From nih-image-request@io.ece.drexel.edu Wed Sep  9 10:23 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA20626;
	Wed, 9 Sep 1998 10:21:21 -0400 (EDT)
Resent-Date: Wed, 9 Sep 1998 10:21:21 -0400 (EDT)
Message-Id: <v03007801b21c3ac9e40d@[144.118.33.245]>
In-Reply-To: <81DAE9E2114@rna.bio.mq.edu.au>
Mime-Version: 1.0
Date: Wed, 9 Sep 1998 09:04:13 -0500
To: nih-image@io.ece.drexel.edu
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: Re: Transferring ROIs to a new image
Resent-Message-ID: <"aikOt3.0.rY4.Uhezr"@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/324
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: 3296
Status: RO

>>Date: Tue, 8 Sep 1998 09:06:15 -0400
>>To: nih-image@io.ece.drexel.edu
>>From: Laird Bloom <lbloom@MIT.EDU>
>>	I'd like to write a macro that allows me to draw a freehand ROI in
>>an image (e.g., the outline of rhodamine-stained cells), open another image
>>(e.g., the FITC channel image of the same cells), and count particles
>>within the same ROI in the second image.  I'd like it to be able to analyze
>>multiple ROIs within the same image, but also to keep the data for each ROI
>>separate.  In the NIH Image archives, I saw a suggestion for copying the
>>two images to a stack, then toggling back and forth between slices to do
>>this analysis.  Has anyone written such a macro using this or another
>>algorithm?
>>Thanks,
>>Laird Bloom
>>MIT Center for Cancer Research
>
>There are a number of approachs available to this including
>the stack method you mention,
>the mapping method suggested by Jonathan Nissanov,
>particular applications as in Doug Morris's site, etc but
>the simplest most useful method is often overlooked,
>probably because this specific application is not explicitly mentioned in the
>manual.
>
>The macro restoreRoi or the restore selection <command 4>(analyse Menu) will
>restore the previously active selection to the current image
>(even if a compound ROI selection made using control/option keys).
>The trick is that the restoration takes effect on the current image even
>if the
>ROI was active on a different but previously active image
>regardless of whether the previous image associated with the ROI was of the
>same dimensions or not.
>It is located in the same position relative to 0,0 ie topleft.
>Thus a ROI established on an image
>(a roi can be associated with any/each open window)
>can be transferred from that image to another, simply by:
>
> activating the image carrying the ROI;
> activate the image to receive the ROI;
> invoke restore selection <command 4>(analyse Menu)
>
>or
>
>selectPic(pid2);killRoi;
>selectPic(pid1);selectPic(pid2);restoreRoi;{transfers ROI from pid1 to 2}
>
>In addition, you can
>selectPic(pid1);
>SetSaveAs('Outline');saveas('aParticularROI');
>selectPic(pid2);open('aParticularROI');
>if you want to have a disk record of the ROI.
>
I agree that the restoreRoi is the simplest approach. For it to work,
though, you must delineate one ROI, analyze  then delineate the next one
and analyze and so forth.

--------------------------------------------------------------------------------
-----------------------
                                  Jonathan Nissanov, Ph.D.
                                      Associate Director
            Computer Vision Center for Vertebrate Brain Mapping,
                a NIH Biomedical Research Technology Resource
                                http://cbis.ece.drexel.edu/ICVC/
--------------------------------------------------------------------------------
-----------------------
Imaging and Computer Vision Center              Tel: 215-895-1381
Drexel University                                                   Fax:
215-895-4987
Phildelphia, PA 19104
yoni@coe.drexel.edu
 -------------------------------------------------------------------------------
------------------------

     And remember, the early bird may get the worm, but the second mouse
gets the cheese.


From nih-image-request@io.ece.drexel.edu Wed Sep  9 11:44 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA28554;
	Wed, 9 Sep 1998 11:43:21 -0400 (EDT)
Resent-Date: Wed, 9 Sep 1998 11:43:21 -0400 (EDT)
Message-ID: <35F6A787.EAB1C51D@netmatters.co.uk>
Date: Wed, 09 Sep 1998 16:06:35 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
Reply-To: brownj@netmatters.co.uk
Organization: brownj@netmatters.co.uk
X-Mailer: Mozilla 4.04 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: Transferring ROIs to a new image
References: <v03020902b21adb8692ae@[18.155.0.117]>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"H_MXh2.0.6T6.cqfzr"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/325
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length:  1451
Status: O

To save and recall multiple ROI of any form you could try the following.

Drop a folder called 'ROI Folder' into you preference folder (or anywhere else
as long as you modify the path name appropriately) and use as many repeats of
the following you require ROI1, ROI2 etc. To apply the ROI in your macro call
the procedures ApplyROI1, ApplyROI2 etc.......

procedure ApplyROI1;
begin
     Open(GetPath('pref'),'ROI Folder:ROI1');
end;

macro '[1] Set Region of Interest 1';
begin
     SetSaveAs('Outline');
     SaveAs(GetPath('pref'),'ROI Folder:ROI');
end;

Jeremy

Laird Bloom wrote:

> Hi,
>         I'd like to write a macro that allows me to draw a freehand ROI in
> an image (e.g., the outline of rhodamine-stained cells), open another image
> (e.g., the FITC channel image of the same cells), and count particles
> within the same ROI in the second image.  I'd like it to be able to analyze
> multiple ROIs within the same image, but also to keep the data for each ROI
> separate.  In the NIH Image archives, I saw a suggestion for copying the
> two images to a stack, then toggling back and forth between slices to do
> this analysis.  Has anyone written such a macro using this or another
> algorithm?
> Thanks,
> Laird Bloom
> MIT Center for Cancer Research

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

Jeremy Brown
Moredun Research Institute / The University Of Edinburgh
http://users.netmatters.co.uk/brownj/ICHomePage.html



From nih-image-request@io.ece.drexel.edu Thu Sep 10 03:25 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id DAA21179;
	Thu, 10 Sep 1998 03:25:51 -0400 (EDT)
Resent-Date: Thu, 10 Sep 1998 03:25:51 -0400 (EDT)
Message-Id: <1.5.4.32.19980910081806.008f1ff0@messv2.univ-pau.fr>
X-Sender: leguer@messv2.univ-pau.fr
X-Mailer: Windows Eudora Light Version 1.5.4 (32)
Mime-Version: 1.0
Date: Thu, 10 Sep 1998 09:18:06 +0100
To: nih-image@io.ece.drexel.edu
From: Yves LE GUER <yves.leguer@univ-pau.fr>
Subject: spatio-temporal image
Resent-Message-ID: <"U6w7Y2.0.ir4.Lntzr"@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/326
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:   778
Status: O

Hi all,

I'm started to use image PC with the Scion CG-7 frame grabber and a Sony
color video camera. 
I'd like to write a macro that allows me to make a spatio-temporal image by
recording the same successive selected vertical (or horizontal) line and
choosing time step beetwen the capture of two lines and the number of lines
in order to reconstruct another image.
Has anyone written such a macro for this ?

Thanks,
_________________________________________________________________________

Yves Le Guer							
Laboratoire de Transferts Thermiques - UPPA			
Helioparc - 2, avenue du President Angot - 64000 PAU - FRANCE	
Tel. : 05 59 84 55 02 (LTT) et 05 59 92 33 76 (IUT GTE)		
Fax :  05 59 84 42 96  Tel. International : 33 5 59 84 55 02	
E-mail : leguer@univ-pau.fr					

From nih-image-d-request@io.ece.drexel.edu Thu Sep 10 03:47 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id DAA23408;
	Thu, 10 Sep 1998 03:47:22 -0400 (EDT)
Date: Thu, 10 Sep 1998 03:47:22 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809100747.DAA23408@io.ECE.Drexel.EDU>
Subject: nih-image-d Digest V98 #58
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/58
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length:  6949
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 58

Today's Topics:
  Re: Transferring ROIs to a new image  [ Jonathan Nissanov <yoni@cbis.ece.dr ]
  Re: Transferring ROIs to a new image  [ Jeremy Brown <brownj@netmatters.co. ]
  spatio-temporal image                 [ Yves LE GUER <yves.leguer@univ-pau. ]

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

Date: Wed, 9 Sep 1998 09:04:13 -0500
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Transferring ROIs to a new image
Message-Id: <v03007801b21c3ac9e40d@[144.118.33.245]>
Content-Type: text/plain; charset="us-ascii"

>>Date: Tue, 8 Sep 1998 09:06:15 -0400
>>To: nih-image@io.ece.drexel.edu
>>From: Laird Bloom <lbloom@MIT.EDU>
>>	I'd like to write a macro that allows me to draw a freehand ROI in
>>an image (e.g., the outline of rhodamine-stained cells), open another image
>>(e.g., the FITC channel image of the same cells), and count particles
>>within the same ROI in the second image.  I'd like it to be able to analyze
>>multiple ROIs within the same image, but also to keep the data for each ROI
>>separate.  In the NIH Image archives, I saw a suggestion for copying the
>>two images to a stack, then toggling back and forth between slices to do
>>this analysis.  Has anyone written such a macro using this or another
>>algorithm?
>>Thanks,
>>Laird Bloom
>>MIT Center for Cancer Research
>
>There are a number of approachs available to this including
>the stack method you mention,
>the mapping method suggested by Jonathan Nissanov,
>particular applications as in Doug Morris's site, etc but
>the simplest most useful method is often overlooked,
>probably because this specific application is not explicitly mentioned in the
>manual.
>
>The macro restoreRoi or the restore selection <command 4>(analyse Menu) will
>restore the previously active selection to the current image
>(even if a compound ROI selection made using control/option keys).
>The trick is that the restoration takes effect on the current image even
>if the
>ROI was active on a different but previously active image
>regardless of whether the previous image associated with the ROI was of the
>same dimensions or not.
>It is located in the same position relative to 0,0 ie topleft.
>Thus a ROI established on an image
>(a roi can be associated with any/each open window)
>can be transferred from that image to another, simply by:
>
> activating the image carrying the ROI;
> activate the image to receive the ROI;
> invoke restore selection <command 4>(analyse Menu)
>
>or
>
>selectPic(pid2);killRoi;
>selectPic(pid1);selectPic(pid2);restoreRoi;{transfers ROI from pid1 to 2}
>
>In addition, you can
>selectPic(pid1);
>SetSaveAs('Outline');saveas('aParticularROI');
>selectPic(pid2);open('aParticularROI');
>if you want to have a disk record of the ROI.
>
I agree that the restoreRoi is the simplest approach. For it to work,
though, you must delineate one ROI, analyze  then delineate the next one
and analyze and so forth.

--------------------------------------------------------------------------------
-----------------------
                                  Jonathan Nissanov, Ph.D.
                                      Associate Director
            Computer Vision Center for Vertebrate Brain Mapping,
                a NIH Biomedical Research Technology Resource
                                http://cbis.ece.drexel.edu/ICVC/
--------------------------------------------------------------------------------
-----------------------
Imaging and Computer Vision Center              Tel: 215-895-1381
Drexel University                                                   Fax:
215-895-4987
Phildelphia, PA 19104
yoni@coe.drexel.edu
 -------------------------------------------------------------------------------
------------------------

     And remember, the early bird may get the worm, but the second mouse
gets the cheese.

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

Date: Wed, 09 Sep 1998 16:06:35 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Transferring ROIs to a new image
Message-ID: <35F6A787.EAB1C51D@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

To save and recall multiple ROI of any form you could try the following.

Drop a folder called 'ROI Folder' into you preference folder (or anywhere else
as long as you modify the path name appropriately) and use as many repeats of
the following you require ROI1, ROI2 etc. To apply the ROI in your macro call
the procedures ApplyROI1, ApplyROI2 etc.......

procedure ApplyROI1;
begin
     Open(GetPath('pref'),'ROI Folder:ROI1');
end;

macro '[1] Set Region of Interest 1';
begin
     SetSaveAs('Outline');
     SaveAs(GetPath('pref'),'ROI Folder:ROI');
end;

Jeremy

Laird Bloom wrote:

> Hi,
>         I'd like to write a macro that allows me to draw a freehand ROI in
> an image (e.g., the outline of rhodamine-stained cells), open another image
> (e.g., the FITC channel image of the same cells), and count particles
> within the same ROI in the second image.  I'd like it to be able to analyze
> multiple ROIs within the same image, but also to keep the data for each ROI
> separate.  In the NIH Image archives, I saw a suggestion for copying the
> two images to a stack, then toggling back and forth between slices to do
> this analysis.  Has anyone written such a macro using this or another
> algorithm?
> Thanks,
> Laird Bloom
> MIT Center for Cancer Research

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

Jeremy Brown
Moredun Research Institute / The University Of Edinburgh
http://users.netmatters.co.uk/brownj/ICHomePage.html

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

Date: Thu, 10 Sep 1998 09:18:06 +0100
From: Yves LE GUER <yves.leguer@univ-pau.fr>
To: nih-image@io.ece.drexel.edu
Subject: spatio-temporal image
Message-Id: <1.5.4.32.19980910081806.008f1ff0@messv2.univ-pau.fr>
Content-Type: text/plain; charset="us-ascii"

Hi all,

I'm started to use image PC with the Scion CG-7 frame grabber and a Sony
color video camera. 
I'd like to write a macro that allows me to make a spatio-temporal image by
recording the same successive selected vertical (or horizontal) line and
choosing time step beetwen the capture of two lines and the number of lines
in order to reconstruct another image.
Has anyone written such a macro for this ?

Thanks,
_________________________________________________________________________

Yves Le Guer							
Laboratoire de Transferts Thermiques - UPPA			
Helioparc - 2, avenue du President Angot - 64000 PAU - FRANCE	
Tel. : 05 59 84 55 02 (LTT) et 05 59 92 33 76 (IUT GTE)		
Fax :  05 59 84 42 96  Tel. International : 33 5 59 84 55 02	
E-mail : leguer@univ-pau.fr					

--------------------------------
End of nih-image-d Digest V98 Issue #58
***************************************

From nih-image-request@io.ece.drexel.edu Thu Sep 10 12:41 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA10857;
	Thu, 10 Sep 1998 12:40:27 -0400 (EDT)
Resent-Date: Thu, 10 Sep 1998 12:40:27 -0400 (EDT)
X-Sender: cozturk@tempest.bme-mri.jhu.edu
Message-Id: <v03007800b21dade563bc@[128.220.160.47]>
In-Reply-To: <1.5.4.32.19980910081806.008f1ff0@messv2.univ-pau.fr>
Mime-Version: 1.0
Date: Thu, 10 Sep 1998 12:27:10 -0400
To: nih-image@io.ece.drexel.edu
From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
Subject: Re: spatio-temporal image
Resent-Message-ID: <"wwRt12.0.vL2.5t_zr"@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/327
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:  1195
Status: O

>Hi all,
>
>I'm started to use image PC with the Scion CG-7 frame grabber and a Sony
>color video camera.
>I'd like to write a macro that allows me to make a spatio-temporal image by
>recording the same successive selected vertical (or horizontal) line and
>choosing time step beetwen the capture of two lines and the number of lines
>in order to reconstruct another image.
>Has anyone written such a macro for this ?
>
>Thanks,
>_________________________________________________________________________
>
>Yves Le Guer
>Laboratoire de Transferts Thermiques - UPPA
>Helioparc - 2, avenue du President Angot - 64000 PAU - FRANCE
>Tel. : 05 59 84 55 02 (LTT) et 05 59 92 33 76 (IUT GTE)
>Fax :  05 59 84 42 96  Tel. International : 33 5 59 84 55 02
>E-mail : leguer@univ-pau.fr


Just capture as usual. (as big fat images!)
Put them in a stack.
Reslice them along vertical and horizontal lines.

Cengizhan





Dr. Cengizhan Ozturk
=======================
Johns Hopkins University - Medical Imaging Lab
407 Traylor Building / 720 Rutland Av.
Baltimore, MD 21205-2196
Phone: (410) 614 5292
Fax:  (410) 502 6915
E-mail: cozturk@mri.jhu.edu
http://www.mri.jhu.edu/~cozturk/
=======================


From nih-image-request@io.ece.drexel.edu Thu Sep 10 13:28 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA14138;
	Thu, 10 Sep 1998 13:27:39 -0400 (EDT)
Resent-Date: Thu, 10 Sep 1998 13:27:39 -0400 (EDT)
X-Sender: mathias@ruby.unibe.ch
Message-Id: <v01510102b21dc505610d@[130.92.130.93]>
Mime-Version: 1.0
Date: Thu, 10 Sep 1998 19:20:16 +0100
To: nih-image@io.ece.drexel.edu
From: mathias@mpi.unibe.ch (mathias rickli)
Subject: adjacent image alignment
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id NAA13213
Resent-Message-ID: <"VqjvR2.0.iE3.zb0-r"@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/328
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="iso-8859-1"
Content-Length:   830
Status: O

I am rather new to the image analysis world and I have two questions.
1) does anyone work on microstructure analysis of heavy clay ceramics?
2) has anyone written a macro to join adjacent, slightly overlapping images
automatically?
My idea is to transform 16 (4x4) or more grayscale SEM images from polished
sections of ceramics into binary Tiff files and then to merge them together
in one file in order to apply object (pore) size measurements. I wonder if
this way of  image treatment exeeds the capacity of even high performance
Mac plattforms.
thanks for answering

cheers
mathias


Mathias Rickli [dipl. Min.]

Mineralogisch-Petrographisches Institut
Universitt Bern
Baltzerstrasse 1
CH-3012 Bern
Switzerland
Tel: +41-31-631-8781
Fax: +41-31-631-4843

home:
Freiestrasse 35
CH-3012 Bern
Switzerland
Tel: +41-31-302-9564



From nih-image-request@io.ece.drexel.edu Thu Sep 10 16:25 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA13515;
	Thu, 10 Sep 1998 16:25:06 -0400 (EDT)
Resent-Date: Thu, 10 Sep 1998 16:25:06 -0400 (EDT)
X-Sender: cozturk@tempest.bme-mri.jhu.edu
Message-Id: <v03007805b21de02c34b5@[128.220.160.47]>
In-Reply-To: <v01510102b21dc505610d@[130.92.130.93]>
Mime-Version: 1.0
Date: Thu, 10 Sep 1998 16:03:34 -0400
To: nih-image@io.ece.drexel.edu
From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
Subject: Re: adjacent image alignment
Resent-Message-ID: <"t_U0a3.0.r36.-13-r"@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/329
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:  6645
Status: O

>I am rather new to the image analysis world and I have two questions.
>1) does anyone work on microstructure analysis of heavy clay ceramics?
>2) has anyone written a macro to join adjacent, slightly overlapping images
>automatically?
>My idea is to transform 16 (4x4) or more grayscale SEM images from polished
>sections of ceramics into binary Tiff files and then to merge them together
>in one file in order to apply object (pore) size measurements. I wonder if
>this way of  image treatment exeeds the capacity of even high performance
>Mac plattforms.
>thanks for answering
>
>cheers
>mathias
-----------------------------------------------------------------
Hi,

A little search on mosaic and image puzzle dig up this from my humble
"the-best-of-NIH-Image" database.
Have fun with it.

Cengizhan

P.S. My Align will be a bad choice for partial to partial alignment.

____________________
included text below
____________________


On Thu, 25 Jul 1996 magyar@cell.biol.ethz.ch wrote:

> Dear Imagers
>
> In our group, we are working among others with the morphological analysis
> of peripheral nerve cross sections. Now, since we want to analyse the
> different parameters of single axons (a more or less regular round shape)
> and their surrounding myelin sheats (looks like a dark ring around the
> axon), I wrote a macro to measure everything as efficient as possible.
> The point is, that we collect the pictures with a CCD camera at a certain
> magnification. If we take a magnification good enought to have a resolution
> of also small axons (63x), then only few (appr. 20) axons are within the
> field of view. If we lower the magnification (20x or 40x), then the
> resolution of the collected picts is not good enought to make reliable
> analysis of all axonal and myelin parameters.
> Now I wrote an other macro, which enables one to fit a new overlapping view
> into an other allready existing pict. This works astounishingly good, so
> that you can nearby not see any transitions. This works by selecting
> certain structures while thresholding in one of the pict and then selecting
> the same stucture at the same threshold level in the other pict (all picts
> are taken in the same angle of view). Using this, you can puzzle together a
> pict of originally e.g. 20 or even more CCD camera gained pictures (only
> limitation is your RAM).
> I am wondering now, whether there are any macros or algorhytms doing the
> same job automaticaly e.g. by pattern recognition or so. Could this work
> perhaps also by comparison of histogramm values, since the picts are
> oriented the same way?
>
> Thanks for thinking...
>
> Josef Peter Magyar
>
>
>*******************************************************************************
>> *     _/_/_/_/_/_/_/_/_/    _/  Eidgenoessische Technische Hochschule
>Zuerich *
> *    _/        _/    _/    _/ Swiss Federal Institute of Technology
>Zurich    *
> *   _/_/_/    _/    _/_/_/_/ Ecole polytechnique federale de Zurich
>*
> *  _/        _/    _/    _/ Politecnico federale di Zurigo
>*
> * _/_/_/_/  _/    _/    _/
>*
> *
>*
>
>*-----------------------------------------------------------------------------*
>> *  Josef Peter Magyar, Ph.D.              |  Tel:   +41/1/633 34 91
>*
> *  Institute of Cell Biology              |         +41/1/633 34 92
>*
> *  Swiss Federal Institute of Technology  |  Fax:   +41/1/633 10 69
>*
> *  ETH-Hoenggerberg HPM E25               |
>*
> *  CH-8093 Zurich, Switzerland            |  eMail:
>magyar@cell.biol.ethz.ch  *
> *                                         |
>*
>
>*******************************************************************************
>>


  There are at least two other programs available to accomplish this
task -- S. Ott wrote one, which has its own webpage and everything,
and I have one at a beta-test stage.

Re the first:

QUOTE:
You might be interested to know that I have released "AutoMatch" a couple of
weeks ago which does exactly the same job in NIH Image. Well it doesn't
give you
a scaled-down map which seems very useful to me. On the other hand, it
gives you
a full "postview" of the previously captured frame. This 1:1 view is very
useful
for moving the stage during live acquisition.

The algorithm can handle frames of any size, by trading accurracy of alignment
versus frame size (of course it does not handle 3000x2000 frames too well...).

AutoMatch has a full-featured graphical user interface (not just those basic
dialogs the macro language provides) and is written entirely in NIH macro code
(yes, you can do that...). Full documentation is included with the package,
and
a paper is submitted to Microsc. Res. Tech. (Ott, S R, Acquisition of High
Resolution Digital Images in Video Microscopy: Automated Image Mosaicing on a
Desktop Microcomputer)

For more information see:
http://wwwzoo.kfunigraz.ac.at/~Swidi/AM/AMhome.html
-----------------------------------------------------
Swidbert R. OTT, MSc
Department of Neurobiology
Institute of Zoology
University of Graz, Austria/Europe
voice: +43 316 380 5602, 5702, 5282
fax:           380 9875

email: ott@balu.kfunigraz.ac.at
WWW: http://wwwzoo.kfunigraz.ac.at/~swidi/home.html
-----------------------------------------------------
ENDQUOTE


The other approach is mine, which isn't as mature but
functions well enough to try out.  I call it "Pan-and-Paint",
as the goal is to be able to just pan the microscopy stage
and paint an image as you go on a video monitor.

Pros:  10 seconds per image, builds a real-time montage as you go,
       works up to a composite of 4x4 times 640x480 greyscale,
       does the time-consuming work in batch mode after the
       operator is done collecting the images -- manual override
       for manual aligning a tricky image is nifty (IMHO)

Cons:  beta-stage so it changes (improves) more or less weekly.
       Batch mode is pretty verbose (but ignorable).
       No web page (yet).

The current shareware executable, documentation, and a worked example
with stack of actual biomedical images (eg, immunohistochemically stained
tissue)  can be obtained by anonymous ftp from host "141.214.135.241", in
directory "/pub/programs/"  which has three equivalent versions --
a macbinary folder, a stuffed version, and a stuffed and binhexed version.

Wade Schuette
University of Michigan
schuette@umich.edu

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


Dr. Cengizhan Ozturk
=======================
Johns Hopkins University - Medical Imaging Lab
407 Traylor Building / 720 Rutland Av.
Baltimore, MD 21205-2196
Phone: (410) 614 5292
Fax:  (410) 502 6915
E-mail: cozturk@mri.jhu.edu
http://www.mri.jhu.edu/~cozturk/
=======================


From nih-image-request@io.ece.drexel.edu Thu Sep 10 17:19 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA17573;
	Thu, 10 Sep 1998 17:18:31 -0400 (EDT)
Resent-Date: Thu, 10 Sep 1998 17:18:31 -0400 (EDT)
Message-Id: <l03010d11b21decf00660@[128.95.250.218]>
Mime-Version: 1.0
Date: Thu, 10 Sep 1998 14:03:00 -0700
To: nih-image@io.ece.drexel.edu
From: Geno Pawlak <gpawlak@ocean.washington.edu>
Subject: Image Capture for PC
Resent-Message-ID: <"6elpQ3.0.n04.yx3-r"@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/330
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:   924
Status: O

Hello,
   I'm new to the list so forgive me if this has already been discussed -
I'm interested in capturing grayscale images realtime (30fps) to RAM on a
PC, most likely from a Hi 8 VCR.  I've worked with a Scion LG-3 card on a
Mac before and it worked wonderfully, however, I've moved to a new job and
have to work with a PC now.  Does anyone have any experience with this card
on a PC?  Capturing from a VCR?  On the Mac, the LG-3 would occassionally
miss a frame, but this wasn't a problem.
  In addition I would like to use my NIH Image macros on the PC, with
Scion's program - will this work ok?
Any other suggestions for framegrabbing hardware are welcome.

Thanks,
Geno


-------------------------------------------
Geno Pawlak
University of Washington
School of Oceanography
Box 357940
Seattle, WA 98195-7940

phone: (206) 543-8543
e-mail: gpawlak@ocean.washington.edu
-------------------------------------------


From nih-image-request@io.ece.drexel.edu Thu Sep 10 19:41 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id TAA27663;
	Thu, 10 Sep 1998 19:41:22 -0400 (EDT)
Resent-Date: Thu, 10 Sep 1998 19:41:22 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: nih-image@io.ece.drexel.edu
Date:          Fri, 11 Sep 1998 9:34:07 GMT+1000
Subject:       Re: spatio-temporal image
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <84CB54A52E0@rna.bio.mq.edu.au>
Resent-Message-ID: <"Gj0cm1.0.IZ6.l56-r"@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/331
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length:  1962
Status: O

>Date: Thu, 10 Sep 1998 12:27:10 -0400
>To: nih-image@io.ece.drexel.edu
>From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
>Subject: Re: spatio-temporal image
>>
>>I'm started to use image PC with the Scion CG-7 frame grabber and a Sony
>>color video camera.
>>I'd like to write a macro that allows me to make a spatio-temporal image by
>>recording the same successive selected vertical (or horizontal) line and
>>choosing time step beetwen the capture of two lines and the number of lines
>>in order to reconstruct another image.
>>Has anyone written such a macro for this ?
>>
>>Thanks,
>>_________________________________________________________________________
>>
>>Yves Le Guer
>>Laboratoire de Transferts Thermiques - UPPA
>>Helioparc - 2, avenue du President Angot - 64000 PAU - FRANCE
>>Tel. : 05 59 84 55 02 (LTT) et 05 59 92 33 76 (IUT GTE)
>>Fax :  05 59 84 42 96  Tel. International : 33 5 59 84 55 02
>>E-mail : leguer@univ-pau.fr
>
>Just capture as usual. (as big fat images!)
>Put them in a stack.
>Reslice them along vertical and horizontal lines.
>
>Dr. Cengizhan Ozturk
>=======================
>Johns Hopkins University - Medical Imaging Lab
>407 Traylor Building / 720 Rutland Av.
>Baltimore, MD 21205-2196
>Phone: (410) 614 5292
>Fax:  (410) 502 6915
>E-mail: cozturk@mri.jhu.edu
>http://www.mri.jhu.edu/~cozturk/
>=======================

Cengizhan, 

your reply "Just capture as usual. (as big fat images!)" etc is right on the 
mark but does also suggest that Yves Le Guer may have missed the obvious ie: 

"capture" & "make movie" will operate on selections (including long thin 
rectangular selections either horizontal or vertical) which will allow much 
faster operation and avoid RAM shortages. Stacks can now be 5000 frames in 
lastest Image versions.
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 Sep 10 20:23 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id UAA00781;
	Thu, 10 Sep 1998 20:23:09 -0400 (EDT)
Resent-Date: Thu, 10 Sep 1998 20:23:09 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: nih-image@io.ece.drexel.edu
Date:          Fri, 11 Sep 1998 10:15:28 GMT+1000
Subject:       Re: adjacent image alignment
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <84D65615701@rna.bio.mq.edu.au>
Resent-Message-ID: <"an15n1.0.CI7.qh6-r"@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/332
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length:  2462
Status: O

>Date: Thu, 10 Sep 1998 16:03:34 -0400
>
>>I am rather new to the image analysis world and I have two questions.
>>1) does anyone work on microstructure analysis of heavy clay ceramics?
>>2) has anyone written a macro to join adjacent, slightly overlapping images
>>automatically?
>>My idea is to transform 16 (4x4) or more grayscale SEM images from polished
>>sections of ceramics into binary Tiff files and then to merge them together
>>in one file in order to apply object (pore) size measurements. I wonder if
>>this way of  image treatment exeeds the capacity of even high performance
>>Mac plattforms.
>>thanks for answering
>>
>>cheers
>>mathias
>-----------------------------------------------------------------

Cengizhan's very comprehensive reply to this question didn't make direct 
reference to an extremely useful mechanism in NIH-Image which is applicable in 
this context, particularly for those new to Image and not everyone would 
followup the web and macro refererence detail.
(I have been unable to raise 141.214.135.241. It may be off "overnight" :-)

"Manual" procedures are commonly sufficient particularly for tiled montages 
where orientation is maintained (eg by microscope stage).

The "paste" with "XOR" option is a very powerful tool in this context.
Make a new image large enough to accomodate the montage 
(The old restriction on maximum image width of 4096 has been removed).
copy and paste the topleft or some other starting component
activate "Show Paste Control(Windows menu"
pan (if necessary) so that next paste will be roughly central in the window.
copy and paste next component with an overlap.
choose "XOR" option in Paste Control Window.
pasted ROI can be moved by mouse or, more importantly, by arrow keys
till it is accurately placed.

"XOR" will make overlapping alignment very apparent as both layers can be 
readily seen until overlap is accurate. If overlap is identical then the 
overlap will suddenly go to white (all zeros).

The paste option can then be switched to "Replace" or 
(else the paste "Undo"ne so that the ROI can then be restoreRoi'd, giving 
accurate position of montage component)

This manual procedure can be quite quick and is accurate to the pixel (if the 
overlaps are properly oriented and undistorted). 
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 Sep 10 21:09 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id VAA04174;
	Thu, 10 Sep 1998 21:09:22 -0400 (EDT)
Resent-Date: Thu, 10 Sep 1998 21:09:22 -0400 (EDT)
From: DrJohnRuss@aol.com
Message-ID: <5bf7dced.35f8745f@aol.com>
Date: Thu, 10 Sep 1998 20:52:47 EDT
To: nih-image@io.ece.drexel.edu
Mime-Version: 1.0
Subject: Re:  adjacent image alignment
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 for Mac sub 84
Resent-Message-ID: <"j6VhX.0.Aj.5I7-r"@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/333
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:  1238
Status: O


In a message dated 9/10/98 5:22:01 PM, Mathias Rickli [dipl. Min.] wrote:

>2) has anyone written a macro to join adjacent, slightly overlapping images
>automatically?
>
>My idea is to transform 16 (4x4) or more grayscale SEM images from polished
>sections of ceramics into binary Tiff files and then to merge them together
>in one file in order to apply object (pore) size measurements. I wonder if
>this way of  image treatment exeeds the capacity of even high performance
>Mac plattforms.

We have a program (Windows NT, not Mac, although it could be recompiled fairly
easily) that will take any array of tiffs - mine are usually 1000x1000 pixels
or larger and I often have arrays up to 8x8 - that have overlaps of 10-30% on
each side and seamlessly stitch them together using cross-correlation in the
overlap regions to determine the best alignment (including rotation). It isn't
fast - a job like the one above takes several hours - but the results are
spectacular. We primarily use it on AFM images, occasionally on SEM, and it
has also been used on aerial reconnaissance photos. The program is not
presently available to others but if there is enough demand we might consider
working out some arrangement for its use.

John Russ

From nih-image-request@io.ece.drexel.edu Fri Sep 11 05:40 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id FAA15389;
	Fri, 11 Sep 1998 05:40:13 -0400 (EDT)
Resent-Date: Fri, 11 Sep 1998 05:40:13 -0400 (EDT)
Message-ID: <35F8FA9A.A3B8EC5B@netmatters.co.uk>
Date: Fri, 11 Sep 1998 10:25:34 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
Reply-To: brownj@netmatters.co.uk
Organization: brownj@netmatters.co.uk
X-Mailer: Mozilla 4.04 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: adjacent image alignment
References: <v03007805b21de02c34b5@[128.220.160.47]>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"AF8YY2.0.TO3.rnE-r"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/334
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length:  3423
Status: O



Cengizhan Ozturk wrote:

> >I am rather new to the image analysis world and I have two questions.
> >1) does anyone work on microstructure analysis of heavy clay ceramics?
> >2) has anyone written a macro to join adjacent, slightly overlapping images
> >automatically?
> >My idea is to transform 16 (4x4) or more grayscale SEM images from polished
> >sections of ceramics into binary Tiff files and then to merge them together
> >in one file in order to apply object (pore) size measurements. I wonder if
> >this way of  image treatment exeeds the capacity of even high performance
> >Mac plattforms.
> >thanks for answering
> >
> >cheers
> >mathias
> -----------------------------------------------------------------
> Hi,
>
> A little search on mosaic and image puzzle dig up this from my humble
> "the-best-of-NIH-Image" database.
> Have fun with it.
>
> Cengizhan
>



> AutoMatch has a full-featured graphical user interface (not just those basic
> dialogs the macro language provides) and is written entirely in NIH macro code
> (yes, you can do that...). Full documentation is included with the package,
> and
> a paper is submitted to Microsc. Res. Tech. (Ott, S R, Acquisition of High
> Resolution Digital Images in Video Microscopy: Automated Image Mosaicing on a
> Desktop Microcomputer)
>
> For more information see:
> http://wwwzoo.kfunigraz.ac.at/~Swidi/AM/AMhome.html
> -----------------------------------------------------
> Swidbert R. OTT, MSc
> Department of Neurobiology
> Institute of Zoology
> University of Graz, Austria/Europe
> voice: +43 316 380 5602, 5702, 5282
> fax:           380 9875
>
>
> --------------------
>
> Dr. Cengizhan Ozturk
> =======================
> Johns Hopkins University - Medical Imaging Lab
> 407 Traylor Building / 720 Rutland Av.
> Baltimore, MD 21205-2196
> Phone: (410) 614 5292
> Fax:  (410) 502 6915
> E-mail: cozturk@mri.jhu.edu
> http://www.mri.jhu.edu/~cozturk/
> =======================

I can personally vouch for Swidbert R. OTT's Automatch Macro. It run well under
both NIH and Object image, is remarkable fast and accurate. I've used it in
conjunction with a 7100/80 AV to mosaic images up to 90 frames at a time. You need
allow 10-15% overlap on tissue sections, in less detailed images you will need to
allow for more overlap. The hardest bit if setting up your stage sensitivity so
that it does not drift but allows you fine control at the same time. Even if the
stage does drift ,Automatch will still work if there is enough overlap. It is very
ram hungry: on my machine, which has 80 MB of physical RAM, 60 -70 MB RAM to NIH
and adjusting your undo and clipboard buffer size to the size the image your going
to create is ok for 20 MB images, i.e. you will need a lot of RAM. It works well
under both Ram Doubler or VM, although you should not give NIH more than your
physical ram. The only disadvantage is if you have already captured the images,
Automatch does both the capturing and assembly, it will not assemble independently
acquired images.

The reference for the paper is ........

Ott, SR (1997) Acquisition of High-Resolution Digital Images in Video Microscopy:
Automated Image Mosaicking on a Desktop Microcomputer. Microscopy Research and
Technique 38: 335-339.



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

Jeremy Brown
Moredun Research Institute / The University Of Edinburgh
http://users.netmatters.co.uk/brownj/ICHomePage.html


From nih-image-d-request@io.ece.drexel.edu Fri Sep 11 05:43 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id FAA15767;
	Fri, 11 Sep 1998 05:43:10 -0400 (EDT)
Date: Fri, 11 Sep 1998 05:43:10 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809110943.FAA15767@io.ECE.Drexel.EDU>
Subject: nih-image-d Digest V98 #59
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/59
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 21759
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 59

Today's Topics:
  Re: spatio-temporal image             [ Cengizhan Ozturk <cozturk@mri.jhu.e ]
  adjacent image alignment              [ mathias@mpi.unibe.ch (mathias rickl ]
  Re: adjacent image alignment          [ Cengizhan Ozturk <cozturk@mri.jhu.e ]
  Image Capture for PC                  [ Geno Pawlak <gpawlak@ocean.washingt ]
  Re: spatio-temporal image             [ GJOSS@rna.bio.mq.edu.au ]
  Re: adjacent image alignment          [ GJOSS@rna.bio.mq.edu.au ]
  Re: adjacent image alignment          [ DrJohnRuss@aol.com ]
  Re: adjacent image alignment          [ Jeremy Brown <brownj@netmatters.co. ]

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

Date: Thu, 10 Sep 1998 12:27:10 -0400
From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: spatio-temporal image
Message-Id: <v03007800b21dade563bc@[128.220.160.47]>
Content-Type: text/plain; charset="us-ascii"

>Hi all,
>
>I'm started to use image PC with the Scion CG-7 frame grabber and a Sony
>color video camera.
>I'd like to write a macro that allows me to make a spatio-temporal image by
>recording the same successive selected vertical (or horizontal) line and
>choosing time step beetwen the capture of two lines and the number of lines
>in order to reconstruct another image.
>Has anyone written such a macro for this ?
>
>Thanks,
>_________________________________________________________________________
>
>Yves Le Guer
>Laboratoire de Transferts Thermiques - UPPA
>Helioparc - 2, avenue du President Angot - 64000 PAU - FRANCE
>Tel. : 05 59 84 55 02 (LTT) et 05 59 92 33 76 (IUT GTE)
>Fax :  05 59 84 42 96  Tel. International : 33 5 59 84 55 02
>E-mail : leguer@univ-pau.fr


Just capture as usual. (as big fat images!)
Put them in a stack.
Reslice them along vertical and horizontal lines.

Cengizhan





Dr. Cengizhan Ozturk
=======================
Johns Hopkins University - Medical Imaging Lab
407 Traylor Building / 720 Rutland Av.
Baltimore, MD 21205-2196
Phone: (410) 614 5292
Fax:  (410) 502 6915
E-mail: cozturk@mri.jhu.edu
http://www.mri.jhu.edu/~cozturk/
=======================

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

Date: Thu, 10 Sep 1998 19:20:16 +0100
From: mathias@mpi.unibe.ch (mathias rickli)
To: nih-image@io.ece.drexel.edu
Subject: adjacent image alignment
Message-Id: <v01510102b21dc505610d@[130.92.130.93]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

I am rather new to the image analysis world and I have two questions.
1) does anyone work on microstructure analysis of heavy clay ceramics?
2) has anyone written a macro to join adjacent, slightly overlapping images
automatically?
My idea is to transform 16 (4x4) or more grayscale SEM images from polished
sections of ceramics into binary Tiff files and then to merge them together
in one file in order to apply object (pore) size measurements. I wonder if
this way of  image treatment exeeds the capacity of even high performance
Mac plattforms.
thanks for answering

cheers
mathias


Mathias Rickli [dipl. Min.]

Mineralogisch-Petrographisches Institut
Universitt Bern
Baltzerstrasse 1
CH-3012 Bern
Switzerland
Tel: +41-31-631-8781
Fax: +41-31-631-4843

home:
Freiestrasse 35
CH-3012 Bern
Switzerland
Tel: +41-31-302-9564

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

Date: Thu, 10 Sep 1998 16:03:34 -0400
From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: adjacent image alignment
Message-Id: <v03007805b21de02c34b5@[128.220.160.47]>
Content-Type: text/plain; charset="us-ascii"

>I am rather new to the image analysis world and I have two questions.
>1) does anyone work on microstructure analysis of heavy clay ceramics?
>2) has anyone written a macro to join adjacent, slightly overlapping images
>automatically?
>My idea is to transform 16 (4x4) or more grayscale SEM images from polished
>sections of ceramics into binary Tiff files and then to merge them together
>in one file in order to apply object (pore) size measurements. I wonder if
>this way of  image treatment exeeds the capacity of even high performance
>Mac plattforms.
>thanks for answering
>
>cheers
>mathias
-----------------------------------------------------------------
Hi,

A little search on mosaic and image puzzle dig up this from my humble
"the-best-of-NIH-Image" database.
Have fun with it.

Cengizhan

P.S. My Align will be a bad choice for partial to partial alignment.

____________________
included text below
____________________


On Thu, 25 Jul 1996 magyar@cell.biol.ethz.ch wrote:

> Dear Imagers
>
> In our group, we are working among others with the morphological analysis
> of peripheral nerve cross sections. Now, since we want to analyse the
> different parameters of single axons (a more or less regular round shape)
> and their surrounding myelin sheats (looks like a dark ring around the
> axon), I wrote a macro to measure everything as efficient as possible.
> The point is, that we collect the pictures with a CCD camera at a certain
> magnification. If we take a magnification good enought to have a resolution
> of also small axons (63x), then only few (appr. 20) axons are within the
> field of view. If we lower the magnification (20x or 40x), then the
> resolution of the collected picts is not good enought to make reliable
> analysis of all axonal and myelin parameters.
> Now I wrote an other macro, which enables one to fit a new overlapping view
> into an other allready existing pict. This works astounishingly good, so
> that you can nearby not see any transitions. This works by selecting
> certain structures while thresholding in one of the pict and then selecting
> the same stucture at the same threshold level in the other pict (all picts
> are taken in the same angle of view). Using this, you can puzzle together a
> pict of originally e.g. 20 or even more CCD camera gained pictures (only
> limitation is your RAM).
> I am wondering now, whether there are any macros or algorhytms doing the
> same job automaticaly e.g. by pattern recognition or so. Could this work
> perhaps also by comparison of histogramm values, since the picts are
> oriented the same way?
>
> Thanks for thinking...
>
> Josef Peter Magyar
>
>
>*******************************************************************************
>> *     _/_/_/_/_/_/_/_/_/    _/  Eidgenoessische Technische Hochschule
>Zuerich *
> *    _/        _/    _/    _/ Swiss Federal Institute of Technology
>Zurich    *
> *   _/_/_/    _/    _/_/_/_/ Ecole polytechnique federale de Zurich
>*
> *  _/        _/    _/    _/ Politecnico federale di Zurigo
>*
> * _/_/_/_/  _/    _/    _/
>*
> *
>*
>
>*-----------------------------------------------------------------------------*
>> *  Josef Peter Magyar, Ph.D.              |  Tel:   +41/1/633 34 91
>*
> *  Institute of Cell Biology              |         +41/1/633 34 92
>*
> *  Swiss Federal Institute of Technology  |  Fax:   +41/1/633 10 69
>*
> *  ETH-Hoenggerberg HPM E25               |
>*
> *  CH-8093 Zurich, Switzerland            |  eMail:
>magyar@cell.biol.ethz.ch  *
> *                                         |
>*
>
>*******************************************************************************
>>


  There are at least two other programs available to accomplish this
task -- S. Ott wrote one, which has its own webpage and everything,
and I have one at a beta-test stage.

Re the first:

QUOTE:
You might be interested to know that I have released "AutoMatch" a couple of
weeks ago which does exactly the same job in NIH Image. Well it doesn't
give you
a scaled-down map which seems very useful to me. On the other hand, it
gives you
a full "postview" of the previously captured frame. This 1:1 view is very
useful
for moving the stage during live acquisition.

The algorithm can handle frames of any size, by trading accurracy of alignment
versus frame size (of course it does not handle 3000x2000 frames too well...).

AutoMatch has a full-featured graphical user interface (not just those basic
dialogs the macro language provides) and is written entirely in NIH macro code
(yes, you can do that...). Full documentation is included with the package,
and
a paper is submitted to Microsc. Res. Tech. (Ott, S R, Acquisition of High
Resolution Digital Images in Video Microscopy: Automated Image Mosaicing on a
Desktop Microcomputer)

For more information see:
http://wwwzoo.kfunigraz.ac.at/~Swidi/AM/AMhome.html
-----------------------------------------------------
Swidbert R. OTT, MSc
Department of Neurobiology
Institute of Zoology
University of Graz, Austria/Europe
voice: +43 316 380 5602, 5702, 5282
fax:           380 9875

email: ott@balu.kfunigraz.ac.at
WWW: http://wwwzoo.kfunigraz.ac.at/~swidi/home.html
-----------------------------------------------------
ENDQUOTE


The other approach is mine, which isn't as mature but
functions well enough to try out.  I call it "Pan-and-Paint",
as the goal is to be able to just pan the microscopy stage
and paint an image as you go on a video monitor.

Pros:  10 seconds per image, builds a real-time montage as you go,
       works up to a composite of 4x4 times 640x480 greyscale,
       does the time-consuming work in batch mode after the
       operator is done collecting the images -- manual override
       for manual aligning a tricky image is nifty (IMHO)

Cons:  beta-stage so it changes (improves) more or less weekly.
       Batch mode is pretty verbose (but ignorable).
       No web page (yet).

The current shareware executable, documentation, and a worked example
with stack of actual biomedical images (eg, immunohistochemically stained
tissue)  can be obtained by anonymous ftp from host "141.214.135.241", in
directory "/pub/programs/"  which has three equivalent versions --
a macbinary folder, a stuffed version, and a stuffed and binhexed version.

Wade Schuette
University of Michigan
schuette@umich.edu

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


Dr. Cengizhan Ozturk
=======================
Johns Hopkins University - Medical Imaging Lab
407 Traylor Building / 720 Rutland Av.
Baltimore, MD 21205-2196
Phone: (410) 614 5292
Fax:  (410) 502 6915
E-mail: cozturk@mri.jhu.edu
http://www.mri.jhu.edu/~cozturk/
=======================

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

Date: Thu, 10 Sep 1998 14:03:00 -0700
From: Geno Pawlak <gpawlak@ocean.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Image Capture for PC
Message-Id: <l03010d11b21decf00660@[128.95.250.218]>
Content-Type: text/plain; charset="us-ascii"

Hello,
   I'm new to the list so forgive me if this has already been discussed -
I'm interested in capturing grayscale images realtime (30fps) to RAM on a
PC, most likely from a Hi 8 VCR.  I've worked with a Scion LG-3 card on a
Mac before and it worked wonderfully, however, I've moved to a new job and
have to work with a PC now.  Does anyone have any experience with this card
on a PC?  Capturing from a VCR?  On the Mac, the LG-3 would occassionally
miss a frame, but this wasn't a problem.
  In addition I would like to use my NIH Image macros on the PC, with
Scion's program - will this work ok?
Any other suggestions for framegrabbing hardware are welcome.

Thanks,
Geno


-------------------------------------------
Geno Pawlak
University of Washington
School of Oceanography
Box 357940
Seattle, WA 98195-7940

phone: (206) 543-8543
e-mail: gpawlak@ocean.washington.edu
-------------------------------------------

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

Date:          Fri, 11 Sep 1998 9:34:07 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: nih-image@io.ece.drexel.edu
Subject:       Re: spatio-temporal image
Message-ID: <84CB54A52E0@rna.bio.mq.edu.au>

>Date: Thu, 10 Sep 1998 12:27:10 -0400
>To: nih-image@io.ece.drexel.edu
>From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
>Subject: Re: spatio-temporal image
>>
>>I'm started to use image PC with the Scion CG-7 frame grabber and a Sony
>>color video camera.
>>I'd like to write a macro that allows me to make a spatio-temporal image by
>>recording the same successive selected vertical (or horizontal) line and
>>choosing time step beetwen the capture of two lines and the number of lines
>>in order to reconstruct another image.
>>Has anyone written such a macro for this ?
>>
>>Thanks,
>>_________________________________________________________________________
>>
>>Yves Le Guer
>>Laboratoire de Transferts Thermiques - UPPA
>>Helioparc - 2, avenue du President Angot - 64000 PAU - FRANCE
>>Tel. : 05 59 84 55 02 (LTT) et 05 59 92 33 76 (IUT GTE)
>>Fax :  05 59 84 42 96  Tel. International : 33 5 59 84 55 02
>>E-mail : leguer@univ-pau.fr
>
>Just capture as usual. (as big fat images!)
>Put them in a stack.
>Reslice them along vertical and horizontal lines.
>
>Dr. Cengizhan Ozturk
>=======================
>Johns Hopkins University - Medical Imaging Lab
>407 Traylor Building / 720 Rutland Av.
>Baltimore, MD 21205-2196
>Phone: (410) 614 5292
>Fax:  (410) 502 6915
>E-mail: cozturk@mri.jhu.edu
>http://www.mri.jhu.edu/~cozturk/
>=======================

Cengizhan, 

your reply "Just capture as usual. (as big fat images!)" etc is right on the 
mark but does also suggest that Yves Le Guer may have missed the obvious ie: 

"capture" & "make movie" will operate on selections (including long thin 
rectangular selections either horizontal or vertical) which will allow much 
faster operation and avoid RAM shortages. Stacks can now be 5000 frames in 
lastest Image versions.
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, 11 Sep 1998 10:15:28 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: nih-image@io.ece.drexel.edu
Subject:       Re: adjacent image alignment
Message-ID: <84D65615701@rna.bio.mq.edu.au>

>Date: Thu, 10 Sep 1998 16:03:34 -0400
>
>>I am rather new to the image analysis world and I have two questions.
>>1) does anyone work on microstructure analysis of heavy clay ceramics?
>>2) has anyone written a macro to join adjacent, slightly overlapping images
>>automatically?
>>My idea is to transform 16 (4x4) or more grayscale SEM images from polished
>>sections of ceramics into binary Tiff files and then to merge them together
>>in one file in order to apply object (pore) size measurements. I wonder if
>>this way of  image treatment exeeds the capacity of even high performance
>>Mac plattforms.
>>thanks for answering
>>
>>cheers
>>mathias
>-----------------------------------------------------------------

Cengizhan's very comprehensive reply to this question didn't make direct 
reference to an extremely useful mechanism in NIH-Image which is applicable in 
this context, particularly for those new to Image and not everyone would 
followup the web and macro refererence detail.
(I have been unable to raise 141.214.135.241. It may be off "overnight" :-)

"Manual" procedures are commonly sufficient particularly for tiled montages 
where orientation is maintained (eg by microscope stage).

The "paste" with "XOR" option is a very powerful tool in this context.
Make a new image large enough to accomodate the montage 
(The old restriction on maximum image width of 4096 has been removed).
copy and paste the topleft or some other starting component
activate "Show Paste Control(Windows menu"
pan (if necessary) so that next paste will be roughly central in the window.
copy and paste next component with an overlap.
choose "XOR" option in Paste Control Window.
pasted ROI can be moved by mouse or, more importantly, by arrow keys
till it is accurately placed.

"XOR" will make overlapping alignment very apparent as both layers can be 
readily seen until overlap is accurate. If overlap is identical then the 
overlap will suddenly go to white (all zeros).

The paste option can then be switched to "Replace" or 
(else the paste "Undo"ne so that the ROI can then be restoreRoi'd, giving 
accurate position of montage component)

This manual procedure can be quite quick and is accurate to the pixel (if the 
overlaps are properly oriented and undistorted). 
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, 10 Sep 1998 20:52:47 EDT
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re:  adjacent image alignment
Message-ID: <5bf7dced.35f8745f@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

In a message dated 9/10/98 5:22:01 PM, Mathias Rickli [dipl. Min.] wrote:

>2) has anyone written a macro to join adjacent, slightly overlapping images
>automatically?
>
>My idea is to transform 16 (4x4) or more grayscale SEM images from polished
>sections of ceramics into binary Tiff files and then to merge them together
>in one file in order to apply object (pore) size measurements. I wonder if
>this way of  image treatment exeeds the capacity of even high performance
>Mac plattforms.

We have a program (Windows NT, not Mac, although it could be recompiled fairly
easily) that will take any array of tiffs - mine are usually 1000x1000 pixels
or larger and I often have arrays up to 8x8 - that have overlaps of 10-30% on
each side and seamlessly stitch them together using cross-correlation in the
overlap regions to determine the best alignment (including rotation). It isn't
fast - a job like the one above takes several hours - but the results are
spectacular. We primarily use it on AFM images, occasionally on SEM, and it
has also been used on aerial reconnaissance photos. The program is not
presently available to others but if there is enough demand we might consider
working out some arrangement for its use.

John Russ

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

Date: Fri, 11 Sep 1998 10:25:34 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: adjacent image alignment
Message-ID: <35F8FA9A.A3B8EC5B@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Cengizhan Ozturk wrote:

> >I am rather new to the image analysis world and I have two questions.
> >1) does anyone work on microstructure analysis of heavy clay ceramics?
> >2) has anyone written a macro to join adjacent, slightly overlapping images
> >automatically?
> >My idea is to transform 16 (4x4) or more grayscale SEM images from polished
> >sections of ceramics into binary Tiff files and then to merge them together
> >in one file in order to apply object (pore) size measurements. I wonder if
> >this way of  image treatment exeeds the capacity of even high performance
> >Mac plattforms.
> >thanks for answering
> >
> >cheers
> >mathias
> -----------------------------------------------------------------
> Hi,
>
> A little search on mosaic and image puzzle dig up this from my humble
> "the-best-of-NIH-Image" database.
> Have fun with it.
>
> Cengizhan
>



> AutoMatch has a full-featured graphical user interface (not just those basic
> dialogs the macro language provides) and is written entirely in NIH macro code
> (yes, you can do that...). Full documentation is included with the package,
> and
> a paper is submitted to Microsc. Res. Tech. (Ott, S R, Acquisition of High
> Resolution Digital Images in Video Microscopy: Automated Image Mosaicing on a
> Desktop Microcomputer)
>
> For more information see:
> http://wwwzoo.kfunigraz.ac.at/~Swidi/AM/AMhome.html
> -----------------------------------------------------
> Swidbert R. OTT, MSc
> Department of Neurobiology
> Institute of Zoology
> University of Graz, Austria/Europe
> voice: +43 316 380 5602, 5702, 5282
> fax:           380 9875
>
>
> --------------------
>
> Dr. Cengizhan Ozturk
> =======================
> Johns Hopkins University - Medical Imaging Lab
> 407 Traylor Building / 720 Rutland Av.
> Baltimore, MD 21205-2196
> Phone: (410) 614 5292
> Fax:  (410) 502 6915
> E-mail: cozturk@mri.jhu.edu
> http://www.mri.jhu.edu/~cozturk/
> =======================

I can personally vouch for Swidbert R. OTT's Automatch Macro. It run well under
both NIH and Object image, is remarkable fast and accurate. I've used it in
conjunction with a 7100/80 AV to mosaic images up to 90 frames at a time. You need
allow 10-15% overlap on tissue sections, in less detailed images you will need to
allow for more overlap. The hardest bit if setting up your stage sensitivity so
that it does not drift but allows you fine control at the same time. Even if the
stage does drift ,Automatch will still work if there is enough overlap. It is very
ram hungry: on my machine, which has 80 MB of physical RAM, 60 -70 MB RAM to NIH
and adjusting your undo and clipboard buffer size to the size the image your going
to create is ok for 20 MB images, i.e. you will need a lot of RAM. It works well
under both Ram Doubler or VM, although you should not give NIH more than your
physical ram. The only disadvantage is if you have already captured the images,
Automatch does both the capturing and assembly, it will not assemble independently
acquired images.

The reference for the paper is ........

Ott, SR (1997) Acquisition of High-Resolution Digital Images in Video Microscopy:
Automated Image Mosaicking on a Desktop Microcomputer. Microscopy Research and
Technique 38: 335-339.



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

Jeremy Brown
Moredun Research Institute / The University Of Edinburgh
http://users.netmatters.co.uk/brownj/ICHomePage.html

--------------------------------
End of nih-image-d Digest V98 Issue #59
***************************************

From nih-image-request@io.ece.drexel.edu Fri Sep 11 08:04 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA27542;
	Fri, 11 Sep 1998 08:04:45 -0400 (EDT)
Resent-Date: Fri, 11 Sep 1998 08:04:45 -0400 (EDT)
Message-Id: <35F90F1B.5FE6@maroon.tc.umn.edu>
Date: Fri, 11 Sep 1998 06:52:59 -0500
From: "Michael J. Herron" <herro001@maroon.tc.umn.edu>
Reply-To: Michael J Herron <herro001@maroon.tc.umn.edu>
Organization: University of Minnesota
X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: adjacent image alignment
References: <5bf7dced.35f8745f@aol.com>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"vGZNj3.0.9S6.WyG-r"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/335
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:   923
Status: O

Dr. Russ,

I was under the impression the the edges of SEM images were too
distorted for this....wrong impression?

Mike

DrJohnRuss@aol.com wrote:
> 

> 
> We have a program (Windows NT, not Mac, although it could be recompiled fairly
> easily) that will take any array of tiffs - mine are usually 1000x1000 pixels
> or larger and I often have arrays up to 8x8 - that have overlaps of 10-30% on
> each side and seamlessly stitch them together using cross-correlation in the
> overlap regions to determine the best alignment (including rotation). It isn't
> fast - a job like the one above takes several hours - but the results are
> spectacular. We primarily use it on AFM images, occasionally on SEM, and it
> has also been used on aerial reconnaissance photos. The program is not
> presently available to others but if there is enough demand we might consider
> working out some arrangement for its use.
> 
> John Russ

From nih-image-request@io.ece.drexel.edu Fri Sep 11 11:51 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA14667;
	Fri, 11 Sep 1998 11:50:54 -0400 (EDT)
Resent-Date: Fri, 11 Sep 1998 11:50:54 -0400 (EDT)
Message-Id: <9809111528.AA16520@acs1.acs.ucalgary.ca>
Subject: Re: adjacent image alignment
To: nih-image@io.ece.drexel.edu
Date: Fri, 11 Sep 98 9:28:24 MDT
From: "Doug S. Phillips" <phillips@ucalgary.ca>
Cc: nih-image@io.ece.drexel.edu
In-Reply-To: <199809110925.FAA13916@io.ECE.Drexel.EDU>; from "nih-image-d-request@io.ece.drexel.edu" at Sep 11, 1998 5:25 am
X-Mailer: ELM [version 2.3 PL11K]
Mime-Version: 1.0
Resent-Message-ID: <"YK4vF3.0.4B3.H8K-r"@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/336
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: multipart/mixed; boundary="----------------------------"
Content-Length:  1133
Status: O


------------------------------
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit


Mathias Rickli asked:

> 2) has anyone written a macro to join adjacent, slightly overlapping imag=
> es automatically? My idea is to transform 16 (4x4) or more grayscale SEM
> images from polished sections of ceramics into binary Tiff files and then to
> merge them together in one file in order to apply object (pore) size
> measurements. I wonder if this way of  image treatment exeeds the capacity of
> even high performance Mac plattforms.

This is well within reach of any modern Mac.  I saw an impressive demo
of image stitching at a QuickTime 3 presentation last night.  Apple 
markets a product called QuickTime VR Authoring Studio 
(http://www.apple.com/quicktime/qtvr/authoringstudio/index.html)
that can do automatic alignment of such images.

Sincerely,   Doug P.

Doug S. Phillips                Internet: phillips@ucalgary.ca
University Computing Services   Phone:(403)220-8445  FAX:(403)282-9199
The University of Calgary       WWW:  http://www.acs.ucalgary.ca/~phillips/


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

From nih-image-request@io.ece.drexel.edu Fri Sep 11 17:37 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA08696;
	Fri, 11 Sep 1998 17:36:50 -0400 (EDT)
Resent-Date: Fri, 11 Sep 1998 17:36:50 -0400 (EDT)
X-Sender: smurfette@mst.lanl.gov
Message-Id: <v03020903b21f44b86d2f@[128.165.243.113]>
Mime-Version: 1.0
Date: Fri, 11 Sep 1998 15:24:44 -0600
To: nih-image@io.ece.drexel.edu
From: Deanna Busick <dnbusick@lanl.gov>
Subject: Particle Analysis Macros
Resent-Message-ID: <"fAZHI.0.At1.gKP-r"@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/337
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:   497
Status: O

Has anyone had any trouble with Matthew Warfel's particle analysis macros?
The macro seems to be running and doing the analysis, but the Size Data
(tab) and Fractal Data (tab) files I get out contain no data, just a number
of carriage returns equal to the number of particles!
Thanks in advance for any help...

Deanna

------------------------
DEANNA BUSICK
MST-11, MS D429
Los Alamos National Laboratory
Los Alamos, NM  87545
e-mail: dnbusick@lanl.gov
ph#:  (505)667-0561
fax:  (505)665-4292



From nih-image-request@io.ece.drexel.edu Fri Sep 11 17:52 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA10040;
	Fri, 11 Sep 1998 17:52:05 -0400 (EDT)
Resent-Date: Fri, 11 Sep 1998 17:52:05 -0400 (EDT)
Message-ID: <19980911214538.19621.qmail@pc241.icsl.ucla.edu>
To: nih-image@io.ece.drexel.edu
cc: jul@seas.ucla.edu
Subject: How do I import images in GE SIGNA 5.x format?
Date: Fri, 11 Sep 1998 14:45:37 -0700
From: Mark Hasegawa-Johnson <mark@pc241.icsl.ucla.edu>
Resent-Message-ID: <"LMRx32.0.GG2.FcP-r"@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/338
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length:   988
Status: O


Pardon the newbie question, but...

I'm trying to read in a stack of MR images from a GE SIGNA machine,
which I believe to be in 5.x format.

Has anybody done this before?  Do you know what I'm doing wrong, or
can you suggest a different approach which worked for you?  

Thank you!!!

----------

Things I've tried so far (both from ftp://codon.nih.gov/pub/nih-image/contrib)

1 - mriconverter doesn't recognize the file (the file is grayed out on
the "file open" menu).

2 - read.GESIGNA macros seem to read in the correct description data
(FOV, slice thickness, image label, etc), but not the correct images.
The m option reads a stack of square images of static; the s option
reads in two one-pixel-height images of static.

-----------

Background:

The HFSE stack was created on a 5.x machine, and tarred to a 4mm tape
using the following commands, suggested by GE:

> cd /usr/g/insite/bin
> ximg -l
 (choose image file from menu)
> cd /usr/g/insite/tmp
> tar -cvf /dev/nrst8 *E*

From nih-image-d-request@io.ece.drexel.edu Sat Sep 12 06:09 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA08540;
	Sat, 12 Sep 1998 06:09:29 -0400 (EDT)
Date: Sat, 12 Sep 1998 06:09:29 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809121009.GAA08540@io.ECE.Drexel.EDU>
Subject: nih-image-d Digest V98 #60
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/60
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length:  5287
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 60

Today's Topics:
  Re: adjacent image alignment          [ "Michael J. Herron" <herro001@maroo ]
  Re: adjacent image alignment          [ "Doug S. Phillips" <phillips@ucalga ]
  Particle Analysis Macros              [ Deanna Busick <dnbusick@lanl.gov> ]
  How do I import images in GE SIGNA 5  [ Mark Hasegawa-Johnson <mark@pc241.i ]

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

Date: Fri, 11 Sep 1998 06:52:59 -0500
From: "Michael J. Herron" <herro001@maroon.tc.umn.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: adjacent image alignment
Message-Id: <35F90F1B.5FE6@maroon.tc.umn.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Dr. Russ,

I was under the impression the the edges of SEM images were too
distorted for this....wrong impression?

Mike

DrJohnRuss@aol.com wrote:
> 

> 
> We have a program (Windows NT, not Mac, although it could be recompiled fairly
> easily) that will take any array of tiffs - mine are usually 1000x1000 pixels
> or larger and I often have arrays up to 8x8 - that have overlaps of 10-30% on
> each side and seamlessly stitch them together using cross-correlation in the
> overlap regions to determine the best alignment (including rotation). It isn't
> fast - a job like the one above takes several hours - but the results are
> spectacular. We primarily use it on AFM images, occasionally on SEM, and it
> has also been used on aerial reconnaissance photos. The program is not
> presently available to others but if there is enough demand we might consider
> working out some arrangement for its use.
> 
> John Russ

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

Date: Fri, 11 Sep 98 9:28:24 MDT
From: "Doug S. Phillips" <phillips@ucalgary.ca>
To: nih-image@io.ece.drexel.edu
Cc: nih-image@io.ece.drexel.edu
Subject: Re: adjacent image alignment
Message-Id: <9809111528.AA16520@acs1.acs.ucalgary.ca>
Content-Type: multipart/mixed; boundary="----------------------------"

Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit


Mathias Rickli asked:

> 2) has anyone written a macro to join adjacent, slightly overlapping imag=
> es automatically? My idea is to transform 16 (4x4) or more grayscale SEM
> images from polished sections of ceramics into binary Tiff files and then to
> merge them together in one file in order to apply object (pore) size
> measurements. I wonder if this way of  image treatment exeeds the capacity of
> even high performance Mac plattforms.

This is well within reach of any modern Mac.  I saw an impressive demo
of image stitching at a QuickTime 3 presentation last night.  Apple 
markets a product called QuickTime VR Authoring Studio 
(http://www.apple.com/quicktime/qtvr/authoringstudio/index.html)
that can do automatic alignment of such images.

Sincerely,   Doug P.

Doug S. Phillips                Internet: phillips@ucalgary.ca
University Computing Services   Phone:(403)220-8445  FAX:(403)282-9199
The University of Calgary       WWW:  http://www.acs.ucalgary.ca/~phillips/


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

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

Date: Fri, 11 Sep 1998 15:24:44 -0600
From: Deanna Busick <dnbusick@lanl.gov>
To: nih-image@io.ece.drexel.edu
Subject: Particle Analysis Macros
Message-Id: <v03020903b21f44b86d2f@[128.165.243.113]>
Content-Type: text/plain; charset="us-ascii"

Has anyone had any trouble with Matthew Warfel's particle analysis macros?
The macro seems to be running and doing the analysis, but the Size Data
(tab) and Fractal Data (tab) files I get out contain no data, just a number
of carriage returns equal to the number of particles!
Thanks in advance for any help...

Deanna

------------------------
DEANNA BUSICK
MST-11, MS D429
Los Alamos National Laboratory
Los Alamos, NM  87545
e-mail: dnbusick@lanl.gov
ph#:  (505)667-0561
fax:  (505)665-4292

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

Date: Fri, 11 Sep 1998 14:45:37 -0700
From: Mark Hasegawa-Johnson <mark@pc241.icsl.ucla.edu>
To: nih-image@io.ece.drexel.edu
cc: jul@seas.ucla.edu
Subject: How do I import images in GE SIGNA 5.x format?
Message-ID: <19980911214538.19621.qmail@pc241.icsl.ucla.edu>

Pardon the newbie question, but...

I'm trying to read in a stack of MR images from a GE SIGNA machine,
which I believe to be in 5.x format.

Has anybody done this before?  Do you know what I'm doing wrong, or
can you suggest a different approach which worked for you?  

Thank you!!!

----------

Things I've tried so far (both from ftp://codon.nih.gov/pub/nih-image/contrib)

1 - mriconverter doesn't recognize the file (the file is grayed out on
the "file open" menu).

2 - read.GESIGNA macros seem to read in the correct description data
(FOV, slice thickness, image label, etc), but not the correct images.
The m option reads a stack of square images of static; the s option
reads in two one-pixel-height images of static.

-----------

Background:

The HFSE stack was created on a 5.x machine, and tarred to a 4mm tape
using the following commands, suggested by GE:

> cd /usr/g/insite/bin
> ximg -l
 (choose image file from menu)
> cd /usr/g/insite/tmp
> tar -cvf /dev/nrst8 *E*

--------------------------------
End of nih-image-d Digest V98 Issue #60
***************************************

From nih-image-request@io.ece.drexel.edu Sun Sep 13 11:15 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA20718;
	Sun, 13 Sep 1998 11:14:44 -0400 (EDT)
Resent-Date: Sun, 13 Sep 1998 11:14:44 -0400 (EDT)
Message-ID: <35FBECD9.7EB6190E@netmatters.co.uk>
Date: Sun, 13 Sep 1998 16:03:39 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
Reply-To: brownj@netmatters.co.uk
Organization: brownj@netmatters.co.uk
X-Mailer: Mozilla 4.04 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: RGB to HSV
References: <l03010d11b21decf00660@[128.95.250.218]>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"5vtpW3.0.kn4.Tvz-r"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/339
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length:   330
Status: O

Is there a macro command for converting a RGB stack into an HSV stack?

If not, does anyone know of a plugin of macro that does this?

Many thanks

Jeremy


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

Jeremy Brown
Moredun Research Institute / The University Of Edinburgh
http://users.netmatters.co.uk/brownj/ICHomePage.html

From nih-image-d-request@io.ece.drexel.edu Mon Sep 14 06:13 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA25216;
	Mon, 14 Sep 1998 06:13:37 -0400 (EDT)
Date: Mon, 14 Sep 1998 06:13:37 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809141013.GAA25216@io.ECE.Drexel.EDU>
Subject: nih-image-d Digest V98 #61
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/61
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length:   983
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 61

Today's Topics:
  RGB to HSV                            [ Jeremy Brown <brownj@netmatters.co. ]

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

Date: Sun, 13 Sep 1998 16:03:39 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: RGB to HSV
Message-ID: <35FBECD9.7EB6190E@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Is there a macro command for converting a RGB stack into an HSV stack?

If not, does anyone know of a plugin of macro that does this?

Many thanks

Jeremy


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

Jeremy Brown
Moredun Research Institute / The University Of Edinburgh
http://users.netmatters.co.uk/brownj/ICHomePage.html

--------------------------------
End of nih-image-d Digest V98 Issue #61
***************************************

From nih-image-request@io.ece.drexel.edu Tue Sep 15 06:13 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA05787;
	Tue, 15 Sep 1998 06:12:42 -0400 (EDT)
Resent-Date: Tue, 15 Sep 1998 06:12:42 -0400 (EDT)
Date: Tue, 15 Sep 1998 20:05:38 +1000
From: "Kwang Y. Han" <ykhan1@student.monash.edu.au>
Subject: Mexican Hat, Sombrero & Top-Hat filters
To: nih-image@io.ece.drexel.edu
Message-id: <000001bde090$63401b20$450ac282@ykhan1>
MIME-version: 1.0
X-Mailer: Microsoft Outlook 8.5, Build 4.71.2377.0
Content-transfer-encoding: 7bit
Importance: Normal
X-MSMail-Priority: Normal
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2120.0
X-Priority: 3 (Normal)
Resent-Message-ID: <"XCEcU2.0.x41.JgZ_r"@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/341
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="iso-8859-1"
Content-Length:   646
Status: O

I am student doing some research on electron diffraction (spot) patterns  
from a TEM. I am confused about the differences (if any) between:

- The Mexican Hat filter
- Sombrero Filter
- the Top-Hat filter.

Could someone provide a suggestion for a reference which clarifies these 
different filters?

Also...I am using NIH image and am unsure whether the Top-Hat filter is 
actually an available plugin/macro under this platform. I have read 
the paper by Bright and Steel (J. Microscopy, Vol.146, p. 191) and would 
like to treat my spot diffraction patterns in the same way. The 
nomenclature is a little confusing.

Plenty thanks in advance

From nih-image-request@io.ece.drexel.edu Tue Sep 15 07:22 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA12242;
	Tue, 15 Sep 1998 07:22:00 -0400 (EDT)
Resent-Date: Tue, 15 Sep 1998 07:22:00 -0400 (EDT)
Message-ID: <35FE4A3A.3EE7@gengenp.rug.ac.be>
Date: Tue, 15 Sep 1998 13:06:34 +0200
From: Gerrit Beemster <gebee@gengenp.rug.ac.be>
Organization: Lab of Genetics
X-Mailer: Mozilla 3.01Gold (WinNT; I)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: capturing images with NIH under executor
References: <9809111528.AA16520@acs1.acs.ucalgary.ca>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"-JuRi2.0.5c2.fea_r"@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/342
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:   566
Status: O

Dear all,

Although the subject may be a bit of, I hope someone out there has some
experience with this. I'm trying to get NIH-Image running on a PC
through Ardi's Executor version 2. It works like a whiz and I'm truly
impressed. However, although I have a scion board installed under
Executor the NIH program doesn't "see" it. Is there an easy fix for this
problem, or is it pretty much a hopeless mission?

Thanks for any response.

-- 
Gerrit Beemster
Department of Genetics
K.L. Ledeganckstraat 35
B-9000 Gent
Belgium

phone: (32)9/2645010
fax:   (32)9/2645349

From nih-image-request@io.ece.drexel.edu Tue Sep 15 08:49 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA20254;
	Tue, 15 Sep 1998 08:49:10 -0400 (EDT)
Resent-Date: Tue, 15 Sep 1998 08:49:10 -0400 (EDT)
Message-Id: <3.0.6.32.19980915082005.007f95d0@PO-Box.mcgill.ca>
X-Sender: mliraj@PO-Box.mcgill.ca
X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32)
Date: Tue, 15 Sep 1998 08:20:05 -0400
To: nih-image@io.ece.drexel.edu
From: "Mario de A. Lira Junior" <mliraj@PO-Box.mcgill.ca>
Subject: Re: capturing images with NIH under executor
In-Reply-To: <35FE4A3A.3EE7@gengenp.rug.ac.be>
References: <9809111528.AA16520@acs1.acs.ucalgary.ca>
Mime-Version: 1.0
Resent-Message-ID: <"a0YqM1.0.4d4.oyb_r"@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/343
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:   307
Status: O

>experience with this. I'm trying to get NIH-Image running on a PC
>through Ardi's Executor version 2. It works like a whiz and I'm truly

Why don't you use the Scion Image por for Windows 9x of NIH-Image ?
Generally running a native version makes for better performance and may
avoid the problem...
Mario

From nih-image-request@io.ece.drexel.edu Tue Sep 15 09:18 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA23091;
	Tue, 15 Sep 1998 09:18:21 -0400 (EDT)
Resent-Date: Tue, 15 Sep 1998 09:18:21 -0400 (EDT)
Message-ID: <35FE65D9.23E0@gengenp.rug.ac.be>
Date: Tue, 15 Sep 1998 15:04:25 +0200
From: Gerrit Beemster <gebee@gengenp.rug.ac.be>
Organization: Lab of Genetics
X-Mailer: Mozilla 3.01Gold (WinNT; I)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: capturing images with NIH under executor
References: <9809111528.AA16520@acs1.acs.ucalgary.ca> <3.0.6.32.19980915082005.007f95d0@PO-Box.mcgill.ca>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"85k8g.0.AI5.BNc_r"@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/344
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:   704
Status: O

Mario de A. Lira Junior wrote:
> 
> >experience with this. I'm trying to get NIH-Image running on a PC
> >through Ardi's Executor version 2. It works like a whiz and I'm truly
> 
> Why don't you use the Scion Image por for Windows 9x of NIH-Image ?
> Generally running a native version makes for better performance and may
> avoid the problem...
> Mario

Yes, but some of the macro's in the contrib directory (I'm specifically
interrested in Automatch) are specific for the mac environment and don't
easily port to the ScionImage for as far as I've been able to work out.

-- 
Gerrit Beemster
Department of Genetics
K.L. Ledeganckstraat 35
B-9000 Gent
Belgium

phone: (32)9/2645010
fax:   (32)9/2645349

From nih-image-d-request@io.ece.drexel.edu Wed Sep 16 06:12 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA27946;
	Wed, 16 Sep 1998 06:12:28 -0400 (EDT)
Date: Wed, 16 Sep 1998 06:12:28 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809161012.GAA27946@io.ECE.Drexel.EDU>
Subject: nih-image-d Digest V98 #62
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/62
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length:  4082
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 62

Today's Topics:
  Mexican Hat, Sombrero & Top-Hat filt  [ "Kwang Y. Han" <ykhan1@student.mona ]
  capturing images with NIH under exec  [ Gerrit Beemster <gebee@gengenp.rug. ]
  Re: capturing images with NIH under   [ "Mario de A. Lira Junior" <mliraj@P ]
  Re: capturing images with NIH under   [ Gerrit Beemster <gebee@gengenp.rug. ]

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

Date: Tue, 15 Sep 1998 20:05:38 +1000
From: "Kwang Y. Han" <ykhan1@student.monash.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Mexican Hat, Sombrero & Top-Hat filters
Message-id: <000001bde090$63401b20$450ac282@ykhan1>
Content-type: text/plain; charset="iso-8859-1"
Content-transfer-encoding: 7bit

I am student doing some research on electron diffraction (spot) patterns  
from a TEM. I am confused about the differences (if any) between:

- The Mexican Hat filter
- Sombrero Filter
- the Top-Hat filter.

Could someone provide a suggestion for a reference which clarifies these 
different filters?

Also...I am using NIH image and am unsure whether the Top-Hat filter is 
actually an available plugin/macro under this platform. I have read 
the paper by Bright and Steel (J. Microscopy, Vol.146, p. 191) and would 
like to treat my spot diffraction patterns in the same way. The 
nomenclature is a little confusing.

Plenty thanks in advance

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

Date: Tue, 15 Sep 1998 13:06:34 +0200
From: Gerrit Beemster <gebee@gengenp.rug.ac.be>
To: nih-image@io.ece.drexel.edu
Subject: capturing images with NIH under executor
Message-ID: <35FE4A3A.3EE7@gengenp.rug.ac.be>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Dear all,

Although the subject may be a bit of, I hope someone out there has some
experience with this. I'm trying to get NIH-Image running on a PC
through Ardi's Executor version 2. It works like a whiz and I'm truly
impressed. However, although I have a scion board installed under
Executor the NIH program doesn't "see" it. Is there an easy fix for this
problem, or is it pretty much a hopeless mission?

Thanks for any response.

-- 
Gerrit Beemster
Department of Genetics
K.L. Ledeganckstraat 35
B-9000 Gent
Belgium

phone: (32)9/2645010
fax:   (32)9/2645349

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

Date: Tue, 15 Sep 1998 08:20:05 -0400
From: "Mario de A. Lira Junior" <mliraj@PO-Box.mcgill.ca>
To: nih-image@io.ece.drexel.edu
Subject: Re: capturing images with NIH under executor
Message-Id: <3.0.6.32.19980915082005.007f95d0@PO-Box.mcgill.ca>
Content-Type: text/plain; charset="us-ascii"

>experience with this. I'm trying to get NIH-Image running on a PC
>through Ardi's Executor version 2. It works like a whiz and I'm truly

Why don't you use the Scion Image por for Windows 9x of NIH-Image ?
Generally running a native version makes for better performance and may
avoid the problem...
Mario

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

Date: Tue, 15 Sep 1998 15:04:25 +0200
From: Gerrit Beemster <gebee@gengenp.rug.ac.be>
To: nih-image@io.ece.drexel.edu
Subject: Re: capturing images with NIH under executor
Message-ID: <35FE65D9.23E0@gengenp.rug.ac.be>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Mario de A. Lira Junior wrote:
> 
> >experience with this. I'm trying to get NIH-Image running on a PC
> >through Ardi's Executor version 2. It works like a whiz and I'm truly
> 
> Why don't you use the Scion Image por for Windows 9x of NIH-Image ?
> Generally running a native version makes for better performance and may
> avoid the problem...
> Mario

Yes, but some of the macro's in the contrib directory (I'm specifically
interrested in Automatch) are specific for the mac environment and don't
easily port to the ScionImage for as far as I've been able to work out.

-- 
Gerrit Beemster
Department of Genetics
K.L. Ledeganckstraat 35
B-9000 Gent
Belgium

phone: (32)9/2645010
fax:   (32)9/2645349

--------------------------------
End of nih-image-d Digest V98 Issue #62
***************************************

From nih-image-request@io.ece.drexel.edu Wed Sep 16 09:10 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA11784;
	Wed, 16 Sep 1998 09:09:29 -0400 (EDT)
Resent-Date: Wed, 16 Sep 1998 09:09:29 -0400 (EDT)
Message-Id: <3.0.6.32.19980916084702.00841280@PO-Box.mcgill.ca>
X-Sender: mliraj@PO-Box.mcgill.ca
X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32)
Date: Wed, 16 Sep 1998 08:47:02 -0400
To: nih-image@io.ece.drexel.edu
From: "Mario de A. Lira Junior" <mliraj@PO-Box.mcgill.ca>
Subject: Re: capturing images with NIH under executor
In-Reply-To: <35FE65D9.23E0@gengenp.rug.ac.be>
References: <9809111528.AA16520@acs1.acs.ucalgary.ca>
	<3.0.6.32.19980915082005.007f95d0@PO-Box.mcgill.ca>
Mime-Version: 1.0
Resent-Message-ID: <"IsV1f2.0.7U2.5Gx_r"@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/345
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:   753
Status: O

>> Why don't you use the Scion Image por for Windows 9x of NIH-Image ?
>> Generally running a native version makes for better performance and may
>> avoid the problem...
>> Mario
>
>Yes, but some of the macro's in the contrib directory (I'm specifically
>interrested in Automatch) are specific for the mac environment and don't
>easily port to the ScionImage for as far as I've been able to work out.

Well, in this case, since both are freeware, you may use both versions, and
use the windows version to capture the files you need, save as tifs, go to
the mac version and do the analysis there... It is a roundabout, but at
least you would be able to start working fast, and could later check out to
see if you can do it in a more direct way...
Mario

From nih-image-request@io.ece.drexel.edu Wed Sep 16 13:00 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA00261;
	Wed, 16 Sep 1998 13:00:20 -0400 (EDT)
Resent-Date: Wed, 16 Sep 1998 13:00:20 -0400 (EDT)
Date: 	Wed, 16 Sep 1998 12:42:29 -0400 (EDT)
Sender: Nora Rooney <nora@email.unc.edu>
From: Nora Maureen Rooney <nora@email.unc.edu>
X-Sender: nora@login4.isis.unc.edu
To: nih-image@io.ece.drexel.edu
Message-ID: <Pine.A41.3.95L.980916124123.36354B-100000@login4.isis.unc.edu>
MIME-Version: 1.0
Resent-Message-ID: <"Nac4S1.0.027.Hh-_r"@io>
Resent-From: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Reply-To: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/346
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:   599
Status: O

I am trying to use the program to decipher cell types on a slide image by
their intensity of stain.  The cell type that I want to differentiate
doesn't become apparent through use of the density slice.  Some parts of
some of these cells becomes red, but not all of them all of the time.  I
am trying to use this because it is difficult to decipher between their
dark brown color and the dark blue nuclei of cells that are not of
interest by simply looking at them.  So, I was hoping to have a more
quantifiable method of determining which cells are of interest.  I would
welcome any suggestions. 


From nih-image-request@io.ece.drexel.edu Wed Sep 16 13:41 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA03516;
	Wed, 16 Sep 1998 13:41:18 -0400 (EDT)
Resent-Date: Wed, 16 Sep 1998 13:41:18 -0400 (EDT)
Mime-Version: 1.0
Message-Id: <v04011712b225a6761d1d@[134.192.129.87]>
In-Reply-To: 
	<Pine.A41.3.95L.980916124123.36354B-100000@login4.isis.unc.edu>
Date: Wed, 16 Sep 1998 13:35:26 -0400
To: nih-image@io.ece.drexel.edu
From: Gloria Hoffman <gehoffma@umaryland.edu>
Subject: Re: Unidentified subject!
Resent-Message-ID: <"VbnNY2.0.OV.-F__r"@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/347
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"
	<Pine.A41.3.95L.980916124123.36354B-100000@login4.isis.unc.edu>
Content-Length:  1418
Status: O

Rather than worry about the program not being "smart" enough why not switch
to a nuclear stain that can be eliminated by adding a filter to the
section. For example if your stain is an immunocytochemical one (ie DAB
which is brown) you might want to use Methyl Green as a counterstain.
Adding a cyan filter will make the computer "blind" to the nuclei so there
won't be any interference. Using a red filter will enhance the nuclear
stain . If you can shift your brown stain to black (ie with Nickel DAB)
then you might want to use Neutral Red as the nuclear stain. It is
eliminated (are at least strongly reduced) by use of a dark red filter.

>I am trying to use the program to decipher cell types on a slide image by
>their intensity of stain.  The cell type that I want to differentiate
>doesn't become apparent through use of the density slice.  Some parts of
>some of these cells becomes red, but not all of them all of the time.  I
>am trying to use this because it is difficult to decipher between their
>dark brown color and the dark blue nuclei of cells that are not of
>interest by simply looking at them.  So, I was hoping to have a more
>quantifiable method of determining which cells are of interest.  I would
>welcome any suggestions.

Gloria E. Hoffman, Ph.D.
Department of Anatomy and Neurobiology
685 W Baltimore St
Baltimore MD 21201
Phone 410 706-2438
Fax 410 706-2512
email gehoffma@umaryland.edu

From nih-image-request@io.ece.drexel.edu Wed Sep 16 20:33 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id UAA15616;
	Wed, 16 Sep 1998 20:33:21 -0400 (EDT)
Resent-Date: Wed, 16 Sep 1998 20:33:21 -0400 (EDT)
Date: Wed, 16 Sep 1998 20:24:56 -0500
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
Subject: Q: explanationof MakeMovie options?
To: nih-image@io.ece.drexel.edu
Message-id: <v03102800b22613523eef@[128.244.12.77]>
MIME-version: 1.0
Resent-Message-ID: <"mKcwY2.0.pO3.PL50s"@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/348
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:   925
Status: O

The NIH Image online manual gives the following for the macro MakeMovie
command:

MakeMovie('str',frames,interval)
Captures a sequence of video frames to a stack. 'str' is some combination
of 'blind', 'buffer', 'time stamp', 'existing', 'trigger first',
'trigger each', and 'dialog'. Frames is the number of frames to capture,
and interval is the interval between frames in seconds. See the
"Movie Making" macro file for examples.

Some of the options are not used in the "Movie Making" macro file. For
example, the 'str' options 'blind', 'buffer', and 'existing' don't appear.
Can anyone explain their usage? Also, the "Movie Making" macro file uses
values of -1 for the frames and interval arguments in one of the example
macros that uses the 'dialog' argument. What is the meaning of this?

Finally, can the MakeMovie command use a sub-second interval, and will this
appear in time stamp?

Thanks.

Bill Christens-Barry


From nih-image-request@io.ece.drexel.edu Thu Sep 17 02:35 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id CAA25393;
	Thu, 17 Sep 1998 02:35:18 -0400 (EDT)
Resent-Date: Thu, 17 Sep 1998 02:35:18 -0400 (EDT)
Message-Id: <199809170626.OAA15859@nero.rph.health.wa.gov.au>
From: "Robert Day" <robday@rph.health.wa.gov.au>
To: nih-image@io.ece.drexel.edu
Date: Thu, 17 Sep 1998 14:17:39 +0800
MIME-Version: 1.0
Content-transfer-encoding: 7BIT
Subject: Re: How do I import images in GE SIGNA 5.x format?
Priority: normal
In-reply-to: <19980911214538.19621.qmail@pc241.icsl.ucla.edu>
X-mailer: Pegasus Mail for Win32 (v3.01b)
Resent-Message-ID: <"d5sMk.0.qk5.JfA0s"@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/349
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:  2006
Status: O

> 
> Pardon the newbie question, but...
> 
> I'm trying to read in a stack of MR images from a GE SIGNA machine,
> which I believe to be in 5.x format.
> 
> Has anybody done this before?  Do you know what I'm doing wrong, or
> can you suggest a different approach which worked for you?  
> 
> Thank you!!!
> 
> ----------
> 
> Things I've tried so far (both from
> ftp://codon.nih.gov/pub/nih-image/contrib)
> 
> 1 - mriconverter doesn't recognize the file (the file is grayed out on the
> "file open" menu).

Possibly mriconverter is looking for a specific creator/type 
signature (I don't use this program so I don't know).  If you have any 
examples it will open, use ResEdit (or something a bit safer :-) to 
look at the signature and change the new files to match.


> 2 - read.GESIGNA macros seem to read in the correct description data
> (FOV, slice thickness, image label, etc), but not the correct images. The
> m option reads a stack of square images of static; the s option reads in
> two one-pixel-height images of static.

There are several possible reasons for this.  
1. The format of GE ximg files has changed in the past.  Get ximg 
to dump the structure of the file and compare that with what the 
macros are doing (or re-write the macro to suit as needed).  The 
command to do this should be :
	ximg -g > imageFileOffsets.h
which will generate a C include file defining the names and offsets 
of the fields in the image headers.

2.  GE has used machines with different byte orders for its 
scanners.  Try byte swapping just to be sure.

3.  The image could have been saved in compressed format.  The 
compression algorithim is given in the Medical Image Format FAQ 
among other places.

In any case, try also the freeware too Dr.RAZZ, as it can read most 
GE files in my experience.  Try :
<http://www.scar.rad.washington.edu/razz/downloads.html>


Rob.

--
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-d-request@io.ece.drexel.edu Thu Sep 17 02:35 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id CAA25433;
	Thu, 17 Sep 1998 02:35:30 -0400 (EDT)
Date: Thu, 17 Sep 1998 02:35:30 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809170635.CAA25433@io.ECE.Drexel.EDU>
Subject: nih-image-d Digest V98 #63
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/63
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length:  7891
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 63

Today's Topics:
  Re: capturing images with NIH under   [ "Mario de A. Lira Junior" <mliraj@P ]
  Unidentified subject!                 [ Nora Maureen Rooney <nora@email.unc ]
  Re: Unidentified subject!             [ Gloria Hoffman <gehoffma@umaryland. ]
  Q: explanationof MakeMovie options?   [ Bill Christens-Barry <wacb@aplcomm. ]
  Re: How do I import images in GE SIG  [ "Robert Day" <robday@rph.health.wa. ]

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

Date: Wed, 16 Sep 1998 08:47:02 -0400
From: "Mario de A. Lira Junior" <mliraj@PO-Box.mcgill.ca>
To: nih-image@io.ece.drexel.edu
Subject: Re: capturing images with NIH under executor
Message-Id: <3.0.6.32.19980916084702.00841280@PO-Box.mcgill.ca>
Content-Type: text/plain; charset="us-ascii"

>> Why don't you use the Scion Image por for Windows 9x of NIH-Image ?
>> Generally running a native version makes for better performance and may
>> avoid the problem...
>> Mario
>
>Yes, but some of the macro's in the contrib directory (I'm specifically
>interrested in Automatch) are specific for the mac environment and don't
>easily port to the ScionImage for as far as I've been able to work out.

Well, in this case, since both are freeware, you may use both versions, and
use the windows version to capture the files you need, save as tifs, go to
the mac version and do the analysis there... It is a roundabout, but at
least you would be able to start working fast, and could later check out to
see if you can do it in a more direct way...
Mario

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

Date: 	Wed, 16 Sep 1998 12:42:29 -0400 (EDT)
From: Nora Maureen Rooney <nora@email.unc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-ID: <Pine.A41.3.95L.980916124123.36354B-100000@login4.isis.unc.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I am trying to use the program to decipher cell types on a slide image by
their intensity of stain.  The cell type that I want to differentiate
doesn't become apparent through use of the density slice.  Some parts of
some of these cells becomes red, but not all of them all of the time.  I
am trying to use this because it is difficult to decipher between their
dark brown color and the dark blue nuclei of cells that are not of
interest by simply looking at them.  So, I was hoping to have a more
quantifiable method of determining which cells are of interest.  I would
welcome any suggestions. 

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

Date: Wed, 16 Sep 1998 13:35:26 -0400
From: Gloria Hoffman <gehoffma@umaryland.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Unidentified subject!
Message-Id: <v04011712b225a6761d1d@[134.192.129.87]>
Content-Type: text/plain; charset="us-ascii"

Rather than worry about the program not being "smart" enough why not switch
to a nuclear stain that can be eliminated by adding a filter to the
section. For example if your stain is an immunocytochemical one (ie DAB
which is brown) you might want to use Methyl Green as a counterstain.
Adding a cyan filter will make the computer "blind" to the nuclei so there
won't be any interference. Using a red filter will enhance the nuclear
stain . If you can shift your brown stain to black (ie with Nickel DAB)
then you might want to use Neutral Red as the nuclear stain. It is
eliminated (are at least strongly reduced) by use of a dark red filter.

>I am trying to use the program to decipher cell types on a slide image by
>their intensity of stain.  The cell type that I want to differentiate
>doesn't become apparent through use of the density slice.  Some parts of
>some of these cells becomes red, but not all of them all of the time.  I
>am trying to use this because it is difficult to decipher between their
>dark brown color and the dark blue nuclei of cells that are not of
>interest by simply looking at them.  So, I was hoping to have a more
>quantifiable method of determining which cells are of interest.  I would
>welcome any suggestions.

Gloria E. Hoffman, Ph.D.
Department of Anatomy and Neurobiology
685 W Baltimore St
Baltimore MD 21201
Phone 410 706-2438
Fax 410 706-2512
email gehoffma@umaryland.edu

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

Date: Wed, 16 Sep 1998 20:24:56 -0500
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
To: nih-image@io.ece.drexel.edu
Subject: Q: explanationof MakeMovie options?
Message-id: <v03102800b22613523eef@[128.244.12.77]>
Content-type: text/plain; charset="us-ascii"

The NIH Image online manual gives the following for the macro MakeMovie
command:

MakeMovie('str',frames,interval)
Captures a sequence of video frames to a stack. 'str' is some combination
of 'blind', 'buffer', 'time stamp', 'existing', 'trigger first',
'trigger each', and 'dialog'. Frames is the number of frames to capture,
and interval is the interval between frames in seconds. See the
"Movie Making" macro file for examples.

Some of the options are not used in the "Movie Making" macro file. For
example, the 'str' options 'blind', 'buffer', and 'existing' don't appear.
Can anyone explain their usage? Also, the "Movie Making" macro file uses
values of -1 for the frames and interval arguments in one of the example
macros that uses the 'dialog' argument. What is the meaning of this?

Finally, can the MakeMovie command use a sub-second interval, and will this
appear in time stamp?

Thanks.

Bill Christens-Barry

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

Date: Thu, 17 Sep 1998 14:17:39 +0800
From: "Robert Day" <robday@rph.health.wa.gov.au>
To: nih-image@io.ece.drexel.edu
Subject: Re: How do I import images in GE SIGNA 5.x format?
Message-Id: <199809170626.OAA15859@nero.rph.health.wa.gov.au>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7BIT

> 
> Pardon the newbie question, but...
> 
> I'm trying to read in a stack of MR images from a GE SIGNA machine,
> which I believe to be in 5.x format.
> 
> Has anybody done this before?  Do you know what I'm doing wrong, or
> can you suggest a different approach which worked for you?  
> 
> Thank you!!!
> 
> ----------
> 
> Things I've tried so far (both from
> ftp://codon.nih.gov/pub/nih-image/contrib)
> 
> 1 - mriconverter doesn't recognize the file (the file is grayed out on the
> "file open" menu).

Possibly mriconverter is looking for a specific creator/type 
signature (I don't use this program so I don't know).  If you have any 
examples it will open, use ResEdit (or something a bit safer :-) to 
look at the signature and change the new files to match.


> 2 - read.GESIGNA macros seem to read in the correct description data
> (FOV, slice thickness, image label, etc), but not the correct images. The
> m option reads a stack of square images of static; the s option reads in
> two one-pixel-height images of static.

There are several possible reasons for this.  
1. The format of GE ximg files has changed in the past.  Get ximg 
to dump the structure of the file and compare that with what the 
macros are doing (or re-write the macro to suit as needed).  The 
command to do this should be :
	ximg -g > imageFileOffsets.h
which will generate a C include file defining the names and offsets 
of the fields in the image headers.

2.  GE has used machines with different byte orders for its 
scanners.  Try byte swapping just to be sure.

3.  The image could have been saved in compressed format.  The 
compression algorithim is given in the Medical Image Format FAQ 
among other places.

In any case, try also the freeware too Dr.RAZZ, as it can read most 
GE files in my experience.  Try :
<http://www.scar.rad.washington.edu/razz/downloads.html>


Rob.

--
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 V98 Issue #63
***************************************

From nih-image-request@io.ece.drexel.edu Thu Sep 17 04:26 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id EAA08060;
	Thu, 17 Sep 1998 04:26:50 -0400 (EDT)
Resent-Date: Thu, 17 Sep 1998 04:26:50 -0400 (EDT)
X-Sender: mathias@ruby.unibe.ch
Message-Id: <v01510103b2268200477b@[130.92.130.93]>
Mime-Version: 1.0
Date: Thu, 17 Sep 1998 10:15:00 +0100
To: nih-image@io.ece.drexel.edu
From: mathias@mpi.unibe.ch (mathias rickli)
Subject: stereology
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id EAA06198
Resent-Message-ID: <"PLSB13.0.zW1.2HC0s"@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/350
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="iso-8859-1"
Content-Length:   504
Status: O

Does anybody combine nih image with stereological methods? In more detail I
wonder if macros are available to estimate quantities such as: mean
particle volume, surface density, mean linear intercept length, star
volume,...
thanks for answering

cheers
mathias

Mathias Rickli [dipl. Min.]

Mineralogisch-Petrographisches Institut
Universitt Bern
Baltzerstrasse 1
CH-3012 Bern
Switzerland
Tel: +41-31-631-8781
Fax: +41-31-631-4843

home:
Freiestrasse 35
CH-3012 Bern
Switzerland
Tel: +41-31-302-9564



From nih-image-request@io.ece.drexel.edu Thu Sep 17 15:30 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA08280;
	Thu, 17 Sep 1998 15:30:01 -0400 (EDT)
Resent-Date: Thu, 17 Sep 1998 15:30:01 -0400 (EDT)
Message-ID: <36016B73.63C29E5@netmatters.co.uk>
Date: Thu, 17 Sep 1998 20:05:14 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
Reply-To: brownj@netmatters.co.uk
Organization: brownj@netmatters.co.uk
X-Mailer: Mozilla 4.04 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: Unidentified subject!
References: <v04011712b225a6761d1d@[134.192.129.87]>
Resent-Message-ID: <"hPZDC2.0.cm1.M-L0s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/351
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: multipart/alternative; boundary="------------C476746C0100839C13B60D38"
Content-Length:  5708
Status: O


--------------C476746C0100839C13B60D38
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Try 'RGB to HSV' from the Stacks menu.

DAB stained cells can be segmented in RGB images, although it is difficult.
However, converting the image to the Hue, Saturation, Intensity model should
make your DAB stained cells show up really nicely in the HUE channel (1) and
the unstained blue nuclei in the Saturation channel (2). DAB is essentially an
unsaturated red colour and can be segmented easily from a blue background.
Haematoxylin staining, for example, is more saturated in the nuclei but is
uniform in Hue. Positive cells should appear bright red on a uniform blue
background in the hue channel. Negative cells may then be counted in the
Saturation channel, in which DAB due to its low saturation value should not
appear.

You may want to use a more intense counterstain if you are using DAB to stain
cell culture preps. Alternatively you can use the intensity channel (3) to
segment DAB stained objects (especially if you are using NiCl2 of CoCl2 to
enhance DAB which should be very dark blue/black).

Hope this helps, it works well for Neospora in tissue sections and Chlamydia
spp in tissue culture.

Jeremy

Gloria Hoffman wrote:

> Rather than worry about the program not being "smart" enough why not switch
> to a nuclear stain that can be eliminated by adding a filter to the
> section. For example if your stain is an immunocytochemical one (ie DAB
> which is brown) you might want to use Methyl Green as a counterstain.
> Adding a cyan filter will make the computer "blind" to the nuclei so there
> won't be any interference. Using a red filter will enhance the nuclear
> stain . If you can shift your brown stain to black (ie with Nickel DAB)
> then you might want to use Neutral Red as the nuclear stain. It is
> eliminated (are at least strongly reduced) by use of a dark red filter.
>
> >I am trying to use the program to decipher cell types on a slide image by
> >their intensity of stain.  The cell type that I want to differentiate
> >doesn't become apparent through use of the density slice.  Some parts of
> >some of these cells becomes red, but not all of them all of the time.  I
> >am trying to use this because it is difficult to decipher between their
> >dark brown color and the dark blue nuclei of cells that are not of
> >interest by simply looking at them.  So, I was hoping to have a more
> >quantifiable method of determining which cells are of interest.  I would
> >welcome any suggestions.
>
> Gloria E. Hoffman, Ph.D.
> Department of Anatomy and Neurobiology
> 685 W Baltimore St
> Baltimore MD 21201
> Phone 410 706-2438
> Fax 410 706-2512
> email gehoffma@umaryland.edu



--------------C476746C0100839C13B60D38
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<HTML>
Try 'RGB to HSV' from the Stacks menu.

<P>DAB stained cells can be segmented in RGB images, although it is difficult.
However, converting the image to the Hue, Saturation, Intensity model should
make your DAB stained cells show up really nicely in the HUE channel (1)
and the unstained blue nuclei in the Saturation channel (2). DAB is essentially
an unsaturated red colour and can be segmented easily from a blue background.
Haematoxylin staining, for example, is more saturated in the nuclei but
is uniform in Hue. Positive cells should appear bright red on a uniform
blue background in the hue channel. Negative cells may then be counted
in the Saturation channel, in which DAB due to its low saturation value
should not appear.

<P>You may want to use a more intense counterstain if you are using DAB
to stain cell culture preps. Alternatively you can use the intensity channel
(3) to segment DAB stained objects (especially if you are using NiCl2 of
CoCl2 to enhance DAB which should be very dark blue/black).

<P>Hope this helps, it works well for <I>Neospora</I> in tissue sections
and <I>Chlamydia</I> <I>spp</I> in tissue culture.

<P>Jeremy

<P>Gloria Hoffman wrote:
<BLOCKQUOTE TYPE=CITE>Rather than worry about the program not being "smart"
enough why not switch
<BR>to a nuclear stain that can be eliminated by adding a filter to the
<BR>section. For example if your stain is an immunocytochemical one (ie
DAB
<BR>which is brown) you might want to use Methyl Green as a counterstain.
<BR>Adding a cyan filter will make the computer "blind" to the nuclei so
there
<BR>won't be any interference. Using a red filter will enhance the nuclear
<BR>stain . If you can shift your brown stain to black (ie with Nickel
DAB)
<BR>then you might want to use Neutral Red as the nuclear stain. It is
<BR>eliminated (are at least strongly reduced) by use of a dark red filter.

<P>>I am trying to use the program to decipher cell types on a slide image
by
<BR>>their intensity of stain.&nbsp; The cell type that I want to differentiate
<BR>>doesn't become apparent through use of the density slice.&nbsp; Some
parts of
<BR>>some of these cells becomes red, but not all of them all of the time.&nbsp;
I
<BR>>am trying to use this because it is difficult to decipher between
their
<BR>>dark brown color and the dark blue nuclei of cells that are not of
<BR>>interest by simply looking at them.&nbsp; So, I was hoping to have
a more
<BR>>quantifiable method of determining which cells are of interest.&nbsp;
I would
<BR>>welcome any suggestions.

<P>Gloria E. Hoffman, Ph.D.
<BR>Department of Anatomy and Neurobiology
<BR>685 W Baltimore St
<BR>Baltimore MD 21201
<BR>Phone 410 706-2438
<BR>Fax 410 706-2512
<BR>email gehoffma@umaryland.edu</BLOCKQUOTE>
&nbsp;</HTML>

--------------C476746C0100839C13B60D38--


From nih-image-request@io.ece.drexel.edu Thu Sep 17 17:13 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA14995;
	Thu, 17 Sep 1998 17:12:52 -0400 (EDT)
Resent-Date: Thu, 17 Sep 1998 17:12:52 -0400 (EDT)
Date: Thu, 17 Sep 1998 13:56:26 -0700 (PDT)
From: Maryam Shariati <shariati@scf-fs.usc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Questions Regarding NIH Image 
Message-ID: <Pine.GSO.4.02.9809171354590.1508-100000@aludra.usc.edu>
MIME-Version: 1.0
Resent-Message-ID: <"owhNy3.0.MM3._TN0s"@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/352
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:  1013
Status: O

Hi,

      I am a Chemical Engineering Ph.D. candidate at USC working on
fluid flow through porous media.  Recently I downloaded the PC version
of the NIH image software from the NIH web site.  I am hoping to use
this software to analyze images captured when a fluid (1), with a
distinct color ( dyed with a dark color), displaces another fluid (2)
with a lighter color ( usually not dyed).  Hence I am planning to
convert the pixel values ( gray scale levels) to concentration using
possibly the Beer-Lambert Law.  I am hoping to get the concentration
gradient across as fluid (1) displaces fluid (2).

Given what I have described, I have a couple of questions :
        o How can one calibrate the system ?
        o Can one store the pixel values using NIH?

You can contact me via email at : shariati@usc.edu.  Thanks a lot for your
consideration and cooperation in this matter.  Your additional suggestions
and advice in this matter are greatly appreciated.

sincerely,

Maryam Shariati
shariati@usc.edu




From nih-image-request@io.ece.drexel.edu Fri Sep 18 02:15 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id CAA29394;
	Fri, 18 Sep 1998 02:15:35 -0400 (EDT)
Resent-Date: Fri, 18 Sep 1998 02:15:35 -0400 (EDT)
Date: Thu, 17 Sep 1998 23:06:36 -0700 (PDT)
From: Pauline Seta Yaralian <yaralian@almaak.usc.edu>
To: nih image <nih-image@io.ece.drexel.edu>
Subject: gray/white segmentation
Message-ID: <Pine.GSO.4.02.9809172305010.1853-100000@almaak.usc.edu>
MIME-Version: 1.0
Resent-Message-ID: <"YhFYw3.0.su6.sXV0s"@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/353
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:   359
Status: O


Is NIH image capable of automatically segmenting gray and white matter?
Also,. is it possible to view 3 planes simultaneously?

Pauline S. Yaralian
Research Assistant
Clinical Neuroscience Laboratory
University of Southern California
Department of Psychology
Los Angeles, Ca. 90089-1061
e mail: yaralian@rcf.usc.edu
Office:(213) 740-2220
Fax:(213) 746-9082

From nih-image-d-request@io.ece.drexel.edu Fri Sep 18 02:16 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id CAA29511;
	Fri, 18 Sep 1998 02:16:25 -0400 (EDT)
Date: Fri, 18 Sep 1998 02:16:25 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809180616.CAA29511@io.ECE.Drexel.EDU>
Subject: nih-image-d Digest V98 #64
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/64
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length:  9371
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 64

Today's Topics:
  stereology                            [ mathias@mpi.unibe.ch (mathias rickl ]
  Re: Unidentified subject!             [ Jeremy Brown <brownj@netmatters.co. ]
  Questions Regarding NIH Image         [ Maryam Shariati <shariati@scf-fs.us ]
  gray/white segmentation               [ Pauline Seta Yaralian <yaralian@alm ]

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

Date: Thu, 17 Sep 1998 10:15:00 +0100
From: mathias@mpi.unibe.ch (mathias rickli)
To: nih-image@io.ece.drexel.edu
Subject: stereology
Message-Id: <v01510103b2268200477b@[130.92.130.93]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Does anybody combine nih image with stereological methods? In more detail I
wonder if macros are available to estimate quantities such as: mean
particle volume, surface density, mean linear intercept length, star
volume,...
thanks for answering

cheers
mathias

Mathias Rickli [dipl. Min.]

Mineralogisch-Petrographisches Institut
Universitt Bern
Baltzerstrasse 1
CH-3012 Bern
Switzerland
Tel: +41-31-631-8781
Fax: +41-31-631-4843

home:
Freiestrasse 35
CH-3012 Bern
Switzerland
Tel: +41-31-302-9564

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

Date: Thu, 17 Sep 1998 20:05:14 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Unidentified subject!
Message-ID: <36016B73.63C29E5@netmatters.co.uk>
Content-Type: multipart/alternative; boundary="------------C476746C0100839C13B60D38"

--------------C476746C0100839C13B60D38
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Try 'RGB to HSV' from the Stacks menu.

DAB stained cells can be segmented in RGB images, although it is difficult.
However, converting the image to the Hue, Saturation, Intensity model should
make your DAB stained cells show up really nicely in the HUE channel (1) and
the unstained blue nuclei in the Saturation channel (2). DAB is essentially an
unsaturated red colour and can be segmented easily from a blue background.
Haematoxylin staining, for example, is more saturated in the nuclei but is
uniform in Hue. Positive cells should appear bright red on a uniform blue
background in the hue channel. Negative cells may then be counted in the
Saturation channel, in which DAB due to its low saturation value should not
appear.

You may want to use a more intense counterstain if you are using DAB to stain
cell culture preps. Alternatively you can use the intensity channel (3) to
segment DAB stained objects (especially if you are using NiCl2 of CoCl2 to
enhance DAB which should be very dark blue/black).

Hope this helps, it works well for Neospora in tissue sections and Chlamydia
spp in tissue culture.

Jeremy

Gloria Hoffman wrote:

> Rather than worry about the program not being "smart" enough why not switch
> to a nuclear stain that can be eliminated by adding a filter to the
> section. For example if your stain is an immunocytochemical one (ie DAB
> which is brown) you might want to use Methyl Green as a counterstain.
> Adding a cyan filter will make the computer "blind" to the nuclei so there
> won't be any interference. Using a red filter will enhance the nuclear
> stain . If you can shift your brown stain to black (ie with Nickel DAB)
> then you might want to use Neutral Red as the nuclear stain. It is
> eliminated (are at least strongly reduced) by use of a dark red filter.
>
> >I am trying to use the program to decipher cell types on a slide image by
> >their intensity of stain.  The cell type that I want to differentiate
> >doesn't become apparent through use of the density slice.  Some parts of
> >some of these cells becomes red, but not all of them all of the time.  I
> >am trying to use this because it is difficult to decipher between their
> >dark brown color and the dark blue nuclei of cells that are not of
> >interest by simply looking at them.  So, I was hoping to have a more
> >quantifiable method of determining which cells are of interest.  I would
> >welcome any suggestions.
>
> Gloria E. Hoffman, Ph.D.
> Department of Anatomy and Neurobiology
> 685 W Baltimore St
> Baltimore MD 21201
> Phone 410 706-2438
> Fax 410 706-2512
> email gehoffma@umaryland.edu



--------------C476746C0100839C13B60D38
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<HTML>
Try 'RGB to HSV' from the Stacks menu.

<P>DAB stained cells can be segmented in RGB images, although it is difficult.
However, converting the image to the Hue, Saturation, Intensity model should
make your DAB stained cells show up really nicely in the HUE channel (1)
and the unstained blue nuclei in the Saturation channel (2). DAB is essentially
an unsaturated red colour and can be segmented easily from a blue background.
Haematoxylin staining, for example, is more saturated in the nuclei but
is uniform in Hue. Positive cells should appear bright red on a uniform
blue background in the hue channel. Negative cells may then be counted
in the Saturation channel, in which DAB due to its low saturation value
should not appear.

<P>You may want to use a more intense counterstain if you are using DAB
to stain cell culture preps. Alternatively you can use the intensity channel
(3) to segment DAB stained objects (especially if you are using NiCl2 of
CoCl2 to enhance DAB which should be very dark blue/black).

<P>Hope this helps, it works well for <I>Neospora</I> in tissue sections
and <I>Chlamydia</I> <I>spp</I> in tissue culture.

<P>Jeremy

<P>Gloria Hoffman wrote:
<BLOCKQUOTE TYPE=CITE>Rather than worry about the program not being "smart"
enough why not switch
<BR>to a nuclear stain that can be eliminated by adding a filter to the
<BR>section. For example if your stain is an immunocytochemical one (ie
DAB
<BR>which is brown) you might want to use Methyl Green as a counterstain.
<BR>Adding a cyan filter will make the computer "blind" to the nuclei so
there
<BR>won't be any interference. Using a red filter will enhance the nuclear
<BR>stain . If you can shift your brown stain to black (ie with Nickel
DAB)
<BR>then you might want to use Neutral Red as the nuclear stain. It is
<BR>eliminated (are at least strongly reduced) by use of a dark red filter.

<P>>I am trying to use the program to decipher cell types on a slide image
by
<BR>>their intensity of stain.&nbsp; The cell type that I want to differentiate
<BR>>doesn't become apparent through use of the density slice.&nbsp; Some
parts of
<BR>>some of these cells becomes red, but not all of them all of the time.&nbsp;
I
<BR>>am trying to use this because it is difficult to decipher between
their
<BR>>dark brown color and the dark blue nuclei of cells that are not of
<BR>>interest by simply looking at them.&nbsp; So, I was hoping to have
a more
<BR>>quantifiable method of determining which cells are of interest.&nbsp;
I would
<BR>>welcome any suggestions.

<P>Gloria E. Hoffman, Ph.D.
<BR>Department of Anatomy and Neurobiology
<BR>685 W Baltimore St
<BR>Baltimore MD 21201
<BR>Phone 410 706-2438
<BR>Fax 410 706-2512
<BR>email gehoffma@umaryland.edu</BLOCKQUOTE>
&nbsp;</HTML>

--------------C476746C0100839C13B60D38--

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

Date: Thu, 17 Sep 1998 13:56:26 -0700 (PDT)
From: Maryam Shariati <shariati@scf-fs.usc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Questions Regarding NIH Image 
Message-ID: <Pine.GSO.4.02.9809171354590.1508-100000@aludra.usc.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi,

      I am a Chemical Engineering Ph.D. candidate at USC working on
fluid flow through porous media.  Recently I downloaded the PC version
of the NIH image software from the NIH web site.  I am hoping to use
this software to analyze images captured when a fluid (1), with a
distinct color ( dyed with a dark color), displaces another fluid (2)
with a lighter color ( usually not dyed).  Hence I am planning to
convert the pixel values ( gray scale levels) to concentration using
possibly the Beer-Lambert Law.  I am hoping to get the concentration
gradient across as fluid (1) displaces fluid (2).

Given what I have described, I have a couple of questions :
        o How can one calibrate the system ?
        o Can one store the pixel values using NIH?

You can contact me via email at : shariati@usc.edu.  Thanks a lot for your
consideration and cooperation in this matter.  Your additional suggestions
and advice in this matter are greatly appreciated.

sincerely,

Maryam Shariati
shariati@usc.edu

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

Date: Thu, 17 Sep 1998 23:06:36 -0700 (PDT)
From: Pauline Seta Yaralian <yaralian@almaak.usc.edu>
To: nih image <nih-image@io.ece.drexel.edu>
Subject: gray/white segmentation
Message-ID: <Pine.GSO.4.02.9809172305010.1853-100000@almaak.usc.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Is NIH image capable of automatically segmenting gray and white matter?
Also,. is it possible to view 3 planes simultaneously?

Pauline S. Yaralian
Research Assistant
Clinical Neuroscience Laboratory
University of Southern California
Department of Psychology
Los Angeles, Ca. 90089-1061
e mail: yaralian@rcf.usc.edu
Office:(213) 740-2220
Fax:(213) 746-9082

--------------------------------
End of nih-image-d Digest V98 Issue #64
***************************************

From nih-image-request@io.ece.drexel.edu Fri Sep 18 06:33 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA22790;
	Fri, 18 Sep 1998 06:33:51 -0400 (EDT)
Resent-Date: Fri, 18 Sep 1998 06:33:51 -0400 (EDT)
From: UPongs@tkc.de
X-Sender: UPongs@mail.tkc.de
Message-Id: <v01540702b227e3ebbdbc@[194.162.166.178]>
Mime-Version: 1.0
Date: Fri, 18 Sep 1998 12:24:06 +0200
To: nih-image@io.ece.drexel.edu
Subject: NIH-Image and DT3155
Resent-Message-ID: <"KAmIf.0.9D5.IGZ0s"@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/354
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:   255
Status: RO

Hi Imagers!

Is there anyone of you, who has experiences with a Data Translation
Framegrabber DT3155 in a Macintosh (which one - 7300, 7500 or ???) together
with NIH-Image?
How can I connect both?

Any ideas and help is really welcome

Uwe Martin Pongs


From nih-image-request@io.ece.drexel.edu Fri Sep 18 11:05 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA15513;
	Fri, 18 Sep 1998 11:04:54 -0400 (EDT)
Resent-Date: Fri, 18 Sep 1998 11:04:54 -0400 (EDT)
Message-Id: <v0300780cb2282348cc0d@[144.118.33.245]>
In-Reply-To: <Pine.GSO.4.02.9809172305010.1853-100000@almaak.usc.edu>
Mime-Version: 1.0
Date: Fri, 18 Sep 1998 10:49:19 -0400
To: nih-image@io.ece.drexel.edu
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: Re: gray/white segmentation
Resent-Message-ID: <"947VN1.0.HQ3.mBd0s"@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/355
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:  1077
Status: O

>Is NIH image capable of automatically segmenting gray and white matter?
>Also,. is it possible to view 3 planes simultaneously?
>
See object image for 3plane view.

--------------------------------------------------------------------------------
-----------------------
                                  Jonathan Nissanov, Ph.D.
                                      Associate Director
            Computer Vision Center for Vertebrate Brain Mapping,
                a NIH Biomedical Research Technology Resource
                                http://cbis.ece.drexel.edu/ICVC/
--------------------------------------------------------------------------------
-----------------------
Imaging and Computer Vision Center              Tel: 215-895-1381
Drexel University                                                   Fax:
215-895-4987
Phildelphia, PA 19104
yoni@coe.drexel.edu
 -------------------------------------------------------------------------------
------------------------

     And remember, the early bird may get the worm, but the second mouse
gets the cheese.


From nih-image-request@io.ece.drexel.edu Fri Sep 18 11:17 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA16996;
	Fri, 18 Sep 1998 11:17:36 -0400 (EDT)
Resent-Date: Fri, 18 Sep 1998 11:17:36 -0400 (EDT)
Message-Id: <199809181506.LAA15716@io.ECE.Drexel.EDU>
From: Chris Liner <cll@douze.geo.utulsa.edu>
Subject: Image/J & linux
To: nih-image@io.ece.drexel.edu
Date: Fri, 18 Sep 98 10:29:31 CDT
Cc: cll@utulsa.edu (Chris Liner)
Mailer: Elm [revision: 70.85]
Resent-Message-ID: <"k3xnt.0.mr3.ZRd0s"@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/356
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length:   379
Status: O

Has anyone on the list got Image/J running under linux?

If so, I would be interested in knowing the procedure. 

Dr. Christopher L. Liner
Associate Professor
Department of Geoscience
University of Tulsa
600 S. College Ave
Tulsa, OK   74104-3189
---------------------------
cll@utulsa.edu
http://douze.utulsa.edu/~cll/ChrisLiner.html
918-631-3028   [phone]
918-631-2091   [fax]

From nih-image-request@io.ece.drexel.edu Fri Sep 18 11:26 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA18055;
	Fri, 18 Sep 1998 11:26:46 -0400 (EDT)
Resent-Date: Fri, 18 Sep 1998 11:26:46 -0400 (EDT)
Message-ID: <3602842F.9363D444@netmatters.co.uk>
Date: Fri, 18 Sep 1998 16:02:57 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
Reply-To: brownj@netmatters.co.uk
Organization: brownj@netmatters.co.uk
X-Mailer: Mozilla 4.04 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: gray/white segmentation
References: <Pine.GSO.4.02.9809172305010.1853-100000@almaak.usc.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"7b6ao2.0.M24.cZd0s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/357
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length:  1289
Status: O



Pauline Seta Yaralian wrote:

> Is NIH image capable of automatically segmenting gray and white matter?
> Also,. is it possible to view 3 planes simultaneously?
>
> Pauline S. Yaralian
> Research Assistant
> Clinical Neuroscience Laboratory
> University of Southern California
> Department of Psychology
> Los Angeles, Ca. 90089-1061
> e mail: yaralian@rcf.usc.edu
> Office:(213) 740-2220
> Fax:(213) 746-908


If by three planes simultaneously you mean X,Y,Z axis images, Object Image
(a spin-off of NIH Image available from
http://simon.bio.uva.nl/object-imageButtons.html or via the NIH site) uses
one of the best approaches to this problem I've ever seen. Under the Sacks
menu  choose slice 2D or slice 3D. These will give you a live 3-planar
view of any image stack. This is extremely useful for 3D data sets. Object
Image is Mac only, if you are using a PC I am afraid that you will have to
make do with drawing a line across you image and then choosing reslice,
repeat this lots of times until you find the point in the 3D image you are
looking for.


Jeremy


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

Jeremy Brown
Moredun Research Institute/Edinburgh University
http://www.netmatters.co.uk/users/brownj/HomePage.html

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



From nih-image-request@io.ece.drexel.edu Fri Sep 18 11:27 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA18194;
	Fri, 18 Sep 1998 11:27:25 -0400 (EDT)
Resent-Date: Fri, 18 Sep 1998 11:27:25 -0400 (EDT)
Message-ID: <3602871F.BE671FB7@netmatters.co.uk>
Date: Fri, 18 Sep 1998 16:15:29 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
Reply-To: brownj@netmatters.co.uk
Organization: brownj@netmatters.co.uk
X-Mailer: Mozilla 4.04 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Plug-in wanted for RGB-HSV conversion
References: <v01540702b227e3ebbdbc@[194.162.166.178]>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"-3AWI.0.b24.eZd0s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/358
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length:   673
Status: O

Hello all,

I still need help with converting RGB images within a macro into HSV images.
Is there a plug-in out there that does the job. Alternatively could anyone
explain how to convert Red Green and Blue images into Hue Saturation intensity
images.

I would also appreciate suggestions for a good cytoplasmic counterstain for
Macrophages, ones that would work with DAB or FITC staining, preferable one
which does not stain acid fast bacteria.

 Jeremy

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

Jeremy Brown
Moredun Research Institute/Edinburgh University
http://www.netmatters.co.uk/users/brownj/HomePage.html

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


From nih-image-request@io.ece.drexel.edu Fri Sep 18 11:57 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA20925;
	Fri, 18 Sep 1998 11:57:04 -0400 (EDT)
Resent-Date: Fri, 18 Sep 1998 11:57:04 -0400 (EDT)
Message-ID: <n1305981720.69163@Administrator>
Date: 18 Sep 1998 17:44:54 +0200
From: "Mark Wunsch" <mwunsch@zmt.uni-bremen.de>
Subject: labeling area measurements
To: "nih questions" <nih-image@io.ece.drexel.edu>
X-Mailer: Mail*Link SMTP-QM 4.1.0
Mime-Version: 1.0
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id LAA19754
Resent-Message-ID: <"K2YrK.0.vq4.__d0s"@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/359
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="ISO-8859-1"; Name="Message Body"
Content-Length:   669
Status: O

                      Betreff:                              Uhrzeit:17:35 Uhr
  MITTEILUNG          labeling area measurements             Datum:18.09.1998

Hello all,
I am studying coral reef communities from underwater video images.
I need to measure the size of individuals of different species by surrounding them manually (contrast usually is low),  i.e. 10 species in a single image.
To transfer the measurements related to the species I would like to find a macro which allows me to label the areas of the individuals with numbers and afterwards to export them to an EXCEL table.
Has anybody experience with this kind of application, knows a macro?
Cheers Mark

From nih-image-request@io.ece.drexel.edu Fri Sep 18 12:14 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA22396;
	Fri, 18 Sep 1998 12:14:06 -0400 (EDT)
Resent-Date: Fri, 18 Sep 1998 12:14:06 -0400 (EDT)
X-Sender: mathias@ruby.unibe.ch
Message-Id: <v01510101b2283b1b7c75@[130.92.130.93]>
Mime-Version: 1.0
Date: Fri, 18 Sep 1998 18:04:20 +0100
To: nih-image@io.ece.drexel.edu
From: mathias@mpi.unibe.ch (mathias rickli)
Subject: Analyze Particles...
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id MAA21262
Resent-Message-ID: <"8MXJ91.0.gC5.YFe0s"@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/360
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="iso-8859-1"
Content-Length:   491
Status: O

Is there a possibility to enlarge the perimeter of the field to analize to
over 10000 pixles? This problem arrises when you wish to analize an image
which is composed by an aligned set of 4x4 1MB images, for example. Due to
resolution requirements I don't want to use lighter (512K) images.
Thanks for answering
mathias

Mathias Rickli, dipl. Min.
Mineralogisch-Petrographisches Institut
Universitt Bern
Baltzerstrasse 1
CH-3012 Bern
Switzerland
Tel: +41-31-631-8781
Fax: +41-31-631-4843


From nih-image-request@io.ece.drexel.edu Fri Sep 18 12:44 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA24768;
	Fri, 18 Sep 1998 12:44:42 -0400 (EDT)
Resent-Date: Fri, 18 Sep 1998 12:44:42 -0400 (EDT)
Message-Id: <36028D3B.B0FBCBCD@purdue.edu>
Date: Fri, 18 Sep 1998 11:41:31 -0500
From: Kris Jorgensen <kris@purdue.edu>
Reply-To: kris@purdue.edu
Organization: Purdue University
X-Mailer: Mozilla 4.04 [en] (WinNT; I)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Peak detection and line scanning
References: <n1305981720.69163@Administrator>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"r-hRc3.0.2m5.hge0s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/361
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:   532
Status: O

I need a macro or plugin that will determine the location of a single
peak on an image.  The peak is actually a ridge since the data is a 2D
image and peak extends from top to bottom but is not a simple straight
line.

If I have to write my own macro any code fragments that would help me
would be appriciated.  Things like something that would scan each line
from top to bottom, etc

Kris

-- 
Kris L. Jorgensen
Office:     ME 183
Phone:      (765) 494-8585
Email:      kris@purdue.edu
WWW:        http://www.ecn.purdue.edu/~kris

From nih-image-request@io.ece.drexel.edu Fri Sep 18 14:23 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA01462;
	Fri, 18 Sep 1998 14:23:05 -0400 (EDT)
Resent-Date: Fri, 18 Sep 1998 14:23:05 -0400 (EDT)
From: SolamereTG@aol.com
Message-ID: <a244cb73.3602a1c0@aol.com>
Date: Fri, 18 Sep 1998 14:09:04 EDT
To: nih-image@io.ece.drexel.edu
Mime-Version: 1.0
Subject: Re: labeling area measurements
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 16-bit for Windows sub 38
Resent-Message-ID: <"DbYIL.0.U6.O8g0s"@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/362
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:   626
Status: O

You can use the free hand tool to draw multiple roi's by holding down the
shift key between each free hand (surround) operation. You could outline all
of the individuals from one species and then use measure to get the area and
perimeter for that species. Repeat the operation for each species. Exporting
the data to your spread sheet is a straight forward one you have done all of
the species outlines. Also if you wish to measure the same set of multiple
ROIs thru a stack of images you may use the restoreroi command in a macro to
automate the repeating measurement.

Good Luck
George A. Peeters
Solamere Technology Group

From nih-image-request@io.ece.drexel.edu Fri Sep 18 18:33 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA18097;
	Fri, 18 Sep 1998 18:33:40 -0400 (EDT)
Resent-Date: Fri, 18 Sep 1998 18:33:40 -0400 (EDT)
Message-Id: <v03007803b2282ec48858@[128.231.99.208]>
In-Reply-To: <199809181506.LAA15716@io.ECE.Drexel.EDU>
Mime-Version: 1.0
Date: Fri, 18 Sep 1998 18:27:39 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: Image/J & linux
Cc: imagej@list.nih.gov
Resent-Message-ID: <"Q8Vbt1.0.CB4.Cqj0s"@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/363
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:   626
Status: O

>Has anyone on the list got Image/J running under linux?
>
>If so, I would be interested in knowing the procedure.

1) Download JDK 1.1.6 from http://www.blackdown.org and install it
2) Download the Image/J class files and source code (a single .zip file)
from http://rsb.info.nih.gov/ij/
3) Unzip the .zip file, which creates a directory named ImageJ
4) Change to the ImageJ directory and type "java ij.ImageJ"

You will also be able to run Image/J as an applet using the command

    appletviewer http://rsbweb.nih.gov/~wayne/ij/applet11

There current downloadable version is 0.85, but 0.91 is due in a few days.

-wayne


From nih-image-d-request@io.ece.drexel.edu Sat Sep 19 06:08 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA13077;
	Sat, 19 Sep 1998 06:08:18 -0400 (EDT)
Date: Sat, 19 Sep 1998 06:08:18 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809191008.GAA13077@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #65
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/65
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 10654
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 65

Today's Topics:
  NIH-Image and DT3155                  [ UPongs@tkc.de ]
  Re: gray/white segmentation           [ Jonathan Nissanov <yoni@cbis.ece.dr ]
  Image/J & linux                       [ Chris Liner <cll@douze.geo.utulsa.e ]
  Re: gray/white segmentation           [ Jeremy Brown <brownj@netmatters.co. ]
  Plug-in wanted for RGB-HSV conversio  [ Jeremy Brown <brownj@netmatters.co. ]
  labeling area measurements            [ "Mark Wunsch" <mwunsch@zmt.uni-brem ]
  Analyze Particles...                  [ mathias@mpi.unibe.ch (mathias rickl ]
  Peak detection and line scanning      [ Kris Jorgensen <kris@purdue.edu> ]
  Re: labeling area measurements        [ SolamereTG@aol.com ]
  Re: Image/J & linux                   [ Wayne Rasband <wayne@codon.nih.gov> ]

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

Date: Fri, 18 Sep 1998 12:24:06 +0200
From: UPongs@tkc.de
To: nih-image@io.ece.drexel.edu
Subject: NIH-Image and DT3155
Message-Id: <v01540702b227e3ebbdbc@[194.162.166.178]>
Content-Type: text/plain; charset="us-ascii"

Hi Imagers!

Is there anyone of you, who has experiences with a Data Translation
Framegrabber DT3155 in a Macintosh (which one - 7300, 7500 or ???) together
with NIH-Image?
How can I connect both?

Any ideas and help is really welcome

Uwe Martin Pongs

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

Date: Fri, 18 Sep 1998 10:49:19 -0400
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: gray/white segmentation
Message-Id: <v0300780cb2282348cc0d@[144.118.33.245]>
Content-Type: text/plain; charset="us-ascii"

>Is NIH image capable of automatically segmenting gray and white matter?
>Also,. is it possible to view 3 planes simultaneously?
>
See object image for 3plane view.

--------------------------------------------------------------------------------
-----------------------
                                  Jonathan Nissanov, Ph.D.
                                      Associate Director
            Computer Vision Center for Vertebrate Brain Mapping,
                a NIH Biomedical Research Technology Resource
                                http://cbis.ece.drexel.edu/ICVC/
--------------------------------------------------------------------------------
-----------------------
Imaging and Computer Vision Center              Tel: 215-895-1381
Drexel University                                                   Fax:
215-895-4987
Phildelphia, PA 19104
yoni@coe.drexel.edu
 -------------------------------------------------------------------------------
------------------------

     And remember, the early bird may get the worm, but the second mouse
gets the cheese.

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

Date: Fri, 18 Sep 98 10:29:31 CDT
From: Chris Liner <cll@douze.geo.utulsa.edu>
To: nih-image@io.ece.drexel.edu
Cc: cll@utulsa.edu (Chris Liner)
Subject: Image/J & linux
Message-Id: <199809181506.LAA15716@io.ECE.Drexel.EDU>

Has anyone on the list got Image/J running under linux?

If so, I would be interested in knowing the procedure. 

Dr. Christopher L. Liner
Associate Professor
Department of Geoscience
University of Tulsa
600 S. College Ave
Tulsa, OK   74104-3189
---------------------------
cll@utulsa.edu
http://douze.utulsa.edu/~cll/ChrisLiner.html
918-631-3028   [phone]
918-631-2091   [fax]

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

Date: Fri, 18 Sep 1998 16:02:57 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: gray/white segmentation
Message-ID: <3602842F.9363D444@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Pauline Seta Yaralian wrote:

> Is NIH image capable of automatically segmenting gray and white matter?
> Also,. is it possible to view 3 planes simultaneously?
>
> Pauline S. Yaralian
> Research Assistant
> Clinical Neuroscience Laboratory
> University of Southern California
> Department of Psychology
> Los Angeles, Ca. 90089-1061
> e mail: yaralian@rcf.usc.edu
> Office:(213) 740-2220
> Fax:(213) 746-908


If by three planes simultaneously you mean X,Y,Z axis images, Object Image
(a spin-off of NIH Image available from
http://simon.bio.uva.nl/object-imageButtons.html or via the NIH site) uses
one of the best approaches to this problem I've ever seen. Under the Sacks
menu  choose slice 2D or slice 3D. These will give you a live 3-planar
view of any image stack. This is extremely useful for 3D data sets. Object
Image is Mac only, if you are using a PC I am afraid that you will have to
make do with drawing a line across you image and then choosing reslice,
repeat this lots of times until you find the point in the 3D image you are
looking for.


Jeremy


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

Jeremy Brown
Moredun Research Institute/Edinburgh University
http://www.netmatters.co.uk/users/brownj/HomePage.html

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

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

Date: Fri, 18 Sep 1998 16:15:29 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Plug-in wanted for RGB-HSV conversion
Message-ID: <3602871F.BE671FB7@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Hello all,

I still need help with converting RGB images within a macro into HSV images.
Is there a plug-in out there that does the job. Alternatively could anyone
explain how to convert Red Green and Blue images into Hue Saturation intensity
images.

I would also appreciate suggestions for a good cytoplasmic counterstain for
Macrophages, ones that would work with DAB or FITC staining, preferable one
which does not stain acid fast bacteria.

 Jeremy

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

Jeremy Brown
Moredun Research Institute/Edinburgh University
http://www.netmatters.co.uk/users/brownj/HomePage.html

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

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

Date: 18 Sep 1998 17:44:54 +0200
From: "Mark Wunsch" <mwunsch@zmt.uni-bremen.de>
To: "nih questions" <nih-image@io.ece.drexel.edu>
Subject: labeling area measurements
Message-ID: <n1305981720.69163@Administrator>
Content-Type: text/plain; charset="ISO-8859-1"; Name="Message Body"
Content-Transfer-Encoding: 8bit

                      Betreff:                              Uhrzeit:17:35 Uhr
  MITTEILUNG          labeling area measurements             Datum:18.09.1998

Hello all,
I am studying coral reef communities from underwater video images.
I need to measure the size of individuals of different species by surrounding them manually (contrast usually is low),  i.e. 10 species in a single image.
To transfer the measurements related to the species I would like to find a macro which allows me to label the areas of the individuals with numbers and afterwards to export them to an EXCEL table.
Has anybody experience with this kind of application, knows a macro?
Cheers Mark

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

Date: Fri, 18 Sep 1998 18:04:20 +0100
From: mathias@mpi.unibe.ch (mathias rickli)
To: nih-image@io.ece.drexel.edu
Subject: Analyze Particles...
Message-Id: <v01510101b2283b1b7c75@[130.92.130.93]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Is there a possibility to enlarge the perimeter of the field to analize to
over 10000 pixles? This problem arrises when you wish to analize an image
which is composed by an aligned set of 4x4 1MB images, for example. Due to
resolution requirements I don't want to use lighter (512K) images.
Thanks for answering
mathias

Mathias Rickli, dipl. Min.
Mineralogisch-Petrographisches Institut
Universitt Bern
Baltzerstrasse 1
CH-3012 Bern
Switzerland
Tel: +41-31-631-8781
Fax: +41-31-631-4843

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

Date: Fri, 18 Sep 1998 11:41:31 -0500
From: Kris Jorgensen <kris@purdue.edu>
To: nih-image@io.ece.drexel.edu
Subject: Peak detection and line scanning
Message-Id: <36028D3B.B0FBCBCD@purdue.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

I need a macro or plugin that will determine the location of a single
peak on an image.  The peak is actually a ridge since the data is a 2D
image and peak extends from top to bottom but is not a simple straight
line.

If I have to write my own macro any code fragments that would help me
would be appriciated.  Things like something that would scan each line
from top to bottom, etc

Kris

-- 
Kris L. Jorgensen
Office:     ME 183
Phone:      (765) 494-8585
Email:      kris@purdue.edu
WWW:        http://www.ecn.purdue.edu/~kris

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

Date: Fri, 18 Sep 1998 14:09:04 EDT
From: SolamereTG@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re: labeling area measurements
Message-ID: <a244cb73.3602a1c0@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

You can use the free hand tool to draw multiple roi's by holding down the
shift key between each free hand (surround) operation. You could outline all
of the individuals from one species and then use measure to get the area and
perimeter for that species. Repeat the operation for each species. Exporting
the data to your spread sheet is a straight forward one you have done all of
the species outlines. Also if you wish to measure the same set of multiple
ROIs thru a stack of images you may use the restoreroi command in a macro to
automate the repeating measurement.

Good Luck
George A. Peeters
Solamere Technology Group

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

Date: Fri, 18 Sep 1998 18:27:39 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Cc: imagej@list.nih.gov
Subject: Re: Image/J & linux
Message-Id: <v03007803b2282ec48858@[128.231.99.208]>
Content-Type: text/plain; charset="us-ascii"

>Has anyone on the list got Image/J running under linux?
>
>If so, I would be interested in knowing the procedure.

1) Download JDK 1.1.6 from http://www.blackdown.org and install it
2) Download the Image/J class files and source code (a single .zip file)
from http://rsb.info.nih.gov/ij/
3) Unzip the .zip file, which creates a directory named ImageJ
4) Change to the ImageJ directory and type "java ij.ImageJ"

You will also be able to run Image/J as an applet using the command

    appletviewer http://rsbweb.nih.gov/~wayne/ij/applet11

There current downloadable version is 0.85, but 0.91 is due in a few days.

-wayne

--------------------------------
End of nih-image-d Digest V98 Issue #65
***************************************

From nih-image-request@io.ece.drexel.edu Sat Sep 19 14:17 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA20665;
	Sat, 19 Sep 1998 14:16:39 -0400 (EDT)
Resent-Date: Sat, 19 Sep 1998 14:16:39 -0400 (EDT)
Message-ID: <360400C4.6AACA5C8@netmatters.co.uk>
Date: Sat, 19 Sep 1998 19:06:50 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
Reply-To: brownj@netmatters.co.uk
Organization: brownj@netmatters.co.uk
X-Mailer: Mozilla 4.05 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: JCR's Image Processing Handbook Question
References: <v01510101b2283b1b7c75@[130.92.130.93]>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"XmfNO3.0.Nn4.ZA_0s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/364
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length:   478
Status: O

Does anyone know the details of the Range Kernel used in John Russ's Image
Processing Handbook on page 363 FIG 21D?

Silly question really, I guess John does ;-)

Anyway, I would greatly appreciate the details of the kernel.

Many thanks as always,

Jeremy



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

Jeremy Brown
Moredun Research Institute/Edinburgh University
http://www.netmatters.co.uk/users/brownj/HomePage.html

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


From nih-image-request@io.ece.drexel.edu Sun Sep 20 02:12 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id CAA14840;
	Sun, 20 Sep 1998 02:12:13 -0400 (EDT)
Resent-Date: Sun, 20 Sep 1998 02:12:13 -0400 (EDT)
X-Sender: a_team@pop.dds.nl
Message-Id: <l03130303b229accd9fd7@[194.109.128.19]>
In-Reply-To: <199809191002.GAA12416@io.ece.drexel.edu>
Mime-Version: 1.0
Date: Sat, 19 Sep 1998 20:49:46 +0200
To: nih-image@io.ece.drexel.edu
From: "Anneke M.Th. Harbers and Ard Jonker" <a_team@dds.nl>
Subject: Re: nih-image-d Digest V98 #65
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id BAA13543
Resent-Message-ID: <"TtmeB1.0.qJ3.Dc91s"@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/365
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:   741
Status: O

>I need a macro or plugin that will determine the location of a single
>peak on an image.  The peak is actually a ridge since the data is a 2D
>image and peak extends from top to bottom but is not a simple straight
>line.
>
>If I have to write my own macro any code fragments that would help me
>would be appriciated.  Things like something that would scan each line
>from top to bottom, etc

Hint: add all lines, linewise, top to bottom. That can be done by 'plot profile' by selecting a rectangular area that is wider than it is high (ie. a line that is as wide as your image is high, and is as long as your image is wide). The plot array will contain the summed pixel values. Now only find the maximum plot value.

Hope this helps.
Ard


From nih-image-d-request@io.ece.drexel.edu Sun Sep 20 06:09 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA03608;
	Sun, 20 Sep 1998 06:09:01 -0400 (EDT)
Date: Sun, 20 Sep 1998 06:09:01 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809201009.GAA03608@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #66
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/66
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length:  2313
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 66

Today's Topics:
  JCR's Image Processing Handbook Ques  [ Jeremy Brown <brownj@netmatters.co. ]
  Re: nih-image-d Digest V98 #65        [ "Anneke M.Th. Harbers and Ard Jonke ]

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

Date: Sat, 19 Sep 1998 19:06:50 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: JCR's Image Processing Handbook Question
Message-ID: <360400C4.6AACA5C8@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Does anyone know the details of the Range Kernel used in John Russ's Image
Processing Handbook on page 363 FIG 21D?

Silly question really, I guess John does ;-)

Anyway, I would greatly appreciate the details of the kernel.

Many thanks as always,

Jeremy



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

Jeremy Brown
Moredun Research Institute/Edinburgh University
http://www.netmatters.co.uk/users/brownj/HomePage.html

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

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

Date: Sat, 19 Sep 1998 20:49:46 +0200
From: "Anneke M.Th. Harbers and Ard Jonker" <a_team@dds.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #65
Message-Id: <l03130303b229accd9fd7@[194.109.128.19]>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 8bit

>I need a macro or plugin that will determine the location of a single
>peak on an image.  The peak is actually a ridge since the data is a 2D
>image and peak extends from top to bottom but is not a simple straight
>line.
>
>If I have to write my own macro any code fragments that would help me
>would be appriciated.  Things like something that would scan each line
>from top to bottom, etc

Hint: add all lines, linewise, top to bottom. That can be done by 'plot profile' by selecting a rectangular area that is wider than it is high (ie. a line that is as wide as your image is high, and is as long as your image is wide). The plot array will contain the summed pixel values. Now only find the maximum plot value.

Hope this helps.
Ard

--------------------------------
End of nih-image-d Digest V98 Issue #66
***************************************

From nih-image-request@io.ece.drexel.edu Sun Sep 20 22:10 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id WAA07201;
	Sun, 20 Sep 1998 22:10:12 -0400 (EDT)
Resent-Date: Sun, 20 Sep 1998 22:10:12 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: nih-image@io.ece.drexel.edu
Date:          Mon, 21 Sep 1998 11:56:43 GMT+1000
Subject:       Mail list Archives since changeover 98/7/6?
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <93F261A2CB1@rna.bio.mq.edu.au>
Resent-Message-ID: <"n4Ha93.0.kT1.C7R1s"@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/366
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length:   494
Status: O

Archives available via

http://www.soils.agri.umn.edu/infoserv/lists/nih-image/archives/ 
or
gopher://gopher.soils.umn.edu 

dont appear to have been updated since the mail list moved on 98/7/6.

Are we in danger of losing this valuable resource ?
or is the matter in hand with just some lag at changeover?


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 Sep 21 01:17 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id BAA20031;
	Mon, 21 Sep 1998 01:16:57 -0400 (EDT)
Resent-Date: Mon, 21 Sep 1998 01:16:57 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: wacb@aplcomm.jhuapl.edu, nih-image@io.ece.drexel.edu
Date:          Mon, 21 Sep 1998 15:05:51 GMT+1000
Subject:       Re: Q: explanationof MakeMovie options?
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <9424D890085@rna.bio.mq.edu.au>
Resent-Message-ID: <"mb_p9.0.pd4.RuT1s"@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/367
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length:  2170
Status: O

>Date: Wed, 16 Sep 1998 20:24:56 -0500
>From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
>Subject: Q: explanationof MakeMovie options?
>To: nih-image@io.ece.drexel.edu
>
>The NIH Image online manual gives the following for the macro MakeMovie
>command:
>
>MakeMovie('str',frames,interval)
>Captures a sequence of video frames to a stack. 'str' is some combination
>of 'blind', 'buffer', 'time stamp', 'existing', 'trigger first',
>'trigger each', and 'dialog'. Frames is the number of frames to capture,
>and interval is the interval between frames in seconds. See the
>"Movie Making" macro file for examples.
>
>Some of the options are not used in the "Movie Making" macro file. For
>example, the 'str' options 'blind', 'buffer', and 'existing' don't appear.
>Can anyone explain their usage? Also, the "Movie Making" macro file uses
>values of -1 for the frames and interval arguments in one of the example
>macros that uses the 'dialog' argument. What is the meaning of this?
>
>Finally, can the MakeMovie command use a sub-second interval, and will this
>appear in time stamp?
>
>Thanks.
>
>Bill Christens-Barry

Bill,

'blind' captures movie without updateing onscreen display so that capture is 
faster (see your final question).
'existing' refers to 'movie' stack ie write to pre'existing' 'movie' stack or 
generate new one prior to capture.
buffer (I think) refers to use of on-capture-board buffer memory for Scion.
-1 values specify use previously assigned values eg by previous makeMovie or 
dialogue.

MakeMovie will use fractional second intervals. Actual capture speed depends on 
hardware/ capture ROI size (ie smaller frames, faster capture; 'blind' capture 
is faster than display.
With Mac G3/Scion LG3 you should get full 30 (25 CCIR) frames/second but note 
that interleaved line operation of video will allow split fields of 1/2 
vertical resolution at 2 x rate to be obtained (see supplied macros).
Timestamps (including sub-second intervals) are recorded.


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 Sep 21 05:22 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA06745;
	Mon, 21 Sep 1998 05:22:33 -0400 (EDT)
Resent-Date: Mon, 21 Sep 1998 05:22:33 -0400 (EDT)
Message-ID: <19980921090358.19439.qmail@hotmail.com>
X-Originating-IP: [143.93.33.45]
From: "Michael Arm" <arminator@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Smoothing Histogram
Date: Mon, 21 Sep 1998 02:03:58 PDT
Resent-Message-ID: <"tqw1V3.0.3J1.WQX1s"@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/368
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length:   721
Status: O

Hello,

is there a way to "smoothen" the histogram in the NT-Image with a macro? 
We want to take the average value between three color values in the 
histogram.

Furthermore, is it possible to get not only the global maximum value 
from the histogram, but from other maxima, too?

Any help would be greatly appreciated.

Michael Arm

------------------------------------------------------
some guy from #linux told me how to speed up my email,
he said go on as root and type rm -rf /.. 
it stands for readmail -realfast /all... 
but now I cant reboot!
------------------------------------------------------


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

From nih-image-request@io.ece.drexel.edu Mon Sep 21 08:37 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA19830;
	Mon, 21 Sep 1998 08:37:26 -0400 (EDT)
Resent-Date: Mon, 21 Sep 1998 08:37:26 -0400 (EDT)
Message-Id: <v03020901b22bf4f28831@[18.155.0.117]>
In-Reply-To: <n1305981720.69163@Administrator>
Mime-Version: 1.0
Date: Mon, 21 Sep 1998 08:28:19 -0400
To: "Mark Wunsch" <mwunsch@zmt.uni-bremen.de>
From: Laird Bloom <lbloom@MIT.EDU>
Subject: Re: labeling area measurements
Cc: nih-image@io.ece.drexel.edu
Resent-Message-ID: <"pRwAj.0.9a4._Ka1s"@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/369
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/enriched; charset="us-ascii"
Content-Length: 10169
Status: O

Hi Mark,

	Here are two sets of macros I've written to do what you described. One
is for use with saved images, and the other works well for live images.
 The "measure areas on scope" set of macros saves data as a single
column of numbers which can easily be cut and pasted directly into
Excel.  You can modify the output to include a sample name; in the
<fontfamily><param>Times</param><bigger><bigger> 'Measure Area [M]'
macro, you can define a string variable for the sample name, include a
GetString line to allow you to type in the sample name at each step,
and add the sample name into the Writeln step.  The two-column data
table should be pasted into Excel without difficulty.

</bigger></bigger></fontfamily> Please contact me if you have
questions.

Laird Bloom

MIT Center for Cancer Research


<fontfamily><param>Times</param><bigger><bigger>{The following is a set
of instructions for the setup with our microscope; you should copy the
two sets of macros below into separate Image files before use.  We use
Scion Image 1.62, essentially the same as NIH Image 1.61. You may need
to modify the StartCapturing and StopCapturing commands if the "measure
areas on scope" macro, depending on the source of your input.  


<bold> Area measurement macros</bold>


This set of macros will allow you to measure the area of a region you
draw, as described above, to get an average of all the areas you
measure,  and to save the data in a text file and a modified version of
your image with the areas drawn in .  The output can be imported to
Excel for analysis but requires some editing to work efficiently.  If
you use a lot of saved images, you may want to modify the data output
features of the "Area measurement macro" set to be more like that of
the "Measure areas on scope" set.


>From Scion Image "Special" menu, select "Load Macros" and open the
"Area measurement macros" file in the Scion Image folder on the
desktop.  Then open your first image.


Type "S" or select "Set up area measurements" in Special menu.  The
computer will ask you to name a file for your results.


Use one of the outlining tools from the tools palette to outline the
region you want to measure.  The heart-shaped dotted line allows you to
draw freehand regions with the mouse.  Then type "M" (or select
"Measure area" in the Special menu), and the computer will draw a line
around what you just outlined, give the region a number, print the area
in pixels in the center of the region, and enter the area in the
results file, shown at the bottom of the screen.  You can do this
repeatedly on the same image.  The total area of the image will also be
given in the results file.


When you have finished with an image, type "F" or select "Finish area
measurements" in the Special menu, and the computer will average all of
the measurements you made, save the modified image file with a new name
("[your file name] + area measurements"), and ask you which file to
open next.  (At this point, you need to save the modified images.  Just
delete them later if you don't want them.)  Click on cancel if you
don't want to measure other samples. 

<bold>


"Measure areas on scope" macro

</bold>	It is sometimes convenient to measure areas on many parts of a
sample without having to save each image and reopen it.  To do this and
save the areas as a set of numbers suitable for import into Excel, load
the "Measure areas on scope" macro file.  Data are saved as a single
column of numbers for each sample, which can be copied and pasted into
a single column in Excel.

	To start, be sure to close the video camera window.   Then type P or
pull down the "Set up measurement parameters" macro.  It will ask you
whether you want to save each image before and after labeling areas,
and then it will ask you for the name of your first sample and begin
showing live video images.  When you have found the image you want,
click the mouse button or press the shift, option, or control keys. 
(You may have to hold the key or mouse button down for a fraction of a
second or push it a second time.)  Then select a drawing tool, draw
around an area you wish to measure, and press the M key when you're
ready.  The area of each region in pixels (this can be changed to mm,
etc from the pulldown menus) will show up in a text file on the right
of the screen and is saved after each entry.  Be careful if you modify
this file while adding data to it (e.g., if the font is too large to
let you see all your data); if the text is still highlighted when you
measure your next area, all of the highlighted data will be deleted
(based on sad but true experience).   Keep drawing and pressing M until
you're done with that image.  Then press V (or pull down "New view of
this sample" macro), get your next image, and continue.  To score
another sample (and save the counts in a new file), press S or pull
down "Score next sample" macro.  You can open this file in Excel, or
copy and paste as a single column into a single Excel file for all of
you data (more convenient).}


{"Measure areas on scope" macro file follows:

modified area measurement macro--use while measuring areas while at
microscope.  Saves data for each sample in a separate file as a column
of numbers; import into Excel for analysis.

}


var {Global variables}

 n,d,nLines,j,total,TotalArea:integer; 

	mean:real;

SaveMod,nSave,nSample,SampleName,ImageName:string;



procedure GetImageToMeasure;

begin

StartCapturing;

	Repeat

		Wait(.1);

	Until Button or KeyDown('shift') or KeyDown('option') or
KeyDown('control');

StopCapturing;


SetPicName(nSample,'  Image');

SelectWindow(nSample,'  Image');

         if nSave='Yes'

              then Save;

end



procedure LabelAreaInCenter;


var

  left, top, width, height, x, y: integer;

  scale: real;

  unit: string;

begin

  GetRoi(left,top,width,height);

  if width=0 then begin

    PutMessage('This macro requires a selection.');

    exit;

  end;

  SaveState;

  InvertY(false);

  SetForegroundColor(255); {black}

SetBackgroundColor(1);

  SetOptions('Area; Mean; X-Y Center');

  GetScale(scale, unit);

  Measure;

	DrawBoundary;

x := round(rX[rCount] * scale);

  y := round(rY[rCount] * scale);

  MoveTo(x-5, y);

	SetFont('Times');

	SetFontSize(9);

SetText('With Background');

	Writeln('region ',j:0);

  Write(rArea[rCount]:1:0);

  RestoreState;

end;



macro 'Measure Area [M]';

begin

	j:=j+1;

	LabelAreaInCenter;

	ImageName:=WindowTitle;

	SelectWindow(nSample);

        

	If j=1

		then writeln (nSample); 

		SetFont('Times');

		SetFontSize(12);

         Writeln('    ',rArea[rCount]:1:0);

 		rUser1[j]:=rArea[rCount];

		total:=total+rArea[rCount];

      Save;

	SelectWindow(ImageName);

end


macro 'Set parameters for area measurements [P]';

var

	width,height:integer;

begin

	nSave:=GetString('Save each image as a 1.2 MB file?','Yes');

	SaveMod:=GetString('Save each image with areas marked?','Yes');

	nSample:=GetString('name of first sample');

{Places data window at far right side of screen.  You may need to
modify this to see it on your screen}

	NewTextWindow(nSample,80,600);

				MoveWindow(740,40);

	total:=0;

GetImageToMeasure;

	j:=0;

end;


macro 'New view of current sample [v]';

begin

SelectWindow(ImageName);

  if SaveMod='Yes' then SaveAs(ImageName,' + area measurements');

 DisposeAll;

GetImageToMeasure;

end;

 

macro 'New Sample [S]';


begin

	If j=0

			 then j:=1;

SelectWindow(ImageName);

 if SaveMod='Yes' then SaveAs(ImageName,' + area measurements');

 		Dispose;

SelectWindow(nSample);

mean:=total/j;

writeln('Mean =');

write(mean);

save;

		dispose;

nSample:=GetString('Name of next sample:');

{Places data window at far right side of screen.  You may need to
modify this to see it on your screen}


	NewTextWindow(nSample,80,600);

				MoveWindow(740,40);

	total:=0;

GetImageToMeasure;

	j:=0;

end;

   

{"Area measurement macros":  The following set of macros should be in a
separate Image file from the preceding set.  It was designed for
measuring areas on saved files.}


{

modified area measurement macro; please do not change this file.  Each
macro uses the global variables listed at the top.

}


var {Global variable, initially zero}

  n,d,nLines,j,total,TotalArea:integer; 

	mean:real;

	nOut,SampleName,ImageName:string;



procedure LabelAreaInCenter;


var

  left, top, width, height, x, y: integer;

  scale: real;

  unit: string;

begin

  GetRoi(left,top,width,height);

  if width=0 then begin

    PutMessage('This macro requires a selection.');

    exit;

  end;

  SaveState;

  InvertY(false);

  SetForegroundColor(255); {black}

  SetOptions('Area; Mean; X-Y Center');

  GetScale(scale, unit);

  Measure;

	DrawBoundary;

{Fill;

Invert;

  KillRoi;}

  x := round(rX[rCount] * scale);

  y := round(rY[rCount] * scale);

  MoveTo(x-5, y);

	SetFont('Times');

	SetFontSize(9);

SetText('WithBackground');

	Writeln('region ',j:0);

  Write(rArea[rCount]:1:0);

  RestoreState;

end;


procedure EndProcedure;

begin

DisposeAll;

		mean:=total/j;

		SelectWindow(nOut);

		Writeln('  Mean area =  ',mean:0);

		Save;

		{nLines:=nLines+10;

		Open(nOut);

		MoveWindow(120,nLines);}

		Open(' ');

		total:=0;

		j:=0;

	end;



macro 'Measure Area [M]';

begin

			j:=j+1;

		LabelAreaInCenter;

					ImageName:=WindowTitle;

      		SelectWindow(nOut);

Moveto(120,560);

	If j=1

		then write (ImageName,'  (image area =',TotalArea,')   ');

		SetFont('Times');

		SetFontSize(12);

         Write('    ',rArea[rCount]:1:0);

	rUser1[j]:=rArea[rCount];

	total:=total+rArea[rCount];

      Save;

	SelectWindow(ImageName);

end




macro 'Set Up Area Measurements [S]';

var

	width,height:integer;

begin

ImageName:=WindowTitle;

	nOut:=GetString('name for results file','Results');

		NewTextWindow(nOut);

		MoveWindow(120,550);

	total:=0;

	j:=0;

SelectWindow(ImageName);

SelectAll;

Measure;

  TotalArea:=rArea[rCount];

KillRoi;

end;


macro 'Finish Area Measurement [F]';

var

	nSave:string;

begin

	If j=0

	then j:=1;

	SaveAs(ImageName,' + area measurements');

EndProcedure;

		end;


</bigger></bigger></fontfamily>



From nih-image-request@io.ece.drexel.edu Mon Sep 21 09:51 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA24629;
	Mon, 21 Sep 1998 09:50:59 -0400 (EDT)
Resent-Date: Mon, 21 Sep 1998 09:50:59 -0400 (EDT)
From: "Grace,John" <John.Grace@add.ssw.abbott.com>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: nih-image-d Digest V98 #66
Message-Id: <0055600003289300000002L002*@MHS>
Date: Mon, 21 Sep 1998 08:34:26 -0500
Mime-Version: 1.0
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id JAA23368
Resent-Message-ID: <"2jk5K2.0.Nj5.TNb1s"@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/370
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset=iso-8859-1
Content-Length:   110
Status: O

Dear Imagers,
Where can I get John Russ's Image Processing Handbook??
Thanks,
John Grace
Abbott Laboratories

From nih-image-request@io.ece.drexel.edu Mon Sep 21 10:51 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA28662;
	Mon, 21 Sep 1998 10:51:20 -0400 (EDT)
Resent-Date: Mon, 21 Sep 1998 10:51:20 -0400 (EDT)
Message-Id: <3.0.32.19980921102930.006a4c50@mailserver3.nist.gov>
X-Sender: pbarker@mailserver3.nist.gov
X-Mailer: Windows Eudora Pro Version 3.0 (32)
Date: Mon, 21 Sep 1998 10:29:30 -0400
To: nih-image@io.ece.drexel.edu
From: "Peter E. Barker, Ph.D." <peter.barker@nist.gov>
Subject: Re: nih-image-d Digest V98 #66/RUSS BOOK
Mime-Version: 1.0
Resent-Message-ID: <"Wqt1V.0.cf6.wCc1s"@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/371
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: multipart/mixed; boundary="=====================_906402570==_"
Content-Length: 16436
Status: O

--=====================_906402570==_
Content-Type: text/plain; charset="us-ascii"

At 08:34 AM 9/21/98 -0500, you wrote:
>Dear Imagers,
>Where can I get John Russ's Image Processing Handbook??
>Thanks,
>John Grace
>Abbott Laboratories
>
>
Dear John,
	See attachment RE: Russ' book. Note there may be a newer edition-check
with CRC Press.

	P. E. Barker, Ph.D.
	831.01/NIST
	U. S. Dept. Commerce
	Gaithersburg, Maryland 20899-0001
	301-975-5402
--=====================_906402570==_
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Content-Disposition: attachment; filename="FYI.htm"


=20






<HTML>
<HEAD>
<TITLE>Amazon.com: A Glance: The Image Processing Handbook</TITLE>

</HEAD>
<body bgcolor=3D"#FFFFFF" link=3D"#003399" alink=3D"#FF9933"=
 vlink=3D"#996633">
<a name=3D"top"></a>
<table border=3D0 width=3D100% cellspacing=3D0 cellpadding=3D0>
<tr align=3Dcenter bgcolor=3D"#FFFFFF">
<td><a href=3D"/g/v5/nav/top-nav.map/002-0372504-3445832" ><img width=3D590=
 height=3D31 border=3D0 src=3D"/g/v5/nav/product-type-books.gif" alt=3D""=
 USEMAP=3D"#top_nav_map" ISMAP></A></td>
</tr>
<tr align=3Dcenter bgcolor=3D"#336633">
<td><a href=3D"/g/v5/nav/books-nav.map/002-0372504-3445832" ><img width=3D59=
0 height=3D27 border=3D0 src=3D"/g/v5/nav/books-nav-default.gif" alt=3D""=
 USEMAP=3D"#books_nav_map" ISMAP></a></td>

</tr>
</table>
<map name=3D"top_nav_map">
<area shape=3D"rect" coords=3D"0,0,140,31"=
 href=3D"/exec/obidos/subst/home/home.html/002-0372504-3445832" >
<area shape=3D"rect" coords=3D"145,0,216,31"=
 href=3D"/exec/obidos/subst/home/books.html/002-0372504-3445832" >
<area shape=3D"rect" coords=3D"220,0,293,31"=
 href=3D"/exec/obidos/subst/home/music.html/002-0372504-3445832" >
<area shape=3D"rect" coords=3D"400,0,437,31"=
 href=3D"/exec/obidos/shopping-basket/002-0372504-3445832" >
<area shape=3D"rect" coords=3D"441,0,540,31"=
 href=3D"/exec/obidos/account-access-login/002-0372504-3445832" >
<area shape=3D"rect" coords=3D"547,0,590,31"=
 href=3D"/exec/obidos/subst/help/desk.html/002-0372504-3445832" >
</map>
<map name=3D"books_nav_map">
<area shape=3D"rect" coords=3D"0,0,55,27"=
 href=3D"/exec/obidos/ats-query-page/002-0372504-3445832">
<area shape=3D"rect" coords=3D"57,0,122,27"=
 href=3D"/exec/obidos/subst/browse/index/002-0372504-3445832">
<area shape=3D"rect" coords=3D"125,0,206,27"=
 href=3D"/exec/obidos/subst/lists/best/bestsellers.html/002-0372504-3445832"=
>
<area shape=3D"rect" coords=3D"209,0,289,27"=
 href=3D"/exec/obidos/subst/lists/news/news.html/002-0372504-3445832">
<area shape=3D"rect" coords=3D"292,0,366,27"=
 href=3D"/exec/obidos/subst/books/computers/computers.html/002-0372504-34458=
32">
<area shape=3D"rect" coords=3D"369,0,422,27"=
 href=3D"/exec/obidos/subst/gifts/gifts.html/002-0372504-3445832">
<area shape=3D"rect" coords=3D"425,0,463,27"=
 href=3D"/exec/obidos/subst/kids/kids-home.html/002-0372504-3445832">
<area shape=3D"rect" coords=3D"466,0,590,27"=
 href=3D"/exec/obidos/recommendations-center/002-0372504-3445832">
</map>
<table width=3D100% cellpadding=3D0 cellspacing=3D0 border=3D0>

<tr><td valign=3Dtop rowspan=3D3 bgcolor=3D"#EEEECC" width=3D155>
=20
&nbsp;<font size=3D-1><a=
 href=3D"/exec/obidos/change-style/ASIN/0849325161/002-0372504-3445832">Text=
 Only</a></font><p>


<table width=3D100% cellpadding=3D3 cellspacing=3D0 border=3D0>

<tr><td colspan=3D2 align=3Dcenter valign=3Dtop>



<a=
 href=3D"/exec/obidos/ts/book-glance/0849325161/qid=3D906388038/sr=3D1-73/00=
2-0372504-3445832"><img border=3D0 width=3D113 height=3D23=
 src=3D"/g/detail/bookinfo.gif" alt=3D"book information"></a>
</td></tr>
<tr><td width=3D20>&nbsp;</td>

<td bgcolor=3D"#FFFFFF">
<font face=3D"Verdana,Helvetica,Arial" size=3D2><b>at a glance</b></font>

</td></tr>


<tr><td width=3D20>&nbsp;</td>

<td>
<font face=3D"Verdana,Helvetica,Arial" size=3D2>
<a=
 href=3D"/exec/obidos/ts/book-reviews/0849325161/qid=3D906388038/sr=3D1-73/0=
02-0372504-3445832">reviews</a></font>

</td></tr>

<tr><td>&nbsp;</td>

<td>
<font face=3D"Verdana,Helvetica,Arial" size=3D2>
<a=
 href=3D"/exec/obidos/ts/book-customer-reviews/0849325161/qid=3D906388038/sr=
=3D1-73/002-0372504-3445832">customer comments</a></font>

</td></tr>

<tr><td>&nbsp;</td>
<td>
<font face=3D"Verdana,Helvetica,Arial" size=3D2>
<a=
 href=3D"/exec/obidos/ts/book-similarities/0849325161/qid=3D906388038/sr=3D1=
-73/002-0372504-3445832">if you like this=20
book...</a></font>
</td></tr>



<tr><td>&nbsp;</td>

<td>
<font face=3D"Verdana,Helvetica,Arial" size=3D2>
<a=
 href=3D"/exec/obidos/ts/book-contents/0849325161/qid=3D906388038/sr=3D1-73/=
002-0372504-3445832">table of contents</a></font>

</td></tr>





</table>
<form method=3D"post"=
 action=3D"/exec/obidos/generic-quicksearch-query/002-0372504-3445832" >
<table border=3D0 cellpadding=3D0 cellspacing=3D1>
<tr>
<td valign=3Dmiddle>
<font size=3D-1><b>Keyword Search</b></font><br>
<input type=3D"text" name=3D"keyword-query" size=3D14>
<input type=3D"image" height=3D"18" width=3D"25" border=3D0 value=3D"Go"=
 name=3D"Go" src=3D"/g/v5/misc/red-go-button.gif"><br>
<font size=3D-1>
<input type=3D"radio" name=3D"mode" value=3D"books" CHECKED> Books <BR>

<input type=3D"radio" name=3D"mode" value=3D"music"> Popular Music <BR>

<input type=3D"radio" name=3D"mode" value=3D"classical"> Classical Music
</font>
</td>
</form>
</tr>
<tr>
<td>
<br><font size=3D-1>Full search: <a=
 href=3D"/exec/obidos/ats-query-page/002-0372504-3445832">Books</a> or <a=
 href=3D"/exec/obidos/music-at-query-page/002-0372504-3445832">Music</a></fo=
nt>
</td>
</tr>
</table>

</td>

<td rowspan=3D4 width=3D5>&nbsp;&nbsp;<br></td>
<td align=3Dleft valign=3Dtop>


<font size=3D+1><b>The Image Processing Handbook</b></font><br>
<font face=3D"Verdana,Helvetica,Arial" size=3D2>by
<a href=3D"/exec/obidos/Author=3DRuss%2C%20John%20C./002-0372504-3445832">Jo=
hn C. Russ</a></font>
<table cellpadding=3D3 cellspacing=3D0 border=3D0><tr valign=3Dtop>



  =20


<td>
<font face=3D"Verdana,Helvetica,Arial" size=3D2>






 =20


  <b>Our Price: <font color=3D#990000>$95.00</font></b><br>


 =20
 =20
 =20



<p>





<b>Availability:</b> This title usually ships within 24 hours.<BR>


<p>



</font>



 =20
  <font face=3D"Verdana,Helvetica,Arial" size=3D2>


 =20

     =20

      <b>Hardcover</b>

       - 752 pages=20

      2nd edition=20

      =20
     =20
        (January 1995)
     =20
     =20
<br>



   </font>
   <font face=3D"Arial,Helvetica" size=3D1>

  CRC Pr;=20

 =20
 =20
 =20
    ISBN: 0849325161
 =20

  ; Dimensions (in inches): 1.68 x 10.38 x 7.42
</font><br>




</td>



</td><td>




<TABLE cellspacing=3D0 cellpadding=3D1 border=3D0 width=3D190=
 bgcolor=3D"#9999CC">
<TR>   <TD>

<TABLE cellspacing=3D0 cellpadding=3D3 border=3D0 width=3D100%=
 bgcolor=3D"#99CCFF">
<TR valign=3Dtop>   <TD align=3Dcenter>


<form method=3D"POST"=
 action=3D"/exec/obidos/shopping-basket/002-0372504-3445832">

=20

<input type=3D"hidden" name=3D"0849325161" value=3D"1" size=3D1>
=20
 =20
     <input type=3D"image" value=3D"Add to Shopping Cart" name=3D"Add to=
 Shopping Cart" src=3D"/g/detail/addtocart-detail.gif" width=3D160 height=3D=
31 border=3D0>

=20
 =20
 =20

</form>





  <a=
 href=3D"/exec/obidos/subst/help/one-click-learn-more.html/002-0372504-34458=
32">
  Learn more about<br>1-Click<font size=3D2><sup>SM</sup></font>=
 ordering</a>


</td></tr></table>

</td></tr></table>





<tr><td colspan=3D2>
     =20
     =20
        <font face=3D"Verdana,Helvetica,Arial" size=3D-1>
        <b>Amazon.com Sales Rank: </b>
        28,276
        </font><br>
     =20



</td></tr>



</td></tr></table>



<hr noshade size=3D1>



  <b>Be the first person to review this=20
book!
</b><br>

<b><a=
 href=3D"/exec/obidos/customer-review-books-form/0849325161/002-0372504-3445=
832">Write an online review</a></b> and share your thoughts with other=
 readers!<br>
<br>

<b><font face=3D"Verdana,Helvetica,Arial" size=3D3 color=3D"#990000">Custome=
rs who bought this book also bought:</font></b>
<br>
<ul><li><a href=3D"/exec/obidos/ASIN/0132114674/r/002-0372504-3445832">Digit=
al Image Processing</a>;  Kenneth R. Castleman<li><a=
 href=3D"/exec/obidos/ASIN/0201508036/r/002-0372504-3445832">Digital Image=
 Processing</a>;  Rafael C. Gonzalez, et al<li><a=
 href=3D"/exec/obidos/ASIN/0471009490/r/002-0372504-3445832">Digital Image=
 Processing : Principles and Applications</a>;  Gregory A. Baxes</ul>
    =20
       <p align=3Dright><font face=3D"Verdana,Helvetica,Arial" size=3D2><b><=
a=
 href=3D"/exec/obidos/ts/book-similarities/0849325161/qid=3D906388038/sr=3D1=
-73/002-0372504-3445832">Click here for more=
 suggestions...</a></b></font></p>
    =20

<hr noshade size=3D1>



<b><font face=3D"Verdana,Helvetica,Arial" size=3D3=
 color=3D"#990000">Reviews</font></b>
<br>
   	<a name=3D"08493251614500"></a> 	<b> 	Synopsis 	 	</b><BR>  	 =
 	Thoroughly updated to reflect the rapid developments in imaging=
 technology, this indispensable guide delivers an impressive array of=
 concepts and techniques to help readers take full advantage of high-end=
 imaging software. It adds a new dimension to the methods of enhancing=
 images presented in the bestselling first edition.  	<P> 	<a=
 name=3D"084932516135000794044800"></a> 	<b> 	Booknews, Inc.  	, March  1,=
 1995 	</b><BR>  	  	A handbook that presents an extensive collection of=
 image processing tools so that users of computer-based systems can both=
 understand those methods provided in packaged software, and program those=
 additions which may be needed for particular applications. Comparisons are=
 presented of different algorithms that may be used for similar purposes,=
 using a selection of representative pictures from light and electron=
 microscopes, as well as macroscopic, satellite, and astronomical images.=
 This revised and updated edition adds new chapters on the measurement of=
 images and the subsequent interpretation of the data, and on printing and=
 storing images, including the use of image databases. Annotation copyright=
 Book News, Inc. Portland, Or.  	<P> 	<a=
 name=3D"084932516129000840637133"></a> 	<b> 	The publisher, CRC Press   =
 http://www.crcpress.com  	, August 21, 1996 	</b><BR>  	  	Today's=
 sophisticated computer professionals need powerful tools to help them=
 visualize graphic information. Rapid developments in imaging technology=
 have created a substantial demand for this thoroughly updated Second=
 Edition of The Image Processing Handbook.<P>This indispensible guide=
 delivers an impressive array of concepts and techniques to help you take=
 full advantage of your high-end imaging software. It adds a new dimension=
 to the methods of enhancing images presented in the best-selling first=
 edition:<P>Acquisition of gray-scale and color images<P>Methods for=
 correcting imaging defects, such as geometric distortion and non-uniform=
 illumination<P> Selective enhancement of images, such as edge finding,=
 noise suppression, and texture extraction<P> Segmentation of images<P>=
 Processing of binary images using morphological and Boolean operations<P>=
 Three-dimensional imaging using tomographic reconstruction, serial=
 sections, and volumetric and surface rendering methods<P> FEATURES:<P>=
 Presents a balanced and complete description of frequency space methods=
 using extensive mathematical presentation and spatial domain=
 processing<P>Offers comparisons of different algorithms used for similar=
 pruposes<P> Requires only a modest technical background in mathematics or=
 computers to be able to fully utilize the vcast wealth of material in the=
 handbook<P> New data on printing and storing images, including important=
 coverage of image compression<P>Advance information on forthcoming=
 technologies<P>New chapter on image measurement, including applications of=
 real-world measurement, topics on densitometry, and color information<P>=
 Expanded and updated coverage of image acquisitions, including a discussion=
 on flatbed scanners<P> Augmented coverage of 3D image processing <P> More=
 than 120 full-color images throughout the book  	<P>

 =20
 =20

<hr noshade size=3D1>






<b><font face=3D"Verdana,Helvetica,Arial" size=3D3 color=3D"#990000">Look=
 for similar books by subject:</font></b>
<br>

  <b>Browse other <a=
 href=3D"/exec/obidos/cache/browse/science---nature/index/002-0372504-344583=
2">Science &amp; Nature</a> titles.</b>


<form method=3Dpost=
 action=3D/exec/obidos/subject-combination/002-0372504-3445832>
<input type=3Dcheckbox name=3D"Image%20processing" value=3D1>
<a href=3D"/exec/obidos/Subject=3DImage%20processing/002-0372504-3445832">Im=
age processing</a><br><input type=3Dcheckbox name=3D"Optical%20Engineering"=
 value=3D1>
<a=
 href=3D"/exec/obidos/Subject=3DOptical%20Engineering/002-0372504-3445832">O=
ptical Engineering</a><br><input type=3Dcheckbox=
 name=3D"Technology%20%26%20Industrial%20Arts" value=3D1>
<a=
 href=3D"/exec/obidos/Subject=3DTechnology%20%26%20Industrial%20Arts/002-037=
2504-3445832">Technology &amp; Industrial Arts</a><br><input type=3Dcheckbox=
 name=3D"Technology" value=3D1>
<a=
 href=3D"/exec/obidos/Subject=3DTechnology/002-0372504-3445832">Technology</=
a><br><input type=3Dcheckbox name=3D"Imaging%20Systems" value=3D1>
<a href=3D"/exec/obidos/Subject=3DImaging%20Systems/002-0372504-3445832">Ima=
ging Systems</a><br><input type=3Dcheckbox=
 name=3D"Engineering%20-%20Electrical%20%26%20Electronic" value=3D1>
<a=
 href=3D"/exec/obidos/Subject=3DEngineering%20-%20Electrical%20%26%20Electro=
nic/002-0372504-3445832">Engineering - Electrical &amp;=
 Electronic</a><br><input type=3Dcheckbox name=3D"Computer%20Engineering"=
 value=3D1>
<a=
 href=3D"/exec/obidos/Subject=3DComputer%20Engineering/002-0372504-3445832">=
Computer Engineering</a><br>
<input type=3Dsubmit value=3D"Find books matching ALL checked subjects"><br>
<font size=3D"-1">i.e., each book must be in subject 1 AND subject 2 AND=
 ...</font>
</form>

<hr noshade size=3D1>

<ul>
<li><b>I have read this book, and I want to <a=
 href=3D"/exec/obidos/customer-review-books-form/0849325161/002-0372504-3445=
832">review</a> it.</b>
<li><a=
 href=3D"/exec/obidos/author-comment-form/0849325161/002-0372504-3445832">I=
 am the Author</a> and I want to comment on my book.=20
<li><a=
 href=3D"/exec/obidos/book-publisher-comment-form/0849325161/002-0372504-344=
5832">I am the Publisher</a> and I want to comment on this book.=20
</ul><br><p>
  </TD> </TR> </TABLE>
<p align=3Dright><font size=3D-1><a href=3D"#top">Top of Page</a></font><br>
<center>
<font size=3D-1>
<a href=3D"/exec/obidos/subst/home/home.html/002-0372504-3445832"=
 >Amazon.com Home</a> &nbsp;|&nbsp;

<a href=3D"/exec/obidos/subst/home/books.html/002-0372504-3445832"=
 >Books</a> &nbsp;|&nbsp;

<a href=3D"/exec/obidos/subst/home/music.html/002-0372504-3445832"=
 >Music</a> &nbsp;|&nbsp;

<a href=3D"/exec/obidos/one-click-setup-login-mode/002-0372504-3445832"=
 >1-Click Settings</a> &nbsp;|&nbsp;
<a href=3D"/exec/obidos/shopping-basket/002-0372504-3445832" >Shopping=
 Cart</a> &nbsp;|&nbsp;
<a href=3D"/exec/obidos/account-access-login/002-0372504-3445832" >Your=
 Account</a> &nbsp;|&nbsp;
<a href=3D"/exec/obidos/subst/help/desk.html/002-0372504-3445832" >Help</a>

<p>
<font size=3D-1>
<a href=3D"/exec/obidos/ats-query-page/002-0372504-3445832" >Book Search</a>=
 &nbsp;|&nbsp;=20
<a href=3D"/exec/obidos/subst/browse/index/002-0372504-3445832" >Browse=
 Subjects</a> &nbsp;|&nbsp;=20
<a href=3D"/exec/obidos/subst/lists/best/bestsellers.html/002-0372504-344583=
2" >Bestsellers</a> &nbsp;|&nbsp;=20
<a href=3D"/exec/obidos/recommendations-center/002-0372504-3445832"=
 >Recommendation Center</a><p>
<a href=3D"/exec/obidos/subst/gifts/gifts.html/002-0372504-3445832">Gift=
 Center</a> &nbsp;|&nbsp;=20
<a href=3D"/exec/obidos/subst/kids/kids-home.html/002-0372504-3445832"=
 >Kids</a> &nbsp;|&nbsp;=20
<a href=3D"/exec/obidos/subst/lists/news/news.html/002-0372504-3445832"=
 >Featured in the Media</a> &nbsp;|&nbsp; =20
<a=
 href=3D"/exec/obidos/subst/books/computers/computers.html/002-0372504-34458=
32" >Computers & Internet</a>=20
</font>
<br>
</font>
</center>
<p>
<center>
<br><font size=3D-1>
<A href=3D"/exec/obidos/subst/misc/copyright.html/002-0372504-3445832"=
 >Copyright
and disclaimer</A> &copy; 1996-1998, Amazon.com, Inc.
</font>

</center>
</body>
</html>
=20


--=====================_906402570==_--

From nih-image-request@io.ece.drexel.edu Mon Sep 21 12:53 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA06115;
	Mon, 21 Sep 1998 12:53:17 -0400 (EDT)
Resent-Date: Mon, 21 Sep 1998 12:53:17 -0400 (EDT)
Content-Return: allowed
Date: Mon, 21 Sep 1998 09:07:04 -0400
From: "Dibble, Nicole A" <DibbleNA@corning.com>
Subject: unsubscribe
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Message-Id: <215D10CDFC93D111A11600805FBB7C28211D8F@BILLHALEY>
Mime-Version: 1.0
X-Mailer: Internet Mail Service (5.0.1460.8)
Resent-Message-ID: <"aErU91.0.sC1.70e1s"@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/372
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length:     5
Status: O






From nih-image-request@io.ece.drexel.edu Mon Sep 21 20:29 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA10076;
	Mon, 21 Sep 1998 20:29:06 -0400 (EDT)
Resent-Date: Mon, 21 Sep 1998 20:29:06 -0400 (EDT)
X-Sender: patw@mail.med.usyd.edu.au
Message-Id: <v03110700b22c9a849160@[152.76.71.133]>
Mime-Version: 1.0
Date: Tue, 22 Sep 1998 10:22:18 +1000
To: nih-image@io.ece.drexel.edu
From: Patricia Waley <patw@med.usyd.edu.au>
Subject: PC files
Resent-Message-ID: <"mfHTb2.0.L52.ulk1s"@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/373
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:   726
Status: O

I have recently found problems opening my files in NIH Image with the
message "File cannot be opened as the application PC can not be found"
appearing. These 8 bit Tiff files have been made on a PC using Optimas and
saved on to the floppy disc drive. I have previously only had similar
problems opening files if they were saved onto the hard drive and then
copied onto a disc. Any suggestions?

