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

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



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

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

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



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

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

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

Hope I got you right...

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



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

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

Another way is to use a macro something like this:

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

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

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

-wayne



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Dear All, 

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

Thanks a lot

Dietrich



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


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


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

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

School of Anatomy
UNSW, Kensington
Sydney 2052
Australia

ph   	9385 2462
fax 	9313 6252


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

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 58

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Hope I got you right...

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

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

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

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

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

Another way is to use a macro something like this:

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

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

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

-wayne

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

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

Dear All, 

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

Thanks a lot

Dietrich



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

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

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

me too!?

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

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

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

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

School of Anatomy
UNSW, Kensington
Sydney 2052
Australia

ph   	9385 2462
fax 	9313 6252

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

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- Eye on Imaging -
May 26-28 
1999


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

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

--MS_Mac_OE_3003993008_821299_MIME_Part--


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

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

Somewhat dated but still valid (except my email)

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

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


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

>Thanks for your time. in advance

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


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


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


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

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

Greg Joss

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


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

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

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

Does the Histogram function work with data in User Columns?  

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

Glen


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

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


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

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 59

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

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

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

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


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

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

--MS_Mac_OE_3003993008_821299_MIME_Part--

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

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

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

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

Somewhat dated but still valid (except my email)

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

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

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

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

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

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

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

>Thanks for your time. in advance

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

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

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

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


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

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

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

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

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

Greg Joss

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

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

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

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

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

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

Does the Histogram function work with data in User Columns?  

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

Glen


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

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

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

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

Glen,

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


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

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

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

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

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

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

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

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

Norbert

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

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

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


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

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

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

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

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

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

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

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

Norbert



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

Thank you

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

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


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


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

Tips by Henry M. Thomas, 

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

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


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

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

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

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

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 60

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

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

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

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

Thank you

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

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

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

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

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


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

Tips by Henry M. Thomas, 

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

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


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

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

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

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

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

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

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

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



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

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

Somewhat dated but still valid (except my email)

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

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


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

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 61

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

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

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

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

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



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

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

Somewhat dated but still valid (except my email)

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

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

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

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

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

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

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

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


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

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

Arnout



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

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 62

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

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

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

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

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

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

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

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

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

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

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

Arnout

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

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

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

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

Regards,
Glen

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



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

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

Thanks

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


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

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


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



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



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

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

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

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

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

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



I look forward to receive any suggestion.

Ruy Jaeger


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



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unsubscribe

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

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nih-image-d Digest				Volume 99 : Issue 63

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

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

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

You can upgrade to QuickTime 3 for free at:

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

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

Regards,
Glen

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

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

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

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

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

Thanks

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

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

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

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

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


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

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

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

>From Ruy Jaeger
University of Sao Paulo
Brazil



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

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

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

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

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

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



I look forward to receive any suggestion.

Ruy Jaeger


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

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

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

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

ard



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

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


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

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

-wayne



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

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 64

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

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

Date: Tue, 16 Mar 1999 12:31:24 +0100
From: Ard Jonker <a.jonker@amc.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Quicktime looping
Message-Id: <l03130307b313f0eb43fd@[145.117.43.50]>
Content-Type: text/plain; charset="us-ascii"

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

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

ard

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

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

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

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

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

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

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

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

-wayne

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

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

Thanks for any help you can provide!   Janet Szczesny


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



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

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

Jeff Linn


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

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

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


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


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

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

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

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


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

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

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

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


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

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


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

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

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


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

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


Gary.


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


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

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

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

Gary.


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unsubscribe


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

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

Thank's for all the help

Sven

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

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


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unsubscribe nih-image


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

Thanks very much

BILL MASON


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Subject: nih-image-d Digest V99 #65
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 99 : Issue 65

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

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

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

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

Thanks for any help you can provide!   Janet Szczesny

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

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

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

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

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

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

Jeff Linn

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

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

Hi,

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