen-Wei Lin
><jenwelin@bio.bu.edu> ]
>  Re: Will LG-3 card work with 7100/80  [ Ben Elkin <elk@igb.fhg.de> ]
>  zoom video optic lens/digital camera  [ Kathleen Annikki Moore
><moorekat@ha ]
>  jpeg images                           [ lillian c becker
><lbecke01@fiu.edu> ]
>  Re: jpeg images + scaling in Scion    [ "j.gregory" <ort056@abdn.ac.uk>
>]
>
>------------------------------
>
>Date: Wed, 18 Aug 1999 12:24:29 +0100
>From: "Jeremy Brown" <jeremy.brown2@ed.ac.uk>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: crop and save under extended name?
>Message-Id: <199908181124.MAA19221@holyrood.ed.ac.uk>
>Content-type: text/plain; charset="ISO-8859-1"
>Content-Transfer-Encoding: 8bit
>
>Try the following,
>
>
>will save as BlahBlah.blah.small
>
>Macro '[C] Crop and Save'
>Var
>Name,wPath,FullPath:string;
>left,top,width,height:Integer;
>begin
>GetRoi(left,top,width,height);
>wPath:= GetPath('window'); name:= WindowTitle;
>FullPath:= concat(wPath, name,);
>SaveAs(FullPath,'.Small');
>Dispose;
>repeat;
>Open('any');
>MakeROI(left,top,width,height);
>wPath:= GetPath('window'); name:= WindowTitle;
>FullPath:= concat(wPath, name,);
>SaveAs(FullPath,'.Small');
>Dispose;
>until button;
>end;
>
>Jeremy
>
>****************************************
>Jeremy Brown
>Research Fellow
>Department of Veterinary Clinical Studies
>Royal (Dick) School of Veterinary Studies
>Easter Bush Veterinary Centre
>Easter Bush
>Roslin
>Midlothian
>EH25 9RG
>Scotland
>UK
>****************************************
>
>
>
>----------
>>From: Ludger Offerhaus <ljo@gfz-potsdam.de>
>>To: nih-image@io.ece.drexel.edu
>>Subject: crop and save under extended name?
>>Date: Wed, Aug 18, 1999, 10:59 am
>>
>
>> Dear imagers!
>>
>> The questions sounds simple to me, but I seem unable to find the answer
>in
>> my manuals.
>>
>> How do I crop a single image and save it under a modified version of the
>> old file name?
>> So e.g. file <monster01.tif> would become <small monster01.tif>
>>
>> If I use Duplicate ('window Title') all I seem to be able to do is
>enter a
>> completely new name, which is a bit of a nuisance, as I want to process
>> tens of files.
>>
>> Thanks in advance!
>> best regards
>> Ludger
>>
>>
>> --
>> Ludger Offerhaus
>> GeoForschungsZentrum Potsdam
>> Telegrafenberg, 14473 Potsdam, Duitsland
>> Tel: +49 (0)331 288 1326 / 1390
>> of (ook awap): 030 32 60 55 68
>> ---
>> ... aan een boom *zo* volgeladen / mist men n, twee pruimpjes niet ...
>> ---
>>
>> 
>
>------------------------------
>
>Date: Wed, 18 Aug 1999 11:22:45 -0400
>From: Jen-Wei Lin <jenwelin@bio.bu.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Will LG-3 card work with 7100/80 upgraded to G3?
>Message-Id: <l03130303b3e07e99aed9@[128.197.80.179]>
>Content-Type: text/plain; charset="us-ascii"
>
>Such is the pain with upgrades.  So we have this old LG-3 card in a
>7100/80.  Has anyone tried to upgrade the computer w/ G3 card and get the
>card to work?  If you do, please also provie info on the Mac OS and NIH
>imaging versions you are using w/ it.
>Thanks in advance.
>
>Jen-Wei
>
>Jen-Wei Lin, Ph.D.
>Biology
>Boston University
>5 Cummington St.
>Boston, MA 02215
>
>TEL:617-353-3443 or -3444
>FAX: 617-353-6340
>
>------------------------------
>
>Date: Wed, 18 Aug 1999 17:49:17 +0200
>From: Ben Elkin <elk@igb.fhg.de>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Will LG-3 card work with 7100/80 upgraded to G3?
>Message-Id: <l03130300b3e0860775d6@[129.233.21.143]>
>Content-Type: text/plain; charset="us-ascii"
>
>>Such is the pain with upgrades.  So we have this old LG-3 card in a
>>7100/80.  Has anyone tried to upgrade the computer w/ G3 card and get the
>>card to work?  If you do, please also provie info on the Mac OS and NIH
>>imaging versions you are using w/ it.
>>Thanks in advance.
>>
>>Jen-Wei
>
>Yes, it works - no problems at all. Currently we have Mac OS 8.6 and NIH
>Image 1.61.
>
>Ben Elkin
>
>=======================================
>elk@igb.fhg.de
>
>http://www.igb.fhg.de/GVT/
>
>Fraunhofer Institute for Interfacial Engineering and Biotechnology
>                    (fuer Grenzflaechen und Bioverfahrenstechnik)
>
>Nobelstr. 12    D-70569 Stuttgart    Germany
>
>Tel. +49 - 711 - 970-4144, -4161
>Fax                 -4200
>
>------------------------------
>
>Date: 	Wed, 18 Aug 1999 12:18:20 -1000
>From: Kathleen Annikki Moore <moorekat@hawaii.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: zoom video optic lens/digital camera?
>Message-ID: <Pine.GSO.4.10.9908181210470.27529-100000@uhunix5>
>Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>Is a zoom video optic lens ( such as used for industrial inspections) with
>magnification range at the monitor of 3.5X to 1350X mounted directly to
>digital camera (with copy stand/optical lights and lower stage area
>accessories etc) adequate for image processing(macro and microscopic).
>Also, I looked in archive at Pixera cameras mixed reviews.  Is there a
>digital camera $1000-$2000 that tethers to powerbook, macs that could be
>used for microscopic image processing yet.  Thank you for any help.
>
>Kathleen Moore
>
>------------------------------
>
>Date: Wed, 18 Aug 1999 18:30:50 -0400 (EDT)
>From: lillian c becker <lbecke01@fiu.edu>
>To: Jonathan WISCO <jjwisco@cajal-1.bu.edu>
>cc: nih-image <nih-image@io.ece.drexel.edu>
>Subject: jpeg images
>Message-ID: <Pine.SOL.3.96.990818182450.23046B-100000@solix4-64>
>Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>Hi,
>
>	Thanks to all of you who sent suggestions about image conversion.
>You were very helpful and kind.
>
>	The new user has another problem.
>
>	I took the advice of several of you and am using Photoshop to
>convert jpeg images to tiff so that I can use the Scion program.  The
>images appear fine.  When I open the converted file in Scion the window
>takes up all of my screen but only shows the upper left one quarter or
>less of my image.  Is there a way to scroll the picture or to reduce the
>size?  The "maginifying glass" only enlarges it.  Anything else I have
>tried changes the color/hues and not the size.  
>
>	Thank you for your suggestions.
>
>TTFN,
>Lill
>
>Lill Becker
>Department of Biology
>Florida International University
>Miami, FL  33199   USA
>
>	*******************************************
>	*Are science and magic mutually exclusive?*
>	*******************************************
>
>------------------------------
>
>Date: Thu, 19 Aug 1999 09:36:53 +0100 (BST)
>From: "j.gregory" <ort056@abdn.ac.uk>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: jpeg images + scaling in Scion
>Message-ID: <SIMEON.9908190953.A@pc10.surg.abdn.ac.uk>
>Content-Type: TEXT/PLAIN; CHARSET=US-ASCII
>
>Hi Lil,
>
>I hope this helps...
>
>Resize your window to the size you want and then from the options menu
>choose 
>'scale to fit window'.   The image doesn't always look too good on the 
>screen, but at least you can see the whole image.
>
>Jenny Gregory
>
>
>> Hi,
>> 
>> 	Thanks to all of you who sent suggestions about image conversion.
>> You were very helpful and kind.
>> 
>> 	The new user has another problem.
>> 
>> 	I took the advice of several of you and am using Photoshop to
>> convert jpeg images to tiff so that I can use the Scion program.  The
>> images appear fine.  When I open the converted file in Scion the window
>> takes up all of my screen but only shows the upper left one quarter or
>> less of my image.  Is there a way to scroll the picture or to reduce the
>> size?  The "maginifying glass" only enlarges it.  Anything else I have
>> tried changes the color/hues and not the size.  
>> 
>> 	Thank you for your suggestions.
>> 
>> TTFN,
>> Lill
>> 
>> Lill Becker
>> Department of Biology
>> Florida International University
>> Miami, FL  33199   USA
>> 
>> 	*******************************************
>> 	*Are science and magic mutually exclusive?*
>> 	*******************************************
>> 
>
>--------------------------------
>End of nih-image-d Digest V99 Issue #189
>****************************************



Elizabeth Stillwell
Department of Cell Biology
1648 Pierce Drive
Emory University
Atlanta, GA 30030

email: estillw@emory.edu
           estillw@learnlink.emory.edu
  
phone:404-727-0445
FAX:   404-727-6256

------------------------------

Date: Thu, 19 Aug 1999 20:33:07 -0400
From: tmcmanus@zeiss.com
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-ID: <00081B3A.C21388@zeiss.com>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
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     SUBSCRIBE

--------------------------------
End of nih-image-d Digest V99 Issue #190
****************************************

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From nih-image-request@io.ece.drexel.edu Fri Aug 20 03:18 EDT 1999
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Date: Fri, 20 Aug 1999 09:09:42 +0100
To: nih-image@io.ece.drexel.edu
From: Lucas Bickel <bickel@mix.ch>
Subject: Re: G3 and Scion LG-3 
In-Reply-To: <199908181000.GAA21402@io.ece.drexel.edu>
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Hi Ralf

I was using exactly that setup for about two months and I can only recomend
it. The G3 is really fast and has no problem handling the LG-3.

Lucas

>We would like to buy a new Mac ("blue" G3).
>Is there any problem using our old LG-3 Frame Grabber (PCI, Rev B) with
>this G3?


From nih-image-request@io.ece.drexel.edu Fri Aug 20 05:18 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: "Dr G. R. Coulton [bs_mp]" <g.coulton@ic.ac.uk>
Subject: 11th International Congress of Histochemistry and
  Cytochemistry (ICHC 2000) 
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Dear All,

11th International Congress of Histochemistry and Cytochemistry (ICHC
2000), 3-8th Sept. 2000, York, UK.

Our web-site problem is now solved so please take a moment to visit the
site at http://www.med.ic.ac.uk/external/ichc_2000

Best wishes

Gary
Dr. Gary Coulton
Molecular Pathology
Division of Biomedical Sciences
Imperial College School of Medicine
The Sir Alexander Fleming Building
South Kensington
London SW7 2AZ

tel 0044 (0)171 594 3190
fax 0044 (0)171 594 3022

e-mail g.coulton@ic.ac.uk

-------------------------------------
Announcing the 11th International Congress of Histochemistry and
Cytochemistry (ICHC 2000)

"Understanding Biocomplexity: The Post-Genome Challenge"

September 3-8, 2000, York, United Kingdom

ICHC 2000 will comprise 27 symposia addressing the latest developments and
applications of histochemistry and cytochemistry in the life sciences
including medicine.

SPEAKERS CONFIRMED (so far)
Lance Liotta (Bethesda)
Roger Tsien (La Jolla)
Dennis Noble (Oxford)
Jonathon Slack (Bath)
Angus Lamond (Dundee)
Johannes hegemann (Dusseldorf)
Paul Nakane (Mountain View)
Fre Bosman (Lausanne)
Margaret Buckingham (Paris)
John Couchman (Alabama)
Jim Coull (Boston)
Roel van Driel (Amsterdam)
David Eppel (Pacific Grove)
Reinhart Gossrau (Berlin)
Martin Green (Bebington)
Tom Just (Copenhagen)
Jeff Lichtman (St. Louis)
Joseph Mazurkiewicz (Albany)
Peter Nielsen (Copenhagen)
John O'Leary (Dublin)
Dennis Baskin (Washington)
Ralf Paus (Berlin)
Francesco Ramirez (New York)
Jim Smith (London)
John Stegeman (Woods Hole)
Hans Tanke (Leiden)
Anthony Thody (Bradford)
David Vaux (Oxford)
Lars-Inge Larsson (Frederiksberg) 
Keith Miller (London)
Mike Grant (Manchester)
Martin Humphries (Manchester)
Paul Martin (London)
Peter Mathiessen (Burnham on Crouch)
David Hinton (Davis) 

For further details of the meeting and how to pre-register please visit our
web-site at http://www.med.ic.ac.uk/external/ichc_2000

Hope to see you there.


From nih-image-request@io.ece.drexel.edu Fri Aug 20 12:18 EDT 1999
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I know we have mentioned little hints like this many times before, but over
time it sometimes bears repeating. I'd like to suggest that when replying
to a message posted to the NIH-Image distribution list, please delete the
bulk of the message to which you are replying, especially if you are
receiving your messages in digest mode. It can indeed be helpful to
understand a reply if you can also see the original query, so keep what's
relevant, but we really don't have to scroll through an entire day
(sometimes more) of old posts, sometimes repeated several times after
multiple replies, to get to the new message. Just a suggestion to help make
the list function "cleaner"... Thanks!

David Morilak



David Morilak, Ph.D.
Dept of Pharmacology
Univ Texas Health Science Center
7703 Floyd Curl Drive
San Antonio, TX 78284-7764

ph: 210-567-4174
FAX: 210-567-4303
E-mail: morilak@uthscsa.edu
At Home: dmorilak@flash.net



From nih-image-request@io.ece.drexel.edu Fri Aug 20 16:24 EDT 1999
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Date: Fri, 20 Aug 1999 13:07:49 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: scaling question
Message-ID: <836310.3144143269@huginn.medicine.washington.edu>
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It sounds like the problem is related to having pixels that are not square.
Image allows you to set the scale and an aspect ratio. I fiddled with it
for quite a while before I figured it out a couple of years ago, and since
then have not done anything with it. It sounds like that may be your
problem.

Sorry that I have not dealt with this for such a long time that I can't
give you specific instructions.

DTL

--On Tue, Aug 17, 1999 3:01 PM +0000 Megan Ferguson
<megan_ferguson@hotmail.com> wrote:

> Hello,
> 
> I am using Image 1.62 to find the area of a black-and-white image of a
> leaf  that I digitized using a flatbed scanner and Photoshop software.
> When I set  the scale in Image using a horizontal scale bar, the
> calculated area is  148.62 cm2.  When I use a vertical scale bar on the
> same image to set the  scale, however, the calculated area is 116.09 cm2.
> I have tried the same  procedure on several different images and there is
> always a discrepancy  between the calculated areas.  Does anyone have any
> ideas of why I come up  with two very different areas depending on which
> axis I set the scale?
> 
> Thanks for your help.
> 
> Megan
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> .
> 
> 
> _______________________________________________________________
> Get Free Email and Do More On The Web. Visit http://www.msn.com
> 





From nih-image-d-request@io.ece.drexel.edu Sat Aug 21 06:18 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #191
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 191

Today's Topics:
  Re: G3 and Scion LG-3                 [ Lucas Bickel <bickel@mix.ch> ]
  11th International Congress of Histo  [ "Dr G. R. Coulton [bs_mp]" <g.coult ]
  please delete old text when replying  [ David Morilak <morilak@uthscsa.edu> ]
  Re: scaling question                  [ David Linker <dtlinker@u.washington ]

------------------------------

Date: Fri, 20 Aug 1999 09:09:42 +0100
From: Lucas Bickel <bickel@mix.ch>
To: nih-image@io.ece.drexel.edu
Subject: Re: G3 and Scion LG-3 
Message-Id: <3.0.6.32.19990820090942.0092e880@pop.mail.yahoo.com>
Content-Type: text/plain; charset="us-ascii"

Hi Ralf

I was using exactly that setup for about two months and I can only recomend
it. The G3 is really fast and has no problem handling the LG-3.

Lucas

>We would like to buy a new Mac ("blue" G3).
>Is there any problem using our old LG-3 Frame Grabber (PCI, Rev B) with
>this G3?

------------------------------

Date: Fri, 20 Aug 1999 09:59:24 +0100
From: "Dr G. R. Coulton [bs_mp]" <g.coulton@ic.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: 11th International Congress of Histochemistry and
  Cytochemistry (ICHC 2000) 
Message-Id: <3.0.3.32.19990820095924.00b47a10@icex4.cc.ic.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Dear All,

11th International Congress of Histochemistry and Cytochemistry (ICHC
2000), 3-8th Sept. 2000, York, UK.

Our web-site problem is now solved so please take a moment to visit the
site at http://www.med.ic.ac.uk/external/ichc_2000

Best wishes

Gary
Dr. Gary Coulton
Molecular Pathology
Division of Biomedical Sciences
Imperial College School of Medicine
The Sir Alexander Fleming Building
South Kensington
London SW7 2AZ

tel 0044 (0)171 594 3190
fax 0044 (0)171 594 3022

e-mail g.coulton@ic.ac.uk

-------------------------------------
Announcing the 11th International Congress of Histochemistry and
Cytochemistry (ICHC 2000)

"Understanding Biocomplexity: The Post-Genome Challenge"

September 3-8, 2000, York, United Kingdom

ICHC 2000 will comprise 27 symposia addressing the latest developments and
applications of histochemistry and cytochemistry in the life sciences
including medicine.

SPEAKERS CONFIRMED (so far)
Lance Liotta (Bethesda)
Roger Tsien (La Jolla)
Dennis Noble (Oxford)
Jonathon Slack (Bath)
Angus Lamond (Dundee)
Johannes hegemann (Dusseldorf)
Paul Nakane (Mountain View)
Fre Bosman (Lausanne)
Margaret Buckingham (Paris)
John Couchman (Alabama)
Jim Coull (Boston)
Roel van Driel (Amsterdam)
David Eppel (Pacific Grove)
Reinhart Gossrau (Berlin)
Martin Green (Bebington)
Tom Just (Copenhagen)
Jeff Lichtman (St. Louis)
Joseph Mazurkiewicz (Albany)
Peter Nielsen (Copenhagen)
John O'Leary (Dublin)
Dennis Baskin (Washington)
Ralf Paus (Berlin)
Francesco Ramirez (New York)
Jim Smith (London)
John Stegeman (Woods Hole)
Hans Tanke (Leiden)
Anthony Thody (Bradford)
David Vaux (Oxford)
Lars-Inge Larsson (Frederiksberg) 
Keith Miller (London)
Mike Grant (Manchester)
Martin Humphries (Manchester)
Paul Martin (London)
Peter Mathiessen (Burnham on Crouch)
David Hinton (Davis) 

For further details of the meeting and how to pre-register please visit our
web-site at http://www.med.ic.ac.uk/external/ichc_2000

Hope to see you there.

------------------------------

Date: Fri, 20 Aug 1999 11:00:59 -0500 (CDT)
From: David Morilak <morilak@uthscsa.edu>
To: nih-image@io.ece.drexel.edu
Subject: please delete old text when replying
Message-id: <l03130301b3e2e54448b2@[129.111.17.122]>
Content-type: text/plain; charset=us-ascii
Content-transfer-encoding: 7BIT

I know we have mentioned little hints like this many times before, but over
time it sometimes bears repeating. I'd like to suggest that when replying
to a message posted to the NIH-Image distribution list, please delete the
bulk of the message to which you are replying, especially if you are
receiving your messages in digest mode. It can indeed be helpful to
understand a reply if you can also see the original query, so keep what's
relevant, but we really don't have to scroll through an entire day
(sometimes more) of old posts, sometimes repeated several times after
multiple replies, to get to the new message. Just a suggestion to help make
the list function "cleaner"... Thanks!

David Morilak



David Morilak, Ph.D.
Dept of Pharmacology
Univ Texas Health Science Center
7703 Floyd Curl Drive
San Antonio, TX 78284-7764

ph: 210-567-4174
FAX: 210-567-4303
E-mail: morilak@uthscsa.edu
At Home: dmorilak@flash.net

------------------------------

Date: Fri, 20 Aug 1999 13:07:49 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: scaling question
Message-ID: <836310.3144143269@huginn.medicine.washington.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

It sounds like the problem is related to having pixels that are not square.
Image allows you to set the scale and an aspect ratio. I fiddled with it
for quite a while before I figured it out a couple of years ago, and since
then have not done anything with it. It sounds like that may be your
problem.

Sorry that I have not dealt with this for such a long time that I can't
give you specific instructions.

DTL

--On Tue, Aug 17, 1999 3:01 PM +0000 Megan Ferguson
<megan_ferguson@hotmail.com> wrote:

> Hello,
> 
> I am using Image 1.62 to find the area of a black-and-white image of a
> leaf  that I digitized using a flatbed scanner and Photoshop software.
> When I set  the scale in Image using a horizontal scale bar, the
> calculated area is  148.62 cm2.  When I use a vertical scale bar on the
> same image to set the  scale, however, the calculated area is 116.09 cm2.
> I have tried the same  procedure on several different images and there is
> always a discrepancy  between the calculated areas.  Does anyone have any
> ideas of why I come up  with two very different areas depending on which
> axis I set the scale?
> 
> Thanks for your help.
> 
> Megan
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> .
> 
> 
> _______________________________________________________________
> Get Free Email and Do More On The Web. Visit http://www.msn.com
> 

--------------------------------
End of nih-image-d Digest V99 Issue #191
****************************************

From nih-image-request@io.ece.drexel.edu Sat Aug 21 07:09 EDT 1999
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Date: Sat, 21 Aug 1999 12:47:17 +0200 (MET DST)
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Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
From: Enric Saiz <enric@icm.csic.es>
Subject: SCALING QUESTION. MEGAN FERGUSON
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Does anyone have any ideas of why I come up
with two very different areas depending on which axis I set the scale?

Thanks for your help.

Megan

DEAR MEGAN,

I THINK THE PROBLEM IS DUE TO THE ASPECT RATIO OF THE CAMERA/SCANNER, THAT
IS USUALLY NOT 1.
YOU MUST FIRST SCALE IMAGE HORIZONTALLY. THEN, USING THAT CALIBRATION,
MESURE THE SAME SCALE PLACED VERTICALLY. MAKE THE RATIO BETWEEN THE VALUE
YOU SHOULD GET (FOR INSTANCE 1) AND THE VALUE YOU GET (FOR INSTANCE, 0.8).
THAT IS THE ASPECT RATIO. GO BACK TO THE SETTING SCALE MENU, INTRODUCE THE
CALCULATED ASPECT RATIO AND SAVE THE FILE. TO MEAKE SURE YOU HAVE DONE IT
CORRECTLY, OPEN THE CALIBRATION FILE AND REPEAT THE MEASUREMENT OF THE
SCALE HORIZONTALLY AND VERTICALLY. IT SHOULD PROVIDE YOU WITH THE SAME
VALUE IN BOTH CASES. IF NOT, COMPUTE THE ASPECT RATIO THE OTHER WAY (I.E.
1/0.8). I ALWAYS MIX UP THE RIGHT WAY!
HOPE IT HELPS
ENRIC




******************************
Enric Saiz
Institut de Cincies del Mar, CSIC
Plaa del Mar s/n
08039 Barcelona
Catalonia, SPAIN

PLEASE NOTE NEW PHONE NUMBERS!!!

Phone: +34+93+2216416
Fax: +34+93+2217340

Visit our Web Page
http://www.icm.csic.es/bio/index_bio.html
******************************



From nih-image-request@io.ece.drexel.edu Sat Aug 21 20:40 EDT 1999
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Date: Sat, 21 Aug 1999 20:36:21 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: 24 bit colour movies
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 >
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>Using Scion mMage I can create a 24-bit Indexed colour Image, but am not
>able to do further manipulations to this image - ie cropping, cutting
>pasteing, stacking, let alone make movies. Does anyone have any
>suggestions how I can make a 24-bit colour movie?

My new ImageJ program at http://rsb.info.nih.gov/ij/ can crop, cut, paste, filter, stack and animate 24-bit RGB images.

-wayne


From nih-image-d-request@io.ece.drexel.edu Sun Aug 22 06:20 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #192
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------------------------------

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nih-image-d Digest				Volume 99 : Issue 192

Today's Topics:
  SCALING QUESTION. MEGAN FERGUSON      [ Enric Saiz <enric@icm.csic.es> ]
  Re: 24 bit colour movies              [ Wayne Rasband <wayne@codon.nih.gov> ]

------------------------------

Date: Sat, 21 Aug 1999 12:47:17 +0200 (MET DST)
From: Enric Saiz <enric@icm.csic.es>
To: nih-image@io.ece.drexel.edu
Subject: SCALING QUESTION. MEGAN FERGUSON
Message-Id: <l03020900b3e44eac42c7@[193.145.218.132]>
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Does anyone have any ideas of why I come up
with two very different areas depending on which axis I set the scale?

Thanks for your help.

Megan

DEAR MEGAN,

I THINK THE PROBLEM IS DUE TO THE ASPECT RATIO OF THE CAMERA/SCANNER, THAT
IS USUALLY NOT 1.
YOU MUST FIRST SCALE IMAGE HORIZONTALLY. THEN, USING THAT CALIBRATION,
MESURE THE SAME SCALE PLACED VERTICALLY. MAKE THE RATIO BETWEEN THE VALUE
YOU SHOULD GET (FOR INSTANCE 1) AND THE VALUE YOU GET (FOR INSTANCE, 0.8).
THAT IS THE ASPECT RATIO. GO BACK TO THE SETTING SCALE MENU, INTRODUCE THE
CALCULATED ASPECT RATIO AND SAVE THE FILE. TO MEAKE SURE YOU HAVE DONE IT
CORRECTLY, OPEN THE CALIBRATION FILE AND REPEAT THE MEASUREMENT OF THE
SCALE HORIZONTALLY AND VERTICALLY. IT SHOULD PROVIDE YOU WITH THE SAME
VALUE IN BOTH CASES. IF NOT, COMPUTE THE ASPECT RATIO THE OTHER WAY (I.E.
1/0.8). I ALWAYS MIX UP THE RIGHT WAY!
HOPE IT HELPS
ENRIC




******************************
Enric Saiz
Institut de Cincies del Mar, CSIC
Plaa del Mar s/n
08039 Barcelona
Catalonia, SPAIN

PLEASE NOTE NEW PHONE NUMBERS!!!

Phone: +34+93+2216416
Fax: +34+93+2217340

Visit our Web Page
http://www.icm.csic.es/bio/index_bio.html
******************************

------------------------------

Date: Sat, 21 Aug 1999 20:36:21 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: 24 bit colour movies
Message-Id: <3.0.5.32.19990821203621.00a0a730@codon.nih.gov>
Content-Type: text/plain; charset="us-ascii"

>Using Scion mMage I can create a 24-bit Indexed colour Image, but am not
>able to do further manipulations to this image - ie cropping, cutting
>pasteing, stacking, let alone make movies. Does anyone have any
>suggestions how I can make a 24-bit colour movie?

My new ImageJ program at http://rsb.info.nih.gov/ij/ can crop, cut, paste, filter, stack and animate 24-bit RGB images.

-wayne

--------------------------------
End of nih-image-d Digest V99 Issue #192
****************************************

From nih-image-request@io.ece.drexel.edu Mon Aug 23 01:42 EDT 1999
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Hi all,

 I have been using Scion Image Beta for a while for TIF images imported
from other
systems. Recently, I have installed on my Pentium II pc the
DataTranslation DT3155
(PIC frame grabber) with a Panasonic video camera. My pc runs under
Windows98. And a small program from DT called Acq2hst is installed,
which
runs sort of fine with GlobalLab, a little bit dated program.
 I'd like to know whether I could run my frame grabber DT3155 with some
additional programs or drivers. At this moment, the image acquisition of
the Scion Image would not work for some reason I do not know.

Thanks in advance,

Jong Kim
jongkim8@shinbiro.com


From nih-image-request@io.ece.drexel.edu Mon Aug 23 05:23 EDT 1999
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                   NIH-image Mailing List Help 
                   ---------------------------
     


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Archive
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Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

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0)  Remember that Archive is case-sensitive.
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then use Unix metacharacters to get more than one file. * matches any string.
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         get latest/*           all 50
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8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
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Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
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--


From nih-image-d-request@io.ece.drexel.edu Tue Aug 24 06:15 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 193

Today's Topics:
  DT3155 and ScionImage                 [ "jjkim" <jjkim@mm.ewha.ac.kr> ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]

------------------------------

Date: Mon, 23 Aug 1999 14:24:13 +0900
From: "jjkim" <jjkim@mm.ewha.ac.kr>
To: nih-image@io.ece.drexel.edu
Subject: DT3155 and ScionImage
Message-ID: <37C0DAFC.9AC48313@mm.ewha.ac.kr>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi all,

 I have been using Scion Image Beta for a while for TIF images imported
from other
systems. Recently, I have installed on my Pentium II pc the
DataTranslation DT3155
(PIC frame grabber) with a Panasonic video camera. My pc runs under
Windows98. And a small program from DT called Acq2hst is installed,
which
runs sort of fine with GlobalLab, a little bit dated program.
 I'd like to know whether I could run my frame grabber DT3155 with some
additional programs or drivers. At this moment, the image acquisition of
the Scion Image would not work for some reason I do not know.

Thanks in advance,

Jong Kim
jongkim8@shinbiro.com

------------------------------

Date: Mon, 23 Aug 1999 05:05:01 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199908230905.FAA06788@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
                   ---------------------------
     


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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

--------------------------------
End of nih-image-d Digest V99 Issue #193
****************************************

From nih-image-request@io.ece.drexel.edu Tue Aug 24 21:57 EDT 1999
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From: kardi@plan.civil.tohoku.ac.jp
Date: Wed, 25 Aug 1999 10:43:53 +0900 (JST)
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Is there any body know how to record XY coordinates and slice number of a
stack in one result?
Thanks.
Kardi Teknomo
kardi@plan.civil.tohoku.ac.jp


From nih-image-d-request@io.ece.drexel.edu Thu Aug 26 06:14 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 194

Today's Topics:
  SliceNumber                           [ kardi@plan.civil.tohoku.ac.jp ]

------------------------------

Date: Wed, 25 Aug 1999 10:43:53 +0900 (JST)
From: kardi@plan.civil.tohoku.ac.jp
To: nih-image@io.ece.drexel.edu
Subject: SliceNumber
Message-Id: <199908250143.KAA29132@plan.civil.tohoku.ac.jp>
Content-Type: text/plain; charset="us-ascii"

Is there any body know how to record XY coordinates and slice number of a
stack in one result?
Thanks.
Kardi Teknomo
kardi@plan.civil.tohoku.ac.jp

--------------------------------
End of nih-image-d Digest V99 Issue #194
****************************************

From nih-image-request@io.ece.drexel.edu Thu Aug 26 08:07 EDT 1999
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From: Peter Bramlage <Peter.Bramlage@rz.hu-berlin.de>
Subject: Camera
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Dear imagers,

Does one of you know a good quality color camera to use on our fluorescence
microscope (Leica)? We don't need a high temporal but a good spatial
resolution.

Any advice is appreciated.

