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From: Ty Wilson <twilson@GIS.Umn.EDU>
To: Multiple recipients of list <nih-image@soils.umn.edu>
Subject: NIH-IMAGE Mailing List Move
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To all members of the nih-image mailing list -


The current list-owners, Ty Wilson, John Ladwig, and Ed Nater, are pleased to
announce:

THE NIH-IMAGE MAILING LIST IS MOVING TO A NEW LOCATION

Jonathan Nissanov and Vaughn Adams of the Computer Vision Center for Vertebrate
Brain Mapping at Drexel University have graciously and generously volunteered to
host the nih-image mailing list in the future. We ask you to support them in
this effort and show them the same patience and kindness you have shown us over
the last few years.

The proposed date and time of the move will be Monday, 29 June, 1998. We
apologize in advance for any inconvenience this changeover will cause to list
members; we have taken several steps (detailed below) to reduce this
inconvenience as much as possible.


=-=-=-=-=-=-=-=

ABOUT THE CHANGEOVER

To facilitate the move and to clean up the membership list, we are asking all
members to subscribe to the new mailing list and to unsubscribe from the old
one. PLEASE NOTE:  You need to make this change yourself; we will *not* do it
for you. Members may make the change to the new list at anytime as of the
posting of this message. Instructions for subscribing to the new mailing list
and unsubscribing from the old one follow at the end of this message.

Prior to the changeover date, we will forward all messages sent to the old list
to the members of the new list. However, until the time of the changeover, all
postings must be sent to the old list. Consequently, those individuals
interested in posting to the list should maintain membership in the old list
until the changeover date and then change their subscriptions after the
changeover has been made.

At the changeover date we will reverse the message flow. From that date, and for
a one week period thereafter, we will forward all messages sent from the new
list to the membership remaining on the old list. After the changeover date,
however, all postings will have to be sent to the new list; messages sent to the
old mailing list will not be forwarded to the new list in order to avoid the
potential for looping messages.


=-=-=-=-=-=-=-=



HOW TO SUBSCRIBE TO THE NEW NIH-IMAGE MAILING LIST:

To subscribe to the new nih-image mailing list, you need to do one of the
following, depending on whether you wish to receive regular postings (each
posting is sent individually) or a digested version (where you receive one
composite posting per day). **Please note** that the commands are somewhat
different from the old list.:

To SUBSCRIBE to the REGULAR LIST, send E-mail to:

     nih-image-request@biomed.drexel.edu

The Subject of the message should contain "Subscribe"

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

To SUBSCRIBE to A DIGESTED VERSION of the list, send E-mail to:

     nih-image-d-request@biomed.drexel.edu.

The Subject of the message should contain "Subscribe".

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


=-=-=-=-=-=-=-=



HOW TO UNSUBSCRIBE FROM THE OLD NIH-IMAGE MAILING LIST:

To unsubscribe, send an email message to:

     listproc@soils.umn.edu

with the message body:

     unsubscribe nih-image

If you have difficulties in unsubscribing, please notify the list-owner at:

     owner-nih-image@soils.umn.edu

and provide a copy of the message returned by the list processor following the
unsuccessful attempt as well as your full name and, if possible, the exact email
address by which you originally subscribed to nih-image. We will gladly remove
you from the list.


=-=-=-=-=-=-=-=



PLEASE REMEMBER:

The old mailing list will be shut down on Monday, 6 July, 1998 (or sooner if all
members have unsubscribed before then). Message forwarding to the old list will
cease at that time. Those individuals who have failed to subscribe to the new
mailing list at that time will no longer receive postings from the mailing list.

From nih-image-request@io.ece.drexel.edu Fri Jun 26 00:38 EDT 1998
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Date: Thu, 25 Jun 1998 23:38:01 -0500 (CDT)
Message-Id: <199806260439.MAA12394@nero.rph.health.wa.gov.au>
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From: "Robert Day" <robday@rph.health.wa.gov.au>
To: Multiple recipients of list <nih-image@soils.umn.edu>
Subject: Re: Sony LANC protocol
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> 
> I am looking for information about the LANC or Control-L protocol
> which is used to control video recorders.
> 

Chris, try the Sony LANC/Control-L page at: 
<http://www.york.ac.uk/~adv3/lanc/lanc.htm>


Rob Day

--
Robert Day		rob.day@nero.rph.health.wa.gov.au
Project Bioengineer	ph  +61 8 9224 3227
Royal Perth Hospital	fax +61 8 9224 1138

From nih-image-request@io.ece.drexel.edu Fri Jun 26 12:32 EDT 1998
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!!  IMPORTANT ANNOUNCEMENT  !!

The email mailing list, nih-image, has moved to a new location. The old list will cease
operation on the 29th of June, 1998, but will continue to forward messages from the new
list until 6 July, 1998.

To continue as a list member, you will have to subscribe to the new list. To do so, you
need to do one of the following, depending on whether you wish to receive regular postings
(each posting is sent individually) or a digested version (where you receive one composite
posting per day). Please note that the commands are somewhat different from the old list.:

To SUBSCRIBE to the REGULAR LIST, send E-mail to:

     nih-image request@biomed.drexel.edu

The Subject of the message should contain "Subscribe"

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

To SUBSCRIBE to A DIGESTED VERSION of the list, send E-mail to:

     nih-image-d-request@biomed.drexel.edu.

The Subject of the message should contain "Subscribe".

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


IF YOU HAVE TROUBLE subscribing to the new list, please send an email message explaining
the problem to nih-image-owner@biomed.drexel.edu.


IN ADDITION, please unsubscribe from the old list. It will help us keep track of the
changeover and it will prevent you from receiving additional messages like this one. To
unsubscribe, send an email message to:

     listproc@soils.umn.edu

with the message body:

     unsubscribe nih-image

If you have difficulties in unsubscribing, please notify the list-owner at:

     owner-nih-image@soils.umn.edu

and provide a copy of the message returned by the list processor following the
unsuccessful attempt and your full name and, if possible, the exact email address by which
you originally subscribed to nih-image.

Thank you all for the patience, kindness, and respect you have shown us (John Ladwig, Ty
Wilson, and Ed Nater) in the past. It has been an honor hosting this list and, although we
take justifiable pride in the quality and usefulness of this list, it is you, the members,
who have made it the high quality resource it has become. Please afford Jonathan Nissanov
and Vaughn Adams the same degree of respect you have shown us and you will ensure its
continued success.


This message will be sent on a daily basis until the list closes.

Thank you all.

Ed
List-owner

--
Edward A. Nater                       phone:  612-625-1725
Professor and                         fax:    612-624-4223
  Director of Graduate Studies        email:  ed.nater@soils.umn.edu
Department of Soil, Water, and Climate, 439 Borlaug Hall
University of Minnesota, St. Paul, MN  55108-6028  USA

"Science advances one funeral at a time."  - Niels Bohr


From nih-image-request@io.ece.drexel.edu Fri Jun 26 14:00 EDT 1998
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Date: Fri, 26 Jun 1998 19:52:58 +0100
To: nih-image@io.ece.drexel.edu
From: Peter Bramlage <Peter.Bramlage@rz.hu-berlin.de>
Subject: Website / Mailing List
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I hope you don't mind if I bother this list once with a mail that is way
off topic. But I believe it could be interesting for some of you.

As some of you may know, I own a small website that deals with the primary
topic of methods in the area of Heart & Vessel Research. I am writing you
to tell you that I added a mailing list just for the topic of Heart &
Vessel Research to my Internetserver (http://www.hvresearch.com). I had the
impression that people are interested in communicating, but are not willing
to use the guestbook for this purpose. Since I believe that communication
is the most important issue in our business I installed this Listserver.

I would like to ask you to help me with the initial etablishment of the
list. For most of us it is nice to subscribe to a mailing list and read the
mails coming in for a while, before participating actively in the
discussion. That is may main concern. People will probably unsubscribe
before a proper discussion can develop. Your task would be to have an open
ear for people on the list and to help when you think help is possible.

To subscribe to the list just send an email to

	requests@hvresearch.com

with

	subscribe listserv

as the body of the message.

I appreciate your help !

... and feel free to give this adress to as many people as you can ;-)

Best Regards, Peter




From nih-image-request@io.ece.drexel.edu Sun Jun 28 02:56 EDT 1998
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Date: Sun, 28 Jun 1998 01:50:54 -0500 (CDT)
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From: John Ladwig <jladwig@soils.umn.edu>
To: Multiple recipients of list <nih-image@soils.umn.edu>
Subject: Administrivia: Getting on, off and around the list
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This message is automatically posted once per month, on the 28th of
the month.  It contains information about list mechanics (subscribing,
subscribing, digests, message archive access, and program distribution
points.

                -jml    NIH-Image mailing list coordinator


[UN]SUBSCRIBING:
================

[Un]Subscription requests should be sent to:

    listproc@soils.umn.edu

with one of the following commands in the *body* of the message:

    subscribe nih-image Your Realname
    unsubscribe nih-image

and *no* Subject: line.  Placing commands in the Subject line will
only get them rejected by the automated list manager, and handed to a
human, who is *no doubt* slower to respond than the list manager.

DIGESTS:
========

Send the following in the body of a message to <listproc@soils.umn.edu>

    set nih-image mail digest

to go back to message-at-a-time mode, send

    set nih-image mail ack

to the same address.


SUSPENDING:
===========

To temporarily suspend your subscription, send the following in the
body of a message to <listproc@soils.umn.edu>

    set nih-image mail postpone

to go back to message-at-a-time or digest mode, send

    set nih-image mail ack
or
    set nih-image mail digest


ADDRESS CHANGES
===============

If your email address has changed, please send mail to
owner-nih-image@soils.umn.edu and ask the human there to change things
around for you.  If you have received an error message regarding your
changed address, be assured that a human being *will* see that error
message, and will handle the changeover.  It may or may not be
immediate, but it's usually handled within a few days.


MESSAGE ARCHIVE ACCESS
======================

Best would be to point your web browser to:

<URL:http://www.soils.agri.umn.edu/infoserv/lists/nih-image/archives/>

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

<URL: gopher://gopher.soils.umn.edu:7151/77/wais-sources/nih-image-archive>

    Computer Information/
     General Information/
      Search Nih-Image Mailing List Current Month's Articles <?>
      Search Nih-Image Mailing List Archives <?>

to search the archived messages for keywords.  The Current Month's
Articles are indexed on an hourly basis, the Archives on a daily basis.

You can also browse the monthly archives in

<URL: gopher://gopher.soils.umn.edu:10082/11/email-lists/nih-image>

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

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

<URL: ftp://ftp.soils.umn.edu:pub/info/email-lists/nih-image/>


The archive of email-retrievable files relevant to NIH Image available
by request from the listprocessor; send the command

    index nih-image

to get a list of the files, and a brief description of each one.


NIH-IMAGE PROGRAM LOCATIONS
===========================

The reference location for NIH-image is <URL:ftp://zippy.nih.gov/pub/nih-image>
Programs, documentation, macro archive, and related information are
stored there.

More information about NIH Image is available on the NIH Image Web
site at <URL:http://rsb.info.nih.gov/nih-image/>



CONTACT/ADMINISTRATIVE INFORMATION
==================================

Questions about the listprocessor system and the NIH-Image discussion
list may be sent to owner-listproc@soils.umn.edu or
owner-nih-image@soils.umn.edu


Your humble List maintainer,
    John Ladwig
    owner-nih-image@soils.umn.edu

From nih-image-request@io.ece.drexel.edu Sun Jun 28 15:59 EDT 1998
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To: Multiple recipients of list <nih-image@soils.umn.edu>
Subject: IMPORTANT: The NIH-Image mailing list is moving
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!!  IMPORTANT ANNOUNCEMENT  !!

The email mailing list, nih-image, has moved to a new location. The old list will cease
operation on the 29th of June, 1998, but will continue to forward messages from the new
list until 6 July, 1998.

     YOU HAVE ** 8 ** DAYS IN WHICH TO MAKE THE CHANGE

To continue as a list member, you will have to subscribe to the new list. To do so, you
need to do one of the following, depending on whether you wish to receive regular postings
(each posting is sent individually) or a digested version (where you receive one composite
posting per day). Please note that the commands are somewhat different from the old list.:

To SUBSCRIBE to the REGULAR LIST, send E-mail to:

     nih-image request@biomed.drexel.edu

The Subject of the message should contain "Subscribe"

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

To SUBSCRIBE to A DIGESTED VERSION of the list, send E-mail to:

     nih-image-d-request@biomed.drexel.edu.

The Subject of the message should contain "Subscribe".

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


IF YOU HAVE TROUBLE subscribing to the new list, please send an email message explaining
the problem to nih-image-owner@biomed.drexel.edu.


IN ADDITION, please unsubscribe from the old list. It will help us keep track of the
changeover and it will prevent you from receiving additional messages like this one. To
unsubscribe, send an email message to:

     listproc@soils.umn.edu

with the message body:

     unsubscribe nih-image

If you have difficulties in unsubscribing, please notify the list-owner at:

     owner-nih-image@soils.umn.edu

and provide a copy of the message returned by the list processor following the
unsuccessful attempt and your full name and, if possible, the exact email address by which
you originally subscribed to nih-image.

Thank you all for the patience, kindness, and respect you have shown us (John Ladwig, Ty
Wilson, and Ed Nater) in the past. It has been an honor hosting this list and, although we
take justifiable pride in the quality and usefulness of this list, it is you, the members,
who have made it the high quality resource it has become. Please afford Jonathan Nissanov
and Vaughn Adams the same degree of respect you have shown us and you will ensure its
continued success.

Thanks,

Ed

--
Edward A. Nater                       phone:  612-625-1725
Professor and                         fax:    612-624-4223
  Director of Graduate Studies        email:  ed.nater@soils.umn.edu
Department of Soil, Water, and Climate, 439 Borlaug Hall
University of Minnesota, St. Paul, MN  55108-6028  USA

"Science advances one funeral at a time."  - Niels Bohr


From nih-image-request@io.ece.drexel.edu Sun Jun 28 16:42 EDT 1998
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	Sun, 28 Jun 1998 16:42:20 -0400 (EDT)
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Date: Sun, 28 Jun 1998 15:41:21 -0500 (CDT)
Message-Id: <199806282018.QAA00076@scionserver.scioncorp.com>
Reply-To: nih-image@soils.umn.edu
Originator: nih-image@soils.umn.edu
Sender: nih-image@soils.umn.edu
From: Jeff Reidler <jreidler@scioncorp.com>
To: Multiple recipients of list <nih-image@soils.umn.edu>
Subject: Scion Image Beta 3
X-Listprocessor-Version: 6.0c -- ListProcessor by Anastasios Kotsikonas
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Dear Imagers,

Scion Corporation has released BETA 3 of Scion Image for Windows 95 and 
NT, 
available at http://www.scioncorp.com in 'Downloads'.  

Thank you for your patience and support.
Jeff

From nih-image-request@io.ece.drexel.edu Mon Jun 29 15:02 EDT 1998
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Date: Mon, 29 Jun 1998 13:49:58 -0500 (CDT)
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From: Ty Wilson <twilson@Gis.Umn.EDU>
To: Multiple recipients of list <nih-image@soils.umn.edu>
Subject: CHANGEOVER IMMINENT!
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======

Dear List Members;

Please take note:

The changeover in the home for the NIH-Image mailing list will occur
*today *at 3:00 pm CST. At the posting of this message, it is
approximately 1:45 pm CST. 

Once the changeover has occurred, all messages posted to the NIH-Image
mailing list *must* be posted to the new list. The old list will no longer
accept postings. In order to post messages, you must be signed up to the
new list. 

We will continue forwarding messages from the new list to the old list for
one week, until 6 July, 1998, at which time we will terminate all message
forwarding. If you have not subscribed to the new list, I urge you to do
so soon. 

Thank you for your patience.

Ed

Instructions for subscription/unsubscription follow:

=======

To continue as a list member, you will have to subscribe to the new list.
To do so, you need to do one of the following, depending on whether you
wish to receive regular postings (each posting is sent individually) or a
digested version (where you receive one composite posting per day). Please
note that the commands are somewhat different from the old list.: 

To SUBSCRIBE to the REGULAR LIST, send E-mail to:

     nih-image request@biomed.drexel.edu

The Subject of the message should contain "Subscribe"

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To SUBSCRIBE to A DIGESTED VERSION of the list, send E-mail to:

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IF YOU HAVE TROUBLE subscribing to the new list, please send an email
message explaining the problem to nih-image-owner@biomed.drexel.edu. 


IN ADDITION, please unsubscribe from the old list. It will help us keep
track of the changeover and it will prevent you from receiving additional
messages like this one. To unsubscribe, send an email message to: 

     listproc@soils.umn.edu

with the message body:

     unsubscribe nih-image

If you have difficulties in unsubscribing, please notify the list-owner at:

     owner-nih-image@soils.umn.edu

and provide a copy of the message returned by the list processor following
the unsuccessful attempt and your full name and, if possible, the exact
email address by which you originally subscribed to nih-image. 

Thank you all for the patience, kindness, and respect you have shown us
(John Ladwig, Ty Wilson, and Ed Nater) in the past. It has been an honor
hosting this list and, although we take justifiable pride in the quality
and usefulness of this list, it is you, the members, who have made it the
high quality resource it has become. Please afford Jonathan Nissanov and
Vaughn Adams the same degree of respect you have shown us and you will
ensure its continued success. 

From nih-image-request@io.ece.drexel.edu Mon Jun 29 15:25 EDT 1998
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From: Brenda Leach <leachb@biology.queensu.ca>
To: Multiple recipients of list <nih-image@soils.umn.edu>
Subject: Image capturing crashes/digitizer problems
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I am trying to capture live video using Image 1.61 on a Performa 5200 CD
with an Adobe Photoshop Plug-in Digitizer. The problem I've always
encountered on this computer (with different Image versions) is that when I
try to use the "start capturing" command, it freezes. Instead, I have to
use "Aquire - Plug-in Digitizer" to get a live image. But this has also
stopped working for me. I just get a black field. I've used both of these
commands on other computers to get images from video tapes, but never
directly from the video camera. Is there some conflict I'm unaware of or a
different digitizer I should be using?
Thanks for any suggestions,

Brenda Leach


From nih-image-request@io.ece.drexel.edu Mon Jun 29 17:08 EDT 1998
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From: Vaughn Adams <vaughn@cbis.ece.drexel.edu>
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Subject: Test - Ignore this
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Please ignore.

-- 
Vaughn Adams
Drexel University 
Electrical and Computer Engineering      Voice: 215-895-1979
32nd and Chestnut Streets                  FAX: 215-895-1695
Philadelphia, Pa 19104                   Email: vaughn@coe.drexel.edu

PGP key available - finger -l vaughn@cbis.ece.drexel.edu

From nih-image-request@io.ece.drexel.edu Mon Jun 29 17:16 EDT 1998
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From: Vaughn Adams <vaughn@cbis.ece.drexel.edu>
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Subject: Archive Test - please ignore
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delete this

-- 
Vaughn Adams
Drexel University 
Electrical and Computer Engineering      Voice: 215-895-1979
32nd and Chestnut Streets                  FAX: 215-895-1695
Philadelphia, Pa 19104                   Email: vaughn@coe.drexel.edu

PGP key available - finger -l vaughn@cbis.ece.drexel.edu

From nih-image-request@io.ece.drexel.edu Tue Jun 30 11:04 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: Welcome
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Dear List Members;


<fontfamily><param>Times</param>We at the Computer Vision Center for
Vertebrate Brain Mapping (http://cbis.ece.drexel.edu/ICVC/) are pleased
to serve as the new hosts of the NIH Image mail list. Ed Nater, John
Ladwig and Ty Wilson have done a fantastic job in establishing and
maintaining the list as an important forum for discussion on NIH Image
issues and on image processing in general. It is a hard act to follow.
Please bear with us while we make the transition. 


Listed below are important information for using the list.


e-mail addresses of importance

--------

nih-image@biomed.drexel.edu   - Sends mail to the list

nih-image-request@biomed.drexel.edu   - Administation for List

nih-image-d-request@biomed.drexel.edu  - Aministration for Digest


Subscribe

---------

To subscribe to the list, send E-mail to
nih-image-request@biomed.drexel.edu.

The Subject of the message should contain "Subscribe".


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

		Subject: subscribe



Subscribe to Digest

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

To subscribe to a digested version of the list, send E-mail to 

nih-image-d-request@biomed.drexel.edu.


The Subject of the message should contain "Subscribe".


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

		Subject: subscribe



Unsubscribe

-----------

To unsubscribe to the list, send E-mail to
nih-image-request@biomed.drexel.edu.

the Subject of the message should contain "unsubscribe".


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

		Subject: unsubscribe



Unsubscribe to Digest

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

To unsubscribe to digested version of the list, send E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "unsubscribe".


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

		Subject: unsubscribe


Help

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

To obtain a listing of help items, send E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "help".


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

		Subject: help




Help on Digest

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

To obtain a listing of help items on digest version of the list, send
E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "help".


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

		Subject: help




Archive

-------

Every submission sent to this list is archived.	 Following are the
commands

used to access the archive.  Send Email to nih-image-request with the
command 

in the Subject line or in the body of the message.


get filename ...

ls directory ...

egrep case_insensitive_regular_expression filename ...

maxfiles nnn

version

quit


Aliases for 'get': send, sendme, getme, gimme, retrieve, mail

Aliases for 'ls': dir, directory, list, show

Aliases for 'egrep': search, grep, fgrep, find

Aliases for 'quit': exit


If you append a non-standard signature, you should use the quit
command

to prevent the archive server from interpreting the signature.


Examples:

     ls latest

     get latest/12

     egrep some.word latest/*

</fontfamily>

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

             Computer Vision Center for Vertebrate Brain Mapping,      
          

               a NIH Biomedical Research Technology Resource

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

                            Jonathan Nissanov, Ph.D.

                              Associate Director  

Imaging and Computer Vision Center              Tel: 215-895-1381

Drexel University                                                  
Fax: 215-895-4987

Phildelphia, PA 19104                                        
yoni@coe.drexel.edu

                        http://cbis.ece.drexel.edu/ICVC/

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

      

     

From nih-image-request@io.ece.drexel.edu Wed Jul  1 14:08 EDT 1998
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	Wed, 1 Jul 1998 14:07:11 -0400 (EDT)
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Message-ID: <359AC0A7.7C8C@pro.via-rs.com.br>
Date: Wed, 01 Jul 1998 15:05:13 -0800
From: Luthero Martins <rsf6675@pro.via-rs.com.br>
Reply-To: luthero@pro.via-rs.com.br
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Group!

        I'm an ophthalmologist in Brazil.  I have a power mac 7600, a
frame
grabber Miro motion DC-20.  I take images from a Canon retinal camera
non-mydriatic CR5-45NM and a Sony 3CCD video camera, with the Adobe
Premiere software.
        I take color images.  I'd like to capture this images directly
from
NIH, that will be Grayscale.
        What I'll need to do this? Somebody knows?

Thanks

Luthero Martins
http://www.oftalmologia-digital.com

From nih-image-request@io.ece.drexel.edu Wed Jul  1 19:22 EDT 1998
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Date: Thu, 2 Jul 1998 09:14:49 +1000
To: nih-image@io.ece.drexel.edu
From: Steve Martin <s.martin@physio.unimelb.EDU.AU>
Subject: New list reply-to setup
Resent-Message-ID: <"IaRvF2.0.k73.xBicr"@io>
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Hi to everyone who has jumped across...

Messages from the new list host seem to have a 'reply-to' of the author of
the posting, not the list.

Is this an oversight, or a deliberate policy change? I only happened to
notice because Eudora no longer filters my 'replyto: NIH-Image' mail.

just wondering...

regards,

Steve

___________________________
Stephen Martin
School of Physiotherapy
The University of Melbourne
200 Berkeley St
Parkville Victoria 3052
AUSTRALIA
ph  +61 3 9344 4171
fax +61 3 9344 4188
___________________________

From nih-image-request@io.ece.drexel.edu Wed Jul  1 20:35 EDT 1998
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Mime-Version: 1.0
Date: Wed, 1 Jul 1998 19:30:46 -0500
To: nih-image@io.ece.drexel.edu
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: Re: New list reply-to setup
Resent-Message-ID: <"QZiTn.0.0t4.2Jjcr"@io>
Resent-From: nih-image@io.ece.drexel.edu
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Not deliberate. We are working on it. Thanks.

>Hi to everyone who has jumped across...
>
>Messages from the new list host seem to have a 'reply-to' of the author of
>the posting, not the list.
>
>Is this an oversight, or a deliberate policy change? I only happened to
>notice because Eudora no longer filters my 'replyto: NIH-Image' mail.
>
>just wondering...
>
>regards,
>
>Steve
>
>___________________________
>Stephen Martin
>School of Physiotherapy
>The University of Melbourne
>200 Berkeley St
>Parkville Victoria 3052
>AUSTRALIA
>ph  +61 3 9344 4171
>fax +61 3 9344 4188
>___________________________


---------------------------------------------------------------------------
             Computer Vision Center for Vertebrate Brain Mapping,

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

     


From nih-image-request@io.ece.drexel.edu Thu Jul  2 11:47 EDT 1998
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	Thu, 2 Jul 1998 11:45:39 -0400 (EDT)
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Message-Id: <v0300782fb1c1548f754f@[144.118.33.245]>
Mime-Version: 1.0
Date: Thu, 2 Jul 1998 10:37:39 -0500
To: nih-image@io.ece.drexel.edu
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: Digest form
Resent-Message-ID: <"eW3_G2.0.6b4.Dbwcr"@io>
Resent-From: nih-image@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
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Dear members.

The digest form appears to vary greatly between different mail systems.
Using Eudora, for example, each digest generates a new mailbox with each
message stored individually. I very much like that mode myself. With some
other systems we are getting less convenient formats. I would appreciate if
those of you using the digest mode would let me know which system you are
using and how the digest appears on that system. You can send your comments
directly to me.

Thanks.

---------------------------------------------------------------------------
             Computer Vision Center for Vertebrate Brain Mapping,

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

     


From nih-image-request@io.ece.drexel.edu Thu Jul  2 11:47 EDT 1998
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	Thu, 2 Jul 1998 11:45:54 -0400 (EDT)
Resent-Date: Thu, 2 Jul 1998 11:45:54 -0400 (EDT)
Message-Id: <v03007830b1c159cfb141@[144.118.33.245]>
Mime-Version: 1.0
Date: Thu, 2 Jul 1998 10:39:35 -0500
To: nih-image@io.ece.drexel.edu
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: Reply to
Resent-Message-ID: <"1MBRz1.0.be4.0dwcr"@io>
Resent-From: nih-image@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
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Status: RO

Dear members.

We have now changed the reply to so it no longer automatically responds to
the author of the posting but rather to the mail list.

Regards,

Yoni

---------------------------------------------------------------------------
             Computer Vision Center for Vertebrate Brain Mapping,

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

     


From nih-image-request@io.ece.drexel.edu Fri Jul  3 06:33 EDT 1998
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	Fri, 3 Jul 1998 06:31:24 -0400 (EDT)
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X-Sender: sdb@pop1.liv.ac.uk
Message-Id: <l03130302b1c260a1e510@[138.253.47.16]>
In-Reply-To: <199807031000.GAA27697@io.ECE.Drexel.EDU>
Mime-Version: 1.0
Date: Fri, 3 Jul 1998 11:22:18 +0100
To: nih-image@io.ece.drexel.edu
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
Subject: Re: Digest form
Resent-Message-ID: <"w6D7T.0.z2.y2Bdr"@io>
Resent-From: nih-image@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
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Status: RO

Dear Jonathan,

>Using Eudora, for example, each digest generates a new mailbox with each
>message stored individually. I very much like that mode myself. With some
>other systems we are getting less convenient formats. I would appreciate if
>those of you using the digest mode would let me know which system you are
>using and how the digest appears on that system.

I use Eudora Light v3.1.3 and the digest appears as with the previous
distribution system -  a single email message containing all the day's
postings. No problem.


___________________________________________________________________

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

Tel: 44-(0)151-794-3874 / 3894 / 3870
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk

___________________________________________________________________


From nih-image-request@io.ece.drexel.edu Sun Jul  5 07:02 EDT 1998
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Subject: long text files
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Hi,

Currently, I need to output very long text results using NIH-Image. When over 32K, I understand, NIH can't handle text files. Having looked around but not being able to locate appropriate routines, I'm in the process of making my own routines, within the NIH-Image macro language. My personal needs are satisfied if I have 

fCreate (creates disk file with length known a priori)
fPutC   (puts a single character)
fPutS   (puts a string)
fFlush  (writes the file to disk)
fClose  (as is)
fSeek   (moves file pointer to a certain location)

Should these routines be useful to anyone, please give some feed back. If useful, I could add some extra features (fGetC, fGetS, fOpen) before releasing the macro. Beta testers also welcome.

Ard


From nih-image-request@io.ece.drexel.edu Sun Jul  5 09:15 EDT 1998
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From: "Mario de A. Lira Junior" <mliraj@PO-Box.mcgill.ca>
Subject: Re: long text files
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Hello,

>Currently, I need to output very long text results using NIH-Image. When
over 32K, I understand, NIH can't handle text >files. Having looked around
but not being able to locate appropriate routines, I'm in the process of
making my own 

I am quite a new user, so I may be very off-base, but I understand that the
program can create the files, although it can't open or edit them...
Best regards,
Mario Lira Junior

From nih-image-request@io.ece.drexel.edu Mon Jul  6 10:23 EDT 1998
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>Currently, I need to output very long text results using NIH-Image. When 
>over 32K, I understand, NIH can't handle text files. Having looked around 
>but not being able to locate appropriate routines, I'm in the process of 
>making my own routines, within the NIH-Image macro language. My personal 
>needs are satisfied if I have 

I'm actually in the process of working on something related. I'm 
attempting to modify the source code of NIH image so that the analyze 
particles function will also create a text file returning the cartesian 
coordinates of the centroids of all particles found. I would have 
preferred to write a macro, but it seemed to me that modifying the source 
code was the only way to go about doing this. I have actually been having 
a little difficulty figuring out how to go about creating and writing to 
a file from NIH Image procedures. If you have any suggestions on how to 
do this (and it sounds like your routines might do the trick), I'd love 
to hear them. Thanks. 




-------------------------
Michael Froimowitz
frommy@mclean.harvard.edu
-------------------------

From nih-image-request@io.ece.drexel.edu Mon Jul  6 11:06 EDT 1998
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Date: Mon, 06 Jul 1998 07:54:47 -0700
From: Joshua McLaughlin <jmclaughlin@popmail.ucsd.edu>
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Subject: Cell Counting
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I was wondering if anyone could give me some help in something I am
trying to do:

I have a SPOT camera and am doing image analysis on Scion's image
program, currently
I am doing some dark-field analysis of some in-situ hybridization
slides, but now I want to do
something new:
We have some blood smears which are stained for immature Red Blood
cells, which stain a dark
purple, mature RBCs stain a light pink.  I would like to simply be able
to count both types of cells within
an AOI.  I have never done any color analysis with Image and would
appreciate any help writing a Macro.

Thank You,
Josh McLaughlin

--
Joshua McLaughlin
UCSD Department of Reproductive Medicine
212 Dickinson St. 0802
San Diego, CA 92103-0802
(619)543-2678
josh@ucsd.edu


From nih-image-request@io.ece.drexel.edu Tue Jul  7 10:21 EDT 1998
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Subject: Re: Cell Counting
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Josh:

Depending on how dark the purple is and how different the purple and pink
are, the simplest solution for you might be to capture two different
grayscale images with different filters to enhance or attenuate the two
different stains. Using a pink or salmon filter might help you enhance the
purple contrast and blend the pink into the background so that you can
count only precursor cells. Selectively capturing pink relative to dark
purple might be trickier, but I suppose you could count total cells and
subtract the counts of the immature ones to get the mature erythrocyte
count. I don't think using a blue filter would differentiate the pink from
purple too well, but you might try it.

The other possibility might be to capture your color image into photoshop
and then use different color channels, but again I don't know how well pink
and purple will be separated.

Good luck!

David Morilak


David Morilak, Ph.D.
Dept of Pharmacology
Univ Texas Health Science Center
7703 Floyd Curl Drive
San Antonio, TX 78284-7764

ph: 210-567-4174
FAX: 210-567-4303
E-mail: morilak@uthscsa.edu


From nih-image-request@io.ece.drexel.edu Tue Jul  7 10:56 EDT 1998
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Hi,

We are using NIH-Image for PC, and are currently doing freehand line
drawing around cell structures in LM and would like to measure the
perimeter in segments, the total perimeter and enclosed area all in one
continuous operation.

At the moment, we are using the Freehand/segmented line selection to make
measurements of the segments and then redrawing the perimeter using the
Freehand Region Tool to get the total perimeter and area measurements.

Is it possible to avoid redrawing the area a second time?

Thanks,

Karen Rethoret
York University, Toronto

From nih-image-request@io.ece.drexel.edu Tue Jul  7 11:39 EDT 1998
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From: "j. s." <jianshi@pop.service.ohio-state.edu>
Subject: CCD camera
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Is there anybody who knows area CCD (white/black) system? I only have a budget around $2000 or less. I need an area CCD (652X488, 12, 14, or 16 bits), and a card. Please email me the brand name, price, and tech info. Thanks much.

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

j. shi

dept. of geological sciences

the ohio state university

columbus, ohio 43210

<color><param>0000,0000,ffff</param>(614)-292-0585/6193 </color>(o)

<color><param>ffff,0000,ffff</param>(614)-688-9686 </color>(h)

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

From nih-image-request@io.ece.drexel.edu Tue Jul  7 15:38 EDT 1998
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From: Fernando <L.TapiaVergara@mailbox.uq.edu.au>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Aanalyze particles self-consistancy?
Date: Wed, 8 Jul 1998 05:25:09 +1000
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------ =_NextPart_000_01BDAA30.C6D76940
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Dear imagers:
Firstly, greetings to all on the new list.

Secondly, I would greatly appreciate if you can help me with this =
bewildering problem:

My binary image consists of a black background fully tessellated by  a =
two-pixel-wide  white line, which constitutes the particles' boundaries. =
Each of the black regions thus created is a "particle".

When I AnalyzeParticles on one computer using the 'label ignore outline =
reset' AnalyzeOptions (which are set by a macro), I obtain the expected =
results. That is, a number of labelled, outlined, 128-greyed, areas =
corresponding to each of the particles that are not touching the edges. =
(The latter are also 128-greyed, but are not counted).

However, when I analyze the same image, using the same macro (and =
therefore the same Analyze Options) on the "headache" computer, all the =
image frame, including the 2-pixel-wide particle boundaries are greyed =
to 128gl. And no particle is counted.

I've tried a number of different Analyze options (I played with all the =
possible combinations of "ignore" and "include"), but can not reproduce =
the results I obtain on my "healthy" computer.

Moreover, the AnalyzeParticles command seems to realize that I am =
bewildered, as it is adding a little of a quiz to the problem:
I am able to get the "expected results" on my headache computer, with =
the original AnalyzeOptions settings when I edit my image adding a very =
wide (30 pixels) border all around the image.
Please, notice that if the border is only 1, 2, 10 or even 15 pixels =
wide, I obtain the headache results.=20

Is there anything that I am missing?
Could it be because of the NIH-image version that I am using?
Or, because of some little differences between different NIH versions?
Are there any options that I am missing?

I appreciate all your attention this far, and thank you in =
advance.


From nih-image-request@io.ece.drexel.edu Tue Jul  7 18:20 EDT 1998
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From: Bill Miller <microbill@mohawk.net>
Subject: Re: CCD camera
In-Reply-To: <3.0.1.32.19980707112824.0069a210@pop.service.ohio-state.ed
	u>
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	<199807071009.GAA22450@io.ECE.Drexel.EDU>
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See Electrim - http://www.electrim.com  and DVC
http://members.aol.com/dvcco/

Both are affordable and do at least what you want - probably more.


Best Regards - Bill Miller


At 11:28 AM 7/7/98 -0400, you wrote:

>>>> 

<excerpt>Is there anybody who knows area CCD (white/black) system? I only
have a budget around $2000 or less. I need an area CCD (652X488, 12, 14,
or 16 bits), and a card. Please email me the brand name, price, and tech
info. Thanks much.

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

j. shi

dept. of geological sciences

the ohio state university

columbus, ohio 43210

<color><param>0000,0000,ffff</param>(614)-292-0585/6193 </color>(o)

<color><param>ffff,0000,ffff</param>(614)-688-9686 </color>(h)

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




</excerpt><<<<<<<<




From nih-image-request@io.ece.drexel.edu Wed Jul  8 01:44 EDT 1998
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Date: Wed, 8 Jul 1998 13:20:39 +0800
To: nih-image@io.ece.drexel.edu
From: Jean-Francois Neron <jfneron@fse.ulaval.ca>
Subject: How to unsuscribe
Resent-Message-ID: <"2zh4f.0.Uh4.oMmer"@io>
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Can someone please post a message explaining how to unsuscribe from the NEW
NIH-Image mailing list. Thanks!

-----------------------------------------------------------------
Jean-Francois Neron, M.Sc.
Department of Human Movement
University of Western Australia
Telephone  011-618-9386-3686
ICQ        4213717                   mailto:jfneron@fse.ulaval.ca
-----------------------------------------------------------------

From nih-image-request@io.ece.drexel.edu Wed Jul  8 10:17 EDT 1998
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Date: Wed, 8 Jul 1998 10:15:37 -0500
To: nih-image@io.ece.drexel.edu
From: Laird Bloom <lbloom@MIT.EDU>
Subject: Help with controlling Optronics camera from Image
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Hi,
We have an Optronics DEI-750 camera connected to a Macintosh G3 via a Scion
CG-7 frame grabber, and we're obtaining images using Scion Image 1.62a.
The Optronics camera controller has no way of saving settings put in
through the camera controller keyboard, which is a nuisance when we're
trying to go back and forth between different lighting conditions (e.g.
brightfield and fluorescence microscopy of the same sample).  We would like
to be able to save the Optronics camera settings and use an Image macro (or
some other Mac program) to send the saved settings back to the camera.  Has
anyone done something like this?

Thanks
Laird Bloom
MIT Center for Cancer Research
lbloom@mit.edu


From nih-image-request@io.ece.drexel.edu Wed Jul  8 10:23 EDT 1998
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From: JLinn24538@aol.com
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Date: Wed, 8 Jul 1998 10:14:30 EDT
To: nih-image@io.ece.drexel.edu
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Trace your outline with the freehand tool then use the 'Save As' an Outline
option.  With that done you can reproduce the outline in the target image (or
a duplicate) as many times as you need to.  If you have multiple discontinuous
outlines then reproduce each as a binary in a new window after drawing it.
Then to reproduce the outline you can use the wand tool.

Jeff Linn

From nih-image-request@io.ece.drexel.edu Wed Jul  8 10:49 EDT 1998
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Date: Wed, 08 Jul 1998 10:39:54 -0500
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To all,

I have recently begun trying to use NIH-image to capture and analyze
images from a Nikon inverted fluorescent microscope.  I am using a low
light level, SIT 66 camera from DAGE-mti, Inc., and capturing the images
with NIH-Image on a PowerMac G3.  Specs for the computer are 32 Meg RAM,
266MHz, and 512K.  The frame grabber is an LG3 from Scion.

The problem I am running into is that the images I'm getting are
incredibly grainy.  In fact, they look worse on the computer screen than
they do when looking through the microscope.  Is there any way to change
the parameters (preferences) of the camera function?

The other question I have is, is there a way to set the software to
capture frames at timed intervals? I would like to be able to take short
exposures at timed intervals.  For example, take a 0.1 second exposure
every 10 sec.  Is there a way to do this?  So far whenever I set the
exposure time the software automatically changes the number of frames
per second.  For example, when I set the camera for a 0.1 second
exposure, the software then automatically sets the computer to capture
10 frames per second.  The problem with this is that I very rapidly
reach the memory limit of the computer and thus cannot capture images
over a long period of time (ie. several minutes).  Any suggestions on
this?

Mary Kimble

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From: Vaughn Adams <vaughn@cbis.ece.drexel.edu>
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Subject: Re: How to unsuscribe
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> Can someone please post a message explaining how to unsuscribe from the NEW
> NIH-Image mailing list. Thanks!

 
Unsubscribe
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                Subject: unsubscribe
 
 
Unsubscribe to Digest
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-- 
Vaughn Adams
Drexel University 
Electrical and Computer Engineering      Voice: 215-895-1979
32nd and Chestnut Streets                  FAX: 215-895-1695
Philadelphia, Pa 19104                   Email: vaughn@coe.drexel.edu

PGP key available - finger -l vaughn@cbis.ece.drexel.edu

From nih-image-request@io.ece.drexel.edu Thu Jul  9 08:01 EDT 1998
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Subject: Window position
Date: Thu, 9 Jul 1998 07:52:41 -0400
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Is there a way to get the position of a window from within a macro? I 
would like to be able to get and store the location of a window, so I can 
position another window in the same locaiton (using the MoveWindow() 
command). Can this be done?

Thanks.

Brett Helbig
Systems Engineer
GORCA Technologies, Inc.
bhelbig@gorca.com

From nih-image-request@io.ece.drexel.edu Thu Jul  9 12:41 EDT 1998
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With the changeover of the Image List host, I now get an unwanted permanent
mailbox created in Eudora each time I receive the NIH Image Digest.
Manually discarding these mailboxes each time is a drag.  I'm using a Mac
9500, System 8.0 and Eudora 4.0 with an existing mailbox set to receive NIH
Image transmissions.  Any suggestions?

_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Jon Goerke, MD                     EMail: goerke@itsa.ucsf.edu
Prof. Physiology, Univ. Calif.     Phone: 415-476-3252
3333 California St., Suite 150,    San Francisco, CA 94118
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From nih-image-request@io.ece.drexel.edu Thu Jul  9 15:34 EDT 1998
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Date: Thu, 09 Jul 1998 12:26:13 -0800
From: Glen MacDonald <glenmac@u.washington.edu>
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Karen,Try 'Restore Selection' if working manually.  In a macro,  use 'RestoreROI' then make the second measurement.



> Subject: Perimeter and area measurement
> Date: Tue, 7 Jul 1998 10:46:40 -0400 (EDT)
> From: Karen Rethoret <rethoret@yorku.ca>
> To: nih-image@io.ece.drexel.edu
>
> Hi,
>
> We are using NIH-Image for PC, and are currently doing freehand line
> drawing around cell structures in LM and would like to measure the
> perimeter in segments, the total perimeter and enclosed area all in one
> continuous operation.
>
> At the moment, we are using the Freehand/segmented line selection to make
> measurements of the segments and then redrawing the perimeter using the
> Freehand Region Tool to get the total perimeter and area measurements.
>
> Is it possible to avoid redrawing the area a second time?
>
> Thanks,
>
> Karen Rethoret
> York University, Toronto
>
> -------------------------------------

   -- Glen MacDonald
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA  98195-7923
glenmac@u.washington.edu
(206) 616-4156
(206) 616-1828 fax
The box said "Requires Windows95 or better". So I bought a Macintosh.

From nih-image-request@io.ece.drexel.edu Thu Jul  9 20:58 EDT 1998
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From: GJOSS@rna.bio.mq.edu.au
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To: nih-image@io.ece.drexel.edu
Date:          Fri, 10 Jul 1998 10:47:27 GMT+1000
Subject:       Re: Window position
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>Date: Thu, 9 Jul 1998 07:52:41 -0400
>
>Is there a way to get the position of a window from within a macro? I 
>would like to be able to get and store the location of a window, so I can 
>position another window in the same locaiton (using the MoveWindow() 
>command). Can this be done?
>
>Thanks.
>
>Brett Helbig
>Systems Engineer
>GORCA Technologies, Inc.
>bhelbig@gorca.com

Brett, 
procedure allignWindows(w1,w2); {alligns window w1 with w2}
	{would return TLcorner coords via x0,y0}
if x0,y0 declaration was made globably or in calling procedure.
to test, create any two windows and position;
 then invoke either by pulldown Special menu or <command><0>.
 (It is not sensitive to mouse use :-)
macro'/0test' uses picNumber but in practice pidNumber would be used.

procedure allignWindows(w1,w2);  {alligns window w1 with w2}
	{would return TLcorner coords via x0,y0}
  var x0,y0,x1,y1,x2,y2:integer;begin
  x0:=84;y0:=40;
  selectPic(w1);
  moveWindow(x0,y0);
  repeat begin
    choosePic(w1);getMouse(x1,y1);
    choosePic(w2);getMouse(x2,y2);
    showMessage(x0,y0,'\',x1,y1,'\',x2,y2,'\',x2-x1,y2-y1);
    selectPic(w1);
    x0:=x0-(x2-x1);y0:=y0-(y2-y1);
    moveWindow(x0,y0);
    end until (x1=x2) and (y1=y2);
  showMessage('corner at\',x0,y0);
  end

macro'/0test';begin allignWindows(1,2);end

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

From nih-image-request@io.ece.drexel.edu Tue Jul 14 12:13 EDT 1998
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Dear listowners,

For several days there a complete silence on the NIH-list.No discussions
, no e-mails where recieved.Whats going on.
I redescribed so that's not the reason I presume.

best wishes of a NIH-list member




-- 
BIOMET
P.M.Houpt -123 Timorstraat.
2585 SE The Hague,The Netherlands.
voice/fax.: 0031703504466

From nih-image-request@io.ece.drexel.edu Tue Jul 14 13:08 EDT 1998
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Date: Tue, 14 Jul 1998 10:59:41 -0600
From: "Michael J. Herron" <herro001@maroon.tc.umn.edu>
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Organization: U of MN
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I got your message...perhaps everyone is on vacation?

How many folk were lost in the transistion to the new list?

Pieter Houpt wrote:
> 
> Dear listowners,
> 
> For several days there a complete silence on the NIH-list.No discussions
> , no e-mails where recieved.Whats going on.
> I redescribed so that's not the reason I presume.
> 
> best wishes of a NIH-list member
> 
> --
> BIOMET
> P.M.Houpt -123 Timorstraat.
> 2585 SE The Hague,The Netherlands.
> voice/fax.: 0031703504466

-- 

     ________________________________________________________
    / Michael J. Herron,  U of MN, Dept. of Dermatology     /
   / herro001@maroon.tc.umn.edu                            /
  / 612-625-8935  Box 98  UMHC, Mpls MN 55455             /
 / http://RASH.med.umn.edu/                              /
/_______________________________________________________/

From nih-image-request@io.ece.drexel.edu Tue Jul 14 13:42 EDT 1998
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archive/latest/12


From nih-image-request@io.ece.drexel.edu Tue Jul 14 13:43 EDT 1998
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ls latest


From nih-image-request@io.ece.drexel.edu Tue Jul 14 13:52 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: mdparadi@MIT.EDU (Marc d. Paradis)
Subject: Irony
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>How many folk were lost in the transistion to the new list?

Isn't this a little like asking everyone not present to raise their hands?  :-)



                Marc d. Paradis
                Dept of Brain & Cognitive Sciences
                M.I.T.

BTW - this is in no way meant as a flame to Michael J. Herron, I am sure
the list administrators have an exact number to his question, but it just
struck me as a little humor which I thouhgt that I would share while the
list is relatively devoid of active content. -MdP


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I am looking for a new or used frame grabber card for use in
a Power Mac 7100/80.  The Scion LG3 would be my preference,
but the AG-5 is also an option.  Other cards may also be
considered.  If you have a spec sheet or web URL that would
help.  Please reply (including price) to (e-mail preferred)
:
Alan J. Townsend, Ph.D., Biochemistry Department, Wake
Forest University School of Medicine, Medical Center Blvd.,
Winston-Salem, N.C.  27157, Phone (336)-716-7658, FAX
(336)-716-7671, E-Mail : atown@wfubmc.edu

From nih-image-d-request@io.ece.drexel.edu Wed Jul 15 06:12 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #10
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 10

Today's Topics:
  silence                               [ Pieter Houpt <houpt@wxs.nl> ]
  Re: silence                           [ "Michael J. Herron" <herro001@maroo ]
  archive                               [ hmthomas@med.cornell.edu (Henry M.  ]
  archive                               [ hmthomas@med.cornell.edu (Henry M.  ]
  Irony                                 [ mdparadi@MIT.EDU (Marc d. Paradis) ]
  NuBus frame grabber wanted            [ "Alan Townsend" <atown@medcenter.wp ]

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

Date: Tue, 14 Jul 1998 18:02:27 +0100
From: Pieter Houpt <houpt@wxs.nl>
To: nih-image@io.ece.drexel.edu
Subject: silence
Message-ID: <35AB8F21.7F51@wxs.nl>
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Dear listowners,

For several days there a complete silence on the NIH-list.No discussions
, no e-mails where recieved.Whats going on.
I redescribed so that's not the reason I presume.

best wishes of a NIH-list member




-- 
BIOMET
P.M.Houpt -123 Timorstraat.
2585 SE The Hague,The Netherlands.
voice/fax.: 0031703504466

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

Date: Tue, 14 Jul 1998 10:59:41 -0600
From: "Michael J. Herron" <herro001@maroon.tc.umn.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: silence
Message-ID: <35AB8E70.3D61@maroon.tc.umn.edu>
Content-Type: text/plain; charset=us-ascii
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I got your message...perhaps everyone is on vacation?

How many folk were lost in the transistion to the new list?

Pieter Houpt wrote:
> 
> Dear listowners,
> 
> For several days there a complete silence on the NIH-list.No discussions
> , no e-mails where recieved.Whats going on.
> I redescribed so that's not the reason I presume.
> 
> best wishes of a NIH-list member
> 
> --
> BIOMET
> P.M.Houpt -123 Timorstraat.
> 2585 SE The Hague,The Netherlands.
> voice/fax.: 0031703504466

-- 

     ________________________________________________________
    / Michael J. Herron,  U of MN, Dept. of Dermatology     /
   / herro001@maroon.tc.umn.edu                            /
  / 612-625-8935  Box 98  UMHC, Mpls MN 55455             /
 / http://RASH.med.umn.edu/                              /
/_______________________________________________________/

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

Date: Tue, 14 Jul 1998 13:34:24 -0400
From: hmthomas@med.cornell.edu (Henry M. Thomas)
To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center)
Subject: archive
Message-Id: <v01540b01b1d10e66c301@[206.152.160.68]>
Content-Type: text/plain; charset="us-ascii"

archive/latest/12

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

Date: Tue, 14 Jul 1998 13:35:50 -0400
From: hmthomas@med.cornell.edu (Henry M. Thomas)
To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center)
Subject: archive
Message-Id: <v01540b02b1d10ec8da07@[206.152.160.68]>
Content-Type: text/plain; charset="us-ascii"

ls latest

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

Date: Tue, 14 Jul 1998 13:50:29 -0400
From: mdparadi@MIT.EDU (Marc d. Paradis)
To: nih-image@io.ece.drexel.edu
Subject: Irony
Message-Id: <v02140b02b1d14a216fe5@[18.42.1.20]>
Content-Type: text/plain; charset="us-ascii"

>How many folk were lost in the transistion to the new list?

Isn't this a little like asking everyone not present to raise their hands?  :-)



                Marc d. Paradis
                Dept of Brain & Cognitive Sciences
                M.I.T.

BTW - this is in no way meant as a flame to Michael J. Herron, I am sure
the list administrators have an exact number to his question, but it just
struck me as a little humor which I thouhgt that I would share while the
list is relatively devoid of active content. -MdP

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

Date: Tue, 14 Jul 1998 14:49:56 -0500
From: "Alan Townsend" <atown@medcenter.wpmail.wfu.edu>
To: nih-image@io.ece.drexel.edu
Subject: NuBus frame grabber wanted
Message-Id: <s5ab6c46.040@medcenter.wpmail.wfu.edu>

I am looking for a new or used frame grabber card for use in
a Power Mac 7100/80.  The Scion LG3 would be my preference,
but the AG-5 is also an option.  Other cards may also be
considered.  If you have a spec sheet or web URL that would
help.  Please reply (including price) to (e-mail preferred)
:
Alan J. Townsend, Ph.D., Biochemistry Department, Wake
Forest University School of Medicine, Medical Center Blvd.,
Winston-Salem, N.C.  27157, Phone (336)-716-7658, FAX
(336)-716-7671, E-Mail : atown@wfubmc.edu

--------------------------------
End of nih-image-d Digest V98 Issue #10
***************************************

From nih-image-request@io.ece.drexel.edu Wed Jul 15 07:21 EDT 1998
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Hello,

Can I use your NIH-image on Power Macintosh G3 series.