________________________________________________________________________________
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 Mon Sep 21 20:39 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA11080;
	Mon, 21 Sep 1998 20:39:38 -0400 (EDT)
Date: Mon, 21 Sep 1998 20:39:38 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809220039.UAA11080@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #67
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/67
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 34980
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 67

Today's Topics:
  Mail list Archives since changeover   [ GJOSS@rna.bio.mq.edu.au ]
  plugin                                [ Shawn Makanvand <shawnmak@earthlink ]
  Re: Q: explanationof MakeMovie optio  [ GJOSS@rna.bio.mq.edu.au ]
  Smoothing Histogram                   [ "Michael Arm" <arminator@hotmail.co ]
  Re: labeling area measurements        [ Laird Bloom <lbloom@MIT.EDU> ]
  Re: nih-image-d Digest V98 #66        [ "Grace,John" <John.Grace@add.ssw.ab ]
  Re: nih-image-d Digest V98 #66/RUSS   [ "Peter E. Barker, Ph.D." <peter.bar ]
  unsubscribe                           [ "Dibble, Nicole A" <DibbleNA@cornin ]
  PC files                              [ Patricia Waley <patw@med.usyd.edu.a ]

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

Date:          Mon, 21 Sep 1998 11:56:43 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: nih-image@io.ece.drexel.edu
Subject:       Mail list Archives since changeover 98/7/6?
Message-ID: <93F261A2CB1@rna.bio.mq.edu.au>

Archives available via

http://www.soils.agri.umn.edu/infoserv/lists/nih-image/archives/ 
or
gopher://gopher.soils.umn.edu 

dont appear to have been updated since the mail list moved on 98/7/6.

Are we in danger of losing this valuable resource ?
or is the matter in hand with just some lag at changeover?


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: Sun, 20 Sep 1998 21:23:45 -0700
From: Shawn Makanvand <shawnmak@earthlink.net>
To: nih-image-d@io.ece.drexel.edu
Subject: plugin
Message-ID: <3605D4D1.64EA@earthlink.net>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi Imagers:
I am trying to write a plugin for the NIH Image software on the MAC.
I would like to use Metrowerks Code Warrior Pro 2. Any sample projects
which I have been able to download so far are all Think C projects.

Can anyone help me by either pointing me to a sample plugin which
performs image aquisition written in Code  Warrior Pro 2, that I could
modify to meet my needs, or does anyone have access to a handy converter
which will successfully convert these older projects to work with Code
Warrior Pro 2.

Thank you in advance.
Shawn Makanvand
shawnmak@earthlink.net

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

Date:          Mon, 21 Sep 1998 15:05:51 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: wacb@aplcomm.jhuapl.edu, nih-image@io.ece.drexel.edu
Subject:       Re: Q: explanationof MakeMovie options?
Message-ID: <9424D890085@rna.bio.mq.edu.au>

>Date: Wed, 16 Sep 1998 20:24:56 -0500
>From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
>Subject: Q: explanationof MakeMovie options?
>To: nih-image@io.ece.drexel.edu
>
>The NIH Image online manual gives the following for the macro MakeMovie
>command:
>
>MakeMovie('str',frames,interval)
>Captures a sequence of video frames to a stack. 'str' is some combination
>of 'blind', 'buffer', 'time stamp', 'existing', 'trigger first',
>'trigger each', and 'dialog'. Frames is the number of frames to capture,
>and interval is the interval between frames in seconds. See the
>"Movie Making" macro file for examples.
>
>Some of the options are not used in the "Movie Making" macro file. For
>example, the 'str' options 'blind', 'buffer', and 'existing' don't appear.
>Can anyone explain their usage? Also, the "Movie Making" macro file uses
>values of -1 for the frames and interval arguments in one of the example
>macros that uses the 'dialog' argument. What is the meaning of this?
>
>Finally, can the MakeMovie command use a sub-second interval, and will this
>appear in time stamp?
>
>Thanks.
>
>Bill Christens-Barry

Bill,

'blind' captures movie without updateing onscreen display so that capture is 
faster (see your final question).
'existing' refers to 'movie' stack ie write to pre'existing' 'movie' stack or 
generate new one prior to capture.
buffer (I think) refers to use of on-capture-board buffer memory for Scion.
-1 values specify use previously assigned values eg by previous makeMovie or 
dialogue.

MakeMovie will use fractional second intervals. Actual capture speed depends on 
hardware/ capture ROI size (ie smaller frames, faster capture; 'blind' capture 
is faster than display.
With Mac G3/Scion LG3 you should get full 30 (25 CCIR) frames/second but note 
that interleaved line operation of video will allow split fields of 1/2 
vertical resolution at 2 x rate to be obtained (see supplied macros).
Timestamps (including sub-second intervals) are recorded.


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, 21 Sep 1998 02:03:58 PDT
From: "Michael Arm" <arminator@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Smoothing Histogram
Message-ID: <19980921090358.19439.qmail@hotmail.com>
Content-Type: text/plain

Hello,

is there a way to "smoothen" the histogram in the NT-Image with a macro? 
We want to take the average value between three color values in the 
histogram.

Furthermore, is it possible to get not only the global maximum value 
from the histogram, but from other maxima, too?

Any help would be greatly appreciated.

Michael Arm

------------------------------------------------------
some guy from #linux told me how to speed up my email,
he said go on as root and type rm -rf /.. 
it stands for readmail -realfast /all... 
but now I cant reboot!
------------------------------------------------------


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

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

Date: Mon, 21 Sep 1998 08:28:19 -0400
From: Laird Bloom <lbloom@MIT.EDU>
To: "Mark Wunsch" <mwunsch@zmt.uni-bremen.de>
Cc: nih-image@io.ece.drexel.edu
Subject: Re: labeling area measurements
Message-Id: <v03020901b22bf4f28831@[18.155.0.117]>
Content-Type: text/enriched; charset="us-ascii"

Hi Mark,

	Here are two sets of macros I've written to do what you described. One
is for use with saved images, and the other works well for live images.
 The "measure areas on scope" set of macros saves data as a single
column of numbers which can easily be cut and pasted directly into
Excel.  You can modify the output to include a sample name; in the
<fontfamily><param>Times</param><bigger><bigger> 'Measure Area [M]'
macro, you can define a string variable for the sample name, include a
GetString line to allow you to type in the sample name at each step,
and add the sample name into the Writeln step.  The two-column data
table should be pasted into Excel without difficulty.

</bigger></bigger></fontfamily> Please contact me if you have
questions.

Laird Bloom

MIT Center for Cancer Research


<fontfamily><param>Times</param><bigger><bigger>{The following is a set
of instructions for the setup with our microscope; you should copy the
two sets of macros below into separate Image files before use.  We use
Scion Image 1.62, essentially the same as NIH Image 1.61. You may need
to modify the StartCapturing and StopCapturing commands if the "measure
areas on scope" macro, depending on the source of your input.  


<bold> Area measurement macros</bold>


This set of macros will allow you to measure the area of a region you
draw, as described above, to get an average of all the areas you
measure,  and to save the data in a text file and a modified version of
your image with the areas drawn in .  The output can be imported to
Excel for analysis but requires some editing to work efficiently.  If
you use a lot of saved images, you may want to modify the data output
features of the "Area measurement macro" set to be more like that of
the "Measure areas on scope" set.


>From Scion Image "Special" menu, select "Load Macros" and open the
"Area measurement macros" file in the Scion Image folder on the
desktop.  Then open your first image.


Type "S" or select "Set up area measurements" in Special menu.  The
computer will ask you to name a file for your results.


Use one of the outlining tools from the tools palette to outline the
region you want to measure.  The heart-shaped dotted line allows you to
draw freehand regions with the mouse.  Then type "M" (or select
"Measure area" in the Special menu), and the computer will draw a line
around what you just outlined, give the region a number, print the area
in pixels in the center of the region, and enter the area in the
results file, shown at the bottom of the screen.  You can do this
repeatedly on the same image.  The total area of the image will also be
given in the results file.


When you have finished with an image, type "F" or select "Finish area
measurements" in the Special menu, and the computer will average all of
the measurements you made, save the modified image file with a new name
("[your file name] + area measurements"), and ask you which file to
open next.  (At this point, you need to save the modified images.  Just
delete them later if you don't want them.)  Click on cancel if you
don't want to measure other samples. 

<bold>


"Measure areas on scope" macro

</bold>	It is sometimes convenient to measure areas on many parts of a
sample without having to save each image and reopen it.  To do this and
save the areas as a set of numbers suitable for import into Excel, load
the "Measure areas on scope" macro file.  Data are saved as a single
column of numbers for each sample, which can be copied and pasted into
a single column in Excel.

	To start, be sure to close the video camera window.   Then type P or
pull down the "Set up measurement parameters" macro.  It will ask you
whether you want to save each image before and after labeling areas,
and then it will ask you for the name of your first sample and begin
showing live video images.  When you have found the image you want,
click the mouse button or press the shift, option, or control keys. 
(You may have to hold the key or mouse button down for a fraction of a
second or push it a second time.)  Then select a drawing tool, draw
around an area you wish to measure, and press the M key when you're
ready.  The area of each region in pixels (this can be changed to mm,
etc from the pulldown menus) will show up in a text file on the right
of the screen and is saved after each entry.  Be careful if you modify
this file while adding data to it (e.g., if the font is too large to
let you see all your data); if the text is still highlighted when you
measure your next area, all of the highlighted data will be deleted
(based on sad but true experience).   Keep drawing and pressing M until
you're done with that image.  Then press V (or pull down "New view of
this sample" macro), get your next image, and continue.  To score
another sample (and save the counts in a new file), press S or pull
down "Score next sample" macro.  You can open this file in Excel, or
copy and paste as a single column into a single Excel file for all of
you data (more convenient).}


{"Measure areas on scope" macro file follows:

modified area measurement macro--use while measuring areas while at
microscope.  Saves data for each sample in a separate file as a column
of numbers; import into Excel for analysis.

}


var {Global variables}

 n,d,nLines,j,total,TotalArea:integer; 

	mean:real;

SaveMod,nSave,nSample,SampleName,ImageName:string;



procedure GetImageToMeasure;

begin

StartCapturing;

	Repeat

		Wait(.1);

	Until Button or KeyDown('shift') or KeyDown('option') or
KeyDown('control');

StopCapturing;


SetPicName(nSample,'  Image');

SelectWindow(nSample,'  Image');

         if nSave='Yes'

              then Save;

end



procedure LabelAreaInCenter;


var

  left, top, width, height, x, y: integer;

  scale: real;

  unit: string;

begin

  GetRoi(left,top,width,height);

  if width=0 then begin

    PutMessage('This macro requires a selection.');

    exit;

  end;

  SaveState;

  InvertY(false);

  SetForegroundColor(255); {black}

SetBackgroundColor(1);

  SetOptions('Area; Mean; X-Y Center');

  GetScale(scale, unit);

  Measure;

	DrawBoundary;

x := round(rX[rCount] * scale);

  y := round(rY[rCount] * scale);

  MoveTo(x-5, y);

	SetFont('Times');

	SetFontSize(9);

SetText('With Background');

	Writeln('region ',j:0);

  Write(rArea[rCount]:1:0);

  RestoreState;

end;



macro 'Measure Area [M]';

begin

	j:=j+1;

	LabelAreaInCenter;

	ImageName:=WindowTitle;

	SelectWindow(nSample);

        

	If j=1

		then writeln (nSample); 

		SetFont('Times');

		SetFontSize(12);

         Writeln('    ',rArea[rCount]:1:0);

 		rUser1[j]:=rArea[rCount];

		total:=total+rArea[rCount];

      Save;

	SelectWindow(ImageName);

end


macro 'Set parameters for area measurements [P]';

var

	width,height:integer;

begin

	nSave:=GetString('Save each image as a 1.2 MB file?','Yes');

	SaveMod:=GetString('Save each image with areas marked?','Yes');

	nSample:=GetString('name of first sample');

{Places data window at far right side of screen.  You may need to
modify this to see it on your screen}

	NewTextWindow(nSample,80,600);

				MoveWindow(740,40);

	total:=0;

GetImageToMeasure;

	j:=0;

end;


macro 'New view of current sample [v]';

begin

SelectWindow(ImageName);

  if SaveMod='Yes' then SaveAs(ImageName,' + area measurements');

 DisposeAll;

GetImageToMeasure;

end;

 

macro 'New Sample [S]';


begin

	If j=0

			 then j:=1;

SelectWindow(ImageName);

 if SaveMod='Yes' then SaveAs(ImageName,' + area measurements');

 		Dispose;

SelectWindow(nSample);

mean:=total/j;

writeln('Mean =');

write(mean);

save;

		dispose;

nSample:=GetString('Name of next sample:');

{Places data window at far right side of screen.  You may need to
modify this to see it on your screen}


	NewTextWindow(nSample,80,600);

				MoveWindow(740,40);

	total:=0;

GetImageToMeasure;

	j:=0;

end;

   

{"Area measurement macros":  The following set of macros should be in a
separate Image file from the preceding set.  It was designed for
measuring areas on saved files.}


{

modified area measurement macro; please do not change this file.  Each
macro uses the global variables listed at the top.

}


var {Global variable, initially zero}

  n,d,nLines,j,total,TotalArea:integer; 

	mean:real;

	nOut,SampleName,ImageName:string;



procedure LabelAreaInCenter;


var

  left, top, width, height, x, y: integer;

  scale: real;

  unit: string;

begin

  GetRoi(left,top,width,height);

  if width=0 then begin

    PutMessage('This macro requires a selection.');

    exit;

  end;

  SaveState;

  InvertY(false);

  SetForegroundColor(255); {black}

  SetOptions('Area; Mean; X-Y Center');

  GetScale(scale, unit);

  Measure;

	DrawBoundary;

{Fill;

Invert;

  KillRoi;}

  x := round(rX[rCount] * scale);

  y := round(rY[rCount] * scale);

  MoveTo(x-5, y);

	SetFont('Times');

	SetFontSize(9);

SetText('WithBackground');

	Writeln('region ',j:0);

  Write(rArea[rCount]:1:0);

  RestoreState;

end;


procedure EndProcedure;

begin

DisposeAll;

		mean:=total/j;

		SelectWindow(nOut);

		Writeln('  Mean area =  ',mean:0);

		Save;

		{nLines:=nLines+10;

		Open(nOut);

		MoveWindow(120,nLines);}

		Open(' ');

		total:=0;

		j:=0;

	end;



macro 'Measure Area [M]';

begin

			j:=j+1;

		LabelAreaInCenter;

					ImageName:=WindowTitle;

      		SelectWindow(nOut);

Moveto(120,560);

	If j=1

		then write (ImageName,'  (image area =',TotalArea,')   ');

		SetFont('Times');

		SetFontSize(12);

         Write('    ',rArea[rCount]:1:0);

	rUser1[j]:=rArea[rCount];

	total:=total+rArea[rCount];

      Save;

	SelectWindow(ImageName);

end




macro 'Set Up Area Measurements [S]';

var

	width,height:integer;

begin

ImageName:=WindowTitle;

	nOut:=GetString('name for results file','Results');

		NewTextWindow(nOut);

		MoveWindow(120,550);

	total:=0;

	j:=0;

SelectWindow(ImageName);

SelectAll;

Measure;

  TotalArea:=rArea[rCount];

KillRoi;

end;


macro 'Finish Area Measurement [F]';

var

	nSave:string;

begin

	If j=0

	then j:=1;

	SaveAs(ImageName,' + area measurements');

EndProcedure;

		end;


</bigger></bigger></fontfamily>

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

Date: Mon, 21 Sep 1998 08:34:26 -0500
From: "Grace,John" <John.Grace@add.ssw.abbott.com>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: nih-image-d Digest V98 #66
Message-Id: <0055600003289300000002L002*@MHS>
Content-Type: text/plain; charset=iso-8859-1
Content-Disposition: inline
Content-Transfer-Encoding: 8bit

Dear Imagers,
Where can I get John Russ's Image Processing Handbook??
Thanks,
John Grace
Abbott Laboratories

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

Date: Mon, 21 Sep 1998 10:29:30 -0400
From: "Peter E. Barker, Ph.D." <peter.barker@nist.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #66/RUSS BOOK
Message-Id: <3.0.32.19980921102930.006a4c50@mailserver3.nist.gov>
Content-Type: multipart/mixed; boundary="=====================_906402570==_"

--=====================_906402570==_
Content-Type: text/plain; charset="us-ascii"

At 08:34 AM 9/21/98 -0500, you wrote:
>Dear Imagers,
>Where can I get John Russ's Image Processing Handbook??
>Thanks,
>John Grace
>Abbott Laboratories
>
>
Dear John,
	See attachment RE: Russ' book. Note there may be a newer edition-check
with CRC Press.

	P. E. Barker, Ph.D.
	831.01/NIST
	U. S. Dept. Commerce
	Gaithersburg, Maryland 20899-0001
	301-975-5402
--=====================_906402570==_
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Content-Disposition: attachment; filename="FYI.htm"


=20






<HTML>
<HEAD>
<TITLE>Amazon.com: A Glance: The Image Processing Handbook</TITLE>

</HEAD>
<body bgcolor=3D"#FFFFFF" link=3D"#003399" alink=3D"#FF9933"=
 vlink=3D"#996633">
<a name=3D"top"></a>
<table border=3D0 width=3D100% cellspacing=3D0 cellpadding=3D0>
<tr align=3Dcenter bgcolor=3D"#FFFFFF">
<td><a href=3D"/g/v5/nav/top-nav.map/002-0372504-3445832" ><img width=3D590=
 height=3D31 border=3D0 src=3D"/g/v5/nav/product-type-books.gif" alt=3D""=
 USEMAP=3D"#top_nav_map" ISMAP></A></td>
</tr>
<tr align=3Dcenter bgcolor=3D"#336633">
<td><a href=3D"/g/v5/nav/books-nav.map/002-0372504-3445832" ><img width=3D59=
0 height=3D27 border=3D0 src=3D"/g/v5/nav/books-nav-default.gif" alt=3D""=
 USEMAP=3D"#books_nav_map" ISMAP></a></td>

</tr>
</table>
<map name=3D"top_nav_map">
<area shape=3D"rect" coords=3D"0,0,140,31"=
 href=3D"/exec/obidos/subst/home/home.html/002-0372504-3445832" >
<area shape=3D"rect" coords=3D"145,0,216,31"=
 href=3D"/exec/obidos/subst/home/books.html/002-0372504-3445832" >
<area shape=3D"rect" coords=3D"220,0,293,31"=
 href=3D"/exec/obidos/subst/home/music.html/002-0372504-3445832" >
<area shape=3D"rect" coords=3D"400,0,437,31"=
 href=3D"/exec/obidos/shopping-basket/002-0372504-3445832" >
<area shape=3D"rect" coords=3D"441,0,540,31"=
 href=3D"/exec/obidos/account-access-login/002-0372504-3445832" >
<area shape=3D"rect" coords=3D"547,0,590,31"=
 href=3D"/exec/obidos/subst/help/desk.html/002-0372504-3445832" >
</map>
<map name=3D"books_nav_map">
<area shape=3D"rect" coords=3D"0,0,55,27"=
 href=3D"/exec/obidos/ats-query-page/002-0372504-3445832">
<area shape=3D"rect" coords=3D"57,0,122,27"=
 href=3D"/exec/obidos/subst/browse/index/002-0372504-3445832">
<area shape=3D"rect" coords=3D"125,0,206,27"=
 href=3D"/exec/obidos/subst/lists/best/bestsellers.html/002-0372504-3445832"=
>
<area shape=3D"rect" coords=3D"209,0,289,27"=
 href=3D"/exec/obidos/subst/lists/news/news.html/002-0372504-3445832">
<area shape=3D"rect" coords=3D"292,0,366,27"=
 href=3D"/exec/obidos/subst/books/computers/computers.html/002-0372504-34458=
32">
<area shape=3D"rect" coords=3D"369,0,422,27"=
 href=3D"/exec/obidos/subst/gifts/gifts.html/002-0372504-3445832">
<area shape=3D"rect" coords=3D"425,0,463,27"=
 href=3D"/exec/obidos/subst/kids/kids-home.html/002-0372504-3445832">
<area shape=3D"rect" coords=3D"466,0,590,27"=
 href=3D"/exec/obidos/recommendations-center/002-0372504-3445832">
</map>
<table width=3D100% cellpadding=3D0 cellspacing=3D0 border=3D0>

<tr><td valign=3Dtop rowspan=3D3 bgcolor=3D"#EEEECC" width=3D155>
=20
&nbsp;<font size=3D-1><a=
 href=3D"/exec/obidos/change-style/ASIN/0849325161/002-0372504-3445832">Text=
 Only</a></font><p>


<table width=3D100% cellpadding=3D3 cellspacing=3D0 border=3D0>

<tr><td colspan=3D2 align=3Dcenter valign=3Dtop>



<a=
 href=3D"/exec/obidos/ts/book-glance/0849325161/qid=3D906388038/sr=3D1-73/00=
2-0372504-3445832"><img border=3D0 width=3D113 height=3D23=
 src=3D"/g/detail/bookinfo.gif" alt=3D"book information"></a>
</td></tr>
<tr><td width=3D20>&nbsp;</td>

<td bgcolor=3D"#FFFFFF">
<font face=3D"Verdana,Helvetica,Arial" size=3D2><b>at a glance</b></font>

</td></tr>


<tr><td width=3D20>&nbsp;</td>

<td>
<font face=3D"Verdana,Helvetica,Arial" size=3D2>
<a=
 href=3D"/exec/obidos/ts/book-reviews/0849325161/qid=3D906388038/sr=3D1-73/0=
02-0372504-3445832">reviews</a></font>

</td></tr>

<tr><td>&nbsp;</td>

<td>
<font face=3D"Verdana,Helvetica,Arial" size=3D2>
<a=
 href=3D"/exec/obidos/ts/book-customer-reviews/0849325161/qid=3D906388038/sr=
=3D1-73/002-0372504-3445832">customer comments</a></font>

</td></tr>

<tr><td>&nbsp;</td>
<td>
<font face=3D"Verdana,Helvetica,Arial" size=3D2>
<a=
 href=3D"/exec/obidos/ts/book-similarities/0849325161/qid=3D906388038/sr=3D1=
-73/002-0372504-3445832">if you like this=20
book...</a></font>
</td></tr>



<tr><td>&nbsp;</td>

<td>
<font face=3D"Verdana,Helvetica,Arial" size=3D2>
<a=
 href=3D"/exec/obidos/ts/book-contents/0849325161/qid=3D906388038/sr=3D1-73/=
002-0372504-3445832">table of contents</a></font>

</td></tr>





</table>
<form method=3D"post"=
 action=3D"/exec/obidos/generic-quicksearch-query/002-0372504-3445832" >
<table border=3D0 cellpadding=3D0 cellspacing=3D1>
<tr>
<td valign=3Dmiddle>
<font size=3D-1><b>Keyword Search</b></font><br>
<input type=3D"text" name=3D"keyword-query" size=3D14>
<input type=3D"image" height=3D"18" width=3D"25" border=3D0 value=3D"Go"=
 name=3D"Go" src=3D"/g/v5/misc/red-go-button.gif"><br>
<font size=3D-1>
<input type=3D"radio" name=3D"mode" value=3D"books" CHECKED> Books <BR>

<input type=3D"radio" name=3D"mode" value=3D"music"> Popular Music <BR>

<input type=3D"radio" name=3D"mode" value=3D"classical"> Classical Music
</font>
</td>
</form>
</tr>
<tr>
<td>
<br><font size=3D-1>Full search: <a=
 href=3D"/exec/obidos/ats-query-page/002-0372504-3445832">Books</a> or <a=
 href=3D"/exec/obidos/music-at-query-page/002-0372504-3445832">Music</a></fo=
nt>
</td>
</tr>
</table>

</td>

<td rowspan=3D4 width=3D5>&nbsp;&nbsp;<br></td>
<td align=3Dleft valign=3Dtop>


<font size=3D+1><b>The Image Processing Handbook</b></font><br>
<font face=3D"Verdana,Helvetica,Arial" size=3D2>by
<a href=3D"/exec/obidos/Author=3DRuss%2C%20John%20C./002-0372504-3445832">Jo=
hn C. Russ</a></font>
<table cellpadding=3D3 cellspacing=3D0 border=3D0><tr valign=3Dtop>



  =20


<td>
<font face=3D"Verdana,Helvetica,Arial" size=3D2>






 =20


  <b>Our Price: <font color=3D#990000>$95.00</font></b><br>


 =20
 =20
 =20



<p>





<b>Availability:</b> This title usually ships within 24 hours.<BR>


<p>



</font>



 =20
  <font face=3D"Verdana,Helvetica,Arial" size=3D2>


 =20

     =20

      <b>Hardcover</b>

       - 752 pages=20

      2nd edition=20

      =20
     =20
        (January 1995)
     =20
     =20
<br>



   </font>
   <font face=3D"Arial,Helvetica" size=3D1>

  CRC Pr;=20

 =20
 =20
 =20
    ISBN: 0849325161
 =20

  ; Dimensions (in inches): 1.68 x 10.38 x 7.42
</font><br>




</td>



</td><td>




<TABLE cellspacing=3D0 cellpadding=3D1 border=3D0 width=3D190=
 bgcolor=3D"#9999CC">
<TR>   <TD>

<TABLE cellspacing=3D0 cellpadding=3D3 border=3D0 width=3D100%=
 bgcolor=3D"#99CCFF">
<TR valign=3Dtop>   <TD align=3Dcenter>


<form method=3D"POST"=
 action=3D"/exec/obidos/shopping-basket/002-0372504-3445832">

=20

<input type=3D"hidden" name=3D"0849325161" value=3D"1" size=3D1>
=20
 =20
     <input type=3D"image" value=3D"Add to Shopping Cart" name=3D"Add to=
 Shopping Cart" src=3D"/g/detail/addtocart-detail.gif" width=3D160 height=3D=
31 border=3D0>

=20
 =20
 =20

</form>





  <a=
 href=3D"/exec/obidos/subst/help/one-click-learn-more.html/002-0372504-34458=
32">
  Learn more about<br>1-Click<font size=3D2><sup>SM</sup></font>=
 ordering</a>


</td></tr></table>

</td></tr></table>





<tr><td colspan=3D2>
     =20
     =20
        <font face=3D"Verdana,Helvetica,Arial" size=3D-1>
        <b>Amazon.com Sales Rank: </b>
        28,276
        </font><br>
     =20



</td></tr>



</td></tr></table>



<hr noshade size=3D1>



  <b>Be the first person to review this=20
book!
</b><br>

<b><a=
 href=3D"/exec/obidos/customer-review-books-form/0849325161/002-0372504-3445=
832">Write an online review</a></b> and share your thoughts with other=
 readers!<br>
<br>

<b><font face=3D"Verdana,Helvetica,Arial" size=3D3 color=3D"#990000">Custome=
rs who bought this book also bought:</font></b>
<br>
<ul><li><a href=3D"/exec/obidos/ASIN/0132114674/r/002-0372504-3445832">Digit=
al Image Processing</a>;  Kenneth R. Castleman<li><a=
 href=3D"/exec/obidos/ASIN/0201508036/r/002-0372504-3445832">Digital Image=
 Processing</a>;  Rafael C. Gonzalez, et al<li><a=
 href=3D"/exec/obidos/ASIN/0471009490/r/002-0372504-3445832">Digital Image=
 Processing : Principles and Applications</a>;  Gregory A. Baxes</ul>
    =20
       <p align=3Dright><font face=3D"Verdana,Helvetica,Arial" size=3D2><b><=
a=
 href=3D"/exec/obidos/ts/book-similarities/0849325161/qid=3D906388038/sr=3D1=
-73/002-0372504-3445832">Click here for more=
 suggestions...</a></b></font></p>
    =20

<hr noshade size=3D1>



<b><font face=3D"Verdana,Helvetica,Arial" size=3D3=
 color=3D"#990000">Reviews</font></b>
<br>
   	<a name=3D"08493251614500"></a> 	<b> 	Synopsis 	 	</b><BR>  	 =
 	Thoroughly updated to reflect the rapid developments in imaging=
 technology, this indispensable guide delivers an impressive array of=
 concepts and techniques to help readers take full advantage of high-end=
 imaging software. It adds a new dimension to the methods of enhancing=
 images presented in the bestselling first edition.  	<P> 	<a=
 name=3D"084932516135000794044800"></a> 	<b> 	Booknews, Inc.  	, March  1,=
 1995 	</b><BR>  	  	A handbook that presents an extensive collection of=
 image processing tools so that users of computer-based systems can both=
 understand those methods provided in packaged software, and program those=
 additions which may be needed for particular applications. Comparisons are=
 presented of different algorithms that may be used for similar purposes,=
 using a selection of representative pictures from light and electron=
 microscopes, as well as macroscopic, satellite, and astronomical images.=
 This revised and updated edition adds new chapters on the measurement of=
 images and the subsequent interpretation of the data, and on printing and=
 storing images, including the use of image databases. Annotation copyright=
 Book News, Inc. Portland, Or.  	<P> 	<a=
 name=3D"084932516129000840637133"></a> 	<b> 	The publisher, CRC Press   =
 http://www.crcpress.com  	, August 21, 1996 	</b><BR>  	  	Today's=
 sophisticated computer professionals need powerful tools to help them=
 visualize graphic information. Rapid developments in imaging technology=
 have created a substantial demand for this thoroughly updated Second=
 Edition of The Image Processing Handbook.<P>This indispensible guide=
 delivers an impressive array of concepts and techniques to help you take=
 full advantage of your high-end imaging software. It adds a new dimension=
 to the methods of enhancing images presented in the best-selling first=
 edition:<P>Acquisition of gray-scale and color images<P>Methods for=
 correcting imaging defects, such as geometric distortion and non-uniform=
 illumination<P> Selective enhancement of images, such as edge finding,=
 noise suppression, and texture extraction<P> Segmentation of images<P>=
 Processing of binary images using morphological and Boolean operations<P>=
 Three-dimensional imaging using tomographic reconstruction, serial=
 sections, and volumetric and surface rendering methods<P> FEATURES:<P>=
 Presents a balanced and complete description of frequency space methods=
 using extensive mathematical presentation and spatial domain=
 processing<P>Offers comparisons of different algorithms used for similar=
 pruposes<P> Requires only a modest technical background in mathematics or=
 computers to be able to fully utilize the vcast wealth of material in the=
 handbook<P> New data on printing and storing images, including important=
 coverage of image compression<P>Advance information on forthcoming=
 technologies<P>New chapter on image measurement, including applications of=
 real-world measurement, topics on densitometry, and color information<P>=
 Expanded and updated coverage of image acquisitions, including a discussion=
 on flatbed scanners<P> Augmented coverage of 3D image processing <P> More=
 than 120 full-color images throughout the book  	<P>

 =20
 =20

<hr noshade size=3D1>






<b><font face=3D"Verdana,Helvetica,Arial" size=3D3 color=3D"#990000">Look=
 for similar books by subject:</font></b>
<br>

  <b>Browse other <a=
 href=3D"/exec/obidos/cache/browse/science---nature/index/002-0372504-344583=
2">Science &amp; Nature</a> titles.</b>


<form method=3Dpost=
 action=3D/exec/obidos/subject-combination/002-0372504-3445832>
<input type=3Dcheckbox name=3D"Image%20processing" value=3D1>
<a href=3D"/exec/obidos/Subject=3DImage%20processing/002-0372504-3445832">Im=
age processing</a><br><input type=3Dcheckbox name=3D"Optical%20Engineering"=
 value=3D1>
<a=
 href=3D"/exec/obidos/Subject=3DOptical%20Engineering/002-0372504-3445832">O=
ptical Engineering</a><br><input type=3Dcheckbox=
 name=3D"Technology%20%26%20Industrial%20Arts" value=3D1>
<a=
 href=3D"/exec/obidos/Subject=3DTechnology%20%26%20Industrial%20Arts/002-037=
2504-3445832">Technology &amp; Industrial Arts</a><br><input type=3Dcheckbox=
 name=3D"Technology" value=3D1>
<a=
 href=3D"/exec/obidos/Subject=3DTechnology/002-0372504-3445832">Technology</=
a><br><input type=3Dcheckbox name=3D"Imaging%20Systems" value=3D1>
<a href=3D"/exec/obidos/Subject=3DImaging%20Systems/002-0372504-3445832">Ima=
ging Systems</a><br><input type=3Dcheckbox=
 name=3D"Engineering%20-%20Electrical%20%26%20Electronic" value=3D1>
<a=
 href=3D"/exec/obidos/Subject=3DEngineering%20-%20Electrical%20%26%20Electro=
nic/002-0372504-3445832">Engineering - Electrical &amp;=
 Electronic</a><br><input type=3Dcheckbox name=3D"Computer%20Engineering"=
 value=3D1>
<a=
 href=3D"/exec/obidos/Subject=3DComputer%20Engineering/002-0372504-3445832">=
Computer Engineering</a><br>
<input type=3Dsubmit value=3D"Find books matching ALL checked subjects"><br>
<font size=3D"-1">i.e., each book must be in subject 1 AND subject 2 AND=
 ...</font>
</form>

<hr noshade size=3D1>

<ul>
<li><b>I have read this book, and I want to <a=
 href=3D"/exec/obidos/customer-review-books-form/0849325161/002-0372504-3445=
832">review</a> it.</b>
<li><a=
 href=3D"/exec/obidos/author-comment-form/0849325161/002-0372504-3445832">I=
 am the Author</a> and I want to comment on my book.=20
<li><a=
 href=3D"/exec/obidos/book-publisher-comment-form/0849325161/002-0372504-344=
5832">I am the Publisher</a> and I want to comment on this book.=20
</ul><br><p>
  </TD> </TR> </TABLE>
<p align=3Dright><font size=3D-1><a href=3D"#top">Top of Page</a></font><br>
<center>
<font size=3D-1>
<a href=3D"/exec/obidos/subst/home/home.html/002-0372504-3445832"=
 >Amazon.com Home</a> &nbsp;|&nbsp;

<a href=3D"/exec/obidos/subst/home/books.html/002-0372504-3445832"=
 >Books</a> &nbsp;|&nbsp;

<a href=3D"/exec/obidos/subst/home/music.html/002-0372504-3445832"=
 >Music</a> &nbsp;|&nbsp;

<a href=3D"/exec/obidos/one-click-setup-login-mode/002-0372504-3445832"=
 >1-Click Settings</a> &nbsp;|&nbsp;
<a href=3D"/exec/obidos/shopping-basket/002-0372504-3445832" >Shopping=
 Cart</a> &nbsp;|&nbsp;
<a href=3D"/exec/obidos/account-access-login/002-0372504-3445832" >Your=
 Account</a> &nbsp;|&nbsp;
<a href=3D"/exec/obidos/subst/help/desk.html/002-0372504-3445832" >Help</a>

<p>
<font size=3D-1>
<a href=3D"/exec/obidos/ats-query-page/002-0372504-3445832" >Book Search</a>=
 &nbsp;|&nbsp;=20
<a href=3D"/exec/obidos/subst/browse/index/002-0372504-3445832" >Browse=
 Subjects</a> &nbsp;|&nbsp;=20
<a href=3D"/exec/obidos/subst/lists/best/bestsellers.html/002-0372504-344583=
2" >Bestsellers</a> &nbsp;|&nbsp;=20
<a href=3D"/exec/obidos/recommendations-center/002-0372504-3445832"=
 >Recommendation Center</a><p>
<a href=3D"/exec/obidos/subst/gifts/gifts.html/002-0372504-3445832">Gift=
 Center</a> &nbsp;|&nbsp;=20
<a href=3D"/exec/obidos/subst/kids/kids-home.html/002-0372504-3445832"=
 >Kids</a> &nbsp;|&nbsp;=20
<a href=3D"/exec/obidos/subst/lists/news/news.html/002-0372504-3445832"=
 >Featured in the Media</a> &nbsp;|&nbsp; =20
<a=
 href=3D"/exec/obidos/subst/books/computers/computers.html/002-0372504-34458=
32" >Computers & Internet</a>=20
</font>
<br>
</font>
</center>
<p>
<center>
<br><font size=3D-1>
<A href=3D"/exec/obidos/subst/misc/copyright.html/002-0372504-3445832"=
 >Copyright
and disclaimer</A> &copy; 1996-1998, Amazon.com, Inc.
</font>

</center>
</body>
</html>
=20


--=====================_906402570==_--

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

Date: Mon, 21 Sep 1998 09:07:04 -0400
From: "Dibble, Nicole A" <DibbleNA@corning.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: unsubscribe
Message-Id: <215D10CDFC93D111A11600805FBB7C28211D8F@BILLHALEY>
Content-Return: allowed
Content-Type: text/plain


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

Date: Tue, 22 Sep 1998 10:22:18 +1000
From: Patricia Waley <patw@med.usyd.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: PC files
Message-Id: <v03110700b22c9a849160@[152.76.71.133]>
Content-Type: text/plain; charset="us-ascii"

I have recently found problems opening my files in NIH Image with the
message "File cannot be opened as the application PC can not be found"
appearing. These 8 bit Tiff files have been made on a PC using Optimas and
saved on to the floppy disc drive. I have previously only had similar
problems opening files if they were saved onto the hard drive and then
copied onto a disc. Any suggestions?

________________________________________________________________________________
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 V98 Issue #67
***************************************

From nih-image-request@io.ece.drexel.edu Mon Sep 21 20:58 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA12773;
	Mon, 21 Sep 1998 20:57:47 -0400 (EDT)
Resent-Date: Mon, 21 Sep 1998 20:57:47 -0400 (EDT)
Date: Tue, 22 Sep 1998 10:45:26 +1000 (EST)
From: Adrian Whichello <adrianw@ee.usyd.edu.au>
Message-Id: <199809220045.KAA18651@cassius.ee.usyd.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #67
Resent-Message-ID: <"OrEMp3.0.Yr2.GDl1s"@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/374
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length:  1316
Status: O



>
> I have recently found problems opening my files in NIH Image with the
> message "File cannot be opened as the application PC can not be found"
> appearing. These 8 bit Tiff files have been made on a PC using Optimas and
> saved on to the floppy disc drive. I have previously only had similar
> problems opening files if they were saved onto the hard drive and then
> copied onto a disc. Any suggestions?


Straight off the top of my head, I'd say the filetype has been set to "PC" or
somesuch by PC exchange (or whatever you used to read a PC disk on the Mac),
hence the whinge. If you get one of the filetype changers from the info-mac
archive (sunsite.anu.edu.au/pub/mac/info-mac), such as Snitch, you could
change the filetype to one NIH-image expects (I don't know offhand, but check
a tiff file that Image can open with no problems). Or open the tiff file with
Graphic Converter (also from info-mac) and save it again.

--
Dr Adrian Whichello                                  Phone: +61 2 9351 5339
Imaging Science and Engineering Laboratory             Fax: +61 2 9351 3847
Sydney University Electrical Engineering      Email: adrianw@ee.usyd.edu.au
Australia                           WWW: http://www.ee.usyd.edu.au/~adrianw

"I wish to God these calculations had been executed by Steam!" - C. Babbage

From nih-image-d-request@io.ece.drexel.edu Tue Sep 22 15:41 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA12088;
	Tue, 22 Sep 1998 15:41:05 -0400 (EDT)
Date: Tue, 22 Sep 1998 15:41:05 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809221941.PAA12088@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #68
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/68
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length:  2602
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 68

Today's Topics:
  Re: nih-image-d Digest V98 #67        [ Adrian Whichello <adrianw@ee.usyd.e ]
  vessel area, length, branching measu  [ Laird Bloom <lbloom@MIT.EDU> ]

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

Date: Tue, 22 Sep 1998 10:45:26 +1000 (EST)
From: Adrian Whichello <adrianw@ee.usyd.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #67
Message-Id: <199809220045.KAA18651@cassius.ee.usyd.edu.au>

>
> I have recently found problems opening my files in NIH Image with the
> message "File cannot be opened as the application PC can not be found"
> appearing. These 8 bit Tiff files have been made on a PC using Optimas and
> saved on to the floppy disc drive. I have previously only had similar
> problems opening files if they were saved onto the hard drive and then
> copied onto a disc. Any suggestions?


Straight off the top of my head, I'd say the filetype has been set to "PC" or
somesuch by PC exchange (or whatever you used to read a PC disk on the Mac),
hence the whinge. If you get one of the filetype changers from the info-mac
archive (sunsite.anu.edu.au/pub/mac/info-mac), such as Snitch, you could
change the filetype to one NIH-image expects (I don't know offhand, but check
a tiff file that Image can open with no problems). Or open the tiff file with
Graphic Converter (also from info-mac) and save it again.

--
Dr Adrian Whichello                                  Phone: +61 2 9351 5339
Imaging Science and Engineering Laboratory             Fax: +61 2 9351 3847
Sydney University Electrical Engineering      Email: adrianw@ee.usyd.edu.au
Australia                           WWW: http://www.ee.usyd.edu.au/~adrianw

"I wish to God these calculations had been executed by Steam!" - C. Babbage

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

Date: Tue, 22 Sep 1998 15:18:04 -0500
From: Laird Bloom <lbloom@MIT.EDU>
To: nih-image-d@io.ece.drexel.edu
Subject: vessel area, length, branching measurements
Message-Id: <v03020900b22db5bd69e6@[18.155.0.106]>
Content-Type: text/plain; charset="us-ascii"

I'm looking for macros to analyze blood vessel morphology, particularly to
measure degrees of branching or branches per unit length.  I've heard of
the BRANching program; can someone tell me where to find it?  Does anyone
know of a program that draws a grid and measures how often vessels cross a
gridline?
Thanks
Laird Bloom
MIT Center for Cancer Research

--------------------------------
End of nih-image-d Digest V98 Issue #68
***************************************

From nih-image-request@io.ece.drexel.edu Wed Sep 23 08:54 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA23269;
	Wed, 23 Sep 1998 08:52:45 -0400 (EDT)
Resent-Date: Wed, 23 Sep 1998 08:52:45 -0400 (EDT)
Date: Wed, 23 Sep 1998 14:34:10 +0200
From: Ard Jonker <a.jonker@AMC.UVA.NL>
Subject: Autowand/AutoOutline touching edge
In-reply-to: <199809221922.PAA08372@io.ece.drexel.edu>
X-Sender: ajonker.public.amc@reddwarf.amc.uva.nl
To: nih-image@io.ece.drexel.edu
Message-id: <l03110702b22e94571ee8@[145.117.43.50]>
MIME-version: 1.0
Content-transfer-encoding: 7BIT
Resent-Message-ID: <"iEGlV2.0.7H5.8kE2s"@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/375
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:   395
Status: O

Hello List,

I want to discard measurements with AutoWand on and AutoOutline, if the outline touches the edge. The result would be similar to measuring one particle which touches the edge in AnalyseParticles: no measurement is taken.

Is there a clever way, short of checking all outline coordinates for the condition of x- and y coordinates both being an image edge coordinate?

Regards, Ard


From nih-image-request@io.ece.drexel.edu Wed Sep 23 12:08 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA10866;
	Wed, 23 Sep 1998 12:08:45 -0400 (EDT)
Resent-Date: Wed, 23 Sep 1998 12:08:45 -0400 (EDT)
Message-ID: <36092776.B0243E80@netmatters.co.uk>
Date: Wed, 23 Sep 1998 16:53:25 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
Reply-To: brownj@netmatters.co.uk
Organization: brownj@netmatters.co.uk
X-Mailer: Mozilla 4.05 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: Autowand/AutoOutline touching edge
References: <l03110702b22e94571ee8@[145.117.43.50]>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"klhTm2.0.NI2.DaH2s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/376
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length:  1951
Status: O



Ard Jonker wrote:

> Hello List,
>
> I want to discard measurements with AutoWand on and AutoOutline, if the outline touches the edge. The result would be similar to measuring one particle which touches the edge in AnalyseParticles: no measurement is taken.
>
> Is there a clever way, short of checking all outline coordinates for the condition of x- and y coordinates both being an image edge coordinate?
>
> Regards, Ard

Ard, the following procedure can be used to delete binary objects touching the edge of a Rectangular ROI. You may be able to make use of it as follow.....

Duplicate the image
Threshold & make binary
Use the procedure below
Analyze particle (X,Y)
Then use the X,Y coordinates (i=1 to rCount) + the threshold & Autooutline on your original image.

In Object image you can then convert each ROI into an object thus saving the roi for further analysis. This is a really nice way of marking up objects non-destructively + you get permanent ROIs and area values stored in the
object file.


Jeremy


Procedure DeleteTouching;
begin
   SetThreshold(1);
   MakeBinary;
   WandAutoMeasure(false);
   GetROI(left,top,width,height);
   MakeLineROI(left,top,left+width-1,top);
   Drawboundary;
   AutoOutline(left,top);
   Clear;
   SetThreshold(1);
   MakeBinary;
   MakeLineROI(left,top,left,top+Height-1);
   Drawboundary;
   AutoOutline(left,top);
   Clear;
   SetThreshold(1);
   MakeBinary;
   MakeLineROI(left+width-1,top,left+width-1,top+Height-1);
   Drawboundary;
   AutoOutline(left+width-1,top);
   Clear;
   SetThreshold(1);
   MakeBinary;
   MakeLineROI(left,top+Height-1,left+width-1,top+Height-1);
   Drawboundary;
   AutoOutline(left,top+Height-1);
   Clear;
   SetThreshold(1);
   MakeBinary;
end;



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

Jeremy Brown
Moredun Research Institute/Edinburgh University
http://www.netmatters.co.uk/users/brownj/HomePage.html

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

From nih-image-request@io.ece.drexel.edu Wed Sep 23 17:48 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA12385;
	Wed, 23 Sep 1998 17:48:42 -0400 (EDT)
Resent-Date: Wed, 23 Sep 1998 17:48:42 -0400 (EDT)
Message-Id: <199809232131.RAA11128@io.ECE.Drexel.EDU>
X-Mailer: Windows Eudora Version 1.4.3
Mime-Version: 1.0
Date: Thu, 24 Sep 1998 09:27:03 +1200
To: nih-image@io.ece.drexel.edu
From: C.J.Trevillian@massey.ac.nz (Cristy Trevillian)
Subject: macro for calibration
Resent-Message-ID: <"2N-2m.0.Mk2.AZM2s"@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/377
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:   936
Status: O

I am an image neophyte and am looking for a macro which will work in
Scion-image to achieve the following steps to calibrate a radiographic image:

The image has a thin circle of stainless steel for calibration.
I need to threshold the image and identify the pixels which are inside the
circle on the image.  
Then use an area based calibration method based on identifying the
co-ordinates of all the pixels inside the circle, then calculate the mean
and standard deviation of the X co-ordinates and the Y co-ordinates.  Then
calculate an aspect ratio using the ratio of the standard deviations of the
X and Y co-ordinates.

I am unfamiliar with writing macros which function inside Scion-image.  Can
anyone help me with a macro for this series of tasks?


Thanks


Cristy Trevillian
Cristy Trevillian BSc BVMS
Assistant Lecturer Equine Studies
Massey University
Private Bag 11222
Palmerston North, New Zealand
64 6 350 5329 extn 7494

From nih-image-request@io.ece.drexel.edu Wed Sep 23 23:18 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id XAA13422;
	Wed, 23 Sep 1998 23:18:06 -0400 (EDT)
Resent-Date: Wed, 23 Sep 1998 23:18:06 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: a.jonker@AMC.UVA.NL, nih-image@io.ece.drexel.edu
Date:          Thu, 24 Sep 1998 13:02:26 GMT+1000
Subject:       Re: Autowand/AutoOutline touching edge
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <98843D70C58@rna.bio.mq.edu.au>
Resent-Message-ID: <"v5W0b2.0.ao2.1NR2s"@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/378
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length:  2886
Status: O

>Received: from SpoolDir by RNA (Mercury 1.43); 23 Sep 98 22:51:39 +1000
>Return-path: <nih-image-request@io.ece.drexel.edu> 
>Received: from io.ece.drexel.edu (144.118.32.3) by rna.bio.mq.edu.au (Mercury 
>1.43) with ESMTP;
>    23 Sep 98 22:51:29 +1000
>Received: (from lists@localhost)
>	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA22869;
>	Wed, 23 Sep 1998 08:49:24 -0400 (EDT)
>Resent-Date: Wed, 23 Sep 1998 08:49:24 -0400 (EDT)
>Date: Wed, 23 Sep 1998 14:34:10 +0200
>From: Ard Jonker <a.jonker@AMC.UVA.NL>
>Subject: Autowand/AutoOutline touching edge
>In-reply-to: <199809221922.PAA08372@io.ece.drexel.edu>
>X-Sender: ajonker.public.amc@reddwarf.amc.uva.nl
>To: nih-image@io.ece.drexel.edu
>Message-id: <l03110702b22e94571ee8@[145.117.43.50]>
>MIME-version: 1.0
>Content-type: text/plain; charset="us-ascii"
>Content-transfer-encoding: 7BIT
>Resent-Message-ID: <"iEGlV2.0.7H5.8kE2s"@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/375
>X-Loop: nih-image@biomed.drexel.edu
>Precedence: list
>Resent-Sender: nih-image-request@io.ece.drexel.edu
>X-PMFLAGS: 34078848 0
>
>Hello List,
>
>I want to discard measurements with AutoWand on and AutoOutline, if the 
>outline touches the edge. The result would be similar to measuring one 
>particle which touches the edge in AnalyseParticles: no
>measurement is taken.
>
>Is there a clever way, short of checking all outline coordinates for the 
>condition of x- and y coordinates both being an image edge coordinate?
>
>Regards, Ard
>

Ard,
    Checking x-y coords would in fact be problematic as x-y coordinates as 
returned by NIH-Image ( and Object-Image etc) do not return coords of outline 
boundary but the coords for a QuickDraw Region which are a pixel outside 
Outline along bottom and right ( see archives for many discussions).

The function below will simply test if the current ROI touches the edge.
(note be wary about changing selectPic to choosePic where restoreRoi is used).

var boundaryId:integer;

function touchBoundary:boolean;
	var pid,n,mean,mode,min,max:integer;
	begin
  pid:=pidNumber;
  if not PidExists(boundaryId) then begin 
    selectAll;duplicate('boundary');
    boundaryId:=pidNumber;selectPic(pid);restoreRoi;
    selectPic(boundaryId);
    setBackGround(0);setForeGround(255);clear;drawBoundary;killroi;
    selectPic(pid);
    end;
  selectPic(boundaryId);restoreRoi;
  measure;getResults(n,mean,mode,min,max);setCounter(rCount-1);
  selectPic(pid);
  if max=0 then touchBoundary:=false else touchBoundary:=true;
  end

macro'/0 does ROI touch [B]oundary'; begin showMessage(touchBoundary);end;

Regards,
        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-d-request@io.ece.drexel.edu Thu Sep 24 06:21 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA26840;
	Thu, 24 Sep 1998 06:21:21 -0400 (EDT)
Date: Thu, 24 Sep 1998 06:21:21 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809241021.GAA26840@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #69
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/69
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length:  7937
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 69

Today's Topics:
  Autowand/AutoOutline touching edge    [ Ard Jonker <a.jonker@AMC.UVA.NL> ]
  Re: Autowand/AutoOutline touching ed  [ Jeremy Brown <brownj@netmatters.co. ]
  macro for calibration                 [ C.J.Trevillian@massey.ac.nz (Cristy ]
  Re: Autowand/AutoOutline touching ed  [ GJOSS@rna.bio.mq.edu.au ]

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

Date: Wed, 23 Sep 1998 14:34:10 +0200
From: Ard Jonker <a.jonker@AMC.UVA.NL>
To: nih-image@io.ece.drexel.edu
Subject: Autowand/AutoOutline touching edge
Message-id: <l03110702b22e94571ee8@[145.117.43.50]>
Content-type: text/plain; charset="us-ascii"
Content-transfer-encoding: 7BIT

Hello List,

I want to discard measurements with AutoWand on and AutoOutline, if the outline touches the edge. The result would be similar to measuring one particle which touches the edge in AnalyseParticles: no measurement is taken.

Is there a clever way, short of checking all outline coordinates for the condition of x- and y coordinates both being an image edge coordinate?

Regards, Ard

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

Date: Wed, 23 Sep 1998 16:53:25 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Autowand/AutoOutline touching edge
Message-ID: <36092776.B0243E80@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Ard Jonker wrote:

> Hello List,
>
> I want to discard measurements with AutoWand on and AutoOutline, if the outline touches the edge. The result would be similar to measuring one particle which touches the edge in AnalyseParticles: no measurement is taken.
>
> Is there a clever way, short of checking all outline coordinates for the condition of x- and y coordinates both being an image edge coordinate?
>
> Regards, Ard

Ard, the following procedure can be used to delete binary objects touching the edge of a Rectangular ROI. You may be able to make use of it as follow.....

Duplicate the image
Threshold & make binary
Use the procedure below
Analyze particle (X,Y)
Then use the X,Y coordinates (i=1 to rCount) + the threshold & Autooutline on your original image.

In Object image you can then convert each ROI into an object thus saving the roi for further analysis. This is a really nice way of marking up objects non-destructively + you get permanent ROIs and area values stored in the
object file.


Jeremy


Procedure DeleteTouching;
begin
   SetThreshold(1);
   MakeBinary;
   WandAutoMeasure(false);
   GetROI(left,top,width,height);
   MakeLineROI(left,top,left+width-1,top);
   Drawboundary;
   AutoOutline(left,top);
   Clear;
   SetThreshold(1);
   MakeBinary;
   MakeLineROI(left,top,left,top+Height-1);
   Drawboundary;
   AutoOutline(left,top);
   Clear;
   SetThreshold(1);
   MakeBinary;
   MakeLineROI(left+width-1,top,left+width-1,top+Height-1);
   Drawboundary;
   AutoOutline(left+width-1,top);
   Clear;
   SetThreshold(1);
   MakeBinary;
   MakeLineROI(left,top+Height-1,left+width-1,top+Height-1);
   Drawboundary;
   AutoOutline(left,top+Height-1);
   Clear;
   SetThreshold(1);
   MakeBinary;
end;



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

Jeremy Brown
Moredun Research Institute/Edinburgh University
http://www.netmatters.co.uk/users/brownj/HomePage.html

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

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

Date: Thu, 24 Sep 1998 09:27:03 +1200
From: C.J.Trevillian@massey.ac.nz (Cristy Trevillian)
To: nih-image@io.ece.drexel.edu
Subject: macro for calibration
Message-Id: <199809232131.RAA11128@io.ECE.Drexel.EDU>
Content-Type: text/plain; charset="us-ascii"

I am an image neophyte and am looking for a macro which will work in
Scion-image to achieve the following steps to calibrate a radiographic image:

The image has a thin circle of stainless steel for calibration.
I need to threshold the image and identify the pixels which are inside the
circle on the image.  
Then use an area based calibration method based on identifying the
co-ordinates of all the pixels inside the circle, then calculate the mean
and standard deviation of the X co-ordinates and the Y co-ordinates.  Then
calculate an aspect ratio using the ratio of the standard deviations of the
X and Y co-ordinates.

I am unfamiliar with writing macros which function inside Scion-image.  Can
anyone help me with a macro for this series of tasks?


Thanks


Cristy Trevillian
Cristy Trevillian BSc BVMS
Assistant Lecturer Equine Studies
Massey University
Private Bag 11222
Palmerston North, New Zealand
64 6 350 5329 extn 7494

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

Date:          Thu, 24 Sep 1998 13:02:26 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: a.jonker@AMC.UVA.NL, nih-image@io.ece.drexel.edu
Subject:       Re: Autowand/AutoOutline touching edge
Message-ID: <98843D70C58@rna.bio.mq.edu.au>

>Received: from SpoolDir by RNA (Mercury 1.43); 23 Sep 98 22:51:39 +1000
>Return-path: <nih-image-request@io.ece.drexel.edu> 
>Received: from io.ece.drexel.edu (144.118.32.3) by rna.bio.mq.edu.au (Mercury 
>1.43) with ESMTP;
>    23 Sep 98 22:51:29 +1000
>Received: (from lists@localhost)
>	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA22869;
>	Wed, 23 Sep 1998 08:49:24 -0400 (EDT)
>Resent-Date: Wed, 23 Sep 1998 08:49:24 -0400 (EDT)
>Date: Wed, 23 Sep 1998 14:34:10 +0200
>From: Ard Jonker <a.jonker@AMC.UVA.NL>
>Subject: Autowand/AutoOutline touching edge
>In-reply-to: <199809221922.PAA08372@io.ece.drexel.edu>
>X-Sender: ajonker.public.amc@reddwarf.amc.uva.nl
>To: nih-image@io.ece.drexel.edu
>Message-id: <l03110702b22e94571ee8@[145.117.43.50]>
>MIME-version: 1.0
>Content-type: text/plain; charset="us-ascii"
>Content-transfer-encoding: 7BIT
>Resent-Message-ID: <"iEGlV2.0.7H5.8kE2s"@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/375
>X-Loop: nih-image@biomed.drexel.edu
>Precedence: list
>Resent-Sender: nih-image-request@io.ece.drexel.edu
>X-PMFLAGS: 34078848 0
>
>Hello List,
>
>I want to discard measurements with AutoWand on and AutoOutline, if the 
>outline touches the edge. The result would be similar to measuring one 
>particle which touches the edge in AnalyseParticles: no
>measurement is taken.
>
>Is there a clever way, short of checking all outline coordinates for the 
>condition of x- and y coordinates both being an image edge coordinate?
>
>Regards, Ard
>

Ard,
    Checking x-y coords would in fact be problematic as x-y coordinates as 
returned by NIH-Image ( and Object-Image etc) do not return coords of outline 
boundary but the coords for a QuickDraw Region which are a pixel outside 
Outline along bottom and right ( see archives for many discussions).

The function below will simply test if the current ROI touches the edge.
(note be wary about changing selectPic to choosePic where restoreRoi is used).

var boundaryId:integer;

function touchBoundary:boolean;
	var pid,n,mean,mode,min,max:integer;
	begin
  pid:=pidNumber;
  if not PidExists(boundaryId) then begin 
    selectAll;duplicate('boundary');
    boundaryId:=pidNumber;selectPic(pid);restoreRoi;
    selectPic(boundaryId);
    setBackGround(0);setForeGround(255);clear;drawBoundary;killroi;
    selectPic(pid);
    end;
  selectPic(boundaryId);restoreRoi;
  measure;getResults(n,mean,mode,min,max);setCounter(rCount-1);
  selectPic(pid);
  if max=0 then touchBoundary:=false else touchBoundary:=true;
  end

macro'/0 does ROI touch [B]oundary'; begin showMessage(touchBoundary);end;

Regards,
        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

--------------------------------
End of nih-image-d Digest V98 Issue #69
***************************************

From nih-image-request@io.ece.drexel.edu Thu Sep 24 12:45 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA05285;
	Thu, 24 Sep 1998 12:45:36 -0400 (EDT)
Resent-Date: Thu, 24 Sep 1998 12:45:36 -0400 (EDT)
Date: Thu, 24 Sep 1998 12:31:50 -0700
From: Abby Pike <Pike_c1@hnrc.tufts.edu>
Subject: subscribe
X-Sender: Pike_c1@email.hnrc.tufts.edu (Unverified)
To: nih-image@io.ece.drexel.edu
Message-id: <3.0.5.32.19980924123150.00798680@email.hnrc.tufts.edu>
MIME-version: 1.0
X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32)
Content-transfer-encoding: 7BIT
Resent-Message-ID: <"v_uL7.0.yl.z7d2s"@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/379
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:    35
Status: O

subscribe nih-image <abby> <pike>

From nih-image-request@io.ece.drexel.edu Thu Sep 24 13:09 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA07369;
	Thu, 24 Sep 1998 13:09:33 -0400 (EDT)
Resent-Date: Thu, 24 Sep 1998 13:09:33 -0400 (EDT)
Reply-To: <FVLamberti@worldnet.att.net>
From: "Francis Lamberti" <FVLamberti@worldnet.att.net>
To: <nih-image@io.ece.drexel.edu>
Subject: request for a "cell" tracking macro
Date: Thu, 24 Sep 1998 09:59:41 -0700
Message-ID: <001b01bde7dc$b8c85500$51b4400c@lamberti>
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
X-Priority: 3 (Normal)
X-MSMail-Priority: Normal
X-Mailer: Microsoft Outlook 8.5, Build 4.71.2377.0
Importance: Normal
In-Reply-To: <199809241015.GAA26131@io.ece.drexel.edu>
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2120.0
Resent-Message-ID: <"jgVQf1.0.WQ1.AZd2s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/380
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Length:  1407
Status: O

Hello Fellow Imagers :
I am using NIH image (and Scion's PC Image) to measure the release of dye
from a gel particle suspended in wash solutions of varying composition.
Currently I have been doing a manual method of creating a stack of
time-lapse images, defining a ROI in the center of each bead, measuring the
Grey level, and then moving to the next image in the stack while retaining
the ROI. A similar series of measurements are performed outside the bead to
obtain background grey levels.  The ratio of these measurements yields the
light transmission through stained bead.  By measuring the diameter of the
bead, (again in each image of the stack, since the bead swell with time),
the concentration of dye can be calculated from the absorbance measurement.

Unfortunately, the beads being spherical tend to move around as they swell
and release dye. To minimize errors in measurements I am forced to move the
ROI of each bead center and each bead background in each image of the stack.

Does anyone out there have or know of a macro that allows one to "track"
cells (or other objects) through a series of images in a stack; create a
mask around cell and measure the grey level at a central ROI in the cell;
the grey level at a ROI outside the cell boundary, and the cell size ??

Any help on any part of this would be greatly appreciated.

Thanks in advance to all

Francis Lamberti
Neocrin Company.

From nih-image-request@io.ece.drexel.edu Thu Sep 24 15:25 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA21808;
	Thu, 24 Sep 1998 15:25:15 -0400 (EDT)
Resent-Date: Thu, 24 Sep 1998 15:25:15 -0400 (EDT)
Date: Thu, 24 Sep 1998 12:32:40 -0700
From: Abby Pike <Pike_c1@hnrc.tufts.edu>
Subject: subscribe
X-Sender: Pike_c1@email.hnrc.tufts.edu (Unverified)
To: nih-image@io.ece.drexel.edu
Message-id: <3.0.5.32.19980924123240.0079c160@email.hnrc.tufts.edu>
MIME-version: 1.0
X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32)
Content-transfer-encoding: 7BIT
Resent-Message-ID: <"uw69H1.0.dw4.yXf2s"@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/381
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:    35
Status: O

subscribe nih-image <abby> <pike>

From nih-image-request@io.ece.drexel.edu Thu Sep 24 15:45 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA23484;
	Thu, 24 Sep 1998 15:45:18 -0400 (EDT)
Resent-Date: Thu, 24 Sep 1998 15:45:18 -0400 (EDT)
Date: Thu, 24 Sep 1998 15:42:09 -0400
From: lipman_pa@hnrc.tufts.edu (Ruth Lipman)
Subject: Re: subscribe
X-Sender: lipman_pa@email.hnrc.tufts.edu
To: nih-image@io.ece.drexel.edu
Message-id: <01J26U9TCGAA9B3SB9@hnrc.tufts.edu>
MIME-version: 1.0
Content-transfer-encoding: 7BIT
Resent-Message-ID: <"KqGkb3.0.tT5.7wf2s"@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/382
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:    67
Status: O

>subscribe nih-image <abby> <pike>

Nope, it came through again.


From nih-image-request@io.ece.drexel.edu Thu Sep 24 16:55 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA28662;
	Thu, 24 Sep 1998 16:55:53 -0400 (EDT)
Resent-Date: Thu, 24 Sep 1998 16:55:53 -0400 (EDT)
Message-Id: <v03007822b2305d7cb6a4@[144.118.33.245]>
In-Reply-To: <3.0.5.32.19980924123240.0079c160@email.hnrc.tufts.edu>
Mime-Version: 1.0
Date: Thu, 24 Sep 1998 16:35:41 -0400
To: nih-image@io.ece.drexel.edu
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: Re: subscribe
Resent-Message-ID: <"uTAa41.0.rc6.Sqg2s"@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/383
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/enriched; charset="us-ascii"
Content-Length:  3792
Status: O

>subscribe nih-image <<abby> <<pike>


<fontfamily><param>Times</param>The following is a reminder to everyone
regarding administrative issues on the list. Those who desire the
digest form, should unsubscribe from the regular list and resubscribe
to the digest list.


e-mail addresses of importance

--------

nih-image@biomed.drexel.edu   - Sends mail to the list

nih-image-request@biomed.drexel.edu   - Administation for List

nih-image-d-request@biomed.drexel.edu  - Aministration for Digest


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".


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

		Subject: unsubscribe



Unsubscribe to Digest

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

To unsubscribe to digested version of the list, send E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "unsubscribe".


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

		Subject: unsubscribe


Help

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

To obtain a listing of help items, send E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "help".


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

		Subject: help




Help on Digest

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

To obtain a listing of help items on digest version of the list, send
E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "help".


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

		Subject: help




Archive

-------

Every submission sent to this list is archived.	 Following are the
commands

used to access the archive.  Send Email to nih-image-request with the
command 

in the Subject line or in the body of the message.


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


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/*

</fontfamily>

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

                                  Jonathan Nissanov, Ph.D.

                                      Associate Director  

            Computer Vision Center for Vertebrate Brain Mapping,

                a NIH Biomedical Research Technology Resource

                                http://cbis.ece.drexel.edu/ICVC/

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

Imaging and Computer Vision Center              Tel: 215-895-1381

Drexel University                                                  
Fax: 215-895-4987

Phildelphia, PA 19104                                        
yoni@coe.drexel.edu

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

      

     And remember, the early bird may get the worm, but the second
mouse gets the cheese.

From nih-image-request@io.ece.drexel.edu Thu Sep 24 20:16 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA11576;
	Thu, 24 Sep 1998 20:16:27 -0400 (EDT)
Resent-Date: Thu, 24 Sep 1998 20:16:27 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: a.jonker@AMC.UVA.NL, nih-image@io.ece.drexel.edu
Date:          Fri, 25 Sep 1998 10:07:45 GMT+1000
Subject:       Re: Autowand/AutoOutline touching edge
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <99D5B8F5EC5@rna.bio.mq.edu.au>
Resent-Message-ID: <"lpCd2.0.CY2.zuj2s"@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/384
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length:  1429
Status: O

>Date: Wed, 23 Sep 1998 14:34:10 +0200
>From: Ard Jonker <a.jonker@AMC.UVA.NL>
>
>I want to discard measurements with AutoWand on and AutoOutline, if the 
>outline touches the edge. The result would be similar to measuring one 
>particle which touches the edge in AnalyseParticles: no
>measurement is taken.
>
>Is there a clever way, short of checking all outline coordinates for the 
>condition of x- and y coordinates both being an image edge coordinate?
>
>Regards, Ard
>

I responded to Ard's post yesterday with a macro which tested for the above by 
measure'ing whether a drawboundary pixel was included in the selection and 
commented that checking of xycoordinate list would have been problematic.

In exchange with Ard, he has since suggested that it would only be necessary to 
test the coords of the bounding rectangle (available via getRoi()). This is a 
much simpler and more elegant solution ( avoids problem with x,ycoordinates 
array values).

function touchBoundary:boolean;
	var x,y,w,h,pw,ph:integer;
	begin getRoi(x,y,w,h);getPicSize(pw,ph);
 if (x<=0) or (y<=0) or (x+w>=pw) or (y+h>=ph) then
 touchBoundary:=true else touchBoundary:=false;
 end

macro'/0 does ROI touch [B]oundary'; begin showMessage(touchBoundary);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 Thu Sep 24 20:54 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA14286;
	Thu, 24 Sep 1998 20:54:34 -0400 (EDT)
Resent-Date: Thu, 24 Sep 1998 20:54:34 -0400 (EDT)
Mime-Version: 1.0
X-Sender: scm@128.250.6.196
Message-Id: <v04011700b230971f981f@[128.250.109.214]>
In-Reply-To: <99D5B8F5EC5@rna.bio.mq.edu.au>
Date: Fri, 25 Sep 1998 10:43:58 +1000
To: nih-image@io.ece.drexel.edu
From: Steve Martin <s.martin@physio.unimelb.EDU.AU>
Subject: Re: Autowand/AutoOutline touching edge
Resent-Message-ID: <"FABSY1.0.VH3.VTk2s"@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/385
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:  1824
Status: O

another thought:
draw a 1 pixel wide line on all boundaries, and select or fill, starting at
1,1. The fill or selection should include areas touching the boundary which
are the same level/binary state. (?)

Steve Martin
School of Physiotherapy
The University of Melbourne

At 8:07 PM +1000 on 25/9/98, GJOSS@rna.bio.mq.edu.au wrote:
> >Date: Wed, 23 Sep 1998 14:34:10 +0200
> >From: Ard Jonker <a.jonker@AMC.UVA.NL>
> >
> >I want to discard measurements with AutoWand on and AutoOutline, if the
> >outline touches the edge. The result would be similar to measuring one
> >particle which touches the edge in AnalyseParticles: no
> >measurement is taken.
> >
> >Is there a clever way, short of checking all outline coordinates for the
> >condition of x- and y coordinates both being an image edge coordinate?
> >
> >Regards, Ard
> >
>
> I responded to Ard's post yesterday with a macro which tested for the
>above by
> measure'ing whether a drawboundary pixel was included in the selection and
> commented that checking of xycoordinate list would have been problematic.
>
> In exchange with Ard, he has since suggested that it would only be
>necessary to
> test the coords of the bounding rectangle (available via getRoi()). This
>is a
> much simpler and more elegant solution ( avoids problem with x,ycoordinates
> array values).
>
> function touchBoundary:boolean;
> 	var x,y,w,h,pw,ph:integer;
> 	begin getRoi(x,y,w,h);getPicSize(pw,ph);
>  if (x<=0) or (y<=0) or (x+w>=pw) or (y+h>=ph) then
>  touchBoundary:=true else touchBoundary:=false;
>  end
>
> macro'/0 does ROI touch [B]oundary'; begin showMessage(touchBoundary);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 Fri Sep 25 00:18 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id AAA01000;
	Fri, 25 Sep 1998 00:18:28 -0400 (EDT)
Resent-Date: Fri, 25 Sep 1998 00:18:28 -0400 (EDT)
Message-ID: <360B1A0A.4F14D237@purdue.edu>
Date: Thu, 24 Sep 1998 23:20:30 -0500
From: Kris Jorgensen <kris@purdue.edu>
X-Mailer: Mozilla 4.05 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image <nih-image@io.ece.drexel.edu>
Subject: get current cell
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"vXMdx2.0.bE7.CSn2s"@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/386
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:   629
Status: O

In Object-Image, I need to get the cell number of the open cell.  While
creating an object in a macro I ask the user for a couple input values that I
need to put into static columns so I need to know which row to put those
values.  If I am always working on the last image listed in the info card then
I can use nCount but if I am working on another image I can't get the cell
number to store this other information.

If anyone has a way to get the current cell please let me know.

Kris
-- 
Kris L. Jorgensen
Office:     ME 183
Phone:      (765) 494-8585
Email:      kris@purdue.edu
WWW:        http://www.ecn.purdue.edu/~kris

From nih-image-request@io.ece.drexel.edu Fri Sep 25 01:12 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id BAA05566;
	Fri, 25 Sep 1998 01:12:22 -0400 (EDT)
Resent-Date: Fri, 25 Sep 1998 01:12:22 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: kris@purdue.edu, nih-image@io.ece.drexel.edu
Date:          Fri, 25 Sep 1998 15:06:42 GMT+1000
Subject:       Re: get current cell
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <9A257552679@rna.bio.mq.edu.au>
Resent-Message-ID: <"caN5N3.0.o91.CHo2s"@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/387
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length:  1331
Status: O

>Date: Thu, 24 Sep 1998 23:20:30 -0500
>From: Kris Jorgensen <kris@purdue.edu>
>
>In Object-Image, I need to get the cell number of the open cell.  While
>creating an object in a macro I ask the user for a couple input values that I
>need to put into static columns so I need to know which row to put those
>values.  If I am always working on the last image listed in the info card then
>I can use nCount but if I am working on another image I can't get the cell
>number to store this other information.
>
>If anyone has a way to get the current cell please let me know.
>
>Kris

Function 'selectedCell' does the job as the name implies :-)
and the following will demonstrate.
Respond '0' or just return to 'cell' query and the 'selectedCell' will be 
shown. Otherwise enter cell/object and cell/object will be selected and shown.

macro'[t]est';
var width, height, slices, pid,cell:integer;
name:string;
begin
cell:=getNumber('cell',0);
if cell<>0 then begin
  selectCell(cell);
  selectObject(getNumber('Object',1));
  GetPicInfo(width, height, slices, pid, name);
  selectPic(pid);
  showCell(cell,true);
  end;
showMessage(selectedCell);
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 Fri Sep 25 05:47 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA27202;
	Fri, 25 Sep 1998 05:47:34 -0400 (EDT)
Resent-Date: Fri, 25 Sep 1998 05:47:34 -0400 (EDT)
X-Sender: pickerin@utct.ct.utwente.nl
Message-Id: <l03010d03b2312108bfe3@[130.89.52.166]>
Mime-Version: 1.0
Date: Fri, 25 Sep 1998 11:32:50 +0100
To: nih-image@io.ece.drexel.edu
From: Jason Pickering <J.P.Pickering@ct.utwente.nl>
Subject: Counting and Sending Pixels
Resent-Message-ID: <"ej4_f1.0.uL6.MFs2s"@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/388
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:  1061
Status: O

Hello everyone,
	I would like to perform a density slice on a live digitized image,
and then count the number of pixels that fall within that density slice.
Then, I would like to use the Scion LG-3's two analog channels to send a
signal proportional to the number of pixels measured. I have written a
macro that sucessfully does this, but I would like to modify the source
code to increase the performance of this routine.

Has anyone had any experience doing something similar? If so, any tips and
possible pitfalls would be very much appreciated.

Thanks,
Jason P. Pickering

___________________________________________________________________________
Jason Pickering				|Email: J.P.Pickering@ct.utwente.nl
Onderzoeker in opleiding		|Tel: xx 31 53 489 3137
Polymeer Materiaalkundevakgroep		|Fax: xx 31 53 489 3823
Universiteit Twente		  	|Priv. addr.:
Faculteit der Chemische Technologie	|van Loenshof 8D
Postbus 217				|7511 HG Enschede
7500 AE Enschede		  	|
The Netherlands				|
__________________________________________________________________________


From nih-image-d-request@io.ece.drexel.edu Fri Sep 25 05:56 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA28066;
	Fri, 25 Sep 1998 05:56:33 -0400 (EDT)
Date: Fri, 25 Sep 1998 05:56:33 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809250956.FAA28066@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #70
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/70
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 15872
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 70

Today's Topics:
  unsubscribe digest                    [ szczesny@umich.edu ]
  subscribe                             [ Abby Pike <Pike_c1@hnrc.tufts.edu> ]
  request for a "cell" tracking macro   [ "Francis Lamberti" <FVLamberti@worl ]
  subscribe                             [ Abby Pike <Pike_c1@hnrc.tufts.edu> ]
  Re: subscribe                         [ lipman_pa@hnrc.tufts.edu (Ruth Lipm ]
  Re: subscribe                         [ Jonathan Nissanov <yoni@cbis.ece.dr ]
  Re: Autowand/AutoOutline touching ed  [ GJOSS@rna.bio.mq.edu.au ]
  Re: Autowand/AutoOutline touching ed  [ Steve Martin <s.martin@physio.unime ]
  get current cell                      [ Kris Jorgensen <kris@purdue.edu> ]
  Re: get current cell                  [ GJOSS@rna.bio.mq.edu.au ]
  Counting and Sending Pixels           [ Jason Pickering <J.P.Pickering@ct.u ]

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

Date: Thu, 24 Sep 1998 10:35:33 -0400
From: szczesny@umich.edu
To: nih-image-d@io.ece.drexel.edu
Subject: unsubscribe digest
Message-ID: <MailDrop1.2d7.980924103533@141-211-226-155.dent.umich.edu>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII


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

Date: Thu, 24 Sep 1998 12:31:50 -0700
From: Abby Pike <Pike_c1@hnrc.tufts.edu>
To: nih-image@io.ece.drexel.edu
Subject: subscribe
Message-id: <3.0.5.32.19980924123150.00798680@email.hnrc.tufts.edu>
Content-type: text/plain; charset="us-ascii"
Content-transfer-encoding: 7BIT

subscribe nih-image <abby> <pike>

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

Date: Thu, 24 Sep 1998 09:59:41 -0700
From: "Francis Lamberti" <FVLamberti@worldnet.att.net>
To: <nih-image@io.ece.drexel.edu>
Subject: request for a "cell" tracking macro
Message-ID: <001b01bde7dc$b8c85500$51b4400c@lamberti>
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 7bit

Hello Fellow Imagers :
I am using NIH image (and Scion's PC Image) to measure the release of dye
from a gel particle suspended in wash solutions of varying composition.
Currently I have been doing a manual method of creating a stack of
time-lapse images, defining a ROI in the center of each bead, measuring the
Grey level, and then moving to the next image in the stack while retaining
the ROI. A similar series of measurements are performed outside the bead to
obtain background grey levels.  The ratio of these measurements yields the
light transmission through stained bead.  By measuring the diameter of the
bead, (again in each image of the stack, since the bead swell with time),
the concentration of dye can be calculated from the absorbance measurement.

Unfortunately, the beads being spherical tend to move around as they swell
and release dye. To minimize errors in measurements I am forced to move the
ROI of each bead center and each bead background in each image of the stack.

Does anyone out there have or know of a macro that allows one to "track"
cells (or other objects) through a series of images in a stack; create a
mask around cell and measure the grey level at a central ROI in the cell;
the grey level at a ROI outside the cell boundary, and the cell size ??

Any help on any part of this would be greatly appreciated.

Thanks in advance to all

Francis Lamberti
Neocrin Company.

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

Date: Thu, 24 Sep 1998 12:32:40 -0700
From: Abby Pike <Pike_c1@hnrc.tufts.edu>
To: nih-image@io.ece.drexel.edu
Subject: subscribe
Message-id: <3.0.5.32.19980924123240.0079c160@email.hnrc.tufts.edu>
Content-type: text/plain; charset="us-ascii"
Content-transfer-encoding: 7BIT

subscribe nih-image <abby> <pike>

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

Date: Thu, 24 Sep 1998 15:42:09 -0400
From: lipman_pa@hnrc.tufts.edu (Ruth Lipman)
To: nih-image@io.ece.drexel.edu
Subject: Re: subscribe
Message-id: <01J26U9TCGAA9B3SB9@hnrc.tufts.edu>
Content-type: text/plain; charset="us-ascii"
Content-transfer-encoding: 7BIT

>subscribe nih-image <abby> <pike>

Nope, it came through again.

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

Date: Thu, 24 Sep 1998 16:35:41 -0400
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: subscribe
Message-Id: <v03007822b2305d7cb6a4@[144.118.33.245]>
Content-Type: text/enriched; charset="us-ascii"

>subscribe nih-image <<abby> <<pike>


<fontfamily><param>Times</param>The following is a reminder to everyone
regarding administrative issues on the list. Those who desire the
digest form, should unsubscribe from the regular list and resubscribe
to the digest list.


e-mail addresses of importance

--------

nih-image@biomed.drexel.edu   - Sends mail to the list

nih-image-request@biomed.drexel.edu   - Administation for List

nih-image-d-request@biomed.drexel.edu  - Aministration for Digest


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".


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

		Subject: unsubscribe



Unsubscribe to Digest

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

To unsubscribe to digested version of the list, send E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "unsubscribe".


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

		Subject: unsubscribe


Help

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

To obtain a listing of help items, send E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "help".


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

		Subject: help




Help on Digest

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

To obtain a listing of help items on digest version of the list, send
E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "help".


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

		Subject: help




Archive

-------

Every submission sent to this list is archived.	 Following are the
commands

used to access the archive.  Send Email to nih-image-request with the
command 

in the Subject line or in the body of the message.


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


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/*

</fontfamily>

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

                                  Jonathan Nissanov, Ph.D.

                                      Associate Director  

            Computer Vision Center for Vertebrate Brain Mapping,

                a NIH Biomedical Research Technology Resource

                                http://cbis.ece.drexel.edu/ICVC/

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

Imaging and Computer Vision Center              Tel: 215-895-1381

Drexel University                                                  
Fax: 215-895-4987

Phildelphia, PA 19104                                        
yoni@coe.drexel.edu

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

      

     And remember, the early bird may get the worm, but the second
mouse gets the cheese.

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

Date:          Fri, 25 Sep 1998 10:07:45 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: a.jonker@AMC.UVA.NL, nih-image@io.ece.drexel.edu
Subject:       Re: Autowand/AutoOutline touching edge
Message-ID: <99D5B8F5EC5@rna.bio.mq.edu.au>

>Date: Wed, 23 Sep 1998 14:34:10 +0200
>From: Ard Jonker <a.jonker@AMC.UVA.NL>
>
>I want to discard measurements with AutoWand on and AutoOutline, if the 
>outline touches the edge. The result would be similar to measuring one 
>particle which touches the edge in AnalyseParticles: no
>measurement is taken.
>
>Is there a clever way, short of checking all outline coordinates for the 
>condition of x- and y coordinates both being an image edge coordinate?
>
>Regards, Ard
>

I responded to Ard's post yesterday with a macro which tested for the above by 
measure'ing whether a drawboundary pixel was included in the selection and 
commented that checking of xycoordinate list would have been problematic.

In exchange with Ard, he has since suggested that it would only be necessary to 
test the coords of the bounding rectangle (available via getRoi()). This is a 
much simpler and more elegant solution ( avoids problem with x,ycoordinates 
array values).

function touchBoundary:boolean;
	var x,y,w,h,pw,ph:integer;
	begin getRoi(x,y,w,h);getPicSize(pw,ph);
 if (x<=0) or (y<=0) or (x+w>=pw) or (y+h>=ph) then
 touchBoundary:=true else touchBoundary:=false;
 end

macro'/0 does ROI touch [B]oundary'; begin showMessage(touchBoundary);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, 25 Sep 1998 10:43:58 +1000
From: Steve Martin <s.martin@physio.unimelb.EDU.AU>
To: nih-image@io.ece.drexel.edu
Subject: Re: Autowand/AutoOutline touching edge
Message-Id: <v04011700b230971f981f@[128.250.109.214]>
Content-Type: text/plain; charset="us-ascii"

another thought:
draw a 1 pixel wide line on all boundaries, and select or fill, starting at
1,1. The fill or selection should include areas touching the boundary which
are the same level/binary state. (?)

Steve Martin
School of Physiotherapy
The University of Melbourne

At 8:07 PM +1000 on 25/9/98, GJOSS@rna.bio.mq.edu.au wrote:
> >Date: Wed, 23 Sep 1998 14:34:10 +0200
> >From: Ard Jonker <a.jonker@AMC.UVA.NL>
> >
> >I want to discard measurements with AutoWand on and AutoOutline, if the
> >outline touches the edge. The result would be similar to measuring one
> >particle which touches the edge in AnalyseParticles: no
> >measurement is taken.
> >
> >Is there a clever way, short of checking all outline coordinates for the
> >condition of x- and y coordinates both being an image edge coordinate?
> >
> >Regards, Ard
> >
>
> I responded to Ard's post yesterday with a macro which tested for the
>above by
> measure'ing whether a drawboundary pixel was included in the selection and
> commented that checking of xycoordinate list would have been problematic.
>
> In exchange with Ard, he has since suggested that it would only be
>necessary to
> test the coords of the bounding rectangle (available via getRoi()). This
>is a
> much simpler and more elegant solution ( avoids problem with x,ycoordinates
> array values).
>
> function touchBoundary:boolean;
> 	var x,y,w,h,pw,ph:integer;
> 	begin getRoi(x,y,w,h);getPicSize(pw,ph);
>  if (x<=0) or (y<=0) or (x+w>=pw) or (y+h>=ph) then
>  touchBoundary:=true else touchBoundary:=false;
>  end
>
> macro'/0 does ROI touch [B]oundary'; begin showMessage(touchBoundary);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: Thu, 24 Sep 1998 23:20:30 -0500
From: Kris Jorgensen <kris@purdue.edu>
To: nih-image <nih-image@io.ece.drexel.edu>
Subject: get current cell
Message-ID: <360B1A0A.4F14D237@purdue.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

In Object-Image, I need to get the cell number of the open cell.  While
creating an object in a macro I ask the user for a couple input values that I
need to put into static columns so I need to know which row to put those
values.  If I am always working on the last image listed in the info card then
I can use nCount but if I am working on another image I can't get the cell
number to store this other information.

If anyone has a way to get the current cell please let me know.

Kris
-- 
Kris L. Jorgensen
Office:     ME 183
Phone:      (765) 494-8585
Email:      kris@purdue.edu
WWW:        http://www.ecn.purdue.edu/~kris

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

Date:          Fri, 25 Sep 1998 15:06:42 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: kris@purdue.edu, nih-image@io.ece.drexel.edu
Subject:       Re: get current cell
Message-ID: <9A257552679@rna.bio.mq.edu.au>

>Date: Thu, 24 Sep 1998 23:20:30 -0500
>From: Kris Jorgensen <kris@purdue.edu>
>
>In Object-Image, I need to get the cell number of the open cell.  While
>creating an object in a macro I ask the user for a couple input values that I
>need to put into static columns so I need to know which row to put those
>values.  If I am always working on the last image listed in the info card then
>I can use nCount but if I am working on another image I can't get the cell
>number to store this other information.
>
>If anyone has a way to get the current cell please let me know.
>
>Kris

Function 'selectedCell' does the job as the name implies :-)
and the following will demonstrate.
Respond '0' or just return to 'cell' query and the 'selectedCell' will be 
shown. Otherwise enter cell/object and cell/object will be selected and shown.

macro'[t]est';
var width, height, slices, pid,cell:integer;
name:string;
begin
cell:=getNumber('cell',0);
if cell<>0 then begin
  selectCell(cell);
  selectObject(getNumber('Object',1));
  GetPicInfo(width, height, slices, pid, name);
  selectPic(pid);
  showCell(cell,true);
  end;
showMessage(selectedCell);
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, 25 Sep 1998 11:32:50 +0100
From: Jason Pickering <J.P.Pickering@ct.utwente.nl>
To: nih-image@io.ece.drexel.edu
Subject: Counting and Sending Pixels
Message-Id: <l03010d03b2312108bfe3@[130.89.52.166]>
Content-Type: text/plain; charset="us-ascii"

Hello everyone,
	I would like to perform a density slice on a live digitized image,
and then count the number of pixels that fall within that density slice.
Then, I would like to use the Scion LG-3's two analog channels to send a
signal proportional to the number of pixels measured. I have written a
macro that sucessfully does this, but I would like to modify the source
code to increase the performance of this routine.

Has anyone had any experience doing something similar? If so, any tips and
possible pitfalls would be very much appreciated.

Thanks,
Jason P. Pickering

___________________________________________________________________________
Jason Pickering				|Email: J.P.Pickering@ct.utwente.nl
Onderzoeker in opleiding		|Tel: xx 31 53 489 3137
Polymeer Materiaalkundevakgroep		|Fax: xx 31 53 489 3823
Universiteit Twente		  	|Priv. addr.:
Faculteit der Chemische Technologie	|van Loenshof 8D
Postbus 217				|7511 HG Enschede
7500 AE Enschede		  	|
The Netherlands				|
__________________________________________________________________________

--------------------------------
End of nih-image-d Digest V98 Issue #70
***************************************

From nih-image-request@io.ece.drexel.edu Fri Sep 25 09:27 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA14910;
	Fri, 25 Sep 1998 09:27:32 -0400 (EDT)
Resent-Date: Fri, 25 Sep 1998 09:27:32 -0400 (EDT)
Message-Id: <360B9980.4E74F69A@purdue.edu>
Date: Fri, 25 Sep 1998 08:24:16 -0500
From: Kris Jorgensen <kris@purdue.edu>
Reply-To: kris@purdue.edu
Organization: Purdue University
X-Mailer: Mozilla 4.04 [en] (WinNT; I)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: get current cell
References: <9A257552679@rna.bio.mq.edu.au>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"jn8r13.0.iK3.dRv2s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/389
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:  1752
Status: O

GJOSS@rna.bio.mq.edu.au wrote:
> 
> >Date: Thu, 24 Sep 1998 23:20:30 -0500
> >From: Kris Jorgensen <kris@purdue.edu>
> >
> >In Object-Image, I need to get the cell number of the open cell.  While
> >creating an object in a macro I ask the user for a couple input values that I
> >need to put into static columns so I need to know which row to put those
> >values.  If I am always working on the last image listed in the info card then
> >I can use nCount but if I am working on another image I can't get the cell
> >number to store this other information.
> >
> >If anyone has a way to get the current cell please let me know.
> >
> >Kris
> 
> Function 'selectedCell' does the job as the name implies :-)
> and the following will demonstrate.
> Respond '0' or just return to 'cell' query and the 'selectedCell' will be
> shown. Otherwise enter cell/object and cell/object will be selected and shown.
> 
> macro'[t]est';
> var width, height, slices, pid,cell:integer;
> name:string;
> begin
> cell:=getNumber('cell',0);
> if cell<>0 then begin
>   selectCell(cell);
>   selectObject(getNumber('Object',1));
>   GetPicInfo(width, height, slices, pid, name);
>   selectPic(pid);
>   showCell(cell,true);
>   end;
> showMessage(selectedCell);
> end

I want to make the process automatic without user intervention. 
selectedCell doesn't return the cell that is currently open since it is
not selected.  All I get is 0.  It is only after the cell is closed and
one of its objects is manually selected will selectedCell work.  I don't
want to rely on the user selecting the cell.  Maybe we need an openCell
function.

-- 
Kris L. Jorgensen
Office:     ME 183
Phone:      (765) 494-8585
Email:      kris@purdue.edu
WWW:        http://www.ecn.purdue.edu/~kris

From nih-image-request@io.ece.drexel.edu Fri Sep 25 10:52 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA21360;
	Fri, 25 Sep 1998 10:52:44 -0400 (EDT)
Resent-Date: Fri, 25 Sep 1998 10:52:44 -0400 (EDT)
X-Authentication-Warning: mail.bio.uva.nl: Host gold.bio.uva.nl [145.18.160.48] claimed to be [145.18.160.48]
Message-Id: <l03110700b23150a0214b@[145.18.160.48]>
In-Reply-To: <360B9980.4E74F69A@purdue.edu>
References: <9A257552679@rna.bio.mq.edu.au>
Mime-Version: 1.0
Date: Fri, 25 Sep 1998 16:43:53 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: get current cell
Resent-Message-ID: <"SiOyj.0.zw4.Ziw2s"@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/390
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:  2350
Status: O

Kris
I can offer you a work-around which may help you (see below).
The problem is that an open cell has no number until it is closed. When it
is closed and you work in insert mode (i.e. not on the last image of the
image list), the cell will obtain the highest number in that image, while
the remaining cells are renumbered (shuffled up). Cells within an image or
stack always have contiguous numbers, but can be random across stack slices.
Below is a macro function which returns the highest cell number of the
front image, so you hopefully can continue until the problem is solved more
elegantly.

Note that a cell index can easily change when cells are deleted or
inserted. Instead of using index-value- pairs, you should consider to put
your additional user information into a dynamic column which maintains
always correctly linked.

By macro, you can create a dynamic column with Makeresultcolumn('name'),
*not* followed by 'PutOperand' or 'PutAlgrorithm'.
You also can use InitColumn('name'), which has a similar effect, but if a
column with this name already exists, it will be cleared without warning.

You also can create dynamic column manually, by choosing Define objects,
clicking on 'NewResult' and supplying the operation 'None'.

OpenCell is indeed a macro which is already implemented in the newest
version (due mid-october; I am currently looking for beta-testers), but it
has the meaning that you can re-open a previously closed cell and
add/delete objects, thus it doesn't address your problem.



function HighestCell: integer;
{in Object-Image, the highest cell number in the current image is returned}

var width, height, slices, pid,
im, foundcell, thecell: real;
name: string;
begin
  foundcell:= 0;
  for im:= 1 to nImages do begin
    thecell := LastCell(im);
    SelectCell(thecell);
    GetPicInfo(width, height, slices, pid, name);
    if PidNumber = Pid then
      foundcell := thecell;
    end;
  HighestCell:= foundcell;
end;

macro 'Show Highest Cell';
begin
  ShowMessage('HighestCell= ', HighestCell);
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 Fri Sep 25 11:49 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA26316;
	Fri, 25 Sep 1998 11:49:05 -0400 (EDT)
Resent-Date: Fri, 25 Sep 1998 11:49:05 -0400 (EDT)
Message-Id: <3.0.6.32.19980925113232.007f7870@PO-Box.mcgill.ca>
X-Sender: mliraj@PO-Box.mcgill.ca
X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32)
Date: Fri, 25 Sep 1998 11:32:32 -0400
To: nih-image@io.ece.drexel.edu
From: "Mario de A. Lira Junior" <mliraj@PO-Box.mcgill.ca>
Subject: Particle analysis
Mime-Version: 1.0
Resent-Message-ID: <"6wQxo.0.E56.dVx2s"@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/391
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:   532
Status: O

Hello List,
I am a beginner on Scion Image (PC side) and one of the measurements I'm
doing is a particle analysis, for which I'll be obtaining both Major and
Minor axis.
I know those measures are for the hypothetical best approach of an ellipse
to the real data.
Would I be reasonably correct and using a Major/Minor value as an
indication of the "sphericity" of the particles ? If so, is it possible to
add a self-created parameter to Particle Analysis like the User1 and such
for full image analysis ?
Thanks for the help,
Mario

From nih-image-d-request@io.ece.drexel.edu Sat Sep 26 06:13 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA14120;
	Sat, 26 Sep 1998 06:13:07 -0400 (EDT)
Date: Sat, 26 Sep 1998 06:13:07 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809261013.GAA14120@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #71
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/71
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length:  6506
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 71

Today's Topics:
  Re: get current cell                  [ Kris Jorgensen <kris@purdue.edu> ]
  Re: get current cell                  [ Norbert Vischer <vischer@bio.uva.nl ]
  Particle analysis                     [ "Mario de A. Lira Junior" <mliraj@P ]
  Image cross-correlation macro         [ Neal Sullivan <NSullivan@concord.tt ]

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

Date: Fri, 25 Sep 1998 08:24:16 -0500
From: Kris Jorgensen <kris@purdue.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: get current cell
Message-Id: <360B9980.4E74F69A@purdue.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

GJOSS@rna.bio.mq.edu.au wrote:
> 
> >Date: Thu, 24 Sep 1998 23:20:30 -0500
> >From: Kris Jorgensen <kris@purdue.edu>
> >
> >In Object-Image, I need to get the cell number of the open cell.  While
> >creating an object in a macro I ask the user for a couple input values that I
> >need to put into static columns so I need to know which row to put those
> >values.  If I am always working on the last image listed in the info card then
> >I can use nCount but if I am working on another image I can't get the cell
> >number to store this other information.
> >
> >If anyone has a way to get the current cell please let me know.
> >
> >Kris
> 
> Function 'selectedCell' does the job as the name implies :-)
> and the following will demonstrate.
> Respond '0' or just return to 'cell' query and the 'selectedCell' will be
> shown. Otherwise enter cell/object and cell/object will be selected and shown.
> 
> macro'[t]est';
> var width, height, slices, pid,cell:integer;
> name:string;
> begin
> cell:=getNumber('cell',0);
> if cell<>0 then begin
>   selectCell(cell);
>   selectObject(getNumber('Object',1));
>   GetPicInfo(width, height, slices, pid, name);
>   selectPic(pid);
>   showCell(cell,true);
>   end;
> showMessage(selectedCell);
> end

I want to make the process automatic without user intervention. 
selectedCell doesn't return the cell that is currently open since it is
not selected.  All I get is 0.  It is only after the cell is closed and
one of its objects is manually selected will selectedCell work.  I don't
want to rely on the user selecting the cell.  Maybe we need an openCell
function.

-- 
Kris L. Jorgensen
Office:     ME 183
Phone:      (765) 494-8585
Email:      kris@purdue.edu
WWW:        http://www.ecn.purdue.edu/~kris

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

Date: Fri, 25 Sep 1998 16:43:53 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: get current cell
Message-Id: <l03110700b23150a0214b@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

Kris
I can offer you a work-around which may help you (see below).
The problem is that an open cell has no number until it is closed. When it
is closed and you work in insert mode (i.e. not on the last image of the
image list), the cell will obtain the highest number in that image, while
the remaining cells are renumbered (shuffled up). Cells within an image or
stack always have contiguous numbers, but can be random across stack slices.
Below is a macro function which returns the highest cell number of the
front image, so you hopefully can continue until the problem is solved more
elegantly.

Note that a cell index can easily change when cells are deleted or
inserted. Instead of using index-value- pairs, you should consider to put
your additional user information into a dynamic column which maintains
always correctly linked.

By macro, you can create a dynamic column with Makeresultcolumn('name'),
*not* followed by 'PutOperand' or 'PutAlgrorithm'.
You also can use InitColumn('name'), which has a similar effect, but if a
column with this name already exists, it will be cleared without warning.

You also can create dynamic column manually, by choosing Define objects,
clicking on 'NewResult' and supplying the operation 'None'.

OpenCell is indeed a macro which is already implemented in the newest
version (due mid-october; I am currently looking for beta-testers), but it
has the meaning that you can re-open a previously closed cell and
add/delete objects, thus it doesn't address your problem.



function HighestCell: integer;
{in Object-Image, the highest cell number in the current image is returned}

var width, height, slices, pid,
im, foundcell, thecell: real;
name: string;
begin
  foundcell:= 0;
  for im:= 1 to nImages do begin
    thecell := LastCell(im);
    SelectCell(thecell);
    GetPicInfo(width, height, slices, pid, name);
    if PidNumber = Pid then
      foundcell := thecell;
    end;
  HighestCell:= foundcell;
end;

macro 'Show Highest Cell';
begin
  ShowMessage('HighestCell= ', HighestCell);
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: Fri, 25 Sep 1998 11:32:32 -0400
From: "Mario de A. Lira Junior" <mliraj@PO-Box.mcgill.ca>
To: nih-image@io.ece.drexel.edu
Subject: Particle analysis
Message-Id: <3.0.6.32.19980925113232.007f7870@PO-Box.mcgill.ca>
Content-Type: text/plain; charset="us-ascii"

Hello List,
I am a beginner on Scion Image (PC side) and one of the measurements I'm
doing is a particle analysis, for which I'll be obtaining both Major and
Minor axis.
I know those measures are for the hypothetical best approach of an ellipse
to the real data.
Would I be reasonably correct and using a Major/Minor value as an
indication of the "sphericity" of the particles ? If so, is it possible to
add a self-created parameter to Particle Analysis like the User1 and such
for full image analysis ?
Thanks for the help,
Mario

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

Date: Fri, 25 Sep 1998 17:09:02 -0400
From: Neal Sullivan <NSullivan@concord.tt.slb.com>
To: nih-image-d@io.ece.drexel.edu
Subject: Image cross-correlation macro
Message-ID: <BB79685FFE22D2118E9900A024EC68F90727BB@prescott.concord.ate.slb.com>
Content-Type: text/plain

Greetings,

I am looking for a SCION IMAGE compatible image cross-correlation
macro...

Thanks in advance

Neal Sullivan
Schlumberger ATE / Verification Systems

--------------------------------
End of nih-image-d Digest V98 Issue #71
***************************************

From nih-image-request@io.ece.drexel.edu Mon Sep 28 08:10 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA22782;
	Mon, 28 Sep 1998 08:10:19 -0400 (EDT)
Resent-Date: Mon, 28 Sep 1998 08:10:19 -0400 (EDT)
X-Sender: pickerin@utct.ct.utwente.nl
Message-Id: <l03010d00b23533d2cce5@[130.89.52.166]>
In-Reply-To: <199809261003.GAA13222@io.ece.drexel.edu>
Mime-Version: 1.0
Date: Mon, 28 Sep 1998 13:43:02 +0100
To: nih-image@io.ece.drexel.edu
From: Jason Pickering <J.P.Pickering@ct.utwente.nl>
Subject: Scion LG-3 Questions
Resent-Message-ID: <"9NiiN2.0.T25.JRt3s"@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/392
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:  1006
Status: O

Dear NIH Imagers,
	Can anyone tell me how to set the scion[4] channel from the source
code? I need to trigger an outside event using the data out channel of the
ScionLG-3 board. I have done this though a macro command such as:

scion[4]:=BitOr(scion[4],8);
scion[4]:=BitOr(scion[4],7);

Any suggestions? Also, any hints as to how to read the scion[3] channel
from the source code? I used similar commands with the macro language, but
I would like to accomplish the same thing with compiled code.

Cheers,
Jason Pickering


___________________________________________________________________________
Jason Pickering				|Email: J.P.Pickering@ct.utwente.nl
Onderzoeker in opleiding		|Tel: xx 31 53 489 3137
Polymeer Materiaalkundevakgroep		|Fax: xx 31 53 489 3823
Universiteit Twente		  	|Priv. addr.:
Faculteit der Chemische Technologie	|van Loenshof 8D
Postbus 217				|7511 HG Enschede
7500 AE Enschede		  	|
The Netherlands				|
__________________________________________________________________________


From nih-image-request@io.ece.drexel.edu Mon Sep 28 13:48 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA18317;
	Mon, 28 Sep 1998 13:48:56 -0400 (EDT)
Resent-Date: Mon, 28 Sep 1998 13:48:56 -0400 (EDT)
Date: Mon, 28 Sep 1998 13:32:59 -0700
From: Abby Pike <Pike_c1@hnrc.tufts.edu>
Subject: measuring
X-Sender: Pike_c1@email.hnrc.tufts.edu
To: nih-image@io.ece.drexel.edu
Message-id: <3.0.5.32.19980928133259.0079b6b0@email.hnrc.tufts.edu>
MIME-version: 1.0
X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32)
Content-transfer-encoding: 7BIT
Resent-Message-ID: <"veqBC2.0.I24.4Py3s"@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/393
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:   340
Status: O

Does anybody know if it is possible to set a distance for how far from the
starting point the free hand drawing tool goes in? For example: to start
from the end of a curved line and following to line untill the drawing tool
has reached .3 of the length of the curve. Any help would be appreciated,
thanks

Abby Pike
Pike_c1@hnrc.tufts.edu

From nih-image-request@io.ece.drexel.edu Mon Sep 28 15:00 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA23550;
	Mon, 28 Sep 1998 14:59:59 -0400 (EDT)
Resent-Date: Mon, 28 Sep 1998 14:59:59 -0400 (EDT)
Date: Mon, 28 Sep 1998 14:37:20 -0400
From: "Richard A. Fluck" <r_fluck@ACAD.FANDM.EDU>
Subject: combining images
X-Sender: R_Fluck@acad.fandm.edu
To: nih-image@io.ece.drexel.edu
Message-id: <l03130306b23586f74c69@[155.68.72.179]>
MIME-version: 1.0
Resent-Message-ID: <"pkQef.0.vK5.qTz3s"@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/394
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:   681
Status: O

I have double-stained cells with two fluorescent dyes that I image with
separate filter sets.  Is there a way, within NIH Image, to capture images
via each filter set and then combine the images in some way so that the
fluorescence within each image shows up as separate colors, for example,
rhodamine as red and Hoechst 33258 as blue?  I see this done often in the
literature but have never done it myself.  Images in the literature also
show yet a third color where the two original images overlap in their
fluorescence.


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 Mon Sep 28 17:26 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA03527;
	Mon, 28 Sep 1998 17:26:40 -0400 (EDT)
Resent-Date: Mon, 28 Sep 1998 17:26:40 -0400 (EDT)
Message-Id: <199809282103.RAA16729@codon.nih.gov>
X-Mailer:  Macintosh Eudora Pro Version 2.1.4-J
Mime-Version: 1.0
Date: Mon, 28 Sep 1998 17:05:02 -0400
To: nih-image@io.ece.drexel.edu
From: tsuyoshi@codon.nih.gov (Tsuyoshi Miyakawa)
Subject: QuickCam & ADB port
Resent-Message-ID: <"tSKCV1.0.UQ.ie_3s"@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/395
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="ISO-2022-JP"
Content-Length:   883
Status: O

Hello Imagers,

I am using Logitech (previously connectix) Color QuickCam
to capture images with NIH Image. QuickCam works using
the power from ADB port and my Powerbook G3 does not
seem to give enough power to it from its ADB port. That is,
my powerbook can capture images from it with NIH Image
when ADB plug of the QuickCam is connected with the ADB
port of another mac.

Does anyone know if there is any way to increase the power
to the ADB port on Powerbooks?
Any suggestions will be greatly appreciated.

Tsuyoshi



________________________________________
Tsuyoshi Miyakawa, Ph. D.
Section on Behavioral Neuropharmacology
Experimental Therapeutics Branch
National Institute of Mental Health
Building 10 Room 4D11
Bethesda, MD 20892-1375
Lab phone#: 301-496-4838 or 301-496-4839
Lab fax#: 301-480-1164
E-mail  tsuyoshi@codon.nih.gov
________________________________________


From nih-image-request@io.ece.drexel.edu Mon Sep 28 19:05 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id TAA11513;
	Mon, 28 Sep 1998 19:05:48 -0400 (EDT)
Resent-Date: Mon, 28 Sep 1998 19:05:48 -0400 (EDT)
From: jludtke@facstaff.wisc.edu
Date: Mon, 28 Sep 1998 17:50:09 -0500
Message-Id: <199809282250.RAA94496@mail1.doit.wisc.edu>
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: combining images
Resent-Message-ID: <"BXGPw2.0.sQ2.nA14s"@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/396
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:   249
Status: O

There is a set of macros in the NIH image folder called "color". You just
"load macro" under the special menu and choose "color". Then, under
special, you should find "color merge two images".

Give it a try.

Jim Ludtke
jludtke@facstaff.wisc.edu


From nih-image-request@io.ece.drexel.edu Mon Sep 28 20:22 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA17576;
	Mon, 28 Sep 1998 20:22:40 -0400 (EDT)
Resent-Date: Mon, 28 Sep 1998 20:22:40 -0400 (EDT)
Message-Id: <m0zNnCc-0003W9C@fwd12.btx.dtag.de>
Date: Tue, 29 Sep 1998 01:59:38 +0200
To: nih-image@io.ece.drexel.edu
Subject: kein Betreff
X-Mailer: T-Online eMail 2.0
MIME-Version: 1.0
Content-Transfer-Encoding: 8BIT
X-Sender: 0421374363-0001@t-online.de
From: 0421374363-0001@t-online.de (Hermann Kleemeyer)
Resent-Message-ID: <"gZyw_1.0.5t3.TE24s"@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/397
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset=ISO-8859-1
Content-Length:    70
Status: O

search NIH-image|listproc/nih-image all TLC&thinlayer chromatography

From nih-image-request@io.ece.drexel.edu Tue Sep 29 04:13 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA26657;
	Tue, 29 Sep 1998 04:13:19 -0400 (EDT)
Resent-Date: Tue, 29 Sep 1998 04:13:19 -0400 (EDT)
Date: 	Tue, 29 Sep 1998 09:57:05 +0200 (CEST)
From: Gary Chinga <gary@nvg.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Quicktime to NIH.Animation...
In-Reply-To: <m0zNnCc-0003W9C@fwd12.btx.dtag.de>
Message-ID: <Pine.NEB.4.05.9809290954410.16226-100000@flode.nvg.ntnu.no>
MIME-Version: 1.0
Resent-Message-ID: <"uGWQx1.0.286.uC94s"@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/398
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:   132
Status: O


HI!

Is it possible to convert a quicktime animation to a TIFF format, such
that I would be able to open it in NIH Image?

Gary.


From nih-image-d-request@io.ece.drexel.edu Tue Sep 29 04:16 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA27175;
	Tue, 29 Sep 1998 04:16:53 -0400 (EDT)
Date: Tue, 29 Sep 1998 04:16:53 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809290816.EAA27175@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #72
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/72
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length:  6149
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 72

Today's Topics:
  Scion LG-3 Questions                  [ Jason Pickering <J.P.Pickering@ct.u ]
  measuring                             [ Abby Pike <Pike_c1@hnrc.tufts.edu> ]
  combining images                      [ "Richard A. Fluck" <r_fluck@ACAD.FA ]
  QuickCam & ADB port                   [ tsuyoshi@codon.nih.gov (Tsuyoshi Mi ]
  Re: combining images                  [ jludtke@facstaff.wisc.edu ]
  kein Betreff                          [ 0421374363-0001@t-online.de (Herman ]
  Quicktime to NIH.Animation...         [ Gary Chinga <gary@nvg.ntnu.no> ]

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

Date: Mon, 28 Sep 1998 13:43:02 +0100
From: Jason Pickering <J.P.Pickering@ct.utwente.nl>
To: nih-image@io.ece.drexel.edu
Subject: Scion LG-3 Questions
Message-Id: <l03010d00b23533d2cce5@[130.89.52.166]>
Content-Type: text/plain; charset="us-ascii"

Dear NIH Imagers,
	Can anyone tell me how to set the scion[4] channel from the source
code? I need to trigger an outside event using the data out channel of the
ScionLG-3 board. I have done this though a macro command such as:

scion[4]:=BitOr(scion[4],8);
scion[4]:=BitOr(scion[4],7);

Any suggestions? Also, any hints as to how to read the scion[3] channel
from the source code? I used similar commands with the macro language, but
I would like to accomplish the same thing with compiled code.

Cheers,
Jason Pickering


___________________________________________________________________________
Jason Pickering				|Email: J.P.Pickering@ct.utwente.nl
Onderzoeker in opleiding		|Tel: xx 31 53 489 3137
Polymeer Materiaalkundevakgroep		|Fax: xx 31 53 489 3823
Universiteit Twente		  	|Priv. addr.:
Faculteit der Chemische Technologie	|van Loenshof 8D
Postbus 217				|7511 HG Enschede
7500 AE Enschede		  	|
The Netherlands				|
__________________________________________________________________________

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

Date: Mon, 28 Sep 1998 13:32:59 -0700
From: Abby Pike <Pike_c1@hnrc.tufts.edu>
To: nih-image@io.ece.drexel.edu
Subject: measuring
Message-id: <3.0.5.32.19980928133259.0079b6b0@email.hnrc.tufts.edu>
Content-type: text/plain; charset="us-ascii"
Content-transfer-encoding: 7BIT

Does anybody know if it is possible to set a distance for how far from the
starting point the free hand drawing tool goes in? For example: to start
from the end of a curved line and following to line untill the drawing tool
has reached .3 of the length of the curve. Any help would be appreciated,
thanks

Abby Pike
Pike_c1@hnrc.tufts.edu

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

Date: Mon, 28 Sep 1998 14:37:20 -0400
From: "Richard A. Fluck" <r_fluck@ACAD.FANDM.EDU>
To: nih-image@io.ece.drexel.edu
Subject: combining images
Message-id: <l03130306b23586f74c69@[155.68.72.179]>
Content-type: text/plain; charset="us-ascii"

I have double-stained cells with two fluorescent dyes that I image with
separate filter sets.  Is there a way, within NIH Image, to capture images
via each filter set and then combine the images in some way so that the
fluorescence within each image shows up as separate colors, for example,
rhodamine as red and Hoechst 33258 as blue?  I see this done often in the
literature but have never done it myself.  Images in the literature also
show yet a third color where the two original images overlap in their
fluorescence.


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: Mon, 28 Sep 1998 17:05:02 -0400
From: tsuyoshi@codon.nih.gov (Tsuyoshi Miyakawa)
To: nih-image@io.ece.drexel.edu
Subject: QuickCam & ADB port
Message-Id: <199809282103.RAA16729@codon.nih.gov>
Content-Type: text/plain; charset="ISO-2022-JP"

Hello Imagers,

I am using Logitech (previously connectix) Color QuickCam
to capture images with NIH Image. QuickCam works using
the power from ADB port and my Powerbook G3 does not
seem to give enough power to it from its ADB port. That is,
my powerbook can capture images from it with NIH Image
when ADB plug of the QuickCam is connected with the ADB
port of another mac.

Does anyone know if there is any way to increase the power
to the ADB port on Powerbooks?
Any suggestions will be greatly appreciated.

Tsuyoshi



________________________________________
Tsuyoshi Miyakawa, Ph. D.
Section on Behavioral Neuropharmacology
Experimental Therapeutics Branch
National Institute of Mental Health
Building 10 Room 4D11
Bethesda, MD 20892-1375
Lab phone#: 301-496-4838 or 301-496-4839
Lab fax#: 301-480-1164
E-mail  tsuyoshi@codon.nih.gov
________________________________________

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

Date: Mon, 28 Sep 1998 17:50:09 -0500
From: jludtke@facstaff.wisc.edu
To: nih-image@io.ece.drexel.edu
Subject: Re: combining images
Message-Id: <199809282250.RAA94496@mail1.doit.wisc.edu>
Content-Type: text/plain; charset="us-ascii"

There is a set of macros in the NIH image folder called "color". You just
"load macro" under the special menu and choose "color". Then, under
special, you should find "color merge two images".

Give it a try.

Jim Ludtke
jludtke@facstaff.wisc.edu

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

Date: Tue, 29 Sep 1998 01:59:38 +0200
From: 0421374363-0001@t-online.de (Hermann Kleemeyer)
To: nih-image@io.ece.drexel.edu
Subject: kein Betreff
Message-Id: <m0zNnCc-0003W9C@fwd12.btx.dtag.de>
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 8BIT

search NIH-image|listproc/nih-image all TLC&thinlayer chromatography

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

Date: 	Tue, 29 Sep 1998 09:57:05 +0200 (CEST)
From: Gary Chinga <gary@nvg.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Quicktime to NIH.Animation...
Message-ID: <Pine.NEB.4.05.9809290954410.16226-100000@flode.nvg.ntnu.no>
Content-Type: TEXT/PLAIN; charset=US-ASCII

HI!

Is it possible to convert a quicktime animation to a TIFF format, such
that I would be able to open it in NIH Image?

Gary.

--------------------------------
End of nih-image-d Digest V98 Issue #72
***************************************

From nih-image-request@io.ece.drexel.edu Tue Sep 29 07:18 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id HAA12404;
	Tue, 29 Sep 1998 07:18:14 -0400 (EDT)
Resent-Date: Tue, 29 Sep 1998 07:18:14 -0400 (EDT)
X-Sender: zuppinge@baba.ethz.ch
Message-Id: <v03110700b2366d40e5cc@[129.132.49.233]>
In-Reply-To: <Pine.NEB.4.05.9809290954410.16226-100000@flode.nvg.ntnu.no>
References: <m0zNnCc-0003W9C@fwd12.btx.dtag.de>
Mime-Version: 1.0
Date: Tue, 29 Sep 1998 13:00:40 +0200
To: nih-image@io.ece.drexel.edu
From: Christian Zuppinger <zuppinge@cell.biol.ethz.ch>
Subject: Re: Quicktime to NIH.Animation...
Resent-Message-ID: <"Djebo1.0.8g2.5uB4s"@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/399
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:   801
Status: O

>HI!
>
>Is it possible to convert a quicktime animation to a TIFF format, such
>that I would be able to open it in NIH Image?
>
>Gary.

It is actually possible to open QuickTime movies directly in
the latest NIH Image version (1.62). However if you have access
to a movie processing software such as Adobe premiere, you can
export a variety of movie formats as a picture series, that can
be opened in NIH Image.


Christian












Dipl Biol
Christian Zuppinger
ETH Hoenggerberg
Institut fuer Zellbiologie, HPM F27
CH-8093 Zurich
Switzerland

Tel: + 441 1 633 33 54
Fax: + 441 1 633 10 69
Email: zuppinge@cell.biol.ethz.ch
or czuppinger@access.ch
WWW:
Institute
http://www.rereth.ethz.ch/biol/zellbiologie/zellbiologie.prof_overview.html
private
http://www.access.ch/whoswho/showwho?czuppinger



From nih-image-request@io.ece.drexel.edu Tue Sep 29 07:37 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id HAA14139;
	Tue, 29 Sep 1998 07:37:32 -0400 (EDT)
Resent-Date: Tue, 29 Sep 1998 07:37:32 -0400 (EDT)
Message-ID: <3610D1EA.8F3AE44D@netmatters.co.uk>
Date: Tue, 29 Sep 1998 12:26:21 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
Reply-To: brownj@netmatters.co.uk
Organization: brownj@netmatters.co.uk
X-Mailer: Mozilla 4.05 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: measuring
References: <3.0.5.32.19980928133259.0079b6b0@email.hnrc.tufts.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"y0q2w1.0.w93.eDC4s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/400
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length:   679
Status: O



Abby Pike wrote:

> Does anybody know if it is possible to set a distance for how far from the
> starting point the free hand drawing tool goes in? For example: to start
> from the end of a curved line and following to line untill the drawing tool
> has reached .3 of the length of the curve. Any help would be appreciated,
> thanks
>
> Abby Pike
> Pike_c1@hnrc.tufts.edu

Try Object Image, if I understand you correctly it has the facility you need.

Jeremy


************************************************
Jeremy Brown
Edinburgh University/Moredun Research Institute
http://www.netmatters.co.uk/users/brownj/HomePage.html
************************************************


From nih-image-request@io.ece.drexel.edu Tue Sep 29 08:02 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA16662;
	Tue, 29 Sep 1998 08:02:19 -0400 (EDT)
Resent-Date: Tue, 29 Sep 1998 08:02:19 -0400 (EDT)
Message-ID: <19980929114614.20773.qmail@hotmail.com>
X-Originating-IP: [143.93.33.45]
From: "Michael Arm" <arminator@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Counting fibres
Date: Tue, 29 Sep 1998 04:46:14 PDT
Resent-Message-ID: <"ZHiAA1.0.Ne3.dYC4s"@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/401
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length:   665
Status: O

Hello,
we are trying to count fibres dispersed on a glass plate. We get the 3d 
image Stack from a confocal microscope.
However, between the fibres are some smaller "dirt"-specks, which we 
don't want to count. We already told Image not to count objects smaller 
than 30 Pixels, however larger "crumbs" are still counted.
How can we get Image to recognize only large objects, that are 
"fibre-like" (i.e. long and thin and not compact like a crumb)?
We already found a cell counting macro, that recognizes circle like 
cells, and leaves out the rest...

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

From nih-image-request@io.ece.drexel.edu Tue Sep 29 10:09 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA28135;
	Tue, 29 Sep 1998 10:09:29 -0400 (EDT)
Resent-Date: Tue, 29 Sep 1998 10:09:29 -0400 (EDT)
Message-ID: <69B43248FE73D11197BB00A0C99AB0678953@jvcserver.vanguardweb.org>
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Reliable Storage and Formats to save
Date: Tue, 29 Sep 1998 09:42:52 -0400
MIME-Version: 1.0
X-Mailer: Internet Mail Service (5.5.1960.3)
Resent-Message-ID: <"0DuwR2.0.FM6.kME4s"@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/402
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length:  1320
Status: O

Hi everyone, 
Basically, a lot of CT and X-ray images will be scanned for 100's of
patient (file size will be min.7 meg to max. 20 meg.). I would like to
save, compress (Stuffit/Winzip), label and store them in reliable
storage like optical or ZIP or any other media which I do not know which
one is better. Later, I would like to search images by name, date and
display as thumbnails and then retrieve for research. We have G3's and
NT boxes as mixed plotforms.

Any suggestion for followings will be appreciated and I will post the
results here:

*	Q1. What will be the best losseless format to save files without
loosing anything? TIFF or JPEG or other
*	Q2. After saving files with selected formats such as TIFF, What
will be the best application to compress and save space? such as Disk
Doubler, Stuffit or Winzip or other
*	Q3. The best reliable media, such as recordable CD, DVD, ZIP or
other? 
*	Q4. After storing images, What will be the best application to
retrieve and display images EASILY? or 
do you suggest any software to search patient names, retrieve and
display stored images EASILY?. 
I have paintshop pro and PhotoDeluxe and we are planning to buy IMAGEPRO
later. 

Appreciated
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-Univ. of Mich.
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087

From nih-image-request@io.ece.drexel.edu Tue Sep 29 10:33 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA00583;
	Tue, 29 Sep 1998 10:33:21 -0400 (EDT)
Resent-Date: Tue, 29 Sep 1998 10:33:21 -0400 (EDT)
From: johannes.barsig@pharma.Novartis.com
X-Lotus-FromDomain: PH@N1
To: nih-image@io.ece.drexel.edu
Message-ID: <4125668E.005269AC.00@nts1.novartis.com>
Date: Tue, 29 Sep 1998 16:08:05 +0100
Subject: wound area measurements
Mime-Version: 1.0
Content-Disposition: inline
Resent-Message-ID: <"zvJCR.0.Ov6.rfE4s"@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/403
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:   609
Status: O

We are tracing wound areas of mice on glass slides. The circles we get
should be digitalized using a graphics tablet. Image should detect, when
the circle is closed an measure the area of the circle. Then, the next
circle could be drawn. In results, the measurements should be listed. The
areas are about two square cm. First question, which graphics tablet would
be best for this task together with NIH Image. Second question, is there a
macro around that could control the sequential measuring process described.
I appreciate every hint.
Johannes Barsig, Ph.D.
Novartis Research Institute
Vienna, Austria


From nih-image-request@io.ece.drexel.edu Tue Sep 29 11:03 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA02984;
	Tue, 29 Sep 1998 11:03:27 -0400 (EDT)
Resent-Date: Tue, 29 Sep 1998 11:03:27 -0400 (EDT)
Message-Id: <3610F469.E9745F44@purdue.edu>
Date: Tue, 29 Sep 1998 09:53:29 -0500
From: Kris Jorgensen <kris@purdue.edu>
Reply-To: kris@purdue.edu
Organization: Purdue University
X-Mailer: Mozilla 4.04 [en] (WinNT; I)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu, Mehmet.Dondurur.ph.d@jvc.org
Subject: Re: Reliable Storage and Formats to save
References: <69B43248FE73D11197BB00A0C99AB0678953@jvcserver.vanguardweb.org>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"pBzOc2.0.qJ.87F4s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/404
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:  1399
Status: O

Mehmet Dondurur, Ph. D. wrote:
> 
> Any suggestion for followings will be appreciated and I will post the
> results here:
> 
> *       Q2. After saving files with selected formats such as TIFF, What
> will be the best application to compress and save space? such as Disk
> Doubler, Stuffit or Winzip or other

I have found that compressing images that are already in a compressed
form (jpeg) generally has only limited usefulness.  Some will actually
get bigger, so the answer to Q1 may be more important.

> *       Q3. The best reliable media, such as recordable CD, DVD, ZIP or
> other?

I would not use a ZIP.  The mean time to failure is far to short for
them or any random access magnetic media.  I would us an optical format
like CD or DVD.  Since you have both Macs and NT machines you can write
them in dual format and still have access to them from both machines.

> *       Q4. After storing images, What will be the best application to
> retrieve and display images EASILY? or
> do you suggest any software to search patient names, retrieve and
> display stored images EASILY?.

You should be able to us something like FileMaker to write your own
database interface to your files.  Again, look at a cross platfrom
solution.

Hope this helps
Kris
-- 
Kris L. Jorgensen
Office:     ME 183
Phone:      (765) 494-8585
Email:      kris@purdue.edu
WWW:        http://www.ecn.purdue.edu/~kris

From nih-image-request@io.ece.drexel.edu Tue Sep 29 12:07 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA09047;
	Tue, 29 Sep 1998 12:07:36 -0400 (EDT)
	<69B43248FE73D11197BB00A0C99AB0678953@jvcserver.vanguardweb.org>
Resent-Date: Tue, 29 Sep 1998 12:07:36 -0400 (EDT)
X-Sender: cgustafs@ece.drexel.edu
Message-Id: <v03110701b236b1bbb83b@[144.118.33.205]>
In-Reply-To: 
	<69B43248FE73D11197BB00A0C99AB0678953@jvcserver.vanguardweb.org>
Mime-Version: 1.0
Date: Tue, 29 Sep 1998 11:54:19 -0400
To: nih-image@io.ece.drexel.edu
From: Carl Gustafson <carl.gustafson@cbis.ece.drexel.edu>
Subject: Re: Reliable Storage and Formats to save
Resent-Message-ID: <"Abxm-1.0.Dk1.X6G4s"@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/405
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:  1958
Status: O

>*	Q1. What will be the best losseless format to save files without
>loosing anything? TIFF or JPEG or other

JPEG is not lossless. TIFF is when the LZW compressed TIFF format is used,
otherwise TIFF isn't compressed.

>*	Q2. After saving files with selected formats such as TIFF, What
>will be the best application to compress and save space? such as Disk
>Doubler, Stuffit or Winzip or other

Choose a compression application that runs on as many platforms as
possible. Stuffit may have a windoze version, there are Mac-based Zippers,
and there are other compressors that originated in the UNIX world that have
MacOS versions.

>*	Q3. The best reliable media, such as recordable CD, DVD, ZIP or
>other?

I wouldn't choose magnetic media for archival storage. This rules out Zip
storage. In addition, I've heard rumors of hardware problems with Zip
mechanisms that damage the media. DVD is too new for my tastes, but CD
seems a reasonable choice.

>*	Q4. After storing images, What will be the best application to
>retrieve and display images EASILY? or
>do you suggest any software to search patient names, retrieve and
>display stored images EASILY?.

Keep a simple FileMaker database with references to storage volume ID, file
path, etc., as well as any other needed data. With FileMaker, you can also
store thumbnails of the images if you wish. Back it up to CD often - you
don't want to have to reconstruct it.



Carl Gustafson
(215) 895-1383
===============================================================================
           the Computer Vision Center for Vertebrate Brain Mapping
===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I'd like to give you my opinion
===============================================================================


From nih-image-request@io.ece.drexel.edu Tue Sep 29 13:51 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA16740;
	Tue, 29 Sep 1998 13:51:17 -0400 (EDT)
Resent-Date: Tue, 29 Sep 1998 13:51:17 -0400 (EDT)
Message-Id: <v03102800b236d47c63d4@DialupEudora>
In-Reply-To: <4125668E.005269AC.00@nts1.novartis.com>
Mime-Version: 1.0
Date: Tue, 29 Sep 1998 12:25:34 -0600
To: nih-image@io.ece.drexel.edu
From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
Subject: Re: wound area measurements
Resent-Message-ID: <"PAgK63.0.cc3.lWH4s"@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/406
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:  1168
Status: O

>We are tracing wound areas of mice on glass slides. The circles we get
>should be digitalized using a graphics tablet. Image should detect, when
>the circle is closed an measure the area of the circle. Then, the next
>circle could be drawn. In results, the measurements should be listed. The
>areas are about two square cm. First question, which graphics tablet would
>be best for this task together with NIH Image. Second question, is there a
>macro around that could control the sequential measuring process described.
>I appreciate every hint.
>Johannes Barsig, Ph.D.
>Novartis Research Institute
>Vienna, Austria

I can reccomend the Wacom digitizing tablet. I have a 15.5*21cm tablet
which works for me, but other sizes are also available. It has a cordless
pen, and relative and absolute positioning, scaling and pressure
sensitivity all can be set to your own liking. Since I have the tablet, I
don't use the mouse anymore.
 For the measuring process you decribe you don't necessarily need a macro,
depending on how you want you output. Outlining each areas and doing
'measure' (apple-1) will generate a list of measurements in the 'results'
window.

Arnout


From nih-image-request@io.ece.drexel.edu Tue Sep 29 14:17 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA18982;
	Tue, 29 Sep 1998 14:17:18 -0400 (EDT)
Resent-Date: Tue, 29 Sep 1998 14:17:18 -0400 (EDT)
Message-Id: <199809291749.NAA14662@kanga.INS.CWRU.Edu>
Date: Tue, 29 Sep 1998 13:49:13 -0400 (EDT)
From: nbd@po.cwru.edu (Nagendu B. Dev)
To: nih-image@io.ece.drexel.edu
Subject: Re: wound area measurements
Reply-To: nbd@po.cwru.edu (Nagendu B. Dev)
Resent-Message-ID: <"ciSQY.0.824.isH4s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/407
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length:   964
Status: O

Dr.Barsig:
If you are interested only in the area measurement for a circle, you could
use sigmascan digitizing tablet with the sigmascan program, areas are
automatically logged into the sigmascan table. Hope, this solves your
problem.
from: nbd@po.cwru.edu
###

Reply to message from johannes.barsig@pharma.Novartis.com of Tue, 29 Sep
>
>We are tracing wound areas of mice on glass slides. The circles we get
>should be digitalized using a graphics tablet. Image should detect, when
>the circle is closed an measure the area of the circle. Then, the next
>circle could be drawn. In results, the measurements should be listed. The
>areas are about two square cm. First question, which graphics tablet would
>be best for this task together with NIH Image. Second question, is there a
>macro around that could control the sequential measuring process described.
>I appreciate every hint.
>Johannes Barsig, Ph.D.
>Novartis Research Institute
>Vienna, Austria
>
>
>
>

From nih-image-request@io.ece.drexel.edu Tue Sep 29 15:20 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA24197;
	Tue, 29 Sep 1998 15:20:40 -0400 (EDT)
Resent-Date: Tue, 29 Sep 1998 15:20:40 -0400 (EDT)
Message-Id: <3610F6A7.55B@cirl.meei.harvard.edu>
Date: Tue, 29 Sep 1998 15:03:03 +0000
From: src <srcramer@cirl.meei.harvard.edu>
Reply-To: srcramer@cirl.meei.harvard.edu
Organization: HMS/MEEI
X-Mailer: Mozilla 3.0 (Macintosh; I; 68K)
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: S-Video and nih-image
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"LRf2n1.0.od5.h_I4s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/408
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:   452
Status: O

To All;

I wondered if anyone had information on how to use the S-Video option
with RGB colors when trying to capture images from within nih-image?  We
are using a microscope/camera setup which is connected to an S-Video
port on a PowerMac 8600.  Is there a seperate video card we need to get
from nih?  Thanks in advance for any information.

Scott Cramer
Woods Hole Oceanographic Institution/Mass. Eye & Ear Infirmary
srcramer@cirl.meei.harvard.edu

From nih-image-request@io.ece.drexel.edu Tue Sep 29 16:58 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA01201;
	Tue, 29 Sep 1998 16:58:55 -0400 (EDT)
Resent-Date: Tue, 29 Sep 1998 16:58:55 -0400 (EDT)
Message-ID: <19980929204608.5529.qmail@pc241.icsl.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Reliable Storage and Formats to save 
In-Reply-To: Your message of "Tue, 29 Sep 1998 11:54:19 EDT."
             <v03110701b236b1bbb83b@[144.118.33.205]> 
Date: Tue, 29 Sep 1998 13:46:08 -0700
From: Mark Hasegawa-Johnson <mark@pc241.icsl.ucla.edu>
Resent-Message-ID: <"gUkXE3.0.rG7.rPK4s"@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/409
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length:   456
Status: O


>>*	Q1. What will be the best losseless format to save files without
>>loosing anything? TIFF or JPEG or other

You should also consider that many medical images store 16 bits of
grayscale data per pixel, while most non-medical formats store up to 8
bits grayscale, or up to 24 bits color.

I usually choose a range of interest for each set of images, quantize
that range of interest to 8-bit precision, and then save as 8-bit
grayscale TIFF.

	  - Mark

From nih-image-request@io.ece.drexel.edu Wed Sep 30 04:59 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA02488;
	Wed, 30 Sep 1998 04:58:58 -0400 (EDT)
Resent-Date: Wed, 30 Sep 1998 04:58:58 -0400 (EDT)
Message-ID: <19980930084539.2826.qmail@hotmail.com>
X-Originating-IP: [143.93.33.45]
From: "Michael Arm" <arminator@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Reliable Storage and Formats to save
Date: Wed, 30 Sep 1998 01:45:39 PDT
Resent-Message-ID: <"fD6tt.0.LE.M_U4s"@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/410
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length:  1613
Status: O


>*	Q1. What will be the best losseless format to save files without
>loosing anything? TIFF or JPEG or other

A1: If you don't want to loose anything, then JPEG is the one NOT to 
choose (since it's compression ALWAYS causes loss in quality.) Save it 
uncompressed, and try a pack-utility like WinZip (see A2)

>*	Q2. After saving files with selected formats such as TIFF, What
>will be the best application to compress and save space? such as Disk
>Doubler, Stuffit or Winzip or other

A2 Use WinZip (or any other ZIP-Archiver) for compression of your 
uncompressed images (compressing already compressed images is not that 
easily possible). Use ZIP since it is understood by most systems and 
since Thumbs can read it (see A4)

>*	Q3. The best reliable media, such as recordable CD, DVD, ZIP or
>other? 

For long term archivation I suggest a DAT tape (only for storage, since 
seek times are pretty long for tapes). For working with these images I 
suggest putting some on Rewritable MO's or CD-RW's


>*	Q4. After storing images, What will be the best application to
>retrieve and display images EASILY? or 
>do you suggest any software to search patient names, retrieve and
>display stored images EASILY?. 

A4 As others suggested, use a FileManager to catalogize your files. 
However, if you found the tape/disk with your ZIPped images, use Thumbs 
Plus (for Windows) at http://www.cerious.com to view the Images directly 
in a ZIP-packed archieve.


I hope this helps.

Sincerely
Michael Arm

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

From nih-image-d-request@io.ece.drexel.edu Wed Sep 30 04:59 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA02569;
	Wed, 30 Sep 1998 04:59:17 -0400 (EDT)
Date: Wed, 30 Sep 1998 04:59:17 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809300859.EAA02569@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #73
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/73
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 16815
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 73

Today's Topics:
  Re: Quicktime to NIH.Animation...     [ Christian Zuppinger <zuppinge@cell. ]
  Re: measuring                         [ Jeremy Brown <brownj@netmatters.co. ]
  Counting fibres                       [ "Michael Arm" <arminator@hotmail.co ]
  Reliable Storage and Formats to save  [ "Mehmet Dondurur, Ph. D." <mehmet.d ]
  wound area measurements               [ johannes.barsig@pharma.Novartis.com ]
  Re: Reliable Storage and Formats to   [ Kris Jorgensen <kris@purdue.edu> ]
  Re: Reliable Storage and Formats to   [ Carl Gustafson <carl.gustafson@cbis ]
  Re: wound area measurements           [ Arnout Ruifrok <arnout@odin.mdacc.t ]
  Re: wound area measurements           [ nbd@po.CWRU.Edu (Nagendu B. Dev) ]
  S-Video and nih-image                 [ src <srcramer@cirl.meei.harvard.edu ]
  Re: Reliable Storage and Formats to   [ Mark Hasegawa-Johnson <mark@pc241.i ]
  Re: Reliable Storage and Formats to   [ "Michael Arm" <arminator@hotmail.co ]

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

Date: Tue, 29 Sep 1998 13:00:40 +0200
From: Christian Zuppinger <zuppinge@cell.biol.ethz.ch>
To: nih-image@io.ece.drexel.edu
Subject: Re: Quicktime to NIH.Animation...
Message-Id: <v03110700b2366d40e5cc@[129.132.49.233]>
Content-Type: text/plain; charset="us-ascii"

>HI!
>
>Is it possible to convert a quicktime animation to a TIFF format, such
>that I would be able to open it in NIH Image?
>
>Gary.

It is actually possible to open QuickTime movies directly in
the latest NIH Image version (1.62). However if you have access
to a movie processing software such as Adobe premiere, you can
export a variety of movie formats as a picture series, that can
be opened in NIH Image.


Christian












Dipl Biol
Christian Zuppinger
ETH Hoenggerberg
Institut fuer Zellbiologie, HPM F27
CH-8093 Zurich
Switzerland

Tel: + 441 1 633 33 54
Fax: + 441 1 633 10 69
Email: zuppinge@cell.biol.ethz.ch
or czuppinger@access.ch
WWW:
Institute
http://www.rereth.ethz.ch/biol/zellbiologie/zellbiologie.prof_overview.html
private
http://www.access.ch/whoswho/showwho?czuppinger

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

Date: Tue, 29 Sep 1998 12:26:21 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: measuring
Message-ID: <3610D1EA.8F3AE44D@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Abby Pike wrote:

> Does anybody know if it is possible to set a distance for how far from the
> starting point the free hand drawing tool goes in? For example: to start
> from the end of a curved line and following to line untill the drawing tool
> has reached .3 of the length of the curve. Any help would be appreciated,
> thanks
>
> Abby Pike
> Pike_c1@hnrc.tufts.edu

Try Object Image, if I understand you correctly it has the facility you need.

Jeremy


************************************************
Jeremy Brown
Edinburgh University/Moredun Research Institute
http://www.netmatters.co.uk/users/brownj/HomePage.html
************************************************

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

Date: Tue, 29 Sep 1998 04:46:14 PDT
From: "Michael Arm" <arminator@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Counting fibres
Message-ID: <19980929114614.20773.qmail@hotmail.com>
Content-Type: text/plain

Hello,
we are trying to count fibres dispersed on a glass plate. We get the 3d 
image Stack from a confocal microscope.
However, between the fibres are some smaller "dirt"-specks, which we 
don't want to count. We already told Image not to count objects smaller 
than 30 Pixels, however larger "crumbs" are still counted.
How can we get Image to recognize only large objects, that are 
"fibre-like" (i.e. long and thin and not compact like a crumb)?
We already found a cell counting macro, that recognizes circle like 
cells, and leaves out the rest...

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

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

Date: Tue, 29 Sep 1998 09:42:52 -0400
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Reliable Storage and Formats to save
Message-ID: <69B43248FE73D11197BB00A0C99AB0678953@jvcserver.vanguardweb.org>
Content-Type: text/plain

Hi everyone, 
Basically, a lot of CT and X-ray images will be scanned for 100's of
patient (file size will be min.7 meg to max. 20 meg.). I would like to
save, compress (Stuffit/Winzip), label and store them in reliable
storage like optical or ZIP or any other media which I do not know which
one is better. Later, I would like to search images by name, date and
display as thumbnails and then retrieve for research. We have G3's and
NT boxes as mixed plotforms.

Any suggestion for followings will be appreciated and I will post the
results here:

*	Q1. What will be the best losseless format to save files without
loosing anything? TIFF or JPEG or other
*	Q2. After saving files with selected formats such as TIFF, What
will be the best application to compress and save space? such as Disk
Doubler, Stuffit or Winzip or other
*	Q3. The best reliable media, such as recordable CD, DVD, ZIP or
other? 
*	Q4. After storing images, What will be the best application to
retrieve and display images EASILY? or 
do you suggest any software to search patient names, retrieve and
display stored images EASILY?. 
I have paintshop pro and PhotoDeluxe and we are planning to buy IMAGEPRO
later. 

Appreciated
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-Univ. of Mich.
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087

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

Date: Tue, 29 Sep 1998 16:08:05 +0100
From: johannes.barsig@pharma.Novartis.com
To: nih-image@io.ece.drexel.edu
Subject: wound area measurements
Message-ID: <4125668E.005269AC.00@nts1.novartis.com>
Content-type: text/plain; charset=us-ascii
Content-Disposition: inline

We are tracing wound areas of mice on glass slides. The circles we get
should be digitalized using a graphics tablet. Image should detect, when
the circle is closed an measure the area of the circle. Then, the next
circle could be drawn. In results, the measurements should be listed. The
areas are about two square cm. First question, which graphics tablet would
be best for this task together with NIH Image. Second question, is there a
macro around that could control the sequential measuring process described.
I appreciate every hint.
Johannes Barsig, Ph.D.
Novartis Research Institute
Vienna, Austria

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

Date: Tue, 29 Sep 1998 09:53:29 -0500
From: Kris Jorgensen <kris@purdue.edu>
To: nih-image@io.ece.drexel.edu, Mehmet.Dondurur.ph.d@jvc.org
Subject: Re: Reliable Storage and Formats to save
Message-Id: <3610F469.E9745F44@purdue.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Mehmet Dondurur, Ph. D. wrote:
> 
> Any suggestion for followings will be appreciated and I will post the
> results here:
> 
> *       Q2. After saving files with selected formats such as TIFF, What
> will be the best application to compress and save space? such as Disk
> Doubler, Stuffit or Winzip or other

I have found that compressing images that are already in a compressed
form (jpeg) generally has only limited usefulness.  Some will actually
get bigger, so the answer to Q1 may be more important.

> *       Q3. The best reliable media, such as recordable CD, DVD, ZIP or
> other?

I would not use a ZIP.  The mean time to failure is far to short for
them or any random access magnetic media.  I would us an optical format
like CD or DVD.  Since you have both Macs and NT machines you can write
them in dual format and still have access to them from both machines.

> *       Q4. After storing images, What will be the best application to
> retrieve and display images EASILY? or
> do you suggest any software to search patient names, retrieve and
> display stored images EASILY?.

You should be able to us something like FileMaker to write your own
database interface to your files.  Again, look at a cross platfrom
solution.

Hope this helps
Kris
-- 
Kris L. Jorgensen
Office:     ME 183
Phone:      (765) 494-8585
Email:      kris@purdue.edu
WWW:        http://www.ecn.purdue.edu/~kris

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

Date: Tue, 29 Sep 1998 11:54:19 -0400
From: Carl Gustafson <carl.gustafson@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Reliable Storage and Formats to save
Message-Id: <v03110701b236b1bbb83b@[144.118.33.205]>
Content-Type: text/plain; charset="us-ascii"

>*	Q1. What will be the best losseless format to save files without
>loosing anything? TIFF or JPEG or other

JPEG is not lossless. TIFF is when the LZW compressed TIFF format is used,
otherwise TIFF isn't compressed.

>*	Q2. After saving files with selected formats such as TIFF, What
>will be the best application to compress and save space? such as Disk
>Doubler, Stuffit or Winzip or other

Choose a compression application that runs on as many platforms as
possible. Stuffit may have a windoze version, there are Mac-based Zippers,
and there are other compressors that originated in the UNIX world that have
MacOS versions.

>*	Q3. The best reliable media, such as recordable CD, DVD, ZIP or
>other?

I wouldn't choose magnetic media for archival storage. This rules out Zip
storage. In addition, I've heard rumors of hardware problems with Zip
mechanisms that damage the media. DVD is too new for my tastes, but CD
seems a reasonable choice.

>*	Q4. After storing images, What will be the best application to
>retrieve and display images EASILY? or
>do you suggest any software to search patient names, retrieve and
>display stored images EASILY?.

Keep a simple FileMaker database with references to storage volume ID, file
path, etc., as well as any other needed data. With FileMaker, you can also
store thumbnails of the images if you wish. Back it up to CD often - you
don't want to have to reconstruct it.



Carl Gustafson
(215) 895-1383
===============================================================================
           the Computer Vision Center for Vertebrate Brain Mapping
===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I'd like to give you my opinion
===============================================================================

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

Date: Tue, 29 Sep 1998 12:25:34 -0600
From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: wound area measurements
Message-Id: <v03102800b236d47c63d4@DialupEudora>
Content-Type: text/plain; charset="us-ascii"

>We are tracing wound areas of mice on glass slides. The circles we get
>should be digitalized using a graphics tablet. Image should detect, when
>the circle is closed an measure the area of the circle. Then, the next
>circle could be drawn. In results, the measurements should be listed. The
>areas are about two square cm. First question, which graphics tablet would
>be best for this task together with NIH Image. Second question, is there a
>macro around that could control the sequential measuring process described.
>I appreciate every hint.
>Johannes Barsig, Ph.D.
>Novartis Research Institute
>Vienna, Austria

I can reccomend the Wacom digitizing tablet. I have a 15.5*21cm tablet
which works for me, but other sizes are also available. It has a cordless
pen, and relative and absolute positioning, scaling and pressure
sensitivity all can be set to your own liking. Since I have the tablet, I
don't use the mouse anymore.
 For the measuring process you decribe you don't necessarily need a macro,
depending on how you want you output. Outlining each areas and doing
'measure' (apple-1) will generate a list of measurements in the 'results'
window.

Arnout

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

Date: Tue, 29 Sep 1998 13:49:13 -0400 (EDT)
From: nbd@po.CWRU.Edu (Nagendu B. Dev)
To: nih-image@io.ece.drexel.edu
Subject: Re: wound area measurements
Message-Id: <199809291749.NAA14662@kanga.INS.CWRU.Edu>

Dr.Barsig:
If you are interested only in the area measurement for a circle, you could
use sigmascan digitizing tablet with the sigmascan program, areas are
automatically logged into the sigmascan table. Hope, this solves your
problem.
from: nbd@po.cwru.edu
###

Reply to message from johannes.barsig@pharma.Novartis.com of Tue, 29 Sep
>
>We are tracing wound areas of mice on glass slides. The circles we get
>should be digitalized using a graphics tablet. Image should detect, when
>the circle is closed an measure the area of the circle. Then, the next
>circle could be drawn. In results, the measurements should be listed. The
>areas are about two square cm. First question, which graphics tablet would
>be best for this task together with NIH Image. Second question, is there a
>macro around that could control the sequential measuring process described.
>I appreciate every hint.
>Johannes Barsig, Ph.D.
>Novartis Research Institute
>Vienna, Austria
>
>
>
>

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

Date: Tue, 29 Sep 1998 15:03:03 +0000
From: src <srcramer@cirl.meei.harvard.edu>
To: nih-image@io.ece.drexel.edu
Subject: S-Video and nih-image
Message-Id: <3610F6A7.55B@cirl.meei.harvard.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

To All;

I wondered if anyone had information on how to use the S-Video option
with RGB colors when trying to capture images from within nih-image?  We
are using a microscope/camera setup which is connected to an S-Video
port on a PowerMac 8600.  Is there a seperate video card we need to get
from nih?  Thanks in advance for any information.

Scott Cramer
Woods Hole Oceanographic Institution/Mass. Eye & Ear Infirmary
srcramer@cirl.meei.harvard.edu

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

Date: Tue, 29 Sep 1998 13:46:08 -0700
From: Mark Hasegawa-Johnson <mark@pc241.icsl.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Reliable Storage and Formats to save 
Message-ID: <19980929204608.5529.qmail@pc241.icsl.ucla.edu>

>>*	Q1. What will be the best losseless format to save files without
>>loosing anything? TIFF or JPEG or other

You should also consider that many medical images store 16 bits of
grayscale data per pixel, while most non-medical formats store up to 8
bits grayscale, or up to 24 bits color.

I usually choose a range of interest for each set of images, quantize
that range of interest to 8-bit precision, and then save as 8-bit
grayscale TIFF.

	  - Mark

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

Date: Wed, 30 Sep 1998 01:45:39 PDT
From: "Michael Arm" <arminator@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Reliable Storage and Formats to save
Message-ID: <19980930084539.2826.qmail@hotmail.com>
Content-Type: text/plain

>*	Q1. What will be the best losseless format to save files without
>loosing anything? TIFF or JPEG or other

A1: If you don't want to loose anything, then JPEG is the one NOT to 
choose (since it's compression ALWAYS causes loss in quality.) Save it 
uncompressed, and try a pack-utility like WinZip (see A2)

>*	Q2. After saving files with selected formats such as TIFF, What
>will be the best application to compress and save space? such as Disk
>Doubler, Stuffit or Winzip or other

A2 Use WinZip (or any other ZIP-Archiver) for compression of your 
uncompressed images (compressing already compressed images is not that 
easily possible). Use ZIP since it is understood by most systems and 
since Thumbs can read it (see A4)

>*	Q3. The best reliable media, such as recordable CD, DVD, ZIP or
>other? 

For long term archivation I suggest a DAT tape (only for storage, since 
seek times are pretty long for tapes). For working with these images I 
suggest putting some on Rewritable MO's or CD-RW's


>*	Q4. After storing images, What will be the best application to
>retrieve and display images EASILY? or 
>do you suggest any software to search patient names, retrieve and
>display stored images EASILY?. 

A4 As others suggested, use a FileManager to catalogize your files. 
However, if you found the tape/disk with your ZIPped images, use Thumbs 
Plus (for Windows) at http://www.cerious.com to view the Images directly 
in a ZIP-packed archieve.


I hope this helps.

Sincerely
Michael Arm

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

--------------------------------
End of nih-image-d Digest V98 Issue #73
***************************************

From nih-image-request@io.ece.drexel.edu Wed Sep 30 05:06 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA03412;
	Wed, 30 Sep 1998 05:06:35 -0400 (EDT)
Resent-Date: Wed, 30 Sep 1998 05:06:35 -0400 (EDT)
Message-ID: <19980930085710.13766.qmail@hotmail.com>
X-Originating-IP: [143.93.33.45]
From: "Michael Arm" <arminator@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Counting Fibres (the complete message)
Date: Wed, 30 Sep 1998 01:57:10 PDT
Resent-Message-ID: <"bGOrd3.0.XZ.8AV4s"@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/411
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length:  1270
Status: O

Sorry, it seemed, as if the last part of my previous mail was cut off.

Hello,
we are trying to count fibres dispersed on a glass plate. We get the 3d 
image Stack from a confocal microscope.
However, between the fibres are some smaller "dirt"-specks, which we 
don't want to count. We already told Image not to count objects smaller 
than 30 Pixels, however larger "crumbs" are still counted.
How can we get Image to recognize only large objects, that are 
"fibre-like" (i.e. long and thin and not compact like a crumb)?
We already found a cell counting macro, that recognizes circle like 
cells, and leaves out the rest...

Is there a way to tell a macro only to count long, thin objects? Putting 
an ellipse into a ROI-selected fibre often doesn't work, since some are 
slightly bent like a parenthesis "("...

Any suggestions would be greatly appreciated.

Sincerely
Michael Arm

------------------------------------------------------
some guy from #linux told me how to speed up my email,
he said go on as root and type rm -rf /.. 
it stands for readmail -realfast /all... 
but now I cant reboot!
------------------------------------------------------


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

From nih-image-request@io.ece.drexel.edu Wed Sep 30 09:10 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA23713;
	Wed, 30 Sep 1998 09:09:55 -0400 (EDT)
Resent-Date: Wed, 30 Sep 1998 09:09:55 -0400 (EDT)
Message-ID: <3612A7AE.C952D464@de.ms.philips.com>
Date: Wed, 30 Sep 1998 14:50:38 -0700
From: Johann Borchers <Johann.Borchers@de.ms.philips.com>
Organization: Philips Medizin Systeme
X-Mailer: Mozilla 4.06 [en] (Win16; I)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: Reliable Storage and Formats to save
References: <199809300850.EAA01432@io.ece.drexel.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"zVaNX.0.jL5.laY4s"@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/412
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset=iso-8859-2
Content-Length:   986
Status: O

> 
> >*      Q1. What will be the best losseless format to save files without
> >loosing anything? TIFF or JPEG or other
> 
> A1: If you don't want to loose anything, then JPEG is the one NOT to
> choose (since it's compression ALWAYS causes loss in quality.) Save it
> uncompressed, and try a pack-utility like WinZip (see A2)
> 

-- 
Dear Imagers,

the ACR-NEMA group proposed a "JPEG Lossles" compression for DICOM 3.0
compliant devices.

Without loss of any pixel-information, you can achieve compression rates
of 2-3 with typical grayscale images.

---------------------------------------------------------------------- 
Johann Borchers                                Voice : 49 40 5078-2071 
Philips Medical Systems Hamburg                  FAX : 49 40 5078-2301 
Medical-Information-Techn.                    Mobile : 49  171 5544566 
                            e-mail : johann.borchers@de.ms.philips.com 
----------------------------------------------------------------------

From nih-image-request@io.ece.drexel.edu Wed Sep 30 09:20 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA24710;
	Wed, 30 Sep 1998 09:20:55 -0400 (EDT)
Resent-Date: Wed, 30 Sep 1998 09:20:55 -0400 (EDT)
From: Stephen Keenan <s.keenan@qub.ac.uk>
Sender: k9425608@qub.ac.uk
To: nih-image@io.ece.drexel.edu
Subject: Watersheds for Scion PC Image?
Message-ID: <SIMEON.9809301444.C@skeenan.qub.ac.uk>
Date: Wed, 30 Sep 1998 14:05:44 -0400 (EDT)
Priority: NORMAL
X-Mailer: Simeon for Windows Version 4.1.2 Build (32)
X-Authentication: none
MIME-Version: 1.0
Resent-Message-ID: <"CYmD42.0.Fg5.SoY4s"@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/413
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:   357
Status: O


Does anyone know if a watersheds pluggin exists for Scion 
PC Image. I know that this pluggin exists for NIH image for the 
Mac but so far I haven'tbeen able to find a pluggin for the PC 
version.
If anyone could point me in the right direction I would be extremely
grateful.

Thanks in advance,

Stephen Keenan,
Ph.D Student,
Queen's University Belfast


From nih-image-request@io.ece.drexel.edu Wed Sep 30 09:40 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA26491;
	Wed, 30 Sep 1998 09:40:11 -0400 (EDT)
Resent-Date: Wed, 30 Sep 1998 09:40:11 -0400 (EDT)
Message-ID: <36123F46.7110EF3@netmatters.co.uk>
Date: Wed, 30 Sep 1998 14:25:12 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
Reply-To: brownj@netmatters.co.uk
Organization: brownj@netmatters.co.uk
X-Mailer: Mozilla 4.05 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: Watersheds for Scion PC Image?
References: <SIMEON.9809301444.C@skeenan.qub.ac.uk>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"XqTmT2.0.I56.33Z4s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/414
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length:   775
Status: O



Stephen Keenan wrote:

> Does anyone know if a watersheds pluggin exists for Scion
> PC Image. I know that this pluggin exists for NIH image for the
> Mac but so far I haven'tbeen able to find a pluggin for the PC
> version.
> If anyone could point me in the right direction I would be extremely
> grateful.
>
> Thanks in advance,
>
> Stephen Keenan,
> Ph.D Student,
> Queen's University Belfast

There should be a watershed command in the binary processes associated
with the Process menu. It is should also be executable via the macro
language.

Jeremy


************************************************
Jeremy Brown
Edinburgh University/Moredun Research Institute
http://www.netmatters.co.uk/users/brownj/HomePage.html
************************************************


From nih-image-request@io.ece.drexel.edu Wed Sep 30 09:52 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA27650;
	Wed, 30 Sep 1998 09:52:19 -0400 (EDT)
Resent-Date: Wed, 30 Sep 1998 09:52:19 -0400 (EDT)
Message-ID: <9D916278299FD111A7E100805FA7C2BA4B9FC7@cheetah.uits.iupui.edu>
From: "Kirk, Todd Jason" <tjkirk@iupui.edu>
To: nih-image@io.ece.drexel.edu
Subject: Meridian InSIGHT and MAC
Date: Wed, 30 Sep 1998 08:30:55 -0500
MIME-Version: 1.0
X-Mailer: Internet Mail Service (5.5.2232.9)
Resent-Message-ID: <"i-SXE3.0.5G6.EAZ4s"@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/415
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length:   622
Status: O

	Has anyone connected a Mac to a Merdian Insight plus? We had a PC
connected to it, now we have a Mac. We used the serial port on the PC to
change filters, open the shutter etc. Now that the Mac is going to be used,
I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but the pin
out seems to be different and it is not sending the data (using the
openserial( ) command), to change the filters etc. Apple said that I have to
become a developer to get this info., and cannot help. It seems simple, has
anyone used a "regular" (DB25 pinout) modem on an apple? Thanks.

Todd Kirk
Indiana University Medical Center

From nih-image-request@io.ece.drexel.edu Wed Sep 30 10:20 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA00138;
	Wed, 30 Sep 1998 10:20:17 -0400 (EDT)
Resent-Date: Wed, 30 Sep 1998 10:20:17 -0400 (EDT)
Date: Wed, 30 Sep 1998 23:59:40 +1000 (EST)
Message-Id: <199809301359.XAA01783@topaz.cqu.edu.au>
X-Sender: mccannc@topaz.cqu.edu.au
X-Mailer: Windows Eudora Light Version 1.5.2
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
From: Cormac <mccannc@topaz.cqu.edu.au>
Subject: Summing Macro
Resent-Message-ID: <"PgX2p.0.mw6.tbZ4s"@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/417
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:   447
Status: O

Greetings imagers,

Does anyone out there know of a macro which can;

- sum up a list of already calculated (area) values (usually less than 50)
from   the results window. 

- take this sum and divide it by the total area of the image and display the
result.

Any help would be much appreciated as I desperately need some code to
include in my final year project.

Thanx in advance,

Cormac McCann
Final year Mechanical Engineering student, CQU.

From nih-image-request@io.ece.drexel.edu Wed Sep 30 10:20 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA00170;
	Wed, 30 Sep 1998 10:20:33 -0400 (EDT)
	<9D916278299FD111A7E100805FA7C2BA4B9FC7@cheetah.uits.iupui.edu>
Resent-Date: Wed, 30 Sep 1998 10:20:33 -0400 (EDT)
X-Authentication-Warning: mail.bio.uva.nl: Host gold.bio.uva.nl [145.18.160.48] claimed to be [145.18.160.48]
Message-Id: <l03110700b237e8a06b17@[145.18.160.48]>
In-Reply-To: 
	<9D916278299FD111A7E100805FA7C2BA4B9FC7@cheetah.uits.iupui.edu>
Mime-Version: 1.0
Date: Wed, 30 Sep 1998 16:02:21 +0200
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Meridian InSIGHT and MAC
Resent-Message-ID: <"XgCq3.0.5t6.kZZ4s"@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/416
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:  1384
Status: O

>	Has anyone connected a Mac to a Merdian Insight plus? We had a PC
>connected to it, now we have a Mac. We used the serial port on the PC to
>change filters, open the shutter etc. Now that the Mac is going to be used,
>I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but the pin
>out seems to be different and it is not sending the data (using the
>openserial( ) command), to change the filters etc. Apple said that I have to
>become a developer to get this info., and cannot help. It seems simple, has
>anyone used a "regular" (DB25 pinout) modem on an apple? Thanks.
>
>Todd Kirk
>Indiana University Medical Center

One complication of the NIH Image serial access is that it alway expects
handshake to  be active. In my version of object-Image (see web site), you
can switch handshake off. This often helped without resoldering the cable.

OpenSerial('Options')
  Besides  parity, speed and stop bits, two more parameters
  are recognized in Object-Image: 'no DTR' disables the
  input hardware handshake 'no XonXoff' disables the input
  software handshake.

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 30 11:39 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA06365;
	Wed, 30 Sep 1998 11:39:08 -0400 (EDT)
Resent-Date: Wed, 30 Sep 1998 11:39:08 -0400 (EDT)
Message-ID: <36124888.45D4A4EE@sdsc.edu>
Date: Wed, 30 Sep 1998 08:04:40 -0700
From: Harvey Karten <kartenh@sdsc.edu>
Reply-To: hjkarten@UCSD.EDU
Organization: UCSD
X-Mailer: Mozilla 4.04 [en] (Win95; U)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re:Reliable format and saving files
References: <199809300855.EAA01981@io.ece.drexel.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"ipC5m3.0.1-._da4s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/418
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:  2433
Status: O

The issue that has not been addressed in the other replies is the matter
of databasing. While FileMaker Pro is a useful tool for storing and
saving text based information, it has only limited ability for dealing
with images. You can create a portal/container for displaying an image,
but FileMaker has no facility for generating the needed thumbnails. It
is best to use FileMaker in conjunction with an image gallery database
product, such as Thumbsplus, Canto Cumulus or a few other lesser
products. I have found Thumbsplus to be the most flexible in being able
to read the widest variety of file formats, including 8, 12 and 16 bits
files. It can read complex Multi-TIFF files (e.g. stacks of double or
triple labeled images in an extended Z-series, etc.).

IImage Gallery Database programs generate thumbnail images of all files
on a disk or series of disks, display them on the screen, and you can
then click on the image of interest. It will bring up the oriignla
image, you can then edit it and re-save it.

As in the case of most Image Gallery Databasing Programs (Thumbsplus,
Canto Cumulus, Extensis Portfolio, Search 3.1, and possibly others)
Thumbsplus will autmoatically scan a disk looking for previously
uncatalogued image files. It will generate a thumbnail image of a size
you choose, read the original collection parameters (possibly including
patient's names, experimental protocol, etc.), and make these available
across a network. It will do all this and more for less than $100. The
next version promises to have direct input to ODBC compliant database
programs. FileMaker Pro will soon be ODBC compliant, so that will make
it easier to work with.

Both FileMaker Pro and Thumbsplus are available for Mac, Windows 95 and
NT platforms.

You can buy Thumbsplus from http://www.cerious.com

No, I don't work Thumbsplus, but I have worked with them and found them
to be the most responsive of companies. They are a small operation, and
are willing to adapt their software to the needs of the scientific
community. And you can't beat the price!

regards, 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

WCBR Program for 1999:
PLEASE NOTE CHANGE OF WEB ADDRESS
http://www.wcbrBrain.org


From nih-image-request@io.ece.drexel.edu Wed Sep 30 12:12 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA09332;
	Wed, 30 Sep 1998 12:12:05 -0400 (EDT)
Resent-Date: Wed, 30 Sep 1998 12:12:05 -0400 (EDT)
Message-Id: <9809301547.AA131782@acs1.acs.ucalgary.ca>
Subject: Re: detecting fibres
To: nih-image@io.ece.drexel.edu
Date: Wed, 30 Sep 98 9:47:42 MDT
From: "Doug S. Phillips" <phillips@ucalgary.ca>
Cc: arminator@hotmail.com
In-Reply-To: <199809300846.EAA00974@io.ece.drexel.edu>; from "nih-image-d-request@io.ece.drexel.edu" at Sep 30, 1998 4:46 am
X-Mailer: ELM [version 2.3 PL11K]
Mime-Version: 1.0
Resent-Message-ID: <"hioo6.0.Pn1.sBb4s"@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/419
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: multipart/mixed; boundary="----------------------------"
Content-Length:  2104
Status: O


------------------------------
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit

Michael Arm <arminator@hotmail.com> wrote:

> How can we get Image to recognize only large objects, that are 
> "fibre-like" (i.e. long and thin and not compact like a crumb)?

Here is a macro I use for the opposite purpose - detecting whether
an object is sufficiently round (aspect ratio less than 4 in the
following example).  By changing the "aspect" value in the 
following, and changing the 

	    if rUser1[j] < aspect then begin

to
	    if rUser1[j] > aspect then begin

it should do what you want.

{=================================================================}
macro 'Find focus';
{Try to measure the position of the white square in each picture of a stack}
var
  i,j,jfocus,numslices: integer;
  aspect: real;
begin

{ Open a window for the data. }
  NewTextWindow('Focus position',250,250);
  MoveWindow(250,320);
  Writeln('Frame,    X,    Y,  Area,  Major,  Minor');
  
  SaveState;
  numslices:=nSlices;
  SetParticleSize(5,500);
  LabelParticles(true);
  OutlineParticles(true);
  
  SetOptions('X-Y Center, Area, Major, Minor');
  for i:=1 to numslices do begin
    ChooseSlice(i);
    ChangeValues(255,255,254);
    SetDensitySlice(215,254);
    MakeBinary;
    Dilate;
    AnalyzeParticles;
    SelectWindow('Focus position');
    aspect:=4.0;
 	if rCount > 0 then begin
          for j:=1 to rCount do begin
            rUser1[j]:=rMajor[j]/rMinor[j];
          end;
	  for j:=1 to rCount do begin
	    if rUser1[j] < aspect then begin
	       aspect:=rUser1[j];
	       jfocus:=j;
	    end;
          end;
   Writeln(i:5:0,',',rX[jfocus]:5:0,',',rY[jfocus]:5:0,',',rArea[jfocus]:5:0,',',rMajor[jfocus]:5:0,',',rMinor[jfocus]:5:0);

	end;
   end;
  RestoreState;
end;
                 Sincerely,
                   Doug P.