Peter




From nih-image-request@io.ece.drexel.edu Thu Aug 26 14:40 EDT 1999
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Message-ID: <709CDBE6CA13D311B4DF0008C7EAD0C62AF011@phsexch13.mgh.harvard.edu>
From: "Carmean, Rebecca" <RCARMEAN@PARTNERS.ORG>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Date: Thu, 26 Aug 1999 14:22:01 -0400
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I was wondering if someone could tell me what kind of scanner is recommended
for scanning Phastgels and DNA gels. Thanks

RCARMEAN@PARTNERS.ORG
Massachusetts General Hospital
Charlestown, MA 02135
617-726-5740


From nih-image-request@io.ece.drexel.edu Thu Aug 26 17:16 EDT 1999
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As a newcomer to this list and the microscopy field, I am wondering how =
adequate NIH Image will be for my long-term confocal microscopy image =
analysis needs.  Rather than paying $$$ for fancy commercial software, I =
would like to get away with pay nothing and use NIH Image. In =
particular, if my microscopy needs stretch further beyond simply =
cropping or annotating images, can NIH Image conduct quantitative =
analyses such as automated object outlining, area quantitation, =
classification of different regions using multi-spectral image data, =
analysis of color/chromophore intensity/localization and frequency?? I =
would appreciate any feedback regarding this matter and advice from =
others' personal experience. My main concern is that NIH Image is not as =
quantitative apt as it may appear to me at first glance.

Thanks.

Hamza


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<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<P><FONT size=3D2>As a newcomer to this list and the microscopy field, I =
am=20
wondering how adequate NIH Image will be for my long-term </FONT><FONT=20
size=3D2>confocal microscopy image analysis needs.&nbsp; Rather than =
paying $$$=20
for fancy commercial software, I would like to get away with =
</FONT><FONT=20
size=3D2>pay nothing and use NIH Image. In particular, if my microscopy =
needs=20
stretch further beyond simply cropping or annotating </FONT><FONT =
size=3D2>images,=20
can NIH Image conduct quantitative analyses such as automated object =
outlining,=20
area quantitation, classification of different regions using =
multi-spectral=20
image data, analysis of color/chromophore intensity/localization and =
frequency??=20
I would appreciate any feedback regarding this matter and advice from =
others'=20
personal experience. My main concern is that NIH Image is not as =
quantitative=20
apt as it may appear to me at first glance.</FONT></P>
<DIV><FONT size=3D2>Thanks.</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>Hamza<BR></FONT></DIV></BODY></HTML>

------=_NextPart_000_003C_01BEEFE4.54722020--


From nih-image-request@io.ece.drexel.edu Thu Aug 26 17:56 EDT 1999
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References: <199908250143.KAA29132@plan.civil.tohoku.ac.jp>
Date: Thu, 26 Aug 1999 17:38:42 -0400
To: nih-image@io.ece.drexel.edu
From: "Gloria.Hoffman" <gehoffma@umaryland.edu>
Subject: Re: Camera
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My experience is that there isn't a good color camera that is both
sensitive to low light and color to begin with. HOWEVER, there are now
excellent ways of having both color and low light capabilities. What is
done is to use cooled black and white cameras that offer great resolution
and then import them into color channels just as confocal microscopes do.
For bright field conversions there are liquid crystal adaptors for these
camers and they will scan an image in red, greed and blue and then merge
the images for superb color rendition. The camera I use for this is the
Sensys camera by Photometrics. It is wonderful for everything! (and it is
pretty reasonable in price now.)

 >Dear imagers,
>
>Does one of you know a good quality color camera to use on our fluorescence
>microscope (Leica)? We don't need a high temporal but a good spatial
>resolution.
>
>Any advice is appreciated.
>
>Peter

**************************************************
"To doubt everything or to believe everything are
two equally convenient solutions; both dispense
with the necessity of reflection."
			H. Poincare
**************************************************
Gloria E. Hoffman, Ph.D.
Department of Anatomy and Neurobiology
685 W Baltimore St
Baltimore MD 21201
Phone 410 706-2438
Lab: 410 706-2440
Fax 410 706-2512
email gehoffma@umaryland.edu


From nih-image-d-request@io.ece.drexel.edu Fri Aug 27 06:15 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #195
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 195

Today's Topics:
  Camera                                [ Peter Bramlage <Peter.Bramlage@rz.h ]
  Unidentified subject!                 [ "Carmean, Rebecca" <RCARMEAN@PARTNE ]
  Unidentified subject!                 [ "Hamza Suria" <hsuria@rri.on.ca> ]
  Re: Camera                            [ "Gloria.Hoffman" <gehoffma@umarylan ]

------------------------------

Date: Thu, 26 Aug 1999 13:43:30 +0200
From: Peter Bramlage <Peter.Bramlage@rz.hu-berlin.de>
To: nih-image@io.ece.drexel.edu
Subject: Camera
Message-Id: <l03130300b3ead84a171e@[141.42.23.131]>
Content-Type: text/plain; charset="us-ascii"

Dear imagers,

Does one of you know a good quality color camera to use on our fluorescence
microscope (Leica)? We don't need a high temporal but a good spatial
resolution.

Any advice is appreciated.

Peter

------------------------------

Date: Thu, 26 Aug 1999 14:22:01 -0400
From: "Carmean, Rebecca" <RCARMEAN@PARTNERS.ORG>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Unidentified subject!
Message-ID: <709CDBE6CA13D311B4DF0008C7EAD0C62AF011@phsexch13.mgh.harvard.edu>
Content-Type: text/plain

I was wondering if someone could tell me what kind of scanner is recommended
for scanning Phastgels and DNA gels. Thanks

RCARMEAN@PARTNERS.ORG
Massachusetts General Hospital
Charlestown, MA 02135
617-726-5740

------------------------------

Date: Thu, 26 Aug 1999 16:59:16 -0400
From: "Hamza Suria" <hsuria@rri.on.ca>
To: <nih-image@io.ece.drexel.edu>
Subject: Unidentified subject!
Message-ID: <003f01bef005$dbacf300$866ef8ce@rri.on.ca>
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As a newcomer to this list and the microscopy field, I am wondering how =
adequate NIH Image will be for my long-term confocal microscopy image =
analysis needs.  Rather than paying $$$ for fancy commercial software, I =
would like to get away with pay nothing and use NIH Image. In =
particular, if my microscopy needs stretch further beyond simply =
cropping or annotating images, can NIH Image conduct quantitative =
analyses such as automated object outlining, area quantitation, =
classification of different regions using multi-spectral image data, =
analysis of color/chromophore intensity/localization and frequency?? I =
would appreciate any feedback regarding this matter and advice from =
others' personal experience. My main concern is that NIH Image is not as =
quantitative apt as it may appear to me at first glance.

Thanks.

Hamza


------=_NextPart_000_003C_01BEEFE4.54722020
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	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content=3D"text/html; charset=3Diso-8859-1" =
http-equiv=3DContent-Type>
<META content=3D"MSHTML 5.00.2314.1000" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<P><FONT size=3D2>As a newcomer to this list and the microscopy field, I =
am=20
wondering how adequate NIH Image will be for my long-term </FONT><FONT=20
size=3D2>confocal microscopy image analysis needs.&nbsp; Rather than =
paying $$$=20
for fancy commercial software, I would like to get away with =
</FONT><FONT=20
size=3D2>pay nothing and use NIH Image. In particular, if my microscopy =
needs=20
stretch further beyond simply cropping or annotating </FONT><FONT =
size=3D2>images,=20
can NIH Image conduct quantitative analyses such as automated object =
outlining,=20
area quantitation, classification of different regions using =
multi-spectral=20
image data, analysis of color/chromophore intensity/localization and =
frequency??=20
I would appreciate any feedback regarding this matter and advice from =
others'=20
personal experience. My main concern is that NIH Image is not as =
quantitative=20
apt as it may appear to me at first glance.</FONT></P>
<DIV><FONT size=3D2>Thanks.</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT size=3D2>Hamza<BR></FONT></DIV></BODY></HTML>

------=_NextPart_000_003C_01BEEFE4.54722020--

------------------------------

Date: Thu, 26 Aug 1999 17:38:42 -0400
From: "Gloria.Hoffman" <gehoffma@umaryland.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Camera
Message-Id: <v04011783b3eb6374fd80@[134.192.131.169]>
Content-Type: text/plain; charset="us-ascii"

My experience is that there isn't a good color camera that is both
sensitive to low light and color to begin with. HOWEVER, there are now
excellent ways of having both color and low light capabilities. What is
done is to use cooled black and white cameras that offer great resolution
and then import them into color channels just as confocal microscopes do.
For bright field conversions there are liquid crystal adaptors for these
camers and they will scan an image in red, greed and blue and then merge
the images for superb color rendition. The camera I use for this is the
Sensys camera by Photometrics. It is wonderful for everything! (and it is
pretty reasonable in price now.)

 >Dear imagers,
>
>Does one of you know a good quality color camera to use on our fluorescence
>microscope (Leica)? We don't need a high temporal but a good spatial
>resolution.
>
>Any advice is appreciated.
>
>Peter

**************************************************
"To doubt everything or to believe everything are
two equally convenient solutions; both dispense
with the necessity of reflection."
			H. Poincare
**************************************************
Gloria E. Hoffman, Ph.D.
Department of Anatomy and Neurobiology
685 W Baltimore St
Baltimore MD 21201
Phone 410 706-2438
Lab: 410 706-2440
Fax 410 706-2512
email gehoffma@umaryland.edu

--------------------------------
End of nih-image-d Digest V99 Issue #195
****************************************

From nih-image-request@io.ece.drexel.edu Fri Aug 27 08:58 EDT 1999
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From: rhawkes@mta.ca (Robert Hawkes)
Subject: NIH Image Capter with ATI Video Cards in Minitower Blue Macs?
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Is it possible to directly capture images into NIH Image from the ATI video
cards which come with current G3 Blue Minitower Macs?  I have looked at the
plug-in descriptions on the NIH Image www site, but don't see any that
sound like they are for this card.

Thanks,

Bob Hawkes
rhawkes@mta.ca



From nih-image-request@io.ece.drexel.edu Fri Aug 27 11:59 EDT 1999
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From: tmcmanus@zeiss.com
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Subject: CG-7 ?
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     If someone is using a CG-7 frame grabber can they acquire time lapse 
     color images and if so how?
     
     Thomas McManus


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Subject: nih-image-d Digest V99 #196
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 196

Today's Topics:
  NIH Image Capter with ATI Video Card  [ rhawkes@mta.ca (Robert Hawkes) ]
  CG-7 ?                                [ tmcmanus@zeiss.com ]

------------------------------

Date: Fri, 27 Aug 1999 09:41:06 -0400
From: rhawkes@mta.ca (Robert Hawkes)
To: nih-image@io.ece.drexel.edu
Subject: NIH Image Capter with ATI Video Cards in Minitower Blue Macs?
Message-Id: <v01540b05b3ec4419da22@[207.179.186.134]>
Content-Type: text/plain; charset="us-ascii"

Is it possible to directly capture images into NIH Image from the ATI video
cards which come with current G3 Blue Minitower Macs?  I have looked at the
plug-in descriptions on the NIH Image www site, but don't see any that
sound like they are for this card.

Thanks,

Bob Hawkes
rhawkes@mta.ca

------------------------------

Date: Fri, 27 Aug 1999 10:23:23 -0400
From: tmcmanus@zeiss.com
To: nih-image@io.ece.drexel.edu
Subject: CG-7 ?
Message-ID: <00084426.C21388@zeiss.com>
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     If someone is using a CG-7 frame grabber can they acquire time lapse 
     color images and if so how?
     
     Thomas McManus

--------------------------------
End of nih-image-d Digest V99 Issue #196
****************************************

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Date: Sat, 28 Aug 1999 10:29:31 -0400
To: nih-image@io.ece.drexel.edu
From: Lance Davidson <lad4x@virginia.edu>
Subject: Re: CG-7 ?
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While the CG-7 and Scion Image (ver. 1.62) can collect color images they
cannot produce a color stack. To work around this we save sequentially
numbered files and reassemble them into a timelapse with another program.

We are using a version of Scion Image and a camera-controlling Photoshop
plugin to collect time-lapse images with the CG-7 with the Dage-MTI DC330
camera. By simultaneously running Photoshop (with the camera controller) we
can set the gain etc. on screen. The following macro will collect a set of
color images as separate tif files. We then batch process the files with
photoshop actions and assemble the "color time-lapse" in Adobe Premiere.
The DC330 is a sort digital/video hybrid 3CCD camera using analog video to
pass a series of video frames which are assembled by Scion image into a
large format color image. 

Even though we've been able to make large format color timelapses we cannot
afford the hardware to play them (even a B&W G3 has its limits ... sigh).
The second macro demonstrates a mouse "button" driven collection of images
(i.e. for reassembly of histological sections).

Good luck,
Lance

{*************************************************************************
**************************************************************************
To ensure this macro runs correctly:
1. start capturing - center your animal.
2. Select the region of interest you want to cover with the time lapse.
3. Start the macro.
4. Fill in the dialog boxes --- store your stack in a responsible place.
5. When prompted, click on the spot where you want the timestamp
( the font style and size may be chosen beforehand from "options").

This macro allows timelapse collection with:
   live focus, 
   saves after every new slice, 
   positioning and customization of the timestamp, 
   average frames, and
   other things I've forgotten to mention.

Changed timelapse procedure to save single tiff files rather than stacks...
990811 added grab color images to files  - mouse driven...

See Lance Davidson (lad4x@virginia.edu) for details.
**************************************************************************}

var
    xpos, ypos: integer;
    firstclock, toggle :integer;
    textStamp: string;
    SleepToTicks : integer;
     nleft, nright, nwidth, nheight: integer;


procedure SleepUntilTicks;
{
}
var
    secs : integer;
begin
    while TickCount < SleepToTicks do begin
         secs := (TickCount - SleepToTicks) / 60;
         ShowMessage(secs);
         if button then begin
            if toggle = 1 then begin
                StartCapturing;
                toggle := 0;
            end;
            if toggle = 0 then begin
                StopCapturing;
                 toggle := 1;
            end;
         end;
    end;
    beep;
end;

procedure SleepUntilMouse;
{
}
begin
    while (NOT button) do begin
    end;
    beep;
end;


procedure StampMeOut;
{
}
var
  hours, minutes, seconds,year, month, day, dayofweek: integer;
begin
    GetTime(year, month, day, hours, minutes,seconds, dayofweek);

    if (firstclock = 1) then begin
          textStamp := GetString('Date, experimental conditions, etc.: ','');
          PutMessage('Click at desired text location...');
          repeat
             GetMouse(xpos,ypos);
          until Button;
          MoveTo(xpos,ypos);

          Write(textStamp,'  ',year, '-', month, '-', day, '  ', hours,
':', minutes, ':',seconds);

    end;
    if (firstclock = 0) then begin
        MoveTo(xpos,ypos);
        Write(hours,':',minutes,':',seconds);
     end;
     firstclock := 0;
end; {Time Stamps...}

procedure avtimelapse(nacc:integer, nFrames:integer, time:
integer,nfile:string) ;
{
}
var
    n, NewStack, Cam : integer;

    interval : integer;
begin
    Requiresversion(1.60);
    SetOption; Multiframes('highres chip',1,nacc);


    interval := 60 * time;
    SleepToTicks := TickCount+interval;
    for n := 1 to nFrames do begin
{
       the camera window should be up front...
}
        StampMeOut;
        SaveAs(n:3);
        Dispose;

        StartCapturing;
        if n < nFrames then SleepUntilTicks;
        SleepToTicks := TickCount+interval;
        StopCapturing;
        SetOption; Multiframes('highres chip',1,nacc);
    end;
    StampMeOut;
    SaveAs((n+1):3);
    Dispose;
end;

procedure colorgrabs(nacc:integer, nFrames:integer,nfile:string) ;
{
}
var
    n, NewStack, Cam : integer;

begin
    Requiresversion(1.60);
    SetOption; Multiframes('none',1,nacc);


    for n := 1 to nFrames do begin
{
       the camera window should be up front...
}
        StampMeOut;
        SaveAs(n:3);
        Dispose;

        StartCapturing;
        if n < nFrames then SleepUntilMouse;
        StopCapturing;
        SetOption; Multiframes('none',1,nacc);
    end;
    StampMeOut;
    SaveAs((n+1):3);
    Dispose;
end;

macro 'Averaging - Color Time Lapse to Folder';
{
}
var
    nacc, nfr, nstr, tim : integer;
    nfile : string;
begin
    toggle := 1;
    firstclock := 1;
   SelectAll;
   GetRoi(nleft, nright, nwidth, nheight);
    nacc := GetNumber('Integrate Frames',8);
    nfr := GetNumber('Number of Slices?',180);
    tim := GetNumber('Delay Between Frames (seconds)?',180);
    nfile:= 'TimeLapse';
    avtimelapse(nacc,nfr,  tim,nfile);
end;

macro 'Make series of color grabs to folder';
{
}
var
    nacc, nfr, nstr, tim : integer;
    nfile : string;
begin
    toggle := 1;
    firstclock := 1;
   SelectAll;
   GetRoi(nleft, nright, nwidth, nheight);
    nacc := 4;
    nfr := GetNumber('Number of Slices?',99);
    nfile:= GetString('Filename for new stack:','Data');
    colorgrabs(nacc,nfr,nfile);
end;

________________________________________________________

Lance Davidson
Research Associate (Postdoctoral Fellow)
Gilmer Hall, Dept. of Biology
University of Virginia
Charlottesville, VA 22903

804-243-2596 lab phone
804-982-5626 fax

See the amazing 3-D Tadpole Head at:
http://www.people.virginia.edu/~lad4x/


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nih-image-d Digest				Volume 99 : Issue 197

Today's Topics:
  Re: CG-7 ?                            [ Lance Davidson <lad4x@virginia.edu> ]

------------------------------

Date: Sat, 28 Aug 1999 10:29:31 -0400
From: Lance Davidson <lad4x@virginia.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: CG-7 ?
Message-Id: <3.0.32.19990828102931.006f8c8c@unix.mail.virginia.edu>
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While the CG-7 and Scion Image (ver. 1.62) can collect color images they
cannot produce a color stack. To work around this we save sequentially
numbered files and reassemble them into a timelapse with another program.

We are using a version of Scion Image and a camera-controlling Photoshop
plugin to collect time-lapse images with the CG-7 with the Dage-MTI DC330
camera. By simultaneously running Photoshop (with the camera controller) we
can set the gain etc. on screen. The following macro will collect a set of
color images as separate tif files. We then batch process the files with
photoshop actions and assemble the "color time-lapse" in Adobe Premiere.
The DC330 is a sort digital/video hybrid 3CCD camera using analog video to
pass a series of video frames which are assembled by Scion image into a
large format color image. 

Even though we've been able to make large format color timelapses we cannot
afford the hardware to play them (even a B&W G3 has its limits ... sigh).
The second macro demonstrates a mouse "button" driven collection of images
(i.e. for reassembly of histological sections).

Good luck,
Lance

{*************************************************************************
**************************************************************************
To ensure this macro runs correctly:
1. start capturing - center your animal.
2. Select the region of interest you want to cover with the time lapse.
3. Start the macro.
4. Fill in the dialog boxes --- store your stack in a responsible place.
5. When prompted, click on the spot where you want the timestamp
( the font style and size may be chosen beforehand from "options").

This macro allows timelapse collection with:
   live focus, 
   saves after every new slice, 
   positioning and customization of the timestamp, 
   average frames, and
   other things I've forgotten to mention.

Changed timelapse procedure to save single tiff files rather than stacks...
990811 added grab color images to files  - mouse driven...

See Lance Davidson (lad4x@virginia.edu) for details.
**************************************************************************}

var
    xpos, ypos: integer;
    firstclock, toggle :integer;
    textStamp: string;
    SleepToTicks : integer;
     nleft, nright, nwidth, nheight: integer;


procedure SleepUntilTicks;
{
}
var
    secs : integer;
begin
    while TickCount < SleepToTicks do begin
         secs := (TickCount - SleepToTicks) / 60;
         ShowMessage(secs);
         if button then begin
            if toggle = 1 then begin
                StartCapturing;
                toggle := 0;
            end;
            if toggle = 0 then begin
                StopCapturing;
                 toggle := 1;
            end;
         end;
    end;
    beep;
end;

procedure SleepUntilMouse;
{
}
begin
    while (NOT button) do begin
    end;
    beep;
end;


procedure StampMeOut;
{
}
var
  hours, minutes, seconds,year, month, day, dayofweek: integer;
begin
    GetTime(year, month, day, hours, minutes,seconds, dayofweek);

    if (firstclock = 1) then begin
          textStamp := GetString('Date, experimental conditions, etc.: ','');
          PutMessage('Click at desired text location...');
          repeat
             GetMouse(xpos,ypos);
          until Button;
          MoveTo(xpos,ypos);

          Write(textStamp,'  ',year, '-', month, '-', day, '  ', hours,
':', minutes, ':',seconds);

    end;
    if (firstclock = 0) then begin
        MoveTo(xpos,ypos);
        Write(hours,':',minutes,':',seconds);
     end;
     firstclock := 0;
end; {Time Stamps...}

procedure avtimelapse(nacc:integer, nFrames:integer, time:
integer,nfile:string) ;
{
}
var
    n, NewStack, Cam : integer;

    interval : integer;
begin
    Requiresversion(1.60);
    SetOption; Multiframes('highres chip',1,nacc);


    interval := 60 * time;
    SleepToTicks := TickCount+interval;
    for n := 1 to nFrames do begin
{
       the camera window should be up front...
}
        StampMeOut;
        SaveAs(n:3);
        Dispose;

        StartCapturing;
        if n < nFrames then SleepUntilTicks;
        SleepToTicks := TickCount+interval;
        StopCapturing;
        SetOption; Multiframes('highres chip',1,nacc);
    end;
    StampMeOut;
    SaveAs((n+1):3);
    Dispose;
end;

procedure colorgrabs(nacc:integer, nFrames:integer,nfile:string) ;
{
}
var
    n, NewStack, Cam : integer;

begin
    Requiresversion(1.60);
    SetOption; Multiframes('none',1,nacc);


    for n := 1 to nFrames do begin
{
       the camera window should be up front...
}
        StampMeOut;
        SaveAs(n:3);
        Dispose;

        StartCapturing;
        if n < nFrames then SleepUntilMouse;
        StopCapturing;
        SetOption; Multiframes('none',1,nacc);
    end;
    StampMeOut;
    SaveAs((n+1):3);
    Dispose;
end;

macro 'Averaging - Color Time Lapse to Folder';
{
}
var
    nacc, nfr, nstr, tim : integer;
    nfile : string;
begin
    toggle := 1;
    firstclock := 1;
   SelectAll;
   GetRoi(nleft, nright, nwidth, nheight);
    nacc := GetNumber('Integrate Frames',8);
    nfr := GetNumber('Number of Slices?',180);
    tim := GetNumber('Delay Between Frames (seconds)?',180);
    nfile:= 'TimeLapse';
    avtimelapse(nacc,nfr,  tim,nfile);
end;

macro 'Make series of color grabs to folder';
{
}
var
    nacc, nfr, nstr, tim : integer;
    nfile : string;
begin
    toggle := 1;
    firstclock := 1;
   SelectAll;
   GetRoi(nleft, nright, nwidth, nheight);
    nacc := 4;
    nfr := GetNumber('Number of Slices?',99);
    nfile:= GetString('Filename for new stack:','Data');
    colorgrabs(nacc,nfr,nfile);
end;

________________________________________________________

Lance Davidson
Research Associate (Postdoctoral Fellow)
Gilmer Hall, Dept. of Biology
University of Virginia
Charlottesville, VA 22903

804-243-2596 lab phone
804-982-5626 fax

See the amazing 3-D Tadpole Head at:
http://www.people.virginia.edu/~lad4x/

--------------------------------
End of nih-image-d Digest V99 Issue #197
****************************************

From nih-image-request@io.ece.drexel.edu Sun Aug 29 18:06 EDT 1999
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For some reason I'm no longer getting an administrative info page with the
digests.  I'm sending this in the hopes that something will be bounced back
to me, and I do apologize if this ends up going out to everyone.

If this should reach a human operator: I would like to unsubscribe from the
list.  Many thanks

D


From nih-image-d-request@io.ece.drexel.edu Mon Aug 30 16:19 EDT 1999
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Subject: nih-image-d Digest V99 #198
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------------------------------

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nih-image-d Digest				Volume 99 : Issue 198

Today's Topics:
  Re: nih-image-d Digest V99 #197       [ "ddarcy" <ddarcy@pomona.edu> ]
  Re: CG-7 ?                            [ "Anneke M.Th. Harbers and Ard Jonke ]

------------------------------

Date: Sun, 29 Aug 1999 14:55:39 -0700
From: "ddarcy" <ddarcy@pomona.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: nih-image-d Digest V99 #197
Message-ID: <003201bef269$3ceceac0$0201a8c0@xanadu>
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	charset="iso-8859-1"
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For some reason I'm no longer getting an administrative info page with the
digests.  I'm sending this in the hopes that something will be bounced back
to me, and I do apologize if this ends up going out to everyone.

If this should reach a human operator: I would like to unsubscribe from the
list.  Many thanks

D

------------------------------

Date: Mon, 30 Aug 1999 21:50:36 +0200
From: "Anneke M.Th. Harbers and Ard Jonker" <a_team@dds.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: CG-7 ?
Message-Id: <l03130303b3f090121679@[194.109.148.162]>
Content-Type: text/plain; charset="us-ascii"

>Even though we've been able to make large format color timelapses we cannot
>afford the hardware to play them (even a B&W G3 has its limits ... sigh).
>The second macro demonstrates a mouse "button" driven collection of images
>(i.e. for reassembly of histological sections).

An alternative for people who do not have Photoshop and  Premiere, is the
full version of Quicktime Pro 4.0. If you have a stack of images in red, a
stack in green and a stack in red, you open each one of them, copy the
contents and paste the contents in a movie (copy scaled, so you get 3
parallel tracks of equal lenght). Set the options of the video tracks to
blend or transparent (experiment with these) and you get a color image. As
QT is quite fast in playing movies, you can have a rather fluent quite
large image.

Ard

--------------------------------
End of nih-image-d Digest V99 Issue #198
****************************************

From nih-image-request@io.ece.drexel.edu Mon Aug 30 16:25 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: "Anneke M.Th. Harbers and Ard Jonker" <a_team@dds.nl>
Subject: Re: CG-7 ?
Resent-Message-ID: <"sPO3Q.0.QU.7Ekot"@io>
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>Even though we've been able to make large format color timelapses we cannot
>afford the hardware to play them (even a B&W G3 has its limits ... sigh).
>The second macro demonstrates a mouse "button" driven collection of images
>(i.e. for reassembly of histological sections).

An alternative for people who do not have Photoshop and  Premiere, is the
full version of Quicktime Pro 4.0. If you have a stack of images in red, a
stack in green and a stack in red, you open each one of them, copy the
contents and paste the contents in a movie (copy scaled, so you get 3
parallel tracks of equal lenght). Set the options of the video tracks to
blend or transparent (experiment with these) and you get a color image. As
QT is quite fast in playing movies, you can have a rather fluent quite
large image.

Ard



From nih-image-request@io.ece.drexel.edu Tue Aug 31 05:06 EDT 1999
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Date: Tue, 31 Aug 1999 10:35:53 +0200 (MET DST)
From: Lars Kildemark <lars@fki.dtu.dk>
To: nih-image@io.ece.drexel.edu
Subject: How is the power spectrum displayed
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Dear Imagers,

I have a short question regarding the gray scale used to display power
spectra. Is the gray scale used to display the power spectra logarithmic?
I am trying to analyse the intensity as a function of frequency and it
mean a great deal for the analysis wether or not a logarithmic gray scale
is used.
 
/Lars
__________________________________________________________
Lars Kildemark Nielsen          | e-mail: lars@kemi.dtu.dk                
Department of Chemistry         | phone : +45 45252363       
Technical University of Denmark | fax   : +45 45934808
Building 206                    |
DK-2800 Lyngby, Denmark         |
__________________________________________________________


From nih-image-request@io.ece.drexel.edu Tue Aug 31 12:45 EDT 1999
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Date: 31 Aug 99 12:34:21 -0400
From: Jonathan WISCO <jjwisco@cajal-1.bu.edu>
Subject: re-slicing MR images from coronal to horizontal
To: Ann Augustine <augustia1@yahoo.com>,
        NIH Image <nih-image@io.ece.drexel.edu>
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We are trying to re-slice coronal MR images to horizontal orientation.  However, the result so far has been a "warped" when in horizontal orientation.  Does anyone have any experience regarding this matter?  
Thanks,

Jonathan J. Wisco and Ann Augustine
Department of Anatomy and Neurobiology
Boston University School of Medicine



From nih-image-request@io.ece.drexel.edu Tue Aug 31 16:13 EDT 1999
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Date: Tue, 31 Aug 1999 15:58:38 -0400
From: "Wade Schuette" <schuette@umich.edu>
To: jjwisco@cajal-1.bu.edu, nih-image@io.ece.drexel.edu, augustia1@yahoo.com
Subject: Re: re-slicing MR images from coronal to horizontal
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No particular experience, but you might try the following to
distinguish
something the computer's doing from an intrinsic property of the 
images themselves:
 
(a) Make a stack of 20 identical images and reslice those, see
     if THAT comes out warped.  If not, problem is probably that
     the original images are already warped as captured,  and
     test b may confirm that.

(b) Reverse the order of images in your stack and see if the 
     Warping reverses as well or not.      If the warping follows
     the images, it's intrinsic;   if the warping changes, it's
probably
     something in NIH Image.

Wade Schuette
Univ. of Michigan



>>> Jonathan WISCO <jjwisco@cajal-1.bu.edu> 08/31 12:45 PM >>>
We are trying to re-slice coronal MR images to horizontal orientation. 
However, the result so far has been a "warped" when in horizontal
orientation.  Does anyone have any experience regarding this matter?  
Thanks,

Jonathan J. Wisco and Ann Augustine
Department of Anatomy and Neurobiology
Boston University School of Medicine



From nih-image-d-request@io.ece.drexel.edu Tue Aug 31 20:59 EDT 1999
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Subject: nih-image-d Digest V99 #199
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 199

Today's Topics:
  How is the power spectrum displayed   [ Lars Kildemark <lars@fki.dtu.dk> ]
  re-slicing MR images from coronal to  [ Jonathan WISCO <jjwisco@cajal-1.bu. ]
  Re: re-slicing MR images from corona  [ "Wade Schuette" <schuette@umich.edu ]
  Re: re-slicing MR images from corona  [ "Robert Day" <robday@rph.health.wa. ]

------------------------------

Date: Tue, 31 Aug 1999 10:35:53 +0200 (MET DST)
From: Lars Kildemark <lars@fki.dtu.dk>
To: nih-image@io.ece.drexel.edu
Subject: How is the power spectrum displayed
Message-ID: <Pine.LNX.3.95.990831102947.24318A-100000@bilayer.fki.dtu.dk>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear Imagers,

I have a short question regarding the gray scale used to display power
spectra. Is the gray scale used to display the power spectra logarithmic?
I am trying to analyse the intensity as a function of frequency and it
mean a great deal for the analysis wether or not a logarithmic gray scale
is used.
 
