From bnhirsch@dapsas1.weizmann.ac.il  Fri Oct  1 12:15:41 1993
Received: from dapsas1.weizmann.ac.il by nx1.soils.umn.edu (5.65c)
	id AA27457; Fri, 1 Oct 1993 03:06:36 -0500
Return-Path: <bnhirsch@dapsas1.weizmann.ac.il>
Received: from [132.76.66.31] by dapsas1.weizmann.ac.il via SMTP (920110.SGI/911001.SGI)
	for nih-image@soils.umn.edu id AA27632; Fri, 1 Oct 93 10:06:42 +0300
Message-Id: <9310010706.AA27632@dapsas1.weizmann.ac.il>
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Fri, 1 Oct 1993 10:15:41 +0200
To: nih-image@soils.umn.edu
From: bnhirsch@dapsas1.weizmann.ac.il (David L. Hirschberg)
Subject: Understanding the dif between integrated and mean density

Forgive me if this issue has come up before.  I am having  trouble
understanding  the difference between integrated and mean density.  I read
the explanation in the 1.51 manual and am still a little confused.  For
what application is each applicable?   

Thank you, David

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
David L. Hirschberg                     bnhirsch@dapsas.weizmann.ac.il
Department of Neurobiology              (972) 834-2127 work
Weizmann Institute of Science           (972) 847-4805 home
Rehovot 76100 Israel                    (972) 834-4131 fax



From wayne@helix.nih.gov  Fri Oct  1 08:55:25 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA01406; Fri, 1 Oct 1993 08:57:00 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA26710; Fri, 1 Oct 93 09:17:12 -0400
Message-Id: <9310011317.AA26710@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Fri, 1 Oct 1993 08:55:25 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: reslicing volume in another plane

>Has anyone out there written macros to reslice a stack in a user specified
>plane?  We are currently looking at high resolution MRI datasets of the
>cochlea (ie. inner ear).  The problem is that each specimen is scanned
>differently, however it happens to rest in the small well it's placed in. 
>It would be real nice if we could resection this volume in user selected
>plane other than the original plane of acquisition.  This would enable us
>to make some critical measurements between specimens.  I though I'd put
>this question out there before I attempt to write any of my own macros.

The are serveral macros for orthogonal reslicing of volumes in the macro
file "Stacks".

--wayne


From brown@alsys1.aecom.yu.edu  Fri Oct  1 05:36:20 1993
Received: from alsys1.aecom.yu.edu by nx1.soils.umn.edu (5.65c)
	id AA02335; Fri, 1 Oct 1993 10:43:30 -0500
Return-Path: <brown@alsys1.aecom.yu.edu>
Received: from [129.98.90.119] (garbo.aecom.yu.edu) by alsys1.aecom.yu.edu with SMTP id AA11361
  (5.67a/IDA-1.5/AECOM-RIT for <nih-image@soils.umn.edu>); Fri, 1 Oct 1993 11:44:22 -0400
From: "Lucy Brown" <brown@aecom.yu.edu>
Date: Fri, 1 Oct 93 11:36:20 CST
Message-Id: <41781.brown@alsys1.aecom.yu.edu>
X-Popmail-Charset: English
To: nih-image@soils.umn.edu
Subject: Re: Understanding the dif between integrated and mean density

On Fri, 1 Oct 1993 03:16:39 -0500, David L. Hirschberg wrote:

>Forgive me if this issue has come up before.  I am having  trouble
>understanding  the difference between integrated and mean density.  I read
>the explanation in the 1.51 manual and am still a little confused.  For
>what application is each applicable?   
>
>Thank you, David
>
>=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>David L. Hirschberg                     bnhirsch@dapsas.weizmann.ac.il
>Department of Neurobiology              (972) 834-2127 work
>Weizmann Institute of Science           (972) 847-4805 home
>Rehovot 76100 Israel                    (972) 834-4131 fax

Integrated optical density is the SUM of the optical density of each pixel 
in your box, or region of interest, with background subtracted.  Mean 
optical density is the sum of all the pixels in your region of interest, 
divided by the number of pixels in your region of interest.  Integrated is 
useful and more sensitive than mean when you're analyzing a gel, and the 
region of interest is a box around a band with some of the background in 
the box.  Also, bands in gels often contain a range of optical densities 
that are not well characterized by a mean.  Mean should be used in material 
where your region of interest is fairly uniform and does not contain 
background.  Mean optical density is used to describe individual brain 
regions with relatively homogeneous densities in autoradiograms, for 
example.


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

Lucy L. Brown, Ph.D.                      email:  brown@aecom.yu.edu
Department of Neurology                   lab  :  (718) 430-3632
Albert Einstein College of Medicine
New York
From brown@alsys1.aecom.yu.edu  Fri Oct  1 05:43:26 1993
Received: from alsys1.aecom.yu.edu by nx1.soils.umn.edu (5.65c)
	id AA02473; Fri, 1 Oct 1993 10:50:20 -0500
Return-Path: <brown@alsys1.aecom.yu.edu>
Received: from [129.98.90.119] (garbo.aecom.yu.edu) by alsys1.aecom.yu.edu with SMTP id AA11581
  (5.67a/IDA-1.5/AECOM-RIT for <nih-image@soils.umn.edu>); Fri, 1 Oct 1993 11:51:29 -0400
From: "Lucy Brown" <brown@aecom.yu.edu>
Date: Fri, 1 Oct 93 11:43:26 CST
Message-Id: <42208.brown@alsys1.aecom.yu.edu>
X-Popmail-Charset: English
To: nih-image@soils.umn.edu
Subject: Automatic threshold

Has anyone written a macro for automatic thresholding?  Russ describes 
automatic thresholding using the change in area and perimeter of the binary 
image formed over a series of threshold-detect values (Russ,1992, The Image 
Procesing Handbook, pgs 258-259).


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

Lucy L. Brown, Ph.D.                      email:  brown@aecom.yu.edu
Department of Neurology                   lab  :  (718) 430-3632
Albert Einstein College of Medicine
New York
From keatinga@med.unc.edu  Fri Oct  1 08:55:23 1993
Received: from med.unc.edu (durham.med.unc.edu) by nx1.soils.umn.edu (5.65c)
	id AA03384; Fri, 1 Oct 1993 11:52:59 -0500
Return-Path: <keatinga@med.unc.edu>
Received: from garner.med.unc.edu by med.unc.edu (4.1/SMI-4.0-ACB-1.0)
	id AA16134; Fri, 1 Oct 93 12:55:28 EDT
Received: by garner.med.unc.edu (4.1/SMI-4.1)
	id AA16052; Fri, 1 Oct 93 12:55:24 EDT
From: keatinga@med.unc.edu (Arthur Keating)
Message-Id: <9310011655.AA16052@garner.med.unc.edu>
Subject: Re: reslicing volume in another plane
To: nih-image@soils.umn.edu
Date: Fri, 1 Oct 93 12:55:23 EDT
In-Reply-To: <9310011317.AA26710@zippy.nimh.nih.gov>; from "Wayne Rasband" at Oct 1, 93 9:10 am
X-Mailer: ELM [version 2.3 PL11]

> 
> >Has anyone out there written macros to reslice a stack in a user specified
> >plane?  We are currently looking at high resolution MRI datasets of the
> >cochlea (ie. inner ear).  The problem is that each specimen is scanned
> >differently, however it happens to rest in the small well it's placed in. 
> >It would be real nice if we could resection this volume in user selected
> >plane other than the original plane of acquisition.  This would enable us
> >to make some critical measurements between specimens.  I though I'd put
> >this question out there before I attempt to write any of my own macros.
> 
> The are serveral macros for orthogonal reslicing of volumes in the macro
> file "Stacks".
> 
> --wayne
> 
> 
> 
 Yes I know.  I'm talking about planes other than orthogonal ones.  I want
to reslice an entire volume repeatedly  as is done when one makes a line
selection and obtains a new section with the slice command.  Any help there?

From @YaleVM.YCC.Yale.Edu:Mike_Schwartz@QUICKMAIL.CIS.YALE.EDU  Fri Oct  1 11:57:49 1993
Received: from YALEVM.YCC.YALE.EDU by nx1.soils.umn.edu (5.65c)
	id AA03422; Fri, 1 Oct 1993 11:57:49 -0500
Return-Path: <@YaleVM.YCC.Yale.Edu:Mike_Schwartz@QUICKMAIL.CIS.YALE.EDU>
Message-Id: <199310011657.AA03422@nx1.soils.umn.edu>
Received: from quickmail.yale.edu by YaleVM.YCC.Yale.Edu (IBM VM SMTP V2R2)
   with TCP; Fri, 01 Oct 93 12:57:16 EDT
Date: 1 Oct 1993 13:00:05 U
From: "Mike Schwartz" <Mike_Schwartz@quickmail.yale.edu>
Subject: Image compression
To: "Image List" <nih-image@soils.umn.edu>

                       Subject:                               Time:9:24 AM
  OFFICE MEMO          Image compression                      Date:10/1/93
I am interested in compressing grey-scale images acquired using Image and a
Perceptics Megagrabber video board.  I do not have the finances to go with a
hardware solution and have been looking at two comercial software packages:
Kodak's Colorsqueeze 2.0 and Storm Technologies Picture Press 2.5.  Picture
Press has a Photoshop plug-in which would be very useful if the plug-in also
works with Image.  However, since I have found a least one Photoshop plug-in
that does not work with Image (the NuVista+ plug-in) I would like to know if
anyone has experience using Picture Press and Image.  Any other comments on
either of these compression programs or advice on alternatives would also be
greatly appreciated.    

Mike Schwartz
Mike Schwartz@qm.yale.edu


From bright@ENH.NIST.GOV  Fri Oct  1 09:53:06 1993
Received: from enh.nist.gov by nx1.soils.umn.edu (5.65c)
	id AA04095; Fri, 1 Oct 1993 13:03:30 -0500
Return-Path: <bright@ENH.NIST.GOV>
Received: from [129.6.98.4] (dsb-mac.nist.gov) by ENH.NIST.GOV (PMDF V4.2-13
 #4653) id <01H3LMOESCRK0001FN@ENH.NIST.GOV>; Fri, 1 Oct 1993 13:53:06 EDT
Date: Fri, 01 Oct 1993 13:53:06 -0400 (EDT)
Date-Warning: Date header was inserted by ENH.NIST.GOV
From: bright@ENH.NIST.GOV
Subject: variance image
To: nih-image@soils.umn.edu
Message-Id: <01H3LMOF6JYA0001FN@ENH.NIST.GOV>
Content-Transfer-Encoding: 7BIT

Hi:o)
  Anyone have a macro that calculates a variance image?  By that I mean
something similar to a smoothing (convolution with all 1's in the kernel),
except the new pixel value is equal to the variance (or standard deviation)
of all the pixels inside the kernel, rather than equal to the sum.
Thanks
--Dave
-------------------------------------------------------------
David S. Bright                        bright@enh.nist.gov  
Microanalysis Research Group 
Chem. A113                                  
National Institute of Standards & Technology (NIST, formerly NBS)
Gaithersburg, MD 20899-0001                                          
USA
301-975-3911 - voice, 301-216-1134 - fax

From wayne@helix.nih.gov  Fri Oct  1 13:41:11 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA04593; Fri, 1 Oct 1993 13:42:46 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA28059; Fri, 1 Oct 93 14:02:58 -0400
Message-Id: <9310011802.AA28059@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Fri, 1 Oct 1993 13:41:11 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Automatic threshold

>Has anyone written a macro for automatic thresholding?  Russ describes 
>automatic thresholding using the change in area and perimeter of the binary 
>image formed over a series of threshold-detect values (Russ,1992, The Image 
>Procesing Handbook, pgs 258-259).

The Threshold command in NIH Image (AutoThreshold in macros) does automatic
thresholding using an Iterative technique, first described by Ridler &
Calvard in "PIcture Thresholding Using an Iterative Selection Method", IEEE
transactions on Systems, Man and Cybernetics, August, 1978. 

--wayne



From Doug.Erickson@m.CC.UTAH.EDU  Fri Oct  1 21:47:18 1993
Received: from fcom.cc.utah.edu by nx1.soils.umn.edu (5.65c)
	id AA05787; Fri, 1 Oct 1993 15:45:21 -0500
Return-Path: <Doug.Erickson@m.CC.UTAH.EDU>
Received: from [128.110.56.10] (emcb010x.utah.edu) by fcom.cc.utah.edu (4.1/SMI-4.0 [uucc-nhj-virtual 18AUG1991])
	id AA05056; Fri, 1 Oct 93 14:44:38 MDT
Message-Id: <9310012044.AA05056@fcom.cc.utah.edu>
Date: Fri, 1 Oct 1993 14:47:18 +0700
To: nih-image@soils.umn.edu
From: Doug.Erickson@m.CC.UTAH.EDU (Doug Erickson)
X-Sender: dme8844@m.cc.utah.edu
Subject: Re: reslicing volume in another plane

> > >Has anyone out there written macros to reslice a stack in a user specified
> > >plane?  It would be real nice if we could resection this volume in user
> > >selected plane other than the original plane of acquisition.

> > The are serveral macros for orthogonal reslicing of volumes in the macro
> > file "Stacks".

> Yes I know.  I'm talking about planes other than orthogonal ones.

I haven't written actually written the macro, but using the "Stacks" <DoReslice>
procedure as a guide, it should be fairly simple to make progressive reslices
parallel to a line selection.  Use the GetRoi command to calculate the slope of
the line selection.  Use this information, along with a parameter for distance
between the output slices, to compute dx and dy.  Specify the number of slices
you want to make, and use MoveRoi(dx,dy) to advance the line of sectioning in-
stead of the "loc" and "max" parameters in the current macro.

This should work for reslicing in any plane perpendicular to the stack images.
If you want to reslice to some oblique plane (I mean one that is neither paral-
lel nor perpendicular to the plane of the stack's images), you could do a kind
of crummy job by using "Reslice Horizontally," with an output spacing of one
pixel.  Then, select the desired plane in the new stack (it might be necessary
to rotate the original image before reslicing horizontally to get exactly the
plane you want--this is why the quality of the end product might get pretty
bad), and apply your new macro.

From Doug.Erickson@m.CC.UTAH.EDU  Fri Oct  1 21:55:05 1993
Received: from fcom.cc.utah.edu by nx1.soils.umn.edu (5.65c)
	id AA05917; Fri, 1 Oct 1993 15:53:08 -0500
Return-Path: <Doug.Erickson@m.CC.UTAH.EDU>
Received: from [128.110.56.10] (emcb010x.utah.edu) by fcom.cc.utah.edu (4.1/SMI-4.0 [uucc-nhj-virtual 18AUG1991])
	id AA05216; Fri, 1 Oct 93 14:52:26 MDT
Message-Id: <9310012052.AA05216@fcom.cc.utah.edu>
Date: Fri, 1 Oct 1993 14:55:05 +0700
To: nih-image@soils.umn.edu
From: Doug.Erickson@m.CC.UTAH.EDU (Doug Erickson)
X-Sender: dme8844@m.cc.utah.edu
Subject: Reslice Command

A week or two ago I asked about the Reslice command, which kept giving me an
error saying "Selection must be within image boundary."  After a little
experimentation, I found that this was caused by setting the slice spacing to
less than one pixel.  To get around this, I set the slice spacing to one pixel, reslice, and then vertically scale the resulting image so that it has the
correct aspect ratio.

Is this by design or is it a bug?

Doug Erickson / Mechanical Engineering

2480 MEB
University of Utah
Salt Lake City, Utah  84112

From brown@alsys1.aecom.yu.edu  Fri Oct  1 11:43:56 1993
Received: from alsys1.aecom.yu.edu by nx1.soils.umn.edu (5.65c)
	id AA06619; Fri, 1 Oct 1993 16:51:15 -0500
Return-Path: <brown@alsys1.aecom.yu.edu>
Received: from [129.98.90.119] (garbo.aecom.yu.edu) by alsys1.aecom.yu.edu with SMTP id AA23026
  (5.67a/IDA-1.5/AECOM-RIT for <nih-image@soils.umn.edu>); Fri, 1 Oct 1993 17:52:23 -0400
From: "Lucy Brown" <brown@aecom.yu.edu>
Date: Fri, 1 Oct 93 17:43:56 CST
Message-Id: <63838.brown@alsys1.aecom.yu.edu>
X-Popmail-Charset: English
To: nih-image@soils.umn.edu
Cc: wayne@helix.nih.gov
Subject: Re: Automatic threshold

On Fri, 1 Oct 1993 13:56:58 -0500, Wayne Rasband wrote:

>
>The Threshold command in NIH Image (AutoThreshold in macros) does automatic
>thresholding using an Iterative technique, first described by Ridler &
>Calvard in "PIcture Thresholding Using an Iterative Selection Method", IEEE
>transactions on Systems, Man and Cybernetics, August, 1978. 
>
>--wayne

Thanks!  Autothreshold sounds good.  But I can't find it.  In what series 
of macros?
From wayne@helix.nih.gov  Fri Oct  1 16:56:59 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA06690; Fri, 1 Oct 1993 16:58:36 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA28678; Fri, 1 Oct 93 17:18:48 -0400
Message-Id: <9310012118.AA28678@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Date: Fri, 1 Oct 1993 16:56:59 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: variance image

>Hi:o)
>  Anyone have a macro that calculates a variance image?  By that=
 I mean
>something similar to a smoothing (convolution with all 1's in the=
 kernel),
>except the new pixel value is equal to the variance (or standard=
 deviation)
>of all the pixels inside the kernel, rather than equal to the sum.

The macro appended to the end of this message doesn't do exactly=
 what
you're asking for, but it's probab;y the best that can be done using=
 the
macro language. A macro that computed the standard deviation for=
 every
pixel instead of for every cell would be hundreds of times slower=
 than this
one.

--wayne


macro 'Make Variance Image=8A';
{
Divides an image into cells, replacing all pixels in each cell by=
 the
standard deviation for that cell. You will need to enter the cell=
 width,
cell height, and estimated maximum standard deviation. The actual=
 maximum
standard deviation is displayed when the macro finishes.
}
var
  x,y,xinc,yinc,width,height:integer;
  cellwidth,cellheight,value:integer;
  maxstd,max:real;
begin
  GetPicSize(width,height);
  xinc:=3DGetNumber('Cell Width:',16);
  yinc:=3DGetNumber('Cell Height:',xinc);
  max:=3DGetNumber('Max std dev:',50);
  maxstd:=3D0;
  y:=3D0;
  repeat
    cellheight:=3Dyinc;
    if (y+cellheight)>height then cellheight:=3Dheight-y;
    x:=3D0;
    repeat
      cellwidth:=3Dxinc;
      if (x+cellwidth)>width then cellwidth:=3Dwidth-x-1;
      MakeRoi(x,y,cellwidth,cellheight);
      measure;
      if rStdDev[rcount]>maxstd
        then maxstd:=3DrStdDev[rcount];
      value:=3Dtrunc(rStdDev[rcount]/max*253)+1;
       if value>254 then value:=3D254;
      SetForeground(value);
      fill;
      ResetCounter;
      x:=3Dx+xinc;
    until x>width;
    y:=3Dy+yinc;
  until y>height;
  KillRoi;
  ShowMessage('max std dev=3D',maxstd:1:2);
end;


From vokey@hg.uleth.ca  Sun Oct  3 06:40:22 1993
Received: from mr.uleth.ca by nx1.soils.umn.edu (5.65c)
	id AA27334; Sun, 3 Oct 1993 13:47:47 -0500
Return-Path: <vokey@hg.uleth.ca>
Received: by hg.uleth.ca (MX V3.3 VAX) id 1983; Sun, 03 Oct 1993 12:40:27 MDT
Date: Sun, 03 Oct 1993 12:40:22 MDT
From: vokey@hg.uleth.ca
To: nih-image@soils.umn.edu
Message-Id: <00973772.ED479580.1983@hg.uleth.ca>
Subject: imagefft

As "/pub/nih-image/nih-image_spinoffs/imagefft" is not binhexed, my system
refuses to allow me to download it.  Could one of you nice (by definition)
image-people binhex a copy of imagefft and upload it so that I may FTP it to my
Mac?  TIA

John R. Vokey <vokey@hg.uleth.ca>
From a337ard@diamond.sara.nl  Mon Oct  4 09:13:14 1993
Received: from vx.cis.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA02244; Mon, 4 Oct 1993 02:16:29 -0500
Return-Path: <a337ard@diamond.sara.nl>
Received: from HASARA5.BITNET (MAILGATE@HASARA5) by vx.cis.umn.edu (PMDF
 V4.2-13 #2574) id <01H3P59FF18WB631QY@vx.cis.umn.edu>; Mon,
 4 Oct 1993 02:17:47 CDT
Received: from diamond.sara.nl by SARA.NL for nih-image@soils.umn.edu; 4 Oct 93
 8:17 MET
Received: by diamond.sara.nl (5.61-AIX-1.2/1.0), id AA124204,
 (for nih-image@soils.umn.edu, from a337ard@diamond.sara.nl);
Date: Mon, 04 Oct 1993 08:13:14 +0100
From: a337ard@diamond.sara.nl (Ard Jonker)
Subject: Re:  Image compression
To: nih-image@soils.umn.edu
Message-Id: <9310040713.AA124204@diamond.sara.nl>
X-Envelope-To: nih-image@soils.umn.edu
Content-Transfer-Encoding: 7BIT

Shareware packages that do jpeg compression (PICT, TIF or alike in,
JPEG out), be it not Plug In,yet cheap are JPEGView and GifConverter.
As far as I know they do not do 'batch' processing, so you have to
save the files one by one (by drag and drop you can open many at one
time, however). So this might only be the solution if your problem is
mainly a storage problem on a small harddisk.
JPEGView saves custom icons(=the icon looks like the picture)
and a preview as well.
As far as I understood, they both require Quicktime to do the compression.
Ard Jonker(a337ard@diamond.sara.nl)
From set@eru.mt.luth.se  Mon Oct  4 11:00:22 1993
Received: from eru.mt.luth.se by nx1.soils.umn.edu (5.65c)
	id AA02934; Mon, 4 Oct 1993 03:59:19 -0500
Return-Path: <set@eru.mt.luth.se>
Received: from [130.240.1.174] (osse217.mt.luth.se) by eru.mt.luth.se with SMTP
	(5.65+bind 1.7+ida 1.4.2/IDA-1.2.8-NS) id AA15740; Mon, 4 Oct 1993 10:00:13 +0100
Message-Id: <199310040900.AA15740@eru.mt.luth.se>
Date: Mon, 4 Oct 1993 10:00:22 +0100
To: nih-image@soils.umn.edu
From: set@mt.luth.se (Sven-Erik Tiberg)
Subject: 64Mb SIMM on Scion 
X-Content-Type: Text/Quoted-Readable


nih-image@soils.umn.edu
We are in for expanding on-board memory to 64MB on a Scion-LG3 PAL frame
grabber. We bought high profile SIMM and could't fit them on the card. Then
I asked Tod Weinberg on Scion about this, and Tod Weinberg answer are as
follow: 

*********************************************
Dear Dr. Tiberg:
 
      There are currently two types of 16 Mb SIMM on the market.  The first
is called composite.  It consists of 32 4 Mbit RAM chips placed on both
sides of the SIMM circuit board.  The composite type of SIMM is generally
too large to be used on a NuBus board like the LG-3.  The second type
consists of 8 16 Mbit RAM chips placed on one side of the SIMM circuit
board.  This is the type of SIMM that will fit on the LG-3.
 
    If you already have the composite type SIMM, you may be able to use them on
the LG-3 by replacing the angled SIMM sockets on the LG-3 with vertical SIMM
sockets.
    The LG-3 is a multilayer board, but a skilled technician should be able to
replace the sockets without damaging the printed circuit board.  We would be
happy to carry out the modification for no charge, though you would have to pay
for shipping in each direction.

Sincerely
 
Tod Weinberg
Scion Corporation
 
*********************************************

I hope that this will be of any help to someone else on this list that are
planning to expand the on-board memory to 64Mb. We will send our card to
Scion for socket replacement, as we will not risk the multilayer PC card. 

*********************************************************
*                                                       *
*       Sven-Erik Tiberg                                *
*       Div. of energy / mashineenginnering             *           
*       Lulea University of Technology                  *
*       Lulea Sweden                                    *
*       email set@eru.mt.luth.se                        *
*       Fax. S-(0)920-91047                             *
*       Tel. S-(0)920-91218, S-(0)10-2189638            *        
*                                                       *
*********************************************************

From wayne@helix.nih.gov  Mon Oct  4 08:49:58 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA06245; Mon, 4 Oct 1993 08:51:39 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA03195; Mon, 4 Oct 93 09:12:01 -0400
Message-Id: <9310041312.AA03195@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Mon, 4 Oct 1993 08:49:58 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: imagefft

>As "/pub/nih-image/nih-image_spinoffs/imagefft" is not binhexed, my system
>refuses to allow me to download it.  Could one of you nice (by definition)
>image-people binhex a copy of imagefft and upload it so that I may FTP it to my
>Mac?  TIA

"/pub/nih-image/nih-image_spinoffs/imagefft" is a directory containing five
files. I have attached a complete listing of the NIH Image related files on
Zippy. Updated versions of this listing are contained in the file
"FileList.txt" in the /pub directory.

--wayne

/pub
total 56
-rw-r--r--   1 wayne    users      19008 Sep 10 08:44 FileList.txt
-rw-r--r--   1 wayne    users          0 Oct  4 08:57 ls-lR
drwxr-xr-x  10 wayne    users       1024 Sep 27 13:39 nih-image
drwxr-xr-x   2 wayne    users       1024 Apr 13 11:04 quicktime
drwxr-xr-x   2 wayne    users       1024 Jul 22 12:27 util

./nih-image:
total 4186
-rw-r--r--   1 wayne    users       5169 Jul 26 09:50 0README.txt
-rw-r--r--   1 wayne    users      13054 Sep 27 13:39 Changes.txt
-rw-r--r--   1 wayne    users        919 Sep 14 16:57 MailingList.txt
drwxrwxrwx   2 wayne    users       1024 Sep 28 11:52 contrib
drwxr-xr-x   5 wayne    users       1024 Sep 22 16:14 documents
drwxr-xr-x   3 wayne    users       1048 Jun 24 14:18 images
-rw-r--r--   1 wayne    users     519115 Sep  9 15:51 nih-image152.hqx
-rw-r--r--   1 wayne    users     417032 Sep  9 15:53 nih-image152_docs.hqx
-rw-r--r--   1 wayne    users     629212 Sep  9 15:55 nih-image152_source.hqx
-rw-r--r--   1 wayne    users     504389 Sep 27 13:37 nih-image153b7.hqx
drwxr-xr-x   4 wayne    users       1024 Jun 15 12:50 nih-image_spinoffs
drwxr-xr-x   2 wayne    users       1024 Sep  9 12:20 plug-ins
drwxr-xr-x   3 wayne    users       1024 Sep  9 12:10 programs
drwxr-xr-x   2 wayne    users       1024 Apr 15 15:07 stacks
drwxr-xr-x   2 wayne    users       1024 Sep 27 13:58 user-macros

./nih-image/contrib:
total 12408
-rw-r--r--   1 wayne    users      13826 Sep  2 12:55 10_Image_Icons.hqx
-rw-r--r--   1 wayne    users     365469 Jun 29 10:48 Contrib_NTH.sit.hqx
-rw-r--r--   1 wayne    users     356172 Jun  3 10:54 Image144Markup.sit.hqx
-rw-r--r--   1 wayne    users     757065 Jun  3 10:56
Image144MarkupSource.sit.hqx
-rw-r--r--   1 wayne    users     460103 Apr 20 10:10 Image149_PAL_NTSC.hqx
-rw-r--r--   1 wayne    users    1323531 Apr 26 10:57 Image149_pal_ntsc.2.hqx
-rw-r--r--   1 wayne    users       3355 Jul 21 15:31
ImageScion1.50b83.ReadMe.txt
-rw-r--r--   1 wayne    users     480176 Jul 21 15:33 ImageScion1.50b83.sit.hqx
-rw-r--r--   1 wayne    users     158351 Apr 26 12:11 ImageTimer.sit.hqx
-rw-r--r--   1 wayne    users       5551 Mar  7  1993 Image_Icons.hqx
-rw-r-----   1 ftp      other      12009 Sep 26 22:10 PreProjection_Macros.hqx
-rw-r--r--   1 wayne    users     855824 Aug 23 07:08 Quantile_Crest.sit.hqx
-rw-r--r--   1 wayne    users       8273 May 24 19:59
Video_presentation_1_49.txt
-rw-r--r--   1 wayne    users       3425 Aug 25 05:15 image_umx_readme
-rw-r-----   1 ftp      other     532248 Sep 28 11:53 nihumx152b3.sit.hqx
-rw-r-----   1 ftp      other     879846 Sep 28 11:51 nihumx152b3source.sit.hqx
-rw-r-----   1 ftp      other      11057 Sep 24 11:42 preproj_macros.hqx

./nih-image/documents:
total 8566
-rw-r--r--   1 wayne    users     435152 May  3 10:19 Nih-image.001.txt
-rw-r--r--   1 wayne    users     561265 Jul 23 11:02 Nih-image.002.txt
-rw-r--r--   1 wayne    users     536162 Sep  7 08:35 Nih-image.txt
-rw-r--r--   1 wayne    users      14390 Mar  8  1993 centris_video.txt
-rw-r--r--   1 wayne    users      19669 Mar 19  1993 ftp-primer.txt
-rw-r--r--   1 wayne    users      38205 Mar 25  1993 mac-ftp-sites.txt
-rw-r--r--   1 wayne    users       9047 May 21 14:32 mac-image-proc.txt
drwxr-xr-x   2 wayne    users       1024 Sep 22 16:14 map_making_tutorial
-rw-r--r--   1 wayne    users      11430 Mar  4  1993 mpw_port.txt
-rw-r--r--   1 wayne    users      19426 Mar  8  1993 quadra_video.txt
-rw-r--r--   1 wayne    users       6380 Sep  2 11:17 reduce-noise.txt
-rw-r--r--   1 wayne    users     126573 Mar 14  1992 tiff5.txt
-rw-r--r--   1 wayne    users    1450351 Mar  4  1993 tiff6.ps.hqx
-rw-r--r--   1 wayne    users    1070958 Mar  4  1993 tiff6.ps.txt
drwxr-xr-x   2 wayne    users       1024 May 21 14:37 v1.49_source
drwxr-xr-x   2 wayne    users       1024 Jun 15 15:46 v1.50b70_source

./nih-image/documents/map_making_tutorial:
total 5844
-rw-r--r--   1 wayne    users       1151 Sep 22 16:11 0ReadMe.Txt
-rw-r--r--   1 wayne    users     630430 Sep 22 16:06 BuildMap.sea.hqx
-rw-r--r--   1 wayne    users      26334 Sep 22 16:06 CLUTFiles.sea.hqx
-rw-r--r--   1 wayne    users     145303 Sep 22 16:06 ClutMake_GrayMap.sea.hqx
-rw-r--r--   1 wayne    users      34979 Sep 22 16:06 DNMapFiles.sea.hqx
-rw-r--r--   1 wayne    users      27609 Sep 22 16:07 GrayLUTs.sea.hqx
-rw-r--r--   1 wayne    users    1815215 Sep 22 16:11 NIHImageFiles.sea.hqx
-rw-r--r--   1 wayne    users     123574 Sep 22 16:11 Text.sea.hqx
-rw-r--r--   1 wayne    users     127340 Sep 22 16:12 USGSColorCodes.sea.hqx

../nih-image/documents/v1.50b70_source:
total 2434
-rw-r--r--   1 wayne    users      74151 Jun 15 15:45 Analysis.p.txt
-rw-r--r--   1 wayne    users      40978 Jun 15 15:45 Background.p.txt
-rw-r--r--   1 wayne    users      33054 Jun 15 15:45 Camera.p.txt
-rw-r--r--   1 wayne    users      65932 Jun 15 15:45 Edit.p.txt
-rw-r--r--   1 wayne    users       8948 Jun 15 15:45 Ellipse.p.txt
-rw-r--r--   1 wayne    users      89856 Jun 15 15:45 File1.p.txt
-rw-r--r--   1 wayne    users      69178 Jun 15 15:45 File2.p.txt
-rw-r--r--   1 wayne    users      46624 Jun 15 15:45 Functions.p.txt
-rw-r--r--   1 wayne    users      37087 Jun 15 15:45 Globals.p.txt
-rw-r--r--   1 wayne    users      60804 Jun 15 15:45 Graphics.p.txt
-rw-r--r--   1 wayne    users      69403 Jun 15 15:45 Image.p.txt
-rw-r--r--   1 wayne    users      13440 Jun 15 15:45 Image.proj.bin
-rw-r--r--   1 wayne    users      53376 Jun 15 15:45 Image.rsrc.bin
-rw-r--r--   1 wayne    users      43806 Jun 15 15:45 Init.p.txt
-rw-r--r--   1 wayne    users       6703 Jun 15 15:45 LeastSquares.p.txt
-rw-r--r--   1 wayne    users      46692 Jun 15 15:46 Lut.p.txt
-rw-r--r--   1 wayne    users      88545 Jun 15 15:46 Macros1.p.txt
-rw-r--r--   1 wayne    users      44531 Jun 15 15:46 Macros2.p.txt
-rw-r--r--   1 wayne    users      20775 Jun 15 15:46 PlugIns.p.txt
-rw-r--r--   1 wayne    users      46775 Jun 15 15:46 Projection.p.txt
-rw-r--r--   1 wayne    users     127872 Jun 15 15:46 Screen.bin
-rw-r--r--   1 wayne    users      41014 Jun 15 15:46 Stacks.p.txt
-rw-r--r--   1 wayne    users      13044 Jun 15 15:46 Text.p.txt
-rw-r--r--   1 wayne    users       9132 Jun 15 15:46 User.p.txt
-rw-r--r--   1 wayne    users      70232 Jun 15 15:46 Utilities.p.txt

./nih-image/images:
total 15498
-rw-r--r--   1 wayne    users    1262976 Jun 24 14:18 16-bit-tiff.bin
-rw-r--r--   1 wayne    users     155520 May  8  1992 1d_gel.bin
-rw-r--r--   1 wayne    users     172651 Mar 14  1992 2d-gel.hqx
-rw-r--r--   1 wayne    users     211251 Oct  8  1992 3d_equation.hqx
-rw-r--r--   1 wayne    users     263040 May  8  1992 abdomen.bin
-rw-r--r--   1 wayne    users      57633 Mar 14  1992 aluminum.hqx
-rw-r--r--   1 wayne    users      11341 Mar 14  1992 angles.hqx
-rw-r--r--   1 wayne    users     147218 Oct  8  1992 arthritis.hqx
-rw-r--r--   1 wayne    users     324434 Mar 14  1992 aupbsn40.hqx
-rw-r--r--   1 wayne    users      30235 Mar 14  1992 blobs.hqx
-rw-r--r--   1 wayne    users     210688 May  8  1992 bloom_county.bin
-rw-r--r--   1 wayne    users     254157 Mar 14  1992 boating_party.hqx
-rw-r--r--   1 wayne    users     125087 Mar 14  1992 brain_renderings.hqx
-rw-r--r--   1 wayne    users      63104 May  8  1992 caution.bin
-rw-r--r--   1 wayne    users      13440 May  8  1992 ceretec_sagittals.bin
-rw-r--r--   1 wayne    users     261807 Mar 14  1992 corr2018.hqx
-rw-r--r--   1 wayne    users      60358 Mar 14  1992 ct_scan.hqx
-rw-r--r--   1 wayne    users     330800 Oct  8  1992 ct_scan2.hqx
-rw-r--r--   1 wayne    users      83328 May  8  1992 fractal.bin
-rw-r--r--   1 wayne    users      38865 Mar 14  1992 gel_with_plots.hqx
-rw-r--r--   1 wayne    users     100480 May  8  1992 george.bin
-rw-r--r--   1 wayne    users     109568 May  8  1992 ige_receptor_model.bin
-rw-r--r--   1 wayne    users      40398 Mar 14  1992 image_menus.hqx
-rw-r--r--   1 wayne    users    1051008 May  8  1992 landsat_scene.bin
-rw-r--r--   1 wayne    users     263680 May 22  1992 lena.bin
-rw-r--r--   1 wayne    users     162999 Mar 14  1992 little_girl.hqx
-rw-r--r--   1 wayne    users     331392 Apr  3  1993 m51_fits.bin
-rw-r--r--   1 wayne    users        183 Apr  3  1993 m51_fits.txt
-rw-r--r--   1 wayne    users      60357 Mar 14  1992 metabolites.hqx
-rw-r--r--   1 wayne    users     230637 Mar 14  1992 molecule.hqx
-rw-r--r--   1 wayne    users     291490 Mar 14  1992 mona_lisa.hqx
-rw-r--r--   1 wayne    users      98688 May  8  1992 morph.bin
-rw-r--r--   1 wayne    users      61623 Mar 14  1992 mri_scan.hqx
-rw-r--r--   1 wayne    users     134272 Dec  8  1992 mu_opiate_receptor.bin
-rw-r--r--   1 wayne    users      12792 Mar 14  1992 pet_scan.hqx
-rw-r--r--   1 wayne    users     128754 Mar 14  1992 porsche.hqx
-rw-r--r--   1 wayne    users      56704 May  8  1992 rat_kidney.bin
-rw-r--r--   1 wayne    users     344006 Mar 14  1992 redrock.hqx
-rw-r--r--   1 wayne    users      50944 Mar  1  1993 silver_lake.bin
-rw-r--r--   1 wayne    users      18168 Mar 14  1992 spots_on_wave.hqx
drwxr-xr-x   2 wayne    users       1024 May 22  1992 wavelet_compression

./nih-image/images/wavelet_compression:
total 3270
-rwxr--r--   1 wayne    users       2488 May 22  1992 README.txt
-rwxr--r--   1 wayne    users     263680 May 22  1992 lena.19_4.bin
-rwxr--r--   1 wayne    users     263680 May 22  1992 lena.30.bin
-rwxr--r--   1 wayne    users     263680 May 22  1992 lena.3_32.bin
-rwxr--r--   1 wayne    users     263680 May 22  1992 lena.61.bin
-rwxr--r--   1 wayne    users     263680 May 22  1992 lena.8_1.bin
-rwxr--r--   1 wayne    users     263680 May 22  1992 lena.raw.bin

./nih-image/nih-image_spinoffs:
total 8724
-rw-r--r--   1 wayne    users     690796 Apr 14  1992 color_image132.hqx
-rw-r--r--   1 wayne    users     488397 Jun 15 10:27 image149vdm.hqx
-rw-r--r--   1 wayne    users     619037 Jun 15 08:54 image149vdm_source.hqx
-rw-r--r--   1 wayne    users     983840 Mar 26  1992 imageKSC.hqx
-rw-r--r--   1 wayne    users     380488 Apr 14 13:30 image_mg144b.hqx
drwxr-xr-x   2 wayne    users       1024 Mar 29  1993 imagefft
drwxr-xr-x   2 wayne    users       1024 Mar 14  1992 imagefractal
-rw-r--r--   1 wayne    users    1223201 Mar 14  1992 munichimage.hqx

./nih-image/nih-image_spinoffs/imagefft:
total 5922
-rw-r--r--   1 wayne    users     835581 Mar 14  1992 ImageFFT128b6.hqx
-rw-r--r--   1 wayne    users     364066 Mar 14  1992 ImageFFTExamples1.hqx
-rw-r--r--   1 wayne    users    1478532 Mar 14  1992 ImageFFTExamples2.sit.hqx
-rw-r--r--   1 wayne    users        275 Mar 29  1993 README.txt
-rw-r--r--   1 wayne    users     305346 Mar 14  1992 Thesis.hqx

./nih-image/nih-image_spinoffs/imagefractal:
total 1114
-rw-r--r--   1 wayne    users       4457 Mar 14  1992 README
-rw-r--r--   1 wayne    users     199293 Mar 14  1992 imagefractal12.hqx
-rw-r--r--   1 wayne    users     341331 Mar 14  1992 source.hqx

./nih-image/plug-ins:
total 1296
-rw-r--r--   1 wayne    users     190897 May 20 12:35 DevelopersKit.cpt.hqx
-rw-r--r--   1 wayne    users      88667 May  4 16:10 LG-3PlugIn.cpt.hqx
-rw-r--r--   1 wayne    users      48130 Jun 16 15:30 MegaGrabberPlugIn.hqx
-rw-r--r--   1 wayne    users      56187 Jun 16 15:31 PixelBufferPlugIn.hqx
-rw-r--r--   1 wayne    users      60347 Jun 16 15:31 PixelHR24PlugIn.hqx
-rw-r--r--   1 wayne    users      12935 Jul 23 16:07 TV-3PlugIn.hqx
-rw-r--r--   1 wayne    users      75360 Sep  9 12:20 cmulti-filter.cpt.hqx
-rw-r--r--   1 wayne    users     100294 Sep  8 08:34 expression30b.cpt.hqx

./nih-image/programs:
total 5240
-rw-r--r--   1 wayne    users     732030 Oct 19  1992 gifconverter221.hqx
-rw-r--r--   1 wayne    users     123361 Mar 14  1992 giffer108.hqx
-rw-r--r--   1 wayne    users     815438 May 25 14:44 ip_lab_demo.cpt.hqx
-rw-r--r--   1 wayne    users     647869 Apr  9  1992 labtoolbox.hqx
-rw-r--r--   1 wayne    users      98670 May 13  1992 macmeasure19.hqx
drwxr-xr-x   2 wayne    users       1024 Jul 23 13:14 ncsa
-rw-r--r--   1 wayne    users     113936 Sep  9 12:11 pics-quicktime.hqx
-rw-r--r--   1 wayne    users      67879 Apr  9  1992 projectionist.hqx

./nih-image/programs/ncsa:
total 11866
-rw-r--r--   1 wayne    users     604490 Oct 29  1992 Image311.hqx
-rw-r--r--   1 wayne    users    3613575 Oct 29  1992 Image_docs.hqx
-rw-r--r--   1 wayne    users     389606 Jul 23 12:03 Layout.Examples.sit.hqx
-rw-r--r--   1 wayne    users     258772 Jul 23 12:03 Layout1.3.mac.sit.hqx
-rw-r--r--   1 wayne    users     259167 Jul 23 12:03 LayoutLCsi1.3.mac.sit.hqx
-rw-r--r--   1 wayne    users       2216 Jul 23 12:03 PalEdit.README
-rw-r--r--   1 wayne    users     112627 Mar 14  1992 PalEdit.hqx
-rw-r--r--   1 wayne    users      58994 Jul 23 12:03 PalEdit.smp.sit.hqx
-rw-r--r--   1 wayne    users     135499 Jul 23 12:03 PalEdit2.0.mac.sit.hqx
-rw-r--r--   1 wayne    users     229468 Jul 23 12:03 PalEdit2.0.msw.sit.hqx
-rw-r--r--   1 wayne    users     298318 Jul 23 12:04 PalEdit2.0.src.sit.hqx

./nih-image/stacks:
total 49398
-rw-r--r--   1 wayne    users     615040 Nov 16  1992 3D-Chromosome_Movie.bin
-rw-r--r--   1 wayne    users       2115 Nov  3  1992 3D_Chromosome.txt
-rw-r--r--   1 wayne    users    6688384 Apr 15 15:05 3D_Knee.cpt.bin
-rw-r--r--   1 wayne    users       3849 Apr 15 15:05 3D_Knee.txt
-rw-r--r--   1 wayne    users    1800832 May  1  1992 Alycia.cpt.bin
-rw-r--r--   1 wayne    users      30592 May  8  1992 Bird_Movie.bin
-rw-r--r--   1 wayne    users    1272576 May  7  1992 CT_Head_Movie.cpt.bin
-rw-r--r--   1 wayne    users     327680 May  7  1992 FluidDynamicsMovie.bin
-rw-r--r--   1 wayne    users       2541 May  7  1992 FluidDynamicsMovie.txt
-rw-r--r--   1 wayne    users     432512 Feb 19  1993 GE_SPECT.cpt.bin
-rw-r--r--   1 wayne    users       1173 Feb 19  1993 GE_SPECT.txt
-rw-r--r--   1 wayne    users        519 May  1  1992 HerpesVirus.txt
-rw-r--r--   1 wayne    users    2469632 Apr 28  1992 HerpesVirusMovie.sit.bin
-rw-r--r--   1 wayne    users    2626845 Sep  4  1992 Hurricanes.sit.hqx
-rw-r--r--   1 wayne    users    8136960 Jul  8  1992 MRI.Axials_1.5mm.bin
-rw-r--r--   1 wayne    users     754944 May  7  1992 MRI_Axials_5mm.bin

./nih-image/user-macros:
total 144
-rw-r--r--   1 wayne    users       5564 Jun  3 21:03 cavalieri_doc.txt
-rw-r--r--   1 wayne    users       6666 Jun  3 21:04 cavalieri_macro.txt
-rw-r--r--   1 wayne    users      13761 Jul 15 09:10 gel_macros_boris.txt
-rw-r--r--   1 wayne    users       4871 Sep  3 13:51 grain_counting.txt
-rw-r--r--   1 wayne    users       2350 Mar  1  1993 image_registration.txt
-rw-r--r--   1 wayne    users       6351 Jun 22 09:26 mac_to_vcr.txt
-rw-r--r--   1 wayne    users      10986 Mar  1  1993 marzhauser_stage.txt
-rw-r--r--   1 wayne    users      10278 Sep 27 13:57 preprojection.txt
-rw-r--r--   1 wayne    users       5336 Mar  1  1993 section_parameters.txt
-rw-r--r--   1 wayne    users       1968 Sep 10 15:31 spots_on_sine_wave.txt

./quicktime:
total 16194
-rw-r--r--   1 wayne    users    8276608 Apr 13 11:03 canyon.bin
-rw-r--r--   1 wayne    users        852 Apr 13 11:03 canyon.txt

./util:
total 2722
-rw-r--r--   1 wayne    users      97137 Dec 11  1992 DepthGauge254.hqx
-rw-r--r--   1 wayne    users     467390 Apr 14 12:04 Disinfectant31.hqx
-rw-r--r--   1 wayne    users     144640 Jan  4  1993 Fetch21.bin
-rw-r--r--   1 wayne    users     196303 Jan  4  1993 Fetch21.hqx
-rw-r--r--   1 wayne    users      47089 Sep  2  1992 MockWrite.hqx
-rw-r--r--   1 wayne    users      66954 Jul 22 12:25 Software_FPU241.hqx
-rw-r--r--   1 wayne    users     117632 Mar 14  1992 Stuffit151.bin
-rw-r--r--   1 wayne    users      50986 Mar 14  1992 Switch-a-Roo.hqx
-rw-r--r--   1 wayne    users     144977 May 11  1992 TiffSniff.hqx


From CHARLEST@macc.wisc.edu  Mon Oct  4 04:59:00 1993
Received: from vms2.macc.wisc.edu by nx1.soils.umn.edu (5.65c)
	id AA06895; Mon, 4 Oct 1993 09:58:30 -0500
Return-Path: <CHARLEST@macc.wisc.edu>
Received: from VMSmail by vms2.macc.wisc.edu; Mon, 04 Oct 93 09:59 CDT
Message-Id: <23100409590462@vms2.macc.wisc.edu>
Date: Mon, 04 Oct 93 09:59 CDT
From: Charles Thomas <CHARLEST@macc.wisc.edu>
Subject: Re: reslicing volume in another plane
To: nih-image@soils.umn.edu
X-Vms-To: IN%"nih-image@soils.umn.edu",CHARLEST

The program SPYGLASS DICER (Spyglass Inc, P.O Box 6338, Champaign, IL  61826;
217-355-6000) will allow you to load your 3D data set, then slice planes through
it from whatever orientation you wish.  You can see these planes one at a time
or just look at the face plane with the rest of the data set displayed.  This
program (in case you've never worked with it) isn't like VoxelView because you
don't get to rotate the data set and see it from different sides.  You can shift
the orientation, but not as a smooth, 360 degree movie.  What Dicer allows you
to do is to reslice your data from any angle, display the surface of your entire
data set and cut chunks out of it to see interior details, make movies showing a
plane moving through your invisible data set showing one plane at a time, and
other things.  I don't believe you can output your resliced planes so that you
can load them into NIH Image, for example.. but my experience with the program
is limited.
 
Hope some of this helps.
 
From keller@micros.mrd.bldrdoc.gov  Mon Oct  4 03:13:37 1993
Received: from central.bldrdoc.gov by nx1.soils.umn.edu (5.65c)
	id AA07046; Mon, 4 Oct 1993 10:13:11 -0500
Return-Path: <keller@micros.mrd.bldrdoc.gov>
Received: from arc1.mrd.bldrdoc.gov by central.bldrdoc.gov (4.1/SMI-DDN)
	id AA15935; Mon, 4 Oct 93 09:14:03 MDT
Received: from micros.mrd.bldrdoc.gov by arc1.mrd.bldrdoc.gov (4.1/SMI-3.2)
	id AA00410; Mon, 4 Oct 93 09:15:35 MDT
Message-Id: <9310041515.AA00410@arc1.mrd.bldrdoc.gov>
Date: Mon, 4 Oct 93 09:13:37 MDT
From: Bob Keller <keller@micros.mrd.bldrdoc.gov>
Subject: Re: grain size measurements
To: nih-image@soils.umn.edu
X-Mailer: LeeMail 1.2.4

>I adapted a protocol to automate cell contour tracing, which might be usefull 
>to you. Basically, the principle is to transform the initial image in an 
>"edge image" (by holding the option key down with the Trace Edges command of 
>Image. Then, I use a special routine (which I called Crest Pathway), which 
>traces the edge of one cell and makes a ROI around it. You have to click on 
>a starting point close to the object of interest, and the routine reiterately
>steps to the darkest neighbour. When it reahces a point already in the path, 
>the iteration ceases and the initial "tail" is eaten.
>
>A version of image containing the Crest Pathway routine is available, 
>together with some example images, on zippy, in the contrib directory.
>
>The name of the file is Quantile_Crest.sit.hqx


Thanks.  We've tried your Crest Pathway routine.  Actually, it's not exactly 
what we need, since Crest measures the size of a single grain, or cell, or 
whatever you're measuring.  (I've also had trouble with it when my binary 
images did not have nice smooth boundaries.  The line would keep going well 
beyond the boundary near where I started and often circle back onto itself 
within a very small area within another boundary itself.  I did vary the size 
of the "detected" region as well, with no luck.  Is it possible to define a 
threshold regime which would tell the line when to change it's course?)  I'm 
going to write a macro to do the grain size measurement myself, using the line 
intercept method which is standard in metallography.

The xy-Quantile routine is great!

Bob Keller
NIST Div. 853
Boulder, CO
keller@micros.mrd.bldrdoc.gov

From chung@mipgsun.mipg.upenn.edu  Mon Oct  4 07:26:20 1993
Received: from NOC4.DCCS.UPENN.EDU by nx1.soils.umn.edu (5.65c)
	id AA07200; Mon, 4 Oct 1993 10:25:18 -0500
Return-Path: <chung@mipgsun.mipg.upenn.edu>
Received: from MIPGSUN.MIPG.UPENN.EDU by noc4.dccs.upenn.edu
	id AA12770; Mon, 4 Oct 93 11:26:24 -0400
Received: by mipgsun.mipg.upenn.edu (4.1/MIPG-1.0)
	id AA23865; Mon, 4 Oct 93 11:26:20 EDT
Date: Mon, 4 Oct 93 11:26:20 EDT
From: chung@mipgsun.mipg.upenn.edu ( Hsiao-Wen Chung 09-17-93)
Message-Id: <9310041526.AA23865@mipgsun.mipg.upenn.edu>
To: nih-image@soils.umn.edu
Subject: IRIS Smartjet


A friend of mine was asking for info about IRIS Smartjet 4012 and 3024
laser printer.  Does anyone know the TELs and FAXs of some agents,
stores, or companies that sell these printers?  Any assistance is
highly appreciated.

Henry Chung
University of Pennsylvania
From Fredboyd@bmec.micro.umn.edu  Mon Oct  4 05:30:16 1993
Received: from mail.tc.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA07883; Mon, 4 Oct 1993 11:39:25 -0500
Return-Path: <Fredboyd@bmec.micro.umn.edu>
Received: from mailbox.mail.umn.edu by mail.tc.umn.edu id SMTP-0012cb0401a029022; Mon, 4 Oct 93 10:24:10 -0500
Date: Mon, 4 Oct 93 10:30:16 CDT
Message-Id: <9310041530.AA11377@mailbox.mail.umn.edu>
Received: from pathobiology-218.med.umn.edu by mailbox.mail.umn.edu; Mon, 4 Oct 93 10:30:16 CDT
From: "Fred Boyd, Ph.D." <Fredboyd@bmec.micro.umn.edu>
To: nih-image@soils.umn.edu
Subject: LG-3 Memory Upgrade

Hi all:
I have just put in 4x1Mb simms on my Lg-3 board.  Image still sees the board as 
a 1Mb board and will only capture/integrate 2 frames at video rate.  What else 
do I have to do?

Fred Boyd, Ph.D.
Assistant Professor
Laboratory Medicine and Pathology
Cell Biology and Neuroanatomy
University of Minnesota
_______________________________________________________________________________
Box 609, UMHC                                Phone (612) 624-8150
420 Delaware St. SE                            FAX (612) 626-2444
Minneapolis, MN   55455

From ruzin@nature.berkeley.edu  Mon Oct  4 02:08:41 1993
Received: from nak.Berkeley.EDU by nx1.soils.umn.edu (5.65c)
	id AA08377; Mon, 4 Oct 1993 12:07:25 -0500
Return-Path: <ruzin@nature.berkeley.edu>
Received: from nature.Berkeley.EDU by nak.berkeley.edu (5.67/1.40)
	id AA22771; Mon, 4 Oct 93 10:08:31 -0700
Received: from [128.32.128.168] (kos5mac13.Berkeley.EDU) by nature.berkeley.edu.cnr-net (4.1/SMI-4.1)
	id AA07818; Mon, 4 Oct 93 10:11:10 PDT
Message-Id: <9310041711.AA07818@nature.berkeley.edu.cnr-net>
Date: Mon, 4 Oct 1993 10:08:41 -0800
To: nih-image@soils.umn.edu
From: ruzin@nature.berkeley.edu (Steven Ruzin)
Subject: Re: imagefft

Where may I find the non-FPU version of Image. I'd like to run it on a LCIII.