 

  $BJ!0fBg3X!!!!9)3XIt!!!!:`NA2=3X2J!!!!9bJ,;R2C9)3X9V:B(J
 
$B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!2#ED!!!!OB8w(J (Kazumitsu Yokota)
   E-mail  yokota@rheo.matse.fukui-u.ac.jp

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>Can I use your NIH-image on Power Macintosh G3 series.

Yes.



Carl Gustafson
(215) 895-1383
===============================================================================
           the Computer Vision Center for Vertebrate Brain Mapping
===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I'd like to give you my opinion
===============================================================================


From nih-image-request@io.ece.drexel.edu Wed Jul 15 07:57 EDT 1998
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An NIH Director's Wednesday Afternoon Lecture Series Event
Sponsor: NIH Inter-Institute Mitochondria Interest Group (MIG)

A Day-long Minisymposium 
Mitochondria: Genetics, Health, and Disease
2 December 1998
Featuring
The Wednesday Afternoon Lecture
by
Dr. Eric A. Schon (Columbia)
Molecular Genetics of Human Mitochondrial Disease




Jack Masur Auditorium, Clinical Center, NIH
For special accommodation needs call 301-594-5595
CME credit awarded 
MITOCHONDRIA: GENETICS, HEALTH, AND DISEASE
MINISYMPOSIUM 2 DECEMBER 1998

Lectures Venue: Masur Auditorium, Clinical Center, NIH
Poster/Exhibitor Venue: Visitor Information Center, Clinical Center, NIH

* 0745 Registration, Poster Set-up, Continental Breakfast in Exhibit Area
* 0830 Dr. David A. Clayton (HHMI): Mitochondrial DNA Control Features
* 0905 Dr. William C. Copeland (NIEHS): Avoidance of Mitochondrial DNA Mutations by DNA Polymerase Gamma
* 0940 Dr. Vilhelm A. Bohr (NIA): Oxidative DNA Damage Repair in Mammalian Mitochondria
* 1015 Poster Session/Coffee Break in Product Exhibit Area
* 1045 Dr. Tracey Rouault (NICHD): Abnormalities of Mitochondrial Iron Metabolism and Human Disease
* 1120 Dr. Steven J. Zullo (NIMH): In situ Localization of the common Human 4977bp Mitochondrial DNA Deletion Mutation
* 1200 Lunch Break
* 1330 Dr. Mariana Gerschenson (NCI): Mitochondrial Genotoxic and Functional Consequences of Chemotherapeutic Drugs
* 1400 Poster Session/Coffee Break in Product Exhibit Area
* 1500 Wednesday Afternoon Lecture: Dr. Eric A. Schon (Columbia):Molecular Genetics of Human Mitochondrial Disease
* 1600 Reception/Poster Session in Product Exhibit Area
* 1700 Poster Session/Product Exhibition Closes

Continental Breakfast, Coffee Breaks, Lunch Break, and Reception sponsored by the
Technical Sales Association
Attendance/Poster Registration Form
Mitochondria: Genetics, Health, and Disease
Wednesday Afternoon Lecture Series Minisymposium
2 December 1998
Masur Auditorium and Visitor Information Center
Clinical Center (Building 10), NIH
Bethesda, MD

Note: There is no registration fee to attend this minisymposium!
Name:
Title:
Affiliation:
Address:
State:
Country:
Postal Code:
Telephone:
Fax:
E-mail:
Web Page URL:
I will attend and present a poster                I will attend but not present a poster________     Poster Title:
Abstract (Abstract Booklet available at the meeting):











Do you need special accommodations while at NIH?______________
For a map of NIH and area, please check the following Web Site: http://www.nih.gov/welcome/maps.html WARNING: Parking is limited on campus, plan to use METRO!
A block of rooms at a special meeting rate has been reserved at The Bethesda Ramada. Call 800-272-6232, or 301-654-2703, before 9 November 1998.  Mention NIH Minisymposium, group # 6210.  For other accommodations in the area, please check the following Web Site: http://www.patsys.com/ftd/city.cgi?pcityid=2521&pcity=Bethesda
Submit advanced registration via Minisymposium web site at http://www-lecb.ncifcrf.gov/~zullo/migDB/symposium.html
or via e-mail to: zullo@helix.nih.gov deadline by e-mail is 8 November 1998 
or via regular mail to: 	Steven J. Zullo, PhD	 postmark deadline is 2 November 1998
			Building 10, Room 2D54
			NIH
			Bethesda, MD 20892

Steven J. Zullo, PhD
Laboratory of Biochemical Genetics
NIMH-NIH; Bldg. 10, Rm. 2D56; 9000 Rockville Pike
Bethesda, MD 20892
301-435-3576; FAX 301-480-9862
zullo@helix.nih.gov
Mitochondria Interest Group Web Page: http://www-lecb.ncifcrf.gov/~zullo/migDB/


From nih-image-request@io.ece.drexel.edu Wed Jul 15 10:39 EDT 1998
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At 08:24 PM 7/15/98 +0900, you wrote:
>Hello,
>
>Can I use your NIH-image on Power Macintosh G3 series.

You can but the "Start Capturing" command does not support the G3's
built-in video digitizer. You can, however, use the Plugin Digitizer
available at "ftp://codon.nih.gov/pub/nih-image/plug-ins/". I have
attempted, without much success, to fix this problem.

Also, NIH Image does not correctly support Scion frame grabbers on G3 Macs.
You need to use Scion's version of the program. This problem will be fixed
in the next NIH Image beta.

-wayne

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Dear List Members,

I have a PowerMac with a built-in frame grabber (low quality). Recently, I installed a Scion frame grabber. Now I cannot seem to access the built-in frame grabber from NIH-Image. Is there a way to do this, or must I ununstall the Scion board?

Mike Smith



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Dear List Members,

I have a PowerMac with a built-in frame grabber (low quality). Recently, I installed a Scion frame grabber. Now I cannot seem to access the built-in frame grabber from NIH-Image. Is there a way to do this, or must I ununstall the Scion board?

Mike Smith



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Subject: nih-image-d Digest V98 #11

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Dear List Members,

I have a PowerMac with a built-in frame grabber (low quality). Recently, I installed a Scion frame grabber. Now I cannot seem to access the built-in frame grabber from NIH-Image. Is there a way to do this, or must I ununstall the Scion board?

Mike Smith



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

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nih-image-d Digest				Volume 98 : Issue 11

Today's Topics:
  Question                              [ yokota@rheo.matse.fukui-u.ac.jp (=? ]
  Re: Question                          [ Carl Gustafson <carl.gustafson@cbis ]
  Please distribute: Call for POSTERS   [ Steve Zullo <zullo@helix.nih.gov> ]
  Re: Question                          [ Wayne Rasband <wayne@codon.nih.gov> ]
  Mac built-in frame grabber            [ "Mike Smith" <MISMITH@brody.med.ecu ]

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

Date: Wed, 15 Jul 1998 20:24:28 +0900
From: yokota@rheo.matse.fukui-u.ac.jp (=?ISO-2022-JP?B?GyRCMiNFRCEhT0I4dxsoSg==?= )
To: nih-image@io.ece.drexel.edu
Subject: Question
Message-Id: <9807151124.AA00061@pp1.rheo.matse.fukui-u.ac.jp>
Content-Type: text/plain; charset=iso-2022-jp

Hello,

Can I use your NIH-image on Power Macintosh G3 series.





 

  $BJ!0fBg3X!!!!9)3XIt!!!!:`NA2=3X2J!!!!9bJ,;R2C9)3X9V:B(J
 
$B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!2#ED!!!!OB8w(J (Kazumitsu Yokota)
   E-mail  yokota@rheo.matse.fukui-u.ac.jp

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

Date: Wed, 15 Jul 1998 07:48:23 -0400
From: Carl Gustafson <carl.gustafson@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Question
Message-Id: <v03110705b1d24776e6a0@[144.118.33.205]>
Content-Type: text/plain; charset="us-ascii"

>Can I use your NIH-image on Power Macintosh G3 series.

Yes.



Carl Gustafson
(215) 895-1383
===============================================================================
           the Computer Vision Center for Vertebrate Brain Mapping
===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I'd like to give you my opinion
===============================================================================

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

Date: Wed, 15 Jul 1998 07:47:58 -0400
From: Steve Zullo <zullo@helix.nih.gov>
To: "nih-image@io.ece.drexel.edu" <nih-image@io.ece.drexel.edu>
Subject: Please distribute: Call for POSTERS and/or ATTENDANCE
Message-ID: <01BDAFC4.E2FD8C00@STEVE-Z>
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An NIH Director's Wednesday Afternoon Lecture Series Event
Sponsor: NIH Inter-Institute Mitochondria Interest Group (MIG)

A Day-long Minisymposium 
Mitochondria: Genetics, Health, and Disease
2 December 1998
Featuring
The Wednesday Afternoon Lecture
by
Dr. Eric A. Schon (Columbia)
Molecular Genetics of Human Mitochondrial Disease




Jack Masur Auditorium, Clinical Center, NIH
For special accommodation needs call 301-594-5595
CME credit awarded 
MITOCHONDRIA: GENETICS, HEALTH, AND DISEASE
MINISYMPOSIUM 2 DECEMBER 1998

Lectures Venue: Masur Auditorium, Clinical Center, NIH
Poster/Exhibitor Venue: Visitor Information Center, Clinical Center, NIH

* 0745 Registration, Poster Set-up, Continental Breakfast in Exhibit Area
* 0830 Dr. David A. Clayton (HHMI): Mitochondrial DNA Control Features
* 0905 Dr. William C. Copeland (NIEHS): Avoidance of Mitochondrial DNA Mutations by DNA Polymerase Gamma
* 0940 Dr. Vilhelm A. Bohr (NIA): Oxidative DNA Damage Repair in Mammalian Mitochondria
* 1015 Poster Session/Coffee Break in Product Exhibit Area
* 1045 Dr. Tracey Rouault (NICHD): Abnormalities of Mitochondrial Iron Metabolism and Human Disease
* 1120 Dr. Steven J. Zullo (NIMH): In situ Localization of the common Human 4977bp Mitochondrial DNA Deletion Mutation
* 1200 Lunch Break
* 1330 Dr. Mariana Gerschenson (NCI): Mitochondrial Genotoxic and Functional Consequences of Chemotherapeutic Drugs
* 1400 Poster Session/Coffee Break in Product Exhibit Area
* 1500 Wednesday Afternoon Lecture: Dr. Eric A. Schon (Columbia):Molecular Genetics of Human Mitochondrial Disease
* 1600 Reception/Poster Session in Product Exhibit Area
* 1700 Poster Session/Product Exhibition Closes

Continental Breakfast, Coffee Breaks, Lunch Break, and Reception sponsored by the
Technical Sales Association
Attendance/Poster Registration Form
Mitochondria: Genetics, Health, and Disease
Wednesday Afternoon Lecture Series Minisymposium
2 December 1998
Masur Auditorium and Visitor Information Center
Clinical Center (Building 10), NIH
Bethesda, MD

Note: There is no registration fee to attend this minisymposium!
Name:
Title:
Affiliation:
Address:
State:
Country:
Postal Code:
Telephone:
Fax:
E-mail:
Web Page URL:
I will attend and present a poster                I will attend but not present a poster________     Poster Title:
Abstract (Abstract Booklet available at the meeting):











Do you need special accommodations while at NIH?______________
For a map of NIH and area, please check the following Web Site: http://www.nih.gov/welcome/maps.html WARNING: Parking is limited on campus, plan to use METRO!
A block of rooms at a special meeting rate has been reserved at The Bethesda Ramada. Call 800-272-6232, or 301-654-2703, before 9 November 1998.  Mention NIH Minisymposium, group # 6210.  For other accommodations in the area, please check the following Web Site: http://www.patsys.com/ftd/city.cgi?pcityid=2521&pcity=Bethesda
Submit advanced registration via Minisymposium web site at http://www-lecb.ncifcrf.gov/~zullo/migDB/symposium.html
or via e-mail to: zullo@helix.nih.gov deadline by e-mail is 8 November 1998 
or via regular mail to: 	Steven J. Zullo, PhD	 postmark deadline is 2 November 1998
			Building 10, Room 2D54
			NIH
			Bethesda, MD 20892

Steven J. Zullo, PhD
Laboratory of Biochemical Genetics
NIMH-NIH; Bldg. 10, Rm. 2D56; 9000 Rockville Pike
Bethesda, MD 20892
301-435-3576; FAX 301-480-9862
zullo@helix.nih.gov
Mitochondria Interest Group Web Page: http://www-lecb.ncifcrf.gov/~zullo/migDB/

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

Date: Wed, 15 Jul 1998 10:28:04 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Question
Message-Id: <3.0.5.32.19980715102804.0079d890@codon.nih.gov>
Content-Type: text/plain; charset="us-ascii"

At 08:24 PM 7/15/98 +0900, you wrote:
>Hello,
>
>Can I use your NIH-image on Power Macintosh G3 series.

You can but the "Start Capturing" command does not support the G3's
built-in video digitizer. You can, however, use the Plugin Digitizer
available at "ftp://codon.nih.gov/pub/nih-image/plug-ins/". I have
attempted, without much success, to fix this problem.

Also, NIH Image does not correctly support Scion frame grabbers on G3 Macs.
You need to use Scion's version of the program. This problem will be fixed
in the next NIH Image beta.

-wayne

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

Date: Wed, 15 Jul 1998 14:59:25 -0400
From: "Mike Smith" <MISMITH@brody.med.ecu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Mac built-in frame grabber
Message-Id: <s5acc3ee.098@brody.med.ecu.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline
Content-Transfer-Encoding: 8bit

Dear List Members,

I have a PowerMac with a built-in frame grabber (low quality). Recently, I installed a Scion frame grabber. Now I cannot seem to access the built-in frame grabber from NIH-Image. Is there a way to do this, or must I ununstall the Scion board?

Mike Smith

--------------------------------
End of nih-image-d Digest V98 Issue #11
***************************************

From nih-image-request@io.ece.drexel.edu Thu Jul 16 06:25 EDT 1998
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Hi,

How can I cancel my subscription to this list ?

thanks,

Tom Vanzieleghem


From nih-image-request@io.ece.drexel.edu Thu Jul 16 09:16 EDT 1998
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From: Paul Human <ctshuman@samiot.uct.ac.za>
Subject: Apple and NIH or Leica and QWin?
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Dear Imager

We run an exclusive Apple Mac network and use NIH-Image (and some of the
spin-off programmes) regularly. Before we chanced upon NIH though, we
purchased an Image Analyser (together with a Fluorescence microscope) from
Leica. The PC unit (a 486 but, due to problems, upgraded with a Pentium
processor only) with its frame grabber (Elvis, 16 bit) has given us more
problems than we care to mention. It has been shipped to the UK twice and
is now currently with the local agents in another city.

To cut a long story short, the agents are offering us a new Pentium II 166
MX with Matrox framegrabber (32 bit) and latest QWin Pro software (includes
QWin gallery) at a price tag of R20,000 (about $3,225).

One of the biggest problems we had with the old system was to get it
networked, with the local agent stating emphatically that we could not
network.  The Pentium on offer will apparantly network, but we would need
to buy the ethernet card as an extra.

My feeling is that we should rather buy a decent framegrabber for the Apple
Mac (am I right in thinking that one could get a similar card to the Matrox
card at around $3,000?). The camera we use (JVC colour) gives S-video and
composite output . We could then use NIH-Image (which I think in many
respects is better than QWin). Networking also would be problem free.

I would appreciate any suggestions in this regard, but basically we seem to
be spending an endless amount of money on a system which is more out of
order than in order.

Specifically, I would appreciate advice on which framegrabber card would be
suitable for hires colour grabbing on the Mac.

Thakns in advance.

____________________________________________________________________
PAUL A HUMAN, M.Sc.
Deputy Director
Cardiovascular Research Unit
University of Cape Town Medical School
OBSERVATORY 7925, Cape Town, South Africa
Voice:+27-21-406 6418  Fax:+27-21-448 5935  Cell:+27-82-770 3612


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Subject: Re: nih-image-d Digest V98 #11
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Tom:

> How can I cancel my subscription to this list ?

Sure.  Just send a message to nih-image-request@biomed.drexel.edu with
Unsubscribe in the Subject.

-- 
Vaughn Adams
Drexel University 
Electrical and Computer Engineering      Voice: 215-895-1979
32nd and Chestnut Streets                  FAX: 215-895-1695
Philadelphia, Pa 19104                   Email: vaughn@coe.drexel.edu

PGP key available - finger -l vaughn@cbis.ece.drexel.edu

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From: SolamereTG@aol.com
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Date: Thu, 16 Jul 1998 11:53:11 EDT
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Dear Dr. Human:

I can recommend the CG-7 board from Scion ($2195). This board has RGB inputs,
or can be used for monochrome. It has a serial/digital I/O to control
peripheral equipment, 2 DAC channels out, and both standard 640x480 capture
and high res capture mode that interpolates the pixels to provide 1280 x 960
pixel image. The board can be used in any PCI platform and comes with the
Scion version of NIH for both Mac OS and Windows 95. 

Another choice would be an ITI IC PCI board with AM DIG-16 for digital cameras
$2300. QED writes software that can take a digital cameras input into ADOBE
photoshop, or NIH image, and archiving software.

I agree NIH image is more flexible than most commercial software available on
the PC or Mac. A major problem is that most commercial vendors rarely mention
it as your best option either because they aren't familiar with it or can't
sell it. Please feel free to contact me if you have questions about the
boards.

Dr. George A. Peeters
Solamere Technology Group
Salt Lake City UT 84103
Solameretg@aol.com
801 322-2645

From nih-image-request@io.ece.drexel.edu Thu Jul 16 17:29 EDT 1998
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Date: Thu, 16 Jul 1998 17:16:30 -0400
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I use ImagePC to analyze electrophoretic gel density. After I measure
the areas with the wand tool.How can I use text tool to label
measurement result on the peak? I use Macintosh computer befor, in Maci
I can use opton button. But, how can I use it in PC systen? 
Thank you for your help.

Pei-Chin Hsieh

From nih-image-request@io.ece.drexel.edu Fri Jul 17 00:12 EDT 1998
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Even though I personally prefer PC's, since your network is exclusively Mac, and
you are obviously more comfortable with Macs, I would recomend putting a decent
frame grabber in a Mac and scrap the PC...  Since your camera only outputs
S-video and composite (NTSC I assume), you can probably get a good frame grabber
for less than $1500 US, unless you are planning to upgrade to a RGB camera some
time in the next few years.  As George Peters mentioned, the Scion boards are a
good choice for use with NIH-Image.  

Chris Tully

Paul Human wrote:
> 
> Dear Imager
> 
> We run an exclusive Apple Mac network and use NIH-Image (and some of the
> spin-off programmes) regularly. Before we chanced upon NIH though, we
> purchased an Image Analyser (together with a Fluorescence microscope) from
> Leica. The PC unit (a 486 but, due to problems, upgraded with a Pentium
> processor only) with its frame grabber (Elvis, 16 bit) has given us more
> problems than we care to mention. It has been shipped to the UK twice and
> is now currently with the local agents in another city.
> 
> To cut a long story short, the agents are offering us a new Pentium II 166
> MX with Matrox framegrabber (32 bit) and latest QWin Pro software (includes
> QWin gallery) at a price tag of R20,000 (about $3,225).
> 
> One of the biggest problems we had with the old system was to get it
> networked, with the local agent stating emphatically that we could not
> network.  The Pentium on offer will apparantly network, but we would need
> to buy the ethernet card as an extra.
> 
> My feeling is that we should rather buy a decent framegrabber for the Apple
> Mac (am I right in thinking that one could get a similar card to the Matrox
> card at around $3,000?). The camera we use (JVC colour) gives S-video and
> composite output . We could then use NIH-Image (which I think in many
> respects is better than QWin). Networking also would be problem free.
> 
> I would appreciate any suggestions in this regard, but basically we seem to
> be spending an endless amount of money on a system which is more out of
> order than in order.
> 
> Specifically, I would appreciate advice on which framegrabber card would be
> suitable for hires colour grabbing on the Mac.
> 
> Thakns in advance.
> 
> ____________________________________________________________________
> PAUL A HUMAN, M.Sc.
> Deputy Director
> Cardiovascular Research Unit
> University of Cape Town Medical School
> OBSERVATORY 7925, Cape Town, South Africa
> Voice:+27-21-406 6418  Fax:+27-21-448 5935  Cell:+27-82-770 3612

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From: nih-image-d-request@io.ece.drexel.edu
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 12

Today's Topics:
  Re: nih-image-d Digest V98 #11        [ Tom Vanzieleghem <Tom.Vanzieleghem@ ]
  Apple and NIH or Leica and QWin?      [ Paul Human <ctshuman@samiot.uct.ac. ]
  Re: nih-image-d Digest V98 #11        [ Vaughn Adams <vaughn@cbis.ece.drexe ]
  Re: Apple and NIH or Leica and QWin?  [ SolamereTG@aol.com ]
  Opton-click with text tool in PC?     [ Pei-Chen Hsieh <ph43@cornell.edu> ]
  Re: Apple and NIH or Leica and QWin?  [ "Christopher P. Tully" <cptully@sis ]

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

Date: Thu, 16 Jul 1998 12:23:03 +0200
From: Tom Vanzieleghem <Tom.Vanzieleghem@elis.rug.ac.be>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #11
Message-ID: <35ADD486.E0B71177@elis.rug.ac.be>
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Hi,

How can I cancel my subscription to this list ?

thanks,

Tom Vanzieleghem

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

Date: Thu, 16 Jul 1998 15:05:56 +0200
From: Paul Human <ctshuman@samiot.uct.ac.za>
To: NIH-Image Mailing List <nih-image@io.ece.drexel.edu>
Subject: Apple and NIH or Leica and QWin?
Message-Id: <l03130301b1d3a58116b6@[196.30.99.11]>
Content-Type: text/plain; charset="us-ascii"

Dear Imager

We run an exclusive Apple Mac network and use NIH-Image (and some of the
spin-off programmes) regularly. Before we chanced upon NIH though, we
purchased an Image Analyser (together with a Fluorescence microscope) from
Leica. The PC unit (a 486 but, due to problems, upgraded with a Pentium
processor only) with its frame grabber (Elvis, 16 bit) has given us more
problems than we care to mention. It has been shipped to the UK twice and
is now currently with the local agents in another city.

To cut a long story short, the agents are offering us a new Pentium II 166
MX with Matrox framegrabber (32 bit) and latest QWin Pro software (includes
QWin gallery) at a price tag of R20,000 (about $3,225).

One of the biggest problems we had with the old system was to get it
networked, with the local agent stating emphatically that we could not
network.  The Pentium on offer will apparantly network, but we would need
to buy the ethernet card as an extra.

My feeling is that we should rather buy a decent framegrabber for the Apple
Mac (am I right in thinking that one could get a similar card to the Matrox
card at around $3,000?). The camera we use (JVC colour) gives S-video and
composite output . We could then use NIH-Image (which I think in many
respects is better than QWin). Networking also would be problem free.

I would appreciate any suggestions in this regard, but basically we seem to
be spending an endless amount of money on a system which is more out of
order than in order.

Specifically, I would appreciate advice on which framegrabber card would be
suitable for hires colour grabbing on the Mac.

Thakns in advance.

____________________________________________________________________
PAUL A HUMAN, M.Sc.
Deputy Director
Cardiovascular Research Unit
University of Cape Town Medical School
OBSERVATORY 7925, Cape Town, South Africa
Voice:+27-21-406 6418  Fax:+27-21-448 5935  Cell:+27-82-770 3612

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

Date: Thu, 16 Jul 1998 09:51:21 -0400 (EDT)
From: Vaughn Adams <vaughn@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #11
Message-Id: <199807161351.JAA28577@cbis.ece.drexel.edu>
Content-Type: text

Tom:

> How can I cancel my subscription to this list ?

Sure.  Just send a message to nih-image-request@biomed.drexel.edu with
Unsubscribe in the Subject.

-- 
Vaughn Adams
Drexel University 
Electrical and Computer Engineering      Voice: 215-895-1979
32nd and Chestnut Streets                  FAX: 215-895-1695
Philadelphia, Pa 19104                   Email: vaughn@coe.drexel.edu

PGP key available - finger -l vaughn@cbis.ece.drexel.edu

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

Date: Thu, 16 Jul 1998 11:53:11 EDT
From: SolamereTG@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re: Apple and NIH or Leica and QWin?
Message-ID: <e0854f9c.35ae21e8@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

Dear Dr. Human:

I can recommend the CG-7 board from Scion ($2195). This board has RGB inputs,
or can be used for monochrome. It has a serial/digital I/O to control
peripheral equipment, 2 DAC channels out, and both standard 640x480 capture
and high res capture mode that interpolates the pixels to provide 1280 x 960
pixel image. The board can be used in any PCI platform and comes with the
Scion version of NIH for both Mac OS and Windows 95. 

Another choice would be an ITI IC PCI board with AM DIG-16 for digital cameras
$2300. QED writes software that can take a digital cameras input into ADOBE
photoshop, or NIH image, and archiving software.

I agree NIH image is more flexible than most commercial software available on
the PC or Mac. A major problem is that most commercial vendors rarely mention
it as your best option either because they aren't familiar with it or can't
sell it. Please feel free to contact me if you have questions about the
boards.

Dr. George A. Peeters
Solamere Technology Group
Salt Lake City UT 84103
Solameretg@aol.com
801 322-2645

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

Date: Thu, 16 Jul 1998 17:16:30 -0400
From: Pei-Chen Hsieh <ph43@cornell.edu>
To: nih-image@io.ece.drexel.edu
Subject: Opton-click with text tool in PC?
Message-ID: <35AE6DAE.6B03@cornell.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

I use ImagePC to analyze electrophoretic gel density. After I measure
the areas with the wand tool.How can I use text tool to label
measurement result on the peak? I use Macintosh computer befor, in Maci
I can use opton button. But, how can I use it in PC systen? 
Thank you for your help.

Pei-Chin Hsieh

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

Date: Thu, 16 Jul 1998 22:08:47 -0600
From: "Christopher P. Tully" <cptully@sisna.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Apple and NIH or Leica and QWin?
Message-ID: <35AECE4F.3D6EF315@sisna.com>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Even though I personally prefer PC's, since your network is exclusively Mac, and
you are obviously more comfortable with Macs, I would recomend putting a decent
frame grabber in a Mac and scrap the PC...  Since your camera only outputs
S-video and composite (NTSC I assume), you can probably get a good frame grabber
for less than $1500 US, unless you are planning to upgrade to a RGB camera some
time in the next few years.  As George Peters mentioned, the Scion boards are a
good choice for use with NIH-Image.  

Chris Tully

Paul Human wrote:
> 
> Dear Imager
> 
> We run an exclusive Apple Mac network and use NIH-Image (and some of the
> spin-off programmes) regularly. Before we chanced upon NIH though, we
> purchased an Image Analyser (together with a Fluorescence microscope) from
> Leica. The PC unit (a 486 but, due to problems, upgraded with a Pentium
> processor only) with its frame grabber (Elvis, 16 bit) has given us more
> problems than we care to mention. It has been shipped to the UK twice and
> is now currently with the local agents in another city.
> 
> To cut a long story short, the agents are offering us a new Pentium II 166
> MX with Matrox framegrabber (32 bit) and latest QWin Pro software (includes
> QWin gallery) at a price tag of R20,000 (about $3,225).
> 
> One of the biggest problems we had with the old system was to get it
> networked, with the local agent stating emphatically that we could not
> network.  The Pentium on offer will apparantly network, but we would need
> to buy the ethernet card as an extra.
> 
> My feeling is that we should rather buy a decent framegrabber for the Apple
> Mac (am I right in thinking that one could get a similar card to the Matrox
> card at around $3,000?). The camera we use (JVC colour) gives S-video and
> composite output . We could then use NIH-Image (which I think in many
> respects is better than QWin). Networking also would be problem free.
> 
> I would appreciate any suggestions in this regard, but basically we seem to
> be spending an endless amount of money on a system which is more out of
> order than in order.
> 
> Specifically, I would appreciate advice on which framegrabber card would be
> suitable for hires colour grabbing on the Mac.
> 
> Thakns in advance.
> 
> ____________________________________________________________________
> PAUL A HUMAN, M.Sc.
> Deputy Director
> Cardiovascular Research Unit
> University of Cape Town Medical School
> OBSERVATORY 7925, Cape Town, South Africa
> Voice:+27-21-406 6418  Fax:+27-21-448 5935  Cell:+27-82-770 3612

--------------------------------
End of nih-image-d Digest V98 Issue #12
***************************************

From nih-image-request@io.ece.drexel.edu Fri Jul 17 09:27 EDT 1998
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Date: Fri, 17 Jul 1998 08:53:56 -0500
To: nih-image@io.ece.drexel.edu
From: Tom Morton <support@scioncorp.com>
Subject: Re: nih-image-d Digest V98 #12
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Hello,

In Beta 3 of Scion Image you need to hold the Scroll Lock key while
clicking with the Text Tool.

Tom

>
>I use ImagePC to analyze electrophoretic gel density. After I measure
>the areas with the wand tool.How can I use text tool to label
>measurement result on the peak? I use Macintosh computer befor, in Maci
>I can use opton button. But, how can I use it in PC systen?
>Thank you for your help.
>
>Pei-Chin Hsieh


-----------------------------------------------------------------------
Tom Morton                                     support@scioncorp.com
Technical Services                             http://www.scioncorp.com
Scion Corporation                              ftp://scioncorp.com
82 Wormans Mill Rd., Suite H                   Phone: (301) 695-7870
Frederick, MD 21701                            Fax:   (301) 695-0035
-----------------------------------------------------------------------


From nih-image-request@io.ece.drexel.edu Fri Jul 17 11:05 EDT 1998
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Date: Fri, 17 Jul 1998 07:47:32 -0700
To: nih-image@io.ece.drexel.edu, Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
From: Glenn Hammonds <rghammonds@earthlink.net>
Subject: Re: Digest form
Resent-Message-ID: <"ZjG6K2.0.Ms1.uLshr"@io>
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Johnathan et al,

After trying it for a while, I'm sorry to report that the new digest format
definitely is not working for me.

I'm using Eudora Pro 3.1.1, and I use filtering to sort mail.  With the new
digests I get a new mailbox for every issue which shows up at the top of
the mail heirarchy instead of in my intended location for NIH Image, and
the naming conventions are somehow messed up such that the name of the
mailbox is not the same as the name of the digest.  The result is a
confusing mess of nearly identical but incorrectly named misplaced
mailboxes, plus packaging.  Ouch!

My "solution" to date has been to dump all the contents of each digest back
into a single NIH Image mailbox, thus losing the digest character as well
as the appropriate "reply-to" address, then delete all those mailboxes,
attachments, original container messages, etc.  In the short run this is
(barely) OK, but in the long run, a single mailbox for individual messages
from the NIH Image list is impractical, and I'm tired of dealing with the
mess.

I would much prefer to go back to the older plain vanilla style of digest.
Could there be two styles of digest offered?

Best,

Glenn Hammonds


From nih-image-request@io.ece.drexel.edu Fri Jul 17 11:34 EDT 1998
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Date: Fri, 17 Jul 1998 10:31:46 -0500
From: "Jud Gurney, M.D." <jgurney@nfinity.com>
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Same for me. Eudora does not handle this digest version without making a new
mailbox each time. I had to unsubscribe and subscribe to the individual
messages.

Jud Gurney
Univ of NE

Glenn Hammonds wrote:

> Johnathan et al,
>
> After trying it for a while, I'm sorry to report that the new digest format
> definitely is not working for me.
>
> I'm using Eudora Pro 3.1.1, and I use filtering to sort mail.  With the new
> digests I get a new mailbox for every issue which shows up at the top of
> the mail heirarchy instead of in my intended location for NIH Image, and
> the naming conventions are somehow messed up such that the name of the
> mailbox is not the same as the name of the digest.  The result is a
> confusing mess of nearly identical but incorrectly named misplaced
> mailboxes, plus packaging.  Ouch!
>
> My "solution" to date has been to dump all the contents of each digest back
> into a single NIH Image mailbox, thus losing the digest character as well
> as the appropriate "reply-to" address, then delete all those mailboxes,
> attachments, original container messages, etc.  In the short run this is
> (barely) OK, but in the long run, a single mailbox for individual messages
> from the NIH Image list is impractical, and I'm tired of dealing with the
> mess.
>
> I would much prefer to go back to the older plain vanilla style of digest.
> Could there be two styles of digest offered?
>
> Best,
>
> Glenn Hammonds
>

From nih-image-request@io.ece.drexel.edu Fri Jul 17 11:35 EDT 1998
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Date: Fri, 17 Jul 1998 11:24:21 -0400
From: "Mike Smith" <MISMITH@brody.med.ecu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Mac built-in frame grabber -Reply
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Dear list Members,

I posted the enclosed question a few days ago.  Though no one replied, I managed to find the answer myself. If anyone else has the same problem, the answer is to hold down the SHIFT key when opening IMAGE. Doing so selects the internal frame grabber.

Mike Smith

>>> "Mike Smith" <MISMITH@brody.med.ecu.edu> 07/15 3:12 pm >>>
Dear List Members,

I have a PowerMac with a built-in frame grabber (low quality). Recently, I installed a Scion frame grabber. Now I cannot seem to access the built-in frame grabber from NIH-Image. Is there a way to do this, or must I ununstall the Scion board?

Mike Smith




From nih-image-request@io.ece.drexel.edu Fri Jul 17 17:36 EDT 1998
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Date: Fri, 17 Jul 1998 16:02:38 -0500
From: scidi <scidi@mci2000.com>
Subject: Re: NuBus frame grabber wanted
To: nih-image@io.ece.drexel.edu
Reply-to: scidi@mci2000.com
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To all on the list:

I have posted this before, but I will try again.  I am in need of a Nubus
VG-5 card or the combination of the LG-3 and TV-3 cards.  I would be
willing to either pay top dollar or to trade for a brand new VG-5 PCI card.
 This is needed ASAP!!!!

Please respond soon!!

Mark R. Molenda, Owner
Scientific Digital Imaging
1407 S 59th St.
Milwaukee, WI  53214

phone (414) 476-2694
fax (414) 645-8037
scidi@mci2000.com

----------
> From: Alan Townsend <atown@medcenter.wpmail.wfu.edu>
> To: nih-image@io.ece.drexel.edu
> Subject: NuBus frame grabber wanted
> Date: Tuesday, July 14, 1998 2:49 PM
> 
> I am looking for a new or used frame grabber card for use in
> a Power Mac 7100/80.  The Scion LG3 would be my preference,
> but the AG-5 is also an option.  Other cards may also be
> considered.  If you have a spec sheet or web URL that would
> help.  Please reply (including price) to (e-mail preferred)
> :
> Alan J. Townsend, Ph.D., Biochemistry Department, Wake
> Forest University School of Medicine, Medical Center Blvd.,
> Winston-Salem, N.C.  27157, Phone (336)-716-7658, FAX
> (336)-716-7671, E-Mail : atown@wfubmc.edu

From nih-image-d-request@io.ece.drexel.edu Sat Jul 18 06:06 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #13
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 13

Today's Topics:
  Re: nih-image-d Digest V98 #12        [ Tom Morton <support@scioncorp.com> ]
  Re: Digest form                       [ Glenn Hammonds <rghammonds@earthlin ]
  Re: Digest form                       [ "Jud Gurney, M.D." <jgurney@nfinity ]
  Mac built-in frame grabber -Reply     [ "Mike Smith" <MISMITH@brody.med.ecu ]
  Re: NuBus frame grabber wanted        [ scidi <scidi@mci2000.com> ]

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

Date: Fri, 17 Jul 1998 08:53:56 -0500
From: Tom Morton <support@scioncorp.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #12
Message-Id: <l03102803b1d50645849f@[10.0.0.239]>
Content-Type: text/plain; charset="us-ascii"

Hello,

In Beta 3 of Scion Image you need to hold the Scroll Lock key while
clicking with the Text Tool.

Tom

>
>I use ImagePC to analyze electrophoretic gel density. After I measure
>the areas with the wand tool.How can I use text tool to label
>measurement result on the peak? I use Macintosh computer befor, in Maci
>I can use opton button. But, how can I use it in PC systen?
>Thank you for your help.
>
>Pei-Chin Hsieh


-----------------------------------------------------------------------
Tom Morton                                     support@scioncorp.com
Technical Services                             http://www.scioncorp.com
Scion Corporation                              ftp://scioncorp.com
82 Wormans Mill Rd., Suite H                   Phone: (301) 695-7870
Frederick, MD 21701                            Fax:   (301) 695-0035
-----------------------------------------------------------------------

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

Date: Fri, 17 Jul 1998 07:47:32 -0700
From: Glenn Hammonds <rghammonds@earthlink.net>
To: nih-image@io.ece.drexel.edu, Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: Re: Digest form
Message-Id: <v03110701b1d11b4bc944@[192.168.0.2]>
Content-Type: text/plain; charset="us-ascii"

Johnathan et al,

After trying it for a while, I'm sorry to report that the new digest format
definitely is not working for me.

I'm using Eudora Pro 3.1.1, and I use filtering to sort mail.  With the new
digests I get a new mailbox for every issue which shows up at the top of
the mail heirarchy instead of in my intended location for NIH Image, and
the naming conventions are somehow messed up such that the name of the
mailbox is not the same as the name of the digest.  The result is a
confusing mess of nearly identical but incorrectly named misplaced
mailboxes, plus packaging.  Ouch!

My "solution" to date has been to dump all the contents of each digest back
into a single NIH Image mailbox, thus losing the digest character as well
as the appropriate "reply-to" address, then delete all those mailboxes,
attachments, original container messages, etc.  In the short run this is
(barely) OK, but in the long run, a single mailbox for individual messages
from the NIH Image list is impractical, and I'm tired of dealing with the
mess.

I would much prefer to go back to the older plain vanilla style of digest.
Could there be two styles of digest offered?

Best,

Glenn Hammonds

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

Date: Fri, 17 Jul 1998 10:31:46 -0500
From: "Jud Gurney, M.D." <jgurney@nfinity.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: Digest form
Message-ID: <35AF6E61.AA495F8C@nfinity.com>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Same for me. Eudora does not handle this digest version without making a new
mailbox each time. I had to unsubscribe and subscribe to the individual
messages.

Jud Gurney
Univ of NE

Glenn Hammonds wrote:

> Johnathan et al,
>
> After trying it for a while, I'm sorry to report that the new digest format
> definitely is not working for me.
>
> I'm using Eudora Pro 3.1.1, and I use filtering to sort mail.  With the new
> digests I get a new mailbox for every issue which shows up at the top of
> the mail heirarchy instead of in my intended location for NIH Image, and
> the naming conventions are somehow messed up such that the name of the
> mailbox is not the same as the name of the digest.  The result is a
> confusing mess of nearly identical but incorrectly named misplaced
> mailboxes, plus packaging.  Ouch!
>
> My "solution" to date has been to dump all the contents of each digest back
> into a single NIH Image mailbox, thus losing the digest character as well
> as the appropriate "reply-to" address, then delete all those mailboxes,
> attachments, original container messages, etc.  In the short run this is
> (barely) OK, but in the long run, a single mailbox for individual messages
> from the NIH Image list is impractical, and I'm tired of dealing with the
> mess.
>
> I would much prefer to go back to the older plain vanilla style of digest.
> Could there be two styles of digest offered?
>
> Best,
>
> Glenn Hammonds
>

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

Date: Fri, 17 Jul 1998 11:24:21 -0400
From: "Mike Smith" <MISMITH@brody.med.ecu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Mac built-in frame grabber -Reply
Message-Id: <s5af3474.051@brody.med.ecu.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline
Content-Transfer-Encoding: 8bit

Dear list Members,

I posted the enclosed question a few days ago.  Though no one replied, I managed to find the answer myself. If anyone else has the same problem, the answer is to hold down the SHIFT key when opening IMAGE. Doing so selects the internal frame grabber.

Mike Smith

>>> "Mike Smith" <MISMITH@brody.med.ecu.edu> 07/15 3:12 pm >>>
Dear List Members,

I have a PowerMac with a built-in frame grabber (low quality). Recently, I installed a Scion frame grabber. Now I cannot seem to access the built-in frame grabber from NIH-Image. Is there a way to do this, or must I ununstall the Scion board?

Mike Smith

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

Date: Fri, 17 Jul 1998 16:02:38 -0500
From: scidi <scidi@mci2000.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: NuBus frame grabber wanted
Message-id: <0EW900MEECXDKX@PM06SM.PMM.MCI.NET>
Content-type: text/plain; charset=ISO-8859-1
Content-transfer-encoding: 7bit

To all on the list:

I have posted this before, but I will try again.  I am in need of a Nubus
VG-5 card or the combination of the LG-3 and TV-3 cards.  I would be
willing to either pay top dollar or to trade for a brand new VG-5 PCI card.
 This is needed ASAP!!!!

Please respond soon!!

Mark R. Molenda, Owner
Scientific Digital Imaging
1407 S 59th St.
Milwaukee, WI  53214

phone (414) 476-2694
fax (414) 645-8037
scidi@mci2000.com

----------
> From: Alan Townsend <atown@medcenter.wpmail.wfu.edu>
> To: nih-image@io.ece.drexel.edu
> Subject: NuBus frame grabber wanted
> Date: Tuesday, July 14, 1998 2:49 PM
> 
> I am looking for a new or used frame grabber card for use in
> a Power Mac 7100/80.  The Scion LG3 would be my preference,
> but the AG-5 is also an option.  Other cards may also be
> considered.  If you have a spec sheet or web URL that would
> help.  Please reply (including price) to (e-mail preferred)
> :
> Alan J. Townsend, Ph.D., Biochemistry Department, Wake
> Forest University School of Medicine, Medical Center Blvd.,
> Winston-Salem, N.C.  27157, Phone (336)-716-7658, FAX
> (336)-716-7671, E-Mail : atown@wfubmc.edu

--------------------------------
End of nih-image-d Digest V98 Issue #13
***************************************

From nih-image-request@io.ece.drexel.edu Sat Jul 18 19:51 EDT 1998
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Date: Sat, 18 Jul 1998 16:28:30 -0700 (PDT)
From: "T. Hickson" <hickson@pangea.Stanford.EDU>
Reply-To: "T. Hickson" <hickson@pangea.Stanford.EDU>
To: nih-image@io.ece.drexel.edu
Subject: image lineations and angle measurement (fwd)
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Hello,

I got this address from the sci.image.processing and I'm hoping that you
can help me out.

I am a mac user.  I'm familiar with NIH-Image and Photoshop.  I have a
series of images that I need to analyze for clusters of lineations.

1.  Are there any plug-ins for Photoshop or macros for NIH-image that can
look for lineations, measure their orientation and dump the data to a text
file?

2.  Is there any commercially available software that might handle this
(such as Prism)?

3.  Is there anyone out there that might like to take a crack at coding an
NIH-Image macro that would do this?

Basically, I think that I can segment my data and generate clusters of
pixels (particles) that have a variety of long-axis orientations on the
image.  I would like to be able to measure the orientation, magnitude, and
density per unit area of each particle within a selected area of the
image, then generate a circular histogram (rose diagram) of the
orientations.  

If you can help me on this, I'd much appreciate it.

Cheers,

Tom Hickson

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

Thomas A. Hickson
Department of Geological and Environmental Sciences
Stanford University
Stanford, CA  94305-2115

Phone:  (650)725-0043
E-mail:  hickson@pangea.stanford.edu
Web site:  http://pangea.stanford.edu/~hickson/hickson.html
New Home:  Geo-Corner (Bldg. 320), Room 319
**************************************************************

	To doubt everything or to believe everything are
	two equally convenient solutions; both dispense
	with the necessity of reflection.
						H. Poincare




From nih-image-d-request@io.ece.drexel.edu Sun Jul 19 21:19 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199807200119.VAA04766@io.ECE.Drexel.EDU>
Subject: nih-image-d Digest V98 #14
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 14

Today's Topics:
  image lineations and angle measureme  [ "T. Hickson" <hickson@pangea.Stanfo ]
  Re: Digest form                       [ David Milstone <milstone@rascal.med ]

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

Date: Sat, 18 Jul 1998 16:28:30 -0700 (PDT)
From: "T. Hickson" <hickson@pangea.Stanford.EDU>
To: nih-image@io.ece.drexel.edu
Subject: image lineations and angle measurement (fwd)
Message-ID: <Pine.OSF.3.93.980718162539.17651A-100000@pangea.Stanford.EDU>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hello,

I got this address from the sci.image.processing and I'm hoping that you
can help me out.

I am a mac user.  I'm familiar with NIH-Image and Photoshop.  I have a
series of images that I need to analyze for clusters of lineations.

1.  Are there any plug-ins for Photoshop or macros for NIH-image that can
look for lineations, measure their orientation and dump the data to a text
file?

2.  Is there any commercially available software that might handle this
(such as Prism)?

3.  Is there anyone out there that might like to take a crack at coding an
NIH-Image macro that would do this?

Basically, I think that I can segment my data and generate clusters of
pixels (particles) that have a variety of long-axis orientations on the
image.  I would like to be able to measure the orientation, magnitude, and
density per unit area of each particle within a selected area of the
image, then generate a circular histogram (rose diagram) of the
orientations.  

If you can help me on this, I'd much appreciate it.

Cheers,

Tom Hickson

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

Thomas A. Hickson
Department of Geological and Environmental Sciences
Stanford University
Stanford, CA  94305-2115

Phone:  (650)725-0043
E-mail:  hickson@pangea.stanford.edu
Web site:  http://pangea.stanford.edu/~hickson/hickson.html
New Home:  Geo-Corner (Bldg. 320), Room 319
**************************************************************

	To doubt everything or to believe everything are
	two equally convenient solutions; both dispense
	with the necessity of reflection.
						H. Poincare

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

Date: Sun, 19 Jul 1998 21:14:38 -0400
From: David Milstone <milstone@rascal.med.harvard.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Digest form
Message-Id: <v03102803b1d84a5b80ac@[134.174.88.145]>
Content-Type: text/plain; charset="us-ascii"

  I am using Eudora Pro 3.1 and find the new digest format O.K but not great.
  I am able to filter a "table of contents" file into any desired mailbox.
  This file then links to the actual posts which are contained in a newly,
  and automatically, created mailbox in my Eudora attachments folder.When I
  trash the "table of contents" file the mailbox containing the corresponding
  posts is automatically moved to the trash. This works fine but seems
  needlessly comlex.  Other than the need to empty the trash to actually
  delete the mailbox containing the posts this system works fine for me.

  Dave


  >Same for me. Eudora does not handle this digest version without making a new
  >mailbox each time. I had to unsubscribe and subscribe to the individual
  >messages.
  >
  >Jud Gurney
  >Univ of NE
  >
  >Glenn Hammonds wrote:
  >
  >> Johnathan et al,
  >>
  >> After trying it for a while, I'm sorry to report that the new digest
format
  >> definitely is not working for me.
  >>
  >> I'm using Eudora Pro 3.1.1, and I use filtering to sort mail.  With
the new
  >> digests I get a new mailbox for every issue which shows up at the top of
  >> the mail heirarchy instead of in my intended location for NIH Image, and
  >> the naming conventions are somehow messed up such that the name of the
  >> mailbox is not the same as the name of the digest.  The result is a
  >> confusing mess of nearly identical but incorrectly named misplaced
  >> mailboxes, plus packaging.  Ouch!
  >>
  >> My "solution" to date has been to dump all the contents of each digest
back
  >> into a single NIH Image mailbox, thus losing the digest character as well
  >> as the appropriate "reply-to" address, then delete all those mailboxes,
  >> attachments, original container messages, etc.  In the short run this is
  >> (barely) OK, but in the long run, a single mailbox for individual messages
  >> from the NIH Image list is impractical, and I'm tired of dealing with the
  >> mess.
  >>
  >> I would much prefer to go back to the older plain vanilla style of digest.
  >> Could there be two styles of digest offered?
  >>
  >> Best,
  >>
  >> Glenn Hammonds

--------------------------------
End of nih-image-d Digest V98 Issue #14
***************************************

From nih-image-request@io.ece.drexel.edu Sun Jul 19 21:22 EDT 1998
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	Sun, 19 Jul 1998 21:21:47 -0400 (EDT)
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Date: Sun, 19 Jul 1998 21:14:38 -0400
To: nih-image@io.ece.drexel.edu
From: David Milstone <milstone@rascal.med.harvard.edu>
Subject: Re: Digest form
Resent-Message-ID: <"3aF6H.0.mt.iafir"@io>
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  I am using Eudora Pro 3.1 and find the new digest format O.K but not great.
  I am able to filter a "table of contents" file into any desired mailbox.
  This file then links to the actual posts which are contained in a newly,
  and automatically, created mailbox in my Eudora attachments folder.When I
  trash the "table of contents" file the mailbox containing the corresponding
  posts is automatically moved to the trash. This works fine but seems
  needlessly comlex.  Other than the need to empty the trash to actually
  delete the mailbox containing the posts this system works fine for me.

  Dave


  >Same for me. Eudora does not handle this digest version without making a new
  >mailbox each time. I had to unsubscribe and subscribe to the individual
  >messages.
  >
  >Jud Gurney
  >Univ of NE
  >
  >Glenn Hammonds wrote:
  >
  >> Johnathan et al,
  >>
  >> After trying it for a while, I'm sorry to report that the new digest
format
  >> definitely is not working for me.
  >>
  >> I'm using Eudora Pro 3.1.1, and I use filtering to sort mail.  With
the new
  >> digests I get a new mailbox for every issue which shows up at the top of
  >> the mail heirarchy instead of in my intended location for NIH Image, and
  >> the naming conventions are somehow messed up such that the name of the
  >> mailbox is not the same as the name of the digest.  The result is a
  >> confusing mess of nearly identical but incorrectly named misplaced
  >> mailboxes, plus packaging.  Ouch!
  >>
  >> My "solution" to date has been to dump all the contents of each digest
back
  >> into a single NIH Image mailbox, thus losing the digest character as well
  >> as the appropriate "reply-to" address, then delete all those mailboxes,
  >> attachments, original container messages, etc.  In the short run this is
  >> (barely) OK, but in the long run, a single mailbox for individual messages
  >> from the NIH Image list is impractical, and I'm tired of dealing with the
  >> mess.
  >>
  >> I would much prefer to go back to the older plain vanilla style of digest.
  >> Could there be two styles of digest offered?
  >>
  >> Best,
  >>
  >> Glenn Hammonds


From nih-image-request@io.ece.drexel.edu Sun Jul 19 23:12 EDT 1998
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	Sun, 19 Jul 1998 23:11:55 -0400 (EDT)
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Message-ID: <F98649A5EE8ED11190160000F802756598CD9D@exchvic3.dsto.defence.gov.au>
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: LUDL MAC2000 (and 2002) controller
Date: Mon, 20 Jul 1998 13:02:12 +1000
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Hi,
Does or has anyone got the code for the RS232C driving of a LUDL 2000
XYZ stage from NIH-IMAGE?
And if so would they like to share it with me?
Otherwise I will have to do it myself.
Thank you.
Noel Goldsmith

From nih-image-request@io.ece.drexel.edu Mon Jul 20 03:03 EDT 1998
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Date: Sun, 19 Jul 1998 23:52:44 -0700
To: nih-image@io.ece.drexel.edu
From: Glenn Hammonds <rghammonds@earthlink.net>
Subject: Re: Digest Form
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I earlier posted that Eudora Pro 3.1.1 was returning a Eudora mailbox for
each issue of the digest.  Thanks to suggestions from Ard Jonker
<a_team@dds.nl> I found a setting that turns off this "feature".  Deselect
the check box Special:Settings:"Receive MIME digests as attachments", and
the digest appears as text.  No further trouble here, and thanks Ard!

Glenn



From nih-image-request@io.ece.drexel.edu Mon Jul 20 08:06 EDT 1998
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Date: Mon, 20 Jul 1998 13:48:13 +0200
To: nih-image@io.ece.drexel.edu
From: Stein Roervik <steinr@chembio.ntnu.no>
Subject: Re: LUDL MAC2000 (and 2002) controller
Resent-Message-ID: <"e0Dzc.0.2G1.3woir"@io>
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>Does or has anyone got the code for the RS232C driving of a LUDL 2000
>XYZ stage from NIH-IMAGE?
>And if so would they like to share it with me?
>Otherwise I will have to do it myself.
>Thank you.
>Noel Goldsmith

I have written such code and posted an example macro to the list in April
1997. Below is the macro I sent. As you see, it is pretty straightforward
to run this stage using serial commands. I also have some Pascal code with
a custom dialog. Contact me off-list if you are interested in this as well.
(I am going on vacation for two weeks from tomorrow morning and will not
reply to email until I am back.)