/Lars
__________________________________________________________
Lars Kildemark Nielsen          | e-mail: lars@kemi.dtu.dk                
Department of Chemistry         | phone : +45 45252363       
Technical University of Denmark | fax   : +45 45934808
Building 206                    |
DK-2800 Lyngby, Denmark         |
__________________________________________________________

------------------------------

Date: 31 Aug 99 12:34:21 -0400
From: Jonathan WISCO <jjwisco@cajal-1.bu.edu>
To: Ann Augustine <augustia1@yahoo.com>,
        NIH Image <nih-image@io.ece.drexel.edu>
Subject: re-slicing MR images from coronal to horizontal
Message-Id: <199908311628.MAA08845@bu.edu>
Content-Type: text/plain; charset="US-Ascii"
Content-Transfer-Encoding: 8bit

We are trying to re-slice coronal MR images to horizontal orientation.  However, the result so far has been a "warped" when in horizontal orientation.  Does anyone have any experience regarding this matter?  
Thanks,

Jonathan J. Wisco and Ann Augustine
Department of Anatomy and Neurobiology
Boston University School of Medicine

------------------------------

Date: Tue, 31 Aug 1999 15:58:38 -0400
From: "Wade Schuette" <schuette@umich.edu>
To: jjwisco@cajal-1.bu.edu, nih-image@io.ece.drexel.edu, augustia1@yahoo.com
Subject: Re: re-slicing MR images from coronal to horizontal
Message-Id: <s7cbfbc3.091@umich.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline

No particular experience, but you might try the following to
distinguish
something the computer's doing from an intrinsic property of the 
images themselves:
 
(a) Make a stack of 20 identical images and reslice those, see
     if THAT comes out warped.  If not, problem is probably that
     the original images are already warped as captured,  and
     test b may confirm that.

(b) Reverse the order of images in your stack and see if the 
     Warping reverses as well or not.      If the warping follows
     the images, it's intrinsic;   if the warping changes, it's
probably
     something in NIH Image.

Wade Schuette
Univ. of Michigan



>>> Jonathan WISCO <jjwisco@cajal-1.bu.edu> 08/31 12:45 PM >>>
We are trying to re-slice coronal MR images to horizontal orientation. 
However, the result so far has been a "warped" when in horizontal
orientation.  Does anyone have any experience regarding this matter?  
Thanks,

Jonathan J. Wisco and Ann Augustine
Department of Anatomy and Neurobiology
Boston University School of Medicine

------------------------------

Date: Wed, 1 Sep 1999 08:48:39 +0800
From: "Robert Day" <robday@rph.health.wa.gov.au>
To: jjwisco@cajal-1.bu.edu, nih-image@io.ece.drexel.edu
Subject: Re: re-slicing MR images from coronal to horizontal
Message-Id: <199909010106.JAA11878@nero.rph.health.wa.gov.au>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7BIT

Jonathan,

You don't specify what sort of "warping" you are getting, but in our 
experience the most common problem when reslicing stacks is getting the 
spacing between slices wrong (or equivalently, the in-slice pixel size 
wrong).

Can you be more specific about your problem ?

Rob.

> We are trying to re-slice coronal MR images to horizontal orientation. 
> However, the result so far has been a "warped" when in horizontal
> orientation.  Does anyone have any experience regarding this matter? 
> Thanks,
> 
> Jonathan J. Wisco and Ann Augustine
> Department of Anatomy and Neurobiology
> Boston University School of Medicine
> 
> 


--
Robert Day		rob.day@nero.rph.health.wa.gov.au
Project Bioengineer	ph  +61 8 9224 3227
Royal Perth Hospital	fax +61 8 9224 1138

--------------------------------
End of nih-image-d Digest V99 Issue #199
****************************************

From nih-image-request@io.ece.drexel.edu Tue Aug 31 21:01 EDT 1999
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From: "Robert Day" <robday@rph.health.wa.gov.au>
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Jonathan,

You don't specify what sort of "warping" you are getting, but in our 
experience the most common problem when reslicing stacks is getting the 
spacing between slices wrong (or equivalently, the in-slice pixel size 
wrong).

Can you be more specific about your problem ?

Rob.

> We are trying to re-slice coronal MR images to horizontal orientation. 
> However, the result so far has been a "warped" when in horizontal
> orientation.  Does anyone have any experience regarding this matter? 
> Thanks,
> 
> Jonathan J. Wisco and Ann Augustine
> Department of Anatomy and Neurobiology
> Boston University School of Medicine
> 
> 


--
Robert Day		rob.day@nero.rph.health.wa.gov.au
Project Bioengineer	ph  +61 8 9224 3227
Royal Perth Hospital	fax +61 8 9224 1138


From nih-image-request@io.ece.drexel.edu Tue Aug 31 22:55 EDT 1999
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From nih-image-request@io.ece.drexel.edu Wed Sep  1 11:38 EDT 1999
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From: Ann Augustine <augustia1@yahoo.com>
Subject: Anyone in Boston?
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I was wondering if there was anyone familiar with NIH Image and
currently using it for Neuroimaging Research in the Boston area.  I am
a graduate student at Boston University trying to become familiar with
this program.  If anyone else is using it, I would greatly appreciate
it if you contacted me.

Ann Augustine

__________________________________________________
Do You Yahoo!?
Bid and sell for free at http://auctions.yahoo.com


From nih-image-d-request@io.ece.drexel.edu Wed Sep  1 19:53 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #200
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 200

Today's Topics:
  unsubscribe                           [ James Keen <jim.keen@mail.tju.edu> ]
  Anyone in Boston?                     [ Ann Augustine <augustia1@yahoo.com> ]
  Multi-page tiff file open/close code  [ "R. Aaron Falk" <rafalk@optomet.com ]

------------------------------

Date: Tue, 31 Aug 1999 22:42:25 -0400
From: James Keen <jim.keen@mail.tju.edu>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
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------------------------------

Date: Wed, 1 Sep 1999 08:21:03 -0700 (PDT)
From: Ann Augustine <augustia1@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: Anyone in Boston?
Message-ID: <19990901152103.9016.rocketmail@send205.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

I was wondering if there was anyone familiar with NIH Image and
currently using it for Neuroimaging Research in the Boston area.  I am
a graduate student at Boston University trying to become familiar with
this program.  If anyone else is using it, I would greatly appreciate
it if you contacted me.

Ann Augustine

__________________________________________________
Do You Yahoo!?
Bid and sell for free at http://auctions.yahoo.com

------------------------------

Date: Wed, 1 Sep 1999 16:47:57 -0700
From: "R. Aaron Falk" <rafalk@optomet.com>
To: <nih-image@io.ece.drexel.edu>
Subject: Multi-page tiff file open/close code
Message-ID: <000b01bef4d4$6aa69a20$0200a8c0@internet>
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 7bit

Dear Imagers,

This question is a bit off the topic, however, I expect that someone in the
group may know an answer. We are building an application that needs to open
and save multi-page tiff files on the PC. In addition, the images we collect
are 10 bit gray scale. We need code examples or references (C, C++, Java,
Visual Basic) on how to do all or part of this process. Any help would be
greatly appreciated.

Take care,
Aaron

*******************************************************************
Dr. R. Aaron Falk
President
OptoMetrix, Inc.
rafalk@optomet.com

--------------------------------
End of nih-image-d Digest V99 Issue #200
****************************************

From nih-image-request@io.ece.drexel.edu Wed Sep  1 19:56 EDT 1999
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From: "R. Aaron Falk" <rafalk@optomet.com>
To: <nih-image@io.ece.drexel.edu>
Subject: Multi-page tiff file open/close code
Date: Wed, 1 Sep 1999 16:47:57 -0700
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Dear Imagers,

This question is a bit off the topic, however, I expect that someone in the
group may know an answer. We are building an application that needs to open
and save multi-page tiff files on the PC. In addition, the images we collect
are 10 bit gray scale. We need code examples or references (C, C++, Java,
Visual Basic) on how to do all or part of this process. Any help would be
greatly appreciated.

Take care,
Aaron

*******************************************************************
Dr. R. Aaron Falk
President
OptoMetrix, Inc.
rafalk@optomet.com


From nih-image-request@io.ece.drexel.edu Wed Sep  1 21:40 EDT 1999
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Date: Wed, 01 Sep 1999 21:36:29 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: Multi-page tiff file open/close code
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At 04:47 PM 9/1/99 -0700, you wrote:
>Dear Imagers,
>
>This question is a bit off the topic, however, I expect that someone in the
>group may know an answer. We are building an application that needs to open
>and save multi-page tiff files on the PC. In addition, the images we collect
>are 10 bit gray scale. We need code examples or references (C, C++, Java,
>Visual Basic) on how to do all or part of this process. Any help would be
>greatly appreciated.

Take a look at the Java source for ImageJ at http://rsb.info.nih.gov/ij/. ImageJ opens and saves multi-image 16-bit tiffs. You source files you want to look at are TiffDecoder.java, TiffEncoder.java, FileInfo.java, ImageReader.java, ImageWriter.java, FileOpener.java and FileSaver.java. 

-wayne


From nih-image-d-request@io.ece.drexel.edu Thu Sep  2 13:07 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #201
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 201

Today's Topics:
  Re: Multi-page tiff file open/close   [ Wayne Rasband <wayne@codon.nih.gov> ]
  looking for software engineer for co  [ "John Gripp" <mrgripper@hotmail.com ]

------------------------------

Date: Wed, 01 Sep 1999 21:36:29 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Multi-page tiff file open/close code
Message-Id: <3.0.5.32.19990901213629.00a2bd60@codon.nih.gov>
Content-Type: text/plain; charset="us-ascii"

At 04:47 PM 9/1/99 -0700, you wrote:
>Dear Imagers,
>
>This question is a bit off the topic, however, I expect that someone in the
>group may know an answer. We are building an application that needs to open
>and save multi-page tiff files on the PC. In addition, the images we collect
>are 10 bit gray scale. We need code examples or references (C, C++, Java,
>Visual Basic) on how to do all or part of this process. Any help would be
>greatly appreciated.

Take a look at the Java source for ImageJ at http://rsb.info.nih.gov/ij/. ImageJ opens and saves multi-image 16-bit tiffs. You source files you want to look at are TiffDecoder.java, TiffEncoder.java, FileInfo.java, ImageReader.java, ImageWriter.java, FileOpener.java and FileSaver.java. 

-wayne

------------------------------

Date: Thu, 02 Sep 1999 09:48:05 PDT
From: "John Gripp" <mrgripper@hotmail.com>
To: nih-image@io.ece.drexel.edu
Cc: rlewis@berkeleyheartlab.com
Subject: looking for software engineer for consultation
Message-ID: <19990902164805.26250.qmail@hotmail.com>
Content-Type: text/plain; format=flowed

I am currently developing some procedures at my lab which utilizes
the NIH Image software platform.  I have been working with a
software engineer who has written several subroutines for the
specific applications we are developing for our research.  Unfortunately, he 
will not be available to see this research to fruition...

Does anyone have a suggestion for finding a consultant who could
assist my group in finalizing our software analysis program???  We
need an individual who is familiar with using and programming for
the NIH Image software format.

Please respond to jgripp@berkeleyheartlab.com if you have some
leads on this situation.

Thanks,

John Gripp

______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com

--------------------------------
End of nih-image-d Digest V99 Issue #201
****************************************

From nih-image-request@io.ece.drexel.edu Thu Sep  2 13:10 EDT 1999
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Subject: looking for software engineer for consultation
Date: Thu, 02 Sep 1999 09:48:05 PDT
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I am currently developing some procedures at my lab which utilizes
the NIH Image software platform.  I have been working with a
software engineer who has written several subroutines for the
specific applications we are developing for our research.  Unfortunately, he 
will not be available to see this research to fruition...

Does anyone have a suggestion for finding a consultant who could
assist my group in finalizing our software analysis program???  We
need an individual who is familiar with using and programming for
the NIH Image software format.

Please respond to jgripp@berkeleyheartlab.com if you have some
leads on this situation.

Thanks,

John Gripp

______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com


From nih-image-request@io.ece.drexel.edu Thu Sep  2 14:40 EDT 1999
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Date: Thu, 2 Sep 1999 14:24:14 -0500
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From: cdm7@psu.edu (Colleen Diane Merritt)
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>Unsubscribe please

-------------------------------------------------------------------

Colleen D. Merritt

Department of Chemical Engineering
Pennsylvania State University
312 Wartik Laboratory
University Park, PA  16802
phone:(814) 863-7182
email:cdm7@psu.edu





From nih-image-request@io.ece.drexel.edu Fri Sep  3 05:24 EDT 1999
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                   NIH-image Mailing List Help 
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Archive
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Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
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Tips by Henry M. Thomas, 

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then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
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Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
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Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
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Examples:
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egrep some.word latest/*
--


From nih-image-d-request@io.ece.drexel.edu Fri Sep  3 06:14 EDT 1999
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 202

Today's Topics:
  unsubscribe                           [ cdm7@psu.edu (Colleen Diane Merritt ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]

------------------------------

Date: Thu, 2 Sep 1999 14:24:14 -0500
From: cdm7@psu.edu (Colleen Diane Merritt)
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <v01530500b3f47f2e1c04@[128.118.22.25]>
Content-Type: text/plain; charset="us-ascii"

>Unsubscribe please

-------------------------------------------------------------------

Colleen D. Merritt

Department of Chemical Engineering
Pennsylvania State University
312 Wartik Laboratory
University Park, PA  16802
phone:(814) 863-7182
email:cdm7@psu.edu

------------------------------

Date: Fri, 3 Sep 1999 05:05:00 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199909030905.FAA27926@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
                   ---------------------------
     


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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

--------------------------------
End of nih-image-d Digest V99 Issue #202
****************************************

From nih-image-request@io.ece.drexel.edu Fri Sep  3 07:50 EDT 1999
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	Fri, 3 Sep 1999 07:50:46 -0400 (EDT)
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Message-ID: <37CFB3DA.A3669092@fundp.ac.be>
Date: Fri, 03 Sep 1999 13:41:15 +0200
From: Gervais Leclerc <gervais.leclerc@fundp.ac.be>
Organization: FUNDP
X-Mailer: Mozilla 4.61 [en] (WinNT; I)
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To: Project Image <nih-image@io.ece.drexel.edu>
Subject: Density calibration with Scion Image Beta 3b
Content-Transfer-Encoding: 8bit
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Hi,

I am trying to write a Scion Image macro which would use the
macrocommand Calibrate. I hope someone can help me. Here is what I wish
to do:

- The images I wish to analyze comprise a grayscale to be used for
density calibration, plus of course the objects whose intensity I wish
to measure.

-The location of both the grayscale and the objects is known.

- I thought I could first use the Calibrate macrocommand to
automatically perform the density calibration. Then I could have used
some combination of Measure, GetResults and cValue to get my calibrated
and uncalibrated measurements.

- The calibration goes well ... until the objects are measured. Then the
calibration curve goes wrong. And stays wrong. The Calibrate Menu first
shows my grayscale measured values with the known values. This is
followed by the mean of the first measured objects accompanied by blanks
in the Known Values column.

- But the Calibration curve and the saved Calibration table both show
that those blank known values are not all blanks. As a result my
Calibration goes awry.

Does anyone have a suggestion to work around that bug?

--
Dr. Gervais Leclerc
Facults Universitaires Notre-Dame de la Paix,
Namur Belgium




From nih-image-d-request@io.ece.drexel.edu Sat Sep  4 06:08 EDT 1999
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	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA23881;
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Date: Sat, 4 Sep 1999 06:08:41 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199909041008.GAA23881@io.ece.drexel.edu>
Subject: nih-image-d Digest V99 #203
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Content-Length: 1868

------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 203

Today's Topics:
  Density calibration with Scion Image  [ Gervais Leclerc <gervais.leclerc@fu ]

------------------------------

Date: Fri, 03 Sep 1999 13:41:15 +0200
From: Gervais Leclerc <gervais.leclerc@fundp.ac.be>
To: Project Image <nih-image@io.ece.drexel.edu>
Subject: Density calibration with Scion Image Beta 3b
Message-ID: <37CFB3DA.A3669092@fundp.ac.be>
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

Hi,

I am trying to write a Scion Image macro which would use the
macrocommand Calibrate. I hope someone can help me. Here is what I wish
to do:

- The images I wish to analyze comprise a grayscale to be used for
density calibration, plus of course the objects whose intensity I wish
to measure.

-The location of both the grayscale and the objects is known.

- I thought I could first use the Calibrate macrocommand to
automatically perform the density calibration. Then I could have used
some combination of Measure, GetResults and cValue to get my calibrated
and uncalibrated measurements.

- The calibration goes well ... until the objects are measured. Then the
calibration curve goes wrong. And stays wrong. The Calibrate Menu first
shows my grayscale measured values with the known values. This is
followed by the mean of the first measured objects accompanied by blanks
in the Known Values column.

- But the Calibration curve and the saved Calibration table both show
that those blank known values are not all blanks. As a result my
Calibration goes awry.

Does anyone have a suggestion to work around that bug?

--
Dr. Gervais Leclerc
Facults Universitaires Notre-Dame de la Paix,
Namur Belgium

--------------------------------
End of nih-image-d Digest V99 Issue #203
****************************************

From nih-image-request@io.ece.drexel.edu Mon Sep  6 03:07 EDT 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id DAA15324;
	Mon, 6 Sep 1999 03:07:14 -0400 (EDT)
Resent-Date: Mon, 6 Sep 1999 03:07:14 -0400 (EDT)
From: mohwco@att.net
Message-Id: <199909060650.CAA12579@io.ece.drexel.edu>
Subject: Homeworkers Needed!
Date: Mon, 6 Sep 1999 03:32:19
Resent-Message-ID: <"_et472.0.g53.SHsqt"@io>
To: nih-image@io.ece.drexel.edu
Resent-From: nih-image@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
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Dear Future Associate,

You Can Work At Home & Set Your Own Hours.  Start earning Big 
Money in a short time
       
                                    NO Newspaper Advertising!

Your job will be to stuff and mail envelopes for our company. You 
will receive $.25 for each and every envelope you stuff and mail 
out.

Just follow our simple instructions and you will be making money 
as easy as
1 2 3

For example stuff and mail 200 envelopes and you will receive 
$50.00. Stuff and mail 1000 and you will receive $250.00. Stuff 
and mail 2000 and you will receive $500.00 and more 

Never before has there been an easier way to make money from 
home!

Our Company's Home Mailing Program is designed for people with 
little or no experience and provides simple, step by step 
instructions.  

There is no prior experience or special skills necessary on your 
part, Just stuffing envelopes.

We need the help of honest and reliable home workers like you.  
Because we are overloaded with work and have more than our staff 
can handle. We have now expanded our mailing program and are 
expecting to reach millions more with our offers throughout the 
US and Canada.

Our system of stuffing and mailing envelopes is very simple and 
easy to do!
You will not be required to buy envelopes or postage stamps.

We will gladly furnish all circulars at no cost to you. We assure 
you that as a participant in our program you will never have to 
mail anything objective or offensive. 

There are no quotas to meet, and there no contracts to sign. You 
can work as much, or as little as you want. Payment for each 
envelope you send out is Guaranteed!

Here is what you will receive when you get your first Package.  
Inside you will find 100 envelopes, 100 labels and 100 sales 
letters ready to stuff and mail

As soon as you are done with stuffing and mailing these first 
letters, your payment will arrive shortly, thereafter. All you 
have to do is to order more free supplies and stuff and mail more 
envelopes to make more money.

Our sales literature which you will be stuffing and mailing will 
contain
information outlining our highly informative manuals that we are
advertising nationwide.  As a free gift you will receive a 
special manual valued at  $24.95, absolutely free, just for 
joining our Home Mailers Program.

Plus you will get your own special code number, so that we will 
know how much you are to get paid.  And to make re-ordering of 
more envelopes, that our company supplies very simple for you.

We are giving you this free bonus because we want you to be 
confident in our company and to ensure that we will be doing 
business with you for a long time.

Benefits Of This Job:

1. You do not have to quit your present job, to earn more money 
at home
2. You can make between $2,500 to $4,500 a month depending on the 
amount of time you are willing to spend stuffing and mailing 
envelopes
3. This is a great opportunity for the students, mothers, 
disabled persons or those who are home bodies.

To secure your position and to show us that you are serious about 
earning extra income at home we require a one-time registration 
fee of $35.00.
This fee covers the cost of your initial start up package,  which 
includes 100 envelopes, 100 labels and 100 sales letters and a 
manual, your registration fee will be refunded back to you 
shortly thereafter.

Money Back Guarantee!

We guarantee that as soon as you stuff and mail your first 300 
envelopes You will be paid $75.00 and your registration fee will 
be refunded.

Many of you wonder why it is necessary to pay a deposit to get a 
job. It is because we are looking for people that seriously want 
to work from home.  

*  If 3.000 people told us they wanted to start working from home 
and we sent out 3.000 packages free to every one.  And then half 
of the people decided not to work, this would be a potential loss 
of more than $60,000 in supply's and shipping that we have sent 
out to people that don't want to work

We have instituted this policy to make sure that you really want 
to work and at least finish your first package.

To Get Started Today Please Enclose Your Registration Fee of $35
Check,Cash Or Money Order and fill out the application below and 
mail to:

MOHW Co	
PMB
11054 Ventura Blvd #126	
Studio City, CA 91604

Name_____________________________________________________

Address___________________________________________________

City____________________________________ State______________

Zip Code________________

Telephone Number(s)_________________________________________

E-mail Address______________________________________________



For all orders, please allow seven (7) days for delivery and up 
to 10 days. Cash and Money Orders will result in faster shipping of your 
package.
 
 
 
 
 
 
 
 
 
 
 
 


From nih-image-request@io.ece.drexel.edu Mon Sep  6 04:07 EDT 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA24292;
	Mon, 6 Sep 1999 04:07:00 -0400 (EDT)
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X-Sender: patw@mail.med.usyd.edu.au
Message-Id: <v03110700b3f51dfd2681@[152.76.71.133]>
Mime-Version: 1.0
Date: Fri, 3 Sep 1999 16:46:22 +1000
To: nih-image@io.ece.drexel.edu
From: Patricia Waley <patw@pathology.usyd.edu.au>
Subject: Thursday Lunch
Resent-Message-ID: <"sIBJB1.0.bK5.t9tqt"@io>
Resent-From: nih-image@io.ece.drexel.edu
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Liz,
Not too many takers for lunch on Thursday. Smita wont be in and the others
( well David any way) think that Friday morning tea would be the best way
to farewell her. I'm in for what its worth.

		Pat

________________________________________________________________________________
Patricia Waley
Centre for Education and Research on Ageing
Concord Hospital
Concord NSW 2139
Ph: (02) 9767 6586
Fax: (02) 9767 8315
Email: patw@pathology.usyd.edu.au
________________________________________________________________________________



From nih-image-d-request@io.ece.drexel.edu Tue Sep  7 06:17 EDT 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA06404;
	Tue, 7 Sep 1999 06:17:29 -0400 (EDT)
Date: Tue, 7 Sep 1999 06:17:29 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199909071017.GAA06404@io.ece.drexel.edu>
Subject: nih-image-d Digest V99 #204
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Content-Length: 6208

------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 204

Today's Topics:
  Homeworkers Needed!                   [ mohwco@att.net ]
  Thursday Lunch                        [ Patricia Waley <patw@pathology.usyd ]

------------------------------

Date: Mon, 6 Sep 1999 03:32:19
From: mohwco@att.net
To: nih-image@io.ece.drexel.edu
Subject: Homeworkers Needed!
Message-Id: <199909060650.CAA12579@io.ece.drexel.edu>

Dear Future Associate,

You Can Work At Home & Set Your Own Hours.  Start earning Big 
Money in a short time
       
                                    NO Newspaper Advertising!

Your job will be to stuff and mail envelopes for our company. You 
will receive $.25 for each and every envelope you stuff and mail 
out.

Just follow our simple instructions and you will be making money 
as easy as
1 2 3

For example stuff and mail 200 envelopes and you will receive 
$50.00. Stuff and mail 1000 and you will receive $250.00. Stuff 
and mail 2000 and you will receive $500.00 and more 

Never before has there been an easier way to make money from 
home!

Our Company's Home Mailing Program is designed for people with 
little or no experience and provides simple, step by step 
instructions.  

There is no prior experience or special skills necessary on your 
part, Just stuffing envelopes.

We need the help of honest and reliable home workers like you.  
Because we are overloaded with work and have more than our staff 
can handle. We have now expanded our mailing program and are 
expecting to reach millions more with our offers throughout the 
US and Canada.

Our system of stuffing and mailing envelopes is very simple and 
easy to do!
You will not be required to buy envelopes or postage stamps.

We will gladly furnish all circulars at no cost to you. We assure 
you that as a participant in our program you will never have to 
mail anything objective or offensive. 

There are no quotas to meet, and there no contracts to sign. You 
can work as much, or as little as you want. Payment for each 
envelope you send out is Guaranteed!

Here is what you will receive when you get your first Package.  
Inside you will find 100 envelopes, 100 labels and 100 sales 
letters ready to stuff and mail

As soon as you are done with stuffing and mailing these first 
letters, your payment will arrive shortly, thereafter. All you 
have to do is to order more free supplies and stuff and mail more 
envelopes to make more money.

Our sales literature which you will be stuffing and mailing will 
contain
information outlining our highly informative manuals that we are
advertising nationwide.  As a free gift you will receive a 
special manual valued at  $24.95, absolutely free, just for 
joining our Home Mailers Program.

Plus you will get your own special code number, so that we will 
know how much you are to get paid.  And to make re-ordering of 
more envelopes, that our company supplies very simple for you.

We are giving you this free bonus because we want you to be 
confident in our company and to ensure that we will be doing 
business with you for a long time.

Benefits Of This Job:

1. You do not have to quit your present job, to earn more money 
at home
2. You can make between $2,500 to $4,500 a month depending on the 
amount of time you are willing to spend stuffing and mailing 
envelopes
3. This is a great opportunity for the students, mothers, 
disabled persons or those who are home bodies.

To secure your position and to show us that you are serious about 
earning extra income at home we require a one-time registration 
fee of $35.00.
This fee covers the cost of your initial start up package,  which 
includes 100 envelopes, 100 labels and 100 sales letters and a 
manual, your registration fee will be refunded back to you 
shortly thereafter.

Money Back Guarantee!

We guarantee that as soon as you stuff and mail your first 300 
envelopes You will be paid $75.00 and your registration fee will 
be refunded.

Many of you wonder why it is necessary to pay a deposit to get a 
job. It is because we are looking for people that seriously want 
to work from home.  

*  If 3.000 people told us they wanted to start working from home 
and we sent out 3.000 packages free to every one.  And then half 
of the people decided not to work, this would be a potential loss 
of more than $60,000 in supply's and shipping that we have sent 
out to people that don't want to work

We have instituted this policy to make sure that you really want 
to work and at least finish your first package.

To Get Started Today Please Enclose Your Registration Fee of $35
Check,Cash Or Money Order and fill out the application below and 
mail to:

MOHW Co	
PMB
11054 Ventura Blvd #126	
Studio City, CA 91604

Name_____________________________________________________

Address___________________________________________________

City____________________________________ State______________

Zip Code________________

Telephone Number(s)_________________________________________

E-mail Address______________________________________________



For all orders, please allow seven (7) days for delivery and up 
to 10 days. Cash and Money Orders will result in faster shipping of your 
package.
 
 
 
 
 
 
 
 
 
 
 
 

------------------------------

Date: Fri, 3 Sep 1999 16:46:22 +1000
From: Patricia Waley <patw@pathology.usyd.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Thursday Lunch
Message-Id: <v03110700b3f51dfd2681@[152.76.71.133]>
Content-Type: text/plain; charset="us-ascii"

Liz,
Not too many takers for lunch on Thursday. Smita wont be in and the others
( well David any way) think that Friday morning tea would be the best way
to farewell her. I'm in for what its worth.

		Pat

________________________________________________________________________________
Patricia Waley
Centre for Education and Research on Ageing
Concord Hospital
Concord NSW 2139
Ph: (02) 9767 6586
Fax: (02) 9767 8315
Email: patw@pathology.usyd.edu.au
________________________________________________________________________________

--------------------------------
End of nih-image-d Digest V99 Issue #204
****************************************

From nih-image-request@io.ece.drexel.edu Tue Sep  7 06:40 EDT 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA10195;
	Tue, 7 Sep 1999 06:40:02 -0400 (EDT)
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X-Sender: reguian@pop-server.ucl.ac.uk
Message-Id: <v01510100b3fa84ffadb5@[192.168.0.69]>
Mime-Version: 1.0
Date: Tue, 7 Sep 1999 11:26:05 +0100
To: nih-image@io.ece.drexel.edu
From: i.evans@ucl.ac.uk (Ian Evans)
Subject: Help - Statistical software for the mac
Resent-Message-ID: <"Kxqmp.0.3s1.sUErt"@io>
Resent-From: nih-image@io.ece.drexel.edu
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Hi,

I realise this is off topic and appologise in advance. Can anyone on the
list point me to a comprehensive stats package for the mac which does
preliminary tests of normality as well as ANOVA and the usual stuff.
Send replies directly to me and I'll post a summary if needed.

Thanks

--------------------------------------------------------------
Ian Evans                               i.evans@ucl.ac.uk
Dept. of Molecular Endocrinology        Tel. 0171 504 9390
University College London.              Fax 0171 580 2737
Mortimer Street
London
W1N 8AA



From nih-image-request@io.ece.drexel.edu Tue Sep  7 10:39 EDT 1999
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Message-ID: <37D51F08.B202D461@ucsd.edu>
Date: Tue, 07 Sep 1999 07:19:52 -0700
From: Paul Grimm <pgrimm@ucsd.edu>
Reply-To: pgrimm@ucsd.edu
Organization: UCSD Pediatric Nephrology
X-Mailer: Mozilla 4.5 (Macintosh; U; PPC)
X-Accept-Language: en
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: Help - Statistical software for the mac
References: <v01510100b3fa84ffadb5@[192.168.0.69]>
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I have used Exel and Statview. Clearly statview is comprehensive and quite easy
to use.

--
Paul C. Grimm
Associate Professor
Pediatric Nephrology
University of California at San Diego

Email pgrimm@ucsd.edu
Phone 619-543-5218
Fax   619-543-3575
Snail mail
UCSD Pediatrics
Mail Stop 0831
9500 Gilman Drive,
La Jolla California
92093-0831

Someone who thinks logically provides a nice contrast to the real world.