Thanks.

Steve...

///////////////////////////////////////////////
|   Steven Ruzin                              |
|   NSF Center of Plant Developmental Biology |
|   Dept Plant Biology                        |
|   Univ California Berkeley                  |
|   e-mail: ruzin@nature.berkeley.edu         |
|   phone:  510-642-6602                      |
///////////////////////////////////////////////

From wayne@helix.nih.gov  Mon Oct  4 12:41:43 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA08828; Mon, 4 Oct 1993 12:43:23 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA04123; Mon, 4 Oct 93 13:03:47 -0400
Message-Id: <9310041703.AA04123@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Mon, 4 Oct 1993 12:41:43 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: LG-3 Memory Upgrade

>Hi all:
>I have just put in 4x1Mb simms on my Lg-3 board.  Image still sees the board
>as 
>a 1Mb board and will only capture/integrate 2 frames at video rate.  What else 
>do I have to do?

You shouldn't have to do anything else since NIH Image checks at startup to
see how much memory the LG-3 has. Are you sure those were 1MB SIMMS you put
in and not 1/4MB SIMMS?

--wayne


From wayne@helix.nih.gov  Mon Oct  4 14:58:30 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA10349; Mon, 4 Oct 1993 15:00:11 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA04844; Mon, 4 Oct 93 15:20:34 -0400
Message-Id: <9310041920.AA04844@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Mon, 4 Oct 1993 14:58:30 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Reslice Command

>A week or two ago I asked about the Reslice command, which kept giving me an
>error saying "Selection must be within image boundary."  After a little
>experimentation, I found that this was caused by setting the slice spacing to
>less than one pixel.  To get around this, I set the slice spacing to one
>pixel, reslice, and then vertically scale the resulting image so that it has
>the
>correct aspect ratio.
>
>Is this by design or is it a bug?

This is a bug that is fixed in V1.53b8, available by FTP from
zippy.nimh.nih.gov.

--wayne


From norm_hurst@maca.sarnoff.com  Mon Oct  4 15:14:02 1993
Received: from nova (nova.sarnoff.com) by nx1.soils.umn.edu (5.65c)
	id AA10528; Mon, 4 Oct 1993 15:14:02 -0500
Return-Path: <norm_hurst@maca.sarnoff.com>
Received: from maca.sarnoff.com by nova (4.1/SMI-4.0)
	id AA21412; Mon, 4 Oct 93 16:14:41 EDT
Message-Id: <9310042014.AA21412@nova>
Date: 4 Oct 1993 11:55:17 U
From: "Norm Hurst" <norm_hurst@maca.sarnoff.com>
Subject: Variance macro
To: nurit_binenbaum@maca.sarnoff.com, scott_casavant@maca.sarnoff.com,
        michael_isnardi@maca.sarnoff.com,
        prashanth_kuchibhotla@maca.sarnoff.com,
        James_Matey.MAILCENTER#u#17@maca.sarnoff.com,
        paul_meehan@maca.sarnoff.com,
        "NIH Image user group" <nih-image@soils.umn.edu>,
        stu_perlman@maca.sarnoff.com, catherine_tsao@maca.sarnoff.com

Variance macro                                            10/4/93
                                                                     11:24 AM

>>>Anyone have a macro that calculates a variance image?

I assume you want the "instantaneous" variance, the variance of a pixel in its
neighborhood.

var(i) = (x(i) - avg(x))^2/(N-1)
   where avg(x) is the average of values in a neighborhood (say 5x5)
   around a pixel x(i), and N is the number of pixels in the
   neighborhood (25). Let's disregard the /(N-1) operation for now --
   it's merely a scaling operation.

x(i) - avg(x) can be found by convolving with an appropriate filter. Here is
the filter for the 5x5 case:
    -1    -1    -1    -1    -1
    -1    -1    -1    -1    -1
    -1    -1    24    -1    -1
    -1    -1    -1    -1    -1
    -1    -1    -1    -1    -1

The squaring operation can be done with a parabolic LUT.  This LUT can include
the scaling operation for those who need calibrated results (modify the
argument to "Square" to be other than 1.0 to scale the LUT).  The macro "Find
Variance [V]" is below.

---------------------
{
Requires the file '5x5 mean diff' to contain:
    -1    -1    -1    -1    -1
    -1    -1    -1    -1    -1
    -1    -1    24    -1    -1
    -1    -1    -1    -1    -1
    -1    -1    -1    -1    -1
This is an impulse filter (all zeros with a 1 in the middle) 
minus a 5x5 average (5x5 1's divided by 25), then scaled so the
smallest tap is 1 (i.e. times 25).
}

procedure Square(scale:real)
{ APPLIES A PARABOLIC LUT}

var i,y:integer;
begin
  for i:= 1 to 254 do begin
    y:= (i-127)*(i-127)*scale/64.25;
    if y > 255 then y:=255;
    RedLUT[i]:=y;
    GreenLUT[i]:= y;
    BlueLUT[i]:=y;
  end;
  UpdateLUT;
  ApplyLUT;
end;


macro 'Find Variance [V]'
begin
  Convolve('5x5 mean diff');  {impulse minus 5x5 average}
  Square(1.0);                {Adjust argument to scale the LUT}
end;



From kyzy@rice.edu  Mon Oct  4 10:31:20 1993
Received: from moe.rice.edu by nx1.soils.umn.edu (5.65c)
	id AA10742; Mon, 4 Oct 1993 15:30:20 -0500
Return-Path: <kyzy@rice.edu>
Received: from [128.42.105.7] (erinna.rice.edu) by moe.rice.edu (AA13618); Mon, 4 Oct 93 15:31:22 CDT
Date: Mon, 4 Oct 93 15:31:20 CDT
Message-Id: <9310042031.AA13618@moe.rice.edu>
To: nih-image@soils.umn.edu
From: kyzy@rice.edu
Subject: Re: imagefft

>Where may I find the non-FPU version of Image. I'd like to run it on a LCIII.
>

  The non-FPU version of NIH-image 1.52 is at /pub/nih-image on zippy.

   But, have you considered adding the FPU chip to your LC-III ? There is a
socket on the LC-III motherboard for the 68882 floating point chip. All you
have to do is buy a 25 MHz 68882 chip from any of the mail-order places and
pop it in its socket (fairly easy to do and safe if you follow the standard
grounding procedures).  Depending on where you buy it, the chip will cost
from 60 to 80 dollars.  I have just upgraded an LCIII with more memory and
the FPU chip, and it now has Mac IIci performance on everything.



------------------------------------------------------------------------
                                 |
Kyriacos Zygourakis, Professor   |   Phone:  (713) 527-8750 Ext. 3509
Dept. of Chemical Engineering    |   FAX:    (713) 285-5478
Rice University                  |   e-mail: kyzy@rice.edu
Houston, Texas 77251-1892        |
                                 |
------------------------------------------------------------------------



From wayne@helix.nih.gov  Mon Oct  4 17:12:49 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA11965; Mon, 4 Oct 1993 17:14:30 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA05452; Mon, 4 Oct 93 17:34:53 -0400
Message-Id: <9310042134.AA05452@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Mon, 4 Oct 1993 17:12:49 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Non-FPU version of NIH Image

>Where may I find the non-FPU version of Image. I'd like to run it on a LCIII.

As of today,  both fpu and non-fpu versions of Image1.52 are on
zippy.nimh.nih.gov. Before today, only the non-fpu version was available,
although it didn't have "non-fpu" in the file name. The non-fpu version
runs on all Macs with 8-bit video, including the PowerPC, and is not
noticably slower than the fpu version for most functions. The fpu version
is faster for a few operations, such as line profile plotting using a wide
line selection.

--wayne


From msachs@admin.ogi.edu  Mon Oct  4 09:33:37 1993
Received: from ogicse.cse.ogi.edu (cse.ogi.edu) by nx1.soils.umn.edu (5.65c)
	id AA12773; Mon, 4 Oct 1993 18:33:12 -0500
Return-Path: <msachs@admin.ogi.edu>
Received: by ogicse.cse.ogi.edu (/\==/\ Smail3.1.25.1 #25.4)
	id <m0ojzPx-0004opC@ogicse.cse.ogi.edu>; Mon, 4 Oct 93 16:34 PDT
Received: from [129.95.74.59] by admin.ogi.edu.ogi.edu (4.1/SMI-4.1)
	id AA18240; Mon, 4 Oct 93 16:33:41 PDT
Date: Mon, 4 Oct 93 16:33:37 PDT
Message-Id: <9310042333.AA18240@admin.ogi.edu.ogi.edu>
To: Multiple recipients of list <nih-image@soils.umn.edu>
From: msachs@admin.ogi.edu (Matthew Sachs)
Subject: How to correctly use Image for densitometry?

Dear Imagers,

Please help a new Image user to use Image correctly.  I regret that the
appellation "Image user" might seem oxymoronic applied to me at present.

Given a MacII CX, Microtek MSF300ZS scanner, Image 1.52, Photoshop 2.5 (and
given the possibility of using a CCD for image capture, if scanner is too
weak a link).

We wish to examine a series of autoradiographic images of gel "bands" of
different intensities and morphologies derived from experimental samples. 
We can follow directions in Image documentation to:

Scan autoradiograms at 75 dpi.
Open in Image, use 2D rolling ball to remove background.
Select "Calibrate" option, select radio button "Uncalibrated OD."
Use Plot Gel macro to obtain profiles of a series of gel lanes.
Draw baselines to make peaks that correspond to bands of interest into
'closed' objects.
Select peaks of interest with the wand tool, and use option-text tool to
place the calculated area of selected peaks onto the lane profiles.  

The questions I have concern how to use peak areas obtained with this
method to CORRECTLY determine the relative amount of material in input
samples.  In some cases, there is an anticipated 1.5-fold difference in the
amount of material of interest in cells grown under different growth
conditions (based on enzyme activity assay); in other cases, hundred-fold
differences are anticipated.

What does experience teach as the best, most efficient way to tackle this
problem?  I anticipate that loading different amounts of each sample, using
different exposures, and possibly defining calibration parameters
empirically using standards are all necessary, but would appreciate
guidance as to what constitutes a sensible protocol to begin this process,
and what controls experts feel are  necessary to assure legitimate
comparisons.

Thank you for any advice you might have on this matter.

Sincerely,

Matthew Sachs
Assistant Professor
Department of Chemistry, Biochemistry and Molecular Biology
Oregon Graduate Institute of Science and Technology
Beaverton, OR

From skim@signal.poly.edu  Mon Oct  4 15:57:56 1993
Received: from signal.poly.edu by nx1.soils.umn.edu (5.65c)
	id AA13143; Mon, 4 Oct 1993 19:01:00 -0500
Return-Path: <skim@signal.poly.edu>
Received: by signal.poly.edu (5.65/1.34)
	id AA09779; Mon, 4 Oct 93 19:57:56 -0400
Date: Mon, 4 Oct 93 19:57:56 -0400
From: skim@signal.poly.edu (Seung Pil Kim)
Message-Id: <9310042357.AA09779@signal.poly.edu>
To: nih-image@soils.umn.edu
Subject: Re: LG-3 Memory Upgrade


> >I have just put in 4x1Mb simms on my Lg-3 board.  Image still sees the board
> >as 
> >a 1Mb board and will only capture/integrate 2 frames at video rate.  What else 
> >do I have to do?
> 
> You shouldn't have to do anything else since NIH Image checks at startup to
> see how much memory the LG-3 has. Are you sure those were 1MB SIMMS you put
> in and not 1/4MB SIMMS?


I had a similar experience when I tried to upgrade memory 1M to 4M for 
my Mac/SE. I found that the resister near the memory module should be 
cut off.  I don't remember the res. number but there is a square
printed beneath it on PCB. 

Hope this helps.

S.P. Kim
From stmwang@hubcap.clemson.edu  Mon Oct  4 16:56:14 1993
Received: from hubcap.clemson.edu by nx1.soils.umn.edu (5.65c)
	id AA13763; Mon, 4 Oct 1993 19:56:01 -0500
Return-Path: <stmwang@hubcap.clemson.edu>
Received: by hubcap.clemson.edu; Mon, 4 Oct 93 20:56:20 -0400 
From: stmwang@hubcap.clemson.edu (Sam Wang)
Message-Id: <9310050056.AA00613@hubcap.clemson.edu>
Subject: Re: QuickImage24
To: nih-image@soils.umn.edu
Date: Mon, 4 Oct 1993 20:56:14 -0400 (EDT)
In-Reply-To: <199310041855.AA09686@nx1.soils.umn.edu> from "nih-image@soils.umn.edu" at Oct 4, 93 01:55:32 pm
X-Mailer: ELM [version 2.4 PL2]
Content-Type: text
Content-Length: 365       

Does anyone use the Mass Micro QuickImage 24 frame capture board
with Image? Latest ad in MacWorld is selling it for $99. It's
supposed to support QuickTime. I am interested to know how well
it might work on a IIcx and on a Centris 610.
-- 
Sam Wang  stmwang@hubcap.clemson.edu    803/656-3924voice 656-0204fax
Art Dept., Clemson University, Clemson, SC 29634-0509
From kartenh@Sdsc.Edu  Tue Oct  5 03:18:42 1993
Received: from Sdsc.Edu (m5.sdsc.edu) by nx1.soils.umn.edu (5.65c)
	id AA15073; Mon, 4 Oct 1993 22:17:45 -0500
Return-Path: <kartenh@Sdsc.Edu>
Date:    Tue, 5 Oct 93 03:18:42 GMT
From: kartenh@Sdsc.Edu (Harvey Karten)
Message-Id: <931005031842.204065b9@m5.sdsc.edu>
Subject: RE: How to correctly use Image for densitometry?
To: nih-image@soils.umn.edu
X-St-Vmsmail-To: ST%"nih-image@soils.umn.edu"
X-St-Vmsmail-Cc: KARTENH

re: questions by Matthew Sachs
If you use a CCD to gather your images, there are several critical operations
that you must attend to if you want to have any hope of accurate
inter-specimen comparison.
1) Get a CCD that allows you to turn the AGC OFF. Many CCDs have an internal 
jumper that has to be correctly repositioned to inactivate the AGC (Automatic
Gain Control).
2) Use a stabilized light source. An AC fluorescent light table is not 
sufficiently stable for this purpose. I have heaerd that a stabilized 
DC fluorescent light source may be ok, but should be recalibrated 
every so often. 
3) When initially setting up your system with the CCD and Good
quality lens, you have to adjust the gain and offset (if using 
a Scion LG-3) to give proper spread of values in your histogram.
(See various texts in video microscopy). 
4) Once you have gotten this standardized, make sure you always 
set it up in exactly the same way each time. It would be adviseable to 
have a graded image with a good 8 bit spread of values for 
calibration each time. Some tips for this are to always use the 
same r egion of the ligth table, same distance from the object, 
same f-stop on the lens, etc. 
5) Despite all these precautions, you may still have problems, 
because of inherent response to bloom on the part of all 
video devices, even if AGC is turned off. Thus, if there is a particularly 
bright portion to your image, some cameras will still modify their
gain even with AGC off. I don't know the reason for this, but 
it may have to do with electrostatic charging of the CCD. 
Perhaps one of our other participants can explain why 
this happens.  
Hope this is of some help. 
				HJK
From rms@acsu.buffalo.edu  Mon Oct  4 19:28:50 1993
Received: from lictor.acsu.buffalo.edu by nx1.soils.umn.edu (5.65c)
	id AA15223; Mon, 4 Oct 1993 22:27:46 -0500
Return-Path: <rms@acsu.buffalo.edu>
Received: from rms@localhost by lictor.acsu.buffalo.edu (8.5/8.5)
	id XAA22135; Mon, 4 Oct 1993 23:28:50 -0400
Date: Mon, 4 Oct 1993 23:28:50 -0400
From: "Robert M. Straubinger" <rms@acsu.buffalo.edu>
Message-Id: <199310050328.XAA22135@lictor.acsu.buffalo.edu>
To: nih-image@soils.umn.edu
Subject: Ratio imaging

I've imported z-series of images from an Olympus confocal into
Image stacks; the stacks consist of pairs of images for each z-slice
(images are taken 2 different wavelengths) in order to determine
pH from a pH - sensitive probe.

I'd like to create a new stack of ratio'ed images. So far, I haven't
found a macro to do it. The preliminary approach I've taken is to 
copy one image and paste it on the other, using Paste Control to
divide one image by the other.

A macro to automate the above would be relatively simple, but I'd like
to solicit comments (better still, macros); a number of other operations
ought to be done, such as mask out background values and saturated pixels.
Also, it would be nice to be able to control the scaling after divide --
either to maximize dynamic range, or to force scaling of all images
to the same range.

If this wheel has been invented already, I'd like to hear about it-

Bob Straubinger
Pharmaceutics
SUNY Buffalo
From mhowland@alsvid.une.edu.au  Wed Oct  6 00:25:12 1993
Received: from alsvid.une.edu.au by nx1.soils.umn.edu (5.65c)
	id AA15853; Mon, 4 Oct 1993 23:24:13 -0500
Return-Path: <mhowland@alsvid.une.edu.au>
Received: from [129.180.146.5] (mac146_5.nr.une.edu.au) by alsvid.une.edu.au with SMTP id AA00959
  (5.65c8+/IDA-1.4.4 for <nih-image@soils.umn.edu>); Tue, 5 Oct 1993 14:25:12 +1000
Date: Tue, 5 Oct 1993 14:25:12 +1000
Message-Id: <199310050425.AA00959@alsvid.une.edu.au>
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: mhowland@alsvid.une.edu.au (Mick Howland)
Subject: Image & AV series Macs

Can Image capture video live through the on board video controller of the
AV series Mac's?
 


_____________________________________________________________
Michael Howland, Faculty of Resource Science & Management
UNE - Northern Rivers, P.O. Box 157, Lismore, NSW, Australia.
Phone: +61-66-203037  Fax: +61-66-212669
E-mail: mhowland@alsvid.une.edu.au
_____________________________________________________________


From herro001@maroon.tc.umn.edu  Tue Oct  5 01:55:04 1993
Received: from maroon.tc.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA20847; Tue, 5 Oct 1993 06:53:58 -0500
Return-Path: <herro001@maroon.tc.umn.edu>
Message-Id: <199310051153.AA20847@nx1.soils.umn.edu>
Received: from rash.med.umn.edu by maroon.tc.umn.edu id SMTP-0012cb16093012531; Tue, 5 Oct 93 06:55:02 -0500
From: "Mike Herron" <herro001@maroon.tc.umn.edu>
Reply-To: "Mike Herron" <herro001@maroon.tc.umn.edu>
To: nih-image@soils.umn.edu
Subject: Re: Non-FPU version of NIH Image
Date: Tue, 5 Oct 93 06:55:04 -0500

In message <9310042134.AA05452@zippy.nimh.nih.gov>  writes:
> >Where may I find the non-FPU version of Image. I'd like to run it on a 
> LCIII.
> 
> As of today,  both fpu and non-fpu versions of Image1.52 are on
> zippy.nimh.nih.gov. Before today, only the non-fpu version was available,
> although it didn't have "non-fpu" in the file name. The non-fpu version
> runs on all Macs with 8-bit video, including the PowerPC, and is not
> noticably slower than the fpu version for most functions. The fpu version
> is faster for a few operations, such as line profile plotting using a wide
> line selection.
> 
> --wayne

Is this right? You/someone tested Image1.52 on a PowerPC?!




 
   ______________________________________________
  / Mike Herron,  U of MN, Dept. of Dermatology /
 / herro001@maroon.tc.umn.edu                  /
/ 612-625-8935  Box 124 UMHC, Mpls MN 55455   /
______________________________________________

From a337ard@diamond.sara.nl  Tue Oct  5 14:39:38 1993
Received: from vx.cis.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA21353; Tue, 5 Oct 1993 07:43:43 -0500
Return-Path: <a337ard@diamond.sara.nl>
Received: from HASARA5.BITNET (MAILGATE@HASARA5) by vx.cis.umn.edu (PMDF
 V4.2-13 #2574) id <01H3QUZUDTWWB6360R@vx.cis.umn.edu>; Tue,
 5 Oct 1993 07:45:18 CDT
Received: from diamond.sara.nl by SARA.NL for nih-image@soils.umn.edu; 5 Oct 93
 13:44 MET
Received: by diamond.sara.nl (5.61-AIX-1.2/1.0), id AA166740,
 (for nih-image@soils.umn.edu, from a337ard@diamond.sara.nl);
Date: Tue, 05 Oct 1993 13:39:38 +0100
From: a337ard@diamond.sara.nl (Ard Jonker)
Subject: Re: Non-FPU version of NIH Image
To: nih-image@soils.umn.edu
Message-Id: <9310051239.AA166740@diamond.sara.nl>
X-Envelope-To: nih-image@soils.umn.edu
Content-Transfer-Encoding: 7BIT

Okay, I'll bite:
Is the powerPC available yet? Where? How much?
From wayne@helix.nih.gov  Tue Oct  5 08:13:21 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA21707; Tue, 5 Oct 1993 08:15:03 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA07159; Tue, 5 Oct 93 08:35:29 -0400
Message-Id: <9310051235.AA07159@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 5 Oct 1993 08:13:21 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Non-FPU version of NIH Image

>Is this right? You/someone tested Image1.52 on a PowerPC?!

I haven't tested Image on a PowerPC, put I don't see any reason why the
non-fpu version wouldn't work. The fpu version won't work because the
PowerPC emulates the 68LC040 processor(used in the Centris 610), which has
no floating point instructions.

--wayne



From wayne@helix.nih.gov  Tue Oct  5 10:02:06 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA22865; Tue, 5 Oct 1993 10:03:52 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA01364; Tue, 5 Oct 93 10:22:25 -0400
Message-Id: <9310051422.AA01364@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 5 Oct 1993 10:02:06 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Non-FPU version of NIH Image

>Okay, I'll bite:
>Is the powerPC available yet? Where? How much?

According to MacWeek, PowerPC Macs will be announced in March at prices
starting around $2000. 

--wayne


From dickinson%g24mac1@relay.nswc.navy.mil  Tue Oct  5 09:07:55 1993
Received: from relay.nswc.navy.mil by nx1.soils.umn.edu (5.65c)
	id AA24464; Tue, 5 Oct 1993 12:07:05 -0500
Return-Path: <dickinson%g24mac1@relay.nswc.navy.mil>
Received: from [128.38.34.152] (ddickensmac.nswc.navy.mil) by relay.nswc.navy.mil (4.1/SMI-4.1)
	id AA14240; Tue, 5 Oct 93 13:07:55 EDT
Date: Tue, 5 Oct 93 13:07:55 EDT
Message-Id: <9310051707.AA14240@relay.nswc.navy.mil>
From: "David Dickinson"  <dickinson%g24mac1@relay.nswc.navy.mil>
Reply-To: "David Dickinson"  <dickinson%g24mac1@relay.nswc.navy.mil>
To: NIH-IMAGE@SOILS.UMN.EDU
Subject: Question on missing results

I am measuring area, x, y, major and minor axis values.

The version of NIH-Image is 1.52.

The count of items measured (displayed in the box on the lower left of the 
screen) is 952. The highest marked item on the image is also 952. However, the 
number of measurements displayed in the results window only goes to 526 and the 
x value of 527. Printing (or copying and pasting to Excel) shows the number of 
measurements to be 582.

The max measurements value is set to 7000. The Undo and Clipboard value is set 
to 1600k.

This process has been repeated multiple times (also with version 1.49) and the 
results are consistant.

Any suggestions on finding the missing values is greatly appreciated.

Thanks in advance.

:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
    David L. Dickinson           dickinson@g24mac1.nswc.navy.mil

    Voice: (703) 663-8691 or DSN 249-8691         FAX: (703) 663-8268

    Lethality and Weapons Effectiveness Branch, G24
    Naval Surface Warfare Center, Dahlgren Division
    Dahlgren, VA  22448
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

From keller@micros.mrd.bldrdoc.gov  Tue Oct  5 05:24:31 1993
Received: from central.bldrdoc.gov by nx1.soils.umn.edu (5.65c)
	id AA24640; Tue, 5 Oct 1993 12:23:45 -0500
Return-Path: <keller@micros.mrd.bldrdoc.gov>
Received: from pascal.mrd.bldrdoc.gov by central.bldrdoc.gov (4.1/SMI-DDN)
	id AA04461; Tue, 5 Oct 93 11:24:47 MDT
Received: from micros.mrd.bldrdoc.gov by pascal.mrd.bldrdoc.gov (4.1/SMI-3.2)
	id AA00275; Tue, 5 Oct 93 11:25:14 MDT
Message-Id: <9310051725.AA00275@pascal.mrd.bldrdoc.gov>
Date: Tue, 5 Oct 93 11:24:31 MDT
From: Bob Keller <keller@micros.mrd.bldrdoc.gov>
Subject: voyager plug-in
To: nih-image@soils.umn.edu
X-Mailer: LeeMail 1.2.4

Where can I find a Voyager decompression plug-in?  It's not in the plug ins 
directory on zippy.

Bob Keller
keller@micros.mrd.bldrdoc.gov

From ikami@liposun.lbl.gov  Tue Oct  5 03:33:29 1993
Received: from lbl.gov by nx1.soils.umn.edu (5.65c)
	id AA24821; Tue, 5 Oct 1993 12:39:06 -0500
Return-Path: <ikami@liposun.lbl.gov>
Received: from liposun.lbl.gov by lbl.gov (4.1/1.39)
	id AA12778; Tue, 5 Oct 93 10:45:57 PDT
Received: from [131.243.32.31] (b1-lipo8.lbl.gov) by liposun.lbl.gov (4.1/SMI-4.0)
	id AA11768; Tue, 5 Oct 93 10:33:30 PDT
Date: Tue, 5 Oct 93 10:33:29 PDT
Message-Id: <9310051733.AA11768@liposun.lbl.gov>
To: nih-image@soils.umn.edu
From: ikami@liposun.lbl.gov (Craig Ikami)
Subject: first timer

We have just acquired a molecular dynamics densitometer. It produces 12 bit
tiff files. We have looked at image v1.44 and would like to know if future
versions of image will support 12 bit acquisition and display? 

                        thanks

From bnhirsch@dapsas1.weizmann.ac.il  Tue Oct  5 22:08:09 1993
Received: from dapsas1.weizmann.ac.il by nx1.soils.umn.edu (5.65c)
	id AA25011; Tue, 5 Oct 1993 12:59:07 -0500
Return-Path: <bnhirsch@dapsas1.weizmann.ac.il>
Received: from [132.76.66.33] by dapsas1.weizmann.ac.il via SMTP (920110.SGI/911001.SGI)
	for nih-image@soils.umn.edu id AA19817; Tue, 5 Oct 93 19:59:10 +0300
Message-Id: <9310051659.AA19817@dapsas1.weizmann.ac.il>
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 5 Oct 1993 20:08:09 +0200
To: nih-image@soils.umn.edu
From: bnhirsch@dapsas1.weizmann.ac.il (David L. Hirschberg)
Subject: Fluorescent Images -Help 

Can someone explain how ccd cameras handle fluorescent images and how can I
use NIH-Image to get the maximum resolution?

I have a Quadra 950 with a Scion LV-3 frame grabber and a Burle CCD camera
(we also have a Sony X-77).  The camera is mounted on a Nikon inverted
scope.  I am currently using Image 153b8.

When I capture phase images I have no problem and my images look fine under
most conditions.  The problem comes whe I want to capture fluorescent
images.  I can see the image clearly through the eye piece and the image is
acceptable on the Sony monitor we have attached to the camera.  Using the
standard acquistition in Image gives me a black screen though.  I tried the
summation and integration modes and still I ended up with a black screen. 
If I turned on the the white light then board started to see enough to
capture something.  

I did download and try the Scion LV-3 plug-in module and was able to get a
very weak image.  Should the plug-in module work better than the standard
method?  Also is there a way to sum images using the plug-in module?

I am trying to image neurites that have been stained with either FITC or
Rhodamine.   The LV-3 board seems to have the most problem when I am
imaging a single neurite  so only a very small portion of the field is
lit-up and the rest is black.  The neurite can be seen clearly through the
eye piece weakly on the monitor but the computor monitor is black.  Even if
I am imaging 100 cells in a field it seems the resolution is not great
after capturing.

So what can I do to capture fluorescent images?  Is Rhodamine better than
Fluorescein?  Is there a way I can change the sensitivity of the Scion
board.  Is there a way to boost the video part of the voltage input the
LV-3 board receives?


Thanks in advance.

David



=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
David L. Hirschberg                     bnhirsch@dapsas.weizmann.ac.il
Department of Neurobiology              (972) 834-2127 work
Weizmann Institute of Science           (972) 847-4805 home
Rehovot 76100 Israel                    (972) 834-4131 fax



From wayne@helix.nih.gov  Tue Oct  5 14:50:08 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA26355; Tue, 5 Oct 1993 14:51:50 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA02166; Tue, 5 Oct 93 15:10:26 -0400
Message-Id: <9310051910.AA02166@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 5 Oct 1993 14:50:08 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Variance macro

Here is a version of Norm Hurst's variance macro that has the convolution
filter inline. To get inline filtering to work right, I had to add width
and height arguments to the NewTextWindow command and to fix the Dispose
command so it works with text windows. These fixes are in V1.53b9 on
zippy.nimh.nih.gov.

--wayne

procedure Square(scale:real)
{ Applies a parabolic LUT}
var i,y:integer;
begin
  for i:= 1 to 254 do begin
    y:= (i-127)*(i-127)*scale/64.25;
    if y > 255 then y:=255;
    RedLUT[i]:=y;
    GreenLUT[i]:= y;
    BlueLUT[i]:=y;
  end;
  UpdateLUT;
  ApplyLUT;
end;

procedure ImpulseFilter;
{This is an impulse filter (all zeros with a 1 in the middle) minus a 5x5
average (5x5 1's divided by 25), then scaled so the smallest tap is 1 (i.e.
times 25).}
begin
  RequiresVersion(1.53);
  NewTextWindow('5x5 mean diff',150,140);
  writeln('-1 -1 -1  -1 -1');
  writeln('-1 -1 -1  -1 -1');
  writeln('-1 -1 24 -1 -1');
  writeln('-1 -1 -1  -1 -1');
  writeln('-1 -1 -1  -1 -1');
  Convolve('');
  Dispose;
end;

macro 'Find Variance [V]'
begin
  ImpulseFilter;       {impulse minus 5x5 average}
  Square(1.0);          {Adjust argument to scale the LUT}
end;


From wayne@helix.nih.gov  Tue Oct  5 15:49:55 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA27019; Tue, 5 Oct 1993 15:51:37 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA02344; Tue, 5 Oct 93 16:10:13 -0400
Message-Id: <9310052010.AA02344@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 5 Oct 1993 15:49:55 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Question on missing results

>The count of items measured (displayed in the box on the lower left of the 
>screen) is 952. The highest marked item on the image is also 952. However, the 
>number of measurements displayed in the results window only goes to 526 and
>the 
>x value of 527. Printing (or copying and pasting to Excel) shows the number of 
>measurements to be 582.
>
>Any suggestions on finding the missing values is greatly appreciated.

>From page 82 of the manual (Program Limitations):

"The maximum number of characters that can be  displayed, printed, or
copied to the clipboard is 32,700. There is no limit to the number of
measurements that can be exported to a text file."

I have updated the description of the Show Results command in the manual to
make this limitation clearer.

--wayne


From wayne@helix.nih.gov  Tue Oct  5 16:51:45 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA27716; Tue, 5 Oct 1993 16:53:27 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA02489; Tue, 5 Oct 93 17:12:03 -0400
Message-Id: <9310052112.AA02489@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 5 Oct 1993 16:51:45 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Ratio imaging

>I've imported z-series of images from an Olympus confocal into
>Image stacks; the stacks consist of pairs of images for each z-slice
>(images are taken 2 different wavelengths) in order to determine
>pH from a pH - sensitive probe.
>
>I'd like to create a new stack of ratio'ed images. So far, I haven't
>found a macro to do it. The preliminary approach I've taken is to 
>copy one image and paste it on the other, using Paste Control to
>divide one image by the other.
>
>A macro to automate the above would be relatively simple, but I'd like
>to solicit comments (better still, macros); a number of other operations
>ought to be done, such as mask out background values and saturated pixels.
>Also, it would be nice to be able to control the scaling after divide --
>either to maximize dynamic range, or to force scaling of all images
>to the same range.

I am about to add a command to the macro language that will make it a lot
easier to write such a macro.  It will perform arithmetic and logical
operations on images, eliminating the need to use Paste Control and
providing the abilty to control scaling. I'm thinking of calling it DoOp
(do operation). It will look something like

    DoOp('Divide', pid1, pid2, pid3, scale, offset)

where the first argument specifies the function to be performed and
pid1,pid2 and pid3 are pic id  numbers. Pixel values resulting from the
operation are multiplied by the scale and then the offset is added.

Here are some examples:

     DoOp('Add', pid1, pid2, pid3, 0.5, 0);          {Compute average of
two images}
     DoOp('Copy', pid1, 0, pid1, 0.5, 128);         {Multiply by .5 and add 128}
     DoOp('AND', pid1, pid2, pid3, 1, 0);            {Logical AND of two images}
  

--wayne


From wayne@helix.nih.gov  Tue Oct  5 16:59:45 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA27755; Tue, 5 Oct 1993 17:01:27 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA02501; Tue, 5 Oct 93 17:20:04 -0400
Message-Id: <9310052120.AA02501@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 5 Oct 1993 16:59:45 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: first timer

>We have just acquired a molecular dynamics densitometer. It produces 12 bit
>tiff files. We have looked at image v1.44 and would like to know if future
>versions of image will support 12 bit acquisition and display? 

The current version of NIH Image (1.52) can import the 16-bit TIFF files
created by Molecular Dynamics scanners. The image data is scaled to 8-bits,
but the 16-bit to 8-bit scaling can be changed using the Rescale(aka Revert
to Saved) command.

--wayne


From kartenh@sdsc.edu  Tue Oct  5 22:55:55 1993
Received: from Sdsc.Edu (sds.sdsc.edu) by nx1.soils.umn.edu (5.65c)
	id AA28428; Tue, 5 Oct 1993 17:55:09 -0500
Return-Path: <kartenh@sdsc.edu>
Message-Id: <199310052255.AA28428@nx1.soils.umn.edu>
Received: from [132.239.67.254] by Sdsc.Edu (sds.sdsc.edu STMG) via INTERNET;
          Tue, 5 Oct 93 22:55:55 GMT
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: kartenh@Sdsc.Edu
Subject: Re: Fluorescent Images -Help
Date:  Tue, 5 Oct 93 22:55:55 GMT

David H. Writes:
>David L. Hirschberg                     bnhirsch@dapsas.weizmann.ac.il
>Department of Neurobiology              (972) 834-2127 work
>Weizmann Institute of Science           (972) 847-4805 home

>So what can I do to capture fluorescent images?  Is Rhodamine better than
>Fluorescein?  Is there a way I can change the sensitivity of the Scion
>board.  Is there a way to boost the video part of the voltage input the
>LV-3 board receives?
>
>

>
>=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
The image you see on your monitor may not reflect the actual values in the
output signal. This most commonly happens when people "adjust" the
brightness and contrast settings on the monitor. Modification of those
settings may provide an image enhancement on the monitor display, but do
not reflect the value that are coming out of the camera and going to the
frame grabber. The use of those controls does not reflect the actual spread
of values that are coming out of the camera. Ideally, you should use a
running histogram when grabbing an image, 
then adjust the gain and offset to give a full spread of the 8 bits of your
frame grabber. 
This is always a bit arbitrary with a fluorescent image, since most
fluorescent images don't actually have that broad a point spread. Your eye
is amazingly sensitive to low light levels. 
You may have to go to an image intensifier to get fluorescent images. If
you are working on an inverted microscope (which I suspect if you are
watching outgrowing neurites), you should be aware that the folded light
path severely reduces the image brightness stil further, again 
emphasizing the need for an intensifier plate.
                                        regards, Harvey K.
                                a.k.a. Reb Hillel of Del Mar

 Harvey J. Karten, M.D.
 Dept. of Neurosciences
 Univ.California San Diego
 La Jolla, CA 92093-0608
 EMail: Kartenh@sdsc.edu
 Phone: (619)-534-4938
 FAX: (619)-534-6602


From a337ard@diamond.sara.nl  Wed Oct  6 09:01:21 1993
Received: from vx.cis.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA03708; Wed, 6 Oct 1993 03:05:59 -0500
Return-Path: <a337ard@diamond.sara.nl>
Received: from HASARA5.BITNET (MAILGATE@HASARA5) by vx.cis.umn.edu (PMDF
 V4.2-13 #2574) id <01H3RZKU2CMOB6397Y@vx.cis.umn.edu>; Wed,
 6 Oct 1993 03:07:33 CDT
Received: from diamond.sara.nl by SARA.NL for nih-image@soils.umn.edu; 6 Oct 93
 9:07 MET
Received: by diamond.sara.nl (5.61-AIX-1.2/1.0), id AA156795,
 (for nih-image@soils.umn.edu, from a337ard);
Date: Wed, 06 Oct 1993 08:01:21 +0100
From: a337ard@diamond.sara.nl (Ard Jonker)
Subject: Re:  Fluorescent Images -Help
To: nih-image@soils.umn.edu
Message-Id: <9310060701.AA156795@diamond.sara.nl>
X-Envelope-To: nih-image@soils.umn.edu
Content-Transfer-Encoding: 7BIT

On the questionn of invisibility of fluorescent images:

Regarding the Sony XC77 (CE) I can say that the image you see is
likeley visible because you look at a video signal. That has been corrected
for the pedestal of the camera (a floor in the camera signal ) that is
caused by dark current. If you were to digitize the signal of the Sony in
127 levels, (As I do) the pedestal or dark current is 24. If you would
digitize with 256 levels (NIH Image) I presume the dark current is 48.
So to optimally visualize the image, grab it, subtract integer (48) from
the image and do an equalization. (or make a histogram and see in which
area of greylevels the interesting part is; if it ranges from a to b, then
subtract a from the image and multiply by 255/(b-a), which is a strech
of the area a..b over the LUT.)
if this too does not work, you have another problem
BTW, you could add the images of subsequent grabs, after subtracting 48
from each image.
The 'official' way to do dark current correction is to grab an image with
obscured camera, and subtract this image from each fluorescent image. I
have found it to be satisfactory to subtract a constant (24 im n my case)
because the variation in the Sony camera is very limited (as opposed to
the Photometrics camera we use; pixelwise-percentage variation is bigger)

ard (a337ard@diamond.sara.nl)
From ptr@GRECO2.POLYTECHNIQUE.FR  Wed Oct  6 12:49:28 1993
Received: from chenas.inria.fr by nx1.soils.umn.edu (5.65c)
	id AA05261; Wed, 6 Oct 1993 05:52:09 -0500
Return-Path: <ptr@GRECO2.POLYTECHNIQUE.FR>
Received: from polytechnique.polytechnique.fr by chenas.inria.fr (5.65c8d/92.02.29)
	via Fnet-EUnet id AA07917; Wed, 6 Oct 1993 11:53:04 +0100 (MET)
Received: by polytechnique.polytechnique.fr (5.65c/SMI-4.1.3)
	id AA14169; Wed, 6 Oct 1993 12:00:52 +0100
Received: from [129.104.27.245] by greco2.noname (4.1/SMI-4.1)
	id AA00446; Wed, 6 Oct 93 11:49:29 +0100
Date: Wed, 6 Oct 93 11:49:28 +0100
Message-Id: <9310061049.AA00446@greco2.noname>
To: nih-image@soils.umn.edu
From: ptr@GRECO2.POLYTECHNIQUE.FR (Peter Goedtkindt)
Subject: Restore selection & Plot bug?

Hallo,

When making a profile plot using the Profile plot tool, then switching to a
next image to do the same operation, using the Restore selection menu
command (or cmd-4), I get inconsistent results. The selection is drawn
where it should be, but the values are nonsense.

When using a rectangular selection, I don't get this problem, and it is
also much faster. Rectangular selections have a big disadvantage that the
direction in which the plot is scanned depends on the relative width and
hight. How can I choose between a vertical or a horizontal profile plot,
independant of the aspect ratio of the selection?

When I have my profile plot, I want to measure the FWHM of the peak. Has
anybody written a Macro that allows this?

Thanks,
Peter Goedtkindt
Universite Paris-Sud 
Laboratoire de Spectroscopie Atomique et Ionique
X-ray Laser group
bat350 
Centre D'Orsay F-91405 Orsay Cedex. France 
Fax.:++33.1.69.41.94.60 - Tel 69.41.77.10
------
And
------
Ecole Polytechnique, Laboratoire d'Utilisation de Lasers Intenses
tel. 69.33.48.95
-----------------------------------------------------------------

From V.A.Moss@vme.glasgow.ac.uk  Wed Oct  6 06:52:16 1993
Received: from hillhead.cent.gla.ac.uk by nx1.soils.umn.edu (5.65c)
	id AA06983; Wed, 6 Oct 1993 06:52:16 -0500
Return-Path: <V.A.Moss@vme.glasgow.ac.uk>
Received: from vme.glasgow.ac.uk by jess.glasgow.ac.uk via JANET 
          with NIFTP (PP) id <24065-0@jess.glasgow.ac.uk>;
          Wed, 6 Oct 1993 12:53:14 +0100
Date: Wed, 6 Oct 93 12:51:18 BST
From: V.A.Moss@vme.glasgow.ac.uk
Subject: Re: Your last message...
To: nih-image@soils.umn.edu
Message-Id: <_6_Oct_93_12:51:18_A101DA@UK.AC.GLA.VME>
In-Reply-To: Your message <9309291242.AA17983@u1.uibk.ac.at>

Dear Dietmar,
   Thanks for your email about my last message being deleted.  I too have
deleted lots of messages, so I am not sure which was my last message.
Any way it was not important.  What it may have been was:-
 
I am putting in a few new changes to MacStereology (moving/zooming and s
shrinking in dialog boxes) and will send you a new version as soon as tested
(in a few days I hope).
 
Alignment of sections can be done manually in Align dialog of MacStereology,
but it may be possible to do an automatc alignment based on the centre of
gravity of objects on adjacent layers.
 
Regards
Vic Moss
From pekr@research.novo.dk  Wed Oct  6 14:34:22 1993
Received: from danpost.uni-c.dk by nx1.soils.umn.edu (5.65c)
	id AA07390; Wed, 6 Oct 1993 07:33:24 -0500
Return-Path: <pekr@research.novo.dk>
Received: from nngate.novo.dk (xpsrv1.novo.dk [129.142.229.2]) by danpost.uni-c.dk (8.6.beta.10/8.6.beta.10) with SMTP id NAA19383 for <nih-image@soils.umn.edu>; Wed, 6 Oct 1993 13:34:23 +0100
Received: by nngate.novo.dk (5.65/DEC-Ultrix/4.3A)
	id AA11275; Wed, 6 Oct 1993 13:34:23 +0100
Date: Wed, 6 Oct 1993 13:34:22 +0100
Message-Id: <9310061234.AA11275@nngate.novo.dk>
From: pekr@research.novo.dk (Peter Kristensen)
To: Internet::nih-image@soils.umn.edu
Subject: Flat bed scanners

The NIH-IMAGE manual notes that the LaCie Silver scanner works well with the 
program. Does anyone have the adress & fax number of the company selling that ?

Other suggestions for flat-bed scanners working well with NIH IMAGE ?	

sincerely

Peter Kristensen
Pathology & Histochemistry
Pharmaceuticals Division
Novo Nordisk A/S
Denmark
<pekr@research.novo.dk>

From eric_s@BIOTEK.MCB.UCONN.EDU  Wed Oct  6 04:40:10 1993
Received: from BIOTEK (biotek.mcb.uconn.edu) by nx1.soils.umn.edu (5.65c)
	id AA07551; Wed, 6 Oct 1993 07:40:52 -0500
Return-Path: <eric_s@BIOTEK.MCB.UCONN.EDU>
Message-Id: <199310061240.AA07551@nx1.soils.umn.edu>
Date: Wed, 6 Oct 1993 08:40:10 -0400
From: eric_s@BIOTEK.MCB.UCONN.EDU
To: nih-image@soils.umn.edu
Subject: looking for Dr. V. A. Moss
X-Vms-To: SMTP%"nih-image@soils.umn.edu"

Sorry to take up air space for this. I couple of weeks ago Dr. Moss
expressed interest in a volume rendering program I have written. All my
messages to him have bounced back - address unknown. Dr Moss, if you
are still interested, I'd be happy to have you look at the program. Please
mail me directly, and hopefully I will be able to return mail to you. Thanks,
	Eric
From wayne@helix.nih.gov  Wed Oct  6 08:22:55 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA08224; Wed, 6 Oct 1993 08:24:39 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA03210; Wed, 6 Oct 93 08:43:18 -0400
Message-Id: <9310061243.AA03210@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Wed, 6 Oct 1993 08:22:55 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Flat bed scanners

>The NIH-IMAGE manual notes that the LaCie Silver scanner works well with the 
>program. Does anyone have the adress & fax number of the company selling that ?

La Cie, Ltd.
8700 SW Creekside Place
Beaverton, OR 97005
800-999-1179
503-520-9000
Fax: 503-520-9100


From rudolfo@hoh.mbl.edu  Wed Oct  6 06:24:48 1993
Received: from AQUA.WHOI.EDU by nx1.soils.umn.edu (5.65c)
	id AA08921; Wed, 6 Oct 1993 09:26:33 -0500
Return-Path: <rudolfo@hoh.mbl.edu>
Received: by aqua.whoi.edu (5.57/Ultrix3.0-C)
	id AA07209; Wed, 6 Oct 93 10:27:33 -0400
Received: from [128.128.172.47] by hoh.mbl.edu. (4.1/SMI-4.1)
	id AA03121; Wed, 6 Oct 93 10:24:49 EDT
Date: Wed, 6 Oct 93 10:24:48 EDT
Message-Id: <9310061424.AA03121@hoh.mbl.edu.>
To: nih-image@soils.umn.edu
From: rudolfo@hoh.mbl.edu (Rudolf Oldenbourg)
X-Sender: rudolfo@hoh.mbl.edu
Subject: Re: Ratio imaging

>I'm thinking of calling it DoOp
>(do operation). It will look something like
>
>    DoOp('Divide', pid1, pid2, pid3, scale, offset)
>
>where the first argument specifies the function to be performed and
>pid1,pid2 and pid3 are pic id  numbers. Pixel values resulting from the
>operation are multiplied by the scale and then the offset is added.
>
>--wayne

This will be a very useful macro command.  In our application of NIH-Image,
we need to do successive image arithmetic operations between slices of a
given stack, storing the result in a new slice.  We (i.e. Guang Mei) have
modified the source code of NIH-Image to do our specific calculations with
the speed of compiled image arithmetic.  With that experience, I'd like to
suggest three features for the above new macro command:

1) For the pid #, allow the use of slices in a stack.

2) Provide for storing the scaling factor and offset value as part of the
result image.
By way of explanation, the original result values from image arithmetic
operations are usually lost, after scaling for display purposes and because
of the restriction of 8 bit data in an image array.  By storing the scale
factor and offset value with the result image, however, one is able to
reproduce the original values.  This is often very useful for quantitative
image analysis.  The recalculated result values will have 8 bit precision
only; however, in most cases this is not a problem, since the intensity
data have only 8 bit pecision to begin with.  We store the scaling values
in the first two pixels of the result image, using an encoding scheme which
is useful in our particular application.  May be there is a better way of
storing those values permanently with the image.

3) May be you can allow for several successive arithmetic operations in one
command, bypassing the (time and memory consuming) need to store
intermidiate results.

>From the desk of

Rudolf Oldenbourg   oldenbourg@mbl.edu     Tel:(508)548-3705 ext 426
Program of Architectural Dynamics in Living Cells
Marine Biological Laboratory, Woods Hole, MA 02543-1031

From wayne@helix.nih.gov  Wed Oct  6 10:10:53 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA09501; Wed, 6 Oct 1993 10:12:37 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA03499; Wed, 6 Oct 93 10:31:16 -0400
Message-Id: <9310061431.AA03499@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Wed, 6 Oct 1993 10:10:53 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Restore selection & Plot bug?

>When making a profile plot using the Profile plot tool, then switching to a
>next image to do the same operation, using the Restore selection menu
>command (or cmd-4), I get inconsistent results. The selection is drawn
>where it should be, but the values are nonsense.

This bug is fixed in version 1.53b10, which is available by anonymous ftp
from zippy.nimh.nih.gov.

>When using a rectangular selection, I don't get this problem, and it is
>also much faster. Rectangular selections have a big disadvantage that the
>direction in which the plot is scanned depends on the relative width and
>hight. How can I choose between a vertical or a horizontal profile plot,
>independant of the aspect ratio of the selection?

You can force the Plot Profile command to do a horizontal plots by holding
the Option key down. It will only do a vertical plots, however,  when the
selection is taller than it is wide and the option key is not held down.

--wayne


From CHARLEST@macc.wisc.edu  Wed Oct  6 05:22:00 1993
Received: from vms2.macc.wisc.edu by nx1.soils.umn.edu (5.65c)
	id AA09661; Wed, 6 Oct 1993 10:21:57 -0500
Return-Path: <CHARLEST@macc.wisc.edu>
Received: from VMSmail by vms2.macc.wisc.edu; Wed, 06 Oct 93 10:22 CDT
Message-Id: <23100610223675@vms2.macc.wisc.edu>
Date: Wed, 06 Oct 93 10:22 CDT
From: Charles Thomas <CHARLEST@macc.wisc.edu>
Subject: Re: Question on missing results
To: nih-image@soils.umn.edu
X-Vms-To: IN%"nih-image@soils.umn.edu",CHARLEST

Lethality and Weapons Effectiveness Branch?
 
Sheesh.  I bet things get done when people see THAT letterhead. :)
 
And I thought we got good service from Pizza Pit when they heard the order was
for "Dr. _______".  :)
 
From CHARLEST@macc.wisc.edu  Wed Oct  6 05:31:00 1993
Received: from vms2.macc.wisc.edu by nx1.soils.umn.edu (5.65c)
	id AA09701; Wed, 6 Oct 1993 10:32:34 -0500
Return-Path: <CHARLEST@macc.wisc.edu>
Received: from VMSmail by vms2.macc.wisc.edu; Wed, 06 Oct 93 10:31 CDT
Message-Id: <23100610313481@vms2.macc.wisc.edu>
Date: Wed, 06 Oct 93 10:31 CDT
From: Charles Thomas <CHARLEST@macc.wisc.edu>
Subject: Re: Restore selection & Plot bug?
To: nih-image@soils.umn.edu
X-Vms-To: IN%"nih-image@soils.umn.edu",CHARLEST

Just an aside...  I had good luck exporting the plot values as a text file and
loading them into DeltaGraph.  From there, you can manipulate your curves and
quantify them at will.
 
 
From dickinson%g24mac1@relay.nswc.navy.mil  Wed Oct  6 07:46:40 1993
Received: from relay.nswc.navy.mil by nx1.soils.umn.edu (5.65c)
	id AA09893; Wed, 6 Oct 1993 10:45:45 -0500
Return-Path: <dickinson%g24mac1@relay.nswc.navy.mil>
Received: from [128.38.34.152] (ddickensmac.nswc.navy.mil) by relay.nswc.navy.mil (4.1/SMI-4.1)
	id AA25586; Wed, 6 Oct 93 11:46:40 EDT
Date: Wed, 6 Oct 93 11:46:40 EDT
Message-Id: <9310061546.AA25586@relay.nswc.navy.mil>
From: "David Dickinson"  <dickinson%g24mac1@relay.nswc.navy.mil>
Reply-To: "David Dickinson"  <dickinson%g24mac1@relay.nswc.navy.mil>
To: nih-image@soils.umn.edu
Subject: Re: Question on missing results

In message <9310052010.AA02344@zippy.nimh.nih.gov>  writes:
 
> >From page 82 of the manual (Program Limitations):
> 
> "The maximum number of characters that can be  displayed, printed, or
> copied to the clipboard is 32,700. There is no limit to the number of
> measurements that can be exported to a text file."
> 
> I have updated the description of the Show Results command in the manual to
> make this limitation clearer.
> 
> --wayne
> 
> 
When I click on Export I see a sub-menu "About Export Plug-ins ...". This tells 
me the plug-ins need to be a Plug-in folder. Where do I find the plug-in to 
export measurements to a tab-delimited text file compatible with Excel? I can't 
find info on this in V1.52 of the manual and none of the titles on the server at
NIH seem to match up.

Thanks for your help.


:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
    David L. Dickinson           dickinson@g24mac1.nswc.navy.mil

    Voice: (703) 663-8691 or DSN 249-8691         FAX: (703) 663-8268

    Lethality and Weapons Effectiveness Branch, G24
    Naval Surface Warfare Center, Dahlgren Division
    Dahlgren, VA  22448
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

From kartenh@sdsc.edu  Wed Oct  6 17:52:36 1993
Received: from Sdsc.Edu (sds.sdsc.edu) by nx1.soils.umn.edu (5.65c)
	id AA11635; Wed, 6 Oct 1993 12:51:43 -0500
Return-Path: <kartenh@sdsc.edu>
Message-Id: <199310061751.AA11635@nx1.soils.umn.edu>
Received: from [132.239.67.254] by Sdsc.Edu (sds.sdsc.edu STMG) via INTERNET;
          Wed, 6 Oct 93 17:52:36 GMT
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: kartenh@Sdsc.Edu
Subject: Re: Your last message...
Date:  Wed, 6 Oct 93 17:52:36 GMT

Re:
>I am putting in a few new changes to MacStereology (moving/zooming and s
>shrinking in dialog boxes) and will send you a new version as soon as tested
>(in a few days I hope).
> 
>Alignment of sections can be done manually in Align dialog of MacStereology,
>but it may be possible to do an automatc alignment based on the centre of
>gravity of objects on adjacent layers.
> 
>Regards
>Vic Moss

What is MacStereology? How does it interact with NIH-Image?
thnaks, Harvey Karten 

 Harvey J. Karten, M.D.
 Dept. of Neurosciences
 Univ.California San Diego
 La Jolla, CA 92093-0608
 EMail: Kartenh@sdsc.edu
 Phone: (619)-534-4938
 FAX: (619)-534-6602


From vokey@hg.uleth.ca  Wed Oct  6 06:07:48 1993
Received: from mr.uleth.ca by nx1.soils.umn.edu (5.65c)
	id AA11721; Wed, 6 Oct 1993 13:04:41 -0500
Return-Path: <vokey@hg.uleth.ca>
Received: by hg.uleth.ca (MX V3.3 VAX) id 13563; Wed, 06 Oct 1993 12:08:21 MDT
Date: Wed, 06 Oct 1993 12:07:48 MDT
From: vokey@hg.uleth.ca
To: nih-image@soils.umn.edu
Message-Id: <009739C9.DF9988E0.13563@hg.uleth.ca>
Subject: Dithering

It is said (in the manual) that Image "uses the Floyd-Stenberg error diffusion
algorithm" to dither images.  Could someone please provide an explanation of
this algorithm?  TIA

John R. Vokey <vokey@hg.uleth.ca>
From herro001@maroon.tc.umn.edu  Wed Oct  6 08:14:22 1993
Received: from maroon.tc.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA11950; Wed, 6 Oct 1993 13:13:18 -0500
Return-Path: <herro001@maroon.tc.umn.edu>
Message-Id: <199310061813.AA11950@nx1.soils.umn.edu>
Received: from rash.med.umn.edu by maroon.tc.umn.edu id SMTP-0012cb30a9c023125; Wed, 6 Oct 93 13:12:47 -0500
From: "Mike Herron" <herro001@maroon.tc.umn.edu>
Reply-To: "Mike Herron" <herro001@maroon.tc.umn.edu>
To: nih-image@soils.umn.edu
Subject: Re: Ratio imaging
Date: Wed, 6 Oct 93 13:14:22 -0500

I would like to second Rudolf's suggestions.  Operations on a stack and storing 
the scaling factor and offset value as part of the resulting image's header (?) 
would be a real improvement.



In message <9310061424.AA03121@hoh.mbl.edu.>  writes:
> >I'm thinking of calling it DoOp
> >(do operation). It will look something like
> >
> >    DoOp('Divide', pid1, pid2, pid3, scale, offset)
> >
> >where the first argument specifies the function to be performed and
> >pid1,pid2 and pid3 are pic id  numbers. Pixel values resulting from the
> >operation are multiplied by the scale and then the offset is added.
> >
> >--wayne
> 
> This will be a very useful macro command.  In our application of NIH-Image,
> we need to do successive image arithmetic operations between slices of a
> given stack, storing the result in a new slice.  We (i.e. Guang Mei) have
> modified the source code of NIH-Image to do our specific calculations with
> the speed of compiled image arithmetic.  With that experience, I'd like to
> suggest three features for the above new macro command:
> 
> 1) For the pid #, allow the use of slices in a stack.
> 
> 2) Provide for storing the scaling factor and offset value as part of the
> result image.
> By way of explanation, the original result values from image arithmetic
> operations are usually lost, after scaling for display purposes and because
> of the restriction of 8 bit data in an image array.  By storing the scale
> factor and offset value with the result image, however, one is able to
> reproduce the original values.  This is often very useful for quantitative
> image analysis.  The recalculated result values will have 8 bit precision
> only; however, in most cases this is not a problem, since the intensity
> data have only 8 bit pecision to begin with.  We store the scaling values
> in the first two pixels of the result image, using an encoding scheme which
> is useful in our particular application.  May be there is a better way of
> storing those values permanently with the image.
> 
> 3) May be you can allow for several successive arithmetic operations in one
> command, bypassing the (time and memory consuming) need to store
> intermidiate results.
> 
> >From the desk of
> 
> Rudolf Oldenbourg   oldenbourg@mbl.edu     Tel:(508)548-3705 ext 426
> Program of Architectural Dynamics in Living Cells
> Marine Biological Laboratory, Woods Hole, MA 02543-1031
> 
> 


 
   ______________________________________________
  / Mike Herron,  U of MN, Dept. of Dermatology /
 / herro001@maroon.tc.umn.edu                  /
/ 612-625-8935  Box 124 UMHC, Mpls MN 55455   /
______________________________________________

From wayne@helix.nih.gov  Wed Oct  6 13:24:17 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA12168; Wed, 6 Oct 1993 13:26:03 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA03881; Wed, 6 Oct 93 13:44:42 -0400
Message-Id: <9310061744.AA03881@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Wed, 6 Oct 1993 13:24:17 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Question on missing results

>When I click on Export I see a sub-menu "About Export Plug-ins ...". This
>tells 
>me the plug-ins need to be a Plug-in folder. Where do I find the plug-in to 
>export measurements to a tab-delimited text file compatible with Excel? I
>can't 
>find info on this in V1.52 of the manual and none of the titles on the server
>at
>NIH seem to match up.

NIH Image has two Export commands in the file menu, use the first one to
export measurements to a text file and the second to use Photoshop
compatible export plug-ins.

--wayne


From a337ard@diamond.sara.nl  Thu Oct  7 08:59:09 1993
Received: from vx.cis.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA20448; Thu, 7 Oct 1993 02:02:24 -0500
Return-Path: <a337ard@diamond.sara.nl>
Received: from HASARA5.BITNET (MAILGATE@HASARA5) by vx.cis.umn.edu (PMDF
 V4.2-13 #2574) id <01H3TBN468LCB7AMAA@vx.cis.umn.edu>; Thu,
 7 Oct 1993 02:03:47 CDT
Received: from diamond.sara.nl by SARA.NL for nih-image@soils.umn.edu; 7 Oct 93
 8:03 MET
Received: by diamond.sara.nl (5.61-AIX-1.2/1.0), id AA173479,
 (for nih-image@soils.umn.edu, from a337ard@diamond.sara.nl);
Date: Thu, 07 Oct 1993 07:59:09 +0100
From: a337ard@diamond.sara.nl (Ard Jonker)
Subject: Re:  Dithering
To: nih-image@soils.umn.edu
Message-Id: <9310070659.AA173479@diamond.sara.nl>
X-Envelope-To: nih-image@soils.umn.edu
Content-Transfer-Encoding: 7BIT

Without going into the detail of the floyd-Steinberg, it comes down to
reducing the number of colors (greylevels) by using the available grey
levels and by propagating the error that has been made to adjacent (right,
left) pixels. The most well known examples are the 'dotty' black and white
images on bw macs, that still 'look like' having shades. Once you have
seen it, you will recognize it. (so, try it on a picture).

ard (a337ard@diamond.sara.nl)
From D.A.Davies@bham.ac.uk  Thu Oct  7 10:38:39 1993
Received: from bham.ac.uk by nx1.soils.umn.edu (5.65c)
	id AA22057; Thu, 7 Oct 1993 04:41:07 -0500
Return-Path: <D.A.Davies@bham.ac.uk>
Received: from sun1.bham.ac.uk by bham.ac.uk with SMTP (PP) 
          id <03434-0@bham.ac.uk>; Thu, 7 Oct 1993 10:38:46 +0100
Received: from [147.188.64.23] (med138.bham.ac.uk) 
          by sun1.bham.ac.uk (5.0/SMI-SVR4) id AA02095;
          Thu, 7 Oct 93 10:39:43 BST
Message-Id: <9310070939.AA02095@sun1.bham.ac.uk>
X-Sender: daviesda@sun1.bham.ac.uk
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Thu, 7 Oct 1993 10:38:39 +0000
To: nih-image@soils.umn.edu
From: D.A.Davies@bham.ac.uk (David Davies)
Subject: Re: Flatbed Scanners and Image
Content-Length: 1046

In response to the request for flatbed scanners that work well with Image,
we use the MirrorScan 600 Plus, an excellent 24bit 600dpi scanner. This
scanner works well with Image via the supplied PhotoShop plug-in to grab
images directly into Image.

Incidentely, for those interested in grabbing frames from video (from a
microscope for example) we also grab images directly into Image using the
PhotoShop plug-in that came with our Radius VideoVision video grabber.
Implementing the PhotoShop plug-in extension to Image was one of the most
useful improvements to Image in our opinion. We use Image a lot in our
Department and just couldn't do our work without it!

David Davies                Tel No   - +44-(0)-21-414-6898
Physiology Department       Fax      - +44-(0)-21-414-6924
The Medical School          Janet    - D.A.Davies@UK.AC.BHAM
University of Birminghan    Internet - D.A.Davies@BHAM.AC.UK
Edgbaston, Birmingham       Talk     - david@med138.bham.ac.uk
B15 2TT                     URL      - http://med152.bham.ac.uk/davies.html


From wayne@helix.nih.gov  Thu Oct  7 08:30:17 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA25976; Thu, 7 Oct 1993 08:32:05 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA04757; Thu, 7 Oct 93 08:50:45 -0400
Message-Id: <9310071250.AA04757@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Thu, 7 Oct 1993 08:30:17 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: QuickImage24

>Does anyone use the Mass Micro QuickImage 24 frame capture board
>with Image? Latest ad in MacWorld is selling it for $99. It's
>supposed to support QuickTime. I am interested to know how well
>it might work on a IIcx and on a Centris 610.

I believe the QuickImage frame grabber is a full size NuBus card, if so, it
won't fit in the Centris 610 since it only accepts 7 inch cards.

--wayne


From ikami@liposun.lbl.gov  Thu Oct  7 03:01:42 1993
Received: from lbl.gov by nx1.soils.umn.edu (5.65c)
	id AA28415; Thu, 7 Oct 1993 12:06:33 -0500
Return-Path: <ikami@liposun.lbl.gov>
Received: from liposun.lbl.gov by lbl.gov (4.1/1.39)
	id AA07264; Thu, 7 Oct 93 10:14:15 PDT
Received: from [131.243.32.28] (b1-lipo5.lbl.gov) by liposun.lbl.gov (4.1/SMI-4.0)
	id AA12335; Thu, 7 Oct 93 10:01:43 PDT
Date: Thu, 7 Oct 93 10:01:42 PDT
Message-Id: <9310071701.AA12335@liposun.lbl.gov>
To: nih-image@soils.umn.edu
From: ikami@liposun.lbl.gov (Craig Ikami)
Subject: Re: first timer

>>We have just acquired a molecular dynamics densitometer. It produces 12 bit
>>tiff files. We have looked at image v1.44 and would like to know if future
>>versions of image will support 12 bit acquisition and display? 
>
>The current version of NIH Image (1.52) can import the 16-bit TIFF files
>created by Molecular Dynamics scanners. The image data is scaled to 8-bits,
>but the 16-bit to 8-bit scaling can be changed using the Rescale(aka Revert
>to Saved) command.
>
Thanks for the response ....


Does this mean it will read our 12 bit tiff files and convert to 8 bit? If
so can we ever have a LUT deeper than 256 ? 

From vokey@hg.uleth.ca  Thu Oct  7 07:23:33 1993
Received: from mr.uleth.ca by nx1.soils.umn.edu (5.65c)
	id AA29554; Thu, 7 Oct 1993 14:19:40 -0500
Return-Path: <vokey@hg.uleth.ca>
Received: by hg.uleth.ca (MX V3.3 VAX) id 17900; Thu, 07 Oct 1993 13:23:48 MDT
Date: Thu, 07 Oct 1993 13:23:33 MDT
From: vokey@hg.uleth.ca
To: nih-image@soils.umn.edu
Message-Id: <00973A9D.9ED8E4C0.17900@hg.uleth.ca>
Subject: Re:  Dithering

Thank you, Ard, for the introduction to the Floyd-Steinberg dithering
technique.  Does anyone have a summary (or psuedocode) of the error propogation
algorithm itself?  I am working on a system that has to move unpredictably
between grey-scale and B&W, and I want to automatically apply the dither
whenever a switch to B&W is detected (the grey-scale image will always be held
in an off-screen pixel-map, only its projection to the screen will be
adjusted).  TIA

John R. Vokey <vokey@hg.uleth.ca>
From vokey@hg.uleth.ca  Thu Oct  7 07:33:57 1993
Received: from mr.uleth.ca by nx1.soils.umn.edu (5.65c)
	id AA29681; Thu, 7 Oct 1993 14:29:45 -0500
Return-Path: <vokey@hg.uleth.ca>
Received: by hg.uleth.ca (MX V3.3 VAX) id 17951; Thu, 07 Oct 1993 13:33:59 MDT
Date: Thu, 07 Oct 1993 13:33:57 MDT
From: vokey@hg.uleth.ca
To: nih-image@soils.umn.edu
Message-Id: <00973A9F.12A62B00.17951@hg.uleth.ca>
Subject: FFT

Is there any way with either ImageFFT or ImageVDM to access directly or save as
text the actual results of the FFT?  As far as I can acertain, only the power
spectrum (in optical -- centred -- form) can be saved, and then only as a
(spatial) image.  Presumably, the complete FFT(x) = a + ib is stored in a
buffer internally and used to produce the observed power spectrum.  Any ideas?
TIA.


John R. Vokey <vokey@hg.uleth.ca>
From wayne@helix.nih.gov  Thu Oct  7 14:51:24 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA29949; Thu, 7 Oct 1993 14:53:10 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA05594; Thu, 7 Oct 93 15:11:53 -0400
Message-Id: <9310071911.AA05594@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Thu, 7 Oct 1993 14:51:24 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re:  Dithering

>Thank you, Ard, for the introduction to the Floyd-Steinberg dithering
>technique.  Does anyone have a summary (or psuedocode) of the error propogation
>algorithm itself?  I am working on a system that has to move unpredictably
>between grey-scale and B&W, and I want to automatically apply the dither
>whenever a switch to B&W is detected (the grey-scale image will always be held
>in an off-screen pixel-map, only its projection to the screen will be
>adjusted).  TIA

Why not look at the real code that NIH Image uses? It's part of the routine
"Filter" in the source file Functions.p. The algorithm is described in the
paper "An Adaptive Algorithm for Spatial Greyscale" by Robert Floyd and
Louis Steinberg, in Proceeding of the S.I.D, Vol.17/2, Second Quarter 1976.

--wayne


From PHILSON@macc.wisc.edu  Thu Oct  7 10:00:00 1993
Received: from vms2.macc.wisc.edu by nx1.soils.umn.edu (5.65c)
	id AA00121; Thu, 7 Oct 1993 15:00:17 -0500
Return-Path: <PHILSON@macc.wisc.edu>
Received: from VMSmail by vms2.macc.wisc.edu; Thu, 07 Oct 93 15:00 CDT
Message-Id: <23100715005034@vms2.macc.wisc.edu>
Date: Thu, 07 Oct 93 15:00 CDT
From: Pierre Hilson <PHILSON@macc.wisc.edu>
Subject: angles
To: NIH-IMAGE@soils.umn.edu
X-Vms-To: IN%"nih-image@nx1.soils.umn.edu",PHILSON

 
 
 
As a new user, I have basic questions.
 
I work with Image version 1.50b75.  I am measuring the orientation
of root growth.  Is there a way to measure angles directionally... by
that I mean from 0 to 360 degrees (or -180 to +180) along the whole
circle.  As it is set up, the program will give the same value if a
segment ends at a given angle with respect to the horizontal above
its starting point or below it.  Is it normal, can it be changed and
how?
 
Thank you for your help.
 
Pierre Hilson
Genetics
University of Wisconsin
EMail: philson@macc.wisc.edu
 
From vokey@hg.uleth.ca  Thu Oct  7 08:09:30 1993
Received: from mr.uleth.ca by nx1.soils.umn.edu (5.65c)
	id AA00217; Thu, 7 Oct 1993 15:05:38 -0500
Return-Path: <vokey@hg.uleth.ca>
Received: by hg.uleth.ca (MX V3.3 VAX) id 18107; Thu, 07 Oct 1993 14:09:47 MDT
Date: Thu, 07 Oct 1993 14:09:30 MDT
From: vokey@hg.uleth.ca
To: nih-image@soils.umn.edu
Message-Id: <00973AA4.0A1365C0.18107@hg.uleth.ca>
Subject: Re:  Dithering

Wayne said:
-->
Why not look at the real code that NIH Image uses? It's part of the routine
"Filter" in the source file Functions.p. The algorithm is described in the
paper "An Adaptive Algorithm for Spatial Greyscale" by Robert Floyd and
Louis Steinberg, in Proceeding of the S.I.D, Vol.17/2, Second Quarter 1976.
<--

Now, why didn't I think of that?  I completely forgot that the source code was
available!  Thanks Wayne, for this advice AND Image.

John R. Vokey <vokey@hg.uleth.ca>
From wayne@helix.nih.gov  Thu Oct  7 15:59:19 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA00649; Thu, 7 Oct 1993 16:01:06 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA05709; Thu, 7 Oct 93 16:19:49 -0400
Message-Id: <9310072019.AA05709@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Thu, 7 Oct 1993 15:59:19 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: angles

>I work with Image version 1.50b75.  I am measuring the orientation
>of root growth.  Is there a way to measure angles directionally... by
>that I mean from 0 to 360 degrees (or -180 to +180) along the whole
>circle.  As it is set up, the program will give the same value if a
>segment ends at a given angle with respect to the horizontal above
>its starting point or below it.  Is it normal, can it be changed and
>how?

How would Image know what direction a particle is pointing? A particle
pointing straight up and a particle pointing straight down will both have a
measured angles of 90 degrees since Image has no way of knowing that the
two particles point in opposite directions. There is a test image in the
images directory on zippy.nimh.nih.gov called angles.hqx that is helpful in
understanding how Image measure angles. 

--wayne


From ptr@GRECO2.POLYTECHNIQUE.FR  Fri Oct  8 12:05:51 1993
Received: from chenas.inria.fr by nx1.soils.umn.edu (5.65c)
	id AA04436; Fri, 8 Oct 1993 05:08:33 -0500
Return-Path: <ptr@GRECO2.POLYTECHNIQUE.FR>
Received: from polytechnique.polytechnique.fr by chenas.inria.fr (5.65c8d/92.02.29)
	via Fnet-EUnet id AA20717; Fri, 8 Oct 1993 11:09:28 +0100 (MET)
Received: by polytechnique.polytechnique.fr (5.65c/SMI-4.1.3)
	id AA06803; Fri, 8 Oct 1993 11:17:18 +0100
Received: from [129.104.27.245] by greco2.noname (4.1/SMI-4.1)
	id AA03791; Fri, 8 Oct 93 11:05:51 +0100
Date: Fri, 8 Oct 93 11:05:51 +0100
Message-Id: <9310081005.AA03791@greco2.noname>
To: nih-image@soils.umn.edu
From: ptr@GRECO2.POLYTECHNIQUE.FR (Peter Goedtkindt)
Subject: Remove density calibration command?

Hallo, I think the subject explains the question.
The only way I found to remove the calibration was to copy the whole image,
close all images (or select an uncalibrated image) open a new image and
paste.
I haven't found any macro command that allows me to uncalibrate more
directly, sorry if I missed it.

ptr.
Peter Goedtkindt
Universite Paris-Sud 
Laboratoire de Spectroscopie Atomique et Ionique
X-ray Laser group
bat350 
Centre D'Orsay F-91405 Orsay Cedex. France 
Fax.:++33.1.69.41.94.60 - Tel 69.41.77.10
------
And
------
Ecole Polytechnique, Laboratoire d'Utilisation de Lasers Intenses
tel. 69.33.48.95
-----------------------------------------------------------------

From esb107@cent1.lancs.ac.uk  Fri Oct  8 12:53:01 1993
Received: from cent1.lancs.ac.uk by nx1.soils.umn.edu (5.65c)
	id AA04705; Fri, 8 Oct 1993 05:52:06 -0500
Return-Path: <esb107@cent1.lancs.ac.uk>
From: "Mr R Herd" <esb107@cent1.lancs.ac.uk>
Message-Id: <14293.9310081053@cent1.lancs.ac.uk>
Received: by cent1.lancs.ac.uk; Fri, 8 Oct 93 11:53:11 +0100
Subject: line plots->data
To: nih-image@soils.umn.edu
Date: Fri, 8 Oct 1993 11:53:01 +0100 (BST)
In-Reply-To: <15085.9310080930@cent1.lancs.ac.uk> from "nih-image@soils.umn.edu" at Oct 8, 93 04:30:35 am
X-Mailer: ELM [version 2.4 PL22]
Mime-Version: 1.0
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Length: 493       

Hi,
I've been trying to digitise topographic maps and recover coordinate data
using the "line plots->data" macros.  As it is they order the data by X or by Y.
Consequently the data cannot be used to replot, for example a contour line.
Is there any easy way to modify the macro so it measures X-Y points along the
line, rather than along the X or Y direction?

Many thanks

Richard Herd

Volcanology Group
Dept. of Environmental Sciences
Lancaster University
Bailrigg
Lancaster
LA1 4YQ
England
From @cc1.kuleuven.ac.be:jvanheld@dbmdec5.ulb.ac.be  Fri Oct  8 13:07:43 1993
Received: from cc1.kuleuven.ac.be by nx1.soils.umn.edu (5.65c)
	id AA04802; Fri, 8 Oct 1993 06:07:49 -0500
Return-Path: <@cc1.kuleuven.ac.be:jvanheld@dbmdec5.ulb.ac.be>
Received: from rc1.vub.ac.be by cc1.kuleuven.ac.be (IBM VM SMTP V2R2) with TCP;
   Fri, 08 Oct 93 12:07:56 +0100
Received: from dec5.ulb.ac.be (dbmdec5) by rc1.vub.ac.be (4.1/RC1-930922)
	id AA22887; Fri, 8 Oct 93 12:09:03 +0100
Received: by dec5.ulb.ac.be (5.65/ULB.920908)
	id AA00433; Fri, 8 Oct 1993 12:07:44 +0100
From: jvanheld@dbm.ulb.ac.be (Jacques VAN HELDEN)
Message-Id: <9310081107.AA00433@dec5.ulb.ac.be>
Subject: Re: grain size measurements
To: nih-image@soils.umn.edu
Date: Fri, 8 Oct 1993 12:07:43 +0100 (WET DST)
Cc: jvanheld@dbm.ulb.ac.be (Jacques VAN HELDEN)
In-Reply-To: <9310041515.AA00410@arc1.mrd.bldrdoc.gov> from "Bob Keller" at Oct 4, 93 10:20:58 am
X-Mailer: ELM [version 2.4 PL22]
Content-Type: text
Content-Length: 1686      

> Thanks.  We've tried your Crest Pathway routine.  Actually, it's not exactly 
> what we need, since Crest measures the size of a single grain, or cell, or 
> whatever you're measuring.  (I've also had trouble with it when my binary 
> images did not have nice smooth boundaries.  The line would keep going well 
> beyond the boundary near where I started and often circle back onto itself 
> within a very small area within another boundary itself.  I did vary the size 
> of the "detected" region as well, with no luck.  Is it possible to define a 
> threshold regime which would tell the line when to change it's course?)  I'm 
> going to write a macro to do the grain size measurement myself, using the line 
> intercept method which is standard in metallography.
> 
> Bob Keller
> NIST Div. 853
> Boulder, CO
> keller@micros.mrd.bldrdoc.gov

In order to avoid small back circling, you could try to increase the 
averaging distance. However this will reduce the resolution (the crest will 
not very well follow strong curves). 
Another parameter to fiddle around with is the maximal angle: if you chose 
1, the crest will rotate of max 45 degrees at each step.

You are not the first user to suggest a threshold in this routine.It seems a 
useful update, but I am not very sure about the best way to do it. What would 
you precisely mean by "threshold regime" ? Would you prefer a threshold on 
the absolute grey value or for the difference between neighbour points (one 
could choose to stop when the crest abruptly steps down) ?

You could maybe contact Sven-Erik Tiberg (set@eru.mt.luth.se), who is 
adaptating a threshold to the routine.

Jacques van Helden
jvanheld@ulb.ac.be
From wayne@helix.nih.gov  Fri Oct  8 08:16:26 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA06932; Fri, 8 Oct 1993 08:18:14 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA06354; Fri, 8 Oct 93 08:37:00 -0400
Message-Id: <9310081237.AA06354@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Fri, 8 Oct 1993 08:16:26 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Remove density calibration command?

>Hallo, I think the subject explains the question.
>The only way I found to remove the calibration was to copy the whole image,
>close all images (or select an uncalibrated image) open a new image and
>paste.
>I haven't found any macro command that allows me to uncalibrate more
>directly, sorry if I missed it.

Check "Remove Calibration" in the Calibrate dialog box and click OK.

--wayne


From wayne@helix.nih.gov  Fri Oct  8 08:30:32 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA07088; Fri, 8 Oct 1993 08:32:21 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA06378; Fri, 8 Oct 93 08:51:06 -0400
Message-Id: <9310081251.AA06378@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Fri, 8 Oct 1993 08:30:32 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: line plots->data

>Hi,
>I've been trying to digitise topographic maps and recover coordinate data
>using the "line plots->data" macros.  As it is they order the data by X or by
>Y.
>Consequently the data cannot be used to replot, for example a contour line.
>Is there any easy way to modify the macro so it measures X-Y points along the
>line, rather than along the X or Y direction?

One way to do this would be to use the wand tool to trace the contour line,
the Measure command to record the coordinates, and then Export the
coordinates to a text file. You can use a graphing program such as
KaleidaGraph to replot the data.

--wayne


From smithj@acad.winthrop.edu  Fri Oct  8 07:56:17 1993
Received: from acad ([192.203.180.3]) by nx1.soils.umn.edu (5.65c)
	id AA08091; Fri, 8 Oct 1993 11:01:14 -0500
Return-Path: <smithj@acad.winthrop.edu>
Message-Id: <199310081601.AA08091@nx1.soils.umn.edu>
Date: Fri, 8 Oct 1993 11:56:17 -0400
From: smithj@acad.winthrop.edu
To: nih-image@soils.umn.edu
Subject: Re: QuickImage24
X-Vms-To: SMTP%"nih-image@soils.umn.edu"

Yes.  I just bought one, and have it in a IIcx w/ RS-170 monochrome
camera.  I can't say about quick-time support, but the two defects I've
seen thus far are that it only assigns about 24 (29?) grey levels (a rather
extreme version of Wayne's comment "favors odd pixel values"); though the 
histogram is otherwise o.k. and that the plug-in doesn't work with Image
(Image reports that there is insufficient video memory).  I'm leaving for the 
coast with my invertebrate class in 2 hours, so more on this Tuesday. It is a full-size Nu-bus card, by the way.
>Does anyone use the Mass Micro QuickImage 24 frame capture board               
>with Image? Latest ad in MacWorld is selling it for $99. It's                  
>supposed to support QuickTime. I am interested to know how well                
>it might work on a IIcx and on a Centris 610.      
                                                     
I believe the QuickImage frame grabber is a full size NuBus card, if so, it
won't fit in the Centris 610 since it only accepts 7 inch cards.

--JSIII
From gmei@hoh.mbl.edu  Fri Oct  8 08:08:00 1993
Received: from AQUA.WHOI.EDU by nx1.soils.umn.edu (5.65c)
	id AA08183; Fri, 8 Oct 1993 11:10:03 -0500
Return-Path: <gmei@hoh.mbl.edu>
Received: by aqua.whoi.edu (5.57/Ultrix3.0-C)
	id AA25567; Fri, 8 Oct 93 12:10:50 -0400
Received: from [128.128.172.219] (SMAC19.MBL.EDU) by hoh.mbl.edu. (4.1/SMI-4.1)
	id AA04934; Fri, 8 Oct 93 12:08:02 EDT
Date: Fri, 8 Oct 93 12:08:00 EDT
Message-Id: <9310081608.AA04934@hoh.mbl.edu.>
To: nih-image@soils.umn.edu
From: gmei@hoh.mbl.edu (Guang Mei)
Subject: Too many constants in enumerated type

Hi, 

I have a question about "constants in enumerated type". When I tried to add
something like "Myadd1C, Myadd2C, ... MyaddnC" (n is an integer) to 

CommandType = (InvertLUTC, UserCodeC, .... PidNumC, SortPaletteC, Myadd1C,
Myadd2C, ... MyaddnC)

in Globals.p (NIH Image 1.52), I always got compile error "Too many
constants in enumerated type" when n is larger than some certain integer.
Is there a limit of number of constants (identifiers?) in this parenthesis?
I am using THINK Pascal 4.0.2.

Thanks for the help. 
 
-------------
Guang Mei   gmei@hoh.mbl.edu     Tel:(508)548-3705 ext 374
Program of Architectural Dynamics in Living Cells
Marine Biological Laboratory, Woods Hole, MA 02543-1031

From wayne@helix.nih.gov  Fri Oct  8 15:36:34 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA01558; Fri, 8 Oct 1993 15:37:37 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA07231; Fri, 8 Oct 93 15:57:09 -0400
Message-Id: <9310081957.AA07231@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Fri, 8 Oct 1993 15:36:34 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Too many constants in enumerated type

>Hi, 
>
>I have a question about "constants in enumerated type". When I tried to add
>something like "Myadd1C, Myadd2C, ... MyaddnC" (n is an integer) to 
>
>CommandType = (InvertLUTC, UserCodeC, .... PidNumC, SortPaletteC, Myadd1C,
>Myadd2C, ... MyaddnC)
>
>in Globals.p (NIH Image 1.52), I always got compile error "Too many
>constants in enumerated type" when n is larger than some certain integer.
>Is there a limit of number of constants (identifiers?) in this parenthesis?
>I am using THINK Pascal 4.0.2.

There seems to be a limit of 256 or so constants in enumerated types. I ran
into this problem when I tried to add a new command to the macro language
today. The short term work-around I used was to recycle some obsolete
commands. The long range solution will be to break CommandType into two
parts: commands and functions.There are 10 obsolete commands starting at
symbol table entry 165(SetArea, SetMean, etc.) and 0ne(SetMinMax) at 185.

--wayne


From glenmac@u.washington.edu  Fri Oct  8 15:01:41 1993
Received: from carson.u.washington.edu by nx1.soils.umn.edu (5.65c)
	id AA05061; Sat, 9 Oct 1993 00:14:14 -0500
Return-Path: <glenmac@u.washington.edu>
Received: by carson.u.washington.edu
	(5.65/UW-NDC Revision: 2.29 ) id AA05061; Fri, 8 Oct 93 22:15:59 -0700
X-Sender: glenmac@carson.u.washington.edu
Date: Fri, 8 Oct 1993 22:01:41 -0700 (PDT)
From: Glen Macdonald <glenmac@u.washington.edu>
Subject: Re: Saving results in Excel file
To: nih-image@soils.umn.edu
Cc: Multiple recipients of list <nih-image@soils.umn.edu>
In-Reply-To: <9310061744.AA03881@zippy.nimh.nih.gov>
Message-Id: <Pine.3.05z.9310082239.A1206-a100000@carson.u.washington.edu>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=us-ascii

The results are now being saved as tab delimited text files.  Would it be
posstible to add the ability to save them as Excel text files, as in the
pas, as an option?  It doesn't bother me, but our lab's many intermittant
users of Image get confused having to open their files through Excel
rather than double clicking on the file itself. 

While I'm asking, how about more user labelled arrays (the manual doen't
mention rMinor and rMajor labels anymore, although they still work), or
the ability to rearrange the order of the arrays in the Measurements so
that data can be better grouped and named for custom applications.  
Thanks much.
Glen MacDonald
Hearing Development Laboratories
University of Washington RL-30
Seattle, WA  98195


From glenmac@u.washington.edu  Fri Oct  8 15:22:19 1993
Received: from carson.u.washington.edu by nx1.soils.umn.edu (5.65c)
	id AA05205; Sat, 9 Oct 1993 00:30:58 -0500
Return-Path: <glenmac@u.washington.edu>
Received: by carson.u.washington.edu
	(5.65/UW-NDC Revision: 2.29 ) id AA06488; Fri, 8 Oct 93 22:32:42 -0700
X-Sender: glenmac@carson.u.washington.edu
Date: Fri, 8 Oct 1993 22:22:19 -0700 (PDT)
From: Glen Macdonald <glenmac@u.washington.edu>
Subject: Re: angles
To: nih-image@soils.umn.edu
Cc: Multiple recipients of list <nih-image@soils.umn.edu>
In-Reply-To: <23100715005034@vms2.macc.wisc.edu>
Message-Id: <Pine.3.05z.9310082216.A1206-b100000@carson.u.washington.edu>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=us-ascii

One way is to write a macro that compares x1,y1 to x2,y2 in order to
determine which quadrant your angle is in.  this inequality check then
determines whether your angles are positive or negative.  I will send you
a macro that does this.  I was measuring the angle of
auditory hair cell stereocilia bundles, which are random in newly
differenctiated cells and then rotate during matureation to a mature
position angle.  This  needed angles 0-180 positive and negative.  

Glen MacDonald
Hearing Development Laboratories
University of Washington RL-30
Seattle, WA  98195

On Thu, 7 Oct 1993, Pierre Hilson wrote:

>  
>  
>  
> As a new user, I have basic questions.
>  
> I work with Image version 1.50b75.  I am measuring the orientation
> of root growth.  Is there a way to measure angles directionally... by
> that I mean from 0 to 360 degrees (or -180 to +180) along the whole
> circle.  As it is set up, the program will give the same value if a
> segment ends at a given angle with respect to the horizontal above
> its starting point or below it.  Is it normal, can it be changed and
> how?
>  
> Thank you for your help.
>  
> Pierre Hilson
> Genetics
> University of Wisconsin
> EMail: philson@macc.wisc.edu
>  



From mt1ntg@fencer.cis.dsto.gov.au  Mon Oct 11 19:46:28 1993
Received: from fencer.cis.dsto.gov.au by nx1.soils.umn.edu (5.65c)
	id AA19279; Sun, 10 Oct 1993 18:44:49 -0500
Return-Path: <mt1ntg@fencer.cis.dsto.gov.au>
Message-Id: <199310102344.AA19279@nx1.soils.umn.edu>
Received: from [160.64.14.216] by fencer.cis.dsto.gov.au with SMTP; 
          Mon, 11 Oct 1993 9:57:19 +1000 (EST)
Date: Mon, 11 Oct 1993 09:46:28 +1000
To: nih-image@soils.umn.edu
From: NoelGoldsmith<mt1ntg@fencer.cis.dsto.gov.au> (Noel Goldsmith)
Subject: Re: Too many constants in enumerated type

>Hi, 
>
>I have a question about "constants in enumerated type". When I tried to add
>something like "Myadd1C, Myadd2C, ... MyaddnC" (n is an integer) to 
>
>CommandType = (InvertLUTC, UserCodeC, .... PidNumC, SortPaletteC, Myadd1C,
>Myadd2C, ... MyaddnC)
>
>in Globals.p (NIH Image 1.52), I always got compile error "Too many
>constants in enumerated type" when n is larger than some certain integer.
>Is there a limit of number of constants (identifiers?) in this parenthesis?
>I am using THINK Pascal 4.0.2.
>
>Thanks for the help. 
> 
>-------------
>Guang Mei   gmei@hoh.mbl.edu     Tel:(508)548-3705 ext 374
>Program of Architectural Dynamics in Living Cells
>Marine Biological Laboratory, Woods Hole, MA 02543-1031

Guang,
Think Pascal has a limit of 256 constants for each enumerated type. This
problem has hit me too.
When you have a program like NIH-Image which is added to by many, such
things are bound to occur. Who would have thought that 256 commands in the
macro interpreter would not have been enough? I see Wayne has suggested the
use of some no-longer used commands.A list of macro commands could be set
up,  but if you look a the source code, it is really the list you need.
What would be nice would be a list of ACTIVE macro-commands for each new
version of NIH-Image.
I understood that the use of the UMX extensions somehow would overcome this
problem, I think the use of this facility requires that your code all lives
in the user unit. I am about to try using the latest version for my code
additions, and will report to the list, (this may take a few weeks as I
have a full plate).

regards
Noel.
Noel T Goldsmith
DSTO
Aeronautical Research Laboratory
506 Lorimer Street
Port Melbourne
Vic 3207
Australia

From kehrer@informatik.uni-ulm.de  Mon Oct 11 11:57:39 1993
Received: from julia.informatik.uni-ulm.de by nx1.soils.umn.edu (5.65c)
	id AA21977; Mon, 11 Oct 1993 04:56:04 -0500
Return-Path: <kehrer@informatik.uni-ulm.de>
Received: from fonzo (kehrer.informatik.uni-ulm.de) by julia.informatik.uni-ulm.de (4.1/UniUlm-info-1.1r)
	id AA03113; Mon, 11 Oct 93 10:57:40 +0100
Date: Mon, 11 Oct 93 10:57:39 +0100
Message-Id: <9310110957.AA03113@julia.informatik.uni-ulm.de>
From: Juergen Kehrer <kehrer@informatik.uni-ulm.de>
To: nih-image@soils.umn.edu
Subject: Raleigh equalisazion?

Hi,
does anybody know something about the "Raleigh equalization". It+s something 
like the "histogram equalization" use in Nih-image, but I need more 
information about the differences and the usage of this equalization.

Thanks for the help.

===============================================================
Juergen Kehrer
University of Ulm/Germany
Dept of Distributed Systems
Internet: kehrer@informatik.uni-ulm.de
===============================================================

From csebeny@goodyear.com  Mon Oct 11 11:05:32 1993
Received: from goodyear.com (goodyear.goodyear.com) by nx1.soils.umn.edu (5.65c)
	id AA27404; Mon, 11 Oct 1993 15:02:42 -0500
Return-Path: <csebeny@goodyear.com>
Received: from rdsrv2 (rdsrv2.goodyear.com) by goodyear.com (4.1/SMI-4.1)
	id AA14583; Mon, 11 Oct 93 16:04:27 EDT
Received: from rds012 by rdsrv2 (4.1/SMI-4.1)
	id AA10000; Mon, 11 Oct 93 16:04:49 EDT
Received: from rds323 ([163.243.12.66]) by rds012 (4.1/SMI-4.1)
	id AA24258; Mon, 11 Oct 93 16:04:08 EDT
X-Mailer: InterCon TCP/Connect II 1.1
Message-Id: <9310111605.AA32995@rds323>
Date: Mon, 11 Oct 1993 16:05:32 -0500
From: Carl Sebeny <csebeny@goodyear.com>
To: nih-image@soils.umn.edu
Cc: csebeny@goodyear.com
Subject: Macro for Particle Centroid & Moment of Inertia


Does anyone have a macro to calulate particle centroid coordinates
and moment of inertia of particles about their centroid?

-----------------------------------------------------------
Joel Lazeration               rdealer1@goodyear.com
Goodyear Tire 


From mmoberg%smhi.dnet.smhi.se@lurch.smhi.se  Tue Oct 12 08:42:23 1993
Received: from palantir.p.tvt.se by nx1.soils.umn.edu (5.65c)
	id AA00866; Tue, 12 Oct 1993 01:40:42 -0500
Return-Path: <mmoberg%smhi.dnet.smhi.se@lurch.smhi.se>
Received: from gatekeeper.smhi.se by palantir.p.tvt.se with smtp
	(Smail3.1.28.1 #2) id m0omdUV-000AD9C; Tue, 12 Oct 93 07:45 WET
Received: by gatekeeper.smhi.se (5.65/DEC-Ultrix/4.3)
	id AA01022; Tue, 12 Oct 1993 07:42:53 +0100
Received: by lurch.smhi.se (5.65/DEC-Ultrix/4.3)
	id AA17554; Tue, 12 Oct 1993 07:42:24 +0100
Date: Tue, 12 Oct 1993 07:42:23 +0100
Message-Id: <9310120642.AA17554@lurch.smhi.se>
From: mmoberg%smhi.dnet.smhi.se@lurch.smhi.se (mmoberg@smhi.se)
To: "nih-image@soils.umn.edu"%LURCH.dnet.smhi.se@lurch.smhi.se
Cc: mmoberg@lurch.smhi.se
Subject: Beginner's LUT-question

Could someone give me a hint on how to create a pseudo-color LUT for NIH-Image 
given that a specified DN will have a specified color in R, G and B.
Thanks!
/mmoberg@smhi.se
From wayne@helix.nih.gov  Tue Oct 12 09:01:46 1993
Received: from zippy.nimh.nih.gov ([128.231.98.32]) by nx1.soils.umn.edu (5.65c)
	id AA04401; Tue, 12 Oct 1993 09:04:53 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA10238; Tue, 12 Oct 93 09:22:41 -0400
Message-Id: <9310121322.AA10238@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Date: Tue, 12 Oct 1993 09:01:46 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Beginner's LUT-question

>Could someone give me a hint on how to create a pseudo-color LUT=
 for NIH-Image=20
>given that a specified DN will have a specified color in R, G and=
 B.

One way to do this is to write a macro that assigns RGB colors to=
 specified
gray values. Here is an example macro that allows you to specify=
 a gray
value and the RGB color you want that value to be displayed in. Not=
 that
this macro modifies only one of the 256 LUT entries. Also note that=
 LUT
entries 0 and 256 can not be modified. They are always mapped to=
 white and
black respectively.=20

To run this macro, Copy it to the Clipboard, Open a new text window=
 in
Image, Paste, Load Macros, and then select 'Change One LUT Entry=8A'=
 from the
Special menu.

--wayne

macro 'Change One LUT Entry=8A';
var
  dn:integer;
begin
  dn:=3DGetNumber('Gray Value(1-254):',128);
  RedLut[dn]:=3DGetNumber('Red(0-255):',255);
  GreenLut[dn]:=3DGetNumber('Green(0-255):',0);
  BlueLut[dn]:=3DGetNumber('Blue(0-255):',0);
  UpdateLUT;
end;


From ptr@GRECO2.POLYTECHNIQUE.FR  Tue Oct 12 17:57:11 1993
Received: from chenas.inria.fr by nx1.soils.umn.edu (5.65c)
	id AA05105; Tue, 12 Oct 1993 10:59:39 -0500
Return-Path: <ptr@GRECO2.POLYTECHNIQUE.FR>
Received: from polytechnique.polytechnique.fr by chenas.inria.fr (5.65c8d/92.02.29)
	via Fnet-EUnet id AA20380; Tue, 12 Oct 1993 17:00:53 +0100 (MET)
Received: by polytechnique.polytechnique.fr (5.65c/SMI-4.1.3)
	id AA07074; Tue, 12 Oct 1993 17:08:45 +0100
Received: from [129.104.27.245] by greco2.noname (4.1/SMI-4.1)
	id AA05665; Tue, 12 Oct 93 16:57:12 +0100
Date: Tue, 12 Oct 93 16:57:11 +0100
Message-Id: <9310121557.AA05665@greco2.noname>
To: nih-image@soils.umn.edu
From: ptr@GRECO2.POLYTECHNIQUE.FR (Peter Goedtkindt)
Subject: Re: Remove density calibration command?

>>Hallo, I think the subject explains the question.
>>The only way I found to remove the calibration was to copy the whole image,
>>close all images (or select an uncalibrated image) open a new image and
>>paste.
>>I haven't found any macro command that allows me to uncalibrate more
>>directly, sorry if I missed it.
>
>Check "Remove Calibration" in the Calibrate dialog box and click OK.
>
>--wayne

Yes, I know how to do this manually, but how to do this in a macro call?

peter

From wayne@helix.nih.gov  Tue Oct 12 12:06:07 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA05734; Tue, 12 Oct 1993 12:07:18 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA10752; Tue, 12 Oct 93 12:27:03 -0400
Message-Id: <9310121627.AA10752@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 12 Oct 1993 12:06:07 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Saving results in Excel file

>The results are now being saved as tab delimited text files.  Would it be
>posstible to add the ability to save them as Excel text files, as in the
>pas, as an option?  It doesn't bother me, but our lab's many intermittant
>users of Image get confused having to open their files through Excel
>rather than double clicking on the file itself. 

The latest 1.53 beta on zippy.nimh.nih.gov allows you to specify (in
Preferences) the four character creator code Image uses for exported text
files. This code determines which application is launched when you
double-click on an exported text file (e.g., measurements, profile plot
data, XY coordinates). Use 'Imag' for Image, 'XCEL' for Excel and 'QKPT'
for KaleidaGraph.

>While I'm asking, how about more user labelled arrays (the manual doen't
>mention rMinor and rMajor labels anymore, although they still work), or
>the ability to rearrange the order of the arrays in the Measurements so
>that data can be better grouped and named for custom applications.

I am considering ways to allow more results data types, including more user
arrays.

--wayne  



From wayne@helix.nih.gov  Tue Oct 12 12:10:37 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA05758; Tue, 12 Oct 1993 12:11:47 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA10764; Tue, 12 Oct 93 12:31:33 -0400
Message-Id: <9310121631.AA10764@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 12 Oct 1993 12:10:37 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Remove density calibration command?

>>>Hallo, I think the subject explains the question.
>>>The only way I found to remove the calibration was to copy the whole image,
>>>close all images (or select an uncalibrated image) open a new image and
>>>paste.
>>>I haven't found any macro command that allows me to uncalibrate more
>>>directly, sorry if I missed it.
>>
>>Check "Remove Calibration" in the Calibrate dialog box and click OK.
>>
>>--wayne
>
>Yes, I know how to do this manually, but how to do this in a macro call?
>

Sorry, I didn't read you original message very carefully. The only other
way I know of to disable density calibration from within a macro is to open
an uncalibrated image and use the PropagateDensity maco command.

--wayne


From huff@MCCLB0.MED.NYU.EDU  Tue Oct 12 09:59:45 1993
Received: from mcclb0.med.nyu.edu by nx1.soils.umn.edu (5.65c)
	id AA06705; Tue, 12 Oct 1993 13:57:12 -0500
Return-Path: <huff@MCCLB0.MED.NYU.EDU>
Received: from DialupEudora (ANNEX1.NET.NYU.EDU) by MCCLB0.MED.NYU.EDU (PMDF
 V4.2-14 #2884) id <01H4126HTPSW001375@MCCLB0.MED.NYU.EDU>; Tue,
 12 Oct 1993 14:58:41 EDT
Date: Tue, 12 Oct 1993 14:59:45 -0500
From: huff@MCCLB0.MED.NYU.EDU (Edward J. Huff)
Subject: RE: Too many constants in enumerated type
To: nih-image@soils.umn.edu
Message-Id: <01H4126IOIZM001375@MCCLB0.MED.NYU.EDU>
X-Envelope-To: nih-image@soils.umn.edu
Content-Transfer-Encoding: 7BIT

Noel T Goldsmith writes
>I understood that the use of the UMX extensions somehow would overcome this
>problem, I think the use of this facility requires that your code all lives
>in the user unit. I am about to try using the latest version for my code
>additions, and will report to the list, (this may take a few weeks as I
>have a full plate).

The UMX facility requires that each pascal programmer create his own new .p
file where the new macro commands go.  This permits integration of code
from a number of people with minimal disruption.  The procedure is easy and
clearly described in UMacroDef.p in the UMX source code.  UMSample.p is a
sample user macro module which you duplicate and modify.

The reason the "too many constants" problem is solved by UMX is because a
new token type was created for user macro tokens, and a new enumerated
type.  This allows for up to 256 user macro commands or functions.
--
Edward J. Huff   huff@mcclb0.med.nyu.edu   (212)998-8465
Keck Laboratory for Biomolecular Imaging
NYU Chemistry Department, 31 Washington Place, New York NY 10003

From sarmienu@rnisd0.DNET.roche.com  Wed Oct 13 03:29:33 1993
Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c)
	id AA12348; Wed, 13 Oct 1993 06:27:57 -0500
Return-Path: <sarmienu@rnisd0.DNET.roche.com>
Received: by gatekeeper.roche.com (5.65/fma-120691);
	id AA15905; Wed, 13 Oct 93 07:29:34 -0400
Received: by mailgate.roche.com (5.65/fma-120691);
	id AA17847; Wed, 13 Oct 93 07:23:14 -0400
From: sarmienu@rnisd0.DNET.roche.com
Message-Id: <9310131123.AA17847@mailgate.roche.com>
Received: from rnisd0.enet; by inet.enet; Wed, 13 Oct 93 07:29:33 EDT
Date: Wed, 13 Oct 93 07:29:33 EDT
To: nih-image@soils.umn.edu
Apparently-To: nih-image@soils.umn.edu
Subject: NIH-Image References

Here is an update in the list of references which quote image. I guess I am now
committed to update the list periodically. Please continue to send me new
references, as they become available, to my address (see below),. If any of you
notice an error, please let me know. 

Thank you to all contributors.

Juan I. Sarmiento
Department of Toxicology and Pathology
Hoffmann-La Roche, INC.
340 Kingsland street
Nutley, NJ 07110
(201) 235 3907
Sarmienu@RNISD0.DNET.ROCHE.COM

P.S. Wayne, thanks for the address for Thomas M. Marschner.


---------------------------------------------------------------------------
              References for NIH-Image


1. Bouabid, R., E.A. Nater, and P. Barak. 1992. 
Measurement of particle and pore size distribution 
in a lamellar B horizon by fluorescence microscopy 
and image analysis. Geoderma 53 (3/4):309-328.

2. Magunda, M.K. 1992. Influence of some physico-
chemical properties on soil strength, stability of 
crusts and soil erosion. Ph.D. Dissertation.

3. Bouabid, R. 1992. Soil solution chemistry, 
mineral weathering, and pedogenesis in sandy 
outwash soils of east-central Minnesota. Ph.D. 
Dissertation.

4. Dyck, RH and Cynader, MS (1993) Histochemical 
localization of synaptic zinc in the developing 
kitten visual cortex. Journal of Comparative 
Neurology, 329, 53-67.

5. Dyck, RH and Cynader MS (1993) An interdigitated 
columnar mosaic of cytochrome oxidase, zinc, and 
neurotransmitter-related molecules in cat and 
monkey visual cortex. Proceedings of the National 
Academy of Science, USA, 90, 9066-9069.

6. Dyck, RH and Cynader MS (1993) Autoradiographic 
localization of serotonin receptor subtypes in cat 
visual cortex: regional, laminar, and columnar 
distributions during postnatal development. Journal 
of Neuroscience, 13, 4316-4338.

7. Biophys. J. 60:629-641 (1991)

8. Gough, A.H. and Taylor, D. L. (1993) Journal of 
Cell Biology, 121:5:1095-1107.

9. T. K. Teague, L.L. Munn, K. Zygourakis and B.W. 
McIntyre "Analysis of Lymphocyte Activation and 
Proliferation by Video Microscopy and Digital 
Imaging," Cytometry, in press (1993).

10. L.L. Munn, M.W. Glacken, B.W. McIntyre and K. 
Zygourakis "Analysis of Lymphocyte Aggregation 
Using Digital Image Analysis," J. Immunol. Methods, 
in press (1993).

11. Hammer, R.P., Pires,W.S., Markou, A. and Koob, 
G.F.: Withdrawal following cocaine self-
administration decreases regional metabolism in 
critical brain reward regions, Synapse, 14: 73-80, 
1993.

12. Hammer, R.P., Margulies, J.E., Lynn, A.B. and 
Brady, L.S.: Chronic fluoxetine treatment up-
regulates dopamine receptors in the mesolimbic 
forebrain of the rat, Depression, 1: 82-87, 1993.

13. Hammer, R.P., Bogic, L. and Handa, R.J.: 
Estrogenic regulation of proenkephalin mRNA 
expression in the ventromedial hypothalamus of the 
adult male rat, Molecular Brain Research, 19: 129-
134, 1993. 

14. Chin DJ; Straubinger RM; Acton S; Nathke I; 
Brodsky FM; 100kDa polypeptides in peripheral 
clathrin-coated vesicles are required for receptor-
mediated endocytosis. Proc. Natl. Acad. Sci. 86: 
9289-93, 1989

15. Chin DJ; Green G; Zon G; Szoka FC; Straubinger 
RM; Rapid nuclear accumulation of injected 
oligodeoxyribonucleotides. New Biologist 2: 1091-
1100, 1990.

16. Xuan-Hui Guo, Edward J. Huff and David C. 
Schwartz. Sizing of Large DNA Molecules by Hook 
Formation in a Loose Matrix. Journal of 
Biomolecular Structure & Dynamics, Volume 11, Issue 
1 (1993) pp 1-10

17. Science, "Ordered Restriction Maps of 
Saccharomyces Cerevisiae Chromosomes Constructed by 
Optical Mapping," David C. Schwartz, Xiaojun Li, 
Luis I. Hernandez, Satyadarshan P. Ramnarain, 
Edward J. Huff, Yu-Ker Wang.

18. Vivino MA, Chintalagiri S, Trus BL, Datiles M, 
"Development of a Scheimpflug Slit Lamp Camera
System for Quantitative Densitometric
Analysis", Eye, Vol 7, number 6

19. Adam DR, Kempner KM, Vivino MA, Tucker EE, 
Jones M, "Measurement of Flow
Velocity in a Phantom by Corrected Doppler Color 
Mapping Technique, using
Transverse Cross-Sectional Imaging", Computers in 
Cardiology 1993, in press

20. Short Term Water Heat storage : Studies of 
Velocity and Temerature Fields and their Importance 
for sizing of the Storage.  Lulea Univ. of 
Technology. Lulea Sweden. 1993:131D

21. Roger Hermansson. An experimental and numerical 
investigation of phenomena that affect the degree 
of therminal stratification.   Lulea Univ. of 
Technology. Lulea Sweden. 1993:127D

22. Velocoimetry ( PIV) in process Metallurgy for 
Steal mills. Gabriella Trandell : Modelling of 
tundish alloying for small lot production.  Lulea 
Univ. of Technology. Lulea Sweden. 1992:100E 

23. D. S. Bright, "Software Tools for examination 
of microanalytical images", pp. 73-78 in MICROBEAM 
ANALYSIS 1990, SAN FRANCISCO Press, CA.