>To: nih-image@soils.umn.edu
>From: steinr@kjemi.unit.no (Stein Roervik)
>Subject: Ludl Macro
>
>Below is a general macro to run the Ludl focus controller.
>It only includes a few basic example functions:
>Do autofocus, read position and move to position.
>All other functions follow the same syntax, so this
>macro should be easy to modify. Read the manual.
>The macro requires NIH image 1.60 or higher.
>
>First press [F1] to verify that the communication is working.
>The reply should read ":A ". Then press [F4] to initialize the unit,
>[f] to do focus or [m] to move to a given position.
>

macro 'test serial [F1]';
var
  CommandString, ReplyChar, ReplyString: string;
begin
  OpenSerial('9600 baud, no parity, eight data, two stop');
  CommandString:= 'window +';
  PutSerial(CommandString,chr(13));
  wait(0.1);
  ReplyString := '';
  repeat
     ReplyChar:= GetSerial;
     ReplyString := concat(ReplyString, ReplyChar);
  until ReplyChar = '';
  ShowMessage('Command: "',CommandString,'"\',
              'Reply: "',ReplyString,'"');
end;

macro 'reset serial [F2]';
begin
  OpenSerial('9600 baud, no parity, eight data, two stop');
  PutSerial(chr(255),chr(82)); {reset Ludl device}
  wait(10); { it takes approx. 9.6 seconds until Ludl device is reset }
  beep;
end;

macro 'flush serial input buffer [F3]';
var i: integer;
    ch, str: string;
begin
  str:= ''; i:= 0;
  repeat
     i:= i+1;
     ch:= GetSerial;
     str:= concat(str,ch);
  until ch='';
  ShowMessage('Buffer: "',str,'"');
end;


function GetLudlValue(CommandString: string): real;
var
  ReplyChar, ReplyString: string;
begin
  PutSerial(CommandString,chr(13));
  wait(0.1);
  ReplyString := '';
  repeat
     ReplyChar:= GetSerial;
     ReplyString := concat(ReplyString, ReplyChar);
  until ReplyChar = '';
  ShowMessage('Ludl request "',CommandString,'"\',
              'Ludl response "',ReplyString,'"');
  GetLudlValue:= StringToNum(ReplyString)/100; {100 steps in a micron}
end;


procedure SendLudlCommand(CommandString: string);
var
  ReplyChar, ReplyString: string;
begin
  PutSerial(CommandString,chr(13));
  wait(0.1);
  ReplyString := '';
  repeat
     ReplyChar:= GetSerial;
     ReplyString := concat(ReplyString, ReplyChar);
  until ReplyChar = '';
  ShowMessage('Ludl command "',CommandString,'"\',
              'Ludl response "',ReplyString,'"');
end;

macro 'init focus driver [F4]';
begin
  OpenSerial('9600 baud, no parity, eight data, two stop');
  SendLudlCommand('window +');
  SendLudlCommand('speed F=5000');
  SendLudlCommand('here F=0');
end;

macro 'do AutoFocus [f]';
begin
  SendLudlCommand('focus');
end;

macro 'do MovePosition [m]';
var Position: real;
begin
  Position:= GetNumber('Move to new position:',GetLudlValue('where F'));
  SendLudlCommand(concat('move F =',round(Position*100)));
end;

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+


From nih-image-request@io.ece.drexel.edu Mon Jul 20 08:49 EDT 1998
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	Mon, 20 Jul 1998 08:49:18 -0400 (EDT)
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From: "Samu Ruuhonen" <samu@nippi.hut.fi>
Organization: HUT/GALA
To: nih-image@io.ece.drexel.edu
Date: Mon, 20 Jul 1998 15:21:42 +0000
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Subject: AutoThreshold -algorithm?
Priority: normal
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I am using ImagePC for thresholding graylevel images taken from a 
paper surface. Does anybody know what is the algorithm that 
"AutoThreshold" -macro command uses to calculate the correct 
threshold value?

Thank you, 
Samu Ruuhonen
Research assist in Helsinki University of Technology
Laboratory of Media Technology

From nih-image-request@io.ece.drexel.edu Mon Jul 20 09:54 EDT 1998
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Hello,

Try holding down the Shift key while invoking Scion Image.  This should
bypass the detection of the Scion frame grabbers and then alow detection of
the AV board.

Tom

>
>Dear list Members,
>
>I posted the enclosed question a few days ago.  Though no one replied, I
>managed to find the answer myself. If anyone else has the same problem,
>the answer is to hold down the SHIFT key when opening IMAGE. Doing so
>selects the internal frame grabber.
>
>Mike Smith
>
>>>> "Mike Smith" <MISMITH@brody.med.ecu.edu> 07/15 3:12 pm >>>
>Dear List Members,
>
>I have a PowerMac with a built-in frame grabber (low quality). Recently, I
>installed a Scion frame grabber. Now I cannot seem to access the built-in
>frame grabber from NIH-Image. Is there a way to do this, or must I
>ununstall the Scion board?
>
>Mike Smith


-----------------------------------------------------------------------
Tom Morton                                     support@scioncorp.com
Technical Services                             http://www.scioncorp.com
Scion Corporation                              ftp://scioncorp.com
82 Wormans Mill Rd., Suite H                   Phone: (301) 695-7870
Frederick, MD 21701                            Fax:   (301) 695-0035
-----------------------------------------------------------------------


From nih-image-request@io.ece.drexel.edu Mon Jul 20 12:11 EDT 1998
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Date: Mon, 20 Jul 1998 09:00:46 -0700
To: nih-image@io.ece.drexel.edu
From: Jon Goerke <goerke@itsa.ucsf.edu>
Subject: Re: Digest Form
Resent-Message-ID: <"MmINn.0.dl6.LZsir"@io>
Resent-From: nih-image@io.ece.drexel.edu
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Four posts to the list have been somewhat critical of the new Digest Form
and its interactions with Eudora.  The basic problem is that it
automatically inserts new Image Digest mailboxes in the Eudora Menu.  Since
my own complaint was posted, however, I've developed a workaround that
seems fairly painless -- and it no longer requires a trip to
Menu/Window/Mailboxes to implement.

I filter each digest into a mailbox as previously ( "from" contains
"NIH-Image" into the mailbox).  Clicking on the new message line appearing
in the NIH-Image mailbox window opens a new-appearing Digest Window
containing an Icon indicating an attached file.  Clicking on this Icon
opens the Digest headed by the ????? index entry.  I click on the topics I
want to see, and then use Menu/Delete to trash what I don't want to save
for future reference, all the way back through the Digest itself.

A singular advantage to the new scheme is that I can save individual posts
directly and easily. The old Digest system required selecting, copying,
opening Simple Text or Word, pasting, and saving.

What appeared to be residual new mailboxes in Menu/Mailbox, even after
Menu/Special/Empty Trash, had disappeared when the Mac System was next
booted.

I'm using Eudora 4.0, but I doubt that the described behavior is specific
to this version.

Put me down for maintaining the current Digest form please.

Jon
_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Jon Goerke, MD                     EMail: goerke@itsa.ucsf.edu
Prof. Physiology, Univ. Calif.     Phone: 415-476-3252
3333 California St., Suite 150,    San Francisco, CA 94118
_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/

From nih-image-request@io.ece.drexel.edu Mon Jul 20 13:44 EDT 1998
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Date: Mon, 20 Jul 1998 12:33:50 -0500 (EST)
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From: Tim Steffens <tsteffen@iupui.edu>
Subject: Test just delete
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just delete this message.

Tim Steffens, CRA
Indiana University Medical Center
tsteffen@iupui.edu



From nih-image-d-request@io.ece.drexel.edu Mon Jul 20 17:47 EDT 1998
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Date: Mon, 20 Jul 1998 17:47:52 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #15
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 15

Today's Topics:
  LUDL MAC2000 (and 2002) controller    [ "Goldsmith, Noel" <Noel.Goldsmith@d ]
  Re: Digest Form                       [ Glenn Hammonds <rghammonds@earthlin ]
  Re: LUDL MAC2000 (and 2002) controll  [ Stein Roervik <steinr@chembio.ntnu. ]
  AutoThreshold -algorithm?             [ "Samu Ruuhonen" <samu@nippi.hut.fi> ]
  Re: nih-image-d Digest V98 #13        [ Tom Morton <support@scioncorp.com> ]
  Re: Digest Form                       [ Jon Goerke <goerke@itsa.ucsf.edu> ]
  Test just delete                      [ Tim Steffens <tsteffen@iupui.edu> ]
  NIH Image for the MAC                 [ "Michael A. Richardson, M.D." <drto ]

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

Date: Mon, 20 Jul 1998 13:02:12 +1000
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: LUDL MAC2000 (and 2002) controller
Message-ID: <F98649A5EE8ED11190160000F802756598CD9D@exchvic3.dsto.defence.gov.au>
Content-Type: text/plain

Hi,
Does or has anyone got the code for the RS232C driving of a LUDL 2000
XYZ stage from NIH-IMAGE?
And if so would they like to share it with me?
Otherwise I will have to do it myself.
Thank you.
Noel Goldsmith

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

Date: Sun, 19 Jul 1998 23:52:44 -0700
From: Glenn Hammonds <rghammonds@earthlink.net>
To: nih-image@io.ece.drexel.edu
Subject: Re: Digest Form
Message-Id: <v03110700b1d898585563@[153.37.20.117]>
Content-Type: text/plain; charset="us-ascii"

I earlier posted that Eudora Pro 3.1.1 was returning a Eudora mailbox for
each issue of the digest.  Thanks to suggestions from Ard Jonker
<a_team@dds.nl> I found a setting that turns off this "feature".  Deselect
the check box Special:Settings:"Receive MIME digests as attachments", and
the digest appears as text.  No further trouble here, and thanks Ard!

Glenn

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

Date: Mon, 20 Jul 1998 13:48:13 +0200
From: Stein Roervik <steinr@chembio.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Re: LUDL MAC2000 (and 2002) controller
Message-Id: <v03102803b1d8dd1ea603@[129.241.39.133]>
Content-Type: text/plain; charset="us-ascii"

>Does or has anyone got the code for the RS232C driving of a LUDL 2000
>XYZ stage from NIH-IMAGE?
>And if so would they like to share it with me?
>Otherwise I will have to do it myself.
>Thank you.
>Noel Goldsmith

I have written such code and posted an example macro to the list in April
1997. Below is the macro I sent. As you see, it is pretty straightforward
to run this stage using serial commands. I also have some Pascal code with
a custom dialog. Contact me off-list if you are interested in this as well.
(I am going on vacation for two weeks from tomorrow morning and will not
reply to email until I am back.)

>To: nih-image@soils.umn.edu
>From: steinr@kjemi.unit.no (Stein Roervik)
>Subject: Ludl Macro
>
>Below is a general macro to run the Ludl focus controller.
>It only includes a few basic example functions:
>Do autofocus, read position and move to position.
>All other functions follow the same syntax, so this
>macro should be easy to modify. Read the manual.
>The macro requires NIH image 1.60 or higher.
>
>First press [F1] to verify that the communication is working.
>The reply should read ":A ". Then press [F4] to initialize the unit,
>[f] to do focus or [m] to move to a given position.
>

macro 'test serial [F1]';
var
  CommandString, ReplyChar, ReplyString: string;
begin
  OpenSerial('9600 baud, no parity, eight data, two stop');
  CommandString:= 'window +';
  PutSerial(CommandString,chr(13));
  wait(0.1);
  ReplyString := '';
  repeat
     ReplyChar:= GetSerial;
     ReplyString := concat(ReplyString, ReplyChar);
  until ReplyChar = '';
  ShowMessage('Command: "',CommandString,'"\',
              'Reply: "',ReplyString,'"');
end;

macro 'reset serial [F2]';
begin
  OpenSerial('9600 baud, no parity, eight data, two stop');
  PutSerial(chr(255),chr(82)); {reset Ludl device}
  wait(10); { it takes approx. 9.6 seconds until Ludl device is reset }
  beep;
end;

macro 'flush serial input buffer [F3]';
var i: integer;
    ch, str: string;
begin
  str:= ''; i:= 0;
  repeat
     i:= i+1;
     ch:= GetSerial;
     str:= concat(str,ch);
  until ch='';
  ShowMessage('Buffer: "',str,'"');
end;


function GetLudlValue(CommandString: string): real;
var
  ReplyChar, ReplyString: string;
begin
  PutSerial(CommandString,chr(13));
  wait(0.1);
  ReplyString := '';
  repeat
     ReplyChar:= GetSerial;
     ReplyString := concat(ReplyString, ReplyChar);
  until ReplyChar = '';
  ShowMessage('Ludl request "',CommandString,'"\',
              'Ludl response "',ReplyString,'"');
  GetLudlValue:= StringToNum(ReplyString)/100; {100 steps in a micron}
end;


procedure SendLudlCommand(CommandString: string);
var
  ReplyChar, ReplyString: string;
begin
  PutSerial(CommandString,chr(13));
  wait(0.1);
  ReplyString := '';
  repeat
     ReplyChar:= GetSerial;
     ReplyString := concat(ReplyString, ReplyChar);
  until ReplyChar = '';
  ShowMessage('Ludl command "',CommandString,'"\',
              'Ludl response "',ReplyString,'"');
end;

macro 'init focus driver [F4]';
begin
  OpenSerial('9600 baud, no parity, eight data, two stop');
  SendLudlCommand('window +');
  SendLudlCommand('speed F=5000');
  SendLudlCommand('here F=0');
end;

macro 'do AutoFocus [f]';
begin
  SendLudlCommand('focus');
end;

macro 'do MovePosition [m]';
var Position: real;
begin
  Position:= GetNumber('Move to new position:',GetLudlValue('where F'));
  SendLudlCommand(concat('move F =',round(Position*100)));
end;

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+

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

Date: Mon, 20 Jul 1998 15:21:42 +0000
From: "Samu Ruuhonen" <samu@nippi.hut.fi>
To: nih-image@io.ece.drexel.edu
Subject: AutoThreshold -algorithm?
Message-ID: <1E2C698500A@nippi.hut.fi>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7BIT

I am using ImagePC for thresholding graylevel images taken from a 
paper surface. Does anybody know what is the algorithm that 
"AutoThreshold" -macro command uses to calculate the correct 
threshold value?

Thank you, 
Samu Ruuhonen
Research assist in Helsinki University of Technology
Laboratory of Media Technology

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

Date: Mon, 20 Jul 1998 09:05:35 -0500
From: Tom Morton <support@scioncorp.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #13
Message-Id: <l03102800b1d8fefedf52@[10.0.0.239]>
Content-Type: text/plain; charset="us-ascii"

Hello,

Try holding down the Shift key while invoking Scion Image.  This should
bypass the detection of the Scion frame grabbers and then alow detection of
the AV board.

Tom

>
>Dear list Members,
>
>I posted the enclosed question a few days ago.  Though no one replied, I
>managed to find the answer myself. If anyone else has the same problem,
>the answer is to hold down the SHIFT key when opening IMAGE. Doing so
>selects the internal frame grabber.
>
>Mike Smith
>
>>>> "Mike Smith" <MISMITH@brody.med.ecu.edu> 07/15 3:12 pm >>>
>Dear List Members,
>
>I have a PowerMac with a built-in frame grabber (low quality). Recently, I
>installed a Scion frame grabber. Now I cannot seem to access the built-in
>frame grabber from NIH-Image. Is there a way to do this, or must I
>ununstall the Scion board?
>
>Mike Smith


-----------------------------------------------------------------------
Tom Morton                                     support@scioncorp.com
Technical Services                             http://www.scioncorp.com
Scion Corporation                              ftp://scioncorp.com
82 Wormans Mill Rd., Suite H                   Phone: (301) 695-7870
Frederick, MD 21701                            Fax:   (301) 695-0035
-----------------------------------------------------------------------

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

Date: Mon, 20 Jul 1998 09:00:46 -0700
From: Jon Goerke <goerke@itsa.ucsf.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Digest Form
Message-Id: <v04011700b1d913c16127@[128.218.160.44]>
Content-Type: text/plain; charset="us-ascii"

Four posts to the list have been somewhat critical of the new Digest Form
and its interactions with Eudora.  The basic problem is that it
automatically inserts new Image Digest mailboxes in the Eudora Menu.  Since
my own complaint was posted, however, I've developed a workaround that
seems fairly painless -- and it no longer requires a trip to
Menu/Window/Mailboxes to implement.

I filter each digest into a mailbox as previously ( "from" contains
"NIH-Image" into the mailbox).  Clicking on the new message line appearing
in the NIH-Image mailbox window opens a new-appearing Digest Window
containing an Icon indicating an attached file.  Clicking on this Icon
opens the Digest headed by the ????? index entry.  I click on the topics I
want to see, and then use Menu/Delete to trash what I don't want to save
for future reference, all the way back through the Digest itself.

A singular advantage to the new scheme is that I can save individual posts
directly and easily. The old Digest system required selecting, copying,
opening Simple Text or Word, pasting, and saving.

What appeared to be residual new mailboxes in Menu/Mailbox, even after
Menu/Special/Empty Trash, had disappeared when the Mac System was next
booted.

I'm using Eudora 4.0, but I doubt that the described behavior is specific
to this version.

Put me down for maintaining the current Digest form please.

Jon
_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Jon Goerke, MD                     EMail: goerke@itsa.ucsf.edu
Prof. Physiology, Univ. Calif.     Phone: 415-476-3252
3333 California St., Suite 150,    San Francisco, CA 94118
_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/

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

Date: Mon, 20 Jul 1998 12:33:50 -0500 (EST)
From: Tim Steffens <tsteffen@iupui.edu>
To: nih-image@io.ece.drexel.edu
Subject: Test just delete
Message-Id: <l03110702b1d8e9e44644@[134.68.114.150]>
Content-Type: text/plain; charset="us-ascii"

just delete this message.

Tim Steffens, CRA
Indiana University Medical Center
tsteffen@iupui.edu

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

Date: Mon, 20 Jul 1998 14:38:59 -0700
From: "Michael A. Richardson, M.D." <drtoad@silcom.com>
To: nih-image@io.ece.drexel.edu
Subject: NIH Image for the MAC
Message-Id: <v03007801b1d969326666@[207.71.218.55]>
Content-Type: text/plain; charset="us-ascii"

Ladies and Gentlemen:

Where can I obtain a copy of NIH image for the MAC (PPC, system 8.1)?


Michael A. Richardson, M.D. FCAP
Department of Laboratory Medicine
Saint Francis Medical Center
601 East Micheltorena Street
Santa Barbara, California  93103
(805) 568-5743
(805) 568-5742
drtoad@silcom.com

--------------------------------
End of nih-image-d Digest V98 Issue #15
***************************************

From nih-image-request@io.ece.drexel.edu Mon Jul 20 17:49 EDT 1998
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Date: Mon, 20 Jul 1998 14:38:59 -0700
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Subject: NIH Image for the MAC
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Ladies and Gentlemen:

Where can I obtain a copy of NIH image for the MAC (PPC, system 8.1)?


Michael A. Richardson, M.D. FCAP
Department of Laboratory Medicine
Saint Francis Medical Center
601 East Micheltorena Street
Santa Barbara, California  93103
(805) 568-5743
(805) 568-5742
drtoad@silcom.com


From nih-image-request@io.ece.drexel.edu Mon Jul 20 18:05 EDT 1998
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Date: Mon, 20 Jul 1998 17:53:27 -0400 (EDT)
From: Jim G Thomas <jgthomas@wam.umd.edu>
Reply-To: Jim G Thomas <jgthomas@wam.umd.edu>
To: nih-image@io.ece.drexel.edu
Subject: movie help
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Hi.  I have a power mac 7600 with 32meg ram.  I am running NIH image 1.61
with around 19meg allocated towards it.  My problem is that I can make
standard movies just fine when I have the picture size at 1/4 (in Video
Control).  If I increase the picture size to 1/2 or full-size I can
still see what is being captured, though it is quite slow.  But when I
try to make a movie, all I get is a black window and hence a black movie.
Any ideas?  Is this just a memory problem?  Or I am not properly
configured.  I do not have scion, if that makes a difference.

jim thomas

From nih-image-request@io.ece.drexel.edu Tue Jul 21 06:16 EDT 1998
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Date: Tue, 21 Jul 1998 11:59:30 +0200
To: support@scioncorp.com, nih-image@io.ece.drexel.edu
From: Francesc Peters <cesc@cucafera.icm.csic.es>
Subject: help with LG-3
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Hi,

We just bought an LG-3 and installed it in a new PowerMac G3 (desktop)
running MacOS 8.0. We installed the ScionImage1.62a provided. The computer
seems to recognize the board fine since we have connected a video to the
board and can capture images without problems. But we can not get to the
settings under File: Acquire to change the grab size and all the other
feature we were used to with the built in boards from apple on other
computers. It keeps saying that there is no quicktime compatible video and
that we need the correct vdig file. I do hold down the shift key to get to
the settings. Do we need to upgrade soft? Put a special plug-in digitizer
from Scion? Take out the other plug-in digitizer or upgrade it (currently
using 1.2.4)? Upgrade to MacOS8.1?

Thanks for your help.

******************************************************************
PLEASE NOTICE NEW PHONE AND FAX NUMBERS!!!

Francesc Peters                           FAX:   34-93-221-7340
Institut de Ciencies del Mar (CSIC)       Phone: 34-93-221-6416 (Ext. 255)
Passeig Joan de Borbo s/n                 cesc@icm.csic.es
E-08039 Barcelona, Catalunya              <http://www.icm.csic.es>
Spain


From nih-image-request@io.ece.drexel.edu Tue Jul 21 06:51 EDT 1998
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Date: Tue, 21 Jul 1998 06:39:39 -0400
To: nih-image@io.ece.drexel.edu
From: Bruce Berkowitz <baberko@med.wayne.edu>
Subject: median stack
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Hi,

Is there a macro around that will calculate and display the pixel by pixel
median of a stack of images? My data are not normally distributed so
displaying the average is not really right and doesn't reflect the
statitisics I have to do.

Thanks!

Bruce Berkowitz
|-------------------------------------------|
|Berkowitz Lab Home Page: http://146.9.7.69 |
|-------------------------------------------|

Bruce Berkowitz, Ph.D.
Department of Anatomy and Cell Biology
Wayne State Univeristy
540 E. Canfield
Detroit, MI 48201

Phone:	(313) 577-9035
FAX:	(313) 577-3125
E-mail:	baberko@med.wayne.edu

From nih-image-request@io.ece.drexel.edu Tue Jul 21 07:36 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Carl Gustafson <carl.gustafson@cbis.ece.drexel.edu>
Subject: Re: NIH Image for the MAC
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>Where can I obtain a copy of NIH image for the MAC (PPC, system 8.1)?

ftp://zippy.nimh.nih.gov/pub/nih-image/




Carl Gustafson
(215) 895-1383
===============================================================================
           the Computer Vision Center for Vertebrate Brain Mapping
===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I'd like to give you my opinion
===============================================================================


From nih-image-request@io.ece.drexel.edu Tue Jul 21 07:38 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Carl Gustafson <carl.gustafson@cbis.ece.drexel.edu>
Subject: Re: help with LG-3
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>board and can capture images without problems. But we can not get to the
>settings under File: Acquire to change the grab size and all the other
>feature we were used to with the built in boards from apple on other
>computers. It keeps saying that there is no quicktime compatible video and
>that we need the correct vdig file. I do hold down the shift key to get to
>the settings. Do we need to upgrade soft? Put a special plug-in digitizer
>from Scion? Take out the other plug-in digitizer or upgrade it (currently
>using 1.2.4)? Upgrade to MacOS8.1?

Unless I am sadly mistaken (could happen), the LG-3 doesn't support this
kind of thing, as there is no built-in vdig for it (and there is no
low-level support on the board, as I recall). I suppose some intrepid
programmer (other than me) could write a vdig, but I doubt it's for the
casual coder.




Carl Gustafson
(215) 895-1383
===============================================================================
           the Computer Vision Center for Vertebrate Brain Mapping
===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I'd like to give you my opinion
===============================================================================


From nih-image-request@io.ece.drexel.edu Tue Jul 21 08:50 EDT 1998
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Date: Tue, 21 Jul 1998 08:44:58 -0400
To: nih-image@io.ece.drexel.edu
From: David Milstone <milstone@rascal.med.harvard.edu>
Subject: Re: Digest Form
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I use the same system with Eudora Pro 3.1 and agree that it is an improvement.

>Four posts to the list have been somewhat critical of the new Digest Form
>and its interactions with Eudora.  The basic problem is that it
>automatically inserts new Image Digest mailboxes in the Eudora Menu.  Since
>my own complaint was posted, however, I've developed a workaround that
>seems fairly painless -- and it no longer requires a trip to
>Menu/Window/Mailboxes to implement.
>
>I filter each digest into a mailbox as previously ( "from" contains
>"NIH-Image" into the mailbox).  Clicking on the new message line appearing
>in the NIH-Image mailbox window opens a new-appearing Digest Window
>containing an Icon indicating an attached file.  Clicking on this Icon
>opens the Digest headed by the ????? index entry.  I click on the topics I
>want to see, and then use Menu/Delete to trash what I don't want to save
>for future reference, all the way back through the Digest itself.
>
>A singular advantage to the new scheme is that I can save individual posts
>directly and easily. The old Digest system required selecting, copying,
>opening Simple Text or Word, pasting, and saving.
>
>What appeared to be residual new mailboxes in Menu/Mailbox, even after
>Menu/Special/Empty Trash, had disappeared when the Mac System was next
>booted.
>
>I'm using Eudora 4.0, but I doubt that the described behavior is specific
>to this version.
>
>Put me down for maintaining the current Digest form please.
>
>Jon
>_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
>Jon Goerke, MD                     EMail: goerke@itsa.ucsf.edu
>Prof. Physiology, Univ. Calif.     Phone: 415-476-3252
>3333 California St., Suite 150,    San Francisco, CA 94118
>_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/



From nih-image-request@io.ece.drexel.edu Tue Jul 21 10:59 EDT 1998
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Date: Tue, 21 Jul 1998 07:48:41 -0700 (PDT)
From: "R. Hard" <rhard@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Course Announcement
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Course Announcement

Title: Optical Microscopy and Imaging in the Biomedical Sciences

When: October 7 - October 15, 1998

Where: Marine Biology Laboratory, Woods Hole, MA, USA

Tuition: $2050 (Includes room and board)

Application Deadline: August 4, 1998

Admission application and information:
     Carol Harnel, Admissions Coordinator
     Marine Biological Laboratory
     7 MBL Street
     Woods Hole, MA 02543-1015
     (508) 289-7401
     Internet: admissions@mbl.edu
     WWW: http://www.mbl.edu (Application forms available via Adobe
                              Acrobat)

Course Director: Colin S. Izzard, State University of New York @ Albany
   Phone: [518] 442 - 4367
   EMail: csizzard@csc.albany.edu

Course Description:

For Whom:
      Designed primarily for research scientists, physicians, postdoctoral 
trainees and advanced graduate students in animal, plant, medical and 
material sciences. Non-biologists seeking a comprehensive introduction to 
microscopy and video-imaging will benefit greatly from this course as
well. There are no specific prerequisites, but an understanding of the basic 
principles of optics is desirable. Limited to 24 students.

  The eight day course consists of lectures, laboratory demonstrations, 
exercises and discussions that will enable the participant to obtain and 
interpret microscope images of high quality, to perform quantitative
optical measurements, and to produce photographic and video records for
documentation and analysis.

Topics to be covered include:
      principles of microscope design and image formation
      bright field, dark field, phase contrast, differential
         interference contrast, interference reflection, and 
         fluorescence microscopy
      confocal scanning microscopy and image deconvolution
      digital image restoration and 3-D reconstruction
      video imaging, recording, enhancement, and intensification
      analog and digital image processing and analysis
      fluorescent probes and ratio-imaging
      laser tweezers and laser scissors

  Applications to live cells will be emphasized; other specimens will be 
covered as well.

  Students will have direct hands-on experience with state-of-the-art 
microscopes, video cameras, recorders and image processing equipment
provided by major optical and electronics companies. Instruction will be
provided by experienced staff from universities and industry.

  Students are encouraged to bring their own biological (primary 
cultures, cell lines, etc.) and material specimens and to discuss
individual research problems with the faculty.


From nih-image-d-request@io.ece.drexel.edu Tue Jul 21 11:05 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #16
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 16

Today's Topics:
  movie help                            [ Jim G Thomas <jgthomas@wam.umd.edu> ]
  help with LG-3                        [ Francesc Peters <cesc@cucafera.icm. ]
  median stack                          [ Bruce Berkowitz <baberko@med.wayne. ]
  Re: NIH Image for the MAC             [ Carl Gustafson <carl.gustafson@cbis ]
  Re: help with LG-3                    [ Carl Gustafson <carl.gustafson@cbis ]
  Re: Digest Form                       [ David Milstone <milstone@rascal.med ]
  Course Announcement                   [ "R. Hard" <rhard@u.washington.edu> ]

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

Date: Mon, 20 Jul 1998 17:53:27 -0400 (EDT)
From: Jim G Thomas <jgthomas@wam.umd.edu>
To: nih-image@io.ece.drexel.edu
Subject: movie help
Message-ID: <Pine.SOL.3.95q.980720175239.27987A-100000@rac6.wam.umd.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi.  I have a power mac 7600 with 32meg ram.  I am running NIH image 1.61
with around 19meg allocated towards it.  My problem is that I can make
standard movies just fine when I have the picture size at 1/4 (in Video
Control).  If I increase the picture size to 1/2 or full-size I can
still see what is being captured, though it is quite slow.  But when I
try to make a movie, all I get is a black window and hence a black movie.
Any ideas?  Is this just a memory problem?  Or I am not properly
configured.  I do not have scion, if that makes a difference.

jim thomas

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

Date: Tue, 21 Jul 1998 11:59:30 +0200
From: Francesc Peters <cesc@cucafera.icm.csic.es>
To: support@scioncorp.com, nih-image@io.ece.drexel.edu
Subject: help with LG-3
Message-Id: <l03130300b1da12b46ed5@[193.145.218.128]>
Content-Type: text/plain; charset="us-ascii"

Hi,

We just bought an LG-3 and installed it in a new PowerMac G3 (desktop)
running MacOS 8.0. We installed the ScionImage1.62a provided. The computer
seems to recognize the board fine since we have connected a video to the
board and can capture images without problems. But we can not get to the
settings under File: Acquire to change the grab size and all the other
feature we were used to with the built in boards from apple on other
computers. It keeps saying that there is no quicktime compatible video and
that we need the correct vdig file. I do hold down the shift key to get to
the settings. Do we need to upgrade soft? Put a special plug-in digitizer
from Scion? Take out the other plug-in digitizer or upgrade it (currently
using 1.2.4)? Upgrade to MacOS8.1?

Thanks for your help.

******************************************************************
PLEASE NOTICE NEW PHONE AND FAX NUMBERS!!!

Francesc Peters                           FAX:   34-93-221-7340
Institut de Ciencies del Mar (CSIC)       Phone: 34-93-221-6416 (Ext. 255)
Passeig Joan de Borbo s/n                 cesc@icm.csic.es
E-08039 Barcelona, Catalunya              <http://www.icm.csic.es>
Spain

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

Date: Tue, 21 Jul 1998 06:39:39 -0400
From: Bruce Berkowitz <baberko@med.wayne.edu>
To: nih-image@io.ece.drexel.edu
Subject: median stack
Message-Id: <3.0.1.32.19980721063939.00772da0@med.wayne.edu>
Content-Type: text/plain; charset="us-ascii"

Hi,

Is there a macro around that will calculate and display the pixel by pixel
median of a stack of images? My data are not normally distributed so
displaying the average is not really right and doesn't reflect the
statitisics I have to do.

Thanks!

Bruce Berkowitz
|-------------------------------------------|
|Berkowitz Lab Home Page: http://146.9.7.69 |
|-------------------------------------------|

Bruce Berkowitz, Ph.D.
Department of Anatomy and Cell Biology
Wayne State Univeristy
540 E. Canfield
Detroit, MI 48201

Phone:	(313) 577-9035
FAX:	(313) 577-3125
E-mail:	baberko@med.wayne.edu

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

Date: Tue, 21 Jul 1998 07:27:07 -0400
From: Carl Gustafson <carl.gustafson@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Image for the MAC
Message-Id: <v03110707b1da2b66be85@[144.118.33.205]>
Content-Type: text/plain; charset="us-ascii"

>Where can I obtain a copy of NIH image for the MAC (PPC, system 8.1)?

ftp://zippy.nimh.nih.gov/pub/nih-image/




Carl Gustafson
(215) 895-1383
===============================================================================
           the Computer Vision Center for Vertebrate Brain Mapping
===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I'd like to give you my opinion
===============================================================================

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

Date: Tue, 21 Jul 1998 07:30:04 -0400
From: Carl Gustafson <carl.gustafson@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: help with LG-3
Message-Id: <v03110708b1da2bb7d19b@[144.118.33.205]>
Content-Type: text/plain; charset="us-ascii"

>board and can capture images without problems. But we can not get to the
>settings under File: Acquire to change the grab size and all the other
>feature we were used to with the built in boards from apple on other
>computers. It keeps saying that there is no quicktime compatible video and
>that we need the correct vdig file. I do hold down the shift key to get to
>the settings. Do we need to upgrade soft? Put a special plug-in digitizer
>from Scion? Take out the other plug-in digitizer or upgrade it (currently
>using 1.2.4)? Upgrade to MacOS8.1?

Unless I am sadly mistaken (could happen), the LG-3 doesn't support this
kind of thing, as there is no built-in vdig for it (and there is no
low-level support on the board, as I recall). I suppose some intrepid
programmer (other than me) could write a vdig, but I doubt it's for the
casual coder.




Carl Gustafson
(215) 895-1383
===============================================================================
           the Computer Vision Center for Vertebrate Brain Mapping
===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I'd like to give you my opinion
===============================================================================

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

Date: Tue, 21 Jul 1998 08:44:58 -0400
From: David Milstone <milstone@rascal.med.harvard.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Digest Form
Message-Id: <v03102804b1da3d8ef39d@[134.174.88.145]>
Content-Type: text/plain; charset="us-ascii"

I use the same system with Eudora Pro 3.1 and agree that it is an improvement.

>Four posts to the list have been somewhat critical of the new Digest Form
>and its interactions with Eudora.  The basic problem is that it
>automatically inserts new Image Digest mailboxes in the Eudora Menu.  Since
>my own complaint was posted, however, I've developed a workaround that
>seems fairly painless -- and it no longer requires a trip to
>Menu/Window/Mailboxes to implement.
>
>I filter each digest into a mailbox as previously ( "from" contains
>"NIH-Image" into the mailbox).  Clicking on the new message line appearing
>in the NIH-Image mailbox window opens a new-appearing Digest Window
>containing an Icon indicating an attached file.  Clicking on this Icon
>opens the Digest headed by the ????? index entry.  I click on the topics I
>want to see, and then use Menu/Delete to trash what I don't want to save
>for future reference, all the way back through the Digest itself.
>
>A singular advantage to the new scheme is that I can save individual posts
>directly and easily. The old Digest system required selecting, copying,
>opening Simple Text or Word, pasting, and saving.
>
>What appeared to be residual new mailboxes in Menu/Mailbox, even after
>Menu/Special/Empty Trash, had disappeared when the Mac System was next
>booted.
>
>I'm using Eudora 4.0, but I doubt that the described behavior is specific
>to this version.
>
>Put me down for maintaining the current Digest form please.
>
>Jon
>_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
>Jon Goerke, MD                     EMail: goerke@itsa.ucsf.edu
>Prof. Physiology, Univ. Calif.     Phone: 415-476-3252
>3333 California St., Suite 150,    San Francisco, CA 94118
>_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/

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

Date: Tue, 21 Jul 1998 07:48:41 -0700 (PDT)
From: "R. Hard" <rhard@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Course Announcement
Message-ID: <Pine.A41.3.95b.980721074632.139598A-100000@homer04.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Course Announcement

Title: Optical Microscopy and Imaging in the Biomedical Sciences

When: October 7 - October 15, 1998

Where: Marine Biology Laboratory, Woods Hole, MA, USA

Tuition: $2050 (Includes room and board)

Application Deadline: August 4, 1998

Admission application and information:
     Carol Harnel, Admissions Coordinator
     Marine Biological Laboratory
     7 MBL Street
     Woods Hole, MA 02543-1015
     (508) 289-7401
     Internet: admissions@mbl.edu
     WWW: http://www.mbl.edu (Application forms available via Adobe
                              Acrobat)

Course Director: Colin S. Izzard, State University of New York @ Albany
   Phone: [518] 442 - 4367
   EMail: csizzard@csc.albany.edu

Course Description:

For Whom:
      Designed primarily for research scientists, physicians, postdoctoral 
trainees and advanced graduate students in animal, plant, medical and 
material sciences. Non-biologists seeking a comprehensive introduction to 
microscopy and video-imaging will benefit greatly from this course as
well. There are no specific prerequisites, but an understanding of the basic 
principles of optics is desirable. Limited to 24 students.

  The eight day course consists of lectures, laboratory demonstrations, 
exercises and discussions that will enable the participant to obtain and 
interpret microscope images of high quality, to perform quantitative
optical measurements, and to produce photographic and video records for
documentation and analysis.

Topics to be covered include:
      principles of microscope design and image formation
      bright field, dark field, phase contrast, differential
         interference contrast, interference reflection, and 
         fluorescence microscopy
      confocal scanning microscopy and image deconvolution
      digital image restoration and 3-D reconstruction
      video imaging, recording, enhancement, and intensification
      analog and digital image processing and analysis
      fluorescent probes and ratio-imaging
      laser tweezers and laser scissors

  Applications to live cells will be emphasized; other specimens will be 
covered as well.

  Students will have direct hands-on experience with state-of-the-art 
microscopes, video cameras, recorders and image processing equipment
provided by major optical and electronics companies. Instruction will be
provided by experienced staff from universities and industry.

  Students are encouraged to bring their own biological (primary 
cultures, cell lines, etc.) and material specimens and to discuss
individual research problems with the faculty.

--------------------------------
End of nih-image-d Digest V98 Issue #16
***************************************

From nih-image-request@io.ece.drexel.edu Tue Jul 21 11:17 EDT 1998
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Date: Tue, 21 Jul 1998 10:12:13 -0700
To: nih-image@io.ece.drexel.edu
From: "Randy M. Wadkins" <rwadkins@saci.org>
Subject: Re: Eudora users
Resent-Message-ID: <"BOTU81.0.r37.CvAjr"@io>
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As someone else pointed out, if you want the mailbox of individual files,
check the box in the Settings->Attachments box that says "receive MIME
digests as attachments".  If you want the old, single message digest,
uncheck this box.

--Randy

>
>------------------------------
>Date: Tue, 21 Jul 1998 08:44:58 -0400
>From: David Milstone <milstone@rascal.med.harvard.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Digest Form
>Message-Id: <v03102804b1da3d8ef39d@[134.174.88.145]>
>Content-Type: text/plain; charset="us-ascii"
>
>I use the same system with Eudora Pro 3.1 and agree that it is an improvement.
>
>>Four posts to the list have been somewhat critical of the new Digest Form
>>and its interactions with Eudora.  The basic problem is that it
>>automatically inserts new Image Digest mailboxes in the Eudora Menu.  Since
>>my own complaint was posted, however, I've developed a workaround that
>>seems fairly painless -- and it no longer requires a trip to
>>Menu/Window/Mailboxes to implement.
******************************************************************
"To be or not to...beeeeeeeeeeeeeee"
--Hamlet vs. Godzilla

Randy M. Wadkins, Ph.D.
Cancer Therapy & Research Center
Institute for Drug Development
14960 Omicron Drive
San Antonio, TX 78245
phone: (210)-677-3835
fax: (210)-677-0058
E-mail:  rwadkins@saci.org
CTRC Homepage: http://www.ccc.saci.org
******************************************************************

From nih-image-request@io.ece.drexel.edu Tue Jul 21 12:23 EDT 1998
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From: "Evdokia Achilleos" <achileos@arnold.Princeton.EDU>
Message-Id: <9807211156.ZM7001@chavi>
Date: 	Tue, 21 Jul 1998 11:56:24 -0400
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I have downloaded nih 1.62 beta Version and have
a couple of questions
1. I can not ge  the plug ins to work -
   even if i place plug ins in the nih.Image folder ,
   I get ``no plug ins '' when I go to the aquire submenu
   Is there something ``extra'' I need to do?
2. Is there a plug-in available for the photoshop unsharp mask
   filter (or an equivalent way of doing it) in NIH
3. Can I change my origin from the lower left corner to
    some known x,y?
Thanks in advance
Evie Achilleos

-- 
Evdokia Achilleos

From nih-image-request@io.ece.drexel.edu Tue Jul 21 14:13 EDT 1998
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Date: Tue, 21 Jul 1998 10:59:06 -0700
From: Jamie Eisenhart <jamie@biomail.ucsd.edu>
Organization: University of California, San Diego
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Hi Bruce,

It sounds like you want to run a median filter on each slice of the stack. That
will calculate the median of each pixel within a 3x3 window. You could try:

macro '2D Median Filter';
var
    i, n: integer;
begin
    n := nSlices;
    for i := 1 to n do begin
        chooseSlice(i);
	filter('median');
    end;
end

Jamie Eisenhart
UCSD Neuroscience

Bruce Berkowitz wrote:
> 
> Hi,
> 
> Is there a macro around that will calculate and display the pixel by pixel
> median of a stack of images? My data are not normally distributed so
> displaying the average is not really right and doesn't reflect the
> statitisics I have to do.
> 
> Thanks!
> 
> Bruce Berkowitz
> |-------------------------------------------|
> |Berkowitz Lab Home Page: http://146.9.7.69 |
> |-------------------------------------------|
> 
> Bruce Berkowitz, Ph.D.
> Department of Anatomy and Cell Biology
> Wayne State Univeristy
> 540 E. Canfield
> Detroit, MI 48201
> 
> Phone:  (313) 577-9035
> FAX:    (313) 577-3125
> E-mail: baberko@med.wayne.edu

From nih-image-request@io.ece.drexel.edu Tue Jul 21 14:31 EDT 1998
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Date: Tue, 21 Jul 1998 14:12:57 -0400
To: nih-image@io.ece.drexel.edu
From: Bruce Berkowitz <baberko@med.wayne.edu>
Subject: Re: median stack
In-Reply-To: <35B4D6EA.D176103D@biomail.ucsd.edu>
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Hi,

Thank you for your response but I don't think that was what I was looking
for. Because my data are not normally distributed I would like to calculate
a median image from a stack of 10 images INSTEAD of calculating one average
image of that stack. 

Bruce


At 10:59 AM 7/21/98 -0700, you wrote:
>Hi Bruce,
>
>It sounds like you want to run a median filter on each slice of the stack.
That
>will calculate the median of each pixel within a 3x3 window. You could try:
>
>macro '2D Median Filter';
>var
>    i, n: integer;
>begin
>    n := nSlices;
>    for i := 1 to n do begin
>        chooseSlice(i);
>	filter('median');
>    end;
>end
>
>Jamie Eisenhart
>UCSD Neuroscience
>
>Bruce Berkowitz wrote:
>> 
>> Hi,
>> 
>> Is there a macro around that will calculate and display the pixel by pixel
>> median of a stack of images? My data are not normally distributed so
>> displaying the average is not really right and doesn't reflect the
>> statitisics I have to do.
>> 
>> Thanks!
>> 
>> Bruce Berkowitz
>> |-------------------------------------------|
>> |Berkowitz Lab Home Page: http://146.9.7.69 |
>> |-------------------------------------------|
>> 
>> Bruce Berkowitz, Ph.D.
>> Department of Anatomy and Cell Biology
>> Wayne State Univeristy
>> 540 E. Canfield
>> Detroit, MI 48201
>> 
>> Phone:  (313) 577-9035
>> FAX:    (313) 577-3125
>> E-mail: baberko@med.wayne.edu
>
>
|-------------------------------------------|
|Berkowitz Lab Home Page: http://146.9.7.69 |
|-------------------------------------------|

Bruce Berkowitz, Ph.D.
Department of Anatomy and Cell Biology
Wayne State Univeristy
540 E. Canfield
Detroit, MI 48201

Phone:	(313) 577-9035
FAX:	(313) 577-3125
E-mail:	baberko@med.wayne.edu

From nih-image-request@io.ece.drexel.edu Tue Jul 21 14:59 EDT 1998
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Date: Tue, 21 Jul 1998 14:50:07 -0400 (EDT)
From: Kanu P Singh <kanu@UDel.Edu>
To: nih-image@io.ece.drexel.edu
Subject: VOID SIZE MEASUREMENT IN POLYMERS
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Hi!

I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of
hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem
that I am facing is that the boundaries of my voids are clear in the
micrographs, but the inside of the voids is the same as the rest of the
image. When I threshold the Images the boundaries appear as white while
all the rest of the image appears black. I have no idea of how to get the
void fraction or the sizes of these voids. 

One option that I have is to outline each void by hand and measure the
major and minor axes of the closest ellipses (the voids are all nearly
spherical). This is a very time consuming process since I have a lot of
micrographs to analyze. 

I would apreciate any ideas that anyone might have to help me out.

-Kanu

From nih-image-request@io.ece.drexel.edu Tue Jul 21 15:21 EDT 1998
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Ah, that is different and would be hard to do efficiently in Image. I do have a
Matlab macro that would do what you want, if that would help.

Jamie

Bruce Berkowitz wrote:
> 
> Hi,
> 
> Thank you for your response but I don't think that was what I was looking
> for. Because my data are not normally distributed I would like to calculate
> a median image from a stack of 10 images INSTEAD of calculating one average
> image of that stack.
> 
> Bruce
> 
> At 10:59 AM 7/21/98 -0700, you wrote:
> >Hi Bruce,
> >
> >It sounds like you want to run a median filter on each slice of the stack.
> That
> >will calculate the median of each pixel within a 3x3 window. You could try:
> >
> >macro '2D Median Filter';
> >var
> >    i, n: integer;
> >begin
> >    n := nSlices;
> >    for i := 1 to n do begin
> >        chooseSlice(i);
> >       filter('median');
> >    end;
> >end
> >
> >Jamie Eisenhart
> >UCSD Neuroscience
> >
> >Bruce Berkowitz wrote:
> >>
> >> Hi,
> >>
> >> Is there a macro around that will calculate and display the pixel by pixel
> >> median of a stack of images? My data are not normally distributed so
> >> displaying the average is not really right and doesn't reflect the
> >> statitisics I have to do.
> >>
> >> Thanks!
> >>
> >> Bruce Berkowitz
> >> |-------------------------------------------|
> >> |Berkowitz Lab Home Page: http://146.9.7.69 |
> >> |-------------------------------------------|
> >>
> >> Bruce Berkowitz, Ph.D.
> >> Department of Anatomy and Cell Biology
> >> Wayne State Univeristy
> >> 540 E. Canfield
> >> Detroit, MI 48201
> >>
> >> Phone:  (313) 577-9035
> >> FAX:    (313) 577-3125
> >> E-mail: baberko@med.wayne.edu
> >
> >
> |-------------------------------------------|
> |Berkowitz Lab Home Page: http://146.9.7.69 |
> |-------------------------------------------|
> 
> Bruce Berkowitz, Ph.D.
> Department of Anatomy and Cell Biology
> Wayne State Univeristy
> 540 E. Canfield
> Detroit, MI 48201
> 
> Phone:  (313) 577-9035
> FAX:    (313) 577-3125
> E-mail: baberko@med.wayne.edu

From nih-image-request@io.ece.drexel.edu Tue Jul 21 15:26 EDT 1998
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Date: Tue, 21 Jul 1998 15:14:34 -0400
To: nih-image@io.ece.drexel.edu
From: Carl Gustafson <carl.gustafson@cbis.ece.drexel.edu>
Subject: Re: VOID SIZE MEASUREMENT IN POLYMERS
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>I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of
>hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem
>that I am facing is that the boundaries of my voids are clear in the
>micrographs, but the inside of the voids is the same as the rest of the
>image. When I threshold the Images the boundaries appear as white while
>all the rest of the image appears black. I have no idea of how to get the
>void fraction or the sizes of these voids.

Can you invert the image, and do an Analyse Particles on the image, which
should now be light, with dark rings?



Carl Gustafson
(215) 895-1383
===============================================================================
           the Computer Vision Center for Vertebrate Brain Mapping
===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I'd like to give you my opinion
===============================================================================


From nih-image-request@io.ece.drexel.edu Tue Jul 21 15:45 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Bruce Berkowitz <baberko@med.wayne.edu>
Subject: Re: median stack
In-Reply-To: <35B4E776.A54349A8@biomail.ucsd.edu>
References: <3.0.1.32.19980721063939.00772da0@med.wayne.edu>
	<3.0.1.32.19980721141257.0077ba6c@med.wayne.edu>
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You imply that it could be done. I don't mind if its not efficient. Any
suggestions? Yes, please send the Matlab macro along if you don't mind.
Thank you again for your time.

At 12:09 PM 7/21/98 -0700, you wrote:
>Ah, that is different and would be hard to do efficiently in Image. I do
have a
>Matlab macro that would do what you want, if that would help.
>
>Jamie
>
>Bruce Berkowitz wrote:
>> 
>> Hi,
>> 
>> Thank you for your response but I don't think that was what I was looking
>> for. Because my data are not normally distributed I would like to calculate
>> a median image from a stack of 10 images INSTEAD of calculating one average
>> image of that stack.
>> 
>> Bruce
>> 
>> At 10:59 AM 7/21/98 -0700, you wrote:
>> >Hi Bruce,
>> >
>> >It sounds like you want to run a median filter on each slice of the stack.
>> That
>> >will calculate the median of each pixel within a 3x3 window. You could
try:
>> >
>> >macro '2D Median Filter';
>> >var
>> >    i, n: integer;
>> >begin
>> >    n := nSlices;
>> >    for i := 1 to n do begin
>> >        chooseSlice(i);
>> >       filter('median');
>> >    end;
>> >end
>> >
>> >Jamie Eisenhart
>> >UCSD Neuroscience
>> >
>> >Bruce Berkowitz wrote:
>> >>
>> >> Hi,
>> >>
>> >> Is there a macro around that will calculate and display the pixel by
pixel
>> >> median of a stack of images? My data are not normally distributed so
>> >> displaying the average is not really right and doesn't reflect the
>> >> statitisics I have to do.
>> >>
>> >> Thanks!
>> >>
>> >> Bruce Berkowitz
>> >> |-------------------------------------------|
>> >> |Berkowitz Lab Home Page: http://146.9.7.69 |
>> >> |-------------------------------------------|
>> >>
>> >> Bruce Berkowitz, Ph.D.
>> >> Department of Anatomy and Cell Biology
>> >> Wayne State Univeristy
>> >> 540 E. Canfield
>> >> Detroit, MI 48201
>> >>
>> >> Phone:  (313) 577-9035
>> >> FAX:    (313) 577-3125
>> >> E-mail: baberko@med.wayne.edu
>> >
>> >
>> |-------------------------------------------|
>> |Berkowitz Lab Home Page: http://146.9.7.69 |
>> |-------------------------------------------|
>> 
>> Bruce Berkowitz, Ph.D.
>> Department of Anatomy and Cell Biology
>> Wayne State Univeristy
>> 540 E. Canfield
>> Detroit, MI 48201
>> 
>> Phone:  (313) 577-9035
>> FAX:    (313) 577-3125
>> E-mail: baberko@med.wayne.edu
>
>
|-------------------------------------------|
|Berkowitz Lab Home Page: http://146.9.7.69 |
|-------------------------------------------|

Bruce Berkowitz, Ph.D.
Department of Anatomy and Cell Biology
Wayne State Univeristy
540 E. Canfield
Detroit, MI 48201

Phone:	(313) 577-9035
FAX:	(313) 577-3125
E-mail:	baberko@med.wayne.edu

From nih-image-request@io.ece.drexel.edu Tue Jul 21 16:08 EDT 1998
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From: Alex_Courtade@huntsman.com
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If your image is clean, perhaps you could threshold the image as normal, and
instead of highlighting the individual voids with the wand, you could highlight
the "black" area of the photo (the area of the whole photo, minus the void
area.) Then you could take the area of the entire image and subtract the "black"
area, leaving you with the area of your voids. Again, I don't have a detailed
description of your images, so I don't know whether this will work, but it's
worth a shot.