From nih-image-request@io.ece.drexel.edu Tue Sep  7 12:39 EDT 1999
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From: Benbowme1@aol.com
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Date: Tue, 7 Sep 1999 12:19:24 EDT
Subject: Re:  Help - Statistical software for the mac
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Ian,
Try JMP, it probably has everything that you want....and much more.
Cheers,
Eric 


From nih-image-d-request@io.ece.drexel.edu Wed Sep  8 06:15 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #205
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 205

Today's Topics:
  Help - Statistical software for the   [ i.evans@ucl.ac.uk (Ian Evans) ]
  Re: Help - Statistical software for   [ Paul Grimm <pgrimm@ucsd.edu> ]
  Re: Help - Statistical software for   [ Benbowme1@aol.com ]

------------------------------

Date: Tue, 7 Sep 1999 11:26:05 +0100
From: i.evans@ucl.ac.uk (Ian Evans)
To: nih-image@io.ece.drexel.edu
Subject: Help - Statistical software for the mac
Message-Id: <v01510100b3fa84ffadb5@[192.168.0.69]>
Content-Type: text/plain; charset="us-ascii"

Hi,

I realise this is off topic and appologise in advance. Can anyone on the
list point me to a comprehensive stats package for the mac which does
preliminary tests of normality as well as ANOVA and the usual stuff.
Send replies directly to me and I'll post a summary if needed.

Thanks

--------------------------------------------------------------
Ian Evans                               i.evans@ucl.ac.uk
Dept. of Molecular Endocrinology        Tel. 0171 504 9390
University College London.              Fax 0171 580 2737
Mortimer Street
London
W1N 8AA

------------------------------

Date: Tue, 07 Sep 1999 07:19:52 -0700
From: Paul Grimm <pgrimm@ucsd.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Help - Statistical software for the mac
Message-ID: <37D51F08.B202D461@ucsd.edu>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

I have used Exel and Statview. Clearly statview is comprehensive and quite easy
to use.

--
Paul C. Grimm
Associate Professor
Pediatric Nephrology
University of California at San Diego

Email pgrimm@ucsd.edu
Phone 619-543-5218
Fax   619-543-3575
Snail mail
UCSD Pediatrics
Mail Stop 0831
9500 Gilman Drive,
La Jolla California
92093-0831

Someone who thinks logically provides a nice contrast to the real world.

------------------------------

Date: Tue, 7 Sep 1999 12:19:24 EDT
From: Benbowme1@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re:  Help - Statistical software for the mac
Message-ID: <736c6887.2506950c@aol.com>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

Ian,
Try JMP, it probably has everything that you want....and much more.
Cheers,
Eric 

--------------------------------
End of nih-image-d Digest V99 Issue #205
****************************************

From nih-image-request@io.ece.drexel.edu Wed Sep  8 08:28 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: Ludger Offerhaus <ljo@gfz-potsdam.de>
Subject: transparent background?
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Dear Imagers!

How can I turn a certain colour (i.c. white) into 'nothing' (i.e. transparent)?

(Explanation: I would like to project a binary image (black lines on a
white background) onto another image (a scanned SEM image of a ceramic
aggregate). Is there a way to make the backgrounds transparent in Image and
then to simply use copy-paste  for the purpose?
A way to do this in object image and use my black lines as an overlay on
the SEM-image would also be very fine, the problem is the colour-to-nothing
conversion.)

thank you!
cheers,
Ludger


--
Ludger Offerhaus
GeoForschungsZentrum Potsdam
Telegrafenberg, 14473 Potsdam, Deutschland
Tel: +49 (0)331 288 1326 / 1390
oder: 030 32 60 55 68 (auch AB)
---



From nih-image-request@io.ece.drexel.edu Wed Sep  8 08:47 EDT 1999
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Date: Wed, 8 Sep 1999 14:41:51 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: transparent background?
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Ludger,
In the image to be pasted, make the area which you want to be transparent
white. Then paste in 'Replace' transfer mode (found in the Paste Control
window).

Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



From nih-image-request@io.ece.drexel.edu Wed Sep  8 08:53 EDT 1999
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From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: transparent background?
Date: Wed, 8 Sep 1999 14:40:53 +0200
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You can use the Image Math option under Process to do that. Use the
logical operator 'or' to combine your original SEM image and the mask
you are using.

Gary.


>-----Original Message-----
>From:	Ludger Offerhaus [SMTP:ljo@gfz-potsdam.de]
>Sent:	8. september 1999 14:11
>To:	nih-image@io.ece.drexel.edu
>Subject:	transparent background?
>
>Dear Imagers!
>
>How can I turn a certain colour (i.c. white) into 'nothing' (i.e.
>transparent)?
>
>(Explanation: I would like to project a binary image (black lines on a
>white background) onto another image (a scanned SEM image of a ceramic
>aggregate). Is there a way to make the backgrounds transparent in Image and
>then to simply use copy-paste  for the purpose?
>A way to do this in object image and use my black lines as an overlay on
>the SEM-image would also be very fine, the problem is the colour-to-nothing
>conversion.)
>
>thank you!
>cheers,
>Ludger
>
>
>--
>Ludger Offerhaus
>GeoForschungsZentrum Potsdam
>Telegrafenberg, 14473 Potsdam, Deutschland
>Tel: +49 (0)331 288 1326 / 1390
>oder: 030 32 60 55 68 (auch AB)
>---
>
>


From nih-image-d-request@io.ece.drexel.edu Thu Sep  9 06:17 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #206
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 206

Today's Topics:
  transparent background?               [ Ludger Offerhaus <ljo@gfz-potsdam.d ]
  Re: transparent background?           [ Norbert Vischer <vischer@bio.uva.nl ]
  RE: transparent background?           [ Gary Chinga <gary.chinga@pfi.no> ]

------------------------------

Date: Wed, 8 Sep 1999 14:10:46 +0200
From: Ludger Offerhaus <ljo@gfz-potsdam.de>
To: nih-image@io.ece.drexel.edu
Subject: transparent background?
Message-Id: <l03130309b3fbffc2d809@[139.17.139.125]>
Content-Type: text/plain; charset="us-ascii"

Dear Imagers!

How can I turn a certain colour (i.c. white) into 'nothing' (i.e. transparent)?

(Explanation: I would like to project a binary image (black lines on a
white background) onto another image (a scanned SEM image of a ceramic
aggregate). Is there a way to make the backgrounds transparent in Image and
then to simply use copy-paste  for the purpose?
A way to do this in object image and use my black lines as an overlay on
the SEM-image would also be very fine, the problem is the colour-to-nothing
conversion.)

thank you!
cheers,
Ludger


--
Ludger Offerhaus
GeoForschungsZentrum Potsdam
Telegrafenberg, 14473 Potsdam, Deutschland
Tel: +49 (0)331 288 1326 / 1390
oder: 030 32 60 55 68 (auch AB)
---

------------------------------

Date: Wed, 8 Sep 1999 14:41:51 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: transparent background?
Message-Id: <l03110703b3fc08280fb5@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

Ludger,
In the image to be pasted, make the area which you want to be transparent
white. Then paste in 'Replace' transfer mode (found in the Paste Control
window).

Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

------------------------------

Date: Wed, 8 Sep 1999 14:40:53 +0200
From: Gary Chinga <gary.chinga@pfi.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: transparent background?
Message-ID: <c=NO%a=_%p=pfi%l=PFINT1-990908124053Z-1213@pfint1.pfi.no>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

You can use the Image Math option under Process to do that. Use the
logical operator 'or' to combine your original SEM image and the mask
you are using.

Gary.


>-----Original Message-----
>From:	Ludger Offerhaus [SMTP:ljo@gfz-potsdam.de]
>Sent:	8. september 1999 14:11
>To:	nih-image@io.ece.drexel.edu
>Subject:	transparent background?
>
>Dear Imagers!
>
>How can I turn a certain colour (i.c. white) into 'nothing' (i.e.
>transparent)?
>
>(Explanation: I would like to project a binary image (black lines on a
>white background) onto another image (a scanned SEM image of a ceramic
>aggregate). Is there a way to make the backgrounds transparent in Image and
>then to simply use copy-paste  for the purpose?
>A way to do this in object image and use my black lines as an overlay on
>the SEM-image would also be very fine, the problem is the colour-to-nothing
>conversion.)
>
>thank you!
>cheers,
>Ludger
>
>
>--
>Ludger Offerhaus
>GeoForschungsZentrum Potsdam
>Telegrafenberg, 14473 Potsdam, Deutschland
>Tel: +49 (0)331 288 1326 / 1390
>oder: 030 32 60 55 68 (auch AB)
>---
>
>

--------------------------------
End of nih-image-d Digest V99 Issue #206
****************************************

From nih-image-request@io.ece.drexel.edu Thu Sep  9 19:47 EDT 1999
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Date: Fri, 10 Sep 1999 01:26:34 +0200
To: nih-image@io.ece.drexel.edu
From: Beat Ludin <ludin@fmi.ch>
Subject: TWAIN
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Does anybody know of a TWAIN plug-in for Scion's PC-port of NIH-Image?
Or has anybody heard of a prospective release date for a 
TWAIN-capable version of ImageJ?

TIA,

	Beat


From nih-image-request@io.ece.drexel.edu Thu Sep  9 23:50 EDT 1999
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At 01:26 AM 9/10/99 +0200, you wrote:
>Does anybody know of a TWAIN plug-in for Scion's PC-port of NIH-Image?
>Or has anybody heard of a prospective release date for a 
>TWAIN-capable version of ImageJ?

ImageJ can acquire images from TWAIN sources such as scanners, digital cameras and frame grabbers using the Java Twain Package at http://internet.sk/gnome/. There are, however, some limitations. Twain is only supported on the PC, it doesn't work with some TWAIN devices, and there is no 16-bit support.

-wayne


From nih-image-request@io.ece.drexel.edu Fri Sep 10 09:31 EDT 1999
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Date: Fri, 10 Sep 1999 13:22:07 GMT
From: Simon <scollins@dmu.ac.uk>
Subject: Point Counting Grids!
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From nih-image-request@io.ece.drexel.edu Fri Sep 10 09:32 EDT 1999
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Date: Fri, 10 Sep 1999 14:10:57 +0100
From: Simon <scollins@dmu.ac.uk>
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Can anyone help please?.

I've been using a modification of the grid option from the 'edit' macro of Image
PC to generate a series of rectilinear point counting grids on NIH Image Ver
1.61 in order to assess the change in fibre density as a function of % depth of
specimen.

However, the material has a natural curvature and therefore a rectilinear grid
is less than ideal. Hence I wish to generate grids comprised of equally spaced
arcs that match the external curvature of the specimen.

Unfortunately as I am dealing with a biological material both the curvature and
the specimen depth varies between individual samples.  I would therefore like to
have the ability to change either the curvature of the arc(albeit with a small
range), or the pixel spacing between the arcs on each grid.

I would welcome any thoughts, ideas etc as to whether it is possible to design a
macro to generate such grids? and if so, how to write such a macro.

Regards

Simon Collins
PhD student
De Montfort University
UK.




From nih-image-request@io.ece.drexel.edu Fri Sep 10 17:05 EDT 1999
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Subject: Calculating "volume"
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I am looking to calculate the integrated area x density of an 
image.  Essentially, what I would like is to know the volume under a 
surface plot.

I am dealing with images that aren't very distinct from the background, so 
I have applied an 8-gray LUT to them...  thus, the background has a value 
of 0, and my regions of interest have distinct intensities.  I am trying to 
compare the area and intensity of 2 images (before and after a reaction).

If anyone knows of a procedure to calculate this information, or can direct 
me to an appropriate resource, I would greatly appreciate it.

Thanks,
	mike

+++++++++++++++++++++++++++++++++
Michael O'Donnell
Hopkins Marine Station, Stanford University
Oceanview Boulevard
Pacific Grove, CA 93950
mooseo@stanford.edu
++++++++++++++++++++++++++++++++


From nih-image-d-request@io.ece.drexel.edu Fri Sep 10 17:06 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #207
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 207

Today's Topics:
  TWAIN                                 [ Beat Ludin <ludin@fmi.ch> ]
  Re: TWAIN                             [ Wayne Rasband <wayne@codon.nih.gov> ]
  Point Counting Grids!                 [ Simon <scollins@dmu.ac.uk> ]
  Point Counting Grids!                 [ Simon <scollins@dmu.ac.uk> ]
  Calculating "volume"                  [ "Michael O'Donnell" <mooseo@stanfor ]

------------------------------

Date: Fri, 10 Sep 1999 01:26:34 +0200
From: Beat Ludin <ludin@fmi.ch>
To: nih-image@io.ece.drexel.edu
Subject: TWAIN
Message-Id: <v04205500b3fdef88a03e@[195.24.84.58]>
Content-Type: text/plain; charset="us-ascii" ; format="flowed"

Does anybody know of a TWAIN plug-in for Scion's PC-port of NIH-Image?
Or has anybody heard of a prospective release date for a 
TWAIN-capable version of ImageJ?

TIA,

	Beat

------------------------------

Date: Thu, 09 Sep 1999 23:44:30 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: TWAIN
Message-Id: <3.0.5.32.19990909234430.00a14100@codon.nih.gov>
Content-Type: text/plain; charset="us-ascii"

At 01:26 AM 9/10/99 +0200, you wrote:
>Does anybody know of a TWAIN plug-in for Scion's PC-port of NIH-Image?
>Or has anybody heard of a prospective release date for a 
>TWAIN-capable version of ImageJ?

ImageJ can acquire images from TWAIN sources such as scanners, digital cameras and frame grabbers using the Java Twain Package at http://internet.sk/gnome/. There are, however, some limitations. Twain is only supported on the PC, it doesn't work with some TWAIN devices, and there is no 16-bit support.

-wayne

------------------------------

Date: Fri, 10 Sep 1999 14:10:57 +0100
From: Simon <scollins@dmu.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Point Counting Grids!
Message-ID: <37D90361.17C2065D@dmu.ac.uk>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Can anyone help please?.

I've been using a modification of the grid option from the 'edit' macro of Image
PC to generate a series of rectilinear point counting grids on NIH Image Ver
1.61 in order to assess the change in fibre density as a function of % depth of
specimen.

However, the material has a natural curvature and therefore a rectilinear grid
is less than ideal. Hence I wish to generate grids comprised of equally spaced
arcs that match the external curvature of the specimen.

Unfortunately as I am dealing with a biological material both the curvature and
the specimen depth varies between individual samples.  I would therefore like to
have the ability to change either the curvature of the arc(albeit with a small
range), or the pixel spacing between the arcs on each grid.

I would welcome any thoughts, ideas etc as to whether it is possible to design a
macro to generate such grids? and if so, how to write such a macro.

Regards

Simon Collins
PhD student
De Montfort University
UK.

------------------------------

Date: Fri, 10 Sep 1999 13:22:07 GMT
From: Simon <scollins@dmu.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Point Counting Grids!
Message-ID: <4DB4A95C8B@curie>


------------------------------

Date: Fri, 10 Sep 1999 13:48:09 -0700
From: "Michael O'Donnell" <mooseo@stanford.edu>
To: nih-image@io.ece.drexel.edu
Subject: Calculating "volume"
Message-Id: <4.2.0.58.19990910134357.009e61f0@mooseo.pobox.stanford.edu>
Content-Type: text/plain; charset="us-ascii"; format=flowed

I am looking to calculate the integrated area x density of an 
image.  Essentially, what I would like is to know the volume under a 
surface plot.

I am dealing with images that aren't very distinct from the background, so 
I have applied an 8-gray LUT to them...  thus, the background has a value 
of 0, and my regions of interest have distinct intensities.  I am trying to 
compare the area and intensity of 2 images (before and after a reaction).

If anyone knows of a procedure to calculate this information, or can direct 
me to an appropriate resource, I would greatly appreciate it.

Thanks,
	mike

+++++++++++++++++++++++++++++++++
Michael O'Donnell
Hopkins Marine Station, Stanford University
Oceanview Boulevard
Pacific Grove, CA 93950
mooseo@stanford.edu
++++++++++++++++++++++++++++++++

--------------------------------
End of nih-image-d Digest V99 Issue #207
****************************************

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Date: Fri, 10 Sep 1999 14:42:39 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
cc: kardi@plan.civil.tohoku.ac.jp
Subject: Re: SliceNumber
Message-ID: <1437870.3145963359@huginn.medicine.washington.edu>
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I am not quite sure what you mean by puttin them in the same result, but
you can put the slice number in one results array, and your x and y
coordinates in another, that hs the same index. Here are som fragments of
macros that do something similar:

macro 'Set up measurements [M]';
begin
ResetCounter;
SetUser1Label('Lumen');
SetUser2Label('Slice_No');
SetOptions('Area, User1, User2');
CurWindow := WindowTitle;
end;

macro 'Measure Lumen [L]';
begin
Measure;
rUser1[rCount] := rArea[rCount];
rUser2[rCount] := SliceNumber;
ShowResults;
KillROI;
SelectWindow(CurWindow);
end;


--On Wed, Aug 25, 1999 10:43 AM +0900 kardi@plan.civil.tohoku.ac.jp wrote:

> 
> Is there any body know how to record XY coordinates and slice number of a
> stack in one result?
> Thanks.
> Kardi Teknomo
> kardi@plan.civil.tohoku.ac.jp
> 





From nih-image-request@io.ece.drexel.edu Fri Sep 10 18:01 EDT 1999
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Date: Fri, 10 Sep 1999 14:47:44 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
cc: "Michael O'Donnell" <mooseo@stanford.edu>
Subject: Re: Calculating "volume"
Message-ID: <1456201.3145963664@huginn.medicine.washington.edu>
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I may be missing something, but if you select the area, there are functions
for the area, and the mean pixel value, and multiplying these two should
give you a "volume".

DTL

--On Fri, Sep 10, 1999 1:48 PM -0700 Michael O'Donnell
<mooseo@stanford.edu> wrote:

> I am looking to calculate the integrated area x density of an 
> image.  Essentially, what I would like is to know the volume under a 
> surface plot.
> 
> I am dealing with images that aren't very distinct from the background,
> so  I have applied an 8-gray LUT to them...  thus, the background has a
> value  of 0, and my regions of interest have distinct intensities.  I am
> trying to  compare the area and intensity of 2 images (before and after a
> reaction).
> 
> If anyone knows of a procedure to calculate this information, or can
> direct  me to an appropriate resource, I would greatly appreciate it.
> 
> Thanks,
>	 mike
> 
> +++++++++++++++++++++++++++++++++
> Michael O'Donnell
> Hopkins Marine Station, Stanford University
> Oceanview Boulevard
> Pacific Grove, CA 93950
> mooseo@stanford.edu
> ++++++++++++++++++++++++++++++++
> 





From nih-image-request@io.ece.drexel.edu Fri Sep 10 18:29 EDT 1999
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Date: Fri, 10 Sep 1999 15:15:33 -0700
To: nih-image@io.ece.drexel.edu
From: "Michael O'Donnell" <mooseo@stanford.edu>
Subject: Re: Calculating "volume"
In-Reply-To: <1456201.3145963664@huginn.medicine.washington.edu>
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No, you're not missing a thing.  That is exactly what I am trying to do.  I 
am really looking for a way to automate the process of taking 6 density 
slices and then having to go over them with the wand tool to measure each 
area element within a particular slice.

Since the background is 0, I would like to come up with a function that 
would find the area x pixel value for all non-zero pixels.

Thanks for your help.

cheers,
         mike

At 02:47 PM 9/10/1999 -0700, you wrote:
>I may be missing something, but if you select the area, there are functions
>for the area, and the mean pixel value, and multiplying these two should
>give you a "volume".
>
>DTL
>
>--On Fri, Sep 10, 1999 1:48 PM -0700 Michael O'Donnell
><mooseo@stanford.edu> wrote:
>
> > I am looking to calculate the integrated area x density of an
> > image.  Essentially, what I would like is to know the volume under a
> > surface plot.
> >
> > I am dealing with images that aren't very distinct from the background,
> > so  I have applied an 8-gray LUT to them...  thus, the background has a
> > value  of 0, and my regions of interest have distinct intensities.  I am
> > trying to  compare the area and intensity of 2 images (before and after a
> > reaction).
> >
> > If anyone knows of a procedure to calculate this information, or can
> > direct  me to an appropriate resource, I would greatly appreciate it.
> >
> > Thanks,
> >       mike
> >
> > +++++++++++++++++++++++++++++++++
> > Michael O'Donnell
> > Hopkins Marine Station, Stanford University
> > Oceanview Boulevard
> > Pacific Grove, CA 93950
> > mooseo@stanford.edu
> > ++++++++++++++++++++++++++++++++
> >
>
>
>

+++++++++++++++++++++++++++++++++
Michael O'Donnell
Hopkins Marine Station, Stanford University
Oceanview Boulevard
Pacific Grove, CA 93950
mooseo@stanford.edu
++++++++++++++++++++++++++++++++


From nih-image-d-request@io.ece.drexel.edu Sat Sep 11 18:02 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 208

Today's Topics:
  Re: SliceNumber                       [ David Linker <dtlinker@u.washington ]
  Re: Calculating "volume"              [ David Linker <dtlinker@u.washington ]
  Re: Calculating "volume"              [ "Michael O'Donnell" <mooseo@stanfor ]
  Help one more time (I hope)           [ lillian c becker <lbecke01@fiu.edu> ]

------------------------------

Date: Fri, 10 Sep 1999 14:42:39 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
cc: kardi@plan.civil.tohoku.ac.jp
Subject: Re: SliceNumber
Message-ID: <1437870.3145963359@huginn.medicine.washington.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

I am not quite sure what you mean by puttin them in the same result, but
you can put the slice number in one results array, and your x and y
coordinates in another, that hs the same index. Here are som fragments of
macros that do something similar:

macro 'Set up measurements [M]';
begin
ResetCounter;
SetUser1Label('Lumen');
SetUser2Label('Slice_No');
SetOptions('Area, User1, User2');
CurWindow := WindowTitle;
end;

macro 'Measure Lumen [L]';
begin
Measure;
rUser1[rCount] := rArea[rCount];
rUser2[rCount] := SliceNumber;
ShowResults;
KillROI;
SelectWindow(CurWindow);
end;


--On Wed, Aug 25, 1999 10:43 AM +0900 kardi@plan.civil.tohoku.ac.jp wrote:

> 
> Is there any body know how to record XY coordinates and slice number of a
> stack in one result?
> Thanks.
> Kardi Teknomo
> kardi@plan.civil.tohoku.ac.jp
> 

------------------------------

Date: Fri, 10 Sep 1999 14:47:44 -0700
From: David Linker <dtlinker@u.washington.edu>
To: nih-image@io.ece.drexel.edu
cc: "Michael O'Donnell" <mooseo@stanford.edu>
Subject: Re: Calculating "volume"
Message-ID: <1456201.3145963664@huginn.medicine.washington.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

I may be missing something, but if you select the area, there are functions
for the area, and the mean pixel value, and multiplying these two should
give you a "volume".

DTL

--On Fri, Sep 10, 1999 1:48 PM -0700 Michael O'Donnell
<mooseo@stanford.edu> wrote:

> I am looking to calculate the integrated area x density of an 
> image.  Essentially, what I would like is to know the volume under a 
> surface plot.
> 
> I am dealing with images that aren't very distinct from the background,
> so  I have applied an 8-gray LUT to them...  thus, the background has a
> value  of 0, and my regions of interest have distinct intensities.  I am
> trying to  compare the area and intensity of 2 images (before and after a
> reaction).
> 
> If anyone knows of a procedure to calculate this information, or can
> direct  me to an appropriate resource, I would greatly appreciate it.
> 
> Thanks,
>	 mike
> 
> +++++++++++++++++++++++++++++++++
> Michael O'Donnell
> Hopkins Marine Station, Stanford University
> Oceanview Boulevard
> Pacific Grove, CA 93950
> mooseo@stanford.edu
> ++++++++++++++++++++++++++++++++
> 

------------------------------

Date: Fri, 10 Sep 1999 15:15:33 -0700
From: "Michael O'Donnell" <mooseo@stanford.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Calculating "volume"
Message-Id: <4.2.0.58.19990910151335.009f0f00@mooseo.pobox.stanford.edu>
Content-Type: text/plain; charset="us-ascii"; format=flowed

No, you're not missing a thing.  That is exactly what I am trying to do.  I 
am really looking for a way to automate the process of taking 6 density 
slices and then having to go over them with the wand tool to measure each 
area element within a particular slice.

Since the background is 0, I would like to come up with a function that 
would find the area x pixel value for all non-zero pixels.

Thanks for your help.

cheers,
         mike

At 02:47 PM 9/10/1999 -0700, you wrote:
>I may be missing something, but if you select the area, there are functions
>for the area, and the mean pixel value, and multiplying these two should
>give you a "volume".
>
>DTL
>
>--On Fri, Sep 10, 1999 1:48 PM -0700 Michael O'Donnell
><mooseo@stanford.edu> wrote:
>
> > I am looking to calculate the integrated area x density of an
> > image.  Essentially, what I would like is to know the volume under a
> > surface plot.
> >
> > I am dealing with images that aren't very distinct from the background,
> > so  I have applied an 8-gray LUT to them...  thus, the background has a
> > value  of 0, and my regions of interest have distinct intensities.  I am
> > trying to  compare the area and intensity of 2 images (before and after a
> > reaction).
> >
> > If anyone knows of a procedure to calculate this information, or can
> > direct  me to an appropriate resource, I would greatly appreciate it.
> >
> > Thanks,
> >       mike
> >
> > +++++++++++++++++++++++++++++++++
> > Michael O'Donnell
> > Hopkins Marine Station, Stanford University
> > Oceanview Boulevard
> > Pacific Grove, CA 93950
> > mooseo@stanford.edu
> > ++++++++++++++++++++++++++++++++
> >
>
>
>

+++++++++++++++++++++++++++++++++
Michael O'Donnell
Hopkins Marine Station, Stanford University
Oceanview Boulevard
Pacific Grove, CA 93950
mooseo@stanford.edu
++++++++++++++++++++++++++++++++

------------------------------

Date: Sat, 11 Sep 1999 17:46:08 -0400 (EDT)
From: lillian c becker <lbecke01@fiu.edu>
To: Jonathan WISCO <jjwisco@cajal-1.bu.edu>, micaela_qoya@yahoo.com,
        nih-image@io.ece.drexel.edu
Subject: Help one more time (I hope)
Message-ID: <Pine.SOL.3.96.990911173121.22039A-100000@solix4-64>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hello,

	First, thank you to all of you who sent helpful suggestions
before.  I had to deal with another project and did not start using your
suggestions until this weekend.  I was about to send you
thanks yous this week.  I am sorry for the delay.

	I am having one more problem.  It is probably something stupid and
small but I have wasted the entire day trying to figure it out and I am
running out of time.

	I am trying to measure areas.  This is how I have been attempting
to do it:

	1) Use Photoshop to convert jpeg files to tiff.

	2) Opening file in Scion.  

	3) Use the line select tool to draw a line on my 1cm scale in the
picture.

	4) In Set Scale I change Known Distance to 1.0 and units to
centimeters.  OK.  Should Measured Distance and Scale have the same
numbers?

	5) I use the ploygonal and freehand selection tools to outline my
area.

	6) I either cntl 1 or Analyze - Measure.

	7)  My area comes up as 0.  

	I somehow got a measurement of 84.---cm^2 on a measurement of my 1
cm^2 scale when I "filled" the image.
What am I missing?  I have been pulling my hair out all day and I am on a
tight deadline.  Please help me.

Loads and Loads of thanks,
Lill


Lill Becker
Department of Biology
Florida International University
Miami, FL  33199   USA

	*******************************************
	*Are science and magic mutually exclusive?*
	*******************************************

--------------------------------
End of nih-image-d Digest V99 Issue #208
****************************************

From nih-image-request@io.ece.drexel.edu Sat Sep 11 18:03 EDT 1999
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Date: Sat, 11 Sep 1999 17:46:08 -0400 (EDT)
From: lillian c becker <lbecke01@fiu.edu>
X-Sender: lbecke01@solix4-64
To: Jonathan WISCO <jjwisco@cajal-1.bu.edu>, micaela_qoya@yahoo.com,
        nih-image@io.ece.drexel.edu
Subject: Help one more time (I hope)
In-Reply-To: <199908192121.RAA17974@bu.edu>
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Hello,

	First, thank you to all of you who sent helpful suggestions
before.  I had to deal with another project and did not start using your
suggestions until this weekend.  I was about to send you
thanks yous this week.  I am sorry for the delay.

	I am having one more problem.  It is probably something stupid and
small but I have wasted the entire day trying to figure it out and I am
running out of time.

	I am trying to measure areas.  This is how I have been attempting
to do it:

	1) Use Photoshop to convert jpeg files to tiff.

	2) Opening file in Scion.  

	3) Use the line select tool to draw a line on my 1cm scale in the
picture.

	4) In Set Scale I change Known Distance to 1.0 and units to
centimeters.  OK.  Should Measured Distance and Scale have the same
numbers?

	5) I use the ploygonal and freehand selection tools to outline my
area.

	6) I either cntl 1 or Analyze - Measure.

	7)  My area comes up as 0.  

	I somehow got a measurement of 84.---cm^2 on a measurement of my 1
cm^2 scale when I "filled" the image.
What am I missing?  I have been pulling my hair out all day and I am on a
tight deadline.  Please help me.

Loads and Loads of thanks,
Lill


Lill Becker
Department of Biology
Florida International University
Miami, FL  33199   USA

	*******************************************
	*Are science and magic mutually exclusive?*
	*******************************************


From nih-image-request@io.ece.drexel.edu Sat Sep 11 21:00 EDT 1999
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Subject: Re: Help one more time (I hope)
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Lillian Becker said:

[snip]
>I am trying to measure areas.
[snip]

>	4) In Set Scale I change Known Distance to 1.0 and units to
>centimeters.  OK.  Should Measured Distance and Scale have the same
>numbers?

No. The 'Scale' number is calculated for you, after you have entered the
'Known Distance' and selected the units.

[snip]
>	7)  My area comes up as 0.
[snip]

Under 'Analyze: Options ...', you will observe 'Digits right of Decimal
Point (0-8)', with default 0 (i.e. no decimals). Make sure that you have
selected your required number of decimals (e.g. 2); otherwise, measurements
<1 will appear to be 0.

Hope this helps.



Doug Mason

Mason Geoscience Pty Ltd
Petrological Services for the Exploration and Mining Industry
email   : drmason@interconnect.com.au
post    : PO Box 78, Glenside  SA  5065, Australia
phone   : +61-8-83901507
fax     : +61-8-83901194



From nih-image-request@io.ece.drexel.edu Sun Sep 12 09:45 EDT 1999
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Date: Sun, 12 Sep 1999 09:29:26 -0400 (EDT)
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Hi,

	I am still having problems with the area measurements but I have
discovered something that may shed some light onto the answer.  Scion will
measure a rectangle made from the retangular selection tool.  It will not,
however, make a measurement from any area selected by the free-hand tool
or the polygonal tool.  Any ideas?  The measurement I got from the "fill"
was actually a measurement made with rectangular tool.

	Thank you for any help you can provide.