24. Bright, D.S., Steel, E.B. and Newbury, D.E. 
(1991), "Visibility of Objects in Noisy Images as a 
Function of Contrast, Noise Level, and Object 
Size", Microbeam Analysis 1991: 185-188.

25. Neuron 11:237-251 (1993).

26.  Richardson ML, Gillespy TG 3rd.  An inexpensive 
computer-based digital imaging teaching  file.  Am J 
Roentgenology 1993;160:1299-1301.

27.  Richardson ML.  Using a personal computer to  create 
anatomic drawings for publication.  Am J  Roentgenology 
1993, in press.

28. Robert Parry, et. al., Computer-Aided Cell Colony 
Counting, BioTechniques,  Vol. 10, No 6, 1991, pages 772-
774.

29. Ricardo Correa-Rotter, et. al., Loading and Transfer 
Control for Northern Hybridization, BioTechniques,  Vol. 
12, No 2, 1992, pages 154-158.

30. Thomas Ford-Holevinski et al., Microcomputer-based 
Three-dimensional Reconstruction of in situ Hybridization 
Autoradiographs, Journal of Chemical Neuroanatomy, Vol 
4, 1991, pages 373-385.

31. Raymond O'Neill et al., Use of Image Analysis to 
Quantitate Changes in Form of Mitochondrial DNA After 
X-irradiation, Applied and Theoretical Electrophoresis, 
1989-1, pages 163-167.   

32. DeVoogd, T.J., Krebs, J.R., Healy, S.D. & Purvis, A. 
"Relations between song repertoire size and the volume of 
brain nuclei related to song: comparative evolutionary 
analyses amongst oscine birds."  In press, Proc. Roy. Soc 
Lon. B.

33. Garlow, S.J., Morilak, D.A., Dean, R.R., 
Roth, B.L. and Ciaranello, R.D. (1993) Production and 
characterization of a specific 5-HT2 receptor antibody. 
Brain Research, 615: 113-120.

34. F. D'Amelio, N.G. Daunton. Effects of 
spaceflight in the adductor longus muscle of rats flown in 
the Soviet biosatellite COSMOS 2044.  A study employing 
neural cell adhesion molecule (N-CAM) 
immunocytochemistry and conventional morphological
techniques (light and electron microscopy). J. Neuropath. 
Exp. Neurol. 51(4):415-431, 1992.

35 Ester Hill, Emily Holton. J. Orthopedic Research. 1993 

36. Reiss, A.L., et. al., "Neuroantomy of Fragile X Syndrome: the Posterior
Fossa, Annals of Neurology, Vol. 29, No. 1, January 1991.

37. Lieberman, D.E., et. al., "Computer Image Enhancement and Analysis of
Cementum Increments as Applied to Teeth of Gazella gazella", Journal of
Archaeological Science, in press (1989).

38. Chiang, P.K., et. al., "Activation of Collagen IV Expression in F9
Teratocarcinoma Cells by 3-Deazaadenosine Analogs", Journal of Biological
Chemistry, Vol. 267, No. 7, March 1992.

39. Correa-Rotter, R., et. al., "Loading and Transfer Control for Northern
Hybridization", BioTechniques, Vol. 12, No. 2 (1992).

40. Masters, D.B., et. al., "High Sensitivity Quantification of RNA from Gels
and Autoradiograms with Affordable Optical Scanning", BioComputing, Vol. 12, No.
6 (1992).

41. Gwon, A.E., et. al., "Lens Regeneration in Juvenile and Adult Rabbits
Measured by Image Analysis", Investigative Ophthalmology & Visual Science, Vol.
33, No. 7, June 1992.

42. Plotorak, M., et. al., "L1 Substrate Enhances Outgrowth of Tyrosine
Hydroxylase-Immunoreactive Neurites in Mesencephalic Cell Culture", Experimental
Neurology 117, 176-184 (1992).                        
From glenmac@u.washington.edu  Wed Oct 13 01:11:12 1993
Received: from carson.u.washington.edu by nx1.soils.umn.edu (5.65c)
	id AA15133; Wed, 13 Oct 1993 10:15:42 -0500
Return-Path: <glenmac@u.washington.edu>
Received: by carson.u.washington.edu
	(5.65/UW-NDC Revision: 2.29 ) id AA22317; Wed, 13 Oct 93 08:12:38 -0700
X-Sender: glenmac@carson.u.washington.edu
Date: Wed, 13 Oct 1993 08:11:12 -0700 (PDT)
From: Glen Macdonald <glenmac@u.washington.edu>
Subject: Re: Saving results in Excel file
To: nih-image@soils.umn.edu
Cc: Multiple recipients of list <nih-image@soils.umn.edu>
In-Reply-To: <9310121627.AA10752@zippy.nimh.nih.gov>
Message-Id: <Pine.3.05z.9310130810.A21693-a100000@carson.u.washington.edu>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=us-ascii



On Tue, 12 Oct 1993, Wayne Rasband wrote:

> 
> The latest 1.53 beta on zippy.nimh.nih.gov allows you to specify (in
> Preferences) the four character creator code Image uses for exported text
> files. This code determines which application is launched when you
> double-click on an exported text file (e.g., measurements, profile plot
> data, XY coordinates). Use 'Imag' for Image, 'XCEL' for Excel and 'QKPT'
> for KaleidaGraph.

Thank you, thank you, thank you, thank you, thank you, thank you.
> 
- Glen> 
> 
> 



From ikami@liposun.lbl.gov  Wed Oct 13 10:01:20 1993
Received: from lbl.gov by nx1.soils.umn.edu (5.65c)
	id AA19611; Wed, 13 Oct 1993 19:05:41 -0500
Return-Path: <ikami@liposun.lbl.gov>
Received: from liposun.lbl.gov by lbl.gov (4.1/1.39)
	id AA10082; Wed, 13 Oct 93 17:14:07 PDT
Received: from [131.243.32.31] (b1-lipo8.lbl.gov) by liposun.lbl.gov (4.1/SMI-4.0)
	id AA13458; Wed, 13 Oct 93 17:01:21 PDT
Date: Wed, 13 Oct 93 17:01:20 PDT
Message-Id: <9310140001.AA13458@liposun.lbl.gov>
To: nih-image@soils.umn.edu
From: ikami@liposun.lbl.gov (Craig Ikami)
Subject: wand tool area

Is it possible to get the area outlined by the wand tool?

From a337ard@diamond.sara.nl  Thu Oct 14 09:18:39 1993
Received: from vx.cis.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA21977; Thu, 14 Oct 1993 02:21:03 -0500
Return-Path: <a337ard@diamond.sara.nl>
Received: from HASARA5.BITNET (MAILGATE@HASARA5) by vx.cis.umn.edu (PMDF
 V4.2-13 #2574) id <01H434DMCXF4B7BAF8@vx.cis.umn.edu>; Thu,
 14 Oct 1993 02:23:14 CDT
Received: from diamond.sara.nl by SARA.NL for nih-image@soils.umn.edu; 14 Oct
 93  8:23 MET
Received: by diamond.sara.nl (5.65/1.37) id AA29776; Thu,
 14 Oct 93 08:18:39 +0100
Date: Thu, 14 Oct 1993 08:18:39 +0100
From: a337ard@diamond.sara.nl (Ard Jonker)
Subject: Re:  NIH-Image References
To: nih-image@soils.umn.edu
Message-Id: <9310140718.AA29776@diamond.sara.nl>
X-Envelope-To: nih-image@soils.umn.edu
Content-Transfer-Encoding: 7BIT

It is very neat of you to maintain a reference list of NIH-image and
to offer to keep it up to date. It would, for convenience, be even
more helpful if the same file would begin with a short notice on the
way Wayne prefers being quoted. (I have a paper submitted, which was
just before the item came up, and now I may comply with Wayne's wishes
when re-submiting)
ard
From sarmienu@rnisd0.DNET.roche.com  Thu Oct 14 04:18:08 1993
Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c)
	id AA24782; Thu, 14 Oct 1993 07:16:34 -0500
Return-Path: <sarmienu@rnisd0.DNET.roche.com>
Received: by gatekeeper.roche.com (5.65/fma-120691);
	id AA22093; Thu, 14 Oct 93 08:18:08 -0400
Received: by mailgate.roche.com (5.65/fma-120691);
	id AA25712; Thu, 14 Oct 93 08:16:48 -0400
From: sarmienu@rnisd0.DNET.roche.com
Message-Id: <9310141216.AA25712@mailgate.roche.com>
Received: from rnisd0.enet; by inet.enet; Thu, 14 Oct 93 08:18:08 EDT
Date: Thu, 14 Oct 93 08:18:08 EDT
To: nih-image@soils.umn.edu
Apparently-To: nih-image@soils.umn.edu
Subject: How to cite NIH-Image: Concensus?

Is there a general consensus in using the following quote when mentioning image
in the materials and methods section of a manuscript?"... analysis performed in
a Macintosh [model] computer using the public domain NIH-Image (written by Wayne
Rasband and available via Internet by anonymous ftp from zippy.nimh.nih.gov or
from Library 9 of the MacApp forum on CompuServe)".

Shouldn't Image be available for a more general audience, say via floppy disk
from the National Library of Medicine? I remember when I first try to get Image,
not having access to E-mail, Internet and never having used Compuserve, it took
me several months to figure out how to get it. Finally somebody handed me a
diskette with an old version of Image. I think the program should be more easy
to obtain. Particularly since it is becoming so popular among scientist. 

Also, I agree with Michael J. Herron that "to appear in a medline search the
words "NIH Image" must appear in either the abstract or the Keywords index...",
Therefore, all people publishing manuscripts using NIH-Image should include the
name of the program in the abstract whenever possible. 

Suggestions and comments to my address below, please

Juan I. Sarmiento
Department of Toxicology and Pathology
Hoffmann-La Roche, INC.
340 Kingsland street
Nutley, NJ 07110
(201) 235 3907
Sarmienu@RNISD0.DNET.ROCHE.COM

From mvivino@helix.nih.gov  Thu Oct 14 04:34:20 1993
Received: from helix.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA24923; Thu, 14 Oct 1993 07:32:44 -0500
Return-Path: <mvivino@helix.nih.gov>
Received: from mavmac.dcrt.nih.gov by helix.nih.gov (5.64/1.35(helix-1.0))
	id AA19807; Thu, 14 Oct 93 08:34:20 -0400
Date: Thu, 14 Oct 93 08:34:20 -0400
Message-Id: <9310141234.AA19807@helix.nih.gov>
X-Sender: mvivino@128.231.2.3
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: mvivino@helix.nih.gov (Mark Vivino)
Subject: Re: wand tool area

>Is it possible to get the area outlined by the wand tool?

Use the Measure command from the analyze menu. Be sure Area is checked
under Options... in the analyze menu


Mark Vivino
NIH/DCRT
mvivino@helix.nih.gov


From wayne@helix.nih.gov  Thu Oct 14 08:43:07 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA25472; Thu, 14 Oct 1993 08:44:21 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA13508; Thu, 14 Oct 93 09:04:13 -0400
Message-Id: <9310141304.AA13508@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Thu, 14 Oct 1993 08:43:07 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: How to cite NIH-Image: Concensus?

>Is there a general consensus in using the following quote when mentioning image
>in the materials and methods section of a manuscript?"... analysis performed in
>a Macintosh [model] computer using the public domain NIH-Image (written by
>Wayne
>Rasband and available via Internet by anonymous ftp from zippy.nimh.nih.gov or
>from Library 9 of the MacApp forum on CompuServe)".

Looks good to me except I would use "NIH Image" instead of NIH-Image.

>Shouldn't Image be available for a more general audience, say via floppy disk
>from the National Library of Medicine? I remember when I first try to get
>Image,
>not having access to E-mail, Internet and never having used Compuserve, it took
>me several months to figure out how to get it. Finally somebody handed me a
>diskette with an old version of Image. I think the program should be more easy
>to obtain. Particularly since it is becoming so popular among scientist.

NIH Image is available on a floppy disk from the National Technical
Information Service (NTIS) for $100. Their phone number is 703-487-4650.
Use order number PB93-504868.

--wayne


From waheeschen@dow.com  Thu Oct 14 06:12:10 1993
Received: from na1.dow.com (na2.dow.com) by nx1.soils.umn.edu (5.65c)
	id AA25718; Thu, 14 Oct 1993 09:10:52 -0500
Return-Path: <waheeschen@dow.com>
Received: by na1.dow.com id AA04159
  (InterLock SMTP Gateway 1.1 for nih-image@soils.umn.edu);
  Thu, 14 Oct 1993 08:58:20 -0500
Message-Id: <199310141358.AA04159@na1.dow.com>
Date: Thu, 14 Oct 1993 10:12:10 -0400
From: waheeschen@dow.com (Bill Heeschen (517)636-4005 PMRC/ASL)
To: nih-image@soils.umn.edu
Subject: re: How to cite NIH Image
X-Vms-To: SMTP%"nih-image@soils.umn.edu"

Folks:

My two cents worth regarding citation of NIH Image.  The nature of NIH Image is 
interesting - it is extremely useful, widely used and well supported, yet it is 
not a commercial product.  I suggest that we treat it with the respect normally 
accorded commercial software or even more respect.  8-)  How about calling it 
NIH Image, not NIH-Image? This is how it is written in the manual except that 
Image is italicized and I can't figure out how to get italics into E-mail.  
Also, I suggest we treat "NIH Image" as a trademark. I have modified Juan 
Sarmiento's citation to reflect my concerns and to address the non-electronic 
distribution issue:

"...using the public domain NIH Image image analysis software (written by Wayne 
Rasband at the U.S. National Institutes of Health and available electronically 
via Internet by anonymous ftp from zippy.nimh.nih.gov or from Library 9 of the 
MacApp forum on CompuServe and on floppy disk from NTIS, 5285 Port Royal Rd., 
Springfield, VA 22161, part number PB93-504868)."

As for an alternate, non-electronic source, the $100 NTIS option listed in 
Appendix I of the manual seems reasonable to me and would be money well spent.  
Once "hooked" with the disk version from NTIS, new users without internet or 
CompuServe would find that the money investment (modem, account, long distance) 
to download from CompuServe still makes NIH Image the best deal around.  With 
no money coming in to Wayne to support physical distribution, the current 
method of distribution (FTP, CompuServe,etc.) is quite reasonable in that it 
allows widespread, rapid response with extremely low time overhead.  Any 
physical distribution system results in a huge relative increase in time (disk 
duplication, mailing) and money (wages, media) for software that is being 
improved at a rate of about once/week.  If it can be done cheaper by the 
National Library of Medicine than NTIS, that would be OK, but for now the NTIS 
option looks reasonable.

By the way, thanks to Juan for compiling the citation list!

Bill

==========================
Bill Heeschen / Analytical Sciences - Materials Characterization
1897-D Building / The Dow Chemical Company
Midland, MI   48667  U.S.A.
phone: (517)636-4005   fax:    (517)636-5453
Email: waheeschen@dow.com
==========================
From m_palchuk@ACAD.FANDM.EDU  Thu Oct 14 07:43:52 1993
Received: from Acad.FandM.EDU by nx1.soils.umn.edu (5.65c)
	id AA26420; Thu, 14 Oct 1993 10:43:09 -0500
Return-Path: <m_palchuk@ACAD.FANDM.EDU>
Received: from [155.68.24.16] (Matvey.FandM.edu) by ACAD.FANDM.EDU (PMDF
 V4.2-11 #3427) id <01H43NXODMJK00BFXN@ACAD.FANDM.EDU>; Thu,
 14 Oct 1993 11:43:52 EDT
Date: Thu, 14 Oct 1993 11:43:52 -0400
From: m_palchuk@ACAD.FANDM.EDU (Matvey Palchuk)
Subject: System configuration
To: NIH-IMAGE@SOILS.UMN.EDU
Message-Id: <01H43NXP3CGY00BFXN@ACAD.FANDM.EDU>
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7BIT

I am a new subscriber to the list and would like to first say a few words
about myself. I am a senior in Franklin & Marshall College, Lancaster, PA
majoring in Biology. I am also a Macintosh software troubleshooter. That's
enough...

Recently our Bio department decided to try to implement image analysis
system based on a Mac and using NIH Image. Neither me nor anyone in the
department has enough knowledge about third-parties hardware and software
necessary for image acquisition and subsequent manipulation.

I would like to know if there is a document somewhere describing  possible
configuration of equipment and software supported by NIH Image. If there is
no such thing, I think it would be a good idea to compile a list of
configuration used by everybody reading this message and make it available
to everyone who wishes to start from ground zero as a reference source.

I would be happy to compile all the responses I receive and post the
summary to the list. If you think it's a good idea, please answer the
following questions and feel free to add or delete anything:

1. Purpose of use. Kind of research or educational process.

2. Method of data acquisition. Hardware (like cameras etc.).

3. Computer. Model. Configuration (RAM, HD, add-ons, etc.).

4. Software used except NIH Image.

5. If you were creating your system today, how would you respond
   to questions 2-4?

Your reply is greatly appreciated. Please send your messages directly to me
at the address    m_palchuk@fandm.edu     and not to the list. I will post
summary.


--
------------------------------------------------------------------------------
                                Matvey Palchuk '94                              
                            Computing Services Manager             
                        CISCS, Franklin & Marshall College

                          Internet: m_palchuk@fandm.edu                     
------------------------------------------------------------------------------


From gmei@hoh.mbl.edu  Thu Oct 14 08:17:55 1993
Received: from AQUA.WHOI.EDU by nx1.soils.umn.edu (5.65c)
	id AA26929; Thu, 14 Oct 1993 11:19:21 -0500
Return-Path: <gmei@hoh.mbl.edu>
Received: by aqua.whoi.edu (5.57/Ultrix3.0-C)
	id AA08886; Thu, 14 Oct 93 12:20:56 -0400
Received: from [128.128.172.215] (SMAC15.MBL.EDU) by hoh.mbl.edu. (4.1/SMI-4.1)
	id AA26716; Thu, 14 Oct 93 12:17:57 EDT
Date: Thu, 14 Oct 93 12:17:55 EDT
Message-Id: <9310141617.AA26716@hoh.mbl.edu.>
To: nih-image@soils.umn.edu
From: gmei@hoh.mbl.edu (Guang Mei)
Subject: Convert HSV to 8-bit color image

Hi:

Does anyone have code (or information about) to convert a stack of HSV
images (Hue, Saturation, Value, 8-bit resolution each) to an 8-bit color
image. We like to include this function into our version of NIH Image 1.52
(either in macro or in User.p).
-------------
Guang Mei   gmei@hoh.mbl.edu     Tel:(508)548-3705 ext 374
Program of Architectural Dynamics in Living Cells
Marine Biological Laboratory, Woods Hole, MA 02543

From jamiel@sybase.com  Thu Oct 14 01:56:05 1993
Received: from halon.sybase.com by nx1.soils.umn.edu (5.65c)
	id AA27310; Thu, 14 Oct 1993 11:52:05 -0500
Return-Path: <jamiel@sybase.com>
Received: from sybase.com (sybgate.sybase.com) by halon.sybase.com (5.0/SMI-SVR4/SybFW4.0)
	id AA27903; Thu, 14 Oct 93 09:55:09 PDT
Received: from ralph.sybgate.sybase.com by sybase.com (4.1/SMI-4.1/SybH3.2)
	id AA01923; Thu, 14 Oct 93 09:53:36 PDT
Received: from [130.214.134.8] by ralph.sybgate.sybase.com (4.1/SMI-4.1/SybEC3.1)
	id AA11499; Thu, 14 Oct 93 09:53:34 PDT
Message-Id: <9310141653.AA11499@ralph.sybgate.sybase.com>
X-Sender: jamiel@ralph.sybase.com
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Thu, 14 Oct 1993 09:56:05 -0800
To: nih-image@soils.umn.edu
From: jamiel@sybase.com (Healthier, More Manageable Hair)
Subject: To the person needing quicktime recorder...
Content-Length: 624

Hi- I apologize for the bandwidth, but I lost the enote from the person who
described the plight of having bought a frame grabber card for research and
finding that the software didn't support grabbing multiple frames. I wrote
and said that I had the apple recorder, and then couldn't find it. In the
mean time, I replied and said sorry, and wither lost or deleted the
original note. Well, I found it, and can send it to you. Write me if (1)
this makes enough sense for you to figure it out and (2) if you still need
it. Again, sorry to everyone else.


jamie

jamiel@sybase.com
"Static- It's all just static"- Bryna Bank


From CMSABEL@minna.acc.iit.edu  Thu Oct 14 07:34:03 1993
Received: from harpo.acc.iit.edu by nx1.soils.umn.edu (5.65c)
	id AA27611; Thu, 14 Oct 1993 12:33:01 -0500
Return-Path: <CMSABEL@minna.acc.iit.edu>
Received: from minna.acc.iit.edu by minna.acc.iit.edu (PMDF V4.2-12 #3556) id
 <01H43PI8JDU88ZG910@minna.acc.iit.edu>; Thu, 14 Oct 1993 12:34:03 CDT
Date: Thu, 14 Oct 1993 12:34:03 -0500 (CDT)
From: CMSABEL@minna.acc.iit.edu
Subject: grain counting macros
To: nih-image@soils.umn.edu
Message-Id: <01H43PI8KGF68ZG910@minna.acc.iit.edu>
X-Vms-To: IN%"nih-image@soils.umn.edu."
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII
Content-Transfer-Encoding: 7BIT

Hi.

I'm a new member of 'the list' and don't know if this has been covered yet.
Has anyone tried the grain-counting macros that Karl Beykirch put up for
anonymous ftp transfer?
I've been trying them, and having some difficulty.  In particular, when 
using the 'Count Grains in Area (F7) macro, it is graying out my entire
selection and counting it as -one- grain.  Perhaps I am not calibrating
the area/grain properly.  I am not macro-literate (yet), so any info
that you can offer is appreciated.
Marc
cmsabel@minna.acc.iit.edu
From ikami@liposun.lbl.gov  Thu Oct 14 04:01:47 1993
Received: from lbl.gov by nx1.soils.umn.edu (5.65c)
	id AA27961; Thu, 14 Oct 1993 13:06:10 -0500
Return-Path: <ikami@liposun.lbl.gov>
Received: from liposun.lbl.gov by lbl.gov (4.1/1.39)
	id AA18503; Thu, 14 Oct 93 11:14:35 PDT
Received: from [131.243.32.31] (b1-lipo8.lbl.gov) by liposun.lbl.gov (4.1/SMI-4.0)
	id AA03509; Thu, 14 Oct 93 11:01:48 PDT
Date: Thu, 14 Oct 93 11:01:47 PDT
Message-Id: <9310141801.AA03509@liposun.lbl.gov>
To: nih-image@soils.umn.edu
From: ikami@liposun.lbl.gov (Craig Ikami)
Subject: Re: wand tool area

>>Is it possible to get the area outlined by the wand tool?
>
>Use the Measure command from the analyze menu. Be sure Area is checked
>under Options... in the analyze menu
>
>
>Mark Vivino
>NIH/DCRT
>mvivino@helix.nih.gov

Sorry for all these beginner questions. 
I am running image 1.52 on an LC III. I have checked the area under options
in the analyze menu and the area numbers i am getting don't seem to make
much sense to me.

From ikami@liposun.lbl.gov  Thu Oct 14 04:08:51 1993
Received: from lbl.gov by nx1.soils.umn.edu (5.65c)
	id AA27999; Thu, 14 Oct 1993 13:13:15 -0500
Return-Path: <ikami@liposun.lbl.gov>
Received: from liposun.lbl.gov by lbl.gov (4.1/1.39)
	id AA18573; Thu, 14 Oct 93 11:21:40 PDT
Received: from [131.243.32.31] (b1-lipo8.lbl.gov) by liposun.lbl.gov (4.1/SMI-4.0)
	id AA03932; Thu, 14 Oct 93 11:08:53 PDT
Date: Thu, 14 Oct 93 11:08:51 PDT
Message-Id: <9310141808.AA03932@liposun.lbl.gov>
To: nih-image@soils.umn.edu
From: ikami@liposun.lbl.gov (Craig Ikami)
Subject: Re: wand tool area

Just a thank-you note for responding to all these first timer questions. We
really like the package. Is there anyone in the San
Francisco/Berkeley/Lawrence Laboratory area who would mind demo'ing his/her
NIH image setup?

                Thanks again in advance 

From BUSCH@zodiac.rutgers.edu  Thu Oct 14 09:41:43 1993
Received: from PISCES.rutgers.edu by nx1.soils.umn.edu (5.65c)
	id AA28125; Thu, 14 Oct 1993 13:21:37 -0500
Return-Path: <BUSCH@zodiac.rutgers.edu>
Received: from zodiac.rutgers.edu by zodiac.rutgers.edu (PMDF V4.2-11 #3450) id
 <01H43RB763HC9YF118@zodiac.rutgers.edu>; Thu, 14 Oct 1993 13:41:43 EDT
Date: Thu, 14 Oct 1993 13:41:43 -0400 (EDT)
From: BUSCH@zodiac.rutgers.edu
Subject: 
To: nih-image@soils.umn.edu
Message-Id: <01H43RB7IYG29YF118@zodiac.rutgers.edu>
X-Envelope-To: nih-image@soils.umn.edu
X-Vms-To: IN%"nih-image@soils.umn.edu"
Mime-Version: 1.0
Content-Transfer-Encoding: 7BIT



Subscribers:

Every now and then, I poke my head into a local laboratory which is working 
with NIH_Image and a Macintosh, (and I might say, some very nice imaging 
equipment), to capture and analyse images of neurons.  This particular 
laboratory is interested in things like the size and shape of the cell 
soma, neurite lengths, number of branches, ... the usual.  After listening 
in on a few conversations recently, it appeared to me that an interesting 
problem has arisen:  How can you tell, from an image, how long a neurite 
is?  This particular question rests in a subclass of the more general 
problem:  Where are the edges of an object?

Let me expand on the general problem.  In the presence of background noise, 
what defines the edges of an object, particularly when the pixel intensity 
defining the object is only modestly above the background.  The detection 
problem is not easy to solve, and many heuristic methods have been 
employed.

In the case of neurite detection, an additional problem arises;  the 
characteristics of the neurites are the data used in determining the 
effects of various substrates, etc. on sprouting, extension, and in 
general cell and neurite viability.  It is critical therefore that an
objective, consistent method be used in determining where the neurites
are, and where they are not (sic).

I wish to propose a partial answer to this problem.  Recently I attended 
a seminar given at the New York Academy of Sciences on wavelets.  I have 
been working with wavelets on the solution of the near infra-red 
tomography problem, and was particularly interested in the contents of 
the seminar.  It struck me that embodied in the material presented 
was the "answer" to the neurite detection problem, and to the more general 
edge detection problem.  The image may be represented as a set of wavelets, 
the coefficients of which represent all the 'information' contained in the 
image.  It turns out that particular properties of these coefficients, 
which I will not go into here, reveal the location of discontinuities in 
the original image, (i.e. where the edges are).  Some work has been done 
on automating the process, but there is still work to be done.  I have 
taken a brief look at the algorithm, and it may be suited to a Mac Quadra
class machine and therefore should be able to be implemented as a macro 
under NIH-image.

It appears to me that the problem of neurite and edge detection in the 
biological sciences must be made rigorous!  Therefore it seems sensible 
to pursue a path in this direction.  Any interested parties may contact 
me directly:

Nathan A. Busch
Department of Chemical Engineering
Rutgers University
Piscataway, NJ

(908) 932-5511
busch@zodiac.rutgers.edu

Nathan.
From Doug.Erickson@m.CC.UTAH.EDU  Thu Oct 14 05:33:25 1993
Received: from fcom.cc.utah.edu by nx1.soils.umn.edu (5.65c)
	id AA28175; Thu, 14 Oct 1993 13:30:57 -0500
Return-Path: <Doug.Erickson@m.CC.UTAH.EDU>
Received: from [128.110.56.17] (emcb017x.utah.edu) by fcom.cc.utah.edu (4.1/SMI-4.0 [uucc-nhj-virtual 18AUG1991])
	id AA21155; Thu, 14 Oct 93 12:30:40 MDT
Message-Id: <9310141830.AA21155@fcom.cc.utah.edu>
Date: Thu, 14 Oct 1993 12:33:25 -0700
To: nih-image@soils.umn.edu
From: Doug.Erickson@m.CC.UTAH.EDU (Doug Erickson)
X-Sender: dme8844@u.cc.utah.edu
Subject: HERESY!  An Image-like program for the PC?

I am hope I don't incur the wrath and ridicule of you all--I love my Mac and
Image has been an _invaluable_ tool for the project I am currently working on.
There are times, however, when all I have handy is a PC.  Does anyone know
of a public domain program that has capabilities similar to Image?

If you can help, please let me know where and how I can get a copy.  Also, if
you have looked for the same thing recently and know that nothing can compare
to Image and that I am wasting my time, I'd like to know that too.

Thanks,

Doug Erickson
U of Utah Dept. of Bioengineering
Doug.Erickson@m.cc.utah.edu


From jladwig@soils.umn.edu  Thu Oct 14 08:59:14 1993
Received: from saturn.soils.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA28504; Thu, 14 Oct 1993 13:59:09 -0500
Return-Path: <jladwig@soils.umn.edu>
Received: by saturn.soils.umn.edu (4.1)
	id AA12047; Thu, 14 Oct 93 13:59:14 CDT
Date: Thu, 14 Oct 93 13:59:14 CDT
From: "John Ladwig" <jladwig@soils.umn.edu>
Message-Id: <9310141859.AA12047@saturn.soils.umn.edu>
To: nih-image@soils.umn.edu
Subject: NIH-Image Message Archives [was: grain counting macros]
In-Reply-To: CMSABEL@minna.acc.iit.edu's message <01H43PI8KGF68ZG910@minna.acc.iit.edu> of 14 October 1993
References: <01H43PI8KGF68ZG910@minna.acc.iit.edu>

>>>>> On Thu, 14 Oct 1993 12:36:13 -0500, CMSABEL@minna.acc.iit.edu said:

    CMSABEL> I'm a new member of 'the list' and don't know if this has
    CMSABEL> been covered yet.  Has anyone tried the grain-counting
    CMSABEL> macros that Karl Beykirch put up for anonymous ftp
    CMSABEL> transfer?  

As a reminder, all past message from the NIH-Image mailing list are
archived, and available via email, FTP, and gopher.

>From the welcome message (which probably no one reads, anyhow) sent at
subscription time:

========================================================================
  Contributions sent to this list are automatically archived. You can
obtain a list of the available archive files by sending an "INDEX
NIH-IMAGE" command to LISTPROC@SOILS.UMN.EDU. These files can then be
retrieved by means of a "GET NIH-IMAGE filename" command.
 
MESSAGE ARCHIVE ACCESS
======================

If you have access to gopher, you can connect to gopher.soils.umn.edu
at port 70 (which can be found under the University of Minnesota "All
the Gophers in the World" listing), and look under:  

    Computer Information/
     General Information/
      Search Nih-Image Mailing List Archives <?>

to search the archived messagesd for keywords, or

    Computer Information/
     General Information/
      Selected Electronic Mailing List Archives/      
       Nih-image*/
               
for the actual archived messages.

The message archives which are available through gopher are also
available via ftp to:

    ftp.soils.umn.edu:pub/info/email-lists/Nih-image*


  Please note that it is presently possible for anybody to determine
that you are signed up to the list through the use of the "REVIEW"
command, which returns the network address and name of all the
subscribers. 
 
  More information on Listprocessor commands can be found in the Help
document, which you can retrieve by sending a "HELP" command to
LISTPROC@SOILS.UMN.EDU.
From mvivino@helix.nih.gov  Thu Oct 14 12:03:08 1993
Received: from helix.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA29091; Thu, 14 Oct 1993 15:01:36 -0500
Return-Path: <mvivino@helix.nih.gov>
Received: from mavmac.dcrt.nih.gov by helix.nih.gov (5.64/1.35(helix-1.0))
	id AA12002; Thu, 14 Oct 93 16:03:08 -0400
Date: Thu, 14 Oct 93 16:03:08 -0400
Message-Id: <9310142003.AA12002@helix.nih.gov>
X-Sender: mvivino@128.231.2.3
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: mvivino@helix.nih.gov (Mark Vivino)
Subject: Re: wand tool area

>Sorry for all these beginner questions. 
>I am running image 1.52 on an LC III. I have checked the area under options
>in the analyze menu and the area numbers i am getting don't seem to make
>much sense to me.

If you want units other than pixels you must scale the image into some unit
like mm or cm with the set scale command. Draw a line of aknown length on
the image with the line tool, then say set scale. Set scale is below
options...

 Otherwise you can remove any scale that is on the image by checking pixels
in the set scale.


Mark Vivino
NIH/DCRT
mvivino@helix.nih.gov


From bright@ENH.NIST.GOV  Thu Oct 14 13:41:59 1993
Received: from enh.nist.gov by nx1.soils.umn.edu (5.65c)
	id AA00144; Thu, 14 Oct 1993 16:41:08 -0500
Return-Path: <bright@ENH.NIST.GOV>
Received: from [129.6.98.4] (dsb-mac.nist.gov) by ENH.NIST.GOV (PMDF V4.2-13
 #4653) id <01H440GKVC74001HYX@ENH.NIST.GOV>; Thu, 14 Oct 1993 17:41:59 EDT
Date: Thu, 14 Oct 1993 17:41:59 -0400 (EDT)
Date-Warning: Date header was inserted by ENH.NIST.GOV
From: bright@ENH.NIST.GOV
Subject: Re: HERESY!  An Image-like program for the PC?
To: nih-image@soils.umn.edu
Message-Id: <01H440GOJYIE001HYX@ENH.NIST.GOV>
Content-Transfer-Encoding: 7BIT

>I am hope I don't incur the wrath and ridicule of you all--I love my Mac and
>Image has been an _invaluable_ tool for the project I am currently working on.
>There are times, however, when all I have handy is a PC.  Does anyone know
>of a public domain program that has capabilities similar to Image?
>
>If you can help, please let me know where and how I can get a copy.  Also, if
>you have looked for the same thing recently and know that nothing can compare
>to Image and that I am wasting my time, I'd like to know that too.
>
>Thanks,
>
>Doug Erickson
>U of Utah Dept. of Bioengineering
>Doug.Erickson@m.cc.utah.edu

Try the National Center for Supercomputing..  PC show or something like that:
FTP host:    ftp.ncsa.uiuc.edu
Questions:  softdev@ncsa.uiuc.edu

:8o)
Dave
-------------------------------------------------------------
David S. Bright                        bright@enh.nist.gov  
Microanalysis Research Group 
Chem. A113                                  
National Institute of Standards & Technology (NIST, formerly NBS)
Gaithersburg, MD 20899-0001                                          
USA
301-975-3911 - voice, 301-216-1134 - fax

From ikami@liposun.lbl.gov  Thu Oct 14 08:18:25 1993
Received: from lbl.gov by nx1.soils.umn.edu (5.65c)
	id AA00560; Thu, 14 Oct 1993 17:22:50 -0500
Return-Path: <ikami@liposun.lbl.gov>
Received: from liposun.lbl.gov by lbl.gov (4.1/1.39)
	id AA21455; Thu, 14 Oct 93 15:31:16 PDT
Received: from [131.243.32.31] (b1-lipo8.lbl.gov) by liposun.lbl.gov (4.1/SMI-4.0)
	id AA08449; Thu, 14 Oct 93 15:18:27 PDT
Date: Thu, 14 Oct 93 15:18:25 PDT
Message-Id: <9310142218.AA08449@liposun.lbl.gov>
To: nih-image@soils.umn.edu
From: ikami@liposun.lbl.gov (Craig Ikami)
Subject: Re: wand tool area

>>Sorry for all these beginner questions. 
>>I am running image 1.52 on an LC III. I have checked the area under options
>>in the analyze menu and the area numbers i am getting don't seem to make
>>much sense to me.
>
>If you want units other than pixels you must scale the image into some unit
>like mm or cm with the set scale command. Draw a line of aknown length on
>the image with the line tool, then say set scale. Set scale is below
>options...
>
> Otherwise you can remove any scale that is on the image by checking pixels
>in the set scale.
>
>
>Mark Vivino
>NIH/DCRT
>mvivino@helix.nih.gov

The measure option is setup on pixels. This is what i get for the wand
measurments. (These are round HDL particles under em).

      area            mean              x               y

1     1.00          100.00          134.50          253.50      
2     1.00          100.00          218.50          209.50       
3     3.00          100.33          331.86          172.83       
4     2.00          100.00          370.43          219.55       
5     0.00            0.00          245.90          330.08       

area 2 is slightly larger than area 1
area 3 is twice the size of area 1
area 4 is about the same size as area 1
area 5 is about the same size as area 1  

The areas seem to be correct when i use the rectangle, ellipse or free
hand. Is there something i am supposed to set for the wand? The outline
looks correct. 

Is there a volume measurement? That is can i circle an area and get some
kind of density/area integration without any averaging?

                        
                                thanks again in advance


From ikami@liposun.lbl.gov  Thu Oct 14 10:29:27 1993
Received: from lbl.gov by nx1.soils.umn.edu (5.65c)
	id AA01609; Thu, 14 Oct 1993 19:33:52 -0500
Return-Path: <ikami@liposun.lbl.gov>
Received: from liposun.lbl.gov by lbl.gov (4.1/1.39)
	id AA22951; Thu, 14 Oct 93 17:42:18 PDT
Received: from [131.243.32.31] (b1-lipo8.lbl.gov) by liposun.lbl.gov (4.1/SMI-4.0)
	id AA10134; Thu, 14 Oct 93 17:29:29 PDT
Date: Thu, 14 Oct 93 17:29:27 PDT
Message-Id: <9310150029.AA10134@liposun.lbl.gov>
To: nih-image@soils.umn.edu
From: ikami@liposun.lbl.gov (Craig Ikami)
Subject: Re: wand tool area

>>Is it possible to get the area outlined by the wand tool?
>
>Use the Measure command from the analyze menu. Be sure Area is checked
>under Options... in the analyze menu
>
>
>Mark Vivino
>NIH/DCRT
>mvivino@helix.nih.gov


ok .. i have some answers. I am reading 12 bit TIFF from Molecular
Dynamics. I turns out that if i use some "diddled" version of NIH image
from Molecular Dynamics, then everything seems ok. If i use the NIH version
, the images look ok but do not seem to computer ok. This is trial by fire
for a first timer.

From @UWAVM.U.WASHINGTON.EDU:tom@peptide.chem.washington.edu  Thu Oct 14 13:59:59 1993
Received: from uwavm.u.washington.edu by nx1.soils.umn.edu (5.65c)
	id AA03304; Thu, 14 Oct 1993 22:58:53 -0500
Return-Path: <@UWAVM.U.WASHINGTON.EDU:tom@peptide.chem.washington.edu>
Received: from peptide.chem.washington.edu by UWAVM.U.WASHINGTON.EDU
   (IBM VM SMTP V2R1) with TCP; Thu, 14 Oct 93 20:59:55 PDT
Received: by peptide.chem.washington.edu (920330.SGI/911001.SGI)
	for @uwavm.u.washington.edu:nih-image@soils.umn.edu id AA22741; Thu, 14 Oct 93 20:59:59 -0700
Date: Thu, 14 Oct 93 20:59:59 -0700
From: tom@peptide.chem.washington.edu (Tom Marschner)
Message-Id: <9310150359.AA22741@peptide.chem.washington.edu>
To: nih-image@soils.umn.edu
Subject: Re: wand tool area

	From nih-image@soils.umn.edu  Thu Oct 14 16:02:25 1993
	Received: from mail.tc.umn.edu by peptide.chem.washington.edu via SMTP (920330.SGI/911001.SGI)
		for tom id AA22176; Thu, 14 Oct 93 16:02:25 -0700
	Received: from nx1.soils.umn.edu by mail.tc.umn.edu id SMTP-0012cbdd366016168; Thu, 14 Oct 93 17:32:07 -0500
	Received: from  (localhost) by nx1.soils.umn.edu (5.65c)
		id AA00634; Thu, 14 Oct 1993 17:29:56 -0500
	Date: Thu, 14 Oct 1993 17:29:56 -0500
	Message-Id: <9310142218.AA08449@liposun.lbl.gov>
	Errors-To: owner-nih-image@soils.umn.edu
	Reply-To: nih-image@soils.umn.edu
	Originator: nih-image@soils.umn.edu
	Sender: nih-image@soils.umn.edu
	Precedence: bulk
	From: ikami%liposun.lbl.gov@relay.tc.umn.edu (Craig Ikami)
	To: Multiple recipients of list <nih-image@nx1.soils.umn.edu>
	Subject: Re: wand tool area
	X-Listprocessor-Version: 6.0 -- ListProcessor by Anastasios Kotsikonas
	X-Comment:  NIH Image Distribution List
	
	>>Sorry for all these beginner questions. 
	>>I am running image 1.52 on an LC III. I have checked the area under options
	>>in the analyze menu and the area numbers i am getting don't seem to make
	>>much sense to me.
	>
	>If you want units other than pixels you must scale the image into some unit
	>like mm or cm with the set scale command. Draw a line of aknown length on
	>the image with the line tool, then say set scale. Set scale is below
	>options...
	>
	> Otherwise you can remove any scale that is on the image by checking pixels
	>in the set scale.
	>
	>
	>Mark Vivino
	>NIH/DCRT
	>mvivino@helix.nih.gov
	
	The measure option is setup on pixels. This is what i get for the wand
	measurments. (These are round HDL particles under em).
	
	      area            mean              x               y
	
	1     1.00          100.00          134.50          253.50      
	2     1.00          100.00          218.50          209.50       
	3     3.00          100.33          331.86          172.83       
	4     2.00          100.00          370.43          219.55       
	5     0.00            0.00          245.90          330.08       
	
	area 2 is slightly larger than area 1
	area 3 is twice the size of area 1
	area 4 is about the same size as area 1
	area 5 is about the same size as area 1  
	
	The areas seem to be correct when i use the rectangle, ellipse or free
	hand. Is there something i am supposed to set for the wand? The outline
	looks correct. 
	
	Is there a volume measurement? That is can i circle an area and get some
	kind of density/area integration without any averaging?
	
	                        
	                                thanks again in advance
	
	

From @UWAVM.U.WASHINGTON.EDU:tom@peptide.chem.washington.edu  Thu Oct 14 14:15:27 1993
Received: from uwavm.u.washington.edu by nx1.soils.umn.edu (5.65c)
	id AA03442; Thu, 14 Oct 1993 23:14:20 -0500
Return-Path: <@UWAVM.U.WASHINGTON.EDU:tom@peptide.chem.washington.edu>
Received: from peptide.chem.washington.edu by UWAVM.U.WASHINGTON.EDU
   (IBM VM SMTP V2R1) with TCP; Thu, 14 Oct 93 21:15:22 PDT
Received: by peptide.chem.washington.edu (920330.SGI/911001.SGI)
	for @uwavm.u.washington.edu:nih-image@soils.umn.edu id AA22793; Thu, 14 Oct 93 21:15:27 -0700
Date: Thu, 14 Oct 93 21:15:27 -0700
From: tom@peptide.chem.washington.edu (Tom Marschner)
Message-Id: <9310150415.AA22793@peptide.chem.washington.edu>
To: nih-image@soils.umn.edu


>>Sorry for all these beginner questions. 
>>I am running image 1.52 on an LC III. I have checked the area under options
>>in the analyze menu and the area numbers i am getting don't seem to make
>>much sense to me.
>
>If you want units other than pixels you must scale the image into some unit
>like mm or cm with the set scale command. Draw a line of aknown length on
>the image with the line tool, then say set scale. Set scale is below
>options...
>
> Otherwise you can remove any scale that is on the image by checking pixels
>in the set scale.
>
>
>Mark Vivino
>NIH/DCRT
>mvivino@helix.nih.gov

Is density slicing or thresholding turned on?  If either is turned on
the measurement is carried out on only the selected pixels.

Tom Marschner
tom@peptide.chem.washington.edu




From ptr@GRECO2.POLYTECHNIQUE.FR  Fri Oct 15 13:09:15 1993
Received: from chenas.inria.fr by nx1.soils.umn.edu (5.65c)
	id AA05892; Fri, 15 Oct 1993 06:11:38 -0500
Return-Path: <ptr@GRECO2.POLYTECHNIQUE.FR>
Received: from polytechnique.polytechnique.fr by chenas.inria.fr (5.65c8d/92.02.29)
	via Fnet-EUnet id AA09323; Fri, 15 Oct 1993 12:13:01 +0100 (MET)
Received: by polytechnique.polytechnique.fr (5.65c/SMI-4.1.3)
	id AA29312; Fri, 15 Oct 1993 12:20:54 +0100
Received: from [129.104.27.245] by greco2.noname (4.1/SMI-4.1)
	id AA10522; Fri, 15 Oct 93 12:09:15 +0100
Date: Fri, 15 Oct 93 12:09:15 +0100
Message-Id: <9310151109.AA10522@greco2.noname>
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: ptr@GRECO2.POLYTECHNIQUE.FR (Peter Goedtkindt)
Subject: Re: NIH-Image Message Archives [was: grain counting macros]


>If you have access to gopher, you can connect to gopher.soils.umn.edu
>at port 70 (which can be found under the University of Minnesota "All
>the Gophers in the World" listing), and look under:  
>
>    Computer Information/
>     General Information/
>      Search Nih-Image Mailing List Archives <?>
>

I'm having difficulties using gopher: he's telling me at manny occasions
that he "cannot resolve host name...". I also get a lot of system errors
using TurboGopher. (Sys 7.1, MacTCP 1.1.1)
I've added all the adresses of the mac-ftp-list to my hosts file in the
system folder, and this improved some connections. Can someone help me out
here? We have a domain name server on the campus, but I have sometimes
problems getting to sites of which I only know the name and not the IP
number. This is why I keep a long list on my mac.
Is there a limit on the size of the Hosts file?
Is MacTCP 2.02 better in some way?  Can someone send it to me so I can try
it out. 

Peter Goedtkindt
Universite Paris-Sud 
Laboratoire de Spectroscopie Atomique et Ionique
X-ray Laser group
bat350 
Centre D'Orsay F-91405 Orsay Cedex. France 
Fax.:++33.1.69.41.94.60 - Tel 69.41.77.10
------
And
------
Ecole Polytechnique, Laboratoire d'Utilisation de Lasers Intenses
tel. 69.33.48.95
-----------------------------------------------------------------


From mvivino@helix.nih.gov  Fri Oct 15 04:56:51 1993
Received: from helix.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA08333; Fri, 15 Oct 1993 07:55:16 -0500
Return-Path: <mvivino@helix.nih.gov>
Received: from mavmac.dcrt.nih.gov by helix.nih.gov (5.64/1.35(helix-1.0))
	id AA02969; Fri, 15 Oct 93 08:56:51 -0400
Date: Fri, 15 Oct 93 08:56:51 -0400
Message-Id: <9310151256.AA02969@helix.nih.gov>
X-Sender: mvivino@128.231.2.3
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: mvivino@helix.nih.gov (Mark Vivino)
Subject: Re: modified software by molecular dynamics, Was: wand tool area

>ok .. i have some answers. I am reading 12 bit TIFF from Molecular
>Dynamics. I turns out that if i use some "diddled" version of NIH image
>from Molecular Dynamics, then everything seems ok. If i use the NIH version
>, the images look ok but do not seem to computer ok. 

 I know that NIH Image does measurements just fine. I can't say how many
hundreds of times i have done them and often tested the software and it is
correct. I can't say anything on software which molecular dynamics
modified.


Mark Vivino
NIH/DCRT
mvivino@helix.nih.gov


From sarmienu@rnisd0.DNET.roche.com  Fri Oct 15 09:32:37 1993
Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c)
	id AA10453; Fri, 15 Oct 1993 12:31:05 -0500
Return-Path: <sarmienu@rnisd0.DNET.roche.com>
Received: by gatekeeper.roche.com (5.65/fma-120691);
	id AA00221; Fri, 15 Oct 93 13:32:38 -0400
Received: by mailgate.roche.com (5.65/fma-120691);
	id AA06359; Fri, 15 Oct 93 13:27:15 -0400
From: sarmienu@rnisd0.DNET.roche.com
Message-Id: <9310151727.AA06359@mailgate.roche.com>
Received: from rnisd0.enet; by inet.enet; Fri, 15 Oct 93 13:32:37 EDT
Date: Fri, 15 Oct 93 13:32:37 EDT
To: nih-image@soils.umn.edu
Apparently-To: nih-image@soils.umn.edu
Subject: More on FDA approval

Everybody on the list knows that I have been confronted with the 
problem of validation of the NIH Image program for FDA approval. 
Because of Image rapid increased popularity in the scientific 
community, it is a matter of time before Image becomes widely 
used in Industry. I have been an advocate of the use of NIH Image 
in the drug industry, particularly in the use of the program in 
toxicologic pathology for morphometric use. The program is 
severely limited in that it must be FDA approved before it can be 
used for some studies. This is in response to an E-mail message by 
Dr. Thomas M. Marschner (see below), that may be of use to some 
of the members of this list. I would like to receive separate replies 
to my address from those of you who have an interest in validating 
the system.

>Dear [Dr. Sarmiento]

>I received you e-mail regarding validation of NIH Image.  We have not
>yet validated the program itself--only the particular measurements
>we are concerned with (area and perimeter).  What this means is that we have
>calibrated the system using rulers, and compared the results  with
>"standards" of known area and perimeter.  We are just now starting to
>think about validation of such things as backups, etc.  We are
>probably a bit naive about this since we currently do not yet have
>any approved drugs (we are still in the development phase).  Any insight
>or recommendations you might have are welcome.  One question I have
>is why your computer people think that validation of a public domain
>program is more difficult that validation of any other program.  It's not
>like Microsoft is going to validate Excel for the few users that may
>be using it for GMP data analysis.  Thanks in advance for any suggestions
>you can make. I will keep you informed of any progress we make in
>validating the software.
>
>Sincerely,
>
>Thomas M. Marschner, Ph.D.
>Senior Scientist
>ProCyte Corporation
>tom@peptide.chem.washington.edu
>                                      Dear Dr. Marschner:
Thank you for replying to my message. I have been frustrated and 
disappointed regarding the use of NIH Image for GLP (good 
laboratory practice) studies because recently, FDA (food and drug

administration) has put many restrictions on computer software 
lately. Widely used commercial software such as EXCEL, for 
example, do not require validation, as there are actually millions of 
users to confirm that the application works as advertised. Programs 
with a limited number of users (e.g. NIH Image), require 
verification of every decision routine in the code. Sometimes, 
vendors are able to provide the code and the warranty that the 
verification of the routines have taken place. There are two parts to 
this verification process: 1) Black box verification, in which the 
original data is compared to the processed data, to confirm that the 
computer has done its job, without errors. 2) The White box 
verification which involves the verification of each "if..." decision 
of the code by a computer expert of programmer. Documents 
verifying that both tests have been performed are send to FDA. The 
way I understand it is that the white box testing does not have to be 
made for every routine in the program.

Further, the code must be supplied with the application for 
validation to FDA. Even though the code for NIH Image is 
available, there are some problems inherited of a public domain 
program: The support to the program depends on one individual, 
Wayne Rasband. If something were to happen to Wayne, physically 
or say he'd just give up, the program will be not validatable, as there 
is not the support of an commercial institution behind the program. 
Wayne has said in the past that he has no intention of going 
commercial, which is just fine for must people that cannot afford 
>$3000 worth of commercial image analysis software. Due to the 
fact that this great program is the result of the generosity of Wayne, 
preclude us from asking him to perform time consuming white or 
black box test that would only limit the time he has available to 
upgrade NIH Image, the way he has been doing for the last few 
years. Ironically, those upgrades are a problem with the FDA 
because if the upgrade is major, a new set of validation documents 
would have to be prepared.

Possibly the best solution, perhaps not the cheapest is to take 
advantage of the availability of the NIH Image code and have an in 
house computer programmer validate the program and perhaps 
customize it to the needs of your operation. However, the upgrades 
that Wayne performs regularly are actually quite valuable, I for one 
would hate to loose that feature. A validation test kit that I prepared

containing multiple tests of the morphometric features of NIH 
Image must be used every time a new project is started and every 
time a new version of NIH Image is obtained. We here have gotten 
an error of less than 1% from test to test.

Another solution to the problem is to acquired a commercially 
available spin-off version of NIH Image. Vic Moss in this list 
suggests: "  There is a program Prism View based on Image, but 
including many new features.  This was developed by John Russ 
(NC State Univ) and his son Christian.  For details I suggest you 
contact John Russ at russ@edu.ncsu.mte.mat". Unfortunately, all 
messages that I have sent to that address have bounced.

Another program such as IP Lab may be an alternatively. They are 
planning to or have made the software compatible with Scion's LG-
3 frame grabber, which is the preferred card for NIH Image. I 
personally, prefer NIH Image. It is much more easy to use, since it 
has the tool bar, it is more intuitive and thus easy to teach to 
technicians and other pathologists in this department. You can call 
Paul Kumpe at signal analytics (703) 281 3277.

Finally, just today, I received the following note from Wayne:

>I just found out that MedVision, one of the Mac imaging programs listed in
>Appended D of the NIH Image manual, has FDA 510K approval for clinical use.
>They just moved to Maine, so the phone number in the manual is incorrect.
>
>--wayne
>
>MedVision
>Evergreen Technologies
>Castine, Maine
>207-326-8300, fax:207-326-8333
>evergreen@applelink.apple.com"

Thank you Wayne...