Doug S. Phillips                Internet: phillips@ucalgary.ca
University Computing Services   Phone:(403)220-8445  FAX:(403)282-9199
The University of Calgary       WWW:  http://www.acs.ucalgary.ca/~phillips/


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

From nih-image-request@io.ece.drexel.edu Wed Sep 30 12:19 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA09909;
	Wed, 30 Sep 1998 12:19:09 -0400 (EDT)
Resent-Date: Wed, 30 Sep 1998 12:19:09 -0400 (EDT)
From: Stephen Keenan <s.keenan@qub.ac.uk>
Sender: k9425608@qub.ac.uk
To: brownj@netmatters.co.uk
cc: nih-image@io.ece.drexel.edu
Subject: Re: Watersheds for Scion PC Image?
In-Reply-To: <36123F46.7110EF3@netmatters.co.uk>
Message-ID: <SIMEON.9809301612.A@skeenan.qub.ac.uk>
Date: Wed, 30 Sep 1998 16:54:12 -0400 (EDT)
Priority: NORMAL
X-Mailer: Simeon for Windows Version 4.1.2 Build (32)
X-Authentication: none
MIME-Version: 1.0
Resent-Message-ID: <"zReQR1.0.2u1.WGb4s"@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/420
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:   294
Status: O

Jeremy,

Thank you for taking the time to answer my request.

I do not seem to have a watersheds command in the binary 
processes associated with my Process menu. 

Do I need to obtain any additional modules/macros to enable this 
function?

Thanks again
----------------------
Stephen Keenan

From nih-image-request@io.ece.drexel.edu Wed Sep 30 12:50 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA12347;
	Wed, 30 Sep 1998 12:50:08 -0400 (EDT)
Resent-Date: Wed, 30 Sep 1998 12:50:08 -0400 (EDT)
Message-Id: <v03007802b2380eba5119@[128.231.99.202]>
In-Reply-To: <SIMEON.9809301612.A@skeenan.qub.ac.uk>
References: <36123F46.7110EF3@netmatters.co.uk>
Mime-Version: 1.0
Date: Wed, 30 Sep 1998 12:39:27 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: Watersheds for Scion PC Image?
Resent-Message-ID: <"CXZsK2.0.Uj2.crb4s"@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/421
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:   270
Status: O

>Jeremy,
>
>Thank you for taking the time to answer my request.
>
>I do not seem to have a watersheds command in the binary
>processes associated with my Process menu.

The Watershed command is in Scion Image for Windows beta 3, but it doesn't
appear to work.

-wayne


From nih-image-request@io.ece.drexel.edu Wed Sep 30 16:12 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA00522;
	Wed, 30 Sep 1998 16:12:03 -0400 (EDT)
Resent-Date: Wed, 30 Sep 1998 16:12:03 -0400 (EDT)
X-Authentication-Warning: morpheus.cis.yale.edu: feke owned process doing -bs
Date: Wed, 30 Sep 1998 15:52:48 -0400 (EDT)
From: Gilbert D Feke <gilbert.feke@yale.edu>
X-Sender: feke@morpheus.cis.yale.edu
To: nih-image@io.ece.drexel.edu
Subject: real-time row&column averaging
Message-ID: <Pine.GSO.3.94.980930154237.4296A-100000@morpheus.cis.yale.edu>
MIME-Version: 1.0
Resent-Message-ID: <"qYFdL1.0.237.Rme4s"@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/422
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:   655
Status: O

I am trying to find some combination of CCD camera, frame grabber (either
digital or analog), DSP, and/or software which allows me to perform
real-time averaging of rows and columns.  For example, if I have a 512x512
image input, then I would like the real-time processing to output both a
1x512 image and a 512x1 image which I can save to memory or disk.  Line
scan cameras are not an option since I need both the row and column
averaging from the same camera.

If anyone has any suggestions of how I could do this or some company I
should contact, please reply. 

Thank you.

Gilbert Feke
Yale University
Dept. of Applied Physics
gilbert.feke@yale.edu

From nih-image-request@io.ece.drexel.edu Wed Sep 30 20:08 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA18849;
	Wed, 30 Sep 1998 20:08:04 -0400 (EDT)
Resent-Date: Wed, 30 Sep 1998 20:08:04 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: arminator@hotmail.com, nih-image@io.ece.drexel.edu
Date:          Thu, 1 Oct 1998 9:50:01 GMT+1000
Subject:       Re: Counting Fibres (the complete message)
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <A2D1A081F85@rna.bio.mq.edu.au>
Resent-Message-ID: <"y-zwK3.0.5F4.2Di4s"@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/423
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length:  2673
Status: O

>From: "Michael Arm" <arminator@hotmail.com>
>To: nih-image@io.ece.drexel.edu
>Subject: Counting Fibres (the complete message)
>Date: Wed, 30 Sep 1998 01:57:10 PDT
>....
>we are trying to count fibres dispersed on a glass plate. We get the 3d 
>image Stack from a confocal microscope.
>However, between the fibres are some smaller "dirt"-specks, which we 
>don't want to count. We already told Image not to count objects smaller 
>than 30 Pixels, however larger "crumbs" are still counted.
>How can we get Image to recognize only large objects, that are 
>"fibre-like" (i.e. long and thin and not compact like a crumb)?
>We already found a cell counting macro, that recognizes circle like 
>cells, and leaves out the rest...
>
>Is there a way to tell a macro only to count long, thin objects? Putting 
>an ellipse into a ROI-selected fibre often doesn't work, since some are 
>slightly bent like a parenthesis "("...
>
>Any suggestions would be greatly appreciated.
>
>Sincerely
>Michael Arm
>
Michael, you cant "tell a macro only to count long, thin objects" but having 
counted objects which satisfy size criteria, you can scan the results tables by 
macro to attempt further qualification of counted particles. You can then count 
those in the results table that meet the further imposed criteria or 
effectively delete them from the table (by shuffling others over them).

It is not clear to me what the significance of the 3D is but I would expect to 
be able to effectively exclude the larger "crumbs" by using the ratio 
rArea[i]/rLength[i]:

for i:= rCount do begin rUser1[i]:=rArea[i]/rLength[i];
{
rLength is particle perimeter for analyzeParticles
for long thin fibre particles,
 rUser1[i] should be average halfwidth << rLength[i]/2 ~= length
}

You might also consider making a binary image, and then a Euclidean distance  
map (binary(Process menu before analyzeParticles. Particles with larger 
cross-sections can be excluded by densitySlice'ing the distance map;
 MakeBinary;
binary('map');enhanceContrast;
setDensitySlice(1,maxHalfwidth);
analyzeParticles;

then rMax[i] will be a measure of particle's maximum halfwidth which in turn 
should be close to average halfwidth in rUser1.

If you really want to nitpick the particles by macro, then use analyzeParticles 
results table locations to autoOutline each particle in turn but you would be 
much better off to use Object-Image in that case as it records rTop,rLeft for 
that autoOutline(rTop[i],rLeft[i]); purpose.


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 Sep 30 20:29 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA20814;
	Wed, 30 Sep 1998 20:29:45 -0400 (EDT)
Resent-Date: Wed, 30 Sep 1998 20:29:45 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: johannes.barsig@pharma.Novartis.com, nih-image@io.ece.drexel.edu
Date:          Thu, 1 Oct 1998 10:16:09 GMT+1000
Subject:       Re: wound area measurements
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <A2D8983212A@rna.bio.mq.edu.au>
Resent-Message-ID: <"NVewJ.0.oj4.lai4s"@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/424
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length:  1430
Status: O

>From: johannes.barsig@pharma.Novartis.com
>To: nih-image@io.ece.drexel.edu
>Date: Tue, 29 Sep 1998 16:08:05 +0100
>Subject: wound area measurements
>
>We are tracing wound areas of mice on glass slides. The circles we get
>should be digitalized using a graphics tablet. Image should detect, when
>the circle is closed an measure the area of the circle. Then, the next
>circle could be drawn. In results, the measurements should be listed. The
>areas are about two square cm. First question, which graphics tablet would
>be best for this task together with NIH Image. Second question, is there a
>macro around that could control the sequential measuring process described.
>I appreciate every hint.
>Johannes Barsig, Ph.D.
>Novartis Research Institute
>Vienna, Austria
>
I would have thought that you would find that an inexpensive video or digital 
camera attached to a dissecting microscope would be a much more flexible and 
efficient approach with potential for (semi)automated analysis by NIH-Image and 
offering much better documentation of results.

Object-Image has a very nice extension to NIH-Image for computer-assisted 
outlining of density-sliced images: points are collected by (option) "sparking" 
to nearest density-sliced edge.
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 Wed Sep 30 20:36 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA21986;
	Wed, 30 Sep 1998 20:36:33 -0400 (EDT)
Date: Wed, 30 Sep 1998 20:36:33 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810010036.UAA21986@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #74
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/74
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 21160
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 74

Today's Topics:
  Counting Fibres (the complete messag  [ "Michael Arm" <arminator@hotmail.co ]
  Re: Reliable Storage and Formats to   [ Johann Borchers <Johann.Borchers@de ]
  Watersheds for Scion PC Image?        [ Stephen Keenan <s.keenan@qub.ac.uk> ]
  Re: Watersheds for Scion PC Image?    [ Jeremy Brown <brownj@netmatters.co. ]
  Meridian InSIGHT and MAC              [ "Kirk, Todd Jason" <tjkirk@iupui.ed ]
  Re: Meridian InSIGHT and MAC          [ Norbert Vischer <vischer@bio.uva.nl ]
  Summing Macro                         [ Cormac <mccannc@topaz.cqu.edu.au> ]
  Re:Reliable format and saving files   [ Harvey Karten <kartenh@sdsc.edu> ]
  Re: detecting fibres                  [ "Doug S. Phillips" <phillips@ucalga ]
  Re: Watersheds for Scion PC Image?    [ Stephen Keenan <s.keenan@qub.ac.uk> ]
  Re: Watersheds for Scion PC Image?    [ Wayne Rasband <wayne@codon.nih.gov> ]
  real-time row&column averaging        [ Gilbert D Feke <gilbert.feke@yale.e ]
  Re: Counting Fibres (the complete me  [ GJOSS@rna.bio.mq.edu.au ]
  Re: wound area measurements           [ GJOSS@rna.bio.mq.edu.au ]

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

Date: Wed, 30 Sep 1998 01:57:10 PDT
From: "Michael Arm" <arminator@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Counting Fibres (the complete message)
Message-ID: <19980930085710.13766.qmail@hotmail.com>
Content-Type: text/plain

Sorry, it seemed, as if the last part of my previous mail was cut off.

Hello,
we are trying to count fibres dispersed on a glass plate. We get the 3d 
image Stack from a confocal microscope.
However, between the fibres are some smaller "dirt"-specks, which we 
don't want to count. We already told Image not to count objects smaller 
than 30 Pixels, however larger "crumbs" are still counted.
How can we get Image to recognize only large objects, that are 
"fibre-like" (i.e. long and thin and not compact like a crumb)?
We already found a cell counting macro, that recognizes circle like 
cells, and leaves out the rest...

Is there a way to tell a macro only to count long, thin objects? Putting 
an ellipse into a ROI-selected fibre often doesn't work, since some are 
slightly bent like a parenthesis "("...

Any suggestions would be greatly appreciated.

Sincerely
Michael Arm

------------------------------------------------------
some guy from #linux told me how to speed up my email,
he said go on as root and type rm -rf /.. 
it stands for readmail -realfast /all... 
but now I cant reboot!
------------------------------------------------------


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

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

Date: Wed, 30 Sep 1998 14:50:38 -0700
From: Johann Borchers <Johann.Borchers@de.ms.philips.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Reliable Storage and Formats to save
Message-ID: <3612A7AE.C952D464@de.ms.philips.com>
Content-Type: text/plain; charset=iso-8859-2
Content-Transfer-Encoding: 7bit

> 
> >*      Q1. What will be the best losseless format to save files without
> >loosing anything? TIFF or JPEG or other
> 
> A1: If you don't want to loose anything, then JPEG is the one NOT to
> choose (since it's compression ALWAYS causes loss in quality.) Save it
> uncompressed, and try a pack-utility like WinZip (see A2)
> 

-- 
Dear Imagers,

the ACR-NEMA group proposed a "JPEG Lossles" compression for DICOM 3.0
compliant devices.

Without loss of any pixel-information, you can achieve compression rates
of 2-3 with typical grayscale images.

---------------------------------------------------------------------- 
Johann Borchers                                Voice : 49 40 5078-2071 
Philips Medical Systems Hamburg                  FAX : 49 40 5078-2301 
Medical-Information-Techn.                    Mobile : 49  171 5544566 
                            e-mail : johann.borchers@de.ms.philips.com 
----------------------------------------------------------------------

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

Date: Wed, 30 Sep 1998 14:05:44 -0400 (EDT)
From: Stephen Keenan <s.keenan@qub.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Watersheds for Scion PC Image?
Message-ID: <SIMEON.9809301444.C@skeenan.qub.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

Does anyone know if a watersheds pluggin exists for Scion 
PC Image. I know that this pluggin exists for NIH image for the 
Mac but so far I haven'tbeen able to find a pluggin for the PC 
version.
If anyone could point me in the right direction I would be extremely
grateful.

Thanks in advance,

Stephen Keenan,
Ph.D Student,
Queen's University Belfast

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

Date: Wed, 30 Sep 1998 14:25:12 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Watersheds for Scion PC Image?
Message-ID: <36123F46.7110EF3@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Stephen Keenan wrote:

> Does anyone know if a watersheds pluggin exists for Scion
> PC Image. I know that this pluggin exists for NIH image for the
> Mac but so far I haven'tbeen able to find a pluggin for the PC
> version.
> If anyone could point me in the right direction I would be extremely
> grateful.
>
> Thanks in advance,
>
> Stephen Keenan,
> Ph.D Student,
> Queen's University Belfast

There should be a watershed command in the binary processes associated
with the Process menu. It is should also be executable via the macro
language.

Jeremy


************************************************
Jeremy Brown
Edinburgh University/Moredun Research Institute
http://www.netmatters.co.uk/users/brownj/HomePage.html
************************************************

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

Date: Wed, 30 Sep 1998 08:30:55 -0500
From: "Kirk, Todd Jason" <tjkirk@iupui.edu>
To: nih-image@io.ece.drexel.edu
Subject: Meridian InSIGHT and MAC
Message-ID: <9D916278299FD111A7E100805FA7C2BA4B9FC7@cheetah.uits.iupui.edu>
Content-Type: text/plain

	Has anyone connected a Mac to a Merdian Insight plus? We had a PC
connected to it, now we have a Mac. We used the serial port on the PC to
change filters, open the shutter etc. Now that the Mac is going to be used,
I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but the pin
out seems to be different and it is not sending the data (using the
openserial( ) command), to change the filters etc. Apple said that I have to
become a developer to get this info., and cannot help. It seems simple, has
anyone used a "regular" (DB25 pinout) modem on an apple? Thanks.

Todd Kirk
Indiana University Medical Center

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

Date: Wed, 30 Sep 1998 16:02:21 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Meridian InSIGHT and MAC
Message-Id: <l03110700b237e8a06b17@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

>	Has anyone connected a Mac to a Merdian Insight plus? We had a PC
>connected to it, now we have a Mac. We used the serial port on the PC to
>change filters, open the shutter etc. Now that the Mac is going to be used,
>I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but the pin
>out seems to be different and it is not sending the data (using the
>openserial( ) command), to change the filters etc. Apple said that I have to
>become a developer to get this info., and cannot help. It seems simple, has
>anyone used a "regular" (DB25 pinout) modem on an apple? Thanks.
>
>Todd Kirk
>Indiana University Medical Center

One complication of the NIH Image serial access is that it alway expects
handshake to  be active. In my version of object-Image (see web site), you
can switch handshake off. This often helped without resoldering the cable.

OpenSerial('Options')
  Besides  parity, speed and stop bits, two more parameters
  are recognized in Object-Image: 'no DTR' disables the
  input hardware handshake 'no XonXoff' disables the input
  software handshake.

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, 30 Sep 1998 23:59:40 +1000 (EST)
From: Cormac <mccannc@topaz.cqu.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Summing Macro
Message-Id: <199809301359.XAA01783@topaz.cqu.edu.au>
Content-Type: text/plain; charset="us-ascii"

Greetings imagers,

Does anyone out there know of a macro which can;

- sum up a list of already calculated (area) values (usually less than 50)
from   the results window. 

- take this sum and divide it by the total area of the image and display the
result.

Any help would be much appreciated as I desperately need some code to
include in my final year project.

Thanx in advance,

Cormac McCann
Final year Mechanical Engineering student, CQU.

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

Date: Wed, 30 Sep 1998 08:04:40 -0700
From: Harvey Karten <kartenh@sdsc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re:Reliable format and saving files
Message-ID: <36124888.45D4A4EE@sdsc.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

The issue that has not been addressed in the other replies is the matter
of databasing. While FileMaker Pro is a useful tool for storing and
saving text based information, it has only limited ability for dealing
with images. You can create a portal/container for displaying an image,
but FileMaker has no facility for generating the needed thumbnails. It
is best to use FileMaker in conjunction with an image gallery database
product, such as Thumbsplus, Canto Cumulus or a few other lesser
products. I have found Thumbsplus to be the most flexible in being able
to read the widest variety of file formats, including 8, 12 and 16 bits
files. It can read complex Multi-TIFF files (e.g. stacks of double or
triple labeled images in an extended Z-series, etc.).

IImage Gallery Database programs generate thumbnail images of all files
on a disk or series of disks, display them on the screen, and you can
then click on the image of interest. It will bring up the oriignla
image, you can then edit it and re-save it.

As in the case of most Image Gallery Databasing Programs (Thumbsplus,
Canto Cumulus, Extensis Portfolio, Search 3.1, and possibly others)
Thumbsplus will autmoatically scan a disk looking for previously
uncatalogued image files. It will generate a thumbnail image of a size
you choose, read the original collection parameters (possibly including
patient's names, experimental protocol, etc.), and make these available
across a network. It will do all this and more for less than $100. The
next version promises to have direct input to ODBC compliant database
programs. FileMaker Pro will soon be ODBC compliant, so that will make
it easier to work with.

Both FileMaker Pro and Thumbsplus are available for Mac, Windows 95 and
NT platforms.

You can buy Thumbsplus from http://www.cerious.com

No, I don't work Thumbsplus, but I have worked with them and found them
to be the most responsive of companies. They are a small operation, and
are willing to adapt their software to the needs of the scientific
community. And you can't beat the price!

regards, 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

WCBR Program for 1999:
PLEASE NOTE CHANGE OF WEB ADDRESS
http://www.wcbrBrain.org

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

Date: Wed, 30 Sep 98 9:47:42 MDT
From: "Doug S. Phillips" <phillips@ucalgary.ca>
To: nih-image@io.ece.drexel.edu
Cc: arminator@hotmail.com
Subject: Re: detecting fibres
Message-Id: <9809301547.AA131782@acs1.acs.ucalgary.ca>
Content-Type: multipart/mixed; boundary="----------------------------"

Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit

Michael Arm <arminator@hotmail.com> wrote:

> How can we get Image to recognize only large objects, that are 
> "fibre-like" (i.e. long and thin and not compact like a crumb)?

Here is a macro I use for the opposite purpose - detecting whether
an object is sufficiently round (aspect ratio less than 4 in the
following example).  By changing the "aspect" value in the 
following, and changing the 

	    if rUser1[j] < aspect then begin

to
	    if rUser1[j] > aspect then begin

it should do what you want.

{=================================================================}
macro 'Find focus';
{Try to measure the position of the white square in each picture of a stack}
var
  i,j,jfocus,numslices: integer;
  aspect: real;
begin

{ Open a window for the data. }
  NewTextWindow('Focus position',250,250);
  MoveWindow(250,320);
  Writeln('Frame,    X,    Y,  Area,  Major,  Minor');
  
  SaveState;
  numslices:=nSlices;
  SetParticleSize(5,500);
  LabelParticles(true);
  OutlineParticles(true);
  
  SetOptions('X-Y Center, Area, Major, Minor');
  for i:=1 to numslices do begin
    ChooseSlice(i);
    ChangeValues(255,255,254);
    SetDensitySlice(215,254);
    MakeBinary;
    Dilate;
    AnalyzeParticles;
    SelectWindow('Focus position');
    aspect:=4.0;
 	if rCount > 0 then begin
          for j:=1 to rCount do begin
            rUser1[j]:=rMajor[j]/rMinor[j];
          end;
	  for j:=1 to rCount do begin
	    if rUser1[j] < aspect then begin
	       aspect:=rUser1[j];
	       jfocus:=j;
	    end;
          end;
   Writeln(i:5:0,',',rX[jfocus]:5:0,',',rY[jfocus]:5:0,',',rArea[jfocus]:5:0,',',rMajor[jfocus]:5:0,',',rMinor[jfocus]:5:0);

	end;
   end;
  RestoreState;
end;
                 Sincerely,
                   Doug P.

Doug S. Phillips                Internet: phillips@ucalgary.ca
University Computing Services   Phone:(403)220-8445  FAX:(403)282-9199
The University of Calgary       WWW:  http://www.acs.ucalgary.ca/~phillips/


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

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

Date: Wed, 30 Sep 1998 16:54:12 -0400 (EDT)
From: Stephen Keenan <s.keenan@qub.ac.uk>
To: brownj@netmatters.co.uk
cc: nih-image@io.ece.drexel.edu
Subject: Re: Watersheds for Scion PC Image?
Message-ID: <SIMEON.9809301612.A@skeenan.qub.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

Jeremy,

Thank you for taking the time to answer my request.

I do not seem to have a watersheds command in the binary 
processes associated with my Process menu. 

Do I need to obtain any additional modules/macros to enable this 
function?

Thanks again
----------------------
Stephen Keenan

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

Date: Wed, 30 Sep 1998 12:39:27 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Watersheds for Scion PC Image?
Message-Id: <v03007802b2380eba5119@[128.231.99.202]>
Content-Type: text/plain; charset="us-ascii"

>Jeremy,
>
>Thank you for taking the time to answer my request.
>
>I do not seem to have a watersheds command in the binary
>processes associated with my Process menu.

The Watershed command is in Scion Image for Windows beta 3, but it doesn't
appear to work.

-wayne

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

Date: Wed, 30 Sep 1998 15:52:48 -0400 (EDT)
From: Gilbert D Feke <gilbert.feke@yale.edu>
To: nih-image@io.ece.drexel.edu
Subject: real-time row&column averaging
Message-ID: <Pine.GSO.3.94.980930154237.4296A-100000@morpheus.cis.yale.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I am trying to find some combination of CCD camera, frame grabber (either
digital or analog), DSP, and/or software which allows me to perform
real-time averaging of rows and columns.  For example, if I have a 512x512
image input, then I would like the real-time processing to output both a
1x512 image and a 512x1 image which I can save to memory or disk.  Line
scan cameras are not an option since I need both the row and column
averaging from the same camera.

If anyone has any suggestions of how I could do this or some company I
should contact, please reply. 

Thank you.

Gilbert Feke
Yale University
Dept. of Applied Physics
gilbert.feke@yale.edu

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

Date:          Thu, 1 Oct 1998 9:50:01 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: arminator@hotmail.com, nih-image@io.ece.drexel.edu
Subject:       Re: Counting Fibres (the complete message)
Message-ID: <A2D1A081F85@rna.bio.mq.edu.au>

>From: "Michael Arm" <arminator@hotmail.com>
>To: nih-image@io.ece.drexel.edu
>Subject: Counting Fibres (the complete message)
>Date: Wed, 30 Sep 1998 01:57:10 PDT
>....
>we are trying to count fibres dispersed on a glass plate. We get the 3d 
>image Stack from a confocal microscope.
>However, between the fibres are some smaller "dirt"-specks, which we 
>don't want to count. We already told Image not to count objects smaller 
>than 30 Pixels, however larger "crumbs" are still counted.
>How can we get Image to recognize only large objects, that are 
>"fibre-like" (i.e. long and thin and not compact like a crumb)?
>We already found a cell counting macro, that recognizes circle like 
>cells, and leaves out the rest...
>
>Is there a way to tell a macro only to count long, thin objects? Putting 
>an ellipse into a ROI-selected fibre often doesn't work, since some are 
>slightly bent like a parenthesis "("...
>
>Any suggestions would be greatly appreciated.
>
>Sincerely
>Michael Arm
>
Michael, you cant "tell a macro only to count long, thin objects" but having 
counted objects which satisfy size criteria, you can scan the results tables by 
macro to attempt further qualification of counted particles. You can then count 
those in the results table that meet the further imposed criteria or 
effectively delete them from the table (by shuffling others over them).

It is not clear to me what the significance of the 3D is but I would expect to 
be able to effectively exclude the larger "crumbs" by using the ratio 
rArea[i]/rLength[i]:

for i:= rCount do begin rUser1[i]:=rArea[i]/rLength[i];
{
rLength is particle perimeter for analyzeParticles
for long thin fibre particles,
 rUser1[i] should be average halfwidth << rLength[i]/2 ~= length
}

You might also consider making a binary image, and then a Euclidean distance  
map (binary(Process menu before analyzeParticles. Particles with larger 
cross-sections can be excluded by densitySlice'ing the distance map;
 MakeBinary;
binary('map');enhanceContrast;
setDensitySlice(1,maxHalfwidth);
analyzeParticles;

then rMax[i] will be a measure of particle's maximum halfwidth which in turn 
should be close to average halfwidth in rUser1.

If you really want to nitpick the particles by macro, then use analyzeParticles 
results table locations to autoOutline each particle in turn but you would be 
much better off to use Object-Image in that case as it records rTop,rLeft for 
that autoOutline(rTop[i],rLeft[i]); purpose.


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, 1 Oct 1998 10:16:09 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: johannes.barsig@pharma.Novartis.com, nih-image@io.ece.drexel.edu
Subject:       Re: wound area measurements
Message-ID: <A2D8983212A@rna.bio.mq.edu.au>

>From: johannes.barsig@pharma.Novartis.com
>To: nih-image@io.ece.drexel.edu
>Date: Tue, 29 Sep 1998 16:08:05 +0100
>Subject: wound area measurements
>
>We are tracing wound areas of mice on glass slides. The circles we get
>should be digitalized using a graphics tablet. Image should detect, when
>the circle is closed an measure the area of the circle. Then, the next
>circle could be drawn. In results, the measurements should be listed. The
>areas are about two square cm. First question, which graphics tablet would
>be best for this task together with NIH Image. Second question, is there a
>macro around that could control the sequential measuring process described.
>I appreciate every hint.
>Johannes Barsig, Ph.D.
>Novartis Research Institute
>Vienna, Austria
>
I would have thought that you would find that an inexpensive video or digital 
camera attached to a dissecting microscope would be a much more flexible and 
efficient approach with potential for (semi)automated analysis by NIH-Image and 
offering much better documentation of results.

Object-Image has a very nice extension to NIH-Image for computer-assisted 
outlining of density-sliced images: points are collected by (option) "sparking" 
to nearest density-sliced edge.
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 V98 Issue #74
***************************************

From nih-image-request@io.ece.drexel.edu Thu Oct  1 00:56 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id AAA13264;
	Thu, 1 Oct 1998 00:56:29 -0400 (EDT)
Resent-Date: Thu, 1 Oct 1998 00:56:29 -0400 (EDT)
Date: 30 Sep 98 21:35:15 -0600
From: Steven Moore <stevem@cipe.com>
Subject: [1]RE>Re: wound area measurements
To: "nih-image" <nih-image@io.ece.drexel.edu>
X-Mailer: QuickMail Pro 1.5.2 (Windows32)
X-Priority: 3
Reply-To: Steven Moore <stevem@cipe.com>
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Message-ID: <1304931229-2795399@mailhost.cipe.com>
Resent-Message-ID: <"weLoP.0.Lm2.SPm4s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/425
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:  1876
Status: O

Thanks for the message!  Please note that I'm out of the office for two weeks. 
I will return on October 15.  If you need immediate attention, call (800)
322-9884.  Press 0 (zero).  Thanks.
Steven Moore, CIPE


On 10/1/98, nih-image wrote:
>>From: johannes.barsig@pharma.Novartis.com
>>To: nih-image@io.ece.drexel.edu
>>Date: Tue, 29 Sep 1998 16:08:05 +0100
>>Subject: wound area measurements
>>
>>We are tracing wound areas of mice on glass slides. The circles we get
>>should be digitalized using a graphics tablet. Image should detect, when
>>the circle is closed an measure the area of the circle. Then, the next
>>circle could be drawn. In results, the measurements should be listed. The
>>areas are about two square cm. First question, which graphics tablet would
>>be best for this task together with NIH Image. Second question, is there a
>>macro around that could control the sequential measuring process described.
>>I appreciate every hint.
>>Johannes Barsig, Ph.D.
>>Novartis Research Institute
>>Vienna, Austria
>>
>I would have thought that you would find that an inexpensive video or digital 
>camera attached to a dissecting microscope would be a much more flexible and 
>efficient approach with potential for (semi)automated analysis by NIH-Image
and 
>offering much better documentation of results.
>
>Object-Image has a very nice extension to NIH-Image for computer-assisted 
>outlining of density-sliced images: points are collected by (option)
"sparking" 
>to nearest density-sliced edge.
>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
>
>.
>

Steven D. Moore, Ph.D.
Director of Evaluation Services
Center for Image Processing in Education
Tucson, AZ 
stevem@cipe.com
http://www.cipe.com
(800) 322-9884 ext. 125


From nih-image-request@io.ece.drexel.edu Thu Oct  1 09:44 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA28877;
	Thu, 1 Oct 1998 09:44:42 -0400 (EDT)
Resent-Date: Thu, 1 Oct 1998 09:44:42 -0400 (EDT)
From: Stephen Keenan <s.keenan@qub.ac.uk>
Sender: k9425608@qub.ac.uk
To: nih-image@io.ece.drexel.edu
cc: nih-image@io.ece.drexel.edu
Subject: Re: Watersheds for Scion PC Image?
In-Reply-To: <v03007802b2380eba5119@[128.231.99.202]>
Message-ID: <SIMEON.9810011419.B@skeenan.qub.ac.uk>
Date: Thu, 1 Oct 1998 14:26:19 -0400 (EDT)
Priority: NORMAL
X-Mailer: Simeon for Windows Version 4.1.2 Build (32)
X-Authentication: none
MIME-Version: 1.0
Resent-Message-ID: <"JtBTH1.0.RS6.XCu4s"@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/426
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:   459
Status: RO

Wayne,

I obtained Scion Image Beta 3b. The Watershed command does seem 
to work for me. The results I obtained aren't very good but I 
suspect this may be something to do with the images I am using.
Thanks for your help.



On Wed, 30 Sep 1998 12:39:27 -0400 Wayne Rasband 
<wayne@codon.nih.gov> wrote:


> The Watershed command is in Scion Image for Windows beta 3, but it doesn't
> appear to work.
> 
> -wayne
> 
> 

----------------------
Stephen Keenan

From nih-image-request@io.ece.drexel.edu Thu Oct  1 09:45 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA28927;
	Thu, 1 Oct 1998 09:44:54 -0400 (EDT)
Resent-Date: Thu, 1 Oct 1998 09:44:54 -0400 (EDT)
Posted-Date: Thu, 01 Oct 1998 15:30:09 +0000
Sender: marmotta@hmg.inpg.fr
Message-Id: <3613A001.3C21@hmg.inpg.fr>
Date: Thu, 01 Oct 1998 15:30:09 +0000
From: MARMOTTANT Philippe <marmotta@hmg.inpg.fr>
Organization: LEGI
X-Mailer: Mozilla 3.01 (X11; I; HP-UX A.09.05 9000/715)
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Seed Fill plug-in ?
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"UWiTH.0.JX6.MEu4s"@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/427
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:   617
Status: O

Hello subcribers,
  To eliminate discontinous edges, resulting from image anaysis of water
drops, I'd like to have a macro that seed fills images, as the paint
bucket does. A Pascal procedure was proposed in the archives , but I
only have a Think C 5.0 language, so I thought about a including a
Photoshop compatible Plug-in.

Does anyone know about a C code that performs this operation as a
Photoshop plug-in ?  

*******************
Philippe Marmottant
Laboratoire des Ecoulements Geophysiques et Industriels
BP 53 X, 38041 Grenoble Cedex FRANCE
Home :
15 bd Marechal Leclerc, 38000 Grenoble
tel : 04 76 00 01 66

From nih-image-request@io.ece.drexel.edu Thu Oct  1 09:46 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA29173;
	Thu, 1 Oct 1998 09:46:38 -0400 (EDT)
Resent-Date: Thu, 1 Oct 1998 09:46:38 -0400 (EDT)
From: David M Roof <roof@mail.med.upenn.edu>
Message-Id: <199810011333.JAA14879@mail.med.upenn.edu>
Subject: serial connections:Meridian InSIGHT and MAC
To: nih-image@io.ece.drexel.edu
Date: Thu, 1 Oct 1998 09:33:13 -0400 (EDT)
X-Mailer: ELM [version 2.4 PL23-upenn3.1]
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"75zj11.0.we6.XIu4s"@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/428
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:   850
Status: O

Re: serial connections

In addition to checking out the features of Object Image, you can learn
all about interfacing Mac serial ports to lab equipment at:
http://www.mindspring.com/~jc1/serial/main.html

-David

> Has anyone connected a Mac to a Merdian Insight plus? We had a PC
>connected to it, now we have a Mac. We used the serial port on the PC to
>change filters, open the shutter etc. Now that the Mac is going to be
>used, I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but
>the pin out seems to be different and it is not sending the data (using
>the openserial( ) command), to change the filters etc. Apple said that I
>have to become a developer to get this info., and cannot help. It seems
>simple, has anyone used a "regular" (DB25 pinout) modem on an apple?
>Thanks. 
> 
>Todd Kirk 
>Indiana University Medical Center

From nih-image-request@io.ece.drexel.edu Thu Oct  1 10:13 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA02444;
	Thu, 1 Oct 1998 10:13:11 -0400 (EDT)
Resent-Date: Thu, 1 Oct 1998 10:13:11 -0400 (EDT)
Message-Id: <199810011359.AA10691@na3.dow.com>
From: "Heeschen, Bill (WA)" <WAHEESCHEN@dow.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Watersheds for Scion PC Image?
Date: Thu, 1 Oct 1998 09:53:08 -0400 
Mime-Version: 1.0
X-Mailer: Internet Mail Service (5.5.1960.3)
Resent-Message-ID: <"vH6Yu1.0.sA.Phu4s"@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/429
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length:   383
Status: O

Folks:
I brought this up with Scion a little while ago and their response was
that this feature is there, but has not been fully debugged, so you
should double-check your results against your original.  I found that it
sometimes appeared to work, other times it crashed the program.  I have
not yet verified the Euclidean Distance Map result.
Bill Heeschen
Dow Chemical
Midland, MI

From nih-image-request@io.ece.drexel.edu Thu Oct  1 10:14 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA02622;
	Thu, 1 Oct 1998 10:14:22 -0400 (EDT)
Resent-Date: Thu, 1 Oct 1998 10:14:22 -0400 (EDT)
Message-ID: <9D916278299FD111A7E100805FA7C2BA4B9FD5@cheetah.uits.iupui.edu>
From: "Kirk, Todd Jason" <tjkirk@iupui.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: serial connections:Meridian InSIGHT and MAC
Date: Thu, 1 Oct 1998 09:00:39 -0500 
MIME-Version: 1.0
X-Mailer: Internet Mail Service (5.5.2232.9)
Resent-Message-ID: <"mDC0H1.0.1D.Diu4s"@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/430
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length:   683
Status: O

Hey,
       Thanks to everyone that replied, listserves are the BEST! What Apple
could not provide me with USRobotics could. I found a pin out on their site
and it works perfectly with the Scion version of NIH Image. Thanks again!
Todd

> -----Original Message-----
> From:	David M Roof [SMTP:roof@mail.med.upenn.edu]
> Sent:	Thursday, October 01, 1998 8:33 AM
> To:	nih-image@io.ece.drexel.edu
> Subject:	serial connections:Meridian InSIGHT and MAC
> 
> Re: serial connections
> 
> In addition to checking out the features of Object Image, you can learn
> all about interfacing Mac serial ports to lab equipment at:
> http://www.mindspring.com/~jc1/serial/main.html
> 
> -David
> 

From nih-image-request@io.ece.drexel.edu Thu Oct  1 13:52 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA23692;
	Thu, 1 Oct 1998 13:52:06 -0400 (EDT)
Resent-Date: Thu, 1 Oct 1998 13:52:06 -0400 (EDT)
Date: Thu, 01 Oct 1998 13:30:40 -0400
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
Subject: Q: calculating best-fitting ellipsoid of a 3D object spanning multiple
 slices?
To: nih-image@io.ece.drexel.edu
Message-id: <v04011700b2396b0a14a6@[128.244.128.68]>
MIME-version: 1.0
Resent-Message-ID: <"tx42z1.0.KD5.smx4s"@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/431
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: 809

I'm looking for a method of calculating (preferably within the macro
language) a best-fitting 3D ellipsoid from contours of an object spanning a
series of slices. I have saved the contour coordinates as a series of
XYcoordinate text files with known slice spacing and scale etc. By
'best-fitting', I mean the ellipsoid that minimizes the sum of square
deviations of points on the contours from the ellipsoid surface. Thus, the
contour coordinates constitute a subset of a complete object surface
description.

Can anyone suggest a method that can be implemented in the macro language?
Standard unix library or source code?

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 Thu Oct  1 16:21 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA06720;
	Thu, 1 Oct 1998 16:21:18 -0400 (EDT)
Date: Thu, 1 Oct 1998 16:21:18 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810012021.QAA06720@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #75
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/75
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 10324

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 75

Today's Topics:
  [1]RE>Re: wound area measurements     [ Steven Moore <stevem@cipe.com> ]
  Re: Watersheds for Scion PC Image?    [ Stephen Keenan <s.keenan@qub.ac.uk> ]
  Seed Fill plug-in ?                   [ MARMOTTANT Philippe <marmotta@hmg.i ]
  serial connections:Meridian InSIGHT   [ David M Roof <roof@mail.med.upenn.e ]
  RE: Watersheds for Scion PC Image?    [ "Heeschen, Bill (WA)" <WAHEESCHEN@d ]
  RE: serial connections:Meridian InSI  [ "Kirk, Todd Jason" <tjkirk@iupui.ed ]
  Q: calculating best-fitting ellipsoi  [ Bill Christens-Barry <wacb@aplcomm. ]
  Re: Q: calculating best-fitting elli  [ Cengizhan Ozturk <cozturk@mri.jhu.e ]

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

Date: 30 Sep 98 21:35:15 -0600
From: Steven Moore <stevem@cipe.com>
To: "nih-image" <nih-image@io.ece.drexel.edu>
Subject: [1]RE>Re: wound area measurements
Message-ID: <1304931229-2795399@mailhost.cipe.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset="US-Ascii"

Thanks for the message!  Please note that I'm out of the office for two weeks. 
I will return on October 15.  If you need immediate attention, call (800)
322-9884.  Press 0 (zero).  Thanks.
Steven Moore, CIPE


On 10/1/98, nih-image wrote:
>>From: johannes.barsig@pharma.Novartis.com
>>To: nih-image@io.ece.drexel.edu
>>Date: Tue, 29 Sep 1998 16:08:05 +0100
>>Subject: wound area measurements
>>
>>We are tracing wound areas of mice on glass slides. The circles we get
>>should be digitalized using a graphics tablet. Image should detect, when
>>the circle is closed an measure the area of the circle. Then, the next
>>circle could be drawn. In results, the measurements should be listed. The
>>areas are about two square cm. First question, which graphics tablet would
>>be best for this task together with NIH Image. Second question, is there a
>>macro around that could control the sequential measuring process described.
>>I appreciate every hint.
>>Johannes Barsig, Ph.D.
>>Novartis Research Institute
>>Vienna, Austria
>>
>I would have thought that you would find that an inexpensive video or digital 
>camera attached to a dissecting microscope would be a much more flexible and 
>efficient approach with potential for (semi)automated analysis by NIH-Image
and 
>offering much better documentation of results.
>
>Object-Image has a very nice extension to NIH-Image for computer-assisted 
>outlining of density-sliced images: points are collected by (option)
"sparking" 
>to nearest density-sliced edge.
>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
>
>.
>

Steven D. Moore, Ph.D.
Director of Evaluation Services
Center for Image Processing in Education
Tucson, AZ 
stevem@cipe.com
http://www.cipe.com
(800) 322-9884 ext. 125

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

Date: Thu, 1 Oct 1998 14:26:19 -0400 (EDT)
From: Stephen Keenan <s.keenan@qub.ac.uk>
To: nih-image@io.ece.drexel.edu
cc: nih-image@io.ece.drexel.edu
Subject: Re: Watersheds for Scion PC Image?
Message-ID: <SIMEON.9810011419.B@skeenan.qub.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

Wayne,

I obtained Scion Image Beta 3b. The Watershed command does seem 
to work for me. The results I obtained aren't very good but I 
suspect this may be something to do with the images I am using.
Thanks for your help.



On Wed, 30 Sep 1998 12:39:27 -0400 Wayne Rasband 
<wayne@codon.nih.gov> wrote:


> The Watershed command is in Scion Image for Windows beta 3, but it doesn't
> appear to work.
> 
> -wayne
> 
> 

----------------------
Stephen Keenan

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

Date: Thu, 01 Oct 1998 15:30:09 +0000
From: MARMOTTANT Philippe <marmotta@hmg.inpg.fr>
To: nih-image@io.ece.drexel.edu
Subject: Seed Fill plug-in ?
Message-Id: <3613A001.3C21@hmg.inpg.fr>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hello subcribers,
  To eliminate discontinous edges, resulting from image anaysis of water
drops, I'd like to have a macro that seed fills images, as the paint
bucket does. A Pascal procedure was proposed in the archives , but I
only have a Think C 5.0 language, so I thought about a including a
Photoshop compatible Plug-in.

Does anyone know about a C code that performs this operation as a
Photoshop plug-in ?  

*******************
Philippe Marmottant
Laboratoire des Ecoulements Geophysiques et Industriels
BP 53 X, 38041 Grenoble Cedex FRANCE
Home :
15 bd Marechal Leclerc, 38000 Grenoble
tel : 04 76 00 01 66

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

Date: Thu, 1 Oct 1998 09:33:13 -0400 (EDT)
From: David M Roof <roof@mail.med.upenn.edu>
To: nih-image@io.ece.drexel.edu
Subject: serial connections:Meridian InSIGHT and MAC
Message-Id: <199810011333.JAA14879@mail.med.upenn.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit

Re: serial connections

In addition to checking out the features of Object Image, you can learn
all about interfacing Mac serial ports to lab equipment at:
http://www.mindspring.com/~jc1/serial/main.html

-David

> Has anyone connected a Mac to a Merdian Insight plus? We had a PC
>connected to it, now we have a Mac. We used the serial port on the PC to
>change filters, open the shutter etc. Now that the Mac is going to be
>used, I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but
>the pin out seems to be different and it is not sending the data (using
>the openserial( ) command), to change the filters etc. Apple said that I
>have to become a developer to get this info., and cannot help. It seems
>simple, has anyone used a "regular" (DB25 pinout) modem on an apple?
>Thanks. 
> 
>Todd Kirk 
>Indiana University Medical Center

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

Date: Thu, 1 Oct 1998 09:53:08 -0400 
From: "Heeschen, Bill (WA)" <WAHEESCHEN@dow.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Watersheds for Scion PC Image?
Message-Id: <199810011359.AA10691@na3.dow.com>
Content-Type: text/plain

Folks:
I brought this up with Scion a little while ago and their response was
that this feature is there, but has not been fully debugged, so you
should double-check your results against your original.  I found that it
sometimes appeared to work, other times it crashed the program.  I have
not yet verified the Euclidean Distance Map result.
Bill Heeschen
Dow Chemical
Midland, MI

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

Date: Thu, 1 Oct 1998 09:00:39 -0500 
From: "Kirk, Todd Jason" <tjkirk@iupui.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: serial connections:Meridian InSIGHT and MAC
Message-ID: <9D916278299FD111A7E100805FA7C2BA4B9FD5@cheetah.uits.iupui.edu>
Content-Type: text/plain

Hey,
       Thanks to everyone that replied, listserves are the BEST! What Apple
could not provide me with USRobotics could. I found a pin out on their site
and it works perfectly with the Scion version of NIH Image. Thanks again!
Todd

> -----Original Message-----
> From:	David M Roof [SMTP:roof@mail.med.upenn.edu]
> Sent:	Thursday, October 01, 1998 8:33 AM
> To:	nih-image@io.ece.drexel.edu
> Subject:	serial connections:Meridian InSIGHT and MAC
> 
> Re: serial connections
> 
> In addition to checking out the features of Object Image, you can learn
> all about interfacing Mac serial ports to lab equipment at:
> http://www.mindspring.com/~jc1/serial/main.html
> 
> -David
> 

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

Date: Thu, 01 Oct 1998 13:30:40 -0400
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
To: nih-image@io.ece.drexel.edu
Subject: Q: calculating best-fitting ellipsoid of a 3D object spanning multiple
 slices?
Message-id: <v04011700b2396b0a14a6@[128.244.128.68]>
Content-type: text/plain; charset="us-ascii"

I'm looking for a method of calculating (preferably within the macro
language) a best-fitting 3D ellipsoid from contours of an object spanning a
series of slices. I have saved the contour coordinates as a series of
XYcoordinate text files with known slice spacing and scale etc. By
'best-fitting', I mean the ellipsoid that minimizes the sum of square
deviations of points on the contours from the ellipsoid surface. Thus, the
contour coordinates constitute a subset of a complete object surface
description.

Can anyone suggest a method that can be implemented in the macro language?
Standard unix library or source code?

Thanks.

Bill Christens-Barry
-------------------------
Bill Christens-Barry, PhD
Johns Hopkins University Applied Physics Laboratory
wacb@aplcomm.jhuapl.edu
-------------------------

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

Date: Thu, 1 Oct 1998 15:48:57 -0400 (EDT)
From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Q: calculating best-fitting ellipsoid of a 3D object spanning multiple slices?
Message-ID: <Pine.SGI.3.91.981001154853.26001D-100000@henryv>
Content-Type: TEXT/PLAIN; charset=US-ASCII

--------------------------------------------
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 Thu, 1 Oct 1998, Bill Christens-Barry wrote:

> I'm looking for a method of calculating (preferably within the macro
> language) a best-fitting 3D ellipsoid from contours of an object spanning a
> series of slices. I have saved the contour coordinates as a series of
> XYcoordinate text files with known slice spacing and scale etc. By
> 'best-fitting', I mean the ellipsoid that minimizes the sum of square
> deviations of points on the contours from the ellipsoid surface. Thus, the
> contour coordinates constitute a subset of a complete object surface
> description.
> 
> Can anyone suggest a method that can be implemented in the macro language?
> Standard unix library or source code?
> 
> Thanks.
> 
> Bill Christens-Barry
> -------------------------
> Bill Christens-Barry, PhD
> Johns Hopkins University Applied Physics Laboratory
> wacb@aplcomm.jhuapl.edu
> -------------------------
> 
> 

--------------------------------
End of nih-image-d Digest V98 Issue #75
***************************************

From nih-image-request@io.ece.drexel.edu Thu Oct  1 16:24 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA06976;
	Thu, 1 Oct 1998 16:24:01 -0400 (EDT)
Resent-Date: Thu, 1 Oct 1998 16:24:01 -0400 (EDT)
Date: Thu, 1 Oct 1998 15:48:57 -0400 (EDT)
From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Q: calculating best-fitting ellipsoid of a 3D object spanning multiple slices?
In-Reply-To: <v04011700b2396b0a14a6@[128.244.128.68]>
Message-ID: <Pine.SGI.3.91.981001154853.26001D-100000@henryv>
MIME-Version: 1.0
Resent-Message-ID: <"XbkS32.0.sv.noz4s"@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/432
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: 1179




--------------------------------------------
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 Thu, 1 Oct 1998, Bill Christens-Barry wrote:

> I'm looking for a method of calculating (preferably within the macro
> language) a best-fitting 3D ellipsoid from contours of an object spanning a
> series of slices. I have saved the contour coordinates as a series of
> XYcoordinate text files with known slice spacing and scale etc. By
> 'best-fitting', I mean the ellipsoid that minimizes the sum of square
> deviations of points on the contours from the ellipsoid surface. Thus, the
> contour coordinates constitute a subset of a complete object surface
> description.
> 
> Can anyone suggest a method that can be implemented in the macro language?
> Standard unix library or source code?
> 
> 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 Thu Oct  1 20:17 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA26474;
	Thu, 1 Oct 1998 20:16:43 -0400 (EDT)
Resent-Date: Thu, 1 Oct 1998 20:16:43 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: marmotta@hmg.inpg.fr, nih-image@io.ece.drexel.edu
Date:          Fri, 2 Oct 1998 9:50:37 GMT+1000
Subject:       Re: Seed Fill plug-in ?
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <A451E023944@rna.bio.mq.edu.au>
Resent-Message-ID: <"WLyrm1.0.km5.FJ15s"@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/433
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1518

>Date: Thu, 01 Oct 1998 15:30:09 +0000
>From: MARMOTTANT Philippe <marmotta@hmg.inpg.fr>
>...
>  To eliminate discontinous edges, resulting from image anaysis of water
>drops, I'd like to have a macro that seed fills images, as the paint
>bucket does. A Pascal procedure was proposed in the archives , but I
>only have a Think C 5.0 language, so I thought about a including a
>Photoshop compatible Plug-in.
>
>Does anyone know about a C code that performs this operation as a
>Photoshop plug-in ?  
>
>*******************
>Philippe Marmottant
>Laboratoire des Ecoulements Geophysiques et Industriels
>BP 53 X, 38041 Grenoble Cedex FRANCE
>Home :
>15 bd Marechal Leclerc, 38000 Grenoble
>tel : 04 76 00 01 66

Object-Image is an extended version of W. Rasband's
image processing program 'NIH-Image'.
           by Norbert Vischer (vischer@bio.uva.nl)
it is available at:
http://simon.bio.uva.nl/Object-Image.html

it has SeedFill(x, y)
  Same as clicking with the paint bucket on (x, y)
along with many other extremely useful extentions.

I am curious as to how you would use a seedFill "To eliminate discontinous 
edges, resulting from image anaysis of water drops, as the paint bucket does".
It seems to me that you would need to segment the drop as a Roi/selection 
before you use seedFill. 

How does it help with segmentation?


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 Oct  2 08:20 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA11850;
	Fri, 2 Oct 1998 08:20:38 -0400 (EDT)
Resent-Date: Fri, 2 Oct 1998 08:20:38 -0400 (EDT)
Posted-Date: Fri, 02 Oct 1998 14:09:15 +0000
Sender: marmotta@hmg.inpg.fr
Message-Id: <3614DE8B.1C2F@hmg.inpg.fr>
Date: Fri, 02 Oct 1998 14:09:15 +0000
From: MARMOTTANT Philippe <marmotta@hmg.inpg.fr>
Organization: LEGI
X-Mailer: Mozilla 3.01 (X11; I; HP-UX A.09.05 9000/715)
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: Seed Fill plug-in ?
References: <A451E023944@rna.bio.mq.edu.au>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"Iek0w2.0.eW2.P8C5s"@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/434
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: 2068

GJOSS@rna.bio.mq.edu.au wrote:
> Object-Image is an extended version of W. Rasband's
> image processing program 'NIH-Image'.
>            by Norbert Vischer (vischer@bio.uva.nl)
> it is available at:
> http://simon.bio.uva.nl/Object-Image.html
> 
> it has SeedFill(x, y)
>   Same as clicking with the paint bucket on (x, y)
> along with many other extremely useful extentions.
> 
> I am curious as to how you would use a seedFill "To eliminate discontinous
> edges, resulting from image anaysis of water drops, as the paint bucket does".
> It seems to me that you would need to segment the drop as a Roi/selection
> before you use seedFill.
> 
> How does it help with segmentation?
> 
> 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

Here are some explanations on my image analysis of non spherical water
drops produced by atomisation experiments:
I first perform a FindEdges-like operation, that I programmed as a C
Photoshop compatible plug-in, by plotting the normalized rms of the 8
neighbouring pixels of each pixel (a filter called Sigma).

A threshold on this result allows to eliminate out-focus drop edges,
because the rms on these edges is lower than with sharp edges. Out-focus
are eliminated because of being outside calibration.

After a squelettonize I then obtain closed and unclosed loops. Unclosed
loops are due to the superposition of an out focus drop with an in-focus
drop. I don't want this edge with an unknown part.

Here is where I perform the SeedFill in black, same color as the edges,
that fills the unclosed loops, and make them disappear. 
I can thus have size measurements on single in-focus drops, represented
by closed loops, with the Analyze particle NIH function.

Hoping I help you see clearer on my segmentation process, 
-- 
*******************
Philippe Marmottant

Laboratoire des Ecoulements Geophysiques et Industriels
Universite Joseph Fourier,
BP 53 X, 38041 Grenoble Cedex France


From nih-image-request@io.ece.drexel.edu Fri Oct  2 11:50 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA02458;
	Fri, 2 Oct 1998 11:50:16 -0400 (EDT)
Resent-Date: Fri, 2 Oct 1998 11:50:16 -0400 (EDT)
From: beverly@umich.edu
Date: Fri, 2 Oct 1998 11:33:34 -0400 (EDT)
X-Sender: beverly@qbert.rs.itd.umich.edu
To: nih-image@io.ece.drexel.edu
Subject: Help with Frame Grabber
Message-ID: <Pine.SOL.3.95.981002112752.21407A-100000@qbert.rs.itd.umich.edu>
MIME-Version: 1.0
Resent-Message-ID: <"Yjo0l2.0.j9.J9F5s"@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/435
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: 1115

To whom it may concern:

We are interested in using the NIH Image program to help us count crystals
through a CCD camera (Panasonic CCD WV-CL300) attached to an optical light
microscope.  We have an old Mac IIcx that we would like to use as computer
to control the program.  However, I can't seem to find a Frame Grabber
Card that I can use on an older mac.  If memory serves correctly, it is
only equipped with NuBus slots.  According to the NIH Image manual, the
VG-5 is a NuBus Card (Appendix B of the manual) however according to the 
tech support specs at the SCION website, this card is PCI only.

Where can I find a NuBus card that we can use in this Mac?  Would this mac
have sufficient computing power to run the program affectively.  We don't
need to capture live video just still images.

Thanks for any support you can provide. I have copied this message to both
Sales and Tech Support because I'm not sure who would be the best group to
talk to about this.

Thanks again

Beverly C. Langevin R.Ph., M.S.

University of Michigan
College of Pharmacy, Room 3018
beverly@umich.edu
Office: (734) 647-2219



From nih-image-d-request@io.ece.drexel.edu Fri Oct  2 11:50 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA02529;
	Fri, 2 Oct 1998 11:50:37 -0400 (EDT)
Date: Fri, 2 Oct 1998 11:50:37 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810021550.LAA02529@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #76
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/76
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 5976

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 76

Today's Topics:
  Re: Seed Fill plug-in ?               [ GJOSS@rna.bio.mq.edu.au ]
  Re: Seed Fill plug-in ?               [ MARMOTTANT Philippe <marmotta@hmg.i ]
  Help with Frame Grabber               [ beverly@umich.edu ]

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

Date:          Fri, 2 Oct 1998 9:50:37 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: marmotta@hmg.inpg.fr, nih-image@io.ece.drexel.edu
Subject:       Re: Seed Fill plug-in ?
Message-ID: <A451E023944@rna.bio.mq.edu.au>

>Date: Thu, 01 Oct 1998 15:30:09 +0000
>From: MARMOTTANT Philippe <marmotta@hmg.inpg.fr>
>...
>  To eliminate discontinous edges, resulting from image anaysis of water
>drops, I'd like to have a macro that seed fills images, as the paint
>bucket does. A Pascal procedure was proposed in the archives , but I
>only have a Think C 5.0 language, so I thought about a including a
>Photoshop compatible Plug-in.
>
>Does anyone know about a C code that performs this operation as a
>Photoshop plug-in ?  
>
>*******************
>Philippe Marmottant
>Laboratoire des Ecoulements Geophysiques et Industriels
>BP 53 X, 38041 Grenoble Cedex FRANCE
>Home :
>15 bd Marechal Leclerc, 38000 Grenoble
>tel : 04 76 00 01 66

Object-Image is an extended version of W. Rasband's
image processing program 'NIH-Image'.
           by Norbert Vischer (vischer@bio.uva.nl)
it is available at:
http://simon.bio.uva.nl/Object-Image.html

it has SeedFill(x, y)
  Same as clicking with the paint bucket on (x, y)
along with many other extremely useful extentions.

I am curious as to how you would use a seedFill "To eliminate discontinous 
edges, resulting from image anaysis of water drops, as the paint bucket does".
It seems to me that you would need to segment the drop as a Roi/selection 
before you use seedFill. 

How does it help with segmentation?


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, 02 Oct 1998 14:09:15 +0000
From: MARMOTTANT Philippe <marmotta@hmg.inpg.fr>
To: nih-image@io.ece.drexel.edu
Subject: Re: Seed Fill plug-in ?
Message-Id: <3614DE8B.1C2F@hmg.inpg.fr>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

GJOSS@rna.bio.mq.edu.au wrote:
> Object-Image is an extended version of W. Rasband's
> image processing program 'NIH-Image'.
>            by Norbert Vischer (vischer@bio.uva.nl)
> it is available at:
> http://simon.bio.uva.nl/Object-Image.html
> 
> it has SeedFill(x, y)
>   Same as clicking with the paint bucket on (x, y)
> along with many other extremely useful extentions.
> 
> I am curious as to how you would use a seedFill "To eliminate discontinous
> edges, resulting from image anaysis of water drops, as the paint bucket does".
> It seems to me that you would need to segment the drop as a Roi/selection
> before you use seedFill.
> 
> How does it help with segmentation?
> 
> 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

Here are some explanations on my image analysis of non spherical water
drops produced by atomisation experiments:
I first perform a FindEdges-like operation, that I programmed as a C
Photoshop compatible plug-in, by plotting the normalized rms of the 8
neighbouring pixels of each pixel (a filter called Sigma).

A threshold on this result allows to eliminate out-focus drop edges,
because the rms on these edges is lower than with sharp edges. Out-focus
are eliminated because of being outside calibration.

After a squelettonize I then obtain closed and unclosed loops. Unclosed
loops are due to the superposition of an out focus drop with an in-focus
drop. I don't want this edge with an unknown part.

Here is where I perform the SeedFill in black, same color as the edges,
that fills the unclosed loops, and make them disappear. 
I can thus have size measurements on single in-focus drops, represented
by closed loops, with the Analyze particle NIH function.

Hoping I help you see clearer on my segmentation process, 
-- 
*******************
Philippe Marmottant

Laboratoire des Ecoulements Geophysiques et Industriels
Universite Joseph Fourier,
BP 53 X, 38041 Grenoble Cedex France

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

Date: Fri, 2 Oct 1998 11:33:34 -0400 (EDT)
From: beverly@umich.edu
To: nih-image@io.ece.drexel.edu
Subject: Help with Frame Grabber
Message-ID: <Pine.SOL.3.95.981002112752.21407A-100000@qbert.rs.itd.umich.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

To whom it may concern:

We are interested in using the NIH Image program to help us count crystals
through a CCD camera (Panasonic CCD WV-CL300) attached to an optical light
microscope.  We have an old Mac IIcx that we would like to use as computer
to control the program.  However, I can't seem to find a Frame Grabber
Card that I can use on an older mac.  If memory serves correctly, it is
only equipped with NuBus slots.  According to the NIH Image manual, the
VG-5 is a NuBus Card (Appendix B of the manual) however according to the 
tech support specs at the SCION website, this card is PCI only.

Where can I find a NuBus card that we can use in this Mac?  Would this mac
have sufficient computing power to run the program affectively.  We don't
need to capture live video just still images.

Thanks for any support you can provide. I have copied this message to both
Sales and Tech Support because I'm not sure who would be the best group to
talk to about this.

Thanks again

Beverly C. Langevin R.Ph., M.S.

University of Michigan
College of Pharmacy, Room 3018
beverly@umich.edu
Office: (734) 647-2219

--------------------------------
End of nih-image-d Digest V98 Issue #76
***************************************

From nih-image-request@io.ece.drexel.edu Fri Oct  2 12:56 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA08290;
	Fri, 2 Oct 1998 12:56:25 -0400 (EDT)
 <Pine.SOL.3.95.981002112752.21407A-100000@qbert.rs.itd.umich.edu>
Resent-Date: Fri, 2 Oct 1998 12:56:25 -0400 (EDT)
Message-Id: <l03020704b23a6b985a50@[192.203.180.76]>
In-Reply-To: 
 <Pine.SOL.3.95.981002112752.21407A-100000@qbert.rs.itd.umich.edu>
Mime-Version: 1.0
Date: Fri, 2 Oct 1998 12:41:13 +0100
To: nih-image@io.ece.drexel.edu
From: Julian Smith III <smithj@winthrop.edu>
Subject: Re: Help with Frame Grabber
Resent-Message-ID: <"bGJHe1.0.Tj1.F7G5s"@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/436
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: 1599

Beverly:
I've used a MacIIcx and a Scion LG-3 frame grabber for monochrome video
capture for several years now.  It works fine. You are correct that the
computer has only NuBus slots.
You may have a little trouble finding a Nubus Scion card, though.  Scion
may have discontinued them, since all of the new macs have PCI.  I would
give them a call and see.
HTH
Julian

>We are interested in using the NIH Image program to help us count crystals
>through a CCD camera (Panasonic CCD WV-CL300) attached to an optical light
>microscope.  We have an old Mac IIcx that we would like to use as computer
>to control the program.  However, I can't seem to find a Frame Grabber
>Card that I can use on an older mac.  If memory serves correctly, it is
>only equipped with NuBus slots.  According to the NIH Image manual, the
>VG-5 is a NuBus Card (Appendix B of the manual) however according to the
>tech support specs at the SCION website, this card is PCI only.
>
>Where can I find a NuBus card that we can use in this Mac?  Would this mac
>have sufficient computing power to run the program affectively.  We don't
>need to capture live video just still images.
>
>Thanks for any support you can provide. I have copied this message to both
>Sales and Tech Support because I'm not sure who would be the best group to
>talk to about this.
>
>Thanks again
>
>Beverly C. Langevin R.Ph., M.S.
>
>University of Michigan
>College of Pharmacy, Room 3018
>beverly@umich.edu
>Office: (734) 647-2219


Julian P.S. Smith III
Biology
Winthrop University
Rock Hill, SC  29733
803-323-2111 x6427 (vox)
803-323-2246 (fax)



From nih-image-d-request@io.ece.drexel.edu Sat Oct  3 06:10 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA00956;
	Sat, 3 Oct 1998 06:10:41 -0400 (EDT)
Date: Sat, 3 Oct 1998 06:10:41 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810031010.GAA00956@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #77
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/77
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 2192

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 77

Today's Topics:
  Re: Help with Frame Grabber           [ Julian Smith III <smithj@winthrop.e ]

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

Date: Fri, 2 Oct 1998 12:41:13 +0100
From: Julian Smith III <smithj@winthrop.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Help with Frame Grabber
Message-Id: <l03020704b23a6b985a50@[192.203.180.76]>
Content-Type: text/plain; charset="us-ascii"

Beverly:
I've used a MacIIcx and a Scion LG-3 frame grabber for monochrome video
capture for several years now.  It works fine. You are correct that the
computer has only NuBus slots.
You may have a little trouble finding a Nubus Scion card, though.  Scion
may have discontinued them, since all of the new macs have PCI.  I would
give them a call and see.
HTH
Julian

>We are interested in using the NIH Image program to help us count crystals
>through a CCD camera (Panasonic CCD WV-CL300) attached to an optical light
>microscope.  We have an old Mac IIcx that we would like to use as computer
>to control the program.  However, I can't seem to find a Frame Grabber
>Card that I can use on an older mac.  If memory serves correctly, it is
>only equipped with NuBus slots.  According to the NIH Image manual, the
>VG-5 is a NuBus Card (Appendix B of the manual) however according to the
>tech support specs at the SCION website, this card is PCI only.
>
>Where can I find a NuBus card that we can use in this Mac?  Would this mac
>have sufficient computing power to run the program affectively.  We don't
>need to capture live video just still images.
>
>Thanks for any support you can provide. I have copied this message to both
>Sales and Tech Support because I'm not sure who would be the best group to
>talk to about this.
>
>Thanks again
>
>Beverly C. Langevin R.Ph., M.S.
>
>University of Michigan
>College of Pharmacy, Room 3018
>beverly@umich.edu
>Office: (734) 647-2219


Julian P.S. Smith III
Biology
Winthrop University
Rock Hill, SC  29733
803-323-2111 x6427 (vox)
803-323-2246 (fax)

--------------------------------
End of nih-image-d Digest V98 Issue #77
***************************************

From nih-image-request@io.ece.drexel.edu Sat Oct  3 12:04 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA00142;
	Sat, 3 Oct 1998 12:04:30 -0400 (EDT)
  <Pine.SOL.3.95.981002112752.21407A-100000@qbert.rs.itd.umich.edu>
Resent-Date: Sat, 3 Oct 1998 12:04:30 -0400 (EDT)
Message-Id: <v04003a00b23c068d9e83@[128.231.128.61]>
In-Reply-To: <l03020704b23a6b985a50@[192.203.180.76]>
References: 
  <Pine.SOL.3.95.981002112752.21407A-100000@qbert.rs.itd.umich.edu>
Mime-Version: 1.0
Date: Sat, 3 Oct 1998 11:54:04 -0500
To: nih-image@io.ece.drexel.edu
From: Mark A Vivino <mvivino@helix.nih.gov>
Subject: NIH'er moving on
Resent-Message-ID: <"LNqPv.0.y27.xWa5s"@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/437
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: 1232

Dear fellow NIH Imagers,

October 9, 1998 will be my last day at NIH. I have over the years enjoyed
being very active on this listserv and in applying NIH Image to many campus
research matters in my work at NIH. I am moving on to Miami, FL where my
wife is doing her fellowship (neuro-ophthalmology) at the Bascom Palmer Eye
Institute/University of Miami. Although I will be signing off from this
account and will remove myself from the listserv under this NIH email
account I have resubscribed under my new email, which is for now:

mvivino@rocketmail.com

As of this time I am looking for consulting, biomedical engineering, or
development work. In these capacities I would be interested in doing some
of the many things I did here at NIH. Among these are, applying NIH Image &
doing modifications to the package, data acquisition, other imaging,
LabView, various collaborative biomedical research & development projects,
and certainly a variety of other things. I am willing to do these via
remote and various on sites and perhaps full time in the Miami area.

Should any of you be interested in contacting me please feel free to do so
at my rocketmail account or my NIH account in the near future.


Sincerely,
Mark A. Vivino



From nih-image-request@io.ece.drexel.edu Sat Oct  3 16:00 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA19239;
	Sat, 3 Oct 1998 16:00:56 -0400 (EDT)
Resent-Date: Sat, 3 Oct 1998 16:00:56 -0400 (EDT)
X-Authentication-Warning: maryann.eng.umd.edu: cgw owned process doing -bs
Date: Sat, 3 Oct 1998 15:49:18 -0400 (EDT)
From: Corey Washington <cgw@Glue.umd.edu>
X-Sender: cgw@maryann.eng.umd.edu
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH'er moving on
In-Reply-To: <v04003a00b23c068d9e83@[128.231.128.61]>
Message-ID: <Pine.OSF.3.95q.981003154841.29242A-100000@maryann.eng.umd.edu>
MIME-Version: 1.0
Resent-Message-ID: <"J828l1.0.rQ4.E_d5s"@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/438
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: 377

Could you please remove my name from the listserv. cgw

_______________________________________________________________________
 Corey Washington		(301) 405-5710 my office
 Dept. of Philosophy            (301) 405-5689 main office
 1123 Skinner Bldg.
 University of Maryland
 College Park, MD 20742-7615
_______________________________________________________________________


From nih-image-request@io.ece.drexel.edu Sat Oct  3 16:27 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA21507;
	Sat, 3 Oct 1998 16:27:38 -0400 (EDT)
 <Pine.OSF.3.95q.981003154841.29242A-100000@maryann.eng.umd.edu>
Resent-Date: Sat, 3 Oct 1998 16:27:38 -0400 (EDT)
Message-Id: <v04003a00b23c44bc8135@[128.231.128.61]>
In-Reply-To: 
 <Pine.OSF.3.95q.981003154841.29242A-100000@maryann.eng.umd.edu>
References: <v04003a00b23c068d9e83@[128.231.128.61]>
Mime-Version: 1.0
Date: Sat, 3 Oct 1998 16:17:51 -0500
To: nih-image@io.ece.drexel.edu
From: Mark A Vivino <mvivino@helix.nih.gov>
Subject: how to (un)subscribe & list info
Resent-Message-ID: <"txEdp2.0.6_4.FOe5s"@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/439
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: 2478

e-mail addresses of importance
--------
nih-image@biomed.drexel.edu   - Sends mail to the list
nih-image-request@biomed.drexel.edu   - Administation for List
nih-image-d-request@biomed.drexel.edu  - Aministration for Digest

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".

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


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

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

Help
--------------------
To obtain a listing of help items, send E-mail to
nih-image-d-request@biomed.drexel.edu.
the Subject of the message should contain "help".

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



Help on Digest
--------------------
To obtain a listing of help items on digest version of the list, send
E-mail to
nih-image-d-request@biomed.drexel.edu.
the Subject of the message should contain "help".

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



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

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

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/*

Mark



From nih-image-request@io.ece.drexel.edu Sat Oct  3 18:10 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA00138;
	Sat, 3 Oct 1998 18:09:59 -0400 (EDT)
Resent-Date: Sat, 3 Oct 1998 18:09:59 -0400 (EDT)
Message-ID: <3616A03A.CA77596D@howard.edu>
Date: Sat, 03 Oct 1998 15:07:55 -0700
From: Bill Eckberg <weckberg@howard.edu>
X-Mailer: Mozilla 4.5b1 (Macintosh; I; PPC)
X-Accept-Language: English [en]
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: frame grabber available
References: <199810031009.GAA00837@io.ece.drexel.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"bdMxs.0.s57.gwf5s"@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/440
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length: 174

If anyone needs a NuBus frame grabber, I have  Scion VG-5 available.
I've gotten a new G3 and had to order a PCI board. Send responses to me,
not to the list.

Bill Eckberg


From nih-image-d-request@io.ece.drexel.edu Sun Oct  4 06:12 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA23258;
	Sun, 4 Oct 1998 06:12:41 -0400 (EDT)
Date: Sun, 4 Oct 1998 06:12:41 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810041012.GAA23258@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #78
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/78
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 6009

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 78

Today's Topics:
  NIH'er moving on                      [ Mark A Vivino <mvivino@helix.nih.go ]
  Re: NIH'er moving on                  [ Corey Washington <cgw@Glue.umd.edu> ]
  how to (un)subscribe & list info      [ Mark A Vivino <mvivino@helix.nih.go ]
  frame grabber available               [ Bill Eckberg <weckberg@howard.edu> ]

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

Date: Sat, 3 Oct 1998 11:54:04 -0500
From: Mark A Vivino <mvivino@helix.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: NIH'er moving on
Message-Id: <v04003a00b23c068d9e83@[128.231.128.61]>
Content-Type: text/plain; charset="us-ascii"

Dear fellow NIH Imagers,

October 9, 1998 will be my last day at NIH. I have over the years enjoyed
being very active on this listserv and in applying NIH Image to many campus
research matters in my work at NIH. I am moving on to Miami, FL where my
wife is doing her fellowship (neuro-ophthalmology) at the Bascom Palmer Eye
Institute/University of Miami. Although I will be signing off from this
account and will remove myself from the listserv under this NIH email
account I have resubscribed under my new email, which is for now:

mvivino@rocketmail.com

As of this time I am looking for consulting, biomedical engineering, or
development work. In these capacities I would be interested in doing some
of the many things I did here at NIH. Among these are, applying NIH Image &
doing modifications to the package, data acquisition, other imaging,
LabView, various collaborative biomedical research & development projects,
and certainly a variety of other things. I am willing to do these via
remote and various on sites and perhaps full time in the Miami area.

Should any of you be interested in contacting me please feel free to do so
at my rocketmail account or my NIH account in the near future.


Sincerely,
Mark A. Vivino

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

Date: Sat, 3 Oct 1998 15:49:18 -0400 (EDT)
From: Corey Washington <cgw@Glue.umd.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH'er moving on
Message-ID: <Pine.OSF.3.95q.981003154841.29242A-100000@maryann.eng.umd.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Could you please remove my name from the listserv. cgw

_______________________________________________________________________
 Corey Washington		(301) 405-5710 my office
 Dept. of Philosophy            (301) 405-5689 main office
 1123 Skinner Bldg.
 University of Maryland
 College Park, MD 20742-7615
_______________________________________________________________________

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

Date: Sat, 3 Oct 1998 16:17:51 -0500
From: Mark A Vivino <mvivino@helix.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: how to (un)subscribe & list info
Message-Id: <v04003a00b23c44bc8135@[128.231.128.61]>
Content-Type: text/plain; charset="us-ascii"

e-mail addresses of importance
--------
nih-image@biomed.drexel.edu   - Sends mail to the list
nih-image-request@biomed.drexel.edu   - Administation for List
nih-image-d-request@biomed.drexel.edu  - Aministration for Digest

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".

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


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

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

Help
--------------------
To obtain a listing of help items, send E-mail to
nih-image-d-request@biomed.drexel.edu.
the Subject of the message should contain "help".

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



Help on Digest
--------------------
To obtain a listing of help items on digest version of the list, send
E-mail to
nih-image-d-request@biomed.drexel.edu.
the Subject of the message should contain "help".

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



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

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

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/*

Mark

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

Date: Sat, 03 Oct 1998 15:07:55 -0700
From: Bill Eckberg <weckberg@howard.edu>
To: nih-image@io.ece.drexel.edu
Subject: frame grabber available
Message-ID: <3616A03A.CA77596D@howard.edu>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

If anyone needs a NuBus frame grabber, I have  Scion VG-5 available.
I've gotten a new G3 and had to order a PCI board. Send responses to me,
not to the list.

Bill Eckberg

--------------------------------
End of nih-image-d Digest V98 Issue #78
***************************************

From nih-image-request@io.ece.drexel.edu Sun Oct  4 16:51 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA10131;
	Sun, 4 Oct 1998 16:51:18 -0400 (EDT)
Resent-Date: Sun, 4 Oct 1998 16:51:18 -0400 (EDT)
From: cadence@imap3.asu.edu
Date: Sun, 04 Oct 1998 13:32:46 -0700 (MST)
Subject: Fixing colors
X-Sender: cadence@general4.asu.edu
To: nih-image@io.ece.drexel.edu
Message-id: <Pine.GSO.3.96.981004132648.11024B-100000@general4.asu.edu>
MIME-version: 1.0
Resent-Message-ID: <"sTPV01.0.F62.hkz5s"@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/441
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: 597

	Hi,
	I'm fairly new to NIH.  I've been importing Leica confocal data into
NIH Image.  My problem is the brightest points if the stained cells (single
fluorescent stain) I'm looking at appear black when I initially import the
data.  I can  solve the problem using the command "Fix Colors", but I have to
ddo that for each data slice and it gets a little time consuming to do that
for 500 or so slices.  Is there a way to automate the process using a macro or
can I fix the problem by changing some value?

Karen Fisher
Arizona State University
Department of Plant Biology
cadence@imap3.asu.edu




From nih-image-request@io.ece.drexel.edu Sun Oct  4 19:16 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id TAA21785;
	Sun, 4 Oct 1998 19:15:35 -0400 (EDT)
Resent-Date: Sun, 4 Oct 1998 19:15:35 -0400 (EDT)
Message-Id: <3.0.5.32.19981004190558.007f8d10@codon.nih.gov>
X-Sender: wayne@codon.nih.gov
X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32)
Date: Sun, 04 Oct 1998 19:05:58 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: Fixing colors
In-Reply-To: <Pine.GSO.3.96.981004132648.11024B-100000@general4.asu.edu>
Mime-Version: 1.0
Resent-Message-ID: <"I0gXA.0.Q_4.6w_5s"@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/442
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: 717

At 01:32 PM 10/4/98 -0700, you wrote:
>	Hi,
>	I'm fairly new to NIH.  I've been importing Leica confocal data into
>NIH Image.  My problem is the brightest points if the stained cells (single
>fluorescent stain) I'm looking at appear black when I initially import the
>data.  I can  solve the problem using the command "Fix Colors", but I have to
>ddo that for each data slice and it gets a little time consuming to do that
>for 500 or so slices.  Is there a way to automate the process using a macro or
>can I fix the problem by changing some value?

This macro should be equivalent to the "Fix Colors" command:

  macro 'Fix Colors';
  begin
    ChangeValues(0,0,1);
    ChangeValues(255,255,254);
  end;

-wayne



From nih-image-request@io.ece.drexel.edu Mon Oct  5 02:22 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id CAA27663;
	Mon, 5 Oct 1998 02:22:14 -0400 (EDT)
Resent-Date: Mon, 5 Oct 1998 02:22:14 -0400 (EDT)
Date: Mon, 5 Oct 1998 12:31:22 +1000 (EST)
Message-Id: <199810050231.MAA06943@topaz.cqu.edu.au>
X-Sender: mccannc@topaz.cqu.edu.au
X-Mailer: Windows Eudora Light Version 1.5.2
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
From: Cormac <mccannc@topaz.cqu.edu.au>
Subject: Macro output
Resent-Message-ID: <"MUzie2.0.gQ6.l966s"@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/443
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: 731

Hi imagers,
           forgive me for being thicker than the offspring of a village
idiot but I am currently trying to use a macro which is supposed to return a
message with calculations in it.  Unfortunately it does not appear to be
doing this and since I am fairly new to NIH I am not exactly sure where this
message is supposed to be.  Is it supposed to be in the info box?

The message goes along the lines of:

Write('The answer is',answer);

I have tried replacing Write with Putmessage and Showmessage but still no
message appears and I am positive that the program is otherwise working
properly.
Can anyone shed some light on this for me?

Thanx in advance,

Cormac McCann
Final year mechanical eng. student, CQU, Aust.




From nih-image-request@io.ece.drexel.edu Mon Oct  5 03:03 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id DAA01467;
	Mon, 5 Oct 1998 03:03:21 -0400 (EDT)
Resent-Date: Mon, 5 Oct 1998 03:03:21 -0400 (EDT)
X-Sender: steinr@pop.chembio.ntnu.no
Message-Id: <v03102805b23e1c7af38b@[129.241.39.133]>
In-Reply-To: <199810050231.MAA06943@topaz.cqu.edu.au>
Mime-Version: 1.0
Date: Mon, 5 Oct 1998 08:51:38 +0200
To: nih-image@io.ece.drexel.edu
From: Stein Roervik <steinr@chembio.ntnu.no>
Subject: Re: Macro output
Resent-Message-ID: <"iFIEr.0.b3.tn66s"@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/444
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: 958

>
>The message goes along the lines of:
>
>Write('The answer is',answer);
>
>I have tried replacing Write with Putmessage and Showmessage but still no
>message appears and I am positive that the program is otherwise working
>properly.
>Can anyone shed some light on this for me?
>

Write(message);		will print the message in an active text window
PutMessage(message);	will display a dialog box with the message
ShowMessage(message);	will show the message in the info-window


+---------------------------------------------------------+
|  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 Mon Oct  5 03:18 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id DAA03036;
	Mon, 5 Oct 1998 03:18:47 -0400 (EDT)
Resent-Date: Mon, 5 Oct 1998 03:18:47 -0400 (EDT)
X-Sender: zuppinge@baba.ethz.ch
Message-Id: <v03110700b23e1ec2f9af@[129.132.49.233]>
Mime-Version: 1.0
Date: Mon, 5 Oct 1998 09:05:17 +0200
To: nih-image@io.ece.drexel.edu
From: Christian Zuppinger <zuppinge@cell.biol.ethz.ch>
Subject: Re: Fixing colors for Leica
Resent-Message-ID: <"sl5AO.0.sQ.P_66s"@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/445
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: 562

Hi,

Leica tif-stacks can be color-fixed within seconds
with one of the functions in the macro 'stacks' that
comes with NIH Image.
This macro does the same operation as Wayne suggested
just in a loop for an entire stack.


C. Zuppinger







Dipl Biol
Christian Zuppinger
ETH Hoenggerberg
Institut fuer Zellbiologie, HPM F27
CH-8093 Zurich
Switzerland

Tel: + 441 1 633 33 54
Fax: + 441 1 633 10 69
Email: zuppinge@cell.biol.ethz.ch
or czuppinger@access.ch
WWW:
Institute http://www.cell.biol.ethz.ch/
private
http://www.access.ch/whoswho/showwho?czuppinger




From nih-image-request@io.ece.drexel.edu Mon Oct  5 05:08 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA12595;
	Mon, 5 Oct 1998 05:08:06 -0400 (EDT)
Resent-Date: Mon, 5 Oct 1998 05:08:06 -0400 (EDT)
X-Sender: sdb@pop1.liv.ac.uk
Message-Id: <l03130303b23e3736aa1a@[138.253.47.16]>
In-Reply-To: <199810021535.LAA00818@io.ece.drexel.edu>
Mime-Version: 1.0
Date: Mon, 5 Oct 1998 09:56:52 +0100
To: nih-image@io.ece.drexel.edu
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
Subject: Re: Help with Frame Grabber
Cc: beverly@umich.edu
Resent-Message-ID: <"wgxsh.0.5l2.yb86s"@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/446
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: 731

>Where can I find a NuBus card that we can use in...
>an old Mac IIcx?

In the past, we have used ScreenMachine framegrabbers in a Mac IIx and a
Mac IIfx. They worked well for grabbing single images. The speed of the
Macs was not a problem for us - we only needed one frame every few seconds.

It was distributed by ProficomP GmbH, but I'm afraid I don't have a web or
email address to hand.

___________________________________________________________________

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

Tel: 44-(0)151-794-3874 / 3894 / 3870
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk

___________________________________________________________________



From nih-image-request@io.ece.drexel.edu Mon Oct  5 06:40 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA21272;
	Mon, 5 Oct 1998 06:40:10 -0400 (EDT)
 <9D916278299FD111A7E100805FA7C2BA4B9FC7@cheetah.uits.iupui.edu>
Resent-Date: Mon, 5 Oct 1998 06:40:10 -0400 (EDT)
X-Sender: steinr@pop.chembio.ntnu.no
Message-Id: <v03102806b23e4c893e33@[129.241.39.133]>
In-Reply-To: 
 <9D916278299FD111A7E100805FA7C2BA4B9FC7@cheetah.uits.iupui.edu>
Mime-Version: 1.0
Date: Mon, 5 Oct 1998 12:27:44 +0200
To: nih-image@io.ece.drexel.edu
From: Stein Roervik <steinr@chembio.ntnu.no>
Subject: Re: Meridian InSIGHT and MAC
Resent-Message-ID: <"EijMn3.0.io4.Ry96s"@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/447
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: 2047

>	Has anyone connected a Mac to a Merdian Insight plus? We had a PC
>connected to it, now we have a Mac. We used the serial port on the PC to
>change filters, open the shutter etc. Now that the Mac is going to be used,
>I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but the pin
>out seems to be different and it is not sending the data (using the
>openserial( ) command), to change the filters etc. Apple said that I have to
>become a developer to get this info., and cannot help. It seems simple, has
>anyone used a "regular" (DB25 pinout) modem on an apple? Thanks.
>
>Todd Kirk
>Indiana University Medical Center

The Mac interfaces to most RS232 compatible devices without any problem.
A standard modem cable (DIN 8 to DB 25) plus a standard DB25 to DB 8
adapter has always worked fine for me. Buy the modem cable in a Mac shop
and the adapter in a PC shop. There might be some magic inside these
adapters; I remember an instance where we were unable to wire DIN 8 to DB 8
directly, but it worked fine with the DIN 8 to DB 25 plus adapter. Your
problems may be because you are using some unstandard cabling.

The pin outs for the Mac modem port is documented in the Inside Mac:
Devices document. You can download it as a PDF file from Apple. There was a
useful document explaining how to properly wire RS232 to RS422 (Mac serial)
posted to this list many years ago, I think I downloaded it from Zippy. I
can have a look in my old file archives and post it to you if you can't
find it. If not I have a print-out somewhere and can fax it to you.

+---------------------------------------------------------+
|  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 Mon Oct  5 08:22 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA00356;
	Mon, 5 Oct 1998 08:22:19 -0400 (EDT)
Resent-Date: Mon, 5 Oct 1998 08:22:19 -0400 (EDT)
Date: Mon, 5 Oct 1998 13:12:21 +0100 (BST)
From: Stamatis Pagakis <spagaki@ns1.nimr.mrc.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Fixing colors
In-Reply-To: <Pine.GSO.3.96.981004132648.11024B-100000@general4.asu.edu>
Message-ID: <Pine.SGI.3.91.981005130735.8747E-100000@membo2.nimr.mrc.ac.uk>
MIME-Version: 1.0
Resent-Message-ID: <"GM0P1.0.P17.sQB6s"@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/448
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: 1436

On Sun, 4 Oct 1998 cadence@imap3.asu.edu wrote:

> 	Hi,
> 	I'm fairly new to NIH.  I've been importing Leica confocal data into
> NIH Image.  My problem is the brightest points if the stained cells (single
> fluorescent stain) I'm looking at appear black when I initially import the
> data.  I can  solve the problem using the command "Fix Colors", but I have to
> ddo that for each data slice and it gets a little time consuming to do that
> for 500 or so slices.  Is there a way to automate the process using a macro or
> can I fix the problem by changing some value?
> 

Hi

If you want to avoid the problem altogether, do not use the "Glowover" 
LUT on the confocal.  The black spots appear where the "Glowover" LUT puts
blue color to indicate PMT saturation.  Use the "Glow"  LUT instead or (if
you really like to see the blue) change the LUT to another one just before
saving the image. 

Regards,


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

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


From nih-image-d-request@io.ece.drexel.edu Mon Oct  5 08:27 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA00930;
	Mon, 5 Oct 1998 08:27:16 -0400 (EDT)
Date: Mon, 5 Oct 1998 08:27:16 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810051227.IAA00930@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #79
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/79
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 10906

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 79

Today's Topics:
  Fixing colors                         [ cadence@imap3.asu.edu ]
  Re: Fixing colors                     [ Wayne Rasband <wayne@codon.nih.gov> ]
  Macro output                          [ Cormac <mccannc@topaz.cqu.edu.au> ]
  Re: Macro output                      [ Stein Roervik <steinr@chembio.ntnu. ]
  Re: Fixing colors for Leica           [ Christian Zuppinger <zuppinge@cell. ]
  Re: Help with Frame Grabber           [ Steve Barrett <S.D.Barrett@liverpoo ]
  Re: Meridian InSIGHT and MAC          [ Stein Roervik <steinr@chembio.ntnu. ]
  Re: Fixing colors                     [ Stamatis Pagakis <spagaki@ns1.nimr. ]

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

Date: Sun, 04 Oct 1998 13:32:46 -0700 (MST)
From: cadence@imap3.asu.edu
To: nih-image@io.ece.drexel.edu
Subject: Fixing colors
Message-id: <Pine.GSO.3.96.981004132648.11024B-100000@general4.asu.edu>
Content-type: TEXT/PLAIN; charset=US-ASCII

	Hi,
	I'm fairly new to NIH.  I've been importing Leica confocal data into
NIH Image.  My problem is the brightest points if the stained cells (single
fluorescent stain) I'm looking at appear black when I initially import the
data.  I can  solve the problem using the command "Fix Colors", but I have to
ddo that for each data slice and it gets a little time consuming to do that
for 500 or so slices.  Is there a way to automate the process using a macro or
can I fix the problem by changing some value?

Karen Fisher
Arizona State University
Department of Plant Biology
cadence@imap3.asu.edu

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

Date: Sun, 04 Oct 1998 19:05:58 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Fixing colors
Message-Id: <3.0.5.32.19981004190558.007f8d10@codon.nih.gov>
Content-Type: text/plain; charset="us-ascii"

At 01:32 PM 10/4/98 -0700, you wrote:
>	Hi,
>	I'm fairly new to NIH.  I've been importing Leica confocal data into
>NIH Image.  My problem is the brightest points if the stained cells (single
>fluorescent stain) I'm looking at appear black when I initially import the
>data.  I can  solve the problem using the command "Fix Colors", but I have to
>ddo that for each data slice and it gets a little time consuming to do that
>for 500 or so slices.  Is there a way to automate the process using a macro or
>can I fix the problem by changing some value?

This macro should be equivalent to the "Fix Colors" command:

  macro 'Fix Colors';
  begin
    ChangeValues(0,0,1);
    ChangeValues(255,255,254);
  end;

-wayne

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

Date: Mon, 5 Oct 1998 12:31:22 +1000 (EST)
From: Cormac <mccannc@topaz.cqu.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Macro output
Message-Id: <199810050231.MAA06943@topaz.cqu.edu.au>
Content-Type: text/plain; charset="us-ascii"

Hi imagers,
           forgive me for being thicker than the offspring of a village
idiot but I am currently trying to use a macro which is supposed to return a
message with calculations in it.  Unfortunately it does not appear to be
doing this and since I am fairly new to NIH I am not exactly sure where this
message is supposed to be.  Is it supposed to be in the info box?

The message goes along the lines of:

Write('The answer is',answer);

I have tried replacing Write with Putmessage and Showmessage but still no
message appears and I am positive that the program is otherwise working
properly.
Can anyone shed some light on this for me?

Thanx in advance,

Cormac McCann
Final year mechanical eng. student, CQU, Aust.

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

Date: Mon, 5 Oct 1998 08:51:38 +0200
From: Stein Roervik <steinr@chembio.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Re: Macro output
Message-Id: <v03102805b23e1c7af38b@[129.241.39.133]>
Content-Type: text/plain; charset="us-ascii"

>
>The message goes along the lines of:
>
>Write('The answer is',answer);
>
>I have tried replacing Write with Putmessage and Showmessage but still no
>message appears and I am positive that the program is otherwise working
>properly.
>Can anyone shed some light on this for me?
>

Write(message);		will print the message in an active text window
PutMessage(message);	will display a dialog box with the message
ShowMessage(message);	will show the message in the info-window


+---------------------------------------------------------+
|  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: Mon, 5 Oct 1998 09:05:17 +0200
From: Christian Zuppinger <zuppinge@cell.biol.ethz.ch>
To: nih-image@io.ece.drexel.edu
Subject: Re: Fixing colors for Leica
Message-Id: <v03110700b23e1ec2f9af@[129.132.49.233]>
Content-Type: text/plain; charset="us-ascii"

Hi,

Leica tif-stacks can be color-fixed within seconds
with one of the functions in the macro 'stacks' that
comes with NIH Image.
This macro does the same operation as Wayne suggested
just in a loop for an entire stack.


C. Zuppinger







Dipl Biol
Christian Zuppinger
ETH Hoenggerberg
Institut fuer Zellbiologie, HPM F27
CH-8093 Zurich
Switzerland

Tel: + 441 1 633 33 54
Fax: + 441 1 633 10 69
Email: zuppinge@cell.biol.ethz.ch
or czuppinger@access.ch
WWW:
Institute http://www.cell.biol.ethz.ch/
private
http://www.access.ch/whoswho/showwho?czuppinger

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

Date: Mon, 5 Oct 1998 09:56:52 +0100
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
To: nih-image@io.ece.drexel.edu
Cc: beverly@umich.edu
Subject: Re: Help with Frame Grabber
Message-Id: <l03130303b23e3736aa1a@[138.253.47.16]>
Content-Type: text/plain; charset="us-ascii"

>Where can I find a NuBus card that we can use in...
>an old Mac IIcx?

In the past, we have used ScreenMachine framegrabbers in a Mac IIx and a
Mac IIfx. They worked well for grabbing single images. The speed of the
Macs was not a problem for us - we only needed one frame every few seconds.

It was distributed by ProficomP GmbH, but I'm afraid I don't have a web or
email address to hand.

___________________________________________________________________

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

Tel: 44-(0)151-794-3874 / 3894 / 3870
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk

___________________________________________________________________

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

Date: Mon, 5 Oct 1998 12:27:44 +0200
From: Stein Roervik <steinr@chembio.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Re: Meridian InSIGHT and MAC
Message-Id: <v03102806b23e4c893e33@[129.241.39.133]>
Content-Type: text/plain; charset="us-ascii"

>	Has anyone connected a Mac to a Merdian Insight plus? We had a PC
>connected to it, now we have a Mac. We used the serial port on the PC to
>change filters, open the shutter etc. Now that the Mac is going to be used,
>I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but the pin
>out seems to be different and it is not sending the data (using the
>openserial( ) command), to change the filters etc. Apple said that I have to
>become a developer to get this info., and cannot help. It seems simple, has
>anyone used a "regular" (DB25 pinout) modem on an apple? Thanks.
>
>Todd Kirk
>Indiana University Medical Center

The Mac interfaces to most RS232 compatible devices without any problem.
A standard modem cable (DIN 8 to DB 25) plus a standard DB25 to DB 8
adapter has always worked fine for me. Buy the modem cable in a Mac shop
and the adapter in a PC shop. There might be some magic inside these
adapters; I remember an instance where we were unable to wire DIN 8 to DB 8
directly, but it worked fine with the DIN 8 to DB 25 plus adapter. Your
problems may be because you are using some unstandard cabling.

The pin outs for the Mac modem port is documented in the Inside Mac:
Devices document. You can download it as a PDF file from Apple. There was a
useful document explaining how to properly wire RS232 to RS422 (Mac serial)
posted to this list many years ago, I think I downloaded it from Zippy. I
can have a look in my old file archives and post it to you if you can't
find it. If not I have a print-out somewhere and can fax it to you.

+---------------------------------------------------------+
|  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: Mon, 5 Oct 1998 13:12:21 +0100 (BST)
From: Stamatis Pagakis <spagaki@ns1.nimr.mrc.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Fixing colors
Message-ID: <Pine.SGI.3.91.981005130735.8747E-100000@membo2.nimr.mrc.ac.uk>
Content-Type: TEXT/PLAIN; charset=US-ASCII

On Sun, 4 Oct 1998 cadence@imap3.asu.edu wrote:

> 	Hi,
> 	I'm fairly new to NIH.  I've been importing Leica confocal data into
> NIH Image.  My problem is the brightest points if the stained cells (single
> fluorescent stain) I'm looking at appear black when I initially import the
> data.  I can  solve the problem using the command "Fix Colors", but I have to
> ddo that for each data slice and it gets a little time consuming to do that
> for 500 or so slices.  Is there a way to automate the process using a macro or
> can I fix the problem by changing some value?
> 

Hi

If you want to avoid the problem altogether, do not use the "Glowover" 
LUT on the confocal.  The black spots appear where the "Glowover" LUT puts
blue color to indicate PMT saturation.  Use the "Glow"  LUT instead or (if
you really like to see the blue) change the LUT to another one just before
saving the image. 

Regards,


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

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

--------------------------------
End of nih-image-d Digest V98 Issue #79
***************************************

From nih-image-request@io.ece.drexel.edu Mon Oct  5 08:57 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA03901;
	Mon, 5 Oct 1998 08:57:02 -0400 (EDT)
Resent-Date: Mon, 5 Oct 1998 08:57:02 -0400 (EDT)
Message-ID: <3618C032.994F05B6@soton.ac.uk>
Date: Mon, 05 Oct 1998 13:48:45 +0100
From: Ashley Pringle <akp1@soton.ac.uk>
Organization: Clinical Neurological Sciences
X-Mailer: Mozilla 4.05 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: Help with Frame Grabber
References: <Pine.SOL.3.95.981002112752.21407A-100000@qbert.rs.itd.umich.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"w-baP.0.Ff.9-B6s"@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/449
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length: 468

We have been quite happily using a MacIIsi for capturing single images
with NIH Image for many years using the Data Translation Quickcapture
frame grabber.

This board is still available and all the detail can be found on this
web page: http://www.datatranslation.com/products/imaging/qc/qc.html

Dr Ashley Pringle
Dept Clinical Neurological Sciences
University of Southampton
Southampton General Hospital
Tremona Rd, Southampton SO16 6YD UK

email: akp1@soton.ac.uk


From nih-image-request@io.ece.drexel.edu Mon Oct  5 10:25 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA12307;
	Mon, 5 Oct 1998 10:25:43 -0400 (EDT)
Resent-Date: Mon, 5 Oct 1998 10:25:43 -0400 (EDT)
Date: Mon, 5 Oct 1998 15:08:02 +0100 (BST)
From: Jan Kreft <Kreft@cardiff.ac.uk>
X-Sender: sabjk@thor
To: nih-image@io.ece.drexel.edu
Subject: cell clusters
Message-ID: <Pine.OSF.3.95q.981005150501.2992A-100000@thor>
MIME-Version: 1.0
Resent-Message-ID: <"tVnxL2.0.xe2.tBD6s"@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/450
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: 368

Hi imagers,

I heard about a macro that analyses cells in cell clusters by Chris
Coulon in a newsgroup but I couldn't find it (not knowing its name).

Any pointers?

Thanks,

Jan.

Jan Kreft				Phone +44 (0)1222 874000 ext. 6036
Cardiff School of Biosciences		Fax   +44 (0)1222 874305
Cardiff	University 			E-mail Kreft@cardiff.ac.uk
PO Box 915, Cardiff CF1 3TL, UK



From nih-image-request@io.ece.drexel.edu Mon Oct  5 11:48 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA20811;
	Mon, 5 Oct 1998 11:47:59 -0400 (EDT)
Resent-Date: Mon, 5 Oct 1998 11:47:59 -0400 (EDT)
From: SCHRANK@TIGGER.STCLOUDSTATE.EDU
Date: Mon, 05 Oct 1998 10:24:35 -0600 (CST)
Subject: Re: nih-image-d Digest V98 #79
To: nih-image@io.ece.drexel.edu
Message-id: <01J2LWOGNRGI005G4E@TIGGER.STCLOUDSTATE.EDU>
X-VMS-To: IN%"nih-image@io.ece.drexel.edu"
X-VMS-Cc: SCHRANK
MIME-version: 1.0
Resent-Message-ID: <"9R-DL3.0.9R4.sHE6s"@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/451
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: 74

Good - will be interesting to see how the cuttings or whatever work out.


From nih-image-request@io.ece.drexel.edu Mon Oct  5 15:43 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA21934;
	Mon, 5 Oct 1998 15:43:04 -0400 (EDT)
Resent-Date: Mon, 5 Oct 1998 15:43:04 -0400 (EDT)
Message-ID: <A0FAC32A7A05D2119A1800805F9A71AD1E20D8@mailhq.icos.com>
From: "Harrison, Janine" <JHarrison@ICOS.com>
To: "'Multiple recipients of list'" <nih-image@io.ece.drexel.edu>
Subject: Calcium ratio imaging experiments
Date: Mon, 5 Oct 1998 12:23:03 -0700 
MIME-Version: 1.0
X-Mailer: Internet Mail Service (5.5.2232.9)
Resent-Message-ID: <"eeu_k2.0.uh3.9lH6s"@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/452
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 924

Hello All-

We have users in our facility who would like to undertake calcium ratio
imaging experiments.

Does anyone have specific recommendations for filter sets (i.e. from Chroma)
for the fura-2/indo-1
class of compounds?

Can NIH-Image be used fairly easily for quantitating ratiometric data?  Or
would a commercial analysis package (such as Metamoph, Axon Inst) be better
suited for extensive experiments?

Responses can be sent directly to me, or the group - - whichever is the most
suitable.

Thanks for any helpful information.

Regards,

Janine

**********************************************************************
     
     Janine Harrison
     Manager, Image Analysis Facility
     ICOS Corporation
     22021 20th Avenue S.E.
     Bothell WA 98021
     
     1-425-485-1900 ext 2318
     1-425-485-1961 FAX
     jharrison@icos.com
     
**********************************************************************


From nih-image-request@io.ece.drexel.edu Mon Oct  5 18:25 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA03370;
	Mon, 5 Oct 1998 18:24:43 -0400 (EDT)
Resent-Date: Mon, 5 Oct 1998 18:24:43 -0400 (EDT)
Date: Mon, 5 Oct 1998 16:03:00 -0600 (MDT)
From: christopher helt <Christopher.Helt@UCHSC.edu>
To: nih-image@io.ece.drexel.edu
Subject: Error 2208 Where is the solution
Message-ID: <Pine.ULT.3.95q.981005155658.6167A-100000@essex.UCHSC.edu>
MIME-Version: 1.0
Resent-Message-ID: <"UvRN42.0.-m6.a6K6s"@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/453
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: 455


I have just downloaded the power PC version of NIH Image and I seem to be
having a problem with it.  When I try click on "start capturing" I get
error number 2208.  I have tried to turn off virtual memory but the
problem persists.  Turning off the ATI video memory extension results in a
message of "unable to load VDIG" in the info box.  Where is the solution
to this problem?


My hardware consists of a power PC macintosh G3
			Thanks,
			Chris Helt


From nih-image-request@io.ece.drexel.edu Mon Oct  5 20:29 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA09548;
	Mon, 5 Oct 1998 20:29:07 -0400 (EDT)
Resent-Date: Mon, 5 Oct 1998 20:29:07 -0400 (EDT)
X-Sender: ad1054@unix.worldpath.net
Message-Id: <v01520d01b23f16cc9182@[206.152.181.158]>
Mime-Version: 1.0
Date: Mon, 5 Oct 1998 20:04:05 -0500
To: nih-image@io.ece.drexel.edu
From: ad1054@worldpath.net (Dr. Christopher Coulon)
Subject: Re: cell clusters
Resent-Message-ID: <"ELDNw1.0.mG.uvL6s"@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/454
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: 1082

Hi Jan,

What is it you need?  I have been working on all sorts of problems
utilizing NIH Image for automating image analysis, grain counting among
them.  I have discovered that every problem is different and requires at
least a modification of an existing macro if not a totally new start.
Please let me know if I can be of help.  Please contact me off list at
ad1054@worldpath.net.

Chris

>Hi imagers,
>
>I heard about a macro that analyses cells in cell clusters by Chris
>Coulon in a newsgroup but I couldn't find it (not knowing its name).
>
>Any pointers?
>
>Thanks,
>
>Jan.
>
>Jan Kreft                               Phone +44 (0)1222 874000 ext. 6036
>Cardiff School of Biosciences           Fax   +44 (0)1222 874305
>Cardiff University                      E-mail Kreft@cardiff.ac.uk
>PO Box 915, Cardiff CF1 3TL, UK

* * * * * * * * * * * * * * * * * *
* 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 Oct  5 20:53 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA16749;
	Mon, 5 Oct 1998 20:53:40 -0400 (EDT)
Resent-Date: Mon, 5 Oct 1998 20:53:40 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: marmotta@hmg.inpg.fr, nih-image@io.ece.drexel.edu
Date:          Tue, 6 Oct 1998 10:39:03 GMT+1000
Subject:       Re: Seed Fill plug-in ?
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <AA5F36E0530@rna.bio.mq.edu.au>
Resent-Message-ID: <"Svpbw3.0.yw2.IPM6s"@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/455
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1309

>Date: Fri, 02 Oct 1998 14:09:15 +0000
>From: MARMOTTANT Philippe <marmotta@hmg.inpg.fr>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Seed Fill plug-in ?

Philippe,

Thankyou for taking the trouble to further explain your technique.

I had mistakenly read "To eliminate discontinous edges, resulting from image 
anaysis of water drops" as implying that you somehow used Seedfill to close (ie 
complete) the discontinous edges. I understand now that you use Seedfill to 
remove those distcontinuous structures from the analysis.

The Seedfill macro available in Object-Image will indeed serve your purpose 
but, particularly as you have skeletonised, the ratio of perimeter to area 
(including enclosed hole) would allow you to disqualify open circles from your 
results table if you wanted to stay with the orginal NIH-Image.

You might also be interested in another extended version of NIH-Image
which has implemented a Hough transform which allows detection/measurement of 
circular objects with indistinct or incomplete boundaries.
ie Image SXM bt Steve Barrett which should be available at 
http://reg.ssci.liv.ac.uk/
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 Oct  5 21:37 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id VAA28855;
	Mon, 5 Oct 1998 21:36:54 -0400 (EDT)
Resent-Date: Mon, 5 Oct 1998 21:36:54 -0400 (EDT)
From: SolamereTG@aol.com
Message-ID: <95c6545.36196ea6@aol.com>
Date: Mon, 5 Oct 1998 21:13:10 EDT
To: nih-image@io.ece.drexel.edu
Mime-Version: 1.0
Subject: Re: Calcium ratio imaging experiments
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 16-bit for Windows sub 38
Resent-Message-ID: <"s8_IB3.0.hX5.YyM6s"@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/456
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: 2289

  to Janine Harrison
      Manager, Image Analysis Facility
      ICOS Corporation
      22021 20th Avenue S.E.
      Bothell WA 98021
      
      1-425-485-1900 ext 2318
      1-425-485-1961 FAX
      jharrison@icos.comt


We have experience using NIH to measure calcium, Na+, and pH in Lymphocytes,
cardiac myocytes, vascular smooth muscle cells, and endothelial cells.  My
recommendation is to spend the money on the front end of the measuring system
(Camera, PMT system, illumination control) and start with NIH Image. You can
always spend more on commercial software if NIH (with the appropriate macros)
can't do what you need. I would be happy to discuss with you your groups
proposed work.However I will be out of my office beginning Wednesday 10/7/98
(morning) but back by next Monday. Please feel free to call tomorrow or after
10/11/98.

sincerely yours,

George A. Peeters M.D.
Pres. Solamere Technology Group
Salt Lake City, UT   84103

801 322-2645

In a message dated 98-10-05 15:31:55 EDT, you write:

<<
 
 Does anyone have specific recommendations for filter sets (i.e. from Chroma)
 for the fura-2/indo-1
 class of compounds?  >>  

This will depend on the experiment. For example, Fura-2 is the most often used
probe for ratio Ca 2+ imaging. This probe will require illumination waveband
switching for each ratio pair and if you wish to collect 15 ratio pairs per
second you will need a progressive scan sensor (not an interlaced detector).
Flo3, and Flo4 are easier to use but not ratioed.
Indo-1 is faster, but would require splitting the detector or an emission wave
band switcher. 
 We have both imaging and photometric equipment used for Ca2+ measurement at
both Genentech, Squibb, Soanes, as well as academic institutions world wide. 
 
 << Can NIH-Image be used fairly easily for quantitating ratiometric data?  Or
 would a commercial analysis package (such as Metamoph, Axon Inst) be better
 suited for extensive experiments?>>   
Yes, we have Macros to ratio of images acquired at video rates (30 fps). A
suitable G-3 platform,  64MB RAM, LG-3 frame grabber, software can run as
little as $2500. This system can control waveband switchers (ours or others),
filter wheels, shutters, electro-physiology, etc. We also have the macros that
control these devices.


From nih-image-d-request@io.ece.drexel.edu Tue Oct  6 01:17 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id BAA29740;
	Tue, 6 Oct 1998 01:17:52 -0400 (EDT)
Date: Tue, 6 Oct 1998 01:17:52 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810060517.BAA29740@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #80
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/80
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 12152

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 80

Today's Topics:
  Re: Help with Frame Grabber           [ Ashley Pringle <akp1@soton.ac.uk> ]
  cell clusters                         [ Jan Kreft <Kreft@cardiff.ac.uk> ]
  Re: nih-image-d Digest V98 #79        [ SCHRANK@TIGGER.STCLOUDSTATE.EDU ]
  Calcium ratio imaging experiments     [ "Harrison, Janine" <JHarrison@ICOS. ]
  Error 2208 Where is the solution      [ christopher helt <Christopher.Helt@ ]
  Re: cell clusters                     [ ad1054@worldpath.net (Dr. Christoph ]
  Re: Seed Fill plug-in ?               [ GJOSS@rna.bio.mq.edu.au ]
  Re: Calcium ratio imaging experiment  [ SolamereTG@aol.com ]
  Re: Macro output                      [ GJOSS@rna.bio.mq.edu.au ]

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

Date: Mon, 05 Oct 1998 13:48:45 +0100
From: Ashley Pringle <akp1@soton.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Help with Frame Grabber
Message-ID: <3618C032.994F05B6@soton.ac.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

We have been quite happily using a MacIIsi for capturing single images
with NIH Image for many years using the Data Translation Quickcapture
frame grabber.

This board is still available and all the detail can be found on this
web page: http://www.datatranslation.com/products/imaging/qc/qc.html

Dr Ashley Pringle
Dept Clinical Neurological Sciences
University of Southampton
Southampton General Hospital
Tremona Rd, Southampton SO16 6YD UK

email: akp1@soton.ac.uk

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

Date: Mon, 5 Oct 1998 15:08:02 +0100 (BST)
From: Jan Kreft <Kreft@cardiff.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: cell clusters
Message-ID: <Pine.OSF.3.95q.981005150501.2992A-100000@thor>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi imagers,

I heard about a macro that analyses cells in cell clusters by Chris
Coulon in a newsgroup but I couldn't find it (not knowing its name).

Any pointers?

Thanks,

Jan.

Jan Kreft				Phone +44 (0)1222 874000 ext. 6036
Cardiff School of Biosciences		Fax   +44 (0)1222 874305
Cardiff	University 			E-mail Kreft@cardiff.ac.uk
PO Box 915, Cardiff CF1 3TL, UK

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

Date: Mon, 05 Oct 1998 10:24:35 -0600 (CST)
From: SCHRANK@TIGGER.STCLOUDSTATE.EDU
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #79
Message-id: <01J2LWOGNRGI005G4E@TIGGER.STCLOUDSTATE.EDU>
Content-type: TEXT/PLAIN; CHARSET=US-ASCII

Good - will be interesting to see how the cuttings or whatever work out.

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

Date: Mon, 5 Oct 1998 12:23:03 -0700 
From: "Harrison, Janine" <JHarrison@ICOS.com>
To: "'Multiple recipients of list'" <nih-image@io.ece.drexel.edu>
Subject: Calcium ratio imaging experiments
Message-ID: <A0FAC32A7A05D2119A1800805F9A71AD1E20D8@mailhq.icos.com>
Content-Type: text/plain

Hello All-

We have users in our facility who would like to undertake calcium ratio
imaging experiments.

Does anyone have specific recommendations for filter sets (i.e. from Chroma)
for the fura-2/indo-1
class of compounds?

Can NIH-Image be used fairly easily for quantitating ratiometric data?  Or
would a commercial analysis package (such as Metamoph, Axon Inst) be better
suited for extensive experiments?

Responses can be sent directly to me, or the group - - whichever is the most
suitable.

Thanks for any helpful information.

Regards,

Janine

**********************************************************************
     
     Janine Harrison
     Manager, Image Analysis Facility
     ICOS Corporation
     22021 20th Avenue S.E.
     Bothell WA 98021
     
     1-425-485-1900 ext 2318
     1-425-485-1961 FAX
     jharrison@icos.com
     
**********************************************************************

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

Date: Mon, 5 Oct 1998 16:03:00 -0600 (MDT)
From: christopher helt <Christopher.Helt@UCHSC.edu>
To: nih-image@io.ece.drexel.edu
Subject: Error 2208 Where is the solution
Message-ID: <Pine.ULT.3.95q.981005155658.6167A-100000@essex.UCHSC.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I have just downloaded the power PC version of NIH Image and I seem to be
having a problem with it.  When I try click on "start capturing" I get
error number 2208.  I have tried to turn off virtual memory but the
problem persists.  Turning off the ATI video memory extension results in a
message of "unable to load VDIG" in the info box.  Where is the solution
to this problem?


My hardware consists of a power PC macintosh G3
			Thanks,
			Chris Helt

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

Date: Mon, 5 Oct 1998 20:04:05 -0500
From: ad1054@worldpath.net (Dr. Christopher Coulon)
To: nih-image@io.ece.drexel.edu
Subject: Re: cell clusters
Message-Id: <v01520d01b23f16cc9182@[206.152.181.158]>
Content-Type: text/plain; charset="us-ascii"

Hi Jan,

What is it you need?  I have been working on all sorts of problems
utilizing NIH Image for automating image analysis, grain counting among
them.  I have discovered that every problem is different and requires at
least a modification of an existing macro if not a totally new start.
Please let me know if I can be of help.  Please contact me off list at
ad1054@worldpath.net.

Chris

>Hi imagers,
>
>I heard about a macro that analyses cells in cell clusters by Chris
>Coulon in a newsgroup but I couldn't find it (not knowing its name).
>
>Any pointers?
>
>Thanks,
>
>Jan.
>
>Jan Kreft                               Phone +44 (0)1222 874000 ext. 6036
>Cardiff School of Biosciences           Fax   +44 (0)1222 874305
>Cardiff University                      E-mail Kreft@cardiff.ac.uk
>PO Box 915, Cardiff CF1 3TL, UK

* * * * * * * * * * * * * * * * * *
* Dr. Christopher Hunt Coulon     *
* The GAIA Group                  *
* 40 Chick Road                   *
* Wolfeboro, New Hampshire 03894  *
* 603 569-0028                    *
* * * * * * * * * * * * * * * * * *

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

Date:          Tue, 6 Oct 1998 10:39:03 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: marmotta@hmg.inpg.fr, nih-image@io.ece.drexel.edu
Subject:       Re: Seed Fill plug-in ?
Message-ID: <AA5F36E0530@rna.bio.mq.edu.au>

>Date: Fri, 02 Oct 1998 14:09:15 +0000
>From: MARMOTTANT Philippe <marmotta@hmg.inpg.fr>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Seed Fill plug-in ?

Philippe,

Thankyou for taking the trouble to further explain your technique.

I had mistakenly read "To eliminate discontinous edges, resulting from image 
anaysis of water drops" as implying that you somehow used Seedfill to close (ie 
complete) the discontinous edges. I understand now that you use Seedfill to 
remove those distcontinuous structures from the analysis.

The Seedfill macro available in Object-Image will indeed serve your purpose 
but, particularly as you have skeletonised, the ratio of perimeter to area 
(including enclosed hole) would allow you to disqualify open circles from your 
results table if you wanted to stay with the orginal NIH-Image.

You might also be interested in another extended version of NIH-Image
which has implemented a Hough transform which allows detection/measurement of 
circular objects with indistinct or incomplete boundaries.
ie Image SXM bt Steve Barrett which should be available at 
http://reg.ssci.liv.ac.uk/
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, 5 Oct 1998 21:13:10 EDT
From: SolamereTG@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re: Calcium ratio imaging experiments
Message-ID: <95c6545.36196ea6@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

  to Janine Harrison
      Manager, Image Analysis Facility
      ICOS Corporation
      22021 20th Avenue S.E.
      Bothell WA 98021
      
      1-425-485-1900 ext 2318
      1-425-485-1961 FAX
      jharrison@icos.comt


We have experience using NIH to measure calcium, Na+, and pH in Lymphocytes,
cardiac myocytes, vascular smooth muscle cells, and endothelial cells.  My
recommendation is to spend the money on the front end of the measuring system
(Camera, PMT system, illumination control) and start with NIH Image. You can
always spend more on commercial software if NIH (with the appropriate macros)
can't do what you need. I would be happy to discuss with you your groups
proposed work.However I will be out of my office beginning Wednesday 10/7/98
(morning) but back by next Monday. Please feel free to call tomorrow or after
10/11/98.

sincerely yours,

George A. Peeters M.D.
Pres. Solamere Technology Group
Salt Lake City, UT   84103

801 322-2645

In a message dated 98-10-05 15:31:55 EDT, you write:

<<
 
 Does anyone have specific recommendations for filter sets (i.e. from Chroma)
 for the fura-2/indo-1
 class of compounds?  >>  

This will depend on the experiment. For example, Fura-2 is the most often used
probe for ratio Ca 2+ imaging. This probe will require illumination waveband
switching for each ratio pair and if you wish to collect 15 ratio pairs per
second you will need a progressive scan sensor (not an interlaced detector).
Flo3, and Flo4 are easier to use but not ratioed.
Indo-1 is faster, but would require splitting the detector or an emission wave
band switcher. 
 We have both imaging and photometric equipment used for Ca2+ measurement at
both Genentech, Squibb, Soanes, as well as academic institutions world wide. 
 
 << Can NIH-Image be used fairly easily for quantitating ratiometric data?  Or
 would a commercial analysis package (such as Metamoph, Axon Inst) be better
 suited for extensive experiments?>>   
Yes, we have Macros to ratio of images acquired at video rates (30 fps). A
suitable G-3 platform,  64MB RAM, LG-3 frame grabber, software can run as
little as $2500. This system can control waveband switchers (ours or others),
filter wheels, shutters, electro-physiology, etc. We also have the macros that
control these devices.

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

Date:          Tue, 6 Oct 1998 14:53:18 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: mccannc@topaz.cqu.edu.au, nih-image@io.ece.drexel.edu
Subject:       Re: Macro output
Message-ID: <AAA30726944@rna.bio.mq.edu.au>

>Date: Mon, 5 Oct 1998 12:31:22 +1000 (EST)
>To: nih-image@io.ece.drexel.edu
>From: Cormac <mccannc@topaz.cqu.edu.au>
>Subject: Macro output
>Hi imagers,
>           forgive me for being thicker than the offspring of a village
>idiot but I am currently trying to use a macro which is supposed to return a
>message with calculations in it.  Unfortunately it does not appear to be
>doing this and since I am fairly new to NIH I am not exactly sure where this
>message is supposed to be.  Is it supposed to be in the info box?
>
>The message goes along the lines of:
>
>Write('The answer is',answer);
>
>I have tried replacing Write with Putmessage and Showmessage but still no
>message appears and I am positive that the program is otherwise working
>properly.
>Can anyone shed some light on this for me?
>
>Thanx in advance,
>
>Cormac McCann
>Final year mechanical eng. student, CQU, Aust.

As one of the other villagers, I thought I should add to Steinr's response:

If the current window is an image window, "write(message);" will output the 
message string at the "current" position which can be controlled by 
moveTo(x,y); 
{ so top left of image would be (0,5) if font is size 9 with "align left"}
note: setForeGround(0);{255} and SetText(string); {'With Background' etc}

If current window is a text window, then cursor will be :
1. where the user last left it
2. at the begining if an existing or new text file is opened
3. at the end if you "selectAll;" with text file the current file.


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 V98 Issue #80
***************************************

From nih-image-request@io.ece.drexel.edu Tue Oct  6 01:18 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id BAA00025;
	Tue, 6 Oct 1998 01:18:40 -0400 (EDT)
Resent-Date: Tue, 6 Oct 1998 01:18:40 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: mccannc@topaz.cqu.edu.au, nih-image@io.ece.drexel.edu
Date:          Tue, 6 Oct 1998 14:53:18 GMT+1000
Subject:       Re: Macro output
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <AAA30726944@rna.bio.mq.edu.au>
Resent-Message-ID: <"DmBVS3.0.2A6.oIQ6s"@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/457
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1681

>Date: Mon, 5 Oct 1998 12:31:22 +1000 (EST)
>To: nih-image@io.ece.drexel.edu
>From: Cormac <mccannc@topaz.cqu.edu.au>
>Subject: Macro output
>Hi imagers,
>           forgive me for being thicker than the offspring of a village
>idiot but I am currently trying to use a macro which is supposed to return a
>message with calculations in it.  Unfortunately it does not appear to be
>doing this and since I am fairly new to NIH I am not exactly sure where this
>message is supposed to be.  Is it supposed to be in the info box?
>
>The message goes along the lines of:
>
>Write('The answer is',answer);
>
>I have tried replacing Write with Putmessage and Showmessage but still no
>message appears and I am positive that the program is otherwise working
>properly.
>Can anyone shed some light on this for me?
>
>Thanx in advance,
>
>Cormac McCann
>Final year mechanical eng. student, CQU, Aust.

As one of the other villagers, I thought I should add to Steinr's response:

If the current window is an image window, "write(message);" will output the 
message string at the "current" position which can be controlled by 
moveTo(x,y); 
{ so top left of image would be (0,5) if font is size 9 with "align left"}
note: setForeGround(0);{255} and SetText(string); {'With Background' etc}

If current window is a text window, then cursor will be :
1. where the user last left it
2. at the begining if an existing or new text file is opened
3. at the end if you "selectAll;" with text file the current file.


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 Tue Oct  6 08:58 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA27845;
	Tue, 6 Oct 1998 08:58:27 -0400 (EDT)
Resent-Date: Tue, 6 Oct 1998 08:58:27 -0400 (EDT)
Message-Id: <199810061235.OAA15085@pinus.slu.se>
X-Sender: jorgenh@pinus.slu.se
Mime-Version: 1.0
Date: Tue, 6 Oct 1998 14:42:32 +0100
To: nih-image@io.ece.drexel.edu
From: Jorgen.Henriksson@farmtox.slu.se ( =?iso-8859-1?Q?J=F6rgen?= Henriksson)
Subject: Scanner and "Save Blank Field"
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id IAA25332
Resent-Message-ID: <"WTmVS2.0.yB6.jwW6s"@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/458
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="iso-8859-1"
Content-Length: 422

Dear listmembers,

I'm new to NIH-Image so I hope that You will forgive me for asking a
question that may have been asked before. I will be using a scanner to
capture my images, and my question is how to proceed if I would like to
correct the images captured by the scanner in the same way as the function
"Save Blank Field" corrects images captured with a camera.

Thank You very much for Your help.

Sincerely, Jrgen



From nih-image-d-request@io.ece.drexel.edu Wed Oct  7 04:53 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA25130;
	Wed, 7 Oct 1998 04:53:12 -0400 (EDT)
Date: Wed, 7 Oct 1998 04:53:12 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810070853.EAA25130@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #81
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/81
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 2229

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 81

Today's Topics:
  Scanner and "Save Blank Field"        [ Jorgen.Henriksson@farmtox.slu.se (  ]
  Unwanted Noise in Image               [ Cormac <mccannc@topaz.cqu.edu.au> ]

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

Date: Tue, 6 Oct 1998 14:42:32 +0100
From: Jorgen.Henriksson@farmtox.slu.se ( =?iso-8859-1?Q?J=F6rgen?= Henriksson)
To: nih-image@io.ece.drexel.edu
Subject: Scanner and "Save Blank Field"
Message-Id: <199810061235.OAA15085@pinus.slu.se>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Dear listmembers,

I'm new to NIH-Image so I hope that You will forgive me for asking a
question that may have been asked before. I will be using a scanner to
capture my images, and my question is how to proceed if I would like to
correct the images captured by the scanner in the same way as the function
"Save Blank Field" corrects images captured with a camera.

Thank You very much for Your help.

Sincerely, Jrgen

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

Date: Wed, 7 Oct 1998 18:36:00 +1000 (EST)
From: Cormac <mccannc@topaz.cqu.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Unwanted Noise in Image
Message-Id: <199810070836.SAA23944@topaz.cqu.edu.au>
Content-Type: text/plain; charset="us-ascii"

Greetings once again Imagers,

                             At the moment I am capturing microscopic images
on the 1.61/PPC version of NIH (I'm unsure as to the type of frame grabber
card that's installed) and while that is working fine, I am getting some
unwanted noise (distortion) down the left hand side of the image.  The
distortion is not there in the 'live' image, only in the captured (saved)
images.  I would like to know how to remove this noise as it is affecting my
analysis.

I am using density slicing and then particle analysis and this noise is
being counted as one of the particles and throwing out my results.  Is there
any way of removing it from the image for good?

Thanks again for any help you can give,

Cormac McCann
Final year mechanical eng. student, CQU, Aust.

--------------------------------
End of nih-image-d Digest V98 Issue #81
***************************************

From nih-image-request@io.ece.drexel.edu Wed Oct  7 04:53 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA24997;
	Wed, 7 Oct 1998 04:53:05 -0400 (EDT)
Resent-Date: Wed, 7 Oct 1998 04:53:05 -0400 (EDT)
Date: Wed, 7 Oct 1998 18:36:00 +1000 (EST)
Message-Id: <199810070836.SAA23944@topaz.cqu.edu.au>
X-Sender: mccannc@topaz.cqu.edu.au
X-Mailer: Windows Eudora Light Version 1.5.2
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
From: Cormac <mccannc@topaz.cqu.edu.au>
Subject: Unwanted Noise in Image
Resent-Message-ID: <"2LpRl2.0.PP2.yVo6s"@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/459
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: 790

Greetings once again Imagers,

                             At the moment I am capturing microscopic images
on the 1.61/PPC version of NIH (I'm unsure as to the type of frame grabber
card that's installed) and while that is working fine, I am getting some
unwanted noise (distortion) down the left hand side of the image.  The
distortion is not there in the 'live' image, only in the captured (saved)
images.  I would like to know how to remove this noise as it is affecting my
analysis.

I am using density slicing and then particle analysis and this noise is
being counted as one of the particles and throwing out my results.  Is there
any way of removing it from the image for good?

Thanks again for any help you can give,

Cormac McCann
Final year mechanical eng. student, CQU, Aust.


From nih-image-request@io.ece.drexel.edu Wed Oct  7 09:06 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA18885;
	Wed, 7 Oct 1998 09:06:15 -0400 (EDT)
Resent-Date: Wed, 7 Oct 1998 09:06:15 -0400 (EDT)
Message-ID: <361BAB6B.3A9@pro.via-rs.com.br>
Date: Wed, 07 Oct 1998 09:57:00 -0800
From: Luthero Martins <rsf6675@pro.via-rs.com.br>
Reply-To: luthero@pro.via-rs.com.br
X-Mailer: Mozilla 3.01Gold (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: question
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"cAXyk.0.NB4.JCs6s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/460
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: 198

Please!

I need to know if there are somebody that work with NIH's software, here
in Brazil.  And if somebody knows some course of NIH.

Thanks

Luthero Martins
http://www.oftlamologia-digital.com


From nih-image-request@io.ece.drexel.edu Wed Oct  7 11:21 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA01192;
	Wed, 7 Oct 1998 11:20:57 -0400 (EDT)
Resent-Date: Wed, 7 Oct 1998 11:20:57 -0400 (EDT)
Message-Id: <199810071455.KAA28776@io.ECE.Drexel.EDU>
From: Chris Liner <cll@douze.geo.utulsa.edu>
Subject: Donation
To: nih-image@io.ece.drexel.edu
Date: Wed, 7 Oct 98 10:19:46 CDT
Cc: cll@utulsa.edu (Chris Liner)
Mailer: Elm [revision: 70.85]
Resent-Message-ID: <"DokWy.0.n17.f3u6s"@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/461
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1221



I have developed a commercial seismic interpretation system
around NIH-Image.  The system is called Cubic and consists of
macros, external utility applications and documentation for
applying NIH-Image to visualize and interpret geophysical data.
Cubic includes an external gridding program that makes it useful
for many kinds of geophysical data (gravity, mag, conductivity, etc.)
as well as subsurface geology (structure maps, isopachs, etc.).
We use the system at U. of Tulsa to teach the fundamentals of 3D seismic
interpretation, including tracking, depth conversion, and
rock property estimation from seismic amplitude.

Cubic currently in use by universities in Arkansas, Texas 
and California.  I am interested in additional donations to a 
U.S. universities before the end of the year.

If anyone on the NIH-Image mail list is interested, please contact
me directly via email.

Information about Cubic can be found at my web site listed below.


Dr. Christopher L. Liner
Associate Professor
Department of Geoscience
University of Tulsa
600 S. College Ave
Tulsa, OK   74104-3189
---------------------------
cll@utulsa.edu
http://douze.utulsa.edu/~cll/ChrisLiner.html
918-631-3028   [phone]
918-631-2091   [fax]


From nih-image-request@io.ece.drexel.edu Wed Oct  7 12:08 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA05427;
	Wed, 7 Oct 1998 12:08:27 -0400 (EDT)
Resent-Date: Wed, 7 Oct 1998 12:08:27 -0400 (EDT)
From: "j.gregory" <ort056@abdn.ac.uk>
Sender: ort056@abdn.ac.uk
To: nih-image@io.ece.drexel.edu
Subject: video capture
Message-ID: <SIMEON.9810071628.A@pc3.abdn.ac.uk>
Date: Wed, 7 Oct 1998 16:55:28 +0100 (BST)
Delivery-Receipt-To: "j.gregory" <ort056@abdn.ac.uk>
Priority: NORMAL
X-Mailer: Simeon for Windows Version 4.0.9
X-Authentication: IMSP
MIME-Version: 1.0
Resent-Message-ID: <"3aIXf1.0.6_.hwu6s"@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/462
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: 585

Hi,

I was wondering if any more experienced imagers could help us,
We are writing a grant application and looking to include video 
capture equipment for use with a PC & Scion image.

We need a field of view (approx 5mm) and a resolution of at least 
5 microns.  We are measuring changes over a period of 2-3 seconds.

If anyone could suggest useful equipment, methods or other 
information, it would be a great help.

Thanks in advance,

Jenny Gregory

----------------------
Jenny Gregory
Department of Orthopaedics
University of Aberdeen
Aberdeen
Scotland

j.gregory@abdn.ac.uk




From nih-image-request@io.ece.drexel.edu Wed Oct  7 13:10 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA21561;
	Wed, 7 Oct 1998 13:09:46 -0400 (EDT)
Resent-Date: Wed, 7 Oct 1998 13:09:46 -0400 (EDT)
From: frautsch@ucla.edu
X-Sender: frautsch@pop.ben2.ucla.edu
Message-Id: <v03102802b2414e21fa9d@[164.67.22.39]>
In-Reply-To: <199810070836.SAA23944@topaz.cqu.edu.au>
Mime-Version: 1.0
Date: Wed, 7 Oct 1998 09:59:52 -0700
To: nih-image@io.ece.drexel.edu
Subject: area of irregularly shaped  ROI
Resent-Message-ID: <"721F2.0.U53.Lnv6s"@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/463
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: 173

i have macros that  compute # and size of cells per unit area using oval or
rectangular ROIs.

If i draw an irregularly shaped ROI.  How do i compute the ROI area?

Sally



From nih-image-request@io.ece.drexel.edu Wed Oct  7 14:15 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA08533;
	Wed, 7 Oct 1998 14:14:55 -0400 (EDT)
Resent-Date: Wed, 7 Oct 1998 14:14:55 -0400 (EDT)
Message-Id: <361BAEAE.25CDBCE8@purdue.edu>
Date: Wed, 07 Oct 1998 13:10:54 -0500
From: Kris Jorgensen <kris@purdue.edu>
Reply-To: kris@purdue.edu
Organization: Purdue University
X-Mailer: Mozilla 4.04 [en] (WinNT; I)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Setting the Z-value in Object Image
References: <199810071455.KAA28776@io.ECE.Drexel.EDU>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"SDUtm3.0.cn6.Cmw6s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/464
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: 800

Hi all:

Is it possible to set the Z value in Object Image?  I would like to use
the export XYZ data and make use of the Z value.  I have thought of
making all the images into a stack, but the distribution of the Z value
is not uniform between images.  To make matters worse, it is actually a
heat transfer coefficient and computed from input provided by the user
and so is not know before hand.  Also, making each image into a stack
with a single image seems a little cumbersome.

If someone has another way of writing to a file the X and Y locations
along with one or more computed values for each point in an object I
could use that instead.

Thanks
Kris

-- 
Kris L. Jorgensen
Office:     ME 183
Phone:      (765) 494-8585
Email:      kris@purdue.edu
WWW:        http://www.ecn.purdue.edu/~kris


From nih-image-request@io.ece.drexel.edu Wed Oct  7 19:12 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id TAA16980;
	Wed, 7 Oct 1998 19:11:46 -0400 (EDT)
Resent-Date: Wed, 7 Oct 1998 19:11:46 -0400 (EDT)
Date: Wed, 7 Oct 1998 18:48:36 -0400 (EDT)
From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
X-Sender: cozturk@henryv
To: frautsch@ucla.edu
cc: nih-image@io.ece.drexel.edu
Subject: Re: area of irregularly shaped ROI
In-Reply-To: <v03102802b2414e21fa9d@[164.67.22.39]>
Message-ID: <Pine.SGI.3.91.981007183441.8347H-100000@henryv>
MIME-Version: 1.0
Resent-Message-ID: <"bv6Xp.0.1_.M_-6s"@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/465
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: 1188


Hi,

There may be quick ways of doing it at image resolution. Roughly, open 
your ROI in an empty image. Fill your ROI with index 1, get its integrated 
density.

Mathematically: You can find the centroid (C), calculate the area by 
summing all the triangles ( cross product CP(i) and CP(i+1) i from 1 to N) 
as you travel along the perimeter. This will handle even if the shape is 
irregular, if you watch the signs. ( Do not forget to divide everything 
by 2 at the end).

One word of caution, the coordinates that you get from NIH-Image ROI  
might be off by 1 pixel at some locations. Please refer to earlier 
discussions about ROI X-Y coordinate corrections.

Good Luck.

--------------------------------------------
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 Wed, 7 Oct 1998 frautsch@ucla.edu wrote:

> i have macros that  compute # and size of cells per unit area using oval or
> rectangular ROIs.
> 
> If i draw an irregularly shaped ROI.  How do i compute the ROI area?
> 
> Sally
> 
> 
> 


From nih-image-request@io.ece.drexel.edu Wed Oct  7 21:11 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id VAA22661;
	Wed, 7 Oct 1998 21:11:05 -0400 (EDT)
Resent-Date: Wed, 7 Oct 1998 21:11:05 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: frautsch@ucla.edu, nih-image@io.ece.drexel.edu
Date:          Thu, 8 Oct 1998 10:28:00 GMT+1000
Subject:       Re: area of irregularly shaped  ROI
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <AD5C7600798@rna.bio.mq.edu.au>
Resent-Message-ID: <"3tNaF2.0.WL2.Fk07s"@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/466
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1031

>From: frautsch@ucla.edu
>Date: Wed, 7 Oct 1998 09:59:52 -0700
>To: nih-image@io.ece.drexel.edu
>
>i have macros that  compute # and size of cells per unit area using oval or
>rectangular ROIs.
>
>If i draw an irregularly shaped ROI.  How do i compute the ROI area?
>
Sally,

The answer is much simpler than you or Cengizhan's response would imply.

A simple 'measure(Analyse menu' will place the area and the coordinates of the 
centroid of the current ROI (including a compound ROI created using 
option/control keys) in both the 'Info' window and the Results Table.

(It is easy enough to check by using 'fill' to make a binary image to allow 
'manual' verification of simple or geometric cases. You can rely on Image's 
accuracy within the accuracy of the image pixels. The variation in the 
xycoordinates list wont affect these results.)



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 Oct  7 23:02 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id WAA06113;
	Wed, 7 Oct 1998 22:32:12 -0400 (EDT)
Resent-Date: Wed, 7 Oct 1998 22:32:12 -0400 (EDT)
Date: Thu, 8 Oct 1998 11:22:27 +1000 (EST)
Message-Id: <199810080122.LAA32197@topaz.cqu.edu.au>
X-Sender: mccannc@topaz.cqu.edu.au (Unverified)
X-Mailer: Windows Eudora Light Version 1.5.2
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
From: Cormac <mccannc@topaz.cqu.edu.au>
Subject: Macro error message
Resent-Message-ID: <"DtWHs1.0.377.kF17s"@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/467
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: 636

Hello again imagers,

                    I am trying to incorporate the line 'Undo EditMenu' into
my Macro program.  When I run the macro, I get an error message saying that
I an "end" or ";" is expected in the Undo EditMenu line.  I have checked and
tried to use the advised corrections but I still recieve the same error
message.  I should note that the macro still actually carries out the Undo
edit function but the rest of the program is halted because of the error
message.

Can anyone out there shed some light on this small but annoying problem?
Thanx in advance,

Cormac McCann
Final year mechanical eng. student, CQU, Aust.


From nih-image-request@io.ece.drexel.edu Thu Oct  8 01:00 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id BAA23155;
	Thu, 8 Oct 1998 01:00:15 -0400 (EDT)
Resent-Date: Thu, 8 Oct 1998 01:00:15 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: mccannc@topaz.cqu.edu.au, nih-image@io.ece.drexel.edu
Date:          Thu, 8 Oct 1998 14:10:47 GMT+1000
Subject:       Re: Macro error message
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <AD97E40648C@rna.bio.mq.edu.au>
Resent-Message-ID: <"dA0261.0.894.3H47s"@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/469
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1331

>Date: Thu, 8 Oct 1998 11:22:27 +1000 (EST)
>>To: nih-image@io.ece.drexel.edu
>From: Cormac <mccannc@topaz.cqu.edu.au>
>Subject: Macro error message
>>
>Hello again imagers,
>
>                    I am trying to incorporate the line 'Undo EditMenu' into
>my Macro program.  When I run the macro, I get an error message saying that
>I an "end" or ";" is expected in the Undo EditMenu line.  I have checked and
>tried to use the advised corrections but I still recieve the same error
>message.  I should note that the macro still actually carries out the Undo
>edit function but the rest of the program is halted because of the error
>message.
>
>Can anyone out there shed some light on this small but annoying problem?
>Thanx in advance,
>
>Cormac McCann
>Final year mechanical eng. student, CQU, Aust.

:-) You are missing a statement end ie ";" or "end" (presumablly soon after the 
"Undo". Note that if you have "the line 'Undo EditMenu' in(to my/your) Macro 
program", it should be just 
"
Undo;
"
not !
"
Undo EditMenu;
"
If you want someone to make inteligent comment, it would be better to paste 
macro into email query (or maillist post).
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 Oct  8 01:00 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id BAA23062;
	Thu, 8 Oct 1998 01:00:06 -0400 (EDT)
Resent-Date: Thu, 8 Oct 1998 01:00:06 -0400 (EDT)
Message-ID: <361C2D4C.5CA0@earthlink.net>
Date: Wed, 07 Oct 1998 20:11:08 -0700
From: Shawn Makanvand <shawnmak@earthlink.net>
Reply-To: shawnmak@earthlink.net
X-Mailer: Mozilla 3.01 (Win95; I)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Plugins
References: <199809241015.GAA26131@io.ece.drexel.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"391bS.0.-64.wG47s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/468
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: 630

Hi folks,

I am new to the Image program and need help creating a plugin project.
I would like to create a plugin using CodeWarrior Pro 2 and am uncertain 
as to how to set up the project parameters.

Does anyone have a blank or basic project which would work on Code
Warrior Pro 2?

I tried downloading and reading the existing projects from the NIH web 
site but was unable to open any of them using the tools I have. They are
written either in Think C or older versions of Code Warrior and I have
not been able to convert any of them.

Any help to get me started would be appreciated.

Thanks.
Shawn M.
shawnmak@earthlink.net


From nih-image-d-request@io.ece.drexel.edu Thu Oct  8 01:00 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id BAA23384;
	Thu, 8 Oct 1998 01:00:40 -0400 (EDT)
Date: Thu, 8 Oct 1998 01:00:40 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810080500.BAA23384@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #82
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/82
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 9877

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 82

Today's Topics:
  question                              [ Luthero Martins <rsf6675@pro.via-rs ]
  Donation                              [ Chris Liner <cll@douze.geo.utulsa.e ]
  video capture                         [ "j.gregory" <ort056@abdn.ac.uk> ]
  area of irregularly shaped ROI        [ frautsch@ucla.edu ]
  Setting the Z-value in Object Image   [ Kris Jorgensen <kris@purdue.edu> ]
  Re: area of irregularly shaped ROI    [ Cengizhan Ozturk <cozturk@mri.jhu.e ]
  Re: area of irregularly shaped ROI    [ GJOSS@rna.bio.mq.edu.au ]
  Macro error message                   [ Cormac <mccannc@topaz.cqu.edu.au> ]
  Plugins                               [ Shawn Makanvand <shawnmak@earthlink ]

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

Date: Wed, 07 Oct 1998 09:57:00 -0800
From: Luthero Martins <rsf6675@pro.via-rs.com.br>
To: nih-image@io.ece.drexel.edu
Subject: question
Message-ID: <361BAB6B.3A9@pro.via-rs.com.br>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Please!

I need to know if there are somebody that work with NIH's software, here
in Brazil.  And if somebody knows some course of NIH.

Thanks

Luthero Martins
http://www.oftlamologia-digital.com

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

Date: Wed, 7 Oct 98 10:19:46 CDT
From: Chris Liner <cll@douze.geo.utulsa.edu>
To: nih-image@io.ece.drexel.edu
Cc: cll@utulsa.edu (Chris Liner)
Subject: Donation
Message-Id: <199810071455.KAA28776@io.ECE.Drexel.EDU>

I have developed a commercial seismic interpretation system
around NIH-Image.  The system is called Cubic and consists of
macros, external utility applications and documentation for
applying NIH-Image to visualize and interpret geophysical data.
Cubic includes an external gridding program that makes it useful
for many kinds of geophysical data (gravity, mag, conductivity, etc.)
as well as subsurface geology (structure maps, isopachs, etc.).
We use the system at U. of Tulsa to teach the fundamentals of 3D seismic
interpretation, including tracking, depth conversion, and
rock property estimation from seismic amplitude.

Cubic currently in use by universities in Arkansas, Texas 
and California.  I am interested in additional donations to a 
U.S. universities before the end of the year.

If anyone on the NIH-Image mail list is interested, please contact
me directly via email.

Information about Cubic can be found at my web site listed below.


Dr. Christopher L. Liner
Associate Professor
Department of Geoscience
University of Tulsa
600 S. College Ave
Tulsa, OK   74104-3189
---------------------------
cll@utulsa.edu
http://douze.utulsa.edu/~cll/ChrisLiner.html
918-631-3028   [phone]
918-631-2091   [fax]

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

Date: Wed, 7 Oct 1998 16:55:28 +0100 (BST)
From: "j.gregory" <ort056@abdn.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: video capture
Message-ID: <SIMEON.9810071628.A@pc3.abdn.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

Hi,

I was wondering if any more experienced imagers could help us,
We are writing a grant application and looking to include video 
capture equipment for use with a PC & Scion image.

We need a field of view (approx 5mm) and a resolution of at least 
5 microns.  We are measuring changes over a period of 2-3 seconds.

If anyone could suggest useful equipment, methods or other 
information, it would be a great help.

Thanks in advance,

Jenny Gregory

----------------------
Jenny Gregory
Department of Orthopaedics
University of Aberdeen
Aberdeen
Scotland

j.gregory@abdn.ac.uk

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

Date: Wed, 7 Oct 1998 09:59:52 -0700
From: frautsch@ucla.edu
To: nih-image@io.ece.drexel.edu
Subject: area of irregularly shaped  ROI
Message-Id: <v03102802b2414e21fa9d@[164.67.22.39]>
Content-Type: text/plain; charset="us-ascii"

i have macros that  compute # and size of cells per unit area using oval or
rectangular ROIs.

If i draw an irregularly shaped ROI.  How do i compute the ROI area?

Sally

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

Date: Wed, 07 Oct 1998 13:10:54 -0500
From: Kris Jorgensen <kris@purdue.edu>
To: nih-image@io.ece.drexel.edu
Subject: Setting the Z-value in Object Image
Message-Id: <361BAEAE.25CDBCE8@purdue.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi all:

Is it possible to set the Z value in Object Image?  I would like to use
the export XYZ data and make use of the Z value.  I have thought of
making all the images into a stack, but the distribution of the Z value
is not uniform between images.  To make matters worse, it is actually a
heat transfer coefficient and computed from input provided by the user
and so is not know before hand.  Also, making each image into a stack
with a single image seems a little cumbersome.

If someone has another way of writing to a file the X and Y locations
along with one or more computed values for each point in an object I
could use that instead.

Thanks
Kris

-- 
Kris L. Jorgensen
Office:     ME 183
Phone:      (765) 494-8585
Email:      kris@purdue.edu
WWW:        http://www.ecn.purdue.edu/~kris

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

Date: Wed, 7 Oct 1998 18:48:36 -0400 (EDT)
From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
To: frautsch@ucla.edu
cc: nih-image@io.ece.drexel.edu
Subject: Re: area of irregularly shaped ROI
Message-ID: <Pine.SGI.3.91.981007183441.8347H-100000@henryv>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi,

There may be quick ways of doing it at image resolution. Roughly, open 
your ROI in an empty image. Fill your ROI with index 1, get its integrated 
density.

Mathematically: You can find the centroid (C), calculate the area by 
summing all the triangles ( cross product CP(i) and CP(i+1) i from 1 to N) 
as you travel along the perimeter. This will handle even if the shape is 
irregular, if you watch the signs. ( Do not forget to divide everything 
by 2 at the end).

One word of caution, the coordinates that you get from NIH-Image ROI  
might be off by 1 pixel at some locations. Please refer to earlier 
discussions about ROI X-Y coordinate corrections.

Good Luck.

--------------------------------------------
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 Wed, 7 Oct 1998 frautsch@ucla.edu wrote:

> i have macros that  compute # and size of cells per unit area using oval or
> rectangular ROIs.
> 
> If i draw an irregularly shaped ROI.  How do i compute the ROI area?
> 
> Sally
> 
> 
> 

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

Date:          Thu, 8 Oct 1998 10:28:00 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: frautsch@ucla.edu, nih-image@io.ece.drexel.edu
Subject:       Re: area of irregularly shaped  ROI
Message-ID: <AD5C7600798@rna.bio.mq.edu.au>

>From: frautsch@ucla.edu
>Date: Wed, 7 Oct 1998 09:59:52 -0700
>To: nih-image@io.ece.drexel.edu
>
>i have macros that  compute # and size of cells per unit area using oval or
>rectangular ROIs.
>
>If i draw an irregularly shaped ROI.  How do i compute the ROI area?
>
Sally,

The answer is much simpler than you or Cengizhan's response would imply.

A simple 'measure(Analyse menu' will place the area and the coordinates of the 
centroid of the current ROI (including a compound ROI created using 
option/control keys) in both the 'Info' window and the Results Table.

(It is easy enough to check by using 'fill' to make a binary image to allow 
'manual' verification of simple or geometric cases. You can rely on Image's 
accuracy within the accuracy of the image pixels. The variation in the 
xycoordinates list wont affect these results.)



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, 8 Oct 1998 11:22:27 +1000 (EST)
From: Cormac <mccannc@topaz.cqu.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Macro error message
Message-Id: <199810080122.LAA32197@topaz.cqu.edu.au>
Content-Type: text/plain; charset="us-ascii"

Hello again imagers,

                    I am trying to incorporate the line 'Undo EditMenu' into
my Macro program.  When I run the macro, I get an error message saying that
I an "end" or ";" is expected in the Undo EditMenu line.  I have checked and
tried to use the advised corrections but I still recieve the same error
message.  I should note that the macro still actually carries out the Undo
edit function but the rest of the program is halted because of the error
message.

Can anyone out there shed some light on this small but annoying problem?
Thanx in advance,

Cormac McCann
Final year mechanical eng. student, CQU, Aust.

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

Date: Wed, 07 Oct 1998 20:11:08 -0700
From: Shawn Makanvand <shawnmak@earthlink.net>
To: nih-image@io.ece.drexel.edu
Subject: Plugins
Message-ID: <361C2D4C.5CA0@earthlink.net>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi folks,

I am new to the Image program and need help creating a plugin project.
I would like to create a plugin using CodeWarrior Pro 2 and am uncertain 
as to how to set up the project parameters.

Does anyone have a blank or basic project which would work on Code
Warrior Pro 2?

I tried downloading and reading the existing projects from the NIH web 
site but was unable to open any of them using the tools I have. They are
written either in Think C or older versions of Code Warrior and I have
not been able to convert any of them.

Any help to get me started would be appreciated.

Thanks.
Shawn M.
shawnmak@earthlink.net

--------------------------------
End of nih-image-d Digest V98 Issue #82
***************************************

From nih-image-request@io.ece.drexel.edu Thu Oct  8 01:33 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id BAA10359;
	Thu, 8 Oct 1998 01:33:20 -0400 (EDT)
Resent-Date: Thu, 8 Oct 1998 01:33:20 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: kris@purdue.edu, nih-image@io.ece.drexel.edu
Date:          Thu, 8 Oct 1998 13:05:54 GMT+1000
Subject:       Re: Setting the Z-value in Object Image
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <AD8695A1250@rna.bio.mq.edu.au>
Resent-Message-ID: <"MMzcY1.0.QI1.Wn47s"@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/470
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 3135

>Date: Wed, 07 Oct 1998 13:10:54 -0500
>From: Kris Jorgensen <kris@purdue.edu>
>Subject: Setting the Z-value in Object Image
>Resent-From: nih-image@io.ece.drexel.edu
>
>Hi all:
>
>Is it possible to set the Z value in Object Image?  I would like to use
>the export XYZ data and make use of the Z value.  I have thought of
>making all the images into a stack, but the distribution of the Z value
>is not uniform between images.  To make matters worse, it is actually a
>heat transfer coefficient and computed from input provided by the user
>and so is not know before hand.  Also, making each image into a stack
>with a single image seems a little cumbersome.
>
>If someone has another way of writing to a file the X and Y locations
>along with one or more computed values for each point in an object I
>could use that instead.
>
>Thanks
>Kris

Kris, 

I hope I haven't misread you this time :-)

For a 3D object to be associated with an image in Object-Image, it is not 
necessary for the image to be a stack. However, to introduce a Z measurement
"Z must be between 1 and nSlices (+/-0.5)". It (the Z dimension) is scaled by 
sliceSpacing which again requires that the underlying image be a stack.
If you have a single frame stack, then -0.5<Z>0.5 pixels and scaled by 
sliceSpacing (can be set to arbitary scaling value).

If you use the mouse to set x,y points you will be unable to speciy z manually 
without a multiframe stack but you have pointed out that Z values are computed.
You may have a 2D object on which you wish to impose the Z dimension or you may 
be also computing the xy coords to go with the Z. 
In the first case, you can merge the Z dimension in by transcribing the 
original 2D object to a new 3D object using SwitchToObject and a 
setMarker(xpos(i),ypos(i),z); looping through npoints of the selectedCell. 
In the second case, you supply all three dimensions in the setMarker(x,y,x) 
loop which creates the object.

While "making each image into a stack with a single image seems a little 
cumbersome", it is not expensive to 
getPicsize(w,h);setNewSize(w,h);selectAll;copy;title:=windowTitle;dispose;
makeNewStack(title);paste;
It is not really necessary to save as stack.

If you are only after exporting the 3D object dimensions for visualisation via 
Rotator or some such program, you could create a dummy stack onto which you 
transcribe the 3D objects from their source 2D object & image as you merge the 
Z dimension.

Perhaps the most straightforward approach is "writing to a file the X and Y 
locations along with one or more computed values for each point in an object" 
to your own textfile with tab delimeters, headings etc. (but you lose some 
advantages of storing processed data in objects).
Readily done with:

var tab:string;i:ineteger;
tab:=chr(9);
newTextFile('xyz');
writeln('heading');
for i:=1 to npoints do writeln(xpos(i),tab,ypos(i),tab,z,tab,other);

Hope this makes a little sense and helps. :-)

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 Oct  8 10:22 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA08620;
	Thu, 8 Oct 1998 10:21:43 -0400 (EDT)
Resent-Date: Thu, 8 Oct 1998 10:21:43 -0400 (EDT)
Message-Id: <v03007800b24271230576@[129.137.148.133]>
In-Reply-To: <AD5C7600798@rna.bio.mq.edu.au>
Mime-Version: 1.0
Date: Thu, 8 Oct 1998 10:05:05 -0400
To: nih-image@io.ece.drexel.edu
From: Marc Steed <steedma@email.uc.edu>
Subject: Re: area of irregularly shaped  ROI
Resent-Message-ID: <"48VNY3.0.va6.KMC7s"@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/471
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: 1581

On a related note:

Is it possible to then scale down (i.e., erode) an irregular-shaped ROI to
a certain percentage of the original, while maintaining the original center
point?

TIA

>>From: frautsch@ucla.edu
>>Date: Wed, 7 Oct 1998 09:59:52 -0700
>>To: nih-image@io.ece.drexel.edu
>>
>>i have macros that  compute # and size of cells per unit area using oval or
>>rectangular ROIs.
>>
>>If i draw an irregularly shaped ROI.  How do i compute the ROI area?
>>
>Sally,
>
>The answer is much simpler than you or Cengizhan's response would imply.
>
>A simple 'measure(Analyse menu' will place the area and the coordinates of
>the
>centroid of the current ROI (including a compound ROI created using
>option/control keys) in both the 'Info' window and the Results Table.
>
>(It is easy enough to check by using 'fill' to make a binary image to allow
>'manual' verification of simple or geometric cases. You can rely on Image's
>accuracy within the accuracy of the image pixels. The variation in the
>xycoordinates list wont affect these results.)
>
>
>
>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


...........................................................................
Marc A. Steed, M.S.
Department of Psychology		513-556-1615 (West Campus)
University of Cincinnati		513-558-5113 (East Campus)
429 Dyer Hall			513-556-1904 (fax)
Cincinnati, OH 45221-0376
...........................................................................



From nih-image-request@io.ece.drexel.edu Thu Oct  8 12:52 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA12169;
	Thu, 8 Oct 1998 12:51:31 -0400 (EDT)
Resent-Date: Thu, 8 Oct 1998 12:51:31 -0400 (EDT)
Message-ID: <A0FAC32A7A05D2119A1800805F9A71AD1E20F3@mailhq.icos.com>
From: "Harrison, Janine" <JHarrison@ICOS.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Calcium ratio imaging experiments
Date: Thu, 8 Oct 1998 09:34:26 -0700 
MIME-Version: 1.0
X-Mailer: Internet Mail Service (5.5.2232.9)
Resent-Message-ID: <"ttaXH2.0.b71.TZE7s"@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/472
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 3306

Hi Dr. Peeters-

I appreciate your response.  I am aware of some of the macros that are
available in Image.  My facility is so busy, however, that we cannot take on
the added responsibility of programming to try and get the entire system to
work.

I was very interested in your comment regarding camera & etc.  Would you be
able to make a recommendation on types of cameras that are best suited for
these ratioing experiments?  We currently are using a one-chip Dage and we
have it cooled to -35degC.  We also use the Dage DSP2000 digital processor
to integrate those samples whose light intensities are very low.

Thanks for your suggestions,

Regards,

Janine

> -----Original Message-----
> From:	SolamereTG@aol.com [SMTP:SolamereTG@aol.com]
> Sent:	Monday, October 05, 1998 6:13 PM
> To:	nih-image@io.ece.drexel.edu
> Subject:	Re: Calcium ratio imaging experiments
> 
>   to Janine Harrison
>       Manager, Image Analysis Facility
>       ICOS Corporation
>       22021 20th Avenue S.E.
>       Bothell WA 98021
>       
>       1-425-485-1900 ext 2318
>       1-425-485-1961 FAX
>       jharrison@icos.comt
> 
> 
> We have experience using NIH to measure calcium, Na+, and pH in
> Lymphocytes,
> cardiac myocytes, vascular smooth muscle cells, and endothelial cells.  My
> recommendation is to spend the money on the front end of the measuring
> system
> (Camera, PMT system, illumination control) and start with NIH Image. You
> can
> always spend more on commercial software if NIH (with the appropriate
> macros)
> can't do what you need. I would be happy to discuss with you your groups
> proposed work.However I will be out of my office beginning Wednesday
> 10/7/98
> (morning) but back by next Monday. Please feel free to call tomorrow or
> after
> 10/11/98.
> 
> sincerely yours,
> 
> George A. Peeters M.D.
> Pres. Solamere Technology Group
> Salt Lake City, UT   84103
> 
> 801 322-2645
> 
> In a message dated 98-10-05 15:31:55 EDT, you write:
> 
> <<
>  
>  Does anyone have specific recommendations for filter sets (i.e. from
> Chroma)
>  for the fura-2/indo-1
>  class of compounds?  >>  
> 
> This will depend on the experiment. For example, Fura-2 is the most often
> used
> probe for ratio Ca 2+ imaging. This probe will require illumination
> waveband
> switching for each ratio pair and if you wish to collect 15 ratio pairs
> per
> second you will need a progressive scan sensor (not an interlaced
> detector).
> Flo3, and Flo4 are easier to use but not ratioed.
> Indo-1 is faster, but would require splitting the detector or an emission
> wave
> band switcher. 
>  We have both imaging and photometric equipment used for Ca2+ measurement
> at
> both Genentech, Squibb, Soanes, as well as academic institutions world
> wide. 
>  
>  << Can NIH-Image be used fairly easily for quantitating ratiometric data?
> Or
>  would a commercial analysis package (such as Metamoph, Axon Inst) be
> better
>  suited for extensive experiments?>>   
> Yes, we have Macros to ratio of images acquired at video rates (30 fps). A
> suitable G-3 platform,  64MB RAM, LG-3 frame grabber, software can run as
> little as $2500. This system can control waveband switchers (ours or
> others),
> filter wheels, shutters, electro-physiology, etc. We also have the macros
> that
> control these devices.


From nih-image-request@io.ece.drexel.edu Thu Oct  8 18:31 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA03520;
	Thu, 8 Oct 1998 18:31:13 -0400 (EDT)
Resent-Date: Thu, 8 Oct 1998 18:31:13 -0400 (EDT)
Message-Id: <199810082215.TAA18877@ceiun01.elogica.com.br>
From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" <ggalindo@elogica.com.br>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: area of irregularly shaped  ROI
Date: Thu, 8 Oct 1998 19:11:42 -0300
X-MSMail-Priority: Normal
X-Priority: 3
X-Mailer: Microsoft Internet Mail 4.70.1155
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"G1nL01.0.hW.ofJ7s"@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/474
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset=ISO-8859-1
Content-Length: 550

Dear Sally,
Could you send to me the macros that compute # and size of cells per unit
area?
Thanks in advance.
Rejane Galindo
Universidade Federal Rural de Pernambuco
Morfologia e Anatomia Vegetal

----------
> From: frautsch@ucla.edu
> To: nih-image@io.ece.drexel.edu
> Subject: area of irregularly shaped  ROI
> Date: Quarta-feira, 07 Outubro, 1998 13:59
> 
> i have macros that  compute # and size of cells per unit area using oval
or
> rectangular ROIs.
> 
> If i draw an irregularly shaped ROI.  How do i compute the ROI area?
> 
> Sally
> 
> 


From nih-image-request@io.ece.drexel.edu Thu Oct  8 18:31 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA03522;
	Thu, 8 Oct 1998 18:31:15 -0400 (EDT)
Resent-Date: Thu, 8 Oct 1998 18:31:15 -0400 (EDT)
Message-Id: <199810082215.TAA12014@ceiun01.elogica.com.br>
From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" <ggalindo@elogica.com.br>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: Donation
Date: Thu, 8 Oct 1998 19:06:05 -0300
X-MSMail-Priority: Normal
X-Priority: 3
X-Mailer: Microsoft Internet Mail 4.70.1155
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"vF_DC3.0.jV.gfJ7s"@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/473
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset=ISO-8859-1
Content-Length: 1720

Dear Chris,
I'm interested to receive more informations about this system, specially
about conductivity. What exactly it does?
Thanks in advance,
Rejane Galindo
Universidade Federal Rural de Pernambuco
Morfologia e Anatomia Vegetal

----------
> From: Chris Liner <cll@douze.geo.utulsa.edu>
> To: nih-image@io.ece.drexel.edu
> Cc: Chris Liner <cll@utulsa.edu>
> Subject: Donation
> Date: Quarta-feira, 07 Outubro, 1998 12:19
> 
> 
> 
> I have developed a commercial seismic interpretation system
> around NIH-Image.  The system is called Cubic and consists of
> macros, external utility applications and documentation for
> applying NIH-Image to visualize and interpret geophysical data.
> Cubic includes an external gridding program that makes it useful
> for many kinds of geophysical data (gravity, mag, conductivity, etc.)
> as well as subsurface geology (structure maps, isopachs, etc.).
> We use the system at U. of Tulsa to teach the fundamentals of 3D seismic
> interpretation, including tracking, depth conversion, and
> rock property estimation from seismic amplitude.
> 
> Cubic currently in use by universities in Arkansas, Texas 
> and California.  I am interested in additional donations to a 
> U.S. universities before the end of the year.
> 
> If anyone on the NIH-Image mail list is interested, please contact
> me directly via email.
> 
> Information about Cubic can be found at my web site listed below.
> 
> 
> Dr. Christopher L. Liner
> Associate Professor
> Department of Geoscience
> University of Tulsa
> 600 S. College Ave
> Tulsa, OK   74104-3189
> ---------------------------
> cll@utulsa.edu
> http://douze.utulsa.edu/~cll/ChrisLiner.html
> 918-631-3028   [phone]
> 918-631-2091   [fax]
> 


From nih-image-d-request@io.ece.drexel.edu Thu Oct  8 18:36 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA04039;
	Thu, 8 Oct 1998 18:36:07 -0400 (EDT)
Date: Thu, 8 Oct 1998 18:36:07 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810082236.SAA04039@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #83
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/83
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 13150

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 83

Today's Topics:
  Re: Macro error message               [ GJOSS@rna.bio.mq.edu.au ]
  Re: Setting the Z-value in Object Im  [ GJOSS@rna.bio.mq.edu.au ]
  Re: area of irregularly shaped ROI    [ Marc Steed <steedma@email.uc.edu> ]
  RE: Calcium ratio imaging experiment  [ "Harrison, Janine" <JHarrison@ICOS. ]
  Re: Donation                          [ "=?ISO-8859-1?Q?Rejane_Magalh=E3es_ ]

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

Date:          Thu, 8 Oct 1998 14:10:47 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: mccannc@topaz.cqu.edu.au, nih-image@io.ece.drexel.edu
Subject:       Re: Macro error message
Message-ID: <AD97E40648C@rna.bio.mq.edu.au>

>Date: Thu, 8 Oct 1998 11:22:27 +1000 (EST)
>>To: nih-image@io.ece.drexel.edu
>From: Cormac <mccannc@topaz.cqu.edu.au>
>Subject: Macro error message
>>
>Hello again imagers,
>
>                    I am trying to incorporate the line 'Undo EditMenu' into
>my Macro program.  When I run the macro, I get an error message saying that
>I an "end" or ";" is expected in the Undo EditMenu line.  I have checked and
>tried to use the advised corrections but I still recieve the same error
>message.  I should note that the macro still actually carries out the Undo
>edit function but the rest of the program is halted because of the error
>message.
>
>Can anyone out there shed some light on this small but annoying problem?
>Thanx in advance,
>
>Cormac McCann
>Final year mechanical eng. student, CQU, Aust.

:-) You are missing a statement end ie ";" or "end" (presumablly soon after the 
"Undo". Note that if you have "the line 'Undo EditMenu' in(to my/your) Macro 
program", it should be just 
"
Undo;
"
not !
"
Undo EditMenu;
"
If you want someone to make inteligent comment, it would be better to paste 
macro into email query (or maillist post).
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, 8 Oct 1998 13:05:54 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: kris@purdue.edu, nih-image@io.ece.drexel.edu
Subject:       Re: Setting the Z-value in Object Image
Message-ID: <AD8695A1250@rna.bio.mq.edu.au>

>Date: Wed, 07 Oct 1998 13:10:54 -0500
>From: Kris Jorgensen <kris@purdue.edu>
>Subject: Setting the Z-value in Object Image
>Resent-From: nih-image@io.ece.drexel.edu
>
>Hi all:
>
>Is it possible to set the Z value in Object Image?  I would like to use
>the export XYZ data and make use of the Z value.  I have thought of
>making all the images into a stack, but the distribution of the Z value
>is not uniform between images.  To make matters worse, it is actually a
>heat transfer coefficient and computed from input provided by the user
>and so is not know before hand.  Also, making each image into a stack
>with a single image seems a little cumbersome.
>
>If someone has another way of writing to a file the X and Y locations
>along with one or more computed values for each point in an object I
>could use that instead.
>
>Thanks
>Kris

Kris, 

I hope I haven't misread you this time :-)

For a 3D object to be associated with an image in Object-Image, it is not 
necessary for the image to be a stack. However, to introduce a Z measurement
"Z must be between 1 and nSlices (+/-0.5)". It (the Z dimension) is scaled by 
sliceSpacing which again requires that the underlying image be a stack.
If you have a single frame stack, then -0.5<Z>0.5 pixels and scaled by 
sliceSpacing (can be set to arbitary scaling value).

If you use the mouse to set x,y points you will be unable to speciy z manually 
without a multiframe stack but you have pointed out that Z values are computed.
You may have a 2D object on which you wish to impose the Z dimension or you may 
be also computing the xy coords to go with the Z. 
In the first case, you can merge the Z dimension in by transcribing the 
original 2D object to a new 3D object using SwitchToObject and a 
setMarker(xpos(i),ypos(i),z); looping through npoints of the selectedCell. 
In the second case, you supply all three dimensions in the setMarker(x,y,x) 
loop which creates the object.

While "making each image into a stack with a single image seems a little 
cumbersome", it is not expensive to 
getPicsize(w,h);setNewSize(w,h);selectAll;copy;title:=windowTitle;dispose;
makeNewStack(title);paste;
It is not really necessary to save as stack.

If you are only after exporting the 3D object dimensions for visualisation via 
Rotator or some such program, you could create a dummy stack onto which you 
transcribe the 3D objects from their source 2D object & image as you merge the 
Z dimension.

Perhaps the most straightforward approach is "writing to a file the X and Y 
locations along with one or more computed values for each point in an object" 
to your own textfile with tab delimeters, headings etc. (but you lose some 
advantages of storing processed data in objects).
Readily done with:

var tab:string;i:ineteger;
tab:=chr(9);
newTextFile('xyz');
writeln('heading');
for i:=1 to npoints do writeln(xpos(i),tab,ypos(i),tab,z,tab,other);

Hope this makes a little sense and helps. :-)

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, 8 Oct 1998 10:05:05 -0400
From: Marc Steed <steedma@email.uc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: area of irregularly shaped  ROI
Message-Id: <v03007800b24271230576@[129.137.148.133]>
Content-Type: text/plain; charset="us-ascii"

On a related note:

Is it possible to then scale down (i.e., erode) an irregular-shaped ROI to
a certain percentage of the original, while maintaining the original center
point?

TIA

>>From: frautsch@ucla.edu
>>Date: Wed, 7 Oct 1998 09:59:52 -0700
>>To: nih-image@io.ece.drexel.edu
>>
>>i have macros that  compute # and size of cells per unit area using oval or
>>rectangular ROIs.
>>
>>If i draw an irregularly shaped ROI.  How do i compute the ROI area?
>>
>Sally,
>
>The answer is much simpler than you or Cengizhan's response would imply.
>
>A simple 'measure(Analyse menu' will place the area and the coordinates of
>the
>centroid of the current ROI (including a compound ROI created using
>option/control keys) in both the 'Info' window and the Results Table.
>
>(It is easy enough to check by using 'fill' to make a binary image to allow
>'manual' verification of simple or geometric cases. You can rely on Image's
>accuracy within the accuracy of the image pixels. The variation in the
>xycoordinates list wont affect these results.)
>
>
>
>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


...........................................................................
Marc A. Steed, M.S.
Department of Psychology		513-556-1615 (West Campus)
University of Cincinnati		513-558-5113 (East Campus)
429 Dyer Hall			513-556-1904 (fax)
Cincinnati, OH 45221-0376
...........................................................................

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

Date: Thu, 8 Oct 1998 09:34:26 -0700 
From: "Harrison, Janine" <JHarrison@ICOS.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Calcium ratio imaging experiments
Message-ID: <A0FAC32A7A05D2119A1800805F9A71AD1E20F3@mailhq.icos.com>
Content-Type: text/plain

Hi Dr. Peeters-

I appreciate your response.  I am aware of some of the macros that are
available in Image.  My facility is so busy, however, that we cannot take on
the added responsibility of programming to try and get the entire system to
work.

I was very interested in your comment regarding camera & etc.  Would you be
able to make a recommendation on types of cameras that are best suited for
these ratioing experiments?  We currently are using a one-chip Dage and we
have it cooled to -35degC.  We also use the Dage DSP2000 digital processor
to integrate those samples whose light intensities are very low.

Thanks for your suggestions,

Regards,

Janine

> -----Original Message-----
> From:	SolamereTG@aol.com [SMTP:SolamereTG@aol.com]
> Sent:	Monday, October 05, 1998 6:13 PM
> To:	nih-image@io.ece.drexel.edu
> Subject:	Re: Calcium ratio imaging experiments
> 
>   to Janine Harrison
>       Manager, Image Analysis Facility
>       ICOS Corporation
>       22021 20th Avenue S.E.
>       Bothell WA 98021
>       
>       1-425-485-1900 ext 2318
>       1-425-485-1961 FAX
>       jharrison@icos.comt
> 
> 
> We have experience using NIH to measure calcium, Na+, and pH in
> Lymphocytes,
> cardiac myocytes, vascular smooth muscle cells, and endothelial cells.  My
> recommendation is to spend the money on the front end of the measuring
> system
> (Camera, PMT system, illumination control) and start with NIH Image. You
> can
> always spend more on commercial software if NIH (with the appropriate
> macros)
> can't do what you need. I would be happy to discuss with you your groups
> proposed work.However I will be out of my office beginning Wednesday
> 10/7/98
> (morning) but back by next Monday. Please feel free to call tomorrow or
> after
> 10/11/98.
> 
> sincerely yours,
> 
> George A. Peeters M.D.
> Pres. Solamere Technology Group
> Salt Lake City, UT   84103
> 
> 801 322-2645
> 
> In a message dated 98-10-05 15:31:55 EDT, you write:
> 
> <<
>  
>  Does anyone have specific recommendations for filter sets (i.e. from
> Chroma)
>  for the fura-2/indo-1
>  class of compounds?  >>  
> 
> This will depend on the experiment. For example, Fura-2 is the most often
> used
> probe for ratio Ca 2+ imaging. This probe will require illumination
> waveband
> switching for each ratio pair and if you wish to collect 15 ratio pairs
> per
> second you will need a progressive scan sensor (not an interlaced
> detector).
> Flo3, and Flo4 are easier to use but not ratioed.
> Indo-1 is faster, but would require splitting the detector or an emission
> wave
> band switcher. 
>  We have both imaging and photometric equipment used for Ca2+ measurement
> at
> both Genentech, Squibb, Soanes, as well as academic institutions world
> wide. 
>  
>  << Can NIH-Image be used fairly easily for quantitating ratiometric data?
> Or
>  would a commercial analysis package (such as Metamoph, Axon Inst) be
> better
>  suited for extensive experiments?>>   
> Yes, we have Macros to ratio of images acquired at video rates (30 fps). A
> suitable G-3 platform,  64MB RAM, LG-3 frame grabber, software can run as
> little as $2500. This system can control waveband switchers (ours or
> others),
> filter wheels, shutters, electro-physiology, etc. We also have the macros
> that
> control these devices.