TTFN,
Lill

Lill Becker
Department of Biology
Florida International University
Miami, FL  33199   USA

	*******************************************
	*Are science and magic mutually exclusive?*
	*******************************************


From nih-image-request@io.ece.drexel.edu Mon Sep 13 05:26 EDT 1999
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                   NIH-image Mailing List Help 
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6)  Send a second email
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then use Unix metacharacters to get more than one file. * matches any string.
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From nih-image-d-request@io.ece.drexel.edu Mon Sep 13 05:28 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 209

Today's Topics:
  Re: Help one more time (I hope)       [ Doug Mason <drmason@interconnect.co ]
  area measurememts amendment           [ lillian c becker <lbecke01@fiu.edu> ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]

------------------------------

Date: Sun, 12 Sep 1999 10:16:50 +1030
From: Doug Mason <drmason@interconnect.com.au>
To: nih-image@io.ece.drexel.edu
Subject: Re: Help one more time (I hope)
Message-Id: <l03110701b40098b4a9e3@[210.8.6.141]>
Content-Type: text/plain; charset="us-ascii"

Lillian Becker said:

[snip]
>I am trying to measure areas.
[snip]

>	4) In Set Scale I change Known Distance to 1.0 and units to
>centimeters.  OK.  Should Measured Distance and Scale have the same
>numbers?

No. The 'Scale' number is calculated for you, after you have entered the
'Known Distance' and selected the units.

[snip]
>	7)  My area comes up as 0.
[snip]

Under 'Analyze: Options ...', you will observe 'Digits right of Decimal
Point (0-8)', with default 0 (i.e. no decimals). Make sure that you have
selected your required number of decimals (e.g. 2); otherwise, measurements
<1 will appear to be 0.

Hope this helps.



Doug Mason

Mason Geoscience Pty Ltd
Petrological Services for the Exploration and Mining Industry
email   : drmason@interconnect.com.au
post    : PO Box 78, Glenside  SA  5065, Australia
phone   : +61-8-83901507
fax     : +61-8-83901194

------------------------------

Date: Sun, 12 Sep 1999 09:29:26 -0400 (EDT)
From: lillian c becker <lbecke01@fiu.edu>
To: nih-image@io.ece.drexel.edu
Subject: area measurememts amendment
Message-ID: <Pine.SOL.3.96.990912092554.15352B-100000@solix4-64>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi,

	I am still having problems with the area measurements but I have
discovered something that may shed some light onto the answer.  Scion will
measure a rectangle made from the retangular selection tool.  It will not,
however, make a measurement from any area selected by the free-hand tool
or the polygonal tool.  Any ideas?  The measurement I got from the "fill"
was actually a measurement made with rectangular tool.

	Thank you for any help you can provide.

TTFN,
Lill

Lill Becker
Department of Biology
Florida International University
Miami, FL  33199   USA

	*******************************************
	*Are science and magic mutually exclusive?*
	*******************************************

------------------------------

Date: Mon, 13 Sep 1999 05:05:01 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199909130905.FAA26976@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
                   ---------------------------
     


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Archive
-------
Every submission sent to this list is archived.	 Following are the commands
used to access the archive.  Send Email to nih-image-request@biomed.drexel.edu
with the command in the Subject line or in the body of the message.

Tips by Henry M. Thomas, 

0)  Remember that Archive is case-sensitive.
1)  Use the proper address for the Archive
        nih-image-request@biomed.drexel.edu
2)  title the Subject line of your email    archive
3)  turn off (or don't send) your email Signature if you have one
4)  In the body of the email write
         ls latest
5)  Send it. latest is a directory containing the latest 50 files. The ls
command returns you a list of the filenumbers of the current 50 files.
(currently in the 800's).  so latest/862 is a filename.
6)  Send a second email
         get latest/862         or whatever filenumber you need
7)   But you probaly want a batch.  If you want more than 16, start the
body of the email with
         archive maxfiles 35    or however many you want
then use Unix metacharacters to get more than one file. * matches any string.
? matches any single character. []'s matches any single character shown in
the brackets.
         get latest/*           all 50
         get latest/8[3-6]?     all from 830 to 869

8)   To search for text (e.g. the word color) in all the files in the


directory latest use egrep
         egrep color latest/*
then use get to get the files you want.
This archive server knows the following commands:

get filename ...
ls directory ...
egrep case_insensitive_regular_expression filename ...
maxfiles nnn
version
quit

Aliases for 'get': send, sendme, getme, gimme, retrieve, mail
Aliases for 'ls': dir, directory, list, show
Aliases for 'egrep': search, grep, fgrep, find
Aliases for 'quit': exit

Lines starting with a '#' are ignored.
Multiple commands per mail are allowed.
Setting maxfiles to zero will remove the limit (to protect you against
yourself no more than maxfiles files will be returned per request).
Egrep supports most common flags.
If you append a non-standard signature, you should use the quit command
to prevent the archive server from interpreting the signature.

Examples:
ls latest
get latest/12
egrep some.word latest/*
--

--------------------------------
End of nih-image-d Digest V99 Issue #209
****************************************

From nih-image-request@io.ece.drexel.edu Mon Sep 13 09:50 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: Doug Mason <drmason@interconnect.com.au>
Subject: Re: area measurememts amendment
Resent-Message-ID: <"mUCgR3.0.Wm1.ArFtt"@io>
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Lill Becker said:

[snip]
>	I am still having problems with the area measurements but I have
>discovered something that may shed some light onto the answer.  Scion will
>measure a rectangle made from the retangular selection tool.  It will not,
>however, make a measurement from any area selected by the free-hand tool
>or the polygonal tool.  Any ideas?  The measurement I got from the "fill"
>was actually a measurement made with rectangular tool.

I have checked NIH-Image v1.60 and Scion Image v1.60, and both applications
work properly. That is, they both generate sensible measurements using a
rectangular, a freehand, and a polygon selection tool. Note that the
measurements will refer to the _entire_ selection area if you have not
density sliced the image; if you have density sliced the image, then only
the area 'hilighted' will be measured.

Note that I have checked Image on the Mac under MacOS v8.1. If you are
running Scion Image on the PC, then I can offer no suggestions.

Good luck,


Doug Mason

Mason Geoscience Pty Ltd
Petrological Services for the Exploration and Mining Industry
email   : drmason@interconnect.com.au
post    : PO Box 78, Glenside  SA  5065, Australia
phone   : +61-8-83901507
fax     : +61-8-83901194



From nih-image-request@io.ece.drexel.edu Mon Sep 13 12:28 EDT 1999
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	Mon, 13 Sep 1999 12:28:21 -0400 (EDT)
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Message-ID: <69DAA178B649D3118F160008C7F3EFFB019A97@SLUHEXCH02>
From: "Bicknese, Alma" <bicknesa@SLUCARE1.SLUH.EDU>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Simple reference?
Date: Mon, 13 Sep 1999 11:05:48 -0500
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I am a beginner attempting to use Image PC in my laboratory.  I am having
difficulty figuring out what should be fairly easy tasks.  I have downloaded
the manual and also the Image tutorial from the NIH webpage, but these don't
explain much.  (For instance, how do I use Image and Photoshop together?)

Is there something like "Image for Dummies" or a more extensive manual
available for people like me?

Thanks
A. Bick


From nih-image-request@io.ece.drexel.edu Mon Sep 13 12:56 EDT 1999
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Date: Mon, 13 Sep 1999 11:33:50 -0500
From: Michael Herron <herro001@maroon.tc.umn.edu>
Reply-To: Michael J Herron <herro001@maroon.tc.umn.edu>
Organization: U of MN, Medicine, Infectious Diseases
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Alma,

No image for dummies...(insert joke here)...

but there are a number of very usefull files you can download at:

http://rsb.info.nih.gov/nih-image/Default.html

and don't be shy to ask specific questions here (at the listserv).

Mike

"Bicknese, Alma" wrote:
> 
> I am a beginner attempting to use Image PC in my laboratory.  I am having
> difficulty figuring out what should be fairly easy tasks.  I have downloaded
> the manual and also the Image tutorial from the NIH webpage, but these don't
> explain much.  (For instance, how do I use Image and Photoshop together?)
> 
> Is there something like "Image for Dummies" or a more extensive manual
> available for people like me?
> 
> Thanks
> A. Bick

-- 

   _________________________________________________
     /  Michael J. Herron                          /
    /     U of MN,Medicine/Infectious Diseases    /
   /        herro001@maroon.tc.umn.edu           /
  /           http://128.101.243.213            /
 /_____________________________________________/


From nih-image-d-request@io.ece.drexel.edu Tue Sep 14 06:14 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #210
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 210

Today's Topics:
  Re: area measurememts amendment       [ Doug Mason <drmason@interconnect.co ]
  Simple reference?                     [ "Bicknese, Alma" <bicknesa@SLUCARE1 ]
  Re: Simple reference?                 [ Michael Herron <herro001@maroon.tc. ]

------------------------------

Date: Mon, 13 Sep 1999 23:00:31 +1030
From: Doug Mason <drmason@interconnect.com.au>
To: nih-image@io.ece.drexel.edu
Subject: Re: area measurememts amendment
Message-Id: <l03110700b4029c97cd9c@[210.8.6.141]>
Content-Type: text/plain; charset="us-ascii"

Lill Becker said:

[snip]
>	I am still having problems with the area measurements but I have
>discovered something that may shed some light onto the answer.  Scion will
>measure a rectangle made from the retangular selection tool.  It will not,
>however, make a measurement from any area selected by the free-hand tool
>or the polygonal tool.  Any ideas?  The measurement I got from the "fill"
>was actually a measurement made with rectangular tool.

I have checked NIH-Image v1.60 and Scion Image v1.60, and both applications
work properly. That is, they both generate sensible measurements using a
rectangular, a freehand, and a polygon selection tool. Note that the
measurements will refer to the _entire_ selection area if you have not
density sliced the image; if you have density sliced the image, then only
the area 'hilighted' will be measured.

Note that I have checked Image on the Mac under MacOS v8.1. If you are
running Scion Image on the PC, then I can offer no suggestions.

Good luck,


Doug Mason

Mason Geoscience Pty Ltd
Petrological Services for the Exploration and Mining Industry
email   : drmason@interconnect.com.au
post    : PO Box 78, Glenside  SA  5065, Australia
phone   : +61-8-83901507
fax     : +61-8-83901194

------------------------------

Date: Mon, 13 Sep 1999 11:05:48 -0500
From: "Bicknese, Alma" <bicknesa@SLUCARE1.SLUH.EDU>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Simple reference?
Message-ID: <69DAA178B649D3118F160008C7F3EFFB019A97@SLUHEXCH02>
Content-Type: text/plain

I am a beginner attempting to use Image PC in my laboratory.  I am having
difficulty figuring out what should be fairly easy tasks.  I have downloaded
the manual and also the Image tutorial from the NIH webpage, but these don't
explain much.  (For instance, how do I use Image and Photoshop together?)

Is there something like "Image for Dummies" or a more extensive manual
available for people like me?

Thanks
A. Bick

------------------------------

Date: Mon, 13 Sep 1999 11:33:50 -0500
From: Michael Herron <herro001@maroon.tc.umn.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Simple reference?
Message-Id: <37DD2757.11A18FD0@tc.umn.edu>
Content-Type: text/plain; charset=us-ascii
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Alma,

No image for dummies...(insert joke here)...

but there are a number of very usefull files you can download at:

http://rsb.info.nih.gov/nih-image/Default.html

and don't be shy to ask specific questions here (at the listserv).

Mike

"Bicknese, Alma" wrote:
> 
> I am a beginner attempting to use Image PC in my laboratory.  I am having
> difficulty figuring out what should be fairly easy tasks.  I have downloaded
> the manual and also the Image tutorial from the NIH webpage, but these don't
> explain much.  (For instance, how do I use Image and Photoshop together?)
> 
> Is there something like "Image for Dummies" or a more extensive manual
> available for people like me?
> 
> Thanks
> A. Bick

-- 

   _________________________________________________
     /  Michael J. Herron                          /
    /     U of MN,Medicine/Infectious Diseases    /
   /        herro001@maroon.tc.umn.edu           /
  /           http://128.101.243.213            /
 /_____________________________________________/

--------------------------------
End of nih-image-d Digest V99 Issue #210
****************************************

From nih-image-request@io.ece.drexel.edu Tue Sep 14 18:09 EDT 1999
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Date: Tue, 14 Sep 1999 17:54:20 -0500
To: nih-image@io.ece.drexel.edu
From: Helen Rodd <hrodd@zoo.utoronto.ca>
Subject: storing images from a Nikon Coolpix digital camera
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Hello,

If I store photos at full size (1600x1200) pixels (in JPEG), I can
only view a portion of the pictures using NIH Image.  If
I rescale the picture to fit the window, the colours
in the photo change.  I can view the entire photo
with NIH Image if I store the photo at the VGA (640x480 pixels)
setting but the image quality is, of course, not as good.

Is there a way to save photos at a higher resolution but
to maintain the colours when I reduce the size of the image
so that I can see the whole thing at one time in NIH Image?

Would it be better to save the files in TIFF format rather
than JPEG?

Thanks very much for any advice,
Helen



From nih-image-request@io.ece.drexel.edu Wed Sep 15 10:50 EDT 1999
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From: "Shiddhartha Nandy" <sn@aii.co.uk>
To: "nih listserver - posting" <nih-image@io.ece.drexel.edu>
Subject: Mac software engineer wanted in UK
Date: Wed, 15 Sep 1999 15:28:25 +0100
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Put together two of the worlds most dynamic industries and you have an
exciting proposition on your hands. On one side is information technology,
providing the means to transform society. On the other is biotechnology, an
industry with an increasingly important place in extending the frontiers of
science, and how we live our lives. Now you have an opportunity to work in
both. Applied Imaging, based at the new International Centre for Life in the
heart of Newcastle, are world leaders in the design and supply of
cytogenetic systems for clinical and research use. Due to recent expansions
we now have the following key positions available.

Software Engineers
A number of positions are available working within a team developing imaging
applications for biotechnology applications.

The positions require previous experience of developing applications on the
Apple Macintosh platform. A working knowledge of image processing is also
required. Experience in the area of biotechnology is not required, as
necessary training will be provided. You will have at least 3 years
experience working with C or C++.
Applied Imaging offers a rewards package which includes a competitive
salary, free life insurance and a range of additional benefits, including
contributory pension.

Email, fax or mail CVs to Paddy O'Kelly (details below) mentioning where you
saw the vacancy

Paddy O'Kelly
Engineering Director
Psok@aii.co.uk

Applied Imaging International
BioScience Centre
Times Square
Newcastle upon Tyne
NE1 4EP
Fax: 0191 202 3101



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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #211
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 211

Today's Topics:
  storing images from a Nikon Coolpix   [ Helen Rodd <hrodd@zoo.utoronto.ca> ]
  Mac software engineer wanted in UK    [ "Shiddhartha Nandy" <sn@aii.co.uk> ]

------------------------------

Date: Tue, 14 Sep 1999 17:54:20 -0500
From: Helen Rodd <hrodd@zoo.utoronto.ca>
To: nih-image@io.ece.drexel.edu
Subject: storing images from a Nikon Coolpix digital camera
Message-Id: <l03130319b40480d40a3f@[128.100.72.213]>
Content-Type: text/plain; charset="us-ascii"

Hello,

If I store photos at full size (1600x1200) pixels (in JPEG), I can
only view a portion of the pictures using NIH Image.  If
I rescale the picture to fit the window, the colours
in the photo change.  I can view the entire photo
with NIH Image if I store the photo at the VGA (640x480 pixels)
setting but the image quality is, of course, not as good.

Is there a way to save photos at a higher resolution but
to maintain the colours when I reduce the size of the image
so that I can see the whole thing at one time in NIH Image?

Would it be better to save the files in TIFF format rather
than JPEG?

Thanks very much for any advice,
Helen

------------------------------

Date: Wed, 15 Sep 1999 15:28:25 +0100
From: "Shiddhartha Nandy" <sn@aii.co.uk>
To: "nih listserver - posting" <nih-image@io.ece.drexel.edu>
Subject: Mac software engineer wanted in UK
Message-ID: <004f01beff86$9218ec40$28807ac1@seer.aii.co.uk>
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Put together two of the worlds most dynamic industries and you have an
exciting proposition on your hands. On one side is information technology,
providing the means to transform society. On the other is biotechnology, an
industry with an increasingly important place in extending the frontiers of
science, and how we live our lives. Now you have an opportunity to work in
both. Applied Imaging, based at the new International Centre for Life in the
heart of Newcastle, are world leaders in the design and supply of
cytogenetic systems for clinical and research use. Due to recent expansions
we now have the following key positions available.

Software Engineers
A number of positions are available working within a team developing imaging
applications for biotechnology applications.

The positions require previous experience of developing applications on the
Apple Macintosh platform. A working knowledge of image processing is also
required. Experience in the area of biotechnology is not required, as
necessary training will be provided. You will have at least 3 years
experience working with C or C++.
Applied Imaging offers a rewards package which includes a competitive
salary, free life insurance and a range of additional benefits, including
contributory pension.

Email, fax or mail CVs to Paddy O'Kelly (details below) mentioning where you
saw the vacancy

Paddy O'Kelly
Engineering Director
Psok@aii.co.uk

Applied Imaging International
BioScience Centre
Times Square
Newcastle upon Tyne
NE1 4EP
Fax: 0191 202 3101

--------------------------------
End of nih-image-d Digest V99 Issue #211
****************************************

From nih-image-request@io.ece.drexel.edu Wed Sep 15 11:30 EDT 1999
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Date: Wed, 15 Sep 1999 16:11:40 +0100
To: nih-image@io.ece.drexel.edu
From: i.evans@ucl.ac.uk (Ian Evans)
Subject: RE: stats package for mac
Resent-Message-ID: <"FmMQW2.0.y43.BQxtt"@io>
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As promised here is a short summary of replies I recieved. Thanks to all
those who replied and apologies again for the off-topic nature of this
post.

Most people recomended Statview (www.statview.com). JMP and Minitab
(ww.minitab.com) were other suggestions, minitab however is no longer being
updated for the mac and no demo version was available. I think Statview is
probably the best option.

Thaks again for your help.

--------------------------------------------------------------
Ian Evans                               i.evans@ucl.ac.uk
Dept. of Molecular Endocrinology        Tel. 0171 504 9390
University College London.              Fax 0171 580 2737
Mortimer Street
London
W1N 8AA



From nih-image-request@io.ece.drexel.edu Wed Sep 15 11:55 EDT 1999
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Subject: Re: RE: stats package for mac
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Date: Wed, 15 Sep 1999 16:38:50 +0100 (BST)
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A bit late now, but for the P.C. (and possibly MAC) try SigmaStat.
It isn't quite as powerful as Minitab or SPSS but it will do most 
things and includes a wizard, through which it will recommend 
tests, will automatically test for normality and recommend an 
appropriate non-parametric test if needed and present the results 
with interpretation, annotating significant results with asterix's.

Very good package for the faint at heart.



From nih-image-request@io.ece.drexel.edu Wed Sep 15 13:06 EDT 1999
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Date: Wed, 15 Sep 1999 09:55:00 -0700
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From: connie temm <ctemm@Ag.Arizona.Edu>
Subject: Re: RE: stats package for mac
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Okay, where do you get it?

you wrote:

>A bit late now, but for the P.C. (and possibly MAC) try SigmaStat.
>It isn't quite as powerful as Minitab or SPSS but it will do most
>things and includes a wizard, through which it will recommend
>tests, will automatically test for normality and recommend an
>appropriate non-parametric test if needed and present the results
>with interpretation, annotating significant results with asterix's.
>
>Very good package for the faint at heart.


Constance J. Temm, Ph.D.      	University of Arizona
Tel.: (520) 621-8643    	Nutritional Sciences Dept.
Fax: 520 621 1396		632 Shantz Building
              			Tucson, AZ 85721  USA






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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 212

Today's Topics:
  RE: stats package for mac             [ i.evans@ucl.ac.uk (Ian Evans) ]
  Re: RE: stats package for mac         [ ort056@abdn.ac.uk ]
  Re: RE: stats package for mac         [ connie temm <ctemm@Ag.Arizona.Edu> ]

------------------------------

Date: Wed, 15 Sep 1999 16:11:40 +0100
From: i.evans@ucl.ac.uk (Ian Evans)
To: nih-image@io.ece.drexel.edu
Subject: RE: stats package for mac
Message-Id: <v01510100b40565a4c3f1@[192.168.0.69]>
Content-Type: text/plain; charset="us-ascii"

As promised here is a short summary of replies I recieved. Thanks to all
those who replied and apologies again for the off-topic nature of this
post.

Most people recomended Statview (www.statview.com). JMP and Minitab
(ww.minitab.com) were other suggestions, minitab however is no longer being
updated for the mac and no demo version was available. I think Statview is
probably the best option.

Thaks again for your help.

--------------------------------------------------------------
Ian Evans                               i.evans@ucl.ac.uk
Dept. of Molecular Endocrinology        Tel. 0171 504 9390
University College London.              Fax 0171 580 2737
Mortimer Street
London
W1N 8AA

------------------------------

Date: Wed, 15 Sep 1999 16:38:50 +0100 (BST)
From: ort056@abdn.ac.uk
To: nih-image@io.ece.drexel.edu
Subject: Re: RE: stats package for mac
Message-ID: <SIMEON.9909151650.M@pc10.surg.abdn.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

A bit late now, but for the P.C. (and possibly MAC) try SigmaStat.
It isn't quite as powerful as Minitab or SPSS but it will do most 
things and includes a wizard, through which it will recommend 
tests, will automatically test for normality and recommend an 
appropriate non-parametric test if needed and present the results 
with interpretation, annotating significant results with asterix's.

Very good package for the faint at heart.

------------------------------

Date: Wed, 15 Sep 1999 09:55:00 -0700
From: connie temm <ctemm@Ag.Arizona.Edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: RE: stats package for mac
Message-Id: <l03130309b4057fbd95cf@[128.196.130.192]>
Content-Type: text/plain; charset="us-ascii"

Okay, where do you get it?

you wrote:

>A bit late now, but for the P.C. (and possibly MAC) try SigmaStat.
>It isn't quite as powerful as Minitab or SPSS but it will do most
>things and includes a wizard, through which it will recommend
>tests, will automatically test for normality and recommend an
>appropriate non-parametric test if needed and present the results
>with interpretation, annotating significant results with asterix's.
>
>Very good package for the faint at heart.


Constance J. Temm, Ph.D.      	University of Arizona
Tel.: (520) 621-8643    	Nutritional Sciences Dept.
Fax: 520 621 1396		632 Shantz Building
              			Tucson, AZ 85721  USA

--------------------------------
End of nih-image-d Digest V99 Issue #212
****************************************

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> Okay, where do you get it?

SigmaStat / SigmaPlot used to be owned by Jandel but has been bought out by SPSS
for more details try:

http://www.spss.com/software/science/sigmaplot/analysis.htm 




From nih-image-request@io.ece.drexel.edu Thu Sep 16 13:44 EDT 1999
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Date: Thu, 16 Sep 1999 12:29:33 -0500
To: nih-image@io.ece.drexel.edu
From: jludtke@facstaff.wisc.edu (Jim Ludtke)
Subject:  CG-7 Scion Frame Grabber
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Hi all,

We have just installed a Scion CG-7 frame grabber on our Power Mac 7600.
Scion sent NIH Image version 1.62 to capture with. The problem I have is
that when I save an image (which looks great) and re-open it with NIH
Image, the image becomes very pixelated. However, if I open the same image
with Photoshop, the image is perfect. Is there a setting in NIH Image that
can fix this problem? It seems to me that I should be able to open an image
in the same program that I collected it with!

Thanks in advance!

Jim Ludtke
jludtke@facstaff.wisc.edu
Department of Pediatrics
U.W. Madison



From nih-image-request@io.ece.drexel.edu Thu Sep 16 18:52 EDT 1999
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From: Ray Hicks <rh208@cus.cam.ac.uk>
Subject: Re: Help one more time (I hope)
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Hi Lill,

You've probably missed your deadline by now, but you're (probably) also
missing the vital "Include Interior Holes" in the "Options..." dialog (from
the "Analysis" menu).  When you filled the shape, the "hole" was filled and
its area measured, when you didn't fill the shape there was nothing to
measure (probably).

I hope someone else got an answer to you in time (and that it's the right one)

Ray

>	I somehow got a measurement of 84.---cm^2 on a measurement of my 1
>cm^2 scale when I "filled" the image.
>What am I missing?  I have been pulling my hair out all day and I am on a
>tight deadline.  Please help me.
>
>Loads and Loads of thanks,
>Lill
>
>
>Lill Becker
>Department of Biology
>Florida International University
>Miami, FL  33199   USA
>
>	*******************************************
>	*Are science and magic mutually exclusive?*
>	*******************************************


                              Ray Hicks
________________________________________________________________________
|University of Cambridge          |Tel              01223 330149        |
|Department of Medicine           |Fax             01223 336846         |
|Level 5, Addenbrookes Hospital   |e-mail         <rh208@cus.cam.ac.uk> |
|Hills Road Cambridge             |Web  http://facsmac.med.cam.ac.uk    |
|CB2                              |ftp server  ftp://131.111.80.78      |
|UK                               |                                     |
|_________________________________|_____________________________________|



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From: nih-image-d-request@io.ece.drexel.edu
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 213

Today's Topics:
  Re: RE: stats package for mac         [ ort056@abdn.ac.uk ]
  CG-7 Scion Frame Grabber              [ jludtke@facstaff.wisc.edu (Jim Ludt ]
  Re: Help one more time (I hope)       [ Ray Hicks <rh208@cus.cam.ac.uk> ]
  IMage and Snapper                     [ David Knecht <knecht@uconn.edu> ]

------------------------------

Date: Thu, 16 Sep 1999 11:21:05 +0100 (BST)
From: ort056@abdn.ac.uk
To: nih-image@io.ece.drexel.edu
Subject: Re: RE: stats package for mac
Message-ID: <SIMEON.9909161105.A@pc10.surg.abdn.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

> Okay, where do you get it?

SigmaStat / SigmaPlot used to be owned by Jandel but has been bought out by SPSS
for more details try:

http://www.spss.com/software/science/sigmaplot/analysis.htm 

------------------------------

Date: Thu, 16 Sep 1999 12:29:33 -0500
From: jludtke@facstaff.wisc.edu (Jim Ludtke)
To: nih-image@io.ece.drexel.edu
Subject:  CG-7 Scion Frame Grabber
Message-Id: <199909161726.MAA34668@mail1.doit.wisc.edu>
Content-Type: text/plain; charset="us-ascii"

Hi all,

We have just installed a Scion CG-7 frame grabber on our Power Mac 7600.
Scion sent NIH Image version 1.62 to capture with. The problem I have is
that when I save an image (which looks great) and re-open it with NIH
Image, the image becomes very pixelated. However, if I open the same image
with Photoshop, the image is perfect. Is there a setting in NIH Image that
can fix this problem? It seems to me that I should be able to open an image
in the same program that I collected it with!

Thanks in advance!

Jim Ludtke
jludtke@facstaff.wisc.edu
Department of Pediatrics
U.W. Madison

------------------------------

Date: Thu, 16 Sep 1999 23:38:14 +0100
From: Ray Hicks <rh208@cus.cam.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Help one more time (I hope)
Message-Id: <l03110709b4071fb6c926@[131.111.80.24]>
Content-Type: text/plain; charset="us-ascii"

Hi Lill,

You've probably missed your deadline by now, but you're (probably) also
missing the vital "Include Interior Holes" in the "Options..." dialog (from
the "Analysis" menu).  When you filled the shape, the "hole" was filled and
its area measured, when you didn't fill the shape there was nothing to
measure (probably).

I hope someone else got an answer to you in time (and that it's the right one)

Ray

>	I somehow got a measurement of 84.---cm^2 on a measurement of my 1
>cm^2 scale when I "filled" the image.
>What am I missing?  I have been pulling my hair out all day and I am on a
>tight deadline.  Please help me.
>
>Loads and Loads of thanks,
>Lill
>
>
>Lill Becker
>Department of Biology
>Florida International University
>Miami, FL  33199   USA
>
>	*******************************************
>	*Are science and magic mutually exclusive?*
>	*******************************************


                              Ray Hicks
________________________________________________________________________
|University of Cambridge          |Tel              01223 330149        |
|Department of Medicine           |Fax             01223 336846         |
|Level 5, Addenbrookes Hospital   |e-mail         <rh208@cus.cam.ac.uk> |
|Hills Road Cambridge             |Web  http://facsmac.med.cam.ac.uk    |
|CB2                              |ftp server  ftp://131.111.80.78      |
|UK                               |                                     |
|_________________________________|_____________________________________|

------------------------------

Date: Thu, 16 Sep 1999 22:24:52 -0400
From: David Knecht <knecht@uconn.edu>
To: nih-image@io.ece.drexel.edu
Subject: IMage and Snapper
Message-Id: <l03130304b406e2f7a8e8@[137.99.71.199]>
Content-Type: text/plain; charset="us-ascii"

Does NIH Image work with the Snapper frame grabber?  Where do you buy a
Snapper?  Does anyone out there use one and can you indicate trade-offs vs.
the Scion?  Is there an easier way of searching archives for a question
like this than the Email procedure documented in the manual.  If so, there
might be less repeat questions as I suspect these are.  Thanks- Dave

Home of the 1999 NCAA Basketball National Champion HUSKIES !!!
************************************************************

Dr. David Knecht
Department of Molecular and Cell Biology
University of Connecticut
75 N. Eagleville Rd.   U-125
Storrs, CT 06269
Knecht@uconnvm.uconn.edu
860-486-2200      860-486-4331 (fax)

************************************************************

--------------------------------
End of nih-image-d Digest V99 Issue #213
****************************************

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Does NIH Image work with the Snapper frame grabber?  Where do you buy a
Snapper?  Does anyone out there use one and can you indicate trade-offs vs.
the Scion?  Is there an easier way of searching archives for a question
like this than the Email procedure documented in the manual.  If so, there
might be less repeat questions as I suspect these are.  Thanks- Dave

Home of the 1999 NCAA Basketball National Champion HUSKIES !!!
************************************************************

Dr. David Knecht
Department of Molecular and Cell Biology
University of Connecticut
75 N. Eagleville Rd.   U-125
Storrs, CT 06269
Knecht@uconnvm.uconn.edu
860-486-2200      860-486-4331 (fax)

************************************************************



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Date: Fri, 17 Sep 1999 08:16:32 -0500 (CDT)
From: Brian McEwen <bmcewen@cowboy.net>
To: nih-image@io.ece.drexel.edu
Subject: re: stat package for Mac
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>SigmaStat / SigmaPlot used to be owned by Jandel but has been bought out
>by SPSS for more details try:
>http://www.spss.com/software/science/sigmaplot/analysis.htm

A couple more:

StatView has a free demo of 5.0, and it is now owned by SAS, see:
http://www.statview.com.

Also there's a neat shareware package, StatSimple, which is quite
well-featured, and is $20.  Has ASCII and pict export of your analyses
and data. It even runs nicely on 68k machines.
The 1.2.1 version supports:
    Descriptive statistics
    Histogram plot
    Student's t-test
    Paired t-test
    Linear regression
    Analysis of Variance (ANOVA)
    Bonferroni modified t-tests
    Dunnet's t-tests
    Fisher's Least Significant Difference tests
    Simple Chi-Square
    Chi-Square 2x2 contingency table 

The finished 2.0 version, which is waiting for a manual update, adds quite
a few more more tests, but I don't have the list handy.  I've been playing
with the demo for about a week and will be buying this one, I think.
You can find this app at:  http://www.aracnet.net/~nidus/statsimple.html
from Nidus Technologies.