Any comments or suggestions will be appreciated

Juan I. Sarmiento
Department of Toxicology and Pathology
Hoffmann-La Roche, INC.
340 Kingsland street
Nutley, NJ 07110
(201) 235 3907
Sarmienu@RNISD0.DNET.ROCHE.COM

The opinions expressed here are solely my own, for which I am 
solely responsible and do not reflect those of Hoffmann-La Roche Inc.
From jcrum%sunstroke@sdsu.edu  Fri Oct 15 08:21:38 1993
Received: from sdsu.edu by nx1.soils.umn.edu (5.65c)
	id AA12668; Fri, 15 Oct 1993 17:22:23 -0500
Return-Path: <jcrum%sunstroke@sdsu.edu>
Received: from sunstroke.sdsu.edu by sdsu.edu; id AA06393
	sendmail 5.64/SDSU-GW-1.11 via SMTP
	Fri, 15 Oct 93 15:21:40 -0700
Received: from .sdsu.edu (lif_sci_n4-mac6.sdsu.edu) by sunstroke.SDSU.EDU (4.1/SDSU-GENERIC.3)
	id AA00771; Fri, 15 Oct 93 15:21:38 PDT
Date: Fri, 15 Oct 93 15:21:38 PDT
From: jcrum%sunstroke@sdsu.edu (John Crum)
Message-Id: <9310152221.AA00771@sunstroke.SDSU.EDU>
Subject: Image capture on SEM
To: nih-image@soils.umn.edu
X-Mailer: SDSUMail [Version 1.9 beta]
X-Type: TEXT

NIH Image Users:

Is anyone out there using NIH Image and a Macintosh to capture images from 
a scanning electron microscope?  If so, what is the resolution (i.e. image 
size) that you are getting?  What hardware (i.e. image capture board and 
Mac) are you using?  What does it cost?

The reason I ask is that our EM facility is in the market for a new SEM.  
A nice feature we have now on our SEM is image capture, using a part of a 
Princeton Gamma Tech EDS system.  The core of that system, though, is a 
Sun 3/60, which doesn't really work well and will need a costly upgrade.  
We can capture images of 512 pixels and 1024 pixels sqaure.  New software 
(on top of hardware upgrade) will capture 2kX2k images.

So, the ultimate question is: should we adapt the system we have now to a 
new SEM, or buy a new Mac/Image based system?

Any advice is greatly appreciated.

jc

From ZALUZEC@anlemc.msd.anl.gov  Fri Oct 15 13:34:47 1993
Received: from anlemc.msd.anl.gov by nx1.soils.umn.edu (5.65c)
	id AA13074; Fri, 15 Oct 1993 18:33:07 -0500
Return-Path: <ZALUZEC@anlemc.msd.anl.gov>
Date: Fri, 15 Oct 1993 18:34:47 -0500 (CDT)
From: "Nestor J. Zaluzec (708)-252-5075, -4964" <ZALUZEC@anlemc.msd.anl.gov>
To: nih-image@soils.umn.edu
Cc: ZALUZEC@anlemc.msd.anl.gov
Message-Id: <931015183447.20201a62@anlemc.msd.anl.gov>
Subject: Image capture on SEM's



There is a good commerical product which will drive your
SEM scanning system and capture images directly into Photoshop
using plug-ins (don't know if the plug-ins will work using NIH Image)

Contact Scott Davilla at "GO4pi@appleline.apple.com"
or call 919-489-1757, Fax: 919-489-1487.

This is not TV rate acquistion but slow scan control of your SEM
giving you the highest quality digitized SEM pictures (up to 4K x 4K)
I've seen on-line. I plan on buying one for my lab when
I scrap up the $$. 

Ball park cost of the hardware boards is about $7K, assuming
you already have the Mac, Display, SEM, and Photoshop.
 
Nestor Zaluzec
ANL EMCenter
From GARRISSJ@ctrvax.Vanderbilt.Edu  Tue Oct 15 15:31:08 1993
Received: from ctrvx1.Vanderbilt.Edu by nx1.soils.umn.edu (5.65c)
	id AA13816; Fri, 15 Oct 1993 20:29:39 -0500
Return-Path: <GARRISSJ@ctrvax.Vanderbilt.Edu>
Received: from ctrvax.Vanderbilt.Edu by ctrvax.Vanderbilt.Edu (PMDF #3899 ) id
 <01H45K9TMHU88WYXDY@ctrvax.Vanderbilt.Edu>; Fri, 15 Oct 1993 20:31:08 CDT
Date: 15 Oct 1993 20:31:08 -0500 (CDT)
From: GARRISSJ@ctrvax.Vanderbilt.Edu
Subject: Message to Unknown Beginner on List (10/15/93)
To: nih-image@soils.umn.edu
Message-Id: <01H45K9TMHUA8WYXDY@ctrvax.Vanderbilt.Edu>
X-Vms-To: IN%"nih-image@soils.umn.edu"
Mime-Version: 1.0
Content-Transfer-Encoding: 7BIT

A beginning user of Image wrote about needing general info. about setting 
up a sytem for image analysis.  I'm sorry, but I lost your msg., but you 
are in precisely the same position as I am.  I need to set up a lab for 
scanning gels and film in biology and can't decide which hardware (cameras, 
scanners, frame grabbers, etc) to use, which software (besides Image) and 
how to link the whole system together so it works.

Our lab has Centris 650's with 8 mb of RAM.  I understand that a high-res
monochrome camera is preferable to color.  Image supports particular 
frame-grabbers and scanners (that much can be seen from the Image Manual).  
It's scary thinking about buying components, though and not being sure if 
the system will work!

One stumbling block seems to be the difficulty in digitizing ethidium 
bromide gels, because UV light while viewing the gel, not regular visible 
light.  Apparently cameras have a hard time picking up the image because of 
low-light conditions.  Sorry to ramble on.  This is the system we are 
thinking of putting together:

	Cohu monochrome camera
	Scion frame-grabber
	Image software with export to Adobe Photoshop & MS Word 
	A dual-purpose illuminator (UV & visible)
	Centris 650 computer
Oh, and the purpose of the lab is for students to run gels, clean them up 
(on screen) and print out the results for their lab notebooks.  The lab 
set-up is not intended for research purposes.

Please comment, anyone.

Thanks.

-------------------------------------------------------------------------
Steve Garrison         Internet username: GARRISSJ@CTRVAX.VANDERBILT.EDU
	Vanderbilt University
	Dept. of Molecular Biology    or.... Learning Technology Center
		615-322-4942                 Vanderbilt University
		                             322-8070
 
-------------------------------------------------------------------------
From rms@acsu.buffalo.edu  Fri Oct 15 17:39:23 1993
Received: from autarch.acsu.buffalo.edu by nx1.soils.umn.edu (5.65c)
	id AA13954; Fri, 15 Oct 1993 20:37:49 -0500
Return-Path: <rms@acsu.buffalo.edu>
Received: from rms@localhost by autarch.acsu.buffalo.edu (8.5/8.5)
	id VAA19083; Fri, 15 Oct 1993 21:39:23 -0400
Date: Fri, 15 Oct 1993 21:39:23 -0400
From: "Robert M. Straubinger" <rms@acsu.buffalo.edu>
Message-Id: <199310160139.VAA19083@autarch.acsu.buffalo.edu>
To: nih-image@soils.umn.edu
Subject: Re:  More on FDA approval


Juan I. Sarmiento writes:

      [deleted discussion of FDA and validation of NIH Image]

We're interested in this topic as well, as (if the gods smile)
we may need to do particle sizing for pre-IND purposes. One 
point brought up:
> Possibly the best solution, perhaps not the cheapest is to take 
> advantage of the availability of the NIH Image code and have an in 
> house computer programmer validate the program and perhaps 
> customize it to the needs of your operation. However, the upgrades 
> that Wayne performs regularly are actually quite valuable, I for one 
> would hate to loose that feature. 
   And these frequent updates likewise may also be a major source of trouble,
since changes thought to be inconsequential might be made without documentation,
perhaps. In your experience, is it possible that if (say) major-release 
versions of the program were 'frozen' in object-library format, then
only new routines would have to be validated?

>A validation test kit that I prepared
>containing multiple tests of the morphometric features of NIH 
>Image must be used every time a new project is started and every 
>time a new version of NIH Image is obtained. We here have gotten 
>an error of less than 1% from test to test.

  If there is general interest, do you think the 'black box'
data could be posted or otherwise made available? Perhaps it
would be relatively painless to assemble a database for
black-box qualification of the program. We recently have
had trouble repeating measurements done with a script developed
for a version somewhere around 1.43, so this question of qualifying
new versions of NIH Image is an important one even outside the 
context of FDA approval.

  If it turns out there is too little interest to keep this discussion
going in the mailing list, and it goes off-line, please keep in mind that
we're interested in how things develop, for the above reasons.

Bob Straubinger
Pharmaceutics
SUNY/Buffalo
From kartenh@Sdsc.Edu  Sat Oct 16 20:51:36 1993
Received: from Sdsc.Edu (m5.sdsc.edu) by nx1.soils.umn.edu (5.65c)
	id AA21711; Sat, 16 Oct 1993 15:50:12 -0500
Return-Path: <kartenh@Sdsc.Edu>
Date:    Sat, 16 Oct 93 20:51:36 GMT
From: kartenh@Sdsc.Edu (Harvey Karten)
Message-Id: <931016205136.204079d8@m5.sdsc.edu>
Subject: RE: Message to Unknown Beginner on List (10/15/93)
To: nih-image@soils.umn.edu
X-St-Vmsmail-To: ST%"nih-image@soils.umn.edu"
X-St-Vmsmail-Cc: KARTENH

I have both a Cohu and a Sony/Dage camera. The Cohu is somewhat more sensitive 
to lower light levels, but is of poorer image quality. It has had to be recalilbrated
recalibrated on several occasions, and gives a crummy 
image when the calibration deteriorates. The Sony/Dage
gives an excellent image, has not deteriorated in image
quality over the past several years, and has proven an 
excellent general workhorse. (I am referring to the B&W-
monochrome camera). If you do decide to go for a color camera, 
you should consider the three chip Sony or the 3 chip 
Panasonic. The one chip color camera from Sony gives a decent image, 
but if you attempt to use it as a monochrome camera, the results
are not satisfactory, when compared to a true monochrome (having 
to do with the way a single chip color CCD is manufactured). If you use 
is as a color camera you will be very disappointed. The image will not 
be as crisp as that with a 3 chip configuration. 
				H. Karten
From @CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu  Sat Oct 16 17:05:00 1993
Received: from cunyvm.cuny.edu by nx1.soils.umn.edu (5.65c)
	id AA23846; Sat, 16 Oct 1993 22:11:04 -0500
Return-Path: <@CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu>
Received: from darban.cc.usm.edu by CUNYVM.CUNY.EDU (IBM VM SMTP V2R2) with TCP;
   Sat, 16 Oct 93 23:11:41 EDT
Received: by darban.cc.usm.edu (5.57/Ultrix3.0-C)
	id AA15680; Sat, 16 Oct 93 22:11:36 -0500
Date: Sat, 16 Oct 93 22:05 CDT
From: GLEN SHEARER <GLEN_SHEARER@bull.cc.usm.edu>
To: nih-image@soils.umn.edu
Really-To: nih-image@soils.umn.edu
Subject: hand scanners
Message-Id: <931016.22072692.038073@USM.CP6>

Any recommendations for hand held scanners that work with
Image?

Glen Shearer<glen_shearer@bull.cc.usm.edu>
From H.Patel@southampton.ac.uk  Mon Oct 18 06:21:11 1993
Received: from sun2.nsfnet-relay.ac.uk by nx1.soils.umn.edu (5.65c)
	id AA07369; Mon, 18 Oct 1993 06:21:11 -0500
Return-Path: <H.Patel@southampton.ac.uk>
Via: uk.ac.southampton; Mon, 18 Oct 1993 12:14:38 +0100
From: "H.Patel" <H.Patel@southampton.ac.uk>
Message-Id: <2894.9310181106@mail.soton.ac.uk>
Date: Mon, 18 Oct 93 12:06:14 BST
To: nih-image@soils.umn.edu
Subject: Re: Another Beginner's Question
In-Reply-To: <9310120642.AA17554@lurch.smhi.se>; from "mmoberg@smhi.se" at Oct 12, 93 1:42 am
X-Mailer: ELM [version 2.3 PL11]



More really basic questions yet again.

I'm trying to use Image for the first time and in a lab where no one has any
working knowledge of it at all.

So 2 questions?

1  I have used ftp to get the image program. What is the difference between the
fpu and non-fpu programs?

2  Is there anyone in the United Kingdom using Image for densitometry. (or
anyone coming anywhere near Southampton who could talk me through it ?)

H.Patel,
Clinical Neurological Sciences,
Southampton General Hospital,
Southampton,
SO9 4XY,
U.K.
From herro001@maroon.tc.umn.edu  Mon Oct 18 01:46:30 1993
Received: from maroon.tc.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA07505; Mon, 18 Oct 1993 06:44:58 -0500
Return-Path: <herro001@maroon.tc.umn.edu>
Message-Id: <199310181144.AA07505@nx1.soils.umn.edu>
Received: from dialup-slip-1-27.gw.umn.edu by maroon.tc.umn.edu id SMTP-0012cc2820f026686; Mon, 18 Oct 93 06:46:26 -0500
From: "Mike Herron" <herro001@maroon.tc.umn.edu>
Reply-To: "Mike Herron" <herro001@maroon.tc.umn.edu>
To: nih-image@soils.umn.edu
Subject: Re: Another Beginner's Question
Date: Mon, 18 Oct 93 06:46:30 -0500

    The fpu version is for Macs _WITH_ an fpu (an fpu does floating point 
calculcations _much_ faster and speeds up a few of the NIH Image functions).  
Any Mac with a true 68040 already has an fpu built in (it is part of the 68040 
chip) A mac with a 68030 (IIsi,LC III, Color Classic, et. al.) may or may not 
have an fpu (you can easily install one for about $80)

  The densitometry thing is so simple I doubt you will need help!  There is a 
macro for scanning gels in the macro folder that does this on electrophoresis 
gels, and there is a pretty good explanation of the whole thing in the manual 
too.  The only slightly confusing aspect is which measurement to use.  There was
a good post on this point recently could someone repost it?


In message <2894.9310181106@mail.soton.ac.uk>  writes:
> 
> 
> More really basic questions yet again.
> 
> I'm trying to use Image for the first time and in a lab where no one has any
> working knowledge of it at all.
> 
> So 2 questions?
> 
> 1  I have used ftp to get the image program. What is the difference between 
> the
> fpu and non-fpu programs?
> 
> 2  Is there anyone in the United Kingdom using Image for densitometry. (or
> anyone coming anywhere near Southampton who could talk me through it ?)
> 
> H.Patel,
> Clinical Neurological Sciences,
> Southampton General Hospital,
> Southampton,
> SO9 4XY,
> U.K.
> 


  _____________________________________________________________
 / Michael J. Herron  University of MN,  Dept. of Dermatology /
/ herro001@staff.tc.umn.edu                                  /
_____________________________________________________________

From smithj@acad.winthrop.edu  Mon Oct 18 05:17:09 1993
Received: from acad ([192.203.180.3]) by nx1.soils.umn.edu (5.65c)
	id AA08163; Mon, 18 Oct 1993 08:18:05 -0500
Return-Path: <smithj@acad.winthrop.edu>
Message-Id: <199310181318.AA08163@nx1.soils.umn.edu>
Date: Mon, 18 Oct 1993 09:17:09 -0400
From: smithj@acad.winthrop.edu
To: nih-image@soils.umn.edu
Subject: Video for TEM?
X-Vms-To: SMTP%"nih-image@soils.umn.edu"

Hi, 
I'm interested in hooking a video camera to my  TEM (JEOL 100B):  
1)To demonstrate procedures such as filament saturation and 'scope 
alignment when teaching my EM class, and 2)  To capture "quickie" 
EM prints to a video printer for students in my cell bio and vertebrate 
histology classes.  I'm looking for about 640x480 pixels and 8 bits, and 
would like something that covers about the same area at each 
magnification as the film camera.  
I know about Gatan's systems, and I've  been told "look at the Fullam 
system before you buy it".  Is there anything else out there that I should 
know about?  Have any of you used either the Gatan system or the Fullam 
system, and how satisfied are you with it?  Any help/feedback would be 
appreciated. 
TIA 
Julian Smith III
(smithj@winthrop.edu)
From Scott.Wurcer@analog.com  Mon Oct 18 06:30:11 1993
Received: from nic.near.net by nx1.soils.umn.edu (5.65c)
	id AA08924; Mon, 18 Oct 1993 09:29:27 -0500
Return-Path: <Scott.Wurcer@analog.com>
Received: from [137.71.23.11] by nic.near.net id aa12160; 18 Oct 93 10:30 EDT
Received: from nwd2sun1.analog.com ([137.71.22.41]) by adi.analog.com
Received: from titania.adsdesign.analog.com by nwd2sun1.analog.com (4.1/SMI-4.1)
Message-Id: <9310181429.AA11453@nwd2sun1.analog.com>
Received: from hermia.adsdesign.analog.com by titania.adsdesign.analog.com
Date: Mon, 18 Oct 93 10:30:11 EDT
From: Scott Wurcer <Scott.Wurcer@analog.com>
To: nih-image@soils.umn.edu
Subject: Plug-Ins

I just finished my first plug-in. It translates packed 12-bit data from a Lynxx
CCD camera into 8-bit. I noticed that in Image the window does not show the
file name, even though Photoshop does. Does 1.53 fix this? BTW I agree with
a previous poster that adding plug-ins is a great addition to Image, at least
it allows me to keep working in C. 
From wayne@helix.nih.gov  Mon Oct 18 10:37:02 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA09694; Mon, 18 Oct 1993 10:38:26 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA18852; Mon, 18 Oct 93 10:58:30 -0400
Message-Id: <9310181458.AA18852@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Mon, 18 Oct 1993 10:37:02 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Plug-Ins

>I just finished my first plug-in. It translates packed 12-bit data from a Lynxx
>CCD camera into 8-bit. I noticed that in Image the window does not show the
>file name, even though Photoshop does. Does 1.53 fix this? BTW I agree with
>a previous poster that adding plug-ins is a great addition to Image, at least
>it allows me to keep working in C. 

Do you plan to make this plug-in available to other NIH Image users? It
would be helpful to others trying to write file import plug-ins to have a
source code example to look at.

The acquistion file name bug will be fixed in the next 1.53 beta (1.53b17
or later), which I will upload to Zippy by the end of the week. I'm adding
on a nifty new command called "Image Math" that does image arithmetic and
allows you to specify the gain and offset values used to convert the result
back to 8-bits. The dialog box uses pop-up menus for specifying the two
source images and the operation to be performed.

--wayne


From sarmienu@rnisd0.DNET.roche.com  Mon Oct 18 08:23:26 1993
Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c)
	id AA10242; Mon, 18 Oct 1993 11:21:58 -0500
Return-Path: <sarmienu@rnisd0.DNET.roche.com>
Received: by gatekeeper.roche.com (5.65/fma-120691);
	id AA12670; Mon, 18 Oct 93 12:23:27 -0400
Received: by mailgate.roche.com (5.65/fma-120691);
	id AA24906; Mon, 18 Oct 93 12:16:48 -0400
From: sarmienu@rnisd0.DNET.roche.com
Message-Id: <9310181616.AA24906@mailgate.roche.com>
Received: from rnisd0.enet; by inet.enet; Mon, 18 Oct 93 12:23:26 EDT
Date: Mon, 18 Oct 93 12:23:26 EDT
To: nih-image@soils.umn.edu
Apparently-To: nih-image@soils.umn.edu
Subject: Updated, Sorted reference list

Use the following quote when mentioning image in the materials and methods
section of a manuscript"... analysis performed in a Macintosh [model] computer
using the public domain NIH Image software program (written by Wayne Rasband at
the U.S. National Institutes of Health and available electronically via Internet
by anonymous ftp from zippy.nimh.nih.gov or from Library 9 of the MacApp forum
on CompuServe and on floppy disk from NTIS, 5285 Port Royal Rd.,Springfield, VA
22161, part number PB93-504868). To appear in a medline search the words "NIH
Image" must appear in either the abstract or the Keywords index. Therefore, all
people publishing manuscripts using NIH Image should include the name of the
program in the abstract whenever possible. 

Here is an update in the list of references which quote image. I have
volunteered to update the list periodically. Please continue to send me new
references, as they become available, to my address (see below),. If any of you
notice an error, please let me know. 

Thank you to all contributors. Suggestions and comments to my address below,
please


Juan I. Sarmiento
Department of Toxicology and Pathology
Hoffmann-La Roche, INC.
340 Kingsland street
Nutley, NJ 07110
(201) 235 3907
Sarmienu@RNISD0.DNET.ROCHE.COM

---------------------------------------------------------------------------
              References for NIH-Image

Adam DR, Kempner KM, Vivino MA, Tucker EE, Jones M, "Measurement of Flow
Velocity in a Phantom by Corrected Doppler Color Mapping Technique, using
Transverse Cross-Sectional Imaging", Computers in Cardiology 1993, in press

Bouabid, R., E.A. Nater, and P. Barak. 1992. Measurement of particle and pore
size distribution in a lamellar B horizon by fluorescence microscopy and image
analysis. Geoderma 53 (3/4):309-328.

Brenneman & collaborators. Nature, March, 1993 (Title has something to do with
VIP)

Bright, D. S. Software Tools for examination of microanalytical images. pp.
73-78 in MICROBEAM ANALYSIS 1990, SAN FRANCISCO Press, CA.

Bright, D.S., Steel, E.B. and Newbury, D.E. (1991), "Visibility of Objects in
Noisy Images as a Function of Contrast, Noise Level, and Object Size", Microbeam
Analysis 1991: 185-188. 

Chiang, P.K., et. al., "Activation of Collagen IV Expression in F9
Teratocarcinoma Cells by 3-Deazaadenosine Analogs", Journal of Biological
Chemistry, Vol. 267, No. 7, March 1992.

Chien, CB; DE Rosenthal, WA Harris, and CE Holt, (1993) "Navigational errors
made by growth cones without filopodia in the embryonic Xenopus brain." Neuron
11:237-251.

Chin DJ; Green G; Zon G; Szoka FC; Straubinger RM; Rapid nuclear accumulation of
injected oligodeoxyribonucleotides. New Biologist 2: 1091- 1100, 1990.

Chin DJ; Straubinger RM; Acton S; Nathke I; Brodsky FM; 100kDa polypeptides in
peripheral clathrin-coated vesicles are required for receptor- mediated
endocytosis. Proc. Natl. Acad. Sci. 86: 9289-93, 1989

Correa-Rotter, R., et. al., "Loading and Transfer Control for Northern
Hybridization", BioTechniques, Vol. 12, No. 2 (1992).

Correa-Rotter, Ricardo et. al., Loading and Transfer Control for Northern
Hybridization, BioTechniques, Vol. 12, No 2, 1992, pages 154-158.

D'Amelio, F. and N.G. Daunton. Effects of spaceflight in the adductor longus
muscle of rats flown in the Soviet biosatellite COSMOS 2044. A study employing
neural cell adhesion molecule (N-CAM) immunocytochemistry and conventional
morphological techniques (light and electron microscopy). J. Neuropath. Exp.
Neurol. 51(4):415-431, 1992.

DeVoogd, T.J., Krebs, J.R., Healy, S.D. & Purvis, A. "Relations between song
repertoire size and the volume of brain nuclei related to song: comparative
evolutionary analyses amongst oscine birds." In press, Proc. Roy. Soc Lon. B.

Dyck, RH and Cynader MS (1993) An interdigitated columnar mosaic of cytochrome
oxidase, zinc, and neurotransmitter-related molecules in cat and monkey visual
cortex. Proceedings of the National Academy of Science, USA, 90, 9066-9069.

Dyck, RH and Cynader MS (1993) Autoradiographic localization of serotonin
receptor subtypes in cat visual cortex: regional, laminar, and columnar
distributions during postnatal development. Journal of Neuroscience, 13,
4316-4338. Biophys. J. 60:629-641 (1991)

Dyck, RH and Cynader, MS (1993) Histochemical localization of synaptic zinc in
the developing kitten visual cortex. Journal of Comparative Neurology, 329,
53-67.

Ford-Holevinski, Thomas et al., Microcomputer-based Three-dimensional
Reconstruction of in situ Hybridization Autoradiographs, Journal of Chemical
Neuroanatomy, Vol 4, 1991, pages 373-385.

Garlow, S.J., Morilak, D.A., Dean, R.R., Roth, B.L. and Ciaranello, R.D. (1993)
Production and characterization of a specific 5-HT2 receptor antibody. Brain
Research, 615: 113-120.

Gough, A.H. and Taylor, D. L. (1993) Journal of Cell Biology, 121:5:1095-1107.
T. K. Teague, L.L. Munn, K. Zygourakis and B.W. McIntyre "Analysis of Lymphocyte
Activation and Proliferation by Video Microscopy and Digital Imaging,"
Cytometry, in press (1993).

Gwon, A.E., et. al., "Lens Regeneration in Juvenile and Adult Rabbits Measured
by Image Analysis", Investigative Ophthalmology & Visual Science, Vol. 33, No.
7, June 1992.

Hammer, R.P., Bogic, L. and Handa, R.J.: Estrogenic regulation of proenkephalin
mRNA expression in the ventromedial hypothalamus of the adult male rat,
Molecular Brain Research, 19: 129- 134, 1993. 

Hammer, R.P., Margulies, J.E., Lynn, A.B. and Brady, L.S.: Chronic fluoxetine
treatment up- regulates dopamine receptors in the mesolimbic forebrain of the
rat, Depression, 1: 82-87, 1993.

Hammer, R.P., Pires,W.S., Markou, A. and Koob, G.F.: Withdrawal following
cocaine self- administration decreases regional metabolism in critical brain
reward regions, Synapse, 14: 73-80, 1993.

Herd, R.A. & Pinkerton, H. 1993. Bubble coalescence in magmas. Lunar and
Planetary Science Conference. XXIV(2). p.641-642. W. Rasband. NIH Image: An
image processing software package for the Macintosh II. Available free of charge
from Wayne Rasband, NIH, Bldg. 36, Rm. 2A03, Bethesda, MD 20892", ref. 3 in

Hermansson, Roger . An experimental and numerical investigation of phenomena
that affect the degree of therminal stratification. Lulea Univ. of Technology.
Lulea Sweden. 1993:127D

Hill, Ester; Emily Holton. J. Orthopedic Research. 1993 

Lieberman, D.E., et. al., "Computer Image Enhancement and Analysis of Cementum
Increments as Applied to Teeth of Gazella gazella", Journal of Archaeological
Science, in press (1989).

Lulea University. Short Term Water Heat storage : Studies of Velocity and
Temperature Fields and their Importance for sizing of the Storage. Lulea Univ.
of Technology. Lulea Sweden. 1993:131D

Magunda, M.K. 1992. Influence of some physico- chemical properties on soil
strength, stability of crusts and soil erosion. Ph.D. Dissertation. Bouabid, R.
1992. Soil solution chemistry, mineral weathering, and pedogenesis in sandy
outwash soils of east-central Minnesota. Ph.D. Dissertation.

Mansfield, John F. & Douglas C. Crawford. Thickness Measurement in the
Analytical Electron Microscope by Macintosh-based analysis of two-beam
convergent beam patterns. IN: Proc. XIIth Int. Cong. for EM (1990) p504-505.

Mansfield, John F. Visit Thaveeprungsriporn & Gary S. Was. Design And
Construction Of An Electron Back-Scattering Pattern Camera For The Environmental
Scanning Electron Microscope. Scanning 15 (1993) pIII36-III37

Masters, D.B., et. al., "High Sensitivity Quantification of RNA from Gels and
Autoradiograms with Affordable Optical Scanning", BioComputing, Vol. 12, No. 6
(1992).

Meiners, S., Marone, M., Rittenhouse, J.L, Geller, H.M. Basic FGF upregulates
tenascin in cultured astrocytes. Dev. Biol., 1993, in press.

Munn, L.L. M.W. Glacken, B.W. McIntyre and K. Zygourakis "Analysis of Lymphocyte
Aggregation Using Digital Image Analysis," J. Immunol. Methods, in press (1993).

O'Neill, R. et al., Use of Image Analysis to Quantitate Changes in Form of
Mitochondrial DNA After X-irradiation, Applied and Theoretical Electrophoresis,
1989-1, pages 163-167. 

Parry, Robert et. al., Computer-Aided Cell Colony Counting, BioTechniques, Vol.
10, No 6, 1991, pages 772- 774.

Plotorak, M., et. al., "L1 Substrate Enhances Outgrowth of Tyrosine
Hydroxylase-Immunoreactive Neurites in Mesencephalic Cell Culture", Experimental
Neurology 117, 176-184 (1992).

Reiss, A.L., et. al., "Neuroantomy of Fragile X Syndrome: the Posterior Fossa,
Annals of Neurology, Vol. 29, No. 1, January 1991.

Richardson ML, Gillespy TG 3rd. An inexpensive computer-based digital imaging
teaching file. Am J Roentgenology 1993;160:1299-1301.

Richardson ML. Using a personal computer to create anatomic drawings for
publication. Am J Roentgenology 1993, in press.

Schwartz, David C., Xiaojun Li, Luis I. Hernandez, Satyadarshan P. Ramnarain,
Edward J. Huff, Yu-Ker Wang. Ordered Restriction Maps of Saccharomyces
Cerevisiae Chromosomes Constructed by Optical Mapping. Science 262:110 (1993)

Velocoimetry ( PIV) in process Metallurgy for Steal mills. Gabriella Trandell :
Modelling of tundish alloying for small lot production. Lulea Univ. of
Technology. Lulea Sweden. 1992:100E 

Vivino MA, Chintalagiri S, Trus BL, Datiles M, "Development of a Scheimpflug
Slit Lamp Camera System for Quantitative Densitometric Analysis", Eye, Vol 7,
number 6

Xuan-Hui Guo, Edward J. Huff and David C. Schwartz. Sizing of Large DNA
Molecules by Hook Formation in a Loose Matrix. Journal of Biomolecular Structure
& Dynamics, Volume 11, Issue 1 (1993) pp 1-10
From mk@nwu.edu  Mon Oct 18 06:03:27 1993
Received: from merle.acns.nwu.edu by nx1.soils.umn.edu (5.65c)
	id AA10569; Mon, 18 Oct 1993 12:02:02 -0500
Return-Path: <mk@nwu.edu>
Received: from aragorn27.acns.nwu.edu by merle.acns.nwu.edu with SMTP
	(1.36.108.4.1.1/16.2) id AA10831; Mon, 18 Oct 93 12:03:29 -0500
Message-Id: <9310181703.AA10831@merle.acns.nwu.edu>
X-Sender: mkhokha@merle.acns.nwu.edu
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Mon, 18 Oct 1993 12:03:27 -0600
To: nih-image@soils.umn.edu
From: mk@nwu.edu (M. Khokha)
Subject: Data Output

Hello Everyone,

I was wondering if anyone had any thoughts about output of image files to
generate figures to submit for application.  I have created and analyzed a
large number of image files and finally gotten some interesting results
that I would now like to publish.  I would also like to create a figure for
the paper that shows some of the images that I generated.  The problem is
how do I turn my image file into something on paper that I can send to a
journal?  Unfortunately the journal that I would like to submit to does not
accept electronic submissions.


>From what I know there are a couple of ways to do this:

A film recorder to create a slide and then turn that into a print.

A dye sublimation printer

Service bureaus that will accept electronic images and then make prints

The problem with theses methods is that they require either multiple steps
so that they take a long time making experimentation on what looks the best
rather impossible or too expensive.

I was wondering what other people do.

Thanks,



Mustafa Khokha (mk@nwu.edu)                       
Markey Program in Developmental Biology  T239   
Northwestern University Medical School                 
303 E. Chicago Ave                               Tel:(312) 503-5232
Chicago  IL 60611-3008                       FAX:(312) 908-5253
U.S.A.


From @CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu  Mon Oct 18 07:09:00 1993
Received: from cunyvm.cuny.edu by nx1.soils.umn.edu (5.65c)
	id AA10708; Mon, 18 Oct 1993 12:12:48 -0500
Return-Path: <@CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu>
Received: from darban.cc.usm.edu by CUNYVM.CUNY.EDU (IBM VM SMTP V2R2) with TCP;
   Mon, 18 Oct 93 13:13:19 EDT
Received: by darban.cc.usm.edu (5.57/Ultrix3.0-C)
	id AA17487; Mon, 18 Oct 93 12:13:07 -0500
Date: Mon, 18 Oct 93 12:09 CDT
From: GLEN SHEARER <GLEN_SHEARER@bull.cc.usm.edu>
To: nih-image@soils.umn.edu
Really-To: soillist
Subject: sequence reader
Message-Id: <931018.12104548.039175@USM.CP6>

Has anyone tried to write a macro to read DNA sequence films
with Image?  It seems that the potential is there in terms of
image manipulations.

Glen Shearer<glen_shearer@bull.cc.usm.edu>
From mvivino@helix.nih.gov  Mon Oct 18 10:32:05 1993
Received: from helix.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA11472; Mon, 18 Oct 1993 13:30:35 -0500
Return-Path: <mvivino@helix.nih.gov>
Received: from mavmac.dcrt.nih.gov by helix.nih.gov (5.64/1.35(helix-1.0))
	id AA07631; Mon, 18 Oct 93 14:32:05 -0400
Date: Mon, 18 Oct 93 14:32:05 -0400
Message-Id: <9310181832.AA07631@helix.nih.gov>
X-Sender: mvivino@128.231.2.3
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: mvivino@helix.nih.gov (Mark Vivino)
Subject: Re: sequence reader

>Has anyone tried to write a macro to read DNA sequence films
>with Image?  It seems that the potential is there in terms of
>image manipulations.

In case anyone has an interest in this, I was given a snipet of 'c' code
several years ago that could read in raw data files from an Applied
Biosystems sequencer. I never bothered to try and port it to NIH Image, but
if someone has the kind of signal processing interest let me know and I'll
see if I can dig it out. Warning though, I doubt it is as nicely flowing
and elegantly programmed as wayne rasband's code.



Mark Vivino
NIH/DCRT
mvivino@helix.nih.gov


From djm@cidmv1.wustl.edu  Mon Oct 18 09:10:47 1993
Received: from wugate.wustl.edu by nx1.soils.umn.edu (5.65c)
	id AA11940; Mon, 18 Oct 1993 14:11:27 -0500
Return-Path: <djm@cidmv1.wustl.edu>
Received: by wugate.wustl.edu (5.67a+/WUSTL-0.3) with DECnet 
	id AA16153; Mon, 18 Oct 1993 14:10:48 -0500
Date: Mon, 18 Oct 1993 14:10:47 -0500
Message-Id: <199310181910.AA16153@wugate.wustl.edu>
From: djm@cidmv1.wustl.edu (D.J. Meyer)
To: "nih-image@soils.umn.edu"@WUGATE.wustl.edu
Subject: Removing Blur though Deconvolution


Hi,
can anyone give me an explanation of how this works?
thank
dj meyer
From jcrum%sunstroke@sdsu.edu  Mon Oct 18 05:20:14 1993
Received: from sdsu.edu by nx1.soils.umn.edu (5.65c)
	id AA12077; Mon, 18 Oct 1993 14:21:38 -0500
Return-Path: <jcrum%sunstroke@sdsu.edu>
Received: from sunstroke.sdsu.edu by sdsu.edu; id AA15810
	sendmail 5.64/SDSU-GW-1.11 via SMTP
	Mon, 18 Oct 93 12:20:16 -0700
Received: from .sdsu.edu (lif_sci_n4-mac5.sdsu.edu) by sunstroke.SDSU.EDU (4.1/SDSU-GENERIC.3)
	id AA07528; Mon, 18 Oct 93 12:20:14 PDT
Date: Mon, 18 Oct 93 12:20:14 PDT
From: jcrum%sunstroke@sdsu.edu (John Crum)
Message-Id: <9310181920.AA07528@sunstroke.SDSU.EDU>
Subject: Re  Data Output
To: nih-image@soils.umn.edu
X-Mailer: SDSUMail [Version 1.9 beta]
X-Type: TEXT

Mustafa Khokha:

If you don't have the hardware (or time), go with the service bureau.  The 
one we use here in San Diego uses a Linotronic L300 to output to film or 
paper.  The costs are farily reasonable.  For an 8.5 X 11 on RC paper the 
costs is $6.00 for 1200dpi and $7.50 for 2400dpi.  Multiple copies of the 
same file run at the same time are 1/2 price.  We have printed grayscale 
images from SuperPaint at both the medium and high resolution and saw little 
difference- 1200dpi is probably the limit of resolution for SuperPaint.  If 
you use them, you must ask them what file formats and what media formats they 
support.  If your files are big (larger than 1.4MB), use a SyQuest drive, as 
most of the service bureaus have them.  Also, many service bureaus also like 
PostScript files, instead of applications files because they can print a PS 
file from any application whereas they have to have the application to print 
a file of that applications format.  For instance, they probably don't have 
NIH Image, so you would have to save the file in another application (that 
they have) or convert your files to PostScript.  They might also take PICT or 
TIFF files, too, but check with them first.

If you have any more question, please feel free to write.

John Crum
San Diego State University

From bbug1@cc.swarthmore.edu  Mon Oct 18 12:06:35 1993
Received: from oak.cc.swarthmore.edu by nx1.soils.umn.edu (5.65c)
	id AA12550; Mon, 18 Oct 1993 15:05:15 -0500
Return-Path: <bbug1@cc.swarthmore.edu>
Received: from [130.58.70.120] (mac05.martin2.swarthmore.edu [130.58.70.120]) by oak.cc.swarthmore.edu (8.6.2/8.6.2) with SMTP id QAA10064 for <nih-image@soils.umn.edu>; Mon, 18 Oct 1993 16:06:35 -0400
Date: Mon, 18 Oct 1993 16:06:35 -0400
Message-Id: <199310182006.QAA10064@oak.cc.swarthmore.edu>
X-Mailer: Eudora/Swarthmore 1.3b116
To: nih-image@soils.umn.edu
From: Bill Bug <bbug1@cc.swarthmore.edu>
Subject: Re: Removing Blur though Deconvolution

>Hi,
>can anyone give me an explanation of how this works?
>thank
>dj meyer

Two references that cleared the haze for me:

1) Castelman, K.R.(1979) Digital image processing. Prentice-Hall,Inc.,
Englewood Cliffs, NY, 429pp.
                * THE general reference on digital imaging techniques; most of  
                        the subsequent work in this field has derived from 
                        algorithms outlined in this book

2) Monck, J.R., Oberhauser,A.F., Keating, T.J., Fernandez, J.M. (1992)
Thin-section ratiometric Ca+2 images obtained by optical sectioning of
fura-2 loaded mast cells
                * This is an extremely well illustrated example of some of the 
                        less computationally-intense methods for applying 
                        digital deconvolution.  They compare and evaluate
                        several methods, testing them on model and real data 
                        sets.


Good luck!!

Cheers,
Bill Bug


*************************
*  Bill Bug             *
*  Dept. of Biology     *
*  Swarthmore College   *
*************************

From John_Mansfield@mse.engin.umich.edu  Mon Oct 18 16:11:54 1993
Received: from mse.engin.umich.edu by nx1.soils.umn.edu (5.65c)
	id AA13205; Mon, 18 Oct 1993 16:11:54 -0500
Return-Path: <John_Mansfield@mse.engin.umich.edu>
Message-Id: <199310182111.AA13205@nx1.soils.umn.edu>
Date: 18 Oct 1993 17:06:32 U
From: "John Mansfield" <John_Mansfield@mse.engin.umich.edu>
Subject: Re: Data Output
To: nih-image@soils.umn.edu

         Reply to:   RE>Data Output
The Kodak Dye Sublimation Printer Model ColorEase PS 300 should do the job for
you very nicely,  Around $7000 university price.


From V112LNKD@ubvms.cc.buffalo.edu  Mon Oct 18 15:27:15 1993
Received: from ubvmsc.cc.buffalo.edu by nx1.soils.umn.edu (5.65c)
	id AA14553; Mon, 18 Oct 1993 18:53:53 -0500
Return-Path: <V112LNKD@ubvms.cc.buffalo.edu>
Received: from ubvms.cc.buffalo.edu by ubvms.cc.buffalo.edu (PMDF V4.2-13
 #3449) id <01H49PA6Q1CK8WXM1U@ubvms.cc.buffalo.edu>; Mon,
 18 Oct 1993 19:27:15 EDT
Date: Mon, 18 Oct 1993 19:27:15 -0400 (EDT)
From: V112LNKD@ubvms.cc.buffalo.edu
Subject: scale to fit window
To: nih-image@soils.umn.edu
Message-Id: <01H49PA6Q1CM8WXM1U@ubvms.cc.buffalo.edu>
Organization: University at Buffalo
X-Vms-To: IN%"nih-image@soils.umn.edu"
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII
Content-Transfer-Encoding: 7BIT

hi, I'm trying to use the scale to fit window function to resize two electrophor
etic gels (so that they may appear the same size, for analysis)...So, i open the
 two images and use the scaling function to get both the same size.  But, how ca
n you keep the new scale of the image...thanks for any advice.....Mark
From @CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu  Tue Oct 19 03:06:00 1993
Received: from cunyvm.cuny.edu by nx1.soils.umn.edu (5.65c)
	id AA20511; Tue, 19 Oct 1993 08:12:05 -0500
Return-Path: <@CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu>
Received: from darban.cc.usm.edu by CUNYVM.CUNY.EDU (IBM VM SMTP V2R2) with TCP;
   Tue, 19 Oct 93 09:12:36 EDT
Received: by darban.cc.usm.edu (5.57/Ultrix3.0-C)
	id AA20241; Tue, 19 Oct 93 08:12:26 -0500
Date: Tue, 19 Oct 93 08:06 CDT
From: GLEN SHEARER <GLEN_SHEARER@bull.cc.usm.edu>
To: nih-image@soils.umn.edu
Really-To: soillist
Subject: VideoSpigot
Message-Id: <931019.08085112.040077@USM.CP6>

Has anyone tried the video capture card called VideoSpigot.  I hear
that the Mac LC card is only about $300.  If this would work well
we could probably afford a board and camera.   Thanks for any info.

Glen Shearer<glen_shearer@bull.cc.usm.edu>
From wayne@helix.nih.gov  Tue Oct 19 09:11:09 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA21127; Tue, 19 Oct 1993 09:12:51 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA28087; Tue, 19 Oct 93 09:32:41 -0400
Message-Id: <9310191332.AA28087@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 19 Oct 1993 09:11:09 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: scale to fit window

>hi, I'm trying to use the scale to fit window function to resize two
>electrophor
>etic gels (so that they may appear the same size, for analysis)...So, i open
>the
> two images and use the scaling function to get both the same size.  But, how
>ca
>n you keep the new scale of the image...thanks for any advice.....Mark

The Scale and Rotate command would probably work better in this situation.
You should avoid the "Nearest Neighbor" option when reducing images since
it is known to alter the mean gray value.

--wayne


From wayne@helix.nih.gov  Tue Oct 19 09:36:14 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA21429; Tue, 19 Oct 1993 09:37:37 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA28673; Tue, 19 Oct 93 09:57:46 -0400
Message-Id: <9310191357.AA28673@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 19 Oct 1993 09:36:14 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: VideoSpigot

>Has anyone tried the video capture card called VideoSpigot.  I hear
>that the Mac LC card is only about $300.  If this would work well
>we could probably afford a board and camera.   Thanks for any info.

I tried a Video Spigot card. The quality of captured 640x480 grayscale
images is greatly inferior to what you get with either the DT QuickCapture
or the Scion LG-3. The Video Spigot was designed for making 160x120 color
QuickTime movies, and should work well for that purpose. NIH Image does not
directly support the Video Spigot, but you can use the conversion utility
in the programs directory on zippy.nimh.nih.gov to convert QuickTime movies
into the PICS format that NIH can read.

--wayne


From ruzin@nature.berkeley.edu  Mon Oct 18 23:55:34 1993
Received: from nak.Berkeley.EDU by nx1.soils.umn.edu (5.65c)
	id AA21617; Tue, 19 Oct 1993 09:53:18 -0500
Return-Path: <ruzin@nature.berkeley.edu>
Received: from nature.Berkeley.EDU by nak.berkeley.edu (5.67/1.40)
	id AA20499; Tue, 19 Oct 93 07:54:42 -0700
Received: from [128.32.128.177] (kos5mac22.Berkeley.EDU) by nature.berkeley.edu.cnr-net (4.1/SMI-4.1)
	id AA14233; Tue, 19 Oct 93 07:57:44 PDT
Message-Id: <9310191457.AA14233@nature.berkeley.edu.cnr-net>
Date: Tue, 19 Oct 1993 07:55:34 -0800
To: nih-image@soils.umn.edu
From: ruzin@nature.berkeley.edu (Steven Ruzin)
Subject: Re: wand tool area

>Just a thank-you note for responding to all these first timer questions. We
>really like the package. Is there anyone in the San
>Francisco/Berkeley/Lawrence Laboratory area who would mind demo'ing his/her
>NIH image setup?
>
>                Thanks again in advance 



I don't know if anyone has responded (I've been out f town) but give me a
call/msg and we can set something up. I have Macs, framers, NIH Image, a
confocal scope... you might like to see. 

Steve...

______________________________________________
|   Steven Ruzin                              |
|   NSF Center of Plant Developmental Biology |
|   Dept Plant Biology                        |
|   Univ California Berkeley                  |
|   e-mail: ruzin@nature.berkeley.edu         |
|   phone:  510-642-6602                      |
|_____________________________________________|

From @CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu  Tue Oct 19 05:05:00 1993
Received: from cunyvm.cuny.edu by nx1.soils.umn.edu (5.65c)
	id AA21869; Tue, 19 Oct 1993 10:10:41 -0500
Return-Path: <@CUNYVM.CUNY.EDU:GLEN_SHEARER@bull.cc.usm.edu>
Received: from darban.cc.usm.edu by CUNYVM.CUNY.EDU (IBM VM SMTP V2R2) with TCP;
   Tue, 19 Oct 93 11:11:11 EDT
Received: by darban.cc.usm.edu (5.57/Ultrix3.0-C)
	id AA20597; Tue, 19 Oct 93 10:11:02 -0500
Date: Tue, 19 Oct 93 10:05 CDT
From: GLEN SHEARER <GLEN_SHEARER@bull.cc.usm.edu>
To: nih-image@soils.umn.edu
Really-To: nih-image@soils.umn.edu
Subject: Re: sequence reader
References: Re: sequence reader
Message-Id: <931019.10080148.040376@USM.CP6>
In-Reply-To: <9310181832.AA07631@helix.nih.gov>

Thanks for the info Mark.

What I had in mind was to scan an autoradiogram of a sequencing
gel with a flat-bed or hand scanner and then use Image on the
TIFF file to have the program read the GATC sequence by doing
some type of density plot of each lane.  If I was about 5X
more clever and had 10X more time, I might give it a try myself.

Glen


Glen Shearer<glen_shearer@bull.cc.usm.edu>
From sarmienu@rnisd0.DNET.roche.com  Tue Oct 19 07:21:50 1993
Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c)
	id AA22003; Tue, 19 Oct 1993 10:20:28 -0500
Return-Path: <sarmienu@rnisd0.DNET.roche.com>
Received: by gatekeeper.roche.com (5.65/fma-120691);
	id AA18574; Tue, 19 Oct 93 11:21:50 -0400
Received: by mailgate.roche.com (5.65/fma-120691);
	id AA02122; Tue, 19 Oct 93 11:19:21 -0400
From: sarmienu@rnisd0.DNET.roche.com
Message-Id: <9310191519.AA02122@mailgate.roche.com>
Received: from rnisd0.enet; by inet.enet; Tue, 19 Oct 93 11:21:50 EDT
Date: Tue, 19 Oct 93 11:21:50 EDT
To: nih-image@soils.umn.edu
Apparently-To: nih-image@soils.umn.edu
Subject: RE:Data Output

This is the second time I post this message, since I did not got it back
as a posted message from the list. It seems to have failed to get through.


I have just recently finished shopping for a dye sublimation 
printer for output of images obtained with NIH Image and 
the Scion card. Images are publication quality. Often I do 
further processing in Photoshop, like adding arrows, or 
magnification bars. Perhaps Wayne could comment on the 
use of Photoshop to reintegrate RGB images from Image 
into a 24 bit color obtained from NIH Image. You can also 
make black and white pictures that can be printed on a 
continuous tone in the dye sublimation printer.

If you have Photoshop, a color monitor, and Quark Express, 
you could reduce* a 640 x 480 image to 8.3 cm wide in 
Photoshop, mounted in QuarkXPress with  other similar 
images and then send the compressed files to a mail printer 
service. Although they cannot guarantee that the printout 
will look the way you want, I think  that your color images 
in Photoshop are pretty good predictors of what the image 
will look like.

*When you reduce the image in Photoshop, your 72 dpi 
image becomes close to 200 dpi which in a continuous tone 
hard copy looks crisp and clear, without jaggies.

Juan I. Sarmiento
Department of Toxicology and Pathology
Hoffmann-La Roche, INC.
340 Kingsland street
Nutley, NJ 07110
(201) 235 3907
Sarmienu@RNISD0.DNET.ROCHE.COM
From sarmienu@rnisd0.DNET.roche.com  Tue Oct 19 07:26:03 1993
Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c)
	id AA22016; Tue, 19 Oct 1993 10:24:36 -0500
Return-Path: <sarmienu@rnisd0.DNET.roche.com>
Received: by gatekeeper.roche.com (5.65/fma-120691);
	id AA18591; Tue, 19 Oct 93 11:26:04 -0400
Received: by mailgate.roche.com (5.65/fma-120691);
	id AA02168; Tue, 19 Oct 93 11:22:07 -0400
From: sarmienu@rnisd0.DNET.roche.com
Message-Id: <9310191522.AA02168@mailgate.roche.com>
Received: from rnisd0.enet; by inet.enet; Tue, 19 Oct 93 11:26:03 EDT
Date: Tue, 19 Oct 93 11:26:03 EDT
To: nih-image@soils.umn.edu
Apparently-To: nih-image@soils.umn.edu
Subject: sequence reader  

This is the second time I post this message, since I did not got it back
as a posted message from the list. It seems to have failed to get through.
                                                                          
>Has anyone tried to write a macro to read DNA sequence films
>with Image?  It seems that the potential is there in terms of
>image manipulations.
>
>Glen Shearer<glen_shearer@bull.cc.usm.edu>   
>
You mean using a flat bed scanner to capture the image of the gel 
radiograph? 

3 years ago I tried to use ScanAnalysis to do this with my wife's 
(Dr. Ulla Sarmiento) sequencing radiographs using the 4 bit Apple 
Scanner. It just could not be done, even at 300 dpi. Perhaps better 
scanners and better software would allow that now. My approach 
was to locate the peaks  of each band in each lane. according to the 
distance migrated data could be sorted. The problem was that at 1 
end the bands were too close together, and at the  other they curved 
to one side, and the program required a rectangular ROI. Perhaps 
with NIH Image you can get around that by using the polygonal 
selection tool. With high resolution scanners (e.g. 600-1200 dpi), 
you might get around the problem of cramped bands. 

Back in those days the troubles were so many that there was no time 
savings using this system in comparison to manual and visual 
reading. 


Juan I. Sarmiento
Department of Toxicology and Pathology
Hoffmann-La Roche, INC.
340 Kingsland street
Nutley, NJ 07110
(201) 235 3907
Sarmienu@RNISD0.DNET.ROCHE.COM

P.S. The sorting of band distances could be easily done in 
Microsoft Excel. A macro could probably be written for that!
From tg3@u.washington.edu  Tue Oct 19 01:02:49 1993
Received: from stein1.u.washington.edu (stein.u.washington.edu) by nx1.soils.umn.edu (5.65c)
	id AA22332; Tue, 19 Oct 1993 11:01:19 -0500
Return-Path: <tg3@u.washington.edu>
Received: from [128.95.15.54] by stein1.u.washington.edu
	(5.65/UW-NDC Revision: 2.29 ) id AA14334; Tue, 19 Oct 93 09:02:49 -0700
Date: Tue, 19 Oct 93 09:02:49 -0800
From: Thurman Gillespy III <tg3@u.washington.edu>
To: nih-image@soils.umn.edu
Subject: Re: Data Output
Message-Id: <Mailstrom.1.03.23993.-3114.tg3@u.washington.edu>
In-Reply-To: Your message <9310181703.AA10831@merle.acns.nwu.edu> of Mon, 18
 Oct 1993 12:21:44 -0500
Content-Type: TEXT/plain; charset=US-ASCII

>   Hello Everyone,
>   
>   I was wondering if anyone had any thoughts about output
>   of image files to generate figures to submit for
>   application.  I have created and analyzed a ...


I regularly submit dye sub prints for publication, using Image as the image
display/image processing software. The results are excellent. Usually, I print
the output as a postscript file, which I submit to the medical photography
folks. Its expensive, ~$10 print, but by far the best way to go that I've
encountered.

Thurman Gillespy III, MD    tg3@u.washington.edu
Department of Radiology
University of Washington

From wsryu@phoenix.Princeton.EDU  Tue Oct 19 07:56:43 1993
Received: from Princeton.EDU by nx1.soils.umn.edu (5.65c)
	id AA22452; Tue, 19 Oct 1993 11:13:55 -0500
Return-Path: <wsryu@phoenix.Princeton.EDU>
Received: from ponyexpress.Princeton.EDU by Princeton.EDU (5.65b/2.99/princeton)
	id AA27639; Tue, 19 Oct 93 11:56:45 -0400
Received: from phoenix.Princeton.EDU by ponyexpress.princeton.edu (5.65c/1.113/newPE)
	id AA13649; Tue, 19 Oct 1993 11:56:44 -0400
From: William Sungho Ryu <wsryu@phoenix.Princeton.EDU>
Received: by phoenix.Princeton.EDU (5.65c/Phoenix_Cluster_Client)
	id AA22471; Tue, 19 Oct 1993 11:56:43 -0400
Date: Tue, 19 Oct 1993 11:56:43 -0400
Message-Id: <199310191556.AA22471@phoenix.Princeton.EDU>
To: nih-image@soils.umn.edu
Subject: 660av Screen Capture.


I am thinking about purchasing a 660av to use NIH Image and was wondering
about the quality of screen capture.

What file type is it?

What is the frame rate for a 640x400 capture?

Is the 660av a poorman's viable alternative to a frame grabber card?