-----
Alex Courtade


____________________Reply Separator____________________
Subject:    VOID SIZE MEASUREMENT IN POLYMERS
Author: Kanu P Singh <kanu@UDel.Edu>
Date:       7/21/98 2:50 PM

Hi!

I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of
hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem
that I am facing is that the boundaries of my voids are clear in the
micrographs, but the inside of the voids is the same as the rest of the
image. When I threshold the Images the boundaries appear as white while
all the rest of the image appears black. I have no idea of how to get the
void fraction or the sizes of these voids. 

One option that I have is to outline each void by hand and measure the
major and minor axes of the closest ellipses (the voids are all nearly
spherical). This is a very time consuming process since I have a lot of
micrographs to analyze. 

I would apreciate any ideas that anyone might have to help me out.

-Kanu

From nih-image-request@io.ece.drexel.edu Tue Jul 21 16:29 EDT 1998
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From: DrJohnRuss@aol.com
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Date: Tue, 21 Jul 1998 16:17:04 EDT
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In a message dated 7/21/98 6:33:18 PM, you wrote:

>Thank you for your response but I don't think that was what I was looking
>for. Because my data are not normally distributed I would like to calculate
>a median image from a stack of 10 images INSTEAD of calculating one average
>image of that stack. 

I think you need to define what you want, and the answer may then be obvious.
for instance do you want to take the pixel values at each x,y location from
all 10 images and find the median value, and repeat this for all pixels? That
doesn't sound like a median image to me, but if that is what you want then it
is easy (but slow) to do. You will have to use a sort procedure in your macro
to get the median (and then since you have an even number of images will have
to probably average the 5th and 6th ranked values).

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From: "Grace,John" <John.Grace@add.ssw.abbott.com>
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Subject: Sum of Values in particle analysis
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Dear imagers,
I am trying to find the amount of ink in spots printed on a card, I also want
the degree of variation/uniformity of the coating of these spots. I have been
thresholding the spot then using the analyze particles command I am getting
the mean intensity, SD and area of the spot.  Is there a way to get the sum
of pixel values in the spot?
Thanks,
John P. Grace
Abbott Laboratories

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Date: 	Tue, 21 Jul 1998 17:48:15 -0400
From: Xudong Cao <xudong@chem-eng.toronto.edu>
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Hi there,
I am trying to evaluate the concentration of my fluorescin labeled 
protein in gels by determining the optic density of the fluorescence 
under the microscope by NIH image analysis software. My question is 
whether the pixels that are represented by the 8-bit integers are in a 
linear relationship, say value 1 represents as twice intensity as that 
of value 2? and how about value 0 (the white color)?  

I would highly appreciate any help from you in this regard.

thanks.

Sincerely,
_______________________________
Xudong CAO
Center for Biomaterials
University of Toronto             	
Phone: (416) 978 0343		 
Fax: (416) 978 1462               

In science one tries to tell people, in such a way as to be 
understood by everyone, something that no one ever knew 
before. But in poetry, it's the exact opposite. 
- Paul Dirac               
                                 


From nih-image-request@io.ece.drexel.edu Tue Jul 21 18:41 EDT 1998
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Unless I am mistaken the total that you want is simply the mean X the area
(which should be the number of pixels if you have not calibrated anything)


-----Original Message-----
From: Grace,John <John.Grace@add.ssw.abbott.com>
To: nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
Date: Tuesday, July 21, 1998 4:22 PM
Subject: Sum of Values in particle analysis


>Dear imagers,
>I am trying to find the amount of ink in spots printed on a card, I also
want
>the degree of variation/uniformity of the coating of these spots. I have
been
>thresholding the spot then using the analyze particles command I am getting
>the mean intensity, SD and area of the spot.  Is there a way to get the sum
>of pixel values in the spot?
>Thanks,
>John P. Grace
>Abbott Laboratories
>
>

From nih-image-request@io.ece.drexel.edu Tue Jul 21 19:51 EDT 1998
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Message-ID: <35B5277A.544C55B6@biomail.ucsd.edu>
Date: Tue, 21 Jul 1998 16:42:50 -0700
From: Jamie Eisenhart <jamie@biomail.ucsd.edu>
Organization: University of California, San Diego
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References: <3.0.1.32.19980721063939.00772da0@med.wayne.edu>
  <3.0.1.32.19980721141257.0077ba6c@med.wayne.edu> <3.0.1.32.19980721153149.00774140@med.wayne.edu>
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I think that the only way to do it in Image would be to do the median
calculation directly in the macro and iterate over each x-y pixel location.
This could take hours. I'll send you my Matlab median routine separately.

Good luck,
Jamie

Bruce Berkowitz wrote:
> 
> You imply that it could be done. I don't mind if its not efficient. Any
> suggestions? Yes, please send the Matlab macro along if you don't mind.
> Thank you again for your time.
> 
> At 12:09 PM 7/21/98 -0700, you wrote:
> >Ah, that is different and would be hard to do efficiently in Image. I do
> have a
> >Matlab macro that would do what you want, if that would help.
> >
> >Jamie

From nih-image-request@io.ece.drexel.edu Tue Jul 21 21:12 EDT 1998
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Date: Tue, 21 Jul 1998 18:07:05 -0700
From: "R. Aaron (Boy) Warnock" <awarnock@cmgm.stanford.edu>
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Howdy,

	We're thinking of replacing our very old COHU SIT 
and therefore have been considering the Dage-MTI and Hamamatsu
cameras. We were considering the Dage VE 1000 SIT system, but
then heard that Dage-MTI was getting out of the "Scientific
imaging" and/or perhaps the "SIT camera" market(s); and have
been advised to avoid them. Any truth to this?

Furthermore, we've been told the Hamamatsu 2400-8 system comes
with no choice of tube grade (but most likely a grade 2). Is 
this also true?

Any additional thoughts about these cameras, and/or the Argus-20
DSP versus the Dage-MTI DSP-2000 would be appreciated.

Thanks in advace,

Aaron


-- 
R. Aaron Warnock
"Nothing more is needed to destroy a man than the conviction
that his life's work is useless." -Antonin Artaud

Lab Address:
Dept. of Pathology L-235	awarnock@cmgm.stanford.edu
Stanford, CA 94305		Tel. (650) 493-5000 x63167

Home Address:
777 Arguello Blvd. #304		Tel. (415) 831-3425
San Francisco, CA 94118

From nih-image-request@io.ece.drexel.edu Tue Jul 21 21:21 EDT 1998
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Date: Tue, 21 Jul 1998 19:16:39 -0600
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To: Kanu P Singh <kanu@UDel.Edu>
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Well, I see too solutions to your problem:
1) The physical solution:  Before photographing your samples, rub them with a
white paste or wax to fill the voids, then photograph.  This should produce
white spots where the voids are on a black background.  The only possible
problem with this approach is if the samples are too delicate to be handled in
this fashion.

2) The computational approcah:  Choose 'Anaylze Particles' from the Analyze
menu, and select 'Include interior holes.'  This should treat the black center
of your voids as a hole in a white particle, and give you the measurements you
want.  The only problem here would be if the boundry is thin enough that it has
breaks in it, preventing the program from identifying the border as an object.

Chris Tully
Image Processing Consultant

Kanu P Singh wrote:
> 
> Hi!
> 
> I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of
> hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem
> that I am facing is that the boundaries of my voids are clear in the
> micrographs, but the inside of the voids is the same as the rest of the
> image. When I threshold the Images the boundaries appear as white while
> all the rest of the image appears black. I have no idea of how to get the
> void fraction or the sizes of these voids.
> 
> One option that I have is to outline each void by hand and measure the
> major and minor axes of the closest ellipses (the voids are all nearly
> spherical). This is a very time consuming process since I have a lot of
> micrographs to analyze.
> 
> I would apreciate any ideas that anyone might have to help me out.
> 
> -Kanu

From nih-image-request@io.ece.drexel.edu Tue Jul 21 22:58 EDT 1998
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No they are not . Your gels must be calibrated ie OD vs grey scale. See the
tutorial at NIH Image home page for a detailed explanation. I believe you
will find it under the "More Documentation" link.
-----Original Message-----
From: Xudong Cao <xudong@chem-eng.toronto.edu>
To: nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
Date: Tuesday, July 21, 1998 5:49 PM
Subject: Image density??


>
>Hi there,
>I am trying to evaluate the concentration of my fluorescin labeled
>protein in gels by determining the optic density of the fluorescence
>under the microscope by NIH image analysis software. My question is
>whether the pixels that are represented by the 8-bit integers are in a
>linear relationship, say value 1 represents as twice intensity as that
>of value 2? and how about value 0 (the white color)?
>
>I would highly appreciate any help from you in this regard.
>
>thanks.
>
>Sincerely,
>_______________________________
>Xudong CAO
>Center for Biomaterials
>University of Toronto
>Phone: (416) 978 0343
>Fax: (416) 978 1462
>
>In science one tries to tell people, in such a way as to be
>understood by everyone, something that no one ever knew
>before. But in poetry, it's the exact opposite.
>- Paul Dirac
>
>
>
>

From nih-image-request@io.ece.drexel.edu Wed Jul 22 05:21 EDT 1998
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From: SangHa Leigh <sleigh@rist.re.kr>
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=========================================================
SangHa Leigh, Ph.D.

Materials Research Division
Research Institute of Industrial Science and Technology (RIST)
P.O. Box 135
Pohang 790-600, Korea

Tel: +82-(0)562-279-6498
Fax: +82-(0)562-279-6199 (Office)
        +82-(0)562-46-0643 (Home)
Cellular: +82-(0)17-342-0643

Personal homepage - http://dol1.eng.sunysb.edu/students/sangha.html
RIST homepage - http://www.rist.re.kr
POSCO homepage - http://www.posco.co.kr
=================================================== 

From nih-image-d-request@io.ece.drexel.edu Wed Jul 22 05:23 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199807220923.FAA21196@io.ECE.Drexel.EDU>
Subject: nih-image-d Digest V98 #17
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 17

Today's Topics:
  Re: Eudora users                      [ "Randy M. Wadkins" <rwadkins@saci.o ]
  Plug-in,Unsharp,and set origin        [ "Evdokia Achilleos" <achileos@arnol ]
  Re: median stack                      [ Jamie Eisenhart <jamie@biomail.ucsd ]
  Re: median stack                      [ Bruce Berkowitz <baberko@med.wayne. ]
  VOID SIZE MEASUREMENT IN POLYMERS     [ Kanu P Singh <kanu@UDel.Edu> ]
  Re: median stack                      [ Jamie Eisenhart <jamie@biomail.ucsd ]
  Re: VOID SIZE MEASUREMENT IN POLYMER  [ Carl Gustafson <carl.gustafson@cbis ]
  Re: median stack                      [ Bruce Berkowitz <baberko@med.wayne. ]
  Re: VOID SIZE MEASUREMENT IN POLYMER  [ Alex_Courtade@huntsman.com ]
  Re: Re: median stack                  [ DrJohnRuss@aol.com ]
  Sum of Values in particle analysis    [ "Grace,John" <John.Grace@add.ssw.ab ]
  Image density??                       [ Xudong Cao <xudong@chem-eng.toronto ]
  Re: Sum of Values in particle analys  [ "Todd Prior" <priort@mcmaster.ca> ]
  Re: median stack                      [ Jamie Eisenhart <jamie@biomail.ucsd ]
  Dage SIT cameras                      [ "R. Aaron (Boy) Warnock" <awarnock@ ]
  Re: VOID SIZE MEASUREMENT IN POLYMER  [ "Christopher P. Tully" <cptully@sis ]
  Re: Image density??                   [ "Todd Prior" <priort@mcmaster.ca> ]
  unsubscribe                           [ SangHa Leigh <sleigh@rist.re.kr> ]

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

Date: Tue, 21 Jul 1998 10:12:13 -0700
From: "Randy M. Wadkins" <rwadkins@saci.org>
To: nih-image@io.ece.drexel.edu
Subject: Re: Eudora users
Message-Id: <v04011700b1da7bc0c61f@[192.238.18.184]>
Content-Type: text/plain; charset="us-ascii"

As someone else pointed out, if you want the mailbox of individual files,
check the box in the Settings->Attachments box that says "receive MIME
digests as attachments".  If you want the old, single message digest,
uncheck this box.

--Randy

>
>------------------------------
>Date: Tue, 21 Jul 1998 08:44:58 -0400
>From: David Milstone <milstone@rascal.med.harvard.edu>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Digest Form
>Message-Id: <v03102804b1da3d8ef39d@[134.174.88.145]>
>Content-Type: text/plain; charset="us-ascii"
>
>I use the same system with Eudora Pro 3.1 and agree that it is an improvement.
>
>>Four posts to the list have been somewhat critical of the new Digest Form
>>and its interactions with Eudora.  The basic problem is that it
>>automatically inserts new Image Digest mailboxes in the Eudora Menu.  Since
>>my own complaint was posted, however, I've developed a workaround that
>>seems fairly painless -- and it no longer requires a trip to
>>Menu/Window/Mailboxes to implement.
******************************************************************
"To be or not to...beeeeeeeeeeeeeee"
--Hamlet vs. Godzilla

Randy M. Wadkins, Ph.D.
Cancer Therapy & Research Center
Institute for Drug Development
14960 Omicron Drive
San Antonio, TX 78245
phone: (210)-677-3835
fax: (210)-677-0058
E-mail:  rwadkins@saci.org
CTRC Homepage: http://www.ccc.saci.org
******************************************************************

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

Date: 	Tue, 21 Jul 1998 11:56:24 -0400
From: "Evdokia Achilleos" <achileos@arnold.Princeton.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Plug-in,Unsharp,and set origin
Message-Id: <9807211156.ZM7001@chavi>
Content-Type: text/plain; charset=us-ascii

I have downloaded nih 1.62 beta Version and have
a couple of questions
1. I can not ge  the plug ins to work -
   even if i place plug ins in the nih.Image folder ,
   I get ``no plug ins '' when I go to the aquire submenu
   Is there something ``extra'' I need to do?
2. Is there a plug-in available for the photoshop unsharp mask
   filter (or an equivalent way of doing it) in NIH
3. Can I change my origin from the lower left corner to
    some known x,y?
Thanks in advance
Evie Achilleos

-- 
Evdokia Achilleos

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

Date: Tue, 21 Jul 1998 10:59:06 -0700
From: Jamie Eisenhart <jamie@biomail.ucsd.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: median stack
Message-ID: <35B4D6EA.D176103D@biomail.ucsd.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi Bruce,

It sounds like you want to run a median filter on each slice of the stack. That
will calculate the median of each pixel within a 3x3 window. You could try:

macro '2D Median Filter';
var
    i, n: integer;
begin
    n := nSlices;
    for i := 1 to n do begin
        chooseSlice(i);
	filter('median');
    end;
end

Jamie Eisenhart
UCSD Neuroscience

Bruce Berkowitz wrote:
> 
> Hi,
> 
> Is there a macro around that will calculate and display the pixel by pixel
> median of a stack of images? My data are not normally distributed so
> displaying the average is not really right and doesn't reflect the
> statitisics I have to do.
> 
> Thanks!
> 
> Bruce Berkowitz
> |-------------------------------------------|
> |Berkowitz Lab Home Page: http://146.9.7.69 |
> |-------------------------------------------|
> 
> Bruce Berkowitz, Ph.D.
> Department of Anatomy and Cell Biology
> Wayne State Univeristy
> 540 E. Canfield
> Detroit, MI 48201
> 
> Phone:  (313) 577-9035
> FAX:    (313) 577-3125
> E-mail: baberko@med.wayne.edu

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

Date: Tue, 21 Jul 1998 14:12:57 -0400
From: Bruce Berkowitz <baberko@med.wayne.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: median stack
Message-Id: <3.0.1.32.19980721141257.0077ba6c@med.wayne.edu>
Content-Type: text/plain; charset="us-ascii"

Hi,

Thank you for your response but I don't think that was what I was looking
for. Because my data are not normally distributed I would like to calculate
a median image from a stack of 10 images INSTEAD of calculating one average
image of that stack. 

Bruce


At 10:59 AM 7/21/98 -0700, you wrote:
>Hi Bruce,
>
>It sounds like you want to run a median filter on each slice of the stack.
That
>will calculate the median of each pixel within a 3x3 window. You could try:
>
>macro '2D Median Filter';
>var
>    i, n: integer;
>begin
>    n := nSlices;
>    for i := 1 to n do begin
>        chooseSlice(i);
>	filter('median');
>    end;
>end
>
>Jamie Eisenhart
>UCSD Neuroscience
>
>Bruce Berkowitz wrote:
>> 
>> Hi,
>> 
>> Is there a macro around that will calculate and display the pixel by pixel
>> median of a stack of images? My data are not normally distributed so
>> displaying the average is not really right and doesn't reflect the
>> statitisics I have to do.
>> 
>> Thanks!
>> 
>> Bruce Berkowitz
>> |-------------------------------------------|
>> |Berkowitz Lab Home Page: http://146.9.7.69 |
>> |-------------------------------------------|
>> 
>> Bruce Berkowitz, Ph.D.
>> Department of Anatomy and Cell Biology
>> Wayne State Univeristy
>> 540 E. Canfield
>> Detroit, MI 48201
>> 
>> Phone:  (313) 577-9035
>> FAX:    (313) 577-3125
>> E-mail: baberko@med.wayne.edu
>
>
|-------------------------------------------|
|Berkowitz Lab Home Page: http://146.9.7.69 |
|-------------------------------------------|

Bruce Berkowitz, Ph.D.
Department of Anatomy and Cell Biology
Wayne State Univeristy
540 E. Canfield
Detroit, MI 48201

Phone:	(313) 577-9035
FAX:	(313) 577-3125
E-mail:	baberko@med.wayne.edu

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

Date: Tue, 21 Jul 1998 14:50:07 -0400 (EDT)
From: Kanu P Singh <kanu@UDel.Edu>
To: nih-image@io.ece.drexel.edu
Subject: VOID SIZE MEASUREMENT IN POLYMERS
Message-ID: <Pine.SOL.3.96.980721144226.19746A-100000@copland.udel.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi!

I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of
hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem
that I am facing is that the boundaries of my voids are clear in the
micrographs, but the inside of the voids is the same as the rest of the
image. When I threshold the Images the boundaries appear as white while
all the rest of the image appears black. I have no idea of how to get the
void fraction or the sizes of these voids. 

One option that I have is to outline each void by hand and measure the
major and minor axes of the closest ellipses (the voids are all nearly
spherical). This is a very time consuming process since I have a lot of
micrographs to analyze. 

I would apreciate any ideas that anyone might have to help me out.

-Kanu

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

Date: Tue, 21 Jul 1998 12:09:42 -0700
From: Jamie Eisenhart <jamie@biomail.ucsd.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: median stack
Message-ID: <35B4E776.A54349A8@biomail.ucsd.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Ah, that is different and would be hard to do efficiently in Image. I do have a
Matlab macro that would do what you want, if that would help.

Jamie

Bruce Berkowitz wrote:
> 
> Hi,
> 
> Thank you for your response but I don't think that was what I was looking
> for. Because my data are not normally distributed I would like to calculate
> a median image from a stack of 10 images INSTEAD of calculating one average
> image of that stack.
> 
> Bruce
> 
> At 10:59 AM 7/21/98 -0700, you wrote:
> >Hi Bruce,
> >
> >It sounds like you want to run a median filter on each slice of the stack.
> That
> >will calculate the median of each pixel within a 3x3 window. You could try:
> >
> >macro '2D Median Filter';
> >var
> >    i, n: integer;
> >begin
> >    n := nSlices;
> >    for i := 1 to n do begin
> >        chooseSlice(i);
> >       filter('median');
> >    end;
> >end
> >
> >Jamie Eisenhart
> >UCSD Neuroscience
> >
> >Bruce Berkowitz wrote:
> >>
> >> Hi,
> >>
> >> Is there a macro around that will calculate and display the pixel by pixel
> >> median of a stack of images? My data are not normally distributed so
> >> displaying the average is not really right and doesn't reflect the
> >> statitisics I have to do.
> >>
> >> Thanks!
> >>
> >> Bruce Berkowitz
> >> |-------------------------------------------|
> >> |Berkowitz Lab Home Page: http://146.9.7.69 |
> >> |-------------------------------------------|
> >>
> >> Bruce Berkowitz, Ph.D.
> >> Department of Anatomy and Cell Biology
> >> Wayne State Univeristy
> >> 540 E. Canfield
> >> Detroit, MI 48201
> >>
> >> Phone:  (313) 577-9035
> >> FAX:    (313) 577-3125
> >> E-mail: baberko@med.wayne.edu
> >
> >
> |-------------------------------------------|
> |Berkowitz Lab Home Page: http://146.9.7.69 |
> |-------------------------------------------|
> 
> Bruce Berkowitz, Ph.D.
> Department of Anatomy and Cell Biology
> Wayne State Univeristy
> 540 E. Canfield
> Detroit, MI 48201
> 
> Phone:  (313) 577-9035
> FAX:    (313) 577-3125
> E-mail: baberko@med.wayne.edu

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

Date: Tue, 21 Jul 1998 15:14:34 -0400
From: Carl Gustafson <carl.gustafson@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: VOID SIZE MEASUREMENT IN POLYMERS
Message-Id: <v0311070bb1da98ee7b50@[144.118.33.205]>
Content-Type: text/plain; charset="us-ascii"

>I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of
>hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem
>that I am facing is that the boundaries of my voids are clear in the
>micrographs, but the inside of the voids is the same as the rest of the
>image. When I threshold the Images the boundaries appear as white while
>all the rest of the image appears black. I have no idea of how to get the
>void fraction or the sizes of these voids.

Can you invert the image, and do an Analyse Particles on the image, which
should now be light, with dark rings?



Carl Gustafson
(215) 895-1383
===============================================================================
           the Computer Vision Center for Vertebrate Brain Mapping
===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I'd like to give you my opinion
===============================================================================

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

Date: Tue, 21 Jul 1998 15:31:49 -0400
From: Bruce Berkowitz <baberko@med.wayne.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: median stack
Message-Id: <3.0.1.32.19980721153149.00774140@med.wayne.edu>
Content-Type: text/plain; charset="us-ascii"

You imply that it could be done. I don't mind if its not efficient. Any
suggestions? Yes, please send the Matlab macro along if you don't mind.
Thank you again for your time.

At 12:09 PM 7/21/98 -0700, you wrote:
>Ah, that is different and would be hard to do efficiently in Image. I do
have a
>Matlab macro that would do what you want, if that would help.
>
>Jamie
>
>Bruce Berkowitz wrote:
>> 
>> Hi,
>> 
>> Thank you for your response but I don't think that was what I was looking
>> for. Because my data are not normally distributed I would like to calculate
>> a median image from a stack of 10 images INSTEAD of calculating one average
>> image of that stack.
>> 
>> Bruce
>> 
>> At 10:59 AM 7/21/98 -0700, you wrote:
>> >Hi Bruce,
>> >
>> >It sounds like you want to run a median filter on each slice of the stack.
>> That
>> >will calculate the median of each pixel within a 3x3 window. You could
try:
>> >
>> >macro '2D Median Filter';
>> >var
>> >    i, n: integer;
>> >begin
>> >    n := nSlices;
>> >    for i := 1 to n do begin
>> >        chooseSlice(i);
>> >       filter('median');
>> >    end;
>> >end
>> >
>> >Jamie Eisenhart
>> >UCSD Neuroscience
>> >
>> >Bruce Berkowitz wrote:
>> >>
>> >> Hi,
>> >>
>> >> Is there a macro around that will calculate and display the pixel by
pixel
>> >> median of a stack of images? My data are not normally distributed so
>> >> displaying the average is not really right and doesn't reflect the
>> >> statitisics I have to do.
>> >>
>> >> Thanks!
>> >>
>> >> Bruce Berkowitz
>> >> |-------------------------------------------|
>> >> |Berkowitz Lab Home Page: http://146.9.7.69 |
>> >> |-------------------------------------------|
>> >>
>> >> Bruce Berkowitz, Ph.D.
>> >> Department of Anatomy and Cell Biology
>> >> Wayne State Univeristy
>> >> 540 E. Canfield
>> >> Detroit, MI 48201
>> >>
>> >> Phone:  (313) 577-9035
>> >> FAX:    (313) 577-3125
>> >> E-mail: baberko@med.wayne.edu
>> >
>> >
>> |-------------------------------------------|
>> |Berkowitz Lab Home Page: http://146.9.7.69 |
>> |-------------------------------------------|
>> 
>> Bruce Berkowitz, Ph.D.
>> Department of Anatomy and Cell Biology
>> Wayne State Univeristy
>> 540 E. Canfield
>> Detroit, MI 48201
>> 
>> Phone:  (313) 577-9035
>> FAX:    (313) 577-3125
>> E-mail: baberko@med.wayne.edu
>
>
|-------------------------------------------|
|Berkowitz Lab Home Page: http://146.9.7.69 |
|-------------------------------------------|

Bruce Berkowitz, Ph.D.
Department of Anatomy and Cell Biology
Wayne State Univeristy
540 E. Canfield
Detroit, MI 48201

Phone:	(313) 577-9035
FAX:	(313) 577-3125
E-mail:	baberko@med.wayne.edu

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

Date: Tue, 21 Jul 1998 14:48:35 -0500
From: Alex_Courtade@huntsman.com
To: nih-image@io.ece.drexel.edu
Subject: Re: VOID SIZE MEASUREMENT IN POLYMERS
Message-ID: <0000665B.CE21466@huntsman.com>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Description: cc:Mail note part

If your image is clean, perhaps you could threshold the image as normal, and
instead of highlighting the individual voids with the wand, you could highlight
the "black" area of the photo (the area of the whole photo, minus the void
area.) Then you could take the area of the entire image and subtract the "black"
area, leaving you with the area of your voids. Again, I don't have a detailed
description of your images, so I don't know whether this will work, but it's
worth a shot.

-----
Alex Courtade


____________________Reply Separator____________________
Subject:    VOID SIZE MEASUREMENT IN POLYMERS
Author: Kanu P Singh <kanu@UDel.Edu>
Date:       7/21/98 2:50 PM

Hi!

I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of
hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem
that I am facing is that the boundaries of my voids are clear in the
micrographs, but the inside of the voids is the same as the rest of the
image. When I threshold the Images the boundaries appear as white while
all the rest of the image appears black. I have no idea of how to get the
void fraction or the sizes of these voids. 

One option that I have is to outline each void by hand and measure the
major and minor axes of the closest ellipses (the voids are all nearly
spherical). This is a very time consuming process since I have a lot of
micrographs to analyze. 

I would apreciate any ideas that anyone might have to help me out.

-Kanu

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

Date: Tue, 21 Jul 1998 16:17:04 EDT
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re:  Re: median stack
Message-ID: <6f909b7b.35b4f741@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

In a message dated 7/21/98 6:33:18 PM, you wrote:

>Thank you for your response but I don't think that was what I was looking
>for. Because my data are not normally distributed I would like to calculate
>a median image from a stack of 10 images INSTEAD of calculating one average
>image of that stack. 

I think you need to define what you want, and the answer may then be obvious.
for instance do you want to take the pixel values at each x,y location from
all 10 images and find the median value, and repeat this for all pixels? That
doesn't sound like a median image to me, but if that is what you want then it
is easy (but slow) to do. You will have to use a sort procedure in your macro
to get the median (and then since you have an even number of images will have
to probably average the 5th and 6th ranked values).

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

Date: Tue, 21 Jul 1998 15:24:36 -0500
From: "Grace,John" <John.Grace@add.ssw.abbott.com>
To: <nih-image@io.ece.drexel.edu>
Subject: Sum of Values in particle analysis
Message-Id: <0055600001401889000002L092*@MHS>
Content-Type: text/plain; charset=iso-8859-1
Content-Disposition: inline
Content-Transfer-Encoding: 8bit

Dear imagers,
I am trying to find the amount of ink in spots printed on a card, I also want
the degree of variation/uniformity of the coating of these spots. I have been
thresholding the spot then using the analyze particles command I am getting
the mean intensity, SD and area of the spot.  Is there a way to get the sum
of pixel values in the spot?
Thanks,
John P. Grace
Abbott Laboratories

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

Date: 	Tue, 21 Jul 1998 17:48:15 -0400
From: Xudong Cao <xudong@chem-eng.toronto.edu>
To: nih-image@io.ece.drexel.edu
Subject: Image density?? 
Message-ID: <Pine.SGI.3.91.980721174738.9916C-100000@chem-eng>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi there,
I am trying to evaluate the concentration of my fluorescin labeled 
protein in gels by determining the optic density of the fluorescence 
under the microscope by NIH image analysis software. My question is 
whether the pixels that are represented by the 8-bit integers are in a 
linear relationship, say value 1 represents as twice intensity as that 
of value 2? and how about value 0 (the white color)?  

I would highly appreciate any help from you in this regard.

thanks.

Sincerely,
_______________________________
Xudong CAO
Center for Biomaterials
University of Toronto             	
Phone: (416) 978 0343		 
Fax: (416) 978 1462               

In science one tries to tell people, in such a way as to be 
understood by everyone, something that no one ever knew 
before. But in poetry, it's the exact opposite. 
- Paul Dirac               
                                 

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

Date: Tue, 21 Jul 1998 18:37:47 -0400
From: "Todd Prior" <priort@mcmaster.ca>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: Sum of Values in particle analysis
Message-ID: <002101bdb4f8$312c0720$ccc07182@MyHost.McMaster.CA>
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 7bit

Unless I am mistaken the total that you want is simply the mean X the area
(which should be the number of pixels if you have not calibrated anything)


-----Original Message-----
From: Grace,John <John.Grace@add.ssw.abbott.com>
To: nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
Date: Tuesday, July 21, 1998 4:22 PM
Subject: Sum of Values in particle analysis


>Dear imagers,
>I am trying to find the amount of ink in spots printed on a card, I also
want
>the degree of variation/uniformity of the coating of these spots. I have
been
>thresholding the spot then using the analyze particles command I am getting
>the mean intensity, SD and area of the spot.  Is there a way to get the sum
>of pixel values in the spot?
>Thanks,
>John P. Grace
>Abbott Laboratories
>
>

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

Date: Tue, 21 Jul 1998 16:42:50 -0700
From: Jamie Eisenhart <jamie@biomail.ucsd.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: median stack
Message-ID: <35B5277A.544C55B6@biomail.ucsd.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

I think that the only way to do it in Image would be to do the median
calculation directly in the macro and iterate over each x-y pixel location.
This could take hours. I'll send you my Matlab median routine separately.

Good luck,
Jamie

Bruce Berkowitz wrote:
> 
> You imply that it could be done. I don't mind if its not efficient. Any
> suggestions? Yes, please send the Matlab macro along if you don't mind.
> Thank you again for your time.
> 
> At 12:09 PM 7/21/98 -0700, you wrote:
> >Ah, that is different and would be hard to do efficiently in Image. I do
> have a
> >Matlab macro that would do what you want, if that would help.
> >
> >Jamie

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

Date: Tue, 21 Jul 1998 18:07:05 -0700
From: "R. Aaron (Boy) Warnock" <awarnock@cmgm.stanford.edu>
To: nih-image@io.ece.drexel.edu
Subject: Dage SIT cameras
Message-ID: <35B53B39.50D0@cmgm.stanford.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Howdy,

	We're thinking of replacing our very old COHU SIT 
and therefore have been considering the Dage-MTI and Hamamatsu
cameras. We were considering the Dage VE 1000 SIT system, but
then heard that Dage-MTI was getting out of the "Scientific
imaging" and/or perhaps the "SIT camera" market(s); and have
been advised to avoid them. Any truth to this?

Furthermore, we've been told the Hamamatsu 2400-8 system comes
with no choice of tube grade (but most likely a grade 2). Is 
this also true?

Any additional thoughts about these cameras, and/or the Argus-20
DSP versus the Dage-MTI DSP-2000 would be appreciated.

Thanks in advace,

Aaron


-- 
R. Aaron Warnock
"Nothing more is needed to destroy a man than the conviction
that his life's work is useless." -Antonin Artaud

Lab Address:
Dept. of Pathology L-235	awarnock@cmgm.stanford.edu
Stanford, CA 94305		Tel. (650) 493-5000 x63167

Home Address:
777 Arguello Blvd. #304		Tel. (415) 831-3425
San Francisco, CA 94118

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

Date: Tue, 21 Jul 1998 19:16:39 -0600
From: "Christopher P. Tully" <cptully@sisna.com>
To: Kanu P Singh <kanu@UDel.Edu>
CC: NIH-Image <nih-image@io.ece.drexel.edu>
Subject: Re: VOID SIZE MEASUREMENT IN POLYMERS
Message-ID: <35B53D77.D9B6FDCB@sisna.com>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Well, I see too solutions to your problem:
1) The physical solution:  Before photographing your samples, rub them with a
white paste or wax to fill the voids, then photograph.  This should produce
white spots where the voids are on a black background.  The only possible
problem with this approach is if the samples are too delicate to be handled in
this fashion.

2) The computational approcah:  Choose 'Anaylze Particles' from the Analyze
menu, and select 'Include interior holes.'  This should treat the black center
of your voids as a hole in a white particle, and give you the measurements you
want.  The only problem here would be if the boundry is thin enough that it has
breaks in it, preventing the program from identifying the border as an object.

Chris Tully
Image Processing Consultant

Kanu P Singh wrote:
> 
> Hi!
> 
> I am trying to use NIH Image to analyze void sizes in my SEM mcrographs of
> hardened phenol-formaldehyde resin ( a thermosetting polymer). The problem
> that I am facing is that the boundaries of my voids are clear in the
> micrographs, but the inside of the voids is the same as the rest of the
> image. When I threshold the Images the boundaries appear as white while
> all the rest of the image appears black. I have no idea of how to get the
> void fraction or the sizes of these voids.
> 
> One option that I have is to outline each void by hand and measure the
> major and minor axes of the closest ellipses (the voids are all nearly
> spherical). This is a very time consuming process since I have a lot of
> micrographs to analyze.
> 
> I would apreciate any ideas that anyone might have to help me out.
> 
> -Kanu

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

Date: Tue, 21 Jul 1998 22:55:50 -0400
From: "Todd Prior" <priort@mcmaster.ca>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: Image density?? 
Message-ID: <001c01bdb51c$3e596680$b3c07182@MyHost.McMaster.CA>
Content-Type: text/plain;
	charset="us-ascii"
Content-Transfer-Encoding: 7bit

No they are not . Your gels must be calibrated ie OD vs grey scale. See the
tutorial at NIH Image home page for a detailed explanation. I believe you
will find it under the "More Documentation" link.
-----Original Message-----
From: Xudong Cao <xudong@chem-eng.toronto.edu>
To: nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
Date: Tuesday, July 21, 1998 5:49 PM
Subject: Image density??


>
>Hi there,
>I am trying to evaluate the concentration of my fluorescin labeled
>protein in gels by determining the optic density of the fluorescence
>under the microscope by NIH image analysis software. My question is
>whether the pixels that are represented by the 8-bit integers are in a
>linear relationship, say value 1 represents as twice intensity as that
>of value 2? and how about value 0 (the white color)?
>
>I would highly appreciate any help from you in this regard.
>
>thanks.
>
>Sincerely,
>_______________________________
>Xudong CAO
>Center for Biomaterials
>University of Toronto
>Phone: (416) 978 0343
>Fax: (416) 978 1462
>
>In science one tries to tell people, in such a way as to be
>understood by everyone, something that no one ever knew
>before. But in poetry, it's the exact opposite.
>- Paul Dirac
>
>
>
>

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

Date: Wed, 22 Jul 1998 18:17:02 +0900
From: SangHa Leigh <sleigh@rist.re.kr>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: unsubscribe
Message-ID: <01BDB59C.EE03E440.sleigh@risnet.rist.re.kr>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit

=========================================================
SangHa Leigh, Ph.D.

Materials Research Division
Research Institute of Industrial Science and Technology (RIST)
P.O. Box 135
Pohang 790-600, Korea

Tel: +82-(0)562-279-6498
Fax: +82-(0)562-279-6199 (Office)
        +82-(0)562-46-0643 (Home)
Cellular: +82-(0)17-342-0643

Personal homepage - http://dol1.eng.sunysb.edu/students/sangha.html
RIST homepage - http://www.rist.re.kr
POSCO homepage - http://www.posco.co.kr
=================================================== 

--------------------------------
End of nih-image-d Digest V98 Issue #17
***************************************

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To: nih-image@io.ece.drexel.edu
From: Bruce Berkowitz <baberko@med.wayne.edu>
Subject: Re:  Re: median stack
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yes, I want to create a new image using the median value at a particular
x,y location from those 10 images, repeated over all pixels. Do you have an
example of a sort routine that will do this?
Thank you for your time!
Bruce

At 04:17 PM 7/21/98 EDT, you wrote:
>
>In a message dated 7/21/98 6:33:18 PM, you wrote:
>
>>Thank you for your response but I don't think that was what I was looking
>>for. Because my data are not normally distributed I would like to calculate
>>a median image from a stack of 10 images INSTEAD of calculating one average
>>image of that stack. 
>
>I think you need to define what you want, and the answer may then be obvious.
>for instance do you want to take the pixel values at each x,y location from
>all 10 images and find the median value, and repeat this for all pixels? That
>doesn't sound like a median image to me, but if that is what you want then it
>is easy (but slow) to do. You will have to use a sort procedure in your macro
>to get the median (and then since you have an even number of images will have
>to probably average the 5th and 6th ranked values).
>
>
|-------------------------------------------|
|Berkowitz Lab Home Page: http://146.9.7.69 |
|-------------------------------------------|

Bruce Berkowitz, Ph.D.
Department of Anatomy and Cell Biology
Wayne State Univeristy
540 E. Canfield
Detroit, MI 48201

Phone:	(313) 577-9035
FAX:	(313) 577-3125
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From nih-image-request@io.ece.drexel.edu Wed Jul 22 07:44 EDT 1998
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From: DrJohnRuss@aol.com
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Date: Wed, 22 Jul 1998 07:34:47 EDT
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In a message dated 7/22/98 10:33:31 AM, you wrote:

>yes, I want to create a new image using the median value at a particular
>x,y location from those 10 images, repeated over all pixels. Do you have an
>example of a sort routine that will do this?

For a small number of values, a shell sort is probably the most efficient and
easy to program. Details and code examples available in any standard numerical
recipes book

From nih-image-request@io.ece.drexel.edu Wed Jul 22 08:23 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Mark A Vivino <mvivino@helix.nih.gov>
Subject: Re: Image density??
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>Hi there,
>I am trying to evaluate the concentration of my fluorescin labeled
>protein in gels by determining the optic density of the fluorescence
>under the microscope by NIH image analysis software. My question is
>whether the pixels that are represented by the 8-bit integers are in a
>linear relationship, say value 1 represents as twice intensity as that
>of value 2? and how about value 0 (the white color)?

You can see in:

http://rsb.info.nih.gov/nih-image/more-docs/Engineering/ImgEngr.html#densitometr
y

As often stated on the list, never make the mistake in assuming a linear
relationship of pixels and concentrations. 100 is not twice 50 and for good
reasons. If pixels represented linear relationships to concentration we
would have pretty ugly looking (poor contrast) images.

Mark


From nih-image-request@io.ece.drexel.edu Wed Jul 22 08:58 EDT 1998
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Subject: pixel range
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Hello to all. 
I am a new user to NIH Image. I am looking for any assistance in how to
determine the percentage of pixels of a specificed color range contained 
within an image. This would be used in histological slide analyses. I 
have used 'Sort by LUT' and individual macros such as 'count 
BluePixels'. Is there a way to specify specific pixel color ranges, then 
count or derive percentages of this range within a ROI? Your help is 
appreciated.

J. Miller, Ph. D. Candidate
Ultrasound Research Imaging Lab
McGill University/RVH
Montreal, Quebec

From nih-image-request@io.ece.drexel.edu Wed Jul 22 09:13 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Steven Hudson <sdh6@po.cwru.edu>
Subject: Macro for circularly averaging an FFT
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Dear discussion group,

Is there a macro available for circularly averaging a 2D FFT and then
outputing the 1D result (i.e. the power spectrum as a function of spatial
frequency)?

Thanking you in advance,
Steve Hudson

Steve Hudson
Assist. Professor of Macromolecular Science
Case Western Reserve University
10900 Euclid Av.
Cleveland, OH 44106-7202
216-368-6373
216-368-4202 Fax
sdh6@po.cwru.edu

From nih-image-request@io.ece.drexel.edu Wed Jul 22 09:37 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Mark A Vivino <mvivino@helix.nih.gov>
Subject: Re: Macro for circularly averaging an FFT
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>Dear discussion group,
>
>Is there a macro available for circularly averaging a 2D FFT and then
>outputing the 1D result (i.e. the power spectrum as a function of spatial
>frequency)?

Don't know if this slow old macro I wrote for someone does all of what you
want, but you can try.

Macro 'circle avg [C]';
var
  OrigPid, WorkPid:Integer;
  i,ignore,ignore2:integer;
  imgleft,imgtop,imgwidth,imgheight, tempwidth,tempheight:integer;
  left,top,width,height,ovalwidth,ovalheight:integer;
  Total:real;
begin
    SetOptions('Mean, User1');
    SetUser1Label('Normalized Mean');
    OrigPid := PidNumber;
    Duplicate('Working');
    WorkPid := PidNumber;
    SelectAll;
    Clear;
    KillROI;
    SelectPic(OrigPid);
    ResetCounter;
    SelectAll;
    GetROI(imgleft,imgtop,imgwidth,imgheight);
    KillROI;
    ChoosePic(origPid);
   	MakeOvalROI(imgwidth/2,imgheight/2,2,2);
    GetROI(ignore,ignore2,Ovalwidth,Ovalheight);
    Copy;
    SelectPic(WorkPid);
    Paste;
    SetThreshold(1);
    Measure;
    Clear;
    SelectPic(OrigPid);
    Ovalwidth := Ovalwidth +2;
    Ovalheight := Ovalheight +2;
    for i := 1 to (imgwidth/2-6) do begin

	MakeOvalROI(imgwidth/2-(OvalWidth-2)/2,imgheight/2-(Ovalheight-2)/2,Ovalwidth,O
valHeight);
      copy;
      ChoosePic(WorkPid);

	MakeOvalROI(imgwidth/2-(OvalWidth-2)/2,imgheight/2-(Ovalheight-2)/2,Ovalwidth,O
valHeight);
      Paste;

MakeOvalROI(imgwidth/2-(OvalWidth-2)/2,imgheight/2-(Ovalheight-2)/2,OvalWidth-1,
OvalHeight-1);
      Ovalwidth := Ovalwidth +2;
      Ovalheight := Ovalheight +2;
      Clear;
      KillROI;
      SetThreshold(1);
      Measure;
     SetThreshold(-1);
      SelectAll;
      Clear;
      KillROI;
      ChoosePic(OrigPid);
       KillROI;
    end;
    Total := 0.00;
    for i := 1 to rCount do begin
      Total := Total + rMean[i];
    end;
    for i := 1 to rCount do begin
      rUser1[i] := rMean[i]/Total;
    end;
    ShowResults;
end;


From nih-image-request@io.ece.drexel.edu Wed Jul 22 09:51 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Mark A Vivino <mvivino@helix.nih.gov>
Subject: Re: pixel range
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>Hello to all.
>I am a new user to NIH Image. I am looking for any assistance in how to
>determine the percentage of pixels of a specificed color range contained
>within an image. This would be used in histological slide analyses. I
>have used 'Sort by LUT' and individual macros such as 'count
>BluePixels'. Is there a way to specify specific pixel color ranges, then
>count or derive percentages of this range within a ROI? Your help is
>appreciated.

Just to start off on a tangent, I often have seen this or a related idea
asked. Fundamentally what a scientist really needs is to know is: which
pixels, or how many pixels, or what percent, have a dominant wavelength
between 400 and 500 nm wavelength (or whatever range). It would be easier
if pixels were not RGB or HSV, or anything else unrelated. Instead they
should be wavelength(s) and density. Unfortunately, this is not the case
but is sort or roughly like that with RGB and then the density is
incorportated and things are sort of lumped all up and its a mess.

I once wrote a macro which looked at the LUT to find which pixels have more
of R than G or B. I then sought and counted those pixels in the image. This
is sort of roughly what you request. Don't know if I can find it because it
was years ago, but thats how I would still implement what you ask.

Mark


From nih-image-request@io.ece.drexel.edu Wed Jul 22 10:19 EDT 1998
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From: Jon Vaughan <jvaughan@hamilton.edu>
Message-Id: <199807221406.KAA11385@hamilton.edu>
Subject: Digest form in elm on unix machine
To: nih-image@io.ece.drexel.edu
Date: Wed, 22 Jul 1998 10:06:20 -0400 (EDT)
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I read the digest using the 'elm' mail program on a unix machine (ELM 2.4 
PL25, using 'more' to page through messages.

Because the digest comes through as a multi-part MIME message, until now I 
have had to read through all the messages of the digest format
of the list, but I have discovered how to skip the messages I don't want
to read: 

at the 

   --Press any key to go on.--

prompt, press the control-c (^C) key combination, and the remainder of 
the message(s) will be skipped. 

-- 
Jonathan Vaughan       Psychology, Hamilton College        jvaughan@hamilton.edu

From nih-image-request@io.ece.drexel.edu Wed Jul 22 10:39 EDT 1998
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From: paul stoodley <P.Stoodley@exeter.ac.uk>
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We calibrated the relative fluorescence intensity [FI] of 
different concentrations of fluorescein measured by 
confocal microscopy. We found a peak FI value at 2mM 
fluorescien. However we had to overcome a couple of 
problems to "standardize" the technique.
1) We used neutral density filters and low magnification to 
mimimize photobleaching effects. We checked this by 
plotting the FI against time of exposure to UV light.
2) Because of light extinction with depth we first did a 
saggital scan to find the brightest point. We then frame 
averaged at that point and used the average FI of the field 
for our value.
3) Because the FI varies with light intensity and contrast 
settings etc. we calibrated just before taking the 
measurements.
Other things to be careful with - fluorescien FI is strongly
influenced by pH. We found FI decreased with alginate 
concentration this could be due to reduced pH or possible 
changes in density. This work is reported in:

deBeer, D., Stoodley, P., and Lewandowski, Z. 1997. 
"Measurement of local diffusion coefficients in biofilms by 
micro-injection and confocal microscopy." Biotech. and 
Bioeng. 53(2):151-158.

We were only interested in relating the relative changes of 
FI to relative changes in fluorescien concentration - not 
making absolute measurements. Confocal laser microscopy is 
also much more controlled than conventional fluorescence. 
However, if you are very careful with your calibration 
steps and run the right controls you might be able to get 
something. Good luck, Paul.


On Wed, 22 Jul 1998 08:16:27 -0500 Mark A Vivino 
<mvivino@helix.nih.gov> wrote:

> >Hi there,
> >I am trying to evaluate the concentration of my fluorescin labeled
> >protein in gels by determining the optic density of the fluorescence
> >under the microscope by NIH image analysis software. My question is
> >whether the pixels that are represented by the 8-bit integers are in a
> >linear relationship, say value 1 represents as twice intensity as that
> >of value 2? and how about value 0 (the white color)?

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

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

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

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Hi List,
I'm looking for an elegant solution to have a prefix on a string, so as to obtain ' 00001' or ' 00012' ie. constant length. I also like to find an elegant way to get a part of a string without character by character moving to another string and then deleting that character from the input string, ie. string1:=concat(string2:3);delete(string2,0,3), which does not seem to work for me.
Please reply by e-mail to a_team@dds.nl
Ard


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|Berkowitz Lab Home Page: http://146.9.7.69 |
|-------------------------------------------|

Bruce Berkowitz, Ph.D.
Department of Anatomy and Cell Biology
Wayne State Univeristy
540 E. Canfield
Detroit, MI 48201

Phone:	(313) 577-9035
FAX:	(313) 577-3125
E-mail:	baberko@med.wayne.edu

From nih-image-request@io.ece.drexel.edu Wed Jul 22 15:55 EDT 1998
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Date: Wed, 22 Jul 1998 12:34:01 -0700 (PDT)
From: David Ehrhardt <ehrhardt@camelot.Stanford.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Re: pixel range
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On Wed, 22 Jul 1998, Mark A Vivino wrote:

> >Hello to all.
> >I am a new user to NIH Image. I am looking for any assistance in how to
> >determine the percentage of pixels of a specificed color range contained
> >within an image. This would be used in histological slide analyses. I
> >have used 'Sort by LUT' and individual macros such as 'count
> >BluePixels'. Is there a way to specify specific pixel color ranges, then
> >count or derive percentages of this range within a ROI? Your help is
> >appreciated.
> 
> Just to start off on a tangent, I often have seen this or a related idea
> asked. Fundamentally what a scientist really needs is to know is: which
> pixels, or how many pixels, or what percent, have a dominant wavelength
> between 400 and 500 nm wavelength (or whatever range). It would be easier
> if pixels were not RGB or HSV, or anything else unrelated. Instead they
> should be wavelength(s) and density. Unfortunately, this is not the case
> but is sort or roughly like that with RGB and then the density is
> incorportated and things are sort of lumped all up and its a mess.
> 
> I once wrote a macro which looked at the LUT to find which pixels have more
> of R than G or B. I then sought and counted those pixels in the image. This
> is sort of roughly what you request. Don't know if I can find it because it
> was years ago, but thats how I would still implement what you ask.
> 
> Mark

This may be hopelessly naive, but Photoshop allows selection of a color
range. You can do a pretty good job isolating parts of a color image with
these selection tools. How does Photoshop define a color range and sort
pixels by that definition?  Could this be incorporated into a macro for
Image? 

-David    

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


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Is there a fix yet for the digitizer error when trying to capture images from the built-in video card in the G3's?

From nih-image-request@io.ece.drexel.edu Wed Jul 22 18:16 EDT 1998
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From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
Subject: Re: pixel range
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>On Wed, 22 Jul 1998, Mark A Vivino wrote:
>
>> >Hello to all.
>> >I am a new user to NIH Image. I am looking for any assistance in how to
>> >determine the percentage of pixels of a specificed color range contained
>> >within an image. This would be used in histological slide analyses. I
>> >have used 'Sort by LUT' and individual macros such as 'count
>> >BluePixels'. Is there a way to specify specific pixel color ranges, then
>> >count or derive percentages of this range within a ROI? Your help is
>> >appreciated.
>>
>> Just to start off on a tangent, I often have seen this or a related idea
>> asked. Fundamentally what a scientist really needs is to know is: which
>> pixels, or how many pixels, or what percent, have a dominant wavelength
>> between 400 and 500 nm wavelength (or whatever range). It would be easier
>> if pixels were not RGB or HSV, or anything else unrelated. Instead they
>> should be wavelength(s) and density. Unfortunately, this is not the case
>> but is sort or roughly like that with RGB and then the density is
>> incorportated and things are sort of lumped all up and its a mess.
>>
>> I once wrote a macro which looked at the LUT to find which pixels have more
>> of R than G or B. I then sought and counted those pixels in the image. This
>> is sort of roughly what you request. Don't know if I can find it because it
>> was years ago, but thats how I would still implement what you ask.
>>
>> Mark
>
>This may be hopelessly naive, but Photoshop allows selection of a color
>range. You can do a pretty good job isolating parts of a color image with
>these selection tools. How does Photoshop define a color range and sort
>pixels by that definition?  Could this be incorporated into a macro for
>Image?
>
>-David
>
>David Ehrhardt
>Carnegie Institution of Washington
>Department of Plant Biology		Phone (650) 325-1521 x261
>260 Panama St., Stanford, CA 94305	FAX (650) 325-6857

If I am not mistaken (I never carefully tested this), photoshop determines
the  R,G and B values in the selected points and adds a range to each value
according to the 'fuzziness' setting (don't ask me how exactly the range is
determined), and then thresholds the whole image according to these values,
resulting in the selection of a 'box'(rectangular prism) (or multiple
boxes) with sides parallel with the RGB axes. This is doable in image by
density slicing in R, G, and B, and 'and'-ing the three color planes.


From nih-image-request@io.ece.drexel.edu Wed Jul 22 18:48 EDT 1998
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From: Bill Miller <microbill@mohawk.net>
Subject: Re: Dage SIT cameras
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Chris - maybe you should have someone from Princeton contact him..