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

Date: Thu, 8 Oct 1998 19:06:05 -0300
From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" <ggalindo@elogica.com.br>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: Donation
Message-Id: <199810082215.TAA12014@ceiun01.elogica.com.br>
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

Dear Chris,
I'm interested to receive more informations about this system, specially
about conductivity. What exactly it does?
Thanks in advance,
Rejane Galindo
Universidade Federal Rural de Pernambuco
Morfologia e Anatomia Vegetal

----------
> From: Chris Liner <cll@douze.geo.utulsa.edu>
> To: nih-image@io.ece.drexel.edu
> Cc: Chris Liner <cll@utulsa.edu>
> Subject: Donation
> Date: Quarta-feira, 07 Outubro, 1998 12:19
> 
> 
> 
> I have developed a commercial seismic interpretation system
> around NIH-Image.  The system is called Cubic and consists of
> macros, external utility applications and documentation for
> applying NIH-Image to visualize and interpret geophysical data.
> Cubic includes an external gridding program that makes it useful
> for many kinds of geophysical data (gravity, mag, conductivity, etc.)
> as well as subsurface geology (structure maps, isopachs, etc.).
> We use the system at U. of Tulsa to teach the fundamentals of 3D seismic
> interpretation, including tracking, depth conversion, and
> rock property estimation from seismic amplitude.
> 
> Cubic currently in use by universities in Arkansas, Texas 
> and California.  I am interested in additional donations to a 
> U.S. universities before the end of the year.
> 
> If anyone on the NIH-Image mail list is interested, please contact
> me directly via email.
> 
> Information about Cubic can be found at my web site listed below.
> 
> 
> Dr. Christopher L. Liner
> Associate Professor
> Department of Geoscience
> University of Tulsa
> 600 S. College Ave
> Tulsa, OK   74104-3189
> ---------------------------
> cll@utulsa.edu
> http://douze.utulsa.edu/~cll/ChrisLiner.html
> 918-631-3028   [phone]
> 918-631-2091   [fax]
> 

--------------------------------
End of nih-image-d Digest V98 Issue #83
***************************************

From nih-image-request@io.ece.drexel.edu Thu Oct  8 20:15 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA12553;
	Thu, 8 Oct 1998 20:14:03 -0400 (EDT)
Resent-Date: Thu, 8 Oct 1998 20:14:03 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: steedma@email.uc.edu, nih-image@io.ece.drexel.edu
Date:          Fri, 9 Oct 1998 9:53:12 GMT+1000
Subject:       Re: area of irregularly shaped  ROI (reduction
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <AED34A57E24@rna.bio.mq.edu.au>
Resent-Message-ID: <"RuTfz3.0.qS2.u_K7s"@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/475
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1629

>Date: Thu, 8 Oct 1998 10:05:05 -0400
>To: nih-image@io.ece.drexel.edu
>From: Marc Steed <steedma@email.uc.edu>
>Subject: Re: area of irregularly shaped  ROI
>..........
>Is it possible to then scale down (i.e., erode) an irregular-shaped ROI to
>a certain percentage of the original, while maintaining the original center
>point?
>
>.............
>Department of Psychology		513-556-1615 (West Campus)
>University of Cincinnati		513-558-5113 (East Campus)
>429 Dyer Hall			513-556-1904 (fax)
>Cincinnati, OH 45221-0376

That is a strange operation(?)
The irregular-shaped ROI needs to be a reasonable shape to avoid splitting to 
multiple parts eg a dumbbell could result in two circles.
Out-of-balance dumbbell could migrate towards the image boundary causing 
failure of macro.

The following will do what you ask:
(It behaves reasonably for reasonable shapes :-)

macro'[r]educe area, retain center of ROI';
  var rp,r:real;x,y,w,h,pi:integer;
  begin getRoi(x,y,w,h); if w=0 then exit('make selection');
  rp:=getNumber('%reduction',33);r:=1-rp/100;
  SetOptions('Area X-Y Center');
  resetCounter;
  measure;pi:=rCount;
  while rArea[rCount]/rArea[pi]>r do begin 
    insetRoi(1);measure;
    moveRoi(rX[pi]-rX[rCount],rY[pi]-rY[rCount]);
    end;
  measure;
  showResults;
  showMessage('reduced',rArea[pi]:6,'\to      ',rArea[rCount]:6
    ,'\',rArea[rCount]/rArea[pi]*100:4:2
    ,'%\at (',rX[rCount]:3:1,',',rY[rCount]:3:1,')');
  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 Thu Oct  8 20:17 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA12753;
	Thu, 8 Oct 1998 20:16:01 -0400 (EDT)
Resent-Date: Thu, 8 Oct 1998 20:16:01 -0400 (EDT)
Message-ID: <361CA8B9.F2F8402D@jingxian.xmu.edu.cn>
Date: Thu, 08 Oct 1998 19:57:46 +0800
From: tianling zheng <wshwzh@jingxian.xmu.edu.cn>
X-Mailer: Mozilla 4.05 [en] (Win95; I)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: remove
References: <199810082219.SAA02082@io.ece.drexel.edu>
Content-Transfer-Encoding: 8bit
Resent-Message-ID: <"xE_GE1.0._c2.Y5L7s"@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/476
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset=iso-8859-1
Content-Length: 13471



nih-image-d-request@io.ece.drexel.edu wrote:

> Subject:
>
> nih-image-d Digest                              Volume 98 : Issue 83
>
> Today's Topics:
>   Re: Macro error message               [ GJOSS@rna.bio.mq.edu.au ]
>   Re: Setting the Z-value in Object Im  [ GJOSS@rna.bio.mq.edu.au ]
>   Re: area of irregularly shaped ROI    [ Marc Steed <steedma@email.uc.edu> ]
>   RE: Calcium ratio imaging experiment  [ "Harrison, Janine" <JHarrison@ICOS. ]
>   Re: Donation                          [ "=?ISO-8859-1?Q?Rejane_Magalh=E3es_ ]
>
>   ------------------------------------------------------------------------
>
> Subject: Re: Macro error message
> Date: Thu, 8 Oct 1998 14:10:47 GMT+1000
> From: GJOSS@rna.bio.mq.edu.au
> To: mccannc@topaz.cqu.edu.au, nih-image@io.ece.drexel.edu
>
> >Date: Thu, 8 Oct 1998 11:22:27 +1000 (EST)
> >>To: nih-image@io.ece.drexel.edu
> >From: Cormac <mccannc@topaz.cqu.edu.au>
> >Subject: Macro error message
> >>
> >Hello again imagers,
> >
> >                    I am trying to incorporate the line 'Undo EditMenu' into
> >my Macro program.  When I run the macro, I get an error message saying that
> >I an "end" or ";" is expected in the Undo EditMenu line.  I have checked and
> >tried to use the advised corrections but I still recieve the same error
> >message.  I should note that the macro still actually carries out the Undo
> >edit function but the rest of the program is halted because of the error
> >message.
> >
> >Can anyone out there shed some light on this small but annoying problem?
> >Thanx in advance,
> >
> >Cormac McCann
> >Final year mechanical eng. student, CQU, Aust.
>
> :-) You are missing a statement end ie ";" or "end" (presumablly soon after the
> "Undo". Note that if you have "the line 'Undo EditMenu' in(to my/your) Macro
> program", it should be just
> "
> Undo;
> "
> not !
> "
> Undo EditMenu;
> "
> If you want someone to make inteligent comment, it would be better to paste
> macro into email query (or maillist post).
> 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
>
>   ------------------------------------------------------------------------
>
> Subject: Re: Setting the Z-value in Object Image
> Date: Thu, 8 Oct 1998 13:05:54 GMT+1000
> From: GJOSS@rna.bio.mq.edu.au
> To: kris@purdue.edu, nih-image@io.ece.drexel.edu
>
> >Date: Wed, 07 Oct 1998 13:10:54 -0500
> >From: Kris Jorgensen <kris@purdue.edu>
> >Subject: Setting the Z-value in Object Image
> >Resent-From: nih-image@io.ece.drexel.edu
> >
> >Hi all:
> >
> >Is it possible to set the Z value in Object Image?  I would like to use
> >the export XYZ data and make use of the Z value.  I have thought of
> >making all the images into a stack, but the distribution of the Z value
> >is not uniform between images.  To make matters worse, it is actually a
> >heat transfer coefficient and computed from input provided by the user
> >and so is not know before hand.  Also, making each image into a stack
> >with a single image seems a little cumbersome.
> >
> >If someone has another way of writing to a file the X and Y locations
> >along with one or more computed values for each point in an object I
> >could use that instead.
> >
> >Thanks
> >Kris
>
> Kris,
>
> I hope I haven't misread you this time :-)
>
> For a 3D object to be associated with an image in Object-Image, it is not
> necessary for the image to be a stack. However, to introduce a Z measurement
> "Z must be between 1 and nSlices (+/-0.5)". It (the Z dimension) is scaled by
> sliceSpacing which again requires that the underlying image be a stack.
> If you have a single frame stack, then -0.5<Z>0.5 pixels and scaled by
> sliceSpacing (can be set to arbitary scaling value).
>
> If you use the mouse to set x,y points you will be unable to speciy z manually
> without a multiframe stack but you have pointed out that Z values are computed.
> You may have a 2D object on which you wish to impose the Z dimension or you may
> be also computing the xy coords to go with the Z.
> In the first case, you can merge the Z dimension in by transcribing the
> original 2D object to a new 3D object using SwitchToObject and a
> setMarker(xpos(i),ypos(i),z); looping through npoints of the selectedCell.
> In the second case, you supply all three dimensions in the setMarker(x,y,x)
> loop which creates the object.
>
> While "making each image into a stack with a single image seems a little
> cumbersome", it is not expensive to
> getPicsize(w,h);setNewSize(w,h);selectAll;copy;title:=windowTitle;dispose;
> makeNewStack(title);paste;
> It is not really necessary to save as stack.
>
> If you are only after exporting the 3D object dimensions for visualisation via
> Rotator or some such program, you could create a dummy stack onto which you
> transcribe the 3D objects from their source 2D object & image as you merge the
> Z dimension.
>
> Perhaps the most straightforward approach is "writing to a file the X and Y
> locations along with one or more computed values for each point in an object"
> to your own textfile with tab delimeters, headings etc. (but you lose some
> advantages of storing processed data in objects).
> Readily done with:
>
> var tab:string;i:ineteger;
> tab:=chr(9);
> newTextFile('xyz');
> writeln('heading');
> for i:=1 to npoints do writeln(xpos(i),tab,ypos(i),tab,z,tab,other);
>
> Hope this makes a little sense and helps. :-)
>
> 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
>
>   ------------------------------------------------------------------------
>
> Subject: Re: area of irregularly shaped ROI
> Date: Thu, 8 Oct 1998 10:05:05 -0400
> From: Marc Steed <steedma@email.uc.edu>
> To: nih-image@io.ece.drexel.edu
>
> On a related note:
>
> Is it possible to then scale down (i.e., erode) an irregular-shaped ROI to
> a certain percentage of the original, while maintaining the original center
> point?
>
> TIA
>
> >>From: frautsch@ucla.edu
> >>Date: Wed, 7 Oct 1998 09:59:52 -0700
> >>To: nih-image@io.ece.drexel.edu
> >>
> >>i have macros that  compute # and size of cells per unit area using oval or
> >>rectangular ROIs.
> >>
> >>If i draw an irregularly shaped ROI.  How do i compute the ROI area?
> >>
> >Sally,
> >
> >The answer is much simpler than you or Cengizhan's response would imply.
> >
> >A simple 'measure(Analyse menu' will place the area and the coordinates of
> >the
> >centroid of the current ROI (including a compound ROI created using
> >option/control keys) in both the 'Info' window and the Results Table.
> >
> >(It is easy enough to check by using 'fill' to make a binary image to allow
> >'manual' verification of simple or geometric cases. You can rely on Image's
> >accuracy within the accuracy of the image pixels. The variation in the
> >xycoordinates list wont affect these results.)
> >
> >
> >
> >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
>
> ...........................................................................
> Marc A. Steed, M.S.
> Department of Psychology                513-556-1615 (West Campus)
> University of Cincinnati                513-558-5113 (East Campus)
> 429 Dyer Hall                   513-556-1904 (fax)
> Cincinnati, OH 45221-0376
> ...........................................................................
>
>   ------------------------------------------------------------------------
>
> Subject: RE: Calcium ratio imaging experiments
> Date: Thu, 8 Oct 1998 09:34:26 -0700
> From: "Harrison, Janine" <JHarrison@ICOS.com>
> To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
>
> Hi Dr. Peeters-
>
> I appreciate your response.  I am aware of some of the macros that are
> available in Image.  My facility is so busy, however, that we cannot take on
> the added responsibility of programming to try and get the entire system to
> work.
>
> I was very interested in your comment regarding camera & etc.  Would you be
> able to make a recommendation on types of cameras that are best suited for
> these ratioing experiments?  We currently are using a one-chip Dage and we
> have it cooled to -35degC.  We also use the Dage DSP2000 digital processor
> to integrate those samples whose light intensities are very low.
>
> Thanks for your suggestions,
>
> Regards,
>
> Janine
>
> > -----Original Message-----
> > From: SolamereTG@aol.com [SMTP:SolamereTG@aol.com]
> > Sent: Monday, October 05, 1998 6:13 PM
> > To:   nih-image@io.ece.drexel.edu
> > Subject:      Re: Calcium ratio imaging experiments
> >
> >   to Janine Harrison
> >       Manager, Image Analysis Facility
> >       ICOS Corporation
> >       22021 20th Avenue S.E.
> >       Bothell WA 98021
> >
> >       1-425-485-1900 ext 2318
> >       1-425-485-1961 FAX
> >       jharrison@icos.comt
> >
> >
> > We have experience using NIH to measure calcium, Na+, and pH in
> > Lymphocytes,
> > cardiac myocytes, vascular smooth muscle cells, and endothelial cells.  My
> > recommendation is to spend the money on the front end of the measuring
> > system
> > (Camera, PMT system, illumination control) and start with NIH Image. You
> > can
> > always spend more on commercial software if NIH (with the appropriate
> > macros)
> > can't do what you need. I would be happy to discuss with you your groups
> > proposed work.However I will be out of my office beginning Wednesday
> > 10/7/98
> > (morning) but back by next Monday. Please feel free to call tomorrow or
> > after
> > 10/11/98.
> >
> > sincerely yours,
> >
> > George A. Peeters M.D.
> > Pres. Solamere Technology Group
> > Salt Lake City, UT   84103
> >
> > 801 322-2645
> >
> > In a message dated 98-10-05 15:31:55 EDT, you write:
> >
> > <<
> >
> >  Does anyone have specific recommendations for filter sets (i.e. from
> > Chroma)
> >  for the fura-2/indo-1
> >  class of compounds?  >>
> >
> > This will depend on the experiment. For example, Fura-2 is the most often
> > used
> > probe for ratio Ca 2+ imaging. This probe will require illumination
> > waveband
> > switching for each ratio pair and if you wish to collect 15 ratio pairs
> > per
> > second you will need a progressive scan sensor (not an interlaced
> > detector).
> > Flo3, and Flo4 are easier to use but not ratioed.
> > Indo-1 is faster, but would require splitting the detector or an emission
> > wave
> > band switcher.
> >  We have both imaging and photometric equipment used for Ca2+ measurement
> > at
> > both Genentech, Squibb, Soanes, as well as academic institutions world
> > wide.
> >
> >  << Can NIH-Image be used fairly easily for quantitating ratiometric data?
> > Or
> >  would a commercial analysis package (such as Metamoph, Axon Inst) be
> > better
> >  suited for extensive experiments?>>
> > Yes, we have Macros to ratio of images acquired at video rates (30 fps). A
> > suitable G-3 platform,  64MB RAM, LG-3 frame grabber, software can run as
> > little as $2500. This system can control waveband switchers (ours or
> > others),
> > filter wheels, shutters, electro-physiology, etc. We also have the macros
> > that
> > control these devices.
>
>   ------------------------------------------------------------------------
>
> Subject: Re: Donation
> Date: Thu, 8 Oct 1998 19:06:05 -0300
> From: "Rejane Magalhes Pimentel Galindo" <ggalindo@elogica.com.br>
> To: <nih-image@io.ece.drexel.edu>
>
> Dear Chris,
> I'm interested to receive more informations about this system, specially
> about conductivity. What exactly it does?
> Thanks in advance,
> Rejane Galindo
> Universidade Federal Rural de Pernambuco
> Morfologia e Anatomia Vegetal
>
> ----------
> > From: Chris Liner <cll@douze.geo.utulsa.edu>
> > To: nih-image@io.ece.drexel.edu
> > Cc: Chris Liner <cll@utulsa.edu>
> > Subject: Donation
> > Date: Quarta-feira, 07 Outubro, 1998 12:19
> >
> >
> >
> > I have developed a commercial seismic interpretation system
> > around NIH-Image.  The system is called Cubic and consists of
> > macros, external utility applications and documentation for
> > applying NIH-Image to visualize and interpret geophysical data.
> > Cubic includes an external gridding program that makes it useful
> > for many kinds of geophysical data (gravity, mag, conductivity, etc.)
> > as well as subsurface geology (structure maps, isopachs, etc.).
> > We use the system at U. of Tulsa to teach the fundamentals of 3D seismic
> > interpretation, including tracking, depth conversion, and
> > rock property estimation from seismic amplitude.
> >
> > Cubic currently in use by universities in Arkansas, Texas
> > and California.  I am interested in additional donations to a
> > U.S. universities before the end of the year.
> >
> > If anyone on the NIH-Image mail list is interested, please contact
> > me directly via email.
> >
> > Information about Cubic can be found at my web site listed below.
> >
> >
> > Dr. Christopher L. Liner
> > Associate Professor
> > Department of Geoscience
> > University of Tulsa
> > 600 S. College Ave
> > Tulsa, OK   74104-3189
> > ---------------------------
> > cll@utulsa.edu
> > http://douze.utulsa.edu/~cll/ChrisLiner.html
> > 918-631-3028   [phone]
> > 918-631-2091   [fax]
> >




From nih-image-request@io.ece.drexel.edu Fri Oct  9 01:35 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id BAA13879;
	Fri, 9 Oct 1998 01:34:23 -0400 (EDT)
Resent-Date: Fri, 9 Oct 1998 01:34:23 -0400 (EDT)
References: TVWTICHR, Company Limited by Guarantee, ACN 009 278 755
Mime-Version: 1.0
Message-Id: <v04011701b2434418ab5e@[130.95.224.88]>
In-Reply-To: <199810070836.SAA23944@topaz.cqu.edu.au>
X-Mailer: Eudora Pro 4.01 for the Mac.
Date: Fri, 9 Oct 1998 13:19:56 +0800
To: nih-image@io.ece.drexel.edu
From: Mike Schon-Hegrad <mike@ichr.uwa.edu.au>
Subject: G3 Upgrade conflict with LG 3??
Cc: karenw@ichr.uwa.edu.au
Resent-Message-ID: <"ofYLl1.0.0_2.OqP7s"@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/477
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: 753

Hi all,

We've been running a successful project using NIH Image on an 8100/80AV
PowerMac with a Scion LG 3 card.

We'd like to upgrade the 8100/80AV to a G3 processor and are looking at the
MAXpower G3 cards for the 8100 from Newertech.

I'm just wondering if anyone else has done this, or if anyone can forsee
any problems with the Scion LG 3 card and this G3 configuration.

Thanks in advance,

Mike
-------------------------------------------------
Mike Schon-Hegrad (Macintosh Administrator)

Central IT Services
TVW Telethon Institute for Child Health Research
Perth, Western Australia
Company limited by guarantee
Phone 61 8 9340 7072         Fax 61 8 9388 3414

WWW: http://www.ichr.uwa.edu.au
-------------------------------------------------


From nih-image-request@io.ece.drexel.edu Fri Oct  9 10:44 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA11389;
	Fri, 9 Oct 1998 10:44:15 -0400 (EDT)
Resent-Date: Fri, 9 Oct 1998 10:44:15 -0400 (EDT)
From: MASandberg@aol.com
Message-ID: <86dd0702.361e1b22@aol.com>
Date: Fri, 9 Oct 1998 10:18:10 EDT
To: nih-image@io.ece.drexel.edu
Mime-Version: 1.0
Subject: Sprintscan plug-in error.
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 for Mac sub 84
Resent-Message-ID: <"qSHTc2.0.n62.8jX7s"@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/478
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: 294

With NIH Image 1.62b and a G3 Powerbook with 192 RAM I can scan one slide with
a Sprintscan 35 plug-in but get an "out of memory" error message when I try to
do a second scan.  If I quit and reopen NIH Image, I can then do the second
scan.  Any advice on how to fix this problem?

Thanks,
MAS


From nih-image-d-request@io.ece.drexel.edu Fri Oct  9 10:49 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA12089;
	Fri, 9 Oct 1998 10:49:54 -0400 (EDT)
Date: Fri, 9 Oct 1998 10:49:54 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810091449.KAA12089@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #84
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/84
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 18826

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 84

Today's Topics:
  Re: area of irregularly shaped ROI    [ "=?ISO-8859-1?Q?Rejane_Magalh=E3es_ ]
  Re: area of irregularly shaped ROI (  [ GJOSS@rna.bio.mq.edu.au ]
  remove                                [ tianling zheng <wshwzh@jingxian.xmu ]
  G3 Upgrade conflict with LG 3??       [ Mike Schon-Hegrad <mike@ichr.uwa.ed ]
  Sprintscan plug-in error.             [ MASandberg@aol.com ]

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

Date: Thu, 8 Oct 1998 19:11:42 -0300
From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" <ggalindo@elogica.com.br>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: area of irregularly shaped  ROI
Message-Id: <199810082215.TAA18877@ceiun01.elogica.com.br>
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

Dear Sally,
Could you send to me the macros that compute # and size of cells per unit
area?
Thanks in advance.
Rejane Galindo
Universidade Federal Rural de Pernambuco
Morfologia e Anatomia Vegetal

----------
> From: frautsch@ucla.edu
> To: nih-image@io.ece.drexel.edu
> Subject: area of irregularly shaped  ROI
> Date: Quarta-feira, 07 Outubro, 1998 13:59
> 
> i have macros that  compute # and size of cells per unit area using oval
or
> rectangular ROIs.
> 
> If i draw an irregularly shaped ROI.  How do i compute the ROI area?
> 
> Sally
> 
> 

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

Date:          Fri, 9 Oct 1998 9:53:12 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: steedma@email.uc.edu, nih-image@io.ece.drexel.edu
Subject:       Re: area of irregularly shaped  ROI (reduction
Message-ID: <AED34A57E24@rna.bio.mq.edu.au>

>Date: Thu, 8 Oct 1998 10:05:05 -0400
>To: nih-image@io.ece.drexel.edu
>From: Marc Steed <steedma@email.uc.edu>
>Subject: Re: area of irregularly shaped  ROI
>..........
>Is it possible to then scale down (i.e., erode) an irregular-shaped ROI to
>a certain percentage of the original, while maintaining the original center
>point?
>
>.............
>Department of Psychology		513-556-1615 (West Campus)
>University of Cincinnati		513-558-5113 (East Campus)
>429 Dyer Hall			513-556-1904 (fax)
>Cincinnati, OH 45221-0376

That is a strange operation(?)
The irregular-shaped ROI needs to be a reasonable shape to avoid splitting to 
multiple parts eg a dumbbell could result in two circles.
Out-of-balance dumbbell could migrate towards the image boundary causing 
failure of macro.

The following will do what you ask:
(It behaves reasonably for reasonable shapes :-)

macro'[r]educe area, retain center of ROI';
  var rp,r:real;x,y,w,h,pi:integer;
  begin getRoi(x,y,w,h); if w=0 then exit('make selection');
  rp:=getNumber('%reduction',33);r:=1-rp/100;
  SetOptions('Area X-Y Center');
  resetCounter;
  measure;pi:=rCount;
  while rArea[rCount]/rArea[pi]>r do begin 
    insetRoi(1);measure;
    moveRoi(rX[pi]-rX[rCount],rY[pi]-rY[rCount]);
    end;
  measure;
  showResults;
  showMessage('reduced',rArea[pi]:6,'\to      ',rArea[rCount]:6
    ,'\',rArea[rCount]/rArea[pi]*100:4:2
    ,'%\at (',rX[rCount]:3:1,',',rY[rCount]:3:1,')');
  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: Thu, 08 Oct 1998 19:57:46 +0800
From: tianling zheng <wshwzh@jingxian.xmu.edu.cn>
To: nih-image@io.ece.drexel.edu
Subject: remove
Message-ID: <361CA8B9.F2F8402D@jingxian.xmu.edu.cn>
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 98 : Issue 83
>
> Today's Topics:
>   Re: Macro error message               [ GJOSS@rna.bio.mq.edu.au ]
>   Re: Setting the Z-value in Object Im  [ GJOSS@rna.bio.mq.edu.au ]
>   Re: area of irregularly shaped ROI    [ Marc Steed <steedma@email.uc.edu> ]
>   RE: Calcium ratio imaging experiment  [ "Harrison, Janine" <JHarrison@ICOS. ]
>   Re: Donation                          [ "=?ISO-8859-1?Q?Rejane_Magalh=E3es_ ]
>
>   ------------------------------------------------------------------------
>
> Subject: Re: Macro error message
> Date: Thu, 8 Oct 1998 14:10:47 GMT+1000
> From: GJOSS@rna.bio.mq.edu.au
> To: mccannc@topaz.cqu.edu.au, nih-image@io.ece.drexel.edu
>
> >Date: Thu, 8 Oct 1998 11:22:27 +1000 (EST)
> >>To: nih-image@io.ece.drexel.edu
> >From: Cormac <mccannc@topaz.cqu.edu.au>
> >Subject: Macro error message
> >>
> >Hello again imagers,
> >
> >                    I am trying to incorporate the line 'Undo EditMenu' into
> >my Macro program.  When I run the macro, I get an error message saying that
> >I an "end" or ";" is expected in the Undo EditMenu line.  I have checked and
> >tried to use the advised corrections but I still recieve the same error
> >message.  I should note that the macro still actually carries out the Undo
> >edit function but the rest of the program is halted because of the error
> >message.
> >
> >Can anyone out there shed some light on this small but annoying problem?
> >Thanx in advance,
> >
> >Cormac McCann
> >Final year mechanical eng. student, CQU, Aust.
>
> :-) You are missing a statement end ie ";" or "end" (presumablly soon after the
> "Undo". Note that if you have "the line 'Undo EditMenu' in(to my/your) Macro
> program", it should be just
> "
> Undo;
> "
> not !
> "
> Undo EditMenu;
> "
> If you want someone to make inteligent comment, it would be better to paste
> macro into email query (or maillist post).
> 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
>
>   ------------------------------------------------------------------------
>
> Subject: Re: Setting the Z-value in Object Image
> Date: Thu, 8 Oct 1998 13:05:54 GMT+1000
> From: GJOSS@rna.bio.mq.edu.au
> To: kris@purdue.edu, nih-image@io.ece.drexel.edu
>
> >Date: Wed, 07 Oct 1998 13:10:54 -0500
> >From: Kris Jorgensen <kris@purdue.edu>
> >Subject: Setting the Z-value in Object Image
> >Resent-From: nih-image@io.ece.drexel.edu
> >
> >Hi all:
> >
> >Is it possible to set the Z value in Object Image?  I would like to use
> >the export XYZ data and make use of the Z value.  I have thought of
> >making all the images into a stack, but the distribution of the Z value
> >is not uniform between images.  To make matters worse, it is actually a
> >heat transfer coefficient and computed from input provided by the user
> >and so is not know before hand.  Also, making each image into a stack
> >with a single image seems a little cumbersome.
> >
> >If someone has another way of writing to a file the X and Y locations
> >along with one or more computed values for each point in an object I
> >could use that instead.
> >
> >Thanks
> >Kris
>
> Kris,
>
> I hope I haven't misread you this time :-)
>
> For a 3D object to be associated with an image in Object-Image, it is not
> necessary for the image to be a stack. However, to introduce a Z measurement
> "Z must be between 1 and nSlices (+/-0.5)". It (the Z dimension) is scaled by
> sliceSpacing which again requires that the underlying image be a stack.
> If you have a single frame stack, then -0.5<Z>0.5 pixels and scaled by
> sliceSpacing (can be set to arbitary scaling value).
>
> If you use the mouse to set x,y points you will be unable to speciy z manually
> without a multiframe stack but you have pointed out that Z values are computed.
> You may have a 2D object on which you wish to impose the Z dimension or you may
> be also computing the xy coords to go with the Z.
> In the first case, you can merge the Z dimension in by transcribing the
> original 2D object to a new 3D object using SwitchToObject and a
> setMarker(xpos(i),ypos(i),z); looping through npoints of the selectedCell.
> In the second case, you supply all three dimensions in the setMarker(x,y,x)
> loop which creates the object.
>
> While "making each image into a stack with a single image seems a little
> cumbersome", it is not expensive to
> getPicsize(w,h);setNewSize(w,h);selectAll;copy;title:=windowTitle;dispose;
> makeNewStack(title);paste;
> It is not really necessary to save as stack.
>
> If you are only after exporting the 3D object dimensions for visualisation via
> Rotator or some such program, you could create a dummy stack onto which you
> transcribe the 3D objects from their source 2D object & image as you merge the
> Z dimension.
>
> Perhaps the most straightforward approach is "writing to a file the X and Y
> locations along with one or more computed values for each point in an object"
> to your own textfile with tab delimeters, headings etc. (but you lose some
> advantages of storing processed data in objects).
> Readily done with:
>
> var tab:string;i:ineteger;
> tab:=chr(9);
> newTextFile('xyz');
> writeln('heading');
> for i:=1 to npoints do writeln(xpos(i),tab,ypos(i),tab,z,tab,other);
>
> Hope this makes a little sense and helps. :-)
>
> 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
>
>   ------------------------------------------------------------------------
>
> Subject: Re: area of irregularly shaped ROI
> Date: Thu, 8 Oct 1998 10:05:05 -0400
> From: Marc Steed <steedma@email.uc.edu>
> To: nih-image@io.ece.drexel.edu
>
> On a related note:
>
> Is it possible to then scale down (i.e., erode) an irregular-shaped ROI to
> a certain percentage of the original, while maintaining the original center
> point?
>
> TIA
>
> >>From: frautsch@ucla.edu
> >>Date: Wed, 7 Oct 1998 09:59:52 -0700
> >>To: nih-image@io.ece.drexel.edu
> >>
> >>i have macros that  compute # and size of cells per unit area using oval or
> >>rectangular ROIs.
> >>
> >>If i draw an irregularly shaped ROI.  How do i compute the ROI area?
> >>
> >Sally,
> >
> >The answer is much simpler than you or Cengizhan's response would imply.
> >
> >A simple 'measure(Analyse menu' will place the area and the coordinates of
> >the
> >centroid of the current ROI (including a compound ROI created using
> >option/control keys) in both the 'Info' window and the Results Table.
> >
> >(It is easy enough to check by using 'fill' to make a binary image to allow
> >'manual' verification of simple or geometric cases. You can rely on Image's
> >accuracy within the accuracy of the image pixels. The variation in the
> >xycoordinates list wont affect these results.)
> >
> >
> >
> >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
>
> ...........................................................................
> Marc A. Steed, M.S.
> Department of Psychology                513-556-1615 (West Campus)
> University of Cincinnati                513-558-5113 (East Campus)
> 429 Dyer Hall                   513-556-1904 (fax)
> Cincinnati, OH 45221-0376
> ...........................................................................
>
>   ------------------------------------------------------------------------
>
> Subject: RE: Calcium ratio imaging experiments
> Date: Thu, 8 Oct 1998 09:34:26 -0700
> From: "Harrison, Janine" <JHarrison@ICOS.com>
> To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
>
> Hi Dr. Peeters-
>
> I appreciate your response.  I am aware of some of the macros that are
> available in Image.  My facility is so busy, however, that we cannot take on
> the added responsibility of programming to try and get the entire system to
> work.
>
> I was very interested in your comment regarding camera & etc.  Would you be
> able to make a recommendation on types of cameras that are best suited for
> these ratioing experiments?  We currently are using a one-chip Dage and we
> have it cooled to -35degC.  We also use the Dage DSP2000 digital processor
> to integrate those samples whose light intensities are very low.
>
> Thanks for your suggestions,
>
> Regards,
>
> Janine
>
> > -----Original Message-----
> > From: SolamereTG@aol.com [SMTP:SolamereTG@aol.com]
> > Sent: Monday, October 05, 1998 6:13 PM
> > To:   nih-image@io.ece.drexel.edu
> > Subject:      Re: Calcium ratio imaging experiments
> >
> >   to Janine Harrison
> >       Manager, Image Analysis Facility
> >       ICOS Corporation
> >       22021 20th Avenue S.E.
> >       Bothell WA 98021
> >
> >       1-425-485-1900 ext 2318
> >       1-425-485-1961 FAX
> >       jharrison@icos.comt
> >
> >
> > We have experience using NIH to measure calcium, Na+, and pH in
> > Lymphocytes,
> > cardiac myocytes, vascular smooth muscle cells, and endothelial cells.  My
> > recommendation is to spend the money on the front end of the measuring
> > system
> > (Camera, PMT system, illumination control) and start with NIH Image. You
> > can
> > always spend more on commercial software if NIH (with the appropriate
> > macros)
> > can't do what you need. I would be happy to discuss with you your groups
> > proposed work.However I will be out of my office beginning Wednesday
> > 10/7/98
> > (morning) but back by next Monday. Please feel free to call tomorrow or
> > after
> > 10/11/98.
> >
> > sincerely yours,
> >
> > George A. Peeters M.D.
> > Pres. Solamere Technology Group
> > Salt Lake City, UT   84103
> >
> > 801 322-2645
> >
> > In a message dated 98-10-05 15:31:55 EDT, you write:
> >
> > <<
> >
> >  Does anyone have specific recommendations for filter sets (i.e. from
> > Chroma)
> >  for the fura-2/indo-1
> >  class of compounds?  >>
> >
> > This will depend on the experiment. For example, Fura-2 is the most often
> > used
> > probe for ratio Ca 2+ imaging. This probe will require illumination
> > waveband
> > switching for each ratio pair and if you wish to collect 15 ratio pairs
> > per
> > second you will need a progressive scan sensor (not an interlaced
> > detector).
> > Flo3, and Flo4 are easier to use but not ratioed.
> > Indo-1 is faster, but would require splitting the detector or an emission
> > wave
> > band switcher.
> >  We have both imaging and photometric equipment used for Ca2+ measurement
> > at
> > both Genentech, Squibb, Soanes, as well as academic institutions world
> > wide.
> >
> >  << Can NIH-Image be used fairly easily for quantitating ratiometric data?
> > Or
> >  would a commercial analysis package (such as Metamoph, Axon Inst) be
> > better
> >  suited for extensive experiments?>>
> > Yes, we have Macros to ratio of images acquired at video rates (30 fps). A
> > suitable G-3 platform,  64MB RAM, LG-3 frame grabber, software can run as
> > little as $2500. This system can control waveband switchers (ours or
> > others),
> > filter wheels, shutters, electro-physiology, etc. We also have the macros
> > that
> > control these devices.
>
>   ------------------------------------------------------------------------
>
> Subject: Re: Donation
> Date: Thu, 8 Oct 1998 19:06:05 -0300
> From: "Rejane Magalhes Pimentel Galindo" <ggalindo@elogica.com.br>
> To: <nih-image@io.ece.drexel.edu>
>
> Dear Chris,
> I'm interested to receive more informations about this system, specially
> about conductivity. What exactly it does?
> Thanks in advance,
> Rejane Galindo
> Universidade Federal Rural de Pernambuco
> Morfologia e Anatomia Vegetal
>
> ----------
> > From: Chris Liner <cll@douze.geo.utulsa.edu>
> > To: nih-image@io.ece.drexel.edu
> > Cc: Chris Liner <cll@utulsa.edu>
> > Subject: Donation
> > Date: Quarta-feira, 07 Outubro, 1998 12:19
> >
> >
> >
> > I have developed a commercial seismic interpretation system
> > around NIH-Image.  The system is called Cubic and consists of
> > macros, external utility applications and documentation for
> > applying NIH-Image to visualize and interpret geophysical data.
> > Cubic includes an external gridding program that makes it useful
> > for many kinds of geophysical data (gravity, mag, conductivity, etc.)
> > as well as subsurface geology (structure maps, isopachs, etc.).
> > We use the system at U. of Tulsa to teach the fundamentals of 3D seismic
> > interpretation, including tracking, depth conversion, and
> > rock property estimation from seismic amplitude.
> >
> > Cubic currently in use by universities in Arkansas, Texas
> > and California.  I am interested in additional donations to a
> > U.S. universities before the end of the year.
> >
> > If anyone on the NIH-Image mail list is interested, please contact
> > me directly via email.
> >
> > Information about Cubic can be found at my web site listed below.
> >
> >
> > Dr. Christopher L. Liner
> > Associate Professor
> > Department of Geoscience
> > University of Tulsa
> > 600 S. College Ave
> > Tulsa, OK   74104-3189
> > ---------------------------
> > cll@utulsa.edu
> > http://douze.utulsa.edu/~cll/ChrisLiner.html
> > 918-631-3028   [phone]
> > 918-631-2091   [fax]
> >

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

Date: Fri, 9 Oct 1998 13:19:56 +0800
From: Mike Schon-Hegrad <mike@ichr.uwa.edu.au>
To: nih-image@io.ece.drexel.edu
Cc: karenw@ichr.uwa.edu.au
Subject: G3 Upgrade conflict with LG 3??
Message-Id: <v04011701b2434418ab5e@[130.95.224.88]>
Content-Type: text/plain; charset="us-ascii"

Hi all,

We've been running a successful project using NIH Image on an 8100/80AV
PowerMac with a Scion LG 3 card.

We'd like to upgrade the 8100/80AV to a G3 processor and are looking at the
MAXpower G3 cards for the 8100 from Newertech.

I'm just wondering if anyone else has done this, or if anyone can forsee
any problems with the Scion LG 3 card and this G3 configuration.

Thanks in advance,

Mike
-------------------------------------------------
Mike Schon-Hegrad (Macintosh Administrator)

Central IT Services
TVW Telethon Institute for Child Health Research
Perth, Western Australia
Company limited by guarantee
Phone 61 8 9340 7072         Fax 61 8 9388 3414

WWW: http://www.ichr.uwa.edu.au
-------------------------------------------------

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

Date: Fri, 9 Oct 1998 10:18:10 EDT
From: MASandberg@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Sprintscan plug-in error.
Message-ID: <86dd0702.361e1b22@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

With NIH Image 1.62b and a G3 Powerbook with 192 RAM I can scan one slide with
a Sprintscan 35 plug-in but get an "out of memory" error message when I try to
do a second scan.  If I quit and reopen NIH Image, I can then do the second
scan.  Any advice on how to fix this problem?

Thanks,
MAS

--------------------------------
End of nih-image-d Digest V98 Issue #84
***************************************

From nih-image-request@io.ece.drexel.edu Fri Oct  9 12:09 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA20912;
	Fri, 9 Oct 1998 12:09:23 -0400 (EDT)
Resent-Date: Fri, 9 Oct 1998 12:09:23 -0400 (EDT)
Message-Id: <l03130321b243dda90cc5@[128.196.130.192]>
Mime-Version: 1.0
Date: Fri, 9 Oct 1998 08:35:59 -0700
To: schlu@alpha.bio.nat.tu-bs.de
From: constance j temm <ctemm@Ag.Arizona.Edu>
Subject: Re: area of irregularly shaped ROI
Cc: nih-image@io.ece.drexel.edu
Resent-Message-ID: <"9nKKs2.0.yc4.o2Z7s"@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/479
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: 1365


Hi,

There may be quick ways of doing it at image resolution. Roughly, open
your ROI in an empty image. Fill your ROI with index 1, get its integrated
density.

Mathematically: You can find the centroid (C), calculate the area by
summing all the triangles ( cross product CP(i) and CP(i+1) i from 1 to N)
as you travel along the perimeter. This will handle even if the shape is
irregular, if you watch the signs. ( Do not forget to divide everything
by 2 at the end).

One word of caution, the coordinates that you get from NIH-Image ROI
might be off by 1 pixel at some locations. Please refer to earlier
discussions about ROI X-Y coordinate corrections.

Good Luck.

--------------------------------------------
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 Wed, 7 Oct 1998 frautsch@ucla.edu wrote:

> i have macros that  compute # and size of cells per unit area using oval or
> rectangular ROIs.
>
> If i draw an irregularly shaped ROI.  How do i compute the ROI area?
>
> Sally
>
>
>

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






From nih-image-request@io.ece.drexel.edu Fri Oct  9 12:53 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA25063;
	Fri, 9 Oct 1998 12:53:23 -0400 (EDT)
Resent-Date: Fri, 9 Oct 1998 12:53:23 -0400 (EDT)
Message-Id: <199810091634.MAA25321@codon.nih.gov>
X-Sender: tsuyoshi@codon.nih.gov (Unverified)
X-Mailer:  Macintosh Eudora Pro Version 2.1.4-J
Mime-Version: 1.0
Date: Fri, 9 Oct 1998 12:36:21 -0400
To: nih-image@io.ece.drexel.edu
From: tsuyoshi@codon.nih.gov (Tsuyoshi Miyakawa)
Subject: 1.62b30 and QT frame Grabber
Resent-Message-ID: <"rGHGw.0.dj5.gkZ7s"@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/480
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="ISO-2022-JP"
Content-Length: 940

Hi,

I am using powerbookG3 and QuickTime compatible
frame grabber, PicPomZV. When I was using NIH Image
1.61, I could not do 'start capturing' because of the
-2208 error. In version 1.62b30, 'start capturing'
works, the live images are perfectly displayed,
but  'make movie' does not work well. That is, when
I run 'make movie', blank rectangles are displayed
while capturing, and relulting stack only contains
completely black slices.

Has anyone expericed this kind of problem with
PicPomZV, or other frame grabbers, using 1.62b30?
If yes, any solutions ?

Thanks.

Tsuyoshi


________________________________________
Tsuyoshi Miyakawa, Ph. D.
Section on Behavioral Neuropharmacology
Experimental Therapeutics Branch
National Institute of Mental Health
Building 10 Room 4D11
Bethesda, MD 20892-1375
Lab phone#: 301-496-4838 or 301-496-4839
Lab fax#: 301-480-1164
E-mail  tsuyoshi@codon.nih.gov
________________________________________



From nih-image-d-request@io.ece.drexel.edu Sat Oct 10 06:14 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA17136;
	Sat, 10 Oct 1998 06:14:18 -0400 (EDT)
Date: Sat, 10 Oct 1998 06:14:18 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810101014.GAA17136@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #85
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/85
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 3302

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 85

Today's Topics:
  Re: area of irregularly shaped ROI    [ constance j temm <ctemm@Ag.Arizona. ]
  1.62b30 and QT frame Grabber          [ tsuyoshi@codon.nih.gov (Tsuyoshi Mi ]

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

Date: Fri, 9 Oct 1998 08:35:59 -0700
From: constance j temm <ctemm@Ag.Arizona.Edu>
To: schlu@alpha.bio.nat.tu-bs.de
Cc: nih-image@io.ece.drexel.edu
Subject: Re: area of irregularly shaped ROI
Message-Id: <l03130321b243dda90cc5@[128.196.130.192]>
Content-Type: text/plain; charset="us-ascii"

Hi,

There may be quick ways of doing it at image resolution. Roughly, open
your ROI in an empty image. Fill your ROI with index 1, get its integrated
density.

Mathematically: You can find the centroid (C), calculate the area by
summing all the triangles ( cross product CP(i) and CP(i+1) i from 1 to N)
as you travel along the perimeter. This will handle even if the shape is
irregular, if you watch the signs. ( Do not forget to divide everything
by 2 at the end).

One word of caution, the coordinates that you get from NIH-Image ROI
might be off by 1 pixel at some locations. Please refer to earlier
discussions about ROI X-Y coordinate corrections.

Good Luck.

--------------------------------------------
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 Wed, 7 Oct 1998 frautsch@ucla.edu wrote:

> i have macros that  compute # and size of cells per unit area using oval or
> rectangular ROIs.
>
> If i draw an irregularly shaped ROI.  How do i compute the ROI area?
>
> Sally
>
>
>

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

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

Date: Fri, 9 Oct 1998 12:36:21 -0400
From: tsuyoshi@codon.nih.gov (Tsuyoshi Miyakawa)
To: nih-image@io.ece.drexel.edu
Subject: 1.62b30 and QT frame Grabber
Message-Id: <199810091634.MAA25321@codon.nih.gov>
Content-Type: text/plain; charset="ISO-2022-JP"

Hi,

I am using powerbookG3 and QuickTime compatible
frame grabber, PicPomZV. When I was using NIH Image
1.61, I could not do 'start capturing' because of the
-2208 error. In version 1.62b30, 'start capturing'
works, the live images are perfectly displayed,
but  'make movie' does not work well. That is, when
I run 'make movie', blank rectangles are displayed
while capturing, and relulting stack only contains
completely black slices.

Has anyone expericed this kind of problem with
PicPomZV, or other frame grabbers, using 1.62b30?
If yes, any solutions ?

Thanks.

Tsuyoshi


________________________________________
Tsuyoshi Miyakawa, Ph. D.
Section on Behavioral Neuropharmacology
Experimental Therapeutics Branch
National Institute of Mental Health
Building 10 Room 4D11
Bethesda, MD 20892-1375
Lab phone#: 301-496-4838 or 301-496-4839
Lab fax#: 301-480-1164
E-mail  tsuyoshi@codon.nih.gov
________________________________________

--------------------------------
End of nih-image-d Digest V98 Issue #85
***************************************

From nih-image-request@io.ece.drexel.edu Mon Oct 12 08:57 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA21587;
	Mon, 12 Oct 1998 08:57:28 -0400 (EDT)
Resent-Date: Mon, 12 Oct 1998 08:57:28 -0400 (EDT)
From: srb22@hermes.cam.ac.uk
Date: Mon, 12 Oct 1998 13:46:53 +0000
To: nih-image@io.ece.drexel.edu
Subject: PCR band quantitation
Message-ID: <724841.3117188813@md8mac01.medschl.cam.ac.uk>
X-Mailer: Mulberry (MacOS) [1.3.2.2, s/n S-100001]
X-Authenticated: srb22 by imap.hermes.cam.ac.uk
X-Licensed-To: University of Cambridge
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"AHGIf.0.cc3.PZV8s"@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/481
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: 560

I was hoping someone could tell me how, after obtaining densitometry values
for PCR bands using NIH image (eth.bromide gels), I use this information
to compare the levels of PCR product between different samples. 
I wish to first adjust the PCR band densities for the band densities of a
housekeeping gene amplified in the same tube. I'm sampling the reaction at 5
different cycles, so both products will have timepoints in the linear range.

Thank you very much for any help
Yours sincerely
Sian Beavan

Research Associate
Dept Medicine
Cambridge University


From nih-image-request@io.ece.drexel.edu Mon Oct 12 17:48 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA02463;
	Mon, 12 Oct 1998 17:48:19 -0400 (EDT)
Resent-Date: Mon, 12 Oct 1998 17:48:19 -0400 (EDT)
X-Authentication-Warning: phoenix.princeton.edu: huntley owned process doing -bs
Date: 	Mon, 12 Oct 1998 17:31:22 -0400 (EDT)
From: "Mark B. Huntley" <huntley@phoenix.Princeton.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Need NUBUS Frame Grabber
Message-ID: <Pine.GSO.4.03.9810121720590.20887-100000@tucson.princeton.edu>
MIME-Version: 1.0
Resent-Message-ID: <"FQjmo1.0.KU6.7Ld8s"@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/482
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: 181


Looking for NUBUS frame grabber for Mac 8100 (Scion LG-3 or VG-5?).  If
you have one available, let me know (huntley@princeton.edu) and we'll
negotiate a price.  Thanks.

-Mark




From nih-image-d-request@io.ece.drexel.edu Tue Oct 13 06:14 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA10814;
	Tue, 13 Oct 1998 06:14:48 -0400 (EDT)
Date: Tue, 13 Oct 1998 06:14:48 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810131014.GAA10814@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #86
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/86
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 1733

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 86

Today's Topics:
  PCR band quantitation                 [ srb22@hermes.cam.ac.uk ]
  Need NUBUS Frame Grabber              [ "Mark B. Huntley" <huntley@phoenix. ]

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

Date: Mon, 12 Oct 1998 13:46:53 +0000
From: srb22@hermes.cam.ac.uk
To: nih-image@io.ece.drexel.edu
Subject: PCR band quantitation
Message-ID: <724841.3117188813@md8mac01.medschl.cam.ac.uk>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

I was hoping someone could tell me how, after obtaining densitometry values
for PCR bands using NIH image (eth.bromide gels), I use this information
to compare the levels of PCR product between different samples. 
I wish to first adjust the PCR band densities for the band densities of a
housekeeping gene amplified in the same tube. I'm sampling the reaction at 5
different cycles, so both products will have timepoints in the linear range.

Thank you very much for any help
Yours sincerely
Sian Beavan

Research Associate
Dept Medicine
Cambridge University

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

Date: 	Mon, 12 Oct 1998 17:31:22 -0400 (EDT)
From: "Mark B. Huntley" <huntley@phoenix.Princeton.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Need NUBUS Frame Grabber
Message-ID: <Pine.GSO.4.03.9810121720590.20887-100000@tucson.princeton.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Looking for NUBUS frame grabber for Mac 8100 (Scion LG-3 or VG-5?).  If
you have one available, let me know (huntley@princeton.edu) and we'll
negotiate a price.  Thanks.

-Mark

--------------------------------
End of nih-image-d Digest V98 Issue #86
***************************************

From nih-image-request@io.ece.drexel.edu Tue Oct 13 10:01 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA04833;
	Tue, 13 Oct 1998 10:01:07 -0400 (EDT)
Resent-Date: Tue, 13 Oct 1998 10:01:07 -0400 (EDT)
Message-Id: <v03020900b248a6b80350@[18.42.0.198]>
In-Reply-To: <199810131015.GAA11106@io.ece.drexel.edu>
Mime-Version: 1.0
Date: Tue, 13 Oct 1998 09:43:18 +0300
To: nih-image@io.ece.drexel.edu
From: Al Lyckman <lyckman@MIT.EDU>
Subject: unsubscribe me
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id JAA27547
Resent-Message-ID: <"ydecq1.0.vk6.RYr8s"@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/483
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="iso-8859-1"
Content-Length: 378

unsubscribe


           ......
         ''''''''''
        || || || || || ||
||||||||||||||||||||||||||||||||||||||||||||||

Alvin W. Lyckman, Ph.D.
Massachusetts Institute of Technology
Department of Brain & Cognitive Sciences
Building E25, Room 235
Cambridge, MA 02139
617.253.8785
lyckman@mit.edu

-- Tous je sais sur la moralit et nos devoirs vient du foot, A. Camus --



From nih-image-request@io.ece.drexel.edu Tue Oct 13 11:48 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA14549;
	Tue, 13 Oct 1998 11:48:10 -0400 (EDT)
Resent-Date: Tue, 13 Oct 1998 11:48:10 -0400 (EDT)
Message-Id: <s6232adf.015@psychiatry.wustl.edu>
X-Mailer: Novell GroupWise 5.2
Date: Tue, 13 Oct 1998 10:26:23 -0500
From: "Bob  Cormier" <cormierb@psychiatry.wustl.edu>
To: nih-image@io.ece.drexel.edu
Subject: LUT Scaling
Mime-Version: 1.0
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id LAA06287
Resent-Message-ID: <"x96AM1.0.dY1.a4t8s"@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/484
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: 361

Hi,
Does anyone have any ideas of how to set the lower and upper limits (calibrated values) for a LUT using macro commands.  For example, I have a series of real value images that have values ranging from .1 to 1.5 in one image, .2 to 2 in another image, and .18 to 1 in another.  How can I set the range of the LUT to .1 to 2 with macro commands?
Thanks,
Bob


From nih-image-request@io.ece.drexel.edu Tue Oct 13 15:18 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA04336;
	Tue, 13 Oct 1998 15:17:58 -0400 (EDT)
Resent-Date: Tue, 13 Oct 1998 15:17:58 -0400 (EDT)
From: "Andreas Becker" <becker@ps1515.chemie.uni-marburg.de>
Organization: =?ISO-8859-1?Q?Inst._f._Pharma./_Tox.;_Universit=E4t;_Marbur?=
To: nih-image@io.ece.drexel.edu
Date: Tue, 13 Oct 1998 20:51:37 +0200
MIME-Version: 1.0
Content-transfer-encoding: 7BIT
Subject: confocal laser scanning microscope 
Reply-to: becker@ps1515.chemie.uni-marburg.de
Priority: normal
In-reply-to: <l03130321b243dda90cc5@[128.196.130.192]>
X-mailer: Pegasus Mail for Win32 (v3.01b)
Message-ID: <919F76267@ps1515.chemie.uni-marburg.de>
Resent-Message-ID: <"xZgzE2.0.q86.V6w8s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/485
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: 334

Our institut is looking for a confocal laser scanning microscope 
with a UV-laser. Do you now any enterprises which distribute this 
kind of device. Do you already have any experience with a certain 
device. 
Please do not reply to the list. Send email to :

becker@ps1515.chemie.uni-marburg.de

Thanks for your help

Andreas Becker


From nih-image-request@io.ece.drexel.edu Wed Oct 14 04:41 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA15493;
	Wed, 14 Oct 1998 04:41:05 -0400 (EDT)
Resent-Date: Wed, 14 Oct 1998 04:41:05 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: cormierb@psychiatry.wustl.edu, nih-image@io.ece.drexel.edu
Date:          Wed, 14 Oct 1998 18:29:52 GMT+1000
Subject:       Re: LUT Scaling
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <B6DD9710195@rna.bio.mq.edu.au>
Resent-Message-ID: <"lq43H3.0.PU2.a169s"@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/486
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 5180

>Date: Tue, 13 Oct 1998 10:26:23 -0500
>From: "Bob  Cormier" <cormierb@psychiatry.wustl.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: LUT Scaling
>
>Hi,
>Does anyone have any ideas of how to set the lower and upper limits 
>(calibrated values) for a LUT using macro commands.  For example, I have a 
>series of real value images that have values ranging fr
>m .1 to 1.5 in one image, .2 to 2 in another image, and .18 to 1 in another.  
>How can I set the range of the LUT to .1 to 2 with macro commands?
>Thanks,
>Bob
>

Bob, 

Calibration sets the transformation used to convert pixel value to some 
external unit value. It doesn't directly affect the LUT.

macro'calibrate image';var desMax,desMin,min,max:real;
begin
desMax:=2;
desMin:=.1;
desMax:=getNumber('desired Maximum',desMax);
desMin:=getNumber('desired Minimum',desMin);
measure;
max:=rMax[rCount];min:=rMin[rCount]; 
calibrate('Straight', 'xxx',0,desmin,255,desMax);
showMessage(min,'<>',max,'\scaled to\',desMin,'<>',desMax);
end

will cause the end of the LUT corresponding to pixel value 255 to be desMax 
external units and 0 end to be desMin external units with linear interpolation.
If applied to a REAL-Value image, the real-value maximum and minimum as shown 
in the Info window or histogram will be calibrated or transformed to the values 
set by calibration, changing all real values read.

For your REAL-Value images, I expect that what you want to achieve is to have 
the same LUT for each of the images with a common minimum/maximum range.

     My understanding of NIH-Image support for REAL-Value images is that it 
doesn't extend that far. NIH-Image carries a REAL-Value image in memory 
(resulting from image-math etc) and displays an integer version of the real 
image the LUT of which is scaled so that min<>max = 0<>255.
There are some limitations with LUT modifications which arise because 0,255 
are used for min/maximum rather than 1,254.
(0,255 are reserved for many LUT operations).

You can do quite a bit of processing with the real-value image using NIH-Image 
imageMath and inspect values via Info window and Histogram, save, save as text 
etc but the visual presentation is actually an integer proxy.

'Duplicate' makes a copy of the scaled integer proxy, so, for intensity-scaled 
presentation, you could make the integer version of each real by 'duplicate' 
and then scale the presented intensity by scaling the pixel values of each 
image.
ie multiply by ratio of actual range:desired range; add scaled offset.

macro'real image to scaled integer intensity';
var desMax,desMin,min,max:real;
begin
desMax:=2;
desMin:=.1;
desMax:=getNumber('desired Maximum',desMax);
desMin:=getNumber('desired Minimum',desMin);
measure;
max:=rMax[rCount];min:=rMin[rCount]; 
duplicate(windowTitle,'.scaled');
multiplyByConstant((max-min)/(desMax-desMin));
addConstant((min-desMin)/(desMax-desMin)*255);
showMessage(min,'<>',max,'\scaled to\',desMin,'<>',desMax);
end

Although you would then have the intensities scaled to the real-value of the 
coresponding real pixel, the image would be a separated integer image proxy and 
the real-values would not be displayed when you inspect the image by cursor.


Another approach which would be better, if processing accomodates it, would be 
to include (generate) pixels of the desired maximum/minimum in each real image 
so that the real image and its proxy integer presentation are scaled desirably.
eg ensure topleft and adjacent pixels are the desired maximum/minimum 
real values. This involves the detail of the real image generation.

 As far as I know, there is no simple way of grafting such values into an 
existing real image eg by putPixel or paste etc. so that the appropriate values 
would need to be inserted in processing.

The following is more of a sledgehammer approach but achieves the desired 
result at the expense of some time and 2 pixels of the real image.
(provided desMax/desMin are at least equal to max/min).
It inserts the desired maximum/minimum real values into the two topleft and 
adjacent pixels by using masks and scaling via imagemath.

macro'scale real image';
var desMax,desMin:real;w,h,p,t,m:integer;
begin
desMax:=2;
desMin:=.1;
desMax:=getNumber('desired Maximum',desMax);
desMin:=getNumber('desired Minimum',desMin);
p:=pidNumber;
getPicSize(w,h);setNewSize(w,h);
setBackGround(1);
makeNewWindow('temp');t:=pidNumber;
putPixel(0,0,0);
putPixel(1,0,0);
imageMath('copy real',t,t,1,0,'mask');m:=pidNumber;
imageMath('mul real',p,m,1,0,p); {clears topleft and adjacent pixels}
selectPic(t);setBackGround(0);clear;putPixel(0,0,1);
imageMath('copy real',t,t,desMax,0,m);
imageMath('add real',p,m,1,0,p); {inserts desMax in topleft}
if desMin<>0.0 then begin
  selectPic(t);putPixel(0,0,0);putPixel(1,0,1);
  imageMath('copy real',t,t,desMin,0,m);
  imageMath('add real',p,m,1,0,p); {inserts desMin in adjacent topleft}
  end;
selectPic(t);dispose;selectPic(m);dispose;selectPic(p);
showMessage('scaled to\',desMin,'<>',desMax);
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-d-request@io.ece.drexel.edu Wed Oct 14 04:44 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA16824;
	Wed, 14 Oct 1998 04:44:35 -0400 (EDT)
Date: Wed, 14 Oct 1998 04:44:35 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810140844.EAA16824@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #87
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/87
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 7992

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 87

Today's Topics:
  unsubscribe me                        [ Al Lyckman <lyckman@mit.edu> ]
  LUT Scaling                           [ "Bob Cormier" <cormierb@psychiatry. ]
  confocal laser scanning microscope    [ "Andreas Becker" <becker@ps1515.che ]
  Re: LUT Scaling                       [ GJOSS@rna.bio.mq.edu.au ]

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

Date: Tue, 13 Oct 1998 09:43:18 +0300
From: Al Lyckman <lyckman@mit.edu>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe me
Message-Id: <v03020900b248a6b80350@[18.42.0.198]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

unsubscribe


           ......
         ''''''''''
        || || || || || ||
||||||||||||||||||||||||||||||||||||||||||||||

Alvin W. Lyckman, Ph.D.
Massachusetts Institute of Technology
Department of Brain & Cognitive Sciences
Building E25, Room 235
Cambridge, MA 02139
617.253.8785
lyckman@mit.edu

-- Tous je sais sur la moralit et nos devoirs vient du foot, A. Camus --

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

Date: Tue, 13 Oct 1998 10:26:23 -0500
From: "Bob  Cormier" <cormierb@psychiatry.wustl.edu>
To: nih-image@io.ece.drexel.edu
Subject: LUT Scaling
Message-Id: <s6232adf.015@psychiatry.wustl.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline
Content-Transfer-Encoding: 8bit

Hi,
Does anyone have any ideas of how to set the lower and upper limits (calibrated values) for a LUT using macro commands.  For example, I have a series of real value images that have values ranging from .1 to 1.5 in one image, .2 to 2 in another image, and .18 to 1 in another.  How can I set the range of the LUT to .1 to 2 with macro commands?
Thanks,
Bob

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

Date: Tue, 13 Oct 1998 20:51:37 +0200
From: "Andreas Becker" <becker@ps1515.chemie.uni-marburg.de>
To: nih-image@io.ece.drexel.edu
Subject: confocal laser scanning microscope 
Message-ID: <919F76267@ps1515.chemie.uni-marburg.de>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7BIT

Our institut is looking for a confocal laser scanning microscope 
with a UV-laser. Do you now any enterprises which distribute this 
kind of device. Do you already have any experience with a certain 
device. 
Please do not reply to the list. Send email to :

becker@ps1515.chemie.uni-marburg.de

Thanks for your help

Andreas Becker

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

Date:          Wed, 14 Oct 1998 18:29:52 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: cormierb@psychiatry.wustl.edu, nih-image@io.ece.drexel.edu
Subject:       Re: LUT Scaling
Message-ID: <B6DD9710195@rna.bio.mq.edu.au>

>Date: Tue, 13 Oct 1998 10:26:23 -0500
>From: "Bob  Cormier" <cormierb@psychiatry.wustl.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: LUT Scaling
>
>Hi,
>Does anyone have any ideas of how to set the lower and upper limits 
>(calibrated values) for a LUT using macro commands.  For example, I have a 
>series of real value images that have values ranging fr
>m .1 to 1.5 in one image, .2 to 2 in another image, and .18 to 1 in another.  
>How can I set the range of the LUT to .1 to 2 with macro commands?
>Thanks,
>Bob
>

Bob, 

Calibration sets the transformation used to convert pixel value to some 
external unit value. It doesn't directly affect the LUT.

macro'calibrate image';var desMax,desMin,min,max:real;
begin
desMax:=2;
desMin:=.1;
desMax:=getNumber('desired Maximum',desMax);
desMin:=getNumber('desired Minimum',desMin);
measure;
max:=rMax[rCount];min:=rMin[rCount]; 
calibrate('Straight', 'xxx',0,desmin,255,desMax);
showMessage(min,'<>',max,'\scaled to\',desMin,'<>',desMax);
end

will cause the end of the LUT corresponding to pixel value 255 to be desMax 
external units and 0 end to be desMin external units with linear interpolation.
If applied to a REAL-Value image, the real-value maximum and minimum as shown 
in the Info window or histogram will be calibrated or transformed to the values 
set by calibration, changing all real values read.

For your REAL-Value images, I expect that what you want to achieve is to have 
the same LUT for each of the images with a common minimum/maximum range.

     My understanding of NIH-Image support for REAL-Value images is that it 
doesn't extend that far. NIH-Image carries a REAL-Value image in memory 
(resulting from image-math etc) and displays an integer version of the real 
image the LUT of which is scaled so that min<>max = 0<>255.
There are some limitations with LUT modifications which arise because 0,255 
are used for min/maximum rather than 1,254.
(0,255 are reserved for many LUT operations).

You can do quite a bit of processing with the real-value image using NIH-Image 
imageMath and inspect values via Info window and Histogram, save, save as text 
etc but the visual presentation is actually an integer proxy.

'Duplicate' makes a copy of the scaled integer proxy, so, for intensity-scaled 
presentation, you could make the integer version of each real by 'duplicate' 
and then scale the presented intensity by scaling the pixel values of each 
image.
ie multiply by ratio of actual range:desired range; add scaled offset.

macro'real image to scaled integer intensity';
var desMax,desMin,min,max:real;
begin
desMax:=2;
desMin:=.1;
desMax:=getNumber('desired Maximum',desMax);
desMin:=getNumber('desired Minimum',desMin);
measure;
max:=rMax[rCount];min:=rMin[rCount]; 
duplicate(windowTitle,'.scaled');
multiplyByConstant((max-min)/(desMax-desMin));
addConstant((min-desMin)/(desMax-desMin)*255);
showMessage(min,'<>',max,'\scaled to\',desMin,'<>',desMax);
end

Although you would then have the intensities scaled to the real-value of the 
coresponding real pixel, the image would be a separated integer image proxy and 
the real-values would not be displayed when you inspect the image by cursor.


Another approach which would be better, if processing accomodates it, would be 
to include (generate) pixels of the desired maximum/minimum in each real image 
so that the real image and its proxy integer presentation are scaled desirably.
eg ensure topleft and adjacent pixels are the desired maximum/minimum 
real values. This involves the detail of the real image generation.

 As far as I know, there is no simple way of grafting such values into an 
existing real image eg by putPixel or paste etc. so that the appropriate values 
would need to be inserted in processing.

The following is more of a sledgehammer approach but achieves the desired 
result at the expense of some time and 2 pixels of the real image.
(provided desMax/desMin are at least equal to max/min).
It inserts the desired maximum/minimum real values into the two topleft and 
adjacent pixels by using masks and scaling via imagemath.

macro'scale real image';
var desMax,desMin:real;w,h,p,t,m:integer;
begin
desMax:=2;
desMin:=.1;
desMax:=getNumber('desired Maximum',desMax);
desMin:=getNumber('desired Minimum',desMin);
p:=pidNumber;
getPicSize(w,h);setNewSize(w,h);
setBackGround(1);
makeNewWindow('temp');t:=pidNumber;
putPixel(0,0,0);
putPixel(1,0,0);
imageMath('copy real',t,t,1,0,'mask');m:=pidNumber;
imageMath('mul real',p,m,1,0,p); {clears topleft and adjacent pixels}
selectPic(t);setBackGround(0);clear;putPixel(0,0,1);
imageMath('copy real',t,t,desMax,0,m);
imageMath('add real',p,m,1,0,p); {inserts desMax in topleft}
if desMin<>0.0 then begin
  selectPic(t);putPixel(0,0,0);putPixel(1,0,1);
  imageMath('copy real',t,t,desMin,0,m);
  imageMath('add real',p,m,1,0,p); {inserts desMin in adjacent topleft}
  end;
selectPic(t);dispose;selectPic(m);dispose;selectPic(p);
showMessage('scaled to\',desMin,'<>',desMax);
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

--------------------------------
End of nih-image-d Digest V98 Issue #87
***************************************

From nih-image-request@io.ece.drexel.edu Thu Oct 15 03:50 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id DAA09974;
	Thu, 15 Oct 1998 03:50:23 -0400 (EDT)
Resent-Date: Thu, 15 Oct 1998 03:50:23 -0400 (EDT)
Mime-Version: 1.0
X-Sender: mantv@alf.uib.no
Message-Id: <v04011701b24b5fb2ae6d@[129.177.231.35]>
Date: Thu, 15 Oct 1998 09:36:38 +0100
To: nih-image@io.ece.drexel.edu
From: Therese Visted <therese.visted@pki.uib.no>
Subject: nih-image
Resent-Message-ID: <"ZscgU3.0.201.ZMQ9s"@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/487
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: 215


My efforts in trying to find the latest version of nih-image has not succeeded.
Could you please help me in getting that information?
Also, how do I get the latest version of nih-image (what url/http/ftp adress)?


From nih-image-request@io.ece.drexel.edu Thu Oct 15 03:50 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id DAA09948;
	Thu, 15 Oct 1998 03:50:20 -0400 (EDT)
Resent-Date: Thu, 15 Oct 1998 03:50:20 -0400 (EDT)
Mime-Version: 1.0
X-Sender: mantv@alf.uib.no (Unverified)
Message-Id: <v04011700b24b6536fa23@[129.177.231.35]>
Date: Thu, 15 Oct 1998 09:41:00 +0100
To: nih-image@io.ece.drexel.edu
From: Therese Visted <therese.visted@pki.uib.no>
Subject: nih-image
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id DAA05640
Resent-Message-ID: <"zaJvJ3.0.TO1.ZQQ9s"@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/488
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="iso-8859-1"
Content-Length: 370


My efforts in trying to find the latest version of nih-image has not succeeded.
Could you please help me in getting that information?
Also, how do I get the latest version of nih-image (what url/http/ftp adress)?
Thank you!
Therese Visted

Institutt for Anatomi og Cellebiologi
rstadveien 19
5009 Bergen

tlf:55-586373
fax:55-586360

e-mail:therese.visted@pki.uib.no


From nih-image-request@io.ece.drexel.edu Thu Oct 15 05:23 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA13636;
	Thu, 15 Oct 1998 05:23:32 -0400 (EDT)
Resent-Date: Thu, 15 Oct 1998 05:23:32 -0400 (EDT)
Message-Id: <199810150906.GAA02006@ceiun01.elogica.com.br>
From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" <ggalindo@elogica.com.br>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: nih-image
Date: Thu, 15 Oct 1998 06:10:26 -0300
X-MSMail-Priority: Normal
X-Priority: 3
X-Mailer: Microsoft Internet Mail 4.70.1155
MIME-Version: 1.0
Content-Transfer-Encoding: 8bit
Resent-Message-ID: <"dlbfe2.0.862.5mR9s"@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/489
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset=ISO-8859-1
Content-Length: 692

Dear Therese,
you can find ScionImage (NIH) in this adress:

http//:www.scioncorp.com
I hope this help
Regards,
Rejane
----------
> De: Therese Visted <therese.visted@pki.uib.no>
> Para: nih-image@io.ece.drexel.edu
> Assunto: nih-image
> Data: Quinta-feira, 15 de Outubro de 1998 05:41
> 
> 
> My efforts in trying to find the latest version of nih-image has not
succeeded.
> Could you please help me in getting that information?
> Also, how do I get the latest version of nih-image (what url/http/ftp
adress)?
> Thank you!
> Therese Visted
> 
> Institutt for Anatomi og Cellebiologi
> rstadveien 19
> 5009 Bergen
> 
> tlf:55-586373
> fax:55-586360
> 
> e-mail:therese.visted@pki.uib.no
> 


From nih-image-request@io.ece.drexel.edu Thu Oct 15 05:53 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA24669;
	Thu, 15 Oct 1998 05:53:45 -0400 (EDT)
Resent-Date: Thu, 15 Oct 1998 05:53:45 -0400 (EDT)
X-Sender: steinr@pop.chembio.ntnu.no
Message-Id: <v0310280eb24b72fb9f57@[129.241.39.133]>
In-Reply-To: <v04011700b24b6536fa23@[129.177.231.35]>
Mime-Version: 1.0
Date: Thu, 15 Oct 1998 11:41:41 +0200
To: nih-image@io.ece.drexel.edu
From: Stein Roervik <steinr@chembio.ntnu.no>
Subject: Re: nih-image
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id FAA19966
Resent-Message-ID: <"Ra2AB2.0.Nu4.1DS9s"@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/490
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="iso-8859-1"
Content-Length: 1055

>My efforts in trying to find the latest version of nih-image has not
>succeeded.
>Could you please help me in getting that information?
>Also, how do I get the latest version of nih-image (what url/http/ftp adress)?
>Thank you!
>Therese Visted
>
>Institutt for Anatomi og Cellebiologi
>rstadveien 19
>5009 Bergen
>
>tlf:55-586373
>fax:55-586360
>
>e-mail:therese.visted@pki.uib.no

http://rsb.info.nih.gov/nih-image/

Jeg bruker programmet svrt mye s du kan ringe eller maile om det er noe
du lurer p. Jeg bruker Mac versjonen. PC versjonen er full av feil og bugs.


+---------------------------------------------------------+
|  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 Oct 15 12:03 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA05877;
	Thu, 15 Oct 1998 12:02:40 -0400 (EDT)
Resent-Date: Thu, 15 Oct 1998 12:02:40 -0400 (EDT)
Date: Thu, 15 Oct 1998 16:32:15 +0100
From: Ranjan Kumar Patro <Ranjan.Patro@UCG.IE>
Subject: DT- Image
In-reply-to: <v0310280eb24b72fb9f57@[129.241.39.133]>
X-Sender: 9698842p@bodkin.ucg.ie (Unverified)
To: nih-image@io.ece.drexel.edu
Message-id: <l03130301b24bc50427d7@[140.203.36.9]>
MIME-version: 1.0
References: <v04011700b24b6536fa23@[129.177.231.35]>
Resent-Message-ID: <"5VKk71.0.Ll6.TSX9s"@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/491
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: 772

Hello Every body!!
I am trying to capture the image by DT board.
Does any body know, where can I get the DT-IMAGE  software from internt or
by FTP.
Thank you in advance.
Ranjan

*****************************************************
*Ranjan Kumar Patro                                     *
*Dept. Of Oceanography                                *
*Martin Ryan  Institute of Marine Sciences  *
*National University of Ireland, Galway       *
*Ireland.                                                        *
*   Voic:  ++353 91 524411, Xt: 3208            *
*     Fax:  ++353 91 528302                           *
*E-mail: ranjan.patro@ucg.ie                         *
*    Web: http://www.angelfire.com/ri/rpatro*
*******************************************************



From nih-image-request@io.ece.drexel.edu Thu Oct 15 17:10 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA03052;
	Thu, 15 Oct 1998 17:09:40 -0400 (EDT)
Resent-Date: Thu, 15 Oct 1998 17:09:40 -0400 (EDT)
Subject: Frame Grabber
Date: Thu, 15 Oct 98 16:49:02 -0400
x-sender: jlr$biol.biol.qc@qc1.qc.edu
x-mailer: Claris Emailer 1.1
From: "Jared L. Rifkin" <jared_rifkin@qc.edu>
To: "anyone" <nih-image@io.ece.drexel.edu>
Mime-Version: 1.0
Message-ID: <2A4E40E154B@qc1.qc.edu>
Resent-Message-ID: <"apETW1.0.wB.e_b9s"@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/492
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: 195

please give me name, address (snailmail or web), phone # of manufacturer 
of scion video card; also of other high resolution videocards.  FOR MAC 
ONLY. 
many thanks in advance for information.


From nih-image-request@io.ece.drexel.edu Thu Oct 15 17:10 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA03305;
	Thu, 15 Oct 1998 17:10:45 -0400 (EDT)
Resent-Date: Thu, 15 Oct 1998 17:10:45 -0400 (EDT)
Subject: Re: Need NUBUS Frame Grabber
Date: Thu, 15 Oct 98 16:50:31 -0400
x-sender: jlr$biol.biol.qc@qc1.qc.edu
x-mailer: Claris Emailer 1.1
From: "Jared L. Rifkin" <jared_rifkin@qc.edu>
To: "anyone" <nih-image@io.ece.drexel.edu>
Mime-Version: 1.0
Message-ID: <2A4EA244E65@qc1.qc.edu>
Resent-Message-ID: <"CiIXu.0.UE.p0c9s"@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/493
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: 55

please give me name,address,phone for manufacturer of


From nih-image-d-request@io.ece.drexel.edu Fri Oct 16 06:22 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA24499;
	Fri, 16 Oct 1998 06:22:06 -0400 (EDT)
Date: Fri, 16 Oct 1998 06:22:06 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810161022.GAA24499@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #88
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/88
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 6174

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 88

Today's Topics:
  nih-image                             [ Therese Visted <therese.visted@pki. ]
  nih-image                             [ Therese Visted <therese.visted@pki. ]
  Re: nih-image                         [ "=?ISO-8859-1?Q?Rejane_Magalh=E3es_ ]
  Re: nih-image                         [ Stein Roervik <steinr@chembio.ntnu. ]
  DT- Image                             [ Ranjan Kumar Patro <Ranjan.Patro@UC ]
  Frame Grabber                         [ "Jared L. Rifkin" <jared_rifkin@qc. ]
  Re: Need NUBUS Frame Grabber          [ "Jared L. Rifkin" <jared_rifkin@qc. ]

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

Date: Thu, 15 Oct 1998 09:36:38 +0100
From: Therese Visted <therese.visted@pki.uib.no>
To: nih-image@io.ece.drexel.edu
Subject: nih-image
Message-Id: <v04011701b24b5fb2ae6d@[129.177.231.35]>
Content-Type: text/plain; charset="us-ascii"

My efforts in trying to find the latest version of nih-image has not succeeded.
Could you please help me in getting that information?
Also, how do I get the latest version of nih-image (what url/http/ftp adress)?

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

Date: Thu, 15 Oct 1998 09:41:00 +0100
From: Therese Visted <therese.visted@pki.uib.no>
To: nih-image@io.ece.drexel.edu
Subject: nih-image
Message-Id: <v04011700b24b6536fa23@[129.177.231.35]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

My efforts in trying to find the latest version of nih-image has not succeeded.
Could you please help me in getting that information?
Also, how do I get the latest version of nih-image (what url/http/ftp adress)?
Thank you!
Therese Visted

Institutt for Anatomi og Cellebiologi
rstadveien 19
5009 Bergen

tlf:55-586373
fax:55-586360

e-mail:therese.visted@pki.uib.no

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

Date: Thu, 15 Oct 1998 06:10:26 -0300
From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" <ggalindo@elogica.com.br>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: nih-image
Message-Id: <199810150906.GAA02006@ceiun01.elogica.com.br>
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 8bit

Dear Therese,
you can find ScionImage (NIH) in this adress:

http//:www.scioncorp.com
I hope this help
Regards,
Rejane
----------
> De: Therese Visted <therese.visted@pki.uib.no>
> Para: nih-image@io.ece.drexel.edu
> Assunto: nih-image
> Data: Quinta-feira, 15 de Outubro de 1998 05:41
> 
> 
> My efforts in trying to find the latest version of nih-image has not
succeeded.
> Could you please help me in getting that information?
> Also, how do I get the latest version of nih-image (what url/http/ftp
adress)?
> Thank you!
> Therese Visted
> 
> Institutt for Anatomi og Cellebiologi
> rstadveien 19
> 5009 Bergen
> 
> tlf:55-586373
> fax:55-586360
> 
> e-mail:therese.visted@pki.uib.no
> 

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

Date: Thu, 15 Oct 1998 11:41:41 +0200
From: Stein Roervik <steinr@chembio.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image
Message-Id: <v0310280eb24b72fb9f57@[129.241.39.133]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

>My efforts in trying to find the latest version of nih-image has not
>succeeded.
>Could you please help me in getting that information?
>Also, how do I get the latest version of nih-image (what url/http/ftp adress)?
>Thank you!
>Therese Visted
>
>Institutt for Anatomi og Cellebiologi
>rstadveien 19
>5009 Bergen
>
>tlf:55-586373
>fax:55-586360
>
>e-mail:therese.visted@pki.uib.no

http://rsb.info.nih.gov/nih-image/

Jeg bruker programmet svrt mye s du kan ringe eller maile om det er noe
du lurer p. Jeg bruker Mac versjonen. PC versjonen er full av feil og bugs.


+---------------------------------------------------------+
|  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, 15 Oct 1998 16:32:15 +0100
From: Ranjan Kumar Patro <Ranjan.Patro@UCG.IE>
To: nih-image@io.ece.drexel.edu
Subject: DT- Image
Message-id: <l03130301b24bc50427d7@[140.203.36.9]>
Content-type: text/plain; charset="us-ascii"

Hello Every body!!
I am trying to capture the image by DT board.
Does any body know, where can I get the DT-IMAGE  software from internt or
by FTP.
Thank you in advance.
Ranjan

*****************************************************
*Ranjan Kumar Patro                                     *
*Dept. Of Oceanography                                *
*Martin Ryan  Institute of Marine Sciences  *
*National University of Ireland, Galway       *
*Ireland.                                                        *
*   Voic:  ++353 91 524411, Xt: 3208            *
*     Fax:  ++353 91 528302                           *
*E-mail: ranjan.patro@ucg.ie                         *
*    Web: http://www.angelfire.com/ri/rpatro*
*******************************************************

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

Date: Thu, 15 Oct 98 16:49:02 -0400
From: "Jared L. Rifkin" <jared_rifkin@qc.edu>
To: "anyone" <nih-image@io.ece.drexel.edu>
Subject: Frame Grabber
Message-ID: <2A4E40E154B@qc1.qc.edu>
Content-Type: text/plain; charset="US-ASCII"

please give me name, address (snailmail or web), phone # of manufacturer 
of scion video card; also of other high resolution videocards.  FOR MAC 
ONLY. 
many thanks in advance for information.

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

Date: Thu, 15 Oct 98 16:50:31 -0400
From: "Jared L. Rifkin" <jared_rifkin@qc.edu>
To: "anyone" <nih-image@io.ece.drexel.edu>
Subject: Re: Need NUBUS Frame Grabber
Message-ID: <2A4EA244E65@qc1.qc.edu>
Content-Type: text/plain; charset="US-ASCII"

please give me name,address,phone for manufacturer of

--------------------------------
End of nih-image-d Digest V98 Issue #88
***************************************

From nih-image-request@io.ece.drexel.edu Fri Oct 16 06:53 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA01851;
	Fri, 16 Oct 1998 06:53:47 -0400 (EDT)
Resent-Date: Fri, 16 Oct 1998 06:53:47 -0400 (EDT)
Message-ID: <01BDF8F8.D61A2F20.t.morris@co.umist.ac.uk>
From: Tim Morris <t.morris@sna.co.umist.ac.uk>
Reply-To: "t.morris@co.umist.ac.uk" <t.morris@sna.co.umist.ac.uk>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: DT-Image
Date: Fri, 16 Oct 1998 11:33:45 +0100
Organization: UMIST
X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"29f-T2.0.tg6.Q4o9s"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/494
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: 630

Ranjan, et al.

I'm using the DT3155 at present. The useful software came with it. But we also had problems setting up the board correctly,
our local distributors were very helpful (sending us updated software etc), and so was the DT website: www.datx.com

Tim.

---------------------------------------------------------------------------------
Dr Tim Morris
Dept of Computation, UMIST, PO Box 88 Manchester, M60 1QD, UK
tel: 0161 200 3376                                              fax: 0161 200 3300
http://www.ap.co.umist.ac.uk/~dtm/IP1.html
---------------------------------------------------------------------------------


From nih-image-request@io.ece.drexel.edu Fri Oct 16 16:37 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA19970;
	Fri, 16 Oct 1998 16:37:24 -0400 (EDT)
Resent-Date: Fri, 16 Oct 1998 16:37:24 -0400 (EDT)
X-Authentication-Warning: pagan.vims.edu: cutter owned process doing -bs
Date: Fri, 16 Oct 1998 16:11:34 -0400 (EDT)
From: Randy Cutter <cutter@vims.edu>
To: nih-image@io.ece.drexel.edu
cc: nih-image-d@io.ece.drexel.edu
Subject: Object-Image: deleting objects, not entire cells
In-Reply-To: <199810021551.LAA02635@io.ece.drexel.edu>
Message-ID: <Pine.SOL.3.96.981016160150.11446A-100000@pagan.vims.edu>
MIME-Version: 1.0
Resent-Message-ID: <"4ZxNE2.0.C_1.TYw9s"@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/495
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: 621


When using Object-Image, is there a way to delete individual objects
within a cell?  There are macro commands SelectCell, SelectObject,
DeleteCell, but apparently no DeleteObject.  Is there a way around this,
because if a cell contains multiple objects, and a mistake is made upon an
object, once the cell is closed, apparently the whole cell must be deleted
if only one object needs to be.  

Thanks,

Randy.

---------------------
Randy Cutter
Virginia Institute of Marine Science
Route 1208 
Gloucester Point, VA 23062 USA

phone 804 684-7365
fax 804 684-7399 or 7045
email:  cutter@vims.edu

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



From nih-image-d-request@io.ece.drexel.edu Sat Oct 17 06:09 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA18246;
	Sat, 17 Oct 1998 06:09:31 -0400 (EDT)
Date: Sat, 17 Oct 1998 06:09:31 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810171009.GAA18246@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #89
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/89
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 2326

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 89

Today's Topics:
  RE: DT-Image                          [ Tim Morris <t.morris@sna.co.umist.a ]
  Object-Image: deleting objects, not   [ Randy Cutter <cutter@vims.edu> ]

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

Date: Fri, 16 Oct 1998 11:33:45 +0100
From: Tim Morris <t.morris@sna.co.umist.ac.uk>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: DT-Image
Message-ID: <01BDF8F8.D61A2F20.t.morris@co.umist.ac.uk>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

Ranjan, et al.

I'm using the DT3155 at present. The useful software came with it. But we also had problems setting up the board correctly,
our local distributors were very helpful (sending us updated software etc), and so was the DT website: www.datx.com

Tim.

---------------------------------------------------------------------------------
Dr Tim Morris
Dept of Computation, UMIST, PO Box 88 Manchester, M60 1QD, UK
tel: 0161 200 3376                                              fax: 0161 200 3300
http://www.ap.co.umist.ac.uk/~dtm/IP1.html
---------------------------------------------------------------------------------

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

Date: Fri, 16 Oct 1998 16:11:34 -0400 (EDT)
From: Randy Cutter <cutter@vims.edu>
To: nih-image@io.ece.drexel.edu
cc: nih-image-d@io.ece.drexel.edu
Subject: Object-Image: deleting objects, not entire cells
Message-ID: <Pine.SOL.3.96.981016160150.11446A-100000@pagan.vims.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

When using Object-Image, is there a way to delete individual objects
within a cell?  There are macro commands SelectCell, SelectObject,
DeleteCell, but apparently no DeleteObject.  Is there a way around this,
because if a cell contains multiple objects, and a mistake is made upon an
object, once the cell is closed, apparently the whole cell must be deleted
if only one object needs to be.  

Thanks,

Randy.

---------------------
Randy Cutter
Virginia Institute of Marine Science
Route 1208 
Gloucester Point, VA 23062 USA

phone 804 684-7365
fax 804 684-7399 or 7045
email:  cutter@vims.edu

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

--------------------------------
End of nih-image-d Digest V98 Issue #89
***************************************

From nih-image-request@io.ece.drexel.edu Sat Oct 17 08:03 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA29593;
	Sat, 17 Oct 1998 08:03:02 -0400 (EDT)
Resent-Date: Sat, 17 Oct 1998 08:03:02 -0400 (EDT)
Date: Sat, 17 Oct 1998 08:50:00 -0300 (ADT)
X-Sender: rhawkes@mailserv.mta.ca
Message-Id: <v01530500b24e09ba39c4@[207.179.158.169]>
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
From: rhawkes@mta.ca (Robert Hawkes)
Subject: looking for fast 25 mm C mount lens
Resent-Message-ID: <"mVOnM.0.B16.jH8As"@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/496
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: 647

I am sorry if this is not directly an NIH Image posting, but we desperately
need to find a source of fast 25 mm C mount lens which can deliver in the
next 10 days.  Preferably, Fujinon C25L (25 mm /f0.85).  All of our regular
suppliers have these backordered by Fujinon for end November, and we need
to ship them for use in a meteor field campaign in Mongolia much earlier
than that.  Any suggestions, those who might have one to sell, etc.
directly to me at
rhawkes@mta.ca
would be appreciated.  We certainly would consider used lenses, if in good
condition.
 Bob Hawkes
 rhawkes@mta.ca
 Physics, Mount Allison University
 Sackville, NB Canada



From nih-image-request@io.ece.drexel.edu Sat Oct 17 09:41 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA04997;
	Sat, 17 Oct 1998 09:41:05 -0400 (EDT)
Resent-Date: Sat, 17 Oct 1998 09:41:05 -0400 (EDT)
Message-ID: <3628A94B.D7A183D3@netmatters.co.uk>
Date: Sat, 17 Oct 1998 14:27:30 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
Reply-To: brownj@netmatters.co.uk
Organization: brownj@netmatters.co.uk
X-Mailer: Mozilla 4.05 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Advise on a commercial product
References: <AED34A57E24@rna.bio.mq.edu.au>
Content-Transfer-Encoding: 8bit
Resent-Message-ID: <"zfDtx3.0.G6.Lk9As"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/497
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset=iso-8859-1; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length: 1101

Hello all,

Sorry to bother you with a non-Image related question but, Has anyone ever
come across a Mac imaging package called Open Lab 2.0 by Improvision. Someone at
the University here is considering purchasing a set-up from them (38 000:
Camera, Z-Focus control, Mac, Software, No Microscope or objectives).
Improvision are claiming that their software can produce con focal images from a
standard fluorescent or white light source by mathematical de-convolution of a z
series of standard images to discard the out of focus information in much the
same way as the optics of a con focal would. To me it sounds possible, but I can
not imagine that it would be as good as the real thing. They are not giving the
module that performs this function away as a demo, for obvious reasons if it
really works. Any
thoughts on the plausibility of this?

Many Thanks in advance,

Jeremy



************************************************
Jeremy Brown
Edinburgh University/Moredun Research Institute
http://www.netmatters.co.uk/users/brownj/HomePage.html
************************************************





From nih-image-request@io.ece.drexel.edu Sat Oct 17 16:47 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA27069;
	Sat, 17 Oct 1998 16:47:19 -0400 (EDT)
Resent-Date: Sat, 17 Oct 1998 16:47:19 -0400 (EDT)
Message-ID: <001f01bdfa0e$2263e4a0$LocalHost@MSN/rchristie>
From: "rchristie" <rchristie@email.msn.com>
To: <nih-image@io.ece.drexel.edu>
Subject: BioRad 1024 z-series
Date: Sat, 17 Oct 1998 16:38:43 -0400
X-Priority: 3
X-MSMail-Priority: Normal
X-Mailer: Microsoft Outlook Express 4.72.2120.0
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2120.0
Resent-Message-ID: <"aIg_u1.0.WK5.6zFAs"@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/498
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 418

I've been using NIH-image to manipulate stacks generated by a BioRad 1024
confocal system.  They are easy enough to open up and play with, but I'm
wondering if anyone has seen a macro to re-save the stack in the BioRad
format, with the header appropriately modified.

Any help would be appreciated,

Rich Christie
rchristie@msn.com
Alzheimer's Research
CNY 6320
Massachusetts General Hospital
Charlestown, MA 02129




From nih-image-d-request@io.ece.drexel.edu Sun Oct 18 06:22 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA00210;
	Sun, 18 Oct 1998 06:22:11 -0400 (EDT)
Date: Sun, 18 Oct 1998 06:22:11 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810181022.GAA00210@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #90
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/90
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 3519

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 90

Today's Topics:
  looking for fast 25 mm C mount lens   [ rhawkes@mta.ca (Robert Hawkes) ]
  Advise on a commercial product        [ Jeremy Brown <brownj@netmatters.co. ]
  BioRad 1024 z-series                  [ "rchristie" <rchristie@email.msn.co ]

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

Date: Sat, 17 Oct 1998 08:50:00 -0300 (ADT)
From: rhawkes@mta.ca (Robert Hawkes)
To: nih-image@io.ece.drexel.edu
Subject: looking for fast 25 mm C mount lens
Message-Id: <v01530500b24e09ba39c4@[207.179.158.169]>
Content-Type: text/plain; charset="us-ascii"

I am sorry if this is not directly an NIH Image posting, but we desperately
need to find a source of fast 25 mm C mount lens which can deliver in the
next 10 days.  Preferably, Fujinon C25L (25 mm /f0.85).  All of our regular
suppliers have these backordered by Fujinon for end November, and we need
to ship them for use in a meteor field campaign in Mongolia much earlier
than that.  Any suggestions, those who might have one to sell, etc.
directly to me at
rhawkes@mta.ca
would be appreciated.  We certainly would consider used lenses, if in good
condition.
 Bob Hawkes
 rhawkes@mta.ca
 Physics, Mount Allison University
 Sackville, NB Canada

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

Date: Sat, 17 Oct 1998 14:27:30 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Advise on a commercial product
Message-ID: <3628A94B.D7A183D3@netmatters.co.uk>
Content-Type: text/plain; charset=iso-8859-1; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 8bit

Hello all,

Sorry to bother you with a non-Image related question but, Has anyone ever
come across a Mac imaging package called Open Lab 2.0 by Improvision. Someone at
the University here is considering purchasing a set-up from them (38 000:
Camera, Z-Focus control, Mac, Software, No Microscope or objectives).
Improvision are claiming that their software can produce con focal images from a
standard fluorescent or white light source by mathematical de-convolution of a z
series of standard images to discard the out of focus information in much the
same way as the optics of a con focal would. To me it sounds possible, but I can
not imagine that it would be as good as the real thing. They are not giving the
module that performs this function away as a demo, for obvious reasons if it
really works. Any
thoughts on the plausibility of this?

Many Thanks in advance,

Jeremy



************************************************
Jeremy Brown
Edinburgh University/Moredun Research Institute
http://www.netmatters.co.uk/users/brownj/HomePage.html
************************************************

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

Date: Sat, 17 Oct 1998 16:38:43 -0400
From: "rchristie" <rchristie@email.msn.com>
To: <nih-image@io.ece.drexel.edu>
Subject: BioRad 1024 z-series
Message-ID: <001f01bdfa0e$2263e4a0$LocalHost@MSN/rchristie>

I've been using NIH-image to manipulate stacks generated by a BioRad 1024
confocal system.  They are easy enough to open up and play with, but I'm
wondering if anyone has seen a macro to re-save the stack in the BioRad
format, with the header appropriately modified.

Any help would be appreciated,

Rich Christie
rchristie@msn.com
Alzheimer's Research
CNY 6320
Massachusetts General Hospital
Charlestown, MA 02129

--------------------------------
End of nih-image-d Digest V98 Issue #90
***************************************

From nih-image-request@io.ece.drexel.edu Sun Oct 18 08:09 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA08228;
	Sun, 18 Oct 1998 08:09:19 -0400 (EDT)
Resent-Date: Sun, 18 Oct 1998 08:09:19 -0400 (EDT)
Date: Sun, 18 Oct 1998 12:52:15 +0100 (BST)
From: Jan Kreft <Kreft@cardiff.ac.uk>
X-Sender: sabjk@thor
To: Jeremy Brown <brownj@netmatters.co.uk>
cc: nih-image@io.ece.drexel.edu
Subject: Re: Advise on a commercial product
In-Reply-To: <3628A94B.D7A183D3@netmatters.co.uk>
Message-ID: <Pine.OSF.3.95q.981018124611.3180B-100000@thor>
X-MIME-Autoconverted: from 8bit to quoted-printable by thor.cf.ac.uk id 
                      MAA26117
MIME-Version: 1.0
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id HAA02239
Resent-Message-ID: <"GSKPH1.0.uZ.wQTAs"@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/499
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/PLAIN; charset="ISO-8859-1"
Content-Length: 1717

Dear Jeremy,

I came across XCosm recently. It seems to do the same job and is for free
(runs on XWindow under Unix/Linux). At least you can ask the developers of
this software what they think about charging 38 000 pounds sterling for
Open Lab.

Have a look at:

www.ibc.wustl.edu/bcl/xcosm

Hope this helps, Jan.

Dr. Jan-Ulrich Kreft			Phone +44 (0)1222 874000 ext. 6036
Cardiff School of Biosciences		Fax   +44 (0)1222 874305
Cardiff University			E-mail Kreft@cardiff.ac.uk
PO Box 915, Cardiff CF1 3TL, UK

On Sat, 17 Oct 1998, Jeremy Brown wrote:

> Hello all,
> 
> Sorry to bother you with a non-Image related question but, Has anyone ever
> come across a Mac imaging package called Open Lab 2.0 by Improvision. Someone at
> the University here is considering purchasing a set-up from them (38 000:
> Camera, Z-Focus control, Mac, Software, No Microscope or objectives).
> Improvision are claiming that their software can produce con focal images from a
> standard fluorescent or white light source by mathematical de-convolution of a z
> series of standard images to discard the out of focus information in much the
> same way as the optics of a con focal would. To me it sounds possible, but I can
> not imagine that it would be as good as the real thing. They are not giving the
> module that performs this function away as a demo, for obvious reasons if it
> really works. Any
> thoughts on the plausibility of this?
> 
> Many Thanks in advance,
> 
> Jeremy
> 
> 
> 
> ************************************************
> Jeremy Brown
> Edinburgh University/Moredun Research Institute
> http://www.netmatters.co.uk/users/brownj/HomePage.html
> ************************************************
> 
> 
> 
> 
> 


From nih-image-request@io.ece.drexel.edu Sun Oct 18 09:01 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA27153;
	Sun, 18 Oct 1998 09:01:15 -0400 (EDT)
Resent-Date: Sun, 18 Oct 1998 09:01:15 -0400 (EDT)
Message-Id: <199810181241.JAA23172@ceiun01.elogica.com.br>
From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" <ggalindo@elogica.com.br>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: nih-image
Date: Sun, 18 Oct 1998 09:17:48 -0200
X-MSMail-Priority: Normal
X-Priority: 3
X-Mailer: Microsoft Internet Mail 4.70.1155
MIME-Version: 1.0
Content-Transfer-Encoding: 8bit
Resent-Message-ID: <"5gVxQ3.0.a85.DBUAs"@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/500
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset=ISO-8859-1
Content-Length: 644

Dear Therese,
did you try 
http://www.scioncorp.com
Good luck,
Rejane

----------
> De: Therese Visted <therese.visted@pki.uib.no>
> Para: nih-image@io.ece.drexel.edu
> Assunto: nih-image
> Data: Quinta-feira, 15 de Outubro de 1998 06:41
> 
> 
> My efforts in trying to find the latest version of nih-image has not
succeeded.
> Could you please help me in getting that information?
> Also, how do I get the latest version of nih-image (what url/http/ftp
adress)?
> Thank you!
> Therese Visted
> 
> Institutt for Anatomi og Cellebiologi
> rstadveien 19
> 5009 Bergen
> 
> tlf:55-586373
> fax:55-586360
> 
> e-mail:therese.visted@pki.uib.no
> 


From nih-image-request@io.ece.drexel.edu Sun Oct 18 19:24 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id TAA17207;
	Sun, 18 Oct 1998 19:24:39 -0400 (EDT)
Resent-Date: Sun, 18 Oct 1998 19:24:39 -0400 (EDT)
Message-Id: <l03010d04b2503ebcde13@[212.238.25.42]>
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Deleting Objects
Date: Sun, 18 Oct 1998 23:07:59 +0000
Resent-Message-ID: <"TxxQ12.0.4U2.MJdAs"@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/501
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: 1018

>When using Object-Image, is there a way to delete individual objects
>within a cell?  There are macro commands SelectCell, SelectObject,
>DeleteCell, but apparently no DeleteObject.  Is there a way around this,
>because if a cell contains multiple objects, and a mistake is made upon an
>object, once the cell is closed, apparently the whole cell must be deleted
>if only one object needs to be.

This is indeed something which needs to be improved in Object-Image.

Meanwhile, you can use the macro command OpenCell(n), which opens the
specified cell so you can add more markers, or delete them with the
backspace key. However, you only can delete them sequentially from back to
front.

So you can highlight a cell with the select tool (Finger cursor, now on the
extended part of the tools window) and then issue

macro 'Open cell';
begin
  OpenCell(SelectedCell);
  ShowCell(SelectedCell);
end;

The cell number of the cell which is open appears in italic.
Note that you need the newest version.

Norbert Vischer



From nih-image-d-request@io.ece.drexel.edu Mon Oct 19 06:17 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA22186;
	Mon, 19 Oct 1998 06:17:58 -0400 (EDT)
Date: Mon, 19 Oct 1998 06:17:58 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810191017.GAA22186@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #91
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/91
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 5236

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 91

Today's Topics:
  Re: Advise on a commercial product    [ Jan Kreft <Kreft@cardiff.ac.uk> ]
  Re: nih-image                         [ "=?ISO-8859-1?Q?Rejane_Magalh=E3es_ ]
  Re: Deleting Objects                  [ Norbert Vischer <vischer@bio.uva.nl ]
  unsubscribe                           [ cbrown@medicine.adelaide.edu.au ]

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

Date: Sun, 18 Oct 1998 12:52:15 +0100 (BST)
From: Jan Kreft <Kreft@cardiff.ac.uk>
To: Jeremy Brown <brownj@netmatters.co.uk>
cc: nih-image@io.ece.drexel.edu
Subject: Re: Advise on a commercial product
Message-ID: <Pine.OSF.3.95q.981018124611.3180B-100000@thor>
Content-type: text/PLAIN; charset="ISO-8859-1"
Content-Transfer-Encoding: 8bit

Dear Jeremy,

I came across XCosm recently. It seems to do the same job and is for free
(runs on XWindow under Unix/Linux). At least you can ask the developers of
this software what they think about charging 38 000 pounds sterling for
Open Lab.

Have a look at:

www.ibc.wustl.edu/bcl/xcosm

Hope this helps, Jan.

Dr. Jan-Ulrich Kreft			Phone +44 (0)1222 874000 ext. 6036
Cardiff School of Biosciences		Fax   +44 (0)1222 874305
Cardiff University			E-mail Kreft@cardiff.ac.uk
PO Box 915, Cardiff CF1 3TL, UK

On Sat, 17 Oct 1998, Jeremy Brown wrote:

> Hello all,
> 
> Sorry to bother you with a non-Image related question but, Has anyone ever
> come across a Mac imaging package called Open Lab 2.0 by Improvision. Someone at
> the University here is considering purchasing a set-up from them (38 000:
> Camera, Z-Focus control, Mac, Software, No Microscope or objectives).
> Improvision are claiming that their software can produce con focal images from a
> standard fluorescent or white light source by mathematical de-convolution of a z
> series of standard images to discard the out of focus information in much the
> same way as the optics of a con focal would. To me it sounds possible, but I can
> not imagine that it would be as good as the real thing. They are not giving the
> module that performs this function away as a demo, for obvious reasons if it
> really works. Any
> thoughts on the plausibility of this?
> 
> Many Thanks in advance,
> 
> Jeremy
> 
> 
> 
> ************************************************
> Jeremy Brown
> Edinburgh University/Moredun Research Institute
> http://www.netmatters.co.uk/users/brownj/HomePage.html
> ************************************************
> 
> 
> 
> 
> 

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

Date: Sun, 18 Oct 1998 09:17:48 -0200
From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" <ggalindo@elogica.com.br>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: nih-image
Message-Id: <199810181241.JAA23172@ceiun01.elogica.com.br>
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 8bit

Dear Therese,
did you try 
http://www.scioncorp.com
Good luck,
Rejane

----------
> De: Therese Visted <therese.visted@pki.uib.no>
> Para: nih-image@io.ece.drexel.edu
> Assunto: nih-image
> Data: Quinta-feira, 15 de Outubro de 1998 06:41
> 
> 
> My efforts in trying to find the latest version of nih-image has not
succeeded.
> Could you please help me in getting that information?
> Also, how do I get the latest version of nih-image (what url/http/ftp
adress)?
> Thank you!
> Therese Visted
> 
> Institutt for Anatomi og Cellebiologi
> rstadveien 19
> 5009 Bergen
> 
> tlf:55-586373
> fax:55-586360
> 
> e-mail:therese.visted@pki.uib.no
> 

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

Date: Sun, 18 Oct 1998 23:07:59 +0000
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Deleting Objects
Message-Id: <l03010d04b2503ebcde13@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

>When using Object-Image, is there a way to delete individual objects
>within a cell?  There are macro commands SelectCell, SelectObject,
>DeleteCell, but apparently no DeleteObject.  Is there a way around this,
>because if a cell contains multiple objects, and a mistake is made upon an
>object, once the cell is closed, apparently the whole cell must be deleted
>if only one object needs to be.

This is indeed something which needs to be improved in Object-Image.

Meanwhile, you can use the macro command OpenCell(n), which opens the
specified cell so you can add more markers, or delete them with the
backspace key. However, you only can delete them sequentially from back to
front.

So you can highlight a cell with the select tool (Finger cursor, now on the
extended part of the tools window) and then issue

macro 'Open cell';
begin
  OpenCell(SelectedCell);
  ShowCell(SelectedCell);
end;

The cell number of the cell which is open appears in italic.
Note that you need the newest version.

Norbert Vischer

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

Date: Mon, 19 Oct 98 08:53:13 +0930
From: cbrown@medicine.adelaide.edu.au
To: <nih-image-d@io.ece.drexel.edu>
Subject: unsubscribe
Message-Id: <9810199087.AA908754606@usbnt01.itd.adelaide.edu.au>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit

unsubscribe

--------------------------------
End of nih-image-d Digest V98 Issue #91
***************************************

From nih-image-request@io.ece.drexel.edu Mon Oct 19 08:37 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA10469;
	Mon, 19 Oct 1998 08:37:46 -0400 (EDT)
Resent-Date: Mon, 19 Oct 1998 08:37:46 -0400 (EDT)
Message-Id: <199810191215.HAA45524@mail1.doit.wisc.edu>
X-Sender: kvogt@facstaff.wisc.edu
X-Mailer: Windows Eudora Pro Version 2.1.2
Mime-Version: 1.0
Date: Mon, 19 Oct 1998 07:11:07 -0500
To: nih-image@io.ece.drexel.edu
From: Kevin Vogt <kvogt@facstaff.wisc.edu>
Subject: Re: nih-image-d Digest V98 #88
Resent-Message-ID: <"HrJD11.0.sg.XroAs"@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/502
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: 185

Hello,

        I have been using gelReader with the nih-image and am having trouble
generating a report when calibrating MW standards.  Does anyone know how
this can be fixed?

Kevin


From nih-image-request@io.ece.drexel.edu Mon Oct 19 11:26 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA06680;
	Mon, 19 Oct 1998 11:26:04 -0400 (EDT)
Resent-Date: Mon, 19 Oct 1998 11:26:04 -0400 (EDT)
Message-ID: <362B523A.6DF1D5CB@sdsc.edu>
Date: Mon, 19 Oct 1998 07:52:42 -0700
From: "Harvey J. Karten" <kartenh@sdsc.edu>
Reply-To: hjkarten@UCSD.EDU
Organization: UCSD
X-Mailer: Mozilla 4.04 [en] (Win95; U)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: Advice on a Commercial Product
References: <199810191015.GAA21214@io.ece.drexel.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"ebBDi1.0.sk6.kFrAs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/503
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: 2631

Jeremy Brown inquired about a deconvolution package for 38,000 English
Pounds
I estimate this to be equal to about $64,000 in U.S. dollars. This
didn't include microscope, motorized stage z-axis, objectives, etc.

Deconvolution is said to be a useful adjunct to confocal. But if you
want a serious assessment, test out how long it would take to collect
the data, then how long to process the data to generate a series of
images. Ask about the flexibility of the system relative to confocal.
Amongst other things, you will find that the time required to generate a
deconvolution image can run to hours of time. This same information is
rapidly available with confocal in a matter of seconds. Since the
procedures are different, there is a different mix of acquisition time
and processing time. There are a whole range of other issues, including
the type of camera you use for acquiring the deconvolution images (8
bit, 12 bit or 16 bit?), the method of obtaining uniform illumination
(scanning laser spot beats a mercury burner in every measure for
uniformity, though can't give a real time image to the user. )

Finally, I suggest that you check out the Olympus Confocal microscope
system. We recently have bought several of them at our university. The
price, including microscope, objectives, fluorescent attachment,
Nomarski optics, z-axis motor, computer, scanning module, control box,
filter set, and computer, was about $100,000. We bought thelaser
directly from Melles Griot for $8,300 (Argon-Krypton 50 RYB laser). You
may be able to negotiate a still better deal, depending upon the
effectiveness of your negotiating ability.

I don't work for Olympus, but we use their equipment, and I strongly
believe that a low price helps advance the technology. Their unit is
equal in image quality to the very expensive Zeiss 510. Obviously, the
Zeiss will give you more bells and whistles for $330,000, but I can
whistle my own tune for $230,000 savings.

Oh, another advantage - you can easily convert the Olympus to a two
photon unit if you happen to have the money for the necessary laser.
There are many benefits to the two photon imaging, which are simply
completely unavailable if you have sunk all you money into a
deconvolution system.

Hope this helps.
Harvey Karten

--
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

WCBR Program for 1999:
PLEASE NOTE CHANGE OF WEB ADDRESS
http://www.wcbrBrain.org



From nih-image-request@io.ece.drexel.edu Mon Oct 19 12:55 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA06768;
	Mon, 19 Oct 1998 12:55:08 -0400 (EDT)
Resent-Date: Mon, 19 Oct 1998 12:55:08 -0400 (EDT)
From: SolamereTG@aol.com
Message-ID: <e44f49c0.362b67a6@aol.com>
Date: Mon, 19 Oct 1998 12:24:06 EDT
To: nih-image@io.ece.drexel.edu
Mime-Version: 1.0
Subject: Re: Advice on a Commercial Product
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 16-bit for Windows sub 38
Resent-Message-ID: <"Ed2cN3.0._V6.wVsAs"@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/504
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: 1108


   I would like to re-iterate Dr. Karten's statement about speed but also
mention another commercially available Confocal, CSU-100 Dual Nipkow Disk
attachment that will work with any microscope, and works well with NIH image.
(Yes, we do sell it in North America, Applied Imaging sells it in Europe). The
image quality in tests at the City of Hope Medical Center showed the image
quality is equal to those made by a Zeiss confocal. The speed is <4 msec per
complete scan & can be sync'ed to video and used with any low light camera
ICCD, cooled, integrating CCD. The confocal sells for $65,000 USD. If you have
a microscope then you would need a laser ($6500 to 8500), and a camera ($3,500
to $26,750). A video rate confocal system that can run on NIH Image without
the need of a full time staff would be under $96,000 and can be moved from
microscope to microscope. I apologize to those who may view this as too
commercial but we are discussing what the available alternatives are. 

Please respond to me directly at Solameretg@aol.com
Dr. George A. Peeters
Solamere Technology Group
Salt Lake City, Utah


From nih-image-request@io.ece.drexel.edu Mon Oct 19 14:19 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA05859;
	Mon, 19 Oct 1998 14:19:28 -0400 (EDT)
Resent-Date: Mon, 19 Oct 1998 14:19:28 -0400 (EDT)
Date: Mon, 19 Oct 1998 13:26:04 -0400
Message-Id: <v01540b01b250e19c5985@[206.152.160.61]>
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center)
From: hmthomas@med.cornell.edu (Henry M. Thomas)
Subject: Re: Advice on a Commercial Product (pseudoconfocal imaging)
Resent-Message-ID: <"yD3UE3.0.3E7.butAs"@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/505
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: 1030


I think the method of reconstructing images by deconvolution is well
accepted. The images are crisp and impressive.  I'm less clear about how to
be sure the parameters for deconvolution are properly set to be accurate at
less than a micron resolution.

Scanalytics' Cellscan (Windows) is a commercial package for pseudo-confocal
imaging.  A collaborator down the hall uses it and is satisfied. Image
reconstruction takes a long time on fast computers (see Karten's email),
but if it can be fit in between experiments, is "cheap".  I'm told that the
current version is packaged in IPLab.

"Scanalytics, Inc.creates scientific image processing software and gel
analysis systems for Apple Macintosh, Windows 95 and Windows NT 4.0
--http://www.iplab.com/"

Henry M. Thomas, III MD (Harry)
Professor of Clinical Medicine,  Pulmonary and Critical Care Division
Department of Medicine, Cornell Univ. Medical School
Director, Pulmonary Research, Burke Rehabilitation Hospital
785 Mamaroneck Ave.  White Plains, NY 10605
(914) 597-2141



From nih-image-d-request@io.ece.drexel.edu Tue Oct 20 06:16 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA16579;
	Tue, 20 Oct 1998 06:16:09 -0400 (EDT)
Date: Tue, 20 Oct 1998 06:16:09 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810201016.GAA16579@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #92
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/92
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 7228

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 92

Today's Topics:
  Unidentified subject!                 [ "Dan Frich"<CSCDJF@arcochem.com> ]
  Re: nih-image-d Digest V98 #88        [ Kevin Vogt <kvogt@facstaff.wisc.edu ]
  Re: Advice on a Commercial Product    [ "Harvey J. Karten" <kartenh@sdsc.ed ]
  Re: Advice on a Commercial Product    [ SolamereTG@aol.com ]
  Re: Advice on a Commercial Product (  [ hmthomas@med.cornell.edu (Henry M.  ]

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

Date: Mon, 19 Oct 1998 07:30:34 -0400
From: "Dan Frich"<CSCDJF@arcochem.com>
To: nih-image-d@io.ece.drexel.edu
Subject: Unidentified subject!
Message-ID: <852566A2.003F1AF3.00@nsns-h01.arcochem.com>
Content-type: text/plain; charset=us-ascii

I was wondering if anyone had any idea how I could correct oversegmentation
when using the watershed function in v 1.61?

Thanks,
Dan Frich
cscdjf@arcochem.com

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

Date: Mon, 19 Oct 1998 07:11:07 -0500
From: Kevin Vogt <kvogt@facstaff.wisc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #88
Message-Id: <199810191215.HAA45524@mail1.doit.wisc.edu>
Content-Type: text/plain; charset="us-ascii"

Hello,

        I have been using gelReader with the nih-image and am having trouble
generating a report when calibrating MW standards.  Does anyone know how
this can be fixed?

Kevin

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

Date: Mon, 19 Oct 1998 07:52:42 -0700
From: "Harvey J. Karten" <kartenh@sdsc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Advice on a Commercial Product
Message-ID: <362B523A.6DF1D5CB@sdsc.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Jeremy Brown inquired about a deconvolution package for 38,000 English
Pounds
I estimate this to be equal to about $64,000 in U.S. dollars. This
didn't include microscope, motorized stage z-axis, objectives, etc.

Deconvolution is said to be a useful adjunct to confocal. But if you
want a serious assessment, test out how long it would take to collect
the data, then how long to process the data to generate a series of
images. Ask about the flexibility of the system relative to confocal.
Amongst other things, you will find that the time required to generate a
deconvolution image can run to hours of time. This same information is
rapidly available with confocal in a matter of seconds. Since the
procedures are different, there is a different mix of acquisition time
and processing time. There are a whole range of other issues, including
the type of camera you use for acquiring the deconvolution images (8
bit, 12 bit or 16 bit?), the method of obtaining uniform illumination
(scanning laser spot beats a mercury burner in every measure for
uniformity, though can't give a real time image to the user. )

Finally, I suggest that you check out the Olympus Confocal microscope
system. We recently have bought several of them at our university. The
price, including microscope, objectives, fluorescent attachment,
Nomarski optics, z-axis motor, computer, scanning module, control box,
filter set, and computer, was about $100,000. We bought thelaser
directly from Melles Griot for $8,300 (Argon-Krypton 50 RYB laser). You
may be able to negotiate a still better deal, depending upon the
effectiveness of your negotiating ability.

I don't work for Olympus, but we use their equipment, and I strongly
believe that a low price helps advance the technology. Their unit is
equal in image quality to the very expensive Zeiss 510. Obviously, the
Zeiss will give you more bells and whistles for $330,000, but I can
whistle my own tune for $230,000 savings.

Oh, another advantage - you can easily convert the Olympus to a two
photon unit if you happen to have the money for the necessary laser.
There are many benefits to the two photon imaging, which are simply
completely unavailable if you have sunk all you money into a
deconvolution system.

Hope this helps.
Harvey Karten

--
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

WCBR Program for 1999:
PLEASE NOTE CHANGE OF WEB ADDRESS
http://www.wcbrBrain.org

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

Date: Mon, 19 Oct 1998 12:24:06 EDT
From: SolamereTG@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re: Advice on a Commercial Product
Message-ID: <e44f49c0.362b67a6@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

   I would like to re-iterate Dr. Karten's statement about speed but also
mention another commercially available Confocal, CSU-100 Dual Nipkow Disk
attachment that will work with any microscope, and works well with NIH image.
(Yes, we do sell it in North America, Applied Imaging sells it in Europe). The
image quality in tests at the City of Hope Medical Center showed the image
quality is equal to those made by a Zeiss confocal. The speed is <4 msec per
complete scan & can be sync'ed to video and used with any low light camera
ICCD, cooled, integrating CCD. The confocal sells for $65,000 USD. If you have
a microscope then you would need a laser ($6500 to 8500), and a camera ($3,500
to $26,750). A video rate confocal system that can run on NIH Image without
the need of a full time staff would be under $96,000 and can be moved from
microscope to microscope. I apologize to those who may view this as too
commercial but we are discussing what the available alternatives are. 

Please respond to me directly at Solameretg@aol.com
Dr. George A. Peeters
Solamere Technology Group
Salt Lake City, Utah

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

Date: Mon, 19 Oct 1998 13:26:04 -0400
From: hmthomas@med.cornell.edu (Henry M. Thomas)
To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center)
Subject: Re: Advice on a Commercial Product (pseudoconfocal imaging)
Message-Id: <v01540b01b250e19c5985@[206.152.160.61]>
Content-Type: text/plain; charset="us-ascii"

I think the method of reconstructing images by deconvolution is well
accepted. The images are crisp and impressive.  I'm less clear about how to
be sure the parameters for deconvolution are properly set to be accurate at
less than a micron resolution.

Scanalytics' Cellscan (Windows) is a commercial package for pseudo-confocal
imaging.  A collaborator down the hall uses it and is satisfied. Image
reconstruction takes a long time on fast computers (see Karten's email),
but if it can be fit in between experiments, is "cheap".  I'm told that the
current version is packaged in IPLab.

"Scanalytics, Inc.creates scientific image processing software and gel
analysis systems for Apple Macintosh, Windows 95 and Windows NT 4.0
--http://www.iplab.com/"

Henry M. Thomas, III MD (Harry)
Professor of Clinical Medicine,  Pulmonary and Critical Care Division
Department of Medicine, Cornell Univ. Medical School
Director, Pulmonary Research, Burke Rehabilitation Hospital
785 Mamaroneck Ave.  White Plains, NY 10605
(914) 597-2141

--------------------------------
End of nih-image-d Digest V98 Issue #92
***************************************

From nih-image-request@io.ece.drexel.edu Tue Oct 20 08:12 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA27212;
	Tue, 20 Oct 1998 08:12:11 -0400 (EDT)
Resent-Date: Tue, 20 Oct 1998 08:12:11 -0400 (EDT)
From: "j.gregory" <ort056@abdn.ac.uk>
Sender: ort056@abdn.ac.uk
To: nih-image@io.ece.drexel.edu
Subject: interior measurements
Message-ID: <SIMEON.9810201300.A@pc10.abdn.ac.uk>
Date: Tue, 20 Oct 1998 13:09:00 +0100 (BST)
Priority: NORMAL
X-Mailer: Simeon for Windows Version 4.0.9
X-Authentication: IMSP
MIME-Version: 1.0
Resent-Message-ID: <"so6H3.0.kF5.8g7Bs"@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/506
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: 480



Whilst there are many automated procedures for measuring the size of an object and the 
space it takes up, does anyone have a macro or method for measuring the largest 
ellipse, rectangle or other regular object(not constrained to horizontal and vertical axis) 
that can fill the interior of an irregular ROI?

Thanks in advance,

Jenny Gregory

----------------------
Jenny Gregory
Department of Orthopaedics
University of Aberdeen
Aberdeen
Scotland

j.gregory@abdn.ac.uk






From nih-image-request@io.ece.drexel.edu Tue Oct 20 08:58 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA13075;
	Tue, 20 Oct 1998 08:58:45 -0400 (EDT)
Resent-Date: Tue, 20 Oct 1998 08:58:45 -0400 (EDT)
Message-ID: <75AC0E50AB70D111830700A02461F8E2655B0D@MCDC-CIN-1>
From: "Baron, Paul A." <pab2@cdc.gov>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Advise on a commercial product
Date: Tue, 20 Oct 1998 08:39:58 -0400
MIME-Version: 1.0
X-Mailer: Internet Mail Service (5.5.2232.9)
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id IAA07023
Resent-Message-ID: <"pnQiC2.0.-j1.GJ8Bs"@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/507
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Length: 1559

I looked at a similar product that appeared to work from a company called
Vay-Tek, 305 West Lowe, Suite 109, PO Box 732, Fairfield Iowa 52556 Phone
515 472 2227 Fax 515 472 8131.  This was several years ago and I don't even
know if they are still in business.

Paul Baron
NIOSH  MS R7
4676 Columbia Parkway
Cincinnati OH 45226
Phone: 513 841 4278
Fax: 513 841 4500
Email: pab2@cdc.gov


 Hello all,

Sorry to bother you with a non-Image related question but, Has anyone ever
come across a Mac imaging package called Open Lab 2.0 by Improvision.
Someone at the University here is considering purchasing a set-up from them
(38 000:
Camera, Z-Focus control, Mac, Software, No Microscope or objectives).
Improvision are claiming that their software can produce con focal images
from a standard fluorescent or white light source by mathematical
de-convolution of a z series of standard images to discard the out of focus
information in much the same way as the optics of a con focal would. To me
it sounds possible, but I can not imagine that it would be as good as the
real thing. They are not giving the module that performs this function away
as a demo, for obvious reasons if it really works. Any thoughts on the
plausibility of this?
Many Thanks in advance,
Jeremy


************************************************
Jeremy Brown
Edinburgh University/Moredun Research Institute
http://www.netmatters.co.uk/users/brownj/HomePage.html
************************************************
	 : Advise on a commercial product >>  << Message: BioRad 1024
z-series >> 


From nih-image-request@io.ece.drexel.edu Tue Oct 20 10:00 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA02817;
	Tue, 20 Oct 1998 10:00:01 -0400 (EDT)
Resent-Date: Tue, 20 Oct 1998 10:00:01 -0400 (EDT)
Date: Tue, 20 Oct 1998 07:41:53 -0600 (CST)
From: "Geoffrey D. Guttmann" <guttmann@duke.usask.ca>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
cc: Paul Baron <pab2@cdc.gov>
Subject: Re: Advise on a commercial product
In-Reply-To: <75AC0E50AB70D111830700A02461F8E2655B0D@MCDC-CIN-1>
Message-ID: <Pine.OSF.4.02A.9810200722270.29739-100000@duke.usask.ca>
MIME-Version: 1.0
Resent-Message-ID: <"Xg445.0.wX6.cC9Bs"@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/508
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: 1351

Hi folks

>I looked at a similar product that appeared to work from a company called
>Vay-Tek, 305 West Lowe, Suite 109, PO Box 732, Fairfield Iowa 52556 Phone
>515 472 2227 Fax 515 472 8131.  This was several years ago and I don't even
>know if they are still in business.
>
>Paul Baron

The answer is Vaytek is very much alive.  I just checked their website.
Below is a contact and address:

Chris MacLean, Ph.D.
VayTek, Inc.
305 West. Lowe, Suite 109
P.O. Box 732
Fairfield, Iowa, 52556-0732

Tel: 515-472-2227 ext.105
Fax: 515-472-8131
E-Mail: cmaclean@vaytek.com
Web: www.vaytek.com

Their product has done well on the PowerMac.
Cheers, geoff

------------------------------------------------------------------------
Geoffrey D. Guttmann, Ph.D	_/_/_/_/     _/_/     _/_/_/_/  _/   _/  
Assistant Professor	       _/	   _/   _/   _/        _/  _/
Dept. of Anatomy and Cell Biology    	  _/    _/  _/        _/ _/
College of Medicine	      _/_/_/_/   _/_/_/_/  _/_/_/_/  _/_/
University of Saskatchewan	   _/   _/    _/	_/  _/ _/
A-315 Health Sciences Building	  _/   _/    _/        _/  _/  _/
107 Wiggins Road	   _/_/_/_/   _/    _/  _/_/_/_/  _/   _/  _/
Saskatoon, SK S7N 5E5 
CANADA				Voice:(306)966-4079   Fax:(306)966-4298   
				E-mail:guttmann@duke.usask.ca	     
------------------------------------------------------------------------


From nih-image-request@io.ece.drexel.edu Tue Oct 20 17:06 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA29747;
	Tue, 20 Oct 1998 17:06:19 -0400 (EDT)
Resent-Date: Tue, 20 Oct 1998 17:06:19 -0400 (EDT)
Message-Id: <l03130300b252b0e501b3@[129.2.37.68]>
Mime-Version: 1.0
Date: Tue, 20 Oct 1998 16:36:34 -0500
To: nih-image@io.ece.drexel.edu
From: Joaquim Garrabou <garrabou@pop.wam.umd.edu>
Subject: Labelling patches
Resent-Message-ID: <"z7x2W3.0.oY4.IHFBs"@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/509
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: 685

Hello everybody,
I have to measure polygons (patches) in several images. I've been looking
at the measure procedures in NIH image and I've realized that NIH
automatically labels all patches or alternativelly you can point go patch
by patch and obtain the measurament. But in either case, one obtain a
sequence of numbers as patch labels. I'd like to introduce my own labels
pointing at the different patches (e.g. e23 or a12) during the measuring
process. Is that possible with NIH?

Thanks for all

Joaquim Garrabou

Joaquim Garrabou
Dpt. of Zoology
University of Maryland at College Park
College Park MD 20742

Voice: 301-405 8021
Fax:   301-314 9358

e-mail: garrabou@wam.umd.edu



From nih-image-request@io.ece.drexel.edu Tue Oct 20 18:46 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA05316;
	Tue, 20 Oct 1998 18:46:16 -0400 (EDT)
Resent-Date: Tue, 20 Oct 1998 18:46:16 -0400 (EDT)
Date: Tue, 20 Oct 1998 15:28:33 -0700 (PDT)
Message-Id: <199810202228.PAA11829@franc.ucdavis.edu>
X-Sender: ez075141@peseta.ucdavis.edu (Unverified)
X-Mailer: Windows Eudora Pro Version 2.1.2
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
From: "Jason A. Melvin" <jamelvin@ucdavis.edu>
Subject: Analysis of Genomic Fingerprints
Resent-Message-ID: <"a4nee.0.N87.9xGBs"@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/510
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: 410

Does anyone use IMAGE to analyze genomic DNA fingerprints? I would like to
know how to generate relative mobility values as well as compare lanes
within one gel to lanes within another gel. Any suggestions would be
appreciated.

Jason



Jason A. Melvin
USDA/ARS
Dept. Plant Pathology
University of California
One Shields Ave.
Davis, CA 95616

tel: 530-752-8679
fax: 530-752-5674
email: jamelvin@ucdavis.edu



From nih-image-request@io.ece.drexel.edu Tue Oct 20 22:10 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id WAA19575;
	Tue, 20 Oct 1998 22:10:00 -0400 (EDT)
Resent-Date: Tue, 20 Oct 1998 22:10:00 -0400 (EDT)
From: wpchan@socrates.berkeley.edu
Date: Tue, 20 Oct 1998 18:52:49 -0700 (PDT)
To: nih-image@io.ece.drexel.edu
Subject: video capture at 30 fps
In-Reply-To: <e44f49c0.362b67a6@aol.com>
Message-ID: <Pine.SOL.3.96.981020184554.15914A-100000@socrates.berkeley.edu>
MIME-Version: 1.0
Resent-Message-ID: <"KRzwV1.0.7H3.1wJBs"@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/511
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: 444

Recently we have bought a Scion LG3 PCI card to put in a Windows NT.  The
highest capture rate that we can get with 'blind capture' in 'make movie'
is 17 fps.  Scion Tech support confirmed that this is probably the highest
one can get on a NT. 

Has anybody successfully get the LG3 PCI to capture to RAM at 30 fps and
if so, under what condition and using what kind of computer?  Thanks.

--Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu)


From nih-image-request@io.ece.drexel.edu Wed Oct 21 05:28 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA13295;
	Wed, 21 Oct 1998 05:28:12 -0400 (EDT)
Resent-Date: Wed, 21 Oct 1998 05:28:12 -0400 (EDT)
Message-ID: <00f301bdfcd3$6185ce60$99efe18f@amendola.unina.it>
From: "Eugenio Amendola" <amendola@unina.it>
To: <nih-image@io.ece.drexel.edu>
Subject: epoxy resin morphology
Date: Wed, 21 Oct 1998 11:15:42 +0200
MIME-Version: 1.0
X-Priority: 3
X-MSMail-Priority: Normal
X-Mailer: Microsoft Outlook Express 4.72.3110.5
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3
Resent-Message-ID: <"gpEUF2.0.MR1.GMQBs"@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/512
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_00F0_01BDFCE4.24992040"
Content-Length: 3352

This is a multi-part message in MIME format.

------=_NextPart_000_00F0_01BDFCE4.24992040
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Hello Imagers,
I would like to ask for some help on the following issue:
I'm performing morphological analysis on mixtures of two different epoxy =
resins, a Shell product and a liquid crystalline epoxy resin synthesized =
in our labs. The mixture, after curing, is optically transparent. The =
composition range of mixtures spans from 0 to 100%.
We are interested in characterizing the phase separation, because the =
high thoughness of the samples could be correlated with a complex =
structure. However, we are unable to detect any definite structural =
feature.
Can someone suggest some staining or etching tecnique suitable to =
differentiate between an amourphous and a liquid crystalline epoxy resin =
in the cured sample. The sample is rigid at room temperature.
TIA in advance to every one,
and congratulation for the job that you are running.
Eugenio=20
-------------------------------------------------------------------------=
------
Dr. Eugenio Amendola
Institute of Composite Materials Technology
C.N.R.
P.le Tecchio 80
80125 Naples, ITALY
Tel: (+) 39 81 768 2511
Fax: (+) 39 81 768 2404
e-mail: amendola@unina.it

------=_NextPart_000_00F0_01BDFCE4.24992040
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,</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT><FONT size=3D2>I would like =
to ask for some=20
help on the following issue:</FONT></DIV>
<DIV><FONT size=3D2>I'm performing morphological analysis on mixtures of =
two=20
different epoxy resins, a Shell product and a liquid crystalline epoxy =
resin=20
synthesized in our labs. The mixture, after curing, is optically =
transparent.=20
The composition range of mixtures spans from 0 to 100%.</FONT></DIV>
<DIV><FONT size=3D2>We are interested in characterizing the phase =
separation,=20
because the high thoughness of the samples could be correlated with a =
complex=20
structure. However, we are unable to detect any definite structural=20
feature.</FONT></DIV>
<DIV><FONT size=3D2>Can someone suggest some staining or etching =
tecnique suitable=20
to differentiate between an amourphous and a liquid crystalline epoxy =
resin in=20
the cured sample. The sample is rigid at room temperature.</FONT></DIV>
<DIV><FONT size=3D2>TIA in advance to every one,</FONT></DIV>
<DIV><FONT size=3D2>and congratulation for the job that you are=20
running.</FONT></DIV>
<DIV><FONT size=3D2>Eugenio&nbsp;</FONT></DIV>
<DIV><FONT color=3D#000000=20
size=3D2>----------------------------------------------------------------=
---------------<BR>Dr.=20
Eugenio Amendola<BR>Institute of Composite Materials=20
Technology<BR>C.N.R.<BR>P.le Tecchio 80<BR>80125 Naples, ITALY<BR>Tel: =
(+) 39 81=20
768 2511<BR>Fax: (+) 39 81 768 2404<BR>e-mail: <A=20
href=3D"mailto:amendola@unina.it">amendola@unina.it</A></FONT></DIV></BOD=
Y></HTML>

------=_NextPart_000_00F0_01BDFCE4.24992040--


From nih-image-d-request@io.ece.drexel.edu Wed Oct 21 05:28 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA13431;
	Wed, 21 Oct 1998 05:28:26 -0400 (EDT)
Date: Wed, 21 Oct 1998 05:28:26 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810210928.FAA13431@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #93
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/93
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 11269

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 93

Today's Topics:
  interior measurements                 [ "j.gregory" <ort056@abdn.ac.uk> ]
  Advise on a commercial product        [ "Baron, Paul A." <pab2@cdc.gov> ]
  Re: Advise on a commercial product    [ "Geoffrey D. Guttmann" <guttmann@du ]
  Labelling patches                     [ Joaquim Garrabou <garrabou@pop.wam. ]
  Analysis of Genomic Fingerprints      [ "Jason A. Melvin" <jamelvin@ucdavis ]
  video capture at 30 fps               [ wpchan@socrates.berkeley.edu ]
  epoxy resin morphology                [ "Eugenio Amendola" <amendola@unina. ]

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

Date: Tue, 20 Oct 1998 13:09:00 +0100 (BST)
From: "j.gregory" <ort056@abdn.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: interior measurements
Message-ID: <SIMEON.9810201300.A@pc10.abdn.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

Whilst there are many automated procedures for measuring the size of an object and the 
space it takes up, does anyone have a macro or method for measuring the largest 
ellipse, rectangle or other regular object(not constrained to horizontal and vertical axis) 
that can fill the interior of an irregular ROI?

Thanks in advance,

Jenny Gregory

----------------------
Jenny Gregory
Department of Orthopaedics
University of Aberdeen
Aberdeen
Scotland

j.gregory@abdn.ac.uk

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

Date: Tue, 20 Oct 1998 08:39:58 -0400
From: "Baron, Paul A." <pab2@cdc.gov>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Advise on a commercial product
Message-ID: <75AC0E50AB70D111830700A02461F8E2655B0D@MCDC-CIN-1>
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

I looked at a similar product that appeared to work from a company called
Vay-Tek, 305 West Lowe, Suite 109, PO Box 732, Fairfield Iowa 52556 Phone
515 472 2227 Fax 515 472 8131.  This was several years ago and I don't even
know if they are still in business.

Paul Baron
NIOSH  MS R7
4676 Columbia Parkway
Cincinnati OH 45226
Phone: 513 841 4278
Fax: 513 841 4500
Email: pab2@cdc.gov


 Hello all,

Sorry to bother you with a non-Image related question but, Has anyone ever
come across a Mac imaging package called Open Lab 2.0 by Improvision.
Someone at the University here is considering purchasing a set-up from them
(38 000:
Camera, Z-Focus control, Mac, Software, No Microscope or objectives).
Improvision are claiming that their software can produce con focal images
from a standard fluorescent or white light source by mathematical
de-convolution of a z series of standard images to discard the out of focus
information in much the same way as the optics of a con focal would. To me
it sounds possible, but I can not imagine that it would be as good as the
real thing. They are not giving the module that performs this function away
as a demo, for obvious reasons if it really works. Any thoughts on the
plausibility of this?
Many Thanks in advance,
Jeremy


************************************************
Jeremy Brown
Edinburgh University/Moredun Research Institute
http://www.netmatters.co.uk/users/brownj/HomePage.html
************************************************
	 : Advise on a commercial product >>  << Message: BioRad 1024
z-series >> 

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

Date: Tue, 20 Oct 1998 07:41:53 -0600 (CST)
From: "Geoffrey D. Guttmann" <guttmann@duke.usask.ca>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
cc: Paul Baron <pab2@cdc.gov>
Subject: Re: Advise on a commercial product
Message-ID: <Pine.OSF.4.02A.9810200722270.29739-100000@duke.usask.ca>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi folks

>I looked at a similar product that appeared to work from a company called
>Vay-Tek, 305 West Lowe, Suite 109, PO Box 732, Fairfield Iowa 52556 Phone
>515 472 2227 Fax 515 472 8131.  This was several years ago and I don't even
>know if they are still in business.
>
>Paul Baron

The answer is Vaytek is very much alive.  I just checked their website.
Below is a contact and address:

Chris MacLean, Ph.D.
VayTek, Inc.
305 West. Lowe, Suite 109
P.O. Box 732
Fairfield, Iowa, 52556-0732

Tel: 515-472-2227 ext.105
Fax: 515-472-8131
E-Mail: cmaclean@vaytek.com
Web: www.vaytek.com

Their product has done well on the PowerMac.
Cheers, geoff

------------------------------------------------------------------------
Geoffrey D. Guttmann, Ph.D	_/_/_/_/     _/_/     _/_/_/_/  _/   _/  
Assistant Professor	       _/	   _/   _/   _/        _/  _/
Dept. of Anatomy and Cell Biology    	  _/    _/  _/        _/ _/
College of Medicine	      _/_/_/_/   _/_/_/_/  _/_/_/_/  _/_/
University of Saskatchewan	   _/   _/    _/	_/  _/ _/
A-315 Health Sciences Building	  _/   _/    _/        _/  _/  _/
107 Wiggins Road	   _/_/_/_/   _/    _/  _/_/_/_/  _/   _/  _/
Saskatoon, SK S7N 5E5 
CANADA				Voice:(306)966-4079   Fax:(306)966-4298   
				E-mail:guttmann@duke.usask.ca	     
------------------------------------------------------------------------

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

Date: Tue, 20 Oct 1998 16:36:34 -0500
From: Joaquim Garrabou <garrabou@pop.wam.umd.edu>
To: nih-image@io.ece.drexel.edu
Subject: Labelling patches
Message-Id: <l03130300b252b0e501b3@[129.2.37.68]>
Content-Type: text/plain; charset="us-ascii"

Hello everybody,
I have to measure polygons (patches) in several images. I've been looking
at the measure procedures in NIH image and I've realized that NIH
automatically labels all patches or alternativelly you can point go patch
by patch and obtain the measurament. But in either case, one obtain a
sequence of numbers as patch labels. I'd like to introduce my own labels
pointing at the different patches (e.g. e23 or a12) during the measuring
process. Is that possible with NIH?

Thanks for all

Joaquim Garrabou

Joaquim Garrabou
Dpt. of Zoology
University of Maryland at College Park
College Park MD 20742

Voice: 301-405 8021
Fax:   301-314 9358

e-mail: garrabou@wam.umd.edu

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

Date: Tue, 20 Oct 1998 15:28:33 -0700 (PDT)
From: "Jason A. Melvin" <jamelvin@ucdavis.edu>
To: nih-image@io.ece.drexel.edu
Subject: Analysis of Genomic Fingerprints
Message-Id: <199810202228.PAA11829@franc.ucdavis.edu>
Content-Type: text/plain; charset="us-ascii"

Does anyone use IMAGE to analyze genomic DNA fingerprints? I would like to
know how to generate relative mobility values as well as compare lanes
within one gel to lanes within another gel. Any suggestions would be
appreciated.

Jason



Jason A. Melvin
USDA/ARS
Dept. Plant Pathology
University of California
One Shields Ave.
Davis, CA 95616

tel: 530-752-8679
fax: 530-752-5674
email: jamelvin@ucdavis.edu

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

Date: Tue, 20 Oct 1998 18:52:49 -0700 (PDT)
From: wpchan@socrates.berkeley.edu
To: nih-image@io.ece.drexel.edu
Subject: video capture at 30 fps
Message-ID: <Pine.SOL.3.96.981020184554.15914A-100000@socrates.berkeley.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Recently we have bought a Scion LG3 PCI card to put in a Windows NT.  The
highest capture rate that we can get with 'blind capture' in 'make movie'
is 17 fps.  Scion Tech support confirmed that this is probably the highest
one can get on a NT. 

Has anybody successfully get the LG3 PCI to capture to RAM at 30 fps and
if so, under what condition and using what kind of computer?  Thanks.

--Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu)

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

Date: Wed, 21 Oct 1998 11:15:42 +0200
From: "Eugenio Amendola" <amendola@unina.it>
To: <nih-image@io.ece.drexel.edu>
Subject: epoxy resin morphology
Message-ID: <00f301bdfcd3$6185ce60$99efe18f@amendola.unina.it>
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_00F0_01BDFCE4.24992040"

This is a multi-part message in MIME format.

------=_NextPart_000_00F0_01BDFCE4.24992040
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Hello Imagers,
I would like to ask for some help on the following issue:
I'm performing morphological analysis on mixtures of two different epoxy =
resins, a Shell product and a liquid crystalline epoxy resin synthesized =
in our labs. The mixture, after curing, is optically transparent. The =
composition range of mixtures spans from 0 to 100%.
We are interested in characterizing the phase separation, because the =
high thoughness of the samples could be correlated with a complex =
structure. However, we are unable to detect any definite structural =
feature.
Can someone suggest some staining or etching tecnique suitable to =
differentiate between an amourphous and a liquid crystalline epoxy resin =
in the cured sample. The sample is rigid at room temperature.
TIA in advance to every one,
and congratulation for the job that you are running.
Eugenio=20
-------------------------------------------------------------------------=
------
Dr. Eugenio Amendola
Institute of Composite Materials Technology
C.N.R.
P.le Tecchio 80
80125 Naples, ITALY
Tel: (+) 39 81 768 2511
Fax: (+) 39 81 768 2404
e-mail: amendola@unina.it

------=_NextPart_000_00F0_01BDFCE4.24992040
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,</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D2></FONT><FONT size=3D2>I would like =
to ask for some=20
help on the following issue:</FONT></DIV>
<DIV><FONT size=3D2>I'm performing morphological analysis on mixtures of =
two=20
different epoxy resins, a Shell product and a liquid crystalline epoxy =
resin=20
synthesized in our labs. The mixture, after curing, is optically =
transparent.=20
The composition range of mixtures spans from 0 to 100%.</FONT></DIV>
<DIV><FONT size=3D2>We are interested in characterizing the phase =
separation,=20
because the high thoughness of the samples could be correlated with a =
complex=20
structure. However, we are unable to detect any definite structural=20
feature.</FONT></DIV>
<DIV><FONT size=3D2>Can someone suggest some staining or etching =
tecnique suitable=20
to differentiate between an amourphous and a liquid crystalline epoxy =
resin in=20
the cured sample. The sample is rigid at room temperature.</FONT></DIV>
<DIV><FONT size=3D2>TIA in advance to every one,</FONT></DIV>
<DIV><FONT size=3D2>and congratulation for the job that you are=20
running.</FONT></DIV>
<DIV><FONT size=3D2>Eugenio&nbsp;</FONT></DIV>
<DIV><FONT color=3D#000000=20
size=3D2>----------------------------------------------------------------=
---------------<BR>Dr.=20
Eugenio Amendola<BR>Institute of Composite Materials=20
Technology<BR>C.N.R.<BR>P.le Tecchio 80<BR>80125 Naples, ITALY<BR>Tel: =
(+) 39 81=20
768 2511<BR>Fax: (+) 39 81 768 2404<BR>e-mail: <A=20
href=3D"mailto:amendola@unina.it">amendola@unina.it</A></FONT></DIV></BOD=
Y></HTML>

------=_NextPart_000_00F0_01BDFCE4.24992040--

--------------------------------
End of nih-image-d Digest V98 Issue #93
***************************************

From nih-image-request@io.ece.drexel.edu Wed Oct 21 08:09 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA21826;
	Wed, 21 Oct 1998 08:09:06 -0400 (EDT)
Resent-Date: Wed, 21 Oct 1998 08:09:06 -0400 (EDT)
X-Sender: cgustafs@ece.drexel.edu
Message-Id: <v03110702b2537c984f04@[144.118.33.205]>
In-Reply-To: <00f301bdfcd3$6185ce60$99efe18f@amendola.unina.it>
Mime-Version: 1.0
Date: Wed, 21 Oct 1998 07:59:21 -0400
To: nih-image@io.ece.drexel.edu
From: Carl Gustafson <carl.gustafson@cbis.ece.drexel.edu>
Subject: Re: epoxy resin morphology
Resent-Message-ID: <"UATK3.0.Xu3.ajSBs"@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/513
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: 1047

...
>However, we are unable to detect any definite structural  feature. Can
>someone suggest some staining or etching tecnique suitable  to
>differentiate between an amourphous and a liquid crystalline epoxy resin
>in  the cured sample.
...

Will some solvent swell the amorphous phase and not the crystalline one?
Are there any substituents on one phase and not on the other that can be
substitued with something that can be made to absorb light differently?

It's been years since I did Real Chemistry.




Carl Gustafson
(215) 895-1383
===============================================================================
           the Computer Vision Center for Vertebrate Brain Mapping
===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I'd like to give you my opinion
===============================================================================



From nih-image-request@io.ece.drexel.edu Wed Oct 21 15:42 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA13324;
	Wed, 21 Oct 1998 15:42:54 -0400 (EDT)
Resent-Date: Wed, 21 Oct 1998 15:42:54 -0400 (EDT)
From: SolamereTG@aol.com
Message-ID: <9b16cd57.362e3253@aol.com>
Date: Wed, 21 Oct 1998 15:13:23 EDT
To: nih-image@io.ece.drexel.edu
Mime-Version: 1.0
Subject: Re: video capture at 30 fps
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 16-bit for Windows sub 38
Resent-Message-ID: <"p_9N51.0._W6.IAZBs"@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/514
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: 348

We use blind capture with  266 and 300 Mhz G-3 desktop models to capture at 30
fps to system Ram. The LG-3 board you have should be able to go into a G-3 and
do the same. I would borrow a G-3 MAC and try it out. You may still use NT but
you may need to capture an ROI rather than the full 640x480 image. 

George Peeters
Solamere Technology Group


From nih-image-request@io.ece.drexel.edu Wed Oct 21 16:28 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA08968;
	Wed, 21 Oct 1998 16:28:31 -0400 (EDT)
Resent-Date: Wed, 21 Oct 1998 16:28:31 -0400 (EDT)
Date: Wed, 21 Oct 1998 16:02:11 -0400 (EDT)
From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
X-Sender: cozturk@henryv
To: nih-image@io.ece.drexel.edu
Subject: Colorcamera info needed
In-Reply-To: <9b16cd57.362e3253@aol.com>
Message-ID: <Pine.SGI.3.91.981021155653.16063B-100000@henryv>
MIME-Version: 1.0
Resent-Message-ID: <"svp7I2.0.Rx5.StZBs"@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/515
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: 651

Hi,

I need a fast color CCD camera for a machine vision/inspection type
of application. I am at least 1 year behind what is the latest in the market.

Anybody has done a recent search ?
Can anybody give some pointers, web pages. 
Please send industrial responses directly to me by e-mail or fax 
(with prices)

My system will be a matrox capture board housed in a PC.

Thanks.

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


From nih-image-request@io.ece.drexel.edu Wed Oct 21 19:15 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id TAA15175;
	Wed, 21 Oct 1998 19:15:29 -0400 (EDT)
Resent-Date: Wed, 21 Oct 1998 19:15:29 -0400 (EDT)
Message-ID: <362E04FB.EE@dri.edu>
Date: Wed, 21 Oct 1998 16:00:05 +0000
From: Pat Arnott <pat@dri.edu>
Reply-To: pat@dri.edu
Organization: Desert Research Institute
X-Mailer: Mozilla 3.0-C-AICK1-2 (Macintosh; U; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #93
References: <199810210928.FAA13290@io.ece.drexel.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"0JvKz.0.OU.yMcBs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/516
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: 818

Hi:

We loaded our lg3 with maximum memory and were able to digitize  frames
to card ram at 30 fps on any of our macs (8100 av, g3).  We could do
this within the memory available in RAM.  

I have also used the g3 av to digitize at 30 fps using adobe premier as
the software, and the built in video card on the mac.  However, the
images are smaller than with the scion board, and you do not have
control of the digitizer offset and gain like with the scion card.  
  
--
      Regards,
                       Pat Arnott
**********************************************************
* W. Patrick Arnott  702-677-3123   -3157 fax
* Atmospheric Sciences Center, Desert Research Institute
* PO Box 60220, RENO NV  89506
* http://www.dri.edu/Projects/replica/webWPA
**********************************************************


From nih-image-request@io.ece.drexel.edu Wed Oct 21 20:54 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA09940;
	Wed, 21 Oct 1998 20:54:33 -0400 (EDT)
Resent-Date: Wed, 21 Oct 1998 20:54:33 -0400 (EDT)
Message-ID: <F98649A5EE8ED11190160000F802756598CEC5@exchvic3.dsto.defence.gov.au>
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: Data from FFT's
Date: Thu, 22 Oct 1998 10:36:41 +1000
MIME-Version: 1.0
X-Mailer: Internet Mail Service (5.5.2232.9)
Resent-Message-ID: <"XIYNN3.0.pe.tudBs"@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/517
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 2025

Hi,
We are using NIH-Image to measure the spacings of groups of striations
observed on fracture surfaces.
The procedure is as follows using the FFT Macros.
Open or display an Image, which is spatially calibrated in microns or mm.
Select the size of square area to be used, Operator decision.
Position the square over the selected group of striations.
Type F  (FFT). (This is now so quick on a G3-300 that it is no longer the
slowest operation) 
Look at the Transform and position the cursor over one of the two distinct
peaks which appear on each side of the centre.
Read the value in the info window which tells about cycles per mm (Or
micron), and also give the angle this makes with the x axis.
Write down the numbers and proceed to the next place.


My question is:
Can I get this data into a macro so I don't have to write it down?
I see it is written in the info window, so it is there, how do I get it into
user1 and user2?

I spent some time reading the manual and could find nothing. I could have a
look at the source code, but thought I would ask first.
I guess this is a measurement which does not yet appear as an option in the
measurements option dialog, and may have to be added.
What I would propose is maybe a mouse click at the desired location to
record these parameters. But I really have no strong feelings about how to
do this job.
After all I am relying on a user decision about the location of the maximum
peak on the transform. For really precise work I suppose we should fit up
some 3-D surfaces across the peak and estimate the peak maximum position, or
fit up some 2-d curves across and up and down to try to locate the maximum.
Of course when you look at the scatter you get when measuring striations all
of this precision becomes academic. The spacing will vary by a factor of 2
or more over a range of very small distances, and the only way you get good
data is by getting lots of numbers. And doing it by using the FFT allows the
accumulation of many measurements, quickly.
Best regards
Noel.


From nih-image-request@io.ece.drexel.edu Thu Oct 22 04:08 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA12202;
	Thu, 22 Oct 1998 04:08:38 -0400 (EDT)
Resent-Date: Thu, 22 Oct 1998 04:08:38 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: Noel.Goldsmith@dsto.defence.gov.au, nih-image@io.ece.drexel.edu
Date:          Thu, 22 Oct 1998 18:00:50 GMT+1000
Subject:       Re: Data from FFT's
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <C2D6AEA324A@rna.bio.mq.edu.au>
Resent-Message-ID: <"J78My3.0.I_1.zLkBs"@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/518
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 3255

>From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
>To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
>Subject: Data from FFT's
>Date: Thu, 22 Oct 1998 10:36:41 +1000
>
>Hi,
>We are using NIH-Image to measure the spacings of groups of striations
>observed on fracture surfaces.
>The procedure is as follows using the FFT Macros.
>Open or display an Image, which is spatially calibrated in microns or mm.
>Select the size of square area to be used, Operator decision.
>Position the square over the selected group of striations.
>Type F  (FFT). (This is now so quick on a G3-300 that it is no longer the
>slowest operation) 
>Look at the Transform and position the cursor over one of the two distinct
>peaks which appear on each side of the centre.
>Read the value in the info window which tells about cycles per mm (Or
>micron), and also give the angle this makes with the x axis.
>Write down the numbers and proceed to the next place.
>
>
>My question is:
>Can I get this data into a macro so I don't have to write it down?
>I see it is written in the info window, so it is there, how do I get it into
>user1 and user2?
>
>I spent some time reading the manual and could find nothing. I could have a
>look at the source code, but thought I would ask first.
>I guess this is a measurement which does not yet appear as an option in the
>measurements option dialog, and may have to be added.
>What I would propose is maybe a mouse click at the desired location to
>record these parameters. But I really have no strong feelings about how to
>do this job.
>After all I am relying on a user decision about the location of the maximum
>peak on the transform. For really precise work I suppose we should fit up
>some 3-D surfaces across the peak and estimate the peak maximum position, or
>fit up some 2-d curves across and up and down to try to locate the maximum.
>Of course when you look at the scatter you get when measuring striations all
>of this precision becomes academic. The spacing will vary by a factor of 2
>or more over a range of very small distances, and the only way you get good
>data is by getting lots of numbers. And doing it by using the FFT allows the
>accumulation of many measurements, quickly.
>Best regards
>Noel.
>
Noel, the FFT window is essentially a spatially scaled image 
with the origin central and using polar coordinates,
so the following macro will mimic the Info window values:

Place the cursor in the FFT window 
and press [t] to demonstrate.

macro'[t]est';
var x,y,c,w,h,scale,AspectRatio,xs,ys,r,theta:integer;
unit:string;begin
invertY(false);
getPicSize(w,h);w:=w/2;
getScale(scale,unit,AspectRatio);
getMouse(x,y);c:=getPixel(x,y);
xs:=x-w;
ys:=w-y;
if ys=0 then if xs>0 then theta:=0 else theta :=180
else theta:=90-arcTan(xs/ys)*45/arcTan(1);
if ys<0 then theta:=theta+180;
r:=sqrt(sqr(xs)+sqr(ys));
if r=0 then r:=999999 else r:=h/r;
showMessage(x,y,c
,'\',(x-w),-(y-w)
,'\',xs,'  ',ys
,'\',scale,unit,AspectRatio
,'\\r:  ',r/scale,unit,' /c (',xs:4:0
,')\theta:  ',theta,'    (',ys:4:0
,')\Value:',c:4:0
);
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 Thu Oct 22 04:12 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA13690;
	Thu, 22 Oct 1998 04:12:24 -0400 (EDT)
Resent-Date: Thu, 22 Oct 1998 04:12:24 -0400 (EDT)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: ort056@abdn.ac.uk, nih-image@io.ece.drexel.edu
Date:          Thu, 22 Oct 1998 18:05:26 GMT+1000
Subject:       Re: interior measurements
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <C2D7E9F4050@rna.bio.mq.edu.au>
Resent-Message-ID: <"2sbyl3.0.0P2.MQkBs"@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/519
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 2173

>From: "j.gregory" <ort056@abdn.ac.uk>
>Date: Tue, 20 Oct 1998 13:09:00 +0100 (BST)
>
>
>Whilst there are many automated procedures for measuring the size of an object 
>and the space it takes up, does anyone have a macro or method for measuring 
>the largest ellipse, rectangle or other regular object(not constrained to 
>horizontal and >vertical axis) that can fill the interior of an irregular ROI?
>
>Thanks in advance,
>
>Jenny Gregory
>
>----------------------
>Jenny Gregory
>Department of Orthopaedics
>University of Aberdeen
>Aberdeen
>Scotland

Jenny, your problem specs seem a little too unconstrained to me :-)
, however, in the absence of other responses,
the following may be of some interest.
_________________________
macro'/0 maximum internal circle of a roi';
var x,y,w,h,d,i,mi,r,xm,xx:integer;
begin
getRoi(x,y,w,h);
if w=0 then exit('selection required');
copy;
d:=trunc(sqrt(sqr(w)+sqr(h))+0.5);
if (d mod 2)=0 then d:=d+3 else d:=d+2;
setForeGround(255);setBackGround(0);
setNewSize(d,d);
makeNewWindow('circle');paste;fill;
binary('edm');
enhanceContrast;
resetCounter;
measure;
r:=rMax[rcount];
showMessage('maximum enclosed circle radius',r);
setDensitySlice(r-1,r);
setOptions('Area X-Y Center Min/Max Major Minor Angle');
analyzeParticles('');
undo;
mi:=2;
for i:=2 to rCount do 
  if rArea[i]>rArea[mi] then mi:=i; 
selectAll;copy;
makeOvalRoi(rX[mi]-r,rY[mi]-r,r+r,r+r);drawBoundary;
if rArea[mi]>3 then begin 
  SetScaling('Same Window Bilinear'{Nearest'});
  makeNewWindow('extend?');
  selectAll;
  y:=trunc(d/2)+1;
  moveRoi(d/2-rX[mi],d/2-rY[mi]);paste;selectAll;
  scaleAndRotate(1,1,rAngle[mi]);
  y:=trunc(d/2)+1;
  getRow(0,y,d);
  x:=y;while lineBuffer[x]>=r-1 do x:=x-1;xm:=x+1; 
  x:=y;while lineBuffer[x]>=r-1 do x:=x+1;xx:=x-1; 
  makeOvalRoi(xm-r,y-r,r+r,r+r);drawBoundary;
  makeOvalRoi(xx-r,y-r,r+r,r+r);drawBoundary;
  makeRoi(xm,y-r,xx-xm+1,r+r);drawBoundary;
  showMessage(r,y,xm,xx);
  tileWindows;
  end;
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-d-request@io.ece.drexel.edu Thu Oct 22 04:15 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA14727;
	Thu, 22 Oct 1998 04:15:15 -0400 (EDT)
Date: Thu, 22 Oct 1998 04:15:15 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810220815.EAA14727@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #94
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/94
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 10544

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 94

Today's Topics:
  Re: epoxy resin morphology            [ Carl Gustafson <carl.gustafson@cbis ]
  Re: video capture at 30 fps           [ SolamereTG@aol.com ]
  Colorcamera info needed               [ Cengizhan Ozturk <cozturk@mri.jhu.e ]
  Re: nih-image-d Digest V98 #93        [ Pat Arnott <pat@dri.edu> ]
  Data from FFT's                       [ "Goldsmith, Noel" <Noel.Goldsmith@d ]
  Re: Data from FFT's                   [ GJOSS@rna.bio.mq.edu.au ]

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

Date: Wed, 21 Oct 1998 07:59:21 -0400
From: Carl Gustafson <carl.gustafson@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: epoxy resin morphology
Message-Id: <v03110702b2537c984f04@[144.118.33.205]>
Content-Type: text/plain; charset="us-ascii"

...
>However, we are unable to detect any definite structural  feature. Can
>someone suggest some staining or etching tecnique suitable  to
>differentiate between an amourphous and a liquid crystalline epoxy resin
>in  the cured sample.
...

Will some solvent swell the amorphous phase and not the crystalline one?
Are there any substituents on one phase and not on the other that can be
substitued with something that can be made to absorb light differently?

It's been years since I did Real Chemistry.




Carl Gustafson
(215) 895-1383
===============================================================================
           the Computer Vision Center for Vertebrate Brain Mapping
===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I'd like to give you my opinion
===============================================================================

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

Date: Wed, 21 Oct 1998 15:13:23 EDT
From: SolamereTG@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re: video capture at 30 fps
Message-ID: <9b16cd57.362e3253@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

We use blind capture with  266 and 300 Mhz G-3 desktop models to capture at 30
fps to system Ram. The LG-3 board you have should be able to go into a G-3 and
do the same. I would borrow a G-3 MAC and try it out. You may still use NT but
you may need to capture an ROI rather than the full 640x480 image. 

George Peeters
Solamere Technology Group

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

Date: Wed, 21 Oct 1998 16:02:11 -0400 (EDT)
From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Colorcamera info needed
Message-ID: <Pine.SGI.3.91.981021155653.16063B-100000@henryv>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi,

I need a fast color CCD camera for a machine vision/inspection type
of application. I am at least 1 year behind what is the latest in the market.

Anybody has done a recent search ?
Can anybody give some pointers, web pages. 
Please send industrial responses directly to me by e-mail or fax 
(with prices)

My system will be a matrox capture board housed in a PC.

Thanks.

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

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

Date: Wed, 21 Oct 1998 16:00:05 +0000
From: Pat Arnott <pat@dri.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #93
Message-ID: <362E04FB.EE@dri.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi:

We loaded our lg3 with maximum memory and were able to digitize  frames
to card ram at 30 fps on any of our macs (8100 av, g3).  We could do
this within the memory available in RAM.  

I have also used the g3 av to digitize at 30 fps using adobe premier as
the software, and the built in video card on the mac.  However, the
images are smaller than with the scion board, and you do not have
control of the digitizer offset and gain like with the scion card.  
  
--
      Regards,
                       Pat Arnott
**********************************************************
* W. Patrick Arnott  702-677-3123   -3157 fax
* Atmospheric Sciences Center, Desert Research Institute
* PO Box 60220, RENO NV  89506
* http://www.dri.edu/Projects/replica/webWPA
**********************************************************

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

Date: Thu, 22 Oct 1998 10:36:41 +1000
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: Data from FFT's
Message-ID: <F98649A5EE8ED11190160000F802756598CEC5@exchvic3.dsto.defence.gov.au>
Content-Type: text/plain

Hi,
We are using NIH-Image to measure the spacings of groups of striations
observed on fracture surfaces.
The procedure is as follows using the FFT Macros.
Open or display an Image, which is spatially calibrated in microns or mm.
Select the size of square area to be used, Operator decision.
Position the square over the selected group of striations.
Type F  (FFT). (This is now so quick on a G3-300 that it is no longer the
slowest operation) 
Look at the Transform and position the cursor over one of the two distinct
peaks which appear on each side of the centre.
Read the value in the info window which tells about cycles per mm (Or
micron), and also give the angle this makes with the x axis.
Write down the numbers and proceed to the next place.


My question is:
Can I get this data into a macro so I don't have to write it down?
I see it is written in the info window, so it is there, how do I get it into
user1 and user2?

I spent some time reading the manual and could find nothing. I could have a
look at the source code, but thought I would ask first.
I guess this is a measurement which does not yet appear as an option in the
measurements option dialog, and may have to be added.
What I would propose is maybe a mouse click at the desired location to
record these parameters. But I really have no strong feelings about how to
do this job.
After all I am relying on a user decision about the location of the maximum
peak on the transform. For really precise work I suppose we should fit up
some 3-D surfaces across the peak and estimate the peak maximum position, or
fit up some 2-d curves across and up and down to try to locate the maximum.
Of course when you look at the scatter you get when measuring striations all
of this precision becomes academic. The spacing will vary by a factor of 2
or more over a range of very small distances, and the only way you get good
data is by getting lots of numbers. And doing it by using the FFT allows the
accumulation of many measurements, quickly.
Best regards
Noel.

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

Date:          Thu, 22 Oct 1998 18:00:50 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: Noel.Goldsmith@dsto.defence.gov.au, nih-image@io.ece.drexel.edu
Subject:       Re: Data from FFT's
Message-ID: <C2D6AEA324A@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: Data from FFT's
>Date: Thu, 22 Oct 1998 10:36:41 +1000
>
>Hi,
>We are using NIH-Image to measure the spacings of groups of striations
>observed on fracture surfaces.
>The procedure is as follows using the FFT Macros.
>Open or display an Image, which is spatially calibrated in microns or mm.
>Select the size of square area to be used, Operator decision.
>Position the square over the selected group of striations.
>Type F  (FFT). (This is now so quick on a G3-300 that it is no longer the
>slowest operation) 
>Look at the Transform and position the cursor over one of the two distinct
>peaks which appear on each side of the centre.
>Read the value in the info window which tells about cycles per mm (Or
>micron), and also give the angle this makes with the x axis.
>Write down the numbers and proceed to the next place.
>
>
>My question is:
>Can I get this data into a macro so I don't have to write it down?
>I see it is written in the info window, so it is there, how do I get it into
>user1 and user2?
>
>I spent some time reading the manual and could find nothing. I could have a
>look at the source code, but thought I would ask first.
>I guess this is a measurement which does not yet appear as an option in the
>measurements option dialog, and may have to be added.
>What I would propose is maybe a mouse click at the desired location to
>record these parameters. But I really have no strong feelings about how to
>do this job.
>After all I am relying on a user decision about the location of the maximum
>peak on the transform. For really precise work I suppose we should fit up
>some 3-D surfaces across the peak and estimate the peak maximum position, or
>fit up some 2-d curves across and up and down to try to locate the maximum.
>Of course when you look at the scatter you get when measuring striations all
>of this precision becomes academic. The spacing will vary by a factor of 2
>or more over a range of very small distances, and the only way you get good
>data is by getting lots of numbers. And doing it by using the FFT allows the
>accumulation of many measurements, quickly.
>Best regards
>Noel.
>
Noel, the FFT window is essentially a spatially scaled image 
with the origin central and using polar coordinates,
so the following macro will mimic the Info window values:

Place the cursor in the FFT window 
and press [t] to demonstrate.

macro'[t]est';
var x,y,c,w,h,scale,AspectRatio,xs,ys,r,theta:integer;
unit:string;begin
invertY(false);
getPicSize(w,h);w:=w/2;
getScale(scale,unit,AspectRatio);
getMouse(x,y);c:=getPixel(x,y);
xs:=x-w;
ys:=w-y;
if ys=0 then if xs>0 then theta:=0 else theta :=180
else theta:=90-arcTan(xs/ys)*45/arcTan(1);
if ys<0 then theta:=theta+180;
r:=sqrt(sqr(xs)+sqr(ys));
if r=0 then r:=999999 else r:=h/r;
showMessage(x,y,c
,'\',(x-w),-(y-w)
,'\',xs,'  ',ys
,'\',scale,unit,AspectRatio
,'\\r:  ',r/scale,unit,' /c (',xs:4:0
,')\theta:  ',theta,'    (',ys:4:0
,')\Value:',c:4:0
);
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

--------------------------------
End of nih-image-d Digest V98 Issue #94
***************************************

From nih-image-request@io.ece.drexel.edu Thu Oct 22 10:23 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA13357;
	Thu, 22 Oct 1998 10:22:59 -0400 (EDT)
Resent-Date: Thu, 22 Oct 1998 10:22:59 -0400 (EDT)
X-Authentication-Warning: rodan.syr.edu: manorato owned process doing -bs
Date: Thu, 22 Oct 1998 09:59:22 -0400 (EDT)
From: "Michael A. Norato" <manorato@mailbox.syr.edu>
X-Sender: manorato@rodan.syr.edu
To: nih-image@io.ece.drexel.edu
Subject: bubble measurements.
Message-ID: <Pine.SOL.3.95.981022095705.6867C-100000@rodan.syr.edu>
MIME-Version: 1.0
Resent-Message-ID: <"pype72.0.2S1.3hpBs"@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/520
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: 225

Does anyone know of an existing macro to measure bubble size
distributions? I want to measure bubbles which are less than 200 microns
in diameter.


mike norato
Dept. Chem. Eng. & Mat. Sci.
Syracuse University

315-443-3286


From nih-image-d-request@io.ece.drexel.edu Fri Oct 23 06:16 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA05247;
	Fri, 23 Oct 1998 06:16:29 -0400 (EDT)
Date: Fri, 23 Oct 1998 06:16:29 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810231016.GAA05247@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #95
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/95
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 3330

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 95

Today's Topics:
  Re: interior measurements             [ GJOSS@rna.bio.mq.edu.au ]
  bubble measurements.                  [ "Michael A. Norato" <manorato@mailb ]

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

Date:          Thu, 22 Oct 1998 18:05:26 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: ort056@abdn.ac.uk, nih-image@io.ece.drexel.edu
Subject:       Re: interior measurements
Message-ID: <C2D7E9F4050@rna.bio.mq.edu.au>

>From: "j.gregory" <ort056@abdn.ac.uk>
>Date: Tue, 20 Oct 1998 13:09:00 +0100 (BST)
>
>
>Whilst there are many automated procedures for measuring the size of an object 
>and the space it takes up, does anyone have a macro or method for measuring 
>the largest ellipse, rectangle or other regular object(not constrained to 
>horizontal and >vertical axis) that can fill the interior of an irregular ROI?
>
>Thanks in advance,
>
>Jenny Gregory
>
>----------------------
>Jenny Gregory
>Department of Orthopaedics
>University of Aberdeen
>Aberdeen
>Scotland

Jenny, your problem specs seem a little too unconstrained to me :-)
, however, in the absence of other responses,
the following may be of some interest.
_________________________
macro'/0 maximum internal circle of a roi';
var x,y,w,h,d,i,mi,r,xm,xx:integer;
begin
getRoi(x,y,w,h);
if w=0 then exit('selection required');
copy;
d:=trunc(sqrt(sqr(w)+sqr(h))+0.5);
if (d mod 2)=0 then d:=d+3 else d:=d+2;
setForeGround(255);setBackGround(0);
setNewSize(d,d);
makeNewWindow('circle');paste;fill;
binary('edm');
enhanceContrast;
resetCounter;
measure;
r:=rMax[rcount];
showMessage('maximum enclosed circle radius',r);
setDensitySlice(r-1,r);
setOptions('Area X-Y Center Min/Max Major Minor Angle');
analyzeParticles('');
undo;
mi:=2;
for i:=2 to rCount do 
  if rArea[i]>rArea[mi] then mi:=i; 
selectAll;copy;
makeOvalRoi(rX[mi]-r,rY[mi]-r,r+r,r+r);drawBoundary;
if rArea[mi]>3 then begin 
  SetScaling('Same Window Bilinear'{Nearest'});
  makeNewWindow('extend?');
  selectAll;
  y:=trunc(d/2)+1;
  moveRoi(d/2-rX[mi],d/2-rY[mi]);paste;selectAll;
  scaleAndRotate(1,1,rAngle[mi]);
  y:=trunc(d/2)+1;
  getRow(0,y,d);
  x:=y;while lineBuffer[x]>=r-1 do x:=x-1;xm:=x+1; 
  x:=y;while lineBuffer[x]>=r-1 do x:=x+1;xx:=x-1; 
  makeOvalRoi(xm-r,y-r,r+r,r+r);drawBoundary;
  makeOvalRoi(xx-r,y-r,r+r,r+r);drawBoundary;
  makeRoi(xm,y-r,xx-xm+1,r+r);drawBoundary;
  showMessage(r,y,xm,xx);
  tileWindows;
  end;
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: Thu, 22 Oct 1998 09:59:22 -0400 (EDT)
From: "Michael A. Norato" <manorato@mailbox.syr.edu>
To: nih-image@io.ece.drexel.edu
Subject: bubble measurements.
Message-ID: <Pine.SOL.3.95.981022095705.6867C-100000@rodan.syr.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Does anyone know of an existing macro to measure bubble size
distributions? I want to measure bubbles which are less than 200 microns
in diameter.


mike norato
Dept. Chem. Eng. & Mat. Sci.
Syracuse University

315-443-3286

--------------------------------
End of nih-image-d Digest V98 Issue #95
***************************************

From nih-image-request@io.ece.drexel.edu Fri Oct 23 06:53 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA09987;
	Fri, 23 Oct 1998 06:53:56 -0400 (EDT)
Resent-Date: Fri, 23 Oct 1998 06:53:56 -0400 (EDT)
X-Sender: sdb@pop1.liv.ac.uk
Message-Id: <l03130300b2560c17fe73@[138.253.47.16]>
In-Reply-To: <199810231002.GAA03423@io.ece.drexel.edu>
Mime-Version: 1.0
Date: Fri, 23 Oct 1998 11:40:13 +0100
To: nih-image@io.ece.drexel.edu
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
Subject: Re: bubble measurements
Cc: "Michael A. Norato" <manorato@mailbox.syr.edu>
Resent-Message-ID: <"NRLos.0.U02.Xq5Cs"@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/521
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: 727

>Does anyone know of an existing macro to measure bubble size
>distributions? I want to measure bubbles which are less than 200 microns
>in diameter.

The NIH Image spin-off 'Image SXM' can analyse circle size distributions. A
copy of the Image SXM installer is in the spin-offs folder on the NIH Image
server. You can find more information about Image SXM from
http://reg.ssci.liv.ac.uk

___________________________________________________________________

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

Tel: 44-(0)151-794-3874 / 3894 / 3870
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk

___________________________________________________________________



From nih-image-request@io.ece.drexel.edu Fri Oct 23 11:59 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA15754;
	Fri, 23 Oct 1998 11:59:38 -0400 (EDT)
Resent-Date: Fri, 23 Oct 1998 11:59:38 -0400 (EDT)
From: MASandberg@aol.com
Message-ID: <82ba1421.3630a107@aol.com>
Date: Fri, 23 Oct 1998 11:30:15 EDT
To: nih-image@io.ece.drexel.edu
Mime-Version: 1.0
Subject: Annular ROI.
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 for Mac sub 84
Resent-Message-ID: <"La2ch1.0.cD3.09ACs"@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/522
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: 544

When I try to save an annular ROI, which I created manually, as an outline in
NIH Image 1.62, I get the error message: "XY Coordinates are not available".
I have also tried to create it automatically with a macro with an option
command between the two makeovalROI commands, but only get the second
(smaller) circle to appear.  I would appreciate any advice on a solution.

Thanks,

Michael A. Sandberg, Ph.D.
Berman-Gund Laboratory for the Study of Retinal Degenerations
Massachusetts Eye and Ear Infirmary
243 Charles Street
Boston, MA 02114


From nih-image-d-request@io.ece.drexel.edu Sat Oct 24 06:09 EDT 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA11464;
	Sat, 24 Oct 1998 06:09:53 -0400 (EDT)
Date: Sat, 24 Oct 1998 06:09:53 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810241009.GAA11464@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #96
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/96
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 2242

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 96

Today's Topics:
  Re: bubble measurements               [ Steve Barrett <S.D.Barrett@liverpoo ]
  Annular ROI.                          [ MASandberg@aol.com ]

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

Date: Fri, 23 Oct 1998 11:40:13 +0100
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
To: nih-image@io.ece.drexel.edu
Cc: "Michael A. Norato" <manorato@mailbox.syr.edu>
Subject: Re: bubble measurements
Message-Id: <l03130300b2560c17fe73@[138.253.47.16]>
Content-Type: text/plain; charset="us-ascii"

>Does anyone know of an existing macro to measure bubble size
>distributions? I want to measure bubbles which are less than 200 microns
>in diameter.

The NIH Image spin-off 'Image SXM' can analyse circle size distributions. A
copy of the Image SXM installer is in the spin-offs folder on the NIH Image
server. You can find more information about Image SXM from
http://reg.ssci.liv.ac.uk

___________________________________________________________________

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

Tel: 44-(0)151-794-3874 / 3894 / 3870
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk

___________________________________________________________________

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

Date: Fri, 23 Oct 1998 11:30:15 EDT
From: MASandberg@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Annular ROI.
Message-ID: <82ba1421.3630a107@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

When I try to save an annular ROI, which I created manually, as an outline in
NIH Image 1.62, I get the error message: "XY Coordinates are not available".
I have also tried to create it automatically with a macro with an option
command between the two makeovalROI commands, but only get the second
(smaller) circle to appear.  I would appreciate any advice on a solution.