William Ryu
Princeton University
From CHARLEST@macc.wisc.edu  Tue Oct 19 07:00:00 1993
Received: from vms2.macc.wisc.edu by nx1.soils.umn.edu (5.65c)
	id AA22777; Tue, 19 Oct 1993 11:59:08 -0500
Return-Path: <CHARLEST@macc.wisc.edu>
Received: from VMSmail by vms2.macc.wisc.edu; Tue, 19 Oct 93 12:00 CDT
Message-Id: <23101912001195@vms2.macc.wisc.edu>
Date: Tue, 19 Oct 93 12:00 CDT
From: Charles Thomas <CHARLEST@macc.wisc.edu>
Subject: Re: wand tool area
To: nih-image@soils.umn.edu
X-Vms-To: IN%"nih-image@soils.umn.edu",CHARLEST

Unless you've calibrated your units differently, the area will be in square
pixels.
 
From sarmienu@rnisd0.DNET.roche.com  Tue Oct 19 09:42:09 1993
Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c)
	id AA23092; Tue, 19 Oct 1993 12:40:44 -0500
Return-Path: <sarmienu@rnisd0.DNET.roche.com>
Received: by gatekeeper.roche.com (5.65/fma-120691);
	id AA19424; Tue, 19 Oct 93 13:42:10 -0400
Received: by mailgate.roche.com (5.65/fma-120691);
	id AA03253; Tue, 19 Oct 93 13:41:05 -0400
From: sarmienu@rnisd0.DNET.roche.com
Message-Id: <9310191741.AA03253@mailgate.roche.com>
Received: from rnisd0.enet; by inet.enet; Tue, 19 Oct 93 13:42:09 EDT
Date: Tue, 19 Oct 93 13:42:09 EDT
To: nih-image@soils.umn.edu
Apparently-To: nih-image@soils.umn.edu
Subject: More on sequencing gels

Actually, I don't know if this will work with your system. The assumption is
that each band has a different xy center in the image:

1. Set the x-y center in the options dialogue box under the analyze menu.
2. Select the area of interest with the polygonal tool. Make sure you select the
A, C, G, and T lanes.
3. Threshold the image to select bands by their grey level.
4. Select Analyze particles from the analyze menu.
5. Show results and option copy.
6. Go to EXCEL and paste.
7. Sort the table by the X values.
8. Create a new column and enter the appropriate base (ACGT) according to
the approximate vertical center of the location of the corresponding lane.
9. Sort the table by the y values.

Your sequence should be organized properly.

Play with it until you get the desired results. You may be able to create macros
in NIH-Image and EXCEL to accomplish this.




Juan I. Sarmiento
Department of Toxicology and Pathology
Hoffmann-La Roche, INC.
340 Kingsland street
Nutley, NJ 07110
(201) 235 3907
Sarmienu@RNISD0.DNET.ROCHE.COM
From bbug1@cc.swarthmore.edu  Tue Oct 19 10:39:00 1993
Received: from oak.cc.swarthmore.edu by nx1.soils.umn.edu (5.65c)
	id AA23473; Tue, 19 Oct 1993 13:37:34 -0500
Return-Path: <bbug1@cc.swarthmore.edu>
Received: from [130.58.70.116] (mac01.martin2.swarthmore.edu [130.58.70.116]) by oak.cc.swarthmore.edu (8.6.2/8.6.2) with SMTP id OAA15177 for <nih-image@soils.umn.edu>; Tue, 19 Oct 1993 14:39:00 -0400
Date: Tue, 19 Oct 1993 14:39:00 -0400
Message-Id: <199310191839.OAA15177@oak.cc.swarthmore.edu>
X-Mailer: Eudora/Swarthmore 1.3b116
To: nih-image@soils.umn.edu
From: Bill Bug <bbug1@cc.swarthmore.edu>
Subject: Re: Removing Blur though Deconvolution

Hello All,

Here's a correction to my reference list on deconvolution techniques as
applied in visible light microscopy.  I've also added a more complete set
of individual examples of digital reconstruction in biological microscopy. 
I'm not an authority in this field, but these are the works that helped to
inform me on the topic.

 1) Castelman, K.R.(1979) Digital image processing. Prentice-Hall,Inc.,
        Englewood Cliffs, NY, 429pp.
                 * THE general reference on digital imaging techniques;
most of  
                        the subsequent work in this field has derived from 
                        algorithms outlined in this book

2) Monck, J.R., Oberhauser,A.F., Keating, T.J., Fernandez, J.M. (1992)
        Thin-section ratiometric Ca+2 images obtained by optical sectioning of
        fura-2 loaded mast cells. J. Cell Biology, v116:3, p745-759.
                 * This is an extremely well illustrated example of some of the 
                        less computationally-intense methods for applying 
                        digital deconvolution.  They compare and evaluate
                        the "nearest-neighbor" and "no-neighbor" methods,
testing them on 
                        model and real data sets.
 
3) Waybill, M.M., Yelamarty, R.V., Zhang,Y., Scaduto, R.C.,Jr., LaNoue,
K.F., Hsu,C.-J.,       
        Smith,B.C., Tillotson,D.L., Yu,F.T.S., and Cheung,J.Y. (1991)
        Nuclear calcium gradients in cultured rat hepatocytes. Am. J. Physiol.
        v261(Endo. Metab. 24), pE49-E57.
                * They evaluate the effectiveness of the "nearest-neighbor"
method for
                        improving the spatial resolution and quantitative
accuracy of
                        fura-2 images in isolated hepatocytes and on model data.
        
4) Agard, D.A., and Sedat, J.W. (1983)
        Three-dimensional architecture of a polytene nucleus. Nature, v302,
p676-681.

5) Carrington, W.A., Fogarty, K.E., and Fay, F.S. (1990)
        3D fluorescence imaging of single cells using image restoration.
In: Nonivasive
        techniques in cell biology, J.K. Foskett and S. Grinstein, eds.,
(Wiley-Liss, New    
        York), p53-72.

                * 4 & 5 present methods for applying more extensive,
computationally-
                        demanding deconvolution techniques that utilize all
the photon data
                        from a axial stack >20 images.  Both papers cite
prior works 
                        which give a more detailed derivation of the
mathematical techniques
                        involved.  Each set of authors also has a chapter
in Handbook of 
                        Biological Confocal Microscopy (J.B. Pawley,ed.,
Plenum Press, New
                        York, 1990) which describes their unique approach
to digital 
                        reconstruction in fluorescent microscopy
                        

I hope these references are of some use to people.  I came to them through
a rather circuitous route but have found them all to be invaluable to the
digital fluorescent imaging we are doing in the lab.


Good luck!!

Cheers,
Bill Bug


*************************
*  Bill Bug             *
*  Dept. of Biology     *
*  Swarthmore College   *
*************************

From wayne@helix.nih.gov  Tue Oct 19 13:46:51 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA23555; Tue, 19 Oct 1993 13:48:15 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA02758; Tue, 19 Oct 93 14:08:25 -0400
Message-Id: <9310191808.AA02758@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 19 Oct 1993 13:46:51 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: 660av Screen Capture.

>I am thinking about purchasing a 660av to use NIH Image and was wondering
>about the quality of screen capture.
>
>What file type is it?

The image capture application that comes with the AV Macs creates QuickTime
movies.

>What is the frame rate for a 640x400 capture?

It is probably no more than 5-10 frames per second and would depend if you
are capturing to RAM or disk.

>Is the 660av a poorman's viable alternative to a frame grabber card?

Like the Video Spigot, it's a good if you wan't to hook up a camcorder to
your Mac and make a color QuickTime movie. (The AV Macs use the same chip
set as the Video Spigot.) You can convert the QuickTime movie into PICS
format to get it into NIH Image.

--wayne


From kartenh@sdsc.edu  Tue Oct 19 19:12:37 1993
Received: from Sdsc.Edu (sds.sdsc.edu) by nx1.soils.umn.edu (5.65c)
	id AA23739; Tue, 19 Oct 1993 14:11:20 -0500
Return-Path: <kartenh@sdsc.edu>
Message-Id: <199310191911.AA23739@nx1.soils.umn.edu>
Received: from [132.239.67.254] by Sdsc.Edu (sds.sdsc.edu STMG) via INTERNET;
          Tue, 19 Oct 93 19:12:37 GMT
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: kartenh@Sdsc.Edu
Subject: Re: 660av Screen Capture.
Date:  Tue, 19 Oct 93 19:12:37 GMT

>>I am thinking about purchasing a 660av to use NIH Image and was wondering
>>about the quality of screen capture.
>>
>>Is the 660av a poorman's viable alternative to a frame grabber card?
>
>Like the Video Spigot, it's a good if you wan't to hook up a camcorder to
>your Mac and make a color QuickTime movie. (The AV Macs use the same chip
>set as the Video Spigot.) You can convert the QuickTime movie into PICS
>format to get it into NIH Image.
>
>--wayne

Does anyone know the actual performance specs of the 660av/840av on a
monochrome image from a decent video camera? Linear resolution, contrast
range, etc. 
                                        Harvey Karten

 Harvey J. Karten, M.D.
 Dept. of Neurosciences
 Univ.California San Diego
 La Jolla, CA 92093-0608
 EMail: Kartenh@sdsc.edu
 Phone: (619)-534-4938
 FAX: (619)-534-6602


From keller@micros.mrd.bldrdoc.gov  Tue Oct 19 09:54:21 1993
Received: from central.bldrdoc.gov by nx1.soils.umn.edu (5.65c)
	id AA24750; Tue, 19 Oct 1993 16:53:11 -0500
Return-Path: <keller@micros.mrd.bldrdoc.gov>
Received: from pascal.mrd.bldrdoc.gov by central.bldrdoc.gov (4.1/SMI-DDN)
	id AA23311; Tue, 19 Oct 93 15:54:35 MDT
Received: from micros.mrd.bldrdoc.gov by pascal.mrd.bldrdoc.gov (4.1/SMI-3.2)
	id AA00422; Tue, 19 Oct 93 15:55:09 MDT
Message-Id: <9310192155.AA00422@pascal.mrd.bldrdoc.gov>
Date: Tue, 19 Oct 93 15:54:21 MDT
From: Bob Keller <keller@micros.mrd.bldrdoc.gov>
Subject: IPLab Spectrum
To: nih-image@soils.umn.edu
X-Mailer: LeeMail 1.2.4

Has anyone tried using IPLab Spectrum, by Signal Analytics Corp?  If so, how 
does it compare with NIH Image?  One difference is that the former can work 
with greater than 256 grey levels, but otherwise it appears quite similar, 
based on the demo version.

Bob Keller
NIST Boulder

From glenmac@u.washington.edu  Tue Oct 19 08:44:15 1993
Received: from carson.u.washington.edu by nx1.soils.umn.edu (5.65c)
	id AA25122; Tue, 19 Oct 1993 17:54:25 -0500
Return-Path: <glenmac@u.washington.edu>
Received: by carson.u.washington.edu
	(5.65/UW-NDC Revision: 2.29 ) id AA21169; Tue, 19 Oct 93 15:55:46 -0700
X-Sender: glenmac@carson.u.washington.edu
Date: Tue, 19 Oct 1993 15:44:15 -0700 (PDT)
From: Glen Macdonald <glenmac@u.washington.edu>
Subject: Re: Data Output
To: nih-image@soils.umn.edu
Cc: Multiple recipients of list <nih-image@soils.umn.edu>
In-Reply-To: <9310181703.AA10831@merle.acns.nwu.edu>
Message-Id: <Pine.3.05z.9310191514.A11603-9100000@carson.u.washington.edu>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=us-ascii

i've used the L300 Linotronic with 640x480 SEM images.  They(the campus
print shop)  will take PICT or TIFF, but only if created with Photoshop.  The
grey scale range and brightness from an Image file probably needs to be
adjusted with photoshop, anyway.  1200 dpi was cheaper than 2400 and gave
a comparable image.  Printing at half or quarter size greatly improves the
resolution and saves money, whereas a full size image suffered from the
jaggies. 


From scudder@cpac.washington.edu  Tue Oct 19 18:46:12 1993
Received: from bailey.cpac.washington.edu by nx1.soils.umn.edu (5.65c)
	id AA28031; Wed, 20 Oct 1993 03:50:10 -0500
Return-Path: <scudder@cpac.washington.edu>
Received: by bailey.cpac.washington.edu
	(5.65/UW-NDC Revision: 2.4 ) id AA01821; Wed, 20 Oct 93 01:50:46 -0700
Date: Wed, 20 Oct 1993 01:46:12 -0700 (PDT)
From: Kurt Scudder <scudder@bailey.cpac.washington.edu>
Subject: Re: VideoSpigot
To: nih-image@soils.umn.edu
In-Reply-To: <9310191357.AA28673@zippy.nimh.nih.gov>
Message-Id: <Pine.3.07.9310200104.D1188-b100000@bailey.cpac.washington.edu>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII



On Tue, 19 Oct 1993, Wayne Rasband wrote:

> >Has anyone tried the video capture card called VideoSpigot.  I hear
> >that the Mac LC card is only about $300.  If this would work well
> >we could probably afford a board and camera.   Thanks for any info.
> 
> I tried a Video Spigot card. The quality of captured 640x480 grayscale
> images is greatly inferior to what you get with either the DT QuickCapture
> or the Scion LG-3. The Video Spigot was designed for making 160x120 color
> QuickTime movies, and should work well for that purpose. NIH Image does not
> directly support the Video Spigot, but you can use the conversion utility
> in the programs directory on zippy.nimh.nih.gov to convert QuickTime movies
> into the PICS format that NIH can read.
> 
> --wayne
> 
> 

	This is the first I have been aware that QuickTime movies could be
brought into NIH-Image. I don't have any plans to do this, but it raises a
simple question: Does Image automatically make 8-bit data out of what I
assume is higher-than-8-bit (i.e., color) images? If so, is the LUT the
same for every image in the movie?

Kurt Scudder
Dept. of Chemistry
University of Washington
scudder@u.washington.edu


From Carl.Gustafson@cbis.ece.drexel.edu  Wed Oct 20 04:39:22 1993
Received: from cbis.ece.drexel.edu by nx1.soils.umn.edu (5.65c)
	id AA29078; Wed, 20 Oct 1993 07:49:40 -0500
Return-Path: <Carl.Gustafson@cbis.ece.drexel.edu>
Received: from n1-5-228-ece-ipc.ece.drexel.edu by cbis.ECE.Drexel.EDU (5.67/1.34)
	id AA14963; Wed, 20 Oct 93 08:39:22 EDT
Date: Wed, 20 Oct 93 08:39:22 EDT
Message-Id: <9310201239.AA14963@cbis.ECE.Drexel.EDU>
To: nih-image@soils.umn.edu
From: Carl.Gustafson@cbis.ece.drexel.edu (Carl Gustafson)
X-Sender: cgustafs@CoE.Drexel.EDU
Subject: Re: Too many constants in enumerated type

>
>There seems to be a limit of 256 or so constants in enumerated types. I ran
>into this problem when I tried to add a new command to the macro language
>today. The short term work-around I used was to recycle some obsolete
>commands. The long range solution will be to break CommandType into two
>parts: commands and functions.There are 10 obsolete commands starting at
>symbol table entry 165(SetArea, SetMean, etc.) and 0ne(SetMinMax) at 185.
>
>--wayne


The really good solution would be to dump Think Pascal and use something
like MPW.

(Ducking and running)

Carl Gustafson

===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Your message here
Philadelphia, Pennsylvania              |   I only speak for myself
===============================================================================

From wayne@helix.nih.gov  Wed Oct 20 08:29:02 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA29449; Wed, 20 Oct 1993 08:30:29 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA08900; Wed, 20 Oct 93 08:50:40 -0400
Message-Id: <9310201250.AA08900@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Wed, 20 Oct 1993 08:29:02 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: VideoSpigot

This is the first I have been aware that QuickTime movies could be
>brought into NIH-Image. I don't have any plans to do this, but it raises a
>simple question: Does Image automatically make 8-bit data out of what I
>assume is higher-than-8-bit (i.e., color) images?

Yes. You convert the QuickTime movie to PICS using the QuickTime<->PICS
utility on zippy.nimh.nih.gov and then open the PICS file as an Image
stack.

>If so, is the LUT the same for every image in the movie?

All slices in the stack use the same LUT since there is only one LUT for
the entire stack.

--wayne





From Scott.Wurcer@analog.com  Wed Oct 20 05:06:06 1993
Received: from nic.near.net by nx1.soils.umn.edu (5.65c)
	id AA29486; Wed, 20 Oct 1993 08:35:23 -0500
Return-Path: <Scott.Wurcer@analog.com>
Received: from [137.71.23.11] by nic.near.net id aa04969; 20 Oct 93 9:06 EDT
Received: from nwd2sun1.analog.com ([137.71.22.41]) by adi.analog.com
Received: from titania.adsdesign.analog.com by nwd2sun1.analog.com (4.1/SMI-4.1)
Message-Id: <9310201304.AA25649@nwd2sun1.analog.com>
Received: from hermia.adsdesign.analog.com by titania.adsdesign.analog.com
Date: Wed, 20 Oct 93 09:06:06 EDT
From: Scott Wurcer <Scott.Wurcer@analog.com>
To: nih-image@soils.umn.edu
Subject: Re: Data Output

I've also had great success using the error-diffusion halftones along with
bicubic spline scaling from Photoshop to get rid of jaggies in blown-up
images. Even 128x128 images can look pretty good at 4x.
From @ibm.gwdg.de:rfritsc@gwdgv1.dnet.gwdg.de  Wed Oct 20 15:34:58 1993
Received: from ibm.gwdg.de by nx1.soils.umn.edu (5.65c)
	id AA29587; Wed, 20 Oct 1993 08:46:13 -0500
Return-Path: <@ibm.gwdg.de:rfritsc@gwdgv1.dnet.gwdg.de>
Message-Id: <199310201346.AA29587@nx1.soils.umn.edu>
Received: from IBM.GWDG.DE by ibm.gwdg.de (IBM VM SMTP R1.2.2MX) with BSMTP id 6162; Wed, 20 Oct 93 14:34:59 MEZ
Received: from dnet.gwdg.de by IBM.GWDG.DE (Mailer R2.08) with BSMTP id 3458;
 Wed, 20 Oct 93 14:34:58 MEZ
Date:    Wed, 20 Oct 1993 14:34:58 +0100
From: "GWDGV1::RFRITSC" <rfritsc@gwdgv1.dnet.gwdg.de>
To: nih-image@soils.umn.edu
Subject: Kodak DCS200/Zeiss Microscope

Dear Image users,
We are trying to set up a system for routine documentation using the Kodak DCS
200 camera. I remember there has been some discussion on this list about using
the Kodak DCS 200 camera for microscopy (via Photoshop plug in). Could anybody
who is using such a setup specify how they connected the camera to a Zeiss
Axiophot microscope? How to compensate for the small CCD chip? The chip has
only 1/4 of the area of film and the adapters we got from Zeiss to connect the
camera to the microscope is for film so we can capture only a small part of the
slide we see in the eyepiece. Any suggestions?
Thanks!

Ruediger Fritsch
Max-Planck-Institut f. biophysikalische Chemie
Am Fassberg
37077 Goettingen
Germany
email rfritsc@gwdgv1.dnet.gwdg.de

From waheeschen@dow.com  Wed Oct 20 06:19:20 1993
Received: from na1.dow.com (na2.dow.com) by nx1.soils.umn.edu (5.65c)
	id AA29894; Wed, 20 Oct 1993 09:18:10 -0500
Return-Path: <waheeschen@dow.com>
Received: by na1.dow.com id AA03041
  (InterLock SMTP Gateway 1.1 for nih-image@soils.umn.edu);
  Wed, 20 Oct 1993 09:05:35 -0500
Message-Id: <199310201405.AA03041@na1.dow.com>
Date: Wed, 20 Oct 1993 10:19:20 -0400
From: waheeschen@dow.com (Bill Heeschen (517)636-4005 PMRC/ASL)
To: nih-image@soils.umn.edu
Subject: Re: Too many constants in enumerated type / MPW vs Think
X-Vms-To: SMTP%"nih-image@soils.umn.edu"

Did I just hear Carl raise his hand to volunteer....  8-)

==========================
Bill Heeschen / Analytical Sciences - Materials Characterization
1897-D Building / The Dow Chemical Company
Midland, MI   48667  U.S.A.
phone: (517)636-4005   fax:    (517)636-5453
Email: waheeschen@dow.com
==========================
From mvivino@helix.nih.gov  Wed Oct 20 06:22:41 1993
Received: from helix.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA29960; Wed, 20 Oct 1993 09:21:14 -0500
Return-Path: <mvivino@helix.nih.gov>
Received: from mavmac.dcrt.nih.gov by helix.nih.gov (5.64/1.35(helix-1.0))
	id AA18813; Wed, 20 Oct 93 10:22:41 -0400
Date: Wed, 20 Oct 93 10:22:41 -0400
Message-Id: <9310201422.AA18813@helix.nih.gov>
X-Sender: mvivino@128.231.2.3
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: mvivino@helix.nih.gov (Mark Vivino)
Subject: Re: IPLab Spectrum

>Has anyone tried using IPLab Spectrum, by Signal Analytics Corp?  If so, how 
>does it compare with NIH Image?  One difference is that the former can work 
>with greater than 256 grey levels, but otherwise it appears quite similar, 
>based on the demo version.

It does do a fourier transform and a few other things, although DIP Station
does these as well or better and they are in your area. If I were adding 50
images together I might use IPLab. IPlab has a few hardware interfaces that
Image does not have, such as for photometrics and others. It has some
interesting color transforms too.


Mark Vivino
NIH/DCRT
mvivino@helix.nih.gov


From mschindl@Physik.TU-Muenchen.DE  Wed Oct 20 16:38:21 1993
Received: from srv.cip.physik.tu-muenchen.de by nx1.soils.umn.edu (5.65c)
	id AA00248; Wed, 20 Oct 1993 09:36:56 -0500
Return-Path: <mschindl@Physik.TU-Muenchen.DE>
Received:  from ss3.cip.physik.tu-muenchen.de
	by srv.cip.physik.tu-muenchen.de with SMTP id AA14185
	for <nih-image@soils.umn.edu> (5.65c/IDA-1.4.4/bs-02);
	Wed, 20 Oct 1993 15:38:22 +0100
Received: by ss3.cip.physik.tu-muenchen.de (4.1/SMI-4.1)
	id AA06294; Wed, 20 Oct 93 15:38:21 +0100
Date: Wed, 20 Oct 93 15:38:21 +0100
From: Mathias.Schindl@Physik.TU-Muenchen.DE
Message-Id: <9310201438.AA06294@ss3.cip.physik.tu-muenchen.de>
To: nih-image@soils.umn.edu
Subject: "Metaphor"

Hi,

has anybody out there ever heard of an image processing system / software 
called "Metaphor" or something like that? 
I would appreciate any little hint or information about it. Thank you.

Mathias Schindl, Ph.D. student
Physics Department, Biophysics Group E22
Technische Universitaet Muenchen, 85747 Garching, Germany
From Carl.Gustafson@cbis.ece.drexel.edu  Wed Oct 20 06:50:08 1993
Received: from cbis.ece.drexel.edu by nx1.soils.umn.edu (5.65c)
	id AA00326; Wed, 20 Oct 1993 09:48:43 -0500
Return-Path: <Carl.Gustafson@cbis.ece.drexel.edu>
Received: from n1-5-228-ece-ipc.ece.drexel.edu by cbis.ECE.Drexel.EDU (5.67/1.34)
	id AA17209; Wed, 20 Oct 93 10:50:08 EDT
Date: Wed, 20 Oct 93 10:50:08 EDT
Message-Id: <9310201450.AA17209@cbis.ECE.Drexel.EDU>
To: nih-image@soils.umn.edu
From: Carl.Gustafson@cbis.ece.drexel.edu (Carl Gustafson)
X-Sender: cgustafs@CoE.Drexel.EDU
Subject: Re: Too many constants in enumerated type / MPW vs Think

>Did I just hear Carl raise his hand to volunteer....  8-)
>
>==========================
>Bill Heeschen / Analytical Sciences - Materials Characterization
>1897-D Building / The Dow Chemical Company
>Midland, MI   48667  U.S.A.
>phone: (517)636-4005   fax:    (517)636-5453
>Email: waheeschen@dow.com
>==========================


Carl was firmly sitting on his hands when he sent that message. Quite a
trick to type that way

What I may do is work on an MPW Tool to convert TP to MPW. This would be
the more general approach, and doesn't require freezing versions. Probably
won't be too difficult; problem is finding time.

Carl Gustafson

===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I only speak for myself
===============================================================================

From djm@cidmv1.wustl.edu  Wed Oct 20 04:55:55 1993
Received: from wugate.wustl.edu by nx1.soils.umn.edu (5.65c)
	id AA00417; Wed, 20 Oct 1993 10:00:12 -0500
Return-Path: <djm@cidmv1.wustl.edu>
Received: by wugate.wustl.edu (5.67a+/WUSTL-0.3) with DECnet 
	id AA04558; Wed, 20 Oct 1993 09:55:55 -0500
Date: Wed, 20 Oct 1993 09:55:55 -0500
Message-Id: <199310201455.AA04558@wugate.wustl.edu>
From: djm@cidmv1.wustl.edu (D.J. Meyer)
To: nih@wugate.wustl.edu
Subject: # of colors on monitor


hi,
i just put a 24bit video card in our IIfx for our imaging needs. now,
nih gives me an error message that the monitor *must* be configured for
256 colors or gray scales. the documentation says it will handle 24
bit images. but not display them? is there a way around this?
8 bit display is not acceptable for what we need to do with our
images.
thanks
dj meyer
djm@cidmv1.wustl.edu
From bbug1@cc.swarthmore.edu  Wed Oct 20 07:26:33 1993
Received: from oak.cc.swarthmore.edu by nx1.soils.umn.edu (5.65c)
	id AA00766; Wed, 20 Oct 1993 10:25:09 -0500
Return-Path: <bbug1@cc.swarthmore.edu>
Received: from [130.58.70.116] (mac01.martin2.swarthmore.edu [130.58.70.116]) by oak.cc.swarthmore.edu (8.6.2/8.6.2) with SMTP id LAA16264 for <nih-image@soils.umn.edu>; Wed, 20 Oct 1993 11:26:33 -0400
Date: Wed, 20 Oct 1993 11:26:33 -0400
Message-Id: <199310201526.LAA16264@oak.cc.swarthmore.edu>
X-Mailer: Eudora/Swarthmore 1.3b116
To: nih-image@soils.umn.edu
From: Bill Bug <bbug1@cc.swarthmore.edu>
Subject: Re: Kodak DCS200/Zeiss Microscope


>The chip(Kodak DCS 200 camera) has only 1/4 of the area of film and the
>adapters we >got from Zeiss to connect the camera to the microscope is for
>film so we can capture >only a small part of the slide we see in the eyepiece.
>Any suggestions?
>Thanks!
>
>Ruediger Fritsch
>Max-Planck-Institut f. biophysikalische Chemie
>Am Fassberg
>37077 Goettingen
>Germany
>email rfritsc@gwdgv1.dnet.gwdg.de


Herr Fritsch,

        We have had been able to get all the optical coupling components we
need to interface our cooled CCD camera (Photometrics, LTD) with a Zeiss
Axioskop from Diagnostic Instruments (6540 Burroughs St., Sterling Heights,
MI, 48314, USA - phone:(313) 731-6000; fax: (313) 731-6469).  Speak with
Patrick Merlo at DI.  He's not only knowledgable of the phyisics involved
in such optical devices, he also has many years experience applying that
knowledge to the specifications of various microscopes.  He should be able
to give you all the pros and cons of using a low power elements (< 1x) to
bring more of the field on to the CCD chip.  Many people actually have a
higher power camera coupling (2.5x) in order to exclude the less well
corrected, outer portion of the objective field from the imaging device.

Good luck!

Cheers,
Bill Bug


*************************
*  Bill Bug             *
*  Dept. of Biology     *
*  Swarthmore College   *
*************************

From kartenh@Sdsc.Edu  Wed Oct 20 15:47:45 1993
Received: from Sdsc.Edu (m5.sdsc.edu) by nx1.soils.umn.edu (5.65c)
	id AA00963; Wed, 20 Oct 1993 10:46:23 -0500
Return-Path: <kartenh@Sdsc.Edu>
Date:    Wed, 20 Oct 93 15:47:45 GMT
From: kartenh@Sdsc.Edu (Harvey Karten)
Message-Id: <931020154745.204074d9@m5.sdsc.edu>
Subject: IPL and AxoVideo
To: nih-image@soils.umn.edu
X-St-Vmsmail-To: ST%"nih-image@soils.umn.edu"

Both IPL and Axovideo (Axon Instruments) include software for Calcium 
ratio  imaging. 
Has anyone developed a complete set of macros for NIH Image 
for this purpose?
				Harvey Karten
 Harvey J. Karten, M.D.
 Dept. Neurosciences 
 UCSD 0608
 La Jolla, CA 92093 
 Phone (619)-534-4938 
 FAX (619)-534-6602 
 E-Mail KARTENH@SDSC.EDU
From keller@micros.mrd.bldrdoc.gov  Wed Oct 20 03:56:51 1993
Received: from central.bldrdoc.gov by nx1.soils.umn.edu (5.65c)
	id AA01096; Wed, 20 Oct 1993 10:55:40 -0500
Return-Path: <keller@micros.mrd.bldrdoc.gov>
Received: from pascal.mrd.bldrdoc.gov by central.bldrdoc.gov (4.1/SMI-DDN)
	id AA04013; Wed, 20 Oct 93 09:57:07 MDT
Received: from micros.mrd.bldrdoc.gov by pascal.mrd.bldrdoc.gov (4.1/SMI-3.2)
	id AA00502; Wed, 20 Oct 93 09:57:46 MDT
Message-Id: <9310201557.AA00502@pascal.mrd.bldrdoc.gov>
Date: Wed, 20 Oct 93 09:56:51 MDT
From: Bob Keller <keller@micros.mrd.bldrdoc.gov>
Subject: Re: IPLab Spectrum
To: nih-image@soils.umn.edu
X-Mailer: LeeMail 1.2.4

>>Has anyone tried using IPLab Spectrum, by Signal Analytics Corp?  
>
>It does do a fourier transform and a few other things, although DIP Station
>does these as well or better and they are in your area. If I were adding 50
>images together I might use IPLab. IPlab has a few hardware interfaces that
>Image does not have, such as for photometrics and others. It has some
>interesting color transforms too.

Thanks for the info.  Where can I find out more about DIP Station?

Bob Keller
NIST Boulder
keller@micros.mrd.bldrdoc.gov

From djm@cidmv1.wustl.edu  Wed Oct 20 07:11:32 1993
Received: from wugate.wustl.edu by nx1.soils.umn.edu (5.65c)
	id AA01773; Wed, 20 Oct 1993 12:10:17 -0500
Return-Path: <djm@cidmv1.wustl.edu>
Received: by wugate.wustl.edu (5.67a+/WUSTL-0.3) with DECnet 
	id AA10976; Wed, 20 Oct 1993 12:11:33 -0500
Date: Wed, 20 Oct 1993 12:11:32 -0500
Message-Id: <199310201711.AA10976@wugate.wustl.edu>
From: djm@cidmv1.wustl.edu (D.J. Meyer)
To: nih@wugate.wustl.edu
Subject: tif or pict


are they both 24bit?
From russ@mat.mte.ncsu.edu  Wed Oct 20 09:16:43 1993
Received: from mat.mte.ncsu.edu by nx1.soils.umn.edu (5.65c)
	id AA01805; Wed, 20 Oct 1993 12:15:32 -0500
Return-Path: <russ@mat.mte.ncsu.edu>
Received: by mat.mte.ncsu.edu (5.57/Ultrix3.0-C)
	id AA09975; Wed, 20 Oct 93 13:16:43 -0400
Date: Wed, 20 Oct 93 13:16:43 -0400
Message-Id: <9310201716.AA09975@mat.mte.ncsu.edu>
To: nih-image@soils.umn.edu
From: russ@mat.mte.ncsu.edu
Subject: Re: "Metaphor"

you may be referring to Metamorph, an image analysis package (software and
boards) that runs on a PC. It is available from Universal Imaging Universal
Imaging Corp, 502 Brandywine Parkway, West Chester, PA 19380, (215)
344-9410; fax: 215-344-9515; ask for Ted Inoue

__________________________________________________
John Russ
(John_Russ@ncsu.edu)   or  (russ@mat.mte.ncsu.edu)
Materials Science and Engineering Department,
North Carolina State Univ., Raleigh, NC 27695-7907
phone: 919-515-3328              fax: 919-515-7724

From kyzy@rice.edu  Wed Oct 20 07:24:09 1993
Received: from moe.rice.edu by nx1.soils.umn.edu (5.65c)
	id AA01891; Wed, 20 Oct 1993 12:22:49 -0500
Return-Path: <kyzy@rice.edu>
Received: from [128.42.105.7] (erinna.rice.edu) by moe.rice.edu (AA10112); Wed, 20 Oct 93 12:24:09 CDT
Date: Wed, 20 Oct 93 12:24:09 CDT
Message-Id: <9310201724.AA10112@moe.rice.edu>
To: nih-image@soils.umn.edu
From: kyzy@rice.edu
Subject: Re: # of colors on monitor

D.J Meyer writes

>i just put a 24bit video card in our IIfx for our imaging needs. now,
>nih gives me an error message that the monitor *must* be configured for
>256 colors or gray scales. the documentation says it will handle 24
>bit images. but not display them? is there a way around this?
>8 bit display is not acceptable for what we need to do with our
>images.

I have experienced a similar problem when I use my Powerbook 180 (4-bit
screen but 8-bit external video) for interactive presentations using Image.
If I configure my external video (LCD display panel) as a second monitor,
Image will not start from my screen since it is not 8-bit deep. So I have
to configure my external video to mirror my Powerbook screen, thus wasting
lots of premium screen space for my presentations (Powerbook has only
640x400 display). Don't ask me why the 180 will not allow me to specify the
external video (LCD panel) as the startup monitor...

Wayne, is there a way around this ?  Can Image be made to refuse to display
8-bit images on a screen that is not 8-bits deep, but
(a) start from a monitor that is 1-bit or 4-bit deep, 
(b) allow you to display 8-bit images on a second 8-bit monitor and 
(b) allow you to display graphics or text on the main 1-bit or 4-bit monitor ?

------------------------------------------------------------------------
                                 |
Kyriacos Zygourakis, Ph.D.       |   Phone:  (713) 527-8750 Ext. 3509
Dept. of Chemical Engineering    |   FAX:    (713) 285-5478
Rice University                  |   e-mail: kyzy@rice.edu
Houston, Texas 77251-1892        |
                                 |
------------------------------------------------------------------------



From mvivino@helix.nih.gov  Wed Oct 20 09:24:30 1993
Received: from helix.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA01897; Wed, 20 Oct 1993 12:23:03 -0500
Return-Path: <mvivino@helix.nih.gov>
Received: from mavmac.dcrt.nih.gov by helix.nih.gov (5.64/1.35(helix-1.0))
	id AA21868; Wed, 20 Oct 93 13:24:30 -0400
Date: Wed, 20 Oct 93 13:24:30 -0400
Message-Id: <9310201724.AA21868@helix.nih.gov>
X-Sender: mvivino@128.231.2.3
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: mvivino@helix.nih.gov (Mark Vivino)
Subject: Re: IPLab Spectrum


>Thanks for the info.  Where can I find out more about DIP Station?

>From the About NIH Image manual:

DIP Station
(Medical image analysis, 16-bits, surface rendering)
Hayden Image Processing Group
Boulder, Colorado
303-449-3433  (whc@po.cwru.edu)


From morilak@cmgm.stanford.edu  Wed Oct 20 03:43:10 1993
Received: from cmgm.Stanford.EDU by nx1.soils.umn.edu (5.65c)
	id AA02057; Wed, 20 Oct 1993 12:35:53 -0500
Return-Path: <morilak@cmgm.stanford.edu>
Received: from  (P159-macplus.Stanford.EDU) by cmgm.stanford.edu (4.1/1.34)
	id AA15051; Wed, 20 Oct 93 10:37:15 PDT
Date: Wed, 20 Oct 1993 10:43:10 PDT
From: QR <morilak@cmgm.stanford.edu>
Subject: MSRS catalog of primary antibodoes
To: nih-image@soils.umn.edu
In-Reply-To: Your message of Thu, 14 Oct 1993 14:08:38 -0500
Message-Id: <MacMS.50878.5758.morilak@cmgm.stanford.edu>

I have received several questions regarding the MSRS catalog of Primary
Antibodies that I mentioned in a previous transmission, so I am sending this
to both the microscopy and NIH image distribution lists. The MSRS catalog is
indeed a catalog of primary antisera, both those available commercially and
those available from individual labs who choose to have their antisera listed.
I have found it to be an extremely useful first reference, though it is, as
might be expected, not 100% comprehensive. I often will call the sources
listed to find out what else they have available that is not in the catalog
(e.g. polyclonals vs monoclonals, different host species, different epitopes
etc.). I ordered it at last years Neuroscience meeting, and an update (I am
told) will be available approximately annually. The cost was somewhere around
$75 (US). (MSRS stands for "Manufacturer's Specifications and Reference
Synopsis"). I don't have a phone number, but here is the address off the order
form:


MSRS catalog of Primary Antibodies
AERIE Corporation
Box 1356
Birmingham, MI  48012-1356 
-------
From wayne@helix.nih.gov  Wed Oct 20 12:42:58 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA02119; Wed, 20 Oct 1993 12:44:23 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA09666; Wed, 20 Oct 93 13:04:36 -0400
Message-Id: <9310201704.AA09666@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Wed, 20 Oct 1993 12:42:58 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: # of colors on monitor

>i just put a 24bit video card in our IIfx for our imaging needs. now,
>nih gives me an error message that the monitor *must* be configured for
>256 colors or gray scales. the documentation says it will handle 24
>bit images. but not display them? is there a way around this?
>8 bit display is not acceptable for what we need to do with our
>images.

NIH Image requires that the monitor be in 8-bit (256 color) mode. I would
suggest using Photoshop for editing and displaying 24-bit color images.
There is a utility in the /pub/util directory on zippy.nimh.nih.gov called
DepthGage that allows you to quickly and easily switch between 8-bit mode
and 24-bit mode.

--wayne


From russ@mat.mte.ncsu.edu  Wed Oct 20 10:46:31 1993
Received: from mat.mte.ncsu.edu by nx1.soils.umn.edu (5.65c)
	id AA02736; Wed, 20 Oct 1993 13:45:15 -0500
Return-Path: <russ@mat.mte.ncsu.edu>
Received: by mat.mte.ncsu.edu (5.57/Ultrix3.0-C)
	id AA10315; Wed, 20 Oct 93 14:46:31 -0400
Date: Wed, 20 Oct 93 14:46:31 -0400
Message-Id: <9310201846.AA10315@mat.mte.ncsu.edu>
To: nih-image@soils.umn.edu
From: russ@mat.mte.ncsu.edu
Subject: Re: # of colors on monitor

Kyriacos Zygourakis writes
>
>I have experienced a similar problem when I use my Powerbook 180 (4-bit
>screen but 8-bit external video) for interactive presentations using Image.
>If I configure my external video (LCD display panel) as a second monitor,
>Image will not start from my screen since it is not 8-bit deep. So I have
>to configure my external video to mirror my Powerbook screen, thus wasting
>lots of premium screen space for my presentations (Powerbook has only
>640x400 display). Don't ask me why the 180 will not allow me to specify the
>external video (LCD panel) as the startup monitor...
>
No problem to do this. I do it all the time, using either an external color
monitor or a Sharp LCD panel as the second screen on my 180. Set the second
monitor up NOT to mirror the screen but as a second monitor. Open monitors
and drag the menu bar from the internal to external monitor. Then depress
the option key (the happy Mac icon will appear). Drag that icon to the
second monitor as well. Now the external monitor (or panel) will be the
primary screen, where the "welcome to mac" message and the menu bars
appear. the nice thing about this is that if you use the powerbook without
the external monitor connected, it reverts to the internal screen, but the
next time you boot up with the second monitor connected, it will use it
without any further fiddling around.

__________________________________________________
John Russ
(John_Russ@ncsu.edu)   or  (russ@mat.mte.ncsu.edu)
Materials Science and Engineering Department,
North Carolina State Univ., Raleigh, NC 27695-7907
phone: 919-515-3328              fax: 919-515-7724

From wayne@helix.nih.gov  Wed Oct 20 14:11:49 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA03011; Wed, 20 Oct 1993 14:13:14 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA09891; Wed, 20 Oct 93 14:33:28 -0400
Message-Id: <9310201833.AA09891@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Wed, 20 Oct 1993 14:11:49 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: tif or pict

>are they both 24bit?

Both can be 1, 8 or 24-bits deep.  NIH Image reads 1, 8 and 24-bit PICT
files, but only writes 8-bit PICTs. Note that reading 24-bit PICTs requires
the QuickTime INIT and doesn't always work.  NIH Image can read
uncompressed 8 and 16-bit TIFF files and writes uncompressed 8-bit TIFF
files.

--wayne


From roper@lamar.ColoState.EDU  Wed Oct 20 09:39:55 1993
Received: from lamar.ColoState.EDU by nx1.soils.umn.edu (5.65c)
	id AA04171; Wed, 20 Oct 1993 16:39:08 -0500
Return-Path: <roper@lamar.ColoState.EDU>
Received: from [129.82.126.25] by lamar.ColoState.EDU (AIX 3.2/UCB 5.64/4.03)
          id AA17373; Wed, 20 Oct 1993 15:39:55 -0600
Date: Wed, 20 Oct 1993 15:39:55 -0600
Message-Id: <9310202139.AA17373@lamar.ColoState.EDU>
To: nih-image@soils.umn.edu
From: roper@lamar.ColoState.EDU
Subject: Re: Kodak DCS200/Zeiss Microscope

>Dear Image users,
>We are trying to set up a system for routine documentation using the Kodak DCS
>200 camera. 

I have the Kodak DCS200 camera attached to a Zeiss Axiophot microscope.  I
had to purchase several hundred dollars of special adapter pieces designed
to connect a Nikon camera to the zeiss TV port, including an extension
tube, a Zeiss eyepiece (10X), and a few adapter pieces.  I am told that
Zeiss is now making an adapter directly for the Kodak camera, but I have no
information on it.  You may wish to contact Dennis Runyan, Technical Sales
Rep, Carl Zeiss Inc, Microscope Division, San Leandro Office, 14751
Catalina St., San Leandro, CA 94577, phone 800-832-3800.  He is familiar
with all the recent adapter stuff, I believe.

To compensate for the small chip, I merely use a lower mag objective than
for a conventional camera back.  You can, of course, view the image through
the ground glass screen of the Kodak (Nikon) camera back to make sure you
have everything you want in the frame. 

I connect the Kodak camera to my Mac Quadra 800 and use PhotoShop to
capture the results.  I can obtain publication-quality (well, nearly so)
prints by sending the resulting image via ftp to my campus's Tektronix dye
sublimation printer (Phase IISD).  The cost for an 8x10 is $3.95.  This
sure beats conventional darkroom methodology in time and money (except for
the expensive Zeiss adapters!).
--------------------------------------------
Stephen Roper, Professor of Anatomy and Neurobiology,
Colorado State University, Ft. Collins CO 80523 
INTERNET: Roper@Lamar.ColoState.Edu
FAX:(303) 491-7907
PHONE: (303) 491-7808

From herro001@maroon.tc.umn.edu  Wed Oct 20 12:14:07 1993
Received: from maroon.tc.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA04503; Wed, 20 Oct 1993 17:22:11 -0500
Return-Path: <herro001@maroon.tc.umn.edu>
Message-Id: <199310202222.AA04503@nx1.soils.umn.edu>
Received: from rash.med.umn.edu by maroon.tc.umn.edu id SMTP-0012cc5b81f012435; Wed, 20 Oct 93 17:13:57 -0500
From: "Mike Herron" <herro001@maroon.tc.umn.edu>
Reply-To: "Mike Herron" <@staff.tc.umn.edu>
To: nih-image@soils.umn.edu
Subject: Re: MSRS catalog of primary antibodoes
Date: Wed, 20 Oct 93 17:14:07 -0500

Do you have any idea how the MSRS compares with the Linscott's Directory as far 
as completeness, accuracy or timely nature of the information? I have used the 
Linscott's directory for years, and have been quite happy with it.

In message <MacMS.50878.5758.morilak@cmgm.stanford.edu>  writes:
> I have received several questions regarding the MSRS catalog of Primary
> Antibodies that I mentioned in a previous transmission, so I am sending this
> to both the microscopy and NIH image distribution lists. The MSRS catalog is
> indeed a catalog of primary antisera, both those available commercially and
> those available from individual labs who choose to have their antisera 
> listed.
> I have found it to be an extremely useful first reference, though it is, as
> might be expected, not 100% comprehensive. I often will call the sources
> listed to find out what else they have available that is not in the catalog
> (e.g. polyclonals vs monoclonals, different host species, different epitopes
> etc.). I ordered it at last years Neuroscience meeting, and an update (I am
> told) will be available approximately annually. The cost was somewhere around
> $75 (US). (MSRS stands for "Manufacturer's Specifications and Reference
> Synopsis"). I don't have a phone number, but here is the address off the 
> order
> form:
> 
> 
> MSRS catalog of Primary Antibodies
> AERIE Corporation
> Box 1356
> Birmingham, MI  48012-1356 
> -------
> 


 
   ______________________________________________
  / Mike Herron,  U of MN, Dept. of Dermatology /
 / herro001@maroon.tc.umn.edu                  /
/ 612-625-8935  Box 124 UMHC, Mpls MN 55455   /
______________________________________________

From morilak@cmgm.stanford.edu  Wed Oct 20 09:47:14 1993
Received: from cmgm.Stanford.EDU by nx1.soils.umn.edu (5.65c)
	id AA05123; Wed, 20 Oct 1993 18:39:51 -0500
Return-Path: <morilak@cmgm.stanford.edu>
Received: from  (P159-macplus.Stanford.EDU) by cmgm.stanford.edu (4.1/1.34)
	id AA22342; Wed, 20 Oct 93 16:41:17 PDT
Date: Wed, 20 Oct 1993 16:47:14 PDT
From: _` <morilak@cmgm.stanford.edu>
Subject: Re: MSRS catalog vs Linscott's
To: nih-image@soils.umn.edu
In-Reply-To: Your message of Wed, 20 Oct 1993 17:28:41 -0500
Message-Id: <MacMS.7186.5758.morilak@cmgm.stanford.edu>

In response to Mike Herron's query, I can't compare the MSRS to the Linscott's
directory as I have not used Linscott's. Maybe someone else could comment?

-David Morilak

P.S. I apologize again for the bizarre "From" headers my messages are
generating. I thought I had the problem fixed, but our mailer seems to have
had something of a psychotic break!
-------
From mt1ntg@fencer.cis.dsto.gov.au  Thu Oct 21 19:50:04 1993
Received: from fencer.cis.dsto.gov.au by nx1.soils.umn.edu (5.65c)
	id AA05195; Wed, 20 Oct 1993 18:48:48 -0500
Return-Path: <mt1ntg@fencer.cis.dsto.gov.au>
Message-Id: <199310202348.AA05195@nx1.soils.umn.edu>
Received: from [160.64.14.216] by fencer.cis.dsto.gov.au with SMTP; 
          Thu, 21 Oct 1993 10:01:41 +1000 (EST)
Date: Thu, 21 Oct 1993 09:50:04 +1000
To: nih-image@soils.umn.edu
From: NoelGoldsmith<mt1ntg@fencer.cis.dsto.gov.au> (Noel Goldsmith)
Subject: Re: Kodak DCS200/Zeiss Microscope

>Dear Image users,
>We are trying to set up a system for routine documentation using the Kodak DCS
>200 camera. I remember there has been some discussion on this list about using
>the Kodak DCS 200 camera for microscopy (via Photoshop plug in). Could anybody
>who is using such a setup specify how they connected the camera to a Zeiss
>Axiophot microscope? How to compensate for the small CCD chip? The chip has
>only 1/4 of the area of film and the adapters we got from Zeiss to connect the
>camera to the microscope is for film so we can capture only a small part of the
>slide we see in the eyepiece. Any suggestions?
>Thanks!
>
>Ruediger Fritsch
>Max-Planck-Institut f. biophysikalische Chemie
>Am Fassberg
>37077 Goettingen
>Germany
>email rfritsc@gwdgv1.dnet.gwdg.de

Ruediger,
I have had some fun here interfacing a variety of cameras to a variety of
lenses, microscopes and so-on.
The essential principles you must keep in mind are as follows.
You need a real image on the chip/chips in focus, which covers the field
you want.
How do you do this when the chip/chips are buried some 30 mm deep in the camera.
I think the DCS200 has similar back focal distance to a 35mm SLR, so if you
use a typical C mount adaptor then you will get a small field of view.
Solution.
Project an image from your microscope onto a piece of card which has a
rectangle on it the same size as your chip. (you might need to turn out the
lights).  Adjust  the distance between the card and the eyepiece or camera
port until the field of view on the chip rectangle is what you need. Focus
this as well as you can, the image is small. Now take a lens, for a trial
use a 50mm enlarger lens or a 50mm lens from an SLR camera. Place this lens
100 mm away from the card and place the ccd chip 100 mm behind the lens.
Remove the card. This will relay the image at 1 magnification (or at 1:1)
into the ccd chip. If you want to get a different scale vary the distances
on each side of the lens. Enlarger lenses are good for this sort of work,
as they are designed to work at ratios around 1:1, whereas ordinary camera
lenses are computed for infinity. The optimum solution will use a process
lens, designed for 1:1 and similar. Of course in this application, the
field need to be covered is small in angular terms and consequently any
lens will work quite well. The problem with this method is that it is not a
compact solution, and requires a bit of machining of tubes etc for a good
permanent set-up. An advantage is that you can make telescoping tubes and
achieve large fields or small fields, with one lens.
Commercial solutions are often expensive, and may be designed to work with
C mount cameras which employ a lens to ccd distance which is around 10mm
and make coupling easier. Commercial solutions may be compact.
Leica, Zeiss and so-on all  have some lenses for adapting cameras to stereo
microscopes and these come in a variety of magnifications, using numbers
such as 0.6. Such a 0.6 lens is a strong positive objective (about a 10x
magnifier) which relays the image smaller, and does so in a fairly compact
way)
Lenses for cameras such as the Sony DXC-930 P which is a 3 chip colour ccd
employ an optical design strategy known a retro-focus, whereby a zoom lens
with a focal length of 8-80 mm say is positioned in front of a window in
the camera, with the focal plane being located some 30mm behind. There is a
relay lens which transfers the image, at the required scale. 
Hope this helps.
Noel
Noel T Goldsmith
DSTO
Aeronautical Research Laboratory
506 Lorimer Street
Port Melbourne
Vic 3207
Australia

From huff@MCCLB0.MED.NYU.EDU  Thu Oct 21 01:10:05 1993
Received: from mcclb0.med.nyu.edu by nx1.soils.umn.edu (5.65c)
	id AA08202; Thu, 21 Oct 1993 05:07:43 -0500
Return-Path: <huff@MCCLB0.MED.NYU.EDU>
Received: from DialupEudora (ANNEX1.NET.NYU.EDU) by MCCLB0.MED.NYU.EDU (PMDF
 V4.2-14 #2884) id <01H4D4ATA09C0027I1@MCCLB0.MED.NYU.EDU>; Thu,
 21 Oct 1993 06:08:56 EDT
Date: Thu, 21 Oct 1993 06:10:05 -0500
From: huff@MCCLB0.MED.NYU.EDU (Edward J. Huff)
Subject: Re: IPL and AxoVideo
To: nih-image@soils.umn.edu
Message-Id: <01H4D4AU37KI0027I1@MCCLB0.MED.NYU.EDU>
X-Envelope-To: nih-image@soils.umn.edu
Content-Transfer-Encoding: 7BIT

>Both IPL and Axovideo (Axon Instruments) include software for Calcium 
>ratio  imaging. 
>Has anyone developed a complete set of macros for NIH Image 
>for this purpose?
>                                Harvey Karten

I developed a User.p which supports 32 bit real images, and
steven@cell.BIH.Harvard.Edu (Steven Blechner) wrote macros that use the
macro commands I provided, and I believe has been doing Calcium ratio
imaging using that package.  I plan to move that code from User.p into
UMPixel32r.p in Image UMX so that the macro commands each have their own
names instead of UserCode(code#,...) but haven't gotten to it yet.  That
package also supports the Scion 1200 board collecting 32fps images onto a
DayStar RAM card and later
integrates them into 16 bit images.
--
Edward J. Huff   huff@mcclb0.med.nyu.edu   (212)998-8465
Keck Laboratory for Biomolecular Imaging
NYU Chemistry Department, 31 Washington Place, New York NY 10003

From sarmienu@rnisd0.DNET.roche.com  Thu Oct 21 03:36:16 1993
Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c)
	id AA08560; Thu, 21 Oct 1993 06:34:53 -0500
Return-Path: <sarmienu@rnisd0.DNET.roche.com>
Received: by gatekeeper.roche.com (5.65/fma-120691);
	id AA28870; Thu, 21 Oct 93 07:36:18 -0400
Received: by mailgate.roche.com (5.65/fma-120691);
	id AA18164; Thu, 21 Oct 93 07:32:23 -0400
From: sarmienu@rnisd0.DNET.roche.com
Message-Id: <9310211132.AA18164@mailgate.roche.com>
Received: from rnisd0.enet; by inet.enet; Thu, 21 Oct 93 07:36:16 EDT
Date: Thu, 21 Oct 93 07:36:16 EDT
To: nih-image@soils.umn.edu
Apparently-To: nih-image@soils.umn.edu
Subject: Linscott's catalogue

Could we get the address (phone number) to obtain the Linscott's catalogue too...
??
Thank you

Juan I. Sarmiento
Department of Toxicology and Pathology
Hoffmann-La Roche, INC.
340 Kingsland street
Nutley, NJ 07110
Sarmienu@RNISD0.DNET.ROCHE.COM
From jladwig@soils.umn.edu  Thu Oct 21 03:19:26 1993
Received: from saturn.soils.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA09238; Thu, 21 Oct 1993 08:19:31 -0500
Return-Path: <jladwig@soils.umn.edu>
Received: by saturn.soils.umn.edu (4.1)
	id AA04542; Thu, 21 Oct 93 08:19:26 CDT
Date: Thu, 21 Oct 93 08:19:26 CDT
From: "John Ladwig" <jladwig@soils.umn.edu>
Message-Id: <9310211319.AA04542@saturn.soils.umn.edu>
To: nih-image@soils.umn.edu
Subject: Re: John Crum - electron microscope images

------- Start of forwarded message -------
Reply to question by John Crum at SDSU:

4pi Analysis in North Carolina makes a board for the Macintosh
computer that will scan an image on an electron microscope and collect
a digital image. Image size can be anything up to 4096x4096 with 14
bits per pixel. Included is a plug-in for Adobe Photoshop to do the
scanning and collect the image. This plug-in also works with NIH Image
and runs faster than in Photoshop. The board also contains all the
hardware to be used as a multi-channel analyzer for EDS analysis. The
NIST/NIH Desktop Spectrum Analysis (DTSA) program runs with this board
to make a complete multichannel analyzer with many simulation and
analysis features. The board from 4pi costs about $5000 and the DTSA
program costs $815 from NIST.