Bill


At 06:07 PM 7/21/98 -0700, you wrote:
>Howdy,
>
>	We're thinking of replacing our very old COHU SIT 
>and therefore have been considering the Dage-MTI and Hamamatsu
>cameras. We were considering the Dage VE 1000 SIT system, but
>then heard that Dage-MTI was getting out of the "Scientific
>imaging" and/or perhaps the "SIT camera" market(s); and have
>been advised to avoid them. Any truth to this?
>
>Furthermore, we've been told the Hamamatsu 2400-8 system comes
>with no choice of tube grade (but most likely a grade 2). Is 
>this also true?
>
>Any additional thoughts about these cameras, and/or the Argus-20
>DSP versus the Dage-MTI DSP-2000 would be appreciated.
>
>Thanks in advace,
>
>Aaron
>
>
>-- 
>R. Aaron Warnock
>"Nothing more is needed to destroy a man than the conviction
>that his life's work is useless." -Antonin Artaud
>
>Lab Address:
>Dept. of Pathology L-235	awarnock@cmgm.stanford.edu
>Stanford, CA 94305		Tel. (650) 493-5000 x63167
>
>Home Address:
>777 Arguello Blvd. #304		Tel. (415) 831-3425
>San Francisco, CA 94118
>
>
>

From nih-image-request@io.ece.drexel.edu Wed Jul 22 20:08 EDT 1998
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Date: Thu, 23 Jul 1998 09:58:58 +1000
To: nih-image@io.ece.drexel.edu
From: Steve Martin <s.martin@physio.unimelb.EDU.AU>
Subject: Re: pixel range
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Dear list,

On Wed, 22 Jul 1998, amongst other things, Mark A Vivino wrote:
>
>It would be easier
>if pixels were not RGB or HSV, or anything else unrelated. Instead they
>should be wavelength(s) and density. Unfortunately, this is not the case

Mark, I found these comments very thought-provoking.

excuse my probable ignorance or niaivity, isn't hue angle related in some
way to wavelength in many cases?

I realise the pixels on our screens are mixtures of rgb, but they usually
do not represent mixtures of rgb brought in from the real world. Unless we
are using spectrophotometers, electronically we most often represent
wavelengths in the real world in rgb because it is convenient to sample it
and then display it that way.

If I digitally photograph or frame grab a sodium yellow flame, isn't the
hue of the resulting image some sort of representation of the original
wavelength(s)?

So if I had a table which converted hue angle to wavelength, perhaps I
could create a real-values image in which pixel values represented the
centres of wavelength ranges. Once I had made the table, I could code it
into Image for all to use (:-) ? Maybe all you need is hue angle, but
wavelength ranges may not be related in a very linear way to hue, I haven't
tried to figure that out.

I am sure there can be lots of dangers in this approach (mixed light
sources etc.) and I am sure the list will hear about them 5 minutes after
this is posted! This could still help out all those people who post to the
list asking how to separate their coloured stains / leaf colours / etc.

I hope this promotes some discussion
even if it is only that I have just re-invented a wheel called hue!

Steve

From nih-image-request@io.ece.drexel.edu Wed Jul 22 22:48 EDT 1998
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Date: Wed, 22 Jul 1998 21:30:35 -0500
From: scidi <scidi@mci2000.com>
Subject: Integration on the LG-3 NuBus Card
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To NIH Users:

I have recently installed NuBus LG-3 and TV-3 cards in my Power Mac 7100. 
I have had relatively few problems, except that when I go to Integrate on
Chip, I get a printout on the Mitsubishi thermal printer that came with the
system instead of the on chip integration.  I can't figure it out.  The
only time I get any type of integration is when I select a small area
within the image.  I do have the Scion integration cable and I am using a
Cohu 4910 CCD camera.  Any help would be greatly appreciated.  Thanks.

Mark R. Molenda
phone (414) 476-2694
fax (414) 645-8037
scidi@mci2000.com

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Subject: nih-image-d Digest V98 #18
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 18

Today's Topics:
  Re: Re: median stack                  [ Bruce Berkowitz <baberko@med.wayne. ]
  Re: Re: Re: median stack              [ DrJohnRuss@aol.com ]
  Re: Image density??                   [ Mark A Vivino <mvivino@helix.nih.go ]
  pixel range                           [ Jeri Miller <jmille@po-box.mcgill.c ]
  Macro for circularly averaging an FF  [ Steven Hudson <sdh6@po.cwru.edu> ]
  Re: Macro for circularly averaging a  [ Mark A Vivino <mvivino@helix.nih.go ]
  Re: pixel range                       [ Mark A Vivino <mvivino@helix.nih.go ]
  Digest form in elm on unix machine    [ Jon Vaughan <jvaughan@hamilton.edu> ]
  Re: Image density??                   [ paul stoodley <P.Stoodley@exeter.ac ]
  zero prefix                           [ "Anneke M.Th. Harbers and Ard Jonke ]
  unsubscribe                           [ Bruce Berkowitz <baberko@med.wayne. ]
  Re: pixel range                       [ David Ehrhardt <ehrhardt@camelot.St ]
  G3                                    [ "STEPHEN MOORMAN" <smoorman@hsc.unt ]
  Unsubscribe                           [ Glenn Kearney <glenn.kearney@stoneb ]
  Re: pixel range                       [ Arnout Ruifrok <arnout@odin.mdacc.t ]
  Re: Dage SIT cameras                  [ Bill Miller <microbill@mohawk.net> ]
  Re: pixel range                       [ Steve Martin <s.martin@physio.unime ]
  Integration on the LG-3 NuBus Card    [ scidi <scidi@mci2000.com> ]

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

Date: Wed, 22 Jul 1998 06:23:20 -0400
From: Bruce Berkowitz <baberko@med.wayne.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re:  Re: median stack
Message-Id: <3.0.1.32.19980722062320.01affe7c@med.wayne.edu>
Content-Type: text/plain; charset="us-ascii"

yes, I want to create a new image using the median value at a particular
x,y location from those 10 images, repeated over all pixels. Do you have an
example of a sort routine that will do this?
Thank you for your time!
Bruce

At 04:17 PM 7/21/98 EDT, you wrote:
>
>In a message dated 7/21/98 6:33:18 PM, you wrote:
>
>>Thank you for your response but I don't think that was what I was looking
>>for. Because my data are not normally distributed I would like to calculate
>>a median image from a stack of 10 images INSTEAD of calculating one average
>>image of that stack. 
>
>I think you need to define what you want, and the answer may then be obvious.
>for instance do you want to take the pixel values at each x,y location from
>all 10 images and find the median value, and repeat this for all pixels? That
>doesn't sound like a median image to me, but if that is what you want then it
>is easy (but slow) to do. You will have to use a sort procedure in your macro
>to get the median (and then since you have an even number of images will have
>to probably average the 5th and 6th ranked values).
>
>
|-------------------------------------------|
|Berkowitz Lab Home Page: http://146.9.7.69 |
|-------------------------------------------|

Bruce Berkowitz, Ph.D.
Department of Anatomy and Cell Biology
Wayne State Univeristy
540 E. Canfield
Detroit, MI 48201

Phone:	(313) 577-9035
FAX:	(313) 577-3125
E-mail:	baberko@med.wayne.edu

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

Date: Wed, 22 Jul 1998 07:34:47 EDT
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re:  Re:  Re: median stack
Message-ID: <1090f786.35b5ce58@aol.com>
Content-type: text/plain; charset=US-ASCII
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In a message dated 7/22/98 10:33:31 AM, you wrote:

>yes, I want to create a new image using the median value at a particular
>x,y location from those 10 images, repeated over all pixels. Do you have an
>example of a sort routine that will do this?

For a small number of values, a shell sort is probably the most efficient and
easy to program. Details and code examples available in any standard numerical
recipes book

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

Date: Wed, 22 Jul 1998 08:16:27 -0500
From: Mark A Vivino <mvivino@helix.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Image density??
Message-Id: <v04003a00b1db96106caa@[128.231.128.61]>
Content-Type: text/plain; charset="us-ascii"

>Hi there,
>I am trying to evaluate the concentration of my fluorescin labeled
>protein in gels by determining the optic density of the fluorescence
>under the microscope by NIH image analysis software. My question is
>whether the pixels that are represented by the 8-bit integers are in a
>linear relationship, say value 1 represents as twice intensity as that
>of value 2? and how about value 0 (the white color)?

You can see in:

http://rsb.info.nih.gov/nih-image/more-docs/Engineering/ImgEngr.html#densitometr
y

As often stated on the list, never make the mistake in assuming a linear
relationship of pixels and concentrations. 100 is not twice 50 and for good
reasons. If pixels represented linear relationships to concentration we
would have pretty ugly looking (poor contrast) images.

Mark

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

Date: Wed, 22 Jul 1998 08:44:12 -0400
From: Jeri Miller <jmille@po-box.mcgill.ca>
To: nih-image@io.ece.drexel.edu
Subject: pixel range
Message-ID: <35B5DE9C.B66@po-box.mcgill.ca>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hello to all. 
I am a new user to NIH Image. I am looking for any assistance in how to
determine the percentage of pixels of a specificed color range contained 
within an image. This would be used in histological slide analyses. I 
have used 'Sort by LUT' and individual macros such as 'count 
BluePixels'. Is there a way to specify specific pixel color ranges, then 
count or derive percentages of this range within a ROI? Your help is 
appreciated.

J. Miller, Ph. D. Candidate
Ultrasound Research Imaging Lab
McGill University/RVH
Montreal, Quebec

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

Date: Wed, 22 Jul 1998 09:02:18 -0400
From: Steven Hudson <sdh6@po.cwru.edu>
To: nih-image@io.ece.drexel.edu
Subject: Macro for circularly averaging an FFT
Message-Id: <3.0.3.32.19980722090218.006c3e40@pop.cwru.edu>
Content-Type: text/plain; charset="us-ascii"

Dear discussion group,

Is there a macro available for circularly averaging a 2D FFT and then
outputing the 1D result (i.e. the power spectrum as a function of spatial
frequency)?

Thanking you in advance,
Steve Hudson

Steve Hudson
Assist. Professor of Macromolecular Science
Case Western Reserve University
10900 Euclid Av.
Cleveland, OH 44106-7202
216-368-6373
216-368-4202 Fax
sdh6@po.cwru.edu

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

Date: Wed, 22 Jul 1998 09:28:51 -0500
From: Mark A Vivino <mvivino@helix.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Macro for circularly averaging an FFT
Message-Id: <v04003a02b1dba781878d@[128.231.128.61]>
Content-Type: text/plain; charset="us-ascii"

>Dear discussion group,
>
>Is there a macro available for circularly averaging a 2D FFT and then
>outputing the 1D result (i.e. the power spectrum as a function of spatial
>frequency)?

Don't know if this slow old macro I wrote for someone does all of what you
want, but you can try.

Macro 'circle avg [C]';
var
  OrigPid, WorkPid:Integer;
  i,ignore,ignore2:integer;
  imgleft,imgtop,imgwidth,imgheight, tempwidth,tempheight:integer;
  left,top,width,height,ovalwidth,ovalheight:integer;
  Total:real;
begin
    SetOptions('Mean, User1');
    SetUser1Label('Normalized Mean');
    OrigPid := PidNumber;
    Duplicate('Working');
    WorkPid := PidNumber;
    SelectAll;
    Clear;
    KillROI;
    SelectPic(OrigPid);
    ResetCounter;
    SelectAll;
    GetROI(imgleft,imgtop,imgwidth,imgheight);
    KillROI;
    ChoosePic(origPid);
   	MakeOvalROI(imgwidth/2,imgheight/2,2,2);
    GetROI(ignore,ignore2,Ovalwidth,Ovalheight);
    Copy;
    SelectPic(WorkPid);
    Paste;
    SetThreshold(1);
    Measure;
    Clear;
    SelectPic(OrigPid);
    Ovalwidth := Ovalwidth +2;
    Ovalheight := Ovalheight +2;
    for i := 1 to (imgwidth/2-6) do begin

	MakeOvalROI(imgwidth/2-(OvalWidth-2)/2,imgheight/2-(Ovalheight-2)/2,Ovalwidth,O
valHeight);
      copy;
      ChoosePic(WorkPid);

	MakeOvalROI(imgwidth/2-(OvalWidth-2)/2,imgheight/2-(Ovalheight-2)/2,Ovalwidth,O
valHeight);
      Paste;

MakeOvalROI(imgwidth/2-(OvalWidth-2)/2,imgheight/2-(Ovalheight-2)/2,OvalWidth-1,
OvalHeight-1);
      Ovalwidth := Ovalwidth +2;
      Ovalheight := Ovalheight +2;
      Clear;
      KillROI;
      SetThreshold(1);
      Measure;
     SetThreshold(-1);
      SelectAll;
      Clear;
      KillROI;
      ChoosePic(OrigPid);
       KillROI;
    end;
    Total := 0.00;
    for i := 1 to rCount do begin
      Total := Total + rMean[i];
    end;
    for i := 1 to rCount do begin
      rUser1[i] := rMean[i]/Total;
    end;
    ShowResults;
end;

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

Date: Wed, 22 Jul 1998 09:40:58 -0500
From: Mark A Vivino <mvivino@helix.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: pixel range
Message-Id: <v04003a03b1dbaa462e5b@[128.231.128.61]>
Content-Type: text/plain; charset="us-ascii"

>Hello to all.
>I am a new user to NIH Image. I am looking for any assistance in how to
>determine the percentage of pixels of a specificed color range contained
>within an image. This would be used in histological slide analyses. I
>have used 'Sort by LUT' and individual macros such as 'count
>BluePixels'. Is there a way to specify specific pixel color ranges, then
>count or derive percentages of this range within a ROI? Your help is
>appreciated.

Just to start off on a tangent, I often have seen this or a related idea
asked. Fundamentally what a scientist really needs is to know is: which
pixels, or how many pixels, or what percent, have a dominant wavelength
between 400 and 500 nm wavelength (or whatever range). It would be easier
if pixels were not RGB or HSV, or anything else unrelated. Instead they
should be wavelength(s) and density. Unfortunately, this is not the case
but is sort or roughly like that with RGB and then the density is
incorportated and things are sort of lumped all up and its a mess.

I once wrote a macro which looked at the LUT to find which pixels have more
of R than G or B. I then sought and counted those pixels in the image. This
is sort of roughly what you request. Don't know if I can find it because it
was years ago, but thats how I would still implement what you ask.

Mark

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

Date: Wed, 22 Jul 1998 10:06:20 -0400 (EDT)
From: Jon Vaughan <jvaughan@hamilton.edu>
To: nih-image@io.ece.drexel.edu
Subject: Digest form in elm on unix machine
Message-Id: <199807221406.KAA11385@hamilton.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit

I read the digest using the 'elm' mail program on a unix machine (ELM 2.4 
PL25, using 'more' to page through messages.

Because the digest comes through as a multi-part MIME message, until now I 
have had to read through all the messages of the digest format
of the list, but I have discovered how to skip the messages I don't want
to read: 

at the 

   --Press any key to go on.--

prompt, press the control-c (^C) key combination, and the remainder of 
the message(s) will be skipped. 

-- 
Jonathan Vaughan       Psychology, Hamilton College        jvaughan@hamilton.edu

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

Date: Wed, 22 Jul 1998 15:29:57 +0100 (GMT Daylight Time)
From: paul stoodley <P.Stoodley@exeter.ac.uk>
To: nih-image@io.ece.drexel.edu
cc: nih-image@io.ece.drexel.edu
Subject: Re: Image density??
Message-ID: <SIMEON.9807221557.A@BS016.ex.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

We calibrated the relative fluorescence intensity [FI] of 
different concentrations of fluorescein measured by 
confocal microscopy. We found a peak FI value at 2mM 
fluorescien. However we had to overcome a couple of 
problems to "standardize" the technique.
1) We used neutral density filters and low magnification to 
mimimize photobleaching effects. We checked this by 
plotting the FI against time of exposure to UV light.
2) Because of light extinction with depth we first did a 
saggital scan to find the brightest point. We then frame 
averaged at that point and used the average FI of the field 
for our value.
3) Because the FI varies with light intensity and contrast 
settings etc. we calibrated just before taking the 
measurements.
Other things to be careful with - fluorescien FI is strongly
influenced by pH. We found FI decreased with alginate 
concentration this could be due to reduced pH or possible 
changes in density. This work is reported in:

deBeer, D., Stoodley, P., and Lewandowski, Z. 1997. 
"Measurement of local diffusion coefficients in biofilms by 
micro-injection and confocal microscopy." Biotech. and 
Bioeng. 53(2):151-158.

We were only interested in relating the relative changes of 
FI to relative changes in fluorescien concentration - not 
making absolute measurements. Confocal laser microscopy is 
also much more controlled than conventional fluorescence. 
However, if you are very careful with your calibration 
steps and run the right controls you might be able to get 
something. Good luck, Paul.


On Wed, 22 Jul 1998 08:16:27 -0500 Mark A Vivino 
<mvivino@helix.nih.gov> wrote:

> >Hi there,
> >I am trying to evaluate the concentration of my fluorescin labeled
> >protein in gels by determining the optic density of the fluorescence
> >under the microscope by NIH image analysis software. My question is
> >whether the pixels that are represented by the 8-bit integers are in a
> >linear relationship, say value 1 represents as twice intensity as that
> >of value 2? and how about value 0 (the white color)?

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

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

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

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

Date: Wed, 22 Jul 1998 20:24:46 +0200
From: "Anneke M.Th. Harbers and Ard Jonker" <a_team@dds.nl>
To: nih-image@io.ece.drexel.edu
Subject: zero prefix
Message-Id: <l03130300b1dbdd8f0190@[194.109.130.97]>
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 8bit

Hi List,
I'm looking for an elegant solution to have a prefix on a string, so as to obtain ' 00001' or ' 00012' ie. constant length. I also like to find an elegant way to get a part of a string without character by character moving to another string and then deleting that character from the input string, ie. string1:=concat(string2:3);delete(string2,0,3), which does not seem to work for me.
Please reply by e-mail to a_team@dds.nl
Ard

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

Date: Wed, 22 Jul 1998 15:20:48 -0400
From: Bruce Berkowitz <baberko@med.wayne.edu>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <3.0.1.32.19980722152048.0077e110@med.wayne.edu>
Content-Type: text/plain; charset="us-ascii"

unsubscribe
|-------------------------------------------|
|Berkowitz Lab Home Page: http://146.9.7.69 |
|-------------------------------------------|

Bruce Berkowitz, Ph.D.
Department of Anatomy and Cell Biology
Wayne State Univeristy
540 E. Canfield
Detroit, MI 48201

Phone:	(313) 577-9035
FAX:	(313) 577-3125
E-mail:	baberko@med.wayne.edu

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

Date: Wed, 22 Jul 1998 12:34:01 -0700 (PDT)
From: David Ehrhardt <ehrhardt@camelot.Stanford.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Re: pixel range
Message-ID: <Pine.GUL.3.95.980722122707.2700A-100000@camelot.Stanford.EDU>
Content-Type: TEXT/PLAIN; charset=US-ASCII

On Wed, 22 Jul 1998, Mark A Vivino wrote:

> >Hello to all.
> >I am a new user to NIH Image. I am looking for any assistance in how to
> >determine the percentage of pixels of a specificed color range contained
> >within an image. This would be used in histological slide analyses. I
> >have used 'Sort by LUT' and individual macros such as 'count
> >BluePixels'. Is there a way to specify specific pixel color ranges, then
> >count or derive percentages of this range within a ROI? Your help is
> >appreciated.
> 
> Just to start off on a tangent, I often have seen this or a related idea
> asked. Fundamentally what a scientist really needs is to know is: which
> pixels, or how many pixels, or what percent, have a dominant wavelength
> between 400 and 500 nm wavelength (or whatever range). It would be easier
> if pixels were not RGB or HSV, or anything else unrelated. Instead they
> should be wavelength(s) and density. Unfortunately, this is not the case
> but is sort or roughly like that with RGB and then the density is
> incorportated and things are sort of lumped all up and its a mess.
> 
> I once wrote a macro which looked at the LUT to find which pixels have more
> of R than G or B. I then sought and counted those pixels in the image. This
> is sort of roughly what you request. Don't know if I can find it because it
> was years ago, but thats how I would still implement what you ask.
> 
> Mark

This may be hopelessly naive, but Photoshop allows selection of a color
range. You can do a pretty good job isolating parts of a color image with
these selection tools. How does Photoshop define a color range and sort
pixels by that definition?  Could this be incorporated into a macro for
Image? 

-David    

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

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

Date: Wed, 22 Jul 1998 15:07:27 -0500
From: "STEPHEN MOORMAN" <smoorman@hsc.unt.edu>
To: nih-image@io.ece.drexel.edu
Subject:  G3
Message-Id: <s5b60129.056@hsc.unt.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline
Content-Transfer-Encoding: 8bit

Is there a fix yet for the digitizer error when trying to capture images from the built-in video card in the G3's?

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

Date: Thu, 23 Jul 1998 09:10:19 +1200
From: Glenn Kearney <glenn.kearney@stonebow.otago.ac.nz>
To: nih-image-d@io.ece.drexel.edu
Subject: Unsubscribe
Message-Id: <l03010d01b1dc05aa4ccd@[139.80.71.22]>
Content-Type: text/plain; charset="us-ascii"

unsubscribe

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

Date: Wed, 22 Jul 1998 17:04:39 -0500
From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: pixel range
Message-Id: <v03102800b1dbc6b345c2@[143.111.62.105]>
Content-Type: text/plain; charset="us-ascii"

>On Wed, 22 Jul 1998, Mark A Vivino wrote:
>
>> >Hello to all.
>> >I am a new user to NIH Image. I am looking for any assistance in how to
>> >determine the percentage of pixels of a specificed color range contained
>> >within an image. This would be used in histological slide analyses. I
>> >have used 'Sort by LUT' and individual macros such as 'count
>> >BluePixels'. Is there a way to specify specific pixel color ranges, then
>> >count or derive percentages of this range within a ROI? Your help is
>> >appreciated.
>>
>> Just to start off on a tangent, I often have seen this or a related idea
>> asked. Fundamentally what a scientist really needs is to know is: which
>> pixels, or how many pixels, or what percent, have a dominant wavelength
>> between 400 and 500 nm wavelength (or whatever range). It would be easier
>> if pixels were not RGB or HSV, or anything else unrelated. Instead they
>> should be wavelength(s) and density. Unfortunately, this is not the case
>> but is sort or roughly like that with RGB and then the density is
>> incorportated and things are sort of lumped all up and its a mess.
>>
>> I once wrote a macro which looked at the LUT to find which pixels have more
>> of R than G or B. I then sought and counted those pixels in the image. This
>> is sort of roughly what you request. Don't know if I can find it because it
>> was years ago, but thats how I would still implement what you ask.
>>
>> Mark
>
>This may be hopelessly naive, but Photoshop allows selection of a color
>range. You can do a pretty good job isolating parts of a color image with
>these selection tools. How does Photoshop define a color range and sort
>pixels by that definition?  Could this be incorporated into a macro for
>Image?
>
>-David
>
>David Ehrhardt
>Carnegie Institution of Washington
>Department of Plant Biology		Phone (650) 325-1521 x261
>260 Panama St., Stanford, CA 94305	FAX (650) 325-6857

If I am not mistaken (I never carefully tested this), photoshop determines
the  R,G and B values in the selected points and adds a range to each value
according to the 'fuzziness' setting (don't ask me how exactly the range is
determined), and then thresholds the whole image according to these values,
resulting in the selection of a 'box'(rectangular prism) (or multiple
boxes) with sides parallel with the RGB axes. This is doable in image by
density slicing in R, G, and B, and 'and'-ing the three color planes.

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

Date: Wed, 22 Jul 1998 18:41:44 -0400
From: Bill Miller <microbill@mohawk.net>
To: nih-image@io.ece.drexel.edu, c.cathcart@sympatico.ca
Subject: Re: Dage SIT cameras
Message-Id: <3.0.5.32.19980722184144.00803920@mohawk.net>
Content-Type: text/plain; charset="us-ascii"

Chris - maybe you should have someone from Princeton contact him..

Bill


At 06:07 PM 7/21/98 -0700, you wrote:
>Howdy,
>
>	We're thinking of replacing our very old COHU SIT 
>and therefore have been considering the Dage-MTI and Hamamatsu
>cameras. We were considering the Dage VE 1000 SIT system, but
>then heard that Dage-MTI was getting out of the "Scientific
>imaging" and/or perhaps the "SIT camera" market(s); and have
>been advised to avoid them. Any truth to this?
>
>Furthermore, we've been told the Hamamatsu 2400-8 system comes
>with no choice of tube grade (but most likely a grade 2). Is 
>this also true?
>
>Any additional thoughts about these cameras, and/or the Argus-20
>DSP versus the Dage-MTI DSP-2000 would be appreciated.
>
>Thanks in advace,
>
>Aaron
>
>
>-- 
>R. Aaron Warnock
>"Nothing more is needed to destroy a man than the conviction
>that his life's work is useless." -Antonin Artaud
>
>Lab Address:
>Dept. of Pathology L-235	awarnock@cmgm.stanford.edu
>Stanford, CA 94305		Tel. (650) 493-5000 x63167
>
>Home Address:
>777 Arguello Blvd. #304		Tel. (415) 831-3425
>San Francisco, CA 94118
>
>
>

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

Date: Thu, 23 Jul 1998 09:58:58 +1000
From: Steve Martin <s.martin@physio.unimelb.EDU.AU>
To: nih-image@io.ece.drexel.edu
Subject: Re: pixel range
Message-Id: <v04011700b1dc26327d36@[128.250.109.214]>
Content-Type: text/plain; charset="us-ascii"

Dear list,

On Wed, 22 Jul 1998, amongst other things, Mark A Vivino wrote:
>
>It would be easier
>if pixels were not RGB or HSV, or anything else unrelated. Instead they
>should be wavelength(s) and density. Unfortunately, this is not the case

Mark, I found these comments very thought-provoking.

excuse my probable ignorance or niaivity, isn't hue angle related in some
way to wavelength in many cases?

I realise the pixels on our screens are mixtures of rgb, but they usually
do not represent mixtures of rgb brought in from the real world. Unless we
are using spectrophotometers, electronically we most often represent
wavelengths in the real world in rgb because it is convenient to sample it
and then display it that way.

If I digitally photograph or frame grab a sodium yellow flame, isn't the
hue of the resulting image some sort of representation of the original
wavelength(s)?

So if I had a table which converted hue angle to wavelength, perhaps I
could create a real-values image in which pixel values represented the
centres of wavelength ranges. Once I had made the table, I could code it
into Image for all to use (:-) ? Maybe all you need is hue angle, but
wavelength ranges may not be related in a very linear way to hue, I haven't
tried to figure that out.

I am sure there can be lots of dangers in this approach (mixed light
sources etc.) and I am sure the list will hear about them 5 minutes after
this is posted! This could still help out all those people who post to the
list asking how to separate their coloured stains / leaf colours / etc.

I hope this promotes some discussion
even if it is only that I have just re-invented a wheel called hue!

Steve

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

Date: Wed, 22 Jul 1998 21:30:35 -0500
From: scidi <scidi@mci2000.com>
To: nih-image@io.ece.drexel.edu
Subject: Integration on the LG-3 NuBus Card
Message-id: <0EWJ00NUI0NM4Y@PM02SM.PMM.MCI.NET>
Content-type: text/plain; charset=ISO-8859-1
Content-transfer-encoding: 7bit

To NIH Users:

I have recently installed NuBus LG-3 and TV-3 cards in my Power Mac 7100. 
I have had relatively few problems, except that when I go to Integrate on
Chip, I get a printout on the Mitsubishi thermal printer that came with the
system instead of the on chip integration.  I can't figure it out.  The
only time I get any type of integration is when I select a small area
within the image.  I do have the Scion integration cable and I am using a
Cohu 4910 CCD camera.  Any help would be greatly appreciated.  Thanks.

Mark R. Molenda
phone (414) 476-2694
fax (414) 645-8037
scidi@mci2000.com

--------------------------------
End of nih-image-d Digest V98 Issue #18
***************************************

From nih-image-request@io.ece.drexel.edu Thu Jul 23 01:03 EDT 1998
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Date: Wed, 22 Jul 1998 22:55:23 -0600
From: "Christopher P. Tully" <cptully@sisna.com>
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Subject: Re: pixel range
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Maybe I'm missing the point here, but couldn't you just take a histogram of your
image, and get the numbers from that?  EVen if you are working in color, taking
the histogram for each of the three color slices in the three slice RGB stack
should get the information you want.

Chris Tully

Jeri Miller wrote:
> 
> Hello to all.
> I am a new user to NIH Image. I am looking for any assistance in how to
> determine the percentage of pixels of a specificed color range contained
> within an image. This would be used in histological slide analyses. I
> have used 'Sort by LUT' and individual macros such as 'count
> BluePixels'. Is there a way to specify specific pixel color ranges, then
> count or derive percentages of this range within a ROI? Your help is
> appreciated.
> 
> J. Miller, Ph. D. Candidate
> Ultrasound Research Imaging Lab
> McGill University/RVH
> Montreal, Quebec

From nih-image-request@io.ece.drexel.edu Thu Jul 23 08:43 EDT 1998
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Date: Thu, 23 Jul 1998 08:31:54 -0400
To: nih-image@io.ece.drexel.edu
From: Laird Bloom <lbloom@MIT.EDU>
Subject: montage macro
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 NIH Image Users:

	Does anyone have a macro that makes a montage of RGB TIFF images?
There was some discussion of ways to do this last summer; has anyone
written the code?

	Ideally, I'd like to be able to make a "contact sheet" (e.g. about
24-35 small images on a page) as a way of keeping track of images I've
recorded.  My computer can't open more than about 10 TIFF images at a time,
but I'd like to be able to make a montage without having to open each file
up individually.  Is there a way to open files in a folder one at a time
without having to give them sequential numbers?

	I'd appreciate help on this.

Thanks very much.

Laird Bloom
MIT Center for Cancer Research


From nih-image-request@io.ece.drexel.edu Thu Jul 23 09:50 EDT 1998
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Date: Thu, 23 Jul 1998 09:37:04 -0500
To: nih-image@io.ece.drexel.edu
From: Mark A Vivino <mvivino@helix.nih.gov>
Subject: Re: pixel range
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Chris Tully asks:
>Maybe I'm missing the point here, but couldn't you just take a histogram
>of your
>image, and get the numbers from that?  EVen if you are working in color,
>taking
>the histogram for each of the three color slices in the three slice RGB stack
>should get the information you want.

Well I'll have to think about it a little more. Roughly the answer seems to
be yes. Specifically I think the answer is not very well. It would be truer
for example if R was a wavelength value from 0 to 255 (or 0 to 100, or 600
to 700 nm) which represented the redness or red wavelengths of of a point,
same for G and B, and you had seperately an intensity plane to take care of
density. Roughly though I think what you say gives as good a simple answer
as can be gotten without forming new image standards and and using a
spectrophotometer, etc. I think using hue might do better.

Mark


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Subject: Fourier Descriptors
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Hi there,

I am looking for a software that can apply Fourier descriptors in ima0ge
analysis.  I have binary images of barley seeds and I am interested in
calculating the area, perimeter, width and length each seed.

If any one knows about such a software and where to get it, please e-mail
me the info or post it in this forum.

Thank you




 
Micheline Ayoub

Plant Science Department
Macdonald Campus of Mcgill University
21111 Lakeshore Rd.
Ste-Anne-de-bellevue, QC, H9X 3V9

Tel: 514-398-7851 ext 8733
Fax: 514-398-7897

From nih-image-request@io.ece.drexel.edu Thu Jul 23 11:38 EDT 1998
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From: "Kirk, Todd Jason" <tjkirk@iupui.edu>
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Date: Thu, 23 Jul 1998 10:22:47 -0500
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Can you do something like?
'0000'+your_num

check the size or your_num to see how many characters or value it has to
see how many zeros to put
if your_num>9 then
'000'+your_num
else
'0000'+your_num

Todd

> -----Original Message-----
> From:	Anneke M.Th. Harbers and Ard Jonker [SMTP:a_team@dds.nl]
> Sent:	Wednesday, July 22, 1998 1:25 PM
> To:	nih-image@io.ece.drexel.edu
> Subject:	zero prefix
> 
> Hi List,
> I'm looking for an elegant solution to have a prefix on a string, so
> as to obtain ' 00001' or ' 00012' ie. constant length. I also like to
> find an elegant way to get a part of a string without character by
> character moving to another string and then deleting that character
> from the input string, ie.
> string1:=concat(string2:3);delete(string2,0,3), which does not seem to
> work for me.
> Please reply by e-mail to a_team@dds.nl
> Ard
> 

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unsubscribe

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>Dear list,
>
>On Wed, 22 Jul 1998, amongst other things, Mark A Vivino wrote:
>>
>>It would be easier
>>if pixels were not RGB or HSV, or anything else unrelated. Instead they
>>should be wavelength(s) and density. Unfortunately, this is not the case
>
>Mark, I found these comments very thought-provoking.
>
>excuse my probable ignorance or niaivity, isn't hue angle related in some
>way to wavelength in many cases?
>
>I realise the pixels on our screens are mixtures of rgb, but they usually
>do not represent mixtures of rgb brought in from the real world. Unless we
>are using spectrophotometers, electronically we most often represent
>wavelengths in the real world in rgb because it is convenient to sample it
>and then display it that way.
>
>If I digitally photograph or frame grab a sodium yellow flame, isn't the
>hue of the resulting image some sort of representation of the original
>wavelength(s)?
>
>So if I had a table which converted hue angle to wavelength, perhaps I
>could create a real-values image in which pixel values represented the
>centres of wavelength ranges. Once I had made the table, I could code it
>into Image for all to use (:-) ? Maybe all you need is hue angle, but
>wavelength ranges may not be related in a very linear way to hue, I haven't
>tried to figure that out.
>
>I am sure there can be lots of dangers in this approach (mixed light
>sources etc.) and I am sure the list will hear about them 5 minutes after
>this is posted! This could still help out all those people who post to the
>list asking how to separate their coloured stains / leaf colours / etc.
>
>I hope this promotes some discussion
>even if it is only that I have just re-invented a wheel called hue!
>
>Steve

In imaging addition of red and green gives yellow. How do you know if the
original color was red plus green or true yellow from an RGB picture? That
is not possible. To really select only yellow, you would have to have a
narrow band-pass filter for only yellow (the exact wavelength). The problem
is that yellow light excites green as well as red cones in the eye (and the
-broad band- elemnts in a RGB camera) and the brain interprets this as
yellow. But the brain also interprets a mix of true (narrow band) red and
true green as yellow. So, in contrast to the ear, the eye (and camera) does
not register the wavelenth of the light, only the relative excitation of
the three types of color-sensitive cones. No way to convert the RGB
information back to wavelength. The problem remains the same irrespective
the color representation (RGB, HSI, etc), all color representations contain
basically the same information, and are interchangable.

Arnout


From nih-image-request@io.ece.drexel.edu Thu Jul 23 14:42 EDT 1998
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From: David Ehrhardt <ehrhardt@camelot.Stanford.EDU>
Reply-To: David Ehrhardt <ehrhardt@camelot.Stanford.EDU>
To: nih-image@io.ece.drexel.edu
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The histogram appraoch does not really answer the question here.  Jeri
needs to know which pixels contain a particular relative amount of each
color component.  A pixel with a particular value of blue might be part of
say a purple or a blue pixel.  I guess what is needed is something like
what Arnout suggested; you classify each pixel as falling within a
certain range of R AND G AND B values.  Possibly more sophisticated
selections could be made by working with relative pixel values to select a
hue across darkness and lightness gradients.  

-David

On Wed, 22 Jul 1998, Christopher P. Tully wrote:

> Maybe I'm missing the point here, but couldn't you just take a histogram of your
> image, and get the numbers from that?  EVen if you are working in color, taking
> the histogram for each of the three color slices in the three slice RGB stack
> should get the information you want.
> 
> Chris Tully
> 
> Jeri Miller wrote:
> > 
> > Hello to all.
> > I am a new user to NIH Image. I am looking for any assistance in how to
> > determine the percentage of pixels of a specificed color range contained
> > within an image. This would be used in histological slide analyses. I
> > have used 'Sort by LUT' and individual macros such as 'count
> > BluePixels'. Is there a way to specify specific pixel color ranges, then
> > count or derive percentages of this range within a ROI? Your help is
> > appreciated.
> > 
> > J. Miller, Ph. D. Candidate
> > Ultrasound Research Imaging Lab
> > McGill University/RVH
> > Montreal, Quebec
> 
> 

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




From nih-image-request@io.ece.drexel.edu Thu Jul 23 14:44 EDT 1998
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Dear Micheline,
I receive a message with a adress that I think have what you need
SPM Image Analysis
http://www.dfm.dtu.dk/spip/
Good luck
Rejane Galindo
Universidade Federal Rural de Pernamnuco
Plant Morphology and Anatomy

----------
> From: Micheline Ayoub <mayoub@po-box.mcgill.ca>
> To: nih-image@io.ece.drexel.edu
> Subject: Fourier Descriptors
> Date: Quinta-feira, 23 Julho, 1998 11:34
> 
> Hi there,
> 
> I am looking for a software that can apply Fourier descriptors in ima0ge
> analysis.  I have binary images of barley seeds and I am interested in
> calculating the area, perimeter, width and length each seed.
> 
> If any one knows about such a software and where to get it, please e-mail
> me the info or post it in this forum.
> 
> Thank you
> 
> 
> 
> 
>  
> Micheline Ayoub
> 
> Plant Science Department
> Macdonald Campus of Mcgill University
> 21111 Lakeshore Rd.
> Ste-Anne-de-bellevue, QC, H9X 3V9
> 
> Tel: 514-398-7851 ext 8733
> Fax: 514-398-7897
> 

From nih-image-request@io.ece.drexel.edu Thu Jul 23 14:55 EDT 1998
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Date: Thu, 23 Jul 1998 14:44:34 -0500
To: nih-image@io.ece.drexel.edu
From: Mark A Vivino <mvivino@helix.nih.gov>
Subject: Re: pixel range
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>In imaging addition of red and green gives yellow. How do you know if the
>original color was red plus green or true yellow from an RGB picture? That
>is not possible. To really select only yellow, you would have to have a
>narrow band-pass filter for only yellow (the exact wavelength). The problem
>is that yellow light excites green as well as red cones in the eye (and the
>-broad band- elemnts in a RGB camera) and the brain interprets this as
>yellow. But the brain also interprets a mix of true (narrow band) red and
>true green as yellow. So, in contrast to the ear, the eye (and camera) does
>not register the wavelenth of the light, only the relative excitation of
>the three types of color-sensitive cones. No way to convert the RGB
>information back to wavelength. The problem remains the same irrespective
>the color representation (RGB, HSI, etc), all color representations contain
>basically the same information, and are interchangable.

Good point! Just read this myself in "Seeing the Light, Optics in Nature,
Photography, Color, Vision and Holography" by David Falk. Wiley books. Nice
easy to read, unlike most IP books.

He shows on page 242 how a 590nm and a mix of 550 and 690 look the same to
the eye.

Oh well, I guess we need a 3D volume to represent a 2D plane. Have width,
height and 300 planes of wavelength for each image. Anything less is a
guess.

Mark


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Dear Micheline,
I receive a message with a adress that I think have what you need
SPM Image Analysis
http://www.dfm.dtu.dk/spip/
Good luck
Rejane Galindo
Universidade Federal Rural de Pernambuco
Plant Morphology and Anatomy


----------
> From: Micheline Ayoub <mayoub@po-box.mcgill.ca>
> To: nih-image@io.ece.drexel.edu
> Subject: Fourier Descriptors
> Date: Quinta-feira, 23 Julho, 1998 11:34
> 
> Hi there,
> 
> I am looking for a software that can apply Fourier descriptors in ima0ge
> analysis.  I have binary images of barley seeds and I am interested in
> calculating the area, perimeter, width and length each seed.
> 
> If any one knows about such a software and where to get it, please e-mail
> me the info or post it in this forum.
> 
> Thank you
> 
> 
> 
> 
>  
> Micheline Ayoub
> 
> Plant Science Department
> Macdonald Campus of Mcgill University
> 21111 Lakeshore Rd.
> Ste-Anne-de-bellevue, QC, H9X 3V9
> 
> Tel: 514-398-7851 ext 8733
> Fax: 514-398-7897
> 

From nih-image-request@io.ece.drexel.edu Thu Jul 23 20:39 EDT 1998
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From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: Display of Changing Numbers.
Date: Fri, 24 Jul 1998 10:29:57 +1000
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Hi,
Thanks to Stein Roervik I am now communicating happily with the Ludl
stage. And it is all fairly painless so far.
When I get it all working well I will share it.
Now I can get the position of the stage by asking it where x y z , and
it returns the appropriate numbers in a string which I can sort out and
scale etc.
The user can push a button on the joystick and this is noted by the
controller and the postion at that point can be recorded.
What I want to do is display a window or a panel in a window which shows
the three numbers with appropriate labels (X Y and Z for instance) and
updates these numbers until I tell it to stop. So that as the stage is
moved with the joystick the numbers roll and follow the position. The
frequency of update might be limited as the stage controller
communicates at 9600 baud. But I guess if I get an update every 0.1
second or so it will be ok.

Now my question.
What is the best method to use in Image.
A text window with big writing. How to delete the old numbers.
An Image window with some hard written labels and the new numbers
overwritten. How to remove the old ones.
The Info window works well but it is in a small font.
So if anyone has tried this sort of thing and is willing to share their
experience I would be grateful.


Best Regards
Noel Goldsmith.

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Subject: nih-image-d Digest V98 #19
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 19

Today's Topics:
  Re: pixel range                       [ "Christopher P. Tully" <cptully@sis ]
  montage macro                         [ Laird Bloom <lbloom@MIT.EDU> ]
  Re: pixel range                       [ Mark A Vivino <mvivino@helix.nih.go ]
  Fourier Descriptors                   [ Micheline Ayoub <mayoub@po-box.mcgi ]
  RE: zero prefix                       [ "Kirk, Todd Jason" <tjkirk@iupui.ed ]
  Unidentified subject!                 [ oscar <oscarm.mozos@umh.es> ]
  Re: pixel range                       [ Arnout Ruifrok <arnout@odin.mdacc.t ]
  Re: pixel range                       [ David Ehrhardt <ehrhardt@camelot.St ]
  Re: Fourier Descriptors               [ "=?ISO-8859-1?Q?Rejane_Magalh=E3es_ ]
  Re: pixel range                       [ Mark A Vivino <mvivino@helix.nih.go ]
  Re: Fourier Descriptors               [ "=?ISO-8859-1?Q?Rejane_Magalh=E3es_ ]
  Display of Changing Numbers.          [ "Goldsmith, Noel" <Noel.Goldsmith@d ]

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

Date: Wed, 22 Jul 1998 22:55:23 -0600
From: "Christopher P. Tully" <cptully@sisna.com>
To: jmille@po-box.mcgill.ca
CC: NIH-Image <nih-image@io.ece.drexel.edu>
Subject: Re: pixel range
Message-ID: <35B6C23B.F9AF6BCF@sisna.com>
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Maybe I'm missing the point here, but couldn't you just take a histogram of your
image, and get the numbers from that?  EVen if you are working in color, taking
the histogram for each of the three color slices in the three slice RGB stack
should get the information you want.

Chris Tully

Jeri Miller wrote:
> 
> Hello to all.
> I am a new user to NIH Image. I am looking for any assistance in how to
> determine the percentage of pixels of a specificed color range contained
> within an image. This would be used in histological slide analyses. I
> have used 'Sort by LUT' and individual macros such as 'count
> BluePixels'. Is there a way to specify specific pixel color ranges, then
> count or derive percentages of this range within a ROI? Your help is
> appreciated.
> 
> J. Miller, Ph. D. Candidate
> Ultrasound Research Imaging Lab
> McGill University/RVH
> Montreal, Quebec

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

Date: Thu, 23 Jul 1998 08:31:54 -0400
From: Laird Bloom <lbloom@MIT.EDU>
To: nih-image@io.ece.drexel.edu
Subject: montage macro
Message-Id: <v03020901b1dcdb74c2e5@[18.155.0.114]>
Content-Type: text/plain; charset="us-ascii"

 NIH Image Users:

	Does anyone have a macro that makes a montage of RGB TIFF images?
There was some discussion of ways to do this last summer; has anyone
written the code?

	Ideally, I'd like to be able to make a "contact sheet" (e.g. about
24-35 small images on a page) as a way of keeping track of images I've
recorded.  My computer can't open more than about 10 TIFF images at a time,
but I'd like to be able to make a montage without having to open each file
up individually.  Is there a way to open files in a folder one at a time
without having to give them sequential numbers?

	I'd appreciate help on this.

Thanks very much.

Laird Bloom
MIT Center for Cancer Research

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

Date: Thu, 23 Jul 1998 09:37:04 -0500
From: Mark A Vivino <mvivino@helix.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: pixel range
Message-Id: <v04003a02b1dcfaab2de5@[128.231.128.61]>
Content-Type: text/plain; charset="us-ascii"

Chris Tully asks:
>Maybe I'm missing the point here, but couldn't you just take a histogram
>of your
>image, and get the numbers from that?  EVen if you are working in color,
>taking
>the histogram for each of the three color slices in the three slice RGB stack
>should get the information you want.

Well I'll have to think about it a little more. Roughly the answer seems to
be yes. Specifically I think the answer is not very well. It would be truer
for example if R was a wavelength value from 0 to 255 (or 0 to 100, or 600
to 700 nm) which represented the redness or red wavelengths of of a point,
same for G and B, and you had seperately an intensity plane to take care of
density. Roughly though I think what you say gives as good a simple answer
as can be gotten without forming new image standards and and using a
spectrophotometer, etc. I think using hue might do better.

Mark

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

Date: Thu, 23 Jul 1998 10:34:38 -0400
From: Micheline Ayoub <mayoub@po-box.mcgill.ca>
To: nih-image@io.ece.drexel.edu
Subject: Fourier Descriptors
Message-Id: <3.0.5.32.19980723103438.007a6950@po-box.mcgill.ca>
Content-Type: text/plain; charset="us-ascii"

Hi there,

I am looking for a software that can apply Fourier descriptors in ima0ge
analysis.  I have binary images of barley seeds and I am interested in
calculating the area, perimeter, width and length each seed.

If any one knows about such a software and where to get it, please e-mail
me the info or post it in this forum.

Thank you




 
Micheline Ayoub

Plant Science Department
Macdonald Campus of Mcgill University
21111 Lakeshore Rd.
Ste-Anne-de-bellevue, QC, H9X 3V9

Tel: 514-398-7851 ext 8733
Fax: 514-398-7897

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

Date: Thu, 23 Jul 1998 10:22:47 -0500
From: "Kirk, Todd Jason" <tjkirk@iupui.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: zero prefix
Message-ID: <9D916278299FD111A7E100805FA7C2BA4B9ED6@cheetah.uits.iupui.edu>
Content-Type: text/plain

Can you do something like?
'0000'+your_num

check the size or your_num to see how many characters or value it has to
see how many zeros to put
if your_num>9 then
'000'+your_num
else
'0000'+your_num

Todd

> -----Original Message-----
> From:	Anneke M.Th. Harbers and Ard Jonker [SMTP:a_team@dds.nl]
> Sent:	Wednesday, July 22, 1998 1:25 PM
> To:	nih-image@io.ece.drexel.edu
> Subject:	zero prefix
> 
> Hi List,
> I'm looking for an elegant solution to have a prefix on a string, so
> as to obtain ' 00001' or ' 00012' ie. constant length. I also like to
> find an elegant way to get a part of a string without character by
> character moving to another string and then deleting that character
> from the input string, ie.
> string1:=concat(string2:3);delete(string2,0,3), which does not seem to
> work for me.
> Please reply by e-mail to a_team@dds.nl
> Ard
> 

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

Date: Thu, 23 Jul 1998 18:19:43 +0200
From: oscar <oscarm.mozos@umh.es>
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-ID: <35B7629F.4AF9351C@umh.es>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

unsubscribe

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

Date: Thu, 23 Jul 1998 13:13:18 -0500
From: Arnout Ruifrok <arnout@odin.mdacc.tmc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: pixel range
Message-Id: <v03102800b1dce3c446aa@[143.111.62.105]>
Content-Type: text/plain; charset="us-ascii"

>Dear list,
>
>On Wed, 22 Jul 1998, amongst other things, Mark A Vivino wrote:
>>
>>It would be easier
>>if pixels were not RGB or HSV, or anything else unrelated. Instead they
>>should be wavelength(s) and density. Unfortunately, this is not the case
>
>Mark, I found these comments very thought-provoking.
>
>excuse my probable ignorance or niaivity, isn't hue angle related in some
>way to wavelength in many cases?
>
>I realise the pixels on our screens are mixtures of rgb, but they usually
>do not represent mixtures of rgb brought in from the real world. Unless we
>are using spectrophotometers, electronically we most often represent
>wavelengths in the real world in rgb because it is convenient to sample it
>and then display it that way.
>
>If I digitally photograph or frame grab a sodium yellow flame, isn't the
>hue of the resulting image some sort of representation of the original
>wavelength(s)?
>
>So if I had a table which converted hue angle to wavelength, perhaps I
>could create a real-values image in which pixel values represented the
>centres of wavelength ranges. Once I had made the table, I could code it
>into Image for all to use (:-) ? Maybe all you need is hue angle, but
>wavelength ranges may not be related in a very linear way to hue, I haven't
>tried to figure that out.
>
>I am sure there can be lots of dangers in this approach (mixed light
>sources etc.) and I am sure the list will hear about them 5 minutes after
>this is posted! This could still help out all those people who post to the
>list asking how to separate their coloured stains / leaf colours / etc.
>
>I hope this promotes some discussion
>even if it is only that I have just re-invented a wheel called hue!
>
>Steve

In imaging addition of red and green gives yellow. How do you know if the
original color was red plus green or true yellow from an RGB picture? That
is not possible. To really select only yellow, you would have to have a
narrow band-pass filter for only yellow (the exact wavelength). The problem
is that yellow light excites green as well as red cones in the eye (and the
-broad band- elemnts in a RGB camera) and the brain interprets this as
yellow. But the brain also interprets a mix of true (narrow band) red and
true green as yellow. So, in contrast to the ear, the eye (and camera) does
not register the wavelenth of the light, only the relative excitation of
the three types of color-sensitive cones. No way to convert the RGB
information back to wavelength. The problem remains the same irrespective
the color representation (RGB, HSI, etc), all color representations contain
basically the same information, and are interchangable.

Arnout

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

Date: Thu, 23 Jul 1998 11:23:53 -0700 (PDT)
From: David Ehrhardt <ehrhardt@camelot.Stanford.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Re: pixel range
Message-ID: <Pine.GUL.3.95.980723105602.3221B-100000@camelot.Stanford.EDU>
Content-Type: TEXT/PLAIN; charset=US-ASCII

The histogram appraoch does not really answer the question here.  Jeri
needs to know which pixels contain a particular relative amount of each
color component.  A pixel with a particular value of blue might be part of
say a purple or a blue pixel.  I guess what is needed is something like
what Arnout suggested; you classify each pixel as falling within a
certain range of R AND G AND B values.  Possibly more sophisticated
selections could be made by working with relative pixel values to select a
hue across darkness and lightness gradients.  