Thanks,

Michael A. Sandberg, Ph.D.
Berman-Gund Laboratory for the Study of Retinal Degenerations
Massachusetts Eye and Ear Infirmary
243 Charles Street
Boston, MA 02114

--------------------------------
End of nih-image-d Digest V98 Issue #96
***************************************

From nih-image-request@io.ece.drexel.edu Mon Oct 26 17:22 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA02798;
	Mon, 26 Oct 1998 17:22:07 -0500 (EST)
Resent-Date: Mon, 26 Oct 1998 17:22:07 -0500 (EST)
Message-Id: <3.0.5.32.19981027105320.00806610@uni.massey.ac.nz>
X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32)
Date: Tue, 27 Oct 1998 10:53:20 +1300
To: nih-image@io.ece.drexel.edu
From: Naomi Boxall <Naomi.Boxall.1@uni.massey.ac.nz>
Subject: Surely not the first....
Mime-Version: 1.0
Resent-Message-ID: <"Pm79q2.0.PN4.azEDs"@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/523
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: 1250

Dear all,

Hi.  I am a very new user of this program and I am doing my Masters In
Veterinary Studies (Epidemiology).  The thesis is built of Image Analysis
and Molecular Epidemiology.  By word of mouth, I have heard that NIH Image
is the best program to use for analysis of EtBr gels (from PFGE).  However
I have come across a few little roadblocks in my path to get the computer
to say in numbers, what I see with my eyes!

I'm sure I can't have been the only one with these problems and would
really appreciate if someone could possibly help out.  

a) How can I calibrate a lambda ladder?  I have read the 'help' file and I
have read the NIH tutorial.  I have no idea what the optical density of the
bands are.  How do I find this out???

b) How can I read the distances from the origin to the peaks without
pointing the mouse over the peak (obtained using the GelPlot2 Macro) and
reading the x-axis value?  Presumably, because the macro delivers the
results by way of graph, then the numerical values for the plot must be
somewhere...where?

Thanks for your time.
Naomi




Naomi S. Boxall BSc
Epicentre
Inst. of Vet, Animal & Biomedical Sciences
Massey University
Palmerston North
New Zealand

064-6-3504008 (W)
Naomi.Boxall.1@uni.massey.ac.nz


From nih-image-request@io.ece.drexel.edu Tue Oct 27 04:29 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA17184;
	Tue, 27 Oct 1998 04:29:52 -0500 (EST)
Resent-Date: Tue, 27 Oct 1998 04:29:52 -0500 (EST)
X-Sender: elk@129.233.21.18
Message-Id: <l03130300b25b3785f82d@[129.233.21.143]>
Mime-Version: 1.0
Date: Tue, 27 Oct 1998 10:04:35 +0100
To: nih-image@io.ece.drexel.edu
From: Ben Elkin <elk@IGB.FhG.de>
Subject: digital photo camera f. microscopy
Resent-Message-ID: <"HKSV12.0.YA1.4qODs"@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/524
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: 1140

Hallo everybody,

we consider equipping still another microscope with a computer-connected
camera. The idea now is to take one of these new digital *photographic*
cameras which begin to penetrate consumer and professional photography
market. They are sensitive enough for our purposes, offer color capture at
the same or higher resolution as compared to video cameras, and cost (which
is important for us now) below 2000 $. That computer can, but must not be
connected to the camera, is also an advantage. The image compression is
usually (or always?) built in, which may be a considerable drawback, but we
could live with it.

The problem is that these cameras have mostly (or always?) built-in lens,
so we don't know how to adapt it to the microscope. Does anybody have the
experience or any ideas?


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 Oct 27 05:02 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA04274;
	Tue, 27 Oct 1998 05:02:54 -0500 (EST)
Resent-Date: Tue, 27 Oct 1998 05:02:54 -0500 (EST)
Date: Tue, 27 Oct 1998 09:48:26 +0000 (GMT)
From: Jan Kreft <Kreft@cardiff.ac.uk>
X-Sender: sabjk@thor
To: nih-image@io.ece.drexel.edu
Subject: Re: digital photo camera f. microscopy
In-Reply-To: <l03130300b25b3785f82d@[129.233.21.143]>
Message-ID: <Pine.OSF.3.95q.981027093428.26928A-100000@thor>
MIME-Version: 1.0
Resent-Message-ID: <"RnGcR.0.fc6.SSPDs"@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/525
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: 2020

Hi Ben,

have a look at Kodak MDS 120 System (Microscopy Documentation System) on
their website www.kodak.com.

They couple a consumer-market digital camera (DC 120, a somewhat dated
model) with a non-removabel lens to a microscope with the help of a
special adaptor. SLR-body digital cameras are a lot more expensive but
better. You can get adaptors for SLR-body cameras (digital or not) to
C-mounts etc. from Diagnostics Instruments (www.diaginc.com). 

There are many useful links for digital cameras and microscopy on:
http://www.mwrn.com/product/image/camera.htm

Hope that helps,

Jan.

Jan Kreft				Phone +44 (0)1222 876036
Cardiff School of Biosciences		Fax   +44 (0)1222 874305
Cardiff	University 			E-mail Kreft@cardiff.ac.uk
PO Box 915, Cardiff CF1 3TL, UK

On Tue, 27 Oct 1998, Ben Elkin wrote:

> Hallo everybody,
> 
> we consider equipping still another microscope with a computer-connected
> camera. The idea now is to take one of these new digital *photographic*
> cameras which begin to penetrate consumer and professional photography
> market. They are sensitive enough for our purposes, offer color capture at
> the same or higher resolution as compared to video cameras, and cost (which
> is important for us now) below 2000 $. That computer can, but must not be
> connected to the camera, is also an advantage. The image compression is
> usually (or always?) built in, which may be a considerable drawback, but we
> could live with it.
> 
> The problem is that these cameras have mostly (or always?) built-in lens,
> so we don't know how to adapt it to the microscope. Does anybody have the
> experience or any ideas?
> 
> 
> 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 Oct 27 05:40 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA23973;
	Tue, 27 Oct 1998 05:40:31 -0500 (EST)
Resent-Date: Tue, 27 Oct 1998 05:40:31 -0500 (EST)
Message-Id: <3.0.32.19981027101754.008c0c00@mail-server>
X-Sender: wtm@mail-server
X-Mailer: Windows Eudora Pro Version 3.0 (32)
Date: Tue, 27 Oct 1998 10:18:00 +0000
To: nih-image@io.ece.drexel.edu
From: Bill Mason <wtm@lsr.co.uk>
Subject: New Digital Cameras for Mac and NIH Image
Mime-Version: 1.0
X-Hops: 1
Resent-Message-ID: <"t9-6h.0.xP3.kwPDs"@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/526
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: 1411

Readers of the list might like to know that our cooled precision digital
CCD cameras for microscopy are now fully supported with a Photoshop and NIH
Image-compatible plugin, as well as a new standalone software package for
the Mac. We offer an outstanding range of high performance cameras for
microscopy employing interline transfer, frame transfer and full frame CCD
chips with a variety of readout speeds. The new plugin which is available
operates with Mac OS7.5 or above or OS8 or above, and utilises a PCI card
on PowerMacs or the new G3 Mac platform. The software support offers full
use of all the camera facilities for control of binning, subarrays,
integration time etc. We also offer RGB filter control for the Mac
environment within NIH Image, for true colour imaging. 

This of course is in addition to our existing Windows 95 PC support.

For further information, please contact us directly rather than sending a
reply to the list! We also have some details on our Web site, the address
of which is given below.

I hope this information is helpful.

Dr. Bill Mason
Life Science Resources Ltd.
Abberley House, Granham's Road
Great Shelford, Cambridge  CB2  5LQ
United Kingdom
Tel 44-(0)1223-845836
Fax 44-(0)1223-840342

In the USA at:
Two Corporate Center Drive
Melville, NY  11747-3157
Tel 516-8445085
Fax 516-8445093
Freephone 1-800-7479530

Email: WTM@LSR.CO.UK
Web Site: http://www.lsr.co.uk


From nih-image-request@io.ece.drexel.edu Tue Oct 27 07:11 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id HAA10898;
	Tue, 27 Oct 1998 07:11:10 -0500 (EST)
Resent-Date: Tue, 27 Oct 1998 07:11:10 -0500 (EST)
X-Sender: steinr@pop.chembio.ntnu.no
Message-Id: <v03102808b25b639f4f9e@[129.241.39.133]>
Mime-Version: 1.0
Date: Tue, 27 Oct 1998 13:53:57 +0200
To: nih-image@io.ece.drexel.edu
From: Stein Roervik <steinr@chembio.ntnu.no>
Subject: Problems with Scion Image for NT
Cc: Gary Chinga <gary.chinga@pfi.no>
Resent-Message-ID: <"3Ttl_3.0.uI.NGRDs"@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/527
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: 949

A friend of me is having problems with Scion Image running on Windows NT
and asked me to post a request to the list if anyone knows any solution to
the problem:

He has a Cinet PC with NT 4.0 and 128 megs RAM. He has installed Scion
Image for PC vers. 1.0.01. The program crashes frequently, several times an
hour. Upon opening, the error message "Error getting handle to NT driver"
appears.

You may forward your reply directly to Gary Chinga <gary.chinga@pfi.no>.

+---------------------------------------------------------+
|  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 Tue Oct 27 10:27 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA19610;
	Tue, 27 Oct 1998 10:27:59 -0500 (EST)
Resent-Date: Tue, 27 Oct 1998 10:27:59 -0500 (EST)
Message-ID: <19981027145337.29598.rocketmail@web4.rocketmail.com>
Date: Tue, 27 Oct 1998 06:53:37 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
Subject: Re: Surely not the first....
To: nih-image@io.ece.drexel.edu
MIME-Version: 1.0
Resent-Message-ID: <"70KwT.0.mh.lyTDs"@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/528
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: 1153


> a) How can I calibrate a lambda ladder?  I have read the 'help' file and I
> have read the NIH tutorial.  I have no idea what the optical density of the
> bands are.  How do I find this out???

You can calibrate your data to any unit you want. OD is directly proportional
to concentration by Beer's law so many use this, but if you have other actual
units, by all means use these.
 
> b) How can I read the distances from the origin to the peaks without
> pointing the mouse over the peak (obtained using the GelPlot2 Macro) and
> reading the x-axis value?  Presumably, because the macro delivers the
> results by way of graph, then the numerical values for the plot must be
> somewhere...where?

The program is setup to read area under the curve as the integral of densities
for a band. I'm sure you can calibrate ("set scale") to distances like mm and
measure distance if you need that as well. This should be very easy. See set
scale in manual.

Mark Vivino
mvivino@rocketmail.com
Consulting Biomedical Engineer 


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


From nih-image-request@io.ece.drexel.edu Tue Oct 27 10:28 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA19672;
	Tue, 27 Oct 1998 10:28:05 -0500 (EST)
Resent-Date: Tue, 27 Oct 1998 10:28:05 -0500 (EST)
Message-ID: <19981027145435.9336.rocketmail@attach1.rocketmail.com>
Date: Tue, 27 Oct 1998 06:54:35 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
Subject: Re: bubble measurements.
To: nih-image@io.ece.drexel.edu
MIME-Version: 1.0
Resent-Message-ID: <"D_Vee1.0.j61.k_TDs"@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/529
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: 468


> Does anyone know of an existing macro to measure bubble size
> distributions? I want to measure bubbles which are less than 200 microns
> in diameter.

Did you try the analyze particles routines? Or did that not work for a variety
of reasons? Do your bubbles touch?

Mark Vivino
mvivino@rocketmail.com
Consulting Biomedical Engineer
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-d-request@io.ece.drexel.edu Tue Oct 27 10:32 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA22224;
	Tue, 27 Oct 1998 10:32:32 -0500 (EST)
Date: Tue, 27 Oct 1998 10:32:32 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810271532.KAA22224@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #97
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/97
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 10398

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 97

Today's Topics:
  Surely not the first....              [ Naomi Boxall <Naomi.Boxall.1@uni.ma ]
  digital photo camera f. microscopy    [ Ben Elkin <elk@IGB.FhG.de> ]
  Re: digital photo camera f. microsco  [ Jan Kreft <Kreft@cardiff.ac.uk> ]
  New Digital Cameras for Mac and NIH   [ Bill Mason <wtm@lsr.co.uk> ]
  Problems with Scion Image for NT      [ Stein Roervik <steinr@chembio.ntnu. ]
  Re: Surely not the first....          [ Mark Vivino <mvivino@rocketmail.com ]

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

Date: Tue, 27 Oct 1998 10:53:20 +1300
From: Naomi Boxall <Naomi.Boxall.1@uni.massey.ac.nz>
To: nih-image@io.ece.drexel.edu
Subject: Surely not the first....
Message-Id: <3.0.5.32.19981027105320.00806610@uni.massey.ac.nz>
Content-Type: text/plain; charset="us-ascii"

Dear all,

Hi.  I am a very new user of this program and I am doing my Masters In
Veterinary Studies (Epidemiology).  The thesis is built of Image Analysis
and Molecular Epidemiology.  By word of mouth, I have heard that NIH Image
is the best program to use for analysis of EtBr gels (from PFGE).  However
I have come across a few little roadblocks in my path to get the computer
to say in numbers, what I see with my eyes!

I'm sure I can't have been the only one with these problems and would
really appreciate if someone could possibly help out.  

a) How can I calibrate a lambda ladder?  I have read the 'help' file and I
have read the NIH tutorial.  I have no idea what the optical density of the
bands are.  How do I find this out???

b) How can I read the distances from the origin to the peaks without
pointing the mouse over the peak (obtained using the GelPlot2 Macro) and
reading the x-axis value?  Presumably, because the macro delivers the
results by way of graph, then the numerical values for the plot must be
somewhere...where?

Thanks for your time.
Naomi




Naomi S. Boxall BSc
Epicentre
Inst. of Vet, Animal & Biomedical Sciences
Massey University
Palmerston North
New Zealand

064-6-3504008 (W)
Naomi.Boxall.1@uni.massey.ac.nz

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

Date: Tue, 27 Oct 1998 10:04:35 +0100
From: Ben Elkin <elk@IGB.FhG.de>
To: nih-image@io.ece.drexel.edu
Subject: digital photo camera f. microscopy
Message-Id: <l03130300b25b3785f82d@[129.233.21.143]>
Content-Type: text/plain; charset="us-ascii"

Hallo everybody,

we consider equipping still another microscope with a computer-connected
camera. The idea now is to take one of these new digital *photographic*
cameras which begin to penetrate consumer and professional photography
market. They are sensitive enough for our purposes, offer color capture at
the same or higher resolution as compared to video cameras, and cost (which
is important for us now) below 2000 $. That computer can, but must not be
connected to the camera, is also an advantage. The image compression is
usually (or always?) built in, which may be a considerable drawback, but we
could live with it.

The problem is that these cameras have mostly (or always?) built-in lens,
so we don't know how to adapt it to the microscope. Does anybody have the
experience or any ideas?


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, 27 Oct 1998 09:48:26 +0000 (GMT)
From: Jan Kreft <Kreft@cardiff.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: digital photo camera f. microscopy
Message-ID: <Pine.OSF.3.95q.981027093428.26928A-100000@thor>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi Ben,

have a look at Kodak MDS 120 System (Microscopy Documentation System) on
their website www.kodak.com.

They couple a consumer-market digital camera (DC 120, a somewhat dated
model) with a non-removabel lens to a microscope with the help of a
special adaptor. SLR-body digital cameras are a lot more expensive but
better. You can get adaptors for SLR-body cameras (digital or not) to
C-mounts etc. from Diagnostics Instruments (www.diaginc.com). 

There are many useful links for digital cameras and microscopy on:
http://www.mwrn.com/product/image/camera.htm

Hope that helps,

Jan.

Jan Kreft				Phone +44 (0)1222 876036
Cardiff School of Biosciences		Fax   +44 (0)1222 874305
Cardiff	University 			E-mail Kreft@cardiff.ac.uk
PO Box 915, Cardiff CF1 3TL, UK

On Tue, 27 Oct 1998, Ben Elkin wrote:

> Hallo everybody,
> 
> we consider equipping still another microscope with a computer-connected
> camera. The idea now is to take one of these new digital *photographic*
> cameras which begin to penetrate consumer and professional photography
> market. They are sensitive enough for our purposes, offer color capture at
> the same or higher resolution as compared to video cameras, and cost (which
> is important for us now) below 2000 $. That computer can, but must not be
> connected to the camera, is also an advantage. The image compression is
> usually (or always?) built in, which may be a considerable drawback, but we
> could live with it.
> 
> The problem is that these cameras have mostly (or always?) built-in lens,
> so we don't know how to adapt it to the microscope. Does anybody have the
> experience or any ideas?
> 
> 
> 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, 27 Oct 1998 10:18:00 +0000
From: Bill Mason <wtm@lsr.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: New Digital Cameras for Mac and NIH Image
Message-Id: <3.0.32.19981027101754.008c0c00@mail-server>
Content-Type: text/plain; charset="us-ascii"

Readers of the list might like to know that our cooled precision digital
CCD cameras for microscopy are now fully supported with a Photoshop and NIH
Image-compatible plugin, as well as a new standalone software package for
the Mac. We offer an outstanding range of high performance cameras for
microscopy employing interline transfer, frame transfer and full frame CCD
chips with a variety of readout speeds. The new plugin which is available
operates with Mac OS7.5 or above or OS8 or above, and utilises a PCI card
on PowerMacs or the new G3 Mac platform. The software support offers full
use of all the camera facilities for control of binning, subarrays,
integration time etc. We also offer RGB filter control for the Mac
environment within NIH Image, for true colour imaging. 

This of course is in addition to our existing Windows 95 PC support.

For further information, please contact us directly rather than sending a
reply to the list! We also have some details on our Web site, the address
of which is given below.

I hope this information is helpful.

Dr. Bill Mason
Life Science Resources Ltd.
Abberley House, Granham's Road
Great Shelford, Cambridge  CB2  5LQ
United Kingdom
Tel 44-(0)1223-845836
Fax 44-(0)1223-840342

In the USA at:
Two Corporate Center Drive
Melville, NY  11747-3157
Tel 516-8445085
Fax 516-8445093
Freephone 1-800-7479530

Email: WTM@LSR.CO.UK
Web Site: http://www.lsr.co.uk

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

Date: Tue, 27 Oct 1998 13:53:57 +0200
From: Stein Roervik <steinr@chembio.ntnu.no>
To: nih-image@io.ece.drexel.edu
Cc: Gary Chinga <gary.chinga@pfi.no>
Subject: Problems with Scion Image for NT
Message-Id: <v03102808b25b639f4f9e@[129.241.39.133]>
Content-Type: text/plain; charset="us-ascii"

A friend of me is having problems with Scion Image running on Windows NT
and asked me to post a request to the list if anyone knows any solution to
the problem:

He has a Cinet PC with NT 4.0 and 128 megs RAM. He has installed Scion
Image for PC vers. 1.0.01. The program crashes frequently, several times an
hour. Upon opening, the error message "Error getting handle to NT driver"
appears.

You may forward your reply directly to Gary Chinga <gary.chinga@pfi.no>.

+---------------------------------------------------------+
|  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: Tue, 27 Oct 1998 06:53:37 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Surely not the first....
Message-ID: <19981027145337.29598.rocketmail@web4.rocketmail.com>
Content-Type: text/plain; charset=us-ascii

> a) How can I calibrate a lambda ladder?  I have read the 'help' file and I
> have read the NIH tutorial.  I have no idea what the optical density of the
> bands are.  How do I find this out???

You can calibrate your data to any unit you want. OD is directly proportional
to concentration by Beer's law so many use this, but if you have other actual
units, by all means use these.
 
> b) How can I read the distances from the origin to the peaks without
> pointing the mouse over the peak (obtained using the GelPlot2 Macro) and
> reading the x-axis value?  Presumably, because the macro delivers the
> results by way of graph, then the numerical values for the plot must be
> somewhere...where?

The program is setup to read area under the curve as the integral of densities
for a band. I'm sure you can calibrate ("set scale") to distances like mm and
measure distance if you need that as well. This should be very easy. See set
scale in manual.

Mark Vivino
mvivino@rocketmail.com
Consulting Biomedical Engineer 


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

--------------------------------
End of nih-image-d Digest V98 Issue #97
***************************************

From nih-image-request@io.ece.drexel.edu Wed Oct 28 03:34 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id DAA04530;
	Wed, 28 Oct 1998 03:34:00 -0500 (EST)
Resent-Date: Wed, 28 Oct 1998 03:34:00 -0500 (EST)
Date: Wed, 28 Oct 1998 09:16:53 +0100
From: Ard Jonker <a.jonker@AMC.UVA.NL>
Subject: Re: digital photo camera f. microscopy
In-reply-to: <199810271503.KAA06277@io.ece.drexel.edu>
X-Sender: ajonker.public.amc@reddwarf.amc.uva.nl
To: nih-image@io.ece.drexel.edu
Message-id: <l03130302b25c8147acf3@[145.117.43.50]>
MIME-version: 1.0
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id DAA26942
Resent-Message-ID: <"5uMpx2.0.Qb6.PEjDs"@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/531
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: 590

>we consider equipping still another microscope with a computer-connected
>camera. The idea now is to take one of these new digital *photographic*
>cameras 

Keep your eye on http://www.imagek.com which has announced (and demonstrated) a digital film under $1000 for your current photocamera body. It takes the place of the ordinary film and after 30 exposures you take it out, connect it to an interface (mac or pc) and drain the cassete. 1280x1024 is said to be the resolution. I have no connections with the company, I'm just very curious for the results when used in microscopy.

Ard



From nih-image-d-request@io.ece.drexel.edu Wed Oct 28 03:34 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id DAA04944;
	Wed, 28 Oct 1998 03:34:42 -0500 (EST)
Date: Wed, 28 Oct 1998 03:34:42 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810280834.DAA04944@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #98
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/98
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 1875

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 98

Today's Topics:
  Re: bubble measurements.              [ Mark Vivino <mvivino@rocketmail.com ]
  Re: digital photo camera f. microsco  [ Vincenzo Della Mea <dellamea@dimi.u ]

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

Date: Tue, 27 Oct 1998 06:54:35 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: bubble measurements.
Message-ID: <19981027145435.9336.rocketmail@attach1.rocketmail.com>
Content-Type: text/plain; charset=us-ascii

> Does anyone know of an existing macro to measure bubble size
> distributions? I want to measure bubbles which are less than 200 microns
> in diameter.

Did you try the analyze particles routines? Or did that not work for a variety
of reasons? Do your bubbles touch?

Mark Vivino
mvivino@rocketmail.com
Consulting Biomedical Engineer
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com

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

Date: Wed, 28 Oct 1998 09:17:47 +0100
From: Vincenzo Della Mea <dellamea@dimi.uniud.it>
To: nih-image@io.ece.drexel.edu
Subject: Re: digital photo camera f. microscopy
Message-Id: <l03130301b25c7e319970@[158.110.70.161]>
Content-Type: text/plain; charset="us-ascii"

>we consider equipping still another microscope with a computer-connected
>camera. The idea now is to take one of these new digital *photographic*
>cameras which begin to penetrate consumer and professional photography

try to look also at Olympus cameras: they are selling a consumer-based
microscope digital camera which is cheap but very nice, with C-mount.
(http://www.olympus-europa.com/mikro/dp10.htm).

Vincenzo

--------------------------------
End of nih-image-d Digest V98 Issue #98
***************************************

From nih-image-request@io.ece.drexel.edu Wed Oct 28 03:34 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id DAA05055;
	Wed, 28 Oct 1998 03:34:53 -0500 (EST)
Resent-Date: Wed, 28 Oct 1998 03:34:53 -0500 (EST)
X-Sender: dellamea@ten.dimi.uniud.it
Message-Id: <l03130301b25c7e319970@[158.110.70.161]>
In-Reply-To: <199810271521.KAA15779@io.ece.drexel.edu>
Mime-Version: 1.0
Date: Wed, 28 Oct 1998 09:17:47 +0100
To: nih-image@io.ece.drexel.edu
From: Vincenzo Della Mea <dellamea@dimi.uniud.it>
Subject: Re: digital photo camera f. microscopy
Resent-Message-ID: <"PXorH3.0.mT6.bDjDs"@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/530
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: 421

>we consider equipping still another microscope with a computer-connected
>camera. The idea now is to take one of these new digital *photographic*
>cameras which begin to penetrate consumer and professional photography

try to look also at Olympus cameras: they are selling a consumer-based
microscope digital camera which is cheap but very nice, with C-mount.
(http://www.olympus-europa.com/mikro/dp10.htm).

Vincenzo



From nih-image-request@io.ece.drexel.edu Wed Oct 28 08:16 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA12203;
	Wed, 28 Oct 1998 08:16:55 -0500 (EST)
Resent-Date: Wed, 28 Oct 1998 08:16:55 -0500 (EST)
Message-ID: <36371457.6CC5557D@sdsc.edu>
Date: Wed, 28 Oct 1998 04:55:51 -0800
From: "Harvey J. Karten" <kartenh@sdsc.edu>
Reply-To: hjkarten@UCSD.EDU
Organization: UCSD
X-Mailer: Mozilla 4.04 [en] (Win95; U)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: Olympus digital camera
References: <199810280833.DAA04104@io.ece.drexel.edu>
Resent-Message-ID: <"gkD9D.0.Ia.JHnDs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/532
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: multipart/alternative; boundary="------------1DB4DE75091445ED637D0443"
Content-Length: 2116


--------------1DB4DE75091445ED637D0443
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Is that a one chip or a three chip camera? Can it be used as a full
resolution monochrome at 1280x1024? What is the effective ASA? Can it be
used for Nomarski? Fluorescence? Dark Field?

Many thanks,
Harvey Karten

Vincenzo Della Mea wrote:
try to look also at Olympus cameras: they are selling a consumer-based
microscope digital camera which is cheap but very nice, with C-mount.
(http://www.olympus-europa.com/mikro/dp10.htm).


--
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

WCBR Program for 1999:
PLEASE NOTE CHANGE OF WEB ADDRESS
http://www.wcbrBrain.org


--------------1DB4DE75091445ED637D0443
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<HTML>
Is that a one chip or a three chip camera? Can it be used as a full resolution
monochrome at 1280x1024? What is the effective ASA? Can it be used for
Nomarski? Fluorescence? Dark Field?

<P>Many thanks,
<BR>Harvey Karten

<P>Vincenzo Della Mea wrote:
<BR><I>try to look also at Olympus cameras: they are selling a consumer-based</I>
<BR><I>microscope digital camera which is cheap but very nice, with C-mount.</I>
<BR><I>(<A HREF="http://www.olympus-europa.com/mikro/dp10.htm">http://www.olympus-europa.com/mikro/dp10.htm</A>).</I>
<BR>&nbsp;

<P>--
<BR>Harvey J. Karten, M.D.
<BR>Dept. of Neurosciences
<BR>University of California at San Diego
<BR>La Jolla, CA 92093-0608
<BR>Phone (Voice): 619-534-4938
<BR>FAX:&nbsp; 619-534-6602
<BR>EMail: HJKarten@ucsd.edu
<BR>Alternate Email: kartenh@sdsc.edu
<BR>Retina Information System: <A HREF="http://www-cajal.ucsd.edu">http://www-cajal.ucsd.edu</A>

<P>WCBR Program for 1999:
<BR>PLEASE NOTE CHANGE OF WEB ADDRESS
<BR><A HREF="http://www.wcbrBrain.org">http://www.wcbrBrain.org</A>
<BR>&nbsp;</HTML>

--------------1DB4DE75091445ED637D0443--


From nih-image-request@io.ece.drexel.edu Wed Oct 28 09:43 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA21664;
	Wed, 28 Oct 1998 09:43:32 -0500 (EST)
Resent-Date: Wed, 28 Oct 1998 09:43:32 -0500 (EST)
X-Authentication-Warning: rodan.syr.edu: manorato owned process doing -bs
Date: Wed, 28 Oct 1998 09:22:14 -0500 (EST)
From: "Michael A. Norato" <manorato@mailbox.syr.edu>
X-Sender: manorato@rodan.syr.edu
To: nih-image@io.ece.drexel.edu
cc: nih-image-d@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #98
In-Reply-To: <199810280836.DAA05729@io.ece.drexel.edu>
Message-ID: <Pine.SOL.3.95.981028092115.3564H-100000@rodan.syr.edu>
MIME-Version: 1.0
Resent-Message-ID: <"jEQtR1.0.Wu2.VYoDs"@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/533
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: 300

I have tried the Analyse particles routines, but it does not appear to
yield an explicit bubbles size distribution.

Sometimes the bubbles touch, but not often.

mike norato
Syracuse University.

On Wed, 28 Oct 1998 nih-image-d-request@io.ece.drexel.edu wrote:


  [NON-Text Body part not included]


From nih-image-d-request@io.ece.drexel.edu Thu Oct 29 06:20 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA29383;
	Thu, 29 Oct 1998 06:20:35 -0500 (EST)
Date: Thu, 29 Oct 1998 06:20:35 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810291120.GAA29383@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #99
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/99
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 4448

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 99

Today's Topics:
  Re: digital photo camera f. microsco  [ Ard Jonker <a.jonker@AMC.UVA.NL> ]
  Re: Olympus digital camera            [ "Harvey J. Karten" <kartenh@sdsc.ed ]
  Re: nih-image-d Digest V98 #98        [ "Michael A. Norato" <manorato@mailb ]

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

Date: Wed, 28 Oct 1998 09:16:53 +0100
From: Ard Jonker <a.jonker@AMC.UVA.NL>
To: nih-image@io.ece.drexel.edu
Subject: Re: digital photo camera f. microscopy
Message-id: <l03130302b25c8147acf3@[145.117.43.50]>
Content-type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 8bit

>we consider equipping still another microscope with a computer-connected
>camera. The idea now is to take one of these new digital *photographic*
>cameras 

Keep your eye on http://www.imagek.com which has announced (and demonstrated) a digital film under $1000 for your current photocamera body. It takes the place of the ordinary film and after 30 exposures you take it out, connect it to an interface (mac or pc) and drain the cassete. 1280x1024 is said to be the resolution. I have no connections with the company, I'm just very curious for the results when used in microscopy.

Ard

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

Date: Wed, 28 Oct 1998 04:55:51 -0800
From: "Harvey J. Karten" <kartenh@sdsc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Olympus digital camera
Message-ID: <36371457.6CC5557D@sdsc.edu>
Content-Type: multipart/alternative; boundary="------------1DB4DE75091445ED637D0443"

--------------1DB4DE75091445ED637D0443
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Is that a one chip or a three chip camera? Can it be used as a full
resolution monochrome at 1280x1024? What is the effective ASA? Can it be
used for Nomarski? Fluorescence? Dark Field?

Many thanks,
Harvey Karten

Vincenzo Della Mea wrote:
try to look also at Olympus cameras: they are selling a consumer-based
microscope digital camera which is cheap but very nice, with C-mount.
(http://www.olympus-europa.com/mikro/dp10.htm).


--
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

WCBR Program for 1999:
PLEASE NOTE CHANGE OF WEB ADDRESS
http://www.wcbrBrain.org


--------------1DB4DE75091445ED637D0443
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<HTML>
Is that a one chip or a three chip camera? Can it be used as a full resolution
monochrome at 1280x1024? What is the effective ASA? Can it be used for
Nomarski? Fluorescence? Dark Field?

<P>Many thanks,
<BR>Harvey Karten

<P>Vincenzo Della Mea wrote:
<BR><I>try to look also at Olympus cameras: they are selling a consumer-based</I>
<BR><I>microscope digital camera which is cheap but very nice, with C-mount.</I>
<BR><I>(<A HREF="http://www.olympus-europa.com/mikro/dp10.htm">http://www.olympus-europa.com/mikro/dp10.htm</A>).</I>
<BR>&nbsp;

<P>--
<BR>Harvey J. Karten, M.D.
<BR>Dept. of Neurosciences
<BR>University of California at San Diego
<BR>La Jolla, CA 92093-0608
<BR>Phone (Voice): 619-534-4938
<BR>FAX:&nbsp; 619-534-6602
<BR>EMail: HJKarten@ucsd.edu
<BR>Alternate Email: kartenh@sdsc.edu
<BR>Retina Information System: <A HREF="http://www-cajal.ucsd.edu">http://www-cajal.ucsd.edu</A>

<P>WCBR Program for 1999:
<BR>PLEASE NOTE CHANGE OF WEB ADDRESS
<BR><A HREF="http://www.wcbrBrain.org">http://www.wcbrBrain.org</A>
<BR>&nbsp;</HTML>

--------------1DB4DE75091445ED637D0443--

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

Date: Wed, 28 Oct 1998 09:22:14 -0500 (EST)
From: "Michael A. Norato" <manorato@mailbox.syr.edu>
To: nih-image@io.ece.drexel.edu
cc: nih-image-d@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #98
Message-ID: <Pine.SOL.3.95.981028092115.3564H-100000@rodan.syr.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I have tried the Analyse particles routines, but it does not appear to
yield an explicit bubbles size distribution.

Sometimes the bubbles touch, but not often.

mike norato
Syracuse University.

On Wed, 28 Oct 1998 nih-image-d-request@io.ece.drexel.edu wrote:


  [NON-Text Body part not included]

--------------------------------
End of nih-image-d Digest V98 Issue #99
***************************************

From nih-image-request@io.ece.drexel.edu Thu Oct 29 07:20 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id HAA29590;
	Thu, 29 Oct 1998 07:20:42 -0500 (EST)
Resent-Date: Thu, 29 Oct 1998 07:20:42 -0500 (EST)
Message-Id: <3.0.5.32.19981029065646.007d86a0@mohawk.net>
X-Sender: microbill@mohawk.net
X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32)
Date: Thu, 29 Oct 1998 06:56:46 -0500
To: nih-image@io.ece.drexel.edu
From: Bill Miller <microbill@mohawk.net>
Subject: Re: digital photo camera f. microscopy
In-Reply-To: <l03130300b25b3785f82d@[129.233.21.143]>
Mime-Version: 1.0
Resent-Message-ID: <"obrVP1.0.xR4.HX5Es"@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/534
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: 1293

See http://www.soundvision.com   digital  made for microscopy w/o lens.



At 10:04 AM 10/27/98 +0100, you wrote:
>Hallo everybody,
>
>we consider equipping still another microscope with a computer-connected
>camera. The idea now is to take one of these new digital *photographic*
>cameras which begin to penetrate consumer and professional photography
>market. They are sensitive enough for our purposes, offer color capture at
>the same or higher resolution as compared to video cameras, and cost (which
>is important for us now) below 2000 $. That computer can, but must not be
>connected to the camera, is also an advantage. The image compression is
>usually (or always?) built in, which may be a considerable drawback, but we
>could live with it.
>
>The problem is that these cameras have mostly (or always?) built-in lens,
>so we don't know how to adapt it to the microscope. Does anybody have the
>experience or any ideas?
>
>
>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 Oct 29 11:05 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA27710;
	Thu, 29 Oct 1998 11:05:50 -0500 (EST)
Resent-Date: Thu, 29 Oct 1998 11:05:50 -0500 (EST)
X-Sender: dellamea@ten.dimi.uniud.it
Message-Id: <l03130302b25e0187bd8d@[158.110.70.237]>
In-Reply-To: <199810291114.GAA26458@io.ece.drexel.edu>
Mime-Version: 1.0
Date: Thu, 29 Oct 1998 16:35:47 +0100
To: nih-image@io.ece.drexel.edu
From: Vincenzo Della Mea <dellamea@dimi.uniud.it>
Subject: Re: Olympus digital camera
Resent-Message-ID: <"kJXHh3.0.zC6.qj8Es"@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/535
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: 607

> Is that a one chip or a three chip camera? Can it be used as a full
>resolution monochrome at 1280x1024? What is the effective ASA? Can it be
>used for Nomarski? Fluorescence? Dark Field?
>
>Many thanks,
>Harvey Karten
>
>Vincenzo Della Mea wrote:
>try to look also at Olympus cameras: they are selling a consumer-based
>microscope digital camera which is cheap but very nice, with C-mount.
>(http://www.olympus-europa.com/mikro/dp10.htm).

I don't know deeply the technical features, I just saw one when it arrived
at Olympus Italy (which is not my company...).

Try to look at the www site.

VIncenzo



From nih-image-request@io.ece.drexel.edu Thu Oct 29 11:29 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA29513;
	Thu, 29 Oct 1998 11:29:24 -0500 (EST)
Resent-Date: Thu, 29 Oct 1998 11:29:24 -0500 (EST)
From: DrJohnRuss@aol.com
Message-ID: <c4fc6d5c.363890a5@aol.com>
Date: Thu, 29 Oct 1998 10:58:29 EST
To: nih-image@io.ece.drexel.edu
Mime-Version: 1.0
Subject: Re:  Re: Olympus digital camera
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 for Mac sub 84
Resent-Message-ID: <"U73ED.0.he6.349Es"@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/536
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: 358


In a message dated 10/29/98 10:53:17 AM, somone wrote:

>try to look also at Olympus cameras: they are selling a consumer-based
>>microscope digital camera which is cheap but very nice, with C-mount.

the preliminary data I saw on this said that it did JPEG compression. If that
"feature" can't be turned off I would strongly suggest NOT using the camera.


From nih-image-request@io.ece.drexel.edu Thu Oct 29 18:56 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA22202;
	Thu, 29 Oct 1998 18:56:45 -0500 (EST)
Resent-Date: Thu, 29 Oct 1998 18:56:45 -0500 (EST)
Message-ID: <19981029232109.3672.rocketmail@web1.rocketmail.com>
Date: Thu, 29 Oct 1998 15:21:09 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
Subject: Re: bubbles continued
To: nih-image@io.ece.drexel.edu
MIME-Version: 1.0
Resent-Message-ID: <"oBcPp2.0.ak2.NkFEs"@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/537
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: 711


> I have tried the Analyse particles routines, but it does not appear to
> yield an explicit bubbles size distribution.

If you have calibrated the image to some units like "mm", then check area for
measurement options you will then get a list of sizes after running the
routine. It isn't a histogram of sizes but that could be done of course, it
will simply be a list in the results window.

Touching particles are another matter and there are multiple ways to handle
this from simple to the very complex.


==
Mark Vivino
mvivino@rocketmail.com
Consulting Biomedical Engineer
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-request@io.ece.drexel.edu Thu Oct 29 20:30 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA10908;
	Thu, 29 Oct 1998 20:30:58 -0500 (EST)
Resent-Date: Thu, 29 Oct 1998 20:30:58 -0500 (EST)
Date: Thu, 29 Oct 1998 17:09:04 -0800 (PST)
From: Lesley Weston <lesley@interchange.ubc.ca>
Reply-To: Lesley Weston <lesley@interchange.ubc.ca>
To: nih-image@io.ece.drexel.edu
Subject: Imagemath
Message-ID: <Pine.GSO.3.95q.981029170729.8471A-100000@interchange.ubc.ca>
MIME-Version: 1.0
Resent-Message-ID: <"Tagt41.0.XH7.p7HEs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/538
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: 424

Can anybody help me with a macro problem concerning Imagemath in a stack
manipulation? Everything seems to work except that I can't pass the parameter
back to tell it where to store the enhanced image. Using something like
"Imagemath('sub',.......,'Image'(i)) to make it store in a new set of
images called "image1", "Image2" etc. doesn't work, and nor daoes anything else
I've tried. Any ideas? Thanks.

Lesley Weston.





From nih-image-request@io.ece.drexel.edu Thu Oct 29 23:28 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id XAA11901;
	Thu, 29 Oct 1998 23:28:58 -0500 (EST)
Resent-Date: Thu, 29 Oct 1998 23:28:58 -0500 (EST)
Date: 	Thu, 29 Oct 1998 18:15:41 -1000
From: Kathleen Annikki Moore <moorekat@hawaii.edu>
X-Sender: moorekat@uhunix4
Reply-To: Kathleen Annikki Moore <moorekat@hawaii.edu>
To: nih-image@io.ece.drexel.edu
Subject: Can a snappy be used for?
Message-ID: <Pine.GSO.3.96.981029144725.7389A-100000@uhunix4>
MIME-Version: 1.0
Resent-Message-ID: <"ykcnk.0.OH1.isJEs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/539
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: 1691

I'm a graduate student looking for a simple solution for capturing
reasonable scientific images from several differing microscopes which each
have a different brand name of video mounted to each individual
microscope.

I've read that 640 x 480 resolution is a minimal standard for video
capture. I've also read that the Capsure card is not appropriate for this
type of work as resolution is 320x240 which is interpolated up to 640x480.

The following is a FAQ answer from Snappy's web site.

A: Actually, video ISN'T 640 x 480. This is a common misconception in the
computer world. .................... NTSC video is an analog signal with
no fixed resolution. The more times you 'sample' the signal the better
your digital representation gets............................ ..we can
calculate based on the bandwidth of video that the point of diminishing
returns is reached around 1500 samples per line. To sample at this
resolution Play designed our own custom chip.......................
 time base correction, spatial and temporal filters, interpolation
algorithms and more................................... Because
NTSC video is only 480 lines tall Snappy interpolates the image vertically
to maintain square pixels. This  algorithm is called Third Order
Polynomial Interpolation.

 My questions: Is an image treated to this inexpensive method of
acquisition reasonable for scientific measurements (I'm working on bone
histmorphometry measurements)?
Will a Snappy framegrabber work well with PC notebooks?
Are there any serious flaws created by using an inexpensive framegrabber
or difficulties in capturing images on notebooks? 
Thank you very much for any answers.    Kathleen Moore





From nih-image-d-request@io.ece.drexel.edu Thu Oct 29 23:36 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id XAA15693;
	Thu, 29 Oct 1998 23:36:05 -0500 (EST)
Date: Thu, 29 Oct 1998 23:36:05 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810300436.XAA15693@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #100
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/100
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 7515

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 100

Today's Topics:
  Re: digital photo camera f. microsco  [ Bill Miller <microbill@mohawk.net> ]
  Re: Olympus digital camera            [ Vincenzo Della Mea <dellamea@dimi.u ]
  Re: Re: Olympus digital camera        [ DrJohnRuss@aol.com ]
  Re: bubbles continued                 [ Mark Vivino <mvivino@rocketmail.com ]
  Imagemath                             [ Lesley Weston <lesley@interchange.u ]
  Can a snappy be used for?             [ Kathleen Annikki Moore <moorekat@ha ]

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

Date: Thu, 29 Oct 1998 06:56:46 -0500
From: Bill Miller <microbill@mohawk.net>
To: nih-image@io.ece.drexel.edu
Subject: Re: digital photo camera f. microscopy
Message-Id: <3.0.5.32.19981029065646.007d86a0@mohawk.net>
Content-Type: text/plain; charset="us-ascii"

See http://www.soundvision.com   digital  made for microscopy w/o lens.



At 10:04 AM 10/27/98 +0100, you wrote:
>Hallo everybody,
>
>we consider equipping still another microscope with a computer-connected
>camera. The idea now is to take one of these new digital *photographic*
>cameras which begin to penetrate consumer and professional photography
>market. They are sensitive enough for our purposes, offer color capture at
>the same or higher resolution as compared to video cameras, and cost (which
>is important for us now) below 2000 $. That computer can, but must not be
>connected to the camera, is also an advantage. The image compression is
>usually (or always?) built in, which may be a considerable drawback, but we
>could live with it.
>
>The problem is that these cameras have mostly (or always?) built-in lens,
>so we don't know how to adapt it to the microscope. Does anybody have the
>experience or any ideas?
>
>
>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, 29 Oct 1998 16:35:47 +0100
From: Vincenzo Della Mea <dellamea@dimi.uniud.it>
To: nih-image@io.ece.drexel.edu
Subject: Re: Olympus digital camera
Message-Id: <l03130302b25e0187bd8d@[158.110.70.237]>
Content-Type: text/plain; charset="us-ascii"

> Is that a one chip or a three chip camera? Can it be used as a full
>resolution monochrome at 1280x1024? What is the effective ASA? Can it be
>used for Nomarski? Fluorescence? Dark Field?
>
>Many thanks,
>Harvey Karten
>
>Vincenzo Della Mea wrote:
>try to look also at Olympus cameras: they are selling a consumer-based
>microscope digital camera which is cheap but very nice, with C-mount.
>(http://www.olympus-europa.com/mikro/dp10.htm).

I don't know deeply the technical features, I just saw one when it arrived
at Olympus Italy (which is not my company...).

Try to look at the www site.

VIncenzo

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

Date: Thu, 29 Oct 1998 10:58:29 EST
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re:  Re: Olympus digital camera
Message-ID: <c4fc6d5c.363890a5@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

In a message dated 10/29/98 10:53:17 AM, somone wrote:

>try to look also at Olympus cameras: they are selling a consumer-based
>>microscope digital camera which is cheap but very nice, with C-mount.

the preliminary data I saw on this said that it did JPEG compression. If that
"feature" can't be turned off I would strongly suggest NOT using the camera.

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

Date: Thu, 29 Oct 1998 15:21:09 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: bubbles continued
Message-ID: <19981029232109.3672.rocketmail@web1.rocketmail.com>
Content-Type: text/plain; charset=us-ascii

> I have tried the Analyse particles routines, but it does not appear to
> yield an explicit bubbles size distribution.

If you have calibrated the image to some units like "mm", then check area for
measurement options you will then get a list of sizes after running the
routine. It isn't a histogram of sizes but that could be done of course, it
will simply be a list in the results window.

Touching particles are another matter and there are multiple ways to handle
this from simple to the very complex.


==
Mark Vivino
mvivino@rocketmail.com
Consulting Biomedical Engineer
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com

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

Date: Thu, 29 Oct 1998 17:09:04 -0800 (PST)
From: Lesley Weston <lesley@interchange.ubc.ca>
To: nih-image@io.ece.drexel.edu
Subject: Imagemath
Message-ID: <Pine.GSO.3.95q.981029170729.8471A-100000@interchange.ubc.ca>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Can anybody help me with a macro problem concerning Imagemath in a stack
manipulation? Everything seems to work except that I can't pass the parameter
back to tell it where to store the enhanced image. Using something like
"Imagemath('sub',.......,'Image'(i)) to make it store in a new set of
images called "image1", "Image2" etc. doesn't work, and nor daoes anything else
I've tried. Any ideas? Thanks.

Lesley Weston.

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

Date: 	Thu, 29 Oct 1998 18:15:41 -1000
From: Kathleen Annikki Moore <moorekat@hawaii.edu>
To: nih-image@io.ece.drexel.edu
Subject: Can a snappy be used for?
Message-ID: <Pine.GSO.3.96.981029144725.7389A-100000@uhunix4>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I'm a graduate student looking for a simple solution for capturing
reasonable scientific images from several differing microscopes which each
have a different brand name of video mounted to each individual
microscope.

I've read that 640 x 480 resolution is a minimal standard for video
capture. I've also read that the Capsure card is not appropriate for this
type of work as resolution is 320x240 which is interpolated up to 640x480.

The following is a FAQ answer from Snappy's web site.

A: Actually, video ISN'T 640 x 480. This is a common misconception in the
computer world. .................... NTSC video is an analog signal with
no fixed resolution. The more times you 'sample' the signal the better
your digital representation gets............................ ..we can
calculate based on the bandwidth of video that the point of diminishing
returns is reached around 1500 samples per line. To sample at this
resolution Play designed our own custom chip.......................
 time base correction, spatial and temporal filters, interpolation
algorithms and more................................... Because
NTSC video is only 480 lines tall Snappy interpolates the image vertically
to maintain square pixels. This  algorithm is called Third Order
Polynomial Interpolation.

 My questions: Is an image treated to this inexpensive method of
acquisition reasonable for scientific measurements (I'm working on bone
histmorphometry measurements)?
Will a Snappy framegrabber work well with PC notebooks?
Are there any serious flaws created by using an inexpensive framegrabber
or difficulties in capturing images on notebooks? 
Thank you very much for any answers.    Kathleen Moore

--------------------------------
End of nih-image-d Digest V98 Issue #100
****************************************

From nih-image-request@io.ece.drexel.edu Fri Oct 30 00:01 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id AAA29028;
	Fri, 30 Oct 1998 00:01:34 -0500 (EST)
Resent-Date: Fri, 30 Oct 1998 00:01:34 -0500 (EST)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: lesley@interchange.ubc.ca, nih-image@io.ece.drexel.edu
Date:          Fri, 30 Oct 1998 14:52:27 GMT+1100
Subject:       Re: Imagemath
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <7062F86C2D@rna.bio.mq.edu.au>
Resent-Message-ID: <"5SQuR3.0.Rr5.gNKEs"@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/540
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1169

>Date: Thu, 29 Oct 1998 17:09:04 -0800 (PST)
>From: Lesley Weston <lesley@interchange.ubc.ca>
>
>Can anybody help me with a macro problem concerning Imagemath in a stack
>manipulation? Everything seems to work except that I can't pass the parameter
>back to tell it where to store the enhanced image. Using something like
>"Imagemath('sub',.......,'Image'(i)) to make it store in a new set of
>images called "image1", "Image2" etc. doesn't work, and nor daoes anything else
>I've tried. Any ideas? Thanks.
>
>Lesley Weston.
>
macro'/0text';var i:integer;
begin i:=3; 
Imagemath('sub',1,2,1,0,concat('Image',i:0));
end

will subtract picNumbers 1,2 to produce 'Image3'.
without the ':0' you would get 'Image...3' {where . is blank}

but if as you suggest, you are doing "stack manipulation" for output,
then you could do imageMath to the n'th slice of an existing stack whose pidNumber is
stackId:= pidNumber;

selectPic(stackId);selectSlice(n);Imagemath('sub',pid1,pid2,1,0,stackId);
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 Oct 30 04:28 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA12471;
	Fri, 30 Oct 1998 04:28:40 -0500 (EST)
Resent-Date: Fri, 30 Oct 1998 04:28:40 -0500 (EST)
X-Sender: sdb@pop1.liv.ac.uk
Message-Id: <l03130305b25f339cff4d@[138.253.47.16]>
In-Reply-To: <199810291101.GAA20187@io.ece.drexel.edu>
Mime-Version: 1.0
Date: Fri, 30 Oct 1998 09:16:00 +0000
To: nih-image@io.ece.drexel.edu
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
Subject: Re: Bubble size distribution
Cc: Michael Norato <manorato@mailbox.syr.edu>
Resent-Message-ID: <"t3S7b.0.DY1.cFOEs"@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/541
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: 831

>I have tried the Analyse particles routines, but it does not appear to
>yield an explicit bubbles size distribution.
>
>Sometimes the bubbles touch, but not often.

The NIH Image spin-off 'Image SXM' can analyse bubble size distributions.
It uses a Hough transform algorithm, and so incomplete or touching bubbles
are detected. A copy of the Image SXM installer is in the spin-offs folder
on the NIH Image server. You can find more information about Image SXM from
http://reg.ssci.liv.ac.uk

___________________________________________________________________

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

Tel: 44-(0)151-794-3874 / 3894 / 3870
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk

___________________________________________________________________



From nih-image-request@io.ece.drexel.edu Fri Oct 30 07:41 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id HAA18416;
	Fri, 30 Oct 1998 07:41:28 -0500 (EST)
Resent-Date: Fri, 30 Oct 1998 07:41:28 -0500 (EST)
From: DrJohnRuss@aol.com
Message-ID: <59632dee.3639af54@aol.com>
Date: Fri, 30 Oct 1998 07:21:40 EST
To: nih-image@io.ece.drexel.edu
Cc: moorekat@hawaii.edu
Mime-Version: 1.0
Subject: Re:  Can a snappy be used for?
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 for Mac sub 84
Resent-Message-ID: <"kQ49s.0.l92.D-QEs"@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/542
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: 2807


In a message dated 10/29/98 11:23:09 PM, moorekat@hawaii.edu wrote:
...
>
>The following is a FAQ answer from Snappy's web site.
>
>A: Actually, video ISN'T 640 x 480. This is a common misconception in the
>computer world. .................... NTSC video is an analog signal with
>no fixed resolution. The more times you 'sample' the signal the better
>your digital representation gets............................ ..we can
>calculate based on the bandwidth of video that the point of diminishing
>returns is reached around 1500 samples per line. To sample at this
>resolution Play designed our own custom chip.......................
> time base correction, spatial and temporal filters, interpolation
>algorithms and more................................... Because
>NTSC video is only 480 lines tall Snappy interpolates the image vertically
>to maintain square pixels. This  algorithm is called Third Order
>Polynomial Interpolation.
>
> My questions: Is an image treated to this inexpensive method of
>acquisition reasonable for scientific measurements (I'm working on bone
>histmorphometry measurements)?
>Will a Snappy framegrabber work well with PC notebooks?
>Are there any serious flaws created by using an inexpensive framegrabber
>or difficulties in capturing images on notebooks? 
...

The snappy answer is correct but perhaps a bit optimistic. It is important to
remember that video is an analog signal and that any digitizer
("framegrabber") samples it. The common use of 640x480 has more to do with the
dimensions of standard VGA displays than anything in the video signal itself.
Based on the bandwidth of the video signal the maximum number of discrete
points that can be sampled along a line is actually about 330, far less than
the 1500 snappy claims. But for visual purposes, the oversampling (empty
magnification) is acceptable to make pretty images. Likewise few video images
have more than 400 scan lines of actual image, although ideally there are 480
between vertical retrace events. 

The simple fact is that a video image digitized with Snappy is quite suitable
for anything that video is good enough for in the first place (digital cameras
are available with much higher resolution). The Snappy does a very good job -
I would recommend not using the 1500 wide pixel image since there really isn't
any more information than in a smaller and more convenient 640x480 size (which
it will also grab), and I would further recommend using the mode in which you
average together 8 frames which reduces noise quite a bit. But the basic
answer is - yes, use the Snappy. It works great and will let you do good image
analysis with a basic PC. I use one with a laptop (generic, running WinNT with
Photoshop and the Image Processing Tool Kit) and am quite pleased with the
results.

John Russ


From nih-image-request@io.ece.drexel.edu Fri Oct 30 09:07 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA27645;
	Fri, 30 Oct 1998 09:07:22 -0500 (EST)
Resent-Date: Fri, 30 Oct 1998 09:07:22 -0500 (EST)
X-Server-Uuid: 9b0d4bf4-4be9-11d2-b9cf-0008c7f450b1
X-Lotus-FromDomain: ARCO
From: "Dan Frich"<CSCDJF@arcochem.com>
To: nih-image@io.ece.drexel.edu
Message-ID: <852566AD.00498551.00@nsns-h01.arcochem.com>
Date: Fri, 30 Oct 1998 08:35:43 -0500
Subject: watershed segmentation
Mime-Version: 1.0
Resent-Message-ID: <"dyThF.0.t54.1CSEs"@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/543
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: 637





I was wondering if anyone could give me any help with the watershed
segmentation routine in v. 1.61.  I am using Image to analyze sizes and
distributions in cellular materials.  To do this, I use watershed
segmentation to yield discrete cells and then use the analyze particles
routine to measure individual cell sizes (areas).  This technique works
extremely well except for the fact that I tend to get some degree of
oversegmentation (splitting of cells that should be counted as only one) in
the watershed routine.  Does anyone have any ideas or experience on how to
correct this problem?

My appreciation in advance,
Dan Frich



From nih-image-request@io.ece.drexel.edu Fri Oct 30 09:54 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA21136;
	Fri, 30 Oct 1998 09:54:21 -0500 (EST)
Resent-Date: Fri, 30 Oct 1998 09:54:21 -0500 (EST)
Message-ID: <01BE03E7.F6BA8460@OAKMONT.SEAS.UPENN.EDU>
From: Eric Johnston <ericdj@seas.upenn.edu>
To: "nih-image@io.ece.drexel.edu" <nih-image@io.ece.drexel.edu>
Subject: RE: analog to digital (was: Can a snappy be used for?)
Date: Fri, 30 Oct 1998 09:30:40 -0500
MIME-Version: 1.0
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id JAA08662
Resent-Message-ID: <"J9iSX1.0.s72.vrSEs"@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/544
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: 2176

Dr Russ

Could you explain further how video bandwidth limits the digitization of a line of video signal to only about 330 pixels?  For that matter, what is "bandwidth"?  Is there is a distinction between "analog bandwidth" and the "digital bandwidth" we hear so much about?

Eric Johnston
Department of Bioengineering
University of Pennsylvania
120 Hayden Hall
3320 Smith Walk
Philadelphia, PA 19104-6392
215-898-1958
(F) 215-573-2071
ericdj@seas.upenn.edu


----------
From:  DrJohnRuss@aol.com [SMTP:DrJohnRuss@aol.com]
Sent:  Friday, October 30, 1998 7:22 AM
To:  nih-image@io.ece.drexel.edu
Cc:  moorekat@hawaii.edu
Subject:  Re:  Can a snappy be used for?


The snappy answer is correct but perhaps a bit optimistic. It is important to
remember that video is an analog signal and that any digitizer
("framegrabber") samples it. The common use of 640x480 has more to do with the
dimensions of standard VGA displays than anything in the video signal itself.
Based on the bandwidth of the video signal the maximum number of discrete
points that can be sampled along a line is actually about 330, far less than
the 1500 snappy claims. But for visual purposes, the oversampling (empty
magnification) is acceptable to make pretty images. Likewise few video images
have more than 400 scan lines of actual image, although ideally there are 480
between vertical retrace events. 

The simple fact is that a video image digitized with Snappy is quite suitable
for anything that video is good enough for in the first place (digital cameras
are available with much higher resolution). The Snappy does a very good job -
I would recommend not using the 1500 wide pixel image since there really isn't
any more information than in a smaller and more convenient 640x480 size (which
it will also grab), and I would further recommend using the mode in which you
average together 8 frames which reduces noise quite a bit. But the basic
answer is - yes, use the Snappy. It works great and will let you do good image
analysis with a basic PC. I use one with a laptop (generic, running WinNT with
Photoshop and the Image Processing Tool Kit) and am quite pleased with the
results.

John Russ



From nih-image-request@io.ece.drexel.edu Fri Oct 30 12:01 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA25302;
	Fri, 30 Oct 1998 12:01:47 -0500 (EST)
Resent-Date: Fri, 30 Oct 1998 12:01:47 -0500 (EST)
From: DrJohnRuss@aol.com
Message-ID: <a4da218f.3639ec04@aol.com>
Date: Fri, 30 Oct 1998 11:40:36 EST
To: nih-image@io.ece.drexel.edu
Mime-Version: 1.0
Subject: Re:  RE: analog to digital (was: Can a snappy be used for?)
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 for Mac sub 84
Resent-Message-ID: <"HqTuL3.0.yv3.9oUEs"@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/545
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: 613


In a message dated 10/30/98 9:39:29 AM, you wrote:

>Could you explain further how video bandwidth limits the digitization of a
line
>of video signal to only about 330 pixels?  For that matter, what is
"bandwidth"?
> Is there is a distinction between "analog bandwidth" and the "digital
bandwidth"
>we hear so much about?

Too long a question for email. Read a good book. Start with Inoue "Video
Microscopy." There is also a lot of information in books like Pratt "Digital
Image Processing", Jain "Fundamentals of Digital Image Proc", Gonzalez&Woods
"Digital Image Proc" and my own "Image Processing Handbook"



From nih-image-request@io.ece.drexel.edu Fri Oct 30 12:44 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA16479;
	Fri, 30 Oct 1998 12:44:11 -0500 (EST)
Resent-Date: Fri, 30 Oct 1998 12:44:11 -0500 (EST)
X-Sender: jreidler@10.0.0.1
Message-Id: <l03102800b25f9f971b49@[10.0.0.248]>
In-Reply-To: <199810300420.XAA07340@io.ece.drexel.edu>
Mime-Version: 1.0
Date: Fri, 30 Oct 1998 12:18:12 -0500
To: nih-image@io.ece.drexel.edu
From: Jeff Reidler <Jreidler@scioncorp.com>
Subject: Re: Snappy in Digest V98 #100
Resent-Message-ID: <"BKLJl.0.Ep.GJVEs"@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/546
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: 1289

Date: 	Thu, 29 Oct 1998 18:15:41 -1000
From: Kathleen Annikki Moore <moorekat@hawaii.edu>
To: nih-image@io.ece.drexel.edu

>I've read that 640 x 480 resolution is a minimal standard for video
>capture. I've also read that the Capsure card is not appropriate for this
>type of work as resolution is 320x240 which is interpolated up to 640x480.
>
>The following is a FAQ answer from Snappy's web site.
>>A: Actually, video ISN'T 640 x 480......
>> The more times you 'sample' the signal the better your digital
>> representation gets.......

> My questions: Is an image treated to this inexpensive method of
>acquisition reasonable for scientific measurements (I'm working on bone
>histmorphometry measurements)?

It depends on the detail you require.
I can send you comparisons of different grabbers and different cameras of
the same image field if you want to see side-by-side comparions of the same
image.  I have a comparison for the Snappy with the CG-7 from Scion.  Reply
to info@scioncorp.com if you are interested.
Jeff

Jeffry A. Reidler, PhD                jreidler@scioncorp.com
Commercial and Applications           http://www.scioncorp.com
Scion Corporation                     tel 301-695-7870
82 Wormans Mill Ct, Suite H           fax 301-695-0035
Frederick, MD  21701  USA



From nih-image-request@io.ece.drexel.edu Fri Oct 30 15:40 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA17452;
	Fri, 30 Oct 1998 15:40:26 -0500 (EST)
Resent-Date: Fri, 30 Oct 1998 15:40:26 -0500 (EST)
Message-Id: <199810302011.MAA09986@oes.edu>
From: "Lynn Huynh" <LynnH@us1.oes.edu>
Organization: Oregon Episcopal School
To: nih-image@io.ece.drexel.edu
Date: Fri, 30 Oct 1998 12:12:02 -0800
MIME-Version: 1.0
Content-transfer-encoding: 7BIT
Subject: tracking asteroids...
Priority: normal
X-mailer: Pegasus Mail for Win32 (v3.01b)
Resent-Message-ID: <"trKrE3.0.501.BvXEs"@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/547
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: 298

hi, i am wondering if anyone knows how to use nih-image to track 
asteroids in photos taken off the net... or rather to make the 
question broader, does anyone have a detailed procedure on how 
to use the stacking feature of the program? 

thank you,
lynn
lynnh@us1.oes.edu
supershiny@hotmail.com


From nih-image-request@io.ece.drexel.edu Fri Oct 30 15:43 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA19060;
	Fri, 30 Oct 1998 15:43:36 -0500 (EST)
Resent-Date: Fri, 30 Oct 1998 15:43:36 -0500 (EST)
Message-Id: <199810302015.MAA09991@oes.edu>
From: "Lynn Huynh" <LynnH@us1.oes.edu>
Organization: Oregon Episcopal School
To: nih-image@io.ece.drexel.edu
Date: Fri, 30 Oct 1998 12:16:01 -0800
MIME-Version: 1.0
Content-transfer-encoding: 7BIT
Subject: electrophoretic gel reading...
Priority: normal
X-mailer: Pegasus Mail for Win32 (v3.01b)
Resent-Message-ID: <"fkhPz.0.4V1.lyXEs"@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/548
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: 426

how do i use nih-image to analyze electrophoretic gels?  i need 
better readings on some gels that i have.  i have been using page 
techniques and will be needing to analyze not just whether the 
band is detectable but also which bands are darker, i will be using 
this information to create a haplotype and do two-point lod score 
analysis with linkage 5.1 software

thank you,
lynn
lynnh@us1.oes.edu
supershiny@hotmail.com


From nih-image-d-request@io.ece.drexel.edu Fri Oct 30 15:46 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA20514;
	Fri, 30 Oct 1998 15:46:33 -0500 (EST)
Date: Fri, 30 Oct 1998 15:46:33 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810302046.PAA20514@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #101
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/101
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 13046

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 101

Today's Topics:
  Re: Imagemath                         [ GJOSS@rna.bio.mq.edu.au ]
  Re: Bubble size distribution          [ Steve Barrett <S.D.Barrett@liverpoo ]
  Re: Can a snappy be used for?         [ DrJohnRuss@aol.com ]
  watershed segmentation                [ "Dan Frich"<CSCDJF@arcochem.com> ]
  RE: analog to digital (was: Can a sn  [ Eric Johnston <ericdj@seas.upenn.ed ]
  Re: RE: analog to digital (was: Can   [ DrJohnRuss@aol.com ]
  Re: Snappy in Digest V98 #100         [ Jeff Reidler <Jreidler@scioncorp.co ]
  tracking asteroids...                 [ "Lynn Huynh" <LynnH@us1.oes.edu> ]

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

Date:          Fri, 30 Oct 1998 14:52:27 GMT+1100
From: GJOSS@rna.bio.mq.edu.au
To: lesley@interchange.ubc.ca, nih-image@io.ece.drexel.edu
Subject:       Re: Imagemath
Message-ID: <7062F86C2D@rna.bio.mq.edu.au>

>Date: Thu, 29 Oct 1998 17:09:04 -0800 (PST)
>From: Lesley Weston <lesley@interchange.ubc.ca>
>
>Can anybody help me with a macro problem concerning Imagemath in a stack
>manipulation? Everything seems to work except that I can't pass the parameter
>back to tell it where to store the enhanced image. Using something like
>"Imagemath('sub',.......,'Image'(i)) to make it store in a new set of
>images called "image1", "Image2" etc. doesn't work, and nor daoes anything else
>I've tried. Any ideas? Thanks.
>
>Lesley Weston.
>
macro'/0text';var i:integer;
begin i:=3; 
Imagemath('sub',1,2,1,0,concat('Image',i:0));
end

will subtract picNumbers 1,2 to produce 'Image3'.
without the ':0' you would get 'Image...3' {where . is blank}

but if as you suggest, you are doing "stack manipulation" for output,
then you could do imageMath to the n'th slice of an existing stack whose pidNumber is
stackId:= pidNumber;

selectPic(stackId);selectSlice(n);Imagemath('sub',pid1,pid2,1,0,stackId);
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, 30 Oct 1998 09:16:00 +0000
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
To: nih-image@io.ece.drexel.edu
Cc: Michael Norato <manorato@mailbox.syr.edu>
Subject: Re: Bubble size distribution
Message-Id: <l03130305b25f339cff4d@[138.253.47.16]>
Content-Type: text/plain; charset="us-ascii"

>I have tried the Analyse particles routines, but it does not appear to
>yield an explicit bubbles size distribution.
>
>Sometimes the bubbles touch, but not often.

The NIH Image spin-off 'Image SXM' can analyse bubble size distributions.
It uses a Hough transform algorithm, and so incomplete or touching bubbles
are detected. A copy of the Image SXM installer is in the spin-offs folder
on the NIH Image server. You can find more information about Image SXM from
http://reg.ssci.liv.ac.uk

___________________________________________________________________

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

Tel: 44-(0)151-794-3874 / 3894 / 3870
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk

___________________________________________________________________

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

Date: Fri, 30 Oct 1998 07:21:40 EST
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Cc: moorekat@hawaii.edu
Subject: Re:  Can a snappy be used for?
Message-ID: <59632dee.3639af54@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

In a message dated 10/29/98 11:23:09 PM, moorekat@hawaii.edu wrote:
...
>
>The following is a FAQ answer from Snappy's web site.
>
>A: Actually, video ISN'T 640 x 480. This is a common misconception in the
>computer world. .................... NTSC video is an analog signal with
>no fixed resolution. The more times you 'sample' the signal the better
>your digital representation gets............................ ..we can
>calculate based on the bandwidth of video that the point of diminishing
>returns is reached around 1500 samples per line. To sample at this
>resolution Play designed our own custom chip.......................
> time base correction, spatial and temporal filters, interpolation
>algorithms and more................................... Because
>NTSC video is only 480 lines tall Snappy interpolates the image vertically
>to maintain square pixels. This  algorithm is called Third Order
>Polynomial Interpolation.
>
> My questions: Is an image treated to this inexpensive method of
>acquisition reasonable for scientific measurements (I'm working on bone
>histmorphometry measurements)?
>Will a Snappy framegrabber work well with PC notebooks?
>Are there any serious flaws created by using an inexpensive framegrabber
>or difficulties in capturing images on notebooks? 
...

The snappy answer is correct but perhaps a bit optimistic. It is important to
remember that video is an analog signal and that any digitizer
("framegrabber") samples it. The common use of 640x480 has more to do with the
dimensions of standard VGA displays than anything in the video signal itself.
Based on the bandwidth of the video signal the maximum number of discrete
points that can be sampled along a line is actually about 330, far less than
the 1500 snappy claims. But for visual purposes, the oversampling (empty
magnification) is acceptable to make pretty images. Likewise few video images
have more than 400 scan lines of actual image, although ideally there are 480
between vertical retrace events. 

The simple fact is that a video image digitized with Snappy is quite suitable
for anything that video is good enough for in the first place (digital cameras
are available with much higher resolution). The Snappy does a very good job -
I would recommend not using the 1500 wide pixel image since there really isn't
any more information than in a smaller and more convenient 640x480 size (which
it will also grab), and I would further recommend using the mode in which you
average together 8 frames which reduces noise quite a bit. But the basic
answer is - yes, use the Snappy. It works great and will let you do good image
analysis with a basic PC. I use one with a laptop (generic, running WinNT with
Photoshop and the Image Processing Tool Kit) and am quite pleased with the
results.

John Russ

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

Date: Fri, 30 Oct 1998 08:35:43 -0500
From: "Dan Frich"<CSCDJF@arcochem.com>
To: nih-image@io.ece.drexel.edu
Subject: watershed segmentation
Message-ID: <852566AD.00498551.00@nsns-h01.arcochem.com>
Content-type: text/plain; charset=us-ascii

I was wondering if anyone could give me any help with the watershed
segmentation routine in v. 1.61.  I am using Image to analyze sizes and
distributions in cellular materials.  To do this, I use watershed
segmentation to yield discrete cells and then use the analyze particles
routine to measure individual cell sizes (areas).  This technique works
extremely well except for the fact that I tend to get some degree of
oversegmentation (splitting of cells that should be counted as only one) in
the watershed routine.  Does anyone have any ideas or experience on how to
correct this problem?

My appreciation in advance,
Dan Frich

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

Date: Fri, 30 Oct 1998 09:30:40 -0500
From: Eric Johnston <ericdj@seas.upenn.edu>
To: "nih-image@io.ece.drexel.edu" <nih-image@io.ece.drexel.edu>
Subject: RE: analog to digital (was: Can a snappy be used for?)
Message-ID: <01BE03E7.F6BA8460@OAKMONT.SEAS.UPENN.EDU>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 8bit

Dr Russ

Could you explain further how video bandwidth limits the digitization of a line of video signal to only about 330 pixels?  For that matter, what is "bandwidth"?  Is there is a distinction between "analog bandwidth" and the "digital bandwidth" we hear so much about?

Eric Johnston
Department of Bioengineering
University of Pennsylvania
120 Hayden Hall
3320 Smith Walk
Philadelphia, PA 19104-6392
215-898-1958
(F) 215-573-2071
ericdj@seas.upenn.edu


----------
From:  DrJohnRuss@aol.com [SMTP:DrJohnRuss@aol.com]
Sent:  Friday, October 30, 1998 7:22 AM
To:  nih-image@io.ece.drexel.edu
Cc:  moorekat@hawaii.edu
Subject:  Re:  Can a snappy be used for?


The snappy answer is correct but perhaps a bit optimistic. It is important to
remember that video is an analog signal and that any digitizer
("framegrabber") samples it. The common use of 640x480 has more to do with the
dimensions of standard VGA displays than anything in the video signal itself.
Based on the bandwidth of the video signal the maximum number of discrete
points that can be sampled along a line is actually about 330, far less than
the 1500 snappy claims. But for visual purposes, the oversampling (empty
magnification) is acceptable to make pretty images. Likewise few video images
have more than 400 scan lines of actual image, although ideally there are 480
between vertical retrace events. 

The simple fact is that a video image digitized with Snappy is quite suitable
for anything that video is good enough for in the first place (digital cameras
are available with much higher resolution). The Snappy does a very good job -
I would recommend not using the 1500 wide pixel image since there really isn't
any more information than in a smaller and more convenient 640x480 size (which
it will also grab), and I would further recommend using the mode in which you
average together 8 frames which reduces noise quite a bit. But the basic
answer is - yes, use the Snappy. It works great and will let you do good image
analysis with a basic PC. I use one with a laptop (generic, running WinNT with
Photoshop and the Image Processing Tool Kit) and am quite pleased with the
results.

John Russ

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

Date: Fri, 30 Oct 1998 11:40:36 EST
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re:  RE: analog to digital (was: Can a snappy be used for?)
Message-ID: <a4da218f.3639ec04@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

In a message dated 10/30/98 9:39:29 AM, you wrote:

>Could you explain further how video bandwidth limits the digitization of a
line
>of video signal to only about 330 pixels?  For that matter, what is
"bandwidth"?
> Is there is a distinction between "analog bandwidth" and the "digital
bandwidth"
>we hear so much about?

Too long a question for email. Read a good book. Start with Inoue "Video
Microscopy." There is also a lot of information in books like Pratt "Digital
Image Processing", Jain "Fundamentals of Digital Image Proc", Gonzalez&Woods
"Digital Image Proc" and my own "Image Processing Handbook"

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

Date: Fri, 30 Oct 1998 12:18:12 -0500
From: Jeff Reidler <Jreidler@scioncorp.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Snappy in Digest V98 #100
Message-Id: <l03102800b25f9f971b49@[10.0.0.248]>
Content-Type: text/plain; charset="us-ascii"

Date: 	Thu, 29 Oct 1998 18:15:41 -1000
From: Kathleen Annikki Moore <moorekat@hawaii.edu>
To: nih-image@io.ece.drexel.edu

>I've read that 640 x 480 resolution is a minimal standard for video
>capture. I've also read that the Capsure card is not appropriate for this
>type of work as resolution is 320x240 which is interpolated up to 640x480.
>
>The following is a FAQ answer from Snappy's web site.
>>A: Actually, video ISN'T 640 x 480......
>> The more times you 'sample' the signal the better your digital
>> representation gets.......

> My questions: Is an image treated to this inexpensive method of
>acquisition reasonable for scientific measurements (I'm working on bone
>histmorphometry measurements)?

It depends on the detail you require.
I can send you comparisons of different grabbers and different cameras of
the same image field if you want to see side-by-side comparions of the same
image.  I have a comparison for the Snappy with the CG-7 from Scion.  Reply
to info@scioncorp.com if you are interested.
Jeff

Jeffry A. Reidler, PhD                jreidler@scioncorp.com
Commercial and Applications           http://www.scioncorp.com
Scion Corporation                     tel 301-695-7870
82 Wormans Mill Ct, Suite H           fax 301-695-0035
Frederick, MD  21701  USA

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

Date: Fri, 30 Oct 1998 12:12:02 -0800
From: "Lynn Huynh" <LynnH@us1.oes.edu>
To: nih-image@io.ece.drexel.edu
Subject: tracking asteroids...
Message-Id: <199810302011.MAA09986@oes.edu>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7BIT

hi, i am wondering if anyone knows how to use nih-image to track 
asteroids in photos taken off the net... or rather to make the 
question broader, does anyone have a detailed procedure on how 
to use the stacking feature of the program? 

thank you,
lynn
lynnh@us1.oes.edu
supershiny@hotmail.com

--------------------------------
End of nih-image-d Digest V98 Issue #101
****************************************

From nih-image-d-request@io.ece.drexel.edu Sat Oct 31 10:36 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA14150;
	Sat, 31 Oct 1998 10:36:40 -0500 (EST)
Date: Sat, 31 Oct 1998 10:36:40 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199810311536.KAA14150@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #102
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/102
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 1508

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 102

Today's Topics:
  electrophoretic gel reading...        [ "Lynn Huynh" <LynnH@us1.oes.edu> ]
  unsubscribe                           [ Sarah Krueger <krueger@fuse.net> ]

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

Date: Fri, 30 Oct 1998 12:16:01 -0800
From: "Lynn Huynh" <LynnH@us1.oes.edu>
To: nih-image@io.ece.drexel.edu
Subject: electrophoretic gel reading...
Message-Id: <199810302015.MAA09991@oes.edu>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7BIT

how do i use nih-image to analyze electrophoretic gels?  i need 
better readings on some gels that i have.  i have been using page 
techniques and will be needing to analyze not just whether the 
band is detectable but also which bands are darker, i will be using 
this information to create a haplotype and do two-point lod score 
analysis with linkage 5.1 software

thank you,
lynn
lynnh@us1.oes.edu
supershiny@hotmail.com

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

Date: Sat, 31 Oct 1998 11:40:51 +0000
From: Sarah Krueger <krueger@fuse.net>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-ID: <363AF740.98A9936C@fuse.net>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

PLEASE TAKE ME OFF THE MAILING LIST

UNSUBSCRIBE TO NIH-IMAGE.

--------------------------------
End of nih-image-d Digest V98 Issue #102
****************************************

From nih-image-request@io.ece.drexel.edu Sat Oct 31 10:39 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA16014;
	Sat, 31 Oct 1998 10:39:51 -0500 (EST)
Resent-Date: Sat, 31 Oct 1998 10:39:51 -0500 (EST)
Message-ID: <363AF740.98A9936C@fuse.net>
Date: Sat, 31 Oct 1998 11:40:51 +0000
From: Sarah Krueger <krueger@fuse.net>
Reply-To: krueger@fuse.net
X-Mailer: Mozilla 4.04 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"DdBsA1.0.BO2.UooEs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/549
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length: 64

PLEASE TAKE ME OFF THE MAILING LIST

UNSUBSCRIBE TO NIH-IMAGE.


From nih-image-request@io.ece.drexel.edu Sat Oct 31 13:01 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA27974;
	Sat, 31 Oct 1998 13:01:20 -0500 (EST)
Resent-Date: Sat, 31 Oct 1998 13:01:20 -0500 (EST)
Date: Sat, 31 Oct 1998 09:44:29 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Modulus operation
In-Reply-To: <199810311537.KAA14644@io.ece.drexel.edu>
Message-ID: <Pine.A41.4.05.9810310932190.147390-100000@homer32.u.washington.edu>
MIME-Version: 1.0
Resent-Message-ID: <"VoQFn2.0.6h4.3oqEs"@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/550
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: 767


Attempts to create a modulus operation have been giving unpredictable
results.  Maybe someone can point out my mistake.  I've been taking the
quotient from division of 2 real vars, then subtracting the truncation of
the quotient:

var
	seglength,Mseglength,quotient,modulo:real;
	Trunk:integer;
begin
	quotient:=MsegLength/segLength;
	Trunk:=trunc(quotient);
	modulo:=quotient-trunk;

end;

If SegLength is passed in as .N*MSegLength [to segment the midline into N
divisions], then sometimes Trunk is N, other times it is N-1.

TIA,
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 Sat Oct 31 21:12 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id VAA11451;
	Sat, 31 Oct 1998 21:12:03 -0500 (EST)
Resent-Date: Sat, 31 Oct 1998 21:12:03 -0500 (EST)
Message-ID: <363BC0C3.5F93@thurston.com>
Date: Sat, 31 Oct 1998 18:00:36 -0800
From: "Patrick T. Pringle" <lespat@thurston.com>
Reply-To: lespat@thurston.com
X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: scanners and pixel aspect ratio
References: <199810311530.KAA10944@io.ece.drexel.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"V8K202.0.Pz.T0yEs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/551
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: 957

Please excuse my naive question. I have been using two different
scanners to obtain images for tree ring analysis. One is a Umax Astra
1200 (600 X 1200 true opt. res.) and the other an Epson that boasts 800
X 1600 TOR. 

1. If I were to want to measure mean density of individual rings
(assuming that's better than modal or integ density for dendro work)
would I have to use the lower optical density value for each scanner in
order to obtain homogeniety in resolution depth along both X and Y
axes?  ...or could I apply a pixel aspect ratio of 1/2 and actually take
advantage of the greater resolution that scanners have in the direction
of scanner head movement (long axis)? 

2. The epson scanner has 12-bit an 16 bit settings (I scan in gray
scale); is one preferable to the other considering I must import to
8-bit NIH or Scion image?  When I do import, how do I know if the image
I am importing is signed or unsigned, etc? 
Thanks
-- 
Pat Pringle
--


From nih-image-d-request@io.ece.drexel.edu Sun Nov  1 06:17 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA25864;
	Sun, 1 Nov 1998 06:17:35 -0500 (EST)
Date: Sun, 1 Nov 1998 06:17:35 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811011117.GAA25864@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #103
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/103
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 2734

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 103

Today's Topics:
  Modulus operation                     [ "G. Macdonald" <glenmac@u.washingto ]
  scanners and pixel aspect ratio       [ "Patrick T. Pringle" <lespat@thurst ]

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

Date: Sat, 31 Oct 1998 09:44:29 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Modulus operation
Message-ID: <Pine.A41.4.05.9810310932190.147390-100000@homer32.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Attempts to create a modulus operation have been giving unpredictable
results.  Maybe someone can point out my mistake.  I've been taking the
quotient from division of 2 real vars, then subtracting the truncation of
the quotient:

var
	seglength,Mseglength,quotient,modulo:real;
	Trunk:integer;
begin
	quotient:=MsegLength/segLength;
	Trunk:=trunc(quotient);
	modulo:=quotient-trunk;

end;

If SegLength is passed in as .N*MSegLength [to segment the midline into N
divisions], then sometimes Trunk is N, other times it is N-1.

TIA,
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: Sat, 31 Oct 1998 18:00:36 -0800
From: "Patrick T. Pringle" <lespat@thurston.com>
To: nih-image@io.ece.drexel.edu
Subject: scanners and pixel aspect ratio
Message-ID: <363BC0C3.5F93@thurston.com>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Please excuse my naive question. I have been using two different
scanners to obtain images for tree ring analysis. One is a Umax Astra
1200 (600 X 1200 true opt. res.) and the other an Epson that boasts 800
X 1600 TOR. 

1. If I were to want to measure mean density of individual rings
(assuming that's better than modal or integ density for dendro work)
would I have to use the lower optical density value for each scanner in
order to obtain homogeniety in resolution depth along both X and Y
axes?  ...or could I apply a pixel aspect ratio of 1/2 and actually take
advantage of the greater resolution that scanners have in the direction
of scanner head movement (long axis)? 

2. The epson scanner has 12-bit an 16 bit settings (I scan in gray
scale); is one preferable to the other considering I must import to
8-bit NIH or Scion image?  When I do import, how do I know if the image
I am importing is signed or unsigned, etc? 
Thanks
-- 
Pat Pringle
--

--------------------------------
End of nih-image-d Digest V98 Issue #103
****************************************

From nih-image-request@io.ece.drexel.edu Sun Nov  1 23:00 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id XAA02255;
	Sun, 1 Nov 1998 23:00:09 -0500 (EST)
Resent-Date: Sun, 1 Nov 1998 23:00:09 -0500 (EST)
From: wpchan@socrates.berkeley.edu
Date: Sun, 1 Nov 1998 19:28:45 -0800 (PST)
To: nih-image@io.ece.drexel.edu
cc: Bill Miller <microbill@mohawk.net>, SolamereTG@aol.com,
        Pat Arnott <pat@dri.edu>
Subject: Re: video capture at 30 fps
In-Reply-To: <Pine.SOL.3.96.981020184554.15914A-100000@socrates.berkeley.edu>
Message-ID: <Pine.SOL.3.96.981101191541.22553F-100000@socrates.berkeley.edu>
MIME-Version: 1.0
Resent-Message-ID: <"9_w8c1.0.1p3.4SIFs"@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/552
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: 2145

Many thanks for all the people that replied to my question.  I further
tested the LG-3 on the Mac and a Pentium machine myself.  It is no doublt
that the Scion LG-3 PCI card is built for the Mac (just look at the length
of the card!). 

On the Mac, a 9500/132 with 90 MB of RAM and ATI graphic card, 'make
movie' with blind capture in NIH-Image 1.61 (NTSC) can easily archive
29.97 frames per sec at 640x480.  The timing is right on the money. 

On a Dell Dimension with a 450 MHz Pentium II and 96 MB of RAM, STB nVidia
8MB VRAM running either Win95 or WinNT, the same procedure can only
accquire video sequences at about 17 fps at 640x480.  The only way to get
it to accquire close to 30 fps is to cut down the size of the ROI for
capturing to about half as suggested by various lister.  Disabling various
services, dropping the color depth of the display or adding more RAM did
not make any differences.  However, the timing of the capture fluctuates
as system resources changes.  Scion Image beta 3b has this strange memory
leak that the system resources (users and GDI as well) drops steadily with
each operation e.g. opening a large stack or make movie.  Eventually, the
capture rate in the make movie procedure will drop below 29.4 fps after a
few of the said operation.  Restarting the program will solve the problem.

The conclusion from this exercise is that since we do want to maintain the
quality of our digitized video by using the LG-3 PCI board, we do have to
use a Mac for capturing full 30 fps at 640x480 with NIH-Image.  For reason
beyond my knowlegde, running Scion Image on a Windoz machine just won't do
it.

--Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu)

On Tue, 20 Oct 1998 wpchan@socrates.berkeley.edu wrote:
> Recently we have bought a Scion LG3 PCI card to put in a Windows NT.  The
> highest capture rate that we can get with 'blind capture' in 'make movie'
> is 17 fps.  Scion Tech support confirmed that this is probably the highest
> one can get on a NT. 
> 
> Has anybody successfully get the LG3 PCI to capture to RAM at 30 fps and
> if so, under what condition and using what kind of computer?  Thanks.


From nih-image-request@io.ece.drexel.edu Mon Nov  2 04:19 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA19184;
	Mon, 2 Nov 1998 04:19:33 -0500 (EST)
Resent-Date: Mon, 2 Nov 1998 04:19:33 -0500 (EST)
X-Sender: bmenard@pop-server.unil.ch
Message-Id: <v03102804b2631ffcd0a2@[130.223.74.27]>
Mime-Version: 1.0
Content-Transfer-Encoding: 8bit
Date: Mon, 2 Nov 1998 09:59:09 +0100
To: nih-image@io.ece.drexel.edu
From: Bertrand Menard <Bertrand.Menard@ie-bpv.unil.ch>
Subject: RE : digital photo camera f. microscopy
Resent-Message-ID: <"3-amA1.0.b74.XINFs"@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/553
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="iso-8859-1"
Content-Length: 1778

Hi Imagers,

I've tried the Kodak digital camera with C-mount on a microscop. I don't
think that's the good cameras for microscopy :
1- It's not a video camera, so you must take a snapshot, wait, look if it's
good, change settings, retry, retry and retry. With video camera, you
change settings in live, you see immediatly if image is good or not. When
it's good, you take it. It's fast and easy.
2- With high magnification, the resolution of the camera (1500*1000) is
highest than the optical resolution. With a 60x oel objective of 1.3
numerical aperture, the optical resolution is approximately the same  than
video resolution (500x700). So high camera resolution is only usefull for
small magnification.

A good product is the digital video camera of Leica : video, very friendly
and usefull software, same price than Kodak with software and PCI card,
very sensitive for fluorescence and resolution of 1400*1200 by
interpolation (700*500 in normal mode). They announce for soon a new one
with real 1400x1200 resolution and a Macintosh version.

That's only my personnal experience.

Best regards.



Bertrand Mnard

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

                           Bertrand MENARD

Institute of Plant Biology                Institut de Biologie et de
        and Physiology                        Physiologie Vgtales
  University of Lausanne                 Universit de Lausanne
  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 Nov  2 09:41 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA24043;
	Mon, 2 Nov 1998 09:41:22 -0500 (EST)
Resent-Date: Mon, 2 Nov 1998 09:41:22 -0500 (EST)
X-Sender: zacchetti.daniele@mail.hsr.it
Message-Id: <l03130300b263703e9c59@[192.167.193.40]>
Mime-Version: 1.0
Date: Mon, 2 Nov 1998 15:24:41 +0100
To: NIH Image mailing list <nih-image@io.ece.drexel.edu>
From: Daniele Zacchetti <zacchetti.daniele@hsr.it>
Subject: Scion image for Windows
Resent-Message-ID: <"9D9yI2.0.VD5.SxRFs"@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/554
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: 306

Does anybody know whether the Scion image source code (Windows95 or NT) is
freely available?
TIA
Daniele

Dr. Daniele Zacchetti, PhD
Cellular Neurophysiology Unit
Dibit, San Raffaele Inst.
via Olgettina 58
20132 Milano, Italy
Phone: +39-02-2643-4812
Fax:+39-02-2643-4813
e-mail: zacchetti.daniele@hsr.it



From nih-image-request@io.ece.drexel.edu Mon Nov  2 10:00 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA26231;
	Mon, 2 Nov 1998 10:00:01 -0500 (EST)
Resent-Date: Mon, 2 Nov 1998 10:00:01 -0500 (EST)
Mime-Version: 1.0
Message-Id: <v04011765b26377f703d0@[134.192.129.87]>
In-Reply-To: <v03102804b2631ffcd0a2@[130.223.74.27]>
Date: Mon, 2 Nov 1998 09:57:56 -0500
To: nih-image@io.ece.drexel.edu
From: Gloria Hoffman <gehoffma@umaryland.edu>
Subject: RE : digital photo camera f. microscopy
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id JAA24286
Resent-Message-ID: <"HaZTX2.0.bx5.WKSFs"@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/555
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="iso-8859-1"
Content-Length: 2448

While somewhat expensive I have been using the Sensys Camera for digital
microscopy. It runs about 20,000 + but is a relatively high resolution
(about 2000 x 1700 pixel resolution)  camera and is a cooled low light
camera as well. There is now a liquid crystal adaptor that will convert the
camera to color  (probably not good for very low light, but should work for
bright fluorescence and does work well for darkfield images). The image
quality is superb!

>Hi Imagers,
>
>I've tried the Kodak digital camera with C-mount on a microscop. I don't
>think that's the good cameras for microscopy :
>1- It's not a video camera, so you must take a snapshot, wait, look if it's
>good, change settings, retry, retry and retry. With video camera, you
>change settings in live, you see immediatly if image is good or not. When
>it's good, you take it. It's fast and easy.
>2- With high magnification, the resolution of the camera (1500*1000) is
>highest than the optical resolution. With a 60x oel objective of 1.3
>numerical aperture, the optical resolution is approximately the same  than
>video resolution (500x700). So high camera resolution is only usefull for
>small magnification.
>
>A good product is the digital video camera of Leica : video, very friendly
>and usefull software, same price than Kodak with software and PCI card,
>very sensitive for fluorescence and resolution of 1400*1200 by
>interpolation (700*500 in normal mode). They announce for soon a new one
>with real 1400x1200 resolution and a Macintosh version.
>
>That's only my personnal experience.
>
>Best regards.
>
>
>
>Bertrand Mnard
>
>*********************************************************************
>
>                           Bertrand MENARD
>
>Institute of Plant Biology                Institut de Biologie et de
>        and Physiology                        Physiologie Vgtales
>  University of Lausanne                 Universit de Lausanne
>  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
>
>*********************************************************************

Gloria E. Hoffman, Ph.D.
Department of Anatomy and Neurobiology
685 W Baltimore St
Baltimore MD 21201
Phone 410 706-2438
Fax 410 706-2512
email gehoffma@umaryland.edu


From nih-image-request@io.ece.drexel.edu Mon Nov  2 10:38 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA04623;
	Mon, 2 Nov 1998 10:38:40 -0500 (EST)
Resent-Date: Mon, 2 Nov 1998 10:38:40 -0500 (EST)
Reply-To: <nedh@lightlink.com>
From: "Ned Horning" <nedh@online.mg>
To: <nih-image@io.ece.drexel.edu>
Subject: RE: Scion image for Windows
Date: Mon, 2 Nov 1998 18:12:00 +0300
Message-ID: <000401be0673$23d0e150$495499d0@nedh>
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
X-Priority: 3 (Normal)
X-MSMail-Priority: Normal
X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0
Importance: Normal
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4
In-Reply-To: <l03130300b263703e9c59@[192.167.193.40]>
Resent-Message-ID: <"E-UhC1.0.Nq6.mpSFs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/556
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Length: 1193

Daniele,

I asked the folks at Scion Corp. about this nearly a year ago and the
response I got was "At this time we will not be releasing any source code
for Scion Image for Windows.  This policy may change in the future but it is
very doubtful." After I received this message my superiors tried to follow
up to see if we could negotiate something but Scion did not respond.

You may want to look at the source code for ImageJ. There are several
advantages to using ImageJ since it does not have some of the limitations of
NIH Image and Scion Image. Wayne is doing a great job with ImageJ and
interest in it seems to be growing.

I wish you luck in your search for the Scion Image source code.

Ned

-----Original Message-----
From:	Daniele Zacchetti [mailto:zacchetti.daniele@hsr.it]
Sent:	Monday, November 02, 1998 5:25 PM
To:	NIH Image mailing list
Subject:	Scion image for Windows

Does anybody know whether the Scion image source code (Windows95 or NT) is
freely available?
TIA
Daniele

Dr. Daniele Zacchetti, PhD
Cellular Neurophysiology Unit
Dibit, San Raffaele Inst.
via Olgettina 58
20132 Milano, Italy
Phone: +39-02-2643-4812
Fax:+39-02-2643-4813
e-mail: zacchetti.daniele@hsr.it




From nih-image-request@io.ece.drexel.edu Mon Nov  2 10:47 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA09498;
	Mon, 2 Nov 1998 10:47:34 -0500 (EST)
Resent-Date: Mon, 2 Nov 1998 10:47:34 -0500 (EST)
X-Sender: jfitz@crgdmail1.cr.usgs.gov
Message-Id: <v03110702b263712c848e@[136.177.34.18]>
Mime-Version: 1.0
Date: Mon, 2 Nov 1998 08:25:08 -0600
To: nih-image@io.ece.drexel.edu
From: "Joan J. Fitzpatrick" <jfitz@usgs.gov>
Subject: unsubscribe
Resent-Message-ID: <"U0VdU1.0.R57.szSFs"@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/557
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: 27

UNSUBSCRIBE TO NIH-IMAGE



From nih-image-request@io.ece.drexel.edu Mon Nov  2 12:35 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA22176;
	Mon, 2 Nov 1998 12:35:22 -0500 (EST)
Resent-Date: Mon, 2 Nov 1998 12:35:22 -0500 (EST)
Message-Id: <v03007800b263967bfedd@[144.118.33.245]>
In-Reply-To: <v03110702b263712c848e@[136.177.34.18]>
Mime-Version: 1.0
Date: Mon, 2 Nov 1998 13:07:27 -0400
To: nih-image@io.ece.drexel.edu
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: Re: unsubscribe
Resent-Message-ID: <"XotsM.0.sk4.RRUFs"@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/558
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/enriched; charset="us-ascii"
Content-Length: 3677

<fontfamily><param>Courier</param>Hi everyone.


The following is a reminder to everyone regarding administrative issues
on the list. Those who desire the digest form, should unsubscribe from
the regular list and resubscribe to the digest list.


e-mail addresses of importance

--------

nih-image@biomed.drexel.edu   - Sends mail to the list

nih-image-request@biomed.drexel.edu   - Administation for List

nih-image-d-request@biomed.drexel.edu  - Aministration for Digest


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".


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

		Subject: unsubscribe



Unsubscribe to Digest

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

To unsubscribe to digested version of the list, send E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "unsubscribe".


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

		Subject: unsubscribe


Help

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

To obtain a listing of help items, send E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "help".


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

		Subject: help




Help on Digest

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

To obtain a listing of help items on digest version of the list, send
E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "help".


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

		Subject: help




Archive

-------

Every submission sent to this list is archived.	 Following are the
commands

used to access the archive.  Send Email to nih-image-request with the
command 

in the Subject line or in the body of the message.


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


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/*






</fontfamily>

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

                                  Jonathan Nissanov, Ph.D.

                                      Associate Director  

            Computer Vision Center for Vertebrate Brain Mapping,

                a NIH Biomedical Research Technology Resource

                                http://cbis.ece.drexel.edu/ICVC/

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

Imaging and Computer Vision Center              Tel: 215-895-1381

Drexel University                                                  
Fax: 215-895-4987

Phildelphia, PA 19104                                        
yoni@coe.drexel.edu

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



From nih-image-request@io.ece.drexel.edu Mon Nov  2 12:39 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA22673;
	Mon, 2 Nov 1998 12:39:32 -0500 (EST)
Resent-Date: Mon, 2 Nov 1998 12:39:32 -0500 (EST)
Message-Id: <363DE87E.7E4A67C2@cirl.meei.harvard.edu>
Date: Mon, 02 Nov 1998 12:14:40 -0500
From: Scott Cramer <srcramer@cirl.meei.harvard.edu>
Reply-To: srcramer@cirl.meei.harvard.edu
Organization: HMS/MEEI/WHOI
X-Mailer: Mozilla 4.05 (Macintosh; I; 68K)
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Unsubscribe
Resent-Message-ID: <"U5Rm63.0.Px4.XXUFs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/559
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: multipart/mixed; boundary="------------98611CBC770253999159B05A"
Content-Length: 931

This is a multi-part message in MIME format.
--------------98611CBC770253999159B05A
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Unsubscribe me please.  Thank you.

--------------98611CBC770253999159B05A
Content-Type: text/x-vcard; charset=us-ascii; name="vcard.vcf"
Content-Transfer-Encoding: 7bit
Content-Description: Card for Scott Cramer
Content-Disposition: attachment; filename="vcard.vcf"

begin:          vcard
fn:             Scott Cramer
n:              Cramer;Scott
org:            Massachusetts Eye & Ear Infirmary
adr;dom:        ;;243 Charles Street;Boston;MA;02114;
email;internet: srcramer@cirl.meei.harvard.edu
title:          Research Assistant II
tel;work:       617-573-4273
tel;fax:        617-573-4275
x-mozilla-cpt:  ;0
x-mozilla-html: FALSE
version:        2.1
end:            vcard


--------------98611CBC770253999159B05A--


From nih-image-request@io.ece.drexel.edu Mon Nov  2 13:07 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA25406;
	Mon, 2 Nov 1998 13:07:34 -0500 (EST)
Resent-Date: Mon, 2 Nov 1998 13:07:34 -0500 (EST)
From: Vaughn Adams <vaughn@cbis.ece.drexel.edu>
Message-Id: <199811021739.MAA18604@cbis.ece.drexel.edu>
Subject: Administrative Help
To: nih-image@io.ece.drexel.edu
Date: Mon, 2 Nov 1998 12:39:27 -0500 (EST)
X-Mailer: ELM [version 2.4ME+ PL48 (25)]
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"EfA4j1.0.MY5.LvUFs"@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/560
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: application/pgp; format=text; x-action=sign
Content-Length: 1106

-----BEGIN PGP SIGNED MESSAGE-----

Nih-Image List members:

List administrative commands will be sent out the 15th of every month.  It
will contain commands to subscribe, unsubscribe and search the archives.  I
hope that this will cut down on the number of unsubscribe requests to the list
itself.  You can get the same information by sending mail to
nih-image-request@biomed.drexel.edu with Help in the subject. 

I would also like to take the opportunity to mention that the nih-mailing list
has reached 779 list members.  

- -- 
Vaughn Adams
Drexel University 
Electrical and Computer Engineering      Voice: 215-895-1979
32nd and Chestnut Streets                  FAX: 215-895-1695
Philadelphia, Pa 19104                   Email: vaughn@coe.drexel.edu

PGP key available - finger -l vaughn@cbis.ece.drexel.edu

-----BEGIN PGP SIGNATURE-----
Version: 2.6.2

iQCVAwUBNj3uSooTfOp6Z5FxAQGjvwQAzBXku1i8qE9/Hc/TMNtlfeNL9A75s2xE
faonRnBbmpr4HR0MKNbM/8bEipfexmJ1lwi0oPHx33RK6T5Xm11ESEufkqri0KlM
nzjm0+IQehy9gMJ7K/6roa3sFzibaK9WLHpY3EYhtchTOJWsesGFe53xmHH1bIcN
3RxTCNPtAIA=
=O58A
-----END PGP SIGNATURE-----


From nih-image-request@io.ece.drexel.edu Mon Nov  2 17:15 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA25097;
	Mon, 2 Nov 1998 17:15:51 -0500 (EST)
Resent-Date: Mon, 2 Nov 1998 17:15:51 -0500 (EST)
Message-ID: <363E29FF.32792D8@netmatters.co.uk>
Date: Mon, 02 Nov 1998 21:54:19 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
Reply-To: brownj@netmatters.co.uk
X-Mailer: Mozilla 4.05 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: tracking asteroids...
References: <199810302011.MAA09986@oes.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"PmwHz.0.ek3.vgYFs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/561
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length: 721

Use ImageMath to determine if the position of the asteroids have changed
between images. Subtract image n from image n+1 the length of the
resultant white/black bits of the images will allow you to calculate the
velocity of the asteroids and direction, assuming you can scale the
images accurately. John Russ's Image Processing hand book covers this
topic very nicely pp273-276.

Jeremy

Lynn Huynh wrote:

> hi, i am wondering if anyone knows how to use nih-image to track
> asteroids in photos taken off the net... or rather to make the
> question broader, does anyone have a detailed procedure on how
> to use the stacking feature of the program?
>
> thank you,
> lynn
> lynnh@us1.oes.edu
> supershiny@hotmail.com





From nih-image-request@io.ece.drexel.edu Mon Nov  2 17:18 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA26446;
	Mon, 2 Nov 1998 17:18:20 -0500 (EST)
Resent-Date: Mon, 2 Nov 1998 17:18:20 -0500 (EST)
Message-ID: <363E1882.62A74C1D@netmatters.co.uk>
Date: Mon, 02 Nov 1998 20:39:39 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
Reply-To: brownj@netmatters.co.uk
X-Mailer: Mozilla 4.05 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: watershed segmentation
References: <852566AD.00498551.00@nsns-h01.arcochem.com>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"NMWXj1.0.0m3.zgYFs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/562
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length: 1234

A good cheat here is to convert your threshold / density slice image into
binary, use AnalyzeParticles (with the label and outline function disabled)
then threshold and makebinary again. This will fill any holes in the cells
which may be contributing to the errors associated with the watershed
algorithm.

If you are interested in the greyscale values of the cells or their internal
components you can use the X,Y location of the center of each cell in
conjunction with Autooutline to apply a ROI to the original image and continue
your analysis.

Jeremy

Dan Frich wrote:

> I was wondering if anyone could give me any help with the watershed
> segmentation routine in v. 1.61.  I am using Image to analyze sizes and
> distributions in cellular materials.  To do this, I use watershed
> segmentation to yield discrete cells and then use the analyze particles
> routine to measure individual cell sizes (areas).  This technique works
> extremely well except for the fact that I tend to get some degree of
> oversegmentation (splitting of cells that should be counted as only one) in
> the watershed routine.  Does anyone have any ideas or experience on how to
> correct this problem?
>
> My appreciation in advance,
> Dan Frich






From nih-image-d-request@io.ece.drexel.edu Mon Nov  2 17:34 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA04636;
	Mon, 2 Nov 1998 17:34:07 -0500 (EST)
Date: Mon, 2 Nov 1998 17:34:07 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811022234.RAA04636@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #104
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/104
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 19331

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 104

Today's Topics:
  Re: video capture at 30 fps           [ wpchan@socrates.berkeley.edu ]
  Use of Scion Image with Imagraph Cor  [ "Twilley, John" <JTwilley@lacma.org ]
  RE : digital photo camera f. microsc  [ Bertrand Menard <Bertrand.Menard@ie ]
  Scion image for Windows               [ Daniele Zacchetti <zacchetti.daniel ]
  RE : digital photo camera f. microsc  [ Gloria Hoffman <gehoffma@umaryland. ]
  RE: Scion image for Windows           [ "Ned Horning" <nedh@online.mg> ]
  unsubscribe                           [ "Joan J. Fitzpatrick" <jfitz@usgs.g ]
  Re: unsubscribe                       [ Jonathan Nissanov <yoni@cbis.ece.dr ]
  Unsubscribe                           [ Scott Cramer <srcramer@cirl.meei.ha ]
  Administrative Help                   [ Vaughn Adams <vaughn@cbis.ece.drexe ]
  Re: tracking asteroids...             [ Jeremy Brown <brownj@netmatters.co. ]

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

Date: Sun, 1 Nov 1998 19:28:45 -0800 (PST)
From: wpchan@socrates.berkeley.edu
To: nih-image@io.ece.drexel.edu
cc: Bill Miller <microbill@mohawk.net>, SolamereTG@aol.com,
        Pat Arnott <pat@dri.edu>
Subject: Re: video capture at 30 fps
Message-ID: <Pine.SOL.3.96.981101191541.22553F-100000@socrates.berkeley.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Many thanks for all the people that replied to my question.  I further
tested the LG-3 on the Mac and a Pentium machine myself.  It is no doublt
that the Scion LG-3 PCI card is built for the Mac (just look at the length
of the card!). 

On the Mac, a 9500/132 with 90 MB of RAM and ATI graphic card, 'make
movie' with blind capture in NIH-Image 1.61 (NTSC) can easily archive
29.97 frames per sec at 640x480.  The timing is right on the money. 

On a Dell Dimension with a 450 MHz Pentium II and 96 MB of RAM, STB nVidia
8MB VRAM running either Win95 or WinNT, the same procedure can only
accquire video sequences at about 17 fps at 640x480.  The only way to get
it to accquire close to 30 fps is to cut down the size of the ROI for
capturing to about half as suggested by various lister.  Disabling various
services, dropping the color depth of the display or adding more RAM did
not make any differences.  However, the timing of the capture fluctuates
as system resources changes.  Scion Image beta 3b has this strange memory
leak that the system resources (users and GDI as well) drops steadily with
each operation e.g. opening a large stack or make movie.  Eventually, the
capture rate in the make movie procedure will drop below 29.4 fps after a
few of the said operation.  Restarting the program will solve the problem.

The conclusion from this exercise is that since we do want to maintain the
quality of our digitized video by using the LG-3 PCI board, we do have to
use a Mac for capturing full 30 fps at 640x480 with NIH-Image.  For reason
beyond my knowlegde, running Scion Image on a Windoz machine just won't do
it.

--Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu)

On Tue, 20 Oct 1998 wpchan@socrates.berkeley.edu wrote:
> Recently we have bought a Scion LG3 PCI card to put in a Windows NT.  The
> highest capture rate that we can get with 'blind capture' in 'make movie'
> is 17 fps.  Scion Tech support confirmed that this is probably the highest
> one can get on a NT. 
> 
> Has anybody successfully get the LG3 PCI to capture to RAM at 30 fps and
> if so, under what condition and using what kind of computer?  Thanks.

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

Date: Sun, 1 Nov 1998 21:31:33 -0800 
From: "Twilley, John" <JTwilley@lacma.org>
To: "'nih-image-d@biomed.drexel.edu'" <nih-image-d@io.ece.drexel.edu>
Subject: Use of Scion Image with Imagraph Corp. frame grabbers
Message-ID: <7366F79ECE20D21197A400805FA7629F0F8F3B@mercury.lacma.org>
Content-Type: text/plain

Does anyone have experience with using the frame averaging capabilities of
the pc version of nih-image during dynamic acquisition on an Imagraph frame
grabber such as the H-Def III, H-Def+ or Acura models?

Is it possible to do this with a macro for those of us who already own a
grabber other than the ones made by Scion?

jtwilley@sprynet.com 

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

Date: Mon, 2 Nov 1998 09:59:09 +0100
From: Bertrand Menard <Bertrand.Menard@ie-bpv.unil.ch>
To: nih-image@io.ece.drexel.edu
Subject: RE : digital photo camera f. microscopy
Message-Id: <v03102804b2631ffcd0a2@[130.223.74.27]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Hi Imagers,

I've tried the Kodak digital camera with C-mount on a microscop. I don't
think that's the good cameras for microscopy :
1- It's not a video camera, so you must take a snapshot, wait, look if it's
good, change settings, retry, retry and retry. With video camera, you
change settings in live, you see immediatly if image is good or not. When
it's good, you take it. It's fast and easy.
2- With high magnification, the resolution of the camera (1500*1000) is
highest than the optical resolution. With a 60x oel objective of 1.3
numerical aperture, the optical resolution is approximately the same  than
video resolution (500x700). So high camera resolution is only usefull for
small magnification.

A good product is the digital video camera of Leica : video, very friendly
and usefull software, same price than Kodak with software and PCI card,
very sensitive for fluorescence and resolution of 1400*1200 by
interpolation (700*500 in normal mode). They announce for soon a new one
with real 1400x1200 resolution and a Macintosh version.

That's only my personnal experience.

Best regards.



Bertrand Mnard

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

                           Bertrand MENARD

Institute of Plant Biology                Institut de Biologie et de
        and Physiology                        Physiologie Vgtales
  University of Lausanne                 Universit de Lausanne
  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

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

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

Date: Mon, 2 Nov 1998 15:24:41 +0100
From: Daniele Zacchetti <zacchetti.daniele@hsr.it>
To: NIH Image mailing list <nih-image@io.ece.drexel.edu>
Subject: Scion image for Windows
Message-Id: <l03130300b263703e9c59@[192.167.193.40]>
Content-Type: text/plain; charset="us-ascii"

Does anybody know whether the Scion image source code (Windows95 or NT) is
freely available?
TIA
Daniele

Dr. Daniele Zacchetti, PhD
Cellular Neurophysiology Unit
Dibit, San Raffaele Inst.
via Olgettina 58
20132 Milano, Italy
Phone: +39-02-2643-4812
Fax:+39-02-2643-4813
e-mail: zacchetti.daniele@hsr.it

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

Date: Mon, 2 Nov 1998 09:57:56 -0500
From: Gloria Hoffman <gehoffma@umaryland.edu>
To: nih-image@io.ece.drexel.edu
Subject: RE : digital photo camera f. microscopy
Message-Id: <v04011765b26377f703d0@[134.192.129.87]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

While somewhat expensive I have been using the Sensys Camera for digital
microscopy. It runs about 20,000 + but is a relatively high resolution
(about 2000 x 1700 pixel resolution)  camera and is a cooled low light
camera as well. There is now a liquid crystal adaptor that will convert the
camera to color  (probably not good for very low light, but should work for
bright fluorescence and does work well for darkfield images). The image
quality is superb!

>Hi Imagers,
>
>I've tried the Kodak digital camera with C-mount on a microscop. I don't
>think that's the good cameras for microscopy :
>1- It's not a video camera, so you must take a snapshot, wait, look if it's
>good, change settings, retry, retry and retry. With video camera, you
>change settings in live, you see immediatly if image is good or not. When
>it's good, you take it. It's fast and easy.
>2- With high magnification, the resolution of the camera (1500*1000) is
>highest than the optical resolution. With a 60x oel objective of 1.3
>numerical aperture, the optical resolution is approximately the same  than
>video resolution (500x700). So high camera resolution is only usefull for
>small magnification.
>
>A good product is the digital video camera of Leica : video, very friendly
>and usefull software, same price than Kodak with software and PCI card,
>very sensitive for fluorescence and resolution of 1400*1200 by
>interpolation (700*500 in normal mode). They announce for soon a new one
>with real 1400x1200 resolution and a Macintosh version.
>
>That's only my personnal experience.
>
>Best regards.
>
>
>
>Bertrand Mnard
>
>*********************************************************************
>
>                           Bertrand MENARD
>
>Institute of Plant Biology                Institut de Biologie et de
>        and Physiology                        Physiologie Vgtales
>  University of Lausanne                 Universit de Lausanne
>  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
>
>*********************************************************************

Gloria E. Hoffman, Ph.D.
Department of Anatomy and Neurobiology
685 W Baltimore St
Baltimore MD 21201
Phone 410 706-2438
Fax 410 706-2512
email gehoffma@umaryland.edu

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

Date: Mon, 2 Nov 1998 18:12:00 +0300
From: "Ned Horning" <nedh@online.mg>
To: <nih-image@io.ece.drexel.edu>
Subject: RE: Scion image for Windows
Message-ID: <000401be0673$23d0e150$495499d0@nedh>
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 7bit

Daniele,

I asked the folks at Scion Corp. about this nearly a year ago and the
response I got was "At this time we will not be releasing any source code
for Scion Image for Windows.  This policy may change in the future but it is
very doubtful." After I received this message my superiors tried to follow
up to see if we could negotiate something but Scion did not respond.

You may want to look at the source code for ImageJ. There are several
advantages to using ImageJ since it does not have some of the limitations of
NIH Image and Scion Image. Wayne is doing a great job with ImageJ and
interest in it seems to be growing.

I wish you luck in your search for the Scion Image source code.

Ned

-----Original Message-----
From:	Daniele Zacchetti [mailto:zacchetti.daniele@hsr.it]
Sent:	Monday, November 02, 1998 5:25 PM
To:	NIH Image mailing list
Subject:	Scion image for Windows

Does anybody know whether the Scion image source code (Windows95 or NT) is
freely available?
TIA
Daniele

Dr. Daniele Zacchetti, PhD
Cellular Neurophysiology Unit
Dibit, San Raffaele Inst.
via Olgettina 58
20132 Milano, Italy
Phone: +39-02-2643-4812
Fax:+39-02-2643-4813
e-mail: zacchetti.daniele@hsr.it

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

Date: Mon, 2 Nov 1998 08:25:08 -0600
From: "Joan J. Fitzpatrick" <jfitz@usgs.gov>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <v03110702b263712c848e@[136.177.34.18]>
Content-Type: text/plain; charset="us-ascii"

UNSUBSCRIBE TO NIH-IMAGE

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

Date: Mon, 2 Nov 1998 13:07:27 -0400
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: unsubscribe
Message-Id: <v03007800b263967bfedd@[144.118.33.245]>
Content-Type: text/enriched; charset="us-ascii"

<fontfamily><param>Courier</param>Hi everyone.


The following is a reminder to everyone regarding administrative issues
on the list. Those who desire the digest form, should unsubscribe from
the regular list and resubscribe to the digest list.


e-mail addresses of importance

--------

nih-image@biomed.drexel.edu   - Sends mail to the list

nih-image-request@biomed.drexel.edu   - Administation for List

nih-image-d-request@biomed.drexel.edu  - Aministration for Digest


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".


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

		Subject: unsubscribe



Unsubscribe to Digest

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

To unsubscribe to digested version of the list, send E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "unsubscribe".


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

		Subject: unsubscribe


Help

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

To obtain a listing of help items, send E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "help".


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

		Subject: help




Help on Digest

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

To obtain a listing of help items on digest version of the list, send
E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "help".


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

		Subject: help




Archive

-------

Every submission sent to this list is archived.	 Following are the
commands

used to access the archive.  Send Email to nih-image-request with the
command 

in the Subject line or in the body of the message.


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


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/*






</fontfamily>

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

                                  Jonathan Nissanov, Ph.D.

                                      Associate Director  

            Computer Vision Center for Vertebrate Brain Mapping,

                a NIH Biomedical Research Technology Resource

                                http://cbis.ece.drexel.edu/ICVC/

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

Imaging and Computer Vision Center              Tel: 215-895-1381

Drexel University                                                  
Fax: 215-895-4987

Phildelphia, PA 19104                                        
yoni@coe.drexel.edu

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

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

Date: Mon, 02 Nov 1998 12:14:40 -0500
From: Scott Cramer <srcramer@cirl.meei.harvard.edu>
To: nih-image@io.ece.drexel.edu
Subject: Unsubscribe
Message-Id: <363DE87E.7E4A67C2@cirl.meei.harvard.edu>
Content-Type: multipart/mixed; boundary="------------98611CBC770253999159B05A"

This is a multi-part message in MIME format.
--------------98611CBC770253999159B05A
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Unsubscribe me please.  Thank you.

--------------98611CBC770253999159B05A
Content-Type: text/x-vcard; charset=us-ascii; name="vcard.vcf"
Content-Transfer-Encoding: 7bit
Content-Description: Card for Scott Cramer
Content-Disposition: attachment; filename="vcard.vcf"

begin:          vcard
fn:             Scott Cramer
n:              Cramer;Scott
org:            Massachusetts Eye & Ear Infirmary
adr;dom:        ;;243 Charles Street;Boston;MA;02114;
email;internet: srcramer@cirl.meei.harvard.edu
title:          Research Assistant II
tel;work:       617-573-4273
tel;fax:        617-573-4275
x-mozilla-cpt:  ;0
x-mozilla-html: FALSE
version:        2.1
end:            vcard


--------------98611CBC770253999159B05A--

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

Date: Mon, 2 Nov 1998 12:39:27 -0500 (EST)
From: Vaughn Adams <vaughn@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Administrative Help
Message-Id: <199811021739.MAA18604@cbis.ece.drexel.edu>
Content-Type: application/pgp; format=text; x-action=sign
Content-Transfer-Encoding: 7bit

-----BEGIN PGP SIGNED MESSAGE-----

Nih-Image List members:

List administrative commands will be sent out the 15th of every month.  It
will contain commands to subscribe, unsubscribe and search the archives.  I
hope that this will cut down on the number of unsubscribe requests to the list
itself.  You can get the same information by sending mail to
nih-image-request@biomed.drexel.edu with Help in the subject. 

I would also like to take the opportunity to mention that the nih-mailing list
has reached 779 list members.  

- -- 
Vaughn Adams
Drexel University 
Electrical and Computer Engineering      Voice: 215-895-1979
32nd and Chestnut Streets                  FAX: 215-895-1695
Philadelphia, Pa 19104                   Email: vaughn@coe.drexel.edu

PGP key available - finger -l vaughn@cbis.ece.drexel.edu

-----BEGIN PGP SIGNATURE-----
Version: 2.6.2

iQCVAwUBNj3uSooTfOp6Z5FxAQGjvwQAzBXku1i8qE9/Hc/TMNtlfeNL9A75s2xE
faonRnBbmpr4HR0MKNbM/8bEipfexmJ1lwi0oPHx33RK6T5Xm11ESEufkqri0KlM
nzjm0+IQehy9gMJ7K/6roa3sFzibaK9WLHpY3EYhtchTOJWsesGFe53xmHH1bIcN
3RxTCNPtAIA=
=O58A
-----END PGP SIGNATURE-----

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

Date: Mon, 02 Nov 1998 21:54:19 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: tracking asteroids...
Message-ID: <363E29FF.32792D8@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Use ImageMath to determine if the position of the asteroids have changed
between images. Subtract image n from image n+1 the length of the
resultant white/black bits of the images will allow you to calculate the
velocity of the asteroids and direction, assuming you can scale the
images accurately. John Russ's Image Processing hand book covers this
topic very nicely pp273-276.

Jeremy

Lynn Huynh wrote:

> hi, i am wondering if anyone knows how to use nih-image to track
> asteroids in photos taken off the net... or rather to make the
> question broader, does anyone have a detailed procedure on how
> to use the stacking feature of the program?
>
> thank you,
> lynn
> lynnh@us1.oes.edu
> supershiny@hotmail.com

--------------------------------
End of nih-image-d Digest V98 Issue #104
****************************************

From nih-image-request@io.ece.drexel.edu Mon Nov  2 18:29 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA03453;
	Mon, 2 Nov 1998 18:29:17 -0500 (EST)
Resent-Date: Mon, 2 Nov 1998 18:29:17 -0500 (EST)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: nih-image@io.ece.drexel.edu, glenmac@u.washington.edu
Date:          Tue, 3 Nov 1998 9:18:36 GMT+1100
Subject:       Re: Modulus operation
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <CAD88E7B46@rna.bio.mq.edu.au>
Resent-Message-ID: <"IOttC3.0.XP6.dqZFs"@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/563
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1726

>Date: Sat, 31 Oct 1998 09:44:29 -0800 (PST)
>From: "G. Macdonald" <glenmac@u.washington.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Modulus operation
>
>Attempts to create a modulus operation have been giving unpredictable
>results.  Maybe someone can point out my mistake.  I've been taking the
>quotient from division of 2 real vars, then subtracting the truncation of
>the quotient:
>
>var
>	seglength,Mseglength,quotient,modulo:real;
>	Trunk:integer;
>begin
>	quotient:=MsegLength/segLength;
>	Trunk:=trunc(quotient);
>	modulo:=quotient-trunk;
>
>end;
>
>If SegLength is passed in as .N*MSegLength [to segment the midline into N
>divisions], then sometimes Trunk is N, other times it is N-1.
>
>TIA,
>Glen
integer<>real conversions can often be trickier than you expect
but I suspect there is an inversion in your statement of your problem.

trunc((rN*rM)/rM) can yield rN-1 if rM uses enough precision bits for (rN*rM) to 
lose precision.

You could set a limit on precision by eg trunc((rN*rM*1.001))/rM).

Note however that the modulus operator is available in NIH-Image macros as well as 
Pascal.

>From Appendix on Macros:
" 
Operators
	+    -    *    /   DIV   MOD   :=    
	=   <   >   <>   <=   >=   AND  OR   NOT


Types
	 INTEGER   REAL  BOOLEAN  STRING

Both integer and real variables are stored internally in extended precision real 
format, which has a range of 1.9 x 10-495 to 1.1 x 10 4932 and 19-20 digits 
precision. Real numbers are automatically converted (by rounding) to integer 
without warning as needed. 
"
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 Nov  2 21:13 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id VAA27035;
	Mon, 2 Nov 1998 21:13:34 -0500 (EST)
Resent-Date: Mon, 2 Nov 1998 21:13:34 -0500 (EST)
Message-ID: <001301be06cd$63dc5900$08778dd2@oemcomputer>
From: "=?iso-2022-jp?B?GyRCNGRFRDdyGyhC?=" <keniwata@d1.dion.ne.jp>
To: <nih-image@io.ece.drexel.edu>
Subject: For western blotting
Date: Tue, 3 Nov 1998 10:57:21 +0900
MIME-Version: 1.0
X-Priority: 3
X-MSMail-Priority: Normal
X-Mailer: Microsoft Outlook Express 4.72.3110.5
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3
Resent-Message-ID: <"c_Pke3.0.vl4.2DcFs"@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/564
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_000F_01BE0718.BAF23E80"
Content-Length: 970

This is a multi-part message in MIME format.

------=_NextPart_000_000F_01BE0718.BAF23E80
Content-Type: text/plain;
	charset="iso-2022-jp"
Content-Transfer-Encoding: 7bit

Hello.
 Dose anyone know the paper which contains NIH image to use for analysing
for Westen blotting?
 Ken Iwata

------=_NextPart_000_000F_01BE0718.BAF23E80
Content-Type: text/html;
	charset="iso-2022-jp"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD W3 HTML//EN">
<HTML>
<HEAD>

<META content=3D"text/html; charset=3DcsISO2022JP" =
http-equiv=3DContent-Type>
<META content=3D'"MSHTML 4.72.3110.7"' name=3DGENERATOR>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT size=3D2>Hello.</FONT></DIV>
<DIV><FONT size=3D2>&nbsp;Dose anyone know the paper which contains NIH =
image to=20
use for analysing for </FONT><FONT size=3D2>Westen =
blotting?</FONT></DIV>
<DIV><FONT size=3D2>&nbsp;Ken Iwata</FONT></DIV></BODY></HTML>

------=_NextPart_000_000F_01BE0718.BAF23E80--


From nih-image-request@io.ece.drexel.edu Mon Nov  2 23:14 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id XAA27809;
	Mon, 2 Nov 1998 23:14:15 -0500 (EST)
Resent-Date: Mon, 2 Nov 1998 23:14:15 -0500 (EST)
Date: Mon, 2 Nov 1998 20:02:41 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: GJOSS@rna.bio.mq.edu.au
cc: rh208@cus.cam.ac.uk, nih-image@io.ece.drexel.edu
Subject: Re: Modulus operation
In-Reply-To: <CAD88E7B46@rna.bio.mq.edu.au>
Message-ID: <Pine.A41.4.05.9811021938280.20938-100000@homer21.u.washington.edu>
MIME-Version: 1.0
Resent-Message-ID: <"6FHAt3.0.fM5.g1eFs"@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/565
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: 419

Dear Greg and Ray, thanks for the responses. Yes, it was rounding errors
that were confounding me. I had over-simplified the statement regarding
setting the segmentation value in my posting.  The MSegLength is the
length of a segment in a segmented line.  SegLength is length of some
fraction of the total length of the segmented line.  I am moving along the
segmented line dividing it in increments of Seglength.






From nih-image-request@io.ece.drexel.edu Mon Nov  2 23:21 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id XAA02073;
	Mon, 2 Nov 1998 23:21:51 -0500 (EST)
Resent-Date: Mon, 2 Nov 1998 23:21:51 -0500 (EST)
Date: Mon, 2 Nov 1998 20:14:10 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: GJOSS@rna.bio.mq.edu.au
cc: rh208@cus.cam.ac.uk, nih-image@io.ece.drexel.edu
Subject: Re: Modulus operation
In-Reply-To: <CAD88E7B46@rna.bio.mq.edu.au>
Message-ID: <Pine.A41.4.05.9811022002480.20938-100000@homer21.u.washington.edu>
MIME-Version: 1.0
Resent-Message-ID: <"Y4oNC1.0.eo6.NCeFs"@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/566
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: 2287

Dear Greg and Ray,
Thanks for the responses.  Yes, it seems to be rounding errors and
transferring quantities between differnt variable types were
confounding me.  The description of the length values being divided was
oversimplified from what I am actually doing,but the warning on an
inversion error is noted just the same. 
Ray, your modulus routine resolved the chronic rounding down.  

Glen

On Tue, 3 Nov 1998 GJOSS@rna.bio.mq.edu.au wrote:

> >Date: Sat, 31 Oct 1998 09:44:29 -0800 (PST)
> >From: "G. Macdonald" <glenmac@u.washington.edu>
> >To: nih-image@io.ece.drexel.edu
> >Subject: Modulus operation
> >
> >Attempts to create a modulus operation have been giving unpredictable
> >results.  Maybe someone can point out my mistake.  I've been taking the
> >quotient from division of 2 real vars, then subtracting the truncation of
> >the quotient:
> >
> >var
> >	seglength,Mseglength,quotient,modulo:real;
> >	Trunk:integer;
> >begin
> >	quotient:=MsegLength/segLength;
> >	Trunk:=trunc(quotient);
> >	modulo:=quotient-trunk;
> >
> >end;
> >
> >If SegLength is passed in as .N*MSegLength [to segment the midline into N
> >divisions], then sometimes Trunk is N, other times it is N-1.
> >
> >TIA,
> >Glen
> integer<>real conversions can often be trickier than you expect
> but I suspect there is an inversion in your statement of your problem.
> 
> trunc((rN*rM)/rM) can yield rN-1 if rM uses enough precision bits for (rN*rM) to 
> lose precision.
> 
> You could set a limit on precision by eg trunc((rN*rM*1.001))/rM).
> 
> Note however that the modulus operator is available in NIH-Image macros as well as 
> Pascal.
> 
> From Appendix on Macros:
> " 
> Operators
> 	+    -    *    /   DIV   MOD   :=    
> 	=   <   >   <>   <=   >=   AND  OR   NOT
> 
> 
> Types
> 	 INTEGER   REAL  BOOLEAN  STRING
> 
> Both integer and real variables are stored internally in extended precision real 
> format, which has a range of 1.9 x 10-495 to 1.1 x 10 4932 and 19-20 digits 
> precision. Real numbers are automatically converted (by rounding) to integer 
> without warning as needed. 
> "
> 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 Tue Nov  3 09:24 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA21009;
	Tue, 3 Nov 1998 09:24:16 -0500 (EST)
Resent-Date: Tue, 3 Nov 1998 09:24:16 -0500 (EST)
Date: Tue, 03 Nov 1998 12:29:18 +0200
From: Ricardo Pujol Borrell <IKHT4@cc.uab.es>
Subject: unsuscribe
To: nih-image@io.ece.drexel.edu
Reply-to: IKHT4@cc.uab.es
Message-id: <363EDAFC.5542EDEE@cc.uab.es>
Organization: Hospital Universitario Germans Trias i Pujol
MIME-version: 1.0
X-Mailer: Mozilla 4.5b2 (Macintosh; I; PPC)
Content-transfer-encoding: 7bit
References: <199811021739.MAA18604@cbis.ece.drexel.edu>
Resent-Message-ID: <"VjtQN.0.Rg4.9vmFs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/567
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; x-mac-creator=4D4F5353; x-mac-type=54455854;
 charset=us-ascii
Content-Length: 205

unsuscribe

--
R. Pujol Borrell MD, PhD
Head Immunology Unit
Hospital Univ. Germans Trias i Pujol/UAB
Crtra. del Canyet s/n
08916 Badalona
Spain

Tel 3493 4978893
Fax 3493 4978843
E-Mail IKHT4@cc.uab.es



From nih-image-d-request@io.ece.drexel.edu Tue Nov  3 09:28 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA21418;
	Tue, 3 Nov 1998 09:28:37 -0500 (EST)
Date: Tue, 3 Nov 1998 09:28:37 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811031428.JAA21418@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #105
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/105
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 9541

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 105

Today's Topics:
  Re: watershed segmentation            [ Jeremy Brown <brownj@netmatters.co. ]
  Re: Modulus operation                 [ GJOSS@rna.bio.mq.edu.au ]
  For western blotting                  [ "=?iso-2022-jp?B?GyRCNGRFRDdyGyhC?= ]
  Re: Modulus operation                 [ "G. Macdonald" <glenmac@u.washingto ]
  Re: Modulus operation                 [ "G. Macdonald" <glenmac@u.washingto ]
  unsuscribe                            [ Ricardo Pujol Borrell <IKHT4@cc.uab ]

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

Date: Mon, 02 Nov 1998 20:39:39 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: watershed segmentation
Message-ID: <363E1882.62A74C1D@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

A good cheat here is to convert your threshold / density slice image into
binary, use AnalyzeParticles (with the label and outline function disabled)
then threshold and makebinary again. This will fill any holes in the cells
which may be contributing to the errors associated with the watershed
algorithm.

If you are interested in the greyscale values of the cells or their internal
components you can use the X,Y location of the center of each cell in
conjunction with Autooutline to apply a ROI to the original image and continue
your analysis.

Jeremy

Dan Frich wrote:

> I was wondering if anyone could give me any help with the watershed
> segmentation routine in v. 1.61.  I am using Image to analyze sizes and
> distributions in cellular materials.  To do this, I use watershed
> segmentation to yield discrete cells and then use the analyze particles
> routine to measure individual cell sizes (areas).  This technique works
> extremely well except for the fact that I tend to get some degree of
> oversegmentation (splitting of cells that should be counted as only one) in
> the watershed routine.  Does anyone have any ideas or experience on how to
> correct this problem?
>
> My appreciation in advance,
> Dan Frich

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

Date:          Tue, 3 Nov 1998 9:18:36 GMT+1100
From: GJOSS@rna.bio.mq.edu.au
To: nih-image@io.ece.drexel.edu, glenmac@u.washington.edu
Subject:       Re: Modulus operation
Message-ID: <CAD88E7B46@rna.bio.mq.edu.au>

>Date: Sat, 31 Oct 1998 09:44:29 -0800 (PST)
>From: "G. Macdonald" <glenmac@u.washington.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Modulus operation
>
>Attempts to create a modulus operation have been giving unpredictable
>results.  Maybe someone can point out my mistake.  I've been taking the
>quotient from division of 2 real vars, then subtracting the truncation of
>the quotient:
>
>var
>	seglength,Mseglength,quotient,modulo:real;
>	Trunk:integer;
>begin
>	quotient:=MsegLength/segLength;
>	Trunk:=trunc(quotient);
>	modulo:=quotient-trunk;
>
>end;
>
>If SegLength is passed in as .N*MSegLength [to segment the midline into N
>divisions], then sometimes Trunk is N, other times it is N-1.
>
>TIA,
>Glen
integer<>real conversions can often be trickier than you expect
but I suspect there is an inversion in your statement of your problem.

trunc((rN*rM)/rM) can yield rN-1 if rM uses enough precision bits for (rN*rM) to 
lose precision.

You could set a limit on precision by eg trunc((rN*rM*1.001))/rM).

Note however that the modulus operator is available in NIH-Image macros as well as 
Pascal.

>From Appendix on Macros:
" 
Operators
	+    -    *    /   DIV   MOD   :=    
	=   <   >   <>   <=   >=   AND  OR   NOT


Types
	 INTEGER   REAL  BOOLEAN  STRING

Both integer and real variables are stored internally in extended precision real 
format, which has a range of 1.9 x 10-495 to 1.1 x 10 4932 and 19-20 digits 
precision. Real numbers are automatically converted (by rounding) to integer 
without warning as needed. 
"
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, 3 Nov 1998 10:57:21 +0900
From: "=?iso-2022-jp?B?GyRCNGRFRDdyGyhC?=" <keniwata@d1.dion.ne.jp>
To: <nih-image@io.ece.drexel.edu>
Subject: For western blotting
Message-ID: <001301be06cd$63dc5900$08778dd2@oemcomputer>
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_000F_01BE0718.BAF23E80"

This is a multi-part message in MIME format.

------=_NextPart_000_000F_01BE0718.BAF23E80
Content-Type: text/plain;
	charset="iso-2022-jp"
Content-Transfer-Encoding: 7bit

Hello.
 Dose anyone know the paper which contains NIH image to use for analysing
for Westen blotting?
 Ken Iwata

------=_NextPart_000_000F_01BE0718.BAF23E80
Content-Type: text/html;
	charset="iso-2022-jp"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD W3 HTML//EN">
<HTML>
<HEAD>

<META content=3D"text/html; charset=3DcsISO2022JP" =
http-equiv=3DContent-Type>
<META content=3D'"MSHTML 4.72.3110.7"' name=3DGENERATOR>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT size=3D2>Hello.</FONT></DIV>
<DIV><FONT size=3D2>&nbsp;Dose anyone know the paper which contains NIH =
image to=20
use for analysing for </FONT><FONT size=3D2>Westen =
blotting?</FONT></DIV>
<DIV><FONT size=3D2>&nbsp;Ken Iwata</FONT></DIV></BODY></HTML>

------=_NextPart_000_000F_01BE0718.BAF23E80--

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

Date: Mon, 2 Nov 1998 20:02:41 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: GJOSS@rna.bio.mq.edu.au
cc: rh208@cus.cam.ac.uk, nih-image@io.ece.drexel.edu
Subject: Re: Modulus operation
Message-ID: <Pine.A41.4.05.9811021938280.20938-100000@homer21.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear Greg and Ray, thanks for the responses. Yes, it was rounding errors
that were confounding me. I had over-simplified the statement regarding
setting the segmentation value in my posting.  The MSegLength is the
length of a segment in a segmented line.  SegLength is length of some
fraction of the total length of the segmented line.  I am moving along the
segmented line dividing it in increments of Seglength.

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

Date: Mon, 2 Nov 1998 20:14:10 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: GJOSS@rna.bio.mq.edu.au
cc: rh208@cus.cam.ac.uk, nih-image@io.ece.drexel.edu
Subject: Re: Modulus operation
Message-ID: <Pine.A41.4.05.9811022002480.20938-100000@homer21.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear Greg and Ray,
Thanks for the responses.  Yes, it seems to be rounding errors and
transferring quantities between differnt variable types were
confounding me.  The description of the length values being divided was
oversimplified from what I am actually doing,but the warning on an
inversion error is noted just the same. 
Ray, your modulus routine resolved the chronic rounding down.  

Glen

On Tue, 3 Nov 1998 GJOSS@rna.bio.mq.edu.au wrote:

> >Date: Sat, 31 Oct 1998 09:44:29 -0800 (PST)
> >From: "G. Macdonald" <glenmac@u.washington.edu>
> >To: nih-image@io.ece.drexel.edu
> >Subject: Modulus operation
> >
> >Attempts to create a modulus operation have been giving unpredictable
> >results.  Maybe someone can point out my mistake.  I've been taking the
> >quotient from division of 2 real vars, then subtracting the truncation of
> >the quotient:
> >
> >var
> >	seglength,Mseglength,quotient,modulo:real;
> >	Trunk:integer;
> >begin
> >	quotient:=MsegLength/segLength;
> >	Trunk:=trunc(quotient);
> >	modulo:=quotient-trunk;
> >
> >end;
> >
> >If SegLength is passed in as .N*MSegLength [to segment the midline into N
> >divisions], then sometimes Trunk is N, other times it is N-1.
> >
> >TIA,
> >Glen
> integer<>real conversions can often be trickier than you expect
> but I suspect there is an inversion in your statement of your problem.
> 
> trunc((rN*rM)/rM) can yield rN-1 if rM uses enough precision bits for (rN*rM) to 
> lose precision.
> 
> You could set a limit on precision by eg trunc((rN*rM*1.001))/rM).
> 
> Note however that the modulus operator is available in NIH-Image macros as well as 
> Pascal.
> 
> From Appendix on Macros:
> " 
> Operators
> 	+    -    *    /   DIV   MOD   :=    
> 	=   <   >   <>   <=   >=   AND  OR   NOT
> 
> 
> Types
> 	 INTEGER   REAL  BOOLEAN  STRING
> 
> Both integer and real variables are stored internally in extended precision real 
> format, which has a range of 1.9 x 10-495 to 1.1 x 10 4932 and 19-20 digits 
> precision. Real numbers are automatically converted (by rounding) to integer 
> without warning as needed. 
> "
> 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, 03 Nov 1998 12:29:18 +0200
From: Ricardo Pujol Borrell <IKHT4@cc.uab.es>
To: nih-image@io.ece.drexel.edu
Subject: unsuscribe
Message-id: <363EDAFC.5542EDEE@cc.uab.es>
Content-type: text/plain; x-mac-creator=4D4F5353; x-mac-type=54455854;
 charset=us-ascii
Content-transfer-encoding: 7bit

unsuscribe

--
R. Pujol Borrell MD, PhD
Head Immunology Unit
Hospital Univ. Germans Trias i Pujol/UAB
Crtra. del Canyet s/n
08916 Badalona
Spain

Tel 3493 4978893
Fax 3493 4978843
E-Mail IKHT4@cc.uab.es

--------------------------------
End of nih-image-d Digest V98 Issue #105
****************************************

From nih-image-request@io.ece.drexel.edu Tue Nov  3 10:57 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA01256;
	Tue, 3 Nov 1998 10:57:31 -0500 (EST)
Resent-Date: Tue, 3 Nov 1998 10:57:31 -0500 (EST)
Message-ID: <363F21FA.7F4BD1A3@earthlink.net>
Date: Tue, 03 Nov 1998 07:32:10 -0800
From: Shawn Makanvand <shawnmak@earthlink.net>
Reply-To: shawnmak@earthlink.net
X-Mailer: Mozilla 4.06 [en] (WinNT; U)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: UNSUBSCRIBE
References: <199811031419.JAA20366@io.ece.drexel.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"BbZng2.0.Sl6.V6oFs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/568
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: 22

UNSUBSCRIBE please.



From nih-image-request@io.ece.drexel.edu Tue Nov  3 14:48 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA24176;
	Tue, 3 Nov 1998 14:48:53 -0500 (EST)
Resent-Date: Tue, 3 Nov 1998 14:48:53 -0500 (EST)
Message-ID: <19981103192416.10573.rocketmail@attach1.rocketmail.com>
Date: Tue, 3 Nov 1998 11:24:16 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
Subject: Re: For western blotting
To: nih-image@io.ece.drexel.edu
MIME-Version: 1.0
Resent-Message-ID: <"VbWJC.0.CH5.RcrFs"@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/570
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: 1575

>  Dose anyone know the paper which contains NIH image to use for analysing
> for Westen blotting?


Well I think this part of the FAQ still has valid links. If not let me know...

   * Is there any help in understanding densitometry and/or gel analysis?

There are a number of documents available explaning anything from portions of
the theoretical prinicples of densitomtry, to step by step help in using the
gel analysis macros. Those interested in densitometry should strive to
understand the "calibrate" command and why it is used. 

For explanation regarding basic underlying principles of densitometry read the
section of Image Engineering on densitometry at:
http://rsb.info.nih.gov/nih-image/more-docs/Engineering/ImgEngr.html#densitometry

For simple explanation on the calibrate command, the NIH Image manual section
should be read:
http://rsb.info.nih.gov/nih-image/manual/menus/analyze.html#calibrate

For basic step by step explanation on the gel macros the NIH Image manual,
techniques section, section should be read:
http://rsb.info.nih.gov/nih-image/manual/tech.html#analyze

For a longer and thorough step by step explanation as to how to use the gel
macros refer to the gel analysis manual at:
http://sunny.dcrt.nih.gov/itc/gel/

Calibrated optical density step tablets are made by Kodak and can be
purchased from Kodak dealers. See Kodak's step table Web page at

http://www.kodak.com/aboutKodak/bu/dai/SIS/stepTab.shtml

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


From nih-image-request@io.ece.drexel.edu Tue Nov  3 14:49 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA24242;
	Tue, 3 Nov 1998 14:49:19 -0500 (EST)
Resent-Date: Tue, 3 Nov 1998 14:49:19 -0500 (EST)
Message-ID: <19981103191254.14852.rocketmail@web1.rocketmail.com>
Date: Tue, 3 Nov 1998 11:12:53 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
Subject: how to (un)subscribe & list info
To: nih-image@io.ece.drexel.edu
MIME-Version: 1.0
Resent-Message-ID: <"DnO1r.0.PA5.jZrFs"@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/569
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: 2778

Seems like most who need this miss it...


e-mail addresses of importance
--------
nih-image@biomed.drexel.edu   - Sends mail to the list
nih-image-request@biomed.drexel.edu   - Administation for List
nih-image-d-request@biomed.drexel.edu  - Aministration for Digest

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".

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


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

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

Help
--------------------
To obtain a listing of help items, send E-mail to
nih-image-d-request@biomed.drexel.edu.
the Subject of the message should contain "help".

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



Help on Digest
--------------------
To obtain a listing of help items on digest version of the list, send
E-mail to
nih-image-d-request@biomed.drexel.edu.
the Subject of the message should contain "help".

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



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

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

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/*

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


From nih-image-request@io.ece.drexel.edu Tue Nov  3 14:55 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA25195;
	Tue, 3 Nov 1998 14:55:55 -0500 (EST)
Resent-Date: Tue, 3 Nov 1998 14:55:55 -0500 (EST)
Message-ID: <19981103192334.17397.rocketmail@web1.rocketmail.com>
Date: Tue, 3 Nov 1998 11:23:34 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
Subject: Re:  RE: analog to digital (was: Can a snappy be used for?)
To: nih-image@io.ece.drexel.edu
MIME-Version: 1.0
Resent-Message-ID: <"Yb8kl1.0.2V5.djrFs"@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/571
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: 1443


> >Could you explain further how video bandwidth limits the digitization of a
> line
> >of video signal to only about 330 pixels?  For that matter, what is
> "bandwidth"?
> > Is there is a distinction between "analog bandwidth" and the "digital
> bandwidth"
> >we hear so much about?
> 
> Too long a question for email. Read a good book. Start with Inoue "Video
> Microscopy." There is also a lot of information in books like Pratt "Digital
> Image Processing", Jain "Fundamentals of Digital Image Proc", Gonzalez&Woods
> "Digital Image Proc" and my own "Image Processing Handbook"

Good set of refs, especially Inoue for this question. Aside from bandwidth
limitations one also has to deal with signal to noise ratios which can ruin
the bit depth. A formula is seen in Inside NIH Image on calculating how many
significant bits one can get from the SNR of a camera, etc. While lots of bits
may be needed for math operations on images, fact is most people out there are
using about 7 real bits or so per pixel, and most don't even have a real eight
bit. Spatial resolution wise, as per question, it is good to deal with digital.

Digital data is transfered or not, analog data only degrades and is the simple
answer to part of your question.
==
Mark Vivino
mvivino@rocketmail.com
Consulting Biomedical Engineer
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-request@io.ece.drexel.edu Tue Nov  3 15:14 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA27036;
	Tue, 3 Nov 1998 15:14:01 -0500 (EST)
Resent-Date: Tue, 3 Nov 1998 15:14:01 -0500 (EST)
Message-ID: <19981103193358.19997.rocketmail@web1.rocketmail.com>
Date: Tue, 3 Nov 1998 11:33:58 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
Subject: Re: electrophoretic gel reading...
To: nih-image@io.ece.drexel.edu
MIME-Version: 1.0
Resent-Message-ID: <"rynck1.0.4p5.OtrFs"@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/572
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: 1871



> how do i use nih-image to analyze electrophoretic gels?  i need 
> better readings on some gels that i have.  i have been using page 
> techniques and will be needing to analyze not just whether the 
> band is detectable but also which bands are darker, i will be using 
> this information to create a haplotype and do two-point lod score 
> analysis with linkage 5.1 software


Again from the faq... I

   * Is there any help in understanding densitometry and/or gel analysis?

There are a number of documents available explaning anything from portions of
the theoretical prinicples of densitomtry, to step by step help in using the
gel analysis macros. Those interested in densitometry should strive to
understand the "calibrate" command and why it is used. 

For explanation regarding basic underlying principles of densitometry read the
section of Image Engineering on densitometry at:
http://rsb.info.nih.gov/nih-image/more-docs/Engineering/ImgEngr.html#densitometry

For simple explanation on the calibrate command, the NIH Image manual section
should be read:
http://rsb.info.nih.gov/nih-image/manual/menus/analyze.html#calibrate

For basic step by step explanation on the gel macros the NIH Image manual,
techniques section, section should be read:
http://rsb.info.nih.gov/nih-image/manual/tech.html#analyze

For a longer and thorough step by step explanation as to how to use the gel
macros refer to the gel analysis manual at:
http://sunny.dcrt.nih.gov/itc/gel/

Calibrated optical density step tablets are made by Kodak and can be
purchased from Kodak dealers. See Kodak's step table Web page at

http://www.kodak.com/aboutKodak/bu/dai/SIS/stepTab.shtml

==
Mark Vivino
mvivino@rocketmail.com
Consulting Biomedical Engineer
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-request@io.ece.drexel.edu Tue Nov  3 20:58 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA18023;
	Tue, 3 Nov 1998 20:58:58 -0500 (EST)
Resent-Date: Tue, 3 Nov 1998 20:58:58 -0500 (EST)
Message-ID: <19981104013818.14801.rocketmail@send1e.yahoomail.com>
Date: Tue, 3 Nov 1998 17:38:18 -0800 (PST)
From: Larisa Haupt <larisahpt@yahoo.com>
Subject: quantifying signal in histology sections
To: nih-image@io.ece.drexel.edu
Cc: malinda@asgard.cbu.edu
MIME-Version: 1.0
Resent-Message-ID: <"2LKXy1.0.9k2.X3xFs"@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/573
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: 898

Hi,

i am in dire need of some help.  I only have access to a digital
camera etc for the next couple of days, and i need to make sure i have
the correct images downloaded to compare and hopefully quantify the
signal in serial tissue sections obtained via in situ-pcr.  Can you
help me and let me know if image is capable of doing this, and most
importantly, how to do this.

I have tried to make sense of the online manual, with some minor
success, if you could give me any pointers and help me out with things
like image size, image type and apecifically the steps involved in
comparing eight serial sections I would greatly appreciate it.

I look forward to your response.

You can also email me at L.Haupt@nhs.gu.edu.au after this week

thanks 

larisa






==

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


From nih-image-request@io.ece.drexel.edu Tue Nov  3 23:19 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id XAA15435;
	Tue, 3 Nov 1998 23:19:57 -0500 (EST)
Resent-Date: Tue, 3 Nov 1998 23:19:57 -0500 (EST)
X-Sender: gtjr@eduserv.unimelb.edu.au
Message-Id: <v03130301b2657b7eedff@[128.250.104.121]>
In-Reply-To: <19981104013818.14801.rocketmail@send1e.yahoomail.com>
Mime-Version: 1.0
Date: Wed, 4 Nov 1998 15:01:32 +1100
To: nih-image@io.ece.drexel.edu
From: Garry Jolley-Rogers <G.jolley-rogers@zoology.unimelb.edu.au>
Subject: Re: quantifying signal in histology sections
Resent-Message-ID: <"JdfEK1.0.4v1.L7zFs"@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/574
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: 2510

Hi Larisa,
	I know the feeling -  In answer to your question - Yes NIH can -
with the only qualification being in the detail. Is your signal   well
differentiated from background? by colour or intensity?  If not - can it be
improved prior to digitization?   As for NIH image- it will allow you to
address most questions that you could ask.  As for image type and size -
try and err on the side of caution. For instance, scan at higher resolution
than you require  then reduce to a  size around twice the size of your
smallest feature of interest(or bits of your feature of interest).  File
format - tiff.  I believe NIH ver 1.6.2 has no restrictions on image width.
Then you'll need to align the sections.  They're are several macros that
will do this.  However, they do vary in  how they work.  What exactly are
you trying to align? with what fidelity?  do you have any fiducial markers?
or features that will serve as markers?

I'm going through the same process at the moment - just on a grander scale
as I've got 100's of serial sections to align. I'm just about to start on
the whole painful process.  If i can help - email me & we can chew the cud
a bit more without jamming this nice mail list.

yours


Garry Jolley-Rogers



At 12:38 PM +1100 on 4/11/98, Larisa Haupt wrote:


> Hi,
>
> i am in dire need of some help.  I only have access to a digital
> camera etc for the next couple of days, and i need to make sure i have
> the correct images downloaded to compare and hopefully quantify the
> signal in serial tissue sections obtained via in situ-pcr.  Can you
> help me and let me know if image is capable of doing this, and most
> importantly, how to do this.
>
> I have tried to make sense of the online manual, with some minor
> success, if you could give me any pointers and help me out with things
> like image size, image type and apecifically the steps involved in
> comparing eight serial sections I would greatly appreciate it.
>
> I look forward to your response.
>
> You can also email me at L.Haupt@nhs.gu.edu.au after this week
>
> thanks
>
> larisa
>
>
>
>
>
>
> ==
>
> _________________________________________________________
> DO YOU YAHOO!?
> Get your free @yahoo.com address at http://mail.yahoo.com


-----------------------------------------------------------
Garry Jolley-Rogers
Dept. of Zoology University of Melbourne
Ph x44846 or x44349 or 98836848 or 93620285

 email :G.jolley-rogers@zoology.unimelb.edu.au
-----------------------------------------------------------



From nih-image-d-request@io.ece.drexel.edu Wed Nov  4 06:25 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA26001;
	Wed, 4 Nov 1998 06:25:09 -0500 (EST)
Date: Wed, 4 Nov 1998 06:25:09 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811041125.GAA26001@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #106
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/106
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 14486

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 106

Today's Topics:
  UNSUBSCRIBE                           [ Shawn Makanvand <shawnmak@earthlink ]
  UNSUBSCRIBE                           [ Pierre-Olivier Tremblay <Pierre-Oli ]
  how to (un)subscribe & list info      [ Mark Vivino <mvivino@rocketmail.com ]
  Re: For western blotting              [ Mark Vivino <mvivino@rocketmail.com ]
  Re: RE: analog to digital (was: Can   [ Mark Vivino <mvivino@rocketmail.com ]
  Re: electrophoretic gel reading...    [ Mark Vivino <mvivino@rocketmail.com ]
  quantifying signal in histology sect  [ Larisa Haupt <larisahpt@yahoo.com> ]
  Re: quantifying signal in histology   [ Garry Jolley-Rogers <G.jolley-roger ]

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

Date: Tue, 03 Nov 1998 07:32:10 -0800
From: Shawn Makanvand <shawnmak@earthlink.net>
To: nih-image@io.ece.drexel.edu
Subject: UNSUBSCRIBE
Message-ID: <363F21FA.7F4BD1A3@earthlink.net>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

UNSUBSCRIBE please.

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

Date: Tue, 3 Nov 1998 12:06:22 -0400
From: Pierre-Olivier Tremblay <Pierre-Olivier.Tremblay@crchul.ulaval.ca>
To: nih-image-d@io.ece.drexel.edu
Subject: UNSUBSCRIBE
Message-Id: <v03007800b264da2a2b70@[132.203.188.94]>
Content-Type: text/plain; charset="us-ascii"

Unsubscribe me from the list

Thank you.

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

Date: Tue, 3 Nov 1998 11:12:53 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
To: nih-image@io.ece.drexel.edu
Subject: how to (un)subscribe & list info
Message-ID: <19981103191254.14852.rocketmail@web1.rocketmail.com>
Content-Type: text/plain; charset=us-ascii

Seems like most who need this miss it...


e-mail addresses of importance
--------
nih-image@biomed.drexel.edu   - Sends mail to the list
nih-image-request@biomed.drexel.edu   - Administation for List
nih-image-d-request@biomed.drexel.edu  - Aministration for Digest

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".

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


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

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

Help
--------------------
To obtain a listing of help items, send E-mail to
nih-image-d-request@biomed.drexel.edu.
the Subject of the message should contain "help".

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



Help on Digest
--------------------
To obtain a listing of help items on digest version of the list, send
E-mail to
nih-image-d-request@biomed.drexel.edu.
the Subject of the message should contain "help".

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



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

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

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/*

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

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

Date: Tue, 3 Nov 1998 11:24:16 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: For western blotting
Message-ID: <19981103192416.10573.rocketmail@attach1.rocketmail.com>
Content-Type: text/plain; charset=us-ascii

>  Dose anyone know the paper which contains NIH image to use for analysing
> for Westen blotting?


Well I think this part of the FAQ still has valid links. If not let me know...

   * Is there any help in understanding densitometry and/or gel analysis?

There are a number of documents available explaning anything from portions of
the theoretical prinicples of densitomtry, to step by step help in using the
gel analysis macros. Those interested in densitometry should strive to
understand the "calibrate" command and why it is used. 

For explanation regarding basic underlying principles of densitometry read the
section of Image Engineering on densitometry at:
http://rsb.info.nih.gov/nih-image/more-docs/Engineering/ImgEngr.html#densitometry

For simple explanation on the calibrate command, the NIH Image manual section
should be read:
http://rsb.info.nih.gov/nih-image/manual/menus/analyze.html#calibrate

For basic step by step explanation on the gel macros the NIH Image manual,
techniques section, section should be read:
http://rsb.info.nih.gov/nih-image/manual/tech.html#analyze

For a longer and thorough step by step explanation as to how to use the gel
macros refer to the gel analysis manual at:
http://sunny.dcrt.nih.gov/itc/gel/

Calibrated optical density step tablets are made by Kodak and can be
purchased from Kodak dealers. See Kodak's step table Web page at

http://www.kodak.com/aboutKodak/bu/dai/SIS/stepTab.shtml

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

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

Date: Tue, 3 Nov 1998 11:23:34 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re:  RE: analog to digital (was: Can a snappy be used for?)
Message-ID: <19981103192334.17397.rocketmail@web1.rocketmail.com>
Content-Type: text/plain; charset=us-ascii

> >Could you explain further how video bandwidth limits the digitization of a
> line
> >of video signal to only about 330 pixels?  For that matter, what is
> "bandwidth"?
> > Is there is a distinction between "analog bandwidth" and the "digital
> bandwidth"
> >we hear so much about?
> 
> Too long a question for email. Read a good book. Start with Inoue "Video
> Microscopy." There is also a lot of information in books like Pratt "Digital
> Image Processing", Jain "Fundamentals of Digital Image Proc", Gonzalez&Woods
> "Digital Image Proc" and my own "Image Processing Handbook"

Good set of refs, especially Inoue for this question. Aside from bandwidth
limitations one also has to deal with signal to noise ratios which can ruin
the bit depth. A formula is seen in Inside NIH Image on calculating how many
significant bits one can get from the SNR of a camera, etc. While lots of bits
may be needed for math operations on images, fact is most people out there are
using about 7 real bits or so per pixel, and most don't even have a real eight
bit. Spatial resolution wise, as per question, it is good to deal with digital.

Digital data is transfered or not, analog data only degrades and is the simple
answer to part of your question.
==
Mark Vivino
mvivino@rocketmail.com
Consulting Biomedical Engineer
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com

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

Date: Tue, 3 Nov 1998 11:33:58 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: electrophoretic gel reading...
Message-ID: <19981103193358.19997.rocketmail@web1.rocketmail.com>
Content-Type: text/plain; charset=us-ascii

> how do i use nih-image to analyze electrophoretic gels?  i need 
> better readings on some gels that i have.  i have been using page 
> techniques and will be needing to analyze not just whether the 
> band is detectable but also which bands are darker, i will be using 
> this information to create a haplotype and do two-point lod score 
> analysis with linkage 5.1 software


Again from the faq... I

   * Is there any help in understanding densitometry and/or gel analysis?

There are a number of documents available explaning anything from portions of
the theoretical prinicples of densitomtry, to step by step help in using the
gel analysis macros. Those interested in densitometry should strive to
understand the "calibrate" command and why it is used. 

For explanation regarding basic underlying principles of densitometry read the
section of Image Engineering on densitometry at:
http://rsb.info.nih.gov/nih-image/more-docs/Engineering/ImgEngr.html#densitometry

For simple explanation on the calibrate command, the NIH Image manual section
should be read:
http://rsb.info.nih.gov/nih-image/manual/menus/analyze.html#calibrate

For basic step by step explanation on the gel macros the NIH Image manual,
techniques section, section should be read:
http://rsb.info.nih.gov/nih-image/manual/tech.html#analyze

For a longer and thorough step by step explanation as to how to use the gel
macros refer to the gel analysis manual at:
http://sunny.dcrt.nih.gov/itc/gel/

Calibrated optical density step tablets are made by Kodak and can be
purchased from Kodak dealers. See Kodak's step table Web page at

http://www.kodak.com/aboutKodak/bu/dai/SIS/stepTab.shtml

==
Mark Vivino
mvivino@rocketmail.com
Consulting Biomedical Engineer
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com

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

Date: Tue, 3 Nov 1998 17:38:18 -0800 (PST)
From: Larisa Haupt <larisahpt@yahoo.com>
To: nih-image@io.ece.drexel.edu
Cc: malinda@asgard.cbu.edu
Subject: quantifying signal in histology sections
Message-ID: <19981104013818.14801.rocketmail@send1e.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

Hi,

i am in dire need of some help.  I only have access to a digital
camera etc for the next couple of days, and i need to make sure i have
the correct images downloaded to compare and hopefully quantify the
signal in serial tissue sections obtained via in situ-pcr.  Can you
help me and let me know if image is capable of doing this, and most
importantly, how to do this.

I have tried to make sense of the online manual, with some minor
success, if you could give me any pointers and help me out with things
like image size, image type and apecifically the steps involved in
comparing eight serial sections I would greatly appreciate it.

I look forward to your response.

You can also email me at L.Haupt@nhs.gu.edu.au after this week

thanks 

larisa






==

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

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

Date: Wed, 4 Nov 1998 15:01:32 +1100
From: Garry Jolley-Rogers <G.jolley-rogers@zoology.unimelb.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Re: quantifying signal in histology sections
Message-Id: <v03130301b2657b7eedff@[128.250.104.121]>
Content-Type: text/plain; charset="us-ascii"

Hi Larisa,
	I know the feeling -  In answer to your question - Yes NIH can -
with the only qualification being in the detail. Is your signal   well
differentiated from background? by colour or intensity?  If not - can it be
improved prior to digitization?   As for NIH image- it will allow you to
address most questions that you could ask.  As for image type and size -
try and err on the side of caution. For instance, scan at higher resolution
than you require  then reduce to a  size around twice the size of your
smallest feature of interest(or bits of your feature of interest).  File
format - tiff.  I believe NIH ver 1.6.2 has no restrictions on image width.
Then you'll need to align the sections.  They're are several macros that
will do this.  However, they do vary in  how they work.  What exactly are
you trying to align? with what fidelity?  do you have any fiducial markers?
or features that will serve as markers?

I'm going through the same process at the moment - just on a grander scale
as I've got 100's of serial sections to align. I'm just about to start on
the whole painful process.  If i can help - email me & we can chew the cud
a bit more without jamming this nice mail list.

yours


Garry Jolley-Rogers



At 12:38 PM +1100 on 4/11/98, Larisa Haupt wrote:


> Hi,
>
> i am in dire need of some help.  I only have access to a digital
> camera etc for the next couple of days, and i need to make sure i have
> the correct images downloaded to compare and hopefully quantify the
> signal in serial tissue sections obtained via in situ-pcr.  Can you
> help me and let me know if image is capable of doing this, and most
> importantly, how to do this.
>
> I have tried to make sense of the online manual, with some minor
> success, if you could give me any pointers and help me out with things
> like image size, image type and apecifically the steps involved in
> comparing eight serial sections I would greatly appreciate it.
>
> I look forward to your response.
>
> You can also email me at L.Haupt@nhs.gu.edu.au after this week
>
> thanks
>
> larisa
>
>
>
>
>
>
> ==
>
> _________________________________________________________
> DO YOU YAHOO!?
> Get your free @yahoo.com address at http://mail.yahoo.com


-----------------------------------------------------------
Garry Jolley-Rogers
Dept. of Zoology University of Melbourne
Ph x44846 or x44349 or 98836848 or 93620285

 email :G.jolley-rogers@zoology.unimelb.edu.au
-----------------------------------------------------------

--------------------------------
End of nih-image-d Digest V98 Issue #106
****************************************

From nih-image-request@io.ece.drexel.edu Wed Nov  4 13:45 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA13136;
	Wed, 4 Nov 1998 13:45:09 -0500 (EST)
Resent-Date: Wed, 4 Nov 1998 13:45:09 -0500 (EST)
Date: 04 Nov 98 11:06:34 -0700
From: Steven Moore <SteveM@cipe.com>
Subject: RE:Scion image for Windows
To: "nih-image" <nih-image@io.ece.drexel.edu>
X-Mailer: QuickMail Pro 1.5.3 (Windows32)
X-Priority: 3
MIME-Version: 1.0
Reply-To: Steven Moore <SteveM@cipe.com>
Message-ID: <1301944690-68027714@mailhost.cipe.com>
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id NAA01441
Resent-Message-ID: <"zWscW2.0.9N.7Y9Gs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/575
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: 1684

My understanding is the Scion does not plan on releasing the source code for Scion Image.

Steven Moore, Ph.D.
Director of Evaluation Services
Center for Image Processing in Education
Tucson, AZ
www.cipe.com


On 11/2/98, nih-image wrote:
>Does anybody know whether the Scion image source >code (Windows95 or NT) is
>freely available?
>TIA
>Daniele
>
>Dr. Daniele Zacchetti, PhD
>Cellular Neurophysiology Unit
>Dibit, San Raffaele Inst.
>via Olgettina 58
>20132 Milano, Italy
>Phone: +39-02-2643-4812
>Fax:+39-02-2643-4813
>e-mail: zacchetti.daniele@hsr.it
>
>
>
>
>RFC822 header
>-----------------------------------
> Return-Path: <nih-image-request@io.ece.drexel.edu>
> Received: from io.ece.drexel.edu (144.118.32.3) by >mailhost.cipe.com
>  with ESMTP (Eudora Internet Mail Server 1.2.1b5); >Mon, 2 Nov 1998 07:32:10 -0700
> Received: (from lists@localhost)
> 	by io.ece.drexel.edu (8.8.8/8.8.8) id >JAA22445;
> 	Mon, 2 Nov 1998 09:27:22 -0500 (EST)
> Resent-Date: Mon, 2 Nov 1998 09:27:22 -0500 (EST)
> X-Sender: zacchetti.daniele@mail.hsr.it
> Message-Id: ><l03130300b263703e9c59@[192.167.193.40]>
> Mime-Version: 1.0
> Content-Type: text/plain; charset="us-ascii"
> Date: Mon, 2 Nov 1998 15:24:41 +0100
> To: NIH Image mailing list <nih-
>image@io.ece.drexel.edu>
> From: Daniele Zacchetti <zacchetti.daniele@hsr.it>
> Subject: Scion image for Windows
> Resent-Message-ID: <"9D9yI2.0.VD5.SxRFs"@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/554
> X-Loop: nih-image@biomed.drexel.edu
> Precedence: list
> Resent-Sender: nih-image-request@io.ece.drexel.edu
> Status: R
> >


From nih-image-request@io.ece.drexel.edu Wed Nov  4 16:57 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA15400;
	Wed, 4 Nov 1998 16:57:33 -0500 (EST)
Resent-Date: Wed, 4 Nov 1998 16:57:33 -0500 (EST)
X-Authentication-Warning: sunspot.ccs.yorku.ca: rethoret owned process doing -bs
Date: Wed, 4 Nov 1998 16:15:53 -0500 (EST)
From: Karen Rethoret <rethoret@yorku.ca>
X-Sender: rethoret@sunspot.ccs.yorku.ca
To: nih-image@io.ece.drexel.edu
Subject: region selection tools
Message-ID: <Pine.SOL.4.05.9811041608250.1300-100000@sunspot.ccs.yorku.ca>
MIME-Version: 1.0
Resent-Message-ID: <"zZXjw2.0._d.LGCGs"@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/576
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: 430



Hello;

In Image for PC


This is probably straight-forward; but can you tell me the best way to
draw a rectangular region in which to do plot profiles that is
oriented
at different angles (not just at right angles?)

Have tried straight-line selection tool also but this is only 8 pixels
wide maximum when vertical or horizontal  (reduces to 1 pixel when line is
tilted).


Thanks in advance,

Karen Rethoret
York University



From nih-image-request@io.ece.drexel.edu Wed Nov  4 18:50 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA21588;
	Wed, 4 Nov 1998 18:50:06 -0500 (EST)
Resent-Date: Wed, 4 Nov 1998 18:50:06 -0500 (EST)
Message-Id: <3.0.5.32.19981105114537.007c3630@uni.massey.ac.nz>
X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32)
Date: Thu, 05 Nov 1998 11:45:37 +1300
To: nih-image@io.ece.drexel.edu
From: Naomi Boxall <Naomi.Boxall.1@uni.massey.ac.nz>
Subject: Extra band...
Mime-Version: 1.0
Resent-Message-ID: <"3VQZB2.0.4K3.X9EGs"@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/577
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: 650

Hi all.

I'm not quite sure if this is the correct forum for my query, but I was
wondering if anyone out there has done PFGE before.  If you have, could you
please suggest a reason (other than a plasmid) for an extra band occurring
on my gel in one isolate (epidemiologically related to the outbreak) which
is the same as the outbreak strain in all other bands.

If not then do you know of anyone I can ask, or any groups I can put this
question to?  Thanks very much,

Naomi
 
Naomi S. Boxall BSc
Epicentre
Inst. of Vet, Animal & Biomedical Sciences
Massey University
Palmerston North
New Zealand

064-6-3504008 (W)
Naomi.Boxall.1@uni.massey.ac.nz


From nih-image-request@io.ece.drexel.edu Wed Nov  4 19:49 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id TAA10913;
	Wed, 4 Nov 1998 19:49:00 -0500 (EST)
Resent-Date: Wed, 4 Nov 1998 19:49:00 -0500 (EST)
From: DrJohnRuss@aol.com
Message-ID: <405655c9.3640efee@aol.com>
Date: Wed, 4 Nov 1998 19:23:10 EST
To: nih-image@io.ece.drexel.edu
Mime-Version: 1.0
Subject: Ann: Updates to Image Processing Tool Kit
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 for Mac sub 84
Resent-Message-ID: <"aukVP1.0.Bf.j0FGs"@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/578
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: 1264

Several updates to the Image Processing Tool Kit are now posted on the web
site at
http://members.aol.com/ImagProcTK/

These are all identical for Mac and PC, and can be downloaded, decompressed
and placed in the same folder as your other plug-ins. The current list of
updates to version 2.5 is

Convolution and deconvolution of blur, motion and other point-spread functions
using Fourier transforms
Color-by-Value which labels features according to the value of any measured
parameter
Several recently published methods for image processing (sharpening, noise
reduction and edge enhancement)
Automatically drawing and labeling a magnification bar on the image
Versions of the Ranking and Variance filters with adjustable size round
neighborhoods.

Bug reports and fixes are also posted on the site.

The next update to be posted (check the web site periodically) will provide
true Phong shading for surface rendering.

In other related news, the third edition of The Image Processing Handbook (CRC
Press, isbn # 0-8493-2532-3) is now available. In addition to lots of new
examples and references, and new sections on digital cameras, surface imaging,
and other topics, the book includes an order card offering a $50 discount on
the Image Processing Tool Kit CD.


From nih-image-d-request@io.ece.drexel.edu Thu Nov  5 06:22 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA09396;
	Thu, 5 Nov 1998 06:22:39 -0500 (EST)
Date: Thu, 5 Nov 1998 06:22:39 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811051122.GAA09396@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #107
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/107
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 5747

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 107

Today's Topics:
  RE:Scion image for Windows            [ Steven Moore <SteveM@cipe.com> ]
  region selection tools                [ Karen Rethoret <rethoret@yorku.ca> ]
  Extra band...                         [ Naomi Boxall <Naomi.Boxall.1@uni.ma ]
  Ann: Updates to Image Processing Too  [ DrJohnRuss@aol.com ]

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

Date: 04 Nov 98 11:06:34 -0700
From: Steven Moore <SteveM@cipe.com>
To: "nih-image" <nih-image@io.ece.drexel.edu>
Subject: RE:Scion image for Windows
Message-ID: <1301944690-68027714@mailhost.cipe.com>
Content-Type: text/plain; charset="US-Ascii"
Content-Transfer-Encoding: 8bit

My understanding is the Scion does not plan on releasing the source code for Scion Image.

Steven Moore, Ph.D.
Director of Evaluation Services
Center for Image Processing in Education
Tucson, AZ
www.cipe.com


On 11/2/98, nih-image wrote:
>Does anybody know whether the Scion image source >code (Windows95 or NT) is
>freely available?
>TIA
>Daniele
>
>Dr. Daniele Zacchetti, PhD
>Cellular Neurophysiology Unit
>Dibit, San Raffaele Inst.
>via Olgettina 58
>20132 Milano, Italy
>Phone: +39-02-2643-4812
>Fax:+39-02-2643-4813
>e-mail: zacchetti.daniele@hsr.it
>
>
>
>
>RFC822 header
>-----------------------------------
> Return-Path: <nih-image-request@io.ece.drexel.edu>
> Received: from io.ece.drexel.edu (144.118.32.3) by >mailhost.cipe.com
>  with ESMTP (Eudora Internet Mail Server 1.2.1b5); >Mon, 2 Nov 1998 07:32:10 -0700
> Received: (from lists@localhost)
> 	by io.ece.drexel.edu (8.8.8/8.8.8) id >JAA22445;
> 	Mon, 2 Nov 1998 09:27:22 -0500 (EST)
> Resent-Date: Mon, 2 Nov 1998 09:27:22 -0500 (EST)
> X-Sender: zacchetti.daniele@mail.hsr.it
> Message-Id: ><l03130300b263703e9c59@[192.167.193.40]>
> Mime-Version: 1.0
> Content-Type: text/plain; charset="us-ascii"
> Date: Mon, 2 Nov 1998 15:24:41 +0100
> To: NIH Image mailing list <nih-
>image@io.ece.drexel.edu>
> From: Daniele Zacchetti <zacchetti.daniele@hsr.it>
> Subject: Scion image for Windows
> Resent-Message-ID: <"9D9yI2.0.VD5.SxRFs"@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/554
> X-Loop: nih-image@biomed.drexel.edu
> Precedence: list
> Resent-Sender: nih-image-request@io.ece.drexel.edu
> Status: R
> >

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

Date: Wed, 4 Nov 1998 16:15:53 -0500 (EST)
From: Karen Rethoret <rethoret@yorku.ca>
To: nih-image@io.ece.drexel.edu
Subject: region selection tools
Message-ID: <Pine.SOL.4.05.9811041608250.1300-100000@sunspot.ccs.yorku.ca>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hello;

In Image for PC


This is probably straight-forward; but can you tell me the best way to
draw a rectangular region in which to do plot profiles that is
oriented
at different angles (not just at right angles?)

Have tried straight-line selection tool also but this is only 8 pixels
wide maximum when vertical or horizontal  (reduces to 1 pixel when line is
tilted).


Thanks in advance,

Karen Rethoret
York University

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

Date: Thu, 05 Nov 1998 11:45:37 +1300
From: Naomi Boxall <Naomi.Boxall.1@uni.massey.ac.nz>
To: nih-image@io.ece.drexel.edu
Subject: Extra band...
Message-Id: <3.0.5.32.19981105114537.007c3630@uni.massey.ac.nz>
Content-Type: text/plain; charset="us-ascii"

Hi all.

I'm not quite sure if this is the correct forum for my query, but I was
wondering if anyone out there has done PFGE before.  If you have, could you
please suggest a reason (other than a plasmid) for an extra band occurring
on my gel in one isolate (epidemiologically related to the outbreak) which
is the same as the outbreak strain in all other bands.