Any more out there? 

Brian


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From: Tom Morton <support@scioncorp.com>
Subject: Re: nih-image-d Digest V99 #213
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Jim,

Scion Image opens 24-bit images as 8-bit color images.  It does this
because you cannot analyze in 24-bit color, only in 8-bit color.  To view
the 24-bit color image, close the Indexed Color image and you are left with
the RGB stack.  Choose RGB to 24-bit color from the stacks menu and the
24-bit color image will be displayed.

Tom

>Date: Thu, 16 Sep 1999 12:29:33 -0500
>From: jludtke@facstaff.wisc.edu (Jim Ludtke)
>To: nih-image@io.ece.drexel.edu
>Subject:  CG-7 Scion Frame Grabber
>Message-Id: <199909161726.MAA34668@mail1.doit.wisc.edu>
>Content-Type: text/plain; charset="us-ascii"
>
>Hi all,
>
>We have just installed a Scion CG-7 frame grabber on our Power Mac 7600.
>Scion sent NIH Image version 1.62 to capture with. The problem I have is
>that when I save an image (which looks great) and re-open it with NIH
>Image, the image becomes very pixelated. However, if I open the same image
>with Photoshop, the image is perfect. Is there a setting in NIH Image that
>can fix this problem? It seems to me that I should be able to open an image
>in the same program that I collected it with!
>
>Thanks in advance!
>
>Jim Ludtke
>jludtke@facstaff.wisc.edu
>Department of Pediatrics
>U.W. Madison
>


-----------------------------------------------------------------------
Tom Morton                                     support@scioncorp.com
Technical Services                             http://www.scioncorp.com
Scion Corporation                              ftp://scioncorp.com
82 Wormans Mill Rd., Suite H                   Phone: (301) 695-7870
Frederick, MD 21701 USA                         Fax:   (301) 695-0035
-----------------------------------------------------------------------



From nih-image-request@io.ece.drexel.edu Fri Sep 17 10:22 EDT 1999
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Date: Fri, 17 Sep 1999 09:03:19 -0500
From: David Morilak <morilak@uthscsa.edu>
Subject: Re: CG-7 Scion Frame Grabber
To: jludtke@facstaff.wisc.edu
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Jim:

It sounds like this could just be a matter of having different image
resolution settings in the different applications. NIH-Image captures and
displays images at a default 72 ppi (I'm not even sure that can be changed).
Photoshop may be opening the image at a higher resolution setting. It's the
same image and all the same information is there, they are just using
different pixel sizes. If this is the case, than the the image itself in
Photoshop should be occupying a lot less screen area than it does in Image.


David Morilak, Ph.D.
Department of Pharmacology
Univ of Texas Health Science Center
7703 Floyd Curl Drive, Mail Code 7764
San Antonio, TX 78229-3900

Phone: 210-567-4174
FAX:   210-567-4303
E-mail: morilak@uthscsa.edu

E-mail at home: dmorilak@flash.net


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From: Lori Ploutz-Snyder <llploutz@syr.edu>
Subject: siemens vision dicom
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I'm trying to use NIH Image to open dicom files (MRI) from the 1.5T siemens
vision system.
I have followed the NIH Image directions, obtained the dicom dictionary,
etc. but can't open the images.
I get part of the header info and then an error message.
Does anyone have any suggestions?

thanks, Lori




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********************************************************
Francis Szele, Ph.D.
Assistant Professor
Neurobiology Core
Children's Memorial Institute for Education and Research
Department of Pediatrics
Northwestern University Medical School
2300 Children's Plaza, 209
Chicago, IL
60614-3394

(773) 880-3791
Fax: (773) 868-8066
F-Szele@nwu.edu

********************************************************
--============_-1274542191==_============--


From nih-image-request@io.ece.drexel.edu Fri Sep 17 11:34 EDT 1999
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Date: Fri, 17 Sep 99 8:14:30 PDT
From: Walter Wolf <wwolfw@hsc.usc.edu>
To: nih-image@io.ece.drexel.edu
Cc: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu
Subject: Re: siemens vision dicom
In-Reply-To: Your message of Fri, 17 Sep 1999 10:43:00 -0400 (EDT)
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Lori:

You wrote:

>I'm trying to use NIH Image to open dicom files (MRI) from the 1.5T siemens
>vision system.
>I have followed the NIH Image directions, obtained the dicom dictionary,
>etc. but can't open the images.
>I get part of the header info and then an error message.
>Does anyone have any suggestions?

We have been opening MRI images obtained on Siemens systems for years with
NIH Image. It is important that you use "Import" and not "open". Then, click
on the Dicom button, and on the image you want to convert. That gives you
both the header information in a Dicom window, and the image, which you can
then save as a TIFF, PICT, or a series of other file formats. 

Let me know if you have further difficulties.

PLEASE NOTE NEW ZIP-CODE AT USC
======================================================================
|  Professor Walter Wolf, Ph.D.          E-Mail: wwolfw@hsc.usc.edu  |
|  Distinguished Professor of Pharmaceutical Sciences		     |
|  Director, Pharmacokinetic Imaging Program                         |
|  Department of Pharmaceutical Sciences, School of Pharmacy	     |
|  University of Southern California           Telephone:323-442-1405|
|  1985 Zonal Ave., Los Angeles, CA 90089-9121 Fax:      323-442-9804|
|                                                                    |
|Center for Noninvasive Pharmacology, Los Angeles Oncologic Institute|
|  MRI at St. Vincent Medical Center     Telephone:    213-484-7235  |
|  2131 Third St., Los Angeles, CA 90057 Fax:          213-484-7447  |
======================================================================
 


From nih-image-request@io.ece.drexel.edu Fri Sep 17 16:38 EDT 1999
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Subject: getting started
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I am preparing to use NIH Image to perform a quantitative analysis on ISH
slides of human and rat ovary sections.  Based on my limited knowledge of
Densitometry, data obtained from one experiment cannot be compared with
that of another, even if background is factored out.  I have been outlining
the oocyte (where signal is) and taking a measurement and then subtracting
the background signal obtained from a "sense" slide.  Does this sound like
the correct procedure?  Also, I am unclear on the meaning of mean gray
area.  Does this directly relate to pixels per unit area or is it the
number of total pixels in the outlined area?  Please help. If it's easier
to discuss this over the phone, you may call me (858)534-4967.
Thank you,
Amy Widger
UCSD Dept of Reproductive Med



From nih-image-request@io.ece.drexel.edu Fri Sep 17 19:29 EDT 1999
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Message-ID: <01BF0128.02441880@carterlab.zoology.wsu.edu>
From: Greg Ragland <gragland@wsunix.wsu.edu>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: time stamp problem
Date: Fri, 17 Sep 1999 16:16:31 -0700
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Hi,

I'm having a problem getting the time stamp to show up against a light background on frames captured with the "make movie" command.  Any ideas on how to rectify this problem would be appreciated.

Thanks

Greg


From nih-image-request@io.ece.drexel.edu Fri Sep 17 21:03 EDT 1999
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From: SolamereTG@aol.com
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Date: Fri, 17 Sep 1999 20:47:41 EDT
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In a message dated 9/17/99 5:26:39 PM, gragland@wsunix.wsu.edu writes:

<< Greg >>

select the color of the letters you want (from the sidebar greyscale) using 
the eyedrop tool. The Paint brush will change color to show you the color 
you've selected.

STG


From nih-image-request@io.ece.drexel.edu Sat Sep 18 02:23 EDT 1999
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Date: Sat, 18 Sep 1999 02:09:48 EDT
Subject: Object image and Scion Image Macros
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Dear List readers:
Has anyone had problems transporting Macros that run in Scion Image (on the 
MAC) over to Object Image (version 1.62.n18)? 
We have written a macro to control a serial device that seems to work 
perfectly well with Scion image but when used with object image it does not. 

The Open Serial  port command is may be suspect. The macro outputs an indexed 
data list into the peripheral device. The device loads the odd data points 
(i.e., 1, 3, 5...) but not the even data points (leaves these as zeros). With 
Scion Image it takes both without problems.


macro 'load list data [l]';
var
s:real
z,k,n,i,j,h:integer;
  select,cmd,linefeed,return,space:string;
begin
  linefeed:=chr(10);
  return:=chr(13);
  space:=chr(32);
s:=Getnumber('Enter step size:',1);
n:=Getnumber('Enter number of steps:',6);
  OpenSerial('9600 baud,no parity,eight data,one stop');
PutSerial('list:stop',return,linefeed);
PutSerial('data:flush',return,linefeed);
PutSerial('pos 0',return,linefeed);
k:=2*n;
i:=1;
  for i:=1 to n do begin
j:=(s*i);                           
cmd:=concat('data',i','j);
showmessage(cmd);
wait(1);
 PutSerial(cmd,return,linefeed);
h:=(s*(n-i));
z:=(n+i);
cmd:=concat('data',z','h);
showmessage(cmd);
wait(1);
 PutSerial(cmd,return,linefeed);
i:=i+1;
end;
end;

Thanks for your help,
Dr. George A. Peeters, 
Solamere Technology Group

WWW.SolamereTech.com
SolamereTG@aol.com


From nih-image-d-request@io.ece.drexel.edu Sat Sep 18 02:24 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #214
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 214

Today's Topics:
  Re: nih-image-d Digest V99 #213       [ Tom Morton <support@scioncorp.com> ]
  re: stat package for Mac              [ Brian McEwen <bmcewen@cowboy.net> ]
  Re: CG-7 Scion Frame Grabber          [ David Morilak <morilak@uthscsa.edu> ]
  siemens vision dicom                  [ Lori Ploutz-Snyder <llploutz@syr.ed ]
  URGENT                                [ Francis Szele <f-szele@nwu.edu> ]
  Re: siemens vision dicom              [ Walter Wolf <wwolfw@hsc.usc.edu> ]
  getting started                       [ Amy Widger <awidger@ucsd.edu> ]
  time stamp problem                    [ Greg Ragland <gragland@wsunix.wsu.e ]
  Re: time stamp problem                [ SolamereTG@aol.com ]
  Object image and Scion Image Macros   [ SolamereTG@aol.com ]

------------------------------

Date: Fri, 17 Sep 1999 08:52:37 -0400
From: Tom Morton <support@scioncorp.com>
To: nih-image@io.ece.drexel.edu, jludtke@facstaff.wisc.edu
Subject: Re: nih-image-d Digest V99 #213
Message-Id: <l03130300b407e972526b@[10.0.0.239]>
Content-Type: text/plain; charset="us-ascii"

Jim,

Scion Image opens 24-bit images as 8-bit color images.  It does this
because you cannot analyze in 24-bit color, only in 8-bit color.  To view
the 24-bit color image, close the Indexed Color image and you are left with
the RGB stack.  Choose RGB to 24-bit color from the stacks menu and the
24-bit color image will be displayed.

Tom

>Date: Thu, 16 Sep 1999 12:29:33 -0500
>From: jludtke@facstaff.wisc.edu (Jim Ludtke)
>To: nih-image@io.ece.drexel.edu
>Subject:  CG-7 Scion Frame Grabber
>Message-Id: <199909161726.MAA34668@mail1.doit.wisc.edu>
>Content-Type: text/plain; charset="us-ascii"
>
>Hi all,
>
>We have just installed a Scion CG-7 frame grabber on our Power Mac 7600.
>Scion sent NIH Image version 1.62 to capture with. The problem I have is
>that when I save an image (which looks great) and re-open it with NIH
>Image, the image becomes very pixelated. However, if I open the same image
>with Photoshop, the image is perfect. Is there a setting in NIH Image that
>can fix this problem? It seems to me that I should be able to open an image
>in the same program that I collected it with!
>
>Thanks in advance!
>
>Jim Ludtke
>jludtke@facstaff.wisc.edu
>Department of Pediatrics
>U.W. Madison
>


-----------------------------------------------------------------------
Tom Morton                                     support@scioncorp.com
Technical Services                             http://www.scioncorp.com
Scion Corporation                              ftp://scioncorp.com
82 Wormans Mill Rd., Suite H                   Phone: (301) 695-7870
Frederick, MD 21701 USA                         Fax:   (301) 695-0035
-----------------------------------------------------------------------

------------------------------

Date: Fri, 17 Sep 1999 08:16:32 -0500 (CDT)
From: Brian McEwen <bmcewen@cowboy.net>
To: nih-image@io.ece.drexel.edu
Subject: re: stat package for Mac
Message-ID: <Pine.LNX.4.10.9909170736380.5002-100000@cowboy.net>
Content-Type: TEXT/PLAIN; charset=US-ASCII

>SigmaStat / SigmaPlot used to be owned by Jandel but has been bought out
>by SPSS for more details try:
>http://www.spss.com/software/science/sigmaplot/analysis.htm

A couple more:

StatView has a free demo of 5.0, and it is now owned by SAS, see:
http://www.statview.com.

Also there's a neat shareware package, StatSimple, which is quite
well-featured, and is $20.  Has ASCII and pict export of your analyses
and data. It even runs nicely on 68k machines.
The 1.2.1 version supports:
    Descriptive statistics
    Histogram plot
    Student's t-test
    Paired t-test
    Linear regression
    Analysis of Variance (ANOVA)
    Bonferroni modified t-tests
    Dunnet's t-tests
    Fisher's Least Significant Difference tests
    Simple Chi-Square
    Chi-Square 2x2 contingency table 

The finished 2.0 version, which is waiting for a manual update, adds quite
a few more more tests, but I don't have the list handy.  I've been playing
with the demo for about a week and will be buying this one, I think.
You can find this app at:  http://www.aracnet.net/~nidus/statsimple.html
from Nidus Technologies.

Any more out there? 

Brian

------------------------------

Date: Fri, 17 Sep 1999 09:03:19 -0500
From: David Morilak <morilak@uthscsa.edu>
To: jludtke@facstaff.wisc.edu
Cc: nih-image@io.ece.drexel.edu
Subject: Re: CG-7 Scion Frame Grabber
Message-id: <01JG2KXYIY3C9ASHP7@uthscsa.edu>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7BIT

Jim:

It sounds like this could just be a matter of having different image
resolution settings in the different applications. NIH-Image captures and
displays images at a default 72 ppi (I'm not even sure that can be changed).
Photoshop may be opening the image at a higher resolution setting. It's the
same image and all the same information is there, they are just using
different pixel sizes. If this is the case, than the the image itself in
Photoshop should be occupying a lot less screen area than it does in Image.


David Morilak, Ph.D.
Department of Pharmacology
Univ of Texas Health Science Center
7703 Floyd Curl Drive, Mail Code 7764
San Antonio, TX 78229-3900

Phone: 210-567-4174
FAX:   210-567-4303
E-mail: morilak@uthscsa.edu

E-mail at home: dmorilak@flash.net

------------------------------

Date: Fri, 17 Sep 1999 10:43:00 -0400 (EDT)
From: Lori Ploutz-Snyder <llploutz@syr.edu>
To: nih-image@io.ece.drexel.edu
Subject: siemens vision dicom
Message-Id: <v03007802b407cac0948b@[128.230.82.189]>
Content-Type: text/plain; charset="us-ascii"

I'm trying to use NIH Image to open dicom files (MRI) from the 1.5T siemens
vision system.
I have followed the NIH Image directions, obtained the dicom dictionary,
etc. but can't open the images.
I get part of the header info and then an error message.
Does anyone have any suggestions?

thanks, Lori

------------------------------


********************************************************
Francis Szele, Ph.D.
Assistant Professor
Neurobiology Core
Children's Memorial Institute for Education and Research
Department of Pediatrics
Northwestern University Medical School
2300 Children's Plaza, 209
Chicago, IL
60614-3394

(773) 880-3791
Fax: (773) 868-8066
F-Szele@nwu.edu

********************************************************
--============_-1274542191==_============--

------------------------------

Date: Fri, 17 Sep 99 8:14:30 PDT
From: Walter Wolf <wwolfw@hsc.usc.edu>
To: nih-image@io.ece.drexel.edu
Cc: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu
Subject: Re: siemens vision dicom
Message-ID: <CMM.0.90.4.937581270.wwolfw@hsc.usc.edu>

Lori:

You wrote:

>I'm trying to use NIH Image to open dicom files (MRI) from the 1.5T siemens
>vision system.
>I have followed the NIH Image directions, obtained the dicom dictionary,
>etc. but can't open the images.
>I get part of the header info and then an error message.
>Does anyone have any suggestions?

We have been opening MRI images obtained on Siemens systems for years with
NIH Image. It is important that you use "Import" and not "open". Then, click
on the Dicom button, and on the image you want to convert. That gives you
both the header information in a Dicom window, and the image, which you can
then save as a TIFF, PICT, or a series of other file formats. 

Let me know if you have further difficulties.

PLEASE NOTE NEW ZIP-CODE AT USC
======================================================================
|  Professor Walter Wolf, Ph.D.          E-Mail: wwolfw@hsc.usc.edu  |
|  Distinguished Professor of Pharmaceutical Sciences		     |
|  Director, Pharmacokinetic Imaging Program                         |
|  Department of Pharmaceutical Sciences, School of Pharmacy	     |
|  University of Southern California           Telephone:323-442-1405|
|  1985 Zonal Ave., Los Angeles, CA 90089-9121 Fax:      323-442-9804|
|                                                                    |
|Center for Noninvasive Pharmacology, Los Angeles Oncologic Institute|
|  MRI at St. Vincent Medical Center     Telephone:    213-484-7235  |
|  2131 Third St., Los Angeles, CA 90057 Fax:          213-484-7447  |
======================================================================
 

------------------------------

Date: Fri, 17 Sep 1999 13:28:31 -0700
From: Amy Widger <awidger@ucsd.edu>
To: nih-image@io.ece.drexel.edu
Subject: getting started
Message-Id: <v04003a01b40852ed1281@[132.239.200.117]>
Content-Type: text/plain; charset="us-ascii"

I am preparing to use NIH Image to perform a quantitative analysis on ISH
slides of human and rat ovary sections.  Based on my limited knowledge of
Densitometry, data obtained from one experiment cannot be compared with
that of another, even if background is factored out.  I have been outlining
the oocyte (where signal is) and taking a measurement and then subtracting
the background signal obtained from a "sense" slide.  Does this sound like
the correct procedure?  Also, I am unclear on the meaning of mean gray
area.  Does this directly relate to pixels per unit area or is it the
number of total pixels in the outlined area?  Please help. If it's easier
to discuss this over the phone, you may call me (858)534-4967.
Thank you,
Amy Widger
UCSD Dept of Reproductive Med

------------------------------

Date: Fri, 17 Sep 1999 16:16:31 -0700
From: Greg Ragland <gragland@wsunix.wsu.edu>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: time stamp problem
Message-ID: <01BF0128.02441880@carterlab.zoology.wsu.edu>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 8bit

Hi,

I'm having a problem getting the time stamp to show up against a light background on frames captured with the "make movie" command.  Any ideas on how to rectify this problem would be appreciated.

Thanks

Greg

------------------------------

Date: Fri, 17 Sep 1999 20:47:41 EDT
From: SolamereTG@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re: time stamp problem
Message-ID: <8dd383a8.25143b2d@aol.com>
Content-Type: text/plain; charset="us-ascii"
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In a message dated 9/17/99 5:26:39 PM, gragland@wsunix.wsu.edu writes:

<< Greg >>

select the color of the letters you want (from the sidebar greyscale) using 
the eyedrop tool. The Paint brush will change color to show you the color 
you've selected.

STG

------------------------------

Date: Sat, 18 Sep 1999 02:09:48 EDT
From: SolamereTG@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Object image and Scion Image Macros
Message-ID: <e640d404.251486ac@aol.com>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

Dear List readers:
Has anyone had problems transporting Macros that run in Scion Image (on the 
MAC) over to Object Image (version 1.62.n18)? 
We have written a macro to control a serial device that seems to work 
perfectly well with Scion image but when used with object image it does not. 

The Open Serial  port command is may be suspect. The macro outputs an indexed 
data list into the peripheral device. The device loads the odd data points 
(i.e., 1, 3, 5...) but not the even data points (leaves these as zeros). With 
Scion Image it takes both without problems.


macro 'load list data [l]';
var
s:real
z,k,n,i,j,h:integer;
  select,cmd,linefeed,return,space:string;
begin
  linefeed:=chr(10);
  return:=chr(13);
  space:=chr(32);
s:=Getnumber('Enter step size:',1);
n:=Getnumber('Enter number of steps:',6);
  OpenSerial('9600 baud,no parity,eight data,one stop');
PutSerial('list:stop',return,linefeed);
PutSerial('data:flush',return,linefeed);
PutSerial('pos 0',return,linefeed);
k:=2*n;
i:=1;
  for i:=1 to n do begin
j:=(s*i);                           
cmd:=concat('data',i','j);
showmessage(cmd);
wait(1);
 PutSerial(cmd,return,linefeed);
h:=(s*(n-i));
z:=(n+i);
cmd:=concat('data',z','h);
showmessage(cmd);
wait(1);
 PutSerial(cmd,return,linefeed);
i:=i+1;
end;
end;

Thanks for your help,
Dr. George A. Peeters, 
Solamere Technology Group

WWW.SolamereTech.com
SolamereTG@aol.com

--------------------------------
End of nih-image-d Digest V99 Issue #214
****************************************

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I want to unsubscribe
Thanks M Brehm


From nih-image-request@io.ece.drexel.edu Sat Sep 18 13:25 EDT 1999
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Date: Sat, 18 Sep 1999 19:12:27 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Object image and Scion Image Macros
Resent-Message-ID: <"6K0Zv1.0.fi3.RVyut"@io>
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>Has anyone had problems transporting Macros that run in Scion Image (on the
>MAC) over to Object Image (version 1.62.n18)?
>The device loads the odd data points
>(i.e., 1, 3, 5...) but not the even data points (leaves these as zeros). With
>Scion Image it takes both without problems.
>Dr. George A. Peeters,
>Solamere Technology Group

The short answer is: remove the line
i := i + 1;
and it will probably work.


The long answer is that Pascal does not recommend to change a loop counter
variable inside the loop, and a compiler is allowed to ignore such a
statement.
NIH Image ignores it, Object-Image executes it.
Reason for the difference is that the built-in single-step debugger in
Object-Image allows the user double-click and manipulate any variable while
stepping, including loop counters.

Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html



From nih-image-d-request@io.ece.drexel.edu Sun Sep 19 06:13 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #215
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 215

Today's Topics:
  unsubscribe                           [ Brehm <mbrehm@zedat.fu-berlin.de> ]
  Re: Object image and Scion Image Mac  [ Norbert Vischer <vischer@bio.uva.nl ]

------------------------------

Date: Sat, 18 Sep 1999 12:12:59 +0200
From: Brehm <mbrehm@zedat.fu-berlin.de>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe 
Message-Id: <3.0.1.32.19990918121259.00733ed0@mail.zedat.fu-berlin.de>
Content-Type: text/plain; charset="us-ascii"

I want to unsubscribe
Thanks M Brehm

------------------------------

Date: Sat, 18 Sep 1999 19:12:27 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Object image and Scion Image Macros
Message-Id: <l03010d02b408ff5e8978@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

>Has anyone had problems transporting Macros that run in Scion Image (on the
>MAC) over to Object Image (version 1.62.n18)?
>The device loads the odd data points
>(i.e., 1, 3, 5...) but not the even data points (leaves these as zeros). With
>Scion Image it takes both without problems.
>Dr. George A. Peeters,
>Solamere Technology Group

The short answer is: remove the line
i := i + 1;
and it will probably work.


The long answer is that Pascal does not recommend to change a loop counter
variable inside the loop, and a compiler is allowed to ignore such a
statement.
NIH Image ignores it, Object-Image executes it.
Reason for the difference is that the built-in single-step debugger in
Object-Image allows the user double-click and manipulate any variable while
stepping, including loop counters.

Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html

--------------------------------
End of nih-image-d Digest V99 Issue #215
****************************************

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I do realize that it is bad form to bother the Group with Admin issues 
but for heaven's sake please take me off this newsgroup. I have gone 
through the official procedure three times with no success. Clearly the 
email account name I used when I subscribed has mutated into the present 
one, but *please* delete d.crook@dial.pipex.com and kba66@dial.pipex.com.

Great news group, but for someone of my limited interests most of the 
posts are of no interest. And as for the envelope-stuffers I have a 
suggestion of my own . . . 


Apologies to all . . .



David Crook PhD


From nih-image-request@io.ece.drexel.edu Mon Sep 20 12:06 EDT 1999
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Date: Mon, 20 Sep 1999 08:54:49 -0700
To: nih-image@io.ece.drexel.edu
From: "Colin J. Saldanha" <colin@physci.ucla.edu>
Subject: Re: nih-image-d Digest V99 #215
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<html>
<font size=3>unsubscribe</font><br>

<font face="Times New Roman, Times">Colin J. Saldanha Ph.D.<br>
Department of Physiological Science<br>
University of California Los Angeles<br>
621 Charles E. Young Drive South<br>
Los Angeles, CA 90095<br>
<br>
(310) 825-4170 (tel)<br>
(310) 206-9184 (fax)</font></html>


From nih-image-request@io.ece.drexel.edu Mon Sep 20 18:40 EDT 1999
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Date: Mon, 20 Sep 1999 16:24:08 -0600
From: Peter Guthrie <Peter.Guthrie@hsc.utah.edu>
Subject: Extra 1.5GB Optical Disks - Free
X-Sender: pguthrie:d@gwpopa.med.utah.edu
To: nih-image@io.ece.drexel.edu, CONFOCAL@LISTSERV.ACSU.BUFFALO.EDU,
        Microscopy@Sparc5.Microscopy.Com
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I have nine un-opened 1.5 GB rewritable optical disks (double-sided) that I
will never use:

Panasonic # LM-R1500A

Originally purchased for use in an Optical Access International optical
disk drive.

If anyone is certain they can use these disks, please contact me.


Peter Guthrie
Department of Neurobiology & Anatomy
University of Utah School of Medicine
50 N Medical Drive
Salt Lake City, UT  84132
(801) 581-8336       (801) 581-4233 fax
Peter.Guthrie@hsc.utah.edu



From nih-image-d-request@io.ece.drexel.edu Tue Sep 21 06:16 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199909211016.GAA06004@io.ece.drexel.edu>
Subject: nih-image-d Digest V99 #216
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 216

Today's Topics:
  UNSUBSCRIBE                           [ David Crook <d.crook@dial.pipex.com ]
  Re: nih-image-d Digest V99 #215       [ "Colin J. Saldanha" <colin@physci.u ]
  Extra 1.5GB Optical Disks - Free      [ Peter Guthrie <Peter.Guthrie@hsc.ut ]

------------------------------

Date: Mon, 20 Sep 1999 10:58:57 +0100
From: David Crook  <d.crook@dial.pipex.com>
To: <nih-image@io.ece.drexel.edu>
Subject: UNSUBSCRIBE
Message-Id: <199909200958.KAA04165@netsrv.lhmc.ac.uk>
Content-Type: text/plain; charset="US-ASCII"

I do realize that it is bad form to bother the Group with Admin issues 
but for heaven's sake please take me off this newsgroup. I have gone 
through the official procedure three times with no success. Clearly the 
email account name I used when I subscribed has mutated into the present 
one, but *please* delete d.crook@dial.pipex.com and kba66@dial.pipex.com.

Great news group, but for someone of my limited interests most of the 
posts are of no interest. And as for the envelope-stuffers I have a 
suggestion of my own . . . 


Apologies to all . . .



David Crook PhD

------------------------------

Date: Mon, 20 Sep 1999 08:54:49 -0700
From: "Colin J. Saldanha" <colin@physci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V99 #215
Message-Id: <4.1.19990920085439.00a2af10@protos.lifesci.ucla.edu>
Content-Type: text/html; charset="us-ascii"

<html>
<font size=3>unsubscribe</font><br>

<font face="Times New Roman, Times">Colin J. Saldanha Ph.D.<br>
Department of Physiological Science<br>
University of California Los Angeles<br>
621 Charles E. Young Drive South<br>
Los Angeles, CA 90095<br>
<br>
(310) 825-4170 (tel)<br>
(310) 206-9184 (fax)</font></html>

------------------------------

Date: Mon, 20 Sep 1999 16:24:08 -0600
From: Peter Guthrie <Peter.Guthrie@hsc.utah.edu>
To: nih-image@io.ece.drexel.edu, CONFOCAL@LISTSERV.ACSU.BUFFALO.EDU,
        Microscopy@Sparc5.Microscopy.Com
Subject: Extra 1.5GB Optical Disks - Free
Message-id: <l03010d04b40c62b7a30a@[155.100.254.98]>
Content-type: text/plain; charset="us-ascii"

I have nine un-opened 1.5 GB rewritable optical disks (double-sided) that I
will never use:

Panasonic # LM-R1500A

Originally purchased for use in an Optical Access International optical
disk drive.

If anyone is certain they can use these disks, please contact me.


Peter Guthrie
Department of Neurobiology & Anatomy
University of Utah School of Medicine
50 N Medical Drive
Salt Lake City, UT  84132
(801) 581-8336       (801) 581-4233 fax
Peter.Guthrie@hsc.utah.edu

--------------------------------
End of nih-image-d Digest V99 Issue #216
****************************************

From nih-image-request@io.ece.drexel.edu Tue Sep 21 06:48 EDT 1999
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Mime-Version: 1.0
Date: Tue, 21 Sep 1999 12:27:40 +0200
To: nih-image@io.ece.drexel.edu
From: Ard Jonker <a.jonker@amc.uva.nl>
Subject: Re:  UNSUBSCRIBE
Resent-Message-ID: <"i8_t51.0.K62.Ixrvt"@io>
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>I do realize that it is bad form to bother the Group with Admin issues
>but for heaven's sake please take me off this newsgroup. I have gone
>through the official procedure three times with no success.
<...>
>Apologies to all . . .

Maybe the Admin posting could have a line added as to where to direct
correspondence to, should unsubscribing (or any admin command) fail. I
guess the most logical one is <mailto://nih-image@io.ece.drexel.edu>

Ard



From nih-image-request@io.ece.drexel.edu Tue Sep 21 10:18 EDT 1999
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Date: Tue, 21 Sep 1999 15:59:48 +0200
From: Ulrich Marti <ulrich.marti@dkf2.unibe.ch>
Subject: Ref. reslicing
To: NIH List <nih-image@io.ece.drexel.edu>
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This is a multi-part message in MIME format.

--Boundary_(ID_zuu+bAetkEr+2KqYdsMMjw)
Content-type: text/plain; x-mac-creator=4D4F5353; x-mac-type=54455854;
 charset=us-ascii
Content-transfer-encoding: 7BIT

Hi there
I am looking for a reference paper to cite on reslicing of Confocal
serials sections.
Thank you for any help.

Ueli

--Boundary_(ID_zuu+bAetkEr+2KqYdsMMjw)
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x-mozilla-cpt:;1
fn:Ulrich Marti
end:vcard

--Boundary_(ID_zuu+bAetkEr+2KqYdsMMjw)--


From nih-image-request@io.ece.drexel.edu Tue Sep 21 11:17 EDT 1999
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From: "Darryl C. Sutton" <dsutton@coe.neu.edu>
Date: Tue, 21 Sep 1999 10:54:11 -0400 (EDT)
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To: nih-image@io.ece.drexel.edu
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Please remove me from your e-mailing list.  