4pi Analysis, Inc.
3500 Westgate Drive
Suite 403
Durham, NC 27707
Phone: 919-489-1757

DTSA information: 
Phone: 301-975-3906 (Bob Myklebust)
email: myklebust@gapnet.nist.gov

 Bob Myklebust
------- End of forwarded message -------
From kartenh@Sdsc.Edu  Thu Oct 21 13:39:54 1993
Received: from Sdsc.Edu (m5.sdsc.edu) by nx1.soils.umn.edu (5.65c)
	id AA09458; Thu, 21 Oct 1993 08:38:42 -0500
Return-Path: <kartenh@Sdsc.Edu>
Date:    Thu, 21 Oct 93 13:39:54 GMT
From: kartenh@Sdsc.Edu (Harvey Karten)
Message-Id: <931021133954.20404251@m5.sdsc.edu>
Subject: Re: IPL and AxoVideo
To: nih-image@soils.umn.edu
X-St-Vmsmail-To: ST%"nih-image@soils.umn.edu"
X-St-Vmsmail-Cc: KARTENH

Edward Huff writes:
"package also supports the Scion 1200 board collecting 32fps images onto a
DayStar RAM card and later
" 
What is the Scion 1200 board? I was only aware of their LG-3.

Also: "
lan to move that code from User.p into
UMPixel32r.p in Image UMX so that the macro commands each have their own
names instead of UserCode(code#,...) "
Look forward to seeing it on Zippy.
					Many thanks, Harvey Karten
 Harvey J. Karten, M.D.
 Dept. Neurosciences 
 UCSD 0608
 La Jolla, CA 92093 
 Phone (619)-534-4938 
 FAX (619)-534-6602 
 E-Mail KARTENH@SDSC.EDU
From @YaleVM.YCC.Yale.Edu:Mike_Schwartz@QUICKMAIL.CIS.YALE.EDU  Mon Oct 21 06:27:31 1993
Received: from YALEVM.YCC.YALE.EDU by nx1.soils.umn.edu (5.65c)
	id AA09913; Thu, 21 Oct 1993 09:27:08 -0500
Return-Path: <@YaleVM.YCC.Yale.Edu:Mike_Schwartz@QUICKMAIL.CIS.YALE.EDU>
Message-Id: <199310211427.AA09913@nx1.soils.umn.edu>
Received: from quickmail.yale.edu by YaleVM.YCC.Yale.Edu (IBM VM SMTP V2R2)
   with TCP; Thu, 21 Oct 93 10:26:36 EDT
Date: 21 Oct 1993 10:27:31 -0400
From: "Mike Schwartz" <Mike_Schwartz@quickmail.yale.edu>
Subject: 4pi Analysis in North Carol
To: "Image List" <nih-image@soils.umn.edu>
Return-Receipt-To: "Mike Schwartz" <Mike_Schwartz@quickmail.yale.edu>

                       Subject:                               Time:10:15 AM
  OFFICE MEMO          4pi Analysis in North Carolina makes_  Date:10/21/93
>4pi Analysis in North Carolina makes a board for the Macintosh
>computer that will scan an image on an electron microscope and collect
>a digital image. Image size can be anything up to 4096x4096 with 14
>bits per pixel. 

What camera do you use  to take advantage of the 4096x4096 resolution and how
do you mount the camera? What printer do you use to obtain hardcopy and are the
resulting prints of publication quality?

Mike Schwartz
Sect. of Neurobiology
Yale Univ. Sch. of Med.
Mike Schwartz@qm.yale.edu


From djm@cidmv1.wustl.edu  Thu Oct 21 06:15:03 1993
Received: from wugate.wustl.edu by nx1.soils.umn.edu (5.65c)
	id AA10589; Thu, 21 Oct 1993 11:13:40 -0500
Return-Path: <djm@cidmv1.wustl.edu>
Received: by wugate.wustl.edu (5.67a+/WUSTL-0.3) with DECnet 
	id AA22037; Thu, 21 Oct 1993 11:15:04 -0500
Date: Thu, 21 Oct 1993 11:15:03 -0500
Message-Id: <199310211615.AA22037@wugate.wustl.edu>
From: djm@cidmv1.wustl.edu (D.J. Meyer)
To: nih@wugate.wustl.edu
Subject: illumination


hi,
we do a lot of processing of retinas, and are frequently using our ccd
camera so the other lab members can watch the surgeries, disections, etc.
we also capture a lot of images. these are shot through binoculars.

i am having a problem with illumination, particularly reflections. the eyes
are as you know, roughly sperical, and we use fiber lights to illuminate 
inside. however, we are getting a lot of reflections no matter what kind
of dish we use to hold the eye. 
i've tried glass petri dishes. beakers. styrofoam. even a plastic bottle cap,
but i can't seem to get the illumination right with the eyes.
grabbing images from the slide microscope works perfectly, but its easy to
get equal illumination from a microscope.
any suggestions on lighting and containers?
thanks
dj meyer
From herro001@maroon.tc.umn.edu  Thu Oct 21 08:38:24 1993
Received: from maroon.tc.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA11806; Thu, 21 Oct 1993 13:36:56 -0500
Return-Path: <herro001@maroon.tc.umn.edu>
Message-Id: <199310211836.AA11806@nx1.soils.umn.edu>
Received: from rash.med.umn.edu by maroon.tc.umn.edu id SMTP-0012cc6d6ff024112; Thu, 21 Oct 93 13:37:54 -0500
From: "Mike Herron" <herro001@maroon.tc.umn.edu>
Reply-To: "Mike Herron" <@staff.tc.umn.edu>
To: nih-image@soils.umn.edu
Subject: Re: illumination
Date: Thu, 21 Oct 93 13:38:24 -0500

How about a polarizer filter?

In message <199310211615.AA22037@wugate.wustl.edu>  writes:
> 
> hi,
> we do a lot of processing of retinas, and are frequently using our ccd
> camera so the other lab members can watch the surgeries, disections, etc.
> we also capture a lot of images. these are shot through binoculars.
> 
> i am having a problem with illumination, particularly reflections. the eyes
> are as you know, roughly sperical, and we use fiber lights to illuminate 
> inside. however, we are getting a lot of reflections no matter what kind
> of dish we use to hold the eye. 
> i've tried glass petri dishes. beakers. styrofoam. even a plastic bottle cap,
> but i can't seem to get the illumination right with the eyes.
> grabbing images from the slide microscope works perfectly, but its easy to
> get equal illumination from a microscope.
> any suggestions on lighting and containers?
> thanks
> dj meyer
> 


 
   ______________________________________________
  / Mike Herron,  U of MN, Dept. of Dermatology /
 / herro001@maroon.tc.umn.edu                  /
/ 612-625-8935  Box 124 UMHC, Mpls MN 55455   /
______________________________________________

From wayne@helix.nih.gov  Thu Oct 21 15:35:57 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA12606; Thu, 21 Oct 1993 15:37:26 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA16471; Thu, 21 Oct 93 15:57:41 -0400
Message-Id: <9310211957.AA16471@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Thu, 21 Oct 1993 15:35:57 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: grain counting macros

>Hi.
>
>I'm a new member of 'the list' and don't know if this has been covered yet.
>Has anyone tried the grain-counting macros that Karl Beykirch put up for
>anonymous ftp transfer?
>I've been trying them, and having some difficulty.  In particular, when 
>using the 'Count Grains in Area (F7) macro, it is graying out my entire
>selection and counting it as -one- grain.  Perhaps I am not calibrating
>the area/grain properly.  I am not macro-literate (yet), so any info
>that you can offer is appreciated.

Send me a sample image and I will see if I can figure out what is going on.
You can either upload it to the contrib directory on Zippy or email it in
binhex format.

--wayne


From glenmac@u.washington.edu  Thu Oct 21 09:40:00 1993
Received: from carson.u.washington.edu by nx1.soils.umn.edu (5.65c)
	id AA13637; Thu, 21 Oct 1993 18:46:27 -0500
Return-Path: <glenmac@u.washington.edu>
Received: by carson.u.washington.edu
	(5.65/UW-NDC Revision: 2.29 ) id AA04781; Thu, 21 Oct 93 16:47:54 -0700
X-Sender: glenmac@carson.u.washington.edu
Date: Thu, 21 Oct 1993 16:40:00 -0700 (PDT)
From: Glen Macdonald <glenmac@u.washington.edu>
Subject: Re: Linscott's catalogue info.
To: nih-image@soils.umn.edu
Cc: Multiple recipients of list <nih-image@soils.umn.edu>
In-Reply-To: <9310211132.AA18164@mailgate.roche.com>
Message-Id: <Pine.3.05z.9310211658.A29519-9100000@carson.u.washington.edu>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=us-ascii

Linscott's Directory
4877 Grange Rd.
Santa Rosa, CA  95404  USA
(707) 544-95555
Subscriptions are $60/yr.  and provides a main book with 3 or 4 quarterly
updates.  It lists monoclonal and polyclonal antibodies by antigen
type,tissues, cytokines, lectins, venoms, etc. and cell cultures,
immunoassay kits, and contract/custome services.  

Glen MacDonald 
Hearing Development Labs
University of WAshington




From pruskyg@hg.uleth.ca  Thu Oct 21 10:17:51 1993
Received: from holly.cc.uleth.ca by nx1.soils.umn.edu (5.65c)
	id AA13831; Thu, 21 Oct 1993 19:14:08 -0500
Return-Path: <pruskyg@hg.uleth.ca>
Received: by holly.cc.uleth.ca; id AA28511; Thu, 21 Oct 1993 18:14:24 -0600
Message-Id: <9310220014.AA28511@holly.cc.uleth.ca>
Date: Thu, 21 Oct 1993 18:17:51 -0800
To: nih-image@soils.umn.edu
From: pruskyg@hg.uleth.ca (Glen Prusky)
X-Sender: pruskyg@pop.uleth.ca
Subject: Sweet wishes

Wayne et al., 
I am an evangelical user and supporter of Image, but there are always
things that could be added to any program to enhance its features to match
one's particular application. I was wondering if anyone out there has
written a macro or if Wayne could incorporate into the program the
following utility: I use image to capture dye-filled neurons on a
fluorescence microscope. The processes of these neurons have the
unfortunate poperty of coursing in and out of the plane of focus at high
magnifications, and at low magnifications, the inherent low resolution of
video results in unsatisfactory images. In order to get around this, I end
up taking a series of images at high magnification at different focal
planes and cutting and pasting to create a 2D image of the cellular
processes. Haig Keshishian (HKESHIS@YALEVM.YCC.YALE.EDU) has encountered a
similar problem and has written code for his DOS-based system to help
rectify this problem. First he captures an image. Then he selects an area
on this image that is out of focus. This and only this area can then be
placed into live capture mode, allowing you to focus on that particular
part of the specimin and then capture that area and paste it into the
original image. This can be done a number of times to give you a completely
focussed 2D image. This has the advantage of maintaining perfect alignment
among pieces of a photomontage, it saves a lot of time since you don't have
to cut and paste together peices of different original images, and the
resulting image has few areas of abrupt changes in background because you
are capturing new areas of the image at the same time under the same
lighting conditions. Confocal microscopy, that allows you to collapse
different planes of an image into 2D, can solve this problem, but for those
of us without such a machine who would like to have this kind of utility,
would do cartwheels if it were part of Image.
I have talked with Haig and he would be happy to share how he accomplished
this feature in his software. I know of many people who use Image in a
similar capacity that I do, so I suspect that a feature such as this in
Image would meet with widespread approval. Keep up the great work!
   
Glen T. Prusky Ph.D.
Department of Psychology
The University of Lethbridge
4401 University Drive
Lethbridge, AB, Canada
T1K 3M4
pruskyg@hg.uleth.ca
Office-403-329-2402
Lab-403-329-2410
Fax-403-329-2410

From rms@acsu.buffalo.edu  Thu Oct 21 17:08:05 1993
Received: from lictor.acsu.buffalo.edu by nx1.soils.umn.edu (5.65c)
	id AA14138; Thu, 21 Oct 1993 20:06:40 -0500
Return-Path: <rms@acsu.buffalo.edu>
Received: from rms@localhost by lictor.acsu.buffalo.edu (8.5/8.5)
	id VAA23789; Thu, 21 Oct 1993 21:08:05 -0400
Date: Thu, 21 Oct 1993 21:08:05 -0400
From: "Robert M. Straubinger" <rms@acsu.buffalo.edu>
Message-Id: <199310220108.VAA23789@lictor.acsu.buffalo.edu>
To: nih-image@soils.umn.edu, nih-image@soils.umn.edu
Subject: Re:  IPL and AxoVideo

H. Karten wrote:
*Has anyone developed a complete set of macros for NIH Image 
*for [the] purpose [of ratio imaging].

Since the exchanges on this list a couple weeks back, we've
made a couple macros to load a stack of alternating-wavelength
images, and create a new stack of ratioed images. The trouble
is that the 'divide' routine currently automatically scales
the resulting image to the widest possible dynamic range (ie.
stretches the max/min ratios to 256/0, respectively), as
best I understand. This creates problems as we need to keep
the scaling uniform through our image series. Otherwise the
calibration curve will mean nothing.

Wayne wrote that he was contemplating a fix for this problem.

Bob Straubinger
Pharmaceutics
SUNY/Buffalo
From kartenh@Sdsc.Edu  Fri Oct 22 03:26:06 1993
Received: from Sdsc.Edu (m5.sdsc.edu) by nx1.soils.umn.edu (5.65c)
	id AA14826; Thu, 21 Oct 1993 22:24:47 -0500
Return-Path: <kartenh@Sdsc.Edu>
Date:    Fri, 22 Oct 93 03:26:06 GMT
From: kartenh@Sdsc.Edu (Harvey Karten)
Message-Id: <931022032606.20407f33@m5.sdsc.edu>
Subject: RE: Sweet wishes
To: nih-image@soils.umn.edu
X-St-Vmsmail-To: ST%"nih-image@soils.umn.edu"
X-St-Vmsmail-Cc: KARTENH

How accurate a reconstruction does this method produce? How does it deal with 
collateral branches in the same ROI but in different focal planes?
						Harvey Karaten
 Harvey J. Karten, M.D.
 Dept. Neurosciences 
 UCSD 0608
 La Jolla, CA 92093 
 Phone (619)-534-4938 
 FAX (619)-534-6602 
 E-Mail KARTENH@SDSC.EDU
From mt1ntg@fencer.cis.dsto.gov.au  Sat Oct 23 02:40:17 1993
Received: from fencer.cis.dsto.gov.au by nx1.soils.umn.edu (5.65c)
	id AA15764; Fri, 22 Oct 1993 01:39:04 -0500
Return-Path: <mt1ntg@fencer.cis.dsto.gov.au>
Message-Id: <199310220639.AA15764@nx1.soils.umn.edu>
Received: from [160.64.14.216] by fencer.cis.dsto.gov.au with SMTP; 
          Fri, 22 Oct 1993 16:52:00 +1000 (EST)
Date: Fri, 22 Oct 1993 16:40:17 +1000
To: nih-image@soils.umn.edu
From: NoelGoldsmith<mt1ntg@fencer.cis.dsto.gov.au> (Noel Goldsmith)
Subject: Re: Sweet wishes

>Wayne et al., 
>I am an evangelical user and supporter of Image, but there are always
>things that could be added to any program to enhance its features to match
>one's particular application. I was wondering if anyone out there has
>written a macro or if Wayne could incorporate into the program the
>following utility: I use image to capture dye-filled neurons on a
>fluorescence microscope. The processes of these neurons have the
>unfortunate poperty of coursing in and out of the plane of focus at high
>magnifications, and at low magnifications, the inherent low resolution of
>video results in unsatisfactory images. In order to get around this, I end
>up taking a series of images at high magnification at different focal
>planes and cutting and pasting to create a 2D image of the cellular
>processes. Haig Keshishian (HKESHIS@YALEVM.YCC.YALE.EDU) has encountered a
>similar problem and has written code for his DOS-based system to help
>rectify this problem. First he captures an image. Then he selects an area
>on this image that is out of focus. This and only this area can then be
>placed into live capture mode, allowing you to focus on that particular
>part of the specimin and then capture that area and paste it into the
>original image. This can be done a number of times to give you a completely
>focussed 2D image. This has the advantage of maintaining perfect alignment
>among pieces of a photomontage, it saves a lot of time since you don't have
>to cut and paste together peices of different original images, and the
>resulting image has few areas of abrupt changes in background because you
>are capturing new areas of the image at the same time under the same
>lighting conditions. Confocal microscopy, that allows you to collapse
>different planes of an image into 2D, can solve this problem, but for those
>of us without such a machine who would like to have this kind of utility,
>would do cartwheels if it were part of Image.
>I have talked with Haig and he would be happy to share how he accomplished
>this feature in his software. I know of many people who use Image in a
>similar capacity that I do, so I suspect that a feature such as this in
>Image would meet with widespread approval. Keep up the great work!
>   
>Glen T. Prusky Ph.D.
>Department of Psychology
>The University of Lethbridge
>4401 University Drive
>Lethbridge, AB, Canada
>T1K 3M4
>pruskyg@hg.uleth.ca
>Office-403-329-2402
>Lab-403-329-2410
>Fax-403-329-2410
Well, I have done this for opaque reflective specimens. This code is not
yet quite mature. I (the place where I work) are considering the financial
implications of commercialisng it. Another much more difficult problem is
how do you cope with constant changes in Image. I am thinking that if we
package our method in a plug in it may do. Or we could put it in NIHUMX,
which would put all of the extra code in one module.
May I recommend the following references for those who want to do a bit of
library digging. As you might guess I am writing a paper on the topic.
  Peiper, R.J., and Korpel, A. (1983) Image Processing for extended depth
of field. Applied Optics 22, 1449-1453.
  Sugimoto, S.A. and Ichioka, Y. (1985) Digital composition of images with
increased depth of focus considering depth information. Applied Optics 24,
2076-2080.
  Hausler, G.  and Korner, E. (1987) Imaging with expanded depth of focus.
Zeiss Information, Vol 29, pp. 1-32. Carl Zeiss, Oberkochen, Germany.
  Itoh, K., Hayashi, A. and Ichioka, Y. (1989) Digitized optical microscopy
with extended depth of field. Applied Optics. 28, 3487-3493.
  Vollath, D., The Influence of the scene parameters and of noise on the
behaviour of automatic focusing algorithms. Journal of Microscopy, Vol.
151, Pt 2, August 1988, pp. 133-146.
 Erteza, A., Sharpness index and its application to focus control. Applied
Optics Vol 15, No. 4, April 1976. pp 877-881.
  Erteza, A., Depth of convergence of a sharpness index autofocus system
Applied Optics Vol 16, No. 8, August 1977. pp 2273-2278.
 Born, M. and Wolf, E., Principles of Optics, Pergamon Press, 1980, pp 435-442.

 Goss, R., Holm, J., Thin Section Photomicrography, Kodak TechBits 1, 1992,
pp 4-7.
  Conrady, A. E. Applied optics and optical design Part 2 Dover
Publications 1960 pp 627-628.
Hope this helps.
Noel
Noel T Goldsmith
DSTO
Aeronautical Research Laboratory
506 Lorimer Street
Port Melbourne
Vic 3207
Australia

From sarmienu@rnisd0.DNET.roche.com  Fri Oct 22 04:07:44 1993
Received: from GATEKEEPER.ROCHE.COM by nx1.soils.umn.edu (5.65c)
	id AA17386; Fri, 22 Oct 1993 07:06:21 -0500
Return-Path: <sarmienu@rnisd0.DNET.roche.com>
Received: by gatekeeper.roche.com (5.65/fma-120691);
	id AA04797; Fri, 22 Oct 93 08:07:47 -0400
Received: by mailgate.roche.com (5.65/fma-120691);
	id AA28363; Fri, 22 Oct 93 08:04:13 -0400
From: sarmienu@rnisd0.DNET.roche.com
Message-Id: <9310221204.AA28363@mailgate.roche.com>
Received: from rnisd0.enet; by inet.enet; Fri, 22 Oct 93 08:07:44 EDT
Date: Fri, 22 Oct 93 08:07:44 EDT
To: nih-image@soils.umn.edu
Apparently-To: nih-image@soils.umn.edu
Subject: IP-Lab Spectrum and LG-3

I thought this may be of some interest:

IP-Lab now supports the frame grabber that we have been using for NIH Image.
This is interesting in that the software is not that expensive and may be used
in addition to or instead of NIH Image. Furthermore, I will be looking into validation for FDA approval for this program as well as PrismView (more expensive).

For more information, contact:

Signal
Analytics Corp., 440 Maple Avenue East, Suite 201, Vienna VA 22180, phone
703-281-3277, fax 703-281-2509. Ask for Dr. Michael Mort. Their email
address via internet is D6196@Applelink.Apple.Com
From mvivino@helix.nih.gov  Fri Oct 22 05:58:56 1993
Received: from helix.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA18040; Fri, 22 Oct 1993 08:57:31 -0500
Return-Path: <mvivino@helix.nih.gov>
Received: from mavmac.dcrt.nih.gov by helix.nih.gov (5.64/1.35(helix-1.0))
	id AA21731; Fri, 22 Oct 93 09:58:56 -0400
Date: Fri, 22 Oct 93 09:58:56 -0400
Message-Id: <9310221358.AA21731@helix.nih.gov>
X-Sender: mvivino@128.231.2.3
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: mvivino@helix.nih.gov (Mark Vivino)
Subject: Re: illumination

>hi,
>we do a lot of processing of retinas, and are frequently 
{deleted}
>i am having a problem with illumination, particularly reflections. {deleted}

Aside from polarisers, what about all the instrumentation that has been
designed exactly for the purpose of looking at the retina? As far as comes
to mind there is an indirect ophthalmoscope, fundus camera and probably
others. These are routinely used here at NIH for studies such as macular
edema, etc.


Mark Vivino
NIH/DCRT
mvivino@helix.nih.gov


From COIN@NIEHS.NIH.GOV  Fri Oct 22 06:52:42 1993
Received: from NIEHS.NIH.GOV (vaxe.niehs.nih.gov) by nx1.soils.umn.edu (5.65c)
	id AA18461; Fri, 22 Oct 1993 09:50:30 -0500
Return-Path: <COIN@NIEHS.NIH.GOV>
Received: from NIEHS.NIH.GOV by NIEHS.NIH.GOV (PMDF V4.2-13 #3461) id
 <01H4ESFZ9ZOW90OASF@NIEHS.NIH.GOV>; Fri, 22 Oct 1993 10:52:42 EDT
Date: Fri, 22 Oct 1993 10:52:42 -0400 (EDT)
From: Patrick Coin <COIN@NIEHS.NIH.GOV>
Subject: cell scoring macro?
To: NIH-IMAGE@SOILS.UMN.EDU
Message-Id: <01H4ESFZA9C290OASF@NIEHS.NIH.GOV>
X-Vms-To: IN%"NIH-IMAGE@SOILS.UMN.EDU"
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII
Content-Transfer-Encoding: 7BIT

Howdy. I'd like to use Image as a semi-automated scoring system for
immuno-stained cells. I have cells on a slide that are either unlabelled (blue
counter- staining) or labelled (brown). These differences show up clearly in 
the
8-bit indexed color when I capture a color image. I would then like to take 
the
crosshair tool and MANUALLY score each cell by clicking on it and have the
program keep count of labelled, unlabelled, and total cells. (I'd like to
differentiate the two by holding down the option key or something.) I know 
there
might be a fancy way to use automated particle counting to do this, but this 
is
too slow and it is too hard to screen out the frequent pieces of junk on the
slide. These are easy to screen out by eye. My main interest in using the
digitizer is to reduce eye strain. This is a serious problem when counting 100
or
200 cells/slide and then counting 20 slides for a single experiment.   So have
any of you macro mavens out there seen a macro to do this? Alternatively, does
anybody have an idea where to start to write a macro to do this?
Many thanks
Patrick Coin
COIN@NIEHS.NIH.GOV
Laboratory of Pulmonary Pathobiology
National Institute of Environmental Health Sciences
(a lesser known part of your friendly National Institutes of Health)
From pruskyg@hg.uleth.ca  Fri Oct 22 02:04:24 1993
Received: from holly.cc.uleth.ca by nx1.soils.umn.edu (5.65c)
	id AA18900; Fri, 22 Oct 1993 11:03:02 -0500
Return-Path: <pruskyg@hg.uleth.ca>
Received: by holly.cc.uleth.ca; id AA00282; Fri, 22 Oct 1993 10:00:58 -0600
Message-Id: <9310221600.AA00282@holly.cc.uleth.ca>
Date: Fri, 22 Oct 1993 10:04:24 -0800
To: nih-image@soils.umn.edu
From: pruskyg@hg.uleth.ca (Glen Prusky)
X-Sender: pruskyg@pop.uleth.ca
Subject: RE: Sweet wishes

>How accurate a reconstruction does this method produce? How does it deal with 
>collateral branches in the same ROI but in different focal planes?
>                                                Harvey Karaten
> Harvey J. Karten, M.D.
> Dept. Neurosciences 
> UCSD 0608
> La Jolla, CA 92093 
> Phone (619)-534-4938 
> FAX (619)-534-6602 
> E-Mail KARTENH@SDSC.EDU
Harvey, 
My brain might be frozen this morning, but I am not sure what you mean by
ROI. This method of capturing an image is much better than cutting and
pasting individual peices of many images together to form a montage.
Basically you rely on your judgement of when an area is in focus. If a
process rapidly moves through the depth of a piece if tissue, then you
simply make smaller boxes and follow that process to its end. Of course it
is not perfect because it is not truly slicing the tissue, but many times
you would like the detail of a higher magnification and the depth of field
of lower magnification. This is one compromize. The kind of tissue that I
use and I think that most people use is a slice of tissue 100-300 uM thick
and most of the time, this procedure works well. I know Haig uses this
technique to follow neurons and muscles in whole fly and grasshopper embyos
with great success. See the covers of The Journal of Neurobiology, Vol 24
#6, June 1993 and the cover of Trends in Neurosciences, Vol 16, #7[181],
July 1993. All of the work in the papers in these journals was done using
this technique. It works extremely well!
Glen Prusky   
Glen T. Prusky Ph.D.
Department of Psychology
The University of Lethbridge
4401 University Drive
Lethbridge, AB, Canada
T1K 3M4
pruskyg@hg.uleth.ca
Office-403-329-2402
Lab-403-329-2410
Fax-403-329-2410

From pruskyg@hg.uleth.ca  Fri Oct 22 02:23:38 1993
Received: from holly.cc.uleth.ca by nx1.soils.umn.edu (5.65c)
	id AA19076; Fri, 22 Oct 1993 11:19:52 -0500
Return-Path: <pruskyg@hg.uleth.ca>
Received: by holly.cc.uleth.ca; id AA00347; Fri, 22 Oct 1993 10:20:12 -0600
Message-Id: <9310221620.AA00347@holly.cc.uleth.ca>
Date: Fri, 22 Oct 1993 10:23:38 -0800
To: nih-image@soils.umn.edu
From: pruskyg@hg.uleth.ca (Glen Prusky)
X-Sender: pruskyg@pop.uleth.ca
Subject: Re: Sweet wishes

Noel Writes:
>Well, I have done this for opaque reflective specimens. This code is not
>yet quite mature. I (the place where I work) are considering the financial
>implications of commercialisng it. Another much more difficult problem is
>how do you cope with constant changes in Image. I am thinking that if we
>package our method in a plug in it may do. Or we could put it in NIHUMX,
>which would put all of the extra code in one module.
>May I recommend the following references for those who want to do a bit of
>library digging. As you might guess I am writing a paper on the topic.
>  Peiper, R.J., and Korpel, A. (1983) Image Processing for extended depth
>of field. Applied Optics 22, 1449-1453.
>  Sugimoto, S.A. and Ichioka, Y. (1985) Digital composition of images with
>increased depth of focus considering depth information. Applied Optics 24,
>2076-2080.
>  Hausler, G.  and Korner, E. (1987) Imaging with expanded depth of focus.
>Zeiss Information, Vol 29, pp. 1-32. Carl Zeiss, Oberkochen, Germany.
>  Itoh, K., Hayashi, A. and Ichioka, Y. (1989) Digitized optical microscopy
>with extended depth of field. Applied Optics. 28, 3487-3493.
>  Vollath, D., The Influence of the scene parameters and of noise on the
>behaviour of automatic focusing algorithms. Journal of Microscopy, Vol.
>151, Pt 2, August 1988, pp. 133-146.
> Erteza, A., Sharpness index and its application to focus control. Applied
>Optics Vol 15, No. 4, April 1976. pp 877-881.
>  Erteza, A., Depth of convergence of a sharpness index autofocus system
>Applied Optics Vol 16, No. 8, August 1977. pp 2273-2278.
> Born, M. and Wolf, E., Principles of Optics, Pergamon Press, 1980, pp 435-442.
>
> Goss, R., Holm, J., Thin Section Photomicrography, Kodak TechBits 1, 1992,
>pp 4-7.
>  Conrady, A. E. Applied optics and optical design Part 2 Dover
>Publications 1960 pp 627-628.
>Hope this helps.
>Noel
>Noel T Goldsmith
>DSTO
>Aeronautical Research Laboratory
>506 Lorimer Street
>Port Melbourne
>Vic 3207
>Australia
Noel,
See my reply to Harvey Karten. In terms of the actual code to accomplish
this within Image, my preference would be to have another option in the
Special menu that simply allowed you to capture images in this manner, just
like you can average, integrate or subtract background. This could be
called something like 'Build Image'. First you would capture an original
and then use the area selection items (probably the box or the elipse would
be fine; Haig's system uses the box) to select the area of the image that
you would like to focus. That area would have live camera input that you
could see over the original image , allowing you to focus that area with
the surrounding areas of the original image, and then paste it in. Just
like in the normal capture mode you could terminate the live video either
by a carriage return or the mouse button, or by using the same average or
integrate settings that were used to capture the original image. This
maintains consistency in the quality of the image across the resulting
montage. If this mode of capture were part of the normal capturing menu,
plug ins would not be necessary. Obviously, to accomplish this, it would
have to be placed in Wayne's queue of priorities for updates. I think that
this would be a very nice addition to the program. What do you think Wayne?

Glen Prusky   
Glen T. Prusky Ph.D.
Department of Psychology
The University of Lethbridge
4401 University Drive
Lethbridge, AB, Canada
T1K 3M4
pruskyg@hg.uleth.ca
Office-403-329-2402
Lab-403-329-2410
Fax-403-329-2410

From morilak@cmgm.stanford.edu  Fri Oct 22 02:53:11 1993
Received: from cmgm.Stanford.EDU by nx1.soils.umn.edu (5.65c)
	id AA19283; Fri, 22 Oct 1993 11:47:25 -0500
Return-Path: <morilak@cmgm.stanford.edu>
Received: from  (P159-macclassic.Stanford.EDU) by cmgm.stanford.edu (4.1/1.34)
	id AA25671; Fri, 22 Oct 93 09:48:49 PDT
From: morilak@cmgm.stanford.edu (David Morilak)
Date: Fri, 22 Oct 1993 09:53:11 PDT
Subject: Re: live paste?
To: nih-image@soils.umn.edu
In-Reply-To: Your message of Fri, 22 Oct 1993 10:05:18 -0500
Message-Id: <MacMS.24071.16838.morilak@cmgm.stanford.edu>

In response to the question about doing a "photomontage" in Image to bring
different focal planes into focus (sorry, I mistakenly deleted the original so
I can't reference the sender), wouldn't the Live Paste function do the trick?
Even if items in different focal planes existed within a ROI, that subregion
could be selected again from the camera window and then refocused in a live
paste. I guess the main limitations would be that rectangular selections only
are allowed, and that if there were huge differences in focal plane, there
might also be an apparent size change, meaning that edges might not line up
exactly right. I gave this a quick and limited try before responding, and it
seemed to work. But, being fairly new at this, I'm more than happy to be
corrected...

David Morilak
Dept of Psychiatry
Stanford Univ
morilak@cmgm.stanford.edu
-------
From bright@ENH.NIST.GOV  Fri Oct 22 10:20:33 1993
Received: from enh.nist.gov by nx1.soils.umn.edu (5.65c)
	id AA19925; Fri, 22 Oct 1993 13:20:20 -0500
Return-Path: <bright@ENH.NIST.GOV>
Received: from [129.6.98.4] (dsb-mac.nist.gov) by ENH.NIST.GOV (PMDF V4.2-13
 #4653) id <01H4EZQPD4Q8002EFP@ENH.NIST.GOV>; Fri, 22 Oct 1993 14:20:33 EDT
Date: Fri, 22 Oct 1993 14:20:33 -0400 (EDT)
Date-Warning: Date header was inserted by ENH.NIST.GOV
From: bright@ENH.NIST.GOV
Subject: Re: 4pi Analysis in North Carol
To: nih-image@soils.umn.edu
Message-Id: <01H4EZQPO46Q002EFP@ENH.NIST.GOV>
Content-Transfer-Encoding: 7BIT

>                       Subject:                               Time:10:15 AM
>  OFFICE MEMO          4pi Analysis in North Carolina makes_  Date:10/21/93
>>4pi Analysis in North Carolina makes a board for the Macintosh
>>computer that will scan an image on an electron microscope and collect
>>a digital image. Image size can be anything up to 4096x4096 with 14
>>bits per pixel. 
>
>What camera do you use  to take advantage of the 4096x4096 resolution and how
>do you mount the camera? What printer do you use to obtain hardcopy and are the
>resulting prints of publication quality?
>
>Mike Schwartz
>Sect. of Neurobiology
>Yale Univ. Sch. of Med.
>Mike Schwartz@qm.yale.edu

The 4Pi board controls the scanning of the beam and gets the signal
(scattered electron count, or whatever) directly from the microscope. 
There is no camera involved, which is why this type of thing is so nice: 
large images and large dynamic range for the data.
:8o)
Dave
-------------------------------------------------------------
David S. Bright                        bright@enh.nist.gov  
Microanalysis Research Group 
Chem. A113                                  
National Institute of Standards & Technology (NIST, formerly NBS)
Gaithersburg, MD 20899-0001                                          
USA
301-975-3911 - voice, 301-216-1134 - fax

From wayne@helix.nih.gov  Fri Oct 22 14:25:05 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA20511; Fri, 22 Oct 1993 14:26:40 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA18210; Fri, 22 Oct 93 14:46:55 -0400
Message-Id: <9310221846.AA18210@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Fri, 22 Oct 1993 14:25:05 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re:  IPL and AxoVideo

>Since the exchanges on this list a couple weeks back, we've
>made a couple macros to load a stack of alternating-wavelength
>images, and create a new stack of ratioed images. The trouble
>is that the 'divide' routine currently automatically scales
>the resulting image to the widest possible dynamic range (ie.
>stretches the max/min ratios to 256/0, respectively), as
>best I understand. This creates problems as we need to keep
>the scaling uniform through our image series. Otherwise the
>calibration curve will mean nothing.
>
>Wayne wrote that he was contemplating a fix for this problem.

There is a new command in the latest beta on Zippy called Image Math that
does image arithmetic between two images and allows you to specify the
scale and offset needed to scale back to 8-bits. There is a corresponding
macro routine that has the form "ImageMath('divide', pic1, pic2, scale,
offset, 'Result')", where pic1 and pic2 are pic numbers or pid numbers. 

--wayne


From wayne@helix.nih.gov  Fri Oct 22 16:20:52 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA21357; Fri, 22 Oct 1993 16:22:38 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA18638; Fri, 22 Oct 93 16:42:41 -0400
Message-Id: <9310222042.AA18638@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Fri, 22 Oct 1993 16:20:52 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Sweet wishes

>See my reply to Harvey Karten. In terms of the actual code to accomplish
>this within Image, my preference would be to have another option in the
>Special menu that simply allowed you to capture images in this manner, just
>like you can average, integrate or subtract background. This could be
>called something like 'Build Image'. First you would capture an original
>and then use the area selection items (probably the box or the elipse would
>be fine; Haig's system uses the box) to select the area of the image that
>you would like to focus. That area would have live camera input that you
>could see over the original image , allowing you to focus that area with
>the surrounding areas of the original image, and then paste it in. Just
>like in the normal capture mode you could terminate the live video either
>by a carriage return or the mouse button, or by using the same average or
>integrate settings that were used to capture the original image. This
>maintains consistency in the quality of the image across the resulting
>montage. If this mode of capture were part of the normal capturing menu,
>plug ins would not be necessary. Obviously, to accomplish this, it would
>have to be placed in Wayne's queue of priorities for updates. I think that
>this would be a very nice addition to the program. What do you think Wayne?

I would like to see someone put this feature into Image so we can see how
difficult it is to implement and how well it works. If it works well and
looks like it would be useful to a lot people then I can put it into the
production version.

--wayne


From kartenh@sdsc.edu  Fri Oct 22 23:41:55 1993
Received: from Sdsc.Edu (sds.sdsc.edu) by nx1.soils.umn.edu (5.65c)
	id AA22022; Fri, 22 Oct 1993 18:40:39 -0500
Return-Path: <kartenh@sdsc.edu>
Message-Id: <199310222340.AA22022@nx1.soils.umn.edu>
Received: from [132.239.67.254] by Sdsc.Edu (sds.sdsc.edu STMG) via INTERNET;
          Fri, 22 Oct 93 23:41:54 GMT
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: kartenh@Sdsc.Edu
Subject: Re: 4pi Analysis in North Carol
Date:  Fri, 22 Oct 93 23:41:55 GMT

>
>The 4Pi board controls the scanning of the beam and gets the signal
>(scattered electron count, or whatever) directly from the microscope. 
>There is no camera involved, which is why this type of thing is so nice: 
>large images and large dynamic range for the data.
>:8o)

Dave
Are you referring tro the output of an SEM or a TEM? That was the nature of
my question. I had assumed that you were referring to a TEM, where the
image is commonly imaged onto a film plane.
        Harvey Karten

 Harvey J. Karten, M.D.
 Dept. of Neurosciences
 Univ.California San Diego
 La Jolla, CA 92093-0608
 EMail: Kartenh@sdsc.edu
 Phone: (619)-534-4938
 FAX: (619)-534-6602


From CMSABEL@minna.acc.iit.edu  Thu Oct 21 12:09:31 1993
Received: from harpo.acc.iit.edu by nx1.soils.umn.edu (5.65c)
	id AA04191; Sat, 23 Oct 1993 22:31:51 -0500
Return-Path: <CMSABEL@minna.acc.iit.edu>
Received: from minna.acc.iit.edu by minna.acc.iit.edu (PMDF V4.2-12 #3556) id
 <01H4DRACW3AO8ZHTTX@minna.acc.iit.edu>; Thu, 21 Oct 1993 17:09:31 CDT
Date: Thu, 21 Oct 1993 17:09:31 -0500 (CDT)
From: CMSABEL@minna.acc.iit.edu
Subject: Re: grain counting macros
To: nih-image@soils.umn.edu
Message-Id: <01H4DRACX5VM8ZHTTX@minna.acc.iit.edu>
X-Vms-To: IN%"nih-image@soils.umn.edu"
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII
Content-Transfer-Encoding: 7BIT

Wayne,

thanks for the offer. I , with the help of a colleague , have been working
on modifying the macro to suit our needs. I think we are very close. So, I 
won't bother you with it at the moment.  If we get it worked out, I'll
upload it (the modified macro)...and if we don't, I'll e-mail you with
specific questions.

Thanks again,

Marc
From sc@wiko-berlin.DE  Sun Oct 24 13:18:55 1993
Received: from sc.ZIB-Berlin.DE by nx1.soils.umn.edu (5.65c)
	id AA07564; Sun, 24 Oct 1993 06:16:04 -0500
Return-Path: <sc@wiko-berlin.DE>
Received: from wiko-berlin.DE ([192.55.244.98]) by sc.ZIB-Berlin.DE (4.1/SMI-4.0-sc/03.06.93)
	id AA01139; Sun, 24 Oct 93 12:17:26 +0100
Received: from [192.55.244.93] (quadra) by wiko-berlin.DE (4.1/SMI-4.0-MHS-6.0)
	id AA21218; Sun, 24 Oct 93 12:18:55 +0100
Date: Sun, 24 Oct 93 12:18:55 +0100
Message-Id: <9310241118.AA21218@wiko-berlin.de>
From: "Scott Camazine"  <sc@wiko-berlin.DE>
To: NIH-IMAGE@soils.umn.edu
Subject: Images

Dear NIH-Image users:
I am new to this list but would like to make a request.  I am trying
to get some interesting high resolution black and white 8-bit images of
medical pathology that I can enhance by applying various palettes with 
PalEdit, Spyglass and similar programs.  I would like to
use these images for lectures and possibly in publications.  The 
contributions I have submitted to the anonymous ftp (zippy.nimh.nih.gov)
are examples of the kind of images I am interested in.  I have acquired
these images by scanning black and white 35mm slides of xrays, CAT scans,
and MRIs that I have access to at the hospitals where I work.  If any
of you have images (preferably in the form of scans at a resolution
of at least 1000 dpi, which would give a file size of several megabytes
for a 35mm slide) which I could use without infringing upon anyone's
copyrights, I would like to hear from you.

I have also been trying to get some nice images of molecules.  I have
been using Alchemy and Chem3D which give pretty space-filling
molecules.  I was wondering if anyone knew who contributed the
image titled "molecule" to the anonymous ftp address.  I would
like to find out what software was used to generate that image.

Thanks,  Scott Camazine  (sc@wiko-berlin.de)


From mt1ntg@fencer.cis.dsto.gov.au  Tue Oct 26 01:08:00 1993
Received: from fencer.cis.dsto.gov.au by nx1.soils.umn.edu (5.65c)
	id AA13627; Mon, 25 Oct 1993 00:06:45 -0500
Return-Path: <mt1ntg@fencer.cis.dsto.gov.au>
Message-Id: <199310250506.AA13627@nx1.soils.umn.edu>
Received: from [160.64.14.216] by fencer.cis.dsto.gov.au with SMTP; 
          Mon, 25 Oct 1993 15:08:06 +1000 (EST)
Date: Mon, 25 Oct 1993 15:08:00 +1000
To: nih-image@soils.umn.edu
From: NoelGoldsmith<mt1ntg@fencer.cis.dsto.gov.au> (Noel Goldsmith)
Subject: Re: Sweet wishes

Glen writes

>Noel,
>See my reply to Harvey Karten. In terms of the actual code to accomplish
>this within Image, my preference would be to have another option in the
>Special menu that simply allowed you to capture images in this manner, just
>like you can average, integrate or subtract background. This could be
>called something like 'Build Image'. First you would capture an original
>and then use the area selection items (probably the box or the elipse would
>be fine; Haig's system uses the box) to select the area of the image that
>you would like to focus. That area would have live camera input that you
>could see over the original image , allowing you to focus that area with
>the surrounding areas of the original image, and then paste it in. Just
>like in the normal capture mode you could terminate the live video either
>by a carriage return or the mouse button, or by using the same average or
>integrate settings that were used to capture the original image. This
>maintains consistency in the quality of the image across the resulting
>montage. If this mode of capture were part of the normal capturing menu,
>plug ins would not be necessary. Obviously, to accomplish this, it would
>have to be placed in Wayne's queue of priorities for updates. I think that
>this would be a very nice addition to the program. What do you think Wayne?
>
>Glen Prusky   


Glen,
I see  now that what you want to do is different to what I do. I want to
get all of the surface of an opaque rough object in focus on one image. You
want to follow a structure through a translucent object so as to produce a
2D of it. The process I use relies on no operator decisions, it knows when
a piece of an image is in the best focus for the z series. I have not tried
this out on specimens like yours, our microscopes work with incident light,
yours with transmitted. Also, by restricting the activity to a simple cut
and paste on the selected area of the image, the speed of the computations
becomes a non-issue. In your response to Harvey Karten you affirm that the
results of the operation you propose are superior to a cut and paste from a
z series. When my procedure is used it works much better than a manual cut
and paste, mainly because my patience and manual dexterity is not as good
as that of the TOM (totally obedient moron ) or computer. The down side on
what I do is that if there is noise in the images, it is favoured in the
montage.
Maybe you could email me some Z series and I will have a go at them if you
like. If you use a mailer like Eudora I think you can enclose images, or
you could turn them into giffs.
Noel.
Noel T Goldsmith
DSTO
Aeronautical Research Laboratory
506 Lorimer Street
Port Melbourne
Vic 3207
Australia

From pierre.trebbia@univ-reims.fr  Mon Oct 25 10:49:06 1993
Received: from cleo.univ-reims.fr by nx1.soils.umn.edu (5.65c)
	id AA14543; Mon, 25 Oct 1993 03:50:22 -0500
Return-Path: <pierre.trebbia@univ-reims.fr>
Message-Id: <199310250850.AA14543@nx1.soils.umn.edu>
Received: from centre01.univ-reims.fr by cleo.univ-reims.fr with SMTP
	(1.37.109.4/16.2) id AA08343; Mon, 25 Oct 93 09:52:20 +0100
Received: from [193.50.208.72] by centre01.univ-reims.fr with SMTP
	(1.37.109.4/16.2) id AA16987; Mon, 25 Oct 93 09:49:06 +0100
Date: Mon, 25 Oct 93 09:49:06 +0100
To: nih-image@soils.umn.edu
From: pierre.trebbia@univ-reims.fr (Pierre TREBBIA)
X-Sender: trebbia@centre01
Subject: Re: grain counting macros

Big problem!
I got (and I'm getting) about 30 times the same message.
Please check what's wrong.

>Wayne,
>
>thanks for the offer. I , with the help of a colleague , have been working
>on modifying the macro to suit our needs. I think we are very close. So, I 
>won't bother you with it at the moment.  If we get it worked out, I'll
>upload it (the modified macro)...and if we don't, I'll e-mail you with
>specific questions.
>
>Thanks again,
>
>Marc

--------------
Pierre Trebbia, LASSI/GRSM, Universite de Reims, F51062 Reims cedex, France
Email : pierre.trebbia@univ-reims.fr
Phone : (33) 26 05 33 62
FAX : (33) 26 05 32 50

From @cc1.kuleuven.ac.be:jvanheld@dbmdec5.ulb.ac.be  Mon Oct 25 11:38:22 1993
Received: from cc1.kuleuven.ac.be by nx1.soils.umn.edu (5.65c)
	id AA14808; Mon, 25 Oct 1993 04:38:50 -0500
Return-Path: <@cc1.kuleuven.ac.be:jvanheld@dbmdec5.ulb.ac.be>
Received: from rc1.vub.ac.be by cc1.kuleuven.ac.be (IBM VM SMTP V2R2) with TCP;
   Mon, 25 Oct 93 10:39:13 +0100
Received: from dec5.ulb.ac.be (dbmdec5) by rc1.vub.ac.be (4.1/RC1-930922)
	id AA09125; Mon, 25 Oct 93 10:40:27 +0100
Received: by dec5.ulb.ac.be (5.65/ULB.920908)
	id AA14535; Mon, 25 Oct 1993 10:38:23 +0100
From: jvanheld@dbm.ulb.ac.be (Jacques VAN HELDEN)
Message-Id: <9310250938.AA14535@dec5.ulb.ac.be>
Subject: Illegal Instruction on Quadra
To: nih-image@soils.umn.edu
Date: Mon, 25 Oct 1993 10:38:22 +0100 (WET DST)
Cc: jvanheld@dbm.ulb.ac.be (Jacques VAN HELDEN)
In-Reply-To: <199310250850.AA14543@nx1.soils.umn.edu> from "Pierre TREBBIA" at Oct 25, 93 03:50:39 am
X-Mailer: ELM [version 2.4 PL22]
Content-Type: text
Content-Length: 581       

Hi everybody,

I have a problem when I want to work on Image sources with a Quadra 800. 
When I use the Measure command, I get an 'Illegal Instruction' error 
message, with the finger pointing to the runtime.lib file. This error 
does not exist on the compiled version (even when compiled on the quadra).

The source error is also absent when I run the sources on a fx.

Has anyone experienced this kind of problem ?
Should I choose special settings in the compile or source options for working 
on sources with the Quadra ?

Thanks,

Jacques van Helden
jvanheld@dbmdec5.ulb.ac.be
From John_Mansfield@mse.engin.umich.edu  Mon Oct 25 09:58:54 1993
Received: from mse.engin.umich.edu by nx1.soils.umn.edu (5.65c)
	id AA16664; Mon, 25 Oct 1993 09:58:54 -0500
Return-Path: <John_Mansfield@mse.engin.umich.edu>
Message-Id: <199310251458.AA16664@nx1.soils.umn.edu>
Date: 25 Oct 1993 10:47:46 U
From: "John Mansfield" <John_Mansfield@mse.engin.umich.edu>
Subject: Re: 660av Screen Capture & 
To: nih-image@soils.umn.edu

Reply_ RE>>660av Screen Capture & 840av too
Reply 
from:
       John Mansfield
       North Campus Electron Microbeam Analysis Laboratory
       University of Michigan
       2455 Hayward
       Ann Arbor MI 48109-2143   Phone: (313)936-3352
       jfmjfm@engin.umich.edu or John_Mansfield@mse.engin.umich.edu
I have tried out the 840av with a VCR  and a good quality TV camera.  The
problem I have is that, as everyone has pointed out, the avs are optimized for
Quicktime. There is no single frame acquisition software that comes with the
machine.
 The only way I could grab a whole 640 by 480 frame was to display the video in
"full screen" mode in the "Video Monitor" application  and then do a command-c.
 You hear the "camera shutter" sound and the next video frame is copied to the
clipboard.  You can then past this image into NIH-Image.  The image quality
isnt as good as the Scion LG-3 board, but it's not too bad compared with the
old early Scion boards we also have.  Too bad there isnt some software to
average a few consecutive video frames as that would help clean up the image
noise and would make the 660av a good buy for low end frame grabbing.  It's
perfect for student labs!  Built in frame grabbing, video and ethernet! What
more do you want? (Yes, I know... the sun and moon and.....)  
Does anyone know if anyone is working on a plug-in for these machines?

John Mansfield.


From glenmac@u.washington.edu  Mon Oct 25 04:22:09 1993
Received: from carson.u.washington.edu by nx1.soils.umn.edu (5.65c)
	id AA18883; Mon, 25 Oct 1993 13:32:36 -0500
Return-Path: <glenmac@u.washington.edu>
Received: by carson.u.washington.edu
	(5.65/UW-NDC Revision: 2.29 ) id AA16497; Mon, 25 Oct 93 11:26:47 -0700
X-Sender: glenmac@carson.u.washington.edu
Date: Mon, 25 Oct 1993 11:22:09 -0700 (PDT)
From: Glen Macdonald <glenmac@u.washington.edu>
Subject: Re: cell scoring macro?
To: nih-image@soils.umn.edu
Cc: Multiple recipients of list <nih-image@soils.umn.edu>
In-Reply-To: <01H4ESFZA9C290OASF@NIEHS.NIH.GOV>
Message-Id: <Pine.3.05z.9310251106.A14086-9100000@carson.u.washington.edu>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=us-ascii

Take a look at the Cavalieri macro in the UserMacros dir on Zippy.  You
may be able to use it as is, simply counting all of one category, then
counting the other label category.  Or, take it apart and use the core
counting code to be able to incorporate an option-click so you can mix
your counts.   Read the Cavalieri doc also in that directory.

Glen MacDonald
Hearing Development Labs
University of Washington


From Joel_Boymel@tpdmgate.amgen.com  Fri Oct 25 06:46:16 1993
Received: from relay1.UU.NET by nx1.soils.umn.edu (5.65c)
	id AA20332; Mon, 25 Oct 1993 15:51:35 -0500
Return-Path: <Joel_Boymel@tpdmgate.amgen.com>
Received: from amgen.com (via ns.amgen.com) by relay1.UU.NET with SMTP 
	(5.61/UUNET-internet-primary) id AA29199; Mon, 25 Oct 93 16:52:48 -0400
Received: from tpdmgate.amgen.com by amgen.com (4.1/SMI-4.1)
	id AA06690; Mon, 25 Oct 93 13:52:43 PDT
Message-Id: <9310252052.AA06690@amgen.com>
Date: 25 Oct 1993 14:46:16 -0800
From: "Joel Boymel" <Joel_Boymel@tpdmgate.amgen.com>
Subject: None
To: "NIH Image" <nih-image@soils.umn.edu>

Mail*Link(r) SMTP               None
help set


From mmoberg%11.59.dnet.smhi.se@lurch.smhi.se  Tue Oct 26 08:37:40 1993
Received: from palantir.p.tvt.se by nx1.soils.umn.edu (5.65c)
	id AA28337; Tue, 26 Oct 1993 01:36:25 -0500
Return-Path: <mmoberg%11.59.dnet.smhi.se@lurch.smhi.se>
Received: from gatekeeper.smhi.se by palantir.p.tvt.se with smtp
	(Smail3.1.28.1 #2) id m0ori5q-000ABsC; Tue, 26 Oct 93 07:41 WET
Received: by gatekeeper.smhi.se (5.65/DEC-Ultrix/4.3)
	id AA00781; Tue, 26 Oct 1993 07:38:18 +0100
Received: by lurch.smhi.se (5.65/DEC-Ultrix/4.3)
	id AA09354; Tue, 26 Oct 1993 07:37:40 +0100
Date: Tue, 26 Oct 1993 07:37:40 +0100
Message-Id: <9310260637.AA09354@lurch.smhi.se>
From: mmoberg%11.59.dnet.smhi.se@lurch.smhi.se (mmoberg@lurch.smhi.se)
To: "nih-image@soils.umn.edu"%LURCH.dnet.smhi.se@lurch.smhi.se
Cc: mmoberg@lurch.smhi.se
Subject: Another LUT-question

I am in need of a function that let me use colour-LUTs from other Image 
processing system in NIH Image. 
A convenient way of defining a LUT is by means of a formatted file (256 lines 
long) that in every line has information about:
	digital count 	Red amount	Green amount	Blue amount

Is there any possibility to include a function in NIH Image that, similar to 
Macro-making, will make a LUT from a text window - e.g. "Load LUT from window"?