If not then do you know of anyone I can ask, or any groups I can put this
question to?  Thanks very much,

Naomi
 
Naomi S. Boxall BSc
Epicentre
Inst. of Vet, Animal & Biomedical Sciences
Massey University
Palmerston North
New Zealand

064-6-3504008 (W)
Naomi.Boxall.1@uni.massey.ac.nz

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

Date: Wed, 4 Nov 1998 19:23:10 EST
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Ann: Updates to Image Processing Tool Kit
Message-ID: <405655c9.3640efee@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

Several updates to the Image Processing Tool Kit are now posted on the web
site at
http://members.aol.com/ImagProcTK/

These are all identical for Mac and PC, and can be downloaded, decompressed
and placed in the same folder as your other plug-ins. The current list of
updates to version 2.5 is

Convolution and deconvolution of blur, motion and other point-spread functions
using Fourier transforms
Color-by-Value which labels features according to the value of any measured
parameter
Several recently published methods for image processing (sharpening, noise
reduction and edge enhancement)
Automatically drawing and labeling a magnification bar on the image
Versions of the Ranking and Variance filters with adjustable size round
neighborhoods.

Bug reports and fixes are also posted on the site.

The next update to be posted (check the web site periodically) will provide
true Phong shading for surface rendering.

In other related news, the third edition of The Image Processing Handbook (CRC
Press, isbn # 0-8493-2532-3) is now available. In addition to lots of new
examples and references, and new sections on digital cameras, surface imaging,
and other topics, the book includes an order card offering a $50 discount on
the Image Processing Tool Kit CD.

--------------------------------
End of nih-image-d Digest V98 Issue #107
****************************************

From nih-image-request@io.ece.drexel.edu Thu Nov  5 10:09 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA22763;
	Thu, 5 Nov 1998 10:09:06 -0500 (EST)
Resent-Date: Thu, 5 Nov 1998 10:09:06 -0500 (EST)
From: "j.gregory" <ort056@abdn.ac.uk>
Sender: ort056@abdn.ac.uk
To: nih-image@io.ece.drexel.edu
Subject: Re: region selection tools
Message-ID: <SIMEON.9811051434.A@pc10.abdn.ac.uk>
Date: Thu, 5 Nov 1998 14:47:34 +0000 (GMT)
Priority: NORMAL
X-Mailer: Simeon for Windows Version 4.0.9
X-Authentication: IMSP
MIME-Version: 1.0
Resent-Message-ID: <"ew7ZR1.0.1v3.JfRGs"@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/579
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: 664

Karen,

If you're in Scion Image then double click on the plotprofile icon 
it the tools menu bar.  Set the line width option (up to 99 
pixels) and then draw the line on the image in any direction you 
choose.


Jenny Gregory


> In Image for PC
> 
> 
> This is probably straight-forward; but can you tell me the best way to
> draw a rectangular region in which to do plot profiles that is
> oriented
> at different angles (not just at right angles?)
> 
> Have tried straight-line selection tool also but this is only 8 pixels
> wide maximum when vertical or horizontal  (reduces to 1 pixel when line is
> tilted).

----------------------
j.gregory@abdn.ac.uk




From nih-image-request@io.ece.drexel.edu Thu Nov  5 11:06 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA11298;
	Thu, 5 Nov 1998 11:06:12 -0500 (EST)
Resent-Date: Thu, 5 Nov 1998 11:06:12 -0500 (EST)
X-Authentication-Warning: d2.hrz.uni-giessen.de: gh43 owned process doing -bs
Date: Thu, 5 Nov 1998 16:40:57 +0100 (CET)
From: Dietmar Tietz <Dietmar.Tietz@agrar.uni-giessen.de>
X-Sender: gh43@d2.hrz.uni-giessen.de
To: nih-image@io.ece.drexel.edu
cc: Naomi.Boxall.1@uni.massey.ac.nz
Subject: Re: Extra band...
In-Reply-To: <3.0.5.32.19981105114537.007c3630@uni.massey.ac.nz>
Message-Id: <Pine.A32.3.96.981105163614.21928A-100000@d2.hrz.uni-giessen.de>
MIME-Version: 1.0
Resent-Message-ID: <"D-rN2.0.ap.vSSGs"@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/580
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: 1000


On Thu, 5 Nov 1998, Naomi Boxall wrote:

> Hi all.
> 
> I'm not quite sure if this is the correct forum for my query, but I was
> wondering if anyone out there has done PFGE before.  If you have, could you
> please suggest a reason (other than a plasmid) for an extra band occurring
> on my gel in one isolate (epidemiologically related to the outbreak) which
> is the same as the outbreak strain in all other bands.
> 
> If not then do you know of anyone I can ask, or any groups I can put this
> question to?  Thanks very much,
> 
> Naomi
>  
> Naomi S. Boxall BSc
> Epicentre
> Inst. of Vet, Animal & Biomedical Sciences
> Massey University
> Palmerston North
> New Zealand
> 
> 064-6-3504008 (W)
> Naomi.Boxall.1@uni.massey.ac.nz
> 
> 

You may want to post your message to the bionet.molbio.methds-reagnts
Internet newsgroup.  For details, please see

http://www.bio.net/hypermail/METHDS-REAGNTS/

Hope you will get the necessary info soon,

Dietmar Tietz
http://www.his.com/~djt/
djt@his.com


From nih-image-request@io.ece.drexel.edu Thu Nov  5 11:07 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA11806;
	Thu, 5 Nov 1998 11:07:24 -0500 (EST)
Resent-Date: Thu, 5 Nov 1998 11:07:24 -0500 (EST)
Message-Id: <3.0.1.32.19981105104220.007b0770@pop.service.ohio-state.edu>
X-Sender: jianshi@pop.service.ohio-state.edu
X-Mailer: Windows Eudora Pro Version 3.0.1 (32)
Date: Thu, 05 Nov 1998 10:42:20 -0500
To: nih-image@io.ece.drexel.edu
From: "j. shi" <jianshi@pop.service.ohio-state.edu>
Subject: Re: region selection tools
In-Reply-To: <Pine.SOL.4.05.9811041608250.1300-100000@sunspot.ccs.yorku.
 ca>
Mime-Version: 1.0
Resent-Message-ID: <"HtB8K1.0.R61.KWSGs"@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/581
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/enriched; charset="us-ascii"
Content-Length: 503

hi, all: is there a new version of NIH image processing software that can handle more than 8 bits (b/w images)? or any other similar package (cheap or free)? mac or pc does't matter. thanks. jerry.

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

j. shi

dept. of geological sciences

the ohio state university

columbus, ohio 43210

<color><param>0000,0000,ffff</param>(614)-292-0585/6193 </color>(o)

<color><param>ffff,0000,ffff</param>(614)-688-9686 </color>(h)

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


From nih-image-request@io.ece.drexel.edu Thu Nov  5 11:47 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA24594;
	Thu, 5 Nov 1998 11:47:31 -0500 (EST)
Resent-Date: Thu, 5 Nov 1998 11:47:31 -0500 (EST)
Message-Id: <199811051627.LAA10913@mcfeely.concentric.net>
Subject: Help with Image capture system
Date: Thu, 5 Nov 98 08:28:32 -0800
From: Your Name <wtdenet@concentric.net>
To: <nih-image@io.ece.drexel.edu>
Mime-Version: 1.0
Resent-Message-ID: <"-2Mh3.0.gU4.f7TGs"@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/582
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: 1671

Hello all,

I hope someone out there can help me with information on how to put 
together a mobile digital image capture system. I have a Macintosh 
Powerbook that I would like to use for capturing images from an analog 
camera. However, I need to know if there are good framegrabber cards 
(scientific quality) that can be used with a Macintosh Powerbook. It 
would be an added plus if NIH-Image controlled the image capture. 
Therefore, I am requesting any information (ie. camera, framegrabber, 
storage) on how to build a digital image capture system using a Macintosh 
Powerbook (or laptop computer). Please e-mail me directly if you feel the 
NIH-Image user group will not benefit from information pertaining to my 
request. 

Thank you,

Wilfred Denetclaw Jr., Ph.D.

---------------------------------------
Department of Anatomy, Box 0452
School of Medicine
University of California, San Francisco
San Francisco, CA 94143-0452
(415)476-1530 (laboratory)
(415)476-4845 (FAX)
wtdenet@concentric.net
---------------------------------------



>>>>-------------------------------//---------------------------------<<<<
Wilfred Denetclaw Jr., Ph.D.             Tina Denetclaw, Pharm.D., BCPS 
Department of Anatomy and                Assistant Clinical Professor
Cardiovascular Research Institute   &    School of Pharmacy (Box 0622)
University of California                 University of California
San Francisco, CA. 94143-0452            San Francisco, CA  94143
(415)476-1530 (Office)                   tdenet@itsa.ucsf.edu (E-mail)
(415)476-3586 (FAX)
wtdenet@concentric.net (E-mail)
>>>>-------------------------------//---------------------------------<<<<




From nih-image-request@io.ece.drexel.edu Thu Nov  5 12:27 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA07156;
	Thu, 5 Nov 1998 12:27:01 -0500 (EST)
Resent-Date: Thu, 5 Nov 1998 12:27:01 -0500 (EST)
Message-ID: <19981105165942.10950.qmail@hotmail.com>
X-Originating-IP: [139.165.30.112]
From: "Enrico BONINO" <e_bonino@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Help with Image capture system
MIME-Version: 1.0
Date: Thu, 05 Nov 1998 08:59:41 PST
Resent-Message-ID: <"pNyHy2.0.627.jcTGs"@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/583
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 669

Wilfred,

Maybe that this is not a good answer at your question, but you can take 
a look at the site http://www.ulg.ac.be/mica/page27.html, where you can 
found a kind of solution that I've developed for acquiring images with a 
"mobile" system.


Enrico BONINO, geologist
------------------------
University of Liege
Dept. of Applied Geology
Lab. MICA Geomaterials Characterization
Avenue des Tilleuls, 45
B-4000 LIEGE
BELGIUM
tel. 0032 (0)4 3669526
fax  0032 (0)4 3669520
E-mail: e_bonino@hotmail.com
http://www.ulg.ac.be/mica
-------------------------


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


From nih-image-request@io.ece.drexel.edu Thu Nov  5 12:39 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA11140;
	Thu, 5 Nov 1998 12:39:51 -0500 (EST)
Resent-Date: Thu, 5 Nov 1998 12:39:51 -0500 (EST)
From: DrJohnRuss@aol.com
Message-ID: <524412e3.3641dc83@aol.com>
Date: Thu, 5 Nov 1998 12:12:35 EST
To: nih-image@io.ece.drexel.edu
Mime-Version: 1.0
Subject: Re:  Help with Image capture system
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 for Mac sub 84
Resent-Message-ID: <"mNPhW2.0.hj.loTGs"@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/584
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: 1150


In a message dated 11/5/98 11:37:48 AM, you wrote:

>I hope someone out there can help me with information on how to put 
>together a mobile digital image capture system. I have a Macintosh 
>Powerbook that I would like to use for capturing images from an analog 
>camera. However, I need to know if there are good framegrabber cards 
>(scientific quality) that can be used with a Macintosh Powerbook. It 
>would be an added plus if NIH-Image controlled the image capture. 
>Therefore, I am requesting any information (ie. camera, framegrabber, 
>storage) on how to build a digital image capture system using a Macintosh 
>Powerbook (or laptop computer). Please e-mail me directly if you feel the 
>NIH-Image user group will not benefit from information pertaining to my 
>request. 

I do lots of image analysis using a Mac Powerbook, but not using a video
camera. Get yourself a good digital camera (I use the Polaroid DMC) with a
SCSI connection. The results will be much better than a video camera (better
resolution, more consistent color, less noise, etc.) and the cost will be
comparable to what a video camera plus frame grabber would cost.


From nih-image-request@io.ece.drexel.edu Thu Nov  5 17:30 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA09029;
	Thu, 5 Nov 1998 17:30:33 -0500 (EST)
Resent-Date: Thu, 5 Nov 1998 17:30:33 -0500 (EST)
Message-Id: <3.0.1.32.19981105170548.007bc970@pop.service.ohio-state.edu>
X-Sender: jianshi@pop.service.ohio-state.edu
X-Mailer: Windows Eudora Pro Version 3.0.1 (32)
Date: Thu, 05 Nov 1998 17:05:48 -0500
To: nih-image@io.ece.drexel.edu
From: "j. shi" <jianshi@pop.service.ohio-state.edu>
Subject: looking for software for higher bits (>8)
In-Reply-To: <3.0.1.32.19981105104220.007b0770@pop.service.ohio-state.ed
 u>
References: <Pine.SOL.4.05.9811041608250.1300-100000@sunspot.ccs.yorku. ca>
Mime-Version: 1.0
Resent-Message-ID: <"ybiZt1.0.hW.u7YGs"@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/585
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/enriched; charset="us-ascii"
Content-Length: 505

hi, all: is there a new version of NIH image processing software that can
handle more than 8 bits (b/w images)? or any other similar package (cheap
or free)? mac or pc does't matter. thanks. jerry.



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

j. shi

dept. of geological sciences

the ohio state university

columbus, ohio 43210

<color><param>0000,0000,ffff</param>(614)-292-0585/6193 </color>(o)

<color><param>ffff,0000,ffff</param>(614)-688-9686 </color>(h)

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


From nih-image-request@io.ece.drexel.edu Thu Nov  5 18:01 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA18857;
	Thu, 5 Nov 1998 18:01:21 -0500 (EST)
 <Pine.SOL.4.05.9811041608250.1300-100000@sunspot.ccs.yorku. ca>
Resent-Date: Thu, 5 Nov 1998 18:01:21 -0500 (EST)
Message-Id: <v03007805b267da6b1cd3@[128.231.99.202]>
In-Reply-To: <3.0.1.32.19981105170548.007bc970@pop.service.ohio-state.edu>
References: <3.0.1.32.19981105104220.007b0770@pop.service.ohio-state.ed u>
 <Pine.SOL.4.05.9811041608250.1300-100000@sunspot.ccs.yorku. ca>
Mime-Version: 1.0
Date: Thu, 5 Nov 1998 18:45:24 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: looking for software for higher bits (>8)
Resent-Message-ID: <"YVGoq3.0.ft2.UaYGs"@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/586
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: 335

>hi, all: is there a new version of NIH image processing software that can
>handle more than 8 bits (b/w images)? or any other similar package (cheap
>or free)? mac or pc does't matter. thanks. jerry.

My new Image/J program at http://rsb.info.nih.gov/ij/ can handle more than
8-bits per pixel. It runs on both Macs and PCs.

-wayne



From nih-image-d-request@io.ece.drexel.edu Fri Nov  6 06:23 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA18983;
	Fri, 6 Nov 1998 06:23:17 -0500 (EST)
Date: Fri, 6 Nov 1998 06:23:17 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811061123.GAA18983@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #108
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/108
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 9744

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 108

Today's Topics:
  Re: region selection tools            [ "j.gregory" <ort056@abdn.ac.uk> ]
  Re: Extra band...                     [ Dietmar Tietz <Dietmar.Tietz@agrar. ]
  Re: region selection tools            [ "j. shi" <jianshi@pop.service.ohio- ]
  Help with Image capture system        [ Your Name <wtdenet@concentric.net> ]
  Re: Help with Image capture system    [ "Enrico BONINO" <e_bonino@hotmail.c ]
  Re: Help with Image capture system    [ DrJohnRuss@aol.com ]
  looking for software for higher bits  [ "j. shi" <jianshi@pop.service.ohio- ]
  Re: looking for software for higher   [ Wayne Rasband <wayne@codon.nih.gov> ]

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

Date: Thu, 5 Nov 1998 14:47:34 +0000 (GMT)
From: "j.gregory" <ort056@abdn.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: region selection tools
Message-ID: <SIMEON.9811051434.A@pc10.abdn.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

Karen,

If you're in Scion Image then double click on the plotprofile icon 
it the tools menu bar.  Set the line width option (up to 99 
pixels) and then draw the line on the image in any direction you 
choose.


Jenny Gregory


> In Image for PC
> 
> 
> This is probably straight-forward; but can you tell me the best way to
> draw a rectangular region in which to do plot profiles that is
> oriented
> at different angles (not just at right angles?)
> 
> Have tried straight-line selection tool also but this is only 8 pixels
> wide maximum when vertical or horizontal  (reduces to 1 pixel when line is
> tilted).

----------------------
j.gregory@abdn.ac.uk

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

Date: Thu, 5 Nov 1998 16:40:57 +0100 (CET)
From: Dietmar Tietz <Dietmar.Tietz@agrar.uni-giessen.de>
To: nih-image@io.ece.drexel.edu
cc: Naomi.Boxall.1@uni.massey.ac.nz
Subject: Re: Extra band...
Message-Id: <Pine.A32.3.96.981105163614.21928A-100000@d2.hrz.uni-giessen.de>
Content-Type: TEXT/PLAIN; charset=US-ASCII

On Thu, 5 Nov 1998, Naomi Boxall wrote:

> Hi all.
> 
> I'm not quite sure if this is the correct forum for my query, but I was
> wondering if anyone out there has done PFGE before.  If you have, could you
> please suggest a reason (other than a plasmid) for an extra band occurring
> on my gel in one isolate (epidemiologically related to the outbreak) which
> is the same as the outbreak strain in all other bands.
> 
> If not then do you know of anyone I can ask, or any groups I can put this
> question to?  Thanks very much,
> 
> Naomi
>  
> Naomi S. Boxall BSc
> Epicentre
> Inst. of Vet, Animal & Biomedical Sciences
> Massey University
> Palmerston North
> New Zealand
> 
> 064-6-3504008 (W)
> Naomi.Boxall.1@uni.massey.ac.nz
> 
> 

You may want to post your message to the bionet.molbio.methds-reagnts
Internet newsgroup.  For details, please see

http://www.bio.net/hypermail/METHDS-REAGNTS/

Hope you will get the necessary info soon,

Dietmar Tietz
http://www.his.com/~djt/
djt@his.com

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

Date: Thu, 05 Nov 1998 10:42:20 -0500
From: "j. shi" <jianshi@pop.service.ohio-state.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: region selection tools
Message-Id: <3.0.1.32.19981105104220.007b0770@pop.service.ohio-state.edu>
Content-Type: text/enriched; charset="us-ascii"

hi, all: is there a new version of NIH image processing software that can handle more than 8 bits (b/w images)? or any other similar package (cheap or free)? mac or pc does't matter. thanks. jerry.

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

j. shi

dept. of geological sciences

the ohio state university

columbus, ohio 43210

<color><param>0000,0000,ffff</param>(614)-292-0585/6193 </color>(o)

<color><param>ffff,0000,ffff</param>(614)-688-9686 </color>(h)

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

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

Date: Thu, 5 Nov 98 08:28:32 -0800
From: Your Name <wtdenet@concentric.net>
To: <nih-image@io.ece.drexel.edu>
Subject: Help with Image capture system
Message-Id: <199811051627.LAA10913@mcfeely.concentric.net>
Content-Type: text/plain; charset="US-ASCII"

Hello all,

I hope someone out there can help me with information on how to put 
together a mobile digital image capture system. I have a Macintosh 
Powerbook that I would like to use for capturing images from an analog 
camera. However, I need to know if there are good framegrabber cards 
(scientific quality) that can be used with a Macintosh Powerbook. It 
would be an added plus if NIH-Image controlled the image capture. 
Therefore, I am requesting any information (ie. camera, framegrabber, 
storage) on how to build a digital image capture system using a Macintosh 
Powerbook (or laptop computer). Please e-mail me directly if you feel the 
NIH-Image user group will not benefit from information pertaining to my 
request. 

Thank you,

Wilfred Denetclaw Jr., Ph.D.

---------------------------------------
Department of Anatomy, Box 0452
School of Medicine
University of California, San Francisco
San Francisco, CA 94143-0452
(415)476-1530 (laboratory)
(415)476-4845 (FAX)
wtdenet@concentric.net
---------------------------------------



>>>>-------------------------------//---------------------------------<<<<
Wilfred Denetclaw Jr., Ph.D.             Tina Denetclaw, Pharm.D., BCPS 
Department of Anatomy and                Assistant Clinical Professor
Cardiovascular Research Institute   &    School of Pharmacy (Box 0622)
University of California                 University of California
San Francisco, CA. 94143-0452            San Francisco, CA  94143
(415)476-1530 (Office)                   tdenet@itsa.ucsf.edu (E-mail)
(415)476-3586 (FAX)
wtdenet@concentric.net (E-mail)
>>>>-------------------------------//---------------------------------<<<<

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

Date: Thu, 05 Nov 1998 08:59:41 PST
From: "Enrico BONINO" <e_bonino@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Help with Image capture system
Message-ID: <19981105165942.10950.qmail@hotmail.com>
Content-Type: text/plain

Wilfred,

Maybe that this is not a good answer at your question, but you can take 
a look at the site http://www.ulg.ac.be/mica/page27.html, where you can 
found a kind of solution that I've developed for acquiring images with a 
"mobile" system.


Enrico BONINO, geologist
------------------------
University of Liege
Dept. of Applied Geology
Lab. MICA Geomaterials Characterization
Avenue des Tilleuls, 45
B-4000 LIEGE
BELGIUM
tel. 0032 (0)4 3669526
fax  0032 (0)4 3669520
E-mail: e_bonino@hotmail.com
http://www.ulg.ac.be/mica
-------------------------


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

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

Date: Thu, 5 Nov 1998 12:12:35 EST
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re:  Help with Image capture system
Message-ID: <524412e3.3641dc83@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

In a message dated 11/5/98 11:37:48 AM, you wrote:

>I hope someone out there can help me with information on how to put 
>together a mobile digital image capture system. I have a Macintosh 
>Powerbook that I would like to use for capturing images from an analog 
>camera. However, I need to know if there are good framegrabber cards 
>(scientific quality) that can be used with a Macintosh Powerbook. It 
>would be an added plus if NIH-Image controlled the image capture. 
>Therefore, I am requesting any information (ie. camera, framegrabber, 
>storage) on how to build a digital image capture system using a Macintosh 
>Powerbook (or laptop computer). Please e-mail me directly if you feel the 
>NIH-Image user group will not benefit from information pertaining to my 
>request. 

I do lots of image analysis using a Mac Powerbook, but not using a video
camera. Get yourself a good digital camera (I use the Polaroid DMC) with a
SCSI connection. The results will be much better than a video camera (better
resolution, more consistent color, less noise, etc.) and the cost will be
comparable to what a video camera plus frame grabber would cost.

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

Date: Thu, 05 Nov 1998 17:05:48 -0500
From: "j. shi" <jianshi@pop.service.ohio-state.edu>
To: nih-image@io.ece.drexel.edu
Subject: looking for software for higher bits (>8)
Message-Id: <3.0.1.32.19981105170548.007bc970@pop.service.ohio-state.edu>
Content-Type: text/enriched; charset="us-ascii"

hi, all: is there a new version of NIH image processing software that can
handle more than 8 bits (b/w images)? or any other similar package (cheap
or free)? mac or pc does't matter. thanks. jerry.



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

j. shi

dept. of geological sciences

the ohio state university

columbus, ohio 43210

<color><param>0000,0000,ffff</param>(614)-292-0585/6193 </color>(o)

<color><param>ffff,0000,ffff</param>(614)-688-9686 </color>(h)

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

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

Date: Thu, 5 Nov 1998 18:45:24 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: looking for software for higher bits (>8)
Message-Id: <v03007805b267da6b1cd3@[128.231.99.202]>
Content-Type: text/plain; charset="us-ascii"

>hi, all: is there a new version of NIH image processing software that can
>handle more than 8 bits (b/w images)? or any other similar package (cheap
>or free)? mac or pc does't matter. thanks. jerry.

My new Image/J program at http://rsb.info.nih.gov/ij/ can handle more than
8-bits per pixel. It runs on both Macs and PCs.

-wayne

--------------------------------
End of nih-image-d Digest V98 Issue #108
****************************************

From nih-image-request@io.ece.drexel.edu Fri Nov  6 11:17 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA05495;
	Fri, 6 Nov 1998 11:17:23 -0500 (EST)
Resent-Date: Fri, 6 Nov 1998 11:17:23 -0500 (EST)
Date: Fri, 06 Nov 1998 10:31:05 -0500
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
Subject: Q: where is current doc / discussion on AverageFrames() macro command?
To: nih-image@io.ece.drexel.edu
Message-id: <v04011700b268c3206ed9@[128.244.128.6]>
MIME-version: 1.0
Resent-Message-ID: <"edI3W1.0.Rf4.dOnGs"@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/587
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: 843

Somewhere, I discovered that I could pass "UseExternalTrigger" into the
AverageFrames() macro command as a string option for acquiring images using
the Scion LG-3 framegrabber.  I've noted that the "Special>Video
Control..." menu item has a "Use External Trigger" item that is surely the
analogous to the macro command option. I am unable, however, to find any
documentation on this is either the NIH Image or the Scion Image dox. I
have no idea where I learned the syntax - it doesn't come up in my gopher
searches of the list archives, and I can't find it in any persoanl email.
Can anyone point me to the definitive doc or other discussion of usage etc?

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 Nov  6 15:41 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA04182;
	Fri, 6 Nov 1998 15:41:42 -0500 (EST)
Resent-Date: Fri, 6 Nov 1998 15:41:42 -0500 (EST)
From: "Herbert M. Geller" <geller@UMDNJ.EDU>
To: nih-image@io.ece.drexel.edu
Message-ID: <SIMEON.9811061513.E@hmgpc.umdnj.edu>
Date: Fri, 6 Nov 1998 15:16:13 -0500 (Eastern Standard Time)
Priority: NORMAL
X-Mailer: Simeon for Win32 Version 4.1.5 Build (43)
X-Authentication: none
MIME-Version: 1.0
Resent-Message-ID: <"v-uvg1.0.zE6.mYrGs"@io>
Resent-From: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Reply-To: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/588
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: 13

set nomail



From nih-image-d-request@io.ece.drexel.edu Sat Nov  7 06:11 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA28184;
	Sat, 7 Nov 1998 06:11:38 -0500 (EST)
Date: Sat, 7 Nov 1998 06:11:38 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811071111.GAA28184@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #109
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/109
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 1878

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 109

Today's Topics:
  Q: where is current doc / discussion  [ Bill Christens-Barry <wacb@aplcomm. ]
  Unidentified subject!                 [ "Herbert M. Geller" <geller@UMDNJ.E ]

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

Date: Fri, 06 Nov 1998 10:31:05 -0500
From: Bill Christens-Barry <wacb@aplcomm.jhuapl.edu>
To: nih-image@io.ece.drexel.edu
Subject: Q: where is current doc / discussion on AverageFrames() macro command?
Message-id: <v04011700b268c3206ed9@[128.244.128.6]>
Content-type: text/plain; charset="us-ascii"

Somewhere, I discovered that I could pass "UseExternalTrigger" into the
AverageFrames() macro command as a string option for acquiring images using
the Scion LG-3 framegrabber.  I've noted that the "Special>Video
Control..." menu item has a "Use External Trigger" item that is surely the
analogous to the macro command option. I am unable, however, to find any
documentation on this is either the NIH Image or the Scion Image dox. I
have no idea where I learned the syntax - it doesn't come up in my gopher
searches of the list archives, and I can't find it in any persoanl email.
Can anyone point me to the definitive doc or other discussion of usage etc?

Thanks.

Bill Christens-Barry
-------------------------
Bill Christens-Barry, PhD
Johns Hopkins University Applied Physics Laboratory
wacb@aplcomm.jhuapl.edu
-------------------------

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

Date: Fri, 6 Nov 1998 15:16:13 -0500 (Eastern Standard Time)
From: "Herbert M. Geller" <geller@UMDNJ.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-ID: <SIMEON.9811061513.E@hmgpc.umdnj.edu>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

set nomail

--------------------------------
End of nih-image-d Digest V98 Issue #109
****************************************

From nih-image-request@io.ece.drexel.edu Mon Nov  9 04:11 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA04609;
	Mon, 9 Nov 1998 04:11:08 -0500 (EST)
Resent-Date: Mon, 9 Nov 1998 04:11:08 -0500 (EST)
Message-ID: <19981109085045.20550.qmail@hotmail.com>
X-Originating-IP: [143.93.33.45]
From: "Michael Arm" <arminator@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Measuring fibres with Object Image
MIME-Version: 1.0
Date: Mon, 09 Nov 1998 00:50:45 PST
Resent-Message-ID: <"YkVFJ1.0.4e6.7qgHs"@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/589
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 1813

Hello Imagers,

We are examining fibres in Image. We got so far, that we can use the 
standard Image to correctly binarize a stack picture, so Image can count 
the fibres and measure them. The stack comes from a Leica confocal 
microscope.

However, the fibres will most often not lie flat, so we tried Object 
Image, and found out by measuring by hand, that a 2D measurement in 
Image NT is not exact enough.
However, there are too many fibres to count by hand in Object Image.

Is there a way to teach Object Image via a macro, to count and measure 
fibres?
The problem is, because sometimes fibres will lie over another, and some 
are bent with the ends pointing upward, and the center lying down, 
making it difficult for a macro to say: "OK, there is a reflection, set 
a startingpoint, go through the stack, until the reflection ends. 
Measure the fibre."
(Well, it would be nice if the macro would do at least THIS).

Now our question: Could a projected and binarized image from ImageNT be 
used on Object Image on our Mac, to use it as a mask, so the computer 
knows where a fibre starts and ends? Is it possible for Object Image to 
automatically detect fibres in 3d and measure them?


And another question: Since I couldn't find a help file in Object Image 
like in NT Image, I tried to mark the fibres by hand (i use a segmented 
line Object for this) and wanted to mark the glass carrier with a 
different colored polygomal object. Then export it to a .rot file and 
view it in Rotater. However, how do I switch over to the 2nd sort of 
object, after I finished marking the fibres with the segmented lines?


Any help to this is really greatly appreciated.

yours sincerely
Michael Arm.


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


From nih-image-request@io.ece.drexel.edu Mon Nov  9 07:12 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id HAA11713;
	Mon, 9 Nov 1998 07:12:44 -0500 (EST)
Resent-Date: Mon, 9 Nov 1998 07:12:44 -0500 (EST)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: arminator@hotmail.com, nih-image@io.ece.drexel.edu
Date:          Mon, 9 Nov 1998 22:57:29 GMT+1100
Subject:       Re: Measuring fibres with Object Image
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <16789F07CF1@rna.bio.mq.edu.au>
Resent-Message-ID: <"6ymj-3.0.hA1.vVjHs"@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/590
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 4187

>From: "Michael Arm" <arminator@hotmail.com>
>To: nih-image@io.ece.drexel.edu
>Subject: Measuring fibres with Object Image
>Date: Mon, 09 Nov 1998 00:50:45 PST
>
>Hello Imagers,
>
>We are examining fibres in Image. We got so far, that we can use the 
>standard Image to correctly binarize a stack picture, so Image can count 
>the fibres and measure them. The stack comes from a Leica confocal 
>microscope.
>
>However, the fibres will most often not lie flat, so we tried Object 
>Image, and found out by measuring by hand, that a 2D measurement in 
>Image NT is not exact enough.
>However, there are too many fibres to count by hand in Object Image.
>
>Is there a way to teach Object Image via a macro, to count and measure 
>fibres?
>The problem is, because sometimes fibres will lie over another, and some 
>are bent with the ends pointing upward, and the center lying down, 
>making it difficult for a macro to say: "OK, there is a reflection, set 
>a startingpoint, go through the stack, until the reflection ends. 
>Measure the fibre."
>(Well, it would be nice if the macro would do at least THIS).
>
>Now our question: Could a projected and binarized image from ImageNT be 
>used on Object Image on our Mac, to use it as a mask, so the computer 
>knows where a fibre starts and ends? Is it possible for Object Image to 
>automatically detect fibres in 3d and measure them?
>

I have writen macros to produce an optimal focus projection from a stack of images 
taken at different focal planes. The quality of focus is measured as the maximum 
local contrast of a column through the stack or alternatively as the maxima or 
mimima of the intensities. A byproduct of the macro is a map of the image showing 
the frame in which the image is best in focus.

Using the optimal focus projection to make a binary mask of the fibres to mask the  
depth contour map, it should be fairly straightforward to segment individual fibres 
together with a record of component (skeletonised) frame segments and the frames 
they traverse.
This should give as good 3D geometry as the stack contains.

The optimal focus projection macro was writen/tested for normal and disecting 
microscope images and works well with subjects that have a primary surface which 
comes to focus such as fish otoliths, hard microfossils, insects etc. As I dont 
have access to a confocal and of course a lot would on the nature of your images, 
it would be best if you could email a small sample stack. I would be happy to have 
a look at processing it to see if the macros are suitable or if some revision might 
be appropriate.

Macros run under NIH-Image (or Object-Image). (haven't tested them on Image NT)
Object-Image rLeft[],rTop[] arrays from analyzeParticles will be particularly 
useful for autoOutline(rLeft[i],rTop[i]); detail reprocessing of individual fibres.

>
>And another question: Since I couldn't find a help file in Object Image 
>like in NT Image, I tried to mark the fibres by hand (i use a segmented 
>line Object for this) and wanted to mark the glass carrier with a 
>different colored polygomal object. Then export it to a .rot file and 
>view it in Rotater. However, how do I switch over to the 2nd sort of 
>object, after I finished marking the fibres with the segmented lines?

? Object-Image has excellent on-line help file (one of the excellent extensions to 
Wayne's standard NIH-Image). The latest version has pull-down help on macro 
reference (standard and Object extensions), text editor and sequence window
(accessed via normal Mac ? help pull-down menu). There are also tutorials at the 
website.
http://simon.bio.uva.nl/object-image.html

As the sequence window help is in the form of an image, and directly answers your 
question I will email as an attachment by separate direct email.
>
>
>Any help to this is really greatly appreciated.
>
>yours sincerely
>Michael Arm.
>
>
>______________________________________________________
>Get Your Private, Free Email at http://www.hotmail.com
>
>
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 Nov  9 09:02 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA21960;
	Mon, 9 Nov 1998 09:02:26 -0500 (EST)
Resent-Date: Mon, 9 Nov 1998 09:02:26 -0500 (EST)
Message-Id: <v03102802b26c9390bc55@[134.174.88.145]>
Mime-Version: 1.0
Date: Mon, 9 Nov 1998 08:48:35 -0400
To: nih-image@io.ece.drexel.edu
From: David Milstone <milstone@rascal.med.harvard.edu>
Subject: NIH Image as Photoshop substitute
Resent-Message-ID: <"kPN5S2.0.vV3.K4lHs"@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/591
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/enriched; charset="us-ascii"
Content-Length: 1266

<fontfamily><param>Geneva</param><bigger>Do you think that NIH Image
would function as a Photoshop substitute for elementary school students
wanting to turn digital camera and scanner output into a school
newspaper, class assignments, etc.? Even with an educational discount
we would have to put out more than $3,000 (I'm told that we really do
need 26 simultaneous-use licenses) for the real thing and this would be
vast overkill for our needs.


We are looking for basic pixel-based manipulations including cropping,
brightness, color correction, etc. Simple drawing functions would also
be useful. Text would probably be handled by other software.


The simplest solution (because the software is familiar to me) would be
outdated versions of Photoshop but these seem scarce.  I thought that
Image could substitute but might be too complicated and that it might
not be easy to simplify the interface.


Any other suggestions? Freeware would be especially welcome.


TIA.


Dave

</bigger></fontfamily>
David S. Milstone, M.D., Ph.D.

Vascular Research Division

Department of Pathology 

Brigham & Women's Hospital

Harvard Medical School

LMRC 421

221 Longwood Ave

Boston, MA 02115

milstone@rascal.med.harvard.edu

(617) 975-0896 (FAX)

(617) 278-0173 (Tel)


From nih-image-request@io.ece.drexel.edu Mon Nov  9 10:06 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA14518;
	Mon, 9 Nov 1998 10:06:58 -0500 (EST)
Resent-Date: Mon, 9 Nov 1998 10:06:58 -0500 (EST)
From: "James C. Fleet" <jim_fleet@uncg.edu>
Sender: jcfleet@uncg.edu
Reply-To: jim_fleet@uncg.edu
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Image as Photoshop substitute
In-Reply-To: <v03102802b26c9390bc55@[134.174.88.145]>
Message-ID: <SIMEON.9811090945.C@oemcomputer.uncg.edu>
Date: Mon, 9 Nov 1998 09:36:45 -0500 (Eastern Standard Time)
Priority: NORMAL
X-Mailer: Simeon for Win32 Version 4.1.2 Build (32)
X-Authentication: none
MIME-Version: 1.0
Resent-Message-ID: <"WO5ut.0.t01.4ulHs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/592
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: 2565

Dave,

I don't think that NIH image is you best solution.  My bet 
is that it isn't user friendly enough for elementary school 
students.

As for Photoshop, why do you need 26 licenses?  Not every 
computer needs to have this.  (In fact, Photoshop probably 
isn't enough anyway - you probably want Pagemaker too 
(although you could also just import into MS Word)). 
Anyway, the kids can do most of their page design and 
layout off the computer.  They would then use the one 
computer with a copy of Photoshop/Pagemaker to do the final 
copy.  In addition, a lower version of Photoshop now comes 
with most flatbed scanners.  My guess is that this is all 
the kids would need.  If you are really concerned about the 
expense, the old fashioned way of cut and paste still works 
just fine.

Just one mans opinion of course.

Jim Fleet

On Mon, 9 Nov 1998 08:48:35 -0400 David Milstone 
<milstone@rascal.med.harvard.edu> wrote:

> <fontfamily><param>Geneva</param><bigger>Do you think that NIH Image
> would function as a Photoshop substitute for elementary school students
> wanting to turn digital camera and scanner output into a school
> newspaper, class assignments, etc.? Even with an educational discount
> we would have to put out more than $3,000 (I'm told that we really do
> need 26 simultaneous-use licenses) for the real thing and this would be
> vast overkill for our needs.
> 
> 
> We are looking for basic pixel-based manipulations including cropping,
> brightness, color correction, etc. Simple drawing functions would also
> be useful. Text would probably be handled by other software.
> 
> 
> The simplest solution (because the software is familiar to me) would be
> outdated versions of Photoshop but these seem scarce.  I thought that
> Image could substitute but might be too complicated and that it might
> not be easy to simplify the interface.
> 
> 
> Any other suggestions? Freeware would be especially welcome.
> 
> 
> TIA.
> 
> 
> Dave
> 
> </bigger></fontfamily>
> David S. Milstone, M.D., Ph.D.
> 
> Vascular Research Division
> 
> Department of Pathology 
> 
> Brigham & Women's Hospital
> 
> Harvard Medical School
> 
> LMRC 421
> 
> 221 Longwood Ave
> 
> Boston, MA 02115
> 
> milstone@rascal.med.harvard.edu
> 
> (617) 975-0896 (FAX)
> 
> (617) 278-0173 (Tel)
> 

----------------------
James C. Fleet, Ph.D.
Director, Graduate Program in Nutrition
Dept. of Nutrition and Foodservice Systems
University of North Carolina at Greensboro
P.O. Box 26170
Greensboro, NC 27402-6170
(O)1-336-334-5313
(F)1-336-334-4129
jim_fleet@uncg.edu


From nih-image-request@io.ece.drexel.edu Mon Nov  9 10:58 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA02081;
	Mon, 9 Nov 1998 10:58:21 -0500 (EST)
Resent-Date: Mon, 9 Nov 1998 10:58:21 -0500 (EST)
Message-Id: <364709A9.E077B5B4@maroon.tc.umn.edu>
Date: Mon, 09 Nov 1998 09:26:34 -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
X-Mailer: Mozilla 4.05 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Image as Photoshop substitute
References: <v03102802b26c9390bc55@[134.174.88.145]>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"GfGO23.0.lG5.ucmHs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/593
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: 1794

Adobe Photo Deluxe is a much cheaper alternative and very friendly compared to PS.

Another cheaper alternative is GraphicsCinvertor a great shareware.

David Milstone wrote:
> 
> Do you think that NIH Image would function as a Photoshop substitute for elementary school students wanting to turn digital camera and scanner output into a school newspaper, class assignments, etc.? Even with an educational discount we would have to put out more than $3,000 (I'm told that we really do need 26 simultaneous-use licenses) for the real thing and this would be vast overkill for our needs.
> 
> We are looking for basic pixel-based manipulations including cropping, brightness, color correction, etc. Simple drawing functions would also be useful. Text would probably be handled by other software.
> 
> The simplest solution (because the software is familiar to me) would be outdated versions of Photoshop but these seem scarce. I thought that Image could substitute but might be too complicated and that it might not be easy to simplify the interface.
> 
> Any other suggestions? Freeware would be especially welcome.
> 
> TIA.
> 
> Dave
> David S. Milstone, M.D., Ph.D.
> Vascular Research Division
> Department of Pathology
> Brigham & Women's Hospital
> Harvard Medical School
> LMRC 421
> 221 Longwood Ave
> Boston, MA 02115
> milstone@rascal.med.harvard.edu
> (617) 975-0896 (FAX)
> (617) 278-0173 (Tel)

-- 
 _____________________________________________________________
   / Michael J. Herron  University of MN,  Dept. of Medicine    /
  /            herro001@maroon.tc.umn.edu                      /
 /           http://134.84.141.41/RASH.html                   /
/     Or my NEW site at    http://128.101.243.213/           /
_____________________________________________________________


From nih-image-request@io.ece.drexel.edu Mon Nov  9 13:14 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA15110;
	Mon, 9 Nov 1998 13:14:03 -0500 (EST)
Resent-Date: Mon, 9 Nov 1998 13:14:03 -0500 (EST)
Message-Id: <v03130301b26cd830bf11@[128.218.158.175]>
In-Reply-To: <v03102802b26c9390bc55@[134.174.88.145]>
Mime-Version: 1.0
Date: Mon, 9 Nov 1998 09:37:33 -0800
To: nih-image@io.ece.drexel.edu
From: Joel Brody <jbrody@itsa.ucsf.edu>
Subject: Re: NIH Image as Photoshop substitute
Resent-Message-ID: <"C9xd83.0.P01.8YoHs"@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/594
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/enriched; charset="us-ascii"
Content-Length: 1937

Dave,


I think that NIH-Image along with Pagemaker or Word would do fine for
your school.  Image can show kids elementary image processing
(particularly Brightness/contrast and sharpen) and most word processors
will do elementary layout.  Thay can also use Image to do simple
animation using stacks.  My kids thought that was fin.


Joel



>>>>

<excerpt><fontfamily><param>Geneva</param><bigger>Do you think that NIH
Image would function as a Photoshop substitute for elementary school
students wanting to turn digital camera and scanner output into a
school newspaper, class assignments, etc.? Even with an educational
discount we would have to put out more than $3,000 (I'm told that we
really do need 26 simultaneous-use licenses) for the real thing and
this would be vast overkill for our needs.


We are looking for basic pixel-based manipulations including cropping,
brightness, color correction, etc. Simple drawing functions would also
be useful. Text would probably be handled by other software.


The simplest solution (because the software is familiar to me) would be
outdated versions of Photoshop but these seem scarce.  I thought that
Image could substitute but might be too complicated and that it might
not be easy to simplify the interface.


Any other suggestions? Freeware would be especially welcome.


TIA.


Dave

</bigger></fontfamily> David S. Milstone, M.D., Ph.D.

Vascular Research Division

Department of Pathology 

Brigham & Women's Hospital

Harvard Medical School

LMRC 421

221 Longwood Ave

Boston, MA 02115

milstone@rascal.med.harvard.edu

(617) 975-0896 (FAX)

(617) 278-0173 (Tel)

</excerpt><<<<<<<<


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


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 Nov  9 13:47 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA25701;
	Mon, 9 Nov 1998 13:47:24 -0500 (EST)
Resent-Date: Mon, 9 Nov 1998 13:47:24 -0500 (EST)
Message-Id: <E788D998AAC8D1119EC10000F8CD1E8A5BDC6A@ntmail23.emn.com>
From: "Calvert, David B" <calvert@eastman.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: NIH Image as Photoshop substitute
Date: Mon, 9 Nov 1998 13:19:28 -0500 
Mime-Version: 1.0
X-Mailer: Internet Mail Service (5.5.1960.3)
Resent-Message-ID: <"qrYfd3.0.724.58pHs"@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/595
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 2063

David,
     It's not freeware - but since you have some $$ you might want to
look at Paint Shop Pro. http://www.jasc.com/  
     I use it everyday for simple presentation layouts, some image
processing, image type conversions etc. In runs standard scanner/camera
interfaces. The latest version has layers like PhotoShop and also
includes an GIF animator, which is great fun.
     Take a look.

(the usual boilerplate: I have no commercial interest in PSP etc).
David B. Calvert
Physical Chemistry Research Laboratory
Eastman Chemical Co.
voice (423) 229-4943
Fax   (423) 229-4558

> -----Original Message-----
> From:	David Milstone [SMTP:milstone@rascal.med.harvard.edu]
> Sent:	Monday, November 09, 1998 7:49 AM
> To:	nih-image@io.ece.drexel.edu
> Subject:	NIH Image as Photoshop substitute
> 
> Do you think that NIH Image would function as a Photoshop substitute
> for elementary school students wanting to turn digital camera and
> scanner output into a school newspaper, class assignments, etc.? Even
> with an educational discount we would have to put out more than $3,000
> (I'm told that we really do need 26 simultaneous-use licenses) for the
> real thing and this would be vast overkill for our needs. 
> 
> We are looking for basic pixel-based manipulations including cropping,
> brightness, color correction, etc. Simple drawing functions would also
> be useful. Text would probably be handled by other software. 
> 
> The simplest solution (because the software is familiar to me) would
> be outdated versions of Photoshop but these seem scarce.  I thought
> that Image could substitute but might be too complicated and that it
> might not be easy to simplify the interface. 
> 
> Any other suggestions? Freeware would be especially welcome. 
> 
> TIA. 
> 
> Dave 
> David S. Milstone, M.D., Ph.D. 
> Vascular Research Division 
> Department of Pathology  
> Brigham & Women's Hospital 
> Harvard Medical School 
> LMRC 421 
> 221 Longwood Ave 
> Boston, MA 02115 
> milstone@rascal.med.harvard.edu 
> (617) 975-0896 (FAX) 
> (617) 278-0173 (Tel) 


From nih-image-d-request@io.ece.drexel.edu Tue Nov 10 06:26 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA09401;
	Tue, 10 Nov 1998 06:26:03 -0500 (EST)
Date: Tue, 10 Nov 1998 06:26:03 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811101126.GAA09401@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #110
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/110
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 18496

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 110

Today's Topics:
  Measuring fibres with Object Image    [ "Michael Arm" <arminator@hotmail.co ]
  Re: Measuring fibres with Object Ima  [ GJOSS@rna.bio.mq.edu.au ]
  NIH Image as Photoshop substitute     [ David Milstone <milstone@rascal.med ]
  Re: NIH Image as Photoshop substitut  [ "James C. Fleet" <jim_fleet@uncg.ed ]
  Re: NIH Image as Photoshop substitut  [ Michael Herron <herro001@maroon.tc. ]
  Re: NIH Image as Photoshop substitut  [ Joel Brody <jbrody@itsa.ucsf.edu> ]
  RE: NIH Image as Photoshop substitut  [ "Calvert, David B" <calvert@eastman ]

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

Date: Mon, 09 Nov 1998 00:50:45 PST
From: "Michael Arm" <arminator@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Measuring fibres with Object Image
Message-ID: <19981109085045.20550.qmail@hotmail.com>
Content-Type: text/plain

Hello Imagers,

We are examining fibres in Image. We got so far, that we can use the 
standard Image to correctly binarize a stack picture, so Image can count 
the fibres and measure them. The stack comes from a Leica confocal 
microscope.

However, the fibres will most often not lie flat, so we tried Object 
Image, and found out by measuring by hand, that a 2D measurement in 
Image NT is not exact enough.
However, there are too many fibres to count by hand in Object Image.

Is there a way to teach Object Image via a macro, to count and measure 
fibres?
The problem is, because sometimes fibres will lie over another, and some 
are bent with the ends pointing upward, and the center lying down, 
making it difficult for a macro to say: "OK, there is a reflection, set 
a startingpoint, go through the stack, until the reflection ends. 
Measure the fibre."
(Well, it would be nice if the macro would do at least THIS).

Now our question: Could a projected and binarized image from ImageNT be 
used on Object Image on our Mac, to use it as a mask, so the computer 
knows where a fibre starts and ends? Is it possible for Object Image to 
automatically detect fibres in 3d and measure them?


And another question: Since I couldn't find a help file in Object Image 
like in NT Image, I tried to mark the fibres by hand (i use a segmented 
line Object for this) and wanted to mark the glass carrier with a 
different colored polygomal object. Then export it to a .rot file and 
view it in Rotater. However, how do I switch over to the 2nd sort of 
object, after I finished marking the fibres with the segmented lines?


Any help to this is really greatly appreciated.

yours sincerely
Michael Arm.


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

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

Date:          Mon, 9 Nov 1998 22:57:29 GMT+1100
From: GJOSS@rna.bio.mq.edu.au
To: arminator@hotmail.com, nih-image@io.ece.drexel.edu
Subject:       Re: Measuring fibres with Object Image
Message-ID: <16789F07CF1@rna.bio.mq.edu.au>

>From: "Michael Arm" <arminator@hotmail.com>
>To: nih-image@io.ece.drexel.edu
>Subject: Measuring fibres with Object Image
>Date: Mon, 09 Nov 1998 00:50:45 PST
>
>Hello Imagers,
>
>We are examining fibres in Image. We got so far, that we can use the 
>standard Image to correctly binarize a stack picture, so Image can count 
>the fibres and measure them. The stack comes from a Leica confocal 
>microscope.
>
>However, the fibres will most often not lie flat, so we tried Object 
>Image, and found out by measuring by hand, that a 2D measurement in 
>Image NT is not exact enough.
>However, there are too many fibres to count by hand in Object Image.
>
>Is there a way to teach Object Image via a macro, to count and measure 
>fibres?
>The problem is, because sometimes fibres will lie over another, and some 
>are bent with the ends pointing upward, and the center lying down, 
>making it difficult for a macro to say: "OK, there is a reflection, set 
>a startingpoint, go through the stack, until the reflection ends. 
>Measure the fibre."
>(Well, it would be nice if the macro would do at least THIS).
>
>Now our question: Could a projected and binarized image from ImageNT be 
>used on Object Image on our Mac, to use it as a mask, so the computer 
>knows where a fibre starts and ends? Is it possible for Object Image to 
>automatically detect fibres in 3d and measure them?
>

I have writen macros to produce an optimal focus projection from a stack of images 
taken at different focal planes. The quality of focus is measured as the maximum 
local contrast of a column through the stack or alternatively as the maxima or 
mimima of the intensities. A byproduct of the macro is a map of the image showing 
the frame in which the image is best in focus.

Using the optimal focus projection to make a binary mask of the fibres to mask the  
depth contour map, it should be fairly straightforward to segment individual fibres 
together with a record of component (skeletonised) frame segments and the frames 
they traverse.
This should give as good 3D geometry as the stack contains.

The optimal focus projection macro was writen/tested for normal and disecting 
microscope images and works well with subjects that have a primary surface which 
comes to focus such as fish otoliths, hard microfossils, insects etc. As I dont 
have access to a confocal and of course a lot would on the nature of your images, 
it would be best if you could email a small sample stack. I would be happy to have 
a look at processing it to see if the macros are suitable or if some revision might 
be appropriate.

Macros run under NIH-Image (or Object-Image). (haven't tested them on Image NT)
Object-Image rLeft[],rTop[] arrays from analyzeParticles will be particularly 
useful for autoOutline(rLeft[i],rTop[i]); detail reprocessing of individual fibres.

>
>And another question: Since I couldn't find a help file in Object Image 
>like in NT Image, I tried to mark the fibres by hand (i use a segmented 
>line Object for this) and wanted to mark the glass carrier with a 
>different colored polygomal object. Then export it to a .rot file and 
>view it in Rotater. However, how do I switch over to the 2nd sort of 
>object, after I finished marking the fibres with the segmented lines?

? Object-Image has excellent on-line help file (one of the excellent extensions to 
Wayne's standard NIH-Image). The latest version has pull-down help on macro 
reference (standard and Object extensions), text editor and sequence window
(accessed via normal Mac ? help pull-down menu). There are also tutorials at the 
website.
http://simon.bio.uva.nl/object-image.html

As the sequence window help is in the form of an image, and directly answers your 
question I will email as an attachment by separate direct email.
>
>
>Any help to this is really greatly appreciated.
>
>yours sincerely
>Michael Arm.
>
>
>______________________________________________________
>Get Your Private, Free Email at http://www.hotmail.com
>
>
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, 9 Nov 1998 08:48:35 -0400
From: David Milstone <milstone@rascal.med.harvard.edu>
To: nih-image@io.ece.drexel.edu
Subject: NIH Image as Photoshop substitute
Message-Id: <v03102802b26c9390bc55@[134.174.88.145]>
Content-Type: text/enriched; charset="us-ascii"

<fontfamily><param>Geneva</param><bigger>Do you think that NIH Image
would function as a Photoshop substitute for elementary school students
wanting to turn digital camera and scanner output into a school
newspaper, class assignments, etc.? Even with an educational discount
we would have to put out more than $3,000 (I'm told that we really do
need 26 simultaneous-use licenses) for the real thing and this would be
vast overkill for our needs.


We are looking for basic pixel-based manipulations including cropping,
brightness, color correction, etc. Simple drawing functions would also
be useful. Text would probably be handled by other software.


The simplest solution (because the software is familiar to me) would be
outdated versions of Photoshop but these seem scarce.  I thought that
Image could substitute but might be too complicated and that it might
not be easy to simplify the interface.


Any other suggestions? Freeware would be especially welcome.


TIA.


Dave

</bigger></fontfamily>
David S. Milstone, M.D., Ph.D.

Vascular Research Division

Department of Pathology 

Brigham & Women's Hospital

Harvard Medical School

LMRC 421

221 Longwood Ave

Boston, MA 02115

milstone@rascal.med.harvard.edu

(617) 975-0896 (FAX)

(617) 278-0173 (Tel)

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

Date: Mon, 9 Nov 1998 09:36:45 -0500 (Eastern Standard Time)
From: "James C. Fleet" <jim_fleet@uncg.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Image as Photoshop substitute
Message-ID: <SIMEON.9811090945.C@oemcomputer.uncg.edu>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

Dave,

I don't think that NIH image is you best solution.  My bet 
is that it isn't user friendly enough for elementary school 
students.

As for Photoshop, why do you need 26 licenses?  Not every 
computer needs to have this.  (In fact, Photoshop probably 
isn't enough anyway - you probably want Pagemaker too 
(although you could also just import into MS Word)). 
Anyway, the kids can do most of their page design and 
layout off the computer.  They would then use the one 
computer with a copy of Photoshop/Pagemaker to do the final 
copy.  In addition, a lower version of Photoshop now comes 
with most flatbed scanners.  My guess is that this is all 
the kids would need.  If you are really concerned about the 
expense, the old fashioned way of cut and paste still works 
just fine.

Just one mans opinion of course.

Jim Fleet

On Mon, 9 Nov 1998 08:48:35 -0400 David Milstone 
<milstone@rascal.med.harvard.edu> wrote:

> <fontfamily><param>Geneva</param><bigger>Do you think that NIH Image
> would function as a Photoshop substitute for elementary school students
> wanting to turn digital camera and scanner output into a school
> newspaper, class assignments, etc.? Even with an educational discount
> we would have to put out more than $3,000 (I'm told that we really do
> need 26 simultaneous-use licenses) for the real thing and this would be
> vast overkill for our needs.
> 
> 
> We are looking for basic pixel-based manipulations including cropping,
> brightness, color correction, etc. Simple drawing functions would also
> be useful. Text would probably be handled by other software.
> 
> 
> The simplest solution (because the software is familiar to me) would be
> outdated versions of Photoshop but these seem scarce.  I thought that
> Image could substitute but might be too complicated and that it might
> not be easy to simplify the interface.
> 
> 
> Any other suggestions? Freeware would be especially welcome.
> 
> 
> TIA.
> 
> 
> Dave
> 
> </bigger></fontfamily>
> David S. Milstone, M.D., Ph.D.
> 
> Vascular Research Division
> 
> Department of Pathology 
> 
> Brigham & Women's Hospital
> 
> Harvard Medical School
> 
> LMRC 421
> 
> 221 Longwood Ave
> 
> Boston, MA 02115
> 
> milstone@rascal.med.harvard.edu
> 
> (617) 975-0896 (FAX)
> 
> (617) 278-0173 (Tel)
> 

----------------------
James C. Fleet, Ph.D.
Director, Graduate Program in Nutrition
Dept. of Nutrition and Foodservice Systems
University of North Carolina at Greensboro
P.O. Box 26170
Greensboro, NC 27402-6170
(O)1-336-334-5313
(F)1-336-334-4129
jim_fleet@uncg.edu

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

Date: Mon, 09 Nov 1998 09:26:34 -0600
From: Michael Herron <herro001@maroon.tc.umn.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Image as Photoshop substitute
Message-Id: <364709A9.E077B5B4@maroon.tc.umn.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Adobe Photo Deluxe is a much cheaper alternative and very friendly compared to PS.

Another cheaper alternative is GraphicsCinvertor a great shareware.

David Milstone wrote:
> 
> Do you think that NIH Image would function as a Photoshop substitute for elementary school students wanting to turn digital camera and scanner output into a school newspaper, class assignments, etc.? Even with an educational discount we would have to put out more than $3,000 (I'm told that we really do need 26 simultaneous-use licenses) for the real thing and this would be vast overkill for our needs.
> 
> We are looking for basic pixel-based manipulations including cropping, brightness, color correction, etc. Simple drawing functions would also be useful. Text would probably be handled by other software.
> 
> The simplest solution (because the software is familiar to me) would be outdated versions of Photoshop but these seem scarce. I thought that Image could substitute but might be too complicated and that it might not be easy to simplify the interface.
> 
> Any other suggestions? Freeware would be especially welcome.
> 
> TIA.
> 
> Dave
> David S. Milstone, M.D., Ph.D.
> Vascular Research Division
> Department of Pathology
> Brigham & Women's Hospital
> Harvard Medical School
> LMRC 421
> 221 Longwood Ave
> Boston, MA 02115
> milstone@rascal.med.harvard.edu
> (617) 975-0896 (FAX)
> (617) 278-0173 (Tel)

-- 
 _____________________________________________________________
   / Michael J. Herron  University of MN,  Dept. of Medicine    /
  /            herro001@maroon.tc.umn.edu                      /
 /           http://134.84.141.41/RASH.html                   /
/     Or my NEW site at    http://128.101.243.213/           /
_____________________________________________________________

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

Date: Mon, 9 Nov 1998 09:37:33 -0800
From: Joel Brody <jbrody@itsa.ucsf.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Image as Photoshop substitute
Message-Id: <v03130301b26cd830bf11@[128.218.158.175]>
Content-Type: text/enriched; charset="us-ascii"

Dave,


I think that NIH-Image along with Pagemaker or Word would do fine for
your school.  Image can show kids elementary image processing
(particularly Brightness/contrast and sharpen) and most word processors
will do elementary layout.  Thay can also use Image to do simple
animation using stacks.  My kids thought that was fin.


Joel



>>>>

<excerpt><fontfamily><param>Geneva</param><bigger>Do you think that NIH
Image would function as a Photoshop substitute for elementary school
students wanting to turn digital camera and scanner output into a
school newspaper, class assignments, etc.? Even with an educational
discount we would have to put out more than $3,000 (I'm told that we
really do need 26 simultaneous-use licenses) for the real thing and
this would be vast overkill for our needs.


We are looking for basic pixel-based manipulations including cropping,
brightness, color correction, etc. Simple drawing functions would also
be useful. Text would probably be handled by other software.


The simplest solution (because the software is familiar to me) would be
outdated versions of Photoshop but these seem scarce.  I thought that
Image could substitute but might be too complicated and that it might
not be easy to simplify the interface.


Any other suggestions? Freeware would be especially welcome.


TIA.


Dave

</bigger></fontfamily> David S. Milstone, M.D., Ph.D.

Vascular Research Division

Department of Pathology 

Brigham & Women's Hospital

Harvard Medical School

LMRC 421

221 Longwood Ave

Boston, MA 02115

milstone@rascal.med.harvard.edu

(617) 975-0896 (FAX)

(617) 278-0173 (Tel)

</excerpt><<<<<<<<


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


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, 9 Nov 1998 13:19:28 -0500 
From: "Calvert, David B" <calvert@eastman.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: NIH Image as Photoshop substitute
Message-Id: <E788D998AAC8D1119EC10000F8CD1E8A5BDC6A@ntmail23.emn.com>
Content-Type: text/plain

David,
     It's not freeware - but since you have some $$ you might want to
look at Paint Shop Pro. http://www.jasc.com/  
     I use it everyday for simple presentation layouts, some image
processing, image type conversions etc. In runs standard scanner/camera
interfaces. The latest version has layers like PhotoShop and also
includes an GIF animator, which is great fun.
     Take a look.

(the usual boilerplate: I have no commercial interest in PSP etc).
David B. Calvert
Physical Chemistry Research Laboratory
Eastman Chemical Co.
voice (423) 229-4943
Fax   (423) 229-4558

> -----Original Message-----
> From:	David Milstone [SMTP:milstone@rascal.med.harvard.edu]
> Sent:	Monday, November 09, 1998 7:49 AM
> To:	nih-image@io.ece.drexel.edu
> Subject:	NIH Image as Photoshop substitute
> 
> Do you think that NIH Image would function as a Photoshop substitute
> for elementary school students wanting to turn digital camera and
> scanner output into a school newspaper, class assignments, etc.? Even
> with an educational discount we would have to put out more than $3,000
> (I'm told that we really do need 26 simultaneous-use licenses) for the
> real thing and this would be vast overkill for our needs. 
> 
> We are looking for basic pixel-based manipulations including cropping,
> brightness, color correction, etc. Simple drawing functions would also
> be useful. Text would probably be handled by other software. 
> 
> The simplest solution (because the software is familiar to me) would
> be outdated versions of Photoshop but these seem scarce.  I thought
> that Image could substitute but might be too complicated and that it
> might not be easy to simplify the interface. 
> 
> Any other suggestions? Freeware would be especially welcome. 
> 
> TIA. 
> 
> Dave 
> David S. Milstone, M.D., Ph.D. 
> Vascular Research Division 
> Department of Pathology  
> Brigham & Women's Hospital 
> Harvard Medical School 
> LMRC 421 
> 221 Longwood Ave 
> Boston, MA 02115 
> milstone@rascal.med.harvard.edu 
> (617) 975-0896 (FAX) 
> (617) 278-0173 (Tel) 

--------------------------------
End of nih-image-d Digest V98 Issue #110
****************************************

From nih-image-request@io.ece.drexel.edu Tue Nov 10 08:33 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA22728;
	Tue, 10 Nov 1998 08:33:12 -0500 (EST)
Resent-Date: Tue, 10 Nov 1998 08:33:12 -0500 (EST)
Date: Tue, 10 Nov 1998 08:10:05 -0500 (EST)
From: Dongbai Guo <dbg@cs.brown.edu>
X-Sender: dbg@mothra
To: nih-image@io.ece.drexel.edu
Subject: gimp is a good substitute for Photoshop.
In-Reply-To: <199811101128.GAA09630@io.ece.drexel.edu>
Message-ID: <Pine.GSO.4.05.9811100801590.22486-100000@mothra>
MIME-Version: 1.0
Resent-Message-ID: <"MicFL.0.yv4.Ej3Is"@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/596
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: 546

It is devoloped under free-ware fundation support, and it is continuely
updating. We use it on unix desktop, in my opinion, it is better than the
unix version of adobe photoshop. It has GNU type license. I don't know if
gimp have a Win95 /Mac version though.
You can check their web page: www.gimp.org
dongbai
 

--------------------------------------------------------------
	Tel:    401-331-6424 (home)
        	401-863-7693 (graphics lab)

	http://www.cs.brown.edu/people/dbg
---------------------------------------------------------------




From nih-image-request@io.ece.drexel.edu Tue Nov 10 10:06 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA01519;
	Tue, 10 Nov 1998 10:06:56 -0500 (EST)
Resent-Date: Tue, 10 Nov 1998 10:06:56 -0500 (EST)
Mime-Version: 1.0
X-Sender: stwang@mail.clemson.edu
Message-Id: <v04011703b26df8860033@[130.127.104.30]>
In-Reply-To: <v03102802b26c9390bc55@[134.174.88.145]>
Date: Tue, 10 Nov 1998 09:29:46 -0500
To: David Milstone <milstone@rascal.med.harvard.edu>
From: Sam Wang <stwang@CLEMSON.EDU>
Subject: Re: NIH Image as Photoshop substitute
Cc: nih-image@io.ece.drexel.edu
Resent-Message-ID: <"9ki4s.0.gg6.3t4Is"@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/597
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: multipart/alternative; boundary="============_-1301414293==_ma============"
Content-Length: 3056

--============_-1301414293==_ma============
Content-Type: text/plain; charset="us-ascii"

Dave,

There are a couple of solutions to your dilemma. One is to use ColorIt, a
very powerful paint software from MicroFrontier in Iowa. It in some aspects
is BETTER than Photoshop - for instance, it was fast, and offered multiple
UNDOs years ago! It is bundled with some scanners, and sold for about $60
each. At one time they gave away a million copies of an earlier version,
for a shipping fee of $8.95 each.

Another solution is to use DeskPaint, a commercial program no longer sold.
Zedcor, who produced it, put it on their web site as freebie about a year
ago, along with DeskDraw. DeskDraw is indeed outdated and not worth using,
but DeskPaint is very capable, even though it has not been updated for a
few years now. The people at Zedcor told me they simply couldn't compete
with the likes of ClarisWorks, which included everything for $45, but the
paint module in ClarisWorks is next to worthless.

Both of these are more FUN to use than Photoshop. The latter is becoming
more a professional tool that requires too much familiarity before it could
be useful or fun.

If Zedcor approves your use of DeskPaint, I can give you a copy of it.
Please contact them first.

Hope this helps.

Sam
--------
Sam Wang                         e-mail: stwang@clemson.edu
Art Dept - Clemson University     voice: 864/656-3924
142 Lee Hall, Clemson, SC 29634     FAX: 864/656-7523
--============_-1301414293==_ma============
Content-Type: text/enriched; charset="us-ascii"

<fontfamily><param>Palatino</param><bigger>Dave,


There are a couple of solutions to your dilemma. One is to use ColorIt,
a very powerful paint software from MicroFrontier in Iowa. It in some
aspects is BETTER than Photoshop - for instance, it was fast, and
offered multiple UNDOs years ago! It is bundled with some scanners, and
sold for about $60 each. At one time they gave away a million copies of
an earlier version, for a shipping fee of $8.95 each.


Another solution is to use DeskPaint, a commercial program no longer
sold. Zedcor, who produced it, put it on their web site as freebie
about a year ago, along with DeskDraw. DeskDraw is indeed outdated and
not worth using, but DeskPaint is very capable, even though it has not
been updated for a few years now. The people at Zedcor told me they
simply couldn't compete with the likes of ClarisWorks, which included
everything for $45, but the paint module in ClarisWorks is next to
worthless.


Both of these are more FUN to use than Photoshop. The latter is
becoming more a professional tool that requires too much familiarity
before it could be useful or fun.


If Zedcor approves your use of DeskPaint, I can give you a copy of it.
Please contact them first.


Hope this helps.


Sam</bigger></fontfamily>

--------

Sam Wang                         e-mail: stwang@clemson.edu

Art Dept - Clemson University     voice: 864/656-3924

142 Lee Hall, Clemson, SC 29634     FAX: 864/656-7523

--============_-1301414293==_ma============--


From nih-image-request@io.ece.drexel.edu Tue Nov 10 11:55 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA04122;
	Tue, 10 Nov 1998 11:55:17 -0500 (EST)
Resent-Date: Tue, 10 Nov 1998 11:55:17 -0500 (EST)
Message-ID: <3648738B.22F253E0@att.net>
Date: Tue, 10 Nov 1998 09:10:35 -0800
From: Chris <kokopellis@att.net>
X-Mailer: Mozilla 4.04 [en] (Win95; I)
MIME-Version: 1.0
To: image <nih-image@io.ece.drexel.edu>
Subject: shortcut for selection size?
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"s4wU21.0.0e3.nM6Is"@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/598
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: 320

Hello all-
Is there a way to set a standard selection size in Image?  I need to
make many (1000's) measurements within a standard area, and I'm
wondering if there's a better way than adjusting the selection area by
hand by looking  in the "info" window until the size is right.

TIA- Christine Cline
Salt Lake City, UT


From nih-image-request@io.ece.drexel.edu Tue Nov 10 12:19 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA15095;
	Tue, 10 Nov 1998 12:19:45 -0500 (EST)
Resent-Date: Tue, 10 Nov 1998 12:19:45 -0500 (EST)
Message-ID: <36487ACC.ABF0E298@att.net>
Date: Tue, 10 Nov 1998 09:41:32 -0800
From: Chris <kokopellis@att.net>
X-Mailer: Mozilla 4.04 [en] (Win95; I)
MIME-Version: 1.0
To: image <nih-image@io.ece.drexel.edu>
Subject: can image count pixels?
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"1ko7U.0.cz6.qp6Is"@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/599
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: 664

Hello again
I'm a new Image user (and new to this newsgroup), so I hope that this
question isn't to irritatingly obvious to more experienced users of this
software.
 
I'm trying to quantitate an area that is dark vs. the light area within
a set area.  I think I can use the "threshold" command (and maybe "make
binary" to convert my grey-scale image to a binary image, but what I'd
like to do next is have IMAGE calculate the number of black pixels
within the area.  Is there a way to do this?

Please reply to me directly unless you think this information would be
of general interest to the readers of the newsgroup.

Thanks-
Christine Cline
Salt Lake City, UT


From nih-image-request@io.ece.drexel.edu Tue Nov 10 13:41 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA19724;
	Tue, 10 Nov 1998 13:41:53 -0500 (EST)
Resent-Date: Tue, 10 Nov 1998 13:41:53 -0500 (EST)
Date: Tue, 10 Nov 1998 10:06:05 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re:NIH Image as Photoshop substitute
In-Reply-To: <199811101127.GAA09578@io.ece.drexel.edu>
Message-ID: <Pine.A41.4.05.9811100958040.30746-100000@homer24.u.washington.edu>
MIME-Version: 1.0
Resent-Message-ID: <"R_N_A2.0.Bx.Q28Is"@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/600
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: 588

Dave, Take a look at Color-It, from MicroFrontier.  Current version is
about US$50. Site licenses are available. It will run plug-ins and does
the levels adjustments and
image manipulations for which Photoshop is commonly used.  I use Color-It
at home and Photoshop at the lab.  My children's elementary school also
uses Color-It on their Macs.

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 Nov 10 14:01 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA28957;
	Tue, 10 Nov 1998 14:01:39 -0500 (EST)
Resent-Date: Tue, 10 Nov 1998 14:01:39 -0500 (EST)
Message-Id: <D209047D0257D21191770000F8C991D904C805@mante35a.nam.dow.com>
From: "Heeschen, Bill (WA)" <WAHEESCHEN@dow.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: shortcut for selection size?
Date: Tue, 10 Nov 1998 13:29:43 -0500
Mime-Version: 1.0
X-Mailer: Internet Mail Service (5.5.1960.3)
Resent-Message-ID: <"ZGhXg3.0.0b3.pO8Is"@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/601
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 1122

Chris:
The "Restore Selection" command (Analyze menu or command-4) will
transfer the active selection area from the most recent image to the
current image:
Set your selection where you want it in your "seed" image
Open the next image
Choose "Restore Selection"
The selection marching ants should appear in the same relative location
as in the seed.

>From here, you can continue on (as long as the selection is still
intact) or go back to your seed and repeat the process.

Alternatively, you can write a simple little macro that creates the
rectangular selection that you want.  If you are going to be doing this
on "thousands" of images over a long period of time, this is the
preferred method.

As for counting pixels in the binary image, you can do it "quick and
dirty" by getting the histogram of the binary image and moving the mouse
over the black and white peaks and noting the two counts, then doing the
math.  The better long-term answer is another quick little macro that
gets the values of Histogram[0] and Histogram[255], then doing the math
for you.

Bill Heeschen
The Dow Chemical Company
Microscopy Group


From nih-image-request@io.ece.drexel.edu Tue Nov 10 18:33 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA26022;
	Tue, 10 Nov 1998 18:33:59 -0500 (EST)
Resent-Date: Tue, 10 Nov 1998 18:33:59 -0500 (EST)
Message-Id: <l03010d00b26e5411a721@[212.238.25.42]>
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Measuring fibres with Object Image
Date: Tue, 10 Nov 1998 22:51:49 +0000
Resent-Message-ID: <"DUknj2.0.Cm2.GFCIs"@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/602
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: 2581

Michael,

In the new version of Object-Image, switching to differently colored
objects is much easier, because there are two collect modes to choose from:
"Multiple" collect mode (bus symbol), is intended for structured point
collection with several objects per cell,
and now also "Single" collect mode (car symbol), intended for random
switching between the available object types, but only allowing one object
per cell.

In your example, prepare the experiment by choosing the 'Define Objects..'
dialog, drag two differently colored 'segmented lines' into the sequence
area (the use of 3d polygons is currently blocked, because the area of such
an object can be ambiguous). Then, click 'Single' and '3D objects' . Once
this preparation is done, set 3D lines into one or several volume stacks.
You can switch to another color by simply clicking onto the desired object
symbol in the floating "Sequence" window. It's also possible to assign
shortcut keys to the object types without using macros, so switching can be
performed by key stroke. Also have a look at the "3d tracing" example in
the "Examples" on the same ftp site, which explains the "live slicing"
collect mode that allows to capture 3 coordinates (x, y and z) with one
mouse click.

All you do by hand, you also can do by macro, if the macro can calculate
the marker positions. An automatic 3D tracer is not yet implemented,
although algorithms to trace tubular 3D structures have been developed in
our lab (see Houtsmuller: The homing cursor; Cytometry? ca. 1990?). I don't
know how many people would be interested in an implementation, and whether
I have the time to do it.
At this moment, you could try to make 2D measurements which you
subsequently connect in 3D by checking for overlaps.

Before using the 'Export XYZ data', look whether you can create appropriate
result columns and simply use 'Export Object Results..'. This provides a
better data structure with correct column names and gives readily
calculated results such as the length of 3D segmented lines or 3D angles.

By the way, we also have a Leica confocal microscope, an old one which
works under OS/9. Because the instrument has a non-standard ftp server
(Fetch doesn't work), I implemented an ftp client into Object-Image to
directly import properly scaled volume images via ftp protocol from this
OS/9 server.

Note that the documentation of Object-Image as well as the web site are
several months old and don't mention some of the new features. Until this
is fixed, look at the help panels under the help menu, or balloon help.

N. Vischer




From nih-image-d-request@io.ece.drexel.edu Wed Nov 11 06:22 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA10615;
	Wed, 11 Nov 1998 06:22:03 -0500 (EST)
Date: Wed, 11 Nov 1998 06:22:03 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811111122.GAA10615@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #111
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/111
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 11854

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 111

Today's Topics:
  gimp is a good substitute for Photos  [ Dongbai Guo <dbg@cs.brown.edu> ]
  Re: NIH Image as Photoshop substitut  [ Sam Wang <stwang@CLEMSON.EDU> ]
  shortcut for selection size?          [ Chris <kokopellis@att.net> ]
  can image count pixels?               [ Chris <kokopellis@att.net> ]
  Re:NIH Image as Photoshop substitute  [ "G. Macdonald" <glenmac@u.washingto ]
  RE: shortcut for selection size?      [ "Heeschen, Bill (WA)" <WAHEESCHEN@d ]
  Re: Measuring fibres with Object Ima  [ Norbert Vischer <vischer@bio.uva.nl ]

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

Date: Tue, 10 Nov 1998 08:10:05 -0500 (EST)
From: Dongbai Guo <dbg@cs.brown.edu>
To: nih-image@io.ece.drexel.edu
Subject: gimp is a good substitute for Photoshop.
Message-ID: <Pine.GSO.4.05.9811100801590.22486-100000@mothra>
Content-Type: TEXT/PLAIN; charset=US-ASCII

It is devoloped under free-ware fundation support, and it is continuely
updating. We use it on unix desktop, in my opinion, it is better than the
unix version of adobe photoshop. It has GNU type license. I don't know if
gimp have a Win95 /Mac version though.
You can check their web page: www.gimp.org
dongbai
 

--------------------------------------------------------------
	Tel:    401-331-6424 (home)
        	401-863-7693 (graphics lab)

	http://www.cs.brown.edu/people/dbg
---------------------------------------------------------------

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

Date: Tue, 10 Nov 1998 09:29:46 -0500
From: Sam Wang <stwang@CLEMSON.EDU>
To: David Milstone <milstone@rascal.med.harvard.edu>
Cc: nih-image@io.ece.drexel.edu
Subject: Re: NIH Image as Photoshop substitute
Message-Id: <v04011703b26df8860033@[130.127.104.30]>
Content-Type: multipart/alternative; boundary="============_-1301414293==_ma============"

--============_-1301414293==_ma============
Content-Type: text/plain; charset="us-ascii"

Dave,

There are a couple of solutions to your dilemma. One is to use ColorIt, a
very powerful paint software from MicroFrontier in Iowa. It in some aspects
is BETTER than Photoshop - for instance, it was fast, and offered multiple
UNDOs years ago! It is bundled with some scanners, and sold for about $60
each. At one time they gave away a million copies of an earlier version,
for a shipping fee of $8.95 each.

Another solution is to use DeskPaint, a commercial program no longer sold.
Zedcor, who produced it, put it on their web site as freebie about a year
ago, along with DeskDraw. DeskDraw is indeed outdated and not worth using,
but DeskPaint is very capable, even though it has not been updated for a
few years now. The people at Zedcor told me they simply couldn't compete
with the likes of ClarisWorks, which included everything for $45, but the
paint module in ClarisWorks is next to worthless.

Both of these are more FUN to use than Photoshop. The latter is becoming
more a professional tool that requires too much familiarity before it could
be useful or fun.

If Zedcor approves your use of DeskPaint, I can give you a copy of it.
Please contact them first.

Hope this helps.

Sam
--------
Sam Wang                         e-mail: stwang@clemson.edu
Art Dept - Clemson University     voice: 864/656-3924
142 Lee Hall, Clemson, SC 29634     FAX: 864/656-7523
--============_-1301414293==_ma============
Content-Type: text/enriched; charset="us-ascii"

<fontfamily><param>Palatino</param><bigger>Dave,


There are a couple of solutions to your dilemma. One is to use ColorIt,
a very powerful paint software from MicroFrontier in Iowa. It in some
aspects is BETTER than Photoshop - for instance, it was fast, and
offered multiple UNDOs years ago! It is bundled with some scanners, and
sold for about $60 each. At one time they gave away a million copies of
an earlier version, for a shipping fee of $8.95 each.


Another solution is to use DeskPaint, a commercial program no longer
sold. Zedcor, who produced it, put it on their web site as freebie
about a year ago, along with DeskDraw. DeskDraw is indeed outdated and
not worth using, but DeskPaint is very capable, even though it has not
been updated for a few years now. The people at Zedcor told me they
simply couldn't compete with the likes of ClarisWorks, which included
everything for $45, but the paint module in ClarisWorks is next to
worthless.


Both of these are more FUN to use than Photoshop. The latter is
becoming more a professional tool that requires too much familiarity
before it could be useful or fun.


If Zedcor approves your use of DeskPaint, I can give you a copy of it.
Please contact them first.


Hope this helps.


Sam</bigger></fontfamily>

--------

Sam Wang                         e-mail: stwang@clemson.edu

Art Dept - Clemson University     voice: 864/656-3924

142 Lee Hall, Clemson, SC 29634     FAX: 864/656-7523

--============_-1301414293==_ma============--

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

Date: Tue, 10 Nov 1998 09:10:35 -0800
From: Chris <kokopellis@att.net>
To: image <nih-image@io.ece.drexel.edu>
Subject: shortcut for selection size?
Message-ID: <3648738B.22F253E0@att.net>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hello all-
Is there a way to set a standard selection size in Image?  I need to
make many (1000's) measurements within a standard area, and I'm
wondering if there's a better way than adjusting the selection area by
hand by looking  in the "info" window until the size is right.

TIA- Christine Cline
Salt Lake City, UT

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

Date: Tue, 10 Nov 1998 09:41:32 -0800
From: Chris <kokopellis@att.net>
To: image <nih-image@io.ece.drexel.edu>
Subject: can image count pixels?
Message-ID: <36487ACC.ABF0E298@att.net>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hello again
I'm a new Image user (and new to this newsgroup), so I hope that this
question isn't to irritatingly obvious to more experienced users of this
software.
 
I'm trying to quantitate an area that is dark vs. the light area within
a set area.  I think I can use the "threshold" command (and maybe "make
binary" to convert my grey-scale image to a binary image, but what I'd
like to do next is have IMAGE calculate the number of black pixels
within the area.  Is there a way to do this?

Please reply to me directly unless you think this information would be
of general interest to the readers of the newsgroup.

Thanks-
Christine Cline
Salt Lake City, UT

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

Date: Tue, 10 Nov 1998 10:06:05 -0800 (PST)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re:NIH Image as Photoshop substitute
Message-ID: <Pine.A41.4.05.9811100958040.30746-100000@homer24.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Dave, Take a look at Color-It, from MicroFrontier.  Current version is
about US$50. Site licenses are available. It will run plug-ins and does
the levels adjustments and
image manipulations for which Photoshop is commonly used.  I use Color-It
at home and Photoshop at the lab.  My children's elementary school also
uses Color-It on their Macs.

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, 10 Nov 1998 13:29:43 -0500
From: "Heeschen, Bill (WA)" <WAHEESCHEN@dow.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: shortcut for selection size?
Message-Id: <D209047D0257D21191770000F8C991D904C805@mante35a.nam.dow.com>
Content-Type: text/plain

Chris:
The "Restore Selection" command (Analyze menu or command-4) will
transfer the active selection area from the most recent image to the
current image:
Set your selection where you want it in your "seed" image
Open the next image
Choose "Restore Selection"
The selection marching ants should appear in the same relative location
as in the seed.

>From here, you can continue on (as long as the selection is still
intact) or go back to your seed and repeat the process.

Alternatively, you can write a simple little macro that creates the
rectangular selection that you want.  If you are going to be doing this
on "thousands" of images over a long period of time, this is the
preferred method.

As for counting pixels in the binary image, you can do it "quick and
dirty" by getting the histogram of the binary image and moving the mouse
over the black and white peaks and noting the two counts, then doing the
math.  The better long-term answer is another quick little macro that
gets the values of Histogram[0] and Histogram[255], then doing the math
for you.

Bill Heeschen
The Dow Chemical Company
Microscopy Group

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

Date: Tue, 10 Nov 1998 22:51:49 +0000
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Measuring fibres with Object Image
Message-Id: <l03010d00b26e5411a721@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

Michael,

In the new version of Object-Image, switching to differently colored
objects is much easier, because there are two collect modes to choose from:
"Multiple" collect mode (bus symbol), is intended for structured point
collection with several objects per cell,
and now also "Single" collect mode (car symbol), intended for random
switching between the available object types, but only allowing one object
per cell.

In your example, prepare the experiment by choosing the 'Define Objects..'
dialog, drag two differently colored 'segmented lines' into the sequence
area (the use of 3d polygons is currently blocked, because the area of such
an object can be ambiguous). Then, click 'Single' and '3D objects' . Once
this preparation is done, set 3D lines into one or several volume stacks.
You can switch to another color by simply clicking onto the desired object
symbol in the floating "Sequence" window. It's also possible to assign
shortcut keys to the object types without using macros, so switching can be
performed by key stroke. Also have a look at the "3d tracing" example in
the "Examples" on the same ftp site, which explains the "live slicing"
collect mode that allows to capture 3 coordinates (x, y and z) with one
mouse click.

All you do by hand, you also can do by macro, if the macro can calculate
the marker positions. An automatic 3D tracer is not yet implemented,
although algorithms to trace tubular 3D structures have been developed in
our lab (see Houtsmuller: The homing cursor; Cytometry? ca. 1990?). I don't
know how many people would be interested in an implementation, and whether
I have the time to do it.
At this moment, you could try to make 2D measurements which you
subsequently connect in 3D by checking for overlaps.

Before using the 'Export XYZ data', look whether you can create appropriate
result columns and simply use 'Export Object Results..'. This provides a
better data structure with correct column names and gives readily
calculated results such as the length of 3D segmented lines or 3D angles.

By the way, we also have a Leica confocal microscope, an old one which
works under OS/9. Because the instrument has a non-standard ftp server
(Fetch doesn't work), I implemented an ftp client into Object-Image to
directly import properly scaled volume images via ftp protocol from this
OS/9 server.

Note that the documentation of Object-Image as well as the web site are
several months old and don't mention some of the new features. Until this
is fixed, look at the help panels under the help menu, or balloon help.

N. Vischer

--------------------------------
End of nih-image-d Digest V98 Issue #111
****************************************

From nih-image-request@io.ece.drexel.edu Wed Nov 11 07:50 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id HAA13084;
	Wed, 11 Nov 1998 07:50:55 -0500 (EST)
Resent-Date: Wed, 11 Nov 1998 07:50:55 -0500 (EST)
From: "j.gregory" <ort056@abdn.ac.uk>
Sender: ort056@abdn.ac.uk
To: nih-image@io.ece.drexel.edu
Subject: Re: can image count pixels?
Message-ID: <SIMEON.9811111254.A@pc10.abdn.ac.uk>
Date: Wed, 11 Nov 1998 12:26:54 +0000 (GMT)
Priority: NORMAL
X-Mailer: Simeon for Windows Version 4.0.9
X-Authentication: IMSP
MIME-Version: 1.0
Resent-Message-ID: <"XZ1pB.0._w.39OIs"@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/603
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: 699

Chris,

I'm using Scion Image - PC spin off of NIH.
In the macros provided with the program, there is one called 
measure.  It includes an option to count the number of black and 
white pixels as suggested by Bill Heeschen.
I've put a copy of it below, just in case.


macro 'Count Black and White Pixels [B]';
{
Counts the number of black and white pixels in the current
selection and stores the counts in the User1 and User2 columns.
}
begin
  RequiresVersion(1.44);
  SetUser1Label('Black');
  SetUser2Label('White');
  Measure;
  rUser1[rCount]:=histogram[255];
  rUser2[rCount]:=histogram[0];
  UpdateResults;
end;

Hope it helps,

Jenny Gregory

----------------------
j.gregory@abdn.ac.uk




From nih-image-request@io.ece.drexel.edu Wed Nov 11 08:29 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA27040;
	Wed, 11 Nov 1998 08:29:06 -0500 (EST)
Resent-Date: Wed, 11 Nov 1998 08:29:06 -0500 (EST)
Message-ID: <19981111125753.27404.rocketmail@web1.rocketmail.com>
Date: Wed, 11 Nov 1998 04:57:53 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
Subject: Re: can image count pixels?
To: nih-image@io.ece.drexel.edu
Cc: kokopellis@att.net
MIME-Version: 1.0
Resent-Message-ID: <"TqOMf2.0.C05.9qOIs"@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/604
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: 1005


> I'm a new Image user (and new to this newsgroup), so I hope that this
> question isn't to irritatingly obvious to more experienced users of this
> software.
>  
> I'm trying to quantitate an area that is dark vs. the light area within
> a set area.  I think I can use the "threshold" command (and maybe "make
> binary" to convert my grey-scale image to a binary image, but what I'd
> like to do next is have IMAGE calculate the number of black pixels
> within the area.  Is there a way to do this?

When NIH Image is in threshold mode and the measure command is issued the
measurement of area will be the black thresholded area. White area would be
the whole area minus the above, so very easy to calculate. Of course you can
use a roi in all of this as well to measure say black area within the roi.
==
Mark Vivino
mvivino@rocketmail.com
Consulting Biomedical Engineer
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-request@io.ece.drexel.edu Wed Nov 11 12:32 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA16253;
	Wed, 11 Nov 1998 12:32:03 -0500 (EST)
Resent-Date: Wed, 11 Nov 1998 12:32:03 -0500 (EST)
Message-Id: <199811111657.KAA25550@mail5.doit.wisc.edu>
X-Sender: dlparker@facstaff.wisc.edu
X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.2 
Date: Wed, 11 Nov 1998 11:00:49 -0600
To: nih-image@io.ece.drexel.edu
From: David Parker <dlparker@facstaff.wisc.edu>
Subject: automation of nih-image
Mime-Version: 1.0
Resent-Message-ID: <"vjZ3X1.0.Cd1.H8SIs"@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/605
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: multipart/alternative;
	types="text/plain,text/html";
	boundary="=====================_3946354==_.ALT"
Content-Length: 3439

--=====================_3946354==_.ALT
Content-Type: text/plain; charset="us-ascii"


Hello!

This question is being posed programmer with experience with many languages,
none being Image's macro language.

I have briefly looked at the documentation, at some posts on a listserver and
at the gopher site for possible macros.


I've been asked to automate a process in nih-image macros language.

The process to automate is to look for a "spark" (NOVA like flash) on an image
and then to calculate several characteristics of the images. The user is
interested in the following attributes: 
>>1. Ratio 
>>2. Duration 
>>3. Time to Peak 
>>4. Full time at half max/min 
>>5. Diameter 
>>6. Full width at half maximum

The scan occurs from left to right. Each image is approximately 512 pixels
across and 1000 pixels long. Once the images have been acquired they are
stored
as TIFFs on a server and then accessed by another workstation running NIH
Image. 

These will depend on being able to find the center of mass of the spark.
Does the macro language facilitate automation for scanning or the parsing of
image file?



Sincerely,
David Parker               dlparker@doit.wisc.edu 

Division of Information Technology, Tools and Methods, Emerging Technologies
Ultratec Building, 5752 Tokay Blvd., Suite 200, Madison, WI 53719-1220 
ICQ-Page Address: http://wwp.mirabilis.com/18694325
            (608) 262-2104 (voice)  (608) 265-6681(fax) 


--=====================_3946354==_.ALT
Content-Type: text/html; charset="us-ascii"

<html><div>Hello!</div>
<br>
<div>This question is being posed programmer with experience with many
languages, none being Image's macro language.</div>
<br>
<div>I have briefly looked at the documentation, at some posts on a
listserver and at the gopher site for possible macros.</div>
<br>
<br>
<div>I've been asked to automate a process in nih-image macros
language.</div>
<br>
<div>The process to automate is to look for a &quot;spark&quot; (NOVA
like flash) on an image and then to calculate several characteristics of
the images. The user is interested in the following attributes: </div>
<div>&gt;&gt;1. Ratio </div>
<div>&gt;&gt;2. Duration </div>
<div>&gt;&gt;3. Time to Peak </div>
<div>&gt;&gt;4. Full time at half max/min </div>
<div>&gt;&gt;5. Diameter </div>
<div>&gt;&gt;6. Full width at half maximum</div>
<br>
<div>The scan occurs from left to right. Each image is approximately 512
pixels across and 1000 pixels long. Once the images have been acquired
they are stored as TIFFs on a server and then accessed by another
workstation running NIH Image. </div>
<br>
<div>These will depend on being able to find the center of mass of the
spark.</div>
<div>Does the macro language facilitate automation for scanning or the
parsing of image file?</div>
<br>
<br>

<br>
Sincerely,<br>
<b><div align="center">
David
Parker&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</b>dlparker@doit.wisc.edu <br>
<br>
Division of Information Technology, Tools and Methods, Emerging
Technologies<br>
Ultratec Building, 5752 Tokay Blvd., Suite 200, Madison, WI 53719-1220
<br>
ICQ-Page Address:
<a href="http://wwp.mirabilis.com/18694325" eudora="autourl"><b>http://wwp.mirabilis.com/18694325<br>
</a></b>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
(608) 262-2104 (voice)&nbsp; (608) 265-6681(fax) <br>
<br>
</html>

--=====================_3946354==_.ALT--


From nih-image-request@io.ece.drexel.edu Wed Nov 11 13:34 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA04751;
	Wed, 11 Nov 1998 13:34:53 -0500 (EST)
Resent-Date: Wed, 11 Nov 1998 13:34:53 -0500 (EST)
Message-Id: <D209047D0257D21191770000F8C991D904C812@mante35a.nam.dow.com>
From: "Heeschen, Bill (WA)" <WAHEESCHEN@dow.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: automation of nih-image
Date: Wed, 11 Nov 1998 12:59:00 -0500
Mime-Version: 1.0
X-Mailer: Internet Mail Service (5.5.1960.3)
Resent-Message-ID: <"44bpQ3.0.Ku5.o1TIs"@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/606
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 1110

David:
The NIH Image macro language will allow you to inspect an image
pixel-by-pixel, however you will find the execution fairly slow.  My
development path is to use the macro language to develop (and debug) the
processing algorithms because of the rapid cycle time (no recompile and
Wayne's macro parser is pretty quick).  Once I am comfortable with it, I
will commit it to source code for the speed improvement.  The source
code is Pascal under CodeWarrior and is freely available from the web
page (http://rsb.info.nih.gov/nih-image/).  The conversion from macro to
source is not too bad as the calls are similarly named.  It does require
some time investment to dig through the source and figure out what
happens when and where - the usual game with following someone else's
logic.  The result, however is a major time improvement, especially for
pixel-by-pixel operations.  Also, the control you have over the whole
program is a lot of fun!  IMHO, Wayne has created a good starting point
for custom image processing solutions.

Bill Heeschen
The Dow Chemical Company
Microscopy group
waheeschen@dow.com


From nih-image-request@io.ece.drexel.edu Wed Nov 11 14:02 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA12564;
	Wed, 11 Nov 1998 14:02:14 -0500 (EST)
Resent-Date: Wed, 11 Nov 1998 14:02:14 -0500 (EST)
Message-ID: <3649D687.4E9E@pop.uky.edu>
Date: Wed, 11 Nov 1998 13:25:11 -0500
From: alex gimelbrant <aagime0@pop.uky.edu>
Organization: U of K
X-Mailer: Mozilla 3.01 (Macintosh; I; 68K)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Image as Photoshop substitute
References: <199811101128.GAA09630@io.ece.drexel.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"QegRJ3.0.xR.NQTIs"@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/607
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: 930

I would like to add another option to the already vast list
of suggested Photoshop substitutes.
You can get GraphicConverter from any shareware source 
(shareware.com , ...). The author keeps putting out new versions,
so it's up to date and not a dead end. In my experience, it has
everything needed for image manipulation, and is pretty easy to 
learn and use. 

The only problem I used to have was low final quality of text
put on image. Since it is the same problem (with the same cause;
see Image FAQ) as with NIH-Image, the way to deal with it might be
of some interest to Image users: The image is converted to higher 
resolution (this operation is in the standard menu of Gr.Conv.), and
the high-resolutuion text on the printout is of publication quality.
It is very memory-consuming, and interpolation involved in the
conversion might distort the data, so all analysis should be done
prior to that step.

Alex Gimelbrant


From nih-image-request@io.ece.drexel.edu Wed Nov 11 14:30 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA21176;
	Wed, 11 Nov 1998 14:30:27 -0500 (EST)
Resent-Date: Wed, 11 Nov 1998 14:30:27 -0500 (EST)
Message-ID: <19981111185423.4975.qmail@hotmail.com>
X-Originating-IP: [130.132.65.250]
From: "John Elsworth" <elsworth@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Autorads: Seeing the light?
MIME-Version: 1.0
Date: Wed, 11 Nov 1998 10:54:23 PST
Resent-Message-ID: <"SITGW2.0.Ib2.HsTIs"@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/608
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 1404

I am just setting up my new imaging equipment (Northern Lights light 
box, Cohu CCD camera 4913 with Nikon Micro-Nikkor 55 mm f2.8 lens) for 
quantifying autoradiograms of brain sections.  My question concerns the 
relative advantages of the different ways of adjusting the brightness 
and contrast of the image on the screen.

The light passing through the film can be adjusted at the light box. 
Alternatively, in Image the offset (brightness) and gain (contrast) can 
be adjusted under Video Control.  What is the best way to balance the 
light box output with the Image settings?  Furthermore, the camera has 8 
different shutter speeds but I suspect that as this is a still image, 
this is not critical.

The Highlight Saturated Pixel option appears to be useful, but it hasn't 
helped me answer the above quesion, as there are different "correct" 
setting for offset and gain for each different light box 
transillumination intensity.
The Display Histogram function would appear to be useful also, however 
the manual suggests spreading out the histogram as much as possible.  To 
my eye, anyway, the best-looking image occurs when there is a "tall but 
not thin" peak to the left in the histogram.
Any insights into any of these issues would be much appreciated.

John Elsworth Ph.D.


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


From nih-image-request@io.ece.drexel.edu Thu Nov 12 03:26 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id DAA28707;
	Thu, 12 Nov 1998 03:26:38 -0500 (EST)
Resent-Date: Thu, 12 Nov 1998 03:26:38 -0500 (EST)
Date: 	Thu, 12 Nov 1998 09:03:59 +0100 (CET)
From: Gary Chinga <gary@nvg.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Morphological operations
In-Reply-To: <199811111657.KAA25550@mail5.doit.wisc.edu>
Message-ID: <Pine.NEB.4.05.9811120857070.17849-100000@flode.nvg.ntnu.no>
MIME-Version: 1.0
Resent-Message-ID: <"nGAr-3.0.qL5.3SfIs"@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/609
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: 265


Hi!

I am wondering if it is possible to perform morphological operations such
as pruning, thinning, thickening or the hit-or-miss transform with Image.
Has somebody out there macroes that can be used in this context.

Thanks.

Gary Chinga
NTNU-Trondheim
Norway.


From nih-image-d-request@io.ece.drexel.edu Thu Nov 12 03:36 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id DAA02215;
	Thu, 12 Nov 1998 03:36:45 -0500 (EST)
Date: Thu, 12 Nov 1998 03:36:45 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811120836.DAA02215@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #112
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/112
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 11777

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 112

Today's Topics:
  Re: can image count pixels?           [ "j.gregory" <ort056@abdn.ac.uk> ]
  Re: can image count pixels?           [ Mark Vivino <mvivino@rocketmail.com ]
  automation of nih-image               [ David Parker <dlparker@facstaff.wis ]
  RE: automation of nih-image           [ "Heeschen, Bill (WA)" <WAHEESCHEN@d ]
  Re: NIH Image as Photoshop substitut  [ alex gimelbrant <aagime0@pop.uky.ed ]
  Autorads: Seeing the light?           [ "John Elsworth" <elsworth@hotmail.c ]
  Morphological operations              [ Gary Chinga <gary@nvg.ntnu.no> ]

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

Date: Wed, 11 Nov 1998 12:26:54 +0000 (GMT)
From: "j.gregory" <ort056@abdn.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: can image count pixels?
Message-ID: <SIMEON.9811111254.A@pc10.abdn.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

Chris,

I'm using Scion Image - PC spin off of NIH.
In the macros provided with the program, there is one called 
measure.  It includes an option to count the number of black and 
white pixels as suggested by Bill Heeschen.
I've put a copy of it below, just in case.


macro 'Count Black and White Pixels [B]';
{
Counts the number of black and white pixels in the current
selection and stores the counts in the User1 and User2 columns.
}
begin
  RequiresVersion(1.44);
  SetUser1Label('Black');
  SetUser2Label('White');
  Measure;
  rUser1[rCount]:=histogram[255];
  rUser2[rCount]:=histogram[0];
  UpdateResults;
end;

Hope it helps,

Jenny Gregory

----------------------
j.gregory@abdn.ac.uk

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

Date: Wed, 11 Nov 1998 04:57:53 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
To: nih-image@io.ece.drexel.edu
Cc: kokopellis@att.net
Subject: Re: can image count pixels?
Message-ID: <19981111125753.27404.rocketmail@web1.rocketmail.com>
Content-Type: text/plain; charset=us-ascii

> I'm a new Image user (and new to this newsgroup), so I hope that this
> question isn't to irritatingly obvious to more experienced users of this
> software.
>  
> I'm trying to quantitate an area that is dark vs. the light area within
> a set area.  I think I can use the "threshold" command (and maybe "make
> binary" to convert my grey-scale image to a binary image, but what I'd
> like to do next is have IMAGE calculate the number of black pixels
> within the area.  Is there a way to do this?

When NIH Image is in threshold mode and the measure command is issued the
measurement of area will be the black thresholded area. White area would be
the whole area minus the above, so very easy to calculate. Of course you can
use a roi in all of this as well to measure say black area within the roi.
==
Mark Vivino
mvivino@rocketmail.com
Consulting Biomedical Engineer
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com

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

Date: Wed, 11 Nov 1998 11:00:49 -0600
From: David Parker <dlparker@facstaff.wisc.edu>
To: nih-image@io.ece.drexel.edu
Subject: automation of nih-image
Message-Id: <199811111657.KAA25550@mail5.doit.wisc.edu>
Content-Type: multipart/alternative;
	types="text/plain,text/html";
	boundary="=====================_3946354==_.ALT"

--=====================_3946354==_.ALT
Content-Type: text/plain; charset="us-ascii"


Hello!

This question is being posed programmer with experience with many languages,
none being Image's macro language.

I have briefly looked at the documentation, at some posts on a listserver and
at the gopher site for possible macros.


I've been asked to automate a process in nih-image macros language.

The process to automate is to look for a "spark" (NOVA like flash) on an image
and then to calculate several characteristics of the images. The user is
interested in the following attributes: 
>>1. Ratio 
>>2. Duration 
>>3. Time to Peak 
>>4. Full time at half max/min 
>>5. Diameter 
>>6. Full width at half maximum

The scan occurs from left to right. Each image is approximately 512 pixels
across and 1000 pixels long. Once the images have been acquired they are
stored
as TIFFs on a server and then accessed by another workstation running NIH
Image. 

These will depend on being able to find the center of mass of the spark.
Does the macro language facilitate automation for scanning or the parsing of
image file?



Sincerely,
David Parker               dlparker@doit.wisc.edu 

Division of Information Technology, Tools and Methods, Emerging Technologies
Ultratec Building, 5752 Tokay Blvd., Suite 200, Madison, WI 53719-1220 
ICQ-Page Address: http://wwp.mirabilis.com/18694325
            (608) 262-2104 (voice)  (608) 265-6681(fax) 


--=====================_3946354==_.ALT
Content-Type: text/html; charset="us-ascii"

<html><div>Hello!</div>
<br>
<div>This question is being posed programmer with experience with many
languages, none being Image's macro language.</div>
<br>
<div>I have briefly looked at the documentation, at some posts on a
listserver and at the gopher site for possible macros.</div>
<br>
<br>
<div>I've been asked to automate a process in nih-image macros
language.</div>
<br>
<div>The process to automate is to look for a &quot;spark&quot; (NOVA
like flash) on an image and then to calculate several characteristics of
the images. The user is interested in the following attributes: </div>
<div>&gt;&gt;1. Ratio </div>
<div>&gt;&gt;2. Duration </div>
<div>&gt;&gt;3. Time to Peak </div>
<div>&gt;&gt;4. Full time at half max/min </div>
<div>&gt;&gt;5. Diameter </div>
<div>&gt;&gt;6. Full width at half maximum</div>
<br>
<div>The scan occurs from left to right. Each image is approximately 512
pixels across and 1000 pixels long. Once the images have been acquired
they are stored as TIFFs on a server and then accessed by another
workstation running NIH Image. </div>
<br>
<div>These will depend on being able to find the center of mass of the
spark.</div>
<div>Does the macro language facilitate automation for scanning or the
parsing of image file?</div>
<br>
<br>

<br>
Sincerely,<br>
<b><div align="center">
David
Parker&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</b>dlparker@doit.wisc.edu <br>
<br>
Division of Information Technology, Tools and Methods, Emerging
Technologies<br>
Ultratec Building, 5752 Tokay Blvd., Suite 200, Madison, WI 53719-1220
<br>
ICQ-Page Address:
<a href="http://wwp.mirabilis.com/18694325" eudora="autourl"><b>http://wwp.mirabilis.com/18694325<br>
</a></b>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
(608) 262-2104 (voice)&nbsp; (608) 265-6681(fax) <br>
<br>
</html>

--=====================_3946354==_.ALT--

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

Date: Wed, 11 Nov 1998 12:59:00 -0500
From: "Heeschen, Bill (WA)" <WAHEESCHEN@dow.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: automation of nih-image
Message-Id: <D209047D0257D21191770000F8C991D904C812@mante35a.nam.dow.com>
Content-Type: text/plain

David:
The NIH Image macro language will allow you to inspect an image
pixel-by-pixel, however you will find the execution fairly slow.  My
development path is to use the macro language to develop (and debug) the
processing algorithms because of the rapid cycle time (no recompile and
Wayne's macro parser is pretty quick).  Once I am comfortable with it, I
will commit it to source code for the speed improvement.  The source
code is Pascal under CodeWarrior and is freely available from the web
page (http://rsb.info.nih.gov/nih-image/).  The conversion from macro to
source is not too bad as the calls are similarly named.  It does require
some time investment to dig through the source and figure out what
happens when and where - the usual game with following someone else's
logic.  The result, however is a major time improvement, especially for
pixel-by-pixel operations.  Also, the control you have over the whole
program is a lot of fun!  IMHO, Wayne has created a good starting point
for custom image processing solutions.

Bill Heeschen
The Dow Chemical Company
Microscopy group
waheeschen@dow.com

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

Date: Wed, 11 Nov 1998 13:25:11 -0500
From: alex gimelbrant <aagime0@pop.uky.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Image as Photoshop substitute
Message-ID: <3649D687.4E9E@pop.uky.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

I would like to add another option to the already vast list
of suggested Photoshop substitutes.
You can get GraphicConverter from any shareware source 
(shareware.com , ...). The author keeps putting out new versions,
so it's up to date and not a dead end. In my experience, it has
everything needed for image manipulation, and is pretty easy to 
learn and use. 

The only problem I used to have was low final quality of text
put on image. Since it is the same problem (with the same cause;
see Image FAQ) as with NIH-Image, the way to deal with it might be
of some interest to Image users: The image is converted to higher 
resolution (this operation is in the standard menu of Gr.Conv.), and
the high-resolutuion text on the printout is of publication quality.
It is very memory-consuming, and interpolation involved in the
conversion might distort the data, so all analysis should be done
prior to that step.

Alex Gimelbrant

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

Date: Wed, 11 Nov 1998 10:54:23 PST
From: "John Elsworth" <elsworth@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Autorads: Seeing the light?
Message-ID: <19981111185423.4975.qmail@hotmail.com>
Content-Type: text/plain

I am just setting up my new imaging equipment (Northern Lights light 
box, Cohu CCD camera 4913 with Nikon Micro-Nikkor 55 mm f2.8 lens) for 
quantifying autoradiograms of brain sections.  My question concerns the 
relative advantages of the different ways of adjusting the brightness 
and contrast of the image on the screen.

The light passing through the film can be adjusted at the light box. 
Alternatively, in Image the offset (brightness) and gain (contrast) can 
be adjusted under Video Control.  What is the best way to balance the 
light box output with the Image settings?  Furthermore, the camera has 8 
different shutter speeds but I suspect that as this is a still image, 
this is not critical.

The Highlight Saturated Pixel option appears to be useful, but it hasn't 
helped me answer the above quesion, as there are different "correct" 
setting for offset and gain for each different light box 
transillumination intensity.
The Display Histogram function would appear to be useful also, however 
the manual suggests spreading out the histogram as much as possible.  To 
my eye, anyway, the best-looking image occurs when there is a "tall but 
not thin" peak to the left in the histogram.
Any insights into any of these issues would be much appreciated.

John Elsworth Ph.D.


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

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

Date: 	Thu, 12 Nov 1998 09:03:59 +0100 (CET)
From: Gary Chinga <gary@nvg.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Morphological operations
Message-ID: <Pine.NEB.4.05.9811120857070.17849-100000@flode.nvg.ntnu.no>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi!

I am wondering if it is possible to perform morphological operations such
as pruning, thinning, thickening or the hit-or-miss transform with Image.
Has somebody out there macroes that can be used in this context.

Thanks.

Gary Chinga
NTNU-Trondheim
Norway.

--------------------------------
End of nih-image-d Digest V98 Issue #112
****************************************

From nih-image-request@io.ece.drexel.edu Thu Nov 12 04:50 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA25833;
	Thu, 12 Nov 1998 04:50:34 -0500 (EST)
Resent-Date: Thu, 12 Nov 1998 04:50:34 -0500 (EST)
Message-Id: <9811120942.AA00163@pp1.rheo.matse.fukui-u.ac.jp>
Date: Thu, 12 Nov 1998 18:42:01 +0900
From: yokota@rheo.matse.fukui-u.ac.jp (=?ISO-2022-JP?B?GyRCMiNFRCEhT0I4dxsoSg==?= )
To: nih-image@io.ece.drexel.edu
Subject: I can't recognize
In-Reply-To: <9810290753.AA00147@pp1.rheo.matse.fukui-u.ac.jp>
Mime-Version: 1.0
X-Mailer: AL-Mail 1.22
Resent-Message-ID: <"SYUrY.0.3Z4.KfgIs"@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/610
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset=iso-2022-jp
Content-Length: 1278


Hello,Imagers.
    EXPLANATION
Before the question, I tell you about my studying.
I want to learn the location of fibers,fibers move high
speed,by the image analysis.
These states are recorded by high speed VTR.
These images are computed in my personal computer
(Power Mac G3).
For the location of moving fibers,it is nesessary 
to change the color to bluck or white(binarization).
And I want to do labeling these images.I want to do
labeling for each frame.

    QUESTION

I want to recognize fibers, but each frame has many noise.
And I can't recognize fibers. 
I hit idea that I decided the point on x-ycoodinate and,if part of white(white 
is fiber) is over 5cm from that point,I recognize the fiber.
And I leave as it is. But it is not 5cm, I don't recognize the fiber.
I want to change to black. Can I do those process by NIH-Image(V.1.62)?
If you have the macro that I can do that process,please contact me by 
below E-mail.

   E-mail yokota@rheo.matse.fukui-u.ac.jp     

Thank you for your help.

     

  $BJ!0fBg3X!!!!9)3XIt!!!!:`NA2=3X2J!!!!9bJ,;R2C9)3X9V:B(J                  $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!2#ED!!!!OB8w(J (Kazumitsu Yokota)     
                E-mail  yokota@rheo.matse.fukui-u.ac.jp
 
     (fukui Univ./ thecnology / material chemical)


From nih-image-request@io.ece.drexel.edu Thu Nov 12 04:52 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA26459;
	Thu, 12 Nov 1998 04:52:17 -0500 (EST)
Resent-Date: Thu, 12 Nov 1998 04:52:17 -0500 (EST)
Date: Thu, 12 Nov 1998 10:26:16 +0100
From: Ard Jonker <a.jonker@AMC.UVA.NL>
Subject: NIH-Image archive Sherlock Plugin available?
In-reply-to: <199811120811.DAA23694@io.ece.drexel.edu>
X-Sender: ajonker.public.amc@reddwarf.amc.uva.nl
To: nih-image@io.ece.drexel.edu
Message-id: <l03130308b27059dde4b7@[145.117.43.50]>
MIME-version: 1.0
Content-transfer-encoding: 7BIT
Resent-Message-ID: <"bzH1U1.0.3t4.vigIs"@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/611
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: 169

Well, the title says it all; maybe I should extend that to 'or is it easy to make one available?'....

It would sure help searching the archives in a mac manner.

Ard



From nih-image-request@io.ece.drexel.edu Thu Nov 12 15:27 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA15627;
	Thu, 12 Nov 1998 15:27:21 -0500 (EST)
Resent-Date: Thu, 12 Nov 1998 15:27:21 -0500 (EST)
Message-ID: <012e01be0e77$18863be0$0100007e@papa>
From: "JP.Plachot" <JP.Plachot@wanadoo.fr>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: nih-image-d Digest V98 #110
Date: Thu, 12 Nov 1998 21:00:27 +0100
MIME-Version: 1.0
Content-Transfer-Encoding: 8bit
X-Priority: 3
X-MSMail-Priority: Normal
X-Mailer: Microsoft Outlook Express 4.72.3110.5
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3
Resent-Message-ID: <"0PXSS2.0.633.mxpIs"@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/613
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain;
	boundary="----------------------------";
	charset="iso-8859-1"
Content-Length: 258

essai
-----Message d'origine-----
De : nih-image-d-request@io.ece.drexel.edu
<nih-image-d-request@io.ece.drexel.edu>
 : nih-image-d@io.ece.drexel.edu <nih-image-d@io.ece.drexel.edu>
Date : mardi 10 novembre 1998 12:18
Objet : nih-image-d Digest V98 #110




From nih-image-request@io.ece.drexel.edu Thu Nov 12 15:27 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA15643;
	Thu, 12 Nov 1998 15:27:28 -0500 (EST)
Resent-Date: Thu, 12 Nov 1998 15:27:28 -0500 (EST)
Message-ID: <00e001be0e76$55aa3360$0100007e@papa>
From: "JP.Plachot" <JP.Plachot@wanadoo.fr>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: nih-image-d Digest V98 #112
Date: Thu, 12 Nov 1998 20:54:25 +0100
MIME-Version: 1.0
Content-Transfer-Encoding: 8bit
X-Priority: 3
X-MSMail-Priority: Normal
X-Mailer: Microsoft Outlook Express 4.72.3110.5
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3
Resent-Message-ID: <"SUCzs1.0.lu2.2spIs"@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/612
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain;
	boundary="----------------------------";
	charset="iso-8859-1"
Content-Length: 258

merci
-----Message d'origine-----
De : nih-image-d-request@io.ece.drexel.edu
<nih-image-d-request@io.ece.drexel.edu>
 : nih-image-d@io.ece.drexel.edu <nih-image-d@io.ece.drexel.edu>
Date : jeudi 12 novembre 1998 09:27
Objet : nih-image-d Digest V98 #112




From nih-image-d-request@io.ece.drexel.edu Fri Nov 13 06:17 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA17079;
	Fri, 13 Nov 1998 06:17:34 -0500 (EST)
Date: Fri, 13 Nov 1998 06:17:34 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811131117.GAA17079@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #113
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/113
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 4756

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 113

Today's Topics:
  I can't recognize                     [ yokota@rheo.matse.fukui-u.ac.jp (=? ]
  NIH-Image archive Sherlock Plugin av  [ Ard Jonker <a.jonker@AMC.UVA.NL> ]
  inhibit redrawing when...             [ Bill Saidel <saidel@crab.rutgers.ed ]
  Re: nih-image-d Digest V98 #112       [ "JP.Plachot" <JP.Plachot@wanadoo.fr ]
  Re: nih-image-d Digest V98 #110       [ "JP.Plachot" <JP.Plachot@wanadoo.fr ]

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

Date: Thu, 12 Nov 1998 18:42:01 +0900
From: yokota@rheo.matse.fukui-u.ac.jp (=?ISO-2022-JP?B?GyRCMiNFRCEhT0I4dxsoSg==?= )
To: nih-image@io.ece.drexel.edu
Subject: I can't recognize
Message-Id: <9811120942.AA00163@pp1.rheo.matse.fukui-u.ac.jp>
Content-Type: text/plain; charset=iso-2022-jp

Hello,Imagers.
    EXPLANATION
Before the question, I tell you about my studying.
I want to learn the location of fibers,fibers move high
speed,by the image analysis.
These states are recorded by high speed VTR.
These images are computed in my personal computer
(Power Mac G3).
For the location of moving fibers,it is nesessary 
to change the color to bluck or white(binarization).
And I want to do labeling these images.I want to do
labeling for each frame.

    QUESTION

I want to recognize fibers, but each frame has many noise.
And I can't recognize fibers. 
I hit idea that I decided the point on x-ycoodinate and,if part of white(white 
is fiber) is over 5cm from that point,I recognize the fiber.
And I leave as it is. But it is not 5cm, I don't recognize the fiber.
I want to change to black. Can I do those process by NIH-Image(V.1.62)?
If you have the macro that I can do that process,please contact me by 
below E-mail.

   E-mail yokota@rheo.matse.fukui-u.ac.jp     

Thank you for your help.

     

  $BJ!0fBg3X!!!!9)3XIt!!!!:`NA2=3X2J!!!!9bJ,;R2C9)3X9V:B(J                  $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!2#ED!!!!OB8w(J (Kazumitsu Yokota)     
                E-mail  yokota@rheo.matse.fukui-u.ac.jp
 
     (fukui Univ./ thecnology / material chemical)

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

Date: Thu, 12 Nov 1998 10:26:16 +0100
From: Ard Jonker <a.jonker@AMC.UVA.NL>
To: nih-image@io.ece.drexel.edu
Subject: NIH-Image archive Sherlock Plugin available?
Message-id: <l03130308b27059dde4b7@[145.117.43.50]>
Content-type: text/plain; charset="us-ascii"
Content-transfer-encoding: 7BIT

Well, the title says it all; maybe I should extend that to 'or is it easy to make one available?'....

It would sure help searching the archives in a mac manner.

Ard

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

Date: Thu, 12 Nov 1998 12:25:31 -0500
From: Bill Saidel <saidel@crab.rutgers.edu>
To: nih-image-d@io.ece.drexel.edu
Subject: inhibit redrawing when...
Message-Id: <3.0.6.32.19981112122531.0085a210@crab.rutgers.edu>
Content-Type: text/plain; charset="us-ascii"

Without recompiling Image, is there a way to inhibit redrawing the image
during the skeletonize function until the function has completed?
**********************************************************************
Dr. Bill Saidel 
Assoc. Prof. 	                  Vocal phone   (609) 225-6336
Department of Biology	FAX  (609) 225-6312
Science Building		email:  saidel@crab.rutgers.edu
315 Penn St.
Rutgers, the State University of New Jersey
Camden, NJ 08102 -1411
http://crab.rutgers.edu/~saidel/saidel.html

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

Date: Thu, 12 Nov 1998 20:54:25 +0100
From: "JP.Plachot" <JP.Plachot@wanadoo.fr>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: nih-image-d Digest V98 #112
Message-ID: <00e001be0e76$55aa3360$0100007e@papa>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
	boundary="----------------------------";
	charset="iso-8859-1"

merci
-----Message d'origine-----
De : nih-image-d-request@io.ece.drexel.edu
<nih-image-d-request@io.ece.drexel.edu>
 : nih-image-d@io.ece.drexel.edu <nih-image-d@io.ece.drexel.edu>
Date : jeudi 12 novembre 1998 09:27
Objet : nih-image-d Digest V98 #112

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

Date: Thu, 12 Nov 1998 21:00:27 +0100
From: "JP.Plachot" <JP.Plachot@wanadoo.fr>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: nih-image-d Digest V98 #110
Message-ID: <012e01be0e77$18863be0$0100007e@papa>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
	boundary="----------------------------";
	charset="iso-8859-1"

essai
-----Message d'origine-----
De : nih-image-d-request@io.ece.drexel.edu
<nih-image-d-request@io.ece.drexel.edu>
 : nih-image-d@io.ece.drexel.edu <nih-image-d@io.ece.drexel.edu>
Date : mardi 10 novembre 1998 12:18
Objet : nih-image-d Digest V98 #110

--------------------------------
End of nih-image-d Digest V98 Issue #113
****************************************

From nih-image-request@io.ece.drexel.edu Fri Nov 13 07:53 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id HAA27747;
	Fri, 13 Nov 1998 07:53:31 -0500 (EST)
Resent-Date: Fri, 13 Nov 1998 07:53:31 -0500 (EST)
Date: Fri, 13 Nov 1998 13:36:23 +0100
From: "U.Marti" <ulrich.marti@dkf2.unibe.ch>
Subject: Second-order stereology
To: NIH List <nih-image@io.ece.drexel.edu>
Reply-to: ulrich.marti@dkf2.unibe.ch
Message-id: <364C27C3.23EF8763@dkf2.unibe.ch>
MIME-version: 1.0
X-Mailer: Mozilla 4.5 (Macintosh; I; PPC)
Content-transfer-encoding: 7bit
X-Accept-Language: en,de
Resent-Message-ID: <"5AOCw2.0.V96.HR2Js"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/614
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; x-mac-type="54455854"; 
              x-mac-creator="4D4F5353"
Content-Length: 182

Hello subscribers

We would like do do some tissue caparisons using second-order
stereology. Is there any macro for NIH image available that could be
used for this work?

Thank you


From nih-image-request@io.ece.drexel.edu Fri Nov 13 16:31 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA18710;
	Fri, 13 Nov 1998 16:31:37 -0500 (EST)
Resent-Date: Fri, 13 Nov 1998 16:31:37 -0500 (EST)
Date: Fri, 13 Nov 1998 15:59:56 -0500 (EST)
From: Lisa Rodrigues <lrodrigu@zoo.utoronto.ca>
To: nih-image@io.ece.drexel.edu
Subject: Video Capture
Message-ID: <Pine.BSI.3.91.981113155635.14153A-100000@zoo.utoronto.ca>
MIME-Version: 1.0
Resent-Message-ID: <"splbd3.0.0p3.Ot9Js"@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/615
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: 369


I am using NIH-Image to analyze behaviors, by directly capturing video 
images from my VCR. However, my problem is that I am only able to view 
the last frame of the digital capture on my desktop. How do I play back 
the entire video capture, frame-by-frame?? Is this possible?

Thank You.


____________________________

Lisa J. Rodrigues
lrodrigu@zoo.utoronto.ca




From nih-image-request@io.ece.drexel.edu Fri Nov 13 19:32 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id TAA05095;
	Fri, 13 Nov 1998 19:32:16 -0500 (EST)
Resent-Date: Fri, 13 Nov 1998 19:32:16 -0500 (EST)
Date: Fri, 13 Nov 1998 16:02:18 -0800 (PST)
From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: G3 digitizer and Image
In-Reply-To: <199810082232.SAA03616@io.ece.drexel.edu>
Message-ID: <Pine.SOL.3.95.981113155321.11457B-100000@protos.lifesci.ucla.edu>
MIME-Version: 1.0
Resent-Message-ID: <"bwnpT2.0.OY.iYCJs"@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/616
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: 1456

Hello,

We bought a G3/266 with a built-in digitizer; we were hoping to replace an
8100/80AV (with built in digitizer). Of course, it turns out Image doesn't
work with the G3 built in digitizer and noone seems to know how to fix
this. So I am gathering my options and would like some info:

1) Does Image work with ANY other quicktime video digitizers on a G3?
Specifically, I do not want to spend the money on the Scion or Data trans
cards, because all I need is grey scale digitization of 640x480 at 1 Hz.
Some would something like an ATI Rage card
or Buz work with Image on a G3? Or any particular card that might cost
under $400?

2) I guess my other option is to try to find a used 8500 and put in a G3
card, would this work?  We have an 8500/120 which works fine, but I don't
know if adding a g3 card would make Image go plooey.

3) I tried capturing video in Premiere and bringing it into Image but all
I get is a single converted frame. This is on a G3/266 with stock 8.1 and
QT 3.02. Any ideas on how to get Image to read a movie file from premiere?

4) Any other ideas would be appreciated as well. 
Thanks,
Stephan

------------------------------
Stephan G. Anagnostaras, Ph.D. 
UCLA Depts. of Neurobiology         
           and Psychology      
stephan@lifesci.ucla.edu    
sanagnos@mediaone.net         
------------------------------
Work, CHS: (310) 794-6609
    Psych: (310) 794-5339
     Home: (310) 306-0294
--------------------------


From nih-image-d-request@io.ece.drexel.edu Sat Nov 14 06:17 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA08794;
	Sat, 14 Nov 1998 06:17:56 -0500 (EST)
Date: Sat, 14 Nov 1998 06:17:56 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811141117.GAA08794@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #114
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/114
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 3474

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 114

Today's Topics:
  Second-order stereology               [ "U.Marti" <ulrich.marti@dkf2.unibe. ]
  Video Capture                         [ Lisa Rodrigues <lrodrigu@zoo.utoron ]
  G3 digitizer and Image                [ Stephan Anagnostaras <stephan@proto ]

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

Date: Fri, 13 Nov 1998 13:36:23 +0100
From: "U.Marti" <ulrich.marti@dkf2.unibe.ch>
To: NIH List <nih-image@io.ece.drexel.edu>
Subject: Second-order stereology
Message-id: <364C27C3.23EF8763@dkf2.unibe.ch>
Content-type: text/plain; charset=us-ascii; x-mac-type="54455854"; 
              x-mac-creator="4D4F5353"
Content-transfer-encoding: 7bit

Hello subscribers

We would like do do some tissue caparisons using second-order
stereology. Is there any macro for NIH image available that could be
used for this work?

Thank you

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

Date: Fri, 13 Nov 1998 15:59:56 -0500 (EST)
From: Lisa Rodrigues <lrodrigu@zoo.utoronto.ca>
To: nih-image@io.ece.drexel.edu
Subject: Video Capture
Message-ID: <Pine.BSI.3.91.981113155635.14153A-100000@zoo.utoronto.ca>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I am using NIH-Image to analyze behaviors, by directly capturing video 
images from my VCR. However, my problem is that I am only able to view 
the last frame of the digital capture on my desktop. How do I play back 
the entire video capture, frame-by-frame?? Is this possible?

Thank You.


____________________________

Lisa J. Rodrigues
lrodrigu@zoo.utoronto.ca

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

Date: Fri, 13 Nov 1998 16:02:18 -0800 (PST)
From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: G3 digitizer and Image
Message-ID: <Pine.SOL.3.95.981113155321.11457B-100000@protos.lifesci.ucla.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hello,

We bought a G3/266 with a built-in digitizer; we were hoping to replace an
8100/80AV (with built in digitizer). Of course, it turns out Image doesn't
work with the G3 built in digitizer and noone seems to know how to fix
this. So I am gathering my options and would like some info:

1) Does Image work with ANY other quicktime video digitizers on a G3?
Specifically, I do not want to spend the money on the Scion or Data trans
cards, because all I need is grey scale digitization of 640x480 at 1 Hz.
Some would something like an ATI Rage card
or Buz work with Image on a G3? Or any particular card that might cost
under $400?

2) I guess my other option is to try to find a used 8500 and put in a G3
card, would this work?  We have an 8500/120 which works fine, but I don't
know if adding a g3 card would make Image go plooey.

3) I tried capturing video in Premiere and bringing it into Image but all
I get is a single converted frame. This is on a G3/266 with stock 8.1 and
QT 3.02. Any ideas on how to get Image to read a movie file from premiere?

4) Any other ideas would be appreciated as well. 
Thanks,
Stephan

- ----------------------------
Stephan G. Anagnostaras, Ph.D. 
UCLA Depts. of Neurobiology         
           and Psychology      
stephan@lifesci.ucla.edu    
sanagnos@mediaone.net         
- ----------------------------
Work, CHS: (310) 794-6609
    Psych: (310) 794-5339
     Home: (310) 306-0294
--------------------------

--------------------------------
End of nih-image-d Digest V98 Issue #114
****************************************

From nih-image-request@io.ece.drexel.edu Sat Nov 14 11:30 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA10890;
	Sat, 14 Nov 1998 11:30:45 -0500 (EST)
Resent-Date: Sat, 14 Nov 1998 11:30:45 -0500 (EST)
Message-ID: <19981114161228.6521.qmail@hotmail.com>
X-Originating-IP: [209.63.112.64]
From: "lynn huynh" <supershiny@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: nih-image stacking feature
MIME-Version: 1.0
Date: Sat, 14 Nov 1998 08:12:28 PST
Resent-Message-ID: <"BAaXy1.0.3A2.JmQJs"@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/617
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 990

i need to know how to use the stacking feature of nih-image to track 
asteroids.  i have tried image math, which will allow fo me to place the 
images on top of each other, all the objects present in one picture will 
show up in white and the objects present in the other picture will show 
up in black, but what i need is to flash the images on top of each 
other, what this requires is that i crop the images so that the fixed 
stars are centered on top of each other, when the images are stacked 
they will not move, non fixed object will appear to "move" across the 
screen if the two pictures are stacked back and forth.  I need to know: 
1. how do i use the stacking feature to stack at a certain rate, not 
controlled by hand, and 2. how do i crop an image and make the pictures 
equally proportional to each other using photoshop.  please help!  thank 
you 

lynn huynh

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


From nih-image-request@io.ece.drexel.edu Sat Nov 14 12:15 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA15881;
	Sat, 14 Nov 1998 12:15:41 -0500 (EST)
Resent-Date: Sat, 14 Nov 1998 12:15:41 -0500 (EST)
Message-ID: <364D9FE1.5145EF75@czd.waw.pl>
Date: Sat, 14 Nov 1998 16:21:05 +0100
From: Robert Prejs <prxx@czd.waw.pl>
X-Mailer: Mozilla 4.08 [en] (Win98; I)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: signoff
References: <199811141104.GAA07122@io.ece.drexel.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"QSxQ_3.0.OQ3.fRRJs"@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/618
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset=iso-8859-2
Content-Length: 30

signoff nih-image-d Digest




From nih-image-request@io.ece.drexel.edu Sat Nov 14 13:30 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA23838;
	Sat, 14 Nov 1998 13:30:33 -0500 (EST)
Resent-Date: Sat, 14 Nov 1998 13:30:33 -0500 (EST)
Message-Id: <l03102800b27378d4df9f@[131.130.80.137]>
In-Reply-To: <199811141110.GAA07959@io.ece.drexel.edu>
Mime-Version: 1.0
Date: Sat, 14 Nov 1998 19:16:18 +0100
To: nih-image@io.ece.drexel.edu
From: Michael Glotzer <mglotzer@nt.imp.univie.ac.at>
Subject: G3 digitizer and Image
Resent-Message-ID: <"1Rh412.0._L5.JWSJs"@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/619
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: 838


>
>3) I tried capturing video in Premiere and bringing it into Image but all
>I get is a single converted frame. This is on a G3/266 with stock 8.1 and
>QT 3.02. Any ideas on how to get Image to read a movie file from premiere?
>
>4) Any other ideas would be appreciated as well.

Assuming Premier can save as qucktime, Image should be able to open it (the
newer versions at least).  THe trick is you have to go to MacOS Easy Open
control panel and delete preferences and then NIH can open a quicktime
movie as a stack.
Good luck,
Michael




___________________________________________________________________

Michael Glotzer
Research Institute of Molecular Pathology
Dr. Bohr-Gasse 7
A-1030 Vienna
AUSTRIA

phone   43-(1)797-30-405   office
phone   43-(1)797-30-525   lab
fax     43-(1)798-7153
email   mglotzer@nt.imp.univie.ac.at



From nih-image-request@io.ece.drexel.edu Sat Nov 14 16:56 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA14709;
	Sat, 14 Nov 1998 16:56:17 -0500 (EST)
Resent-Date: Sat, 14 Nov 1998 16:56:17 -0500 (EST)
Message-Id: <l03130300b273a60bfc87@[194.252.64.62]>
Mime-Version: 1.0
Date: Sat, 14 Nov 1998 23:38:25 +0200
To: nih-image <nih-image@io.ece.drexel.edu>
From: Matti Haveri <mhaveri@walli.uwasa.fi>
Subject: How to open DICOM with a given density range
Resent-Message-ID: <"DLqa2.0.X43.2YVJs"@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/620
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: 536

How can I open DICOM images with a given Window/Level?

I can do this with File/Import/Custom/Set/Fixed Scale -command but this
isn't practical because each DICOM file can have different Offset which
must be manually calculated.

If I open DICOM with File/Import/DICOM then there seems to be no
possibility to open just a given density range? (I can adjust Brightness &
Contrast but the result is not pretty because the whole density range is
imported).

--
Matti Haveri <mhaveri@walli.uwasa.fi>
<http://www.walli.uwasa.fi/~mhaveri/>



From nih-image-request@io.ece.drexel.edu Sat Nov 14 22:43 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id WAA18554;
	Sat, 14 Nov 1998 22:43:02 -0500 (EST)
Resent-Date: Sat, 14 Nov 1998 22:43:02 -0500 (EST)
Message-Id: <9811149111.AA911100457@chppm-ccmail.apgea.army.mil>
X-Mailer: ccMail Link to SMTP R6.01.01
Date: Sat, 14 Nov 98 22:25:48 -0500
From: "Mike Terry"<mike_terry_at_chppm4__apgea@chppm-ccmail.apgea.army.mil>
Cc: <nih-image@io.ece.drexel.edu>,
        <mike_terry_at_chppm4__apgea@chppm-ccmail.apgea.army.mil>
Subject: Automating the analysis of a multilane gel
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"1fP_P1.0.P84.oeaJs"@io>
To: nih-image@io.ece.drexel.edu
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/621
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: 1549


     I have not yet used Nih-image.  Can anyone help with the following?
     
     1) the task I have is to automate is the analysis of a single 
     multilane gel.  There may only be three bands per lane, which may be 
     the same three bands in each lane (if all bands are present in any 
     particular lane).  For now, the Mac is the desired platform where this 
     automated system is to eventually run.  But I do not have convenient 
     access to a Mac while developing the automated system.  So, does it 
     make sense to run the Mac version of Nih-image on the Ardi Executor 
     (win32 version) Mac emulation system, running  on a pc running NT, 
     while developing the automated system for the Mac?
     
     2) I checked the abbreviated tutorial at scrc.cit.nih.gov/imaging.  
     What I think(?) we would like to do for the Mac (at least initially) 
     would be to automate the steps in II thru IV.  Perhaps, the operator 
     of the the automated system would select the image file.  Then the 
     automated system would calibrate (apparently necessary even for 
     comparisons between lanes on the same gel), select all the lanes, 
     "plot" all the lanes, automatically isolate signal from noise 
     (apparently automatically draw base line and drop lines), use the wand 
     to quantitate peak areas, and save results.
     Can this sequence of steps be automated?
     
     Thanks,
     Mike Terry, Ph.D.
     USACHPPM
     APG, MD
     410 436-8288 (Tel)
     mike_terry@chppm-ccmail.apgea.army.mil



From nih-image-request@io.ece.drexel.edu Sat Nov 14 23:05 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id XAA20838;
	Sat, 14 Nov 1998 23:04:59 -0500 (EST)
Resent-Date: Sat, 14 Nov 1998 23:04:59 -0500 (EST)
Message-Id: <3.0.5.32.19981114225356.00827640@codon.nih.gov>
X-Sender: wayne@codon.nih.gov
X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32)
Date: Sat, 14 Nov 1998 22:53:56 -0500
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: How to open DICOM with a given density range
In-Reply-To: <l03130300b273a60bfc87@[194.252.64.62]>
Mime-Version: 1.0
Resent-Message-ID: <"gE7-22.0.Oh4.dyaJs"@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/622
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: 744

At 11:38 PM 11/14/98 +0200, you wrote:
>How can I open DICOM images with a given Window/Level?
>
>I can do this with File/Import/Custom/Set/Fixed Scale -command but this
>isn't practical because each DICOM file can have different Offset which
>must be manually calculated.
>
>If I open DICOM with File/Import/DICOM then there seems to be no
>possibility to open just a given density range? (I can adjust Brightness &
>Contrast but the result is not pretty because the whole density range is
>imported).

Adjust brightness/contrast and then select Rescale (Revert), which re-imports the image using new window/level settings. You might also want to try Image/J (http://rsb.info.nih.gov/ij/), which imports DICOM files as 16-bit images.

-wayne


From nih-image-d-request@io.ece.drexel.edu Sun Nov 15 06:24 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA02591;
	Sun, 15 Nov 1998 06:24:19 -0500 (EST)
Date: Sun, 15 Nov 1998 06:24:19 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811151124.GAA02591@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #115
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/115
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 7300

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 115

Today's Topics:
  nih-image stacking feature            [ "lynn huynh" <supershiny@hotmail.co ]
  signoff                               [ Robert Prejs <prxx@czd.waw.pl> ]
  G3 digitizer and Image                [ Michael Glotzer <mglotzer@nt.imp.un ]
  How to open DICOM with a given densi  [ Matti Haveri <mhaveri@walli.uwasa.f ]
  Automating the analysis of a multila  [ "Mike Terry"<mike_terry_at_chppm4__ ]
  Re: How to open DICOM with a given d  [ Wayne Rasband <wayne@codon.nih.gov> ]

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

Date: Sat, 14 Nov 1998 08:12:28 PST
From: "lynn huynh" <supershiny@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: nih-image stacking feature
Message-ID: <19981114161228.6521.qmail@hotmail.com>
Content-Type: text/plain

i need to know how to use the stacking feature of nih-image to track 
asteroids.  i have tried image math, which will allow fo me to place the 
images on top of each other, all the objects present in one picture will 
show up in white and the objects present in the other picture will show 
up in black, but what i need is to flash the images on top of each 
other, what this requires is that i crop the images so that the fixed 
stars are centered on top of each other, when the images are stacked 
they will not move, non fixed object will appear to "move" across the 
screen if the two pictures are stacked back and forth.  I need to know: 
1. how do i use the stacking feature to stack at a certain rate, not 
controlled by hand, and 2. how do i crop an image and make the pictures 
equally proportional to each other using photoshop.  please help!  thank 
you 

lynn huynh

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

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

Date: Sat, 14 Nov 1998 16:21:05 +0100
From: Robert Prejs <prxx@czd.waw.pl>
To: nih-image@io.ece.drexel.edu
Subject: signoff
Message-ID: <364D9FE1.5145EF75@czd.waw.pl>
Content-Type: text/plain; charset=iso-8859-2
Content-Transfer-Encoding: 7bit

signoff nih-image-d Digest

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

Date: Sat, 14 Nov 1998 19:16:18 +0100
From: Michael Glotzer <mglotzer@nt.imp.univie.ac.at>
To: nih-image@io.ece.drexel.edu
Subject: G3 digitizer and Image
Message-Id: <l03102800b27378d4df9f@[131.130.80.137]>
Content-Type: text/plain; charset="us-ascii"

>
>3) I tried capturing video in Premiere and bringing it into Image but all
>I get is a single converted frame. This is on a G3/266 with stock 8.1 and
>QT 3.02. Any ideas on how to get Image to read a movie file from premiere?
>
>4) Any other ideas would be appreciated as well.

Assuming Premier can save as qucktime, Image should be able to open it (the
newer versions at least).  THe trick is you have to go to MacOS Easy Open
control panel and delete preferences and then NIH can open a quicktime
movie as a stack.
Good luck,
Michael




___________________________________________________________________

Michael Glotzer
Research Institute of Molecular Pathology
Dr. Bohr-Gasse 7
A-1030 Vienna
AUSTRIA

phone   43-(1)797-30-405   office
phone   43-(1)797-30-525   lab
fax     43-(1)798-7153
email   mglotzer@nt.imp.univie.ac.at

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

Date: Sat, 14 Nov 1998 23:38:25 +0200
From: Matti Haveri <mhaveri@walli.uwasa.fi>
To: nih-image <nih-image@io.ece.drexel.edu>
Subject: How to open DICOM with a given density range
Message-Id: <l03130300b273a60bfc87@[194.252.64.62]>
Content-Type: text/plain; charset="us-ascii"

How can I open DICOM images with a given Window/Level?

I can do this with File/Import/Custom/Set/Fixed Scale -command but this
isn't practical because each DICOM file can have different Offset which
must be manually calculated.

If I open DICOM with File/Import/DICOM then there seems to be no
possibility to open just a given density range? (I can adjust Brightness &
Contrast but the result is not pretty because the whole density range is
imported).

--
Matti Haveri <mhaveri@walli.uwasa.fi>
<http://www.walli.uwasa.fi/~mhaveri/>

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

Date: Sat, 14 Nov 98 22:25:48 -0500
From: "Mike Terry"<mike_terry_at_chppm4__apgea@chppm-ccmail.apgea.army.mil>
To: nih-image@io.ece.drexel.edu
Cc: <nih-image@io.ece.drexel.edu>,
        <mike_terry_at_chppm4__apgea@chppm-ccmail.apgea.army.mil>
Subject: Automating the analysis of a multilane gel
Message-Id: <9811149111.AA911100457@chppm-ccmail.apgea.army.mil>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit

     I have not yet used Nih-image.  Can anyone help with the following?
     
     1) the task I have is to automate is the analysis of a single 
     multilane gel.  There may only be three bands per lane, which may be 
     the same three bands in each lane (if all bands are present in any 
     particular lane).  For now, the Mac is the desired platform where this 
     automated system is to eventually run.  But I do not have convenient 
     access to a Mac while developing the automated system.  So, does it 
     make sense to run the Mac version of Nih-image on the Ardi Executor 
     (win32 version) Mac emulation system, running  on a pc running NT, 
     while developing the automated system for the Mac?
     
     2) I checked the abbreviated tutorial at scrc.cit.nih.gov/imaging.  
     What I think(?) we would like to do for the Mac (at least initially) 
     would be to automate the steps in II thru IV.  Perhaps, the operator 
     of the the automated system would select the image file.  Then the 
     automated system would calibrate (apparently necessary even for 
     comparisons between lanes on the same gel), select all the lanes, 
     "plot" all the lanes, automatically isolate signal from noise 
     (apparently automatically draw base line and drop lines), use the wand 
     to quantitate peak areas, and save results.
     Can this sequence of steps be automated?
     
     Thanks,
     Mike Terry, Ph.D.
     USACHPPM
     APG, MD
     410 436-8288 (Tel)
     mike_terry@chppm-ccmail.apgea.army.mil

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

Date: Sat, 14 Nov 1998 22:53:56 -0500
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: How to open DICOM with a given density range
Message-Id: <3.0.5.32.19981114225356.00827640@codon.nih.gov>
Content-Type: text/plain; charset="us-ascii"

At 11:38 PM 11/14/98 +0200, you wrote:
>How can I open DICOM images with a given Window/Level?
>
>I can do this with File/Import/Custom/Set/Fixed Scale -command but this
>isn't practical because each DICOM file can have different Offset which
>must be manually calculated.
>
>If I open DICOM with File/Import/DICOM then there seems to be no
>possibility to open just a given density range? (I can adjust Brightness &
>Contrast but the result is not pretty because the whole density range is
>imported).

Adjust brightness/contrast and then select Rescale (Revert), which re-imports the image using new window/level settings. You might also want to try Image/J (http://rsb.info.nih.gov/ij/), which imports DICOM files as 16-bit images.

-wayne

--------------------------------
End of nih-image-d Digest V98 Issue #115
****************************************

From nih-image-request@io.ece.drexel.edu Sun Nov 15 12:14 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA06999;
	Sun, 15 Nov 1998 12:14:52 -0500 (EST)
Resent-Date: Sun, 15 Nov 1998 12:14:52 -0500 (EST)
Message-Id: <l03130300b274b74b8b5e@[194.252.64.55]>
Mime-Version: 1.0
Date: Sun, 15 Nov 1998 19:01:24 +0200
To: nih-image <nih-image@io.ece.drexel.edu>
From: Matti Haveri <mhaveri@walli.uwasa.fi>
Subject: Re: How to open DICOM with a given density range
Resent-Message-ID: <"T9U2B.0.xM1.ZZmJs"@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/623
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: 1027

>>How can I open DICOM images with a given Window/Level?
>>
>>I can do this with File/Import/Custom/Set/Fixed Scale -command but this
>>isn't practical because each DICOM file can have different Offset which
>>must be manually calculated.
>>
>>If I open DICOM with File/Import/DICOM then there seems to be no
>>possibility to open just a given density range? (I can adjust Brightness &
>>Contrast but the result is not pretty because the whole density range is
>>imported).
>
>Adjust brightness/contrast and then select Rescale (Revert), which
>re-imports the image using new window/level settings. You might also want
>to try Image/J (http://rsb.info.nih.gov/ij/), which imports DICOM files as
>16-bit images.

Oh, I see, but how can I rescale _several_ images to the same density range?

If I import 20 images as DICOM (Open all), choose windows to stack, adjust
brightness/contrast for one slice and try to Rescale I get an "File I/O
error".

--
Matti Haveri <mhaveri@walli.uwasa.fi>
<http://www.walli.uwasa.fi/~mhaveri/>



From nih-image-request@io.ece.drexel.edu Sun Nov 15 21:24 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id VAA28694;
	Sun, 15 Nov 1998 21:24:44 -0500 (EST)
Resent-Date: Sun, 15 Nov 1998 21:24:44 -0500 (EST)
Date: Sun, 15 Nov 1998 21:02:16 -0500 (EST)
From: nih-image-owner@io.ece.drexel.edu
Message-Id: <199811160202.VAA26171@io.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Resent-Message-ID: <"Mx5wQ1.0.3P6.gUuJs"@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/624
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1997

                   NIH-image Mailing List Help 

nih-image@biomed.drexel.edu   - Sends mail to the list
nih-image-request@biomed.drexel.edu   - Administation for List
nih-image-d-request@biomed.drexel.edu  - Aministration for Digest


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".

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


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

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

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

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 Mon Nov 16 06:15 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA23385;
	Mon, 16 Nov 1998 06:15:19 -0500 (EST)
Resent-Date: Mon, 16 Nov 1998 06:15:19 -0500 (EST)
Message-ID: <3650141B.1BEF@dv.kp.dlr.de>
Date: Mon, 16 Nov 1998 12:01:31 +0000
From: Stephan Sous <Stephan.Sous@dlr.de>
Organization: DLR
X-Mailer: Mozilla 3.01 [de] (Macintosh; I; 68K)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: ShowResults (read permission)
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"J4De03.0.5E5.RM0Ks"@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/625
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: 446

Hi Imagers,

I hope somebody can help.

I set the measurement options 'area, x-y-center', measure about 2500
particles. If the particles are bigger than 10 and smaller than 26
(pixel x pixel),I want to delete this particles from the image with the
aid of the x-y-position (auto-outline and so ...). 
If the ShowResults-window (file) is bigger than 1400 counts (entries), I
have no access (cannot read) to the higher entries. 

Yhanks in advance


From nih-image-d-request@io.ece.drexel.edu Mon Nov 16 06:22 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA24400;
	Mon, 16 Nov 1998 06:22:30 -0500 (EST)
Date: Mon, 16 Nov 1998 06:22:30 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811161122.GAA24400@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #116
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/116
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 6171

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 116

Today's Topics:
  Re: How to open DICOM with a given d  [ Matti Haveri <mhaveri@walli.uwasa.f ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
  Photoshop planes <-> NIH image stack  [ Peter Ahnelt <peter.ahnelt@univie.a ]
  ShowResults (read permission)         [ Stephan Sous <Stephan.Sous@dlr.de> ]

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

Date: Sun, 15 Nov 1998 19:01:24 +0200
From: Matti Haveri <mhaveri@walli.uwasa.fi>
To: nih-image <nih-image@io.ece.drexel.edu>
Subject: Re: How to open DICOM with a given density range
Message-Id: <l03130300b274b74b8b5e@[194.252.64.55]>
Content-Type: text/plain; charset="us-ascii"

>>How can I open DICOM images with a given Window/Level?
>>
>>I can do this with File/Import/Custom/Set/Fixed Scale -command but this
>>isn't practical because each DICOM file can have different Offset which
>>must be manually calculated.
>>
>>If I open DICOM with File/Import/DICOM then there seems to be no
>>possibility to open just a given density range? (I can adjust Brightness &
>>Contrast but the result is not pretty because the whole density range is
>>imported).
>
>Adjust brightness/contrast and then select Rescale (Revert), which
>re-imports the image using new window/level settings. You might also want
>to try Image/J (http://rsb.info.nih.gov/ij/), which imports DICOM files as
>16-bit images.

Oh, I see, but how can I rescale _several_ images to the same density range?

If I import 20 images as DICOM (Open all), choose windows to stack, adjust
brightness/contrast for one slice and try to Rescale I get an "File I/O
error".

--
Matti Haveri <mhaveri@walli.uwasa.fi>
<http://www.walli.uwasa.fi/~mhaveri/>

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

Date: Sun, 15 Nov 1998 21:02:16 -0500 (EST)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199811160202.VAA26171@io.ece.drexel.edu>

                   NIH-image Mailing List Help 

nih-image@biomed.drexel.edu   - Sends mail to the list
nih-image-request@biomed.drexel.edu   - Administation for List
nih-image-d-request@biomed.drexel.edu  - Aministration for Digest


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".

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


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

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

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

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, 16 Nov 1998 09:12:38 +0100
From: Peter Ahnelt <peter.ahnelt@univie.ac.at>
To: nih-image-d@io.ece.drexel.edu
Subject: Photoshop planes <-> NIH image stacks?
Message-Id: <l03130300b2758d8e7d74@[131.130.51.13]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Hello!

An obvious advantage of Photoshop is the versatility of its plane tools,
including color handling transparency modes etc..

NIH image on the other hand has lots of Macros ready for stack=plane
processing.

So:
Is there anybody out there who could write some conversion
to a) import PS-plane files as NIH-Stacks ?
b) export stacks as PS-plane files ?
c) export PS-planes as .TIF stack files importable by NIH ?

It might be even worthwhile to include this in the NIH import options.

Would be nice ...

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: Mon, 16 Nov 1998 12:01:31 +0000
From: Stephan Sous <Stephan.Sous@dlr.de>
To: nih-image@io.ece.drexel.edu
Subject: ShowResults (read permission)
Message-ID: <3650141B.1BEF@dv.kp.dlr.de>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi Imagers,

I hope somebody can help.

I set the measurement options 'area, x-y-center', measure about 2500
particles. If the particles are bigger than 10 and smaller than 26
(pixel x pixel),I want to delete this particles from the image with the
aid of the x-y-position (auto-outline and so ...). 
If the ShowResults-window (file) is bigger than 1400 counts (entries), I
have no access (cannot read) to the higher entries. 

Yhanks in advance

--------------------------------
End of nih-image-d Digest V98 Issue #116
****************************************

From nih-image-request@io.ece.drexel.edu Mon Nov 16 10:24 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA18552;
	Mon, 16 Nov 1998 10:24:47 -0500 (EST)
Resent-Date: Mon, 16 Nov 1998 10:24:47 -0500 (EST)
Message-Id: <l03130300b275e0f4d9a7@[192.98.93.254]>
In-Reply-To: <3.0.5.32.19981115164557.0082ae60@codon.nih.gov>
References: <l03130300b274b74b8b5e@[194.252.64.55]>
Mime-Version: 1.0
Date: Mon, 16 Nov 1998 17:00:33 +0200
To: nih-image@io.ece.drexel.edu
From: Matti Haveri <mhaveri@walli.uwasa.fi>
Subject: Re: How to open DICOM with a given density range
Resent-Message-ID: <"qLFvn2.0.Yt3.Sq3Ks"@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/626
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: 1384

>>Oh, I see, but how can I rescale _several_ images to the same density range?
>>
>>If I import 20 images as DICOM (Open all), choose windows to stack, adjust
>>brightness/contrast for one slice and try to Rescale I get an "File I/O
>>error".
>
>The Rescale command does not work with stacks. Acoording to the manual,
>when importing DICOMS using the "Open All" option, you can hold the shift
>key down to fix 16-bit to 8-bit scaling.

What I basically want to do is to open DICOM CT-slices to 1029-1099
densities (i.e. in Hounsfield units W/L 70/40).

It seems that the best way to accomplish this is to DICOM import the slices
with Shift down (fixed 16-bit to 8-bit scaling), then brightness/contrast
one image to 1029-1099 with the mouse, choose Options/Propagate/LUT and
Rescale each image separately?

Is it possible to adjust brightness/contrast numerically (it is impossible
to get exactly to right values via the mouse)?

What still I miss is the possibility to DICOM-import a selected density
range just like it is possible via Custom import/Fixed Scale. The problem
with Custom import is that the Offset may be different for each CT slice.
Custom import also doesn't automatically calibrate densities to Hounfield
units like DICOM import does (although the HU-info gets lost when
Rescaling).

--
Matti Haveri <mhaveri@walli.uwasa.fi>
<http://www.walli.uwasa.fi/~mhaveri/>



From nih-image-request@io.ece.drexel.edu Mon Nov 16 14:03 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA06718;
	Mon, 16 Nov 1998 14:03:22 -0500 (EST)
Resent-Date: Mon, 16 Nov 1998 14:03:22 -0500 (EST)
Date: Mon, 16 Nov 1998 10:41:15 -0800 (PST)
From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: Image and G3
In-Reply-To: <199811161120.GAA24063@io.ece.drexel.edu>
Message-ID: <Pine.SOL.3.95.981116104003.21960A-100000@protos.lifesci.ucla.edu>
MIME-Version: 1.0
Resent-Message-ID: <"adKSe3.0.xB1.H77Ks"@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/627
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: 496

Hi, 
can anyone tell me definitively if the ATI XClaim VR 4mb Rage II PCI
video in/out card will work with Image?

Thanks! All help is greatly appreciated!

Stephan


------------------------------
Stephan G. Anagnostaras, Ph.D. 
UCLA Depts. of Neurobiology         
           and Psychology      
stephan@lifesci.ucla.edu    
sanagnos@mediaone.net         
------------------------------
Work, CHS: (310) 794-6609
    Psych: (310) 794-5339
     Home: (310) 306-0294
--------------------------


From nih-image-request@io.ece.drexel.edu Tue Nov 17 01:18 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id BAA12000;
	Tue, 17 Nov 1998 01:18:04 -0500 (EST)
Resent-Date: Tue, 17 Nov 1998 01:18:04 -0500 (EST)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: Stephan.Sous@dlr.de, nih-image@io.ece.drexel.edu
Date:          Tue, 17 Nov 1998 16:48:51 GMT+1100
Subject:       Re: ShowResults (read permission)
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <22171922636@rna.bio.mq.edu.au>
Resent-Message-ID: <"yhS7p1.0.o02.rsGKs"@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/628
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1692

>Date: Mon, 16 Nov 1998 12:01:31 +0000
>From: Stephan Sous <Stephan.Sous@dlr.de>
>.......
>I set the measurement options 'area, x-y-center', measure about 2500
>particles. If the particles are bigger than 10 and smaller than 26
>(pixel x pixel),I want to delete this particles from the image with the
>aid of the x-y-position (auto-outline and so ...). 
>If the ShowResults-window (file) is bigger than 1400 counts (entries), I
>have no access (cannot read) to the higher entries. 
>
>....

Stephan,

NIH-Image uses Mac OS facilities to display text that are limited to 32K so that 
you cant display all characters of the results table but never-the-less the values 
are still in the results table (provided your MaxMeasurements is large enough; 
standard max results table size is/was 8000 measurements). Your macro code to 
access 
if (rArea[i]<10) or (rArea[i]>26) then begin
autoOutline(rX[i],rY[i]); 
getRoi(x,y,w,h); if w<>0 then fill else exit(concat('particle',i,' not found??');
end;
etc will still work

You can increase the number of Results table entries you can see by reducing 
characters per line eg by reducing precision or viewing 'area, x-y-center' 
alternatly rather than together.
A more effective way of viewing is to save results to disk and then open in an 
editor (such as bbedit) or spreadsheet (Xcell).

If your image has illshaped particles where the centroid rX[i],rY[i] falls outside 
the particle, then Object-Image has rLeft[i],rTop[i] in the Results table for this 
purpose.
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 Tue Nov 17 01:55 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id BAA16421;
	Tue, 17 Nov 1998 01:55:11 -0500 (EST)
Resent-Date: Tue, 17 Nov 1998 01:55:11 -0500 (EST)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: Stephan.Sous@dlr.de, nih-image@io.ece.drexel.edu
Date:          Tue, 17 Nov 1998 17:25:09 GMT+1100
Subject:       Re: ShowResults (read permission) (postscript)
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <2220C3A3CBC@rna.bio.mq.edu.au>
Resent-Message-ID: <"tchVQ2.0.933.fOHKs"@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/629
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1333

>Date: Mon, 16 Nov 1998 12:01:31 +0000
>From: Stephan Sous <Stephan.Sous@dlr.de>
>.....
>I set the measurement options 'area, x-y-center', measure about 2500
>particles. If the particles are bigger than 10 and smaller than 26
>(pixel x pixel),I want to delete this particles from the image with the
>aid of the x-y-position (auto-outline and so ...). 
>If the ShowResults-window (file) is bigger than 1400 counts (entries), I
>have no access (cannot read) to the higher entries. 
>
>....

What I should have also pointed out previously :-) :

You can also achieve your result by taking advantage of the coloring of the 
particles examined by analyzeParticles (to threshold-1 or lower-1)
and of the 'outline' option.

setParticleSize(10,26);
analyzeParticles('outline reset');
setThreshold(254);
analyzeParticles('outline include reset');

will result in the particles 10<=>26 being colored 254 and 
those originally thresholded or sliced but outside this size range 
being colored threshold-1.

 You can then use changeValues to convert the image to a binary mask for either 
counted or excluded particles to be applied to the original 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


From nih-image-d-request@io.ece.drexel.edu Tue Nov 17 01:55 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id BAA16610;
	Tue, 17 Nov 1998 01:55:51 -0500 (EST)
Date: Tue, 17 Nov 1998 01:55:51 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811170655.BAA16610@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #117
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/117
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 6582

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 117

Today's Topics:
  Re: How to open DICOM with a given d  [ Matti Haveri <mhaveri@walli.uwasa.f ]
  Image and G3                          [ Stephan Anagnostaras <stephan@proto ]
  Re: ShowResults (read permission)     [ GJOSS@rna.bio.mq.edu.au ]
  Re: ShowResults (read permission) (p  [ GJOSS@rna.bio.mq.edu.au ]

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

Date: Mon, 16 Nov 1998 17:00:33 +0200
From: Matti Haveri <mhaveri@walli.uwasa.fi>
To: nih-image@io.ece.drexel.edu
Subject: Re: How to open DICOM with a given density range
Message-Id: <l03130300b275e0f4d9a7@[192.98.93.254]>
Content-Type: text/plain; charset="us-ascii"

>>Oh, I see, but how can I rescale _several_ images to the same density range?
>>
>>If I import 20 images as DICOM (Open all), choose windows to stack, adjust
>>brightness/contrast for one slice and try to Rescale I get an "File I/O
>>error".
>
>The Rescale command does not work with stacks. Acoording to the manual,
>when importing DICOMS using the "Open All" option, you can hold the shift
>key down to fix 16-bit to 8-bit scaling.

What I basically want to do is to open DICOM CT-slices to 1029-1099
densities (i.e. in Hounsfield units W/L 70/40).

It seems that the best way to accomplish this is to DICOM import the slices
with Shift down (fixed 16-bit to 8-bit scaling), then brightness/contrast
one image to 1029-1099 with the mouse, choose Options/Propagate/LUT and
Rescale each image separately?

Is it possible to adjust brightness/contrast numerically (it is impossible
to get exactly to right values via the mouse)?

What still I miss is the possibility to DICOM-import a selected density
range just like it is possible via Custom import/Fixed Scale. The problem
with Custom import is that the Offset may be different for each CT slice.
Custom import also doesn't automatically calibrate densities to Hounfield
units like DICOM import does (although the HU-info gets lost when
Rescaling).

--
Matti Haveri <mhaveri@walli.uwasa.fi>
<http://www.walli.uwasa.fi/~mhaveri/>

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

Date: Mon, 16 Nov 1998 10:41:15 -0800 (PST)
From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: Image and G3
Message-ID: <Pine.SOL.3.95.981116104003.21960A-100000@protos.lifesci.ucla.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi, 
can anyone tell me definitively if the ATI XClaim VR 4mb Rage II PCI
video in/out card will work with Image?

Thanks! All help is greatly appreciated!

Stephan


- ----------------------------
Stephan G. Anagnostaras, Ph.D. 
UCLA Depts. of Neurobiology         
           and Psychology      
stephan@lifesci.ucla.edu    
sanagnos@mediaone.net         
- ----------------------------
Work, CHS: (310) 794-6609
    Psych: (310) 794-5339
     Home: (310) 306-0294
--------------------------

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

Date:          Tue, 17 Nov 1998 16:48:51 GMT+1100
From: GJOSS@rna.bio.mq.edu.au
To: Stephan.Sous@dlr.de, nih-image@io.ece.drexel.edu
Subject:       Re: ShowResults (read permission)
Message-ID: <22171922636@rna.bio.mq.edu.au>

>Date: Mon, 16 Nov 1998 12:01:31 +0000
>From: Stephan Sous <Stephan.Sous@dlr.de>
>.......
>I set the measurement options 'area, x-y-center', measure about 2500
>particles. If the particles are bigger than 10 and smaller than 26
>(pixel x pixel),I want to delete this particles from the image with the
>aid of the x-y-position (auto-outline and so ...). 
>If the ShowResults-window (file) is bigger than 1400 counts (entries), I
>have no access (cannot read) to the higher entries. 
>
>....

Stephan,

NIH-Image uses Mac OS facilities to display text that are limited to 32K so that 
you cant display all characters of the results table but never-the-less the values 
are still in the results table (provided your MaxMeasurements is large enough; 
standard max results table size is/was 8000 measurements). Your macro code to 
access 
if (rArea[i]<10) or (rArea[i]>26) then begin
autoOutline(rX[i],rY[i]); 
getRoi(x,y,w,h); if w<>0 then fill else exit(concat('particle',i,' not found??');
end;
etc will still work

You can increase the number of Results table entries you can see by reducing 
characters per line eg by reducing precision or viewing 'area, x-y-center' 
alternatly rather than together.
A more effective way of viewing is to save results to disk and then open in an 
editor (such as bbedit) or spreadsheet (Xcell).

If your image has illshaped particles where the centroid rX[i],rY[i] falls outside 
the particle, then Object-Image has rLeft[i],rTop[i] in the Results table for this 
purpose.
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, 17 Nov 1998 17:25:09 GMT+1100
From: GJOSS@rna.bio.mq.edu.au
To: Stephan.Sous@dlr.de, nih-image@io.ece.drexel.edu
Subject:       Re: ShowResults (read permission) (postscript)
Message-ID: <2220C3A3CBC@rna.bio.mq.edu.au>

>Date: Mon, 16 Nov 1998 12:01:31 +0000
>From: Stephan Sous <Stephan.Sous@dlr.de>
>.....
>I set the measurement options 'area, x-y-center', measure about 2500
>particles. If the particles are bigger than 10 and smaller than 26
>(pixel x pixel),I want to delete this particles from the image with the
>aid of the x-y-position (auto-outline and so ...). 
>If the ShowResults-window (file) is bigger than 1400 counts (entries), I
>have no access (cannot read) to the higher entries. 
>
>....

What I should have also pointed out previously :-) :

You can also achieve your result by taking advantage of the coloring of the 
particles examined by analyzeParticles (to threshold-1 or lower-1)
and of the 'outline' option.

setParticleSize(10,26);
analyzeParticles('outline reset');
setThreshold(254);
analyzeParticles('outline include reset');

will result in the particles 10<=>26 being colored 254 and 
those originally thresholded or sliced but outside this size range 
being colored threshold-1.

 You can then use changeValues to convert the image to a binary mask for either 
counted or excluded particles to be applied to the original 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

--------------------------------
End of nih-image-d Digest V98 Issue #117
****************************************

From nih-image-request@io.ece.drexel.edu Tue Nov 17 11:37 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA17380;
	Tue, 17 Nov 1998 11:37:11 -0500 (EST)
Resent-Date: Tue, 17 Nov 1998 11:37:11 -0500 (EST)
Mime-Version: 1.0
X-Sender: tmitchel@mail.med.upenn.edu (Unverified)
Message-Id: <v04020a00b2774e0cf45a@[130.91.204.125]>
Date: Tue, 17 Nov 1998 11:04:24 -0500
To: nih-image@io.ece.drexel.edu
From: "Thomas W. Mitchell, V.M.D., Ph.D." <tmitchel@mail.med.upenn.edu>
Subject: I/O error
Resent-Message-ID: <"yPzm51.0.3S3.IyPKs"@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/630
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: 829

This has been covered in this list server, and I did attempt to answer my
question using the available archives.  I have a macro for area analysis,
and when I am saving a flat field, I continually get the following error
message:

A File I/O error has occurred.  No such volume.  Result code = -35.

>From the zippy-obtained Systems error software, I know this is a volume
searching error.  To the best of my ability, I have tried to identify the
volume searching error, but no luck.  Any suggestions?

Tom


Thomas W. Mitchell, V.M.D., Ph.D.
Center for Neurodegenerative Disease Research
University of Pennsylvania School of Medicine
Department of Pathology and Laboratory Medicine
3600 Spruce Street - 3rd Floor Maloney
Philadelphia, PA  19104

Phone:	215-573-3258 (-2840)
FAX:	215-349-5909
email:	tmitchel@mail.med.upenn.edu


From nih-image-request@io.ece.drexel.edu Tue Nov 17 15:25 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA14450;
	Tue, 17 Nov 1998 15:25:02 -0500 (EST)
Resent-Date: Tue, 17 Nov 1998 15:25:02 -0500 (EST)
Date: Tue, 17 Nov 1998 11:36:01 -0800 (PST)
From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: Iomega Buz works with Image in a G3
In-Reply-To: <199811170648.BAA15502@io.ece.drexel.edu>
Message-ID: <Pine.SOL.3.95.981117112904.20136A-100000@protos.lifesci.ucla.edu>
MIME-Version: 1.0
Resent-Message-ID: <"kuLMc3.0.Tx1.g0TKs"@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/631
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: 1077

Hello all,

Just thought I would update you on my search for a cheap digitizer to work
with Image on a G3.  As we know, the G3 built in digitizer does not work.
Also, I didn't end up trying the ATI card, because it only supports
320x240. Well, I came across the Buz, and I thought what the heck.

Well, the good news is that it works fine with Image on the G3. it
supports 720 x 480 and cost me $259. Also it has some other goodies which
may be useful in other work, as it has on the fly MPEG compression and a
high-speed SCSI port on it as well for capturing directly to a jaz or zip.
of course, the usual caveats about cheap frame grabbers apply (i.e.gain
control, etc) but for what we are using it for those aren't a problem.

Cheers,
Stephan


------------------------------
Stephan G. Anagnostaras, Ph.D. 
UCLA Depts. of Neurobiology         
           and Psychology      
stephan@lifesci.ucla.edu    
sanagnos@mediaone.net         
------------------------------
Work, CHS: (310) 794-6609
    Psych: (310) 794-5339
     Home: (310) 306-0294
--------------------------


From nih-image-request@io.ece.drexel.edu Tue Nov 17 15:43 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA16309;
	Tue, 17 Nov 1998 15:43:23 -0500 (EST)
Resent-Date: Tue, 17 Nov 1998 15:43:23 -0500 (EST)
X-Authentication-Warning: umbc7.umbc.edu: lei owned process doing -bs
Date: Tue, 17 Nov 1998 14:58:39 -0500 (EST)
From: "Dr. Tianhu Lei; MEDIC-UMAB" <lei@umbc.edu>
To: nih-image@io.ece.drexel.edu
Subject: gray level setting
Message-ID: <Pine.SGI.3.96A.981117145148.21538A-100000@umbc7.umbc.edu>
MIME-Version: 1.0
Resent-Message-ID: <"Pl-2F.0.Ok2.rPTKs"@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/632
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: 365


Dear Sir/Madam:

My laptop computer can only display image with 16 gray levels.
When I open NIH Image, I always get the following message:

	To run image, the main monitor must be set to 
	256 colors or 256 gray levels.

Can I change gray level setting of NIH Image (from 256 to 16) 
such that I can use it in my laptop computer (Powerbook 180)?

Thanks.

T. Lei


From nih-image-request@io.ece.drexel.edu Tue Nov 17 16:41 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA22218;
	Tue, 17 Nov 1998 16:41:08 -0500 (EST)
Resent-Date: Tue, 17 Nov 1998 16:41:08 -0500 (EST)
Message-Id: <l03010d02b277a14d9993@[212.238.25.42]>
In-Reply-To: <Pine.SGI.3.96A.981117145148.21538A-100000@umbc7.umbc.edu>
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: gray level setting
Date: Tue, 17 Nov 1998 20:56:49 +0000
Resent-Message-ID: <"LwxpC.0._I4.nCUKs"@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/633
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: 518

>Dear Sir/Madam:
>
>My laptop computer can only display image with 16 gray levels.
>When I open NIH Image, I always get the following message:
>
>	To run image, the main monitor must be set to
>	256 colors or 256 gray levels.
>
>Can I change gray level setting of NIH Image (from 256 to 16)
>such that I can use it in my laptop computer (Powerbook 180)?
>
>Thanks.
>
>T. Lei

Do you use an old version of Image? Newer versions even run on older
Powerbooks like the PB140, which has only black and white.

N. Vischer



From nih-image-request@io.ece.drexel.edu Tue Nov 17 18:18 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA02387;
	Tue, 17 Nov 1998 18:18:58 -0500 (EST)
Resent-Date: Tue, 17 Nov 1998 18:18:58 -0500 (EST)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: tmitchel@mail.med.upenn.edu, nih-image@io.ece.drexel.edu
Date:          Wed, 18 Nov 1998 9:41:35 GMT+1100
Subject:       Re: I/O error
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <23253CB7CE3@rna.bio.mq.edu.au>
Resent-Message-ID: <"f2cuH2.0.co6.whVKs"@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/634
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 2118

>Date: Tue, 17 Nov 1998 11:04:24 -0500
>To: nih-image@io.ece.drexel.edu
>From: "Thomas W. Mitchell, V.M.D., Ph.D." <tmitchel@mail.med.upenn.edu>
>
>This has been covered in this list server, and I did attempt to answer my
>question using the available archives.  I have a macro for area analysis,
>and when I am saving a flat field, I continually get the following error
>message:
>
>A File I/O error has occurred.  No such volume.  Result code = -35.
>
>From the zippy-obtained Systems error software, I know this is a volume
>searching error.  To the best of my ability, I have tried to identify the
>volume searching error, but no luck.  Any suggestions?
>
>Tom
>
>
>Thomas W. Mitchell, V.M.D., Ph.D.
>Center for Neurodegenerative Disease Research
>University of Pennsylvania School of Medicine
>Department of Pathology and Laboratory Medicine
>3600 Spruce Street - 3rd Floor Maloney
>Philadelphia, PA  19104
>
>Phone:	215-573-3258 (-2840)
>FAX:	215-349-5909
>email:	tmitchel@mail.med.upenn.edu
>
Tom, you didn't give much info on macro code but my guess would be that the 'name' 
you are attempting to save has included a colon ':' so that Image is treating it as 
a fully qualified name and searching for a volume.

>From Object-Image help:
SaveAs('name')
  Saves the current image using the specified file name.
  Use SetSave to specify the format. Uses the window
  title as the file name when saving a text file or if
  SaveAs is used with no argument. When saving images,
  the dialog box should only be displayed the first time
  SaveAs is called within a macro. For both image and
  text windows, 'name' can be a full folder path (e.g.,
  'HD400:Images:MyImage'). In this case, no dialog box is
  displayed.

eg 
macro'/0test';begin SaveAs('name:suffix'); end

fails with exactly that message because it is looking for a drive called 'name' on 
which to save 'suffix'.

You cannot have imbedded colons in a filename.





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 Tue Nov 17 18:44 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA05724;
	Tue, 17 Nov 1998 18:44:18 -0500 (EST)
Resent-Date: Tue, 17 Nov 1998 18:44:18 -0500 (EST)
X-Sender: jayers@pop.dac.neu.edu
Message-Id: <l03102802b277af7ad2e9@[129.10.11.90]>
Mime-Version: 1.0
Date: Tue, 17 Nov 1998 17:57:54 -0500
To: nih-image@io.ece.drexel.edu
From: Joseph Ayers <lobster@neu.edu>
Subject: MacOS Scientific Software Petition
Resent-Message-ID: <"Vxljc3.0.x4.30WKs"@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/635
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: 341

Check out the:

MacOS Scientific Software Petition  at:

http://members.aol.com/mattspete/


Joseph Ayers, Director
Marine Science Center
Northeastern University
East Point, Nahant, MA 01908
(781) 581-7370 (office), (781) 581-6076 (fax)
(781) 586-9128 (lab), (617) 755-7523 (cellular)
Internet: lobster@neu.edu
http://www.dac.neu.edu/msc/



From nih-image-request@io.ece.drexel.edu Tue Nov 17 21:25 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id VAA23085;
	Tue, 17 Nov 1998 21:25:38 -0500 (EST)
Resent-Date: Tue, 17 Nov 1998 21:25:38 -0500 (EST)
Date: Wed, 18 Nov 1998 11:59:48 +1000 (EST)
Message-Id: <199811180159.LAA01755@topaz.cqu.edu.au>
X-Sender: mccannc@topaz.cqu.edu.au
X-Mailer: Windows Eudora Light Version 1.5.2
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
From: Cormac <mccannc@topaz.cqu.edu.au>
Subject: THANKSALOT!
Resent-Message-ID: <"AGTfM.0.H_4.YeYKs"@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/636
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: 304

This is just a quick note to thank all those who replied to my queries and
questions over the last semester as it really helped me out.  I have
finished my stint at Uni and can now become a professional bum with an
engineering degree.