-David

On Wed, 22 Jul 1998, Christopher P. Tully wrote:

> Maybe I'm missing the point here, but couldn't you just take a histogram of your
> image, and get the numbers from that?  EVen if you are working in color, taking
> the histogram for each of the three color slices in the three slice RGB stack
> should get the information you want.
> 
> Chris Tully
> 
> Jeri Miller wrote:
> > 
> > Hello to all.
> > I am a new user to NIH Image. I am looking for any assistance in how to
> > determine the percentage of pixels of a specificed color range contained
> > within an image. This would be used in histological slide analyses. I
> > have used 'Sort by LUT' and individual macros such as 'count
> > BluePixels'. Is there a way to specify specific pixel color ranges, then
> > count or derive percentages of this range within a ROI? Your help is
> > appreciated.
> > 
> > J. Miller, Ph. D. Candidate
> > Ultrasound Research Imaging Lab
> > McGill University/RVH
> > Montreal, Quebec
> 
> 

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

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

Date: Thu, 23 Jul 1998 15:33:45 -0300
From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" <ggalindo@elogica.com.br>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: Fourier Descriptors
Message-Id: <199807231828.PAA02162@ceiun01.elogica.com.br>
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

Dear Micheline,
I receive a message with a adress that I think have what you need
SPM Image Analysis
http://www.dfm.dtu.dk/spip/
Good luck
Rejane Galindo
Universidade Federal Rural de Pernamnuco
Plant Morphology and Anatomy

----------
> From: Micheline Ayoub <mayoub@po-box.mcgill.ca>
> To: nih-image@io.ece.drexel.edu
> Subject: Fourier Descriptors
> Date: Quinta-feira, 23 Julho, 1998 11:34
> 
> Hi there,
> 
> I am looking for a software that can apply Fourier descriptors in ima0ge
> analysis.  I have binary images of barley seeds and I am interested in
> calculating the area, perimeter, width and length each seed.
> 
> If any one knows about such a software and where to get it, please e-mail
> me the info or post it in this forum.
> 
> Thank you
> 
> 
> 
> 
>  
> Micheline Ayoub
> 
> Plant Science Department
> Macdonald Campus of Mcgill University
> 21111 Lakeshore Rd.
> Ste-Anne-de-bellevue, QC, H9X 3V9
> 
> Tel: 514-398-7851 ext 8733
> Fax: 514-398-7897
> 

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

Date: Thu, 23 Jul 1998 14:44:34 -0500
From: Mark A Vivino <mvivino@helix.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: pixel range
Message-Id: <v04003a00b1dd421bf923@[128.231.128.61]>
Content-Type: text/plain; charset="us-ascii"

>In imaging addition of red and green gives yellow. How do you know if the
>original color was red plus green or true yellow from an RGB picture? That
>is not possible. To really select only yellow, you would have to have a
>narrow band-pass filter for only yellow (the exact wavelength). The problem
>is that yellow light excites green as well as red cones in the eye (and the
>-broad band- elemnts in a RGB camera) and the brain interprets this as
>yellow. But the brain also interprets a mix of true (narrow band) red and
>true green as yellow. So, in contrast to the ear, the eye (and camera) does
>not register the wavelenth of the light, only the relative excitation of
>the three types of color-sensitive cones. No way to convert the RGB
>information back to wavelength. The problem remains the same irrespective
>the color representation (RGB, HSI, etc), all color representations contain
>basically the same information, and are interchangable.

Good point! Just read this myself in "Seeing the Light, Optics in Nature,
Photography, Color, Vision and Holography" by David Falk. Wiley books. Nice
easy to read, unlike most IP books.

He shows on page 242 how a 590nm and a mix of 550 and 690 look the same to
the eye.

Oh well, I guess we need a 3D volume to represent a 2D plane. Have width,
height and 300 planes of wavelength for each image. Anything less is a
guess.

Mark

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

Date: Thu, 23 Jul 1998 16:18:14 -0300
From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" <ggalindo@elogica.com.br>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: Fourier Descriptors
Message-Id: <199807231925.QAA14158@ceiun01.elogica.com.br>
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

Dear Micheline,
I receive a message with a adress that I think have what you need
SPM Image Analysis
http://www.dfm.dtu.dk/spip/
Good luck
Rejane Galindo
Universidade Federal Rural de Pernambuco
Plant Morphology and Anatomy


----------
> From: Micheline Ayoub <mayoub@po-box.mcgill.ca>
> To: nih-image@io.ece.drexel.edu
> Subject: Fourier Descriptors
> Date: Quinta-feira, 23 Julho, 1998 11:34
> 
> Hi there,
> 
> I am looking for a software that can apply Fourier descriptors in ima0ge
> analysis.  I have binary images of barley seeds and I am interested in
> calculating the area, perimeter, width and length each seed.
> 
> If any one knows about such a software and where to get it, please e-mail
> me the info or post it in this forum.
> 
> Thank you
> 
> 
> 
> 
>  
> Micheline Ayoub
> 
> Plant Science Department
> Macdonald Campus of Mcgill University
> 21111 Lakeshore Rd.
> Ste-Anne-de-bellevue, QC, H9X 3V9
> 
> Tel: 514-398-7851 ext 8733
> Fax: 514-398-7897
> 

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

Date: Fri, 24 Jul 1998 10:29:57 +1000
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Image Mailing List'" <nih-image@io.ece.drexel.edu>
Subject: Display of Changing Numbers.
Message-ID: <F98649A5EE8ED11190160000F802756598CDA9@exchvic3.dsto.defence.gov.au>
Content-Type: text/plain

Hi,
Thanks to Stein Roervik I am now communicating happily with the Ludl
stage. And it is all fairly painless so far.
When I get it all working well I will share it.
Now I can get the position of the stage by asking it where x y z , and
it returns the appropriate numbers in a string which I can sort out and
scale etc.
The user can push a button on the joystick and this is noted by the
controller and the postion at that point can be recorded.
What I want to do is display a window or a panel in a window which shows
the three numbers with appropriate labels (X Y and Z for instance) and
updates these numbers until I tell it to stop. So that as the stage is
moved with the joystick the numbers roll and follow the position. The
frequency of update might be limited as the stage controller
communicates at 9600 baud. But I guess if I get an update every 0.1
second or so it will be ok.

Now my question.
What is the best method to use in Image.
A text window with big writing. How to delete the old numbers.
An Image window with some hard written labels and the new numbers
overwritten. How to remove the old ones.
The Info window works well but it is in a small font.
So if anyone has tried this sort of thing and is willing to share their
experience I would be grateful.


Best Regards
Noel Goldsmith.

--------------------------------
End of nih-image-d Digest V98 Issue #19
***************************************

From nih-image-request@io.ece.drexel.edu Fri Jul 24 09:50 EDT 1998
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Date: Fri, 24 Jul 1998 06:36:12 -0700 (PDT)
From: first last <w2072y@yahoo.com>
Subject: brightness values over time
To: nih-image@io.ece.drexel.edu
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Dear users of NIH image:

I have stacks of gray scale images, representing a time lapse, and I
would like to measure the values for the brightness of single pixels
or for the average brightness of a small ROI, respectively, for each
frame in the image stack.
The results of these measurements should be written in a column to a
text window for later saving to an ASCII file.

I could not find a macro for doing this and I would highly appreciate
any suggestions of how to write such a macro.

Thank you very much in advance.





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

From nih-image-request@io.ece.drexel.edu Fri Jul 24 10:08 EDT 1998
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Date: Fri, 24 Jul 1998 09:57:38 -0400
From: "J.P. Simmons" <simmons@cindy.ml.wpafb.af.mil>
Message-Id: <9807241357.AA17033@cindy.ml.wpafb.af.mil>
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Subject: montage macro
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I don't know how to do that with NIH Image, but if you're running on a Mac,
there's a software package by the name of GraphicConverter (shareware) that
will do exactly this. You may also want to look at the commercial software
Extensis Fetch.

Jeff Simmons
UES, Inc.


>NIH Image Users:
>
>	Does anyone have a macro that makes a montage of RGB TIFF images?
>There was some discussion of ways to do this last summer; has anyone
>written the code?
>
>	Ideally, I'd like to be able to make a "contact sheet" (e.g. about
>24-35 small images on a page) as a way of keeping track of images I've
>recorded.  My computer can't open more than about 10 TIFF images at a time,
>but I'd like to be able to make a montage without having to open each file
>up individually.  Is there a way to open files in a folder one at a time
>without having to give them sequential numbers?
>
>	I'd appreciate help on this.
>
>Thanks very much.
>
>Laird Bloom
>MIT Center for Cancer Research

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Date: Fri, 24 Jul 1998 08:10:16 -0700 (PDT)
From: "R. Hard" <rhard@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: 2nd Announcement-Optical Microscopy Course
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Course Announcement

Title: Optical Microscopy and Imaging in the Biomedical Sciences

When: October 7 - October 15, 1998

Where: Marine Biology Laboratory, Woods Hole, MA, USA

Tuition: $2050 (Includes room and board)

Application Deadline: August 4, 1998

Admission application and information:
     Carol Harnel, Admissions Coordinator
     Marine Biological Laboratory
     7 MBL Street
     Woods Hole, MA 02543-1015
     (508) 289-7401
     Internet: admissions@mbl.edu
     WWW: http://www.mbl.edu (Application forms available via Adobe
                              Acrobat)

Course Director: Colin S. Izzard, State University of New York @ Albany
   Phone: [518] 442 - 4367
   EMail: csizzard@csc.albany.edu

Course Description:

For Whom:
      Designed primarily for research scientists, physicians, postdoctoral 
trainees and advanced graduate students in animal, plant, medical and 
material sciences. Non-biologists seeking a comprehensive introduction to 
microscopy and video-imaging will benefit greatly from this course as
well. There are no specific prerequisites, but an understanding of the basic 
principles of optics is desirable. Limited to 24 students.

  The eight day course consists of lectures, laboratory demonstrations, 
exercises and discussions that will enable the participant to obtain and 
interpret microscope images of high quality, to perform quantitative
optical measurements, and to produce photographic and video records for
documentation and analysis.

Topics to be covered include:
      principles of microscope design and image formation
      bright field, dark field, phase contrast, differential
         interference contrast, interference reflection, and 
         fluorescence microscopy
      confocal scanning microscopy and image deconvolution
      digital image restoration and 3-D reconstruction
      video imaging, recording, enhancement, and intensification
      analog and digital image processing and analysis
      fluorescent probes and ratio-imaging
      laser tweezers and laser scissors

  Applications to live cells will be emphasized; other specimens will be 
covered as well.

  Students will have direct hands-on experience with state-of-the-art 
microscopes, video cameras, recorders and image processing equipment
provided by major optical and electronics companies. Instruction will be provided
by experienced staff from universities and industry.

  Students are encouraged to bring their own biological (primary 
cultures, cell lines, etc.) and material specimens and to discuss
individual research problems with the faculty.


From nih-image-request@io.ece.drexel.edu Fri Jul 24 11:51 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
Subject: Re: montage macro
Cc: Laird Bloom <lbloom@MIT.EDU>
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>	Does anyone have a macro that makes a montage of RGB TIFF images?
>There was some discussion of ways to do this last summer; has anyone
>written the code?

'Image SXM' is a version of NIH Image that has been extended for use with
scanning microscope images such as those from SEMs or SPMs. It also has a
number of general features which users may find useful. One is the ability
to browse through the images in a folder, creating 'contact sheets' that
can be double-clicked to load the original image, or printed out
automatically.

Information about Image SXM can be found at http://reg.ssci.liv.ac.uk.
A copy of the Image SXM installer is in the spin-offs folder of the NIH
Image server.


___________________________________________________________________

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

Tel: 44-(0)151-794-3874 / 3894 / 3870
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk

___________________________________________________________________


From nih-image-request@io.ece.drexel.edu Fri Jul 24 15:55 EDT 1998
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Subject: real result and thresholding
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Is there a way in Image to threshold the real result of image subtraction
such that negative values are all converted to zero?  Since the real
result is mapped to values from 0-255 for display, the LUT has those
values.  Should I work with a macro to examine each pixel value?

Thanks,

Randy.

---------------------
Randy Cutter
Virginia Institute of Marine Science
Route 1208 
Gloucester Point, VA 23062 USA

phone 804 684-7365
fax 804 684-7399 or 7045
email:  cutter@vims.edu

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


From nih-image-request@io.ece.drexel.edu Fri Jul 24 16:56 EDT 1998
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From: "Mariann Roetzheim" <roetzheimm@marotz.com>
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Subject: Question!
Date: Fri, 24 Jul 1998 13:54:03 -0700
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Hello,
My name is Elizabeth and I am a new user of Scion Image analysis beta
version three. I have run into what I consider a bug, where I have outlined
area of interest using the oval, polygonal, or freehand selection tool and
the area measures 0.00sq inches no matter how much I select of the image.
The only tool that will give me a measurement is the rectangle. Has anyone
else run into this problem? I am also looking for the mean gray value. Any
answers or input would be helpful. 
Thank you
Elizabeth Roetzheim 

roetzheimm@marotz.com

From nih-image-request@io.ece.drexel.edu Fri Jul 24 21:50 EDT 1998
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Paul G. Mermelstein Ph.D.
Department of Molecular and Cellular Physiology
Stanford University School of Medicine
Beckman Center Room B101
Stanford, CA 94305
phone: (650) 725-7564
fax: (650) 498-5663
email: pmerm@stanford.edu


From nih-image-d-request@io.ece.drexel.edu Sat Jul 25 06:11 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #20
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 20

Today's Topics:
  brightness values over time           [ first last <w2072y@yahoo.com> ]
  montage macro                         [ "J.P. Simmons" <simmons@cindy.ml.wp ]
  2nd Announcement-Optical Microscopy   [ "R. Hard" <rhard@u.washington.edu> ]
  Re: montage macro                     [ Steve Barrett <S.D.Barrett@liverpoo ]
  real result and thresholding          [ Randy Cutter <cutter@vims.edu> ]
  Question!                             [ "Mariann Roetzheim" <roetzheimm@mar ]
  subscribe                             [ Paul G Mermelstein <pmerm@stanford. ]

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

Date: Fri, 24 Jul 1998 06:36:12 -0700 (PDT)
From: first last <w2072y@yahoo.com>
To: nih-image@io.ece.drexel.edu
Subject: brightness values over time
Message-ID: <19980724133612.22265.rocketmail@send1a.yahoomail.com>
Content-Type: text/plain; charset=us-ascii

Dear users of NIH image:

I have stacks of gray scale images, representing a time lapse, and I
would like to measure the values for the brightness of single pixels
or for the average brightness of a small ROI, respectively, for each
frame in the image stack.
The results of these measurements should be written in a column to a
text window for later saving to an ASCII file.

I could not find a macro for doing this and I would highly appreciate
any suggestions of how to write such a macro.

Thank you very much in advance.





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

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

Date: Fri, 24 Jul 1998 09:57:38 -0400
From: "J.P. Simmons" <simmons@cindy.ml.wpafb.af.mil>
To: nih-image@io.ece.drexel.edu
Subject: montage macro
Message-Id: <9807241357.AA17033@cindy.ml.wpafb.af.mil>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Content-Md5: ojMfNMmjy49Q8MoSy5LZSA==

I don't know how to do that with NIH Image, but if you're running on a Mac,
there's a software package by the name of GraphicConverter (shareware) that
will do exactly this. You may also want to look at the commercial software
Extensis Fetch.

Jeff Simmons
UES, Inc.


>NIH Image Users:
>
>	Does anyone have a macro that makes a montage of RGB TIFF images?
>There was some discussion of ways to do this last summer; has anyone
>written the code?
>
>	Ideally, I'd like to be able to make a "contact sheet" (e.g. about
>24-35 small images on a page) as a way of keeping track of images I've
>recorded.  My computer can't open more than about 10 TIFF images at a time,
>but I'd like to be able to make a montage without having to open each file
>up individually.  Is there a way to open files in a folder one at a time
>without having to give them sequential numbers?
>
>	I'd appreciate help on this.
>
>Thanks very much.
>
>Laird Bloom
>MIT Center for Cancer Research

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

Date: Fri, 24 Jul 1998 08:10:16 -0700 (PDT)
From: "R. Hard" <rhard@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: 2nd Announcement-Optical Microscopy Course
Message-ID: <Pine.A41.3.95b.980724080744.40206B-100000@homer29.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Course Announcement

Title: Optical Microscopy and Imaging in the Biomedical Sciences

When: October 7 - October 15, 1998

Where: Marine Biology Laboratory, Woods Hole, MA, USA

Tuition: $2050 (Includes room and board)

Application Deadline: August 4, 1998

Admission application and information:
     Carol Harnel, Admissions Coordinator
     Marine Biological Laboratory
     7 MBL Street
     Woods Hole, MA 02543-1015
     (508) 289-7401
     Internet: admissions@mbl.edu
     WWW: http://www.mbl.edu (Application forms available via Adobe
                              Acrobat)

Course Director: Colin S. Izzard, State University of New York @ Albany
   Phone: [518] 442 - 4367
   EMail: csizzard@csc.albany.edu

Course Description:

For Whom:
      Designed primarily for research scientists, physicians, postdoctoral 
trainees and advanced graduate students in animal, plant, medical and 
material sciences. Non-biologists seeking a comprehensive introduction to 
microscopy and video-imaging will benefit greatly from this course as
well. There are no specific prerequisites, but an understanding of the basic 
principles of optics is desirable. Limited to 24 students.

  The eight day course consists of lectures, laboratory demonstrations, 
exercises and discussions that will enable the participant to obtain and 
interpret microscope images of high quality, to perform quantitative
optical measurements, and to produce photographic and video records for
documentation and analysis.

Topics to be covered include:
      principles of microscope design and image formation
      bright field, dark field, phase contrast, differential
         interference contrast, interference reflection, and 
         fluorescence microscopy
      confocal scanning microscopy and image deconvolution
      digital image restoration and 3-D reconstruction
      video imaging, recording, enhancement, and intensification
      analog and digital image processing and analysis
      fluorescent probes and ratio-imaging
      laser tweezers and laser scissors

  Applications to live cells will be emphasized; other specimens will be 
covered as well.

  Students will have direct hands-on experience with state-of-the-art 
microscopes, video cameras, recorders and image processing equipment
provided by major optical and electronics companies. Instruction will be provided
by experienced staff from universities and industry.

  Students are encouraged to bring their own biological (primary 
cultures, cell lines, etc.) and material specimens and to discuss
individual research problems with the faculty.

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

Date: Fri, 24 Jul 1998 16:42:56 +0100
From: Steve Barrett <S.D.Barrett@liverpool.ac.uk>
To: nih-image@io.ece.drexel.edu
Cc: Laird Bloom <lbloom@mit.edu>
Subject: Re: montage macro
Message-Id: <l03130316b1de5b054f24@[138.253.47.16]>
Content-Type: text/plain; charset="us-ascii"

>	Does anyone have a macro that makes a montage of RGB TIFF images?
>There was some discussion of ways to do this last summer; has anyone
>written the code?

'Image SXM' is a version of NIH Image that has been extended for use with
scanning microscope images such as those from SEMs or SPMs. It also has a
number of general features which users may find useful. One is the ability
to browse through the images in a folder, creating 'contact sheets' that
can be double-clicked to load the original image, or printed out
automatically.

Information about Image SXM can be found at http://reg.ssci.liv.ac.uk.
A copy of the Image SXM installer is in the spin-offs folder of the NIH
Image server.


___________________________________________________________________

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

Tel: 44-(0)151-794-3874 / 3894 / 3870
Fax: 44-(0)151-708-0662
Email: S.D.Barrett@liv.ac.uk

___________________________________________________________________

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

Date: Fri, 24 Jul 1998 15:07:10 -0400 (EDT)
From: Randy Cutter <cutter@vims.edu>
To: nih-image@io.ece.drexel.edu
Subject: real result and thresholding
Message-ID: <Pine.SOL.3.96.980724150308.22815B-100000@pagan.vims.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Is there a way in Image to threshold the real result of image subtraction
such that negative values are all converted to zero?  Since the real
result is mapped to values from 0-255 for display, the LUT has those
values.  Should I work with a macro to examine each pixel value?

Thanks,

Randy.

---------------------
Randy Cutter
Virginia Institute of Marine Science
Route 1208 
Gloucester Point, VA 23062 USA

phone 804 684-7365
fax 804 684-7399 or 7045
email:  cutter@vims.edu

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

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

Date: Fri, 24 Jul 1998 13:54:03 -0700
From: "Mariann Roetzheim" <roetzheimm@marotz.com>
To: <nih-image@io.ece.drexel.edu>
Subject: Question!
Message-ID: <B0000131173@marotzpdc.marotz.com>
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

Hello,
My name is Elizabeth and I am a new user of Scion Image analysis beta
version three. I have run into what I consider a bug, where I have outlined
area of interest using the oval, polygonal, or freehand selection tool and
the area measures 0.00sq inches no matter how much I select of the image.
The only tool that will give me a measurement is the rectangle. Has anyone
else run into this problem? I am also looking for the mean gray value. Any
answers or input would be helpful. 
Thank you
Elizabeth Roetzheim 

roetzheimm@marotz.com

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

Date: Fri, 24 Jul 1998 18:44:02 -0800
From: Paul G Mermelstein <pmerm@stanford.edu>
To: nih-image@io.ece.drexel.edu
Subject: subscribe
Message-Id: <l03110700b1def6e0f19e@[171.65.23.170]>
Content-Type: text/plain; charset="us-ascii"

Paul G. Mermelstein Ph.D.
Department of Molecular and Cellular Physiology
Stanford University School of Medicine
Beckman Center Room B101
Stanford, CA 94305
phone: (650) 725-7564
fax: (650) 498-5663
email: pmerm@stanford.edu

--------------------------------
End of nih-image-d Digest V98 Issue #20
***************************************

From nih-image-request@io.ece.drexel.edu Sat Jul 25 11:04 EDT 1998
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Date: Sat, 25 Jul 1998 10:17:23 -0400
To: nih-image@io.ece.drexel.edu
From: Sam Wang <stwang@CLEMSON.EDU>
Subject: Re: montage macro
Resent-Message-ID: <"eIMpT3.0.ec6.85Vkr"@io>
Resent-From: nih-image@io.ece.drexel.edu
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>>	Does anyone have a macro that makes a montage of RGB TIFF images?
>>There was some discussion of ways to do this last summer; has anyone
>>written the code?
>>
>>	Ideally, I'd like to be able to make a "contact sheet" (e.g. about
>>24-35 small images on a page) as a way of keeping track of images I've
>>recorded.  My computer can't open more than about 10 TIFF images at a time,
>>but I'd like to be able to make a montage without having to open each file
>>up individually.  Is there a way to open files in a folder one at a time
>>without having to give them sequential numbers?
>>
>>	I'd appreciate help on this.
>>
>>Thanks very much.
>>
>>Laird Bloom
>>MIT Center for Cancer Research

On the Mac, there is a great $25 graphics shareware called iView that does
everything you mentioned plus. It's up on the usual Archive sites.

--
Sam Wang
Clemson University
Art Department - Lee Hall
Clemson, SC 29634-0509
864/656-3924    FAX 864/656-7523

From nih-image-d-request@io.ece.drexel.edu Sun Jul 26 06:15 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #21
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 21

Today's Topics:
  Re: montage macro                     [ Sam Wang <stwang@CLEMSON.EDU> ]

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

Date: Sat, 25 Jul 1998 10:17:23 -0400
From: Sam Wang <stwang@CLEMSON.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Re: montage macro
Message-Id: <v04011700b1df987153e4@[204.189.110.43]>
Content-Type: text/plain; charset="us-ascii"

>>	Does anyone have a macro that makes a montage of RGB TIFF images?
>>There was some discussion of ways to do this last summer; has anyone
>>written the code?
>>
>>	Ideally, I'd like to be able to make a "contact sheet" (e.g. about
>>24-35 small images on a page) as a way of keeping track of images I've
>>recorded.  My computer can't open more than about 10 TIFF images at a time,
>>but I'd like to be able to make a montage without having to open each file
>>up individually.  Is there a way to open files in a folder one at a time
>>without having to give them sequential numbers?
>>
>>	I'd appreciate help on this.
>>
>>Thanks very much.
>>
>>Laird Bloom
>>MIT Center for Cancer Research

On the Mac, there is a great $25 graphics shareware called iView that does
everything you mentioned plus. It's up on the usual Archive sites.

--
Sam Wang
Clemson University
Art Department - Lee Hall
Clemson, SC 29634-0509
864/656-3924    FAX 864/656-7523

--------------------------------
End of nih-image-d Digest V98 Issue #21
***************************************

From nih-image-request@io.ece.drexel.edu Sun Jul 26 10:43 EDT 1998
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Date: Sun, 26 Jul 1998 16:35:07 +0200
From: Ilya Reviakine <I.Reviakine@chem.rug.nl>
X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX 6.3 IP32)
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To: nih-image@io.ece.drexel.edu
Subject: PRINTING THE FILE NAME ON THE IMAGE
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Hi everyone - 

	How does one print the file name with the image or text? 

	This question has been posted previously, but I could not fine the
answer to it among the archives.

					Thank you in advance,
							Ilya Reviakine.

-- 

	I.Reviakine@chem.rug.nl	                                    
	Ilya Reviakine, BSc (Biochemistry), Computer Science Minor  
	Dept. of Biophysical Chemistry                              
	University of Groningen
	Nijenborgh, 4                                    
	9747 AG Groningen, the Netherlands.                                 
	
	Phone:	31 (050)363-4220; 363-4213
	Fax:	31 (050)363-4800
                                                                    
	http://rugbe2.chem.rug.nl/~reviakin

From nih-image-d-request@io.ece.drexel.edu Mon Jul 27 06:15 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 22

Today's Topics:
  PRINTING THE FILE NAME ON THE IMAGE   [ Ilya Reviakine <I.Reviakine@chem.ru ]

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

Date: Sun, 26 Jul 1998 16:35:07 +0200
From: Ilya Reviakine <I.Reviakine@chem.rug.nl>
To: nih-image@io.ece.drexel.edu
Subject: PRINTING THE FILE NAME ON THE IMAGE
Message-ID: <35BB3E9B.CB6C0951@chem.rug.nl>
Content-Type: text/plain; charset=us-ascii
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Hi everyone - 

	How does one print the file name with the image or text? 

	This question has been posted previously, but I could not fine the
answer to it among the archives.

					Thank you in advance,
							Ilya Reviakine.

-- 

	I.Reviakine@chem.rug.nl	                                    
	Ilya Reviakine, BSc (Biochemistry), Computer Science Minor  
	Dept. of Biophysical Chemistry                              
	University of Groningen
	Nijenborgh, 4                                    
	9747 AG Groningen, the Netherlands.                                 
	
	Phone:	31 (050)363-4220; 363-4213
	Fax:	31 (050)363-4800
                                                                    
	http://rugbe2.chem.rug.nl/~reviakin

--------------------------------
End of nih-image-d Digest V98 Issue #22
***************************************

From nih-image-request@io.ece.drexel.edu Mon Jul 27 12:35 EDT 1998
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From: Alex_Courtade@huntsman.com
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Subject: derivative processing and particle size histogram macros
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I am analyzing rubber void images (taken using an SEM) with Scion beta 3. I
threshold the image, and then do a particle size/ count. I was wondering if
someone has any NIH Image/ Scion macros that can generate a histogram of
particle size vs # of particles. Is this even within the program's capability?
If not, does anyone have any other routines or programs that can do this?

I was also wondering if anyone has any derivative processing (differential
processing) macros that could be used. I know that derivative processing units
are available for electron microscopes, but can it be performed by software?
Thanks for any feedback.

From nih-image-request@io.ece.drexel.edu Mon Jul 27 12:47 EDT 1998
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From: "Mario de A. Lira Junior" <mliraj@PO-Box.mcgill.ca>
Subject: Re: derivative processing and particle size histogram macros
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Alex,

>someone has any NIH Image/ Scion macros that can generate a histogram of
>particle size vs # of particles. Is this even within the program's
capability?

I'll be using the same kind of processing, but my idea is to simply save
the measurements file, and then import into SAS or some other program, and
proceed with the analysis from there. You probably would be able to do this
even on a spreadsheet program, such as Excel or Quattro Pro.

From nih-image-request@io.ece.drexel.edu Tue Jul 28 01:41 EDT 1998
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Date: Mon, 27 Jul 1998 23:35:08 -0600
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Subject: Re: PRINTING THE FILE NAME ON THE IMAGE
References: <35BB3E9B.CB6C0951@chem.rug.nl>
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To be blunt, read the documentation.  Amoung the macros included with the
distribution versions of Image for Macs is a file called 'Editing Macros.txt'
which includes a macro titled 'Draw File Name in each Image,' which I think will
do what you want.  If not, it should be a good starting place for writing your
own macro.

I found this information by going to the NIH Image home page
(http://rsb.info.nih.gov/nih-image/Default.html) and clicking on 'More
Documentation' and then clicking on 'Macros Distributed with NIH Image' and
scanning the list of included macros.  There is also a reference to the 'File
Paths Demo' macro in the 'Input/Output Macros' included with Image under the
description of the GetFileInfo() macro command on the 'Macro Commands' page
(http://rsb.info.nih.gov/nih-image/more-docs/commands.html).

Chris Tully


Ilya Reviakine wrote:
> 
> Hi everyone -
> 
>         How does one print the file name with the image or text?
> 
>         This question has been posted previously, but I could not fine the
> answer to it among the archives.
> 
>                                         Thank you in advance,
>                                                         Ilya Reviakine.
> 
> --
> 
>         I.Reviakine@chem.rug.nl
>         Ilya Reviakine, BSc (Biochemistry), Computer Science Minor
>         Dept. of Biophysical Chemistry
>         University of Groningen
>         Nijenborgh, 4
>         9747 AG Groningen, the Netherlands.
> 
>         Phone:  31 (050)363-4220; 363-4213
>         Fax:    31 (050)363-4800
> 
>         http://rugbe2.chem.rug.nl/~reviakin

From nih-image-d-request@io.ece.drexel.edu Tue Jul 28 06:12 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #23
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 23

Today's Topics:
  derivative processing and particle s  [ Alex_Courtade@huntsman.com ]
  Re: derivative processing and partic  [ "Mario de A. Lira Junior" <mliraj@P ]
  Re: PRINTING THE FILE NAME ON THE IM  [ "Christopher P. Tully" <cptully@sis ]

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

Date: Mon, 27 Jul 1998 10:54:32 -0500
From: Alex_Courtade@huntsman.com
To: nih-image@io.ece.drexel.edu
Subject: derivative processing and particle size histogram macros
Message-ID: <00009EF3.CE21466@huntsman.com>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
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I am analyzing rubber void images (taken using an SEM) with Scion beta 3. I
threshold the image, and then do a particle size/ count. I was wondering if
someone has any NIH Image/ Scion macros that can generate a histogram of
particle size vs # of particles. Is this even within the program's capability?
If not, does anyone have any other routines or programs that can do this?

I was also wondering if anyone has any derivative processing (differential
processing) macros that could be used. I know that derivative processing units
are available for electron microscopes, but can it be performed by software?
Thanks for any feedback.

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

Date: Mon, 27 Jul 1998 12:25:33 -0400
From: "Mario de A. Lira Junior" <mliraj@PO-Box.mcgill.ca>
To: nih-image@io.ece.drexel.edu
Subject: Re: derivative processing and particle size histogram macros
Message-Id: <3.0.1.32.19980727122533.006b9a84@PO-Box.mcgill.ca>
Content-Type: text/plain; charset="us-ascii"

Alex,

>someone has any NIH Image/ Scion macros that can generate a histogram of
>particle size vs # of particles. Is this even within the program's
capability?

I'll be using the same kind of processing, but my idea is to simply save
the measurements file, and then import into SAS or some other program, and
proceed with the analysis from there. You probably would be able to do this
even on a spreadsheet program, such as Excel or Quattro Pro.

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

Date: Mon, 27 Jul 1998 23:35:08 -0600
From: "Christopher P. Tully" <cptully@sisna.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: PRINTING THE FILE NAME ON THE IMAGE
Message-ID: <35BD630C.7DECA269@sisna.com>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

To be blunt, read the documentation.  Amoung the macros included with the
distribution versions of Image for Macs is a file called 'Editing Macros.txt'
which includes a macro titled 'Draw File Name in each Image,' which I think will
do what you want.  If not, it should be a good starting place for writing your
own macro.

I found this information by going to the NIH Image home page
(http://rsb.info.nih.gov/nih-image/Default.html) and clicking on 'More
Documentation' and then clicking on 'Macros Distributed with NIH Image' and
scanning the list of included macros.  There is also a reference to the 'File
Paths Demo' macro in the 'Input/Output Macros' included with Image under the
description of the GetFileInfo() macro command on the 'Macro Commands' page
(http://rsb.info.nih.gov/nih-image/more-docs/commands.html).

Chris Tully


Ilya Reviakine wrote:
> 
> Hi everyone -
> 
>         How does one print the file name with the image or text?
> 
>         This question has been posted previously, but I could not fine the
> answer to it among the archives.
> 
>                                         Thank you in advance,
>                                                         Ilya Reviakine.
> 
> --
> 
>         I.Reviakine@chem.rug.nl
>         Ilya Reviakine, BSc (Biochemistry), Computer Science Minor
>         Dept. of Biophysical Chemistry
>         University of Groningen
>         Nijenborgh, 4
>         9747 AG Groningen, the Netherlands.
> 
>         Phone:  31 (050)363-4220; 363-4213
>         Fax:    31 (050)363-4800
> 
>         http://rugbe2.chem.rug.nl/~reviakin

--------------------------------
End of nih-image-d Digest V98 Issue #23
***************************************

From nih-image-request@io.ece.drexel.edu Tue Jul 28 10:42 EDT 1998
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Date: Tue, 28 Jul 1998 10:27:30 -0400 (EDT)
From: Kanu P Singh <kanu@UDel.Edu>
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To: nih-image@io.ece.drexel.edu
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Hi Alex,
I am working on the void distribution in hardened Phenolic resins. I
would appreciate if you could let me know what kind of analysis you are
doing for your study of rubber voids. I have some SEM pictures of my
samples. I was wondering if you could tell me what kind of information can
be obtained from them regarding the void sizes and volume fractions. I
would also appreciate any information that you could give me regarding
existing literature on void fraction studies through electron microscopy.
Thanks,
Kanu


From nih-image-d-request@io.ece.drexel.edu Wed Jul 29 06:14 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #24
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------------------------------

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nih-image-d Digest				Volume 98 : Issue 24

Today's Topics:
  NIH image processing                  [ Kanu P Singh <kanu@UDel.Edu> ]

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

Date: Tue, 28 Jul 1998 10:27:30 -0400 (EDT)
From: Kanu P Singh <kanu@UDel.Edu>
To: nih-image@io.ece.drexel.edu
cc: Alex_Courtade@huntsman.com
Subject: NIH image processing
Message-ID: <Pine.SOL.3.96.980728101617.13269A-100000@copland.udel.edu>
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Hi Alex,
I am working on the void distribution in hardened Phenolic resins. I
would appreciate if you could let me know what kind of analysis you are
doing for your study of rubber voids. I have some SEM pictures of my
samples. I was wondering if you could tell me what kind of information can
be obtained from them regarding the void sizes and volume fractions. I
would also appreciate any information that you could give me regarding
existing literature on void fraction studies through electron microscopy.
Thanks,
Kanu

--------------------------------
End of nih-image-d Digest V98 Issue #24
***************************************

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*********************************************************************
Rafael Edgardo Carazo Salas 
EMBL
Meyerhofstrasse 1
69117 Heidelberg
Tel :: (00496221) 38 72 84
Fax :: (00496221) 38 75 12
*********************************************************************

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From nih-image-request@io.ece.drexel.edu Wed Jul 29 09:28 EDT 1998
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From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>
Subject: Image comparison
Date: Wed, 29 Jul 1998 09:10:00 -0400
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Hello,
I have two B&W identical images: one is original and second
one is interpolated. Both are same size and have same number
of pixels as well. To my eyes, both looked same but  I want
to compare them pixel by pixel to how much they are
different. Main goal is to see how much interpolated image
is identical or close to the original one. Can I do that with
NIH or other application?.

Thanks
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-U of Michigan
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087

From nih-image-request@io.ece.drexel.edu Wed Jul 29 09:29 EDT 1998
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To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>
Subject: Image enhancment
Date: Wed, 29 Jul 1998 09:11:49 -0400
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Hello,
Is there any way to enhance (sharpening edges) images in
folder in one shot rather than enhancing one image a time
using one of the filters?.
I have B&W CAT scan images-100's of them. Any  suggestion is
appreciated.

Thanks
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-U of M
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087

From nih-image-request@io.ece.drexel.edu Wed Jul 29 10:36 EDT 1998
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I am chiefly looking at the voids in some polypropylene samples. It's
essentially industrial analysis. The void size/ distribution apparently can have
some important effects on the physical properties of the sample. 

I am only a summer intern, and unfortunately I don't know what specific
information can be obtained from the void size/ volume. As far as existing
literature of void fraction studies in electron microscopy, I'm pretty much in
the dark as well. Perhaps someone else out there is aware of some of these
studies?


____________________Reply Separator____________________
Subject:    NIH image processing
Author: Kanu P Singh <kanu@UDel.Edu>
Date:       7/28/98 10:27 AM

Hi Alex,
I am working on the void distribution in hardened Phenolic resins. I
would appreciate if you could let me know what kind of analysis you are
doing for your study of rubber voids. I have some SEM pictures of my
samples. I was wondering if you could tell me what kind of information can
be obtained from them regarding the void sizes and volume fractions. I
would also appreciate any information that you could give me regarding
existing literature on void fraction studies through electron microscopy.
Thanks,
Kanu


From nih-image-request@io.ece.drexel.edu Wed Jul 29 14:03 EDT 1998
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Date: Wed, 29 Jul 1998 18:55:18  -127532
From: "Swidbert R OTT" <sro21@hermes.cam.ac.uk>
To: nih-image@io.ece.drexel.edu
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You may subtract one from the other in NIH Image, using some offset, e.g.
127 (to push those difference pixels that are negative back into range).

Swidi

--------------------------------------------------
Swidbert R OTT
Department of Zoology
University of Cambridge
Downing Street
Cambridge CB2 3EJ
ENGLAND

From nih-image-request@io.ece.drexel.edu Wed Jul 29 14:42 EDT 1998
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To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Image comparison
Date: Wed, 29 Jul 1998 14:21:52 -0400
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I am sorry I could not understand exactly what you mean. Do you mean
use:
Image math
then
substarct image
or what is the exact steps please?

> ----------
> From: 	Swidbert R OTT[SMTP:sro21@hermes.cam.ac.uk]
> Reply To: 	nih-image@io.ece.drexel.edu
> Sent: 	Wednesday, July 29, 1998 2:55 PM
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	Re: Image comparison
> 
> You may subtract one from the other in NIH Image, using some offset,
> e.g.
> 127 (to push those difference pixels that are negative back into
> range).
> 
> Swidi
> 
> --------------------------------------------------
> Swidbert R OTT
> Department of Zoology
> University of Cambridge
> Downing Street
> Cambridge CB2 3EJ
> ENGLAND
> 

From nih-image-request@io.ece.drexel.edu Wed Jul 29 16:46 EDT 1998
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Subject: Re: G3
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>Is there a fix yet for the digitizer error when trying to capture images
>from the built-in video card in the G3's?

I tried to fix this problem by capturing to screen memory rather than
offscreen memory but it only works when then monitor is set to 256 colors
and only for single frames. I'm open to suggestions for what to try next.

-wayne


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============================================================
Dr. Ruy G. Jaeger                       Phone 55-11-8187902
                                              55-11-8187912

Patologia Bucal                         FAX   55-11-8187413
FOUSP
                 E-mail rgjaeger@siso.fo.usp.br
      Av Prof. Lineu Prestes 2227 Cidade Universitaria
                   Sao Paulo SP 05508-900
                             BRAZIL
============================================================


From nih-image-request@io.ece.drexel.edu Thu Jul 30 04:35 EDT 1998
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From: Paul Human <ctshuman@samiot.uct.ac.za>
Subject: Avid Cinema and G3 drivers?
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Dear Imagers

Firstly, thank you to all the responses I received concerning the Mac and
NIH or Leica and QWin issue. To my dismay, we have gone with the Leica
system due to corporate political issues and I think already we are seeing
the disadvantage of that decision. Nevertheless, we will be adding
framegrabber cards to some of our existing Macs and the information this
list has provided will certainly help in this area.

Secondly, we have a Apple 6500/300 with an Avid Cinema card as well as a
few G3's with their standard AV input/output. Although these are obviously
not what one needs for individual framegrabs, they do nevertheless provide
a suitable picture (in many ways better than we are getting with the Leica
system with its Matrox Millenium card) which would be usable for simple
morphometric analysis of LM specimens. My question is, are there drivers
available which would allow direct capture from these cards into NIH? At
present we have to use third party applications to grab an image and then
save it on disk to get it into NIH.

Thanks in advance.

Paul

____________________________________________________________________
PAUL A HUMAN, M.Sc.
Deputy Director
Cardiovascular Research Unit
University of Cape Town Medical School
OBSERVATORY 7925, Cape Town, South Africa
Voice:+27-21-406 6418  Fax:+27-21-448 5935  Cell:+27-82-770 3612


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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #25
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 25

Today's Topics:
  unsubscribe                           [ Glenn Kearney <glenn.kearney@stoneb ]
  Re: unsubscribe                       [ Rafael Carazo-Salas <Rafael.Carazos ]
  How to unsubscribe                    [ Mark A Vivino <mvivino@helix.nih.go ]
  Image comparison                      [ "Mehmet Dondurur, Ph. D." <mehmet.d ]
  Image enhancment                      [ "Mehmet Dondurur, Ph. D." <mehmet.d ]
  Re:NIH image processing               [ Alex_Courtade@huntsman.com ]
  Re: Image comparison                  [ "Swidbert R OTT" <sro21@hermes.cam. ]
  RE: Image comparison                  [ "Mehmet Dondurur, Ph. D." <mehmet.d ]
  Re: G3                                [ Wayne Rasband <wayne@codon.nih.gov> ]
  Subscribe                             [ rgjaeger@fo.usp.br (Ruy Jaeger) ]
  Avid Cinema and G3 drivers?           [ Paul Human <ctshuman@samiot.uct.ac. ]

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

Date: Wed, 29 Jul 1998 22:49:43 +1200
From: Glenn Kearney <glenn.kearney@stonebow.otago.ac.nz>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <l03010d00b1e4aebefb44@[139.80.71.22]>
Content-Type: text/plain; charset="us-ascii"


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

Date: Wed, 29 Jul 1998 13:44:24 +0200 (MDT)
From: Rafael Carazo-Salas <Rafael.Carazosalas@EMBL-Heidelberg.de>
To: nih-image@io.ece.drexel.edu
Subject: Re: unsubscribe
Message-ID: <Pine.SGI.3.96.980729134420.7011B-100000@hawk.EMBL-Heidelberg.DE>
Content-Type: TEXT/PLAIN; charset=US-ASCII

*********************************************************************
Rafael Edgardo Carazo Salas 
EMBL
Meyerhofstrasse 1
69117 Heidelberg
Tel :: (00496221) 38 72 84
Fax :: (00496221) 38 75 12
*********************************************************************

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

Date: Wed, 29 Jul 1998 08:01:50 -0500
From: Mark A Vivino <mvivino@helix.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: How to unsubscribe
Message-Id: <v04003a00b1e4cd89893e@[128.231.128.61]>
Content-Type: text/plain; charset="us-ascii"

Whatever you do, do not send the request to:
    nih-image@io.ece.drexel.edu


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

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


Unsubscribe to Digest
--------------------
To unsubscribe to digested version of the list, send E-mail to
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As in:          To: nih-image-d-request@biomed.drexel.edu
                Subject: unsubscribe

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

Date: Wed, 29 Jul 1998 09:10:00 -0400
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>
Subject: Image comparison
Message-ID: <69B43248FE73D11197BB00A0C99AB06788CC@jvcserver.vanguardweb.org>
Content-Type: text/plain

Hello,
I have two B&W identical images: one is original and second
one is interpolated. Both are same size and have same number
of pixels as well. To my eyes, both looked same but  I want
to compare them pixel by pixel to how much they are
different. Main goal is to see how much interpolated image
is identical or close to the original one. Can I do that with
NIH or other application?.

Thanks
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-U of Michigan
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087

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

Date: Wed, 29 Jul 1998 09:11:49 -0400
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>
Subject: Image enhancment
Message-ID: <69B43248FE73D11197BB00A0C99AB06788CD@jvcserver.vanguardweb.org>
Content-Type: text/plain

Hello,
Is there any way to enhance (sharpening edges) images in
folder in one shot rather than enhancing one image a time
using one of the filters?.
I have B&W CAT scan images-100's of them. Any  suggestion is
appreciated.

Thanks
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-U of M
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087

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

Date: Wed, 29 Jul 1998 09:13:09 -0700
From: Alex_Courtade@huntsman.com
To: Kanu P Singh <kanu@UDel.Edu>, nih-image@io.ece.drexel.edu
Subject: Re:NIH image processing
Message-ID: <0000BC12.CE21466@huntsman.com>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Description: cc:Mail note part

I am chiefly looking at the voids in some polypropylene samples. It's
essentially industrial analysis. The void size/ distribution apparently can have
some important effects on the physical properties of the sample. 

I am only a summer intern, and unfortunately I don't know what specific
information can be obtained from the void size/ volume. As far as existing
literature of void fraction studies in electron microscopy, I'm pretty much in
the dark as well. Perhaps someone else out there is aware of some of these
studies?


____________________Reply Separator____________________
Subject:    NIH image processing
Author: Kanu P Singh <kanu@UDel.Edu>
Date:       7/28/98 10:27 AM

Hi Alex,
I am working on the void distribution in hardened Phenolic resins. I
would appreciate if you could let me know what kind of analysis you are
doing for your study of rubber voids. I have some SEM pictures of my
samples. I was wondering if you could tell me what kind of information can
be obtained from them regarding the void sizes and volume fractions. I
would also appreciate any information that you could give me regarding
existing literature on void fraction studies through electron microscopy.
Thanks,
Kanu

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

Date: Wed, 29 Jul 1998 18:55:18  -127532
From: "Swidbert R OTT" <sro21@hermes.cam.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Image comparison
Message-ID: <437379.3110727318@neuron06.zoo.cam.ac.uk>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

You may subtract one from the other in NIH Image, using some offset, e.g.
127 (to push those difference pixels that are negative back into range).

Swidi

--------------------------------------------------
Swidbert R OTT
Department of Zoology
University of Cambridge
Downing Street
Cambridge CB2 3EJ
ENGLAND

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

Date: Wed, 29 Jul 1998 14:21:52 -0400
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Image comparison
Message-ID: <69B43248FE73D11197BB00A0C99AB06788CE@jvcserver.vanguardweb.org>
Content-Type: text/plain

I am sorry I could not understand exactly what you mean. Do you mean
use:
Image math
then
substarct image
or what is the exact steps please?

> ----------
> From: 	Swidbert R OTT[SMTP:sro21@hermes.cam.ac.uk]
> Reply To: 	nih-image@io.ece.drexel.edu
> Sent: 	Wednesday, July 29, 1998 2:55 PM
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	Re: Image comparison
> 
> You may subtract one from the other in NIH Image, using some offset,
> e.g.
> 127 (to push those difference pixels that are negative back into
> range).
> 
> Swidi
> 
> --------------------------------------------------
> Swidbert R OTT
> Department of Zoology
> University of Cambridge
> Downing Street
> Cambridge CB2 3EJ
> ENGLAND
> 

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

Date: Wed, 29 Jul 1998 16:40:33 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: G3
Message-Id: <v03007810b1e5363f61b1@[128.231.99.217]>
Content-Type: text/plain; charset="us-ascii"

>Is there a fix yet for the digitizer error when trying to capture images
>from the built-in video card in the G3's?

I tried to fix this problem by capturing to screen memory rather than
offscreen memory but it only works when then monitor is set to 256 colors
and only for single frames. I'm open to suggestions for what to try next.

-wayne

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

Date: Wed, 29 Jul 1998 17:50:04 -0300
From: rgjaeger@fo.usp.br (Ruy Jaeger)
To: nih-image@io.ece.drexel.edu
Subject: Subscribe
Message-Id: <199807292044.RAA16457@siso.fo.usp.br>
Content-Type: text/plain; charset="us-ascii"

============================================================
Dr. Ruy G. Jaeger                       Phone 55-11-8187902
                                              55-11-8187912

Patologia Bucal                         FAX   55-11-8187413
FOUSP
                 E-mail rgjaeger@siso.fo.usp.br
      Av Prof. Lineu Prestes 2227 Cidade Universitaria
                   Sao Paulo SP 05508-900
                             BRAZIL
============================================================

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

Date: Thu, 30 Jul 1998 10:24:28 +0200
From: Paul Human <ctshuman@samiot.uct.ac.za>
To: NIH-Image Mailing List <nih-image@io.ece.drexel.edu>
Subject: Avid Cinema and G3 drivers?
Message-Id: <l03130300b1e5dc2d9caa@[196.30.99.11]>
Content-Type: text/plain; charset="us-ascii"

Dear Imagers

Firstly, thank you to all the responses I received concerning the Mac and
NIH or Leica and QWin issue. To my dismay, we have gone with the Leica
system due to corporate political issues and I think already we are seeing
the disadvantage of that decision. Nevertheless, we will be adding
framegrabber cards to some of our existing Macs and the information this
list has provided will certainly help in this area.

Secondly, we have a Apple 6500/300 with an Avid Cinema card as well as a
few G3's with their standard AV input/output. Although these are obviously
not what one needs for individual framegrabs, they do nevertheless provide
a suitable picture (in many ways better than we are getting with the Leica
system with its Matrox Millenium card) which would be usable for simple
morphometric analysis of LM specimens. My question is, are there drivers
available which would allow direct capture from these cards into NIH? At
present we have to use third party applications to grab an image and then
save it on disk to get it into NIH.

Thanks in advance.

Paul

____________________________________________________________________
PAUL A HUMAN, M.Sc.
Deputy Director
Cardiovascular Research Unit
University of Cape Town Medical School
OBSERVATORY 7925, Cape Town, South Africa
Voice:+27-21-406 6418  Fax:+27-21-448 5935  Cell:+27-82-770 3612

--------------------------------
End of nih-image-d Digest V98 Issue #25
***************************************

From nih-image-request@io.ece.drexel.edu Thu Jul 30 06:08 EDT 1998
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Date: Thu, 30 Jul 1998 10:56:14 +0100
From: "Swidbert R OTT" <sro21@hermes.cam.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: RE: Image comparison
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--On Wed, Jul 29, 1998 2:21 pm -0400 "Mehmet Dondurur, Ph. D."
<mehmet.dondurur.ph.d@jvc.org> wrote: 

> I am sorry I could not understand exactly what you mean. Do you mean
> use:
> Image math
> then
> substarct image
> or what is the exact steps please?

You go to menu "Process" item "Image math..." to bring up a dialog box. 
You specify your two windows containing the two images you want to compare
by using the two popup-menues.  You select "-" as the operator fom the
pop-up menu of operators (next to the pop-up menue for the second image). 
You leave the offset (the number field next to the "+" in the dialog) as
it is by default (128).  You can crank up (scale, magnify) the differences
by setting the number in the field next to the "X" to something bigger
than 1.

The whole operation is:

C=((A-B)*k)+128     where A and B are your source images, C is the
                    one containing the differences, and k is the
                    multiplicative (scaling) factor.

I hope this helps.

Swidi

From nih-image-request@io.ece.drexel.edu Thu Jul 30 06:24 EDT 1998
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	<69B43248FE73D11197BB00A0C99AB06788CC@jvcserver.vanguardweb.org>
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	<69B43248FE73D11197BB00A0C99AB06788CC@jvcserver.vanguardweb.org>
Mime-Version: 1.0
Date: Thu, 30 Jul 1998 11:15:28 +0100
To: nih-image@io.ece.drexel.edu
From: Clive Washington <Clive.Washington@nottingham.ac.uk>
Subject: Re: Image comparison
Resent-Message-ID: <"CDiyt3.0.t52.RT4mr"@io>
Resent-From: nih-image@io.ece.drexel.edu
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>Hello,
>I have two B&W identical images: one is original and second
>one is interpolated. Both are same size and have same number
>of pixels as well. To my eyes, both looked same but  I want
>to compare them pixel by pixel to how much they are
>different. Main goal is to see how much interpolated image
>is identical or close to the original one. Can I do that with
>NIH or other application?.

Just use the image maths function to subtract one image from the other.
>
>Thanks
>Dr. Mehmet Dondurur
>Research Scientist
>Jobst Vascular Center-U of Michigan
>Mehmet.Dondurur.ph.d@jvc.org
>(419) 471-2087


////////////////////////COLLOID ENGINEERING GROUP///////////////////////////

Dr. Clive Washington,                                      Tel. 0115 9515034
Senior Lecturer in Pharmaceutics,			   Fax  0115 9515102
Department of Pharmaceutical Sciences,
University of Nottingham,
University Park,                       Email pazcw@unix.ccc.nottingham.ac.uk
Nottingham NG7 2RD.         http://reliant.pharm.nottingham.ac.uk/clive.html

                  "It's mail, Jim, but not as we know it."