M Moberg, mmoberg@smhi.se
From bonnot@jouy.inra.fr  Tue Oct 26 17:02:52 1993
Received: from chenas.inria.fr by nx1.soils.umn.edu (5.65c)
	id AA01372; Tue, 26 Oct 1993 08:54:24 -0500
Return-Path: <bonnot@jouy.inra.fr>
Received: from inra.inra.fr by chenas.inria.fr (5.65c8d/92.02.29)
	via Fnet-EUnet id AA26453; Tue, 26 Oct 1993 14:55:40 +0100 (MET)
Received: from jouy.jouy.inra.fr by inra.inra.fr, Tue, 26 Oct 93 14:55:15 +0100
Received: from [134.214.101.173] (bio2.insa-lyon.fr) by jouy.jouy.inra.fr, Tue, 26 Oct 93 14:52:55 +0100
Message-Id: <9310261352.AA01017@jouy.jouy.inra.fr>
X-Sender: bonnot@jouy.inra.fr (Unverified)
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 26 Oct 1993 16:02:52 +0100
To: nih-image@soils.umn.edu
From: bonnot@jouy.inra.fr
Subject: about projections

I am attempting to make 3D reconstruction of aphid gut circonvolutions from
histological slices. In order to better see the outer gut loops I tried to
project my stack using the z axis for rotation and find this projection
does not   work as expected. All what I get is a rotating frontal
projection (from front to back); the way th ex or y axis projection works
lets me think (it's what I need) that z projection would project the stack
from a lateral point of view while turning around the object.
I probably don't have understood everything. does someone has other
solution than reslicing repetitively my stack to constitute a longitudinal
sliced stack using a macro (it would be perhaps better to return back to
the microtome).
Thanks for any suggestions

########################################################
# Guy Bonnot              phone: +33 - 72 43 83 56     #
# INRA - INSA                  fax: +33 - 72 43 85 11  #
# Biologie 406           internet: bonnot@lyon.inra.fr #
# 20, av. A. Einstein             =bonnot@jouy.inra.fr #
# 69621 Villeurbanne cedex                             #
# France                                               #
########################################################


From RBLYSTON@VM1.TUCC.TRINITY.EDU  Tue Oct 26 05:43:37 1993
Received: from vm1.tucc.trinity.edu by nx1.soils.umn.edu (5.65c)
	id AA02295; Tue, 26 Oct 1993 10:43:30 -0500
Return-Path: <RBLYSTON@VM1.TUCC.TRINITY.EDU>
Message-Id: <199310261543.AA02295@nx1.soils.umn.edu>
Received: from VM1.tucc.trinity.edu by VM1.TUCC.TRINITY.EDU (IBM VM SMTP V2R2)
   with BSMTP id 9085; Tue, 26 Oct 93 10:44:35 CDT
Received: from TRINITY.EDU (RBLYSTON) by VM1.tucc.trinity.edu (Mailer R2.10
 ptf000) with BSMTP id 9084; Tue, 26 Oct 93 10:44:34 CDT
Date:         Tue, 26 Oct 93 10:43:37 CDT
From: rblyston <RBLYSTON@VM1.TUCC.TRINITY.EDU>
Subject:      Re: about projections
To: nih-image@soils.umn.edu
In-Reply-To:  Message of Tue, 26 Oct 1993 09:04:41 -0500 from
 <bonnot%jouy.inra.fr@relay.tc.umn.edu>

To Guy Bonnet:  Which version of Image are you using? and have you looked at
SpyGlass?  It might do what you want.  Blystone in Texas

**********************
ROBERT V. BLYSTONE                    PHONE:(210)736-7243
DEPARTMENT OF BIOLOGY                   FAX:(210)736-7229
Trinity University                   E-Mail:RBlyston@Trinity.edu
715 Stadium Drive
San Antonio, TX, 78212
From bonnot@jouy.inra.fr  Tue Oct 26 20:31:10 1993
Received: from chenas.inria.fr by nx1.soils.umn.edu (5.65c)
	id AA03196; Tue, 26 Oct 1993 12:22:41 -0500
Return-Path: <bonnot@jouy.inra.fr>
Received: from inra.inra.fr by chenas.inria.fr (5.65c8d/92.02.29)
	via Fnet-EUnet id AA10899; Tue, 26 Oct 1993 18:23:57 +0100 (MET)
Received: from jouy.jouy.inra.fr by inra.inra.fr, Tue, 26 Oct 93 18:23:32 +0100
Received: from [134.214.101.173] (bio2.insa-lyon.fr) by jouy.jouy.inra.fr, Tue, 26 Oct 93 18:21:13 +0100
Message-Id: <9310261721.AA04583@jouy.jouy.inra.fr>
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Tue, 26 Oct 1993 19:31:10 +0100
To: nih-image@soils.umn.edu
From: bonnot@jouy.inra.fr
Subject: Re: about projections

>To Guy Bonnet:  Which version of Image are you using? and have you looked at
>SpyGlass?  It might do what you want.  Blystone in Texas
>
>**********************
>ROBERT V. BLYSTONE                    PHONE:(210)736-7243
>DEPARTMENT OF BIOLOGY                   FAX:(210)736-7229
>Trinity University                   E-Mail:RBlyston@Trinity.edu
>715 Stadium Drive
>San Antonio, TX, 78212

Thank you.

I use NIH Image 1.52.
How to access to SpyGlass? . I never see this program in catalogs in France.

########################################################
# Guy Bonnot              phone: +33 - 72 43 83 56     #
# INRA - INSA                  fax: +33 - 72 43 85 11  #
# Biologie 406           internet: bonnot@lyon.inra.fr #
# 20, av. A. Einstein             =bonnot@jouy.inra.fr #
# 69621 Villeurbanne cedex                             #
# France                                               #
########################################################


From CHARLEST@macc.wisc.edu  Tue Oct 26 08:26:00 1993
Received: from vms2.macc.wisc.edu by nx1.soils.umn.edu (5.65c)
	id AA03746; Tue, 26 Oct 1993 13:26:21 -0500
Return-Path: <CHARLEST@macc.wisc.edu>
Received: from VMSmail by vms2.macc.wisc.edu; Tue, 26 Oct 93 13:26 CDT
Message-Id: <23102613265529@vms2.macc.wisc.edu>
Date: Tue, 26 Oct 93 13:26 CDT
From: Charles Thomas <CHARLEST@macc.wisc.edu>
Subject: Re: about projections
To: nih-image@soils.umn.edu
X-Vms-To: IN%"nih-image@soils.umn.edu",CHARLEST

Spyglass, Inc.
P.O. Box 6338
Champaign, IL  61826
(217) 355-6000
USA
 
 
We have used Spyglass Dicer in limited applications and have found it very
useful.  It allows you to show 2D planes through your specimen at any
orientation, view surfaces, cut chunks out of volumes to see inner details, etc.
 
It makes a very nice compliment to Voxel View/Mac and NIH-Image.
 
Feel free to call or Email me directly with any specific questions.
 
 
Charles Thomas
Integrated Microscopy Resource
University of Wisconsin, Madison
608-263-8481
 
P.S. I have made a demonstration video tape outlining many of Spyglass Dicer's
features.  I could arrange to have it sent to you if it would be helpful.
 
 
From RBLYSTON@VM1.TUCC.TRINITY.EDU  Tue Oct 26 08:31:16 1993
Received: from vm1.tucc.trinity.edu by nx1.soils.umn.edu (5.65c)
	id AA03881; Tue, 26 Oct 1993 13:38:37 -0500
Return-Path: <RBLYSTON@VM1.TUCC.TRINITY.EDU>
Message-Id: <199310261838.AA03881@nx1.soils.umn.edu>
Received: from VM1.tucc.trinity.edu by VM1.TUCC.TRINITY.EDU (IBM VM SMTP V2R2)
   with BSMTP id 1732; Tue, 26 Oct 93 13:39:43 CDT
Received: from TRINITY.EDU (RBLYSTON) by VM1.tucc.trinity.edu (Mailer R2.10
 ptf000) with BSMTP id 1731; Tue, 26 Oct 93 13:39:41 CDT
Date:         Tue, 26 Oct 93 13:31:16 CDT
From: RBlystone <RBLYSTON@VM1.TUCC.TRINITY.EDU>
Subject:      Re: about projections
To: nih-image@soils.umn.edu
In-Reply-To:  Message of Tue, 26 Oct 1993 12:34:28 -0500 from
 <bonnot%jouy.inra.fr@relay.tc.umn.edu>

To Guy:  Obviously you are using the most current full version of Image.
Spyglass is a commercial product. Its Email address is D5717@applelink.apple.co
m.  FAX is 217-355-8925 and regular phone 217-355-1665.  Address is P.O. Box
6388  Champaign, IL.  61826 USA   A person to speak to is Brand Fortner.
SpyGlass has an interesting application called Dicer and it can be used to
create animated rotations.  There is another early version of SpyGlass that is
public domain called NCSA Dataslice.  You can find that at ftp.ncsa.uiuc.edu.
I find SpyGlass very useful for rotations of histological reconstructions of se
rial sections.

Blystone in Texas

**********************
ROBERT V. BLYSTONE                    PHONE:(210)736-7243
DEPARTMENT OF BIOLOGY                   FAX:(210)736-7229
Trinity University                   E-Mail:RBlyston@Trinity.edu
715 Stadium Drive
San Antonio, TX, 78212
From NSafford@scigen.co.uk  Tue Oct 26 19:11:59 1993
Received: from eros.Britain.EU.net by nx1.soils.umn.edu (5.65c)
	id AA04320; Tue, 26 Oct 1993 14:21:37 -0500
Return-Path: <NSafford@scigen.co.uk>
Received: from scigen.co.uk by eros.britain.eu.net with UUCP 
          id <sg.02292-0@eros.britain.eu.net>; Tue, 26 Oct 1993 19:20:58 +0000
Received: from [192.9.200.40] (sg_quadra_800) by scigen.co.uk (4.1/SMI-4.1) 
          id AA08412; Tue, 26 Oct 93 19:11:23 GMT
Message-Id: <9310261911.AA08412@ scigen.co.uk>
Date: Tue, 26 Oct 1993 19:11:59 +0000
To: nih-image@soils.umn.edu
From: NSafford@scigen.co.uk (Nick Safford)
X-Sender: nas1@jasper
Subject: Re: 660av Screen Capture.


>>>I am thinking about purchasing a 660av to use NIH Image and was wondering
>>>about the quality of screen capture.
>>>
>>>Is the 660av a poorman's viable alternative to a frame grabber card?
>>
>>Like the Video Spigot, it's a good if you wan't to hook up a camcorder to
>>your Mac and make a color QuickTime movie. (The AV Macs use the same chip
>>set as the Video Spigot.) You can convert the QuickTime movie into PICS
>>format to get it into NIH Image.
>>
>>--wayne
>
>Does anyone know the actual performance specs of the 660av/840av on a
>monochrome image from a decent video camera? Linear resolution, contrast
>range, etc. 
>                                        Harvey Karten
>
> Harvey J. Karten, M.D.
> Dept. of Neurosciences
> Univ.California San Diego
> La Jolla, CA 92093-0608
> EMail: Kartenh@sdsc.edu
> Phone: (619)-534-4938
> FAX: (619)-534-6602


For what it's worth, I've tried the 840AV against a Scion (and also
QuickImage, QuickCapture, VideoSpigot).

As I recall the order of quality goes:

QuickCapture, Scion LG-3

Quadra 840AV

QuickImage

VideoSpigot.

This is using the S-video input on the Quadra. The composite is not nearly
as good (not surprisingly).

The biggest problem with the 840AV's internal grabber (which I imagine is
similar/identical to the 660) is that it's 16 bit (5 bits per gun and one
that gets thrown away) and you do get obvious 'oatmeal' effects from this,
as the greyscale information is really only 5 bits. For scientific purposes
this is obviously a drawback. The resolution is pretty good - subjective
sharpness is better than on the Scion but this is only because the contrast
I achieved was higher (too high) with the 840AV. The true resolution is
just about the same.

Writing code to grab frames through the Quicktime routines is pretty easy,
although I haven't done it myself in Pascal. I'm thinking of doing some
kind of rudimentary photoshop plugin BUT as far as I'm aware you HAVE to be
working with your monitor set to 16 bit to use it. This will make Image
feel uncomfortable. (It might be possible to do something nasty with
getting the code to switch modes on the way in and out of the plugin in the
hope that Image won't notice the horrid thing you've done). The 16 bit
display requirement is because the grabber stuffs its 16 bit data straight
into VRAM.

It's really quite fast. You can get full speed, full frame video onto your
monitor (ie into your VRAM) and it's pretty amazing to look at (no lag!).
Using sequential buffering on an 840av we nearly got full speed video into
main RAM (rather than VRAM) - but not quite. You wouln't get so close with
a 660av. This was PAL format - I'm not sure how this would work in NTSC
format, as NTSC is a higher framing rate (but fewer lines, so the data rate
you have to sustain is only 18Mb/sec instead of about 22Mb/sec). You
clearly can't put data at these rates onto disc; Apple say you can get 1/4
frame onto disc at a sustained 30 fps.

Hope this is of some use to somebody.

Nick Safford                    (NSafford@scigen.co.uk)
Scientific Generics             Phone   0223 424425
King's Court                    Fax     0223 424281
Kirkwood Road
Cambridge
CB4 2PF
UK

From philp@physiol.su.oz.au  Wed Oct 27 21:40:27 1993
Received: from cortex.physiol.su.OZ.AU by nx1.soils.umn.edu (5.65c)
	id AA07063; Tue, 26 Oct 1993 20:39:18 -0500
Return-Path: <philp@physiol.su.oz.au>
Received: by cortex.physiol.su.oz.au (5.57/Ultrix3.0-C)
	id AA05190; Wed, 27 Oct 93 11:40:27 +1000
Date: Wed, 27 Oct 93 11:40:27 +1000
From: philp@physiol.su.oz.au (Philip Poronnik)
Message-Id: <9310270140.AA05190@cortex.physiol.su.oz.au>
To: nih-image@soils.umn.edu
Subject: edge detection


Hi out there,

does anyone have/know of an edge detection or edge following macro or
algorithm to run under Image.  The problem I have is that I am 
trying to follow volume changes in a clump of cells.  At the moment
I just trace around the perimeter and measure the number of pixels
inside - infortunately I have literally thousands of images and some
sort of automation would be more than appropriate.  these are bright
field images so it is very difficult to use a mask.  I would rather be 
able to define an edge and let a macro just follow it around.

Any help would be more than appreciated

thanks

philp
From @cc1.kuleuven.ac.be:jvanheld@dbmdec5.ulb.ac.be  Wed Oct 27 12:45:03 1993
Received: from cc1.kuleuven.ac.be by nx1.soils.umn.edu (5.65c)
	id AA10828; Wed, 27 Oct 1993 06:35:06 -0500
Return-Path: <@cc1.kuleuven.ac.be:jvanheld@dbmdec5.ulb.ac.be>
Received: from rc1.vub.ac.be by cc1.kuleuven.ac.be (IBM VM SMTP V2R2) with TCP;
   Wed, 27 Oct 93 12:34:23 +0100
Received: from dec5.ulb.ac.be (dbmdec5) by rc1.vub.ac.be (4.1/RC1-930922)
	id AA24902; Wed, 27 Oct 93 12:35:42 +0100
Received: by dec5.ulb.ac.be (5.65/ULB.920908)
	id AA06516; Wed, 27 Oct 1993 11:45:04 +0100
From: jvanheld@dbm.ulb.ac.be (Jacques VAN HELDEN)
Message-Id: <9310271045.AA06516@dec5.ulb.ac.be>
Subject: Re: edge detection
To: nih-image@soils.umn.edu
Date: Wed, 27 Oct 1993 11:45:03 +0100 (WET DST)
Cc: jvanheld@dbm.ulb.ac.be (Jacques VAN HELDEN)
In-Reply-To: <9310270140.AA05190@cortex.physiol.su.oz.au> from "Philip Poronnik" at Oct 26, 93 08:39:39 pm
X-Mailer: ELM [version 2.4 PL22]
Content-Type: text
Content-Length: 515       

Hi,

there is a routine I developed specially for tracing cell edges on bright 
field images. It is not a macro but a Pascal routine, which is integrated in 
NIH-Image. The compiled version, as well as the source code, are on zippy, 
in the contrib directory. The name of the file is Quantile_Crest.sit.hqx
The archive includes an example stack. In this example, the edge finding is
 based on cell fluorescence, but it also works with bright field images.

Good luck,

Jacques van Helden
jvanheld@dbmdec5.ulb.ac.be
From wayne@helix.nih.gov  Wed Oct 27 16:39:31 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA16303; Wed, 27 Oct 1993 16:41:09 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA16654; Wed, 27 Oct 93 17:01:47 -0400
Message-Id: <9310272101.AA16654@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Wed, 27 Oct 1993 16:39:31 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: 660av Screen Capture.

>For what it's worth, I've tried the 840AV against a Scion (and also
>QuickImage, QuickCapture, VideoSpigot).

Have you tried the Movie Movie card from Sigma Designs. It got a good write
up in the latest MacUser and is only $300.

>Writing code to grab frames through the Quicktime routines is pretty easy,
>although I haven't done it myself in Pascal. I'm thinking of doing some
>kind of rudimentary photoshop plugin BUT as far as I'm aware you HAVE to be
>working with your monitor set to 16 bit to use it.

I you sure of this? I thought the QuickTime capture program that comes with
the AV Macs (Video Fusion?) requires that the monitor be in 8-bit mode. I
would love to see a plug-in that uses QuickTime to capture images,
particularly one that came with source code so I could see how it was done.
I assume it would also work with any capture card with a QuickTime driver,
such as the Video Spigot and the Movie Movie.

--wayne


From mhowland@alsvid.une.edu.au  Thu Oct 28 21:49:45 1993
Received: from alsvid.une.edu.au by nx1.soils.umn.edu (5.65c)
	id AA18040; Wed, 27 Oct 1993 20:48:31 -0500
Return-Path: <mhowland@alsvid.une.edu.au>
Received: from [129.180.146.5] (mac146_5.nr.une.edu.au) by alsvid.une.edu.au with SMTP id AA27807
  (5.65c8+/IDA-1.4.4 for <nih-image@soils.umn.edu>); Thu, 28 Oct 1993 11:49:45 +1000
Date: Thu, 28 Oct 1993 11:49:45 +1000
Message-Id: <199310280149.AA27807@alsvid.une.edu.au>
X-Sender: mhowland@pophost.nr.une.edu.au
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: mhowland@alsvid.une.edu.au (Mick Howland)
Subject: source code

What version of Think Pascal is the source code for Image written in. I
have v4.0 and it doesn't seem to be able to open the Image project.


_____________________________________________________________
Michael Howland, Faculty of Resource Science & Management
UNE - Northern Rivers, P.O. Box 157, Lismore, NSW, Australia.
Phone: +61-66-203037  Fax: +61-66-212669
E-mail: mhowland@alsvid.une.edu.au
_____________________________________________________________


From huff@MCCLB0.MED.NYU.EDU  Thu Oct 28 02:27:00 1993
Received: from mcclb0.med.nyu.edu by nx1.soils.umn.edu (5.65c)
	id AA21830; Thu, 28 Oct 1993 06:24:35 -0500
Return-Path: <huff@MCCLB0.MED.NYU.EDU>
Received: from [128.122.250.23] (EDHUFF.DIAL.NET.NYU.EDU) by MCCLB0.MED.NYU.EDU
 (PMDF V4.2-14 #2884) id <01H4MZ0HI2BK0031CA@MCCLB0.MED.NYU.EDU>; Thu,
 28 Oct 1993 07:25:48 EDT
Date: Thu, 28 Oct 1993 07:27:00 -0500
From: huff@MCCLB0.MED.NYU.EDU (Edward J. Huff)
Subject: Re: source code
To: nih-image@soils.umn.edu
Message-Id: <01H4MZ0IL6HU0031CA@MCCLB0.MED.NYU.EDU>
X-Envelope-To: nih-image@soils.umn.edu
Content-Transfer-Encoding: 7BIT

>What version of Think Pascal is the source code for Image written in. I
>have v4.0 and it doesn't seem to be able to open the Image project.

V4.0.1 is used.  I don't know if lack of the update prevents opening the
project.   I just uploaded the updater to zippy.nimh.nih.gov into
/pub/nih-image/contrib, file name ThP_4.0.1_TCL_1.1.2_Update.sea.hqx.

--
Edward J. Huff   huff@mcclb0.med.nyu.edu   (212)998-8465
Keck Laboratory for Biomolecular Imaging
NYU Chemistry Department, 31 Washington Place, New York NY 10003

From husemoj@ccsmtp.ccf.org  Thu Oct 28 03:54:37 1993
Received: from ccfadm.eeg.ccf.org by nx1.soils.umn.edu (5.65c)
	id AA22470; Thu, 28 Oct 1993 07:55:24 -0500
Return-Path: <husemoj@ccsmtp.ccf.org>
Received: from ccsmtp.ccf.org by ccfadm.eeg.ccf.org with SMTP
	(1.37.109.4/16.2) id AA04370; Thu, 28 Oct 93 08:54:53 -0400
Received: from cc:Mail by ccsmtp.ccf.org (1.30/SMTPLink)
	id A10072; Thu, 28 Oct 93 08:54:37 EST
Date: Thu, 28 Oct 93 08:54:37 EST
From: John Husemoller <husemoj@ccsmtp.ccf.org>
Message-Id: <9310280854.A10072@ccsmtp.ccf.org>
To: wayne%helix.nih.gov@relay.tc.umn.edu, nih-image@soils.umn.edu
Subject: Re: image documents corrupted?-Please Help

I had a system crash just after I saved several documents I had scanned and 
worked with in Image 1.53b7.  After the restart, These images and every image 
after them (listed alphabetically) in the same folder was corrupted somehow. 
Several of these files weren't even open, and the ones before the corrupted 
ones(again listed alphabetically) are completley fine  I can see with any 
number of utilities that these documents are ~70k and show the correct file and 
creator codes, in the finder they show up as 2k TIFF Image documents and give 
an I/O error of( -83 or -73 or something like that-I can't exactly remember) 
when I open them in image.  I'm running on a quad 700, sys7.1 HSU 2.1, standard 
inits, and working off of a bernoulli drive.  ANY help would be greatly 
appreciated.

Thanks,
John

From NSafford@scigen.co.uk  Thu Oct 28 16:39:17 1993
Received: from eros.Britain.EU.net by nx1.soils.umn.edu (5.65c)
	id AA25441; Thu, 28 Oct 1993 12:24:24 -0500
Return-Path: <NSafford@scigen.co.uk>
Received: from scigen.co.uk by eros.britain.eu.net with UUCP 
          id <sg.28801-0@eros.britain.eu.net>; Thu, 28 Oct 1993 16:51:01 +0000
Received: from [192.9.200.40] (sg_quadra_800) by scigen.co.uk (4.1/SMI-4.1) 
          id AA12493; Thu, 28 Oct 93 16:38:38 GMT
Message-Id: <9310281638.AA12493@ scigen.co.uk>
Date: Thu, 28 Oct 1993 16:39:17 +0000
To: nih-image@soils.umn.edu
From: NSafford@scigen.co.uk (Nick Safford)
X-Sender: nas1@jasper
Subject: Re: 660av Screen Capture.



>Have you tried the Movie Movie card from Sigma Designs. It got a good write
>up in the latest MacUser and is only $300.
 
No, but I'm interested!

>I you sure of this? I thought the QuickTime capture program that comes with
>the AV Macs (Video Fusion?) requires that the monitor be in 8-bit mode. I
>would love to see a plug-in that uses QuickTime to capture images,
>particularly one that came with source code so I could see how it was done.
>I assume it would also work with any capture card with a QuickTime driver,
>such as the Video Spigot and the Movie Movie.
>
>--wayne


I think you may be right - I think my initial assessment was hasty. I'll be
investigating capture modes other than 16 bit shortly. Further
investigation of the chipset specs leads me to believe that it ought to be
possible to capture decent 8 bit greyscale. I don't need to do that right
now, but doubtless very soon I will.

Nick Safford                    (NSafford@scigen.co.uk)
Scientific Generics             Phone   0223 424425
King's Court                    Fax     0223 424281
Kirkwood Road
Cambridge
CB4 2PF
UK

From pruskyg@hg.uleth.ca  Thu Oct 28 04:24:02 1993
Received: from holly.cc.uleth.ca by nx1.soils.umn.edu (5.65c)
	id AA25991; Thu, 28 Oct 1993 13:21:14 -0500
Return-Path: <pruskyg@hg.uleth.ca>
Received: by holly.cc.uleth.ca; id AA12479; Thu, 28 Oct 1993 12:20:22 -0600
Message-Id: <9310281820.AA12479@holly.cc.uleth.ca>
Date: Thu, 28 Oct 1993 12:24:02 -0800
To: nih-image@soils.umn.edu
From: pruskyg@hg.uleth.ca (Glen Prusky)
X-Sender: pruskyg@pop.uleth.ca
Subject: Re: sweet dreams (re:David Morilak)

>Glen:
>
>Sorry, I misplaced (i.e. deleted) your original message, so I couldn't refer
>to you directly in the following message, which I have submitted to the NIH
>Image mailing list. Is Live Paste something you might be able to use for the 
>purpose you describe??
>
>David Morilak
>
>
>
>From: morilak%cmgm.stanford.edu@relay.tc.umn.edu (David Morilak)
>To: Multiple recipients of list <nih-image@nx1.soils.umn.edu>
>Subject: Re: live paste?
>X-Listprocessor-Version: 6.0 -- ListProcessor by Anastasios Kotsikonas
>X-Comment:  NIH Image Distribution List
>
>In response to the question about doing a "photomontage" in Image to bring
>different focal planes into focus (sorry, I mistakenly deleted the original so
>I can't reference the sender), wouldn't the Live Paste function do the trick?
>Even if items in different focal planes existed within a ROI, that subregion
>could be selected again from the camera window and then refocused in a live
>paste. I guess the main limitations would be that rectangular selections only
>are allowed, and that if there were huge differences in focal plane, there
>might also be an apparent size change, meaning that edges might not line up
>exactly right. I gave this a quick and limited try before responding, and it
>seemed to work. But, being fairly new at this, I'm more than happy to be
>corrected...
>
>David Morilak
>Dept of Psychiatry
>Stanford Univ
>morilak@cmgm.stanford.edu
>-------
>-------
David,
Thanks for your interest in this feature. I think that the live paste
function could easily be beefed-up to do what I am proposing. It does allow
you to select part of a field and then independently control the focus of
the live image in that selected area. That is step one in the process.
However, there are two limitations with it as it currently exists in order
to easily produce 2D photomontages. First, it does not give you the option
of pasting the selected area into the exact X-Y coordinates that it came
from in the camera window. You still must align the images by hand or
remember the coordinates from the camera window as you move the selected
area in image that you are building. Second, it only allows you to grab one
frame. Most times you want to average or integrate the capture of your
image to reduce noise or increase gain. You can do this, of course, with
the original image, but you can not use the same parameters in live paste
mode; it only allows you to grab one frame. I think that it would be
relatively easy to encorporate these simple features into the live paste
window  that 1, Allows you to automatically paste the selection from the
camera window into the same coordinates in the new window and 2, Allows you
to control the input parameters of the live paste in the same way that you
can in the capture window. Wayne, is this possible? There may already be
utilities that I do not know about that could accomplish this that could be
controlled with a macro. Does such a Macro exist?  Thanks a million, Glen! 

Glen T. Prusky Ph.D., Department of Psychology, The University of Lethbridge
4401 University Drive, Lethbridge, AB, Canada T1K 3M4
pruskyg@hg.uleth.ca  Office-403-329-2402  Lab-403-329-2410  Fax-403-329-2410

From MEZY301@utxvms.cc.utexas.edu  Thu Oct 28 09:36:38 1993
Received: from orange.cc.utexas.edu by nx1.soils.umn.edu (5.65c)
	id AA26680; Thu, 28 Oct 1993 14:37:42 -0500
Return-Path: <MEZY301@utxvms.cc.utexas.edu>
Received: from utxvms.cc.utexas.edu by utxvms.cc.utexas.edu (PMDF V4.2-12
 #4544) id <01H4NDWJPBQ88WXE9L@utxvms.cc.utexas.edu>; Thu,
 28 Oct 1993 14:36:39 CDT
Date: Thu, 28 Oct 1993 14:36:38 -0500 (CDT)
From: MEZY301@utxvms.cc.utexas.edu
Subject: Re: sweet dreams (re:David Morilak)
To: nih-image@soils.umn.edu
Message-Id: <01H4NDWJRGW28WXE9L@utxvms.cc.utexas.edu>
X-Envelope-To: nih-image@soils.umn.edu
X-Vms-To: IN%"nih-image@soils.umn.edu"
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII
Content-Transfer-Encoding: 7BIT


I have compiled a long list of useful macros, as well as a couple different
working versions of Image.  I just discovered I can keep my "Image Macros" file
in the System Folder which means I don't have to have multiple copies for each
version of Image I run.  My question how big can this "Image Macros" file get,
how many macros can Image load in this manner???  



Peter J. Joyce                                Office Phone (512) 471-5724
email=<mezy301@utxvms.utexas.edu              Office: ETC 4.148



From mhowland@alsvid.une.edu.au  Fri Oct 29 21:43:11 1993
Received: from alsvid.une.edu.au by nx1.soils.umn.edu (5.65c)
	id AA29422; Thu, 28 Oct 1993 20:42:16 -0500
Return-Path: <mhowland@alsvid.une.edu.au>
Received: from [129.180.146.5] (mac146_5.nr.une.edu.au) by alsvid.une.edu.au with SMTP id AA19172
  (5.65c8+/IDA-1.4.4 for <nih-image@soils.umn.edu>); Fri, 29 Oct 1993 11:43:11 +1000
Date: Fri, 29 Oct 1993 11:43:11 +1000
Message-Id: <199310290143.AA19172@alsvid.une.edu.au>
X-Sender: mhowland@pophost.nr.une.edu.au
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: mhowland@alsvid.une.edu.au (Mick Howland)
Subject: Re: source code

>>What version of Think Pascal is the source code for Image written in. I
>>have v4.0 and it doesn't seem to be able to open the Image project.
>
>V4.0.1 is used.  I don't know if lack of the update prevents opening the
>project.   I just uploaded the updater to zippy.nimh.nih.gov into
>/pub/nih-image/contrib, file name ThP_4.0.1_TCL_1.1.2_Update.sea.hqx.
>
Thanks, thing are now working fine.


_____________________________________________________________
Michael Howland, Faculty of Resource Science & Management
UNE - Northern Rivers, P.O. Box 157, Lismore, NSW, Australia.
Phone: +61-66-203037  Fax: +61-66-212669
E-mail: mhowland@alsvid.une.edu.au
_____________________________________________________________


From huff@MCCLB0.MED.NYU.EDU  Thu Oct 28 17:35:30 1993
Received: from mcclb0.med.nyu.edu by nx1.soils.umn.edu (5.65c)
	id AA29811; Thu, 28 Oct 1993 21:33:05 -0500
Return-Path: <huff@MCCLB0.MED.NYU.EDU>
Received: from [128.122.250.23] (EDHUFF.DIAL.NET.NYU.EDU) by MCCLB0.MED.NYU.EDU
 (PMDF V4.2-14 #2884) id <01H4NUQN7ZN4003861@MCCLB0.MED.NYU.EDU>; Thu,
 28 Oct 1993 22:34:17 EDT
Date: Thu, 28 Oct 1993 22:35:30 -0500
From: huff@MCCLB0.MED.NYU.EDU (Edward J. Huff)
Subject: Live paste to camera coordinates
To: nih-image@soils.umn.edu
Message-Id: <01H4NUQVA592003861@MCCLB0.MED.NYU.EDU>
X-Envelope-To: nih-image@soils.umn.edu
Content-Transfer-Encoding: 7BIT

Select a region on the camera window, copy, then switch to the destination
image and type command 4 (restore selection).  Then paste.
--
Edward J. Huff   huff@mcclb0.med.nyu.edu   (212)998-8465
Keck Laboratory for Biomolecular Imaging
NYU Chemistry Department, 31 Washington Place, New York NY 10003

From huff@MCCLB0.MED.NYU.EDU  Thu Oct 28 17:35:37 1993
Received: from mcclb0.med.nyu.edu by nx1.soils.umn.edu (5.65c)
	id AA29820; Thu, 28 Oct 1993 21:33:13 -0500
Return-Path: <huff@MCCLB0.MED.NYU.EDU>
Received: from [128.122.250.23] (EDHUFF.DIAL.NET.NYU.EDU) by MCCLB0.MED.NYU.EDU
 (PMDF V4.2-14 #2884) id <01H4NUQN7ZN4003861@MCCLB0.MED.NYU.EDU>; Thu,
 28 Oct 1993 22:34:24 EDT
Date: Thu, 28 Oct 1993 22:35:37 -0500
From: huff@MCCLB0.MED.NYU.EDU (Edward J. Huff)
Subject: Macro file size limitations
To: nih-image@soils.umn.edu
Message-Id: <01H4NUR01CFU003861@MCCLB0.MED.NYU.EDU>
X-Envelope-To: nih-image@soils.umn.edu
Content-Transfer-Encoding: 7BIT

There is a limit on the number of macros, and a limit on the file size.

Text edit restricts files to 32k bytes, and the text windows are implemented
with text edit.

My version of 1.44 (markup) lifts the file size restriction and doubles the
number of macros, but the scrolling menu got a little unreasonable.  A few
seconds to get down to the bottom...  

[That version also fixed the else if "feature".  In the present version,
you must write "else begin ...", never "else if" or "else repeat". 
1.44markup fixes that at the expense of a slightly slower macro processor. 
Now that the segment size limitation of the amount of code in Macros1.p has
been lifted, this fix ought to be incorporated...  Or at least the program
should give a macro error if "else" is followed by "if" or "repeat".]

I think a good fix for all of these restrictions would be to create a
hierarchal menu under special with one hierarchal menu item for each macro
file.  Thus, the 32k file size limit need not be removed, and the number of
macros per file limit need not be removed.  But you can still have
essentially unliminted number of macros and essentially unlimited file
space.  Each macro set would have its own global variables.  They could
communicate by stuffing values into a scratch image.
--
Edward J. Huff   huff@mcclb0.med.nyu.edu   (212)998-8465
Keck Laboratory for Biomolecular Imaging
NYU Chemistry Department, 31 Washington Place, New York NY 10003

From robday@uniwa.uwa.edu.au  Fri Oct 29 19:05:35 1993
Received: from uniwa.uwa.edu.au by nx1.soils.umn.edu (5.65c)
	id AA00259; Thu, 28 Oct 1993 22:04:24 -0500
Return-Path: <robday@uniwa.uwa.edu.au>
Received: from localhost (robday@localhost) by uniwa.uwa.edu.au (8.6.3/8.6.2) id LAA27825 for nih-image@soils.umn.edu; Fri, 29 Oct 1993 11:05:37 +0800
From: Robert Day <robday@uniwa.uwa.edu.au>
Message-Id: <199310290305.LAA27825@uniwa.uwa.edu.au>
Subject: Errors (?) in length of skeletonised image
To: nih-image@soils.umn.edu
Date: Fri, 29 Oct 1993 11:05:35 +0800 (WST)
X-Mailer: ELM [version 2.4 PL11]
Mime-Version: 1.0
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Length: 811       

We have been using Image to do histomorphometry on trabecular bone in
vertebral bodies.

In the course of this work, we are wanting to measure the length of a
skeletonised network of trabeculae.  We have tried using the analyse
particles selection with Area and Length/Perimeter checked, but the
results don't seem right.  To check the results, we then drew a series
of straight 1 pixel wide lines and tried to measure them.  Vertical
lines have almost the right area, and slightly overestimated perimeters.
Horizontal lines are a little worse, and lines at any other angle are
way off (30 %).

Does anyone know what we are doing wrong, or how to get correct length
measurements of a skeletonised network out of Image ?

Steve Edmondston
Rob Day (robday@uniwa.uwa.edu.au)

Royal Perth Hospital
Perth  Australia
From bab6@cornell.edu  Fri Oct 29 02:13:13 1993
Received: from POSTOFFICE.MAIL.CORNELL.EDU by nx1.soils.umn.edu (5.65c)
	id AA03388; Fri, 29 Oct 1993 06:11:54 -0500
Return-Path: <bab6@cornell.edu>
Received: from [128.253.111.209] by postoffice.mail.cornell.edu with SMTP id AA17979
  (5.67a/IDA-1.5 for <nih-image@nx1.soils.umn.edu>); Fri, 29 Oct 1993 07:13:08 -0400
Message-Id: <199310291113.AA17979@postoffice.mail.cornell.edu>
Date: Fri, 29 Oct 1993 07:13:13 -0500
To: Multiple recipients of list <nih-image@soils.umn.edu>
From: bab6@cornell.edu (Barry Ball)
X-Sender: bab6@postoffice.mail.cornell.edu
Subject: CCD cameras

We are interested in obtaining a slide scanner for image acquisition from
both color and B&W 35-mm format slides and negatives.  We might also use
the scanner for digitizing images from larger format films, but only on an
occassional basis.  Does anyone have experience with particular hardware in
this area and if so what type of equipment are you using.

Any information would be helpful.

Thanks,


bab6@cornell.edu (Barry Ball)

From enater@soils.umn.edu  Fri Oct 29 03:03:52 1993
Received: from forsoil.soils.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA04136; Fri, 29 Oct 1993 08:00:49 -0500
Return-Path: <enater@soils.umn.edu>
Received: by forsoil.soils.umn.edu (4.1)
	id AA02345; Fri, 29 Oct 93 08:03:53 CDT
From: "Ed Nater" <enater@soils.umn.edu>
Message-Id: <9310291303.AA02345@forsoil.soils.umn.edu>
Subject: ImageFractal Problems
To: nih-image@soils.umn.edu (Image newsletter)
Date: Fri, 29 Oct 1993 08:03:52 -0500 (CDT)
X-Mailer: ELM [version 2.4 PL22]
Mime-Version: 1.0
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Length: 1398      

We are having a couple of problems while running NIH-ImageFractal and hope
someone in netland can help. 

Our application is trying to assess the fractal nature of the pore network
in soils. The images are large (3.4 Mb) fluorescent images of a soil pore
network. Our setup is a Quadra 950 with 32 Mb RAM running system 7.1. In
order to accommodate the images, the application memory size has been
expanded to 20,000 Kb with a minimum size of 10,000 Kb, and the Undo and
Clipboard Buffer Size has been expanded to 5,000 Kb. 

The two problems we have been experiencing are: 

(1) When we try to run the Grid-Screen fractal analysis (under the Fractal
menu item) the program dies and gives a type 1 error. There seems to be no
way around this particular bomb. 

(2) We would also like to run the Caliper and the GridXY methods of
analysis (also under the Fractal menu item) on the whole image. Although
they seem to work properly, they *only* work on one selected particle at a
time (each image has several hundred pa rticles). Does anyone know if
there is a way to get these items to measure all particles in an image at
a single stroke? 

Thanks for the help.

Ed


-- 
Ed Nater                              Soil Science Department
Associate Professor                   University of Minnesota
Soil Genesis/Clay Mineralogy          St. Paul, MN  55108   U.S.A.  
Internet: ed.nater@soils.umn.edu

From CHARLEST@macc.wisc.edu  Fri Oct 29 04:55:00 1993
Received: from vms2.macc.wisc.edu by nx1.soils.umn.edu (5.65c)
	id AA05124; Fri, 29 Oct 1993 09:55:25 -0500
Return-Path: <CHARLEST@macc.wisc.edu>
Received: from VMSmail by vms2.macc.wisc.edu; Fri, 29 Oct 93 09:55 CDT
Message-Id: <23102909555482@vms2.macc.wisc.edu>
Date: Fri, 29 Oct 93 09:55 CDT
From: Charles Thomas <CHARLEST@macc.wisc.edu>
Subject: Harvey Karten
To: nih-image@soils.umn.edu
X-Vms-To: image,CHARLEST

Two things...
 
If anyone (including Harvey himself) can get me Harvey Karten's email address, I
would be most grateful.
 
Secondly, the instructions I got a month or two back on how to access old NIH
Image email group posts from gopher don't seem to be working for me.
 
Under Univeristy of Minnesota, Computer Information, General, I don't see a
folder for NIH Image messages.
 
Thanks, as always.
 
 
Charles Thomas
Charlest@macc.wisc.edu
608-263-8481
 
 
P.S. I'm looking for Harvey in regard to a Ludl Mac 1000 stage drive we have.
Nothing to fret about. :)
 
 
From jladwig@soils.umn.edu  Fri Oct 29 06:36:51 1993
Received: from saturn.soils.umn.edu by nx1.soils.umn.edu (5.65c)
	id AA05965; Fri, 29 Oct 1993 11:37:10 -0500
Return-Path: <jladwig@soils.umn.edu>
Received: by saturn.soils.umn.edu (4.1)
	id AA08292; Fri, 29 Oct 93 11:36:51 CDT
Date: Fri, 29 Oct 93 11:36:51 CDT
From: "John Ladwig" <jladwig@soils.umn.edu>
Message-Id: <9310291636.AA08292@saturn.soils.umn.edu>
To: nih-image@soils.umn.edu
Subject: Re: Harvey Karten
In-Reply-To: Charles Thomas's message <23102909555482@vms2.macc.wisc.edu> of 29 October 1993
References: <23102909555482@vms2.macc.wisc.edu>

>>>>> On Fri, 29 Oct 1993 09:57:19 -0500, Charles Thomas <CHARLEST@macc.wisc.edu> said:

    Charles> If anyone (including Harvey himself) can get me Harvey
    Charles> Karten's email address, I would be most grateful.
 
kartenh@Sdsc.Edu  (From the Gopher archives)

    Charles> Secondly, the instructions I got a month or two back on
    Charles> how to access old NIH Image email group posts from gopher
    Charles> don't seem to be working for me.
 
    Charles> Under Univeristy of Minnesota, Computer Information,
    Charles> General, I don't see a folder for NIH Image messages.

It's there if you connect to the UMN *Soil Science* gopher
(gopher.soils.umn.edu). 
 
The path from the UMN "mother" gopher is:

Other Gopher and Information Servers/
 North America/
  USA/
   minnesota/
    University of Minnesota Soil Science Gopher Information Service/
     Computer Information/
      General Information/
       Search Nih-Image Mailing List Archives <?>
or
       Selected Electronic Mailing List Archives/
	Nih-image/
From kartenh@sdsc.edu  Fri Oct 29 17:10:46 1993
Received: from Sdsc.Edu (sds.sdsc.edu) by nx1.soils.umn.edu (5.65c)
	id AA06291; Fri, 29 Oct 1993 12:09:42 -0500
Return-Path: <kartenh@sdsc.edu>
Message-Id: <199310291709.AA06291@nx1.soils.umn.edu>
Received: from [132.239.67.254] by Sdsc.Edu (sds.sdsc.edu STMG) via INTERNET;
          Fri, 29 Oct 93 17:10:45 GMT
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
To: nih-image@soils.umn.edu
From: kartenh@Sdsc.Edu
Subject: Re: Harvey Karten
Date:  Fri, 29 Oct 93 17:10:46 GMT

\
>If anyone (including Harvey himself) can get me Harvey Karten's email address,
>I
>would be most grateful.

Dear Charles, 
        From himself, (but not the black Irishman), 
                        How can I help you on the Ludl 1000? 
                                        regards, Harvey Karten 

 Harvey J. Karten, M.D.
 Dept. of Neurosciences
 Univ.California San Diego
 La Jolla, CA 92093-0608
 EMail: Kartenh@sdsc.edu
 Phone: (619)-534-4938
 FAX: (619)-534-6602


From wayne@helix.nih.gov  Fri Oct 29 12:14:08 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA06327; Fri, 29 Oct 1993 12:15:55 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA03655; Fri, 29 Oct 93 12:36:33 -0400
Message-Id: <9310291636.AA03655@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Fri, 29 Oct 1993 12:14:08 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Harvey Karten

>If anyone (including Harvey himself) can get me Harvey Karten's email address,
>I
>would be most grateful.

You can get a list (with email addresses) of all subscribers to the NIH
Image mailing list be sending a message containing the line "recipients
nih-image" to listserv@soils.umn.edu.

--wayne


From wayne@helix.nih.gov  Fri Oct 29 13:11:50 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA06925; Fri, 29 Oct 1993 13:13:31 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA03811; Fri, 29 Oct 93 13:34:15 -0400
Message-Id: <9310291734.AA03811@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Fri, 29 Oct 1993 13:11:50 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Macro file size limitations

>There is a limit on the number of macros, and a limit on the file size.

The maximum number of macros per file is 100 and the maximum macro file
size is 30,000 bytes.

>My version of 1.44 (markup) lifts the file size restriction and doubles the
>number of macros, but the scrolling menu got a little unreasonable.  A few
>seconds to get down to the bottom...
>
>[That version also fixed the else if "feature".  In the present version,
>you must write "else begin ...", never "else if" or "else repeat".
>1.44markup fixes that at the expense of a slightly slower macro processor.
>Now that the segment size limitation of the amount of code in Macros1.p has
>been lifted, this fix ought to be incorporated...  Or at least the program
>should give a macro error if "else" is followed by "if" or "repeat".]

The latest NIH Image beta (1.53b33) reports an error if an "else" is
followed by either "if" or "repeat".

--wayne


From hammer@wana.pbrc.Hawaii.Edu  Fri Oct 29 13:47:46 1993
Received: from wana.pbrc.Hawaii.Edu by nx1.soils.umn.edu (5.65c)
	id AA07304; Fri, 29 Oct 1993 13:47:46 -0500
Return-Path: <hammer@wana.pbrc.Hawaii.Edu>
Received: from [128.171.24.10] (McHammer.pbrc.Hawaii.Edu) by wana.pbrc.Hawaii.Edu (4.1/SMI-4.1)
	id AA20414; Fri, 29 Oct 93 08:48:52 HST
Date: Fri, 29 Oct 93 08:48:51 HST
Message-Id: <9310291848.AA20414@wana.pbrc.Hawaii.Edu>
To: Multiple recipients of list <nih-image@soils.umn.edu>
From: Ron Hammer <hammer@wana.pbrc.Hawaii.Edu>
Subject: Voxel View/Mac

If anyone is interested, Vital Images (515-472-7726) has a demo version of
Voxel View/Mac which does everything except save files. Sample data sets
are included. The Mac version sells for $1295 (a scaled down, less
expensive form of the SGI version).

Thanks to Charles Thomas for answering my questions about Voxel View/Mac.

Ron Hammer

From wayne@helix.nih.gov  Fri Oct 29 16:43:27 1993
Received: from zippy.nimh.nih.gov by nx1.soils.umn.edu (5.65c)
	id AA09071; Fri, 29 Oct 1993 16:45:08 -0500
Return-Path: <wayne@helix.nih.gov>
Received: from pico.nimh.nih.gov by zippy.nimh.nih.gov (1.37.109.4/zippy-1.0)
	id AA04383; Fri, 29 Oct 93 17:05:53 -0400
Message-Id: <9310292105.AA04383@zippy.nimh.nih.gov>
X-Sender: wayne@128.231.98.32
Mime-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Date: Fri, 29 Oct 1993 16:43:27 +0000
To: nih-image@soils.umn.edu
From: wayne@helix.nih.gov(Wayne Rasband)
Subject: Re: Errors (?) in length of skeletonised image

>We have been using Image to do histomorphometry on trabecular bone in
>vertebral bodies.
>
>In the course of this work, we are wanting to measure the length of a
>skeletonised network of trabeculae.  We have tried using the analyse
>particles selection with Area and Length/Perimeter checked, but the
>results don't seem right.  To check the results, we then drew a series
>of straight 1 pixel wide lines and tried to measure them.  Vertical
>lines have almost the right area, and slightly overestimated perimeters.
>Horizontal lines are a little worse, and lines at any other angle are
>way off (30 %).
>
>Does anyone know what we are doing wrong, or how to get correct length
>measurements of a skeletonised network out of Image ?

You get these errors because, for example, a horizontal line and a diagonal
line are both drawn using the same number of pixels.  In this example

#####
#
 #
   #
    #
      #

both lines have the same area in pixels (5), but the diagonal line is
longer. Bert Smit (SMIT@CABO.AGRO.nl), an NIH Image user in the Netherlands
figured out a conversion factor to correct for these errors, assuming the
line segments are at random angles. He was trying to measure the lengths of
plant roots.

You might also consider using a program that is better at morhometrics,
such as PrismView, which is now available for Signal Analytics, the IPLab
people. PrismView measures about 50 particle features, including length.

--wayne


From honig@leland.Stanford.EDU  Sun Oct 31 09:08:52 1993
Received: from cardinal.Stanford.EDU by nx1.soils.umn.edu (5.65c)
	id AA28717; Sun, 31 Oct 1993 19:07:40 -0600
Return-Path: <honig@leland.Stanford.EDU>
Received: from localhost (honig@localhost) by cardinal.Stanford.EDU (8.5/8.5) id RAA10338; Sun, 31 Oct 1993 17:08:53 -0800
From: "Lawrence S. Honig" <honig@leland.Stanford.EDU>
Message-Id: <199311010108.RAA10338@cardinal.Stanford.EDU>
Subject: Re: Errors apparent in handling "Results meaurements"
To: nih-image@soils.umn.edu
Date: Sun, 31 Oct 1993 17:08:52 -0800 (PST)
In-Reply-To: <9310292105.AA04383@zippy.nimh.nih.gov> from "Wayne Rasband" at Oct 29, 93 04:50:42 pm
X-Mailer: ELM [version 2.4 PL21]
Mime-Version: 1.0
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Length: 1072      

To Wayne Rasband  -     
	I seem to have uncovered an error in handling of Results Measurements
in version 1.52.  
	Firstly, in preface... NIH Image seems to have a great difficulty 
handling large (>64K ?) results of measurements files... For example, if one
makes more than about 371 measurements (with my options which include:
number, average, int density, bak, min/max, user1 and user2) , then one cannot 
use "ShowResults" to see more than the first 371 .. However the program does 
correctly save the entire (1000 plus) set of measurements. 
	Secondly, MORE IMPORTANTLY, but probably related to the above (?), 
if one tries to "Delete a measurement" such as measurement 1 to 10 (i.e. 
early measurements) , one is unable to do so as far as I can tell... 
	That is, normally it is no problem to delete any specified measurement, 
but in big result files, it no longer seems possible (the program just deletes
the last measurement done, instead of the measurement number specified!)  
	My compliments regarding the program in general...
		Thanks ....
			Larry Honig

From honig@leland.Stanford.EDU  Sun Oct 31 09:10:37 1993
Received: from cardinal.Stanford.EDU by nx1.soils.umn.edu (5.65c)
	id AA28735; Sun, 31 Oct 1993 19:09:24 -0600
Return-Path: <honig@leland.Stanford.EDU>
Received: from localhost (honig@localhost) by cardinal.Stanford.EDU (8.5/8.5) id RAA10447; Sun, 31 Oct 1993 17:10:38 -0800
From: "Lawrence S. Honig" <honig@leland.Stanford.EDU>
Message-Id: <199311010110.RAA10447@cardinal.Stanford.EDU>
Subject: Re: Errors apparent in handling "Results meaurements" (fwd)
To: nih-image@soils.umn.edu
Date: Sun, 31 Oct 1993 17:10:37 -0800 (PST)
X-Mailer: ELM [version 2.4 PL21]
Mime-Version: 1.0
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Length: 1517      

Forwarded message:
>From honig Sun Oct 31 17:08:52 1993
Subject: Re: Errors apparent in handling "Results meaurements"
To: nih-image@soils.umn.edu
Date: Sun, 31 Oct 1993 17:08:52 -0800 (PST)
In-Reply-To: <9310292105.AA04383@zippy.nimh.nih.gov> from "Wayne Rasband" at Oct 29, 93 04:50:42 pm
X-Mailer: ELM [version 2.4 PL21]
MIME-Version: 1.0
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Length: 1073      

To Wayne Rasband  -     
	I seem to have uncovered an error in handling of Results Measurements
in version 1.52.  
	Firstly, in preface... NIH Image seems to have a great difficulty 
handling large (>64K ?) results of measurements files... For example, if one
makes more than about 371 measurements (with my options which include:
number, average, int density, bak, min/max, user1 and user2) , then one cannot 
use "ShowResults" to see more than the first 371 .. However the program does 
correctly save the entire (1000 plus) set of measurements. 
	Secondly, MORE IMPORTANTLY, but probably related to the above (?), 
if one tries to "Delete a measurement" such as measurement 1 to 10 (i.e. 
early measurements) , one is unable to do so as far as I can tell... 
	That is, normally it is no problem to delete any specified measurement, 
but in big result files, it no longer seems possible (the program just deletes
the last measurement done, instead of the measurement number specified!)  
	My compliments regarding the program in general...
		Thanks ....
			Larry Honig