Cormac McCann
Mechanical Engineering student, CQU, QLD, Australia.


From nih-image-d-request@io.ece.drexel.edu Wed Nov 18 06:33 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA20470;
	Wed, 18 Nov 1998 06:33:28 -0500 (EST)
Date: Wed, 18 Nov 1998 06:33:28 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811181133.GAA20470@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #118
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/118
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 8324

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 118

Today's Topics:
  I/O error                             [ "Thomas W. Mitchell, V.M.D., Ph.D." ]
  Iomega Buz works with Image in a G3   [ Stephan Anagnostaras <stephan@proto ]
  gray level setting                    [ "Dr. Tianhu Lei; MEDIC-UMAB" <lei@u ]
  Re: gray level setting                [ Norbert Vischer <vischer@bio.uva.nl ]
  Re: I/O error                         [ GJOSS@rna.bio.mq.edu.au ]
  MacOS Scientific Software Petition    [ Joseph Ayers <lobster@neu.edu> ]
  THANKSALOT!                           [ Cormac <mccannc@topaz.cqu.edu.au> ]

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

Date: Tue, 17 Nov 1998 11:04:24 -0500
From: "Thomas W. Mitchell, V.M.D., Ph.D." <tmitchel@mail.med.upenn.edu>
To: nih-image@io.ece.drexel.edu
Subject: I/O error
Message-Id: <v04020a00b2774e0cf45a@[130.91.204.125]>
Content-Type: text/plain; charset="us-ascii"

This has been covered in this list server, and I did attempt to answer my
question using the available archives.  I have a macro for area analysis,
and when I am saving a flat field, I continually get the following error
message:

A File I/O error has occurred.  No such volume.  Result code = -35.

>From the zippy-obtained Systems error software, I know this is a volume
searching error.  To the best of my ability, I have tried to identify the
volume searching error, but no luck.  Any suggestions?

Tom


Thomas W. Mitchell, V.M.D., Ph.D.
Center for Neurodegenerative Disease Research
University of Pennsylvania School of Medicine
Department of Pathology and Laboratory Medicine
3600 Spruce Street - 3rd Floor Maloney
Philadelphia, PA  19104

Phone:	215-573-3258 (-2840)
FAX:	215-349-5909
email:	tmitchel@mail.med.upenn.edu

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

Date: Tue, 17 Nov 1998 11:36:01 -0800 (PST)
From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: Iomega Buz works with Image in a G3
Message-ID: <Pine.SOL.3.95.981117112904.20136A-100000@protos.lifesci.ucla.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hello all,

Just thought I would update you on my search for a cheap digitizer to work
with Image on a G3.  As we know, the G3 built in digitizer does not work.
Also, I didn't end up trying the ATI card, because it only supports
320x240. Well, I came across the Buz, and I thought what the heck.

Well, the good news is that it works fine with Image on the G3. it
supports 720 x 480 and cost me $259. Also it has some other goodies which
may be useful in other work, as it has on the fly MPEG compression and a
high-speed SCSI port on it as well for capturing directly to a jaz or zip.
of course, the usual caveats about cheap frame grabbers apply (i.e.gain
control, etc) but for what we are using it for those aren't a problem.

Cheers,
Stephan


- ----------------------------
Stephan G. Anagnostaras, Ph.D. 
UCLA Depts. of Neurobiology         
           and Psychology      
stephan@lifesci.ucla.edu    
sanagnos@mediaone.net         
- ----------------------------
Work, CHS: (310) 794-6609
    Psych: (310) 794-5339
     Home: (310) 306-0294
--------------------------

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

Date: Tue, 17 Nov 1998 14:58:39 -0500 (EST)
From: "Dr. Tianhu Lei; MEDIC-UMAB" <lei@umbc.edu>
To: nih-image@io.ece.drexel.edu
Subject: gray level setting
Message-ID: <Pine.SGI.3.96A.981117145148.21538A-100000@umbc7.umbc.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear Sir/Madam:

My laptop computer can only display image with 16 gray levels.
When I open NIH Image, I always get the following message:

	To run image, the main monitor must be set to 
	256 colors or 256 gray levels.

Can I change gray level setting of NIH Image (from 256 to 16) 
such that I can use it in my laptop computer (Powerbook 180)?

Thanks.

T. Lei

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

Date: Tue, 17 Nov 1998 20:56:49 +0000
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: gray level setting
Message-Id: <l03010d02b277a14d9993@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

>Dear Sir/Madam:
>
>My laptop computer can only display image with 16 gray levels.
>When I open NIH Image, I always get the following message:
>
>	To run image, the main monitor must be set to
>	256 colors or 256 gray levels.
>
>Can I change gray level setting of NIH Image (from 256 to 16)
>such that I can use it in my laptop computer (Powerbook 180)?
>
>Thanks.
>
>T. Lei

Do you use an old version of Image? Newer versions even run on older
Powerbooks like the PB140, which has only black and white.

N. Vischer

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

Date:          Wed, 18 Nov 1998 9:41:35 GMT+1100
From: GJOSS@rna.bio.mq.edu.au
To: tmitchel@mail.med.upenn.edu, nih-image@io.ece.drexel.edu
Subject:       Re: I/O error
Message-ID: <23253CB7CE3@rna.bio.mq.edu.au>

>Date: Tue, 17 Nov 1998 11:04:24 -0500
>To: nih-image@io.ece.drexel.edu
>From: "Thomas W. Mitchell, V.M.D., Ph.D." <tmitchel@mail.med.upenn.edu>
>
>This has been covered in this list server, and I did attempt to answer my
>question using the available archives.  I have a macro for area analysis,
>and when I am saving a flat field, I continually get the following error
>message:
>
>A File I/O error has occurred.  No such volume.  Result code = -35.
>
>From the zippy-obtained Systems error software, I know this is a volume
>searching error.  To the best of my ability, I have tried to identify the
>volume searching error, but no luck.  Any suggestions?
>
>Tom
>
>
>Thomas W. Mitchell, V.M.D., Ph.D.
>Center for Neurodegenerative Disease Research
>University of Pennsylvania School of Medicine
>Department of Pathology and Laboratory Medicine
>3600 Spruce Street - 3rd Floor Maloney
>Philadelphia, PA  19104
>
>Phone:	215-573-3258 (-2840)
>FAX:	215-349-5909
>email:	tmitchel@mail.med.upenn.edu
>
Tom, you didn't give much info on macro code but my guess would be that the 'name' 
you are attempting to save has included a colon ':' so that Image is treating it as 
a fully qualified name and searching for a volume.

>From Object-Image help:
SaveAs('name')
  Saves the current image using the specified file name.
  Use SetSave to specify the format. Uses the window
  title as the file name when saving a text file or if
  SaveAs is used with no argument. When saving images,
  the dialog box should only be displayed the first time
  SaveAs is called within a macro. For both image and
  text windows, 'name' can be a full folder path (e.g.,
  'HD400:Images:MyImage'). In this case, no dialog box is
  displayed.

eg 
macro'/0test';begin SaveAs('name:suffix'); end

fails with exactly that message because it is looking for a drive called 'name' on 
which to save 'suffix'.

You cannot have imbedded colons in a filename.





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, 17 Nov 1998 17:57:54 -0500
From: Joseph Ayers <lobster@neu.edu>
To: nih-image@io.ece.drexel.edu
Subject: MacOS Scientific Software Petition
Message-Id: <l03102802b277af7ad2e9@[129.10.11.90]>
Content-Type: text/plain; charset="us-ascii"

Check out the:

MacOS Scientific Software Petition  at:

http://members.aol.com/mattspete/


Joseph Ayers, Director
Marine Science Center
Northeastern University
East Point, Nahant, MA 01908
(781) 581-7370 (office), (781) 581-6076 (fax)
(781) 586-9128 (lab), (617) 755-7523 (cellular)
Internet: lobster@neu.edu
http://www.dac.neu.edu/msc/

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

Date: Wed, 18 Nov 1998 11:59:48 +1000 (EST)
From: Cormac <mccannc@topaz.cqu.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: THANKSALOT!
Message-Id: <199811180159.LAA01755@topaz.cqu.edu.au>
Content-Type: text/plain; charset="us-ascii"

This is just a quick note to thank all those who replied to my queries and
questions over the last semester as it really helped me out.  I have
finished my stint at Uni and can now become a professional bum with an
engineering degree.

Cormac McCann
Mechanical Engineering student, CQU, QLD, Australia.

--------------------------------
End of nih-image-d Digest V98 Issue #118
****************************************

From nih-image-request@io.ece.drexel.edu Wed Nov 18 07:49 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id HAA28889;
	Wed, 18 Nov 1998 07:49:08 -0500 (EST)
Resent-Date: Wed, 18 Nov 1998 07:49:08 -0500 (EST)
X-Sender: steinr@pop.chembio.ntnu.no
Message-Id: <v0310283fb2786a1bfa36@[129.241.39.133]>
Mime-Version: 1.0
Date: Wed, 18 Nov 1998 14:30:08 +0200
To: nih-image@io.ece.drexel.edu
From: Stein Roervik <steinr@chembio.ntnu.no>
Subject: Microscope recommendations wanted
Resent-Message-ID: <"twIGu2.0.8R6.vqhKs"@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/637
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: 1531

I am looking for a microscope which is to be used for measuring reflectance
in a metallic material according to an ASTM standard. The microscope must
meet the following criteria:

- using reflective lighting (the samples to be examined are non-transparent)
- XY-stage interchangable with a stage that rotates around the image center,
  or preferrably these two combined if that is possible
- connection possibilities for a photometer with accuracy as high as 0.01 %
- an inverted model is preferred but not mandatory

I have been in contact with the standard microscope suppliers (Zeiss,
Leica, Nikon, Olympus) but none seem to be able to supply a model that
combines all desired functionality. The budget is around $75 000, which
should be high enough to not be the limiting factor.

Regarding photometers, are digital models accurate enough ?
Can a good digital camera be used, or will non-linearity be a problem ?
The photometer must be able to measure accurately as little as 0.5 %
reflectance. I guess we need some photomultiplier or similar.

+---------------------------------------------------------+
|  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 Wed Nov 18 08:15 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA02115;
	Wed, 18 Nov 1998 08:15:54 -0500 (EST)
Resent-Date: Wed, 18 Nov 1998 08:15:54 -0500 (EST)
Message-ID: <3652C321.A91D1CEB@soton.ac.uk>
Date: Wed, 18 Nov 1998 12:52:44 +0000
From: Ashley Pringle <akp1@soton.ac.uk>
Organization: Clinical Neurological Sciences
X-Mailer: Mozilla 4.05 (Macintosh; I; PPC)
MIME-Version: 1.0
To: NIH Image mailing list <nih-image@io.ece.drexel.edu>
Subject: Scale-to-fit window
Resent-Message-ID: <"tlBWI2.0.Y.nIiKs"@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/638
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: multipart/alternative; boundary="------------262519205C0D6E9DD1B31CC7"
Content-Length: 1790


--------------262519205C0D6E9DD1B31CC7
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Dear Imagers

Hopefully this is a nice easy question to answer.  I need to write a
macro to run on several Macs with different monitor resolutions.  At the
moment, all our analysis is done manually, using the scale to fit window
command from the option menu - which rescales differently dpending on
the monitor resolution.  I cannot find a macro-command that correlates
to this function, and was wondering what the easiest way round the
problem would be.

Thanks in advance

Ash

Dr Ashley Pringle
Research Fellow
Dept Clinical Neurological Sciences
University of Southampton
Southampton General Hospital
Tremona Rd, Southampton SO16 6YD UK

Tel: +44 (0)1703 794875
email: akp1@soton.ac.uk


--------------262519205C0D6E9DD1B31CC7
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<HTML>
Dear Imagers

<P>Hopefully this is a nice easy question to answer.&nbsp; I need to write
a macro to run on several Macs with different monitor resolutions.&nbsp;
At the moment, all our analysis is done manually, using the scale to fit
window command from the option menu - which rescales differently dpending
on the monitor resolution.&nbsp; I cannot find a macro-command that correlates
to this function, and was wondering what the easiest way round the problem
would be.

<P>Thanks in advance

<P>Ash

<P><B>Dr Ashley Pringle</B>
<BR>Research Fellow
<BR>Dept Clinical Neurological Sciences
<BR>University of Southampton
<BR>Southampton General Hospital
<BR>Tremona Rd, Southampton SO16 6YD UK

<P>Tel: +44 (0)1703 794875
<BR>email: akp1@soton.ac.uk
<BR>&nbsp;</HTML>

--------------262519205C0D6E9DD1B31CC7--


From nih-image-request@io.ece.drexel.edu Wed Nov 18 10:02 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA13523;
	Wed, 18 Nov 1998 10:02:58 -0500 (EST)
Resent-Date: Wed, 18 Nov 1998 10:02:58 -0500 (EST)
Message-ID: <c=US%a=_%p=Indiana_Universi%l=PYRITE-981118143753Z-4477@pyrite.igs.indiana.edu>
From: "Barwood, Henry" <hbarwood@pyrite.igs.indiana.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Macro for Mac or PC?
Date: Wed, 18 Nov 1998 09:37:53 -0500
X-Mailer:  Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63
Encoding: 6 TEXT
Resent-Message-ID: <"-L4MU1.0.oS2.FhjKs"@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/639
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 240

I'm curious is a macro written for the Mac version of Image will work on
either the Java or Scion PC version as well? If not, is there a way to
convert macros so that they are interchangeable? TIA.

Henry Barwood
Indiana Geological Survey


From nih-image-request@io.ece.drexel.edu Wed Nov 18 10:08 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA14271;
	Wed, 18 Nov 1998 10:08:50 -0500 (EST)
Resent-Date: Wed, 18 Nov 1998 10:08:50 -0500 (EST)
Message-ID: <3652960E.FF1A44DC@maine.rr.com>
Date: Wed, 18 Nov 1998 09:40:30 +0000
From: Marcia Goldfarb <anatekep@maine.rr.com>
X-Mailer: Mozilla 4.5 (Macintosh; I; PPC)
MIME-Version: 1.0
To: Nih-image <nih-image@io.ece.drexel.edu>
Subject: list
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"y82Sz3.0.Cg2._njKs"@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/640
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: 247

I have not received any mail from the list  for 2 weeks. Have I been
accidently cut off? or is the list no longer functioning? Do I need to
subscribe again?

Marcia Goldfarb

Anatek-EP
17 Bishop St
Portland,ME 04103

email: anatekep@maine.rr.com


From nih-image-request@io.ece.drexel.edu Wed Nov 18 10:17 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA15346;
	Wed, 18 Nov 1998 10:17:16 -0500 (EST)
Resent-Date: Wed, 18 Nov 1998 10:17:16 -0500 (EST)
X-Authentication-Warning: mail.bio.uva.nl: Host gold.bio.uva.nl [145.18.160.48] claimed to be [145.18.160.48]
Message-Id: <l03110702b2787f5555a9@[145.18.160.48]>
In-Reply-To: <3652C321.A91D1CEB@soton.ac.uk>
Mime-Version: 1.0
Date: Wed, 18 Nov 1998 15:55:25 +0100
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Scale-to-fit window
Resent-Message-ID: <"4p0W2.0.Jx2.0xjKs"@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/641
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: 1295


Ash,

a few additional zooming features can be found in Object-Image:

Zoom(factor, top, left)
  zooms the window by factor 1, 2, 3, 4, 8, 16, 32 or 64.
  The pixel addressed by (top, left) will appear at top left
  in the zoomed window. Zoom(0, 0, 0) performs 'fit window
  to screen and fit entire image into window'.

MoveWindow(x, y, width, height)
  Moves current window to global screen coordinates x, y.
  Width and  height (optional) control the window size.
  Moving is ignored if x = y = 0.

Another feature is the 'Quick ZoomOut feature':
press simultaneously the command key and space bar. A temporary
"fit-to-screen" is performed. In the overview, the normally visible field
is shown as frame and can be dragged to a different position of interest.
The zooming factor can be changed with a pop-up menu. Then, release the two
keys, and the window will show the new field at the desired magnification.
You can synchronously zoom tiled windows when including the option key.


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 Nov 18 10:57 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA19805;
	Wed, 18 Nov 1998 10:57:24 -0500 (EST)
Resent-Date: Wed, 18 Nov 1998 10:57:24 -0500 (EST)
Message-Id: <D209047D0257D21191770000F8C991D904C846@mante35a.nam.dow.com>
From: "Heeschen, Bill (WA)" <WAHEESCHEN@dow.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Macro for Mac or PC?
Date: Wed, 18 Nov 1998 10:16:40 -0500
Mime-Version: 1.0
X-Mailer: Internet Mail Service (5.5.1960.3)
Resent-Message-ID: <"JjfHr2.0.Lk3.lJkKs"@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/642
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 1154

I have had reasonably good luck moving macros between NIH Image  and
Scion Image.  There are some interesting problems which I have discussed
with Scion and they plan to fix.  Some of the less-common routines are
still not implemented in a "bulletproof" manner (like watershed
segmentation), but most things are working.  For me, the biggest problem
right now is that variable names cannot be re-declared in called
subroutines.  For example, I like to use i,j,k as local counters, so
they get declared in almost every macro and subroutine.  When they have
been declared in the macro, then declared again in a called subroutine,
unexpected results can occur, especially when the subroutine is called
within a DO loop.  This is contrary to regular Pascal and they plan to
fix it in their first full release (remember that they are at beta 3
right now).  There are also some platform specific differences, like the
serial port calls.

Best suggestion is to simply load them and run on disposable images -
don't start doing real work until you know your macros are performing as
expected.

Good luck,
Bill Heeschen
Microscopy group
The Dow Chemical Company


From nih-image-request@io.ece.drexel.edu Wed Nov 18 18:19 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA27722;
	Wed, 18 Nov 1998 18:19:50 -0500 (EST)
Resent-Date: Wed, 18 Nov 1998 18:19:50 -0500 (EST)
Date: Wed, 18 Nov 1998 16:32:56 -0600 (CST)
From: Steve Eglen <eglen@thalamus.wustl.edu>
Message-Id: <199811182232.QAA21749@thalamus.wustl.edu>
To: nih-image@io.ece.drexel.edu
Subject: How do you open an image in macro with Keep LUT checked?
Resent-Message-ID: <"fnMRi3.0.ya5.HeqKs"@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/643
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 709

[using version 1.58b30]

Hi,

I have a set of PICT files that I'd like to make into a stack.  The manual
tells me that I should check the `keep LUT' item to remap the pixel values.
This works fine when I open the images one by one `by hand'.  When
writing a macro however, what is the command to set this option before using
the Open('File') macro?

Thanks in advance for any help,
Stephen Eglen

PS.  is there a broken link in the macro pages?  If I go to
http://rsb.info.nih.gov/nih-image/more-docs/macros.html
and then try to click on `Input/Output Macros' I get the
following error:

Could not open 
ftp://codon.nih.gov/pub/nih-image/macros/Input%2fOutput%20Macros.txt.

(This was under both IE 4 and 2)


From nih-image-request@io.ece.drexel.edu Thu Nov 19 04:22 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA05063;
	Thu, 19 Nov 1998 04:22:49 -0500 (EST)
Resent-Date: Thu, 19 Nov 1998 04:22:49 -0500 (EST)
Date: 	Thu, 19 Nov 1998 10:06:27 +0100 (CET)
From: Gary Chinga <gary@nvg.ntnu.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Re: Macro for Mac or PC?
In-Reply-To: <c=US%a=_%p=Indiana_Universi%l=PYRITE-981118143753Z-4477@pyrite.igs.indiana.edu>
Message-ID: <Pine.NEB.4.05.9811191002470.1583-100000@flode.nvg.ntnu.no>
MIME-Version: 1.0
Resent-Message-ID: <"xl1IG3.0.1i.W_zKs"@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/644
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: 469


I used to write my macroes at home in my Mac and then use them in a PC (at
Work). I have not found any problems yet.  any problems yet.


Gary.
NTNU-Trondheim
Norway.


On Wed, 18 Nov 1998, Barwood, Henry wrote:

> I'm curious is a macro written for the Mac version of Image will work on
> either the Java or Scion PC version as well? If not, is there a way to
> convert macros so that they are interchangeable? TIA.
> 
> Henry Barwood
> Indiana Geological Survey
> 


From nih-image-d-request@io.ece.drexel.edu Thu Nov 19 04:26 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA05661;
	Thu, 19 Nov 1998 04:26:40 -0500 (EST)
Date: Thu, 19 Nov 1998 04:26:40 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811190926.EAA05661@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #119
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/119
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 11927

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 119

Today's Topics:
  Microscope recommendations wanted     [ Stein Roervik <steinr@chembio.ntnu. ]
  Scale-to-fit window                   [ Ashley Pringle <akp1@soton.ac.uk> ]
  Macro for Mac or PC?                  [ "Barwood, Henry" <hbarwood@pyrite.i ]
  list                                  [ Marcia Goldfarb <anatekep@maine.rr. ]
  Re: Scale-to-fit window               [ Norbert Vischer <vischer@bio.uva.nl ]
  RE: Macro for Mac or PC?              [ "Heeschen, Bill (WA)" <WAHEESCHEN@d ]
  Animation or rotating 3D object from  [ "Mehmet Dondurur, Ph. D." <mehmet.d ]
  How do you open an image in macro wi  [ Steve Eglen <eglen@thalamus.wustl.e ]
  Re: Macro for Mac or PC?              [ Gary Chinga <gary@nvg.ntnu.no> ]

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

Date: Wed, 18 Nov 1998 14:30:08 +0200
From: Stein Roervik <steinr@chembio.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Microscope recommendations wanted
Message-Id: <v0310283fb2786a1bfa36@[129.241.39.133]>
Content-Type: text/plain; charset="us-ascii"

I am looking for a microscope which is to be used for measuring reflectance
in a metallic material according to an ASTM standard. The microscope must
meet the following criteria:

- using reflective lighting (the samples to be examined are non-transparent)
- XY-stage interchangable with a stage that rotates around the image center,
  or preferrably these two combined if that is possible
- connection possibilities for a photometer with accuracy as high as 0.01 %
- an inverted model is preferred but not mandatory

I have been in contact with the standard microscope suppliers (Zeiss,
Leica, Nikon, Olympus) but none seem to be able to supply a model that
combines all desired functionality. The budget is around $75 000, which
should be high enough to not be the limiting factor.

Regarding photometers, are digital models accurate enough ?
Can a good digital camera be used, or will non-linearity be a problem ?
The photometer must be able to measure accurately as little as 0.5 %
reflectance. I guess we need some photomultiplier or similar.

+---------------------------------------------------------+
|  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: Wed, 18 Nov 1998 12:52:44 +0000
From: Ashley Pringle <akp1@soton.ac.uk>
To: NIH Image mailing list <nih-image@io.ece.drexel.edu>
Subject: Scale-to-fit window
Message-ID: <3652C321.A91D1CEB@soton.ac.uk>
Content-Type: multipart/alternative; boundary="------------262519205C0D6E9DD1B31CC7"

--------------262519205C0D6E9DD1B31CC7
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Dear Imagers

Hopefully this is a nice easy question to answer.  I need to write a
macro to run on several Macs with different monitor resolutions.  At the
moment, all our analysis is done manually, using the scale to fit window
command from the option menu - which rescales differently dpending on
the monitor resolution.  I cannot find a macro-command that correlates
to this function, and was wondering what the easiest way round the
problem would be.

Thanks in advance

Ash

Dr Ashley Pringle
Research Fellow
Dept Clinical Neurological Sciences
University of Southampton
Southampton General Hospital
Tremona Rd, Southampton SO16 6YD UK

Tel: +44 (0)1703 794875
email: akp1@soton.ac.uk


--------------262519205C0D6E9DD1B31CC7
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<HTML>
Dear Imagers

<P>Hopefully this is a nice easy question to answer.&nbsp; I need to write
a macro to run on several Macs with different monitor resolutions.&nbsp;
At the moment, all our analysis is done manually, using the scale to fit
window command from the option menu - which rescales differently dpending
on the monitor resolution.&nbsp; I cannot find a macro-command that correlates
to this function, and was wondering what the easiest way round the problem
would be.

<P>Thanks in advance

<P>Ash

<P><B>Dr Ashley Pringle</B>
<BR>Research Fellow
<BR>Dept Clinical Neurological Sciences
<BR>University of Southampton
<BR>Southampton General Hospital
<BR>Tremona Rd, Southampton SO16 6YD UK

<P>Tel: +44 (0)1703 794875
<BR>email: akp1@soton.ac.uk
<BR>&nbsp;</HTML>

--------------262519205C0D6E9DD1B31CC7--

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

Date: Wed, 18 Nov 1998 09:37:53 -0500
From: "Barwood, Henry" <hbarwood@pyrite.igs.indiana.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Macro for Mac or PC?
Message-ID: <c=US%a=_%p=Indiana_Universi%l=PYRITE-981118143753Z-4477@pyrite.igs.indiana.edu>

I'm curious is a macro written for the Mac version of Image will work on
either the Java or Scion PC version as well? If not, is there a way to
convert macros so that they are interchangeable? TIA.

Henry Barwood
Indiana Geological Survey

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

Date: Wed, 18 Nov 1998 09:40:30 +0000
From: Marcia Goldfarb <anatekep@maine.rr.com>
To: Nih-image <nih-image@io.ece.drexel.edu>
Subject: list
Message-ID: <3652960E.FF1A44DC@maine.rr.com>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

I have not received any mail from the list  for 2 weeks. Have I been
accidently cut off? or is the list no longer functioning? Do I need to
subscribe again?

Marcia Goldfarb

Anatek-EP
17 Bishop St
Portland,ME 04103

email: anatekep@maine.rr.com

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

Date: Wed, 18 Nov 1998 15:55:25 +0100
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Scale-to-fit window
Message-Id: <l03110702b2787f5555a9@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

Ash,

a few additional zooming features can be found in Object-Image:

Zoom(factor, top, left)
  zooms the window by factor 1, 2, 3, 4, 8, 16, 32 or 64.
  The pixel addressed by (top, left) will appear at top left
  in the zoomed window. Zoom(0, 0, 0) performs 'fit window
  to screen and fit entire image into window'.

MoveWindow(x, y, width, height)
  Moves current window to global screen coordinates x, y.
  Width and  height (optional) control the window size.
  Moving is ignored if x = y = 0.

Another feature is the 'Quick ZoomOut feature':
press simultaneously the command key and space bar. A temporary
"fit-to-screen" is performed. In the overview, the normally visible field
is shown as frame and can be dragged to a different position of interest.
The zooming factor can be changed with a pop-up menu. Then, release the two
keys, and the window will show the new field at the desired magnification.
You can synchronously zoom tiled windows when including the option key.


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, 18 Nov 1998 10:16:40 -0500
From: "Heeschen, Bill (WA)" <WAHEESCHEN@dow.com>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Macro for Mac or PC?
Message-Id: <D209047D0257D21191770000F8C991D904C846@mante35a.nam.dow.com>
Content-Type: text/plain

I have had reasonably good luck moving macros between NIH Image  and
Scion Image.  There are some interesting problems which I have discussed
with Scion and they plan to fix.  Some of the less-common routines are
still not implemented in a "bulletproof" manner (like watershed
segmentation), but most things are working.  For me, the biggest problem
right now is that variable names cannot be re-declared in called
subroutines.  For example, I like to use i,j,k as local counters, so
they get declared in almost every macro and subroutine.  When they have
been declared in the macro, then declared again in a called subroutine,
unexpected results can occur, especially when the subroutine is called
within a DO loop.  This is contrary to regular Pascal and they plan to
fix it in their first full release (remember that they are at beta 3
right now).  There are also some platform specific differences, like the
serial port calls.

Best suggestion is to simply load them and run on disposable images -
don't start doing real work until you know your macros are performing as
expected.

Good luck,
Bill Heeschen
Microscopy group
The Dow Chemical Company

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

Date: Wed, 18 Nov 1998 10:53:03 -0500
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'nih-image-d@io.ece.drexel.edu'" <nih-image-d@io.ece.drexel.edu>
Subject: Animation or rotating 3D object from four flat images
Message-ID: <69B43248FE73D11197BB00A0C99AB0678986@jvcserver.vanguardweb.org>
Content-Type: text/plain

Hi to all,
I am not sure to ask this question here. Please except my apologies. I
thought one of you can help me if possible.
I have four 3D views (front, back, left and right) of blood vessel as
TIF (four flat images containing 3D views of blood vessel). These images
were scanned from x-ray films and saved as TIF files. I want to make
animation by rotating these views as 3D. Obviously, I have to create
more views by interpolation.  I cannot get any other views to make
animation since I have only four views and stuck with them. Is it
possible or impossible to rotate 3D object from four flat images?. Any
help is appreciated.

Thanks
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-U of M
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087

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

Date: Wed, 18 Nov 1998 16:32:56 -0600 (CST)
From: Steve Eglen <eglen@thalamus.wustl.edu>
To: nih-image@io.ece.drexel.edu
Subject: How do you open an image in macro with Keep LUT checked?
Message-Id: <199811182232.QAA21749@thalamus.wustl.edu>

[using version 1.58b30]

Hi,

I have a set of PICT files that I'd like to make into a stack.  The manual
tells me that I should check the `keep LUT' item to remap the pixel values.
This works fine when I open the images one by one `by hand'.  When
writing a macro however, what is the command to set this option before using
the Open('File') macro?

Thanks in advance for any help,
Stephen Eglen

PS.  is there a broken link in the macro pages?  If I go to
http://rsb.info.nih.gov/nih-image/more-docs/macros.html
and then try to click on `Input/Output Macros' I get the
following error:

Could not open 
ftp://codon.nih.gov/pub/nih-image/macros/Input%2fOutput%20Macros.txt.

(This was under both IE 4 and 2)

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

Date: 	Thu, 19 Nov 1998 10:06:27 +0100 (CET)
From: Gary Chinga <gary@nvg.ntnu.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Re: Macro for Mac or PC?
Message-ID: <Pine.NEB.4.05.9811191002470.1583-100000@flode.nvg.ntnu.no>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I used to write my macroes at home in my Mac and then use them in a PC (at
Work). I have not found any problems yet.  any problems yet.


Gary.
NTNU-Trondheim
Norway.


On Wed, 18 Nov 1998, Barwood, Henry wrote:

> I'm curious is a macro written for the Mac version of Image will work on
> either the Java or Scion PC version as well? If not, is there a way to
> convert macros so that they are interchangeable? TIA.
> 
> Henry Barwood
> Indiana Geological Survey
> 

--------------------------------
End of nih-image-d Digest V98 Issue #119
****************************************

From nih-image-request@io.ece.drexel.edu Thu Nov 19 08:20 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA05420;
	Thu, 19 Nov 1998 08:20:48 -0500 (EST)
Resent-Date: Thu, 19 Nov 1998 08:20:48 -0500 (EST)
Message-Id: <l03130302b279c80dd18b@[134.1.14.69]>
Mime-Version: 1.0
Date: Thu, 19 Nov 1998 14:06:23 +0100
To: nih-image@io.ece.drexel.edu
From: "Nuria Teixido" <nteixido@awi-bremerhaven.de>
Subject: from raster to vector images
Resent-Message-ID: <"2gkX-.0.bY.tP1Ls"@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/645
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: 635

I'm working with drawings that I use to scann and the resulting raster
images are imported to NIH program where they are submitted to binarization
and skeletonization processes. I need to vectorize the images and to export
to file format compatible with Arc/info Geographical Information System
(GIS) programm. But my question is how to convert the raster image to
vector image. If somebody knows it, it will be very helpfull for us.

Thanks

Nuria teixido

Nuria Teixido
Alfred-Wegener-Institut
Columbusstrasse
27568 Bremerhaven
Deutschland
Tel. Nr. 00-49-471-4831-319
Fax. Nr. 00-49-471-4831-149
e-mail:nteixido@awi-bremerhaven.de



From nih-image-request@io.ece.drexel.edu Thu Nov 19 08:38 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA08198;
	Thu, 19 Nov 1998 08:38:20 -0500 (EST)
Resent-Date: Thu, 19 Nov 1998 08:38:20 -0500 (EST)
X-Sender: elk@129.233.21.18
Message-Id: <l03130300b279ca3f17e9@[129.233.21.143]>
In-Reply-To: <l03130302b279c80dd18b@[134.1.14.69]>
Mime-Version: 1.0
Date: Thu, 19 Nov 1998 14:18:26 +0100
To: nih-image@io.ece.drexel.edu
From: Ben Elkin <elk@IGB.FhG.de>
Subject: Re: from raster to vector images
Resent-Message-ID: <"Qc5xE1.0.8E1._g1Ls"@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/646
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: 950

>I'm working with drawings that I use to scann and the resulting raster
>images are imported to NIH program where they are submitted to binarization
>and skeletonization processes. I need to vectorize the images and to export
>to file format compatible with Arc/info Geographical Information System
>(GIS) programm. But my question is how to convert the raster image to
>vector image. If somebody knows it, it will be very helpfull for us.
>

Shareware GraphicConverter ( http://www.lemkesoft.de ) would produce a
vectorized image consisting of many straight lines. Perhaps it would be
enough for your purpose.


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 Nov 19 08:59 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA10929;
	Thu, 19 Nov 1998 08:59:15 -0500 (EST)
Resent-Date: Thu, 19 Nov 1998 08:59:15 -0500 (EST)
Message-Id: <36541F1B.E7CB58C@maroon.tc.umn.edu>
Date: Thu, 19 Nov 1998 07:37:46 -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
X-Mailer: Mozilla 4.05 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: from raster to vector images
References: <l03130302b279c80dd18b@[134.1.14.69]>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"riXIZ1.0.Z-1.ny1Ls"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/647
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: 1076

GraphicConvertor will vectorize it, and save it as pict or HPGL.

Nuria Teixido wrote:
> 
> I'm working with drawings that I use to scann and the resulting raster
> images are imported to NIH program where they are submitted to binarization
> and skeletonization processes. I need to vectorize the images and to export
> to file format compatible with Arc/info Geographical Information System
> (GIS) programm. But my question is how to convert the raster image to
> vector image. If somebody knows it, it will be very helpfull for us.
> 
> Thanks
> 
> Nuria teixido
> 
> Nuria Teixido
> Alfred-Wegener-Institut
> Columbusstrasse
> 27568 Bremerhaven
> Deutschland
> Tel. Nr. 00-49-471-4831-319
> Fax. Nr. 00-49-471-4831-149
> e-mail:nteixido@awi-bremerhaven.de

-- 

   _________________________________________________
     /  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 Nov 19 09:47 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA16978;
	Thu, 19 Nov 1998 09:47:19 -0500 (EST)
Resent-Date: Thu, 19 Nov 1998 09:47:19 -0500 (EST)
Message-ID: <19981119142434.12792.qmail@hotmail.com>
X-Originating-IP: [139.165.30.123]
From: "Enrico BONINO" <e_bonino@hotmail.com>
To: ermapper-l@ermapper.com
Cc: CIPA-L@uibk.ac.at, arcwatch@esri.com, imagrs-l@gis.psu.edu,
        majordomo@avenza.com, nih-image@io.ece.drexel.edu, starqui@tin.it
Subject: GEOVISION 99 2nd circular
MIME-Version: 1.0
Date: Thu, 19 Nov 1998 06:24:32 PST
Resent-Message-ID: <"T93Vq2.0.DX3.Hf2Ls"@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/649
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 2247



Dear colleagues,

GEOVISION 99
International Symposium on Imaging Applications in Geology
Liege (BELGIUM), 6-7 may 1999

The second circular for GEOVISION 99 is now available from :

http://www.lgih.ulg.ac.be/geovision/circular2/circular2.htm

Check it or bookmark it today and have a look at the topics that will be 
treated during this unique conference!


INTRODUCTION

Geovision is the very first congress of its kind. The idea of organising 
this meeting came from the striking evidence that more and more imaging 
techniques are developed or used in the earth sciences. Video 
microscopy, electrical tomography or airborne and space infrared imaging 
are only but a few of these emerging techniques requiring a thorough 
understanding of imaging principles and a good mastership of the 
processing algorithms.

We strongly believe that bringing together earth scientists involved in 
digital imaging, whatever their field of applications, is the best way 
to help people tighten new relationships and discover new potentials for 
geo-imaging. The leading researchers and major scientific societies 
supporting Geovision '99 give us the feeling that this will be a great 
event.

Looking forward to welcoming you in Lige,

			The Organizers

KEYNOTE LECTURES

 Richard Bedell, Homestake Mining Company, NEVADA, UNITED STATES:
 "Geological Imaging: Principles and applications "

 Serge Beucher, Ecole des Mines de Paris, FRANCE:
 " Mathematical Morphology and Geology: when image analysis uses the
vocabulary of earth science. A review of some applications "

 Torleif Dahlin, Lund University, SWEDEN:
 " Development of resistivity imaging techniques "

 Wim Spakman, University of Utrecht, NETHERLANDS:
 " Tomography of the Earth's interior with seismic travel times "


--------------------------------------------------------------
GEOVISION 99
Website : http://www.lgih.ulg.ac.be/geovision
Address :

Universit de Lige-Sart Tilman
Gologie de l'Ingnieur - Bat. B19
4000 LIEGE - BELGIUM
tel. : +32-4-3662216
fax : +32-4-3662817
email: fcheslet@ulg.ac.be

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




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


From nih-image-request@io.ece.drexel.edu Thu Nov 19 09:48 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA17136;
	Thu, 19 Nov 1998 09:48:41 -0500 (EST)
Resent-Date: Thu, 19 Nov 1998 09:48:41 -0500 (EST)
Message-ID: <c=US%a=_%p=Indiana_Universi%l=PYRITE-981119142844Z-4749@pyrite.igs.indiana.edu>
From: "Barwood, Henry" <hbarwood@pyrite.igs.indiana.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Macro for Mac or PC?
Date: Thu, 19 Nov 1998 09:28:44 -0500
X-Mailer:  Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63
Encoding: 11 TEXT
Resent-Message-ID: <"jK_8Z.0.OV3.ie2Ls"@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/648
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 303

Dear Gary,
You wrote:
>
>I used to write my macroes at home in my Mac and then use them in a PC (at
>Work). I have not found any problems yet.  any problems yet.
>

Thanks for helping me out. The general consensus is that Mac and PC
Macros are generally interchangeable (with a few exceptions).

Henry


From nih-image-request@io.ece.drexel.edu Thu Nov 19 16:01 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA19986;
	Thu, 19 Nov 1998 16:01:01 -0500 (EST)
Resent-Date: Thu, 19 Nov 1998 16:01:01 -0500 (EST)
Message-Id: <199811192030.PAA17201@io.ECE.Drexel.EDU>
From: Chris Liner <cll@douze.geo.utulsa.edu>
Subject: 2 questions
To: nih-image@io.ece.drexel.edu
Date: Thu, 19 Nov 98 14:56:23 CST
Cc: cll@utulsa.edu (Chris Liner)
Mailer: Elm [revision: 70.85]
Resent-Message-ID: <"xLZhq2.0.wC4.708Ls"@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/650
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1088

Here are two unrelated questions that have been 
puzzling me.

1. Has anyone noticed that pixel-operation macros 
run a whole lot slower in ScionImage than NIH Image.
I have some fairly involved pixel read/scan/operate/write
kind of macros that run about 100-200 times faster under Image 
than ScionImage.  The test is on a G3 using VirtualPC.
I attribute some of the speed loss to VirtualPC, but
other things like ffts run at basically equivalent speeds.
Any insight is appreciated.

2. With ObjectImage, is there any way to collect the density 
value at the points defined by a 3-D point object?  What I would
like to generate is a list of (x,y,z,density) values for export
to a spreadsheet.

Thanks in advance for any help.


Dr. Christopher L. Liner
Associate Professor
Department of Geoscience
University of Tulsa
600 S. College Ave
Tulsa, OK   74104-3189
---------------------------
cll@utulsa.edu
http://douze.utulsa.edu/~cll/ChrisLiner.html
918-631-3028   [phone]
918-631-2091   [fax]

"Education is an ornament in prosperity,
and a refuge in adversity" - Aristotle (384-322 BC)


From nih-image-request@io.ece.drexel.edu Thu Nov 19 20:52 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA11590;
	Thu, 19 Nov 1998 20:52:25 -0500 (EST)
Resent-Date: Thu, 19 Nov 1998 20:52:25 -0500 (EST)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: cll@douze.geo.utulsa.edu, nih-image@io.ece.drexel.edu
Date:          Fri, 20 Nov 1998 12:21:59 GMT+1100
Subject:       Re: 2 questions
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <265038A782D@rna.bio.mq.edu.au>
Resent-Message-ID: <"GdTDr3.0._R2.pECLs"@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/651
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1770

>From: Chris Liner <cll@douze.geo.utulsa.edu>
>Subject: 2 questions
>To: nih-image@io.ece.drexel.edu
>Date: Thu, 19 Nov 98 14:56:23 CST
>
>Here are two unrelated questions that have been 
>puzzling me.
>
>1. Has anyone noticed that pixel-operation macros 
>run a whole lot slower in ScionImage than NIH Image.
>.............

>2. With ObjectImage, is there any way to collect the density 
>value at the points defined by a 3-D point object?  What I would
>like to generate is a list of (x,y,z,density) values for export
>to a spreadsheet.
>.........

Basic macro code to access pixel associated with Objects in Object-Image is:

macro'/0test';var i,c:integer;begin
  for i:=1 to nCount do 
    begin
    SelectCell(i);
    selectSlice(ZPos(1));
    c:=getPixel(XPos(1),YPos(1));
    showMessage(i,XPos(1),  YPos(1),  ZPos(1),c);
    SetValue ('Color', i, c);
    end;
  end

in the above, all except {'/0test','Color', i, c} are keywords defined in 
Macro Ref or Macro Ref online help files.

As XYZPos can be fractional pixel positions, you may wish to do interpolation by 
accessing neighbours in each slice, taking note of fractional position using
f:= XPos(j) mod 1

I took simple approach of specifying XYZPos in Define Objects and defining a static 
column 'Color' for test.
Show Obj Results lists results.
Export Obj Results exports results.

For Objects which were ROIs or polygons then you would replace the getPixel by

ObjectToRoi;measure;
GetResults(n,mean,mode,min,max);
SetValue ('Color', i, mean);

or

ObjectToRoi;measure;
SetValue ('Color', i, rMean[rCount]);

etc



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 Nov 20 04:33 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA02618;
	Fri, 20 Nov 1998 04:33:23 -0500 (EST)
Resent-Date: Fri, 20 Nov 1998 04:33:23 -0500 (EST)
From: "j.gregory" <ort056@abdn.ac.uk>
Sender: ort056@abdn.ac.uk
To: nih-image@io.ece.drexel.edu
Subject: Re: Macro for Mac or PC?
Message-ID: <SIMEON.9811200929.A@pc10.abdn.ac.uk>
Date: Fri, 20 Nov 1998 09:07:29 +0000 (GMT)
Priority: NORMAL
X-Mailer: Simeon for Windows Version 4.0.9
X-Authentication: IMSP
MIME-Version: 1.0
Resent-Message-ID: <"qUJAS.0.147.p3JLs"@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/652
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: 718

> I'm curious is a macro written for the Mac version of Image will work on
> either the Java or Scion PC version as well? If not, is there a way to
> convert macros so that they are interchangeable? TIA.
> 
> Henry Barwood
> Indiana Geological Survey


I keep seeing 'edm' in NIH Macros but can't find any reference to it in Scion image.
if anyone knows a workaround or way to replace it, please tell me. 

--------------------------------------------------------------------------
Jennifer Gregory BSc.              
Department of Orthopaedics         
University of Aberdeen              
Aberdeen
AB25 2ZD
UK

email: j.gregory@abdn.ac.uk
--------------------------------------------------------------------------



From nih-image-d-request@io.ece.drexel.edu Fri Nov 20 04:49 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA04728;
	Fri, 20 Nov 1998 04:49:34 -0500 (EST)
Date: Fri, 20 Nov 1998 04:49:34 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811200949.EAA04728@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #120
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/120
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 12000

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 120

Today's Topics:
  from raster to vector images          [ "Nuria Teixido" <nteixido@awi-breme ]
  Re: from raster to vector images      [ Ben Elkin <elk@IGB.FhG.de> ]
  Re: from raster to vector images      [ Michael Herron <herro001@maroon.tc. ]
  RE: Macro for Mac or PC?              [ "Barwood, Henry" <hbarwood@pyrite.i ]
  GEOVISION 99 2nd circular             [ "Enrico BONINO" <e_bonino@hotmail.c ]
  2 questions                           [ Chris Liner <cll@douze.geo.utulsa.e ]
  Re: 2 questions                       [ GJOSS@rna.bio.mq.edu.au ]
  Re: Macro for Mac or PC?              [ "j.gregory" <ort056@abdn.ac.uk> ]

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

Date: Thu, 19 Nov 1998 14:06:23 +0100
From: "Nuria Teixido" <nteixido@awi-bremerhaven.de>
To: nih-image@io.ece.drexel.edu
Subject: from raster to vector images
Message-Id: <l03130302b279c80dd18b@[134.1.14.69]>
Content-Type: text/plain; charset="us-ascii"

I'm working with drawings that I use to scann and the resulting raster
images are imported to NIH program where they are submitted to binarization
and skeletonization processes. I need to vectorize the images and to export
to file format compatible with Arc/info Geographical Information System
(GIS) programm. But my question is how to convert the raster image to
vector image. If somebody knows it, it will be very helpfull for us.

Thanks

Nuria teixido

Nuria Teixido
Alfred-Wegener-Institut
Columbusstrasse
27568 Bremerhaven
Deutschland
Tel. Nr. 00-49-471-4831-319
Fax. Nr. 00-49-471-4831-149
e-mail:nteixido@awi-bremerhaven.de

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

Date: Thu, 19 Nov 1998 14:18:26 +0100
From: Ben Elkin <elk@IGB.FhG.de>
To: nih-image@io.ece.drexel.edu
Subject: Re: from raster to vector images
Message-Id: <l03130300b279ca3f17e9@[129.233.21.143]>
Content-Type: text/plain; charset="us-ascii"

>I'm working with drawings that I use to scann and the resulting raster
>images are imported to NIH program where they are submitted to binarization
>and skeletonization processes. I need to vectorize the images and to export
>to file format compatible with Arc/info Geographical Information System
>(GIS) programm. But my question is how to convert the raster image to
>vector image. If somebody knows it, it will be very helpfull for us.
>

Shareware GraphicConverter ( http://www.lemkesoft.de ) would produce a
vectorized image consisting of many straight lines. Perhaps it would be
enough for your purpose.


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, 19 Nov 1998 07:37:46 -0600
From: Michael Herron <herro001@maroon.tc.umn.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: from raster to vector images
Message-Id: <36541F1B.E7CB58C@maroon.tc.umn.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

GraphicConvertor will vectorize it, and save it as pict or HPGL.

Nuria Teixido wrote:
> 
> I'm working with drawings that I use to scann and the resulting raster
> images are imported to NIH program where they are submitted to binarization
> and skeletonization processes. I need to vectorize the images and to export
> to file format compatible with Arc/info Geographical Information System
> (GIS) programm. But my question is how to convert the raster image to
> vector image. If somebody knows it, it will be very helpfull for us.
> 
> Thanks
> 
> Nuria teixido
> 
> Nuria Teixido
> Alfred-Wegener-Institut
> Columbusstrasse
> 27568 Bremerhaven
> Deutschland
> Tel. Nr. 00-49-471-4831-319
> Fax. Nr. 00-49-471-4831-149
> e-mail:nteixido@awi-bremerhaven.de

-- 

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

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

Date: Thu, 19 Nov 1998 09:28:44 -0500
From: "Barwood, Henry" <hbarwood@pyrite.igs.indiana.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Macro for Mac or PC?
Message-ID: <c=US%a=_%p=Indiana_Universi%l=PYRITE-981119142844Z-4749@pyrite.igs.indiana.edu>

Dear Gary,
You wrote:
>
>I used to write my macroes at home in my Mac and then use them in a PC (at
>Work). I have not found any problems yet.  any problems yet.
>

Thanks for helping me out. The general consensus is that Mac and PC
Macros are generally interchangeable (with a few exceptions).

Henry

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

Date: Thu, 19 Nov 1998 06:24:32 PST
From: "Enrico BONINO" <e_bonino@hotmail.com>
To: ermapper-l@ermapper.com
Cc: CIPA-L@uibk.ac.at, arcwatch@esri.com, imagrs-l@gis.psu.edu,
        majordomo@avenza.com, nih-image@io.ece.drexel.edu, starqui@tin.it
Subject: GEOVISION 99 2nd circular
Message-ID: <19981119142434.12792.qmail@hotmail.com>
Content-Type: text/plain

Dear colleagues,

GEOVISION 99
International Symposium on Imaging Applications in Geology
Liege (BELGIUM), 6-7 may 1999

The second circular for GEOVISION 99 is now available from :

http://www.lgih.ulg.ac.be/geovision/circular2/circular2.htm

Check it or bookmark it today and have a look at the topics that will be 
treated during this unique conference!


INTRODUCTION

Geovision is the very first congress of its kind. The idea of organising 
this meeting came from the striking evidence that more and more imaging 
techniques are developed or used in the earth sciences. Video 
microscopy, electrical tomography or airborne and space infrared imaging 
are only but a few of these emerging techniques requiring a thorough 
understanding of imaging principles and a good mastership of the 
processing algorithms.

We strongly believe that bringing together earth scientists involved in 
digital imaging, whatever their field of applications, is the best way 
to help people tighten new relationships and discover new potentials for 
geo-imaging. The leading researchers and major scientific societies 
supporting Geovision '99 give us the feeling that this will be a great 
event.

Looking forward to welcoming you in Lige,

			The Organizers

KEYNOTE LECTURES

 Richard Bedell, Homestake Mining Company, NEVADA, UNITED STATES:
 "Geological Imaging: Principles and applications "

 Serge Beucher, Ecole des Mines de Paris, FRANCE:
 " Mathematical Morphology and Geology: when image analysis uses the
vocabulary of earth science. A review of some applications "

 Torleif Dahlin, Lund University, SWEDEN:
 " Development of resistivity imaging techniques "

 Wim Spakman, University of Utrecht, NETHERLANDS:
 " Tomography of the Earth's interior with seismic travel times "


--------------------------------------------------------------
GEOVISION 99
Website : http://www.lgih.ulg.ac.be/geovision
Address :

Universit de Lige-Sart Tilman
Gologie de l'Ingnieur - Bat. B19
4000 LIEGE - BELGIUM
tel. : +32-4-3662216
fax : +32-4-3662817
email: fcheslet@ulg.ac.be

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




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

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

Date: Thu, 19 Nov 98 14:56:23 CST
From: Chris Liner <cll@douze.geo.utulsa.edu>
To: nih-image@io.ece.drexel.edu
Cc: cll@utulsa.edu (Chris Liner)
Subject: 2 questions
Message-Id: <199811192030.PAA17201@io.ECE.Drexel.EDU>

Here are two unrelated questions that have been 
puzzling me.

1. Has anyone noticed that pixel-operation macros 
run a whole lot slower in ScionImage than NIH Image.
I have some fairly involved pixel read/scan/operate/write
kind of macros that run about 100-200 times faster under Image 
than ScionImage.  The test is on a G3 using VirtualPC.
I attribute some of the speed loss to VirtualPC, but
other things like ffts run at basically equivalent speeds.
Any insight is appreciated.

2. With ObjectImage, is there any way to collect the density 
value at the points defined by a 3-D point object?  What I would
like to generate is a list of (x,y,z,density) values for export
to a spreadsheet.

Thanks in advance for any help.


Dr. Christopher L. Liner
Associate Professor
Department of Geoscience
University of Tulsa
600 S. College Ave
Tulsa, OK   74104-3189
---------------------------
cll@utulsa.edu
http://douze.utulsa.edu/~cll/ChrisLiner.html
918-631-3028   [phone]
918-631-2091   [fax]

"Education is an ornament in prosperity,
and a refuge in adversity" - Aristotle (384-322 BC)

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

Date:          Fri, 20 Nov 1998 12:21:59 GMT+1100
From: GJOSS@rna.bio.mq.edu.au
To: cll@douze.geo.utulsa.edu, nih-image@io.ece.drexel.edu
Subject:       Re: 2 questions
Message-ID: <265038A782D@rna.bio.mq.edu.au>

>From: Chris Liner <cll@douze.geo.utulsa.edu>
>Subject: 2 questions
>To: nih-image@io.ece.drexel.edu
>Date: Thu, 19 Nov 98 14:56:23 CST
>
>Here are two unrelated questions that have been 
>puzzling me.
>
>1. Has anyone noticed that pixel-operation macros 
>run a whole lot slower in ScionImage than NIH Image.
>.............

>2. With ObjectImage, is there any way to collect the density 
>value at the points defined by a 3-D point object?  What I would
>like to generate is a list of (x,y,z,density) values for export
>to a spreadsheet.
>.........

Basic macro code to access pixel associated with Objects in Object-Image is:

macro'/0test';var i,c:integer;begin
  for i:=1 to nCount do 
    begin
    SelectCell(i);
    selectSlice(ZPos(1));
    c:=getPixel(XPos(1),YPos(1));
    showMessage(i,XPos(1),  YPos(1),  ZPos(1),c);
    SetValue ('Color', i, c);
    end;
  end

in the above, all except {'/0test','Color', i, c} are keywords defined in 
Macro Ref or Macro Ref online help files.

As XYZPos can be fractional pixel positions, you may wish to do interpolation by 
accessing neighbours in each slice, taking note of fractional position using
f:= XPos(j) mod 1

I took simple approach of specifying XYZPos in Define Objects and defining a static 
column 'Color' for test.
Show Obj Results lists results.
Export Obj Results exports results.

For Objects which were ROIs or polygons then you would replace the getPixel by

ObjectToRoi;measure;
GetResults(n,mean,mode,min,max);
SetValue ('Color', i, mean);

or

ObjectToRoi;measure;
SetValue ('Color', i, rMean[rCount]);

etc



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, 20 Nov 1998 09:07:29 +0000 (GMT)
From: "j.gregory" <ort056@abdn.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Macro for Mac or PC?
Message-ID: <SIMEON.9811200929.A@pc10.abdn.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

> I'm curious is a macro written for the Mac version of Image will work on
> either the Java or Scion PC version as well? If not, is there a way to
> convert macros so that they are interchangeable? TIA.
> 
> Henry Barwood
> Indiana Geological Survey


I keep seeing 'edm' in NIH Macros but can't find any reference to it in Scion image.
if anyone knows a workaround or way to replace it, please tell me. 

--------------------------------------------------------------------------
Jennifer Gregory BSc.              
Department of Orthopaedics         
University of Aberdeen              
Aberdeen
AB25 2ZD
UK

email: j.gregory@abdn.ac.uk
--------------------------------------------------------------------------

--------------------------------
End of nih-image-d Digest V98 Issue #120
****************************************

From nih-image-request@io.ece.drexel.edu Fri Nov 20 05:18 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA08576;
	Fri, 20 Nov 1998 05:18:18 -0500 (EST)
Resent-Date: Fri, 20 Nov 1998 05:18:18 -0500 (EST)
Message-ID: <19981120095327.6661.qmail@hotmail.com>
X-Originating-IP: [143.93.33.45]
From: "Michael Arm" <arminator@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: 2 questions
MIME-Version: 1.0
Date: Fri, 20 Nov 1998 01:53:27 PST
Resent-Message-ID: <"AV0rC2.0.fJ1.wmJLs"@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/653
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 1300

>Here are two unrelated questions that have been 
>puzzling me.
>
>1. Has anyone noticed that pixel-operation macros 
>run a whole lot slower in ScionImage than NIH Image.
>I have some fairly involved pixel read/scan/operate/write
>kind of macros that run about 100-200 times faster under Image 
>than ScionImage.  The test is on a G3 using VirtualPC.
>I attribute some of the speed loss to VirtualPC, but
>other things like ffts run at basically equivalent speeds.
>Any insight is appreciated.

I don't know what causes this, but we wrote a macro, that scans pixel 
for pixel in a binary image if it's black or white (it HAS TO be done 
this way with our macro). We started it on two computers at the same 
Time (a Pentium 133 with 32 MB RAM and Windows NT, and a 350 MHz Pentium 
II with 128 MB RAM and Windows 98).

Both PC's finished after 13 minutes at nearly the same time. Strange, 
isn't it?

Michael Arm

------------------------------------------------------
some guy from #linux told me how to speed up my email,
he said go on as root and type rm -rf /.. 
it stands for readmail -realfast /all... 
but now I cant reboot!
------------------------------------------------------


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


From nih-image-request@io.ece.drexel.edu Fri Nov 20 09:18 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA07356;
	Fri, 20 Nov 1998 09:18:17 -0500 (EST)
Resent-Date: Fri, 20 Nov 1998 09:18:17 -0500 (EST)
Message-ID: <69B43248FE73D11197BB00A0C99AB067898F@jvcserver.vanguardweb.org>
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>
Subject: Pixel to Voxel conversion
Date: Fri, 20 Nov 1998 08:37:45 -0500
MIME-Version: 1.0
X-Mailer: Internet Mail Service (5.5.1960.3)
Resent-Message-ID: <"BoZpm2.0.4z.EBNLs"@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/654
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 504

Hello,
I know this is difficult question and not related to NIH. Please excuse
me. 
I have four flat images of 3D blood vessel in TIF format. 
I want to rotate/animate blood vessel by creating more views. 
I guess what is needed is a computer program that would convert
four images into "voxels", or pixels in three-dimensional space. 
Has anybody done that?.
Any suggestion please.

Thanks
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-U of M
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087


From nih-image-request@io.ece.drexel.edu Fri Nov 20 12:25 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA22267;
	Fri, 20 Nov 1998 12:25:35 -0500 (EST)
Resent-Date: Fri, 20 Nov 1998 12:25:35 -0500 (EST)
Message-Id: <199811201647.LAA19261@io.ECE.Drexel.EDU>
From: Chris Liner <cll@douze.geo.utulsa.edu>
Subject: 3D Object (x,y,z,c) macro
To: nih-image@io.ece.drexel.edu
Date: Fri, 20 Nov 98 11:09:14 CST
Cc: cll@utulsa.edu (Chris Liner)
Mailer: Elm [revision: 70.85]
Resent-Message-ID: <"us0iu1.0.Mj4.lqPLs"@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/655
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1245

Thanks to Gregg Joss's quick reply, 
I now have a macro set that will extract
the color values at points defined by 
a 3D point object.  Since it may be of 
wider interest (and is short), here it is:

macro '/1Make Color Column';
begin
  MakeResultColumn('Color');
end

macro'/2Generate [x,y,z,c] Results';
  var i,c,ix,iy,iz:integer;
begin
    for i:=1 to nCount do 
      begin
      SelectCell(i);
      ix := trunc(XPos(1));
      iy := trunc(YPos(1));
      iz := trunc(YPos(1));
      selectSlice(ZPos(1));
      c:=getPixel(ix,iy);
      showMessage(i,ix,iy,iz,c);
      SetValue ('Color', i, c);
    end;
    ShowObjectResults;
end

macro '/3Delete Color Column';
begin
  DeleteColumn('Color');
end


The first macro is run once per work session,
the second as many times as you need, and 
the third once at the end of the work session.

Many thanks to G. Joss for the help.



Dr. Christopher L. Liner
Associate Professor
Department of Geoscience
University of Tulsa
600 S. College Ave
Tulsa, OK   74104-3189
---------------------------
cll@utulsa.edu
http://douze.utulsa.edu/~cll/ChrisLiner.html
918-631-3028   [phone]
918-631-2091   [fax]

"Education is an ornament in prosperity,
and a refuge in adversity" - Aristotle (384-322 BC)


From nih-image-request@io.ece.drexel.edu Fri Nov 20 16:25 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA10954;
	Fri, 20 Nov 1998 16:25:08 -0500 (EST)
Resent-Date: Fri, 20 Nov 1998 16:25:08 -0500 (EST)
Message-Id: <199811202058.PAA08679@io.ECE.Drexel.EDU>
From: Chris Liner <cll@douze.geo.utulsa.edu>
Subject: 3D object densities
To: nih-image@io.ece.drexel.edu
Date: Fri, 20 Nov 98 15:22:51 CST
Cc: cll@utulsa.edu (Chris Liner)
Mailer: Elm [revision: 70.85]
Resent-Message-ID: <"9mlxx3.0.o72.hVTLs"@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/656
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 952

Here is the latest (final?) form of the macro for
getting the density values associated with 3D point
objects in ObjectImage.  Credit goes to G. Joss and 
N. Visher.

macro 'Density of 3D points [A]';
var x, y, z, im, value, cell: real;
begin
  InitColumn('Dens.');
    for im := 1 to nImages do begin
      for cell := firstcell(im) to LastCell(im) do begin
        ShowCell(cell);
        SelectObject(1);{optional}
        x := trunc( XPos(1) );
        y := trunc( YPos(1) );
        z := ZPos(1);
        SelectSlice(z); {optional}
        value := GetPixel(x, y);
        SetValue('Dens.', cell, value);
     end;
    {Close;} {optional, to make room for next image}
  end;
end;


Dr. Christopher L. Liner
Associate Professor
Department of Geoscience
University of Tulsa
600 S. College Ave
Tulsa, OK   74104-3189
---------------------------
cll@utulsa.edu
http://douze.utulsa.edu/~cll/ChrisLiner.html
918-631-3028   [phone]
918-631-2091   [fax]


From nih-image-request@io.ece.drexel.edu Sat Nov 21 00:20 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id AAA03283;
	Sat, 21 Nov 1998 00:20:58 -0500 (EST)
Resent-Date: Sat, 21 Nov 1998 00:20:58 -0500 (EST)
From: SolamereTG@aol.com
Message-ID: <da0cd243.36564a01@aol.com>
Date: Sat, 21 Nov 1998 00:05:05 EST
To: nih-image@io.ece.drexel.edu
Mime-Version: 1.0
Subject: Re: Pixel to Voxel conversion
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 16-bit for Windows sub 38
Resent-Message-ID: <"fSGLp2.0.OI.3faLs"@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/657
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: 333


to Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-U of M

NIH has a set of macros that can reslice the images in a number of ways, see
MRI macros in the standard set. To form a 3d projection from a stack of images
you can use Project... under the stack menu .  
Good Luck

George A. Peeters
Solamere Technology Group


From nih-image-d-request@io.ece.drexel.edu Sat Nov 21 00:22 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id AAA03542;
	Sat, 21 Nov 1998 00:22:33 -0500 (EST)
Date: Sat, 21 Nov 1998 00:22:33 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811210522.AAA03542@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #121
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/121
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 7535

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 121

Today's Topics:
  Re: 2 questions                       [ "Michael Arm" <arminator@hotmail.co ]
  Image EELS in EFTEM                   [ Markus Drechsler <b7drma@rz.uni-jen ]
  Pixel to Voxel conversion             [ "Mehmet Dondurur, Ph. D." <mehmet.d ]
  3D Object (x,y,z,c) macro             [ Chris Liner <cll@douze.geo.utulsa.e ]
  3D object densities                   [ Chris Liner <cll@douze.geo.utulsa.e ]
  Re: Pixel to Voxel conversion         [ SolamereTG@aol.com ]

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

Date: Fri, 20 Nov 1998 01:53:27 PST
From: "Michael Arm" <arminator@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: 2 questions
Message-ID: <19981120095327.6661.qmail@hotmail.com>
Content-Type: text/plain

>Here are two unrelated questions that have been 
>puzzling me.
>
>1. Has anyone noticed that pixel-operation macros 
>run a whole lot slower in ScionImage than NIH Image.
>I have some fairly involved pixel read/scan/operate/write
>kind of macros that run about 100-200 times faster under Image 
>than ScionImage.  The test is on a G3 using VirtualPC.
>I attribute some of the speed loss to VirtualPC, but
>other things like ffts run at basically equivalent speeds.
>Any insight is appreciated.

I don't know what causes this, but we wrote a macro, that scans pixel 
for pixel in a binary image if it's black or white (it HAS TO be done 
this way with our macro). We started it on two computers at the same 
Time (a Pentium 133 with 32 MB RAM and Windows NT, and a 350 MHz Pentium 
II with 128 MB RAM and Windows 98).

Both PC's finished after 13 minutes at nearly the same time. Strange, 
isn't it?

Michael Arm

------------------------------------------------------
some guy from #linux told me how to speed up my email,
he said go on as root and type rm -rf /.. 
it stands for readmail -realfast /all... 
but now I cant reboot!
------------------------------------------------------


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

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

Date: Fri, 20 Nov 1998 14:29:29 +0100
From: Markus Drechsler <b7drma@rz.uni-jena.de>
To: nih-image-d@io.ece.drexel.edu
Subject: Image EELS in EFTEM
Message-Id: <3.0.5.32.19981120142929.0092eb80@pop3.uni-jena.de>
Content-Type: text/plain; charset="us-ascii"

Hello imagers,

is there anybody who uses Image to work with a Zeiss EM902A EFTEM? Are
there any macros for ESI, Image-EELS etc. which enable direct access to the
spectrometer unit and the EELS photomultiplier of the EM? 
Which frame grabber and camera can be used for EM application?

Any help would be greatly appreciated.
Thanks in advance
Markus



*******************************************
Dr. Markus Drechsler                      
Friedrich-Schiller-Universitaet Jena              
Institut fuer Pharmazie   
Lehrstuhl fuer Pharmazeutische Technologie               
Lessingstr.8    
D-07743 Jena           
     	
Tel:   ++49/3641/9-49903
       ++49/3641/9-49914
       ++49/3641/9-49915
e-mail:b7drma@rz.uni-jena.de

Sekretariat
Tel:   ++49/3641/9-49900
Fax:   ++49/3641/9-49902

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

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

Date: Fri, 20 Nov 1998 08:37:45 -0500
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>
Subject: Pixel to Voxel conversion
Message-ID: <69B43248FE73D11197BB00A0C99AB067898F@jvcserver.vanguardweb.org>
Content-Type: text/plain

Hello,
I know this is difficult question and not related to NIH. Please excuse
me. 
I have four flat images of 3D blood vessel in TIF format. 
I want to rotate/animate blood vessel by creating more views. 
I guess what is needed is a computer program that would convert
four images into "voxels", or pixels in three-dimensional space. 
Has anybody done that?.
Any suggestion please.

Thanks
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-U of M
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087

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

Date: Fri, 20 Nov 98 11:09:14 CST
From: Chris Liner <cll@douze.geo.utulsa.edu>
To: nih-image@io.ece.drexel.edu
Cc: cll@utulsa.edu (Chris Liner)
Subject: 3D Object (x,y,z,c) macro
Message-Id: <199811201647.LAA19261@io.ECE.Drexel.EDU>

Thanks to Gregg Joss's quick reply, 
I now have a macro set that will extract
the color values at points defined by 
a 3D point object.  Since it may be of 
wider interest (and is short), here it is:

macro '/1Make Color Column';
begin
  MakeResultColumn('Color');
end

macro'/2Generate [x,y,z,c] Results';
  var i,c,ix,iy,iz:integer;
begin
    for i:=1 to nCount do 
      begin
      SelectCell(i);
      ix := trunc(XPos(1));
      iy := trunc(YPos(1));
      iz := trunc(YPos(1));
      selectSlice(ZPos(1));
      c:=getPixel(ix,iy);
      showMessage(i,ix,iy,iz,c);
      SetValue ('Color', i, c);
    end;
    ShowObjectResults;
end

macro '/3Delete Color Column';
begin
  DeleteColumn('Color');
end


The first macro is run once per work session,
the second as many times as you need, and 
the third once at the end of the work session.

Many thanks to G. Joss for the help.



Dr. Christopher L. Liner
Associate Professor
Department of Geoscience
University of Tulsa
600 S. College Ave
Tulsa, OK   74104-3189
---------------------------
cll@utulsa.edu
http://douze.utulsa.edu/~cll/ChrisLiner.html
918-631-3028   [phone]
918-631-2091   [fax]

"Education is an ornament in prosperity,
and a refuge in adversity" - Aristotle (384-322 BC)

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

Date: Fri, 20 Nov 98 15:22:51 CST
From: Chris Liner <cll@douze.geo.utulsa.edu>
To: nih-image@io.ece.drexel.edu
Cc: cll@utulsa.edu (Chris Liner)
Subject: 3D object densities
Message-Id: <199811202058.PAA08679@io.ECE.Drexel.EDU>

Here is the latest (final?) form of the macro for
getting the density values associated with 3D point
objects in ObjectImage.  Credit goes to G. Joss and 
N. Visher.

macro 'Density of 3D points [A]';
var x, y, z, im, value, cell: real;
begin
  InitColumn('Dens.');
    for im := 1 to nImages do begin
      for cell := firstcell(im) to LastCell(im) do begin
        ShowCell(cell);
        SelectObject(1);{optional}
        x := trunc( XPos(1) );
        y := trunc( YPos(1) );
        z := ZPos(1);
        SelectSlice(z); {optional}
        value := GetPixel(x, y);
        SetValue('Dens.', cell, value);
     end;
    {Close;} {optional, to make room for next image}
  end;
end;


Dr. Christopher L. Liner
Associate Professor
Department of Geoscience
University of Tulsa
600 S. College Ave
Tulsa, OK   74104-3189
---------------------------
cll@utulsa.edu
http://douze.utulsa.edu/~cll/ChrisLiner.html
918-631-3028   [phone]
918-631-2091   [fax]

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

Date: Sat, 21 Nov 1998 00:05:05 EST
From: SolamereTG@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re: Pixel to Voxel conversion
Message-ID: <da0cd243.36564a01@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

to Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-U of M

NIH has a set of macros that can reslice the images in a number of ways, see
MRI macros in the standard set. To form a 3d projection from a stack of images
you can use Project... under the stack menu .  
Good Luck

George A. Peeters
Solamere Technology Group

--------------------------------
End of nih-image-d Digest V98 Issue #121
****************************************

From nih-image-request@io.ece.drexel.edu Sat Nov 21 22:40 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id WAA04516;
	Sat, 21 Nov 1998 22:40:42 -0500 (EST)
Resent-Date: Sat, 21 Nov 1998 22:40:42 -0500 (EST)
X-Warning: UCONNVM.UConn.Edu: Host 182.hartford-06-07rs.ct.dial-access.att.net claimed to be [12.79.36.233]
Message-Id: <l03130308b27d350ee1a6@[12.79.36.233]>
Mime-Version: 1.0
Date: Sat, 21 Nov 1998 22:27:13 -0500
To: nih-image@io.ece.drexel.edu
From: David Knecht <knecht@uconnvm.uconn.edu>
Subject: 3D smoothing in Image
Resent-Message-ID: <"2mKPA3.0.VS.7BuLs"@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/658
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: 268

Has anyone written a macro that will perform a 3D smoothing routine on a stack?

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 Sun Nov 22 05:43 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA23058;
	Sun, 22 Nov 1998 05:43:35 -0500 (EST)
Resent-Date: Sun, 22 Nov 1998 05:43:35 -0500 (EST)
Message-Id: <199811221027.FAA21006@io.ECE.Drexel.EDU>
Date:     Sun,  22 Nov 98 12:26 +0200
From: DVORAH@AGRI.HUJI.AC.IL
To: nih-image@io.ece.drexel.edu
Subject:  RE: from raster to vector images
Resent-Message-ID: <"HNWIs.0.V85.LS-Ls"@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/659
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 101

1. Corel Draw has a very nice bectorization program
2. Arc/Info has it's own vectorization program.


From nih-image-request@io.ece.drexel.edu Sun Nov 22 11:15 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA01799;
	Sun, 22 Nov 1998 11:15:09 -0500 (EST)
Resent-Date: Sun, 22 Nov 1998 11:15:09 -0500 (EST)
Message-Id: <l03102801b27de54bb734@[162.38.196.42]>
Mime-Version: 1.0
X-Mailer: Eudora Light F3.1l
Date: Sun, 22 Nov 1998 17:00:07 +0100
To: nih-image@io.ece.drexel.edu
From: olivier bricaud <obricaud@crit.univ-montp2.fr>
Subject: Stereo-4D macros
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id LAA00205
Resent-Message-ID: <"Ybndb2.0.Y3.wM3Ms"@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/660
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="iso-8859-1"
Content-Length: 437

Hello,

Can you tell me, please where i can download the 4d-stereo macros for NIH
image?

Thanks a lot

Olivier

Olivier BRICAUD
Laboratoire de Neurogntique du Dveloppement
Universit des Sciences et Techniques du Languedoc
CC 103
Place Eugne Bataillon
F-34095 Montpellier Cedex 05
FRANCE


Tel : (+33) (0)4 67 14 32 53
Fax : (+33) (0)4 67 14 39 28
E-mail : obricaud@crit.univ-montp2.fr
URL: http://www.univ-montp2.fr/~neurodvpmt/



From nih-image-d-request@io.ece.drexel.edu Mon Nov 23 06:23 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA15639;
	Mon, 23 Nov 1998 06:23:35 -0500 (EST)
Date: Mon, 23 Nov 1998 06:23:35 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811231123.GAA15639@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #122
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/122
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 2084

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 122

Today's Topics:
  3D smoothing in Image                 [ David Knecht <knecht@uconnvm.uconn. ]
  RE: from raster to vector images      [ DVORAH@AGRI.HUJI.AC.IL ]
  Stereo-4D macros                      [ olivier bricaud <obricaud@crit.univ ]

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

Date: Sat, 21 Nov 1998 22:27:13 -0500
From: David Knecht <knecht@uconnvm.uconn.edu>
To: nih-image@io.ece.drexel.edu
Subject: 3D smoothing in Image
Message-Id: <l03130308b27d350ee1a6@[12.79.36.233]>
Content-Type: text/plain; charset="us-ascii"

Has anyone written a macro that will perform a 3D smoothing routine on a stack?

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:     Sun,  22 Nov 98 12:26 +0200
From: DVORAH@AGRI.HUJI.AC.IL
To: nih-image@io.ece.drexel.edu
Subject:  RE: from raster to vector images
Message-Id: <199811221027.FAA21006@io.ECE.Drexel.EDU>

1. Corel Draw has a very nice bectorization program
2. Arc/Info has it's own vectorization program.

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

Date: Sun, 22 Nov 1998 17:00:07 +0100
From: olivier bricaud <obricaud@crit.univ-montp2.fr>
To: nih-image@io.ece.drexel.edu
Subject: Stereo-4D macros
Message-Id: <l03102801b27de54bb734@[162.38.196.42]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Hello,

Can you tell me, please where i can download the 4d-stereo macros for NIH
image?

Thanks a lot

Olivier

Olivier BRICAUD
Laboratoire de Neurogntique du Dveloppement
Universit des Sciences et Techniques du Languedoc
CC 103
Place Eugne Bataillon
F-34095 Montpellier Cedex 05
FRANCE


Tel : (+33) (0)4 67 14 32 53
Fax : (+33) (0)4 67 14 39 28
E-mail : obricaud@crit.univ-montp2.fr
URL: http://www.univ-montp2.fr/~neurodvpmt/

--------------------------------
End of nih-image-d Digest V98 Issue #122
****************************************

From nih-image-request@io.ece.drexel.edu Mon Nov 23 09:43 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA11218;
	Mon, 23 Nov 1998 09:43:43 -0500 (EST)
Resent-Date: Mon, 23 Nov 1998 09:43:43 -0500 (EST)
Message-ID: <10B622A095EFD111BF7B00A0C98313F141C68E@pathem0.path.uab.edu>
From: Margaret Amsler <mamsler@PATH.UAB.EDU>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: dot blot imaging
Date: Mon, 23 Nov 1998 08:20:19 -0600
MIME-Version: 1.0
X-Mailer: Internet Mail Service (5.5.2232.9)
Resent-Message-ID: <"QHtTr.0.2-1.XzMMs"@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/661
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 1456

Hi!  I am a new NIH Image user and a new reader of this group.  I apologize
in advance if this particular topic has been dealt with already.  
I am seeking advice for analyzing my dot blot results which reflect gene
expression in a nuclear run-on experiment.  
The pertinent step in a run-on involves hybridizing radiolabeled RNA with
DNA bound to a nytran membrane with a resulting dot blot.  A typical
experiment involves 6 treatment groups and each group has a maximum of 32
different DNA samples.  The DNA samples are arranged on the membrane in 4
columns of 8 rows- all 6 strips bear the same samples.  The hybridized 6 hot
blots are placed on a sheet of 8x10" AR film for a time.  The developed film
consists of  6 blocks of 32 dots of varying intensity based on the amount of

hybridization/expression/signal.  The film is scanned using HP Desk Scan II.
I am trying to use Scion Image to then analyze the varying intensities.  I
am using a gelblot macro but find it extremely laborious. I can only get it
to work if I assign a single column as 'lane 1' at a time.  This way there
are 24 lanes with 8 curves each 'wand adjust'.    Would you have any
suggestions on how to make the process more efficient?  Could I analyze each
strip of 32 dots at once or even better all 6 strips at once?  Is there a
macro for reading a 96 well plate??  Essentially my dots can be thought of
as two 96 well plates.  
Thanks much for any assistance!

Maggie Amsler



From nih-image-request@io.ece.drexel.edu Mon Nov 23 18:19 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA07120;
	Mon, 23 Nov 1998 18:19:56 -0500 (EST)
Resent-Date: Mon, 23 Nov 1998 18:19:56 -0500 (EST)
Message-Id: <l03110700b27f96821b35@[134.76.211.69]>
Mime-Version: 1.0
Date: Mon, 23 Nov 1998 23:48:09 +0100
To: nih-image@io.ece.drexel.edu
From: Donna Arndt-Jovin <djovin@mpc186.mpibpc.gwdg.de>
Resent-Message-ID: <"OavBe3.0.vv.6PUMs"@io>
Resent-From: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Reply-To: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/662
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: 227

set nih-image mail postpone

Donna Arndt-Jovin
MPI for Biophysical Chemistry
Dept. of Molecular Biology
Am Fassberg
D-37070 Goettingen, Germany
tel: +49-551-201-1393
fax: +49-551-201-1467
e-mail: djovin@mpc186.mpibpc.gwdg.de



From nih-image-d-request@io.ece.drexel.edu Tue Nov 24 06:34 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA24638;
	Tue, 24 Nov 1998 06:34:01 -0500 (EST)
Date: Tue, 24 Nov 1998 06:34:01 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811241134.GAA24638@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #123
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/123
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 3534

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 123

Today's Topics:
  dot blot imaging                      [ Margaret Amsler <mamsler@PATH.UAB.E ]
  Slice construction                    [ "Mehmet Dondurur, Ph. D." <mehmet.d ]
  Unidentified subject!                 [ Donna Arndt-Jovin <djovin@mpc186.mp ]

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

Date: Mon, 23 Nov 1998 08:20:19 -0600
From: Margaret Amsler <mamsler@PATH.UAB.EDU>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: dot blot imaging
Message-ID: <10B622A095EFD111BF7B00A0C98313F141C68E@pathem0.path.uab.edu>
Content-Type: text/plain

Hi!  I am a new NIH Image user and a new reader of this group.  I apologize
in advance if this particular topic has been dealt with already.  
I am seeking advice for analyzing my dot blot results which reflect gene
expression in a nuclear run-on experiment.  
The pertinent step in a run-on involves hybridizing radiolabeled RNA with
DNA bound to a nytran membrane with a resulting dot blot.  A typical
experiment involves 6 treatment groups and each group has a maximum of 32
different DNA samples.  The DNA samples are arranged on the membrane in 4
columns of 8 rows- all 6 strips bear the same samples.  The hybridized 6 hot
blots are placed on a sheet of 8x10" AR film for a time.  The developed film
consists of  6 blocks of 32 dots of varying intensity based on the amount of

hybridization/expression/signal.  The film is scanned using HP Desk Scan II.
I am trying to use Scion Image to then analyze the varying intensities.  I
am using a gelblot macro but find it extremely laborious. I can only get it
to work if I assign a single column as 'lane 1' at a time.  This way there
are 24 lanes with 8 curves each 'wand adjust'.    Would you have any
suggestions on how to make the process more efficient?  Could I analyze each
strip of 32 dots at once or even better all 6 strips at once?  Is there a
macro for reading a 96 well plate??  Essentially my dots can be thought of
as two 96 well plates.  
Thanks much for any assistance!

Maggie Amsler

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

Date: Mon, 23 Nov 1998 15:19:51 -0500
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'nih-image-d@io.ece.drexel.edu'" <nih-image-d@io.ece.drexel.edu>
Subject: Slice construction
Message-ID: <69B43248FE73D11197BB00A0C99AB0678996@jvcserver.vanguardweb.org>
Content-Type: text/plain

Hi to all,
Is there any macro to construct a CT slice from given two slices?
Basically, You have two cross sectional CT slices (slice1 and 2).By
using slice 1 and 2, I would like to create 3rd slice in between slice 1
and 2 by interpolation or other methods.
Is this possible with NIH or other programs.
Many thanks for any suggestion.


Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-U of M
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087

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

Date: Mon, 23 Nov 1998 23:48:09 +0100
From: Donna Arndt-Jovin <djovin@mpc186.mpibpc.gwdg.de>
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <l03110700b27f96821b35@[134.76.211.69]>
Content-Type: text/plain; charset="us-ascii"

set nih-image mail postpone

Donna Arndt-Jovin
MPI for Biophysical Chemistry
Dept. of Molecular Biology
Am Fassberg
D-37070 Goettingen, Germany
tel: +49-551-201-1393
fax: +49-551-201-1467
e-mail: djovin@mpc186.mpibpc.gwdg.de

--------------------------------
End of nih-image-d Digest V98 Issue #123
****************************************

From nih-image-request@io.ece.drexel.edu Tue Nov 24 10:59 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA22775;
	Tue, 24 Nov 1998 10:59:30 -0500 (EST)
Resent-Date: Tue, 24 Nov 1998 10:59:30 -0500 (EST)
Date: Tue, 24 Nov 1998 15:23:23 +0000 (GMT)
From: Jan Kreft <sabjk@thor.cf.ac.uk>
X-Sender: sabjk@thor
To: nih-image@io.ece.drexel.edu
Subject: Canny edge detector
Message-ID: <Pine.OSF.3.95q.981124151845.27997A-100000@thor>
MIME-Version: 1.0
Resent-Message-ID: <"vTYad.0.se4.B_iMs"@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/663
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: 270

Dear all,

has anybody implemented the Canny edge detector in NIH-Image already?

TIA, Jan.

Jan Kreft				Phone +44 (0)1222 876036
Cardiff School of Biosciences		Fax   +44 (0)1222 874305
Cardiff	University 			E-mail Kreft@cardiff.ac.uk
PO Box 915, Cardiff CF1 3TL, UK



From nih-image-request@io.ece.drexel.edu Tue Nov 24 14:55 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA16639;
	Tue, 24 Nov 1998 14:55:50 -0500 (EST)
Resent-Date: Tue, 24 Nov 1998 14:55:50 -0500 (EST)
X-Sender: d306604@nobel.si.uqam.ca
Message-Id: <l03130300b280b968d688@[132.208.139.22]>
Mime-Version: 1.0
Date: Tue, 24 Nov 1998 14:29:58 -0500
To: Nih mailing list <nih-image@io.ece.drexel.edu>
From: Dominique Berube <Berube.Dominique@uqam.ca>
Subject: Convex Hull
Resent-Message-ID: <"jMHLi.0.RP3.IdmMs"@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/664
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: 336


Hello all,

I searched the archives about a possible convex hull macro. I found code to
implement directly into the program (from manuel Urrutia Avisrror)but I
would rather stay with the
macros. I think that some work was done but I couldn't find anything usable
in the archives or the ftp site.  Anyone knows something?

Thank you.



From nih-image-d-request@io.ece.drexel.edu Wed Nov 25 06:20 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA23337;
	Wed, 25 Nov 1998 06:20:36 -0500 (EST)
Date: Wed, 25 Nov 1998 06:20:36 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811251120.GAA23337@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #124
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/124
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 1565

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 124

Today's Topics:
  Canny edge detector                   [ Jan Kreft <sabjk@thor.cf.ac.uk> ]
  Convex Hull                           [ Dominique Berube <Berube.Dominique@ ]

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

Date: Tue, 24 Nov 1998 15:23:23 +0000 (GMT)
From: Jan Kreft <sabjk@thor.cf.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Canny edge detector
Message-ID: <Pine.OSF.3.95q.981124151845.27997A-100000@thor>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear all,

has anybody implemented the Canny edge detector in NIH-Image already?

TIA, Jan.

Jan Kreft				Phone +44 (0)1222 876036
Cardiff School of Biosciences		Fax   +44 (0)1222 874305
Cardiff	University 			E-mail Kreft@cardiff.ac.uk
PO Box 915, Cardiff CF1 3TL, UK

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

Date: Tue, 24 Nov 1998 14:29:58 -0500
From: Dominique Berube <Berube.Dominique@uqam.ca>
To: Nih mailing list <nih-image@io.ece.drexel.edu>
Subject: Convex Hull
Message-Id: <l03130300b280b968d688@[132.208.139.22]>
Content-Type: text/plain; charset="us-ascii"

Hello all,

I searched the archives about a possible convex hull macro. I found code to
implement directly into the program (from manuel Urrutia Avisrror)but I
would rather stay with the
macros. I think that some work was done but I couldn't find anything usable
in the archives or the ftp site.  Anyone knows something?

Thank you.

--------------------------------
End of nih-image-d Digest V98 Issue #124
****************************************

From nih-image-request@io.ece.drexel.edu Wed Nov 25 08:15 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA05820;
	Wed, 25 Nov 1998 08:15:08 -0500 (EST)
Resent-Date: Wed, 25 Nov 1998 08:15:08 -0500 (EST)
Message-Id: <l03130301b281adc406e5@[134.1.14.69]>
In-Reply-To: <199811221027.FAA21006@io.ECE.Drexel.EDU>
Mime-Version: 1.0
Date: Wed, 25 Nov 1998 13:59:28 +0100
To: nih-image@io.ece.drexel.edu
From: "Nuria Teixido" <nteixido@awi-bremerhaven.de>
Subject: Corel Draw
Resent-Message-ID: <"MNLfT3.0.jp.Nt_Ms"@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/665
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: 623

Hello,

This is the student who sent a message to NIH group to ask for the
possibility to convert raster to vector modul. We have Corel Draw 7.0 and
OCR-TRACE (in German) and maybe makes me to go slowly in solving the step.

I have been trying to import the images and convert them to vector with
bitmaps vectorization but it didn't work. I really would be very gratefull
if you could say me something more about the process.

Thank you,

Nuria

Nuria Teixido
Alfred-Wegener-Institut
Columbusstrasse
27568 Bremerhaven
Deutschland
Tel. Nr. 00-49-471-4831-319
Fax. Nr. 00-49-471-4831-149
e-mail:nteixido@awi-bremerhaven.de



From nih-image-request@io.ece.drexel.edu Wed Nov 25 18:13 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA27368;
	Wed, 25 Nov 1998 18:13:12 -0500 (EST)
Resent-Date: Wed, 25 Nov 1998 18:13:12 -0500 (EST)
From: Lynn_N_Li@notes.seagate.com
X-Lotus-FromDomain: SEAGATE@INTERNET
To: nih-image@io.ece.drexel.edu
Message-ID: <882566C7.007D84B2.00@sv-gw1.stsv.seagate.com>
Date: Wed, 25 Nov 1998 16:50:37 -0600
Subject: MFM data import
Mime-Version: 1.0
Content-Disposition: inline
Resent-Message-ID: <"bIWYW2.0.SC6.Cf8Ns"@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/666
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: 419

I am new to NIH-image. I have downloaded a PC version Scion Image to do
some off-line analysis of  the MFM image by Digital Intruments' D 3000
microscope.
when I go to menu File-Import-custom, I need to skip a 8192 bytes header
and a 512by 512 AFM image, which totals 270336 bytes. But the offset option
will not allow me to put in any number larger than 99999 bytes. So what
should I do to get around it?

thank you



From nih-image-request@io.ece.drexel.edu Wed Nov 25 20:37 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA11523;
	Wed, 25 Nov 1998 20:37:06 -0500 (EST)
Resent-Date: Wed, 25 Nov 1998 20:37:06 -0500 (EST)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: Lynn_N_Li@notes.seagate.com, nih-image@io.ece.drexel.edu
Date:          Thu, 26 Nov 1998 12:27:38 GMT+1100
Subject:       Re: MFM data import
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <2F525975CEA@rna.bio.mq.edu.au>
Resent-Message-ID: <"-55g93.0.NS2.FtANs"@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/667
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1752

>From: Lynn_N_Li@notes.seagate.com
>To: nih-image@io.ece.drexel.edu
>Date: Wed, 25 Nov 1998 16:50:37 -0600
>Subject: MFM data import
>
>I am new to NIH-image. I have downloaded a PC version Scion Image to do
>some off-line analysis of  the MFM image by Digital Intruments' D 3000
>microscope.
>when I go to menu File-Import-custom, I need to skip a 8192 bytes header
>and a 512by 512 AFM image, which totals 270336 bytes. But the offset option
>will not allow me to put in any number larger than 99999 bytes. So what
>should I do to get around it?
>
Lynn,
      The Mac NIH-Image doesnt have that restriction on data entry to setCustom for 
Import. :-)

I would expect (I haven't tested this on PC version) that the macro interface would 
not face the same user interface problem. The following macro can used to import 
mid slices from very large TIFF(header=768) stacks (on the Mac). 

Changeing or overriding the default width,height,offset and using fromSlice=2 
should work for you.

macro'[F9] Import slices from stack';
var width,height,offset,fromSlice,slices:integer;
begin
width:=256;height:=256;
offset:=768;{Tiff header}
fromSlice:=1;slices:=1;
width:=getNumber('width',width);
height:=getNumber('height',height);
offset:=getNumber('offset',offset);
fromSlice:=getNumber('fromSlice',fromSlice);
slices:=getNumber('slices',slices);
showMessage
('\width',width
,'\height',height
,'\offset',offset
,'\fromSlice',fromSlice
,'\slices',slices
);
SetCustom(width,height,offset+(fromSlice-1)*width*height,slices);
Import(''); {invokes user dialogue for file}
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-d-request@io.ece.drexel.edu Thu Nov 26 06:19 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA14979;
	Thu, 26 Nov 1998 06:19:32 -0500 (EST)
Date: Thu, 26 Nov 1998 06:19:32 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811261119.GAA14979@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #125
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/125
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 4062

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 125

Today's Topics:
  Corel Draw                            [ "Nuria Teixido" <nteixido@awi-breme ]
  MFM data import                       [ Lynn_N_Li@notes.seagate.com ]
  Re: MFM data import                   [ GJOSS@rna.bio.mq.edu.au ]

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

Date: Wed, 25 Nov 1998 13:59:28 +0100
From: "Nuria Teixido" <nteixido@awi-bremerhaven.de>
To: nih-image@io.ece.drexel.edu
Subject: Corel Draw
Message-Id: <l03130301b281adc406e5@[134.1.14.69]>
Content-Type: text/plain; charset="us-ascii"

Hello,

This is the student who sent a message to NIH group to ask for the
possibility to convert raster to vector modul. We have Corel Draw 7.0 and
OCR-TRACE (in German) and maybe makes me to go slowly in solving the step.

I have been trying to import the images and convert them to vector with
bitmaps vectorization but it didn't work. I really would be very gratefull
if you could say me something more about the process.

Thank you,

Nuria

Nuria Teixido
Alfred-Wegener-Institut
Columbusstrasse
27568 Bremerhaven
Deutschland
Tel. Nr. 00-49-471-4831-319
Fax. Nr. 00-49-471-4831-149
e-mail:nteixido@awi-bremerhaven.de

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

Date: Wed, 25 Nov 1998 16:50:37 -0600
From: Lynn_N_Li@notes.seagate.com
To: nih-image@io.ece.drexel.edu
Subject: MFM data import
Message-ID: <882566C7.007D84B2.00@sv-gw1.stsv.seagate.com>
Content-type: text/plain; charset=us-ascii
Content-Disposition: inline

I am new to NIH-image. I have downloaded a PC version Scion Image to do
some off-line analysis of  the MFM image by Digital Intruments' D 3000
microscope.
when I go to menu File-Import-custom, I need to skip a 8192 bytes header
and a 512by 512 AFM image, which totals 270336 bytes. But the offset option
will not allow me to put in any number larger than 99999 bytes. So what
should I do to get around it?

thank you

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

Date:          Thu, 26 Nov 1998 12:27:38 GMT+1100
From: GJOSS@rna.bio.mq.edu.au
To: Lynn_N_Li@notes.seagate.com, nih-image@io.ece.drexel.edu
Subject:       Re: MFM data import
Message-ID: <2F525975CEA@rna.bio.mq.edu.au>

>From: Lynn_N_Li@notes.seagate.com
>To: nih-image@io.ece.drexel.edu
>Date: Wed, 25 Nov 1998 16:50:37 -0600
>Subject: MFM data import
>
>I am new to NIH-image. I have downloaded a PC version Scion Image to do
>some off-line analysis of  the MFM image by Digital Intruments' D 3000
>microscope.
>when I go to menu File-Import-custom, I need to skip a 8192 bytes header
>and a 512by 512 AFM image, which totals 270336 bytes. But the offset option
>will not allow me to put in any number larger than 99999 bytes. So what
>should I do to get around it?
>
Lynn,
      The Mac NIH-Image doesnt have that restriction on data entry to setCustom for 
Import. :-)

I would expect (I haven't tested this on PC version) that the macro interface would 
not face the same user interface problem. The following macro can used to import 
mid slices from very large TIFF(header=768) stacks (on the Mac). 

Changeing or overriding the default width,height,offset and using fromSlice=2 
should work for you.

macro'[F9] Import slices from stack';
var width,height,offset,fromSlice,slices:integer;
begin
width:=256;height:=256;
offset:=768;{Tiff header}
fromSlice:=1;slices:=1;
width:=getNumber('width',width);
height:=getNumber('height',height);
offset:=getNumber('offset',offset);
fromSlice:=getNumber('fromSlice',fromSlice);
slices:=getNumber('slices',slices);
showMessage
('\width',width
,'\height',height
,'\offset',offset
,'\fromSlice',fromSlice
,'\slices',slices
);
SetCustom(width,height,offset+(fromSlice-1)*width*height,slices);
Import(''); {invokes user dialogue for file}
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

--------------------------------
End of nih-image-d Digest V98 Issue #125
****************************************

From nih-image-request@io.ece.drexel.edu Thu Nov 26 10:00 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA09139;
	Thu, 26 Nov 1998 10:00:03 -0500 (EST)
Resent-Date: Thu, 26 Nov 1998 10:00:03 -0500 (EST)
Message-Id: <3.0.6.32.19981126094100.007b6e70@po-box.mcgill.ca>
X-Sender: mayoub@po-box.mcgill.ca
X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32)
Date: Thu, 26 Nov 1998 09:41:00 -0500
To: nih-image@io.ece.drexel.edu
From: Micheline Ayoub <mayoub@po-box.mcgill.ca>
Subject: unsubscribe
Mime-Version: 1.0
Resent-Message-ID: <"RU_MX1.0.Hj1.2ZMNs"@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/668
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: 181


Micheline Ayoub
Plant Science Dpt. R2-004
Macdoanld Campus
McGill University
21111 Lakeshore Rd.
Ste-Anne-de-Bellevue, Quebec
H9X 3V9
Tel: 514-398-7851 ext 8733
Fax: 514-398-7897


From nih-image-d-request@io.ece.drexel.edu Fri Nov 27 03:18 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id DAA16222;
	Fri, 27 Nov 1998 03:18:57 -0500 (EST)
Date: Fri, 27 Nov 1998 03:18:57 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811270818.DAA16222@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #126
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/126
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 1167

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 126

Today's Topics:
  unsubscribe                           [ Micheline Ayoub <mayoub@po-box.mcgi ]
  unsubscribe                           [ "Thorsen, Anders" <anders.thorsen@i ]

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

Date: Thu, 26 Nov 1998 09:41:00 -0500
From: Micheline Ayoub <mayoub@po-box.mcgill.ca>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <3.0.6.32.19981126094100.007b6e70@po-box.mcgill.ca>
Content-Type: text/plain; charset="us-ascii"

Micheline Ayoub
Plant Science Dpt. R2-004
Macdoanld Campus
McGill University
21111 Lakeshore Rd.
Ste-Anne-de-Bellevue, Quebec
H9X 3V9
Tel: 514-398-7851 ext 8733
Fax: 514-398-7897

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

Date: Fri, 27 Nov 1998 08:59:04 +0100
From: "Thorsen, Anders" <anders.thorsen@imr.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: unsubscribe
Message-ID: <E389805C564CD111A6EF00805F15D0300780DB@hipost.imr.no>
Content-Type: text/plain

unsubscribe

--------------------------------
End of nih-image-d Digest V98 Issue #126
****************************************

From nih-image-request@io.ece.drexel.edu Fri Nov 27 03:18 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id DAA16235;
	Fri, 27 Nov 1998 03:18:59 -0500 (EST)
Resent-Date: Fri, 27 Nov 1998 03:18:59 -0500 (EST)
Message-ID: <E389805C564CD111A6EF00805F15D0300780DB@hipost.imr.no>
From: "Thorsen, Anders" <anders.thorsen@imr.no>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: unsubscribe
Date: Fri, 27 Nov 1998 08:59:04 +0100
MIME-Version: 1.0
X-Mailer: Internet Mail Service (5.0.1460.8)
Resent-Message-ID: <"76K7q.0.1O3.YlbNs"@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/669
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 13

unsubscribe


From nih-image-request@io.ece.drexel.edu Fri Nov 27 04:07 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA21652;
	Fri, 27 Nov 1998 04:07:04 -0500 (EST)
Resent-Date: Fri, 27 Nov 1998 04:07:04 -0500 (EST)
Message-Id: <3.0.5.32.19981127185403.007b6dd0@email.aims.gov.au>
X-Sender: aburja@email.aims.gov.au
X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32)
Date: Fri, 27 Nov 1998 18:54:03 +1000
To: nih-image@io.ece.drexel.edu
From: Adam Burja <aburja@aims.gov.au>
Subject: unsubscribe
Mime-Version: 1.0
Resent-Message-ID: <"yjDGw2.0.nw4.zYcNs"@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/670
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: 1



From nih-image-request@io.ece.drexel.edu Fri Nov 27 21:37 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id VAA04679;
	Fri, 27 Nov 1998 21:37:00 -0500 (EST)
Resent-Date: Fri, 27 Nov 1998 21:37:00 -0500 (EST)
From: wpchan@socrates.berkeley.edu
Date: Fri, 27 Nov 1998 18:25:09 -0800 (PST)
To: nih-image@io.ece.drexel.edu
Subject: Re: video capture at 30 fps
In-Reply-To: <Pine.SOL.3.96.981101191541.22553F-100000@socrates.berkeley.edu>
Message-ID: <Pine.SOL.3.96.981127181536.6505A-100000@socrates.berkeley.edu>
MIME-Version: 1.0
Resent-Message-ID: <"e_1JM1.0.rj.FyrNs"@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/671
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: 719

We have just got a G3/333 with 768MB of RAM running MacOS 8.5.  Even with
Virtual Memory and File Sharing off, with Scion-Image 1.62 and the Scion
LG-3, I can only get 29.97 frames per sec at 592x457 but not at 640x480,
using 'make movie' with blind capture.

I tried turning off a lot of the extensions but still no improvement. 
What have I done wrong?  Any advice are appreciated.  Thanks. 

--Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu)

On Sun, 1 Nov 1998 wpchan@socrates.berkeley.edu wrote:
> On the Mac, a 9500/132 with 90 MB of RAM and ATI graphic card, 'make
> movie' with blind capture in NIH-Image 1.61 (NTSC) can easily archive
> 29.97 frames per sec at 640x480.  The timing is right on the money. 


From nih-image-d-request@io.ece.drexel.edu Fri Nov 27 21:37 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id VAA04789;
	Fri, 27 Nov 1998 21:37:36 -0500 (EST)
Date: Fri, 27 Nov 1998 21:37:36 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811280237.VAA04789@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #127
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/127
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 1676

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 127

Today's Topics:
  unsubscribe                           [ Adam Burja <aburja@aims.gov.au> ]
  Re: video capture at 30 fps           [ wpchan@socrates.berkeley.edu ]

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

Date: Fri, 27 Nov 1998 18:54:03 +1000
From: Adam Burja <aburja@aims.gov.au>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <3.0.5.32.19981127185403.007b6dd0@email.aims.gov.au>
Content-Type: text/plain; charset="us-ascii"


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

Date: Fri, 27 Nov 1998 18:25:09 -0800 (PST)
From: wpchan@socrates.berkeley.edu
To: nih-image@io.ece.drexel.edu
Subject: Re: video capture at 30 fps
Message-ID: <Pine.SOL.3.96.981127181536.6505A-100000@socrates.berkeley.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

We have just got a G3/333 with 768MB of RAM running MacOS 8.5.  Even with
Virtual Memory and File Sharing off, with Scion-Image 1.62 and the Scion
LG-3, I can only get 29.97 frames per sec at 592x457 but not at 640x480,
using 'make movie' with blind capture.

I tried turning off a lot of the extensions but still no improvement. 
What have I done wrong?  Any advice are appreciated.  Thanks. 

--Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu)

On Sun, 1 Nov 1998 wpchan@socrates.berkeley.edu wrote:
> On the Mac, a 9500/132 with 90 MB of RAM and ATI graphic card, 'make
> movie' with blind capture in NIH-Image 1.61 (NTSC) can easily archive
> 29.97 frames per sec at 640x480.  The timing is right on the money. 

--------------------------------
End of nih-image-d Digest V98 Issue #127
****************************************

From nih-image-request@io.ece.drexel.edu Sat Nov 28 11:19 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA26297;
	Sat, 28 Nov 1998 11:19:44 -0500 (EST)
Resent-Date: Sat, 28 Nov 1998 11:19:44 -0500 (EST)
Mime-Version: 1.0
X-Sender: pauln@maine.maine.edu
Message-Id: <v04102f01b285d00743ef@[130.111.130.210]>
Date: Sat, 28 Nov 1998 11:08:34 -0500
To: nih-image@io.ece.drexel.edu
From: Paul Nakroshis <pauln@usm.maine.edu>
Subject: ATI XClaim VR
Resent-Message-ID: <"XEus4.0.J56.902Os"@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/672
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" ; format="flowed"
Content-Length: 562

Hello,

is there some trick to get NIH-Image to recognize the ATI XClaim VR graphics
card? Perhaps some plugin needed? I am running Image on a powermac 9600/233 
with
128 MB ram.

-paul
=================================================================
Paul Nakroshis                             pauln@usm.maine.edu
Department of Physics                      207.780.4158 (OFFICE)
Room 252 Science Building		   207.780.5607 (FAX)
University of Southern Maine
PO Box 9300
Portland, ME  04104-9300
=================================================================


From nih-image-d-request@io.ece.drexel.edu Sun Nov 29 06:11 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA14060;
	Sun, 29 Nov 1998 06:11:21 -0500 (EST)
Date: Sun, 29 Nov 1998 06:11:21 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811291111.GAA14060@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #128
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/128
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 2627

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 128

Today's Topics:
  3-D Newborn Skull ?                   [ "Corrina Cory" <spe4czc@forest.cf.a ]
  ATI XClaim VR                         [ Paul Nakroshis <pauln@usm.maine.edu ]

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

Date: Fri, 27 Nov 1998 16:49:09 GMT0BST
From: "Corrina Cory" <spe4czc@forest.cf.ac.uk>
To: nih-image-d@io.ece.drexel.edu
Subject: 3-D Newborn Skull ?
Message-ID: <6D37FAF7F08@NPRDCF1S.CF.AC.UK>

Hello,

I know that many human bones and organs have been scanned using MRI 
or CT and this information has been used to make a representative 3-D
model by stacking the slices. 

I am looking for a 3-D model of a newborn babies skull. 

If anyone knows if this has already been done I would appreciate it 
if you could e-mail any details of the model or any ideas of other 
contacts that may have this information.

Is it relatively simple to use NIH Image to import the MRI files and 
create a 3-D image?.  I have checked the archives but although there 
is some information on MRI scans I need more basic information like 
where do I start?  Is it as simple as saving the raw MRI 
data in a particular format,  opening it in NIH Image with a bit of 
manipulation to get the 3-D Image or is it very time consuming?

Thanks for your help

Corrina Cory

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Corrina Cory BEng MPhil 
PhD Research
Forensic Bioengineering
Medical Engineering Research Unit
UWCC
The Parade
PO Box 688
Cardiff CF2 3TE
WALES, UK

Tel    +44(0) 1222 875926
Fax    +44(0) 1222 874533
E-mail Cory@Cardiff.ac.uk 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

Date: Sat, 28 Nov 1998 11:08:34 -0500
From: Paul Nakroshis <pauln@usm.maine.edu>
To: nih-image@io.ece.drexel.edu
Subject: ATI XClaim VR
Message-Id: <v04102f01b285d00743ef@[130.111.130.210]>
Content-Type: text/plain; charset="us-ascii" ; format="flowed"

Hello,

is there some trick to get NIH-Image to recognize the ATI XClaim VR graphics
card? Perhaps some plugin needed? I am running Image on a powermac 9600/233 
with
128 MB ram.

-paul
=================================================================
Paul Nakroshis                             pauln@usm.maine.edu
Department of Physics                      207.780.4158 (OFFICE)
Room 252 Science Building		   207.780.5607 (FAX)
University of Southern Maine
PO Box 9300
Portland, ME  04104-9300
=================================================================

--------------------------------
End of nih-image-d Digest V98 Issue #128
****************************************

From nih-image-request@io.ece.drexel.edu Mon Nov 30 00:03 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id AAA26791;
	Mon, 30 Nov 1998 00:03:08 -0500 (EST)
Resent-Date: Mon, 30 Nov 1998 00:03:08 -0500 (EST)
Date: Sun, 29 Nov 1998 23:40:37 -0500 (EST)
From: nih-image-request@io.ece.drexel.edu
Message-Id: <199811300440.XAA24270@io.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: unsubscribe
References: <199811300440.XAA06258@kanga.INS.CWRU.Edu>
In-Reply-To: <199811300440.XAA06258@kanga.INS.CWRU.Edu>
X-Loop: nih-image@biomed.drexel.edu
Resent-Message-ID: <"Ew6tl2.0.Xx5.F7YOs"@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/673
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1122

WARNING:
	Please try to use 'nih-image-request@biomed.drexel.edu'
	the next time when issuing (un)subscribe requests.

                   32760 nbd@po.CWRU.Edu
nbd@po.CWRU.Edu

You have been removed from the list.

If this wasn't your intention or you are having problems getting yourself
unsubscribed, reply to this mail now (quoting it entirely (for diagnostic
purposes), and of course adding any comments you see fit).

Transcript of unsubscription request follows:
-- 
>From nbd@kanga.INS.CWRU.Edu  Sun Nov 29 23:40:34 1998
>Received: from kanga.INS.CWRU.Edu (nbd@kanga.INS.CWRU.Edu [129.22.8.32])
>	by io.ECE.Drexel.EDU (8.8.8/8.8.8) with ESMTP id XAA24235
>	for <nih-image@io.ece.drexel.edu>; Sun, 29 Nov 1998 23:40:33 -0500 (EST)
>Received: (nbd@localhost) by kanga.INS.CWRU.Edu (8.8.6+cwru/CWRU-2.5-bsdi)
>	id XAA06258; Sun, 29 Nov 1998 23:40:25 -0500 (EST) (from nbd)
>Message-Id: <199811300440.XAA06258@kanga.INS.CWRU.Edu>
>Date: Sun, 29 Nov 1998 23:40:25 -0500 (EST)
>From: nbd@po.CWRU.Edu (Nagendu B. Dev)
>To: nih-image@io.ece.drexel.edu
>Subject: unsubscribe
>Reply-To: nih-image@io.ece.drexel.edu
>
>###
>


From nih-image-request@io.ece.drexel.edu Mon Nov 30 15:06 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA17920;
	Mon, 30 Nov 1998 15:06:28 -0500 (EST)
Resent-Date: Mon, 30 Nov 1998 15:06:28 -0500 (EST)
Date: Mon, 30 Nov 1998 11:42:08 -0800 (PST)
From: Lesley Weston <lesley@interchange.ubc.ca>
To: nih-image@io.ece.drexel.edu
Subject: Re: unsubscribe
In-Reply-To: <199811300440.XAA24270@io.ece.drexel.edu>
Message-ID: <Pine.GSO.3.95q.981130113915.24727A-100000@interchange.ubc.ca>
MIME-Version: 1.0
Resent-Message-ID: <"l0wUS2.0.3y3.QKlOs"@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/674
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: 1495

I'm not sure if this was meant for me, since it seems to be addressed to the
whole list. However, I do *not* want to be removed from the list, and I haven't
sent anything suggesting I do. Please leave me on the list. Thanks.
Lesley Weston.



On Sun, 29 Nov 1998 nih-image-request@io.ece.drexel.edu wrote:

> WARNING:
> 	Please try to use 'nih-image-request@biomed.drexel.edu'
> 	the next time when issuing (un)subscribe requests.
> 
>                    32760 nbd@po.CWRU.Edu
> nbd@po.CWRU.Edu
> 
> You have been removed from the list.
> 
> If this wasn't your intention or you are having problems getting yourself
> unsubscribed, reply to this mail now (quoting it entirely (for diagnostic
> purposes), and of course adding any comments you see fit).
> 
> Transcript of unsubscription request follows:
> -- 
> >From nbd@kanga.INS.CWRU.Edu  Sun Nov 29 23:40:34 1998
> >Received: from kanga.INS.CWRU.Edu (nbd@kanga.INS.CWRU.Edu [129.22.8.32])
> >	by io.ECE.Drexel.EDU (8.8.8/8.8.8) with ESMTP id XAA24235
> >	for <nih-image@io.ece.drexel.edu>; Sun, 29 Nov 1998 23:40:33 -0500 (EST)
> >Received: (nbd@localhost) by kanga.INS.CWRU.Edu (8.8.6+cwru/CWRU-2.5-bsdi)
> >	id XAA06258; Sun, 29 Nov 1998 23:40:25 -0500 (EST) (from nbd)
> >Message-Id: <199811300440.XAA06258@kanga.INS.CWRU.Edu>
> >Date: Sun, 29 Nov 1998 23:40:25 -0500 (EST)
> >From: nbd@po.CWRU.Edu (Nagendu B. Dev)
> >To: nih-image@io.ece.drexel.edu
> >Subject: unsubscribe
> >Reply-To: nih-image@io.ece.drexel.edu
> >
> >###
> >
> 
> 


From nih-image-d-request@io.ece.drexel.edu Mon Nov 30 15:12 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA18365;
	Mon, 30 Nov 1998 15:12:32 -0500 (EST)
Date: Mon, 30 Nov 1998 15:12:32 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199811302012.PAA18365@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #129
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/129
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 5474

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 129

Today's Topics:
  Re: unsubscribe                       [ nih-image-request@io.ece.drexel.edu ]
  Scale And Rotate                      [ wgr2@cus.cam.ac.uk (Dr Gareth Rees) ]
  Re: unsubscribe                       [ Lesley Weston <lesley@interchange.u ]

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

Date: Sun, 29 Nov 1998 23:40:37 -0500 (EST)
From: nih-image-request@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: Re: unsubscribe
Message-Id: <199811300440.XAA24270@io.ece.drexel.edu>

WARNING:
	Please try to use 'nih-image-request@biomed.drexel.edu'
	the next time when issuing (un)subscribe requests.

                   32760 nbd@po.CWRU.Edu
nbd@po.CWRU.Edu

You have been removed from the list.

If this wasn't your intention or you are having problems getting yourself
unsubscribed, reply to this mail now (quoting it entirely (for diagnostic
purposes), and of course adding any comments you see fit).

Transcript of unsubscription request follows:
-- 
>From nbd@kanga.INS.CWRU.Edu  Sun Nov 29 23:40:34 1998
>Received: from kanga.INS.CWRU.Edu (nbd@kanga.INS.CWRU.Edu [129.22.8.32])
>	by io.ECE.Drexel.EDU (8.8.8/8.8.8) with ESMTP id XAA24235
>	for <nih-image@io.ece.drexel.edu>; Sun, 29 Nov 1998 23:40:33 -0500 (EST)
>Received: (nbd@localhost) by kanga.INS.CWRU.Edu (8.8.6+cwru/CWRU-2.5-bsdi)
>	id XAA06258; Sun, 29 Nov 1998 23:40:25 -0500 (EST) (from nbd)
>Message-Id: <199811300440.XAA06258@kanga.INS.CWRU.Edu>
>Date: Sun, 29 Nov 1998 23:40:25 -0500 (EST)
>From: nbd@po.CWRU.Edu (Nagendu B. Dev)
>To: nih-image@io.ece.drexel.edu
>Subject: unsubscribe
>Reply-To: nih-image@io.ece.drexel.edu
>
>###
>

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

Date: Mon, 30 Nov 1998 09:34:23 +0000
From: wgr2@cus.cam.ac.uk (Dr Gareth Rees)
To: nih-image-d@io.ece.drexel.edu
Subject: Scale And Rotate
Message-Id: <E0zkPio-0007ey-00@taurus.cus.cam.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Hello imagers,

I have a problem using the ScaleAndRotate operation from within macros. I
am trying to write a macro to perform a known linear transformation on data
(change of scale, offset, plus skew), for which I need to use the
ScaleAndRotate operation. My problem is that I do not know how to predict
the effect of issuing the command 
        ScaleAndRotate(1,1,theta).
In general, this produces an image in which the new x' and y' coordinates
are given in terms of the old ones by
        x' = x cos(theta) - y sin(theta) + a
        y' = x sin(theta) + y cos(theta) + b,
but my problem is to know how Image chooses the values of a and b. In other
words, which pixel in the image will NOT have its position changed by this
operation? SOMETIMES, it is the pixel at ((w-1)/2,(h-1)/2), where w and h
are the width and height of the image respectively - but not always.

Has anyone out there got experience of this problem, and more importantly,
its solution?

Gareth Rees

___________________________________________________________________________
Dr W Gareth Rees                              Telephone        01223 336540
Remote Sensing Group                          International +44 1223 336540
Scott Polar Research Institute                Facsimile        01223 336549
Lensfield Road                                International +44 1223 336549
Cambridge CB2 1ER                             Direct line (voice, fax,
United Kingdom                                  answer machine)      336575
___________________________________________________________________________

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

Date: Mon, 30 Nov 1998 11:42:08 -0800 (PST)
From: Lesley Weston <lesley@interchange.ubc.ca>
To: nih-image@io.ece.drexel.edu
Subject: Re: unsubscribe
Message-ID: <Pine.GSO.3.95q.981130113915.24727A-100000@interchange.ubc.ca>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I'm not sure if this was meant for me, since it seems to be addressed to the
whole list. However, I do *not* want to be removed from the list, and I haven't
sent anything suggesting I do. Please leave me on the list. Thanks.
Lesley Weston.



On Sun, 29 Nov 1998 nih-image-request@io.ece.drexel.edu wrote:

> WARNING:
> 	Please try to use 'nih-image-request@biomed.drexel.edu'
> 	the next time when issuing (un)subscribe requests.
> 
>                    32760 nbd@po.CWRU.Edu
> nbd@po.CWRU.Edu
> 
> You have been removed from the list.
> 
> If this wasn't your intention or you are having problems getting yourself
> unsubscribed, reply to this mail now (quoting it entirely (for diagnostic
> purposes), and of course adding any comments you see fit).
> 
> Transcript of unsubscription request follows:
> -- 
> >From nbd@kanga.INS.CWRU.Edu  Sun Nov 29 23:40:34 1998
> >Received: from kanga.INS.CWRU.Edu (nbd@kanga.INS.CWRU.Edu [129.22.8.32])
> >	by io.ECE.Drexel.EDU (8.8.8/8.8.8) with ESMTP id XAA24235
> >	for <nih-image@io.ece.drexel.edu>; Sun, 29 Nov 1998 23:40:33 -0500 (EST)
> >Received: (nbd@localhost) by kanga.INS.CWRU.Edu (8.8.6+cwru/CWRU-2.5-bsdi)
> >	id XAA06258; Sun, 29 Nov 1998 23:40:25 -0500 (EST) (from nbd)
> >Message-Id: <199811300440.XAA06258@kanga.INS.CWRU.Edu>
> >Date: Sun, 29 Nov 1998 23:40:25 -0500 (EST)
> >From: nbd@po.CWRU.Edu (Nagendu B. Dev)
> >To: nih-image@io.ece.drexel.edu
> >Subject: unsubscribe
> >Reply-To: nih-image@io.ece.drexel.edu
> >
> >###
> >
> 
> 

--------------------------------
End of nih-image-d Digest V98 Issue #129
****************************************

From nih-image-request@io.ece.drexel.edu Mon Nov 30 17:52 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA01669;
	Mon, 30 Nov 1998 17:52:05 -0500 (EST)
Resent-Date: Mon, 30 Nov 1998 17:52:05 -0500 (EST)
Message-Id: <v0300781ab288bc1f68ee@[144.118.33.245]>
Mime-Version: 1.0
Date: Mon, 30 Nov 1998 14:20:57 -0700
To: nih-image@io.ece.drexel.edu
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: A reminder about unsubscribing
Resent-Message-ID: <"9VKPe2.0.pz6.VdnOs"@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/675
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/enriched; charset="us-ascii"
Content-Length: 1186

<fontfamily><param>Courier</param>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</fontfamily>


note this address differs from the discussion address.

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

                                  Jonathan Nissanov, Ph.D.

                                      Associate Director  

            Computer Vision Center for Vertebrate Brain Mapping,

                a NIH Biomedical Research Technology Resource

                                http://cbis.ece.drexel.edu/ICVC/

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

Imaging and Computer Vision Center              Tel: 215-895-1381

Drexel University                                                  
Fax: 215-895-4987

Phildelphia, PA 19104                                        
yoni@coe.drexel.edu

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



From nih-image-request@io.ece.drexel.edu Tue Dec  1 01:51 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id BAA16695;
	Tue, 1 Dec 1998 01:51:14 -0500 (EST)
Resent-Date: Tue, 1 Dec 1998 01:51:14 -0500 (EST)
X-Sender: eilamt@post
Message-Id: <v02140b02b2893cfdb219@[132.66.44.130]>
Mime-Version: 1.0
Date: Tue, 1 Dec 1998 08:29:07 +0200
To: nih-image@io.ece.drexel.edu
From: eilamt@post.tau.ac.il (Tamar Eilam)
Subject: Re: unsubscribe
Resent-Message-ID: <"MFVFC1.0.VU3.vouOs"@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/676
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: 1324

>WARNING:
>        Please try to use 'nih-image-request@biomed.drexel.edu'
>        the next time when issuing (un)subscribe requests.
>
>                   32760 nbd@po.CWRU.Edu
>nbd@po.CWRU.Edu
>
>You have been removed from the list.
>
>If this wasn't your intention or you are having problems getting yourself
>unsubscribed, reply to this mail now (quoting it entirely (for diagnostic
>purposes), and of course adding any comments you see fit).
>
>Transcript of unsubscription request follows:
>--
>>From nbd@kanga.INS.CWRU.Edu  Sun Nov 29 23:40:34 1998
>>Received: from kanga.INS.CWRU.Edu (nbd@kanga.INS.CWRU.Edu [129.22.8.32])
>>       by io.ECE.Drexel.EDU (8.8.8/8.8.8) with ESMTP id XAA24235
>>       for <nih-image@io.ece.drexel.edu>; Sun, 29 Nov 1998 23:40:33 -0500
>>(EST)
>>Received: (nbd@localhost) by kanga.INS.CWRU.Edu (8.8.6+cwru/CWRU-2.5-bsdi)
>>       id XAA06258; Sun, 29 Nov 1998 23:40:25 -0500 (EST) (from nbd)
>>Message-Id: <199811300440.XAA06258@kanga.INS.CWRU.Edu>
>>Date: Sun, 29 Nov 1998 23:40:25 -0500 (EST)
>>From: nbd@po.CWRU.Edu (Nagendu B. Dev)
>>To: nih-image@io.ece.drexel.edu
>>Subject: unsubscribe
>>Reply-To: nih-image@io.ece.drexel.edu
>>
>>###
>>
I do *not* want to be removed from the list, and I haven't
sent anything suggesting I do. Please leave me on the list. Thanks
Tamar Eilam



From nih-image-request@io.ece.drexel.edu Tue Dec  1 07:31 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id HAA22359;
	Tue, 1 Dec 1998 07:31:44 -0500 (EST)
Resent-Date: Tue, 1 Dec 1998 07:31:44 -0500 (EST)
X-Authentication-Warning: mail.bio.uva.nl: Host gold.bio.uva.nl [145.18.160.48] claimed to be [145.18.160.48]
Message-Id: <l03110700b2898bccbfb1@[145.18.160.48]>
In-Reply-To: <v02140b02b2893cfdb219@[132.66.44.130]>
Mime-Version: 1.0
Date: Tue, 1 Dec 1998 13:16:47 +0100
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Exchanging 640 MB MO media between Mac and PC
Resent-Message-ID: <"cL5VI2.0.Wv4.TqzOs"@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/677
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: 763

We want to exchange magneto-optical media between Macs and the PC which
controls our confocal microscope (a Zeiss 510). On both machines, a 640MB
MO drive is hooked up, but I don't succeed to interchange the media. When I
format a cartridge on the Mac in "PC-format", the PC refuses it.

My questions are:
has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC?
What is the difference between "D" and "F" cartridges?
Norbert Vischer


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 Dec  1 08:26 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA28155;
	Tue, 1 Dec 1998 08:26:40 -0500 (EST)
Resent-Date: Tue, 1 Dec 1998 08:26:40 -0500 (EST)
Message-Id: <l03110701b2899a857f36@[128.100.71.77]>
In-Reply-To: <l03110700b2898bccbfb1@[145.18.160.48]>
References: <v02140b02b2893cfdb219@[132.66.44.130]>
Mime-Version: 1.0
Date: Tue, 1 Dec 1998 08:09:15 -0500
To: nih-image@io.ece.drexel.edu
From: yip@ibme.utoronto.ca (Christopher Yip)
Subject: Re: Exchanging 640 MB MO media between Mac and PC
Resent-Message-ID: <"xvumk1.0.DM6.Je-Os"@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/678
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: 1508

>We want to exchange magneto-optical media between Macs and the PC which
>controls our confocal microscope (a Zeiss 510). On both machines, a 640MB
>MO drive is hooked up, but I don't succeed to interchange the media. When I
>format a cartridge on the Mac in "PC-format", the PC refuses it.
>
>My questions are:
>has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC?
>What is the difference between "D" and "F" cartridges?
>Norbert Vischer
>
>
>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've had no problems with 230 MB MO disks - what I usually do is use the PC
to format them if I want a DOS-formatted version and then use Software
Architect's DOS Mounter on my Macs to see them.  (I'm assuming that MacOS's
PC Exchange will also work).

Never tried it with the 640 MB MO's though.

Chris.

Christopher M. Yip, Ph.D., P.Eng.
Assistant Professor
Department of Chemical Engineering and Applied Chemistry
Institute of Biomaterials and Biomedical Engineering
Department of Biochemistry
University of Toronto
407 Rosebrugh Building, 4 Taddle Creek Rd.
Toronto, Ontario CANADA M5S 3G9
Office:(416) 978-7853; Lab:(416) 946-5022; Fax: (416) 978-4317;
e-mail: yip@ibme.utoronto.ca
WWW: http://goldie.ibme.utoronto.ca







From nih-image-request@io.ece.drexel.edu Tue Dec  1 08:28 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA28349;
	Tue, 1 Dec 1998 08:28:10 -0500 (EST)
Resent-Date: Tue, 1 Dec 1998 08:28:10 -0500 (EST)
Message-ID: <3663E636.CABCA198@soton.ac.uk>
Date: Tue, 01 Dec 1998 12:50:59 +0000
From: Ashley Pringle <akp1@soton.ac.uk>
Organization: Clinical Neurological Sciences
X-Mailer: Mozilla 4.05 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: Exchanging 640 MB MO media between Mac and PC
References: <l03110700b2898bccbfb1@[145.18.160.48]>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"L5e2a3.0.cN6.ge-Os"@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/679
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; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Length: 348



We have had the same problem for several years and have never been
successful in solving.  In the end we gave up, bought a CD writer, and
wrote the MAC TIFF files in an ISO9660 format, which is readable across
both platforms.

Ashley Pringle
Research Fellow
Dept Clinical Neurological Sciences
University of Southampton

email: akp1@soton.ac.uk


From nih-image-request@io.ece.drexel.edu Tue Dec  1 09:03 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA01982;
	Tue, 1 Dec 1998 09:03:38 -0500 (EST)
Resent-Date: Tue, 1 Dec 1998 09:03:38 -0500 (EST)
From: paul stoodley <P.Stoodley@exeter.ac.uk>
Sender: P.Stoodley@exeter.ac.uk
To: nih-image@io.ece.drexel.edu
cc: nih-image@io.ece.drexel.edu
Subject: Re: Exchanging 640 MB MO media between Mac and PC
In-Reply-To: <3663E636.CABCA198@soton.ac.uk>
Message-ID: <SIMEON.9812011341.A@BS016.ex.ac.uk>
Date: Tue, 1 Dec 1998 13:44:41 +0000 (GMT Standard Time)
Priority: NORMAL
X-Mailer: Simeon for Win32 Version 4.1.2 Build (32)
X-Authentication: IMSP
MIME-Version: 1.0
Resent-Message-ID: <"qcgN1.0.ND7.P7_Os"@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/680
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: 1171

Along the same lines of interchanging image files between 
PC and Mac:

We have a HP CD writer attached to a PC. We copy the images 
from the Mac onto our server and then write them to a CD 
in an ISO9660 format. However, we have had some problems:
1) Although we can see long names on the PC they get 
conveted to 8 characters with a ~ symbol so I can not see 
the names correctly on the Mac. I am using adaptec software 
and have not yet found any options for defining long file 
names in the software.

2) Another thing that I have noticed is that on write only 
CD's, on which files have been added at different times, 
sometimes Explorer will only see one of the folders. If I 
eject and then reinsert the disc I might get a folder that 
was added at another time but not all of the folders. I 
guess to avoid this the trick is only to write once and 
then go onto another CD.


----------------------
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.


From nih-image-d-request@io.ece.drexel.edu Tue Dec  1 09:18 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA03425;
	Tue, 1 Dec 1998 09:18:33 -0500 (EST)
Date: Tue, 1 Dec 1998 09:18:33 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812011418.JAA03425@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #130
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/130
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 8885

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 130

Today's Topics:
  A reminder about unsubscribing        [ Jonathan Nissanov <yoni@cbis.ece.dr ]
  Re: unsubscribe                       [ eilamt@post.tau.ac.il (Tamar Eilam) ]
  Exchanging 640 MB MO media between M  [ Norbert Vischer <vischer@bio.uva.nl ]
  Re: Exchanging 640 MB MO media betwe  [ yip@ibme.utoronto.ca (Christopher Y ]
  Re: Exchanging 640 MB MO media betwe  [ Ashley Pringle <akp1@soton.ac.uk> ]
  Re: Exchanging 640 MB MO media betwe  [ paul stoodley <P.Stoodley@exeter.ac ]

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

Date: Mon, 30 Nov 1998 14:20:57 -0700
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: A reminder about unsubscribing
Message-Id: <v0300781ab288bc1f68ee@[144.118.33.245]>
Content-Type: text/enriched; charset="us-ascii"

<fontfamily><param>Courier</param>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</fontfamily>


note this address differs from the discussion address.

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

                                  Jonathan Nissanov, Ph.D.

                                      Associate Director  

            Computer Vision Center for Vertebrate Brain Mapping,

                a NIH Biomedical Research Technology Resource

                                http://cbis.ece.drexel.edu/ICVC/

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

Imaging and Computer Vision Center              Tel: 215-895-1381

Drexel University                                                  
Fax: 215-895-4987

Phildelphia, PA 19104                                        
yoni@coe.drexel.edu

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

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

Date: Tue, 1 Dec 1998 08:29:07 +0200
From: eilamt@post.tau.ac.il (Tamar Eilam)
To: nih-image@io.ece.drexel.edu
Subject: Re: unsubscribe
Message-Id: <v02140b02b2893cfdb219@[132.66.44.130]>
Content-Type: text/plain; charset="us-ascii"

>WARNING:
>        Please try to use 'nih-image-request@biomed.drexel.edu'
>        the next time when issuing (un)subscribe requests.
>
>                   32760 nbd@po.CWRU.Edu
>nbd@po.CWRU.Edu
>
>You have been removed from the list.
>
>If this wasn't your intention or you are having problems getting yourself
>unsubscribed, reply to this mail now (quoting it entirely (for diagnostic
>purposes), and of course adding any comments you see fit).
>
>Transcript of unsubscription request follows:
>--
>>From nbd@kanga.INS.CWRU.Edu  Sun Nov 29 23:40:34 1998
>>Received: from kanga.INS.CWRU.Edu (nbd@kanga.INS.CWRU.Edu [129.22.8.32])
>>       by io.ECE.Drexel.EDU (8.8.8/8.8.8) with ESMTP id XAA24235
>>       for <nih-image@io.ece.drexel.edu>; Sun, 29 Nov 1998 23:40:33 -0500
>>(EST)
>>Received: (nbd@localhost) by kanga.INS.CWRU.Edu (8.8.6+cwru/CWRU-2.5-bsdi)
>>       id XAA06258; Sun, 29 Nov 1998 23:40:25 -0500 (EST) (from nbd)
>>Message-Id: <199811300440.XAA06258@kanga.INS.CWRU.Edu>
>>Date: Sun, 29 Nov 1998 23:40:25 -0500 (EST)
>>From: nbd@po.CWRU.Edu (Nagendu B. Dev)
>>To: nih-image@io.ece.drexel.edu
>>Subject: unsubscribe
>>Reply-To: nih-image@io.ece.drexel.edu
>>
>>###
>>
I do *not* want to be removed from the list, and I haven't
sent anything suggesting I do. Please leave me on the list. Thanks
Tamar Eilam

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

Date: Tue, 1 Dec 1998 13:16:47 +0100
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Exchanging 640 MB MO media between Mac and PC
Message-Id: <l03110700b2898bccbfb1@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

We want to exchange magneto-optical media between Macs and the PC which
controls our confocal microscope (a Zeiss 510). On both machines, a 640MB
MO drive is hooked up, but I don't succeed to interchange the media. When I
format a cartridge on the Mac in "PC-format", the PC refuses it.

My questions are:
has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC?
What is the difference between "D" and "F" cartridges?
Norbert Vischer


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, 1 Dec 1998 08:09:15 -0500
From: yip@ibme.utoronto.ca (Christopher Yip)
To: nih-image@io.ece.drexel.edu
Subject: Re: Exchanging 640 MB MO media between Mac and PC
Message-Id: <l03110701b2899a857f36@[128.100.71.77]>
Content-Type: text/plain; charset="us-ascii"

>We want to exchange magneto-optical media between Macs and the PC which
>controls our confocal microscope (a Zeiss 510). On both machines, a 640MB
>MO drive is hooked up, but I don't succeed to interchange the media. When I
>format a cartridge on the Mac in "PC-format", the PC refuses it.
>
>My questions are:
>has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC?
>What is the difference between "D" and "F" cartridges?
>Norbert Vischer
>
>
>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've had no problems with 230 MB MO disks - what I usually do is use the PC
to format them if I want a DOS-formatted version and then use Software
Architect's DOS Mounter on my Macs to see them.  (I'm assuming that MacOS's
PC Exchange will also work).

Never tried it with the 640 MB MO's though.

Chris.

Christopher M. Yip, Ph.D., P.Eng.
Assistant Professor
Department of Chemical Engineering and Applied Chemistry
Institute of Biomaterials and Biomedical Engineering
Department of Biochemistry
University of Toronto
407 Rosebrugh Building, 4 Taddle Creek Rd.
Toronto, Ontario CANADA M5S 3G9
Office:(416) 978-7853; Lab:(416) 946-5022; Fax: (416) 978-4317;
e-mail: yip@ibme.utoronto.ca
WWW: http://goldie.ibme.utoronto.ca

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

Date: Tue, 01 Dec 1998 12:50:59 +0000
From: Ashley Pringle <akp1@soton.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Exchanging 640 MB MO media between Mac and PC
Message-ID: <3663E636.CABCA198@soton.ac.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

We have had the same problem for several years and have never been
successful in solving.  In the end we gave up, bought a CD writer, and
wrote the MAC TIFF files in an ISO9660 format, which is readable across
both platforms.

Ashley Pringle
Research Fellow
Dept Clinical Neurological Sciences
University of Southampton

email: akp1@soton.ac.uk

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

Date: Tue, 1 Dec 1998 13:44:41 +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: Exchanging 640 MB MO media between Mac and PC
Message-ID: <SIMEON.9812011341.A@BS016.ex.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

Along the same lines of interchanging image files between 
PC and Mac:

We have a HP CD writer attached to a PC. We copy the images 
from the Mac onto our server and then write them to a CD 
in an ISO9660 format. However, we have had some problems:
1) Although we can see long names on the PC they get 
conveted to 8 characters with a ~ symbol so I can not see 
the names correctly on the Mac. I am using adaptec software 
and have not yet found any options for defining long file 
names in the software.

2) Another thing that I have noticed is that on write only 
CD's, on which files have been added at different times, 
sometimes Explorer will only see one of the folders. If I 
eject and then reinsert the disc I might get a folder that 
was added at another time but not all of the folders. I 
guess to avoid this the trick is only to write once and 
then go onto another CD.


----------------------
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.

--------------------------------
End of nih-image-d Digest V98 Issue #130
****************************************

From nih-image-request@io.ece.drexel.edu Tue Dec  1 13:03 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA20405;
	Tue, 1 Dec 1998 13:03:03 -0500 (EST)
Resent-Date: Tue, 1 Dec 1998 13:03:03 -0500 (EST)
From: wpchan@socrates.berkeley.edu
Date: Tue, 1 Dec 1998 09:21:40 -0800 (PST)
X-Sender: wpchan@socrates
To: nih-image@io.ece.drexel.edu
Subject: Re: Exchanging 640 MB MO media between Mac and PC
In-Reply-To: <l03110700b2898bccbfb1@[145.18.160.48]>
Message-ID: <Pine.SOL.3.96.981201090430.10730B-100000@socrates>
MIME-Version: 1.0
Resent-Message-ID: <"fSfVd2.0.eA4.mM2Ps"@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/681
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: 912

We have recently brough a DynaMO 640.  DOS mounter and Ringowin were
bundled with it.  The former allows us to use a PC formatted MO on the
Mac and the latter lets us use Mac formatted MO on the PC.  Both utilities
also allow other cross-platform removables such as floppy or Syquest cart.
to be mounted.  The MO that we use are 2K-sector and formatted with the
DynaMO supplied driver both on the Mac and on the PC.

--Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu)

On Tue, 1 Dec 1998, Norbert Vischer wrote:
> We want to exchange magneto-optical media between Macs and the PC which
> controls our confocal microscope (a Zeiss 510). On both machines, a 640MB
> MO drive is hooked up, but I don't succeed to interchange the media. When I
> format a cartridge on the Mac in "PC-format", the PC refuses it.
> 
> My questions are:
> has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC?


From nih-image-request@io.ece.drexel.edu Tue Dec  1 14:48 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA29943;
	Tue, 1 Dec 1998 14:48:29 -0500 (EST)
Resent-Date: Tue, 1 Dec 1998 14:48:29 -0500 (EST)
Message-Id: <9812011914.AA13359@ch1d2301nwk>
Mime-Version: 1.0 (NeXT Mail 3.3 v124.8483.6)
Content-Transfer-Encoding: 7bit
X-Nextstep-Mailer: Mail 3.3 (Enhance 1.3)
From: Rand Dvorak <Rand.Dvorak@wdr.com>
Date: Tue,  1 Dec 98 13:14:33 -0600
To: nih-image@io.ece.drexel.edu
Subject: SONY XC-77 CCD Camera modules for sale
Resent-Message-ID: <"Wem8V2.0.LK6.sy3Ps"@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/682
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: multipart/alternative; boundary=NeXT-Mail-1035837613-7
Content-Length: 1233

--NeXT-Mail-1035837613-7
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline



Hello,

I have 6 Sony XC-77 ccd camera modules I would like to 
sell.  The price is $100 per unit,  a 50mm lens is also included
in the price.  You pay shipping by UPS, from zip code 60604.
Call UPS and determine shipping from 60604 to your zip code.
I can also ship COD if necessary.  Please respond by e-mail
to:

Rand.Dvorak@wdr.com 

if you are interested in purchasing one of these units, as I don't 
subscribe to this list.


Regards,
Rand Dvorak

--NeXT-Mail-1035837613-7
Content-Type: text/enriched; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline



<smaller>Hello,


I have 6 Sony XC-77 ccd camera modules I would like to 

sell.  The price is $100 per unit,  a 50mm lens is also included

in the price.  You pay shipping by UPS, from zip code 60604.

Call UPS and determine shipping from 60604 to your zip code.

I can also ship COD if necessary.  Please respond by e-mail

to:


Rand.Dvorak@wdr.com 


if you are interested in purchasing one of these units, as I don't 

subscribe to this list.



Regards,

Rand Dvorak

</smaller>

--NeXT-Mail-1035837613-7--


From nih-image-request@io.ece.drexel.edu Tue Dec  1 16:48 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA12424;
	Tue, 1 Dec 1998 16:48:20 -0500 (EST)
Resent-Date: Tue, 1 Dec 1998 16:48:20 -0500 (EST)
From: dmc4@cornell.edu
X-Sender: dmc4@postoffice.mail.cornell.edu
Message-Id: <v04003000b28a0be5dbce@[132.236.171.219]>
Mime-Version: 1.0
Date: Tue, 1 Dec 1998 16:20:39 -0500
To: nih-image@io.ece.drexel.edu
Subject: frame grabbers
Resent-Message-ID: <"4tiNE1.0.YI2.Zq5Ps"@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/683
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: 834

Hi,

We are in the process of trying to set up a gel documentation system. We
have a Powermac 6100/60 that is currently unused and was supposed to be
dedicated to gel documentation. However, it has a nubus slot and Scion no
longer makes a nubus framegrabber. Other than buying a new computer with a
PCI slot, which seems kind of wasteful since it will be dedicated to
securing gel images, are there any other options.. do any other companies
make equivalent framegrabbers that would work with a nubus slot?
Any suggestions would be greatly appreciated.

Thanks,
Donna Cassidy-Hanley



-----------------------------------------------------------------------------
Donna Cassidy-Hanley, PhD.
Section of Genetics and Development
Cornell University
Ithaca, New York 14853
e-mail: dmc4@cornell.edu
phone: 607-254-4837
fax: 607-255-6249



From nih-image-request@io.ece.drexel.edu Tue Dec  1 17:07 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA14616;
	Tue, 1 Dec 1998 17:07:20 -0500 (EST)
Resent-Date: Tue, 1 Dec 1998 17:07:20 -0500 (EST)
Message-ID: <19981201214140.6243.qmail@hotmail.com>
X-Originating-IP: [209.150.98.242]
From: "Michael R. Whaley, CQE" <mrwhaley@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: SONY XC-77 CCD Camera modules for sale
MIME-Version: 1.0
Date: Tue, 01 Dec 1998 13:41:34 PST
Resent-Message-ID: <"Zj2ZE.0.Iv2.JB6Ps"@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/684
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 1285



>From: Rand Dvorak <Rand.Dvorak@wdr.com>
>Date: Tue,  1 Dec 98 13:14:33 -0600
>To: nih-image@io.ece.drexel.edu
>Subject: SONY XC-77 CCD Camera modules for sale
>Reply-To: nih-image@io.ece.drexel.edu
>
>
>
>Hello,
>
>I have 6 Sony XC-77 ccd camera modules I would like to 
>sell.  The price is $100 per unit,  a 50mm lens is also included
>in the price.  You pay shipping by UPS, from zip code 60604.
>Call UPS and determine shipping from 60604 to your zip code.
>I can also ship COD if necessary.  Please respond by e-mail
>to:
>
>Rand.Dvorak@wdr.com 
>
>if you are interested in purchasing one of these units, as I don't 
>subscribe to this list.
>
>
>Regards,
>Rand Dvorak
>\

Mr. Dvorak:

Is the XC-77 a 2/3" CCD?  I could find some similar numbers, but not the 
one you have.  Also, does this unit have a "C" mount for lenses or 
adapters?  I am very interested in this unit, and just need to know if 
it will meet my need.  Thanks.



Michael R. Whaley, CQE
Supplier Quality Analyst
Magna International
Cosma Body and Chassis Systems
Marada Industries
151 Airport Drive
Westminster, Maryland  21157
410-840-1717 (Voice) 410-876-0256 (Fax)
michael_whaley@asqnet.org


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


From nih-image-request@io.ece.drexel.edu Tue Dec  1 17:11 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA15061;
	Tue, 1 Dec 1998 17:11:01 -0500 (EST)
Resent-Date: Tue, 1 Dec 1998 17:11:01 -0500 (EST)
Date: Tue, 01 Dec 1998 21:46:49 +0000 (GMT)
From: RANJAN PATRO OCE DEPT <Ranjan.Patro@NUIGALWAY.IE>
Subject: Thershold
To: NIH-IMAGE@io.ece.drexel.edu
Message-id: <01J4U6QYK1IQ005S9G@bodkin.nuigalway.ie>
X-VMS-To: NIH-IMAGE@IO.ECE.DREXEL.EDU
MIME-version: 1.0
Resent-Message-ID: <"nc1-m1.0.w_2.LF6Ps"@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/685
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 847

Hi Everybody!

I am using DT-image to analyse the area and radius of  Bubbles.
But if I change the THERSHOLD value than I am getting different measurement
value. Is there anybody know, what value of thershloding is accurate?
Thanks in advance.
Ciao,
Ranjan
***********************************************
* Ranjan Kumar Patro                          *
* Dept of Oceanography,                       *
* Martin Ryan Marine Science Institute        *
* National University of Ireland,             *
* Galway                                      *
* Voice : 353 91 524411,                      *
*                 ext:3208                    *
* Fax   : 353 91 528302                       *
* e-mail: ranjan.patro@nuigalway.ie           *             
* Web   : http://www.angelfire.com/ri/rpatro  *
***********************************************


From nih-image-request@io.ece.drexel.edu Tue Dec  1 18:23 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA21288;
	Tue, 1 Dec 1998 18:23:11 -0500 (EST)
Resent-Date: Tue, 1 Dec 1998 18:23:11 -0500 (EST)
Message-ID: <366472D7.263D@pop.uky.edu>
Date: Tue, 01 Dec 1998 17:51:56 -0500
From: alex gimelbrant <aagime0@pop.uky.edu>
Organization: U of K
X-Mailer: Mozilla 3.01 (Macintosh; I; 68K)
MIME-Version: 1.0
To: Nih mailing list <nih-image@io.ece.drexel.edu>
Subject: counting pixels of different colors
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"wqPYN.0.XU4.OC7Ps"@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/686
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset=koi8-r
Content-Length: 1119

Dear Imagers,

I need to quantitate a number of  images of double-labeled cells.
They are 8-bit images merged from monochromes generated
by a confocal microscope in "green" and "red" channels.

What I need to do is to count the number of  "red" pixels, "green" ones,
and "yellow" ones (these are the result of overlap of green and red) in
order
to calculate the extent to which these two stainings overlap.

The way I am doing it is I 
(1) Hue-sort the LUT, 
(2) density slice the LUT until all pixels I deem of a certain color are
covered, 
(3) count all pixels within the density slice.

I am not happy with the second part, since it seems to be subjective.
Besides, it is time consuming, and I cannot use a macro with
one-size-fit-all
density slices, since (sorted) LUTs vary between images  (they also
contain
a lot of darker bands, as well, so sometimes I have to omit parts of a
density
slice in order to ignore noise).
Is there any "objective" or at least consistent way to select pixels of
certain color 
(ideally, something like "all red/green/etc with brightness above
certain level" )?

TIA
Alex Gimelbrant


From nih-image-request@io.ece.drexel.edu Wed Dec  2 02:05 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id CAA05078;
	Wed, 2 Dec 1998 02:05:11 -0500 (EST)
Resent-Date: Wed, 2 Dec 1998 02:05:11 -0500 (EST)
Message-Id: <3664D656.A7A6EF58@mail.biu.ac.il>
Date: Wed, 02 Dec 1998 07:55:34 +0200
From: "Dr. Ron Goldstein" <goldst@mail.biu.ac.il>
X-Mailer: Mozilla 4.5 [en] (Win95; I)
X-Accept-Language: en
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #130
References: <199812011342.IAA29904@io.ece.drexel.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"30uyG.0.Fe.S4EPs"@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/687
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: 1509

Hi,

My two cents worth.

It is probably much easier to connect the Mac with the PC using a cheap
LAN program called DAVE (www.thursby.com). It allows PC's to be seen as
Mac's from the Mac, and the Mac to be seen as a PC from the PC"s in
Windows 95. It also interfaces with Linux/Samba. Then, you could save
your files via Ethernet directly to the Mac MO from the Zeiss. I have
used it to write CD's on a PC with Mac files, with no problem.

Good luck,

-Ron

------------------------------------------------------------------------
> 
> Subject: Exchanging 640 MB MO media between Mac and PC
> Date: Tue, 1 Dec 1998 13:16:47 +0100
> From: Norbert Vischer <vischer@bio.uva.nl>
> To: nih-image@io.ece.drexel.edu
> 
> We want to exchange magneto-optical media between Macs and the PC which
> controls our confocal microscope (a Zeiss 510). On both machines, a 640MB
> MO drive is hooked up, but I don't succeed to interchange the media. When I
> format a cartridge on the Mac in "PC-format", the PC refuses it.
> 
> My questions are:
> has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC?
> What is the difference between "D" and "F" cartridges?
> Norbert Vischer
> 
> 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 Dec  2 02:41 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id CAA08837;
	Wed, 2 Dec 1998 02:41:10 -0500 (EST)
Resent-Date: Wed, 2 Dec 1998 02:41:10 -0500 (EST)
Message-ID: <32A291D8.317D@wxs.nl>
Date: Mon, 02 Dec 1996 08:22:51 +0000
From: "P.M. Houpt" <houpt@wxs.nl>
Organization: BIOMET
X-Mailer: Mozilla 3.01-C-WXS-Mac (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: frame grabbers
References: <v04003000b28a0be5dbce@[132.236.171.219]>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"xeT1m.0.yg1.HhEPs"@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/688
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: 296

Hi Donna,

Try to find a framegrabber card Called AV card , it is specially made
for the 6100 and 7100 series.Ask Apple , here in my country they are
very cheap ( less $50). I have the software for it.

best wishes,

Pieter Houpt
-- 

BIOMET
The Hague , The Netherlands.
voice/fax : 00703504466


From nih-image-request@io.ece.drexel.edu Wed Dec  2 03:10 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id DAA12059;
	Wed, 2 Dec 1998 03:10:42 -0500 (EST)
Resent-Date: Wed, 2 Dec 1998 03:10:42 -0500 (EST)
Message-ID: <36657006.599D@cris.enel.it>
Date: Wed, 02 Dec 1998 08:51:18 -0800
From: "Zuccala David" <zuccala@cris.enel.it>
Reply-To: zuccala@cris.enel.it
Organization: ENEL Ricerca - Polo Idraulico e Strutturale
X-Mailer: Mozilla 3.01Gold (Win16; I)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Re: Exchanging 640 MB MO media between Mac and PC
References: <199812011407.JAA02430@io.ece.drexel.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"XcvtI3.0.aO2.34FPs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/689
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: 1525

Dear Norbert,
> We want to exchange magneto-optical media between Macs and the PC which
> controls our confocal microscope (a Zeiss 510). On both machines, a 640MB
> MO drive is hooked up, but I don't succeed to interchange the media. When I
> format a cartridge on the Mac in "PC-format", the PC refuses it.

There is no a widely accepted standard for logical format of MO
cartridges; each software producer uses a different format, so you have
no guarantee to be able to read data across MAC and PCs, but also across
PCs connected to different drivers.
Thank to writable CDs, MOs are becoming obsolete and this problem in the
future will disappear.

Dear Paul 
> We have a HP CD writer attached to a PC. We copy the images
> from the Mac onto our server and then write them to a CD
> in an ISO9660 format. However, we have had some problems:
> 1) Although we can see long names on the PC they get
> conveted to 8 characters with a ~ symbol so I can not see
> the names correctly on the Mac. I am using adaptec software
> and have not yet found any options for defining long file
> names in the software.

Toast software for Mac allows to generate extended ISO9660 format that
supports long names. I could see these long names on Mac and UNIX
platforms. I never tried with Windows 95 PCs.

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  (office)


From nih-image-d-request@io.ece.drexel.edu Wed Dec  2 06:24 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA01291;
	Wed, 2 Dec 1998 06:24:51 -0500 (EST)
Date: Wed, 2 Dec 1998 06:24:51 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812021124.GAA01291@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #131
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/131
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 13127

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 131

Today's Topics:
  Re: Exchanging 640 MB MO media betwe  [ wpchan@socrates.berkeley.edu ]
  SONY XC-77 CCD Camera modules for sa  [ Rand Dvorak <Rand.Dvorak@wdr.com> ]
  frame grabbers                        [ dmc4@cornell.edu ]
  Re: SONY XC-77 CCD Camera modules fo  [ "Michael R. Whaley, CQE" <mrwhaley@ ]
  Thershold                             [ RANJAN PATRO OCE DEPT <Ranjan.Patro ]
  counting pixels of different colors   [ alex gimelbrant <aagime0@pop.uky.ed ]
  Re: nih-image-d Digest V98 #130       [ "Dr. Ron Goldstein" <goldst@mail.bi ]
  Re: frame grabbers                    [ "P.M. Houpt" <houpt@wxs.nl> ]
  Re: Exchanging 640 MB MO media betwe  [ "Zuccala David" <zuccala@cris.enel. ]

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

Date: Tue, 1 Dec 1998 09:21:40 -0800 (PST)
From: wpchan@socrates.berkeley.edu
To: nih-image@io.ece.drexel.edu
Subject: Re: Exchanging 640 MB MO media between Mac and PC
Message-ID: <Pine.SOL.3.96.981201090430.10730B-100000@socrates>
Content-Type: TEXT/PLAIN; charset=US-ASCII

We have recently brough a DynaMO 640.  DOS mounter and Ringowin were
bundled with it.  The former allows us to use a PC formatted MO on the
Mac and the latter lets us use Mac formatted MO on the PC.  Both utilities
also allow other cross-platform removables such as floppy or Syquest cart.
to be mounted.  The MO that we use are 2K-sector and formatted with the
DynaMO supplied driver both on the Mac and on the PC.

--Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu)

On Tue, 1 Dec 1998, Norbert Vischer wrote:
> We want to exchange magneto-optical media between Macs and the PC which
> controls our confocal microscope (a Zeiss 510). On both machines, a 640MB
> MO drive is hooked up, but I don't succeed to interchange the media. When I
> format a cartridge on the Mac in "PC-format", the PC refuses it.
> 
> My questions are:
> has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC?

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

Date: Tue,  1 Dec 98 13:14:33 -0600
From: Rand Dvorak <Rand.Dvorak@wdr.com>
To: nih-image@io.ece.drexel.edu
Subject: SONY XC-77 CCD Camera modules for sale
Message-Id: <9812011914.AA13359@ch1d2301nwk>
Content-Type: multipart/alternative; boundary=NeXT-Mail-1035837613-7
Content-Transfer-Encoding: 7bit

--NeXT-Mail-1035837613-7
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline



Hello,

I have 6 Sony XC-77 ccd camera modules I would like to 
sell.  The price is $100 per unit,  a 50mm lens is also included
in the price.  You pay shipping by UPS, from zip code 60604.
Call UPS and determine shipping from 60604 to your zip code.
I can also ship COD if necessary.  Please respond by e-mail
to:

Rand.Dvorak@wdr.com 

if you are interested in purchasing one of these units, as I don't 
subscribe to this list.


Regards,
Rand Dvorak

--NeXT-Mail-1035837613-7
Content-Type: text/enriched; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Disposition: inline



<smaller>Hello,


I have 6 Sony XC-77 ccd camera modules I would like to 

sell.  The price is $100 per unit,  a 50mm lens is also included

in the price.  You pay shipping by UPS, from zip code 60604.

Call UPS and determine shipping from 60604 to your zip code.

I can also ship COD if necessary.  Please respond by e-mail

to:


Rand.Dvorak@wdr.com 


if you are interested in purchasing one of these units, as I don't 

subscribe to this list.



Regards,

Rand Dvorak

</smaller>

--NeXT-Mail-1035837613-7--

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

Date: Tue, 1 Dec 1998 16:20:39 -0500
From: dmc4@cornell.edu
To: nih-image@io.ece.drexel.edu
Subject: frame grabbers
Message-Id: <v04003000b28a0be5dbce@[132.236.171.219]>
Content-Type: text/plain; charset="us-ascii"

Hi,

We are in the process of trying to set up a gel documentation system. We
have a Powermac 6100/60 that is currently unused and was supposed to be
dedicated to gel documentation. However, it has a nubus slot and Scion no
longer makes a nubus framegrabber. Other than buying a new computer with a
PCI slot, which seems kind of wasteful since it will be dedicated to
securing gel images, are there any other options.. do any other companies
make equivalent framegrabbers that would work with a nubus slot?
Any suggestions would be greatly appreciated.

Thanks,
Donna Cassidy-Hanley



-----------------------------------------------------------------------------
Donna Cassidy-Hanley, PhD.
Section of Genetics and Development
Cornell University
Ithaca, New York 14853
e-mail: dmc4@cornell.edu
phone: 607-254-4837
fax: 607-255-6249

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

Date: Tue, 01 Dec 1998 13:41:34 PST
From: "Michael R. Whaley, CQE" <mrwhaley@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: SONY XC-77 CCD Camera modules for sale
Message-ID: <19981201214140.6243.qmail@hotmail.com>
Content-Type: text/plain

>From: Rand Dvorak <Rand.Dvorak@wdr.com>
>Date: Tue,  1 Dec 98 13:14:33 -0600
>To: nih-image@io.ece.drexel.edu
>Subject: SONY XC-77 CCD Camera modules for sale
>Reply-To: nih-image@io.ece.drexel.edu
>
>
>
>Hello,
>
>I have 6 Sony XC-77 ccd camera modules I would like to 
>sell.  The price is $100 per unit,  a 50mm lens is also included
>in the price.  You pay shipping by UPS, from zip code 60604.
>Call UPS and determine shipping from 60604 to your zip code.
>I can also ship COD if necessary.  Please respond by e-mail
>to:
>
>Rand.Dvorak@wdr.com 
>
>if you are interested in purchasing one of these units, as I don't 
>subscribe to this list.
>
>
>Regards,
>Rand Dvorak
>\

Mr. Dvorak:

Is the XC-77 a 2/3" CCD?  I could find some similar numbers, but not the 
one you have.  Also, does this unit have a "C" mount for lenses or 
adapters?  I am very interested in this unit, and just need to know if 
it will meet my need.  Thanks.



Michael R. Whaley, CQE
Supplier Quality Analyst
Magna International
Cosma Body and Chassis Systems
Marada Industries
151 Airport Drive
Westminster, Maryland  21157
410-840-1717 (Voice) 410-876-0256 (Fax)
michael_whaley@asqnet.org


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

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

Date: Tue, 01 Dec 1998 21:46:49 +0000 (GMT)
From: RANJAN PATRO OCE DEPT <Ranjan.Patro@NUIGALWAY.IE>
To: NIH-IMAGE@io.ece.drexel.edu
Subject: Thershold
Message-id: <01J4U6QYK1IQ005S9G@bodkin.nuigalway.ie>

Hi Everybody!

I am using DT-image to analyse the area and radius of  Bubbles.
But if I change the THERSHOLD value than I am getting different measurement
value. Is there anybody know, what value of thershloding is accurate?
Thanks in advance.
Ciao,
Ranjan
***********************************************
* Ranjan Kumar Patro                          *
* Dept of Oceanography,                       *
* Martin Ryan Marine Science Institute        *
* National University of Ireland,             *
* Galway                                      *
* Voice : 353 91 524411,                      *
*                 ext:3208                    *
* Fax   : 353 91 528302                       *
* e-mail: ranjan.patro@nuigalway.ie           *             
* Web   : http://www.angelfire.com/ri/rpatro  *
***********************************************

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

Date: Tue, 01 Dec 1998 17:51:56 -0500
From: alex gimelbrant <aagime0@pop.uky.edu>
To: Nih mailing list <nih-image@io.ece.drexel.edu>
Subject: counting pixels of different colors
Message-ID: <366472D7.263D@pop.uky.edu>
Content-Type: text/plain; charset=koi8-r
Content-Transfer-Encoding: 7bit

Dear Imagers,

I need to quantitate a number of  images of double-labeled cells.
They are 8-bit images merged from monochromes generated
by a confocal microscope in "green" and "red" channels.

What I need to do is to count the number of  "red" pixels, "green" ones,
and "yellow" ones (these are the result of overlap of green and red) in
order
to calculate the extent to which these two stainings overlap.

The way I am doing it is I 
(1) Hue-sort the LUT, 
(2) density slice the LUT until all pixels I deem of a certain color are
covered, 
(3) count all pixels within the density slice.

I am not happy with the second part, since it seems to be subjective.
Besides, it is time consuming, and I cannot use a macro with
one-size-fit-all
density slices, since (sorted) LUTs vary between images  (they also
contain
a lot of darker bands, as well, so sometimes I have to omit parts of a
density
slice in order to ignore noise).
Is there any "objective" or at least consistent way to select pixels of
certain color 
(ideally, something like "all red/green/etc with brightness above
certain level" )?

TIA
Alex Gimelbrant

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

Date: Wed, 02 Dec 1998 07:55:34 +0200
From: "Dr. Ron Goldstein" <goldst@mail.biu.ac.il>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #130
Message-Id: <3664D656.A7A6EF58@mail.biu.ac.il>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi,

My two cents worth.

It is probably much easier to connect the Mac with the PC using a cheap
LAN program called DAVE (www.thursby.com). It allows PC's to be seen as
Mac's from the Mac, and the Mac to be seen as a PC from the PC"s in
Windows 95. It also interfaces with Linux/Samba. Then, you could save
your files via Ethernet directly to the Mac MO from the Zeiss. I have
used it to write CD's on a PC with Mac files, with no problem.

Good luck,

-Ron

------------------------------------------------------------------------
> 
> Subject: Exchanging 640 MB MO media between Mac and PC
> Date: Tue, 1 Dec 1998 13:16:47 +0100
> From: Norbert Vischer <vischer@bio.uva.nl>
> To: nih-image@io.ece.drexel.edu
> 
> We want to exchange magneto-optical media between Macs and the PC which
> controls our confocal microscope (a Zeiss 510). On both machines, a 640MB
> MO drive is hooked up, but I don't succeed to interchange the media. When I
> format a cartridge on the Mac in "PC-format", the PC refuses it.
> 
> My questions are:
> has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC?
> What is the difference between "D" and "F" cartridges?
> Norbert Vischer
> 
> 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, 02 Dec 1996 08:22:51 +0000
From: "P.M. Houpt" <houpt@wxs.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: frame grabbers
Message-ID: <32A291D8.317D@wxs.nl>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi Donna,

Try to find a framegrabber card Called AV card , it is specially made
for the 6100 and 7100 series.Ask Apple , here in my country they are
very cheap ( less $50). I have the software for it.

best wishes,

Pieter Houpt
-- 

BIOMET
The Hague , The Netherlands.
voice/fax : 00703504466

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

Date: Wed, 02 Dec 1998 08:51:18 -0800
From: "Zuccala David" <zuccala@cris.enel.it>
To: nih-image@io.ece.drexel.edu
Subject: Re: Exchanging 640 MB MO media between Mac and PC
Message-ID: <36657006.599D@cris.enel.it>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Dear Norbert,
> We want to exchange magneto-optical media between Macs and the PC which
> controls our confocal microscope (a Zeiss 510). On both machines, a 640MB
> MO drive is hooked up, but I don't succeed to interchange the media. When I
> format a cartridge on the Mac in "PC-format", the PC refuses it.

There is no a widely accepted standard for logical format of MO
cartridges; each software producer uses a different format, so you have
no guarantee to be able to read data across MAC and PCs, but also across
PCs connected to different drivers.
Thank to writable CDs, MOs are becoming obsolete and this problem in the
future will disappear.

Dear Paul 
> We have a HP CD writer attached to a PC. We copy the images
> from the Mac onto our server and then write them to a CD
> in an ISO9660 format. However, we have had some problems:
> 1) Although we can see long names on the PC they get
> conveted to 8 characters with a ~ symbol so I can not see
> the names correctly on the Mac. I am using adaptec software
> and have not yet found any options for defining long file
> names in the software.

Toast software for Mac allows to generate extended ISO9660 format that
supports long names. I could see these long names on Mac and UNIX
platforms. I never tried with Windows 95 PCs.

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  (office)

--------------------------------
End of nih-image-d Digest V98 Issue #131
****************************************

From nih-image-request@io.ece.drexel.edu Wed Dec  2 10:25 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA24532;
	Wed, 2 Dec 1998 10:25:22 -0500 (EST)
Resent-Date: Wed, 2 Dec 1998 10:25:22 -0500 (EST)
Message-Id: <l03102800b28b031e5aca@[131.130.80.137]>
In-Reply-To: <199812021118.GAA00463@io.ece.drexel.edu>
Mime-Version: 1.0
Date: Wed, 2 Dec 1998 15:54:33 +0100
To: nih-image@io.ece.drexel.edu
From: Michael Glotzer <mglotzer@nt.imp.univie.ac.at>
Subject: setting quicktime parameters from within a macro
Resent-Message-ID: <"Usg3D2.0.9J5.HJLPs"@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/690
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: 831

Hi Imagers,
I would like to specify the settings of the "compression settings" dialog
box that comes up when you save a stack as a quicktime file.  There are a
number of settings:
1) compressor
	 choices are none, photojpeg, etc
2) a sub dialog
	choices ae colr, greyscale, best depth
3) quality
	a numeric value is set with a slider
4) then comes a bunch of other settings that concern motion

My questions:
a) is it possible to set 1,2, and 3 from within a macro?
b) what are the motion settings for?

Thanks for your help
Michael




___________________________________________________________________

Michael Glotzer
Research Institute of Molecular Pathology
Dr. Bohr-Gasse 7
A-1030 Vienna
AUSTRIA

phone   43-(1)797-30-405   office
phone   43-(1)797-30-525   lab
fax     43-(1)798-7153
email   mglotzer@nt.imp.univie.ac.at



From nih-image-request@io.ece.drexel.edu Wed Dec  2 10:33 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA25174;
	Wed, 2 Dec 1998 10:33:00 -0500 (EST)
Resent-Date: Wed, 2 Dec 1998 10:33:00 -0500 (EST)
From: "Herbert M. Geller" <geller@UMDNJ.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #130
In-Reply-To: <3664D656.A7A6EF58@mail.biu.ac.il>
Message-ID: <SIMEON.9812012107.B@hmgpc.umdnj.edu>
Date: Tue, 1 Dec 1998 21:12:07 -0500 (Eastern Standard Time)
Priority: NORMAL
X-Mailer: Simeon for Win32 Version 4.1.5 Build (43)
X-Authentication: none
MIME-Version: 1.0
Resent-Message-ID: <"dlJKq3.0.PW5.jRLPs"@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/691
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: 1437

V
On Wed, 02 Dec 1998 07:55:34 +0200 "Dr. Ron Goldstein" 
<goldst@mail.biu.ac.il> wrote:

> Hi,
> 
> My two cents worth.
> 
> It is probably much easier to connect the Mac with the PC using a cheap
> LAN program called DAVE (www.thursby.com). It allows PC's to be seen as
> Mac's from the Mac, and the Mac to be seen as a PC from the PC"s in
> Windows 95. It also interfaces with Linux/Samba. Then, you could save
> your files via Ethernet directly to the Mac MO from the Zeiss. I have
> used it to write CD's on a PC with Mac files, with no problem.

> > We want to exchange magneto-optical media between Macs and the PC which
> > controls our confocal microscope (a Zeiss 510). On both machines, a 640MB
> > MO drive is hooked up, but I don't succeed to interchange the media. When I
> > format a cartridge on the Mac in "PC-format", the PC refuses it.

If both of these machines are on a network, we have found 
that COPStalk works smoothly to allow Windows machines 
to see the Appletalk network, which includes reading and 
writing to Macs from the PC.

Information can be gotten at:
http://www.copstalk.com/index.shtml
----------------------------------------------------------
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-request@io.ece.drexel.edu Wed Dec  2 18:08 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA05386;
	Wed, 2 Dec 1998 18:08:57 -0500 (EST)
Resent-Date: Wed, 2 Dec 1998 18:08:57 -0500 (EST)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: aagime0@pop.uky.edu, nih-image@io.ece.drexel.edu
Date:          Thu, 3 Dec 1998 9:42:39 GMT+1100
Subject:       Re: counting pixels of different colors
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <39A712B453A@rna.bio.mq.edu.au>
Resent-Message-ID: <"rCQKu2.0.NZ.D7SPs"@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/692
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 2396

>Date: Tue, 01 Dec 1998 17:51:56 -0500
>From: alex gimelbrant <aagime0@pop.uky.edu>
>..........
>I need to quantitate a number of  images of double-labeled cells.
>They are 8-bit images merged from monochromes generated
>by a confocal microscope in "green" and "red" channels.
>
>What I need to do is to count the number of  "red" pixels, "green" ones,
>and "yellow" ones (these are the result of overlap of green and red) in
>order
>to calculate the extent to which these two stainings overlap.
>
>The way I am doing it is I 
>(1) Hue-sort the LUT, 
>(2) density slice the LUT until all pixels I deem of a certain color are
>covered, 
>(3) count all pixels within the density slice.
>
>I am not happy with the second part, since it seems to be subjective.
>Besides, it is time consuming, and I cannot use a macro with
>one-size-fit-all
>density slices, since (sorted) LUTs vary between images  (they also
>contain
>a lot of darker bands, as well, so sometimes I have to omit parts of a
>density
>slice in order to ignore noise).
>Is there any "objective" or at least consistent way to select pixels of
>certain color 
>(ideally, something like "all red/green/etc with brightness above
>certain level" )?
>

Alex,
     
It would be best to work with the orginal "green" and "red" channel images as they 
are presumeably both 8-bit. Then you could threshold (ie "something like "all 
red/green with brightness above certain level"") each channel and makebinary 
separately to get red/green maps. A simple paste with "And" option would then give 
the overlap map.

The "8-bit color images merged from monochromes" are likely to be formed by bin 
counting the pixel intensities in RGB space to 32 level (5-bit) bins and then 
successively bisecting the 32 R x 32 G x 32 B space into 254 (256-2 white/black) 
"equally" populated regions. The central coordinate of each region is then used as 
the bin color.

You can recover the red/green channels by using "8-bit color to RGB"(stack menu. 

The red and green channels will then be 32 level (5-bit) posterised
 (the blue channel should be empty).

You can then threshold each of the red and green slices(1,2) of the RGB stack and
AND them together to find overlap.
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 Dec  2 20:17 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA19111;
	Wed, 2 Dec 1998 20:17:58 -0500 (EST)
Resent-Date: Wed, 2 Dec 1998 20:17:58 -0500 (EST)
Message-Id: <199812030058.IAA31651@nero.rph.health.wa.gov.au>
From: "Robert Day" <robday@rph.health.wa.gov.au>
To: nih-image@io.ece.drexel.edu
Date: Thu, 3 Dec 1998 08:49:42 +0800
MIME-Version: 1.0
Content-transfer-encoding: 7BIT
Subject: Re: Exchanging 640 MB MO media between Mac and PC
Priority: normal
References: <3663E636.CABCA198@soton.ac.uk>
In-reply-to: <SIMEON.9812011341.A@BS016.ex.ac.uk>
X-mailer: Pegasus Mail for Win32 (v3.01b)
Resent-Message-ID: <"WaZ5i1.0.A14.i3UPs"@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/693
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: 1767


> We have a HP CD writer attached to a PC. We copy the images 
> from the Mac onto our server and then write them to a CD 
> in an ISO9660 format. However, we have had some problems:
> 1) Although we can see long names on the PC they get 
> conveted to 8 characters with a ~ symbol so I can not see 
> the names correctly on the Mac. I am using adaptec software 
> and have not yet found any options for defining long file 
> names in the software.

If you are using EasyCD Pro, which is what Adaptec was selling 
most recently, then under the filenames tab there should be an 
option for "Joliet (Win95 long file names)".  This a typically broken 
Microsoft version of the Rock Ridge extensions to iso9600, but if 
you keep under 31 characters the names will show up on the Mac.  
I do this a lot and it works OK for Mac win95 and Unix, even if it 
does play around with the case of names - damn Microsoft :-(

> 2) Another thing that I have noticed is that on write only 
> CD's, on which files have been added at different times, 
> sometimes Explorer will only see one of the folders. If I 
> eject and then reinsert the disc I might get a folder that 
> was added at another time but not all of the folders. I 
> guess to avoid this the trick is only to write once and 
> then go onto another CD.

This can be a problem with multi-session CDs, in some drives.  Try 
making a multi-session mode 1 CD instead.  I know you're 
supposed to use mode 2 for multi-session, but sometinmes the 
Adaptec software seems to get it wrong.  Partly because of this 
problem we switched to Nero, and this has been a much better 
product.


Rob.

--
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-d-request@io.ece.drexel.edu Thu Dec  3 06:26 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA29134;
	Thu, 3 Dec 1998 06:26:17 -0500 (EST)
Date: Thu, 3 Dec 1998 06:26:17 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812031126.GAA29134@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #132
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/132
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 8198

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 132

Today's Topics:
  setting quicktime parameters from wi  [ Michael Glotzer <mglotzer@nt.imp.un ]
  Re: nih-image-d Digest V98 #130       [ "Herbert M. Geller" <geller@UMDNJ.E ]
  Re: counting pixels of different col  [ GJOSS@rna.bio.mq.edu.au ]
  Re: Exchanging 640 MB MO media betwe  [ "Robert Day" <robday@rph.health.wa. ]

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

Date: Wed, 2 Dec 1998 15:54:33 +0100
From: Michael Glotzer <mglotzer@nt.imp.univie.ac.at>
To: nih-image@io.ece.drexel.edu
Subject: setting quicktime parameters from within a macro
Message-Id: <l03102800b28b031e5aca@[131.130.80.137]>
Content-Type: text/plain; charset="us-ascii"

Hi Imagers,
I would like to specify the settings of the "compression settings" dialog
box that comes up when you save a stack as a quicktime file.  There are a
number of settings:
1) compressor
	 choices are none, photojpeg, etc
2) a sub dialog
	choices ae colr, greyscale, best depth
3) quality
	a numeric value is set with a slider
4) then comes a bunch of other settings that concern motion

My questions:
a) is it possible to set 1,2, and 3 from within a macro?
b) what are the motion settings for?