Thanks


From nih-image-d-request@io.ece.drexel.edu Wed Sep 22 06:14 EDT 1999
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Date: Wed, 22 Sep 1999 06:14:22 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #217
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 217

Today's Topics:
  Re: UNSUBSCRIBE                       [ Ard Jonker <a.jonker@amc.uva.nl> ]
  Ref. reslicing                        [ Ulrich Marti <ulrich.marti@dkf2.uni ]
  unsubscribe                           [ "Darryl C. Sutton" <dsutton@coe.neu ]

------------------------------

Date: Tue, 21 Sep 1999 12:27:40 +0200
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re:  UNSUBSCRIBE
Message-Id: <l03130304b40d0cc272d1@[145.117.53.66]>
Content-Type: text/plain; charset="us-ascii"

>I do realize that it is bad form to bother the Group with Admin issues
>but for heaven's sake please take me off this newsgroup. I have gone
>through the official procedure three times with no success.
<...>
>Apologies to all . . .

Maybe the Admin posting could have a line added as to where to direct
correspondence to, should unsubscribing (or any admin command) fail. I
guess the most logical one is <mailto://nih-image@io.ece.drexel.edu>

Ard

------------------------------

Date: Tue, 21 Sep 1999 15:59:48 +0200
From: Ulrich Marti <ulrich.marti@dkf2.unibe.ch>
To: NIH List <nih-image@io.ece.drexel.edu>
Subject: Ref. reslicing
Message-id: <37E78F50.E5E3B5A1@dkf2.unibe.ch>
Content-type: MULTIPART/MIXED; BOUNDARY="Boundary_(ID_zuu+bAetkEr+2KqYdsMMjw)"

This is a multi-part message in MIME format.

--Boundary_(ID_zuu+bAetkEr+2KqYdsMMjw)
Content-type: text/plain; x-mac-creator=4D4F5353; x-mac-type=54455854;
 charset=us-ascii
Content-transfer-encoding: 7BIT

Hi there
I am looking for a reference paper to cite on reslicing of Confocal
serials sections.
Thank you for any help.

Ueli

--Boundary_(ID_zuu+bAetkEr+2KqYdsMMjw)
Content-type: text/x-vcard; name=ulrich.marti.vcf; charset=us-ascii
Content-description: Card for Ulrich Marti
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begin:vcard 
n:Marti;Ulrich
tel;fax:+41(031) 632 89 66
tel;home:+41(031) 829 09 54
tel;work:+41(031) 632 95 45
x-mozilla-html:FALSE
org:University Hospital Berne;Endocrinology Research Lab
version:2.1
email;internet:ulrich.marti@dkf2.unibe.ch
title:Ph.D.
adr;quoted-printable:;;Childern's Hospital=0D=0AG3-812;Berne;;CH-3010;Switzerland
x-mozilla-cpt:;1
fn:Ulrich Marti
end:vcard

--Boundary_(ID_zuu+bAetkEr+2KqYdsMMjw)--

------------------------------

Date: Tue, 21 Sep 1999 10:54:11 -0400 (EDT)
From: "Darryl C. Sutton" <dsutton@coe.neu.edu>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <199909211454.KAA00914@K.coe.neu.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-MD5: aIM3u3PLqhNjoYPhqx7IcA==

Please remove me from your e-mailing list.  

Thanks

--------------------------------
End of nih-image-d Digest V99 Issue #217
****************************************

From nih-image-request@io.ece.drexel.edu Wed Sep 22 09:42 EDT 1999
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Date: Wed, 22 Sep 1999 09:30:21 -0400
To: nih-image@io.ece.drexel.edu
From: Andrew <astewar2@caregroup.harvard.edu>
Subject: Unsuscribe 
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Please UNSUSCRIBE me from this list please.

Thank you,
Andrew


From nih-image-d-request@io.ece.drexel.edu Thu Sep 23 02:16 EDT 1999
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Date: Thu, 23 Sep 1999 02:16:41 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199909230616.CAA13013@io.ece.drexel.edu>
Subject: nih-image-d Digest V99 #218
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 218

Today's Topics:
  Unsuscribe                            [ Andrew <astewar2@caregroup.harvard. ]
  UNSUBSCRIBE                           [ "Dagmar Iber" <iber_dagmar@hotmail. ]

------------------------------

Date: Wed, 22 Sep 1999 09:30:21 -0400
From: Andrew <astewar2@caregroup.harvard.edu>
To: nih-image@io.ece.drexel.edu
Subject: Unsuscribe 
Message-Id: <3.0.5.32.19990922093021.008149a0@pop.bidmc.harvard.edu>
Content-Type: text/plain; charset="us-ascii"

Please UNSUSCRIBE me from this list please.

Thank you,
Andrew

------------------------------

Date: Thu, 23 Sep 1999 08:02:26 CEST
From: "Dagmar Iber" <iber_dagmar@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: UNSUBSCRIBE
Message-ID: <19990923060226.30558.qmail@hotmail.com>
Content-Type: text/plain; charset=iso-8859-1; format=flowed

Hello,

please unsubscribe me from the list.

Thanks, dagmar

______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com

--------------------------------
End of nih-image-d Digest V99 Issue #218
****************************************

From nih-image-request@io.ece.drexel.edu Thu Sep 23 02:21 EDT 1999
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From: "Dagmar Iber" <iber_dagmar@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: UNSUBSCRIBE
Date: Thu, 23 Sep 1999 08:02:26 CEST
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Hello,

please unsubscribe me from the list.

Thanks, dagmar

______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com


From nih-image-request@io.ece.drexel.edu Thu Sep 23 05:26 EDT 1999
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Date: Thu, 23 Sep 1999 05:05:01 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
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From nih-image-request@io.ece.drexel.edu Thu Sep 23 09:25 EDT 1999
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From: "Eugenio Amendola" <amendola@unina.it>
To: "NIH-Image mailing list" <nih-image@io.ece.drexel.edu>
Subject: MAC or PC?
Date: Thu, 23 Sep 1999 15:08:30 +0200
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This is a multi-part message in MIME format.

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Content-Type: text/plain;
	charset="iso-8859-1"
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Dear friends,
I'm reading this list with interest since a little while, and first of =
all I would like to thank the organizer for this.
Comeing to the topic, I'm aware that I'm going to stirr the hornet's =
nest, but...
it is the same old story: Mac vs. PC.
For some practical reasons (lower price and wider software availability) =
I prefer to buy PC, but on the other hand I use Image and some spinn off =
that I find very nice and usefull.
How match both the necessities?
I've checked about MAC emulators on PC, testing a demo of executor (Ardi =
company). Even though the demo worked, it really emulates only old 68xxx =
processor. Quite dissapointing!
Does any one know about a reliable and reasonably fast MAC emulator for =
PC??

Thank you in advance to whoever bothers to answer.
Sincerely
Eugenio Amendola
----------------------------
----------------------------
Dr. Eugenio Amendola
Italian National Council of Research
Institute of Composite Materials Technology
P.le Tecchio 80, 80125 Naples
ITALY
Tel:       (+) 39 081 7682511
fax:       (+) 39 081 7682404
email:    amendola@unina.it
url:        143.225.239.86

------=_NextPart_000_0009_01BF05D5.7ECB7860
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	charset="iso-8859-1"
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content=3D"text/html; charset=3Diso-8859-1" =
http-equiv=3DContent-Type>
<META content=3D"MSHTML 5.00.2014.210" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#c8e0d8>
<DIV><FONT face=3DArial size=3D2>Dear friends,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I'm reading this list with interest =
since a little=20
while, and first of all I would like to thank the organizer for=20
this.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Comeing to the topic, I'm aware that =
I'm going to=20
stirr the hornet's nest, but...</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>it is the same old story: Mac vs. =
PC.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>For some practical reasons (lower price =
and wider=20
software availability) I prefer to buy PC, but on the other hand I use =
Image and=20
some spinn off that I find very nice and usefull.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>How match both the =
necessities?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I've checked about MAC emulators on PC, =
testing a=20
demo of executor (Ardi company). Even though the demo worked, it really =
emulates=20
only old 68xxx processor. Quite dissapointing!</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Does any one know about a reliable and =
reasonably=20
fast MAC emulator for PC??</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Thank you in advance to whoever bothers =
to=20
answer.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Sincerely</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Eugenio Amendola</FONT></DIV>
<DIV><FONT face=3DArial=20
size=3D2>----------------------------<BR>----------------------------<BR>=
Dr.=20
Eugenio Amendola<BR>Italian National Council of Research<BR>Institute of =

Composite Materials Technology<BR>P.le Tecchio 80, 80125=20
Naples<BR>ITALY<BR>Tel:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (+) 39 081=20
7682511<BR>fax:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (+) 39 081=20
7682404<BR>email:&nbsp;&nbsp;&nbsp; <A=20
href=3D"mailto:amendola@unina.it">amendola@unina.it</A><BR>url:&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
143.225.239.86</FONT></DIV></BODY></HTML>

------=_NextPart_000_0009_01BF05D5.7ECB7860--


From nih-image-request@io.ece.drexel.edu Thu Sep 23 09:42 EDT 1999
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To: nih-image@io.ece.drexel.edu
From: "=?iso-8859-1?Q?=22Dr._Luis_F._Hern=E1ndez=22?="  <lhernan@criba.edu.ar>
Subject: Re:MAC or PC?
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Dr.  Eugenio Amendola wrote:
Does any one know about a reliable and reasonably  fast MAC emulator for
PC??   Thank you in advance to whoever bothers to  answer. Sincerely
Eugenio Amendola

For my experience and after several tries with  Executor (Ardi company) and
Gemulator (http://www.emulators.com/ ) the answer is:
"The best reliable and reasonably fast MAC emulator is a true MAC (ranging
from a good old and reliable SE30 to a G4)"



_______________________________________________________
Dr. Luis F. Hernandez, Ph.D.
Laboratorio de Botanica
Departamento de Agronomia
U N I V E R S I D A D  N A C I O N A L  D E L  S U R
8000. Bahia Blanca - ARGENTINA

<mailto: lhernan@criba.edu.ar>
Telefonos (0291) 453-4775/453-0024
FAX: 54 - 0291 - 452-1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.



From nih-image-request@io.ece.drexel.edu Thu Sep 23 09:54 EDT 1999
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Message-ID: <19990923133517.15335.rocketmail@web601.yahoomail.com>
Date: Thu, 23 Sep 1999 06:35:17 -0700 (PDT)
From: steve spencer <stephen_spencer@yahoo.com>
Subject: Re: MAC or PC?
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Unfortuniatly until the bugs are fixed from scion
image I would suggest just buying an expensive
macintosh if you are planning on doing analysis that
requires the use of an imaging program such as NIH
image.
Or buy a pc instal linux and use one of the many image
based programs designed for linux. i.e MEDx brains2 (
which I have heard may be ported to linux) afni  etc.
steve

--- Eugenio Amendola <amendola@unina.it> wrote:
> Dear friends,
> I'm reading this list with interest since a little
> while, and first of all I would like to thank the
> organizer for this.
> Comeing to the topic, I'm aware that I'm going to
> stirr the hornet's nest, but...
> it is the same old story: Mac vs. PC.
> For some practical reasons (lower price and wider
> software availability) I prefer to buy PC, but on
> the other hand I use Image and some spinn off that I
> find very nice and usefull.
> How match both the necessities?
> I've checked about MAC emulators on PC, testing a
> demo of executor (Ardi company). Even though the
> demo worked, it really emulates only old 68xxx
> processor. Quite dissapointing!
> Does any one know about a reliable and reasonably
> fast MAC emulator for PC??
> 
> Thank you in advance to whoever bothers to answer.
> Sincerely
> Eugenio Amendola
> ----------------------------
> ----------------------------
> Dr. Eugenio Amendola
> Italian National Council of Research
> Institute of Composite Materials Technology
> P.le Tecchio 80, 80125 Naples
> ITALY
> Tel:       (+) 39 081 7682511
> fax:       (+) 39 081 7682404
> email:    amendola@unina.it
> url:        143.225.239.86
> 

__________________________________________________
Do You Yahoo!?
Bid and sell for free at http://auctions.yahoo.com


From nih-image-request@io.ece.drexel.edu Thu Sep 23 10:30 EDT 1999
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Please "UNSUBSCRIBE" or remove me from your e-mailing list.

Thanks 


From nih-image-request@io.ece.drexel.edu Thu Sep 23 11:03 EDT 1999
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If you want to do image analysis and know that NIH Image meets
your needs, I would highly suggest buying a mac.  The G4s
don't seem too expensive considering what you get.  Any extra
cost might be offset by the price of NIH Image (free) and the ease of
installing/running it.
-Lori

>
>--- Eugenio Amendola <amendola@unina.it> wrote:
>> Dear friends,
>> I'm reading this list with interest since a little
>> while, and first of all I would like to thank the
>> organizer for this.
>> Comeing to the topic, I'm aware that I'm going to
>> stirr the hornet's nest, but...
>> it is the same old story: Mac vs. PC.
>> For some practical reasons (lower price and wider
>> software availability) I prefer to buy PC, but on
>> the other hand I use Image and some spinn off that I
>> find very nice and usefull.
>> How match both the necessities?
>> I've checked about MAC emulators on PC, testing a
>> demo of executor (Ardi company). Even though the
>> demo worked, it really emulates only old 68xxx
>> processor. Quite dissapointing!
>> Does any one know about a reliable and reasonably
>> fast MAC emulator for PC??
>>
>> Thank you in advance to whoever bothers to answer.
>> Sincerely
>> Eugenio Amendola
>> ----------------------------
>> ----------------------------
>> Dr. Eugenio Amendola
>> Italian National Council of Research
>> Institute of Composite Materials Technology
>> P.le Tecchio 80, 80125 Naples
>> ITALY
>> Tel:       (+) 39 081 7682511
>> fax:       (+) 39 081 7682404
>> email:    amendola@unina.it
>> url:        143.225.239.86
>>
>
>__________________________________________________
>Do You Yahoo!?
>Bid and sell for free at http://auctions.yahoo.com


Lori Ploutz-Snyder, Ph.D.
Exercise Science
Room 201 Women's Building
Syracuse University
Syracuse, NY  13244
(315) 443-9800
fax (315) 443-9375



From nih-image-request@io.ece.drexel.edu Thu Sep 23 11:09 EDT 1999
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Date: Wed, 22 Sep 1999 07:51:41 -0700
From: "Mark C. Olm" <olm1@ix.netcom.com>
Reply-To: olm1@ix.netcom.com
Organization: Consulting Geophysicist
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I get an error message when attempting to print many images, which can
then be imported into even a program like lview and printed with no
problem.
The message is :   "StretchDIBits Failed"
Can anyone help me to understand the reason and a solution.
Thank You;  Mark  (olm1@ix.netcom.com)


From nih-image-request@io.ece.drexel.edu Thu Sep 23 14:12 EDT 1999
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Date: Thu, 23 Sep 1999 10:52:59 -0700 (PDT)
From: Chris Poklemba <poklembc@ucs.orst.edu>
To: NIH-Image mailing list <nih-image@io.ece.drexel.edu>
Subject: Re: MAC or PC?
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We now have a G4 and use the PC emulator 'Virtual PC' which works
incredibly smooth and seamless.




From nih-image-d-request@io.ece.drexel.edu Fri Sep 24 03:15 EDT 1999
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Date: Fri, 24 Sep 1999 03:15:19 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199909240715.DAA12235@io.ece.drexel.edu>
Subject: nih-image-d Digest V99 #219
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 219

Today's Topics:
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
  MAC or PC?                            [ "Eugenio Amendola" <amendola@unina. ]
  Re:MAC or PC?                         [ "=?iso-8859-1?Q?=22Dr._Luis_F._Hern ]
  Re: MAC or PC?                        [ steve spencer <stephen_spencer@yaho ]
  unsubscribe                           [ "Darryl C. Sutton" <dsutton@coe.neu ]
  Re: MAC or PC?                        [ Lori Ploutz-Snyder <llploutz@syr.ed ]
  printing error message                [ "Mark C. Olm" <olm1@ix.netcom.com> ]
  Re: MAC or PC?                        [ Chris Poklemba <poklembc@ucs.orst.e ]
  Extended Focal Imaging                [ brownlee <brownlee@bluemoon.astro.w ]
  Focus Macro                           [ Bertrand Menard <Bertrand.Menard@ie ]

------------------------------

Date: Thu, 23 Sep 1999 05:05:01 -0400 (EDT)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199909230905.FAA10878@io.ece.drexel.edu>

                   NIH-image Mailing List Help 
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0)  Remember that Archive is case-sensitive.
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Examples:
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--

------------------------------

Date: Thu, 23 Sep 1999 15:08:30 +0200
From: "Eugenio Amendola" <amendola@unina.it>
To: "NIH-Image mailing list" <nih-image@io.ece.drexel.edu>
Subject: MAC or PC?
Message-ID: <000c01bf05c4$bdc81ac0$99efe18f@unina.it>
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_0009_01BF05D5.7ECB7860"

This is a multi-part message in MIME format.

------=_NextPart_000_0009_01BF05D5.7ECB7860
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Dear friends,
I'm reading this list with interest since a little while, and first of =
all I would like to thank the organizer for this.
Comeing to the topic, I'm aware that I'm going to stirr the hornet's =
nest, but...
it is the same old story: Mac vs. PC.
For some practical reasons (lower price and wider software availability) =
I prefer to buy PC, but on the other hand I use Image and some spinn off =
that I find very nice and usefull.
How match both the necessities?
I've checked about MAC emulators on PC, testing a demo of executor (Ardi =
company). Even though the demo worked, it really emulates only old 68xxx =
processor. Quite dissapointing!
Does any one know about a reliable and reasonably fast MAC emulator for =
PC??

Thank you in advance to whoever bothers to answer.
Sincerely
Eugenio Amendola
----------------------------
----------------------------
Dr. Eugenio Amendola
Italian National Council of Research
Institute of Composite Materials Technology
P.le Tecchio 80, 80125 Naples
ITALY
Tel:       (+) 39 081 7682511
fax:       (+) 39 081 7682404
email:    amendola@unina.it
url:        143.225.239.86

------=_NextPart_000_0009_01BF05D5.7ECB7860
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content=3D"text/html; charset=3Diso-8859-1" =
http-equiv=3DContent-Type>
<META content=3D"MSHTML 5.00.2014.210" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#c8e0d8>
<DIV><FONT face=3DArial size=3D2>Dear friends,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I'm reading this list with interest =
since a little=20
while, and first of all I would like to thank the organizer for=20
this.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Comeing to the topic, I'm aware that =
I'm going to=20
stirr the hornet's nest, but...</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>it is the same old story: Mac vs. =
PC.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>For some practical reasons (lower price =
and wider=20
software availability) I prefer to buy PC, but on the other hand I use =
Image and=20
some spinn off that I find very nice and usefull.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>How match both the =
necessities?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I've checked about MAC emulators on PC, =
testing a=20
demo of executor (Ardi company). Even though the demo worked, it really =
emulates=20
only old 68xxx processor. Quite dissapointing!</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Does any one know about a reliable and =
reasonably=20
fast MAC emulator for PC??</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Thank you in advance to whoever bothers =
to=20
answer.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Sincerely</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Eugenio Amendola</FONT></DIV>
<DIV><FONT face=3DArial=20
size=3D2>----------------------------<BR>----------------------------<BR>=
Dr.=20
Eugenio Amendola<BR>Italian National Council of Research<BR>Institute of =

Composite Materials Technology<BR>P.le Tecchio 80, 80125=20
Naples<BR>ITALY<BR>Tel:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (+) 39 081=20
7682511<BR>fax:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; (+) 39 081=20
7682404<BR>email:&nbsp;&nbsp;&nbsp; <A=20
href=3D"mailto:amendola@unina.it">amendola@unina.it</A><BR>url:&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
143.225.239.86</FONT></DIV></BODY></HTML>

------=_NextPart_000_0009_01BF05D5.7ECB7860--

------------------------------

Date: Thu, 23 Sep 1999 10:26:36 -0300
From: "=?iso-8859-1?Q?=22Dr._Luis_F._Hern=E1ndez=22?="  <lhernan@criba.edu.ar>
To: nih-image@io.ece.drexel.edu
Subject: Re:MAC or PC?
Message-Id: <v03130300b40fd9d11626@[170.210.187.214]>
Content-Type: text/plain; charset="us-ascii"

Dr.  Eugenio Amendola wrote:
Does any one know about a reliable and reasonably  fast MAC emulator for
PC??   Thank you in advance to whoever bothers to  answer. Sincerely
Eugenio Amendola

For my experience and after several tries with  Executor (Ardi company) and
Gemulator (http://www.emulators.com/ ) the answer is:
"The best reliable and reasonably fast MAC emulator is a true MAC (ranging
from a good old and reliable SE30 to a G4)"



_______________________________________________________
Dr. Luis F. Hernandez, Ph.D.
Laboratorio de Botanica
Departamento de Agronomia
U N I V E R S I D A D  N A C I O N A L  D E L  S U R
8000. Bahia Blanca - ARGENTINA

<mailto: lhernan@criba.edu.ar>
Telefonos (0291) 453-4775/453-0024
FAX: 54 - 0291 - 452-1942
_______________________________________________________
The box said: "Requires Windows 98 or better".....
So I bought a Macintosh.

------------------------------

Date: Thu, 23 Sep 1999 06:35:17 -0700 (PDT)
From: steve spencer <stephen_spencer@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: MAC or PC?
Message-ID: <19990923133517.15335.rocketmail@web601.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

Unfortuniatly until the bugs are fixed from scion
image I would suggest just buying an expensive
macintosh if you are planning on doing analysis that
requires the use of an imaging program such as NIH
image.
Or buy a pc instal linux and use one of the many image
based programs designed for linux. i.e MEDx brains2 (
which I have heard may be ported to linux) afni  etc.
steve

--- Eugenio Amendola <amendola@unina.it> wrote:
> Dear friends,
> I'm reading this list with interest since a little
> while, and first of all I would like to thank the
> organizer for this.
> Comeing to the topic, I'm aware that I'm going to
> stirr the hornet's nest, but...
> it is the same old story: Mac vs. PC.
> For some practical reasons (lower price and wider
> software availability) I prefer to buy PC, but on
> the other hand I use Image and some spinn off that I
> find very nice and usefull.
> How match both the necessities?
> I've checked about MAC emulators on PC, testing a
> demo of executor (Ardi company). Even though the
> demo worked, it really emulates only old 68xxx
> processor. Quite dissapointing!
> Does any one know about a reliable and reasonably
> fast MAC emulator for PC??
> 
> Thank you in advance to whoever bothers to answer.
> Sincerely
> Eugenio Amendola
> ----------------------------
> ----------------------------
> Dr. Eugenio Amendola
> Italian National Council of Research
> Institute of Composite Materials Technology
> P.le Tecchio 80, 80125 Naples
> ITALY
> Tel:       (+) 39 081 7682511
> fax:       (+) 39 081 7682404
> email:    amendola@unina.it
> url:        143.225.239.86
> 

__________________________________________________
Do You Yahoo!?
Bid and sell for free at http://auctions.yahoo.com

------------------------------

Date: Thu, 23 Sep 1999 10:17:31 -0400 (EDT)
From: "Darryl C. Sutton" <dsutton@coe.neu.edu>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <199909231417.KAA05569@Bars.coe.neu.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-MD5: xqPdB/YbmjDml7O4cDMkZQ==

Please "UNSUBSCRIBE" or remove me from your e-mailing list.

Thanks 

------------------------------

Date: Thu, 23 Sep 1999 10:43:30 -0400 (EDT)
From: Lori Ploutz-Snyder <llploutz@syr.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: MAC or PC?
Message-Id: <v03007800b40fb36488e3@[128.230.82.189]>
Content-Type: text/plain; charset="us-ascii"

If you want to do image analysis and know that NIH Image meets
your needs, I would highly suggest buying a mac.  The G4s
don't seem too expensive considering what you get.  Any extra
cost might be offset by the price of NIH Image (free) and the ease of
installing/running it.
-Lori

>
>--- Eugenio Amendola <amendola@unina.it> wrote:
>> Dear friends,
>> I'm reading this list with interest since a little
>> while, and first of all I would like to thank the
>> organizer for this.
>> Comeing to the topic, I'm aware that I'm going to
>> stirr the hornet's nest, but...
>> it is the same old story: Mac vs. PC.
>> For some practical reasons (lower price and wider
>> software availability) I prefer to buy PC, but on
>> the other hand I use Image and some spinn off that I
>> find very nice and usefull.
>> How match both the necessities?
>> I've checked about MAC emulators on PC, testing a
>> demo of executor (Ardi company). Even though the
>> demo worked, it really emulates only old 68xxx
>> processor. Quite dissapointing!
>> Does any one know about a reliable and reasonably
>> fast MAC emulator for PC??
>>
>> Thank you in advance to whoever bothers to answer.
>> Sincerely
>> Eugenio Amendola
>> ----------------------------
>> ----------------------------
>> Dr. Eugenio Amendola
>> Italian National Council of Research
>> Institute of Composite Materials Technology
>> P.le Tecchio 80, 80125 Naples
>> ITALY
>> Tel:       (+) 39 081 7682511
>> fax:       (+) 39 081 7682404
>> email:    amendola@unina.it
>> url:        143.225.239.86
>>
>
>__________________________________________________
>Do You Yahoo!?
>Bid and sell for free at http://auctions.yahoo.com


Lori Ploutz-Snyder, Ph.D.
Exercise Science
Room 201 Women's Building
Syracuse University
Syracuse, NY  13244
(315) 443-9800
fax (315) 443-9375

------------------------------

Date: Wed, 22 Sep 1999 07:51:41 -0700
From: "Mark C. Olm" <olm1@ix.netcom.com>
To: NIH List <nih-image@io.ece.drexel.edu>
Subject: printing error message
Message-ID: <37E8ECFD.AFEA6327@ix.netcom.com>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

I get an error message when attempting to print many images, which can
then be imported into even a program like lview and printed with no
problem.
The message is :   "StretchDIBits Failed"
Can anyone help me to understand the reason and a solution.
Thank You;  Mark  (olm1@ix.netcom.com)

------------------------------

Date: Thu, 23 Sep 1999 10:52:59 -0700 (PDT)
From: Chris Poklemba <poklembc@ucs.orst.edu>
To: NIH-Image mailing list <nih-image@io.ece.drexel.edu>
Subject: Re: MAC or PC?
Message-ID: <Pine.OSF.4.05.9909231050230.31044-100000@ucs.orst.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

We now have a G4 and use the PC emulator 'Virtual PC' which works
incredibly smooth and seamless.

------------------------------

Date: Thu, 23 Sep 1999 13:29:00 -0700
From: brownlee <brownlee@bluemoon.astro.washington.edu>
To: nih-image-d@io.ece.drexel.edu
Subject: Extended Focal Imaging
Message-Id: <v04210108b4103d49e3dc@[128.95.99.35]>
Content-Type: text/plain; charset="us-ascii" ; format="flowed"

Does anyone know of a NIH Image or photoshop plugin that add can add 
optical microscope images taken at various depths of focus to 
increase the total depth of field? Soft-imaging in Germany  has a 
product called "Extended Focal Imaging" 
http://www.soft-imaging.De/eng/hotshots/efi/efi_e.htm that does this 
but  it is a PC-only product.  They do not say how it works but it 
must involve frequency filtering and some clever way of combining the 
filtered images.  The examples  on their home page look very good.

Don Brownlee
Don Brownlee
Dept. of Astronomy
BOX 351580
University of Washington
Seattle, WA 98195

phone (206) 543-8575
fax   (206 685-0403
brownlee@astro.washington.edu

------------------------------

Date: Fri, 24 Sep 1999 09:05:49 +0200
From: Bertrand Menard <Bertrand.Menard@ie-bpv.unil.ch>
To: nih-image@io.ece.drexel.edu
Subject: Focus Macro
Message-Id: <v03102800b410d189f44a@[130.223.74.35]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Hi imagers,

Does someone know an algorithm, or better a macro, which could detect
focused and out of focus zones of an image ? Or could compare 2 images to
find the best focused zones ?

Thank you very much.



Bertrand

**********************************************************

                             Bertrand MENARD


    University of Lausanne                   Universit de Lausanne
        Institut of Ecology                         Institut d'cologie
Plant Biology and Physiology       Biologie et Physiologie Vgtales
      Batiment de Biologie                     Batiment de Biologie
     CH-1015 LAUSANNE                  CH-1015 LAUSANNE
            Switzerland                                       Suisse

                           Tel : 00 41 21 692 42 19
                           Fax : 00 41 21 692 41 95

                  E-Mail : Bertrand.Menard@ie-bpv.unil.ch

**********************************************************

--------------------------------
End of nih-image-d Digest V99 Issue #219
****************************************

From nih-image-request@io.ece.drexel.edu Fri Sep 24 03:21 EDT 1999
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Date: Fri, 24 Sep 1999 09:05:49 +0200
To: nih-image@io.ece.drexel.edu
From: Bertrand Menard <Bertrand.Menard@ie-bpv.unil.ch>
Subject: Focus Macro
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Hi imagers,

Does someone know an algorithm, or better a macro, which could detect
focused and out of focus zones of an image ? Or could compare 2 images to
find the best focused zones ?

Thank you very much.



Bertrand

**********************************************************

                             Bertrand MENARD


    University of Lausanne                   Universit de Lausanne
        Institut of Ecology                         Institut d'cologie
Plant Biology and Physiology       Biologie et Physiologie Vgtales
      Batiment de Biologie                     Batiment de Biologie
     CH-1015 LAUSANNE                  CH-1015 LAUSANNE
            Switzerland                                       Suisse

                           Tel : 00 41 21 692 42 19
                           Fax : 00 41 21 692 41 95

                  E-Mail : Bertrand.Menard@ie-bpv.unil.ch

**********************************************************



From nih-image-request@io.ece.drexel.edu Fri Sep 24 04:32 EDT 1999
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Date: Fri, 24 Sep 1999 09:18:38 +0100
To: nih-image@io.ece.drexel.edu
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
Subject: Re: Extended Focal Imaging and Focus Macro
Resent-Message-ID: <"A6RIy1.0.OW5.gEpwt"@io>
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Don Brownlee asked:

>Does anyone know of a NIH Image or photoshop plugin that add can add
>optical microscope images taken at various depths of focus to
>increase the total depth of field?

and Bertrand Menard asked:

>Does someone know an algorithm, or better a macro, which could detect
>focused and out of focus zones of an image ? Or could compare 2 images to
>find the best focused zones?

I have written an NIH Image spin-off application, Image SXM, that has been
extended to handle SEM, SPM and SAM images. It includes a routine to
produce a composite image from a stack of images focussed at different
depths of the sample. The algorithm is being modified, with feedback from
users, to improve its performance. This new version will be released soon,
or I can send it to anyone interested in beta-testing.