////////////////////////COLLOID ENGINEERING GROUP///////////////////////////


From nih-image-request@io.ece.drexel.edu Thu Jul 30 08:39 EDT 1998
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Message-ID: <69B43248FE73D11197BB00A0C99AB06788D3@jvcserver.vanguardweb.org>
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Image comparison
Date: Thu, 30 Jul 1998 08:17:58 -0400
MIME-Version: 1.0
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Yes sir,
It is more than enough and appreciated for great help.
Cheers
Mehmet

> ----------
> From: 	Swidbert R OTT[SMTP:sro21@hermes.cam.ac.uk]
> Reply To: 	nih-image@io.ece.drexel.edu
> Sent: 	Thursday, July 30, 1998 5:56 AM
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	RE: Image comparison
> 
> --On Wed, Jul 29, 1998 2:21 pm -0400 "Mehmet Dondurur, Ph. D."
> <mehmet.dondurur.ph.d@jvc.org> wrote: 
> 
> > I am sorry I could not understand exactly what you mean. Do you mean
> > use:
> > Image math
> > then
> > substarct image
> > or what is the exact steps please?
> 
> You go to menu "Process" item "Image math..." to bring up a dialog
> box. 
> You specify your two windows containing the two images you want to
> compare
> by using the two popup-menues.  You select "-" as the operator fom the
> pop-up menu of operators (next to the pop-up menue for the second
> image). 
> You leave the offset (the number field next to the "+" in the dialog)
> as
> it is by default (128).  You can crank up (scale, magnify) the
> differences
> by setting the number in the field next to the "X" to something bigger
> than 1.
> 
> The whole operation is:
> 
> C=((A-B)*k)+128     where A and B are your source images, C is the
>                     one containing the differences, and k is the
>                     multiplicative (scaling) factor.
> 
> I hope this helps.
> 
> Swidi
> 

From nih-image-request@io.ece.drexel.edu Thu Jul 30 09:59 EDT 1998
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	Thu, 30 Jul 1998 09:58:49 -0400 (EDT)
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Mime-Version: 1.0
Date: Thu, 30 Jul 1998 09:46:19 -0500
To: nih-image@io.ece.drexel.edu
From: Mark A Vivino <mvivino@helix.nih.gov>
Subject: NIH'er seeking new employment
Resent-Message-ID: <"y6yMY.0.Bi6.Wa7mr"@io>
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Sorry for the use of bandwidth, but thought I would give this a shot.

Biomedical Engineer, MSEE, seeking new employment opportunity. Trained and
with experience in broad areas of electrical engineering, computing,
biomedicine, imaging, data and signal acquisition. Ten years experience
collaborating in clinical and basic science research, development of
diagnostic tools and methodologies. Open to combining current skills with
other kinds of work like networking or other.

Much of my work over the years has been with the National Eye Institute,
National Heart Lung and Blood Institute, National Institute of Neurological
Disorders and Stroke and many other clinical and basic science labs on the
NIH campus.

I have extensive experience with the NIH Image package.

Geographical and other preferences: Since my wife has an offer in Miami, FL
this is now my first choice to relocate. However nothing is etched in
concrete, and as her position is temporary, I am open to other possible
locations. I am eligible to transfer as a federal employee as well.

Note: I am on a vacation trip from Aug 1 until Aug 23. I will probably
repost this again upon my return. But please feel free to drop me a line or
a contact.

How to contact: Mark Vivino
Email: mvivino@rocketmail.com
  Or mvivino@helix.nih.gov
Phone current w: 301-402-2633


Thanks in advance.


From nih-image-request@io.ece.drexel.edu Thu Jul 30 13:51 EDT 1998
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Date: Thu, 30 Jul 1998 10:37:00 -0700
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Mark A Vivino wrote:
> 
> Sorry for the use of bandwidth, but thought I would give this a shot.
> 
> Biomedical Engineer, MSEE, seeking new employment opportunity. Trained and
> with experience in broad areas of electrical engineering, computing,
> biomedicine, imaging, data and signal acquisition. Ten years experience
> collaborating in clinical and basic science research, development of
> diagnostic tools and methodologies. Open to combining current skills with
> other kinds of work like networking or other.
> 
> Much of my work over the years has been with the National Eye Institute,
> National Heart Lung and Blood Institute, National Institute of Neurological
> Disorders and Stroke and many other clinical and basic science labs on the
> NIH campus.
> 
> I have extensive experience with the NIH Image package.
> 
> Geographical and other preferences: Since my wife has an offer in Miami, FL
> this is now my first choice to relocate. However nothing is etched in
> concrete, and as her position is temporary, I am open to other possible
> locations. I am eligible to transfer as a federal employee as well.
> 
> Note: I am on a vacation trip from Aug 1 until Aug 23. I will probably
> repost this again upon my return. But please feel free to drop me a line or
> a contact.
> 
> How to contact: Mark Vivino
> Email: mvivino@rocketmail.com
>   Or mvivino@helix.nih.gov
> Phone current w: 301-402-2633
> 
> Thanks in advance.
Mark: 
You have done a great job for the people over the years. Best wishes for
future endeavor.--Dev, N.B; San Diego

From nih-image-d-request@io.ece.drexel.edu Fri Jul 31 06:14 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #26
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 26

Today's Topics:
  RE: Image comparison                  [ "Swidbert R OTT" <sro21@hermes.cam. ]
  Re: Image comparison                  [ Clive Washington <Clive.Washington@ ]
  RE: Image comparison                  [ "Mehmet Dondurur, Ph. D." <mehmet.d ]
  NIH'er seeking new employment         [ Mark A Vivino <mvivino@helix.nih.go ]
  Re: NIH'er seeking new employment     [ "n.b.dev" <nbdev@genetronics.com> ]

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

Date: Thu, 30 Jul 1998 10:56:14 +0100
From: "Swidbert R OTT" <sro21@hermes.cam.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: RE: Image comparison
Message-ID: <488223.3110784974@neuron05.zoo.cam.ac.uk>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

--On Wed, Jul 29, 1998 2:21 pm -0400 "Mehmet Dondurur, Ph. D."
<mehmet.dondurur.ph.d@jvc.org> wrote: 

> I am sorry I could not understand exactly what you mean. Do you mean
> use:
> Image math
> then
> substarct image
> or what is the exact steps please?

You go to menu "Process" item "Image math..." to bring up a dialog box. 
You specify your two windows containing the two images you want to compare
by using the two popup-menues.  You select "-" as the operator fom the
pop-up menu of operators (next to the pop-up menue for the second image). 
You leave the offset (the number field next to the "+" in the dialog) as
it is by default (128).  You can crank up (scale, magnify) the differences
by setting the number in the field next to the "X" to something bigger
than 1.

The whole operation is:

C=((A-B)*k)+128     where A and B are your source images, C is the
                    one containing the differences, and k is the
                    multiplicative (scaling) factor.

I hope this helps.

Swidi

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

Date: Thu, 30 Jul 1998 11:15:28 +0100
From: Clive Washington <Clive.Washington@nottingham.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Image comparison
Message-Id: <l03110701b1e5f81d75d8@[128.243.184.1]>
Content-Type: text/plain; charset="us-ascii"

>Hello,
>I have two B&W identical images: one is original and second
>one is interpolated. Both are same size and have same number
>of pixels as well. To my eyes, both looked same but  I want
>to compare them pixel by pixel to how much they are
>different. Main goal is to see how much interpolated image
>is identical or close to the original one. Can I do that with
>NIH or other application?.

Just use the image maths function to subtract one image from the other.
>
>Thanks
>Dr. Mehmet Dondurur
>Research Scientist
>Jobst Vascular Center-U of Michigan
>Mehmet.Dondurur.ph.d@jvc.org
>(419) 471-2087


////////////////////////COLLOID ENGINEERING GROUP///////////////////////////

Dr. Clive Washington,                                      Tel. 0115 9515034
Senior Lecturer in Pharmaceutics,			   Fax  0115 9515102
Department of Pharmaceutical Sciences,
University of Nottingham,
University Park,                       Email pazcw@unix.ccc.nottingham.ac.uk
Nottingham NG7 2RD.         http://reliant.pharm.nottingham.ac.uk/clive.html

                  "It's mail, Jim, but not as we know it."

////////////////////////COLLOID ENGINEERING GROUP///////////////////////////

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

Date: Thu, 30 Jul 1998 08:17:58 -0400
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Image comparison
Message-ID: <69B43248FE73D11197BB00A0C99AB06788D3@jvcserver.vanguardweb.org>
Content-Type: text/plain

Yes sir,
It is more than enough and appreciated for great help.
Cheers
Mehmet

> ----------
> From: 	Swidbert R OTT[SMTP:sro21@hermes.cam.ac.uk]
> Reply To: 	nih-image@io.ece.drexel.edu
> Sent: 	Thursday, July 30, 1998 5:56 AM
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	RE: Image comparison
> 
> --On Wed, Jul 29, 1998 2:21 pm -0400 "Mehmet Dondurur, Ph. D."
> <mehmet.dondurur.ph.d@jvc.org> wrote: 
> 
> > I am sorry I could not understand exactly what you mean. Do you mean
> > use:
> > Image math
> > then
> > substarct image
> > or what is the exact steps please?
> 
> You go to menu "Process" item "Image math..." to bring up a dialog
> box. 
> You specify your two windows containing the two images you want to
> compare
> by using the two popup-menues.  You select "-" as the operator fom the
> pop-up menu of operators (next to the pop-up menue for the second
> image). 
> You leave the offset (the number field next to the "+" in the dialog)
> as
> it is by default (128).  You can crank up (scale, magnify) the
> differences
> by setting the number in the field next to the "X" to something bigger
> than 1.
> 
> The whole operation is:
> 
> C=((A-B)*k)+128     where A and B are your source images, C is the
>                     one containing the differences, and k is the
>                     multiplicative (scaling) factor.
> 
> I hope this helps.
> 
> Swidi
> 

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

Date: Thu, 30 Jul 1998 09:46:19 -0500
From: Mark A Vivino <mvivino@helix.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: NIH'er seeking new employment
Message-Id: <v04003a01b1e63645cc1e@[128.231.128.61]>
Content-Type: text/plain; charset="us-ascii"

Sorry for the use of bandwidth, but thought I would give this a shot.

Biomedical Engineer, MSEE, seeking new employment opportunity. Trained and
with experience in broad areas of electrical engineering, computing,
biomedicine, imaging, data and signal acquisition. Ten years experience
collaborating in clinical and basic science research, development of
diagnostic tools and methodologies. Open to combining current skills with
other kinds of work like networking or other.

Much of my work over the years has been with the National Eye Institute,
National Heart Lung and Blood Institute, National Institute of Neurological
Disorders and Stroke and many other clinical and basic science labs on the
NIH campus.

I have extensive experience with the NIH Image package.

Geographical and other preferences: Since my wife has an offer in Miami, FL
this is now my first choice to relocate. However nothing is etched in
concrete, and as her position is temporary, I am open to other possible
locations. I am eligible to transfer as a federal employee as well.

Note: I am on a vacation trip from Aug 1 until Aug 23. I will probably
repost this again upon my return. But please feel free to drop me a line or
a contact.

How to contact: Mark Vivino
Email: mvivino@rocketmail.com
  Or mvivino@helix.nih.gov
Phone current w: 301-402-2633


Thanks in advance.

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

Date: Thu, 30 Jul 1998 10:37:00 -0700
From: "n.b.dev" <nbdev@genetronics.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH'er seeking new employment
Message-ID: <35C0AF3C.13E8@genetronics.com>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Mark A Vivino wrote:
> 
> Sorry for the use of bandwidth, but thought I would give this a shot.
> 
> Biomedical Engineer, MSEE, seeking new employment opportunity. Trained and
> with experience in broad areas of electrical engineering, computing,
> biomedicine, imaging, data and signal acquisition. Ten years experience
> collaborating in clinical and basic science research, development of
> diagnostic tools and methodologies. Open to combining current skills with
> other kinds of work like networking or other.
> 
> Much of my work over the years has been with the National Eye Institute,
> National Heart Lung and Blood Institute, National Institute of Neurological
> Disorders and Stroke and many other clinical and basic science labs on the
> NIH campus.
> 
> I have extensive experience with the NIH Image package.
> 
> Geographical and other preferences: Since my wife has an offer in Miami, FL
> this is now my first choice to relocate. However nothing is etched in
> concrete, and as her position is temporary, I am open to other possible
> locations. I am eligible to transfer as a federal employee as well.
> 
> Note: I am on a vacation trip from Aug 1 until Aug 23. I will probably
> repost this again upon my return. But please feel free to drop me a line or
> a contact.
> 
> How to contact: Mark Vivino
> Email: mvivino@rocketmail.com
>   Or mvivino@helix.nih.gov
> Phone current w: 301-402-2633
> 
> Thanks in advance.
Mark: 
You have done a great job for the people over the years. Best wishes for
future endeavor.--Dev, N.B; San Diego

--------------------------------
End of nih-image-d Digest V98 Issue #26
***************************************

From nih-image-d-request@io.ece.drexel.edu Sun Aug  2 06:10 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #27
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 27

Today's Topics:
  UNSUBSCRIBE                           [ Ilya Reviakine <I.Reviakine@chem.ru ]

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

Date: Sat, 01 Aug 1998 00:58:08 +0200
From: Ilya Reviakine <I.Reviakine@chem.rug.nl>
To: nih-image-d@io.ece.drexel.edu
Subject: UNSUBSCRIBE
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-- 

	I.Reviakine@chem.rug.nl	                                    
	Ilya Reviakine, BSc (Biochemistry), Computer Science Minor  
	Dept. of Biophysical Chemistry                              
	University of Groningen
	Nijenborgh, 4                                    
	9747 AG Groningen, the Netherlands.                                 
	
	Phone:	31 (050)363-4220; 363-4213
	Fax:	31 (050)363-4800
                                                                    
	http://rugbe2.chem.rug.nl/~reviakin

--------------------------------
End of nih-image-d Digest V98 Issue #27
***************************************

From nih-image-request@io.ece.drexel.edu Mon Aug  3 09:52 EDT 1998
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Date: Mon, 03 Aug 1998 09:35:10 +0000
From: Marcia Goldfarb <anatekep@maine.rr.com>
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I have just upgraded my computer from a 7100 PowerMac to a G3. I believe
I am using Nih-image 1.61 for powermac. Every so often I have a problem
with printing results. That is after several times of printing, the
computer says it can no longer find the printer. I have to quit, shut
down, restart , select chooser and reselect the printer. Needless to say
this is annoying. Would this have anything to do with a G3- Nih-image
conflict? I am having no luck in tracking this problem down.  Thanks for
any help.

Marcia Goldfarb
Anatek-EP
17 Bishop St
Portland, ME o4103

email: anatekep@maine.rr.com

From nih-image-request@io.ece.drexel.edu Mon Aug  3 11:27 EDT 1998
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As far as I can tell, the printing problem is specific to the G3 and has nothing to do with NIH Image.  It usually manifests itself as a message saying it can't find the desktop print spooler.  I have an 8600/300 running the same version of the OS with the same extensions loaded and I never have this problem.  I suspect Apple will fix this with the next version of laserwriter 8.  

I still haven't found a good fix for acquiring images from the G3 built in video card.

From nih-image-request@io.ece.drexel.edu Mon Aug  3 11:43 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Stein Roervik <steinr@chembio.ntnu.no>
Subject: Re: PCI to NuBus adapters
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>Imagers,
>Does anyone know if a Scion LG-3 NuBus card will run at 30 fps in a PCI
>machine with a PCI to NuBus adapter, or will it run at NuBus speed?
>
It will run at or slightly below NuBus speed. If your PCI machine is
faster, that will counteract any overhead in the translation process, so
you will get a higher capture speed on a fast PCI with an adapter than on a
slow NuBus Mac. The only PCI to NuBus adapters I know of are from
SecondWave and quite expensive ($900) so you would spend the money better
on upgrading your LG-3 card.

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+


From nih-image-request@io.ece.drexel.edu Mon Aug  3 18:56 EDT 1998
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From: John Jamieson <j.jamieson@unsw.edu.au>
Subject: Re: G3
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I had a similar problem with a new G3 using the serial Localtalk printer
connection.  Here is what Apple Australia suggested:

"Try trashing the LocalTalk PCI extension, restart the G3 and you should 
find that the problem is resolved."

This fixed my problem immediately.

At 09:35 03/08/98 +0000, you wrote:
>I have just upgraded my computer from a 7100 PowerMac to a G3. I believe
>I am using Nih-image 1.61 for powermac. Every so often I have a problem
>with printing results. That is after several times of printing, the
>computer says it can no longer find the printer. I have to quit, shut
>down, restart , select chooser and reselect the printer. Needless to say
>this is annoying. Would this have anything to do with a G3- Nih-image
>conflict? I am having no luck in tracking this problem down.  Thanks for
>any help.
>
>Marcia Goldfarb
>Anatek-EP
>17 Bishop St
>Portland, ME o4103
>
>email: anatekep@maine.rr.com
>
>
>
John Jamieson
Prince of Wales Medical Research Institute
Randwick   NSW    AUSTRALIA
tel: 61-2-9382-2696
fax: 61-2-9382-2723
email: j.jamieson@unsw.edu.au

From nih-image-request@io.ece.drexel.edu Tue Aug  4 00:09 EDT 1998
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From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: mehmet.dondurur.ph.d@jvc.org, nih-image@io.ece.drexel.edu
Date:          Tue, 4 Aug 1998 14:00:46 GMT+1000
Subject:       Batch Processing of Images
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>From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
>To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>
>Subject: Image enhancment
>Date: Wed, 29 Jul 1998 09:11:49 -0400
>...........
>Is there any way to enhance (sharpening edges) images in
>folder in one shot rather than enhancing one image a time
>using one of the filters?.
>I have B&W CAT scan images-100's of them. Any  suggestion is
>appreciated.
>
>Date: Thu, 23 Jul 1998 08:31:54 -0400
>To: nih-image@io.ece.drexel.edu
>From: Laird Bloom <lbloom@MIT.EDU>
>Subject: montage macro
......
 My computer can't open more than about 10 TIFF images at a time,
>but I'd like to be able to make a montage without having to open each file
>up individually.  Is there a way to open files in a folder one at a time
>without having to give them sequential numbers?

The above posts caused me to rethink some macro techniques I had used to do 
batch processing of images in NIH-Image and Object-Image.
Using 'recent' extentions to macros, I have implemented a 'simple to use' macro 
suite which allows the user to make selections of files and directory contents. 
The selection process  builds a 'tobeProcessed filelist' which can be listed 
and processed without the need for structured filenames.

It will be emailed separately to Mehmet Dondurur as an attachment in 
anticipation of some feedback on its usefulness and the documentation.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

From nih-image-d-request@io.ece.drexel.edu Tue Aug  4 06:07 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #28
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 28

Today's Topics:
  G3                                    [ Marcia Goldfarb <anatekep@maine.rr. ]
  G3 printing                           [ "STEPHEN MOORMAN" <smoorman@hsc.unt ]
  Re: PCI to NuBus adapters             [ Stein Roervik <steinr@chembio.ntnu. ]
  Re: G3                                [ John Jamieson <j.jamieson@unsw.edu. ]
  Batch Processing of Images            [ GJOSS@rna.bio.mq.edu.au ]

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

Date: Mon, 03 Aug 1998 09:35:10 +0000
From: Marcia Goldfarb <anatekep@maine.rr.com>
To: Nih-image <nih-image@io.ece.drexel.edu>
Subject: G3
Message-ID: <35C5844D.57592B27@maine.rr.com>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
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I have just upgraded my computer from a 7100 PowerMac to a G3. I believe
I am using Nih-image 1.61 for powermac. Every so often I have a problem
with printing results. That is after several times of printing, the
computer says it can no longer find the printer. I have to quit, shut
down, restart , select chooser and reselect the printer. Needless to say
this is annoying. Would this have anything to do with a G3- Nih-image
conflict? I am having no luck in tracking this problem down.  Thanks for
any help.

Marcia Goldfarb
Anatek-EP
17 Bishop St
Portland, ME o4103

email: anatekep@maine.rr.com

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

Date: Mon, 03 Aug 1998 10:13:17 -0500
From: "STEPHEN MOORMAN" <smoorman@hsc.unt.edu>
To: nih-image@io.ece.drexel.edu
Subject: G3 printing
Message-Id: <s5c58e21.053@hsc.unt.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline
Content-Transfer-Encoding: 8bit

As far as I can tell, the printing problem is specific to the G3 and has nothing to do with NIH Image.  It usually manifests itself as a message saying it can't find the desktop print spooler.  I have an 8600/300 running the same version of the OS with the same extensions loaded and I never have this problem.  I suspect Apple will fix this with the next version of laserwriter 8.  

I still haven't found a good fix for acquiring images from the G3 built in video card.

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

Date: Mon, 3 Aug 1998 17:30:42 +0200
From: Stein Roervik <steinr@chembio.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Re: PCI to NuBus adapters
Message-Id: <v03102807b1eb88193665@[129.241.39.133]>
Content-Type: text/plain; charset="us-ascii"

>Imagers,
>Does anyone know if a Scion LG-3 NuBus card will run at 30 fps in a PCI
>machine with a PCI to NuBus adapter, or will it run at NuBus speed?
>
It will run at or slightly below NuBus speed. If your PCI machine is
faster, that will counteract any overhead in the translation process, so
you will get a higher capture speed on a fast PCI with an adapter than on a
slow NuBus Mac. The only PCI to NuBus adapters I know of are from
SecondWave and quite expensive ($900) so you would spend the money better
on upgrading your LG-3 card.

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+

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

Date: Tue, 04 Aug 1998 08:49:01 +1000
From: John Jamieson <j.jamieson@unsw.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Re: G3
Message-Id: <3.0.5.32.19980804084901.007a31a0@pop3.unsw.edu.au>
Content-Type: text/plain; charset="us-ascii"

I had a similar problem with a new G3 using the serial Localtalk printer
connection.  Here is what Apple Australia suggested:

"Try trashing the LocalTalk PCI extension, restart the G3 and you should 
find that the problem is resolved."

This fixed my problem immediately.

At 09:35 03/08/98 +0000, you wrote:
>I have just upgraded my computer from a 7100 PowerMac to a G3. I believe
>I am using Nih-image 1.61 for powermac. Every so often I have a problem
>with printing results. That is after several times of printing, the
>computer says it can no longer find the printer. I have to quit, shut
>down, restart , select chooser and reselect the printer. Needless to say
>this is annoying. Would this have anything to do with a G3- Nih-image
>conflict? I am having no luck in tracking this problem down.  Thanks for
>any help.
>
>Marcia Goldfarb
>Anatek-EP
>17 Bishop St
>Portland, ME o4103
>
>email: anatekep@maine.rr.com
>
>
>
John Jamieson
Prince of Wales Medical Research Institute
Randwick   NSW    AUSTRALIA
tel: 61-2-9382-2696
fax: 61-2-9382-2723
email: j.jamieson@unsw.edu.au

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

Date:          Tue, 4 Aug 1998 14:00:46 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: mehmet.dondurur.ph.d@jvc.org, nih-image@io.ece.drexel.edu
Subject:       Batch Processing of Images
Message-ID: <4C0E8FC1C9F@rna.bio.mq.edu.au>

>From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
>To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>
>Subject: Image enhancment
>Date: Wed, 29 Jul 1998 09:11:49 -0400
>...........
>Is there any way to enhance (sharpening edges) images in
>folder in one shot rather than enhancing one image a time
>using one of the filters?.
>I have B&W CAT scan images-100's of them. Any  suggestion is
>appreciated.
>
>Date: Thu, 23 Jul 1998 08:31:54 -0400
>To: nih-image@io.ece.drexel.edu
>From: Laird Bloom <lbloom@MIT.EDU>
>Subject: montage macro
......
 My computer can't open more than about 10 TIFF images at a time,
>but I'd like to be able to make a montage without having to open each file
>up individually.  Is there a way to open files in a folder one at a time
>without having to give them sequential numbers?

The above posts caused me to rethink some macro techniques I had used to do 
batch processing of images in NIH-Image and Object-Image.
Using 'recent' extentions to macros, I have implemented a 'simple to use' macro 
suite which allows the user to make selections of files and directory contents. 
The selection process  builds a 'tobeProcessed filelist' which can be listed 
and processed without the need for structured filenames.

It will be emailed separately to Mehmet Dondurur as an attachment in 
anticipation of some feedback on its usefulness and the documentation.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

--------------------------------
End of nih-image-d Digest V98 Issue #28
***************************************

From nih-image-request@io.ece.drexel.edu Tue Aug  4 11:11 EDT 1998
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Date: Tue, 04 Aug 1998 15:53:58 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
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References: <4C0E8FC1C9F@rna.bio.mq.edu.au>
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In addition to Object Image and NIH Image I also use Image-Pro Plus for the Mac.
The colour segmentation system used in the later was one of the few things
that I
feel gives this $3000 package an edge over Image. So I've implemented the point
and click colour segmentation bit in Object Image. Click on one of the objects you
want to segment in the index colour image and Object Image will segment the RGB
image on the basis of independent density slices in each channel. Unlike Image-Pro
Plus, you can easily discard any of the channels you don't want. You can also
record your settings for use in batch processing. I still have to add a few
features like the ability to segment several types of object in the same image,
but if any one is interested I've sent it to Wayne for uploading to the NIH site.

I welcome any feed back :-)


Jeremy Brown

From nih-image-request@io.ece.drexel.edu Tue Aug  4 11:11 EDT 1998
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Greg,

This sounds good. It would be nice to batch process images by folder rather than
by sequentially numbered file names. Could I get a copy?

Jeremy Brown




GJOSS@rna.bio.mq.edu.au wrote:

> >From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
> >To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>
> >Subject: Image enhancment
> >Date: Wed, 29 Jul 1998 09:11:49 -0400
> >...........
> >Is there any way to enhance (sharpening edges) images in
> >folder in one shot rather than enhancing one image a time
> >using one of the filters?.
> >I have B&W CAT scan images-100's of them. Any  suggestion is
> >appreciated.
> >
> >Date: Thu, 23 Jul 1998 08:31:54 -0400
> >To: nih-image@io.ece.drexel.edu
> >From: Laird Bloom <lbloom@MIT.EDU>
> >Subject: montage macro
> ......
>  My computer can't open more than about 10 TIFF images at a time,
> >but I'd like to be able to make a montage without having to open each file
> >up individually.  Is there a way to open files in a folder one at a time
> >without having to give them sequential numbers?
>
> The above posts caused me to rethink some macro techniques I had used to do
> batch processing of images in NIH-Image and Object-Image.
> Using 'recent' extentions to macros, I have implemented a 'simple to use' macro
> suite which allows the user to make selections of files and directory contents.
> The selection process  builds a 'tobeProcessed filelist' which can be listed
> and processed without the need for structured filenames.
>
> It will be emailed separately to Mehmet Dondurur as an attachment in
> anticipation of some feedback on its usefulness and the documentation.
> Greg Joss,
> School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
> Macquarie University,          Email gjoss@rna.bio.mq.edu.au
> North Ryde, (Sydney,) NSW 2109, Australia





From nih-image-request@io.ece.drexel.edu Tue Aug  4 11:49 EDT 1998
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From: ablocker@pasteur.fr (Ariel Blocker)
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Dear List Managers and Users,
Maybe I am stupid folks but when we swapped to the new list I, who was
previously receiving only digests and not individual messages, started
getting only individual messages (which is pretty troublesome when you go
away on holidays for 2 weeks and return to find your mailbox clogged up
with alomst exclusively list news). I subsbribed to
nih-image@biomed.drexel.edu and use Eudora 1.5.3, is this like normal and
if so what do I do to get back on a 1 digesty per day track? I would
appreciate your advice before I drown in messages...
Sincerely,
Ariel Blocker.


From nih-image-request@io.ece.drexel.edu Tue Aug  4 13:00 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: "Malinda E.C. Fitzgerald" <malinda@cbu.edu>
Subject: Re: Eudora users
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I have always received individual messages and never received lists!  I
just thought that was the way it was!  Malinda (I use Eudora 3.0)

Malinda E.C. Fitzgerald, Ph.D.
Associate Professor
Department of Biology
650 E Parkway So.
Christian Brothers University
Memphis, TN   38104
901-321-3262 office
901-321-4433 fax


From nih-image-request@io.ece.drexel.edu Tue Aug  4 13:23 EDT 1998
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Message-ID: <69B43248FE73D11197BB00A0C99AB06788E0@jvcserver.vanguardweb.org>
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Eudora users
Date: Tue, 4 Aug 1998 12:59:51 -0400 
MIME-Version: 1.0
X-Mailer: Internet Mail Service (5.5.1960.3)
Resent-Message-ID: <"KXoxy1.0.cz.9-pnr"@io>
Resent-From: nih-image@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
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Status: RO

Hi,
I am in same situation like your. 
What is the solution to get the list?
Could you please let me know if you find out how to get the list?

Thanks
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-U of M
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087


> ----------
> From: 	Malinda E.C. Fitzgerald[SMTP:malinda@cbu.edu]
> Reply To: 	nih-image@io.ece.drexel.edu
> Sent: 	Tuesday, August 04, 1998 12:19 PM
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	Re: Eudora users
> 
> I have always received individual messages and never received lists!
> I
> just thought that was the way it was!  Malinda (I use Eudora 3.0)
> 
> Malinda E.C. Fitzgerald, Ph.D.
> Associate Professor
> Department of Biology
> 650 E Parkway So.
> Christian Brothers University
> Memphis, TN   38104
> 901-321-3262 office
> 901-321-4433 fax
> 
> 

From nih-image-request@io.ece.drexel.edu Tue Aug  4 14:17 EDT 1998
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	Tue, 4 Aug 1998 14:17:27 -0400 (EDT)
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Message-Id: <v03007802b1ecfbc6242c@[144.118.33.245]>
Mime-Version: 1.0
Date: Tue, 4 Aug 1998 13:01:39 -0500
To: nih-image@io.ece.drexel.edu
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: ADMINISTRATA
Resent-Message-ID: <"BWw-1.0.X02.6oqnr"@io>
Resent-From: nih-image@io.ece.drexel.edu
Reply-To: nih-image@io.ece.drexel.edu
X-Mailing-List: <nih-image@biomed.drexel.edu> archive/latest/170
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Status: RO

<fontfamily><param>Times</param>Hi everyone.


The following is a reminder to everyone regarding administrative issues
on the list. Those who desire the digest form, should unsubscribe from
the regular list and resubscribe to the digest list.


e-mail addresses of importance

--------

nih-image@biomed.drexel.edu   - Sends mail to the list

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Subscribe

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Help

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

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Help on Digest

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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 with the
command 

in the Subject line or in the body of the message.


get filename ...

ls directory ...

egrep case_insensitive_regular_expression filename ...

maxfiles nnn

version

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Aliases for 'get': send, sendme, getme, gimme, retrieve, mail

Aliases for 'ls': dir, directory, list, show

Aliases for 'egrep': search, grep, fgrep, find

Aliases for 'quit': exit


If you append a non-standard signature, you should use the quit
command

to prevent the archive server from interpreting the signature.


Examples:

     ls latest

     get latest/12

     egrep some.word latest/*

</fontfamily>


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

                                  Jonathan Nissanov, Ph.D.

                                      Associate Director  

            Computer Vision Center for Vertebrate Brain Mapping,

                a NIH Biomedical Research Technology Resource

                                http://cbis.ece.drexel.edu/ICVC/

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

Imaging and Computer Vision Center              Tel: 215-895-1381

Drexel University                                                  
Fax: 215-895-4987

Phildelphia, PA 19104                                        
yoni@coe.drexel.edu

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

      

     

From nih-image-request@io.ece.drexel.edu Tue Aug  4 15:13 EDT 1998
Received: (from lists@localhost)
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	Tue, 4 Aug 1998 15:11:45 -0400 (EDT)
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Mime-Version: 1.0
Date: Tue, 4 Aug 1998 13:35:27 -0500
To: nih-image@io.ece.drexel.edu
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: Digest Issue
Resent-Message-ID: <"wy5P1.0.4g2.nHrnr"@io>
Resent-From: nih-image@io.ece.drexel.edu
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Hi everyone.

A Digestion of the Digest Issue. Digests are handled differently by
depending on settings and email applications.Note that it is likely that
you are able to control their appearance on your end by adjusting the
preferences for  MIME digests.  Here is how they appear according to
various users. Thank you everyone for your messages on the subject.

Email software

Elm v 2.4. Multi-part MIME. You can skip messages at the

--Press any key to go on.--

prompt, press the control-c (^C) key combination, and the remainder of the
message(s) will be skipped.

Unix-Pine. Two modes. Single message with header at top or with each
message a seperate attachment with one message consisting of table of
content.

Eudora Light v 3.1.3. Single message.

Eudora Pro v 3.1.1. New mailbox with seperate messages (this can be
filtered and made into a submailbox). Or, if you prefer a single message,
under Special setting deselect "Receive MIME digests as attachments".

Pegasus. New mailbox with seperate messages.

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

     


From nih-image-request@io.ece.drexel.edu Tue Aug  4 15:22 EDT 1998
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Resent-Date: Tue, 4 Aug 1998 15:21:24 -0400 (EDT)
From: Alex_Courtade@huntsman.com
Mime-Version: 1.0
Date: Tue, 4 Aug 1998 13:51:27 -0500
Message-ID: <0000FFFF.CE21466@huntsman.com>
Subject: Scion (beta 3) problems w/ major, minor axes
To: nih-image@io.ece.drexel.edu
Content-Transfer-Encoding: 7bit
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This message is specifically directed at any of the PC Scion Image users out
there, so most  Mac NIH Image users can probably ignore this.

I have been using (trying to, at least) Scion Beta 3 for particle analysis. The
particles I am analyzing are somewhat oval shaped, fairly well defined, and
usually a few hundred pixels in area (they don't appear small on the screen.) I
have been trying to get Scion to give me the lengths of the major/ minor axes of
the best fitting oval for the particle, but every time I attempt this I get
error codes like "-1.#IO" instead of a measurement. Whether or not I have
calibrated my scale to the proper units doesn't seem to have an effect.

Has anyone else had this problem? Is there some way to get the major/ minor axes
to work? I even drew perfect elipses on a blank image as a test, and it didn't
even give me the measurements for that.

__________________________________

Alex Courtade
Huntsman Corporation
7114 N. Lamar Blvd
Austin, TX 78752

Phone: (512) 483-0190
Email: alex_courtade@huntsman.com

__________________________________

From nih-image-d-request@io.ece.drexel.edu Wed Aug  5 06:12 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA20069;
	Wed, 5 Aug 1998 06:12:06 -0400 (EDT)
Date: Wed, 5 Aug 1998 06:12:06 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199808051012.GAA20069@io.ECE.Drexel.EDU>
Subject: nih-image-d Digest V98 #29
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Reply-To: nih-image@io.ece.drexel.edu
Content-Type: multipart/digest; boundary="----------------------------"
Content-Length: 14367
Status: O

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 29

Today's Topics:
  Re: Batch Processing of Images        [ Jeremy Brown <brownj@netmatters.co. ]
  Point and click colour segmentation   [ Jeremy Brown <brownj@netmatters.co. ]
  Re: Eudora users                      [ ablocker@pasteur.fr (Ariel Blocker) ]
  Re: Eudora users                      [ "Malinda E.C. Fitzgerald" <malinda@ ]
  RE: Eudora users                      [ "Mehmet Dondurur, Ph. D." <mehmet.d ]
  ADMINISTRATA                          [ Jonathan Nissanov <yoni@cbis.ece.dr ]
  Digest Issue                          [ Jonathan Nissanov <yoni@cbis.ece.dr ]
  Scion (beta 3) problems w/ major, mi  [ Alex_Courtade@huntsman.com ]

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

Date: Tue, 04 Aug 1998 15:23:28 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Batch Processing of Images
Message-ID: <35C72780.B9F9B06E@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Greg,

This sounds good. It would be nice to batch process images by folder rather than
by sequentially numbered file names. Could I get a copy?

Jeremy Brown




GJOSS@rna.bio.mq.edu.au wrote:

> >From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
> >To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>
> >Subject: Image enhancment
> >Date: Wed, 29 Jul 1998 09:11:49 -0400
> >...........
> >Is there any way to enhance (sharpening edges) images in
> >folder in one shot rather than enhancing one image a time
> >using one of the filters?.
> >I have B&W CAT scan images-100's of them. Any  suggestion is
> >appreciated.
> >
> >Date: Thu, 23 Jul 1998 08:31:54 -0400
> >To: nih-image@io.ece.drexel.edu
> >From: Laird Bloom <lbloom@MIT.EDU>
> >Subject: montage macro
> ......
>  My computer can't open more than about 10 TIFF images at a time,
> >but I'd like to be able to make a montage without having to open each file
> >up individually.  Is there a way to open files in a folder one at a time
> >without having to give them sequential numbers?
>
> The above posts caused me to rethink some macro techniques I had used to do
> batch processing of images in NIH-Image and Object-Image.
> Using 'recent' extentions to macros, I have implemented a 'simple to use' macro
> suite which allows the user to make selections of files and directory contents.
> The selection process  builds a 'tobeProcessed filelist' which can be listed
> and processed without the need for structured filenames.
>
> It will be emailed separately to Mehmet Dondurur as an attachment in
> anticipation of some feedback on its usefulness and the documentation.
> Greg Joss,
> School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
> Macquarie University,          Email gjoss@rna.bio.mq.edu.au
> North Ryde, (Sydney,) NSW 2109, Australia

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

Date: Tue, 04 Aug 1998 15:53:58 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Point and click colour segmentation
Message-ID: <35C72EA5.5980097F@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

In addition to Object Image and NIH Image I also use Image-Pro Plus for the Mac.
The colour segmentation system used in the later was one of the few things
that I
feel gives this $3000 package an edge over Image. So I've implemented the point
and click colour segmentation bit in Object Image. Click on one of the objects you
want to segment in the index colour image and Object Image will segment the RGB
image on the basis of independent density slices in each channel. Unlike Image-Pro
Plus, you can easily discard any of the channels you don't want. You can also
record your settings for use in batch processing. I still have to add a few
features like the ability to segment several types of object in the same image,
but if any one is interested I've sent it to Wayne for uploading to the NIH site.

I welcome any feed back :-)


Jeremy Brown

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

Date: Tue, 4 Aug 1998 17:27:44 +0200 (MET DST)
From: ablocker@pasteur.fr (Ariel Blocker)
To: nih-image@io.ece.drexel.edu
Subject: Re: Eudora users
Message-Id: <v01530504b1ecf51f23dd@[157.99.96.127]>
Content-Type: text/plain; charset="us-ascii"

Dear List Managers and Users,
Maybe I am stupid folks but when we swapped to the new list I, who was
previously receiving only digests and not individual messages, started
getting only individual messages (which is pretty troublesome when you go
away on holidays for 2 weeks and return to find your mailbox clogged up
with alomst exclusively list news). I subsbribed to
nih-image@biomed.drexel.edu and use Eudora 1.5.3, is this like normal and
if so what do I do to get back on a 1 digesty per day track? I would
appreciate your advice before I drown in messages...
Sincerely,
Ariel Blocker.

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

Date: Tue, 4 Aug 1998 11:19:19 -0500 (CDT)
From: "Malinda E.C. Fitzgerald" <malinda@cbu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Eudora users
Message-Id: <v03007800b1eca070c504@[205.129.119.164]>
Content-Type: text/plain; charset="us-ascii"

I have always received individual messages and never received lists!  I
just thought that was the way it was!  Malinda (I use Eudora 3.0)

Malinda E.C. Fitzgerald, Ph.D.
Associate Professor
Department of Biology
650 E Parkway So.
Christian Brothers University
Memphis, TN   38104
901-321-3262 office
901-321-4433 fax

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

Date: Tue, 4 Aug 1998 12:59:51 -0400 
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Eudora users
Message-ID: <69B43248FE73D11197BB00A0C99AB06788E0@jvcserver.vanguardweb.org>
Content-Type: text/plain

Hi,
I am in same situation like your. 
What is the solution to get the list?
Could you please let me know if you find out how to get the list?

Thanks
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-U of M
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087


> ----------
> From: 	Malinda E.C. Fitzgerald[SMTP:malinda@cbu.edu]
> Reply To: 	nih-image@io.ece.drexel.edu
> Sent: 	Tuesday, August 04, 1998 12:19 PM
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	Re: Eudora users
> 
> I have always received individual messages and never received lists!
> I
> just thought that was the way it was!  Malinda (I use Eudora 3.0)
> 
> Malinda E.C. Fitzgerald, Ph.D.
> Associate Professor
> Department of Biology
> 650 E Parkway So.
> Christian Brothers University
> Memphis, TN   38104
> 901-321-3262 office
> 901-321-4433 fax
> 
> 

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

Date: Tue, 4 Aug 1998 13:01:39 -0500
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: ADMINISTRATA
Message-Id: <v03007802b1ecfbc6242c@[144.118.33.245]>
Content-Type: text/enriched; charset="us-ascii"

<fontfamily><param>Times</param>Hi everyone.


The following is a reminder to everyone regarding administrative issues
on the list. Those who desire the digest form, should unsubscribe from
the regular list and resubscribe to the digest list.


e-mail addresses of importance

--------

nih-image@biomed.drexel.edu   - Sends mail to the list

nih-image-request@biomed.drexel.edu   - Administation for List

nih-image-d-request@biomed.drexel.edu  - Aministration for Digest


Subscribe

---------

To subscribe to the list, send E-mail to
nih-image-request@biomed.drexel.edu.

The Subject of the message should contain "Subscribe".


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

		Subject: subscribe



Subscribe to Digest

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

To subscribe to a digested version of the list, send E-mail to 

nih-image-d-request@biomed.drexel.edu.


The Subject of the message should contain "Subscribe".


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		Subject: subscribe



Unsubscribe

-----------

To unsubscribe to the list, send E-mail to
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Unsubscribe to Digest

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

To unsubscribe to digested version of the list, send E-mail to 

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Help

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

To obtain a listing of help items, send E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "help".


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

		Subject: help




Help on Digest

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

To obtain a listing of help items on digest version of the list, send
E-mail to 

nih-image-d-request@biomed.drexel.edu.

the Subject of the message should contain "help".


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

		Subject: help




Archive

-------

Every submission sent to this list is archived.	 Following are the
commands

used to access the archive.  Send Email to nih-image-request with the
command 

in the Subject line or in the body of the message.


get filename ...

ls directory ...

egrep case_insensitive_regular_expression filename ...

maxfiles nnn

version

quit


Aliases for 'get': send, sendme, getme, gimme, retrieve, mail

Aliases for 'ls': dir, directory, list, show

Aliases for 'egrep': search, grep, fgrep, find

Aliases for 'quit': exit


If you append a non-standard signature, you should use the quit
command

to prevent the archive server from interpreting the signature.


Examples:

     ls latest

     get latest/12

     egrep some.word latest/*

</fontfamily>


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

                                  Jonathan Nissanov, Ph.D.

                                      Associate Director  

            Computer Vision Center for Vertebrate Brain Mapping,

                a NIH Biomedical Research Technology Resource

                                http://cbis.ece.drexel.edu/ICVC/

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

Imaging and Computer Vision Center              Tel: 215-895-1381

Drexel University                                                  
Fax: 215-895-4987

Phildelphia, PA 19104                                        
yoni@coe.drexel.edu

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

      

     

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

Date: Tue, 4 Aug 1998 13:35:27 -0500
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Digest Issue
Message-Id: <v03007803b1ecff5dfc31@[144.118.33.245]>
Content-Type: text/plain; charset="us-ascii"

Hi everyone.

A Digestion of the Digest Issue. Digests are handled differently by
depending on settings and email applications.Note that it is likely that
you are able to control their appearance on your end by adjusting the
preferences for  MIME digests.  Here is how they appear according to
various users. Thank you everyone for your messages on the subject.

Email software

Elm v 2.4. Multi-part MIME. You can skip messages at the

--Press any key to go on.--

prompt, press the control-c (^C) key combination, and the remainder of the
message(s) will be skipped.

Unix-Pine. Two modes. Single message with header at top or with each
message a seperate attachment with one message consisting of table of
content.

Eudora Light v 3.1.3. Single message.

Eudora Pro v 3.1.1. New mailbox with seperate messages (this can be
filtered and made into a submailbox). Or, if you prefer a single message,
under Special setting deselect "Receive MIME digests as attachments".

Pegasus. New mailbox with seperate messages.

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

     

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

Date: Tue, 4 Aug 1998 13:51:27 -0500
From: Alex_Courtade@huntsman.com
To: nih-image@io.ece.drexel.edu
Subject: Scion (beta 3) problems w/ major, minor axes
Message-ID: <0000FFFF.CE21466@huntsman.com>
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Description: cc:Mail note part

This message is specifically directed at any of the PC Scion Image users out
there, so most  Mac NIH Image users can probably ignore this.

I have been using (trying to, at least) Scion Beta 3 for particle analysis. The
particles I am analyzing are somewhat oval shaped, fairly well defined, and
usually a few hundred pixels in area (they don't appear small on the screen.) I
have been trying to get Scion to give me the lengths of the major/ minor axes of
the best fitting oval for the particle, but every time I attempt this I get
error codes like "-1.#IO" instead of a measurement. Whether or not I have
calibrated my scale to the proper units doesn't seem to have an effect.

Has anyone else had this problem? Is there some way to get the major/ minor axes
to work? I even drew perfect elipses on a blank image as a test, and it didn't
even give me the measurements for that.

__________________________________

Alex Courtade
Huntsman Corporation
7114 N. Lamar Blvd
Austin, TX 78752

Phone: (512) 483-0190
Email: alex_courtade@huntsman.com

__________________________________

--------------------------------
End of nih-image-d Digest V98 Issue #29
***************************************

From nih-image-request@io.ece.drexel.edu Wed Aug  5 11:41 EDT 1998
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Date: Wed, 05 Aug 1998 11:23:03 -0400
From: Julie Mann <juliem@netreach.net>
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Greg,

I'd love to receive a copy, too, if that's possible!

julie mann


Subject:
        Re: Batch Processing of Images
   Date:
        Tue, 04 Aug 1998 15:23:28 +0000
   From:
        Jeremy Brown <brownj@netmatters.co.uk>
     To:
        nih-image@io.ece.drexel.edu

Greg,

This sounds good. It would be nice to batch process images by folder
rather than
by sequentially numbered file names. Could I get a copy?

Jeremy Brown




GJOSS@rna.bio.mq.edu.au wrote:

> >From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
> >To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>
> >Subject: Image enhancment
> >Date: Wed, 29 Jul 1998 09:11:49 -0400
> >...........
> >Is there any way to enhance (sharpening edges) images in
> >folder in one shot rather than enhancing one image a time
> >using one of the filters?.
> >I have B&W CAT scan images-100's of them. Any  suggestion is
> >appreciated.
> >
> >Date: Thu, 23 Jul 1998 08:31:54 -0400
> >To: nih-image@io.ece.drexel.edu
> >From: Laird Bloom <lbloom@MIT.EDU>
> >Subject: montage macro
> ......
>  My computer can't open more than about 10 TIFF images at a time,
> >but I'd like to be able to make a montage without having to open each
file
> >up individually.  Is there a way to open files in a folder one at a
time
> >without having to give them sequential numbers?
>
> The above posts caused me to rethink some macro techniques I had used
to do
> batch processing of images in NIH-Image and Object-Image.
> Using 'recent' extentions to macros, I have implemented a 'simple to
use' macro
> suite which allows the user to make selections of files and directory
contents.
> The selection process  builds a 'tobeProcessed filelist' which can be
listed
> and processed without the need for structured filenames.
>
> It will be emailed separately to Mehmet Dondurur as an attachment in
> anticipation of some feedback on its usefulness and the documentation.

> 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 Aug  5 11:59 EDT 1998
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Date: Thu, 06 Aug 1998 01:49:58 +1000
From: "Kwang Y. Han" <ykhan1@student.monash.edu.au>
Subject: Measuring spot distances in electron diffraction patterns (EDP)
To: nih-image@io.ece.drexel.edu
Message-id: <000001bdc088$b2c54580$640ac282@ykhan1>
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I am hoping someone could point out to me a more accurate way of measuring
spot distances in EDP for single-crystal materials.

This is how i did:
1) manually threshold the inverted TIFF image to obtain all the desired
spots
2) perform 'Analyze Particles...'
3) click 'Show Results'
4) import the results to Excel and calculate the distances

The distance between 2 specific spots appears to depend very much on my
threshold value.

Should I be locating the centroid or geometrical centre of each spot?
I am not sure if top-hat filter or Hough transform can help to reduce
variability in measurements? If so, how should it be done?

Thanks ahead for any suggestions..

From nih-image-request@io.ece.drexel.edu Wed Aug  5 16:54 EDT 1998
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	Wed, 5 Aug 1998 16:53:58 -0400 (EDT)
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From: "Toby Chai, M.D., 8-5544, S8D18" <TCHAI@surgery1.umaryland.edu>
Organization: UMAB, Surgery
To: nih-image@io.ece.drexel.edu
Date: Wed, 5 Aug 1998 16:35:24 -0500
MIME-Version: 1.0
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Subject: Video Capture with Futura II LX Card
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I am trying to get NIH Image to work on a Mac PowerPC 8100 with a 
Futura II LX Video Capture card and a video camera hooked up to a 
fluorescence microscope.  The machine currently is running Oncor 
program which is working (it's capturing video feed fine).  
However, when I run NIH Image (1.61), I get the error message that I 
must use a frame grabber, etc.  How do I "configure" the Mac so that 
NIH Image recognizes the already present  video card/video signal?  I 
looked briefly through Oncor's manuals, but it didn't really help me. 
 I did "turn off" the Oncor init file and rebooting the computer, but 
still could not get NIH Imageto capture the video feed.  So 
basically, I want to use NIH Image software instead of Oncor.

Thanks in advance.

T. Chai, M.D.
Division of Urology
University of Maryland

From nih-image-request@io.ece.drexel.edu Wed Aug  5 16:55 EDT 1998
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Message-ID: <001d01bdc0b0$d248b7c0$0f0a13c0@oemcomputer>
From: "Joan Main" <Joan.Main@gte.net>
To: <GJOSS@rna.bio.mq.edu.au>, <mehmet.dondurur.ph.d@jvc.org>,
        <nih-image@io.ece.drexel.edu>
Subject: Re:       Batch Processing of Images
Date: Tue, 4 Aug 1998 22:03:14 -0700
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HI,
I have been using a program called hijaak pro which catalogs and labels each
image I process.  I am processing 100-200 ultrasound iimages for time
intensity information.  I set up a file for each study.  The hijaak pro
program catalogs, labels allows thumbnail viewing and printing for later
analysis.  This may help you.  I am stacking 30 frames for analysis at a
time .  IMSI manufactures this program. Hope this is helpful
jmain@acuson.com or joan.main@gte.net good luck

-----Original Message-----
From: GJOSS@rna.bio.mq.edu.au <GJOSS@rna.bio.mq.edu.au>
To: mehmet.dondurur.ph.d@jvc.org <mehmet.dondurur.ph.d@jvc.org>;
nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
Date: Tuesday, August 04, 1998 7:00 AM
Subject: Batch Processing of Images


>>From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
>>To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>
>>Subject: Image enhancment
>>Date: Wed, 29 Jul 1998 09:11:49 -0400
>>...........
>>Is there any way to enhance (sharpening edges) images in
>>folder in one shot rather than enhancing one image a time
>>using one of the filters?.
>>I have B&W CAT scan images-100's of them. Any  suggestion is
>>appreciated.
>>
>>Date: Thu, 23 Jul 1998 08:31:54 -0400
>>To: nih-image@io.ece.drexel.edu
>>From: Laird Bloom <lbloom@MIT.EDU>
>>Subject: montage macro
>......
> My computer can't open more than about 10 TIFF images at a time,
>>but I'd like to be able to make a montage without having to open each file
>>up individually.  Is there a way to open files in a folder one at a time
>>without having to give them sequential numbers?
>
>The above posts caused me to rethink some macro techniques I had used to do
>batch processing of images in NIH-Image and Object-Image.
>Using 'recent' extentions to macros, I have implemented a 'simple to use'
macro
>suite which allows the user to make selections of files and directory
contents.
>The selection process  builds a 'tobeProcessed filelist' which can be
listed
>and processed without the need for structured filenames.
>
>It will be emailed separately to Mehmet Dondurur as an attachment in
>anticipation of some feedback on its usefulness and the documentation.
>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 Aug  6 05:49 EDT 1998
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Date: Thu, 6 Aug 1998 11:29:28 +0100
To: nih-image@io.ece.drexel.edu
From: "Jed.Mosenfelder" <Jed.Mosenfelder@uni-bayreuth.de>
Subject: dumb question about IP toolkit 2.5
Resent-Message-ID: <"lMa_g.0.B63.PYNor"@io>
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Has anyone tried threshholding greyscale images using the IPTK plugins in
Adobe photoshop. It's driving me crazy because, contrary to the manual, the
threshholded pixels do not appear highlighted in a color that you can
easily distinguish (they appear in some shade of grey rather than red), so
it's basically impossible to see what you're doing. I wonder if i'm missing
something obvious. Anyway i'm using Photoshop 3.0 on a 90 MhZ mac. I'd
really prefer to use NIH Image but the plugin filters in this toolkit that
i want to use run unbelievably slow in Image, because it doesn't read the
powerPC code (very disappointing!). Thanks much in advance for any help
from the experts out there....

cheers,

jed


-X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X
Jed Leigh Mosenfelder	e-mail: Jed.Mosenfelder@uni-bayreuth.de
Bayerisches Geoinstitut	Tel: +49-921-553712 (office)
Universitaet Bayreuth		     -553700 (dept. secretary)
D-95440 Bayreuth 			     -5160186 (home)
Germany			Fax:+49-921-553769
:-)----:-)----:-)----:-)----:-)----:-)----:-)----:-)----:-)----:-)----:-)


From nih-image-d-request@io.ece.drexel.edu Thu Aug  6 05:55 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #30
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 30

Today's Topics:
  Greg's batch processing macros        [ Julie Mann <juliem@netreach.net> ]
  Measuring spot distances in electron  [ "Kwang Y. Han" <ykhan1@student.mona ]
  Video Capture with Futura II LX Card  [ "Toby Chai, M.D., 8-5544, S8D18" <T ]
  Re: Batch Processing of Images        [ "Joan Main" <Joan.Main@gte.net> ]
  dumb question about IP toolkit 2.5    [ "Jed.Mosenfelder" <Jed.Mosenfelder@ ]

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

Date: Wed, 05 Aug 1998 11:23:03 -0400
From: Julie Mann <juliem@netreach.net>
To: nih-image@io.ece.drexel.edu
Subject: Greg's batch processing macros
Message-ID: <35C878D7.8A6A83F1@netreach.net>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Greg,

I'd love to receive a copy, too, if that's possible!

julie mann


Subject:
        Re: Batch Processing of Images
   Date:
        Tue, 04 Aug 1998 15:23:28 +0000
   From:
        Jeremy Brown <brownj@netmatters.co.uk>
     To:
        nih-image@io.ece.drexel.edu

Greg,

This sounds good. It would be nice to batch process images by folder
rather than
by sequentially numbered file names. Could I get a copy?