Thanks for your help
Michael




___________________________________________________________________

Michael Glotzer
Research Institute of Molecular Pathology
Dr. Bohr-Gasse 7
A-1030 Vienna
AUSTRIA

phone   43-(1)797-30-405   office
phone   43-(1)797-30-525   lab
fax     43-(1)798-7153
email   mglotzer@nt.imp.univie.ac.at

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

Date: Tue, 1 Dec 1998 21:12:07 -0500 (Eastern Standard Time)
From: "Herbert M. Geller" <geller@UMDNJ.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #130
Message-ID: <SIMEON.9812012107.B@hmgpc.umdnj.edu>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

V
On Wed, 02 Dec 1998 07:55:34 +0200 "Dr. Ron Goldstein" 
<goldst@mail.biu.ac.il> wrote:

> Hi,
> 
> My two cents worth.
> 
> It is probably much easier to connect the Mac with the PC using a cheap
> LAN program called DAVE (www.thursby.com). It allows PC's to be seen as
> Mac's from the Mac, and the Mac to be seen as a PC from the PC"s in
> Windows 95. It also interfaces with Linux/Samba. Then, you could save
> your files via Ethernet directly to the Mac MO from the Zeiss. I have
> used it to write CD's on a PC with Mac files, with no problem.

> > We want to exchange magneto-optical media between Macs and the PC which
> > controls our confocal microscope (a Zeiss 510). On both machines, a 640MB
> > MO drive is hooked up, but I don't succeed to interchange the media. When I
> > format a cartridge on the Mac in "PC-format", the PC refuses it.

If both of these machines are on a network, we have found 
that COPStalk works smoothly to allow Windows machines 
to see the Appletalk network, which includes reading and 
writing to Macs from the PC.

Information can be gotten at:
http://www.copstalk.com/index.shtml
----------------------------------------------------------
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/

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

Date:          Thu, 3 Dec 1998 9:42:39 GMT+1100
From: GJOSS@rna.bio.mq.edu.au
To: aagime0@pop.uky.edu, nih-image@io.ece.drexel.edu
Subject:       Re: counting pixels of different colors
Message-ID: <39A712B453A@rna.bio.mq.edu.au>

>Date: Tue, 01 Dec 1998 17:51:56 -0500
>From: alex gimelbrant <aagime0@pop.uky.edu>
>..........
>I need to quantitate a number of  images of double-labeled cells.
>They are 8-bit images merged from monochromes generated
>by a confocal microscope in "green" and "red" channels.
>
>What I need to do is to count the number of  "red" pixels, "green" ones,
>and "yellow" ones (these are the result of overlap of green and red) in
>order
>to calculate the extent to which these two stainings overlap.
>
>The way I am doing it is I 
>(1) Hue-sort the LUT, 
>(2) density slice the LUT until all pixels I deem of a certain color are
>covered, 
>(3) count all pixels within the density slice.
>
>I am not happy with the second part, since it seems to be subjective.
>Besides, it is time consuming, and I cannot use a macro with
>one-size-fit-all
>density slices, since (sorted) LUTs vary between images  (they also
>contain
>a lot of darker bands, as well, so sometimes I have to omit parts of a
>density
>slice in order to ignore noise).
>Is there any "objective" or at least consistent way to select pixels of
>certain color 
>(ideally, something like "all red/green/etc with brightness above
>certain level" )?
>

Alex,
     
It would be best to work with the orginal "green" and "red" channel images as they 
are presumeably both 8-bit. Then you could threshold (ie "something like "all 
red/green with brightness above certain level"") each channel and makebinary 
separately to get red/green maps. A simple paste with "And" option would then give 
the overlap map.

The "8-bit color images merged from monochromes" are likely to be formed by bin 
counting the pixel intensities in RGB space to 32 level (5-bit) bins and then 
successively bisecting the 32 R x 32 G x 32 B space into 254 (256-2 white/black) 
"equally" populated regions. The central coordinate of each region is then used as 
the bin color.

You can recover the red/green channels by using "8-bit color to RGB"(stack menu. 

The red and green channels will then be 32 level (5-bit) posterised
 (the blue channel should be empty).

You can then threshold each of the red and green slices(1,2) of the RGB stack and
AND them together to find overlap.
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, 3 Dec 1998 08:49:42 +0800
From: "Robert Day" <robday@rph.health.wa.gov.au>
To: nih-image@io.ece.drexel.edu
Subject: Re: Exchanging 640 MB MO media between Mac and PC
Message-Id: <199812030058.IAA31651@nero.rph.health.wa.gov.au>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7BIT

> We have a HP CD writer attached to a PC. We copy the images 
> from the Mac onto our server and then write them to a CD 
> in an ISO9660 format. However, we have had some problems:
> 1) Although we can see long names on the PC they get 
> conveted to 8 characters with a ~ symbol so I can not see 
> the names correctly on the Mac. I am using adaptec software 
> and have not yet found any options for defining long file 
> names in the software.

If you are using EasyCD Pro, which is what Adaptec was selling 
most recently, then under the filenames tab there should be an 
option for "Joliet (Win95 long file names)".  This a typically broken 
Microsoft version of the Rock Ridge extensions to iso9600, but if 
you keep under 31 characters the names will show up on the Mac.  
I do this a lot and it works OK for Mac win95 and Unix, even if it 
does play around with the case of names - damn Microsoft :-(

> 2) Another thing that I have noticed is that on write only 
> CD's, on which files have been added at different times, 
> sometimes Explorer will only see one of the folders. If I 
> eject and then reinsert the disc I might get a folder that 
> was added at another time but not all of the folders. I 
> guess to avoid this the trick is only to write once and 
> then go onto another CD.

This can be a problem with multi-session CDs, in some drives.  Try 
making a multi-session mode 1 CD instead.  I know you're 
supposed to use mode 2 for multi-session, but sometinmes the 
Adaptec software seems to get it wrong.  Partly because of this 
problem we switched to Nero, and this has been a much better 
product.


Rob.

--
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 V98 Issue #132
****************************************

From nih-image-request@io.ece.drexel.edu Thu Dec  3 09:47 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA22167;
	Thu, 3 Dec 1998 09:47:57 -0500 (EST)
Resent-Date: Thu, 3 Dec 1998 09:47:57 -0500 (EST)
Message-ID: <69B43248FE73D11197BB00A0C99AB06789AC@jvcserver.vanguardweb.org>
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>,
        "'NIH wayne'"
	 <wayne@helix.nih.gov>
Subject: Interpolation Macro
Date: Thu, 3 Dec 1998 09:03:43 -0500 
MIME-Version: 1.0
X-Mailer: Internet Mail Service (5.5.1960.3)
Resent-Message-ID: <"Kt6xP2.0.GQ4.snfPs"@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/694
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 429

Hi,
Is it possible to interpolate two CT slices, creating 3rd one in NIH?. I
have two B&W images and I want to create third image by interpolating
given two images. Is there any macro to interpolate 150 plus slices?.
Which interpolation approach is the best (bilinear or nearest neighboor
or other methods).

Thanks
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-U of M
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087


From nih-image-request@io.ece.drexel.edu Thu Dec  3 10:22 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA26699;
	Thu, 3 Dec 1998 10:22:18 -0500 (EST)
Resent-Date: Thu, 3 Dec 1998 10:22:18 -0500 (EST)
Message-Id: <9812031452.AA396380@mail.biu.ac.il>
From: "Giller Dima" <giller@PHYSNET.PH.BIU.AC.IL>
Organization: Physics Dept, Bar-Ilan University
To: nih-image@io.ece.drexel.edu
Date: Thu, 3 Dec 1998 16:52:05 IST+2
Subject:  Problem with NIH(Scion)-Image
Reply-To: giller@PHYSNET.PH.BIU.AC.IL
Priority: normal
X-Mailer: Pegasus Mail for Win32 (v3.01d)
Resent-Message-ID: <"XEBrk.0.Wa5.-MgPs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/695
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 788


Hello! 
In our work we use frame grabber AG-5 of Scion corporation and 
the program "Scion Image" that helps us a lot.  I would like to ask 
you some question about  "NIH (Scion)-Image".When I write the 
macro and try to copy a group of images with real values into a 
stack,I face some problem. LUT of all slices remains unchanged but 
the values inside the image do change (this problem doesn't exist for 
images with integer values).
I will very appreciate if you could explain me how I should deal with 
this problem.
   Thanks a lot. 
_____________________________________________________

Dima Giller
Institute of Superconductivity
Department of Physics, Bar-Ilan University
Ramat-Gan, Israel 52900
tel: (972) (3) 5317325  fax:(972) (3) 5353298
email: giller@physnet.ph.biu.ac.il


From nih-image-request@io.ece.drexel.edu Thu Dec  3 13:35 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA15559;
	Thu, 3 Dec 1998 13:35:30 -0500 (EST)
Resent-Date: Thu, 3 Dec 1998 13:35:30 -0500 (EST)
Date: Thu, 3 Dec 1998 12:50:40 -0500 (EST)
X-Authentication-Warning: pop.uky.edu: [128.163.85.61] didn't use HELO protocol
Message-Id: <2.2.16.19981203125039.34a79670@pop.uky.edu>
X-Sender: bcler1@pop.uky.edu
X-Mailer: Windows Eudora Pro Version 2.2 (16)
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu
From: "Bill Clerici, Ph.D." <bcler1@pop.uky.edu>
Subject: Quantification of fluorescein in single cells
Resent-Message-ID: <"ZRDYJ1.0.vo2.xziPs"@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/696
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: 2110

I would like to quantify the fluorescence of single cells examined at 600x
magnification after treatment with a fluorescein probe. Pilot cells
fluoresce very intensely under experimental conditions, while control cells
are not visually detectable. However, I am not certain how best to calibrate
the system and measure the cells. I have the Kodak control scales
recommended by the NIH Image manual, and, calibrated the microscope/ NIH
Image system (at 100x and 600x) using the microscope's normal white light on
full intensity, with and without each of two neutral density filters.
However, since it is not white light that will be measured from the cell, I,
then, attempted to calibrate using the same filter and magnification
combinations, utilizing the UV light source. I could calibrate at 100x using
the UV light source with no neutral density filters, but, if either ND
filter was used (as will be used with cells), then the light was too dark.
At 600x, the magnification needed for the experiment, the light intensity
was too dark, even without any neutral density filters. My question is "How
should the system be calibrated?" Since we are exciting the cells at one
wavelength (488 nm) and, measuring emissions at another (530 nm), are any of
these conditions appropriate? I would very much appreciate any advice as to
the best (or, even an adequate) method of calibrating the system for such
conditions. Also, once values are measured for standard areas within each
cell, should the background intensity be subtracted from that of the cell,
or should a ratio of cell to background intensity be calculated?

Thank you, very much, for your help.
Sincerely,
Bill Clerici

--------------------------------------------
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 Thu Dec  3 14:02 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA17993;
	Thu, 3 Dec 1998 14:02:54 -0500 (EST)
Resent-Date: Thu, 3 Dec 1998 14:02:54 -0500 (EST)
Message-Id: <m0zldRf-000KG0C@post.cis.smu.edu>
X-Mailer: Microsoft Outlook Express for Macintosh - 4.01 (295) 
Date: Thu, 03 Dec 1998 12:23:51 -0500
Subject: Help with grain-size analysis
From: "Peter A. Scholle" <pscholle@post.cis.smu.edu>
To: nih-image@io.ece.drexel.edu
Mime-version: 1.0
X-Priority: 3
Content-transfer-encoding: 7bit
Resent-Message-ID: <"TS0kl.0.Cd3.fWjPs"@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/697
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: 636

I am a new user of Image 1.61 and could use some help.  I am trying to do
automated grain- and pore-size analysis on digital scanning electron
micrographs of very fine-grained rocks (chalks).  I basically need to
construct a histogram of the principal (longest and shortest) axes of all
the
grains in the image.  I have been able to threshold the image to distinguish
between grains and pores but have not figured out how to get the grain size
measurements.  Any help would be much appreciated.

Dr. Peter A. Scholle
Dept. of Geological Sciences
Southern Methodist University
Dallas, TX 75275 U.S.A.
214-768-4011
pscholle@mail.smu.edu


From nih-image-request@io.ece.drexel.edu Thu Dec  3 16:31 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA00509;
	Thu, 3 Dec 1998 16:31:14 -0500 (EST)
Resent-Date: Thu, 3 Dec 1998 16:31:14 -0500 (EST)
Message-Id: <l03010d00b28c9143baa4@[212.238.25.42]>
In-Reply-To: <m0zldRf-000KG0C@post.cis.smu.edu>
Mime-Version: 1.0
Date: Thu, 3 Dec 1998 22:00:21 +0100
To: nih-image@io.ece.drexel.edu
From: Norbert Vischer <vischer@bio.uva.nl>
Subject: Re: Help with grain-size analysis
Resent-Message-ID: <"8pDX33.0.wm6.JjlPs"@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/698
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: 1115

There is a set of macro commands available in Object-Image for the creation
of histograms. An example is shown in the file 'sort particles' in
'Examples.sea', where particle analysis is performed and the particle
diameter is plotted as histogram. Similarly, one can mark long and short
axes of the best-fitting ellipse and put them into a histogram.

The macro syntax allows you to combine several parameters in a single
graphics, each one shown in the desired color and with statistic values
like mean and stdev.

The advantage compared to exporting data to Excel is that Object-Image
integrates macros, direct and derived results and non-destructive markers
into a single file, so you can update the histogram any time with a single
keystroke. No intermediate files need to be created, and you need not to
care about data organisation and non-existing results ('zero' is different
from 'nothing'). You also can trace a result back to the corresponding
image, and kill or modify the markers.

If you are interested I can give you more hints.


look at:
http://simon.bio.uva.nl/object-image.html

Norbert Vischer



From nih-image-d-request@io.ece.drexel.edu Fri Dec  4 06:28 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA14402;
	Fri, 4 Dec 1998 06:28:45 -0500 (EST)
Date: Fri, 4 Dec 1998 06:28:45 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812041128.GAA14402@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #133
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/133
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 7264

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 133

Today's Topics:
  Interpolation Macro                   [ "Mehmet Dondurur, Ph. D." <mehmet.d ]
  Problem with NIH(Scion)-Image         [ "Giller Dima" <giller@PHYSNET.PH.BI ]
  Quantification of fluorescein in sin  [ "Bill Clerici, Ph.D." <bcler1@pop.u ]
  Help with grain-size analysis         [ "Peter A. Scholle" <pscholle@post.c ]
  Re: Help with grain-size analysis     [ Norbert Vischer <vischer@bio.uva.nl ]

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

Date: Thu, 3 Dec 1998 09:03:43 -0500 
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>,
        "'NIH wayne'"
	 <wayne@helix.nih.gov>
Subject: Interpolation Macro
Message-ID: <69B43248FE73D11197BB00A0C99AB06789AC@jvcserver.vanguardweb.org>
Content-Type: text/plain

Hi,
Is it possible to interpolate two CT slices, creating 3rd one in NIH?. I
have two B&W images and I want to create third image by interpolating
given two images. Is there any macro to interpolate 150 plus slices?.
Which interpolation approach is the best (bilinear or nearest neighboor
or other methods).

Thanks
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-U of M
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087

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

Date: Thu, 3 Dec 1998 16:52:05 IST+2
From: "Giller Dima" <giller@PHYSNET.PH.BIU.AC.IL>
To: nih-image@io.ece.drexel.edu
Subject:  Problem with NIH(Scion)-Image
Message-Id: <9812031452.AA396380@mail.biu.ac.il>

Hello! 
In our work we use frame grabber AG-5 of Scion corporation and 
the program "Scion Image" that helps us a lot.  I would like to ask 
you some question about  "NIH (Scion)-Image".When I write the 
macro and try to copy a group of images with real values into a 
stack,I face some problem. LUT of all slices remains unchanged but 
the values inside the image do change (this problem doesn't exist for 
images with integer values).
I will very appreciate if you could explain me how I should deal with 
this problem.
   Thanks a lot. 
_____________________________________________________

Dima Giller
Institute of Superconductivity
Department of Physics, Bar-Ilan University
Ramat-Gan, Israel 52900
tel: (972) (3) 5317325  fax:(972) (3) 5353298
email: giller@physnet.ph.biu.ac.il

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

Date: Thu, 3 Dec 1998 12:50:40 -0500 (EST)
From: "Bill Clerici, Ph.D." <bcler1@pop.uky.edu>
To: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu
Subject: Quantification of fluorescein in single cells
Message-Id: <2.2.16.19981203125039.34a79670@pop.uky.edu>
Content-Type: text/plain; charset="us-ascii"

I would like to quantify the fluorescence of single cells examined at 600x
magnification after treatment with a fluorescein probe. Pilot cells
fluoresce very intensely under experimental conditions, while control cells
are not visually detectable. However, I am not certain how best to calibrate
the system and measure the cells. I have the Kodak control scales
recommended by the NIH Image manual, and, calibrated the microscope/ NIH
Image system (at 100x and 600x) using the microscope's normal white light on
full intensity, with and without each of two neutral density filters.
However, since it is not white light that will be measured from the cell, I,
then, attempted to calibrate using the same filter and magnification
combinations, utilizing the UV light source. I could calibrate at 100x using
the UV light source with no neutral density filters, but, if either ND
filter was used (as will be used with cells), then the light was too dark.
At 600x, the magnification needed for the experiment, the light intensity
was too dark, even without any neutral density filters. My question is "How
should the system be calibrated?" Since we are exciting the cells at one
wavelength (488 nm) and, measuring emissions at another (530 nm), are any of
these conditions appropriate? I would very much appreciate any advice as to
the best (or, even an adequate) method of calibrating the system for such
conditions. Also, once values are measured for standard areas within each
cell, should the background intensity be subtracted from that of the cell,
or should a ratio of cell to background intensity be calculated?

Thank you, very much, for your help.
Sincerely,
Bill Clerici

--------------------------------------------
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: Thu, 03 Dec 1998 12:23:51 -0500
From: "Peter A. Scholle" <pscholle@post.cis.smu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Help with grain-size analysis
Message-Id: <m0zldRf-000KG0C@post.cis.smu.edu>
Content-type: text/plain; charset="US-ASCII"
Content-transfer-encoding: 7bit

I am a new user of Image 1.61 and could use some help.  I am trying to do
automated grain- and pore-size analysis on digital scanning electron
micrographs of very fine-grained rocks (chalks).  I basically need to
construct a histogram of the principal (longest and shortest) axes of all
the
grains in the image.  I have been able to threshold the image to distinguish
between grains and pores but have not figured out how to get the grain size
measurements.  Any help would be much appreciated.

Dr. Peter A. Scholle
Dept. of Geological Sciences
Southern Methodist University
Dallas, TX 75275 U.S.A.
214-768-4011
pscholle@mail.smu.edu

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

Date: Thu, 3 Dec 1998 22:00:21 +0100
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Help with grain-size analysis
Message-Id: <l03010d00b28c9143baa4@[212.238.25.42]>
Content-Type: text/plain; charset="us-ascii"

There is a set of macro commands available in Object-Image for the creation
of histograms. An example is shown in the file 'sort particles' in
'Examples.sea', where particle analysis is performed and the particle
diameter is plotted as histogram. Similarly, one can mark long and short
axes of the best-fitting ellipse and put them into a histogram.

The macro syntax allows you to combine several parameters in a single
graphics, each one shown in the desired color and with statistic values
like mean and stdev.

The advantage compared to exporting data to Excel is that Object-Image
integrates macros, direct and derived results and non-destructive markers
into a single file, so you can update the histogram any time with a single
keystroke. No intermediate files need to be created, and you need not to
care about data organisation and non-existing results ('zero' is different
from 'nothing'). You also can trace a result back to the corresponding
image, and kill or modify the markers.

If you are interested I can give you more hints.


look at:
http://simon.bio.uva.nl/object-image.html

Norbert Vischer

--------------------------------
End of nih-image-d Digest V98 Issue #133
****************************************

From nih-image-request@io.ece.drexel.edu Fri Dec  4 11:02 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA08974;
	Fri, 4 Dec 1998 11:02:04 -0500 (EST)
Resent-Date: Fri, 4 Dec 1998 11:02:04 -0500 (EST)
Date: Fri, 4 Dec 1998 15:11:36 +0000 (BST)
From: Dan Lovegrove <Dan.Lovegrove@earth.ox.ac.uk>
X-Sender: danl@cook
Reply-To: Dan Lovegrove <Dan.Lovegrove@earth.ox.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Best Fit Ellipses
Message-ID: <Pine.GSO.3.96.981204150653.14926J-100000@cook>
Organisation: Department of Earth Sciences University of Oxford UK.
MIME-Version: 1.0
Resent-Message-ID: <"jROR_.0.1A1.0l_Ps"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/699
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: 583


I was wondering exactly how NIH image calculates the major and minor axes
etc. of best fit ellipses to irregularly shaped particles.
Cheers
Dan Lovegrove

################################

Castle Milk Stout - Brewed to be Rich and Dark

Dan Lovegrove Esq.                                
Department of Earth Sciences                  
University of Oxford                          
Parks Road                                    
OXFORD
OX1 3PR
email: danl@earth.ox.ac.uk
telephone: (01865) 272000
direct line: (01865) 272056
fax: (01865) 272072


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



From nih-image-request@io.ece.drexel.edu Fri Dec  4 11:32 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA11564;
	Fri, 4 Dec 1998 11:32:31 -0500 (EST)
Resent-Date: Fri, 4 Dec 1998 11:32:31 -0500 (EST)
From: DrJohnRuss@aol.com
Message-ID: <18cc33e7.3668044e@aol.com>
Date: Fri, 4 Dec 1998 10:48:30 EST
To: nih-image@io.ece.drexel.edu
Mime-Version: 1.0
Subject: Ann: Application notes on-line
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 for Mac sub 84
Resent-Message-ID: <"UMDw82.0.Vx1.bI0Qs"@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/700
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: 547

Users of the Image Processing Tool Kit may download several *.pdf files
containing application notes on topics such as deconvolution to remove image
blur, hysteresis thresholding, automatic counting for stereological analysis
using grids, coloring features by the magnitude of any measured parameter,
measuring feature fractal dimension, and converting images of graphs to
numeric data. Either click on the "Application Notes" link at the main web
page (http://members.aol.com/ImagProcTK) or go directly to
http://members.aol.com/IPTK/index.html


From nih-image-request@io.ece.drexel.edu Fri Dec  4 12:07 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA14120;
	Fri, 4 Dec 1998 12:07:05 -0500 (EST)
Resent-Date: Fri, 4 Dec 1998 12:07:05 -0500 (EST)
Message-Id: <v03007801b28dbff2d1f9@[128.231.99.220]>
In-Reply-To: <Pine.GSO.3.96.981204150653.14926J-100000@cook>
Mime-Version: 1.0
Date: Fri, 4 Dec 1998 12:37:54 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: Best Fit Ellipses
Resent-Message-ID: <"DLLvs.0.mp2.Gw0Qs"@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/701
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: 209

>I was wondering exactly how NIH image calculates the major and minor axes
>etc. of best fit ellipses to irregularly shaped particles.

Look at the source ("ellipse.p") to see exactly how it's done.

-wayne



From nih-image-d-request@io.ece.drexel.edu Sat Dec  5 05:19 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA10923;
	Sat, 5 Dec 1998 05:19:39 -0500 (EST)
Date: Sat, 5 Dec 1998 05:19:39 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812051019.FAA10923@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #134
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/134
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 4943

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 134

Today's Topics:
  Best Fit Ellipses                     [ Dan Lovegrove <Dan.Lovegrove@earth. ]
  Ann: Application notes on-line        [ DrJohnRuss@aol.com ]
  Re: Best Fit Ellipses                 [ Wayne Rasband <wayne@codon.nih.gov> ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]

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

Date: Fri, 4 Dec 1998 15:11:36 +0000 (BST)
From: Dan Lovegrove <Dan.Lovegrove@earth.ox.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Best Fit Ellipses
Message-ID: <Pine.GSO.3.96.981204150653.14926J-100000@cook>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I was wondering exactly how NIH image calculates the major and minor axes
etc. of best fit ellipses to irregularly shaped particles.
Cheers
Dan Lovegrove

################################

Castle Milk Stout - Brewed to be Rich and Dark

Dan Lovegrove Esq.                                
Department of Earth Sciences                  
University of Oxford                          
Parks Road                                    
OXFORD
OX1 3PR
email: danl@earth.ox.ac.uk
telephone: (01865) 272000
direct line: (01865) 272056
fax: (01865) 272072


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

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

Date: Fri, 4 Dec 1998 10:48:30 EST
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Ann: Application notes on-line
Message-ID: <18cc33e7.3668044e@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

Users of the Image Processing Tool Kit may download several *.pdf files
containing application notes on topics such as deconvolution to remove image
blur, hysteresis thresholding, automatic counting for stereological analysis
using grids, coloring features by the magnitude of any measured parameter,
measuring feature fractal dimension, and converting images of graphs to
numeric data. Either click on the "Application Notes" link at the main web
page (http://members.aol.com/ImagProcTK) or go directly to
http://members.aol.com/IPTK/index.html

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

Date: Fri, 4 Dec 1998 12:37:54 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Best Fit Ellipses
Message-Id: <v03007801b28dbff2d1f9@[128.231.99.220]>
Content-Type: text/plain; charset="us-ascii"

>I was wondering exactly how NIH image calculates the major and minor axes
>etc. of best fit ellipses to irregularly shaped particles.

Look at the source ("ellipse.p") to see exactly how it's done.

-wayne

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

Date: Sat, 5 Dec 1998 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: <199812051005.FAA09162@io.ece.drexel.edu>

                   NIH-image Mailing List Help 

nih-image@biomed.drexel.edu   - Sends mail to the list
nih-image-request@biomed.drexel.edu   - Administation for List
nih-image-d-request@biomed.drexel.edu  - Aministration for Digest


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".

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


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

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

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

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 V98 Issue #134
****************************************

From nih-image-request@io.ece.drexel.edu Sat Dec  5 05:19 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA10934;
	Sat, 5 Dec 1998 05:19:41 -0500 (EST)
Resent-Date: Sat, 5 Dec 1998 05:19:41 -0500 (EST)
Date: Sat, 5 Dec 1998 05:05:01 -0500 (EST)
From: nih-image-owner@io.ece.drexel.edu
Message-Id: <199812051005.FAA09162@io.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Resent-Message-ID: <"Epdvs.0.QF2.GLGQs"@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/702
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1997

                   NIH-image Mailing List Help 

nih-image@biomed.drexel.edu   - Sends mail to the list
nih-image-request@biomed.drexel.edu   - Administation for List
nih-image-d-request@biomed.drexel.edu  - Aministration for Digest


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".

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


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

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

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

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 Mon Dec  7 12:06 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA00212;
	Mon, 7 Dec 1998 12:06:44 -0500 (EST)
Resent-Date: Mon, 7 Dec 1998 12:06:44 -0500 (EST)
X-Sender: merchant@mail.persci.com
Message-Id: <l03110701b291a3b913a5@[199.5.159.182]>
Mime-Version: 1.0
Date: Mon, 7 Dec 1998 10:29:07 -0500
To: CONFOCAL@LISTSERV.ACSU.BUFFALO.EDU
From: Merchant <merchant@persci.com>
Subject: HSEMB 99 conference (Session on Imaging)
Cc: Microscopy@sparc5.microscopy.com, nih-image@io.ece.drexel.edu
Resent-Message-ID: <"Z2pif2.0.1c6.V90Rs"@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/703
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: 1874


>********************************
>
>ANNOUNCEMENT:  Special session on Image Analysis for Optical Microscopy
>
>The Houston Society for Engineering in Medicine and Biology (HSEMB) is
>holding its 17th annual Houston Conference on Biomedical Engineering at the
>University of Houston on February 11-12, 1999.  This conference is usually
>well-attended and very informative, and draws attendees from a wide variety
>of biomedical engineering fields and from a fairly wide geographic area as
>well.  We are organizing and chairing a session tentatively entitled "Image
>Analysis for Optical Microscopy" as part of the Medical Image Processing
>topic.  We would like to encourage submissions from parties performing
>research on the analysis of microscope images (brightfield, fluorescence,
>or confocal) for this session.
>
>Other topics of potential interest at the conference include Lasers &
>Optics, Neural Networks, Biosignal Processing, Medical Physics, Ultrasound,
>and Computational Biology.  Further information can be found at
>http://www.hsemb.org/.  The abstract submission deadline is December 11,
>1998.  Our session will consist of oral presentations (approximately 15-20
>minutes apiece).  Only one-page abstracts are published by the conference.
>
>Please e-mail Fatima Merchant (merchant@persci.com) or Mark Schulze
>(schulze@persci.com) for more information about submitting a paper to this
>special session.
>
>*****************************


 <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>

 Fatima Merchant, Ph.D.
 Senior Research Engineer
 Perceptive Scientific Instruments, Inc.
 2525 South Shore Blvd., Suite 100
 League City, Texas 77573

 Telephone:	(281) 334-3027 Ext: 219
 Toll Free:	(800) 288-3027 Ext: 219
 Facsimile:	(281) 538-2222
 Email:		merchant@persci.com

 <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>



From nih-image-d-request@io.ece.drexel.edu Tue Dec  8 06:27 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA02187;
	Tue, 8 Dec 1998 06:27:05 -0500 (EST)
Date: Tue, 8 Dec 1998 06:27:05 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812081127.GAA02187@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #135
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/135
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 2541

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 135

Today's Topics:
  HSEMB 99 conference (Session on Imag  [ Merchant <merchant@persci.com> ]

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

Date: Mon, 7 Dec 1998 10:29:07 -0500
From: Merchant <merchant@persci.com>
To: CONFOCAL@LISTSERV.ACSU.BUFFALO.EDU
Cc: Microscopy@sparc5.microscopy.com, nih-image@io.ece.drexel.edu
Subject: HSEMB 99 conference (Session on Imaging)
Message-Id: <l03110701b291a3b913a5@[199.5.159.182]>
Content-Type: text/plain; charset="us-ascii"

>********************************
>
>ANNOUNCEMENT:  Special session on Image Analysis for Optical Microscopy
>
>The Houston Society for Engineering in Medicine and Biology (HSEMB) is
>holding its 17th annual Houston Conference on Biomedical Engineering at the
>University of Houston on February 11-12, 1999.  This conference is usually
>well-attended and very informative, and draws attendees from a wide variety
>of biomedical engineering fields and from a fairly wide geographic area as
>well.  We are organizing and chairing a session tentatively entitled "Image
>Analysis for Optical Microscopy" as part of the Medical Image Processing
>topic.  We would like to encourage submissions from parties performing
>research on the analysis of microscope images (brightfield, fluorescence,
>or confocal) for this session.
>
>Other topics of potential interest at the conference include Lasers &
>Optics, Neural Networks, Biosignal Processing, Medical Physics, Ultrasound,
>and Computational Biology.  Further information can be found at
>http://www.hsemb.org/.  The abstract submission deadline is December 11,
>1998.  Our session will consist of oral presentations (approximately 15-20
>minutes apiece).  Only one-page abstracts are published by the conference.
>
>Please e-mail Fatima Merchant (merchant@persci.com) or Mark Schulze
>(schulze@persci.com) for more information about submitting a paper to this
>special session.
>
>*****************************


 <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>

 Fatima Merchant, Ph.D.
 Senior Research Engineer
 Perceptive Scientific Instruments, Inc.
 2525 South Shore Blvd., Suite 100
 League City, Texas 77573

 Telephone:	(281) 334-3027 Ext: 219
 Toll Free:	(800) 288-3027 Ext: 219
 Facsimile:	(281) 538-2222
 Email:		merchant@persci.com

 <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>

--------------------------------
End of nih-image-d Digest V98 Issue #135
****************************************

From nih-image-request@io.ece.drexel.edu Tue Dec  8 13:51 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA11275;
	Tue, 8 Dec 1998 13:51:43 -0500 (EST)
Resent-Date: Tue, 8 Dec 1998 13:51:43 -0500 (EST)
From: sandri@pas.matrix.com.br
Message-ID: <366D6CCB.2CA4@pas.matrix.com.br>
Date: Tue, 08 Dec 1998 16:15:42 -0200
Reply-To: sandri@pas.matrix.com.br
X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: Quit!
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"ug5nY1.0.ks1.XmMRs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/704
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: 13

unsubscribe


From nih-image-d-request@io.ece.drexel.edu Wed Dec  9 06:25 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA04786;
	Wed, 9 Dec 1998 06:25:05 -0500 (EST)
Date: Wed, 9 Dec 1998 06:25:05 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812091125.GAA04786@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #136
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/136
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 587

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 136

Today's Topics:
  Quit!                                 [ sandri@pas.matrix.com.br ]

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

Date: Tue, 08 Dec 1998 16:15:42 -0200
From: sandri@pas.matrix.com.br
To: nih-image@io.ece.drexel.edu
Subject: Quit!
Message-ID: <366D6CCB.2CA4@pas.matrix.com.br>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

unsubscribe

--------------------------------
End of nih-image-d Digest V98 Issue #136
****************************************

From nih-image-request@io.ece.drexel.edu Wed Dec  9 11:37 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA04871;
	Wed, 9 Dec 1998 11:37:20 -0500 (EST)
Resent-Date: Wed, 9 Dec 1998 11:37:20 -0500 (EST)
From: "Angelika Zohlen" <vxt_anzo@luecology.ecol.lu.se>
Organization: Dpt of Ecology, Lund Univ, Sweden
To: nih-image@io.ece.drexel.edu
Date: Wed, 9 Dec 1998 17:10:48 +0200
MIME-Version: 1.0
Subject: leaf area measurements
Reply-to: vxt_anzo@luecology.ecol.lu.se
Priority: normal
X-mailer: Pegasus Mail for Windows (v2.23)
Message-ID: <4B215D68F4@Luecology.ecol.lu.se>
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from Quoted-printable to 8bit by io.ECE.Drexel.EDU id LAA02304
Resent-Message-ID: <"CBOvp1.0.Ba.Z3gRs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/705
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset=ISO-8859-1
Content-Length: 653

Hello,
I am looking for a scanner to measure leaf areas in situ and roots. I
dont think that a scan board is suitable because its a bit clumsy
and heavy. Does anybody know if their are scanners available where the
electronic part is separate from the board or if there are different
scanning systems for measuring in the field? 
Any information is appreciated.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Angelika Zohlen
Soil-Plant Research, Dept. of Ecology
Lund University, Ecology Building 
S-22362 Lund, Sweden

Tel. +46/(0)46/2224247, Fax  +46/(0)46/2224423, E-mail vxt_anzo@luecology.ecol.lu.se


From nih-image-request@io.ece.drexel.edu Wed Dec  9 17:49 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA05248;
	Wed, 9 Dec 1998 17:49:10 -0500 (EST)
Resent-Date: Wed, 9 Dec 1998 17:49:10 -0500 (EST)
X-Authentication-Warning: pagan.vims.edu: cutter owned process doing -bs
Date: Wed, 9 Dec 1998 17:25:59 -0500 (EST)
From: Randy Cutter <cutter@vims.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #121
In-Reply-To: <199811210522.AAA03619@io.ece.drexel.edu>
Message-ID: <Pine.SOL.3.96.981209171743.18403A-100000@pagan.vims.edu>
MIME-Version: 1.0
Resent-Message-ID: <"uF3Xv.0.Ti.MalRs"@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/707
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: 761

I have been registering stacks using Image 1.62 very successfully with 
grayscale or 8-bit color images.  The grayscale stacks do
not elucidate many of the features which I would like to portray, and the
8-bit indexed color images look rather bad.  I have tried other software,
including Image-Pro Plus and Adobe After Effects, but they don't allow
registration upon stacks by definition of fiducial points upon the
multiple images in the stacks.  Does anyone have suggestions concerning
registration of 24-bit color image stacks?  Thank you.

Randy.

---------------------
Randy Cutter
Virginia Institute of Marine Science
Route 1208 
Gloucester Point, VA 23062 USA

phone 804 684-7365
fax 804 684-7399 or 7045
email:  cutter@vims.edu

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



From nih-image-request@io.ece.drexel.edu Wed Dec  9 17:49 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA05292;
	Wed, 9 Dec 1998 17:49:26 -0500 (EST)
Resent-Date: Wed, 9 Dec 1998 17:49:26 -0500 (EST)
Message-ID: <366EF878.269B@pop.uky.edu>
Date: Wed, 09 Dec 1998 17:23:51 -0500
From: alex gimelbrant <aagime0@pop.uky.edu>
Organization: U of K
X-Mailer: Mozilla 3.01 (Macintosh; I; 68K)
MIME-Version: 1.0
To: NIH-Image mailing list <nih-image@io.ece.drexel.edu>
Subject: Automatic thresholding
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"j7N203.0.2e.kXlRs"@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/706
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: 327

Dear Imagers,

Can anyone explain how automatic thresholding works, or point me to some
description of it?

(That's what the online manual says:

... The threshold is automatically set based on an analysis of the
histogram of the current selection, or of the entire image if there is
no selection. ...)

TIA,

Alex Gimelbrant


From nih-image-d-request@io.ece.drexel.edu Thu Dec 10 06:21 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA21900;
	Thu, 10 Dec 1998 06:21:05 -0500 (EST)
Date: Thu, 10 Dec 1998 06:21:05 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812101121.GAA21900@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #137
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/137
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 3141

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 137

Today's Topics:
  leaf area measurements                [ "Angelika Zohlen" <vxt_anzo@luecolo ]
  Automatic thresholding                [ alex gimelbrant <aagime0@pop.uky.ed ]
  Re: nih-image-d Digest V98 #121       [ Randy Cutter <cutter@vims.edu> ]

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

Date: Wed, 9 Dec 1998 17:10:48 +0200
From: "Angelika Zohlen" <vxt_anzo@luecology.ecol.lu.se>
To: nih-image@io.ece.drexel.edu
Subject: leaf area measurements
Message-ID: <4B215D68F4@Luecology.ecol.lu.se>
Content-type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 8bit

Hello,
I am looking for a scanner to measure leaf areas in situ and roots. I
dont think that a scan board is suitable because its a bit clumsy
and heavy. Does anybody know if their are scanners available where the
electronic part is separate from the board or if there are different
scanning systems for measuring in the field? 
Any information is appreciated.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Angelika Zohlen
Soil-Plant Research, Dept. of Ecology
Lund University, Ecology Building 
S-22362 Lund, Sweden

Tel. +46/(0)46/2224247, Fax  +46/(0)46/2224423, E-mail vxt_anzo@luecology.ecol.lu.se

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

Date: Wed, 09 Dec 1998 17:23:51 -0500
From: alex gimelbrant <aagime0@pop.uky.edu>
To: NIH-Image mailing list <nih-image@io.ece.drexel.edu>
Subject: Automatic thresholding
Message-ID: <366EF878.269B@pop.uky.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Dear Imagers,

Can anyone explain how automatic thresholding works, or point me to some
description of it?

(That's what the online manual says:

... The threshold is automatically set based on an analysis of the
histogram of the current selection, or of the entire image if there is
no selection. ...)

TIA,

Alex Gimelbrant

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

Date: Wed, 9 Dec 1998 17:25:59 -0500 (EST)
From: Randy Cutter <cutter@vims.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #121
Message-ID: <Pine.SOL.3.96.981209171743.18403A-100000@pagan.vims.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I have been registering stacks using Image 1.62 very successfully with 
grayscale or 8-bit color images.  The grayscale stacks do
not elucidate many of the features which I would like to portray, and the
8-bit indexed color images look rather bad.  I have tried other software,
including Image-Pro Plus and Adobe After Effects, but they don't allow
registration upon stacks by definition of fiducial points upon the
multiple images in the stacks.  Does anyone have suggestions concerning
registration of 24-bit color image stacks?  Thank you.

Randy.

---------------------
Randy Cutter
Virginia Institute of Marine Science
Route 1208 
Gloucester Point, VA 23062 USA

phone 804 684-7365
fax 804 684-7399 or 7045
email:  cutter@vims.edu

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

--------------------------------
End of nih-image-d Digest V98 Issue #137
****************************************

From nih-image-request@io.ece.drexel.edu Thu Dec 10 10:08 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA14868;
	Thu, 10 Dec 1998 10:08:37 -0500 (EST)
Resent-Date: Thu, 10 Dec 1998 10:08:37 -0500 (EST)
Message-Id: <s66f85e9.017@mednet.swmed.edu>
X-Mailer: Novell GroupWise 5.5
Date: Thu, 10 Dec 1998 08:27:19 -0600
From: "Daniel Blander" <DBLAND@mednet.swmed.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: frame grabber
Mime-Version: 1.0
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id JAA10679
Resent-Message-ID: <"UlTX5.0.0d2.DfzRs"@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/708
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: 306

I have an old macintosh with whichi am trying to set up color image analysis using NIH image.  I need a color frame grabber on a NuBus board (Scion LG3 or equivalent).  Is there anyone out there who has one or knows how i can get one??

Daniel Blander
Instructor in Urology
UT Southwestern Medical School


From nih-image-d-request@io.ece.drexel.edu Fri Dec 11 06:19 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA15073;
	Fri, 11 Dec 1998 06:19:23 -0500 (EST)
Date: Fri, 11 Dec 1998 06:19:23 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812111119.GAA15073@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #138
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/138
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 945

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 138

Today's Topics:
  frame grabber                         [ "Daniel Blander" <DBLAND@mednet.swm ]

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

Date: Thu, 10 Dec 1998 08:27:19 -0600
From: "Daniel Blander" <DBLAND@mednet.swmed.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: frame grabber
Message-Id: <s66f85e9.017@mednet.swmed.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline
Content-Transfer-Encoding: 8bit

I have an old macintosh with whichi am trying to set up color image analysis using NIH image.  I need a color frame grabber on a NuBus board (Scion LG3 or equivalent).  Is there anyone out there who has one or knows how i can get one??

Daniel Blander
Instructor in Urology
UT Southwestern Medical School

--------------------------------
End of nih-image-d Digest V98 Issue #138
****************************************

From nih-image-request@io.ece.drexel.edu Fri Dec 11 13:27 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA02446;
	Fri, 11 Dec 1998 13:27:10 -0500 (EST)
Resent-Date: Fri, 11 Dec 1998 13:27:10 -0500 (EST)
Message-Id: <199812111808.NAA00561@io.ece.drexel.edu>
X-Mailer: Microsoft Outlook Express for Macintosh - 4.01 (295)
Date: Fri, 11 Dec 1998 19:10:09 +0100
Subject: Trigger problems
From: "Johan Jersblad" <jersblad@msi.se>
To: nih-image@io.ece.drexel.edu
MIME-Version: 1.0
X-Priority: 3
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id NAA00561
Resent-Message-ID: <"1CLBg.0.u8.O-LSs"@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/709
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="ISO-8859-1"
Content-Length: 1233

Dear list,

This is the first time I write here and it is a cry for help.

Equipment: LG3 framegrabber, PPC Mac, CCD camera SONY XC8500-CE, Scion Image
1.62a.

The only thing we want to do is to trigger our CCD camera at a given time to
get a frame.
This doesnt work.

What we have tried is the following; 

1. The camera is in normal mode, meaning that it is continously aquiring
   fields.  The framegrabber is triggered. Every time we trigger the
framegrabber we
   get a picture. Seems normal.

2. The camera is in RR mode. (RR-reset.restart) 
   We DONT trigger the camera, BUT we trigger the framegrabber.
   Result: Nothing happens. It still says "Waiting for trigger" in the
   window.  We dont understand completely. 
   I would expect a black picture, or something from the memory.

3. The camera is in RR mode.
   We trigger the camera.
   We wait 100ms.
   We trigger the framegrabber.
   Result: nothing happens.
   We trigger the framegrabber again.
   We see a new picture.
   I dont understand anything.


Has anybody out there done this or does anyone have any expirience whitin
this field, or does anyone have a relative that has got a friend whose
husband works for........etc.

Yours sincerely,

Johan Jersblad


From nih-image-request@io.ece.drexel.edu Fri Dec 11 15:03 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA10945;
	Fri, 11 Dec 1998 15:03:37 -0500 (EST)
Resent-Date: Fri, 11 Dec 1998 15:03:37 -0500 (EST)
Message-Id: <v03020900b2971af4013b@[18.155.0.117]>
Mime-Version: 1.0
Date: Fri, 11 Dec 1998 14:58:45 -0400
To: nih-image@io.ece.drexel.edu
From: Laird Bloom <lbloom@MIT.EDU>
Subject: counting cells in tissue sections
Resent-Message-ID: <"C22aT3.0._I2.6UNSs"@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/710
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: 515

NIH Image users:
	Does anyone know a good way to adapt the cell counting macro to
counting cells in tissue sections?  There are two problems I'm trying to
solve:  first, the cells touch each other, and second, they're stained with
a surface marker, so each one looks like a ring of stain around a blank
nucleus.  It's obvious to the eye where individual cells are, but without
drawing circles around each one manually, how can I tell the computer what
to count?
Thanks,
Laird Bloom
MIT Center for Cancer Research



From nih-image-request@io.ece.drexel.edu Fri Dec 11 15:20 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA12616;
	Fri, 11 Dec 1998 15:20:51 -0500 (EST)
Resent-Date: Fri, 11 Dec 1998 15:20:51 -0500 (EST)
Message-Id: <s6713581.020@umich.edu>
X-Mailer: Novell GroupWise 5.2
Date: Fri, 11 Dec 1998 15:08:15 -0500
From: "Wade Schuette" <schuette@umich.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: counting cells in tissue sections
Mime-Version: 1.0
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id PAA11417
Resent-Message-ID: <"-hBat3.0.Yo2.PlNSs"@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/711
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: 677

Can you email a small section of one image? (say 200 x 200 pixels)
to me at  "schuette@umich.edu" ?  
Wade



>>> Laird Bloom <lbloom@MIT.EDU> 12/11 3:03 PM >>>
NIH Image users:
	Does anyone know a good way to adapt the cell counting macro to
counting cells in tissue sections?  There are two problems I'm trying to
solve:  first, the cells touch each other, and second, they're stained with
a surface marker, so each one looks like a ring of stain around a blank
nucleus.  It's obvious to the eye where individual cells are, but without
drawing circles around each one manually, how can I tell the computer what
to count?
Thanks,
Laird Bloom
MIT Center for Cancer Research




From nih-image-d-request@io.ece.drexel.edu Sat Dec 12 06:11 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA04916;
	Sat, 12 Dec 1998 06:11:20 -0500 (EST)
Date: Sat, 12 Dec 1998 06:11:20 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812121111.GAA04916@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #139
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/139
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 4152

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 139

Today's Topics:
  Trigger problems                      [ "Johan Jersblad" <jersblad@msi.se> ]
  unsubscribe                           [ Michal Ondrejcek <ondrejc@fzu.cz> ]
  counting cells in tissue sections     [ Laird Bloom <lbloom@MIT.EDU> ]
  Re: counting cells in tissue section  [ "Wade Schuette" <schuette@umich.edu ]

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

Date: Fri, 11 Dec 1998 19:10:09 +0100
From: "Johan Jersblad" <jersblad@msi.se>
To: nih-image@io.ece.drexel.edu
Subject: Trigger problems
Message-Id: <199812111808.NAA00561@io.ece.drexel.edu>
Content-Type: text/plain; charset="ISO-8859-1"
Content-Transfer-Encoding: 8bit

Dear list,

This is the first time I write here and it is a cry for help.

Equipment: LG3 framegrabber, PPC Mac, CCD camera SONY XC8500-CE, Scion Image
1.62a.

The only thing we want to do is to trigger our CCD camera at a given time to
get a frame.
This doesnt work.

What we have tried is the following; 

1. The camera is in normal mode, meaning that it is continously aquiring
   fields.  The framegrabber is triggered. Every time we trigger the
framegrabber we
   get a picture. Seems normal.

2. The camera is in RR mode. (RR-reset.restart) 
   We DONT trigger the camera, BUT we trigger the framegrabber.
   Result: Nothing happens. It still says "Waiting for trigger" in the
   window.  We dont understand completely. 
   I would expect a black picture, or something from the memory.

3. The camera is in RR mode.
   We trigger the camera.
   We wait 100ms.
   We trigger the framegrabber.
   Result: nothing happens.
   We trigger the framegrabber again.
   We see a new picture.
   I dont understand anything.


Has anybody out there done this or does anyone have any expirience whitin
this field, or does anyone have a relative that has got a friend whose
husband works for........etc.

Yours sincerely,

Johan Jersblad

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

Date: Fri, 11 Dec 1998 13:39:12 -0500 (EST)
From: Michal Ondrejcek <ondrejc@fzu.cz>
To: nih-image-d@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <v03110700b296c294e9b0@[128.174.102.118]>
Content-Type: text/plain; charset="us-ascii"


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

Date: Fri, 11 Dec 1998 14:58:45 -0400
From: Laird Bloom <lbloom@MIT.EDU>
To: nih-image@io.ece.drexel.edu
Subject: counting cells in tissue sections
Message-Id: <v03020900b2971af4013b@[18.155.0.117]>
Content-Type: text/plain; charset="us-ascii"

NIH Image users:
	Does anyone know a good way to adapt the cell counting macro to
counting cells in tissue sections?  There are two problems I'm trying to
solve:  first, the cells touch each other, and second, they're stained with
a surface marker, so each one looks like a ring of stain around a blank
nucleus.  It's obvious to the eye where individual cells are, but without
drawing circles around each one manually, how can I tell the computer what
to count?
Thanks,
Laird Bloom
MIT Center for Cancer Research

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

Date: Fri, 11 Dec 1998 15:08:15 -0500
From: "Wade Schuette" <schuette@umich.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: counting cells in tissue sections
Message-Id: <s6713581.020@umich.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline
Content-Transfer-Encoding: 8bit

Can you email a small section of one image? (say 200 x 200 pixels)
to me at  "schuette@umich.edu" ?  
Wade



>>> Laird Bloom <lbloom@MIT.EDU> 12/11 3:03 PM >>>
NIH Image users:
	Does anyone know a good way to adapt the cell counting macro to
counting cells in tissue sections?  There are two problems I'm trying to
solve:  first, the cells touch each other, and second, they're stained with
a surface marker, so each one looks like a ring of stain around a blank
nucleus.  It's obvious to the eye where individual cells are, but without
drawing circles around each one manually, how can I tell the computer what
to count?
Thanks,
Laird Bloom
MIT Center for Cancer Research

--------------------------------
End of nih-image-d Digest V98 Issue #139
****************************************

From nih-image-request@io.ece.drexel.edu Sat Dec 12 08:07 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA16301;
	Sat, 12 Dec 1998 08:07:05 -0500 (EST)
Resent-Date: Sat, 12 Dec 1998 08:07:05 -0500 (EST)
Message-ID: <19981212124138.19441.rocketmail@web1.rocketmail.com>
Date: Sat, 12 Dec 1998 04:41:38 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
Subject: Re: Trigger problems
To: nih-image@io.ece.drexel.edu
MIME-Version: 1.0
Resent-Message-ID: <"FsGPa2.0.gg3.VVcSs"@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/712
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: 686

---Johan Jersblad <jersblad@msi.se> wrote:
> Equipment: LG3 framegrabber, PPC Mac, CCD camera SONY XC8500-CE, Scion Image
> 1.62a.
> 
> The only thing we want to do is to trigger our CCD camera at a given time to
> get a frame.

Once triggered the frame grabber waits until it gets a vertical refresh, then
begins capture of video. No refresh no capture.

One can run into trouble if the camera trys to have ways set on putting out
video and the frame grabber is not expecting that.


==
Mark Vivino
mvivino@rocketmail.com
Consulting Biomedical Engineer
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com


From nih-image-request@io.ece.drexel.edu Sat Dec 12 10:49 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA02420;
	Sat, 12 Dec 1998 10:49:59 -0500 (EST)
Resent-Date: Sat, 12 Dec 1998 10:49:59 -0500 (EST)
Message-Id: <3.0.5.32.19981212163522.01273e80@krzsun.med-rz.uni-sb.de>
X-Sender: phblin@krzsun.med-rz.uni-sb.de
X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32)
Date: Sat, 12 Dec 1998 16:35:22 +0100
To: nih-image@io.ece.drexel.edu
From: Bernd Lindemann <phblin@med-rz.uni-sb.de>
Subject: distortion in space
Mime-Version: 1.0
Resent-Message-ID: <"WDvQY.0.dH.eteSs"@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/713
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: 2309



I have followed exchanges in this discussion group with interest, even
though not since July 1998. My question is not directly concerned with
macros in NIH-image, but may nevertheless be of interest to some of you.

I am working with synapses in tissues. The synapses can be stained (with
the fluorescent tracer FM1-43) and then show up as fluorescent spots. I
take stacks of images to record the 3-D distribution of the spots. A
program I have written scans the stack for spots, numbers the spots (about
100 per stack) and records their properties (x, y, z -coordinates, peak
intensity, diameter, slope). Thus each spot has its own identity, it is an
object (with a "type" structure in my programming language).  Illustrations
are found on my web-site:

http://www.med-rz.uni-sb.de/med_fak/physiol2/LDM/index.html


When the tissue is stimulated, some of the synapses are activated and the
fluorescence of those activated (perhaps 10 or 20 out of 100) decreases or
disappears. This is recorded by repetitive acquisition of the stack. To
follow individual spots through an experiment with several stimulations,
thats the purpose of this work. 

Unfortunately, there is a complication due to movement of spots: driven by
local swelling and shrinking of cells some spots cannot maintain their
coordinates and change their inter-spot distances. The travel can be up to
10% of the stack diameter. Thus, even though the movement of spots is
limited, spot identity is not always obvious. While the spots can sometimes
be traced by inspection, this should be automated by programming. 

Notably, the time of acquisition of a stack is longer than the time it
takes to deform the pattern of spots. Thus, it is impossible to get a
continuous record. 

I am wondering whether one might compare two stacks by cross-correlation,
looking for parts which have not changed, then reconstruct the remainder
starting with those parts which have not changed. This would mean to go for
the most likely model of the distortion. However, there may be better
possibilities to deal with the distortion in space. Perhaps people working
with distortion in electron microscopy images know suitable programming
strategies?

I shall welcome your ideas and advice about this.

Thanks in advance for your comments,   Bernd Lindemann.





From nih-image-d-request@io.ece.drexel.edu Sun Dec 13 06:12 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA17570;
	Sun, 13 Dec 1998 06:12:01 -0500 (EST)
Date: Sun, 13 Dec 1998 06:12:01 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812131112.GAA17570@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #140
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/140
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 3972

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 140

Today's Topics:
  Re: Trigger problems                  [ Mark Vivino <mvivino@rocketmail.com ]
  distortion in space                   [ Bernd Lindemann <phblin@med-rz.uni- ]

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

Date: Sat, 12 Dec 1998 04:41:38 -0800 (PST)
From: Mark Vivino <mvivino@rocketmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Trigger problems
Message-ID: <19981212124138.19441.rocketmail@web1.rocketmail.com>
Content-Type: text/plain; charset=us-ascii

---Johan Jersblad <jersblad@msi.se> wrote:
> Equipment: LG3 framegrabber, PPC Mac, CCD camera SONY XC8500-CE, Scion Image
> 1.62a.
> 
> The only thing we want to do is to trigger our CCD camera at a given time to
> get a frame.

Once triggered the frame grabber waits until it gets a vertical refresh, then
begins capture of video. No refresh no capture.

One can run into trouble if the camera trys to have ways set on putting out
video and the frame grabber is not expecting that.


==
Mark Vivino
mvivino@rocketmail.com
Consulting Biomedical Engineer
_________________________________________________________
DO YOU YAHOO!?
Get your free @yahoo.com address at http://mail.yahoo.com

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

Date: Sat, 12 Dec 1998 16:35:22 +0100
From: Bernd Lindemann <phblin@med-rz.uni-sb.de>
To: nih-image@io.ece.drexel.edu
Subject: distortion in space
Message-Id: <3.0.5.32.19981212163522.01273e80@krzsun.med-rz.uni-sb.de>
Content-Type: text/plain; charset="us-ascii"

I have followed exchanges in this discussion group with interest, even
though not since July 1998. My question is not directly concerned with
macros in NIH-image, but may nevertheless be of interest to some of you.

I am working with synapses in tissues. The synapses can be stained (with
the fluorescent tracer FM1-43) and then show up as fluorescent spots. I
take stacks of images to record the 3-D distribution of the spots. A
program I have written scans the stack for spots, numbers the spots (about
100 per stack) and records their properties (x, y, z -coordinates, peak
intensity, diameter, slope). Thus each spot has its own identity, it is an
object (with a "type" structure in my programming language).  Illustrations
are found on my web-site:

http://www.med-rz.uni-sb.de/med_fak/physiol2/LDM/index.html


When the tissue is stimulated, some of the synapses are activated and the
fluorescence of those activated (perhaps 10 or 20 out of 100) decreases or
disappears. This is recorded by repetitive acquisition of the stack. To
follow individual spots through an experiment with several stimulations,
thats the purpose of this work. 

Unfortunately, there is a complication due to movement of spots: driven by
local swelling and shrinking of cells some spots cannot maintain their
coordinates and change their inter-spot distances. The travel can be up to
10% of the stack diameter. Thus, even though the movement of spots is
limited, spot identity is not always obvious. While the spots can sometimes
be traced by inspection, this should be automated by programming. 

Notably, the time of acquisition of a stack is longer than the time it
takes to deform the pattern of spots. Thus, it is impossible to get a
continuous record. 

I am wondering whether one might compare two stacks by cross-correlation,
looking for parts which have not changed, then reconstruct the remainder
starting with those parts which have not changed. This would mean to go for
the most likely model of the distortion. However, there may be better
possibilities to deal with the distortion in space. Perhaps people working
with distortion in electron microscopy images know suitable programming
strategies?

I shall welcome your ideas and advice about this.

Thanks in advance for your comments,   Bernd Lindemann.

--------------------------------
End of nih-image-d Digest V98 Issue #140
****************************************

From nih-image-request@io.ece.drexel.edu Mon Dec 14 02:44 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id CAA03106;
	Mon, 14 Dec 1998 02:44:23 -0500 (EST)
Resent-Date: Mon, 14 Dec 1998 02:44:23 -0500 (EST)
X-Sender: bmenard@pop-server.unil.ch
Message-Id: <v03102802b29a68ff2357@[130.223.74.27]>
In-Reply-To: <199812111808.NAA00561@io.ece.drexel.edu>
Mime-Version: 1.0
Content-Transfer-Encoding: 8bit
Date: Mon, 14 Dec 1998 08:22:26 +0100
To: Johan Jersblad <jersblad@msi.se>, nih-image@io.ece.drexel.edu
From: Bertrand Menard <Bertrand.Menard@ie-bpv.unil.ch>
Subject: Re: Trigger problems
Resent-Message-ID: <"IFU181.0.kG.jpBTs"@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/714
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="iso-8859-1"
Content-Length: 1403

Dear Johan,

I couldn't directly help you, but I could give you an idea. I have a
similar problem with my JVc camera and my CG7 framegrabber (problem is the
same with a LG3). When I use the integration mode of the camera, if I plug
directly the output trigger of the camera to the framegrabber, I only
obtain black image. The problem is that the trigger signal of the camera is
a TTL edge growing from +0V to 5. The signal that is waiting by the CG7 is
a falling of a TTL edge from +5V to 0. So Stein Roervik gave me the schema
of a simple circuit to delay the TTL edge.

So I could give you an advise, test your signals with an oscilloscope.

Good luck.



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 Dec 14 08:08 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA00763;
	Mon, 14 Dec 1998 08:08:08 -0500 (EST)
Resent-Date: Mon, 14 Dec 1998 08:08:08 -0500 (EST)
Message-ID: <36755057.756@pro.via-rs.com.br>
Date: Mon, 14 Dec 1998 10:52:23 -0700
From: Luthero Martins <rsf6675@pro.via-rs.com.br>
Reply-To: luthero@pro.via-rs.com.br
X-Mailer: Mozilla 3.01Gold (Macintosh; I; PPC)
MIME-Version: 1.0
To: nih-image@io.ece.drexel.edu
Subject: ophthalmologist
References: <199812131107.GAA16996@io.ece.drexel.edu>
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"aeJkB1.0.t27.baGTs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/715
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: 83

Please!

I'm looking for ophthalmologist in the group.  

Thanks

Luthero Martins


From nih-image-request@io.ece.drexel.edu Mon Dec 14 08:59 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA05679;
	Mon, 14 Dec 1998 08:59:20 -0500 (EST)
Resent-Date: Mon, 14 Dec 1998 08:59:20 -0500 (EST)
Message-Id: <199812141339.HAA32972@mail5.doit.wisc.edu>
X-Sender: dlparker@facstaff.wisc.edu
X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.2 
Date: Mon, 14 Dec 1998 07:45:15 -0600
To: nih-image@io.ece.drexel.edu
From: David Parker <dlparker@facstaff.wisc.edu>
Subject: unsubscribe
In-Reply-To: <199812131111.GAA17419@io.ece.drexel.edu>
Mime-Version: 1.0
Resent-Message-ID: <"appCF2.0.xv.eKHTs"@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/716
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: 13

unsubscribe


From nih-image-request@io.ece.drexel.edu Mon Dec 14 10:57 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA15543;
	Mon, 14 Dec 1998 10:57:56 -0500 (EST)
Resent-Date: Mon, 14 Dec 1998 10:57:56 -0500 (EST)
Message-Id: <v0300780bb29ad2e6a077@[144.118.33.245]>
Mime-Version: 1.0
Date: Mon, 14 Dec 1998 07:37:12 -0700
To: nih-image@io.ece.drexel.edu
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: unsubscribe_yoni@cbis.ece.drexel.edu
Resent-Message-ID: <"qfG582.0.hI3.-0JTs"@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/717
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: 821


--------------------------------------------------------------------------------
-----------------------
                                  Jonathan Nissanov, Ph.D.
                                      Associate Director
            Computer Vision Center for Vertebrate Brain Mapping,
                a NIH Biomedical Research Technology Resource
                                http://cbis.ece.drexel.edu/ICVC/
--------------------------------------------------------------------------------
-----------------------
Imaging and Computer Vision Center              Tel: 215-895-1381
Drexel University                                                   Fax:
215-895-4987
Phildelphia, PA 19104
yoni@coe.drexel.edu
 -------------------------------------------------------------------------------
------------------------



From nih-image-request@io.ece.drexel.edu Mon Dec 14 23:14 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id XAA16651
	for cshtest@io.ece.drexel.edu; Mon, 14 Dec 1998 23:14:24 -0500 (EST)
Resent-Date: Mon, 14 Dec 1998 23:14:24 -0500 (EST)
X-Sender: driska4@pop3.netaxs.com
Message-Id: <l03020902b29b8f778f34@[207.8.207.90]>
Mime-Version: 1.0
Date: Mon, 14 Dec 1998 23:04:25 -0500
To: nih-image@io.ece.drexel.edu
From: Steve Driska <driska4@netaxs.com>
Subject: Can a number be typed into the Results window?
Resent-Message-ID: <"ksQVb1.0.0n3.E1UTs"@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/718
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: 671



I can't find a way to type in a number into the results scrreen.  It seems
like it would be easy.

What I'm trying to do is play video into NIH Image ( a quick time movie)
which the program opens as a stack.  I want to trace the objects in the
picture to measure their length.  This I can do.  What I need to do is
this:  The video has a time/date stamp as part of the image.  I would like
to manually read the time, and enter it into column of the results, so that
it is matched with the length measurement.

Is there a simple way, or will I have to learn to do macros?

Thanks a lot,

	Steve Driska



Steve Driska            driska4@netaxs.com
                   



From nih-image-d-request@io.ece.drexel.edu Mon Dec 14 23:17 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id XAA17065;
	Mon, 14 Dec 1998 23:17:08 -0500 (EST)
Date: Mon, 14 Dec 1998 23:17:08 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812150417.XAA17065@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #141
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/141
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 5135

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 141

Today's Topics:
  Re: Trigger problems                  [ Bertrand Menard <Bertrand.Menard@ie ]
  ophthalmologist                       [ Luthero Martins <rsf6675@pro.via-rs ]
  unsubscribe                           [ David Parker <dlparker@facstaff.wis ]
  unsubscribe_yoni@cbis.ece.drexel.edu  [ Jonathan Nissanov <yoni@cbis.ece.dr ]
  Can a number be typed into the Resul  [ Steve Driska <driska4@netaxs.com> ]

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

Date: Mon, 14 Dec 1998 08:22:26 +0100
From: Bertrand Menard <Bertrand.Menard@ie-bpv.unil.ch>
To: Johan Jersblad <jersblad@msi.se>, nih-image@io.ece.drexel.edu
Subject: Re: Trigger problems
Message-Id: <v03102802b29a68ff2357@[130.223.74.27]>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

Dear Johan,

I couldn't directly help you, but I could give you an idea. I have a
similar problem with my JVc camera and my CG7 framegrabber (problem is the
same with a LG3). When I use the integration mode of the camera, if I plug
directly the output trigger of the camera to the framegrabber, I only
obtain black image. The problem is that the trigger signal of the camera is
a TTL edge growing from +0V to 5. The signal that is waiting by the CG7 is
a falling of a TTL edge from +5V to 0. So Stein Roervik gave me the schema
of a simple circuit to delay the TTL edge.

So I could give you an advise, test your signals with an oscilloscope.

Good luck.



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

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

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

Date: Mon, 14 Dec 1998 10:52:23 -0700
From: Luthero Martins <rsf6675@pro.via-rs.com.br>
To: nih-image@io.ece.drexel.edu
Subject: ophthalmologist
Message-ID: <36755057.756@pro.via-rs.com.br>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Please!

I'm looking for ophthalmologist in the group.  

Thanks

Luthero Martins

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

Date: Mon, 14 Dec 1998 07:45:15 -0600
From: David Parker <dlparker@facstaff.wisc.edu>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <199812141339.HAA32972@mail5.doit.wisc.edu>
Content-Type: text/plain; charset="us-ascii"

unsubscribe

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

Date: Mon, 14 Dec 1998 07:37:12 -0700
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe_yoni@cbis.ece.drexel.edu
Message-Id: <v0300780bb29ad2e6a077@[144.118.33.245]>
Content-Type: text/plain; charset="us-ascii"

--------------------------------------------------------------------------------
-----------------------
                                  Jonathan Nissanov, Ph.D.
                                      Associate Director
            Computer Vision Center for Vertebrate Brain Mapping,
                a NIH Biomedical Research Technology Resource
                                http://cbis.ece.drexel.edu/ICVC/
--------------------------------------------------------------------------------
-----------------------
Imaging and Computer Vision Center              Tel: 215-895-1381
Drexel University                                                   Fax:
215-895-4987
Phildelphia, PA 19104
yoni@coe.drexel.edu
 -------------------------------------------------------------------------------
------------------------

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

Date: Mon, 14 Dec 1998 23:04:25 -0500
From: Steve Driska <driska4@netaxs.com>
To: nih-image@io.ece.drexel.edu
Subject: Can a number be typed into the Results window?
Message-Id: <l03020902b29b8f778f34@[207.8.207.90]>
Content-Type: text/plain; charset="us-ascii"

I can't find a way to type in a number into the results scrreen.  It seems
like it would be easy.

What I'm trying to do is play video into NIH Image ( a quick time movie)
which the program opens as a stack.  I want to trace the objects in the
picture to measure their length.  This I can do.  What I need to do is
this:  The video has a time/date stamp as part of the image.  I would like
to manually read the time, and enter it into column of the results, so that
it is matched with the length measurement.

Is there a simple way, or will I have to learn to do macros?

Thanks a lot,

	Steve Driska



Steve Driska            driska4@netaxs.com
                   

--------------------------------
End of nih-image-d Digest V98 Issue #141
****************************************

From nih-image-request@io.ece.drexel.edu Tue Dec 15 04:26 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id EAA17698
	for cshtest@io.ece.drexel.edu; Tue, 15 Dec 1998 04:26:26 -0500 (EST)
Resent-Date: Tue, 15 Dec 1998 04:26:26 -0500 (EST)
X-Sender: md1rjsh@swineshaw.shef.ac.uk
Message-Id: <l03130300b29bd5e98093@[143.167.91.113]>
Mime-Version: 1.0
Date: Tue, 15 Dec 1998 09:06:56 +0000
To: nih-image@io.ece.drexel.edu
From: Rachael Simpson <R.J.Simpson@sheffield.ac.uk>
Subject: using scion image
Resent-Message-ID: <"p5bY83.0.Gs3.ZSYTs"@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/719
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: 1003

Dear Scion,
>>
>>My name is Rachael Simpson and I am Currently working on an MD project
>>at Sheffield Children's Hospital, England. I am trained in
>>Orthopaedics and my MD project is looking at the evaluation of
>>clubfoot deformity in children. As part of this project, I am
>>evaluating foot function using pedobarography. This essentially gives
>>me an imprint of the child's foot with a plot of points over the
>>surface showing the change in position of the pressure through the
>>foot with walking.

>> Essentially what I would like to do using the NIH image
>>programme, is to convert the plot on the foot into graphical form. I
>>thought it may be possible to do this by first scanning the image in
>>and then superimposing a graph around this and then to remove the
>>foot image leaving only the plot in place. I am writing to see
>>whether anyone has any experience of such a method or how I might go
>>about it. I would be grateful for any help that can be offered. Thank
>>you. Rachael.



From nih-image-request@io.ece.drexel.edu Tue Dec 15 10:36 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA22602
	for cshtest@io.ece.drexel.edu; Tue, 15 Dec 1998 10:36:44 -0500 (EST)
Resent-Date: Tue, 15 Dec 1998 10:36:44 -0500 (EST)
Message-Id: <199812151510.JAA22800@mail1.doit.wisc.edu>
X-Sender: kvogt@facstaff.wisc.edu
X-Mailer: Windows Eudora Pro Version 2.1.2
Mime-Version: 1.0
Date: Tue, 15 Dec 1998 09:06:10 -0600
To: nih-image@io.ece.drexel.edu
From: Kevin Vogt <kvogt@facstaff.wisc.edu>
Subject: Re: nih-image-d Digest V98 #141
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id KAA20246
Resent-Message-ID: <"ReIEF3.0.Ty4.CmdTs"@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/720
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset="iso-8859-1"
Content-Length: 5310

unsubscribe
At 11:15 PM 12/14/98 -0500, you wrote:
>Content-Type: text/plain
>MIME-Version: 1.0
>
>nih-image-d Digest				Volume 98 : Issue 141
>
>Today's Topics:
>  Re: Trigger problems                  [ Bertrand Menard <Bertrand.Menard@ie ]
>  ophthalmologist                       [ Luthero Martins <rsf6675@pro.via-rs ]
>  unsubscribe                           [ David Parker <dlparker@facstaff.wis ]
>  unsubscribe_yoni@cbis.ece.drexel.edu  [ Jonathan Nissanov <yoni@cbis.ece.dr ]
>  Can a number be typed into the Resul  [ Steve Driska <driska4@netaxs.com> ]
>Date: Mon, 14 Dec 1998 08:22:26 +0100
>From: Bertrand Menard <Bertrand.Menard@ie-bpv.unil.ch>
>To: Johan Jersblad <jersblad@msi.se>, nih-image@io.ece.drexel.edu
>Subject: Re: Trigger problems
>Message-Id: <v03102802b29a68ff2357@[130.223.74.27]>
>Content-Type: text/plain; charset="iso-8859-1"
>MIME-Version: 1.0

>X-MIME-Autoconverted: from 8bit to quoted-printable by mail2.doit.wisc.edu
id WAA91880
>
>Dear Johan,
>
>I couldn't directly help you, but I could give you an idea. I have a
>similar problem with my JVc camera and my CG7 framegrabber (problem is the
>same with a LG3). When I use the integration mode of the camera, if I plug
>directly the output trigger of the camera to the framegrabber, I only
>obtain black image. The problem is that the trigger signal of the camera is
>a TTL edge growing from +0V to 5. The signal that is waiting by the CG7 is
>a falling of a TTL edge from +5V to 0. So Stein Roervik gave me the schema
>of a simple circuit to delay the TTL edge.
>
>So I could give you an advise, test your signals with an oscilloscope.
>
>Good luck.
>
>
>
>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
>
>**********************************************************
>Date: Mon, 14 Dec 1998 10:52:23 -0700
>From: Luthero Martins <rsf6675@pro.via-rs.com.br>
>To: nih-image@io.ece.drexel.edu
>Subject: ophthalmologist
>Message-ID: <36755057.756@pro.via-rs.com.br>
>Content-Type: text/plain; charset=us-ascii
>MIME-Version: 1.0
>Content-Transfer-Encoding: 7bit
>
>Please!
>
>I'm looking for ophthalmologist in the group.  
>
>Thanks
>
>Luthero Martins
>Date: Mon, 14 Dec 1998 07:45:15 -0600
>From: David Parker <dlparker@facstaff.wisc.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: unsubscribe
>Message-Id: <199812141339.HAA32972@mail5.doit.wisc.edu>
>Content-Type: text/plain; charset="us-ascii"
>MIME-Version: 1.0
>
>unsubscribe
>Date: Mon, 14 Dec 1998 07:37:12 -0700
>From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: unsubscribe_yoni@cbis.ece.drexel.edu
>Message-Id: <v0300780bb29ad2e6a077@[144.118.33.245]>
>Content-Type: text/plain; charset="us-ascii"
>MIME-Version: 1.0
>
>---------------------------------------------------------------------------
-----
>-----------------------
>                                  Jonathan Nissanov, Ph.D.
>                                      Associate Director
>            Computer Vision Center for Vertebrate Brain Mapping,
>                a NIH Biomedical Research Technology Resource
>                                http://cbis.ece.drexel.edu/ICVC/
>---------------------------------------------------------------------------
-----
>-----------------------
>Imaging and Computer Vision Center              Tel: 215-895-1381
>Drexel University                                                   Fax:
>215-895-4987
>Phildelphia, PA 19104
>yoni@coe.drexel.edu
>
-------------------------------------------------------------------------------
>------------------------
>Date: Mon, 14 Dec 1998 23:04:25 -0500
>From: Steve Driska <driska4@netaxs.com>
>To: nih-image@io.ece.drexel.edu
>Subject: Can a number be typed into the Results window?
>Message-Id: <l03020902b29b8f778f34@[207.8.207.90]>
>Content-Type: text/plain; charset="us-ascii"
>MIME-Version: 1.0
>
>I can't find a way to type in a number into the results scrreen.  It seems
>like it would be easy.
>
>What I'm trying to do is play video into NIH Image ( a quick time movie)
>which the program opens as a stack.  I want to trace the objects in the
>picture to measure their length.  This I can do.  What I need to do is
>this:  The video has a time/date stamp as part of the image.  I would like
>to manually read the time, and enter it into column of the results, so that
>it is matched with the length measurement.
>
>Is there a simple way, or will I have to learn to do macros?
>
>Thanks a lot,
>
>	Steve Driska
>
>
>
>Steve Driska            driska4@netaxs.com
>                   
>
Kevin Vogt	
262-1360	
University of Wisconsin-Madison	
Dept. of Biomolecular Chemistry
580 MSC
1300 University Ave.
Madison, WI 53706


From nih-image-d-request@io.ece.drexel.edu Wed Dec 16 07:49 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id HAA28383;
	Wed, 16 Dec 1998 07:49:52 -0500 (EST)
Date: Wed, 16 Dec 1998 07:49:52 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812161249.HAA28383@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #142
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/142
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 7309

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 142

Today's Topics:
  using scion image                     [ Rachael Simpson <R.J.Simpson@sheffi ]
  Re: nih-image-d Digest V98 #141       [ Kevin Vogt <kvogt@facstaff.wisc.edu ]

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

Date: Tue, 15 Dec 1998 09:06:56 +0000
From: Rachael Simpson <R.J.Simpson@sheffield.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: using scion image
Message-Id: <l03130300b29bd5e98093@[143.167.91.113]>
Content-Type: text/plain; charset="us-ascii"

Dear Scion,
>>
>>My name is Rachael Simpson and I am Currently working on an MD project
>>at Sheffield Children's Hospital, England. I am trained in
>>Orthopaedics and my MD project is looking at the evaluation of
>>clubfoot deformity in children. As part of this project, I am
>>evaluating foot function using pedobarography. This essentially gives
>>me an imprint of the child's foot with a plot of points over the
>>surface showing the change in position of the pressure through the
>>foot with walking.

>> Essentially what I would like to do using the NIH image
>>programme, is to convert the plot on the foot into graphical form. I
>>thought it may be possible to do this by first scanning the image in
>>and then superimposing a graph around this and then to remove the
>>foot image leaving only the plot in place. I am writing to see
>>whether anyone has any experience of such a method or how I might go
>>about it. I would be grateful for any help that can be offered. Thank
>>you. Rachael.

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

Date: Tue, 15 Dec 1998 09:06:10 -0600
From: Kevin Vogt <kvogt@facstaff.wisc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #141
Message-Id: <199812151510.JAA22800@mail1.doit.wisc.edu>
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit

unsubscribe
At 11:15 PM 12/14/98 -0500, you wrote:
>Content-Type: text/plain
>MIME-Version: 1.0
>
>nih-image-d Digest				Volume 98 : Issue 141
>
>Today's Topics:
>  Re: Trigger problems                  [ Bertrand Menard <Bertrand.Menard@ie ]
>  ophthalmologist                       [ Luthero Martins <rsf6675@pro.via-rs ]
>  unsubscribe                           [ David Parker <dlparker@facstaff.wis ]
>  unsubscribe_yoni@cbis.ece.drexel.edu  [ Jonathan Nissanov <yoni@cbis.ece.dr ]
>  Can a number be typed into the Resul  [ Steve Driska <driska4@netaxs.com> ]
>Date: Mon, 14 Dec 1998 08:22:26 +0100
>From: Bertrand Menard <Bertrand.Menard@ie-bpv.unil.ch>
>To: Johan Jersblad <jersblad@msi.se>, nih-image@io.ece.drexel.edu
>Subject: Re: Trigger problems
>Message-Id: <v03102802b29a68ff2357@[130.223.74.27]>
>Content-Type: text/plain; charset="iso-8859-1"
>MIME-Version: 1.0

>X-MIME-Autoconverted: from 8bit to quoted-printable by mail2.doit.wisc.edu
id WAA91880
>
>Dear Johan,
>
>I couldn't directly help you, but I could give you an idea. I have a
>similar problem with my JVc camera and my CG7 framegrabber (problem is the
>same with a LG3). When I use the integration mode of the camera, if I plug
>directly the output trigger of the camera to the framegrabber, I only
>obtain black image. The problem is that the trigger signal of the camera is
>a TTL edge growing from +0V to 5. The signal that is waiting by the CG7 is
>a falling of a TTL edge from +5V to 0. So Stein Roervik gave me the schema
>of a simple circuit to delay the TTL edge.
>
>So I could give you an advise, test your signals with an oscilloscope.
>
>Good luck.
>
>
>
>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
>
>**********************************************************
>Date: Mon, 14 Dec 1998 10:52:23 -0700
>From: Luthero Martins <rsf6675@pro.via-rs.com.br>
>To: nih-image@io.ece.drexel.edu
>Subject: ophthalmologist
>Message-ID: <36755057.756@pro.via-rs.com.br>
>Content-Type: text/plain; charset=us-ascii
>MIME-Version: 1.0
>Content-Transfer-Encoding: 7bit
>
>Please!
>
>I'm looking for ophthalmologist in the group.  
>
>Thanks
>
>Luthero Martins
>Date: Mon, 14 Dec 1998 07:45:15 -0600
>From: David Parker <dlparker@facstaff.wisc.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: unsubscribe
>Message-Id: <199812141339.HAA32972@mail5.doit.wisc.edu>
>Content-Type: text/plain; charset="us-ascii"
>MIME-Version: 1.0
>
>unsubscribe
>Date: Mon, 14 Dec 1998 07:37:12 -0700
>From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: unsubscribe_yoni@cbis.ece.drexel.edu
>Message-Id: <v0300780bb29ad2e6a077@[144.118.33.245]>
>Content-Type: text/plain; charset="us-ascii"
>MIME-Version: 1.0
>
>---------------------------------------------------------------------------
-----
>-----------------------
>                                  Jonathan Nissanov, Ph.D.
>                                      Associate Director
>            Computer Vision Center for Vertebrate Brain Mapping,
>                a NIH Biomedical Research Technology Resource
>                                http://cbis.ece.drexel.edu/ICVC/
>---------------------------------------------------------------------------
-----
>-----------------------
>Imaging and Computer Vision Center              Tel: 215-895-1381
>Drexel University                                                   Fax:
>215-895-4987
>Phildelphia, PA 19104
>yoni@coe.drexel.edu
>
-------------------------------------------------------------------------------
>------------------------
>Date: Mon, 14 Dec 1998 23:04:25 -0500
>From: Steve Driska <driska4@netaxs.com>
>To: nih-image@io.ece.drexel.edu
>Subject: Can a number be typed into the Results window?
>Message-Id: <l03020902b29b8f778f34@[207.8.207.90]>
>Content-Type: text/plain; charset="us-ascii"
>MIME-Version: 1.0
>
>I can't find a way to type in a number into the results scrreen.  It seems
>like it would be easy.
>
>What I'm trying to do is play video into NIH Image ( a quick time movie)
>which the program opens as a stack.  I want to trace the objects in the
>picture to measure their length.  This I can do.  What I need to do is
>this:  The video has a time/date stamp as part of the image.  I would like
>to manually read the time, and enter it into column of the results, so that
>it is matched with the length measurement.
>
>Is there a simple way, or will I have to learn to do macros?
>
>Thanks a lot,
>
>	Steve Driska
>
>
>
>Steve Driska            driska4@netaxs.com
>                   
>
Kevin Vogt	
262-1360	
University of Wisconsin-Madison	
Dept. of Biomolecular Chemistry
580 MSC
1300 University Ave.
Madison, WI 53706

--------------------------------
End of nih-image-d Digest V98 Issue #142
****************************************

From nih-image-request@io.ece.drexel.edu Wed Dec 16 09:06 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA05679
	for cshtest@io.ece.drexel.edu; Wed, 16 Dec 1998 09:06:50 -0500 (EST)
Resent-Date: Wed, 16 Dec 1998 09:06:50 -0500 (EST)
From: "Richard M. Clark" <richard.m.clark@luton.ac.uk>
Organization: University of Luton
To: nih-image@io.ece.drexel.edu
Date: Wed, 16 Dec 1998 13:43:43 GMT
MIME-Version: 1.0
Content-transfer-encoding: 7BIT
Subject: Request for IP info...
Reply-to: richard.m.clark@luton.ac.uk
Priority: normal
X-mailer: Pegasus Mail for Windows (v2.53/R1)
Message-ID: <13E1883C85@novell.science.luton.ac.uk>
Resent-Message-ID: <"3OU7y1.0.9q.CZxTs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/721
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: 1219

To all members of nih-image list...

I used to be a member of this list but un-subscribed due to email 
problems - I am now back on the list and wanted to ask some quick 
questions....

I am an Image Processing researcher who is working on combining some 
AI techniques with IP for 'intelligent machine vision' .... I am 
currently working on 'feature extraction' techniques and was 
wondering if anyone has/knows-of any papers which cover 'feature 
extraction' algorithms/techniques etc....

I am also interested in writing papers, articles etc regarding my 
research and have done a lot of work so far regarding 'wavelets and 
image processing' - I am currently experimenting with wavelets and 
will have some pretty good results during next year .... is there 
anyone who publishes image processing 'documents' or 'journals' (or 
AI related) who is looking for material from 'researchers' within 
this area?

Many thanks, 

Richard M. Clark
______________________________________________


Richard M. Clark,
Research Student,
University of Luton,
Department of Computing and Information Systems,
Room: B303 - (01582) 734111 extn 2071

NOVELL:   richard.m.clark@luton.ac.uk
HOME:     rmclark@luton34.freeserve.co.uk


From nih-image-request@io.ece.drexel.edu Wed Dec 16 11:56 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA20714
	for cshtest@io.ece.drexel.edu; Wed, 16 Dec 1998 11:56:08 -0500 (EST)
Resent-Date: Wed, 16 Dec 1998 11:56:08 -0500 (EST)
Date: Wed, 16 Dec 1998 11:26:12 -0500
Message-Id: <9812161626.AA25860@aquila.fccc.edu>
Reply-To: JD_Tisdall@fccc.edu
From: "James D. Tisdall" <JD_Tisdall@fccc.edu>
To: nih-image@io.ece.drexel.edu
Subject: mean fragment length in gel
Cc: JD_Tisdall@fccc.edu
Resent-Message-ID: <"6Hw-c.0.GP4.HzzTs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/722
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 529


Hi,
	I just subscribed. I wasn't sure how to proceed
after looking at manuals and faqs and macros, and I am a
new user:

	We have gels where each lane has all telomeres,
so lanes look like big smudges.  We want to calculate the
mean telomere length in each lane.  Is there a macro
that already exists for this purpose?

	Thanks for your help,

Jim


James D. Tisdall
The Fox Chase Cancer Center		Phone: (215) 728-3660
7701 Burholme Avenue			FAX:   (215) 728-2513
Philadelphia, Pennsylvania 19111 USA	Email: JD_Tisdall@fccc.edu


From nih-image-request@io.ece.drexel.edu Wed Dec 16 13:20 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA28988
	for cshtest@io.ece.drexel.edu; Wed, 16 Dec 1998 13:20:24 -0500 (EST)
Resent-Date: Wed, 16 Dec 1998 13:20:24 -0500 (EST)
Message-ID: <B0000001115@rpa.fmrp.usp.br>
X-Mailer: Microsoft Outlook Express for Macintosh - 4.02 (298) 
Date: Wed, 16 Dec 1998 15:55:17 -0200
Subject: unsubscribe
From: "Lenaldo Branco Rocha" <lenaldo@rpa.fmrp.usp.br>
To: nih-image@io.ece.drexel.edu
Mime-version: 1.0
X-Priority: 3
Content-transfer-encoding: 7bit
Resent-Message-ID: <"obBJH.0.sN6.pF_Ts"@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/723
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: 1



From nih-image-request@io.ece.drexel.edu Wed Dec 16 13:38 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA01173
	for cshtest@io.ece.drexel.edu; Wed, 16 Dec 1998 13:38:54 -0500 (EST)
Resent-Date: Wed, 16 Dec 1998 13:38:54 -0500 (EST)
Date: Wed, 16 Dec 1998 13:17:28 -0500 (EST)
From: Colette Baril <colette@zoo.utoronto.ca>
To: nih-image@io.ece.drexel.edu
Subject: Questions on Iomega Buzz boxes
Message-ID: <Pine.BSI.3.91.981216130828.13096A-100000@zoo.utoronto.ca>
MIME-Version: 1.0
Resent-Message-ID: <"OgreV1.0.c-6.sa_Ts"@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/724
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: 469

Hi,

We are looking into using NIH image to analyse video tapes of guppy 
behaviour.  As an alternative to using a Scion or Data Translation card 
for AV input, we were considering the use of the Iomega Buzz (an external AV 
converter).  What we need to know is whether the Buzz is compatible with 
NIH-image software in terms of image resolution, speed, etc.  Any 
information that could be shared on this matter would be great.

Thanks,

Colette Baril
Univ. Toronto


From nih-image-d-request@io.ece.drexel.edu Thu Dec 17 06:19 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA07912;
	Thu, 17 Dec 1998 06:19:40 -0500 (EST)
Date: Thu, 17 Dec 1998 06:19:40 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812171119.GAA07912@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #143
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/143
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 3955

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 143

Today's Topics:
  Request for IP info...                [ "Richard M. Clark" <richard.m.clark ]
  mean fragment length in gel           [ "James D. Tisdall" <JD_Tisdall@fccc ]
  unsubscribe                           [ "Lenaldo Branco Rocha" <lenaldo@rpa ]
  Questions on Iomega Buzz boxes        [ Colette Baril <colette@zoo.utoronto ]

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

Date: Wed, 16 Dec 1998 13:43:43 GMT
From: "Richard M. Clark" <richard.m.clark@luton.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Request for IP info...
Message-ID: <13E1883C85@novell.science.luton.ac.uk>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7BIT

To all members of nih-image list...

I used to be a member of this list but un-subscribed due to email 
problems - I am now back on the list and wanted to ask some quick 
questions....

I am an Image Processing researcher who is working on combining some 
AI techniques with IP for 'intelligent machine vision' .... I am 
currently working on 'feature extraction' techniques and was 
wondering if anyone has/knows-of any papers which cover 'feature 
extraction' algorithms/techniques etc....

I am also interested in writing papers, articles etc regarding my 
research and have done a lot of work so far regarding 'wavelets and 
image processing' - I am currently experimenting with wavelets and 
will have some pretty good results during next year .... is there 
anyone who publishes image processing 'documents' or 'journals' (or 
AI related) who is looking for material from 'researchers' within 
this area?

Many thanks, 

Richard M. Clark
______________________________________________


Richard M. Clark,
Research Student,
University of Luton,
Department of Computing and Information Systems,
Room: B303 - (01582) 734111 extn 2071

NOVELL:   richard.m.clark@luton.ac.uk
HOME:     rmclark@luton34.freeserve.co.uk

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

Date: Wed, 16 Dec 1998 11:26:12 -0500
From: "James D. Tisdall" <JD_Tisdall@fccc.edu>
To: nih-image@io.ece.drexel.edu
Cc: JD_Tisdall@fccc.edu
Subject: mean fragment length in gel
Message-Id: <9812161626.AA25860@aquila.fccc.edu>

Hi,
	I just subscribed. I wasn't sure how to proceed
after looking at manuals and faqs and macros, and I am a
new user:

	We have gels where each lane has all telomeres,
so lanes look like big smudges.  We want to calculate the
mean telomere length in each lane.  Is there a macro
that already exists for this purpose?

	Thanks for your help,

Jim


James D. Tisdall
The Fox Chase Cancer Center		Phone: (215) 728-3660
7701 Burholme Avenue			FAX:   (215) 728-2513
Philadelphia, Pennsylvania 19111 USA	Email: JD_Tisdall@fccc.edu

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

Date: Wed, 16 Dec 1998 15:55:17 -0200
From: "Lenaldo Branco Rocha" <lenaldo@rpa.fmrp.usp.br>
To: nih-image@io.ece.drexel.edu
Subject:  unsubscribe
Message-ID: <B0000001115@rpa.fmrp.usp.br>
Content-type: text/plain; charset="US-ASCII"
Content-transfer-encoding: 7bit


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

Date: Wed, 16 Dec 1998 13:17:28 -0500 (EST)
From: Colette Baril <colette@zoo.utoronto.ca>
To: nih-image@io.ece.drexel.edu
Subject: Questions on Iomega Buzz boxes
Message-ID: <Pine.BSI.3.91.981216130828.13096A-100000@zoo.utoronto.ca>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi,

We are looking into using NIH image to analyse video tapes of guppy 
behaviour.  As an alternative to using a Scion or Data Translation card 
for AV input, we were considering the use of the Iomega Buzz (an external AV 
converter).  What we need to know is whether the Buzz is compatible with 
NIH-image software in terms of image resolution, speed, etc.  Any 
information that could be shared on this matter would be great.

Thanks,

Colette Baril
Univ. Toronto

--------------------------------
End of nih-image-d Digest V98 Issue #143
****************************************

From nih-image-request@io.ece.drexel.edu Thu Dec 17 06:27 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA08835
	for cshtest@io.ece.drexel.edu; Thu, 17 Dec 1998 06:27:28 -0500 (EST)
Resent-Date: Thu, 17 Dec 1998 06:27:28 -0500 (EST)
Date: Thu, 17 Dec 1998 11:12:17 +0000
From: "Dr. Patrick Felle" <patrick.felle@ucd.ie>
Subject: unsubscribe
To: nih-image@io.ece.drexel.edu
Reply-to: patrick.felle@ucd.ie
Message-id: <3678E709.C87FC99A@ucd.ie>
Organization: University College Dublin
MIME-version: 1.0
X-Mailer: Mozilla 4.5 (Macintosh; I; PPC)
Content-transfer-encoding: 7bit
X-Accept-Language: en-GB,fr-FR,Irish
References: <199812150407.XAA15558@io.ece.drexel.edu>
Resent-Message-ID: <"3JKUH3.0._l1.OSEUs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/725
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: 13

unsubscribe


From nih-image-request@io.ece.drexel.edu Thu Dec 17 09:56 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA25233
	for cshtest@io.ece.drexel.edu; Thu, 17 Dec 1998 09:56:39 -0500 (EST)
Resent-Date: Thu, 17 Dec 1998 09:56:39 -0500 (EST)
Date: 	Thu, 17 Dec 1998 09:34:09 -0500 (EST)
Sender: Nora Rooney <nora@email.unc.edu>
From: Nora Maureen Rooney <nora@email.unc.edu>
X-Sender: nora@login6.isis.unc.edu
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
In-Reply-To: <199812171117.GAA07668@io.ece.drexel.edu>
Message-ID: <Pine.A41.3.95L.981217093355.97224B-100000@login6.isis.unc.edu>
MIME-Version: 1.0
Resent-Message-ID: <"BTvNi2.0.-f5.rPHUs"@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/726
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: 1



From nih-image-request@io.ece.drexel.edu Thu Dec 17 10:35 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA28782
	for cshtest@io.ece.drexel.edu; Thu, 17 Dec 1998 10:35:40 -0500 (EST)
Resent-Date: Thu, 17 Dec 1998 10:35:40 -0500 (EST)
From: Vaughn Adams <vaughn@cbis.ece.drexel.edu>
Message-Id: <199812171514.KAA19314@cbis.ece.drexel.edu>
Subject: ADMIN: Unsubscribe filter
To: nih-image@io.ece.drexel.edu
Date: Thu, 17 Dec 1998 10:14:39 -0500 (EST)
X-Mailer: ELM [version 2.4ME+ PL48 (25)]
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"31vgM3.0.qa6.d_HUs"@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/727
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: 702

List members:

I have added an "unsubscribe" filter to reject those really annoying 
unsubscribe messages that get sent to the list.  It should take care of the
majority of the requests.

To get help on administrative commands like unsubscribing, send email to
nih-image-request@biomed.drexel.edu.  Enter "help" for the subject.  If you
get the digested version, use nih-image-d-request@biomed.drexel.edu instead.

-- 
Vaughn Adams
Drexel University 
Electrical and Computer Engineering      Voice: 215-895-1979
32nd and Chestnut Streets                  FAX: 215-895-1695
Philadelphia, Pa 19104                   Email: vaughn@coe.drexel.edu

PGP key available - finger -l vaughn@cbis.ece.drexel.edu


From nih-image-request@io.ece.drexel.edu Thu Dec 17 15:48 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA28078
	for cshtest@io.ece.drexel.edu; Thu, 17 Dec 1998 15:48:04 -0500 (EST)
Resent-Date: Thu, 17 Dec 1998 15:48:04 -0500 (EST)
Date: Thu, 17 Dec 1998 12:32:03 -0800 (PST)
From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: Buz & behavior
In-Reply-To: <199812171117.GAA07612@io.ece.drexel.edu>
Message-ID: <Pine.SOL.3.95.981217123022.11913B-100000@protos.lifesci.ucla.edu>
MIME-Version: 1.0
Resent-Message-ID: <"KS7Rh2.0.nQ6.LfMUs"@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/728
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: 635


Hi,

the Iomega buz works fine with Image (even on a G3). I use it for behavior
as well and there is no problem with it, it supports 720 x 480 as well
which is a little better than the standard.  i would be interested in
talking to others who are using Image to analyze behavior as well.

Cheers,
Stephan
------------------------------
Stephan G. Anagnostaras, Ph.D. 
UCLA Depts. of Neurobiology         
           and Psychology      
stephan@lifesci.ucla.edu    
sanagnos@mediaone.net         
------------------------------
Work, CHS: (310) 794-6609
    Psych: (310) 794-5339
     Home: (310) 306-0294
--------------------------


From nih-image-request@io.ece.drexel.edu Fri Dec 18 06:45 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA12471
	for cshtest@io.ece.drexel.edu; Fri, 18 Dec 1998 06:45:00 -0500 (EST)
Resent-Date: Fri, 18 Dec 1998 06:45:00 -0500 (EST)
From: ebonino@physun.geo.ulg.ac.be
Date: Fri, 18 Dec 1998 11:36:07 -0100
Message-Id: <199812181236.LAA11290@phylune.geo.ulg.ac.be>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Mime-Version: 1.0
Content-Transfer-Encoding: 7bit
Content-MD5: hdeBTR4qbJ4p96fDbDRqhQ==
Resent-Message-ID: <"QsDVW2.0.ZP.BHYUs"@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/729
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: 13

unsubscribe


From nih-image-d-request@io.ece.drexel.edu Fri Dec 18 06:51 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA12575;
	Fri, 18 Dec 1998 06:51:00 -0500 (EST)
Date: Fri, 18 Dec 1998 06:51:00 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812181151.GAA12575@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #144
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/144
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 3544

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 144

Today's Topics:
  unsubscribe                           [ "Dr. Patrick Felle" <patrick.felle@ ]
  unsubscribe                           [ Nora Maureen Rooney <nora@email.unc ]
  ADMIN: Unsubscribe filter             [ Vaughn Adams <vaughn@cbis.ece.drexe ]
  Buz & behavior                        [ Stephan Anagnostaras <stephan@proto ]
  unsubscribe                           [ ebonino@physun.geo.ulg.ac.be ]

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

Date: Thu, 17 Dec 1998 11:12:17 +0000
From: "Dr. Patrick Felle" <patrick.felle@ucd.ie>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-id: <3678E709.C87FC99A@ucd.ie>
Content-type: text/plain; charset=us-ascii
Content-transfer-encoding: 7bit

unsubscribe

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

Date: 	Thu, 17 Dec 1998 09:34:09 -0500 (EST)
From: Nora Maureen Rooney <nora@email.unc.edu>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-ID: <Pine.A41.3.95L.981217093355.97224B-100000@login6.isis.unc.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII


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

Date: Thu, 17 Dec 1998 10:14:39 -0500 (EST)
From: Vaughn Adams <vaughn@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: Unsubscribe filter
Message-Id: <199812171514.KAA19314@cbis.ece.drexel.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit

List members:

I have added an "unsubscribe" filter to reject those really annoying 
unsubscribe messages that get sent to the list.  It should take care of the
majority of the requests.

To get help on administrative commands like unsubscribing, send email to
nih-image-request@biomed.drexel.edu.  Enter "help" for the subject.  If you
get the digested version, use nih-image-d-request@biomed.drexel.edu instead.

-- 
Vaughn Adams
Drexel University 
Electrical and Computer Engineering      Voice: 215-895-1979
32nd and Chestnut Streets                  FAX: 215-895-1695
Philadelphia, Pa 19104                   Email: vaughn@coe.drexel.edu

PGP key available - finger -l vaughn@cbis.ece.drexel.edu

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

Date: Thu, 17 Dec 1998 12:32:03 -0800 (PST)
From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: Buz & behavior
Message-ID: <Pine.SOL.3.95.981217123022.11913B-100000@protos.lifesci.ucla.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi,

the Iomega buz works fine with Image (even on a G3). I use it for behavior
as well and there is no problem with it, it supports 720 x 480 as well
which is a little better than the standard.  i would be interested in
talking to others who are using Image to analyze behavior as well.

Cheers,
Stephan
- ----------------------------
Stephan G. Anagnostaras, Ph.D. 
UCLA Depts. of Neurobiology         
           and Psychology      
stephan@lifesci.ucla.edu    
sanagnos@mediaone.net         
- ----------------------------
Work, CHS: (310) 794-6609
    Psych: (310) 794-5339
     Home: (310) 306-0294
--------------------------

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

Date: Fri, 18 Dec 1998 11:36:07 -0100
From: ebonino@physun.geo.ulg.ac.be
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <199812181236.LAA11290@phylune.geo.ulg.ac.be>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-MD5: hdeBTR4qbJ4p96fDbDRqhQ==

unsubscribe

--------------------------------
End of nih-image-d Digest V98 Issue #144
****************************************

From nih-image-request@io.ece.drexel.edu Fri Dec 18 08:20 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id IAA18297
	for cshtest@io.ece.drexel.edu; Fri, 18 Dec 1998 08:19:56 -0500 (EST)
Resent-Date: Fri, 18 Dec 1998 08:19:56 -0500 (EST)
Message-Id: <v01540b00b29fd8d387ff@[151.100.42.80]>
Mime-Version: 1.0
Date: Fri, 18 Dec 1998 13:03:37 +0300
To: nih-image@io.ece.drexel.edu
From: ippoliti@axrma.uniroma1.it (Rodolfo Ippoliti)
Subject: unsuscribe
Resent-Message-ID: <"wlnwq2.0.gD2.jLZUs"@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/730
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: 190



Dr. Rodolfo Ippoliti
Dept. of Biochemical Sciences
University of Rome La Sapienza
P.le Aldo Moro 5
00185 Rome
Italy

Tel:+39+6+4450291
FAX:+39+6+4440062
Email:ippoliti@axrma.uniroma1.it



From nih-image-request@io.ece.drexel.edu Fri Dec 18 12:25 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA20695
	for cshtest@io.ece.drexel.edu; Fri, 18 Dec 1998 12:25:33 -0500 (EST)
Resent-Date: Fri, 18 Dec 1998 12:25:33 -0500 (EST)
Message-ID: <009901be2aa7$6679dcc0$1d80d9c2@seer.aii.co.uk>
From: "Shiddhartha Nandy" <sn@aii.co.uk>
To: <nih-image@io.ece.drexel.edu>
Subject: TCL file format info required
Date: Fri, 18 Dec 1998 16:56:47 -0000
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
X-Priority: 3
X-MSMail-Priority: Normal
X-Mailer: Microsoft Outlook Express 4.72.3110.5
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3
X-MDaemon-Deliver-To: nih-image@biomed.drexel.edu
X-Return-Path: sn@aii.co.uk
Resent-Message-ID: <"N8hnv2.0.m94.kceUs"@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/731
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Length: 138

Hi,

Does anyone have information on the TCL image file format used with 
BDS Imaging systems?

Thanks
Shiddhartha Nandy
sn01@aii.co.uk



From nih-image-request@io.ece.drexel.edu Fri Dec 18 13:00 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id NAA25171
	for cshtest@io.ece.drexel.edu; Fri, 18 Dec 1998 13:00:03 -0500 (EST)
Resent-Date: Fri, 18 Dec 1998 13:00:03 -0500 (EST)
Date: Fri, 18 Dec 1998 12:47:30 -0500 (EST)
From: Hideyo Inouye <inouye@amy.bc.edu>
To: nih-image@io.ece.drexel.edu
Cc: Hideyo Inouye <inouye@amy.bc.edu>
Subject: arc integration 
In-Reply-To: <009901be2aa7$6679dcc0$1d80d9c2@seer.aii.co.uk>
Message-Id: <Pine.ULT.3.91.981218124329.3012B-100000@amy.bc.edu>
Mime-Version: 1.0
Resent-Message-ID: <"12yYv2.0.3l5.9KfUs"@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/732
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: 382

Dear Colleagues, 

 Are there any capablities on nih-image to do arc integration along the 
angular direction and to plot the data as a function of radial direction ?

Sincerely 

Hideyo Inouye
Department of Biology, Higgins Hall 510
Boston College, 140 Commonwealth Avenue,
Chestnut Hill, MA 02167-3811
Email: inouye@amy.bc.edu  http://amy.bc.edu:8080/
Phone: +1 (617)552-0213   


From nih-image-request@io.ece.drexel.edu Fri Dec 18 14:04 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA02031
	for cshtest@io.ece.drexel.edu; Fri, 18 Dec 1998 14:04:21 -0500 (EST)
Resent-Date: Fri, 18 Dec 1998 14:04:21 -0500 (EST)
From: DrJohnRuss@aol.com
Message-ID: <46eee9bc.367aa379@aol.com>
Date: Fri, 18 Dec 1998 13:48:25 EST
To: nih-image@io.ece.drexel.edu
Mime-Version: 1.0
Subject: Re:  arc integration
Content-transfer-encoding: 7bit
X-Mailer: AOL 3.0 for Mac sub 84
Resent-Message-ID: <"BACQL3.0.C7.xEgUs"@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/733
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: 300


In a message dated 12/18/98 12:56:15 PM, you wrote:

> Are there any capablities on nih-image to do arc integration along the 
>angular direction and to plot the data as a function of radial direction ?

I have a macro that will do that, and will post it if enough people are
interested.
John Russ


From nih-image-d-request@io.ece.drexel.edu Sat Dec 19 06:10 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA23657;
	Sat, 19 Dec 1998 06:10:30 -0500 (EST)
Date: Sat, 19 Dec 1998 06:10:30 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812191110.GAA23657@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #145
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/145
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 2729

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 145

Today's Topics:
  unsuscribe                            [ ippoliti@axrma.uniroma1.it (Rodolfo ]
  TCL file format info required         [ "Shiddhartha Nandy" <sn@aii.co.uk> ]
  arc integration                       [ Hideyo Inouye <inouye@amy.bc.edu> ]
  Re: arc integration                   [ DrJohnRuss@aol.com ]

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

Date: Fri, 18 Dec 1998 13:03:37 +0300
From: ippoliti@axrma.uniroma1.it (Rodolfo Ippoliti)
To: nih-image@io.ece.drexel.edu
Subject: unsuscribe
Message-Id: <v01540b00b29fd8d387ff@[151.100.42.80]>
Content-Type: text/plain; charset="us-ascii"

Dr. Rodolfo Ippoliti
Dept. of Biochemical Sciences
University of Rome La Sapienza
P.le Aldo Moro 5
00185 Rome
Italy

Tel:+39+6+4450291
FAX:+39+6+4440062
Email:ippoliti@axrma.uniroma1.it

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

Date: Fri, 18 Dec 1998 16:56:47 -0000
From: "Shiddhartha Nandy" <sn@aii.co.uk>
To: <nih-image@io.ece.drexel.edu>
Subject: TCL file format info required
Message-ID: <009901be2aa7$6679dcc0$1d80d9c2@seer.aii.co.uk>
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 7bit

Hi,

Does anyone have information on the TCL image file format used with 
BDS Imaging systems?

Thanks
Shiddhartha Nandy
sn01@aii.co.uk

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

Date: Fri, 18 Dec 1998 12:47:30 -0500 (EST)
From: Hideyo Inouye <inouye@amy.bc.edu>
To: nih-image@io.ece.drexel.edu
Cc: Hideyo Inouye <inouye@amy.bc.edu>
Subject: arc integration 
Message-Id: <Pine.ULT.3.91.981218124329.3012B-100000@amy.bc.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear Colleagues, 

 Are there any capablities on nih-image to do arc integration along the 
angular direction and to plot the data as a function of radial direction ?

Sincerely 

Hideyo Inouye
Department of Biology, Higgins Hall 510
Boston College, 140 Commonwealth Avenue,
Chestnut Hill, MA 02167-3811
Email: inouye@amy.bc.edu  http://amy.bc.edu:8080/
Phone: +1 (617)552-0213   

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

Date: Fri, 18 Dec 1998 13:48:25 EST
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re:  arc integration
Message-ID: <46eee9bc.367aa379@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

In a message dated 12/18/98 12:56:15 PM, you wrote:

> Are there any capablities on nih-image to do arc integration along the 
>angular direction and to plot the data as a function of radial direction ?

I have a macro that will do that, and will post it if enough people are
interested.
John Russ

--------------------------------
End of nih-image-d Digest V98 Issue #145
****************************************

From nih-image-request@io.ece.drexel.edu Sat Dec 19 18:41 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA24670
	for cshtest@io.ece.drexel.edu; Sat, 19 Dec 1998 18:41:28 -0500 (EST)
Resent-Date: Sat, 19 Dec 1998 18:41:28 -0500 (EST)
Reply-To: <FVLamberti@worldnet.att.net>
From: "Francis Lamberti" <FVLamberti@worldnet.att.net>
To: <DrJohnRuss@aol.com>, <nih-image@io.ece.drexel.edu>
Subject: RE: arc integration
Date: Sat, 19 Dec 1998 15:30:37 -0800
Message-ID: <000201be2ba7$95033220$2a50480c@758151725worldnet.att.net>
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
X-Priority: 3 (Normal)
X-MSMail-Priority: Normal
X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4
Importance: Normal
In-Reply-To: <46eee9bc.367aa379@aol.com>
Resent-Message-ID: <"_Xvi22.0.eZ5.cP3Vs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/734
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Length: 786

Dr. John Russ :
Yes I would be interested in this macro.  I am trying to measure the rate of
diffusion of a fluorescently labeled protein into capsules of different
permeabilities, and this would definitely be useful for these studies.

Thanks in advance

Francis Lamberti

> -----Original Message-----
> From: DrJohnRuss@aol.com [mailto:DrJohnRuss@aol.com]
> Sent: Friday, December 18, 1998 10:48 AM
> To: nih-image@io.ece.drexel.edu
> Subject: Re: arc integration
>
>
> In a message dated 12/18/98 12:56:15 PM, you wrote:
>
> > Are there any capablities on nih-image to do arc integration along the
> >angular direction and to plot the data as a function of radial
> direction ?
>
> I have a macro that will do that, and will post it if enough people are
> interested.
> John Russ
>


From nih-image-request@io.ece.drexel.edu Sun Dec 20 05:19 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA14831
	for cshtest@io.ece.drexel.edu; Sun, 20 Dec 1998 05:19:42 -0500 (EST)
Resent-Date: Sun, 20 Dec 1998 05:19:42 -0500 (EST)
Date: Sun, 20 Dec 1998 05:05:00 -0500 (EST)
From: nih-image-owner@io.ece.drexel.edu
Message-Id: <199812201005.FAA12779@io.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Resent-Message-ID: <"CFtD4.0.z73.FlCVs"@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/735
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1997

                   NIH-image Mailing List Help 

nih-image@biomed.drexel.edu   - Sends mail to the list
nih-image-request@biomed.drexel.edu   - Administation for List
nih-image-d-request@biomed.drexel.edu  - Aministration for Digest


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".

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


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

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

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

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 Sun Dec 20 10:35 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA23934;
	Sun, 20 Dec 1998 10:35:53 -0500 (EST)
Resent-Date: Sun, 20 Dec 1998 10:35:53 -0500 (EST)
Date: Sun, 20 Dec 1998 10:15:37 -0500 (EST)
From: R Wade Schuette <schuette@umich.edu>
X-Sender: schuette@frogger.rs.itd.umich.edu
To: NIH Image List <nih-image@io.ece.drexel.edu>
Subject: RGB spectral response curvers?
Message-ID: <Pine.SOL.3.95.981220100637.6896B-100000@frogger.rs.itd.umich.edu>
MIME-Version: 1.0
Resent-Message-ID: <"_MFnO2.0.Y75.UIHVs"@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/736
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: 490

Does anyone have the spectral-response curves for the
R, G, and B channels for some digital camera?  
(or know where I could download them?) 

I'm looking at the impact of color correction and "color
temperature" on scoring of immunohistochemically stained
pathology sections, and need to find the full sensitivity
curves as a function of wavelength for each of the R,G,
and B channels for at least some representative camera.

Thanks!

Wade Schuette  (schuette@umich.edu)
Ann Arbor, MI.



From nih-image-d-request@io.ece.drexel.edu Sun Dec 20 10:38 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA24338;
	Sun, 20 Dec 1998 10:38:18 -0500 (EST)
Date: Sun, 20 Dec 1998 10:38:18 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812201538.KAA24338@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #146
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/146
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 4671

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 146

Today's Topics:
  RE: arc integration                   [ "Francis Lamberti" <FVLamberti@worl ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
  RGB spectral response curvers?        [ R Wade Schuette <schuette@umich.edu ]

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

Date: Sat, 19 Dec 1998 15:30:37 -0800
From: "Francis Lamberti" <FVLamberti@worldnet.att.net>
To: <DrJohnRuss@aol.com>, <nih-image@io.ece.drexel.edu>
Subject: RE: arc integration
Message-ID: <000201be2ba7$95033220$2a50480c@758151725worldnet.att.net>
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 7bit

Dr. John Russ :
Yes I would be interested in this macro.  I am trying to measure the rate of
diffusion of a fluorescently labeled protein into capsules of different
permeabilities, and this would definitely be useful for these studies.

Thanks in advance

Francis Lamberti

> -----Original Message-----
> From: DrJohnRuss@aol.com [mailto:DrJohnRuss@aol.com]
> Sent: Friday, December 18, 1998 10:48 AM
> To: nih-image@io.ece.drexel.edu
> Subject: Re: arc integration
>
>
> In a message dated 12/18/98 12:56:15 PM, you wrote:
>
> > Are there any capablities on nih-image to do arc integration along the
> >angular direction and to plot the data as a function of radial
> direction ?
>
> I have a macro that will do that, and will post it if enough people are
> interested.
> John Russ
>

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

Date: Sun, 20 Dec 1998 05:05:00 -0500 (EST)
From: nih-image-owner@io.ece.drexel.edu
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Message-Id: <199812201005.FAA12779@io.ece.drexel.edu>

                   NIH-image Mailing List Help 

nih-image@biomed.drexel.edu   - Sends mail to the list
nih-image-request@biomed.drexel.edu   - Administation for List
nih-image-d-request@biomed.drexel.edu  - Aministration for Digest


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".

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


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

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

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

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: Sun, 20 Dec 1998 10:15:37 -0500 (EST)
From: R Wade Schuette <schuette@umich.edu>
To: NIH Image List <nih-image@io.ece.drexel.edu>
Subject: RGB spectral response curvers?
Message-ID: <Pine.SOL.3.95.981220100637.6896B-100000@frogger.rs.itd.umich.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Does anyone have the spectral-response curves for the
R, G, and B channels for some digital camera?  
(or know where I could download them?) 

I'm looking at the impact of color correction and "color
temperature" on scoring of immunohistochemically stained
pathology sections, and need to find the full sensitivity
curves as a function of wavelength for each of the R,G,
and B channels for at least some representative camera.

Thanks!

Wade Schuette  (schuette@umich.edu)
Ann Arbor, MI.

--------------------------------
End of nih-image-d Digest V98 Issue #146
****************************************

From nih-image-request@io.ece.drexel.edu Mon Dec 21 09:14 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA22733;
	Mon, 21 Dec 1998 09:14:35 -0500 (EST)
Resent-Date: Mon, 21 Dec 1998 09:14:35 -0500 (EST)
Message-Id: <199812211358.OAA14246@naxos.unice.fr>
Subject: arc integration again
Date: Mon, 21 Dec 98 14:53:02 +0100
x-mailer: Claris Emailer 2.0Fv1 , 3 juillet 1997
From: Legrand <legrand@naxos.unice.fr>
To: <nih-image@io.ece.drexel.edu>
Mime-Version: 1.0
Resent-Message-ID: <"TJuPE3.0.Ko4.CBbVs"@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/737
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: 289

I would certainly be interested by a macro for arc integration... Please

Olivier LEGRAND
Laboratoire de Physique de la Matiere Condensee
CNRS - UMR 6622
Universite de Nice-Sophia Antipolis
Parc Valrose    F-06108 Nice cedex 2 FRANCE
tel.: +33 (0)4 92 07 67 87
fax : +33 (0)4 92 07 67 54


From nih-image-request@io.ece.drexel.edu Mon Dec 21 14:53 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA04602;
	Mon, 21 Dec 1998 14:53:15 -0500 (EST)
Resent-Date: Mon, 21 Dec 1998 14:53:15 -0500 (EST)
Message-ID: <367EA1A8.14F9@pop.uky.edu>
Date: Mon, 21 Dec 1998 14:29:45 -0500
From: alex gimelbrant <aagime0@pop.uky.edu>
Organization: U of K
X-Mailer: Mozilla 3.01 (Macintosh; I; 68K)
MIME-Version: 1.0
To: NIH-Image mailing list <nih-image@io.ece.drexel.edu>
Subject: BDS-Image TCL file format
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"JBb9R3.0.YO.M6gVs"@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/738
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: 562

There was a request several days ago concerning the format
of the TCL files from BDS-Image. I do not have the
email of the author handy, so I post that to the list.

That's what I used to import them to NIH image:
(alternatively, you can save the files in TIFF from 
BDS/Oncor/Whatever-it-is-now Image)

macro 'Import  1300x1000 TCL';
var
  HdrSize,width,height:integer;
begin
  HdrSize:=512;
  width:= 1300;
  height:=1000;
  SetImport('16-bit Unsigned');
  SetImport('Invert');
  SetCustom(width, height, HdrSize, 100);
  Import('');
end;

Hope it helps.

AG


From nih-image-d-request@io.ece.drexel.edu Mon Dec 21 23:39 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id XAA04039;
	Mon, 21 Dec 1998 23:39:46 -0500 (EST)
Date: Mon, 21 Dec 1998 23:39:46 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812220439.XAA04039@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #147
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/147
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 5586

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 147

Today's Topics:
  There is an e-card waiting for you i  [ NetCard <netcard@netcard.com.br> ]
  There is an e-card waiting for you i  [ NetCard <netcard@netcard.com.br> ]
  arc integration again                 [ Legrand <legrand@naxos.unice.fr> ]
  BDS-Image TCL file format             [ alex gimelbrant <aagime0@pop.uky.ed ]
  Quantitative IHC stain scoring        [ R Wade Schuette <schuette@umich.edu ]

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

Date: Mon, 21 Dec 1998 07:38:55 -0500 (EST)
From: NetCard <netcard@netcard.com.br>
To: Group <nih-image-d@io.ece.drexel.edu>
Subject: There is an e-card waiting for you in NetCard!
Message-Id: <199812211238.HAA16077@charon.minerva.net>

Hello Group

You just receive a NetCard's virtual postcard.
NetCard is the brazilian card site in the Internet

To read it, access the web address
http://www.netcard.com.br/cgi-bin/ler.pl?ident=221941892
in your browser.

The card will be available for 12 (twelve) days.

===================================================
 NetCard - The brazilian card site in the Internet
---------------------------------------------------
      WWW: http://www.netcard.com.br
      E-mail: netcard@netcard.com.br
===================================================
 

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

Date: Mon, 21 Dec 1998 07:39:38 -0500 (EST)
From: NetCard <netcard@netcard.com.br>
To: Group <nih-image-d@io.ece.drexel.edu>
Subject: There is an e-card waiting for you in NetCard!
Message-Id: <199812211239.HAA17178@charon.minerva.net>

Hello Group

You just receive a NetCard's virtual postcard.
NetCard is the brazilian card site in the Internet

To read it, access the web address
http://www.netcard.com.br/cgi-bin/ler.pl?ident=191957466
in your browser.

The card will be available for 12 (twelve) days.

===================================================
 NetCard - The brazilian card site in the Internet
---------------------------------------------------
      WWW: http://www.netcard.com.br
      E-mail: netcard@netcard.com.br
===================================================
 

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

Date: Mon, 21 Dec 98 14:53:02 +0100
From: Legrand <legrand@naxos.unice.fr>
To: <nih-image@io.ece.drexel.edu>
Subject: arc integration again
Message-Id: <199812211358.OAA14246@naxos.unice.fr>
Content-Type: text/plain; charset="US-ASCII"

I would certainly be interested by a macro for arc integration... Please

Olivier LEGRAND
Laboratoire de Physique de la Matiere Condensee
CNRS - UMR 6622
Universite de Nice-Sophia Antipolis
Parc Valrose    F-06108 Nice cedex 2 FRANCE
tel.: +33 (0)4 92 07 67 87
fax : +33 (0)4 92 07 67 54

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

Date: Mon, 21 Dec 1998 14:29:45 -0500
From: alex gimelbrant <aagime0@pop.uky.edu>
To: NIH-Image mailing list <nih-image@io.ece.drexel.edu>
Subject: BDS-Image TCL file format
Message-ID: <367EA1A8.14F9@pop.uky.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

There was a request several days ago concerning the format
of the TCL files from BDS-Image. I do not have the
email of the author handy, so I post that to the list.

That's what I used to import them to NIH image:
(alternatively, you can save the files in TIFF from 
BDS/Oncor/Whatever-it-is-now Image)

macro 'Import  1300x1000 TCL';
var
  HdrSize,width,height:integer;
begin
  HdrSize:=512;
  width:= 1300;
  height:=1000;
  SetImport('16-bit Unsigned');
  SetImport('Invert');
  SetCustom(width, height, HdrSize, 100);
  Import('');
end;

Hope it helps.

AG

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

Date: Mon, 21 Dec 1998 23:30:23 -0500 (EST)
From: R Wade Schuette <schuette@umich.edu>
To: NIH Image List <nih-image@io.ece.drexel.edu>
cc: schuette@umich.edu
Subject: Quantitative IHC stain scoring
Message-ID: <Pine.SOL.3.95.981221232103.28999A-100000@seawolf.rs.itd.umich.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Fellow Imagers -- I posted a new paper of mine for your comments.

I am seeking someone with a lab interested in producing test
slides and images to pursue this study of quantitative scoring.

Title:
A Novel, Quantitative, Automated Technique for Identifying and Scoring
Stained Regions in Immunohistochemical Specimens with Dual Stains
----------------
Abstract

Reliable, reproducible quantitative scoring of immunohistochemically
stained images has been difficult,  due in part to the fact that the stain
and counterstains in common use have overlapping colors.     This paper
presents the mathematical basis for completely and reproducibly
identifying the amount of each stain at each pixel of the
image, regardless of image depth and overlapping stains.   The technique
allows closed-form reconstruction of an image of each stain alone, which
can be quantified, or ratio of the two stains, which produces a
substantially higher signal-to-noise ratio than other techniques now in
use. The technique is only valid for images with two different stains.
Preliminary empirical investigation is encouraging that this technique can
be used in practice.

The full paper (5 pages, 22K) is now available for download or viewing
as an Adobe Acrobat "pdf" document  at:
http://www-personal.umich.edu/~schuette/imaging/vpaper.pdf

keywords:  quantitative image analysis, IHC, automated scoring techniques

Wade Schuette
University of Michigan
Medical Center Information Technologies
Ann Arbor, MI USA
schuette@umich.edu

--------------------------------
End of nih-image-d Digest V98 Issue #147
****************************************

From nih-image-request@io.ece.drexel.edu Mon Dec 21 23:40 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id XAA04273;
	Mon, 21 Dec 1998 23:40:50 -0500 (EST)
Resent-Date: Mon, 21 Dec 1998 23:40:50 -0500 (EST)
Date: Mon, 21 Dec 1998 23:30:23 -0500 (EST)
From: R Wade Schuette <schuette@umich.edu>
X-Sender: schuette@seawolf.rs.itd.umich.edu
To: NIH Image List <nih-image@io.ece.drexel.edu>
cc: schuette@umich.edu
Subject: Quantitative IHC stain scoring
Message-ID: <Pine.SOL.3.95.981221232103.28999A-100000@seawolf.rs.itd.umich.edu>
MIME-Version: 1.0
Resent-Message-ID: <"cgnYs3.0.1d.d1oVs"@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/739
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: 1515


Fellow Imagers -- I posted a new paper of mine for your comments.

I am seeking someone with a lab interested in producing test
slides and images to pursue this study of quantitative scoring.

Title:
A Novel, Quantitative, Automated Technique for Identifying and Scoring
Stained Regions in Immunohistochemical Specimens with Dual Stains
----------------
Abstract

Reliable, reproducible quantitative scoring of immunohistochemically
stained images has been difficult,  due in part to the fact that the stain
and counterstains in common use have overlapping colors.     This paper
presents the mathematical basis for completely and reproducibly
identifying the amount of each stain at each pixel of the
image, regardless of image depth and overlapping stains.   The technique
allows closed-form reconstruction of an image of each stain alone, which
can be quantified, or ratio of the two stains, which produces a
substantially higher signal-to-noise ratio than other techniques now in
use. The technique is only valid for images with two different stains.
Preliminary empirical investigation is encouraging that this technique can
be used in practice.

The full paper (5 pages, 22K) is now available for download or viewing
as an Adobe Acrobat "pdf" document  at:
http://www-personal.umich.edu/~schuette/imaging/vpaper.pdf

keywords:  quantitative image analysis, IHC, automated scoring techniques

Wade Schuette
University of Michigan
Medical Center Information Technologies
Ann Arbor, MI USA
schuette@umich.edu



From nih-image-request@io.ece.drexel.edu Tue Dec 22 10:52 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA20845;
	Tue, 22 Dec 1998 10:52:46 -0500 (EST)
Resent-Date: Tue, 22 Dec 1998 10:52:46 -0500 (EST)
Message-Id: <s67f6813.053@mednet.swmed.edu>
X-Mailer: Novell GroupWise 5.5
Date: Tue, 22 Dec 1998 09:36:16 -0600
From: "Daniel Blander" <DBLAND@mednet.swmed.edu>
To: <nih-image@io.ece.drexel.edu>
Subject:  unsubscribe
Mime-Version: 1.0
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id KAA18722
Resent-Message-ID: <"F_Vfd1.0.ja4.tnxVs"@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/740
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: 13

unsubscribe


From nih-image-request@io.ece.drexel.edu Tue Dec 22 10:54 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA21147;
	Tue, 22 Dec 1998 10:54:37 -0500 (EST)
Resent-Date: Tue, 22 Dec 1998 10:54:37 -0500 (EST)
Message-id: <16919155@donner.Dartmouth.EDU>
Date: 22 Dec 98 10:41:06 EST
From: Charles.P.Daghlian@Dartmouth.EDU (Charles P. Daghlian)
Reply-To: daghlian@Dartmouth.EDU
Subject: G3 , vdig, OS 8.1 vs 8.5
To: nih-image@io.ece.drexel.edu
MIME-Version: 1.0
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id KAA19329
Resent-Message-ID: <"_kYAy2.0.Gk4.RsxVs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/741
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain; charset=iso-8859-1
Content-Length: 1056

After having installed OS 8.5 on a G3 all-in-one with a built in digitizer, I find that we are back to having the Start Digitizing command not work. On this same machine with OS 8.1 loaded, the 1.62b30 version of Image works fine. Now it gives a -108 error, then crashes with a type 1 error. The same thing happens with a G3 333 with built-in digitizer.

Does anyone know why this happens? What is different in 8.5? I know Wayne has made adjustments to get Image to work, at least in part, with the built-in digitizers in the G3 machines.Is this a new problem? It would be nice if the G3s would work as well as the 7500-8500 series.

I know the real solution is to try not to be so cheap and buy yet another card from Scion, but hope springs eternal.

regards,

Chuck
********************************************
Charles P. Daghlian, Ph. D.
Director, Rippel E. M. Facility
7605 Remsen
Dartmouth College
Hanover, NH 03755
603-646-1039
http://www.dartmouth.edu/~emczar/
http://www.dartmouth.edu/~daghlian/paleo/
********************************************


From nih-image-request@io.ece.drexel.edu Tue Dec 22 14:39 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA17317;
	Tue, 22 Dec 1998 14:39:13 -0500 (EST)
Resent-Date: Tue, 22 Dec 1998 14:39:13 -0500 (EST)
Message-Id: <s67fac84.076@war.wyeth.com>
X-Mailer: Novell GroupWise 4.1
Date: Tue, 22 Dec 1998 14:28:06 -0500
From: Michael Vinegra <VINEGRM@war.wyeth.com>
To: nih-image@io.ece.drexel.edu
Subject: Commmercial autorad packages
Mime-Version: 1.0
Content-Disposition: inline
Resent-Message-ID: <"gMcD33.0.at3.YB_Vs"@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/742
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text/plain
Content-Length: 1735

Can anyone suggest GREAT out-of-the-box autoradiography software capable of doing grain counting and densitometry on whole rat brain slices on the Mac?  I need something idiot proof, that I can plop on a PowerMac 8500 and leave to be used by a variety of non-collaborating scientists that can't be messed up by the lowest common denominator of computer literacy.  

In the past I've used NIH-Image and IPlab Spectrum to do these tasks, but the level of knowledge involved in the users has resulted in people screwing up macros and scripts that I need to fix repeatedly, and people fighting over who broke who's script.  I need a simple point and click interface, and I need it to be able to capture from my existing setup seamlessly (Dage ccd-72 greyscale camera on a scion LG-7 board, c-mounted to a ChromaPro lightbox with appropriate masks and magnifying lenses)

Michael Vinegra
Acute Neurodegeneration
CNS Disorders
Wyeth-Ayerst Research
Princeton NJ
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         


From nih-image-d-request@io.ece.drexel.edu Wed Dec 23 06:14 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA19720;
	Wed, 23 Dec 1998 06:14:29 -0500 (EST)
Date: Wed, 23 Dec 1998 06:14:29 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812231114.GAA19720@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #148
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/148
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 4193

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 148

Today's Topics:
  unsubscribe                           [ "Daniel Blander" <DBLAND@mednet.swm ]
  G3 , vdig, OS 8.1 vs 8.5              [ Charles.P.Daghlian@Dartmouth.EDU (C ]
  Commmercial autorad packages          [ Michael Vinegra <VINEGRM@war.wyeth. ]

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

Date: Tue, 22 Dec 1998 09:36:16 -0600
From: "Daniel Blander" <DBLAND@mednet.swmed.edu>
To: <nih-image@io.ece.drexel.edu>
Subject:  unsubscribe
Message-Id: <s67f6813.053@mednet.swmed.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline
Content-Transfer-Encoding: 8bit

unsubscribe

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

Date: 22 Dec 98 10:41:06 EST
From: Charles.P.Daghlian@Dartmouth.EDU (Charles P. Daghlian)
To: nih-image@io.ece.drexel.edu
Subject: G3 , vdig, OS 8.1 vs 8.5
Message-id: <16919155@donner.Dartmouth.EDU>
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

After having installed OS 8.5 on a G3 all-in-one with a built in digitizer, I find that we are back to having the Start Digitizing command not work. On this same machine with OS 8.1 loaded, the 1.62b30 version of Image works fine. Now it gives a -108 error, then crashes with a type 1 error. The same thing happens with a G3 333 with built-in digitizer.

Does anyone know why this happens? What is different in 8.5? I know Wayne has made adjustments to get Image to work, at least in part, with the built-in digitizers in the G3 machines.Is this a new problem? It would be nice if the G3s would work as well as the 7500-8500 series.

I know the real solution is to try not to be so cheap and buy yet another card from Scion, but hope springs eternal.

regards,

Chuck
********************************************
Charles P. Daghlian, Ph. D.
Director, Rippel E. M. Facility
7605 Remsen
Dartmouth College
Hanover, NH 03755
603-646-1039
http://www.dartmouth.edu/~emczar/
http://www.dartmouth.edu/~daghlian/paleo/
********************************************

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

Date: Tue, 22 Dec 1998 14:28:06 -0500
From: Michael Vinegra <VINEGRM@war.wyeth.com>
To: nih-image@io.ece.drexel.edu
Subject: Commmercial autorad packages
Message-Id: <s67fac84.076@war.wyeth.com>
Content-Type: text/plain
Content-Disposition: inline

Can anyone suggest GREAT out-of-the-box autoradiography software capable of doing grain counting and densitometry on whole rat brain slices on the Mac?  I need something idiot proof, that I can plop on a PowerMac 8500 and leave to be used by a variety of non-collaborating scientists that can't be messed up by the lowest common denominator of computer literacy.  

In the past I've used NIH-Image and IPlab Spectrum to do these tasks, but the level of knowledge involved in the users has resulted in people screwing up macros and scripts that I need to fix repeatedly, and people fighting over who broke who's script.  I need a simple point and click interface, and I need it to be able to capture from my existing setup seamlessly (Dage ccd-72 greyscale camera on a scion LG-7 board, c-mounted to a ChromaPro lightbox with appropriate masks and magnifying lenses)

Michael Vinegra
Acute Neurodegeneration
CNS Disorders
Wyeth-Ayerst Research
Princeton NJ
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         

--------------------------------
End of nih-image-d Digest V98 Issue #148
****************************************

From nih-image-request@io.ece.drexel.edu Wed Dec 23 10:36 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id KAA27373;
	Wed, 23 Dec 1998 10:36:09 -0500 (EST)
Resent-Date: Wed, 23 Dec 1998 10:36:09 -0500 (EST)
Mime-Version: 1.0
Message-Id: <v04011705b2a6becd5b4a@[134.192.129.87]>
In-Reply-To: 
 <Pine.SOL.3.95.981221232103.28999A-100000@seawolf.rs.itd.umich.edu>
Date: Wed, 23 Dec 1998 10:38:06 -0500
To: nih-image@io.ece.drexel.edu
From: Gloria Hoffman <gehoffma@umaryland.edu>
Subject: Re: Quantitative IHC stain scoring
Resent-Message-ID: <"pkt-I1.0.o76.bgGWs"@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/743
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"
 <Pine.SOL.3.95.981221232103.28999A-100000@seawolf.rs.itd.umich.edu>
Content-Length: 1775

I'd be interested in reviewing that one

>Fellow Imagers -- I posted a new paper of mine for your comments.
>
>I am seeking someone with a lab interested in producing test
>slides and images to pursue this study of quantitative scoring.
>
>Title:
>A Novel, Quantitative, Automated Technique for Identifying and Scoring
>Stained Regions in Immunohistochemical Specimens with Dual Stains
>----------------
>Abstract
>
>Reliable, reproducible quantitative scoring of immunohistochemically
>stained images has been difficult,  due in part to the fact that the stain
>and counterstains in common use have overlapping colors.     This paper
>presents the mathematical basis for completely and reproducibly
>identifying the amount of each stain at each pixel of the
>image, regardless of image depth and overlapping stains.   The technique
>allows closed-form reconstruction of an image of each stain alone, which
>can be quantified, or ratio of the two stains, which produces a
>substantially higher signal-to-noise ratio than other techniques now in
>use. The technique is only valid for images with two different stains.
>Preliminary empirical investigation is encouraging that this technique can
>be used in practice.
>
>The full paper (5 pages, 22K) is now available for download or viewing
>as an Adobe Acrobat "pdf" document  at:
>http://www-personal.umich.edu/~schuette/imaging/vpaper.pdf
>
>keywords:  quantitative image analysis, IHC, automated scoring techniques
>
>Wade Schuette
>University of Michigan
>Medical Center Information Technologies
>Ann Arbor, MI USA
>schuette@umich.edu

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 Wed Dec 23 11:22 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id LAA04362;
	Wed, 23 Dec 1998 11:21:34 -0500 (EST)
Resent-Date: Wed, 23 Dec 1998 11:21:34 -0500 (EST)
Date: Wed, 23 Dec 1998 10:08:29 -0600 (CST)
Date-warning: Date header was inserted by uthscsa.edu
From: David Morilak <morilak@uthscsa.edu>
Subject: Re: Commercial autorad packages
X-Sender: morilak@arwen.uthscsa.edu
To: nih-image@io.ece.drexel.edu
Cc: VINEGRM@war.wyeth.com
Message-id: <l03130300b2a66aff7e3a@[129.111.17.122]>
MIME-version: 1.0
Content-transfer-encoding: 7BIT
Resent-Message-ID: <"Gze5f2.0.aX.cLHWs"@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/744
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: 3380

Michael:

	Please don't take any personal offense at this reply, because
certainly none is intended, but I'm a little taken aback by your query to
provide an idiot-proof out-of-the-box scientific method which will
presumably generate high level scientific results independent of (or
perhaps in spite of) a lack of user training or knowledge. I'm not sure my
comments will contribute anything useful to your search, but as a
grant-funded PI, as we all must do, I constantly train new post-docs,
students and techs in all aspects of my work, including image acquisition
and analysis. (At some point, of course, my most difficult and painful task
becomes training the old lab members to train the new lab members). It
might be constructive to consider the issues you raise in the context of
the inevitable tradeoff between utility/productivity (ie what a procedure
gains for you in your work) and expertise/resources required (ie what it
costs to get that utility). In other words, I have concluded once again
that you get what you pay for, or more precisely, you pay for everything
you get.
	I can think of no more useful, simple (and free) image analysis
package than NIH-Image. You asked for something for "doing grain counting
and densitometry on whole rat brain slices on the Mac" - a pretty
sophisticated task by any definition, with data generated presumably as a
result of very sophisticated bench procedures employed in the service of an
important and expensive research project. We certainly wouldn't expect
anyone with no skills and no training to conduct in situ hybridization or
radioligand binding experiments, so why would we expect such individuals to
process and analyze the results of such experiments? If this is the kind of
work you need accomplished, there is no way to avoid requiring an
appropriate degree of expertise and knowledge on the part of the scientists
you employ to use this technique. This obviously requires an investment of
time and resources to train the users. Calibration, definition and
elimination of noise/background/inappropriate labelling, regional
delineation, not to mention statistical weighting (detertmining mean
integrated density, proportional area of silver grain coverage, etc) and
analysis require knowledge, some subjective understanding of the process
and material being analyzed, as well as an understanding and use of
reliable conventions for making objective decisions. I would submit that
the use of computerized image analysis is by no means an "idiot-proof"
process, nor should it be. It is a terribly sophisticated tool that is only
as good as the scientists who implement it. I would suggest asking your
division or whatever entity is responsible for maintaining the hardware
used in your analyses to also invest in a program of user training. Then,
to avoid the problems you described, you could require taht anyone using
your system will have gone through a minimum level of training and possess
a degree of expertise that you can trust. Without being flippant (well, not
too much anyway), I would suggest that the only way to idiot-proof such a
scientific technique is to idiot-proof the users!

Sincerely,

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-d-request@io.ece.drexel.edu Thu Dec 24 06:15 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA14515;
	Thu, 24 Dec 1998 06:15:04 -0500 (EST)
Date: Thu, 24 Dec 1998 06:15:04 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812241115.GAA14515@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #149
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/149
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 6186

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 149

Today's Topics:
  Re: Quantitative IHC stain scoring    [ Gloria Hoffman <gehoffma@umaryland. ]
  Re: Commercial autorad packages       [ David Morilak <morilak@uthscsa.edu> ]

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

Date: Wed, 23 Dec 1998 10:38:06 -0500
From: Gloria Hoffman <gehoffma@umaryland.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Quantitative IHC stain scoring
Message-Id: <v04011705b2a6becd5b4a@[134.192.129.87]>
Content-Type: text/plain; charset="us-ascii"

I'd be interested in reviewing that one

>Fellow Imagers -- I posted a new paper of mine for your comments.
>
>I am seeking someone with a lab interested in producing test
>slides and images to pursue this study of quantitative scoring.
>
>Title:
>A Novel, Quantitative, Automated Technique for Identifying and Scoring
>Stained Regions in Immunohistochemical Specimens with Dual Stains
>----------------
>Abstract
>
>Reliable, reproducible quantitative scoring of immunohistochemically
>stained images has been difficult,  due in part to the fact that the stain
>and counterstains in common use have overlapping colors.     This paper
>presents the mathematical basis for completely and reproducibly
>identifying the amount of each stain at each pixel of the
>image, regardless of image depth and overlapping stains.   The technique
>allows closed-form reconstruction of an image of each stain alone, which
>can be quantified, or ratio of the two stains, which produces a
>substantially higher signal-to-noise ratio than other techniques now in
>use. The technique is only valid for images with two different stains.
>Preliminary empirical investigation is encouraging that this technique can
>be used in practice.
>
>The full paper (5 pages, 22K) is now available for download or viewing
>as an Adobe Acrobat "pdf" document  at:
>http://www-personal.umich.edu/~schuette/imaging/vpaper.pdf
>
>keywords:  quantitative image analysis, IHC, automated scoring techniques
>
>Wade Schuette
>University of Michigan
>Medical Center Information Technologies
>Ann Arbor, MI USA
>schuette@umich.edu

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: Wed, 23 Dec 1998 10:08:29 -0600 (CST)
From: David Morilak <morilak@uthscsa.edu>
To: nih-image@io.ece.drexel.edu
Cc: VINEGRM@war.wyeth.com
Subject: Re: Commercial autorad packages
Message-id: <l03130300b2a66aff7e3a@[129.111.17.122]>
Content-type: text/plain; charset=us-ascii
Content-transfer-encoding: 7BIT

Michael:

	Please don't take any personal offense at this reply, because
certainly none is intended, but I'm a little taken aback by your query to
provide an idiot-proof out-of-the-box scientific method which will
presumably generate high level scientific results independent of (or
perhaps in spite of) a lack of user training or knowledge. I'm not sure my
comments will contribute anything useful to your search, but as a
grant-funded PI, as we all must do, I constantly train new post-docs,
students and techs in all aspects of my work, including image acquisition
and analysis. (At some point, of course, my most difficult and painful task
becomes training the old lab members to train the new lab members). It
might be constructive to consider the issues you raise in the context of
the inevitable tradeoff between utility/productivity (ie what a procedure
gains for you in your work) and expertise/resources required (ie what it
costs to get that utility). In other words, I have concluded once again
that you get what you pay for, or more precisely, you pay for everything
you get.
	I can think of no more useful, simple (and free) image analysis
package than NIH-Image. You asked for something for "doing grain counting
and densitometry on whole rat brain slices on the Mac" - a pretty
sophisticated task by any definition, with data generated presumably as a
result of very sophisticated bench procedures employed in the service of an
important and expensive research project. We certainly wouldn't expect
anyone with no skills and no training to conduct in situ hybridization or
radioligand binding experiments, so why would we expect such individuals to
process and analyze the results of such experiments? If this is the kind of
work you need accomplished, there is no way to avoid requiring an
appropriate degree of expertise and knowledge on the part of the scientists
you employ to use this technique. This obviously requires an investment of
time and resources to train the users. Calibration, definition and
elimination of noise/background/inappropriate labelling, regional
delineation, not to mention statistical weighting (detertmining mean
integrated density, proportional area of silver grain coverage, etc) and
analysis require knowledge, some subjective understanding of the process
and material being analyzed, as well as an understanding and use of
reliable conventions for making objective decisions. I would submit that
the use of computerized image analysis is by no means an "idiot-proof"
process, nor should it be. It is a terribly sophisticated tool that is only
as good as the scientists who implement it. I would suggest asking your
division or whatever entity is responsible for maintaining the hardware
used in your analyses to also invest in a program of user training. Then,
to avoid the problems you described, you could require taht anyone using
your system will have gone through a minimum level of training and possess
a degree of expertise that you can trust. Without being flippant (well, not
too much anyway), I would suggest that the only way to idiot-proof such a
scientific technique is to idiot-proof the users!

Sincerely,

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

--------------------------------
End of nih-image-d Digest V98 Issue #149
****************************************

From nih-image-request@io.ece.drexel.edu Sun Dec 27 21:06 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id VAA19500;
	Sun, 27 Dec 1998 21:05:51 -0500 (EST)
Resent-Date: Sun, 27 Dec 1998 21:05:51 -0500 (EST)
Message-ID: <3686E537.7599@thurston.com>
Date: Sun, 27 Dec 1998 17:56:10 -0800
From: "Patrick T. Pringle" <lespat@thurston.com>
Reply-To: lespat@thurston.com
X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC)
MIME-Version: 1.0
To: NIH forum <nih-image@io.ece.drexel.edu>
Subject: NIH mean density scans and line width of measuring too
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"F00851.0.JY4.lFkXs"@io>
Resent-From: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/745
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: 964

Holiday Greetings!
Has anyone come up with a satisfactory line width for obtaining mean
density of tree rings in a scanned image, say using NIH or Scion Image?
We have been pretty much relying on measuring the ring width and
latewood width with single pixel wide lines up until now, but it seems a
pity not to at least collect the density information since one is making
the measurements anyway. Somewhere I read or heard that the maximum line
width shown in the NIH toolbar is 99 pixels. I have tried a few
measurements using that width, but the beginning and ending
points invariably "reach out" into the next ring because the line is too
fat.  I suppose one solution to be simply to choose a narrower line, say
10-20 pixels wide and accept that some overlap onto the next ring is
going to happen and that the errors that result are minimal. 
Any thoughts on this would be welcome.
Thanks.
-- 
Pat Pringle

lespat@thurston.com 
pat.pringle@wadnr.gov (Pat's wk)


From nih-image-d-request@io.ece.drexel.edu Tue Dec 29 06:14 EST 1998
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id GAA13194;
	Tue, 29 Dec 1998 06:14:36 -0500 (EST)
Date: Tue, 29 Dec 1998 06:14:36 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199812291114.GAA13194@io.ece.drexel.edu>
Subject: nih-image-d Digest V98 #150
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume98/150
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 1623

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 150

Today's Topics:
  NIH mean density scans and line widt  [ "Patrick T. Pringle" <lespat@thurst ]

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

Date: Sun, 27 Dec 1998 17:56:10 -0800
From: "Patrick T. Pringle" <lespat@thurston.com>
To: NIH forum <nih-image@io.ece.drexel.edu>
Subject: NIH mean density scans and line width of measuring too
Message-ID: <3686E537.7599@thurston.com>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Holiday Greetings!
Has anyone come up with a satisfactory line width for obtaining mean
density of tree rings in a scanned image, say using NIH or Scion Image?
We have been pretty much relying on measuring the ring width and
latewood width with single pixel wide lines up until now, but it seems a
pity not to at least collect the density information since one is making
the measurements anyway. Somewhere I read or heard that the maximum line
width shown in the NIH toolbar is 99 pixels. I have tried a few
measurements using that width, but the beginning and ending
points invariably "reach out" into the next ring because the line is too
fat.  I suppose one solution to be simply to choose a narrower line, say
10-20 pixels wide and accept that some overlap onto the next ring is
going to happen and that the errors that result are minimal. 
Any thoughts on this would be welcome.
Thanks.
-- 
Pat Pringle

lespat@thurston.com 
pat.pringle@wadnr.gov (Pat's wk)

--------------------------------
End of nih-image-d Digest V98 Issue #150
****************************************

From nih-image-request@io.ece.drexel.edu Mon Jan  4 16:29 EST 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA23523;
	Mon, 4 Jan 1999 16:28:03 -0500 (EST)
Resent-Date: Mon, 4 Jan 1999 16:28:03 -0500 (EST)
Date: Mon, 04 Jan 1999 15:01:43 -0600 (CST)
Date-warning: Date header was inserted by uthscsa.edu
From: David Morilak <morilak@uthscsa.edu>
Subject: Image in 99??
X-Sender: morilak@arwen.uthscsa.edu
To: nih-image-d-request@io.ece.drexel.edu
Cc: nih-image@io.ece.drexel.edu
Message-id: <l03130306b2b6867542b5@[129.111.17.122]>
MIME-version: 1.0
Content-transfer-encoding: 7BIT
Resent-Message-ID: <"Q5MKo.0.G05.XmIas"@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/746
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: 918

Hi:

I'm just checking in since I have not received anything from the NIH-Image
mailing list (I am subscribed to receive messages in digest mode) since
12/31/98... I'm wondering if

a) the list has experienced a premature Y2k melt-down
b) The New Year dawned, and I got inadvertently kicked off the list
c) I pissed somebody off and got advertently kicked off the list
d) all imagers are snorkeling in the Caribbean or skiing in the Rockies,
and there have actually been NO messages posted to the NIH list since the
dawn of '99
or
e) Our mail server shredded all messages received between 1/1/99 and 1/4/99

Any ideas as to which is most likely? (and please lie to me if it's c!)

Thanks, and Happy New Year!

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 Jan  4 16:43 EST 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA25161;
	Mon, 4 Jan 1999 16:43:08 -0500 (EST)
Resent-Date: Mon, 4 Jan 1999 16:43:08 -0500 (EST)
From: Vaughn Adams <vaughn@cbis.ece.drexel.edu>
Message-Id: <199901042122.QAA20822@cbis.ece.drexel.edu>
Subject: Re: Image in 99??
In-Reply-To: <l03130306b2b6867542b5@[129.111.17.122]> from David Morilak at "Jan 4, 1999  3: 1:43 pm"
To: nih-image@io.ece.drexel.edu
Date: Mon, 4 Jan 1999 16:22:24 -0500 (EST)
Cc: morilak@uthscsa.edu
X-Mailer: ELM [version 2.4ME+ PL48 (25)]
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Resent-Message-ID: <"3rV0L1.0.9b5.X4Jas"@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/747
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: 1137

David:

> I'm just checking in since I have not received anything from the NIH-Image
> mailing list (I am subscribed to receive messages in digest mode) since
> 12/31/98... I'm wondering if
> 
> a) the list has experienced a premature Y2k melt-down
> b) The New Year dawned, and I got inadvertently kicked off the list
> c) I pissed somebody off and got advertently kicked off the list
> d) all imagers are snorkeling in the Caribbean or skiing in the Rockies,
> and there have actually been NO messages posted to the NIH list since the
> dawn of '99
> or
> e) Our mail server shredded all messages received between 1/1/99 and 1/4/99
> 
> Any ideas as to which is most likely? (and please lie to me if it's c!)

The correct answer is D.  Everybody went to the Caribbean.  The list members
who live in the Caribean went mountain climbing in Alaska.


-- 
Vaughn Adams
Drexel University 
Electrical and Computer Engineering      Voice: 215-895-1979
32nd and Chestnut Streets                  FAX: 215-895-1695
Philadelphia, Pa 19104                   Email: vaughn@coe.drexel.edu

PGP key available - finger -l vaughn@cbis.ece.drexel.edu


From nih-image-request@io.ece.drexel.edu Mon Jan  4 17:04 EST 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id RAA27417;
	Mon, 4 Jan 1999 17:04:37 -0500 (EST)
Resent-Date: Mon, 4 Jan 1999 17:04:37 -0500 (EST)
Message-Id: <l03130300b2b6e65fa10b@[128.196.130.192]>
In-Reply-To: <l03130306b2b6867542b5@[129.111.17.122]>
Mime-Version: 1.0
Date: Mon, 4 Jan 1999 14:43:28 -0700
To: nih-image@io.ece.drexel.edu
From: connie temm <ctemm@Ag.Arizona.Edu>
Subject: Re: Image in 99??
Resent-Message-ID: <"CV9KB3.0.wF6.lRJas"@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/748
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: 244

d1/2: all imagers would rather be snorkeling or skiing

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






From nih-image-request@io.ece.drexel.edu Mon Jan  4 18:21 EST 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id SAA05855;
	Mon, 4 Jan 1999 18:21:42 -0500 (EST)
Resent-Date: Mon, 4 Jan 1999 18:21:42 -0500 (EST)
Date: Mon, 4 Jan 1999 15:02:29 -0800 (PST)
From: David Ehrhardt <ehrhardt@camelot.Stanford.EDU>
To: nih-image@io.ece.drexel.edu
cc: nih-image-d-request@io.ece.drexel.edu
Subject: Re: Image in 99??
In-Reply-To: <l03130306b2b6867542b5@[129.111.17.122]>
Message-ID: <Pine.GUL.3.95.990104150017.13729B-100000@camelot.Stanford.EDU>
MIME-Version: 1.0
Resent-Message-ID: <"kqI0L.0.h11.1dKas"@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/749
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: 1086

> Hi:
> 
> I'm just checking in since I have not received anything from the NIH-Image
> mailing list (I am subscribed to receive messages in digest mode) since
> 12/31/98... I'm wondering if
> 
> a) the list has experienced a premature Y2k melt-down
> b) The New Year dawned, and I got inadvertently kicked off the list
> c) I pissed somebody off and got advertently kicked off the list
> d) all imagers are snorkeling in the Caribbean or skiing in the Rockies,
> and there have actually been NO messages posted to the NIH list since the
> dawn of '99
> or
> e) Our mail server shredded all messages received between 1/1/99 and 1/4/99
> 
> Any ideas as to which is most likely? (and please lie to me if it's c!)
> 
> Thanks, and Happy New Year!
> 
> David Morilak

I was actually snorkeling during this time and I saw a lot of suspicious
pasty-skinned people who looked like they spent a lot of time in darkened
rooms.


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 Mon Jan  4 20:29 EST 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id UAA18525;
	Mon, 4 Jan 1999 20:29:43 -0500 (EST)
Resent-Date: Mon, 4 Jan 1999 20:29:43 -0500 (EST)
Message-Id: <3.0.5.32.19990104201057.00bb64d0@s.imap.itd.umich.edu>
X-Sender: schuette@s.imap.itd.umich.edu
X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32)
Date: Mon, 04 Jan 1999 20:10:57 -0500
To: nih-image@io.ece.drexel.edu
From: Wade & Cheryll Schuette <schuette@s.imap.itd.umich.edu>
Subject: Quantitative immunoperoxidase staining
In-Reply-To: <l03130306b2b6867542b5@[129.111.17.122]>
Mime-Version: 1.0
Resent-Message-ID: <"-F27H1.0.924.cRMas"@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/750
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: 677

Maybe it just seems like snorkeling, as the snow mountains
are 3-4 meters high at the edge of our parking lot...  

Anyway, what _I_ did on my holiday break was to finally crack
segmenting images of immunoperoxidase stained pathology slides
to separate the  brown peroxidase and blue counterstain objectively and
quantitatively.  

I posted the example under "98.001" on my web page
http://www-personal.umich.edu/~schuette/imaging

I'd be interested in hearing from anyone else on the list who's
working on this problem.

Wade Schuette
University of Michigan
Sunny (14 inches worth) Ann Arbor, Michigan

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


From nih-image-request@io.ece.drexel.edu Tue Jan  5 01:25 EST 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id BAA21275;
	Tue, 5 Jan 1999 01:24:53 -0500 (EST)
Resent-Date: Tue, 5 Jan 1999 01:24:53 -0500 (EST)
From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: lespat@thurston.com, nih-image@io.ece.drexel.edu
Date:          Tue, 5 Jan 1999 17:01:32 GMT+1100
Subject:       Re: NIH mean density scans and line width of measuring too
Priority: normal
X-mailer: Pegasus Mail/Mac (v2.2.1)
Message-ID: <6B9F84B5792@rna.bio.mq.edu.au>
Resent-Message-ID: <"G7cTJ1.0.Ia4.ZjQas"@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/751
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 2515

>Date: Sun, 27 Dec 1998 17:56:10 -0800
>From: "Patrick T. Pringle" <lespat@thurston.com>
>To: NIH forum <nih-image@io.ece.drexel.edu>
>Subject: NIH mean density scans and line width of measuring too
>....
>Has anyone come up with a satisfactory line width for obtaining mean
>density of tree rings in a scanned image, say using NIH or Scion Image?
>We have been pretty much relying on measuring the ring width and
>latewood width with single pixel wide lines up until now, but it seems a
>pity not to at least collect the density information since one is making
>the measurements anyway. Somewhere I read or heard that the maximum line
>width shown in the NIH toolbar is 99 pixels. I have tried a few
>measurements using that width, but the beginning and ending
>points invariably "reach out" into the next ring because the line is too
>fat.  I suppose one solution to be simply to choose a narrower line, say
>10-20 pixels wide and accept that some overlap onto the next ring is
>going to happen and that the errors that result are minimal. 
>Any thoughts on this would be welcome.
>Thanks.
>-- 
>Pat Pringle
>

A GrowthRingsMacro I wrote in '96 attempted to make the best use of the available 
data. This is probably more complex than you want. It involved:

Radial analysis of the maximum available sector or full 360 degree data using a 
first pass radial analysis with a narrow profilePlot line (n=6<>8pixels) to 
generate a (more or less) linearised 2D profile map where one dimension was 
distance from core and other dimension was angle around sector.

This preliminary profile along this first pass radial was then used to trace 
(usually 3 well spaced) of these approximately linearised rings using either 
density sliceing and wand or manually using a segemented line selection.
These were then in turn used to morph (or interpolate) their shape over the whole 
profile so that the whole sector data was linearised using the radially integrated 
data.

The linearised profile was then plotprofiled to give accurate integrated peak 
spacing and densities. (peaks can be automatically found by derivative passing 
through zero).

The morphing data was inverted to remap the determined rings back over the original 
image for easy verification.

A lot depends on the nature of the project, your images, patience etc :-)


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 Tue Jan  5 05:18 EST 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id FAA17705;
	Tue, 5 Jan 1999 05:18:42 -0500 (EST)
Resent-Date: Tue, 5 Jan 1999 05:18:42 -0500 (EST)
Date: Tue, 5 Jan 1999 05:05:01 -0500 (EST)
From: nih-image-owner@io.ece.drexel.edu
Message-Id: <199901051005.FAA15920@io.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: ADMIN: list commands
Resent-Message-ID: <"zXAT7.0.yu3.FFUas"@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/752
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1997

                   NIH-image Mailing List Help 

nih-image@biomed.drexel.edu   - Sends mail to the list
nih-image-request@biomed.drexel.edu   - Administation for List
nih-image-d-request@biomed.drexel.edu  - Aministration for Digest


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".

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


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

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

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

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 Tue Jan  5 09:51 EST 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA19308;
	Tue, 5 Jan 1999 09:51:30 -0500 (EST)
Resent-Date: Tue, 5 Jan 1999 09:51:30 -0500 (EST)
X-Authentication-Warning: asgard.cbu.edu: malinda owned process doing -bs
Date: Tue, 5 Jan 1999 08:23:28 -0600 (CST)
From: Malinda Fitzgerald <malinda@cbu.edu>
X-Sender: malinda@asgard
To: nih-image@io.ece.drexel.edu
cc: nih-image-d-request@io.ece.drexel.edu
Subject: Re: Image in 99??
In-Reply-To: <Pine.GUL.3.95.990104150017.13729B-100000@camelot.Stanford.EDU>
Message-ID: <Pine.GSO.3.96.990105081930.4367A-100000@asgard>
MIME-Version: 1.0
Resent-Message-ID: <"wHQbH2.0.xr3.W2Yas"@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/753
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: 282

I just surfaced from the chaos of the holidays and speaking as a one that
spends way too much time working on my computer I wish I was
snorkling!!Sounds like a good idea.  How about an image retreat?  We could
all bring our laptops and discuss how to analyze coral reefs!  Malinda


From nih-image-d-request@io.ece.drexel.edu Tue Jan  5 09:56 EST 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id JAA19991;
	Tue, 5 Jan 1999 09:56:17 -0500 (EST)
Date: Tue, 5 Jan 1999 09:56:17 -0500 (EST)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199901051456.JAA19991@io.ece.drexel.edu>
Subject: nih-image-d Digest V99 #1
X-Loop: nih-image-d@biomed.drexel.edu
X-Mailing-List: <nih-image-d@biomed.drexel.edu> archive/volume99/1
Precedence: list
MIME-Version: 1.0
To: nih-image-d@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 12169

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

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 1

Today's Topics:
  Image in 99??                         [ David Morilak <morilak@uthscsa.edu> ]
  Re: Image in 99??                     [ Vaughn Adams <vaughn@cbis.ece.drexe ]
  Re: Image in 99??                     [ connie temm <ctemm@Ag.Arizona.Edu> ]
  Re: Image in 99??                     [ David Ehrhardt <ehrhardt@camelot.St ]
  Quantitative immunoperoxidase staini  [ Wade & Cheryll Schuette <schuette@s ]
  Re: NIH mean density scans and line   [ GJOSS@rna.bio.mq.edu.au ]
  ADMIN: list commands                  [ nih-image-owner@io.ece.drexel.edu ]
  Re: Image in 99??                     [ Malinda Fitzgerald <malinda@cbu.edu ]

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

Date: Mon, 04 Jan 1999 15:01:43 -0600 (CST)
From: David Morilak <morilak@uthscsa.edu>
To: nih-image-d-request@io.ece.drexel.edu
Cc: nih-image@io.ece.drexel.edu
Subject: Image in 99??
Message-id: <l03130306b2b6867542b5@[129.111.17.122]>
Content-type: text/plain; charset=us-ascii
Content-transfer-encoding: 7BIT

Hi:

I'm just checking in since I have not received anything from the NIH-Image
mailing list (I am subscribed to receive messages in digest mode) since
12/31/98... I'm wondering if

a) the list has experienced a premature Y2k melt-down
b) The New Year dawned, and I got inadvertently kicked off the list
c) I pissed somebody off and got advertently kicked off the list
d) all imagers are snorkeling in the Caribbean or skiing in the Rockies,
and there have actually been NO messages posted to the NIH list since the
dawn of '99
or
e) Our mail server shredded all messages received between 1/1/99 and 1/4/99

Any ideas as to which is most likely? (and please lie to me if it's c!)

Thanks, and Happy New Year!

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, 4 Jan 1999 16:22:24 -0500 (EST)
From: Vaughn Adams <vaughn@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Cc: morilak@uthscsa.edu
Subject: Re: Image in 99??
Message-Id: <199901042122.QAA20822@cbis.ece.drexel.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit

David:

> I'm just checking in since I have not received anything from the NIH-Image
> mailing list (I am subscribed to receive messages in digest mode) since
> 12/31/98... I'm wondering if
> 
> a) the list has experienced a premature Y2k melt-down
> b) The New Year dawned, and I got inadvertently kicked off the list
> c) I pissed somebody off and got advertently kicked off the list
> d) all imagers are snorkeling in the Caribbean or skiing in the Rockies,
> and there have actually been NO messages posted to the NIH list since the
> dawn of '99
> or
> e) Our mail server shredded all messages received between 1/1/99 and 1/4/99
> 
> Any ideas as to which is most likely? (and please lie to me if it's c!)

The correct answer is D.  Everybody went to the Caribbean.  The list members
who live in the Caribean went mountain climbing in Alaska.


-- 
Vaughn Adams
Drexel University 
Electrical and Computer Engineering      Voice: 215-895-1979
32nd and Chestnut Streets                  FAX: 215-895-1695
Philadelphia, Pa 19104                   Email: vaughn@coe.drexel.edu

PGP key available - finger -l vaughn@cbis.ece.drexel.edu

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

Date: Mon, 4 Jan 1999 14:43:28 -0700
From: connie temm <ctemm@Ag.Arizona.Edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Image in 99??
Message-Id: <l03130300b2b6e65fa10b@[128.196.130.192]>
Content-Type: text/plain; charset="us-ascii"

d1/2: all imagers would rather be snorkeling or skiing

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

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

Date: Mon, 4 Jan 1999 15:02:29 -0800 (PST)
From: David Ehrhardt <ehrhardt@camelot.Stanford.EDU>
To: nih-image@io.ece.drexel.edu
cc: nih-image-d-request@io.ece.drexel.edu
Subject: Re: Image in 99??
Message-ID: <Pine.GUL.3.95.990104150017.13729B-100000@camelot.Stanford.EDU>
Content-Type: TEXT/PLAIN; charset=US-ASCII

> Hi:
> 
> I'm just checking in since I have not received anything from the NIH-Image
> mailing list (I am subscribed to receive messages in digest mode) since
> 12/31/98... I'm wondering if
> 
> a) the list has experienced a premature Y2k melt-down
> b) The New Year dawned, and I got inadvertently kicked off the list
> c) I pissed somebody off and got advertently kicked off the list
> d) all imagers are snorkeling in the Caribbean or skiing in the Rockies,
> and there have actually been NO messages posted to the NIH list since the
> dawn of '99
> or
> e) Our mail server shredded all messages received between 1/1/99 and 1/4/99
> 
> Any ideas as to which is most likely? (and please lie to me if it's c!)
> 
> Thanks, and Happy New Year!
> 
> David Morilak

I was actually snorkeling during this time and I saw a lot of suspicious
pasty-skinned people who looked like they spent a lot of time in darkened
rooms.


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: Mon, 04 Jan 1999 20:10:57 -0500
From: Wade & Cheryll Schuette <schuette@s.imap.itd.umich.edu>
To: nih-image@io.ece.drexel.edu
Subject: Quantitative immunoperoxidase staining
Message-Id: <3.0.5.32.19990104201057.00bb64d0@s.imap.itd.umich.edu>
Content-Type: text/plain; charset="us-ascii"

Maybe it just seems like snorkeling, as the snow mountains
are 3-4 meters high at the edge of our parking lot...  

Anyway, what _I_ did on my holiday break was to finally crack
segmenting images of immunoperoxidase stained pathology slides
to separate the  brown peroxidase and blue counterstain objectively and
quantitatively.  

I posted the example under "98.001" on my web page
http://www-personal.umich.edu/~schuette/imaging

I'd be interested in hearing from anyone else on the list who's
working on this problem.

Wade Schuette
University of Michigan
Sunny (14 inches worth) Ann Arbor, Michigan

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

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

Date:          Tue, 5 Jan 1999 17:01:32 GMT+1100
From: GJOSS@rna.bio.mq.edu.au
To: lespat@thurston.com, nih-image@io.ece.drexel.edu
Subject:       Re: NIH mean density scans and line width of measuring too
Message-ID: <6B9F84B5792@rna.bio.mq.edu.au>

>Date: Sun, 27 Dec 1998 17:56:10 -0800
>From: "Patrick T. Pringle" <lespat@thurston.com>
>To: NIH forum <nih-image@io.ece.drexel.edu>
>Subject: NIH mean density scans and line width of measuring too
>....
>Has anyone come up with a satisfactory line width for obtaining mean
>density of tree rings in a scanned image, say using NIH or Scion Image?
>We have been pretty much relying on measuring the ring width and
>latewood width with single pixel wide lines up until now, but it seems a
>pity not to at least collect the density information since one is making
>the measurements anyway. Somewhere I read or heard that the maximum line
>width shown in the NIH toolbar is 99 pixels. I have tried a few
>measurements using that width, but the beginning and ending
>points invariably "reach out" into the next ring because the line is too
>fat.  I suppose one solution to be simply to choose a narrower line, say
>10-20 pixels wide and accept that some overlap onto the next ring is
>going to happen and that the errors that result are minimal. 
>Any thoughts on this would be welcome.
>Thanks.
>-- 
>Pat Pringle
>

A GrowthRingsMacro I wrote in '96 attempted to make the best use of the available 
data. This is probably more complex than you want. It involved:

Radial analysis of the maximum available sector or full 360 degree data using a 
first pass radial analysis with a narrow profilePlot line (n=6<>8pixels) to 
generate a (more or less) linearised 2D profile map where one dimension was 
distance from core and other dimension was angle around sector.

This preliminary profile along this first pass radial was then used to trace 
(usually 3 well spaced) of these approximately linearised rings using either 
density sliceing and wand or manually using a segemented line selection.
These were then in turn used to morph (or interpolate) their shape over the whole 
profile so that the whole sector data was linearised using the radially integrated 
data.

The linearised profile was then plotprofiled to give accurate integrated peak 
spacing and densities. (peaks can be automatically found by derivative passing 
through zero).

The morphing data was inverted to remap the determined rings back over the original 
image for easy verification.

A lot depends on the nature of the project, your images, patience etc :-)


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, 5 Jan 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: <199901051005.FAA15920@io.ece.drexel.edu>

                   NIH-image Mailing List Help 

nih-image@biomed.drexel.edu   - Sends mail to the list
nih-image-request@biomed.drexel.edu   - Administation for List
nih-image-d-request@biomed.drexel.edu  - Aministration for Digest


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".

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


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

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

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

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, 5 Jan 1999 08:23:28 -0600 (CST)
From: Malinda Fitzgerald <malinda@cbu.edu>
To: nih-image@io.ece.drexel.edu
cc: nih-image-d-request@io.ece.drexel.edu
Subject: Re: Image in 99??
Message-ID: <Pine.GSO.3.96.990105081930.4367A-100000@asgard>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I just surfaced from the chaos of the holidays and speaking as a one that
spends way too much time working on my computer I wish I was
snorkling!!Sounds like a good idea.  How about an image retreat?  We could
all bring our laptops and discuss how to analyze coral reefs!  Malinda

--------------------------------
End of nih-image-d Digest V99 Issue #1
**************************************

From nih-image-request@io.ece.drexel.edu Tue Jan  5 12:50 EST 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id MAA08171;
	Tue, 5 Jan 1999 12:49:08 -0500 (EST)
Resent-Date: Tue, 5 Jan 1999 12:49:08 -0500 (EST)
Date: Tue, 5 Jan 1999 12:21:16 -0500 (EST)
From: RICHARD RHIEW <rbr16@columbia.edu>
Sender: rbr16@columbia.edu
To: nih-image@io.ece.drexel.edu
Subject: pixel to meter conversion???
Message-ID: <Pine.GSO.3.95qL.990105122010.9189A-100000@merhaba.cc.columbia.edu>
MIME-Version: 1.0
Resent-Message-ID: <"7C32v1.0.RO1.Xeaas"@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/754
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: 80

is there a conversion to go from 1 pixel to
meters/micrometers/inches,etc???




From nih-image-request@io.ece.drexel.edu Tue Jan  5 15:00 EST 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id OAA21357;
	Tue, 5 Jan 1999 14:59:37 -0500 (EST)
Resent-Date: Tue, 5 Jan 1999 14:59:37 -0500 (EST)
Date: Tue, 5 Jan 1999 20:34:12 +0100 (MET)
Message-Id: <199901051934.UAA10225@isidoro.unileon.es>
X-Sender: dbcmjv@isidoro.unileon.es
X-Mailer: Windows Eudora Light Version 1.5.2
Mime-Version: 1.0
To: nih-image@io.ece.drexel.edu
From: Maria Dolores Julian <dbcmjv@unileon.es>
Subject: in situ hybridization
Resent-Message-ID: <"ZNo1G1.0.tX4.rdcas"@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/755
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: 2175

Dear colleagues:
I am analyzing some in situ hybridization films from brain sections and
would appreciate any clarification of my doubts as well as any further
suggestions.  The version of Image that I have available is 1.22.

1.- How do you get more reliable results?, using the gray scale or with the
threshold?, or do you vary this depending on the region to be studied and/or
the probe (oligoprobe or riboprobe).
2.- After selecting a region with the mouse, the program gives us two
columns with two different values (area and mean).  I have been told to use
the mean value (ignoring the area) when using the gray scale, whereas, when
using the threshold, the value to be used is the product obtained
multiplying the area by the mean; is that correct?
3.- Does anyone subtract the background? Do you think it is
important/necessary? (Some people believe it is especially important when
using riboprobes because the labeling is more intense and uneven between
sections).  And, if so, when and how do you do it?  In this regard I have
been tested to measure the background of a similar region between the
dentate gyrus and CA1 when analyzing the hippocampus (riboprobe labeled)
using the threshold method.  In these cases, the area for the value is zero
or a very small number (0.001, etc.); however, the values for the mean
column, although sometimes are also zero, are otherwise bigger than the area
value as, for example, 0.2, etc.  Consequently, subtracting the background
for each section I would have a very different result if I consider the
value of this background as the product of the area by the mean or if I only
consider the value of its mean column.
4.-  In my studies I am analyzing brains of different sizes (male/female,
young/adult) and thus their different regions would be bigger or smaller
depending on the sex/age. Does the Image program compensate these
differences in anyway or, by the contrary, it would give a bigger value for
a male brain region (because it has a bigger surface) than for a female that
has a higher labeling from the probe (because its surface is smaller)?

Thank you very much in advance for your replays (dbcmjv@unileon.es).


From nih-image-request@io.ece.drexel.edu Tue Jan  5 15:58 EST 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id PAA26805;
	Tue, 5 Jan 1999 15:57:06 -0500 (EST)
Resent-Date: Tue, 5 Jan 1999 15:57:06 -0500 (EST)
Date: Tue, 5 Jan 99 12:33:06 PST
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: in situ hybridization
In-Reply-To: Your message of Tue, 5 Jan 1999 20:34:12 +0100 (MET)
Message-ID: <CMM.0.90.4.915568386.wwolfw@hsc.usc.edu>
Resent-Message-ID: <"vWxnX.0.nt5.TSdas"@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/756
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 1244

Correction:

In item 4, where you wrote:

>might be difficult for clinical courses that are taught by faculty from
>various different departments.

please change 1 word: clinical to interdisciplinary. It should read:

might be difficult for interdisciplinary that are taught by faculty from
different departments.

I also suggest deleting "various", as "various" and "different" is redundant.

Walter
======================================================================
|  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 90033    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 Tue Jan  5 16:02 EST 1999
Received: (from lists@localhost)
	by io.ece.drexel.edu (8.8.8/8.8.8) id QAA27422;
	Tue, 5 Jan 1999 16:02:11 -0500 (EST)
Resent-Date: Tue, 5 Jan 1999 16:02:11 -0500 (EST)
Date: Tue, 5 Jan 99 12:38:00 PST
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: in situ hybridization
In-Reply-To: Your message of Tue, 5 Jan 1999 20:34:12 +0100 (MET)
Message-ID: <CMM.0.90.4.915568680.wwolfw@hsc.usc.edu>
Resent-Message-ID: <"NH_5z3.0.916.uWdas"@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/757
X-Loop: nih-image@biomed.drexel.edu
Precedence: list
Resent-Sender: nih-image-request@io.ece.drexel.edu
Content-Type: text
Content-Length: 951

Dear Colleagues:

It appears that a reply to a different message went to this list-server. My
appologies. 

======================================================================
|  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 90033    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  |
======================================================================