For more information on Image SXM, see http://reg.ssci.liv.ac.uk

___________________________________________________________________
Dr Steve Barrett
Surface Science Research Centre
University of Liverpool
Liverpool L69 3BX
United Kingdom

Tel: 44-(0)151-794-3894 / 3874 / 3541
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk
___________________________________________________________________



From nih-image-request@io.ece.drexel.edu Fri Sep 24 09:47 EDT 1999
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Date: Fri, 24 Sep 1999 09:30:27 -0400
To: nih-image@io.ece.drexel.edu
From: "Phil Allen" <pallen@rics.bwh.harvard.edu>
Subject: Re: Focus Macro
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Bertrand-

I'm confused about your request.  Do you want to find the image most in
focus out of a stack of images or are you interested in defining areas
within an image that can be classified as in (or out) of focus.  Also, what
kind of images are you considering?  Brightfield, fluorescence, EM?

In my experience with bright field images, the image with the maximal
variance is usually the one we would define as in focus by eye.
Unfortunately it doesn't work as well with standard fluorescence images,
and I haven't tried it yet with confocal data.

Phil Allen
>Hi imagers,
>
>Does someone know an algorithm, or better a macro, which could detect
>focused and out of focus zones of an image ? Or could compare 2 images to
>find the best focused zones ?
>
>Thank you very much.
>
>
>
>Bertrand
>
>**********************************************************
>
>                             Bertrand MENARD
>
>
>    University of Lausanne                   Universit de Lausanne
>        Institut of Ecology                         Institut d'cologie
>Plant Biology and Physiology       Biologie et Physiologie Vgtales
>      Batiment de Biologie                     Batiment de Biologie
>     CH-1015 LAUSANNE                  CH-1015 LAUSANNE
>            Switzerland                                       Suisse
>
>                           Tel : 00 41 21 692 42 19
>                           Fax : 00 41 21 692 41 95
>
>                  E-Mail : Bertrand.Menard@ie-bpv.unil.ch
>
>**********************************************************


________________
Philip G. Allen; Ph.D.
Scientific Director
Brigham and Women's Hospital Confocal Facility &
Hematology Division
LMRC 301
221 Longwood Ave.
Boston, MA 02115

617-278-0321 (office)
       -734-2248 (fax)



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Steve Barrett wrote:

>I have written an NIH Image spin-off application, Image SXM, that has been
>extended to handle SEM, SPM and SAM images. It includes a routine to
>produce a composite image from a stack of images focussed at different
>depths of the sample. The algorithm is being modified, with feedback from
>users, to improve its performance. This new version will be released soon,
>or I can send it to anyone interested in beta-testing.

Has this been, or it be, released in either ImageJ or a PC version?
Thanks.

Henry Barwood
>
>


From nih-image-request@io.ece.drexel.edu Fri Sep 24 09:59 EDT 1999
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From: Harvey Karten <hjkarten@ucsd.edu>
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The recent thread asking about Mac vs. PC reflects the continuing
outstanding value of NIH-Image. There is no question but that NIH-Image
is best run on a Mac. The PC version is helpful, but remains buggy, and
is not being updated. However, the limitations of an 8 bit image
processing program, in conjunction with platform limitations are
significant. I strongly suggest that more NIH-Image users start looking
more seriously at ImageJ by Wayne Rasband, author of NIH-Image.

ImageJ is a Java based program that will run on Mac, PC, UNIX, Linus,
O/S2. It handles 16 bit images with facility, provides RGB support, and
is expandable via plugins. It is actively being developed, whereas
NIH-Image is now frozen at version 1.62. Wayne has stated that he will
not do any further development of NIH-Image. The sooner the scientific
community joins in to the new level of image processing, the more rapid
will be the expansion of ImageJ.

regards, Harvey J. Karten
UCSD


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From: Walter Wolf <wwolfw@hsc.usc.edu>
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The comment by Dr. Karten, that ImageJ, a Java based program, should be used
more actively is important. However, for those of us who are users, and not
developers, the absence of a good manual that would "walk us by the hand" and
allow us to use ImageJ properly is critical. 

We have been unable to find people who understand Pascal in order to write
new macros that would allow us to process our dynamic MRI data the way that
would be most convenient. Clearly, using Java-based programs should be much
more effective, and likely to allow greater use of NIH Image / ImageJ, which
is a wonderful program. 

We look forward to the day when a manual becomes available that would allow
us to make full and good use of the features of ImageJ. 

PLEASE NOTE NEW ZIP-CODE AT USC
======================================================================
|  Professor Walter Wolf, Ph.D.          E-Mail: wwolfw@hsc.usc.edu  |
|  Distinguished Professor of Pharmaceutical Sciences		     |
|  Director, Pharmacokinetic Imaging Program                         |
|  Department of Pharmaceutical Sciences, School of Pharmacy	     |
|  University of Southern California           Telephone:323-442-1405|
|  1985 Zonal Ave., Los Angeles, CA 90089-9121 Fax:      323-442-9804|
|                                                                    |
|Center for Noninvasive Pharmacology, Los Angeles Oncologic Institute|
|  MRI at St. Vincent Medical Center     Telephone:    213-484-7235  |
|  2131 Third St., Los Angeles, CA 90057 Fax:          213-484-7447  |
======================================================================
 


From nih-image-request@io.ece.drexel.edu Fri Sep 24 10:59 EDT 1999
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Date: Fri, 24 Sep 1999 08:41:39 -0600
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I am setting up a new system and am in the process of buying  a Scion
VG-5 board for a PC. I would like to do the same kind of things that I
could do with the Mac I had for my old system. I am planning on using
Scion PC Image to capture and process images. However, it appears from
the recent PC v Mac discussions that PC image is buggy. I would like to
give ImageJ ago but was wondering if the software will run a Scion Image
board. I am hoping that ImageJ on a PC will run as smoothly as NIH Image
did on the Mac. Does anybody know if I can capture / integrate etc. on a
Scion board right out of ImageJ like I did with Scion Image?

Paul Stoodley
Research Associate
Center for Biofilm Engineering


From nih-image-request@io.ece.drexel.edu Fri Sep 24 11:32 EDT 1999
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I believe that Image SXM (downloadable from the NIH page) can detect and
combine Focused regions of different images - this based on pixel
contrast...


> Does anyone know of a NIH Image or photoshop plugin that add can add
> optical microscope images taken at various depths of focus to
> increase the total depth of field? Soft-imaging in Germany  has a
> product called "Extended Focal Imaging"
> http://www.soft-imaging.De/eng/hotshots/efi/efi_e.htm that does this
> but  it is a PC-only product.  They do not say how it works but it
> must involve frequency filtering and some clever way of combining the
> filtered images.  The examples  on their home page look very good.
> 
> Don Brownlee

> Hi imagers,
> 
> Does someone know an algorithm, or better a macro, which could detect
> focused and out of focus zones of an image ? Or could compare 2 images to
> find the best focused zones ?
> 
> Thank you very much.
> 
> Bertrand


From nih-image-request@io.ece.drexel.edu Fri Sep 24 11:35 EDT 1999
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Subject: RE: Mac vs. PC
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I have not yet switched to Image-J because, as far as I can tell, I have to
acquire my images using some other program so that I can then analyze them
in Image-J.  I would have thought that image acquisition would have been a
priority.  I would like to be able to use the same software to acquire and
analyze an image and I would very much like to use Image-J for these.


Stephen J. Moorman, Ph.D.
Assistant Professor of Anatomy
Case Western Reserve University
10900 Euclid Ave.
Cleveland, OH 44106-4930

Office: 216-368-2855
Fax: 216-368-4378
e-mail: sjm8@po.cwru.edu

http://mediswww.cwru.edu/dept/anatomy/moorman/



From nih-image-request@io.ece.drexel.edu Fri Sep 24 11:40 EDT 1999
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OK, I know ImageJ is the thing of the future.  But Java has always been
unstable for me.

Just now, I tried running ImageJ  (with freshly intalled MRJ 2.1.4)  and
it will not run...


I am trying to be hip and with it...what am I doing wrong?


-- 

   _________________________________________________
     /  Michael J. Herron                          /
    /     U of MN,Medicine/Infectious Diseases    /
   /        herro001@maroon.tc.umn.edu           /
  /           http://128.101.243.213            /
 /_____________________________________________/


From nih-image-request@io.ece.drexel.edu Fri Sep 24 11:45 EDT 1999
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Harvey J. Karten's remarks encouraged us to switch ASAP.

I have spent a lot of time developing macros that work well for my requirements
on NIH Image for the Mac. As soon as ImageJ will allow me to port the macros
easily and supports Watershed techniques (NIH Image does but ImageJ not yet) it
may be worth my while to move over. Until then I just want to thank Wayne R for
all the work on BOTH applications

--
Paul C. Grimm
Associate Professor
Pediatric Nephrology
University of California at San Diego

Email pgrimm@ucsd.edu
Phone 619-543-5218
Fax   619-543-3575
Snail mail
UCSD Pediatrics
Mail Stop 0831
9500 Gilman Drive,
La Jolla California
92093-0831

Someone who thinks logically provides a nice contrast to the real world.



From nih-image-request@io.ece.drexel.edu Fri Sep 24 12:02 EDT 1999
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I concur.  

"Stephen J. Moorman" wrote:
> 
> I have not yet switched to Image-J because, as far as I can tell, I have to
> acquire my images using some other program so that I can then analyze them
> in Image-J.  I would have thought that image acquisition would have been a
> priority.  I would like to be able to use the same software to acquire and
> analyze an image and I would very much like to use Image-J for these.
> 
> Stephen J. Moorman, Ph.D.
> Assistant Professor of Anatomy
> Case Western Reserve University
> 10900 Euclid Ave.
> Cleveland, OH 44106-4930
> 
> Office: 216-368-2855
> Fax: 216-368-4378
> e-mail: sjm8@po.cwru.edu
> 
> http://mediswww.cwru.edu/dept/anatomy/moorman/

-- 

   _________________________________________________
     /  Michael J. Herron                          /
    /     U of MN,Medicine/Infectious Diseases    /
   /        herro001@maroon.tc.umn.edu           /
  /           http://128.101.243.213            /
 /_____________________________________________/


From nih-image-d-request@io.ece.drexel.edu Sat Sep 25 06:15 EDT 1999
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V99 #220
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 220

Today's Topics:
  Re: Extended Focal Imaging and Focus  [ Steve Barrett <S.D.Barrett@liverpoo ]
  Re: Focus Macro                       [ "Phil Allen" <pallen@rics.bwh.harva ]
  RE: Extended Focal Imaging and Focus  [ "Barwood, Henry" <hbarwood@pyrite.i ]
  Mac vs. PC                            [ Harvey Karten <hjkarten@ucsd.edu> ]
  Re: Mac vs. PC                        [ Walter Wolf <wwolfw@hsc.usc.edu> ]
  RE: Mac vs. PC                        [ "Stoodley, Paul" <paul_s@erc.montan ]
  combining in-focus slices             [ Duncan Young <dyoung@post.cis.smu.e ]
  RE: Mac vs. PC                        [ "Stephen J. Moorman" <sjm8@po.cwru. ]
  ImageJ woes                           [ Michael Herron <herro001@maroon.tc. ]
  Re: Image vs ImageJ                   [ Paul Grimm <pgrimm@ucsd.edu> ]
  Re: Mac vs. PC                        [ Michael Herron <herro001@maroon.tc. ]

------------------------------

Date: Fri, 24 Sep 1999 09:18:38 +0100
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Extended Focal Imaging and Focus Macro
Message-Id: <l03130319b410e00de435@[138.253.47.16]>
Content-Type: text/plain; charset="us-ascii"

Don Brownlee asked:

>Does anyone know of a NIH Image or photoshop plugin that add can add
>optical microscope images taken at various depths of focus to
>increase the total depth of field?

and Bertrand Menard asked:

>Does someone know an algorithm, or better a macro, which could detect
>focused and out of focus zones of an image ? Or could compare 2 images to
>find the best focused zones?

I have written an NIH Image spin-off application, Image SXM, that has been
extended to handle SEM, SPM and SAM images. It includes a routine to
produce a composite image from a stack of images focussed at different
depths of the sample. The algorithm is being modified, with feedback from
users, to improve its performance. This new version will be released soon,
or I can send it to anyone interested in beta-testing.

For more information on Image SXM, see http://reg.ssci.liv.ac.uk

___________________________________________________________________
Dr Steve Barrett
Surface Science Research Centre
University of Liverpool
Liverpool L69 3BX
United Kingdom

Tel: 44-(0)151-794-3894 / 3874 / 3541
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk
___________________________________________________________________

------------------------------

Date: Fri, 24 Sep 1999 09:30:27 -0400
From: "Phil Allen" <pallen@rics.bwh.harvard.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Focus Macro
Message-Id: <l03130305b4112c9c398f@[134.174.88.4]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Bertrand-

I'm confused about your request.  Do you want to find the image most in
focus out of a stack of images or are you interested in defining areas
within an image that can be classified as in (or out) of focus.  Also, what
kind of images are you considering?  Brightfield, fluorescence, EM?

In my experience with bright field images, the image with the maximal
variance is usually the one we would define as in focus by eye.
Unfortunately it doesn't work as well with standard fluorescence images,
and I haven't tried it yet with confocal data.

Phil Allen
>Hi imagers,
>
>Does someone know an algorithm, or better a macro, which could detect
>focused and out of focus zones of an image ? Or could compare 2 images to
>find the best focused zones ?
>
>Thank you very much.
>
>
>
>Bertrand
>
>**********************************************************
>
>                             Bertrand MENARD
>
>
>    University of Lausanne                   Universit de Lausanne
>        Institut of Ecology                         Institut d'cologie
>Plant Biology and Physiology       Biologie et Physiologie Vgtales
>      Batiment de Biologie                     Batiment de Biologie
>     CH-1015 LAUSANNE                  CH-1015 LAUSANNE
>            Switzerland                                       Suisse
>
>                           Tel : 00 41 21 692 42 19
>                           Fax : 00 41 21 692 41 95
>
>                  E-Mail : Bertrand.Menard@ie-bpv.unil.ch
>
>**********************************************************


________________
Philip G. Allen; Ph.D.
Scientific Director
Brigham and Women's Hospital Confocal Facility &
Hematology Division
LMRC 301
221 Longwood Ave.
Boston, MA 02115

617-278-0321 (office)
       -734-2248 (fax)

------------------------------

Date: Fri, 24 Sep 1999 08:36:19 -0500
From: "Barwood, Henry" <hbarwood@pyrite.igs.indiana.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Extended Focal Imaging and Focus Macro
Message-ID: <c=US%a=_%p=Indiana_Universi%l=PYRITE-990924133619Z-9144@pyrite.igs.indiana.edu>

Steve Barrett wrote:

>I have written an NIH Image spin-off application, Image SXM, that has been
>extended to handle SEM, SPM and SAM images. It includes a routine to
>produce a composite image from a stack of images focussed at different
>depths of the sample. The algorithm is being modified, with feedback from
>users, to improve its performance. This new version will be released soon,
>or I can send it to anyone interested in beta-testing.

Has this been, or it be, released in either ImageJ or a PC version?
Thanks.

Henry Barwood
>
>

------------------------------

Date: Fri, 24 Sep 1999 06:40:30 -0700
From: Harvey Karten <hjkarten@ucsd.edu>
To: nih-image@io.ece.drexel.edu
Subject: Mac vs. PC
Message-ID: <37EB7F4E.ACFD07B@ucsd.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

The recent thread asking about Mac vs. PC reflects the continuing
outstanding value of NIH-Image. There is no question but that NIH-Image
is best run on a Mac. The PC version is helpful, but remains buggy, and
is not being updated. However, the limitations of an 8 bit image
processing program, in conjunction with platform limitations are
significant. I strongly suggest that more NIH-Image users start looking
more seriously at ImageJ by Wayne Rasband, author of NIH-Image.

ImageJ is a Java based program that will run on Mac, PC, UNIX, Linus,
O/S2. It handles 16 bit images with facility, provides RGB support, and
is expandable via plugins. It is actively being developed, whereas
NIH-Image is now frozen at version 1.62. Wayne has stated that he will
not do any further development of NIH-Image. The sooner the scientific
community joins in to the new level of image processing, the more rapid
will be the expansion of ImageJ.

regards, Harvey J. Karten
UCSD

------------------------------

Date: Fri, 24 Sep 99 7:13:05 PDT
From: Walter Wolf <wwolfw@hsc.usc.edu>
To: nih-image@io.ece.drexel.edu
Cc: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu
Subject: Re: Mac vs. PC
Message-ID: <CMM.0.90.4.938182385.wwolfw@hsc.usc.edu>

The comment by Dr. Karten, that ImageJ, a Java based program, should be used
more actively is important. However, for those of us who are users, and not
developers, the absence of a good manual that would "walk us by the hand" and
allow us to use ImageJ properly is critical. 

We have been unable to find people who understand Pascal in order to write
new macros that would allow us to process our dynamic MRI data the way that
would be most convenient. Clearly, using Java-based programs should be much
more effective, and likely to allow greater use of NIH Image / ImageJ, which
is a wonderful program. 

We look forward to the day when a manual becomes available that would allow
us to make full and good use of the features of ImageJ. 

PLEASE NOTE NEW ZIP-CODE AT USC
======================================================================
|  Professor Walter Wolf, Ph.D.          E-Mail: wwolfw@hsc.usc.edu  |
|  Distinguished Professor of Pharmaceutical Sciences		     |
|  Director, Pharmacokinetic Imaging Program                         |
|  Department of Pharmaceutical Sciences, School of Pharmacy	     |
|  University of Southern California           Telephone:323-442-1405|
|  1985 Zonal Ave., Los Angeles, CA 90089-9121 Fax:      323-442-9804|
|                                                                    |
|Center for Noninvasive Pharmacology, Los Angeles Oncologic Institute|
|  MRI at St. Vincent Medical Center     Telephone:    213-484-7235  |
|  2131 Third St., Los Angeles, CA 90057 Fax:          213-484-7447  |
======================================================================
 

------------------------------

Date: Fri, 24 Sep 1999 08:41:39 -0600
From: "Stoodley, Paul" <paul_s@erc.montana.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Mac vs. PC
Message-ID: <28C8B514497ED111AF510000F803473E0105CA29@power.coe.montana.edu>
Content-Type: text/plain

I am setting up a new system and am in the process of buying  a Scion
VG-5 board for a PC. I would like to do the same kind of things that I
could do with the Mac I had for my old system. I am planning on using
Scion PC Image to capture and process images. However, it appears from
the recent PC v Mac discussions that PC image is buggy. I would like to
give ImageJ ago but was wondering if the software will run a Scion Image
board. I am hoping that ImageJ on a PC will run as smoothly as NIH Image
did on the Mac. Does anybody know if I can capture / integrate etc. on a
Scion board right out of ImageJ like I did with Scion Image?

Paul Stoodley
Research Associate
Center for Biofilm Engineering

------------------------------

Date: Fri, 24 Sep 1999 09:08:32 -0500
From: Duncan Young <dyoung@post.cis.smu.edu>
To: nih-image@io.ece.drexel.edu
Subject: combining in-focus slices
Message-ID: <37EB85DF.3BB2@mail.smu.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

I believe that Image SXM (downloadable from the NIH page) can detect and
combine Focused regions of different images - this based on pixel
contrast...


> Does anyone know of a NIH Image or photoshop plugin that add can add
> optical microscope images taken at various depths of focus to
> increase the total depth of field? Soft-imaging in Germany  has a
> product called "Extended Focal Imaging"
> http://www.soft-imaging.De/eng/hotshots/efi/efi_e.htm that does this
> but  it is a PC-only product.  They do not say how it works but it
> must involve frequency filtering and some clever way of combining the
> filtered images.  The examples  on their home page look very good.
> 
> Don Brownlee

> Hi imagers,
> 
> Does someone know an algorithm, or better a macro, which could detect
> focused and out of focus zones of an image ? Or could compare 2 images to
> find the best focused zones ?
> 
> Thank you very much.
> 
> Bertrand

------------------------------

Date: Fri, 24 Sep 1999 11:18:48 -0400
From: "Stephen J. Moorman" <sjm8@po.cwru.edu>
To: nih-image@io.ece.drexel.edu
Subject: RE: Mac vs. PC
Message-Id: <l03130300b41145f35584@[129.22.112.180]>
Content-Type: text/plain; charset="us-ascii"

I have not yet switched to Image-J because, as far as I can tell, I have to
acquire my images using some other program so that I can then analyze them
in Image-J.  I would have thought that image acquisition would have been a
priority.  I would like to be able to use the same software to acquire and
analyze an image and I would very much like to use Image-J for these.


Stephen J. Moorman, Ph.D.
Assistant Professor of Anatomy
Case Western Reserve University
10900 Euclid Ave.
Cleveland, OH 44106-4930

Office: 216-368-2855
Fax: 216-368-4378
e-mail: sjm8@po.cwru.edu

http://mediswww.cwru.edu/dept/anatomy/moorman/

------------------------------

Date: Fri, 24 Sep 1999 10:24:17 -0500
From: Michael Herron <herro001@maroon.tc.umn.edu>
To: NIH Image Mailing List <nih-image@io.ece.drexel.edu>
Subject: ImageJ woes
Message-Id: <37EB979E.61A7A724@tc.umn.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

OK, I know ImageJ is the thing of the future.  But Java has always been
unstable for me.

Just now, I tried running ImageJ  (with freshly intalled MRJ 2.1.4)  and
it will not run...


I am trying to be hip and with it...what am I doing wrong?


-- 

   _________________________________________________
     /  Michael J. Herron                          /
    /     U of MN,Medicine/Infectious Diseases    /
   /        herro001@maroon.tc.umn.edu           /
  /           http://128.101.243.213            /
 /_____________________________________________/

------------------------------

Date: Fri, 24 Sep 1999 08:29:38 -0700
From: Paul Grimm <pgrimm@ucsd.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Image vs ImageJ
Message-ID: <37EB98E1.D81646EF@ucsd.edu>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Harvey J. Karten's remarks encouraged us to switch ASAP.

I have spent a lot of time developing macros that work well for my requirements
on NIH Image for the Mac. As soon as ImageJ will allow me to port the macros
easily and supports Watershed techniques (NIH Image does but ImageJ not yet) it
may be worth my while to move over. Until then I just want to thank Wayne R for
all the work on BOTH applications

--
Paul C. Grimm
Associate Professor
Pediatric Nephrology
University of California at San Diego

Email pgrimm@ucsd.edu
Phone 619-543-5218
Fax   619-543-3575
Snail mail
UCSD Pediatrics
Mail Stop 0831
9500 Gilman Drive,
La Jolla California
92093-0831

Someone who thinks logically provides a nice contrast to the real world.

------------------------------

Date: Fri, 24 Sep 1999 10:46:10 -0500
From: Michael Herron <herro001@maroon.tc.umn.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Mac vs. PC
Message-Id: <37EB9CBE.A53A6E39@tc.umn.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

I concur.  

"Stephen J. Moorman" wrote:
> 
> I have not yet switched to Image-J because, as far as I can tell, I have to
> acquire my images using some other program so that I can then analyze them
> in Image-J.  I would have thought that image acquisition would have been a
> priority.  I would like to be able to use the same software to acquire and
> analyze an image and I would very much like to use Image-J for these.
> 
> Stephen J. Moorman, Ph.D.
> Assistant Professor of Anatomy
> Case Western Reserve University
> 10900 Euclid Ave.
> Cleveland, OH 44106-4930
> 
> Office: 216-368-2855
> Fax: 216-368-4378
> e-mail: sjm8@po.cwru.edu
> 
> http://mediswww.cwru.edu/dept/anatomy/moorman/

-- 

   _________________________________________________
     /  Michael J. Herron                          /
    /     U of MN,Medicine/Infectious Diseases    /
   /        herro001@maroon.tc.umn.edu           /
  /           http://128.101.243.213            /
 /_____________________________________________/

--------------------------------
End of nih-image-d Digest V99 Issue #220
****************************************

From nih-image-request@io.ece.drexel.edu Mon Sep 27 07:51 EDT 1999
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	Mon, 27 Sep 1999 07:51:37 -0400 (EDT)
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Date: Mon, 27 Sep 1999 13:32:30 +0200
To: nih-image@io.ece.drexel.edu
From: Bertrand Menard <Bertrand.Menard@ie-bpv.unil.ch>
Subject: Focus macro (suite)
Resent-Message-ID: <"QDKqP.0.FX5.SNrxt"@io>
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Hi imagers,

More precisely, I would like to eliminate the out of focus parts of my images.

Than you.


Bertrand

**********************************************************

                             Bertrand MENARD


    University of Lausanne                   Universit de Lausanne
        Institut of Ecology                         Institut d'cologie
Plant Biology and Physiology       Biologie et Physiologie Vgtales
      Batiment de Biologie                     Batiment de Biologie
     CH-1015 LAUSANNE                  CH-1015 LAUSANNE
            Switzerland                                       Suisse

                           Tel : 00 41 21 692 42 19
                           Fax : 00 41 21 692 41 95

                  E-Mail : Bertrand.Menard@ie-bpv.unil.ch

**********************************************************



From nih-image-request@io.ece.drexel.edu Mon Sep 27 10:04 EDT 1999
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From: "Peter van Loon" <mushpvl@wish.net>
To: "NIH discussiegroep" <nih-image@io.ece.drexel.edu>
Subject: What means tokenized?
Date: Mon, 27 Sep 1999 15:45:36 +0200
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This is a multi-part message in MIME format.

------=_NextPart_000_0226_01BF08FF.578CEF40
Content-Type: text/plain;
	charset="x-user-defined"
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Hello,

I make macro's in Object-Image. (Thank you Norbert Vischer for this =
fantastic spin-off,=20
with the very usefull debugging tool). Unfortunately the used =
text-editor in NIH and Object-Image=20
has a limitation of 32K (Apple's built in editor). So I have to be very =
efficient whenever I write these macro's.=20
When I load the macro's, the info window gives information about =
filesize and tells me that it is tokenized=20
(whatever it means?. It seems to be limited to 20K. Sometimes I reach =
this limitation earlier then the=20
32K filesize limitation.=20
How can I prevent reaching this tokenized limit?
Are there future plans of using a different editor without a 32K =
limitation (whenever possible)?

Regards,

Peter van Loon
Mushroom Experimental Station
Horst, The Netherlands
Mushpvl@wish.net=20

------=_NextPart_000_0226_01BF08FF.578CEF40
Content-Type: text/html;
	charset="x-user-defined"
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD W3 HTML//EN">
<HTML>
<HEAD>

<META content=3D"text/html; charset=3Dx-user-defined" =
http-equiv=3DContent-Type>
<META content=3D'"MSHTML 4.72.3110.7"' name=3DGENERATOR>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT color=3D#000000 face=3DArial size=3D2>Hello,<BR></FONT></DIV>
<DIV><FONT color=3D#000000 face=3DArial size=3D2>I make macro's in =
Object-Image.=20
(Thank you Norbert Vischer for this fantastic spin-off, <BR>with the =
very=20
usefull debugging tool). Unfortunately the used text-editor in NIH and=20
Object-Image <BR>has a limitation of 32K (Apple's built in editor). So I =
have to=20
be very efficient whenever I write these macro's. <BR>When I load the =
macro's,=20
the info window gives information about filesize and tells me that it is =

tokenized <BR>(whatever it means?. It seems to be limited to 20K. =
Sometimes I=20
reach this limitation earlier then the <BR>32K filesize limitation. =
<BR>How can=20
I prevent reaching this tokenized limit?</FONT><FONT color=3D#000000 =
face=3DArial=20
size=3D2><BR>Are there future plans of using a different editor without =
a 32K=20
limitation (whenever possible)?</FONT></DIV>
<DIV><FONT color=3D#000000 face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000000 face=3DArial size=3D2>Regards,</FONT></DIV>
<DIV><FONT color=3D#000000 face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT color=3D#000000 face=3DArial size=3D2>Peter van =
Loon</FONT></DIV>
<DIV><FONT color=3D#000000 face=3DArial size=3D2>Mushroom Experimental=20
Station</FONT></DIV>
<DIV><FONT color=3D#000000 face=3DArial size=3D2>Horst, The =
Netherlands</FONT></DIV>
<DIV><FONT color=3D#000000 face=3DArial size=3D2><A=20
href=3D"mailto:Mushpvl@wish.net">Mushpvl@wish.net</A> =
</FONT></DIV></BODY></HTML>

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From nih-image-request@io.ece.drexel.edu Mon Sep 27 11:16 EDT 1999
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Date: Mon, 27 Sep 1999 17:10:32 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: What means tokenized?
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>     Hello,
> I make macro's in Object-Image.  (Thank you Norbert Vischer for this
>fantastic spin-off,
>with the very  usefull debugging tool). Unfortunately the used text-editor
>in NIH and  Object-Image
>has a limitation of 32K (Apple's built in editor). So I have to  be very
>efficient whenever I write these macro's.
>When I load the macro's,  the info window gives information about filesize
>and tells me that it is  tokenized
>(whatever it means?. It seems to be limited to 20K. Sometimes I  reach
>this limitation earlier then the
>32K filesize limitation.
>How can  I prevent reaching this tokenized limit?
>Are there future plans of using a different editor without a 32K
>limitation (whenever possible)?   Regards,   Peter van Loon Mushroom
>Experimental  Station Horst, The Netherlands Mushpvl@wish.net


Peter:

The macro text is dissolved into a stream of tokens, so it can be executed
more efficiently. Usually, the token stream is shorter than the macro text,
as variable names only occupy 2 bytes and comment is skipped. However, if
you use a lot of string literals like s := 'This is a string literal', you
can easily reach the 20k limit.
Object-Image uses slightly more memory because of the extended set of macro
commands.
I can extend the stream size from 20 to 32K for you, but I don't have any
plans to go beyond 32K. I'd rather implement a way to read/write from/to a
generic file, so you can more easily interpret or manipulate files (text or
other, any size) without using the Import-work-around.

Here is an example how a macro is converted into a token stream:

Macro text:
===========

macro 'first macro';
var
  aa, bb: integer;
begin
  aa := 2;
  bb := aa * 3;

The above macro text fragment is converted into a token stream of 56 bytes:

TokenStream
===========
byte  Token             original text
----  -----             ------
0     MacroT              macro 'first macro';
1     StringLiteral
      (11)
13    NullT
14    SemiColon
15    NewLineT
16    VarT                var
17    NewLineT
18    Identifier            aa, bb: integer;
      (2)
21    Comma
22    Identifier
      (2)
25    Colon
26    IntegerT
27    SemiColon
28    NewLineT
29    beginT               begin
30    NewLineT
31    Identifier              aa := 2;
      (2)
34    AssignOp
35    NumLiteral
      (4)
40    SemiColon
41    NewLine
42    Identifier              bb := aa * 3;
      (2)
45    AssignOp
46    Identifier
      (2)
49    MulOp
50    NumericLiteral
      (4)
55    SemiColon
56    NewLine

Norbert Vischer                  University of Amsterdam
scientific engineer              Molecular Cell Biology
                                 Kruislaan 316
tel. +31-20-525-6267(fax 6271)   NL-1098 SM Amsterdam
e-mail: vischer@bio.uva.nl       The Netherlands
http://simon.bio.uva.nl/object-image.html