Jeremy Brown




GJOSS@rna.bio.mq.edu.au wrote:

> >From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
> >To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>
> >Subject: Image enhancment
> >Date: Wed, 29 Jul 1998 09:11:49 -0400
> >...........
> >Is there any way to enhance (sharpening edges) images in
> >folder in one shot rather than enhancing one image a time
> >using one of the filters?.
> >I have B&W CAT scan images-100's of them. Any  suggestion is
> >appreciated.
> >
> >Date: Thu, 23 Jul 1998 08:31:54 -0400
> >To: nih-image@io.ece.drexel.edu
> >From: Laird Bloom <lbloom@MIT.EDU>
> >Subject: montage macro
> ......
>  My computer can't open more than about 10 TIFF images at a time,
> >but I'd like to be able to make a montage without having to open each
file
> >up individually.  Is there a way to open files in a folder one at a
time
> >without having to give them sequential numbers?
>
> The above posts caused me to rethink some macro techniques I had used
to do
> batch processing of images in NIH-Image and Object-Image.
> Using 'recent' extentions to macros, I have implemented a 'simple to
use' macro
> suite which allows the user to make selections of files and directory
contents.
> The selection process  builds a 'tobeProcessed filelist' which can be
listed
> and processed without the need for structured filenames.
>
> It will be emailed separately to Mehmet Dondurur as an attachment in
> anticipation of some feedback on its usefulness and the documentation.

> 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, 06 Aug 1998 01:49:58 +1000
From: "Kwang Y. Han" <ykhan1@student.monash.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Measuring spot distances in electron diffraction patterns (EDP)
Message-id: <000001bdc088$b2c54580$640ac282@ykhan1>
Content-type: text/plain; charset="iso-8859-1"
Content-transfer-encoding: 7bit

I am hoping someone could point out to me a more accurate way of measuring
spot distances in EDP for single-crystal materials.

This is how i did:
1) manually threshold the inverted TIFF image to obtain all the desired
spots
2) perform 'Analyze Particles...'
3) click 'Show Results'
4) import the results to Excel and calculate the distances

The distance between 2 specific spots appears to depend very much on my
threshold value.

Should I be locating the centroid or geometrical centre of each spot?
I am not sure if top-hat filter or Hough transform can help to reduce
variability in measurements? If so, how should it be done?

Thanks ahead for any suggestions..

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

Date: Wed, 5 Aug 1998 16:35:24 -0500
From: "Toby Chai, M.D., 8-5544, S8D18" <TCHAI@surgery1.umaryland.edu>
To: nih-image@io.ece.drexel.edu
Subject: Video Capture with Futura II LX Card
Message-ID: <74C71F31767@surgery1.umaryland.edu>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7BIT

I am trying to get NIH Image to work on a Mac PowerPC 8100 with a 
Futura II LX Video Capture card and a video camera hooked up to a 
fluorescence microscope.  The machine currently is running Oncor 
program which is working (it's capturing video feed fine).  
However, when I run NIH Image (1.61), I get the error message that I 
must use a frame grabber, etc.  How do I "configure" the Mac so that 
NIH Image recognizes the already present  video card/video signal?  I 
looked briefly through Oncor's manuals, but it didn't really help me. 
 I did "turn off" the Oncor init file and rebooting the computer, but 
still could not get NIH Imageto capture the video feed.  So 
basically, I want to use NIH Image software instead of Oncor.

Thanks in advance.

T. Chai, M.D.
Division of Urology
University of Maryland

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

Date: Tue, 4 Aug 1998 22:03:14 -0700
From: "Joan Main" <Joan.Main@gte.net>
To: <GJOSS@rna.bio.mq.edu.au>, <mehmet.dondurur.ph.d@jvc.org>,
        <nih-image@io.ece.drexel.edu>
Subject: Re:       Batch Processing of Images
Message-ID: <001d01bdc0b0$d248b7c0$0f0a13c0@oemcomputer>
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 7bit

HI,
I have been using a program called hijaak pro which catalogs and labels each
image I process.  I am processing 100-200 ultrasound iimages for time
intensity information.  I set up a file for each study.  The hijaak pro
program catalogs, labels allows thumbnail viewing and printing for later
analysis.  This may help you.  I am stacking 30 frames for analysis at a
time .  IMSI manufactures this program. Hope this is helpful
jmain@acuson.com or joan.main@gte.net good luck

-----Original Message-----
From: GJOSS@rna.bio.mq.edu.au <GJOSS@rna.bio.mq.edu.au>
To: mehmet.dondurur.ph.d@jvc.org <mehmet.dondurur.ph.d@jvc.org>;
nih-image@io.ece.drexel.edu <nih-image@io.ece.drexel.edu>
Date: Tuesday, August 04, 1998 7:00 AM
Subject: Batch Processing of Images


>>From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
>>To: "'NIH User Group'" <nih-image@io.ece.drexel.edu>
>>Subject: Image enhancment
>>Date: Wed, 29 Jul 1998 09:11:49 -0400
>>...........
>>Is there any way to enhance (sharpening edges) images in
>>folder in one shot rather than enhancing one image a time
>>using one of the filters?.
>>I have B&W CAT scan images-100's of them. Any  suggestion is
>>appreciated.
>>
>>Date: Thu, 23 Jul 1998 08:31:54 -0400
>>To: nih-image@io.ece.drexel.edu
>>From: Laird Bloom <lbloom@MIT.EDU>
>>Subject: montage macro
>......
> My computer can't open more than about 10 TIFF images at a time,
>>but I'd like to be able to make a montage without having to open each file
>>up individually.  Is there a way to open files in a folder one at a time
>>without having to give them sequential numbers?
>
>The above posts caused me to rethink some macro techniques I had used to do
>batch processing of images in NIH-Image and Object-Image.
>Using 'recent' extentions to macros, I have implemented a 'simple to use'
macro
>suite which allows the user to make selections of files and directory
contents.
>The selection process  builds a 'tobeProcessed filelist' which can be
listed
>and processed without the need for structured filenames.
>
>It will be emailed separately to Mehmet Dondurur as an attachment in
>anticipation of some feedback on its usefulness and the documentation.
>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, 6 Aug 1998 11:29:28 +0100
From: "Jed.Mosenfelder" <Jed.Mosenfelder@uni-bayreuth.de>
To: nih-image@io.ece.drexel.edu
Subject: dumb question about IP toolkit 2.5
Message-Id: <v03007800b1ee22ab7200@[132.180.124.75]>
Content-Type: text/plain; charset="us-ascii"

Has anyone tried threshholding greyscale images using the IPTK plugins in
Adobe photoshop. It's driving me crazy because, contrary to the manual, the
threshholded pixels do not appear highlighted in a color that you can
easily distinguish (they appear in some shade of grey rather than red), so
it's basically impossible to see what you're doing. I wonder if i'm missing
something obvious. Anyway i'm using Photoshop 3.0 on a 90 MhZ mac. I'd
really prefer to use NIH Image but the plugin filters in this toolkit that
i want to use run unbelievably slow in Image, because it doesn't read the
powerPC code (very disappointing!). Thanks much in advance for any help
from the experts out there....

cheers,

jed


-X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X--X
Jed Leigh Mosenfelder	e-mail: Jed.Mosenfelder@uni-bayreuth.de
Bayerisches Geoinstitut	Tel: +49-921-553712 (office)
Universitaet Bayreuth		     -553700 (dept. secretary)
D-95440 Bayreuth 			     -5160186 (home)
Germany			Fax:+49-921-553769
:-)----:-)----:-)----:-)----:-)----:-)----:-)----:-)----:-)----:-)----:-)

--------------------------------
End of nih-image-d Digest V98 Issue #30
***************************************

From nih-image-request@io.ece.drexel.edu Thu Aug  6 08:26 EDT 1998
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From: DrJohnRuss@aol.com
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In a message dated 8/6/98 9:40:10 AM, Jed.Mosenfelder@uni-bayreuth.de wrote:

>Has anyone tried threshholding greyscale images using the IPTK plugins in
>Adobe photoshop. It's driving me crazy because, contrary to the manual, the
>threshholded pixels do not appear highlighted in a color that you can
>easily distinguish (they appear in some shade of grey rather than red), so
>it's basically impossible to see what you're doing. I wonder if i'm missing
>something obvious.

It sounds as though you have a 256 color display depth. With thousands or
millions the preview of the thresholded region appears with a color overlay.

John Russ

From nih-image-request@io.ece.drexel.edu Thu Aug  6 17:35 EDT 1998
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Subject: Re: nih-image-d Digest V98 #29
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Hello,

Beta 3b fixes this problem.  It was released on our website yesterday at
http://www.scioncorp.com



>
>This message is specifically directed at any of the PC Scion Image users out
>there, so most  Mac NIH Image users can probably ignore this.
>
>I have been using (trying to, at least) Scion Beta 3 for particle
>analysis. The
>particles I am analyzing are somewhat oval shaped, fairly well defined, and
>usually a few hundred pixels in area (they don't appear small on the
>screen.) I
>have been trying to get Scion to give me the lengths of the major/ minor
>axes of
>the best fitting oval for the particle, but every time I attempt this I get
>error codes like "-1.#IO" instead of a measurement. Whether or not I have
>calibrated my scale to the proper units doesn't seem to have an effect.
>
>Has anyone else had this problem? Is there some way to get the major/
>minor axes
>to work? I even drew perfect elipses on a blank image as a test, and it didn't
>even give me the measurements for that.
>
>__________________________________
>
>Alex Courtade
>Huntsman Corporation
>7114 N. Lamar Blvd
>Austin, TX 78752
>
>Phone: (512) 483-0190
>Email: alex_courtade@huntsman.com
>
>__________________________________
>
>--------------------------------



-----------------------------------------------------------------------
Tom Morton                                     support@scioncorp.com
Technical Services                             http://www.scioncorp.com
Scion Corporation                              ftp://scioncorp.com
82 Wormans Mill Rd., Suite H                   Phone: (301) 695-7870
Frederick, MD 21701                            Fax:   (301) 695-0035
-----------------------------------------------------------------------


From nih-image-request@io.ece.drexel.edu Thu Aug  6 17:48 EDT 1998
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Date: Thu, 6 Aug 1998 17:18:57 -0400
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To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center)
From: hmthomas@med.cornell.edu (Henry M. Thomas)
Subject: Skewed normal distribution
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This problem is mathematical, but started in NIH Image.  I described the
distribution of intensities in an ROI by the mean, standard deviation, and
skewness of the distribution of pixel intensities.  Now, I would like to
generate the curve described by those 3 parameters.  I've got the equation
for a symmetrical normal distribution {y=3.989*e^(-x*x/2)} but don't know
how to put in the skewness term.

Any advice as to the actual equation or where to look?  Standard statistics
books don't help.  Maybe engineering, where similar parameters are called
first, second and third moments.

Thanks in advance, Harry.

Henry M. Thomas, III MD (Harry)
Professor of Clinical Medicine  Pulmonary and Critical Care Division
Department of Medicine, Cornell Univ. Medical School
Director, Pulmonary Research, Burke Rehabilitation Hospital
785 Mamaroneck Ave.  White Plains, NY 10605
(914) 597-2141


From nih-image-request@io.ece.drexel.edu Thu Aug  6 19:51 EDT 1998
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Date: Thu, 06 Aug 1998 18:40:22 -0500
From: "Michael J. Herron" <herro001@maroon.tc.umn.edu>
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Organization: U of MN
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Geez!  That is something that has been bothering me for a long time.  I
thought it was a "feature".  Glad to hear there is a way around it.


DrJohnRuss@AOL.COM wrote:
> 
> In a message dated 8/6/98 9:40:10 AM, Jed.Mosenfelder@uni-bayreuth.de wrote:
> 
> >Has anyone tried threshholding greyscale images using the IPTK plugins in
> >Adobe photoshop. It's driving me crazy because, contrary to the manual, the
> >threshholded pixels do not appear highlighted in a color that you can
> >easily distinguish (they appear in some shade of grey rather than red), so
> >it's basically impossible to see what you're doing. I wonder if i'm missing
> >something obvious.
> 
> It sounds as though you have a 256 color display depth. With thousands or
> millions the preview of the thresholded region appears with a color overlay.
> 
> John Russ

--
   _____________________________________________________________
  / Michael J. Herron  University of MN,  Dept. of Dermatology /
 / herro001@maroon.tc.umn.edu                                 /
/http://134.84.141.41/RASH.html                              /
_____________________________________________________________

From nih-image-request@io.ece.drexel.edu Thu Aug  6 20:10 EDT 1998
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Message-ID: <F98649A5EE8ED11190160000F802756598CDCA@exchvic3.dsto.defence.gov.au>
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Kwang Y. Han'" <ykhan1@student.monash.edu.au>,
        "'Image Mailing List'"
  <nih-image@io.ece.drexel.edu>
Subject: RE: Measuring spot distances in electron diffraction patterns (ED
	P)
Date: Fri, 7 Aug 1998 09:59:42 +1000 
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Kwang,
Mail me an image and I will have a look.
What you are doing looks fine, but maybe you have a centre to edge
gradient which you must remove before thresholding. This would explain
the shift in positions with a change in thresholding.
Its a bit hard to tell what you need to be doing without the data.
Noel.
> ----------
> From: 	Kwang Y. Han
> Sent: 	Thursday, 6 August 1998 1:49 AM
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	Measuring spot distances in electron diffraction
> patterns (EDP)
> 
> I am hoping someone could point out to me a more accurate way of
> measuring
> spot distances in EDP for single-crystal materials.
> 
> This is how i did:
> 1) manually threshold the inverted TIFF image to obtain all the
> desired
> spots
> 2) perform 'Analyze Particles...'
> 3) click 'Show Results'
> 4) import the results to Excel and calculate the distances
> 
> The distance between 2 specific spots appears to depend very much on
> my
> threshold value.
> 
> Should I be locating the centroid or geometrical centre of each spot?
> I am not sure if top-hat filter or Hough transform can help to reduce
> variability in measurements? If so, how should it be done?
> 
> Thanks ahead for any suggestions..
> 

From nih-image-d-request@io.ece.drexel.edu Fri Aug  7 06:13 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #31
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 31

Today's Topics:
  Re: dumb question about IP toolkit 2  [ DrJohnRuss@aol.com ]
  Re: nih-image-d Digest V98 #29        [ Tom Morton <support@scioncorp.com> ]
  Skewed normal distribution            [ hmthomas@med.cornell.edu (Henry M.  ]
  Re: dumb question about IP toolkit 2  [ "Michael J. Herron" <herro001@maroo ]
  RE: Measuring spot distances in elec  [ "Goldsmith, Noel" <Noel.Goldsmith@d ]

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

Date: Thu, 6 Aug 1998 08:07:31 EDT
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re:  dumb question about IP toolkit 2.5
Message-ID: <4fc7f694.35c99c86@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

In a message dated 8/6/98 9:40:10 AM, Jed.Mosenfelder@uni-bayreuth.de wrote:

>Has anyone tried threshholding greyscale images using the IPTK plugins in
>Adobe photoshop. It's driving me crazy because, contrary to the manual, the
>threshholded pixels do not appear highlighted in a color that you can
>easily distinguish (they appear in some shade of grey rather than red), so
>it's basically impossible to see what you're doing. I wonder if i'm missing
>something obvious.

It sounds as though you have a 256 color display depth. With thousands or
millions the preview of the thresholded region appears with a color overlay.

John Russ

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

Date: Wed, 5 Aug 1998 08:46:48 -0500
From: Tom Morton <support@scioncorp.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #29
Message-Id: <l03102800b1ee12847781@[10.0.0.239]>
Content-Type: text/plain; charset="us-ascii"

Hello,

Beta 3b fixes this problem.  It was released on our website yesterday at
http://www.scioncorp.com



>
>This message is specifically directed at any of the PC Scion Image users out
>there, so most  Mac NIH Image users can probably ignore this.
>
>I have been using (trying to, at least) Scion Beta 3 for particle
>analysis. The
>particles I am analyzing are somewhat oval shaped, fairly well defined, and
>usually a few hundred pixels in area (they don't appear small on the
>screen.) I
>have been trying to get Scion to give me the lengths of the major/ minor
>axes of
>the best fitting oval for the particle, but every time I attempt this I get
>error codes like "-1.#IO" instead of a measurement. Whether or not I have
>calibrated my scale to the proper units doesn't seem to have an effect.
>
>Has anyone else had this problem? Is there some way to get the major/
>minor axes
>to work? I even drew perfect elipses on a blank image as a test, and it didn't
>even give me the measurements for that.
>
>__________________________________
>
>Alex Courtade
>Huntsman Corporation
>7114 N. Lamar Blvd
>Austin, TX 78752
>
>Phone: (512) 483-0190
>Email: alex_courtade@huntsman.com
>
>__________________________________
>
>--------------------------------



-----------------------------------------------------------------------
Tom Morton                                     support@scioncorp.com
Technical Services                             http://www.scioncorp.com
Scion Corporation                              ftp://scioncorp.com
82 Wormans Mill Rd., Suite H                   Phone: (301) 695-7870
Frederick, MD 21701                            Fax:   (301) 695-0035
-----------------------------------------------------------------------

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

Date: Thu, 6 Aug 1998 17:18:57 -0400
From: hmthomas@med.cornell.edu (Henry M. Thomas)
To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center)
Subject: Skewed normal distribution
Message-Id: <v01540b00b1ef90fa9672@[206.152.160.79]>
Content-Type: text/plain; charset="us-ascii"

This problem is mathematical, but started in NIH Image.  I described the
distribution of intensities in an ROI by the mean, standard deviation, and
skewness of the distribution of pixel intensities.  Now, I would like to
generate the curve described by those 3 parameters.  I've got the equation
for a symmetrical normal distribution {y=3.989*e^(-x*x/2)} but don't know
how to put in the skewness term.

Any advice as to the actual equation or where to look?  Standard statistics
books don't help.  Maybe engineering, where similar parameters are called
first, second and third moments.

Thanks in advance, Harry.

Henry M. Thomas, III MD (Harry)
Professor of Clinical Medicine  Pulmonary and Critical Care Division
Department of Medicine, Cornell Univ. Medical School
Director, Pulmonary Research, Burke Rehabilitation Hospital
785 Mamaroneck Ave.  White Plains, NY 10605
(914) 597-2141

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

Date: Thu, 06 Aug 1998 18:40:22 -0500
From: "Michael J. Herron" <herro001@maroon.tc.umn.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: dumb question about IP toolkit 2.5
Message-ID: <35CA3EE5.4CE8@maroon.tc.umn.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Geez!  That is something that has been bothering me for a long time.  I
thought it was a "feature".  Glad to hear there is a way around it.


DrJohnRuss@AOL.COM wrote:
> 
> In a message dated 8/6/98 9:40:10 AM, Jed.Mosenfelder@uni-bayreuth.de wrote:
> 
> >Has anyone tried threshholding greyscale images using the IPTK plugins in
> >Adobe photoshop. It's driving me crazy because, contrary to the manual, the
> >threshholded pixels do not appear highlighted in a color that you can
> >easily distinguish (they appear in some shade of grey rather than red), so
> >it's basically impossible to see what you're doing. I wonder if i'm missing
> >something obvious.
> 
> It sounds as though you have a 256 color display depth. With thousands or
> millions the preview of the thresholded region appears with a color overlay.
> 
> John Russ

--
   _____________________________________________________________
  / Michael J. Herron  University of MN,  Dept. of Dermatology /
 / herro001@maroon.tc.umn.edu                                 /
/http://134.84.141.41/RASH.html                              /
_____________________________________________________________

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

Date: Fri, 7 Aug 1998 09:59:42 +1000 
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Kwang Y. Han'" <ykhan1@student.monash.edu.au>,
        "'Image Mailing List'"
	 <nih-image@io.ece.drexel.edu>
Subject: RE: Measuring spot distances in electron diffraction patterns (ED
	P)
Message-ID: <F98649A5EE8ED11190160000F802756598CDCA@exchvic3.dsto.defence.gov.au>
Content-Type: text/plain

Kwang,
Mail me an image and I will have a look.
What you are doing looks fine, but maybe you have a centre to edge
gradient which you must remove before thresholding. This would explain
the shift in positions with a change in thresholding.
Its a bit hard to tell what you need to be doing without the data.
Noel.
> ----------
> From: 	Kwang Y. Han
> Sent: 	Thursday, 6 August 1998 1:49 AM
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	Measuring spot distances in electron diffraction
> patterns (EDP)
> 
> I am hoping someone could point out to me a more accurate way of
> measuring
> spot distances in EDP for single-crystal materials.
> 
> This is how i did:
> 1) manually threshold the inverted TIFF image to obtain all the
> desired
> spots
> 2) perform 'Analyze Particles...'
> 3) click 'Show Results'
> 4) import the results to Excel and calculate the distances
> 
> The distance between 2 specific spots appears to depend very much on
> my
> threshold value.
> 
> Should I be locating the centroid or geometrical centre of each spot?
> I am not sure if top-hat filter or Hough transform can help to reduce
> variability in measurements? If so, how should it be done?
> 
> Thanks ahead for any suggestions..
> 

--------------------------------
End of nih-image-d Digest V98 Issue #31
***************************************

From nih-image-request@io.ece.drexel.edu Fri Aug  7 09:37 EDT 1998
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Message-ID: <35CAFD32.DEBB3212@ix.urz.uni-heidelberg.de>
Date: Fri, 07 Aug 1998 15:12:18 +0200
From: Thomas Ehmer <tehmer@ix.urz.uni-heidelberg.de>
X-Mailer: Mozilla 4.05 [en] (WinNT; I)
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To: NIH-image Mailinglist <nih-image@io.ece.drexel.edu>
Subject: translate scanned b/w curves in xy (ascii) coordinates ?
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What: A question about transfering paper plots in computer coordinates.
Problem: translate b/w curves with marching line alg. automatically in
xy coordinates

Hello.

In our lab, we often have plots from an analogue plotter (xy-plots,
single trace)
After having scanned the paper plots and having converted them into b/w
pictures, it would be great to have a tool that transfers/translates the
black pixel-trace into worksheet readable xy coordinates (ascii).
I know about the capabilities from the SigmaScanPro program from Jandel
Scientific, but unfortunately we do not have any funds to buy it.
Has anyone already written a tool using kind of the marching line
algorithm, so one only needs to click the trace and to give the start
direction, and the software outputs a table of xy cooridnates?

Thanks in advance, Thomas

--
Thomas Ehmer, Dipl.-Phys.     FON:+49 6221 544084
2nd Institute of Physiolgy    FAX:+49 6221 544123
University of Heidelberg      just have look at...
INF 326                       www.rzuser.uni-heidelberg.de/~jm0/fink
D-69120 Heidelberg, Germany
----


From nih-image-request@io.ece.drexel.edu Fri Aug  7 10:18 EDT 1998
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From: Jan Kreft <Kreft@cardiff.ac.uk>
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To: NIH-image Mailinglist <nih-image@io.ece.drexel.edu>
Subject: Re: translate scanned b/w curves in xy (ascii) coordinates ?
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Hi,

there was a report on a freeware program called Tracer that is supposed to
do exactly that in a computer mag (c't 12/98). I haven't tested it. It's
Win95 only. Have a look at:

http://www.ntu.edu.sg/home/akarol/data.htm

Hope this helps,

Jan.

Dr. Jan-Ulrich Kreft			Phone +44 1222 874000 ext. 6036
School of Pure and Applied Biology	Fax   +44 1222 874305
Cardiff University			E-mail Kreft@cardiff.ac.uk
PO Box 915, Cardiff CF1 3TL, UK

On Fri, 7 Aug 1998, Thomas Ehmer wrote:

> What: A question about transfering paper plots in computer coordinates.
> Problem: translate b/w curves with marching line alg. automatically in
> xy coordinates
> 
> Hello.
> 
> In our lab, we often have plots from an analogue plotter (xy-plots,
> single trace)
> After having scanned the paper plots and having converted them into b/w
> pictures, it would be great to have a tool that transfers/translates the
> black pixel-trace into worksheet readable xy coordinates (ascii).
> I know about the capabilities from the SigmaScanPro program from Jandel
> Scientific, but unfortunately we do not have any funds to buy it.
> Has anyone already written a tool using kind of the marching line
> algorithm, so one only needs to click the trace and to give the start
> direction, and the software outputs a table of xy cooridnates?
> 
> Thanks in advance, Thomas
> 
> --
> Thomas Ehmer, Dipl.-Phys.     FON:+49 6221 544084
> 2nd Institute of Physiolgy    FAX:+49 6221 544123
> University of Heidelberg      just have look at...
> INF 326                       www.rzuser.uni-heidelberg.de/~jm0/fink
> D-69120 Heidelberg, Germany
> ----
> 
> 
> 

From nih-image-request@io.ece.drexel.edu Fri Aug  7 11:23 EDT 1998
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From: "Michael G. Miller" <mmiller@arches.uga.edu>
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To: nih-image@io.ece.drexel.edu
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I'm trying to help a faculty member here who is using nih-image
to work with mri image data from a local hospital.

The image data is provided on 4mm DAT tapes. Currently we read
those on a unix system (it's just raw data files, not tar) and
transfer them to his Mac. He has acquired an 4mm DAT drive
to do backups using the Retrospect software. I've taken a quick
look around the web and could not find any software to read
the mri image DAT tapes directly on the MAC (since it is not
tar format the various Mac tar programs do not work).

Does anyone know of software that will allow a mac to read 
raw data files off a DAT tape?

Thanks in advance for any information, Michael

Michael G. Miller	
UCNS Client Services	
University of Georgia	
mmiller@arches.uga.edu
706.542.5359


From nih-image-request@io.ece.drexel.edu Fri Aug  7 11:55 EDT 1998
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From: Ray Hicks <rh208@cus.cam.ac.uk>
Subject: Re: translate scanned b/w curves in xy (ascii) coordinates ?
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Hi Thomas,

there used to be a macro for this that ran with Image (as I remember the
plot was ANDed with a grid of lines normal to the x axis, breaking the data
line up into dots, co-ordinates for these could then be found using analyse
particles).


There is also a program that does this for you  called dataThief, it allows
you to calibrate the plot axes, and then either click where you want
measurementsto be taken, or automatically trace a line, exporting the data
as text.

I haven't used it "in anger" but I remembered mention of it a few years ago
on this list, and found  it at:
 ftp://codon.nih.gov/pub/nih-image/programs/dataThief_2.0b.hqx

I gave it a go and it seems to be just what you want.

Good luck

Ray

ps have you tried digitising the voltage that goes into the chart recorder
in the first place?  It shouldn't be too expensive ($20-30? - at least for
a pc),and would probably give better results than any plot/scan/trace
methods where there are plenty of places for non-linearity and errors to
creep in.


>What: A question about transfering paper plots in computer coordinates.
>Problem: translate b/w curves with marching line alg. automatically in
>xy coordinates
>
>Hello.
>
>In our lab, we often have plots from an analogue plotter (xy-plots,
>single trace)
>After having scanned the paper plots and having converted them into b/w
>pictures, it would be great to have a tool that transfers/translates the
>black pixel-trace into worksheet readable xy coordinates (ascii).
>I know about the capabilities from the SigmaScanPro program from Jandel
>Scientific, but unfortunately we do not have any funds to buy it.
>Has anyone already written a tool using kind of the marching line
>algorithm, so one only needs to click the trace and to give the start
>direction, and the software outputs a table of xy cooridnates?
>
>Thanks in advance, Thomas
>
>--
>Thomas Ehmer, Dipl.-Phys.     FON:+49 6221 544084
>2nd Institute of Physiolgy    FAX:+49 6221 544123
>University of Heidelberg      just have look at...
>INF 326                       www.rzuser.uni-heidelberg.de/~jm0/fink
>D-69120 Heidelberg, Germany
>----


                              Ray Hicks
________________________________________________________________________
|University of Cambridge          |Tel              01223 330149        |
|Department of Medicine           |Fax             01223 336846         |
|Level 5, Addenbrookes Hospital   |e-mail         <rh208@cus.cam.ac.uk> |
|Hills Road Cambridge             |Web  http://facsmac.med.cam.ac.uk    |
|CB2                              |ftp server  ftp://131.111.80.78      |
|UK                               |                                     |
|_________________________________|_____________________________________|


From nih-image-request@io.ece.drexel.edu Fri Aug  7 15:51 EDT 1998
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Date: Fri, 07 Aug 1998 13:41:24 -0600
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Thomas-

Take look at a program called DataThief at this url:
http://archives.math.utk.edu/software/mac/graphingAids/.directory.html

I think it will do everything you need.

Chris Tully

Thomas Ehmer wrote:
> 
> What: A question about transfering paper plots in computer coordinates.
> Problem: translate b/w curves with marching line alg. automatically in
> xy coordinates
> 
> Hello.
> 
> In our lab, we often have plots from an analogue plotter (xy-plots,
> single trace)
> After having scanned the paper plots and having converted them into b/w
> pictures, it would be great to have a tool that transfers/translates the
> black pixel-trace into worksheet readable xy coordinates (ascii).
> I know about the capabilities from the SigmaScanPro program from Jandel
> Scientific, but unfortunately we do not have any funds to buy it.
> Has anyone already written a tool using kind of the marching line
> algorithm, so one only needs to click the trace and to give the start
> direction, and the software outputs a table of xy cooridnates?
> 
> Thanks in advance, Thomas
> 
> --
> Thomas Ehmer, Dipl.-Phys.     FON:+49 6221 544084
> 2nd Institute of Physiolgy    FAX:+49 6221 544123
> University of Heidelberg      just have look at...
> INF 326                       www.rzuser.uni-heidelberg.de/~jm0/fink
> D-69120 Heidelberg, Germany
> ----

From nih-image-d-request@io.ece.drexel.edu Sat Aug  8 06:13 EDT 1998
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 32

Today's Topics:
  translate scanned b/w curves in xy (  [ Thomas Ehmer <tehmer@ix.urz.uni-hei ]
  Re: translate scanned b/w curves in   [ Jan Kreft <Kreft@cardiff.ac.uk> ]
  Reading DAT tapes on a Mac            [ "Michael G. Miller" <mmiller@arches ]
  Re: translate scanned b/w curves in   [ Ray Hicks <rh208@cus.cam.ac.uk> ]
  Re: translate scanned b/w curves in   [ "Christoopher P. Tully" <cptully@us ]

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

Date: Fri, 07 Aug 1998 15:12:18 +0200
From: Thomas Ehmer <tehmer@ix.urz.uni-heidelberg.de>
To: NIH-image Mailinglist <nih-image@io.ece.drexel.edu>
Subject: translate scanned b/w curves in xy (ascii) coordinates ?
Message-ID: <35CAFD32.DEBB3212@ix.urz.uni-heidelberg.de>
Content-Type: text/plain; charset=us-ascii
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What: A question about transfering paper plots in computer coordinates.
Problem: translate b/w curves with marching line alg. automatically in
xy coordinates

Hello.

In our lab, we often have plots from an analogue plotter (xy-plots,
single trace)
After having scanned the paper plots and having converted them into b/w
pictures, it would be great to have a tool that transfers/translates the
black pixel-trace into worksheet readable xy coordinates (ascii).
I know about the capabilities from the SigmaScanPro program from Jandel
Scientific, but unfortunately we do not have any funds to buy it.
Has anyone already written a tool using kind of the marching line
algorithm, so one only needs to click the trace and to give the start
direction, and the software outputs a table of xy cooridnates?

Thanks in advance, Thomas

--
Thomas Ehmer, Dipl.-Phys.     FON:+49 6221 544084
2nd Institute of Physiolgy    FAX:+49 6221 544123
University of Heidelberg      just have look at...
INF 326                       www.rzuser.uni-heidelberg.de/~jm0/fink
D-69120 Heidelberg, Germany
----

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

Date: Fri, 7 Aug 1998 15:02:25 +0100 (BST)
From: Jan Kreft <Kreft@cardiff.ac.uk>
To: NIH-image Mailinglist <nih-image@io.ece.drexel.edu>
Subject: Re: translate scanned b/w curves in xy (ascii) coordinates ?
Message-ID: <Pine.OSF.3.95q.980807145809.6142A-100000@thor>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi,

there was a report on a freeware program called Tracer that is supposed to
do exactly that in a computer mag (c't 12/98). I haven't tested it. It's
Win95 only. Have a look at:

http://www.ntu.edu.sg/home/akarol/data.htm

Hope this helps,

Jan.

Dr. Jan-Ulrich Kreft			Phone +44 1222 874000 ext. 6036
School of Pure and Applied Biology	Fax   +44 1222 874305
Cardiff University			E-mail Kreft@cardiff.ac.uk
PO Box 915, Cardiff CF1 3TL, UK

On Fri, 7 Aug 1998, Thomas Ehmer wrote:

> What: A question about transfering paper plots in computer coordinates.
> Problem: translate b/w curves with marching line alg. automatically in
> xy coordinates
> 
> Hello.
> 
> In our lab, we often have plots from an analogue plotter (xy-plots,
> single trace)
> After having scanned the paper plots and having converted them into b/w
> pictures, it would be great to have a tool that transfers/translates the
> black pixel-trace into worksheet readable xy coordinates (ascii).
> I know about the capabilities from the SigmaScanPro program from Jandel
> Scientific, but unfortunately we do not have any funds to buy it.
> Has anyone already written a tool using kind of the marching line
> algorithm, so one only needs to click the trace and to give the start
> direction, and the software outputs a table of xy cooridnates?
> 
> Thanks in advance, Thomas
> 
> --
> Thomas Ehmer, Dipl.-Phys.     FON:+49 6221 544084
> 2nd Institute of Physiolgy    FAX:+49 6221 544123
> University of Heidelberg      just have look at...
> INF 326                       www.rzuser.uni-heidelberg.de/~jm0/fink
> D-69120 Heidelberg, Germany
> ----
> 
> 
> 

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

Date: Fri, 7 Aug 1998 11:05:59 -0400 (EDT)
From: "Michael G. Miller" <mmiller@arches.uga.edu>
To: nih-image@io.ece.drexel.edu
Subject: Reading DAT tapes on a Mac
Message-ID: <Pine.A41.3.96.980807110040.50996A-100000@archa15.cc.uga.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I'm trying to help a faculty member here who is using nih-image
to work with mri image data from a local hospital.

The image data is provided on 4mm DAT tapes. Currently we read
those on a unix system (it's just raw data files, not tar) and
transfer them to his Mac. He has acquired an 4mm DAT drive
to do backups using the Retrospect software. I've taken a quick
look around the web and could not find any software to read
the mri image DAT tapes directly on the MAC (since it is not
tar format the various Mac tar programs do not work).

Does anyone know of software that will allow a mac to read 
raw data files off a DAT tape?

Thanks in advance for any information, Michael

Michael G. Miller	
UCNS Client Services	
University of Georgia	
mmiller@arches.uga.edu
706.542.5359

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

Date: Fri, 7 Aug 1998 16:43:19 +0100
From: Ray Hicks <rh208@cus.cam.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: translate scanned b/w curves in xy (ascii) coordinates ?
Message-Id: <l03110702b1f0ca52f365@[131.111.80.24]>
Content-Type: text/plain; charset="us-ascii"

Hi Thomas,

there used to be a macro for this that ran with Image (as I remember the
plot was ANDed with a grid of lines normal to the x axis, breaking the data
line up into dots, co-ordinates for these could then be found using analyse
particles).


There is also a program that does this for you  called dataThief, it allows
you to calibrate the plot axes, and then either click where you want
measurementsto be taken, or automatically trace a line, exporting the data
as text.

I haven't used it "in anger" but I remembered mention of it a few years ago
on this list, and found  it at:
 ftp://codon.nih.gov/pub/nih-image/programs/dataThief_2.0b.hqx

I gave it a go and it seems to be just what you want.

Good luck

Ray

ps have you tried digitising the voltage that goes into the chart recorder
in the first place?  It shouldn't be too expensive ($20-30? - at least for
a pc),and would probably give better results than any plot/scan/trace
methods where there are plenty of places for non-linearity and errors to
creep in.


>What: A question about transfering paper plots in computer coordinates.
>Problem: translate b/w curves with marching line alg. automatically in
>xy coordinates
>
>Hello.
>
>In our lab, we often have plots from an analogue plotter (xy-plots,
>single trace)
>After having scanned the paper plots and having converted them into b/w
>pictures, it would be great to have a tool that transfers/translates the
>black pixel-trace into worksheet readable xy coordinates (ascii).
>I know about the capabilities from the SigmaScanPro program from Jandel
>Scientific, but unfortunately we do not have any funds to buy it.
>Has anyone already written a tool using kind of the marching line
>algorithm, so one only needs to click the trace and to give the start
>direction, and the software outputs a table of xy cooridnates?
>
>Thanks in advance, Thomas
>
>--
>Thomas Ehmer, Dipl.-Phys.     FON:+49 6221 544084
>2nd Institute of Physiolgy    FAX:+49 6221 544123
>University of Heidelberg      just have look at...
>INF 326                       www.rzuser.uni-heidelberg.de/~jm0/fink
>D-69120 Heidelberg, Germany
>----


                              Ray Hicks
________________________________________________________________________
|University of Cambridge          |Tel              01223 330149        |
|Department of Medicine           |Fax             01223 336846         |
|Level 5, Addenbrookes Hospital   |e-mail         <rh208@cus.cam.ac.uk> |
|Hills Road Cambridge             |Web  http://facsmac.med.cam.ac.uk    |
|CB2                              |ftp server  ftp://131.111.80.78      |
|UK                               |                                     |
|_________________________________|_____________________________________|

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

Date: Fri, 07 Aug 1998 13:41:24 -0600
From: "Christoopher P. Tully" <cptully@usa.net>
To: nih-image@io.ece.drexel.edu
Subject: Re: translate scanned b/w curves in xy (ascii) coordinates ?
Message-ID: <35CB5864.745C0ADE@usa.net>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Thomas-

Take look at a program called DataThief at this url:
http://archives.math.utk.edu/software/mac/graphingAids/.directory.html

I think it will do everything you need.

Chris Tully

Thomas Ehmer wrote:
> 
> What: A question about transfering paper plots in computer coordinates.
> Problem: translate b/w curves with marching line alg. automatically in
> xy coordinates
> 
> Hello.
> 
> In our lab, we often have plots from an analogue plotter (xy-plots,
> single trace)
> After having scanned the paper plots and having converted them into b/w
> pictures, it would be great to have a tool that transfers/translates the
> black pixel-trace into worksheet readable xy coordinates (ascii).
> I know about the capabilities from the SigmaScanPro program from Jandel
> Scientific, but unfortunately we do not have any funds to buy it.
> Has anyone already written a tool using kind of the marching line
> algorithm, so one only needs to click the trace and to give the start
> direction, and the software outputs a table of xy cooridnates?
> 
> Thanks in advance, Thomas
> 
> --
> Thomas Ehmer, Dipl.-Phys.     FON:+49 6221 544084
> 2nd Institute of Physiolgy    FAX:+49 6221 544123
> University of Heidelberg      just have look at...
> INF 326                       www.rzuser.uni-heidelberg.de/~jm0/fink
> D-69120 Heidelberg, Germany
> ----

--------------------------------
End of nih-image-d Digest V98 Issue #32
***************************************

From nih-image-request@io.ece.drexel.edu Mon Aug 10 06:50 EDT 1998
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Date: Mon, 10 Aug 1998 11:35:53 +0100
To: nih-image@io.ece.drexel.edu
From: Clive Washington <Clive.Washington@nottingham.ac.uk>
Subject: Re: Skewed normal distribution
Resent-Message-ID: <"amz0g2.0.F8.Eoipr"@io>
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>This problem is mathematical, but started in NIH Image.  I described the
>distribution of intensities in an ROI by the mean, standard deviation, and
>skewness of the distribution of pixel intensities.  Now, I would like to
>generate the curve described by those 3 parameters.  I've got the equation
>for a symmetrical normal distribution {y=3.989*e^(-x*x/2)} but don't know
>how to put in the skewness term.

I'm not sure about this but I think you'll find that you cannot reconstruct
in this way.  The normal distribution is unique so can be reconstructed
knowing mean x and standard deviation.  But there are an infinite number of
different curves which can generate a particular skewedness.  Admittedly
they may not be smooth.  For example if you take a normal and just pull up
one channel a bit, the value of skewedness will increase.  If you drop it
down again and pull up another channel it will also increase similarly, and
you won't be able to distinguish one from the other.  So there is no unique
solution.

You might be better fitting a more explicit form to your data.   The
simplest skewed form is the lognormal, which has a tail to larger X.  I
haven't got the formula to hand but it's in the books.  I expect there are
others - consult the particle size literature, esp. Terry Allen's book
'particle size measurement' since particle people have to deal with this
sort of data frequently.

////////////////////////COLLOID ENGINEERING GROUP///////////////////////////

Dr. Clive Washington,                                      Tel. 0115 9515034
Senior Lecturer in Pharmaceutics,			   Fax  0115 9515102
Department of Pharmaceutical Sciences,
University of Nottingham,
University Park,                       Email pazcw@unix.ccc.nottingham.ac.uk
Nottingham NG7 2RD.         http://reliant.pharm.nottingham.ac.uk/clive.html

                  "It's mail, Jim, but not as we know it."

////////////////////////COLLOID ENGINEERING GROUP///////////////////////////


From nih-image-request@io.ece.drexel.edu Mon Aug 10 07:12 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Stein Roervik <steinr@chembio.ntnu.no>
Subject: Clicking Zip disks
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Now it has finally happened, the dreaded thing I have heard happened to
other users of Zip drives: The drive goes clicking when a Zip disk is
inserted, and destroys all subsequent disks that are inserted.
(Fortunately, I tested the drive with a blank disk after the clicking disk
to avoid further data loss, as recommended on the Iomega web-pages). I have
used 85+ disks without any problems since I bought my first Zip.

I remember there was a thread about this last winter, but I am unable to
locate it in the archives. So, is there any way to recover the data on the
initial clicking disk ?

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+


From nih-image-request@io.ece.drexel.edu Mon Aug 10 09:34 EDT 1998
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From: rhawkes@mta.ca (Robert Hawkes)
Subject: PowerBook, PCI Expansion and Frame Rate
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I have recently acquired a PowerBook G3 / 233 MHz with a Magma PCI
expansion system (3 slot, portable) which we are using with a SCION LG-3
video digitizer. Even though the G3 should be faster than the 9600/233 we
use in the lab, I can only get 12 fps from NIH (or Scion) Image, even with
virtual memory and extensions turned off. I am using system 8.1.

I would very much appreciate any suggestions.

Bob Hawkes
rhawkes@mta.ca


From nih-image-request@io.ece.drexel.edu Mon Aug 10 10:45 EDT 1998
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From: Stein Roervik <steinr@chembio.ntnu.no>
Subject: Re: PowerBook, PCI Expansion and Frame Rate
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>I have recently acquired a PowerBook G3 / 233 MHz with a Magma PCI
>expansion system (3 slot, portable) which we are using with a SCION LG-3
>video digitizer. Even though the G3 should be faster than the 9600/233 we
>use in the lab, I can only get 12 fps from NIH (or Scion) Image, even with
>virtual memory and extensions turned off. I am using system 8.1.
>
>I would very much appreciate any suggestions.
>
>Bob Hawkes
>rhawkes@mta.ca

Try reducing the number of colors on the screen. Makes a big difference.

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+


From nih-image-request@io.ece.drexel.edu Mon Aug 10 12:53 EDT 1998
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Date: Mon, 10 Aug 1998 10:37:29 -0600 (CST)
From: "Geoffrey D. Guttmann" <guttmann@duke.usask.ca>
To: nih-image@io.ece.drexel.edu
Subject: Re: Clicking Zip disks
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Hi folks
	The same problem happened to me.  The drive was in warranty so
Iomega replaced the Zip drive.  The cost to recover the data was US$425
but they offered a 50% discount since the drive was under warranty.  Maybe
somebody can set up a cheaper Zip disk recovery service.
Cheers, geoff

>Now it has finally happened, the dreaded thing I have heard happened to
>other users of Zip drives: The drive goes clicking when a Zip disk is
>inserted, and destroys all subsequent disks that are inserted.
>(Fortunately, I tested the drive with a blank disk after the clicking disk
>to avoid further data loss, as recommended on the Iomega web-pages). I have
>used 85+ disks without any problems since I bought my first Zip.
>
>I remember there was a thread about this last winter, but I am unable to
>locate it in the archives. So, is there any way to recover the data on the
>initial clicking disk ?

------------------------------------------------------------------------
Geoffrey D. Guttmann, Ph.D	_/_/_/_/     _/_/     _/_/_/_/  _/   _/  
Assistant Professor	       _/	   _/   _/   _/        _/  _/
Dept. of Anatomy and Cell Biology    	  _/    _/  _/        _/ _/
College of Medicine	      _/_/_/_/   _/_/_/_/  _/_/_/_/  _/_/
University of Saskatchewan	   _/   _/    _/	_/  _/ _/
A-315 Health Sciences Building	  _/   _/    _/        _/  _/  _/
107 Wiggins Road	   _/_/_/_/   _/    _/  _/_/_/_/  _/   _/  _/
Saskatoon, SK S7N 5E5 
CANADA				Voice:(306)966-4079   Fax:(306)966-4298   
				E-mail:guttmann@duke.usask.ca	     
------------------------------------------------------------------------

From nih-image-request@io.ece.drexel.edu Mon Aug 10 13:41 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: hmthomas@med.cornell.edu (Henry M. Thomas)
Subject: Re: Skewed normal distribution
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>>This problem is mathematical, but started in NIH Image.  I described the
>>distribution of intensities in an ROI by the mean, standard deviation, and
>>skewness of the distribution of pixel intensities.  Now, I would like to
>>generate the curve described by those 3 parameters.  I've got the equation
>>for a symmetrical normal distribution {y=3.989*e^(-x*x/2)} but don't know
>>how to put in the skewness term.
>
>I'm not sure about this but I think you'll find that you cannot reconstruct
>in this way.  The normal distribution is unique so can be reconstructed
>knowing mean x and standard deviation.  But there are an infinite number of
>different curves which can generate a particular skewedness.  Admittedly
>they may not be smooth.  For example if you take a normal and just pull up
>one channel a bit, the value of skewedness will increase.  If you drop it
>down again and pull up another channel it will also increase similarly, and
>you won't be able to distinguish one from the other.  So there is no unique
>solution.

   Thank you for your thought experiment with a normal curve.  I believe
that            your logic applies to the SD of the the normal curve as
well: there are an infinite number of actual distributions with the same
mean and SD. What I'm looking for is a formula with 3 independent variables
(mean, S.D. and skewness), which will generate a unique "standard" skewed
normal (Gaussian) curve, the way mean and SD generate a standard normal
curve.

>
>You might be better fitting a more explicit form to your data.   The
>simplest skewed form is the lognormal, which has a tail to larger X.  I
>haven't got the formula to hand but it's in the books.  I expect there are
>others - consult the particle size literature, esp. Terry Allen's book
>'particle size measurement' since particle people have to deal with this
>sort of data frequently.

     I'll try a log transformation, and also check the book. Thank you. Harry.

>
>////////////////////////COLLOID ENGINEERING GROUP///////////////////////////
>
>Dr. Clive Washington,                                      Tel. 0115 9515034
>Senior Lecturer in Pharmaceutics,                          Fax  0115 9515102
>Department of Pharmaceutical Sciences,
>University of Nottingham,
>University Park,                       Email pazcw@unix.ccc.nottingham.ac.uk
>Nottingham NG7 2RD.         http://reliant.pharm.nottingham.ac.uk/clive.html
>
>                  "It's mail, Jim, but not as we know it."
>
>////////////////////////COLLOID ENGINEERING GROUP///////////////////////////

Henry M. Thomas, III MD (Harry)
Professor of Clinical Medicine,  Pulmonary and Critical Care Division
Department of Medicine, Cornell Univ. Medical School
Director, Pulmonary Research, Burke Rehabilitation Hospital
785 Mamaroneck Ave.  White Plains, NY 10605
(914) 597-2141


From nih-image-request@io.ece.drexel.edu Mon Aug 10 13:42 EDT 1998
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Date: Mon, 10 Aug 1998 11:31:19 -0600
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My experieneces were with an internal IDE zip on a Wintel box, but they
may be relavent:

1) when the drive started clicking, I was unable to read any disks on
that drive, but had no problems reading them on other zip drives.
2) Taking the Zip drive out of the computer case and putting it back in
cured the problem TEMPORARILY - I'd try gently knocking on the case of
an external drive.  However, the drive did eventually die and have to be
replaced (in fact, the replacement was DOA, and had to be replaced as
well...).

3) At this point, I think long and hard before buying any more Zip
drives.  First because at 100 - 200 MB of images per experiment Zips get
used up fast, and second because CD-R disks are cheaper and less prone
to being killed by a defective drive.  

Chris Tully

Geoffrey D. Guttmann wrote:
> 
> Hi folks
>         The same problem happened to me.  The drive was in warranty so
> Iomega replaced the Zip drive.  The cost to recover the data was US$425
> but they offered a 50% discount since the drive was under warranty.  Maybe
> somebody can set up a cheaper Zip disk recovery service.
> Cheers, geoff
> 
> >Now it has finally happened, the dreaded thing I have heard happened to
> >other users of Zip drives: The drive goes clicking when a Zip disk is
> >inserted, and destroys all subsequent disks that are inserted.
> >(Fortunately, I tested the drive with a blank disk after the clicking disk
> >to avoid further data loss, as recommended on the Iomega web-pages). I have
> >used 85+ disks without any problems since I bought my first Zip.
> >
> >I remember there was a thread about this last winter, but I am unable to
> >locate it in the archives. So, is there any way to recover the data on the
> >initial clicking disk ?
> 
> ------------------------------------------------------------------------
> Geoffrey D. Guttmann, Ph.D      _/_/_/_/     _/_/     _/_/_/_/  _/   _/
> Assistant Professor            _/          _/   _/   _/        _/  _/
> Dept. of Anatomy and Cell Biology         _/    _/  _/        _/ _/
> College of Medicine           _/_/_/_/   _/_/_/_/  _/_/_/_/  _/_/
> University of Saskatchewan         _/   _/    _/        _/  _/ _/
> A-315 Health Sciences Building    _/   _/    _/        _/  _/  _/
> 107 Wiggins Road           _/_/_/_/   _/    _/  _/_/_/_/  _/   _/  _/
> Saskatoon, SK S7N 5E5
> CANADA                          Voice:(306)966-4079   Fax:(306)966-4298
>                                 E-mail:guttmann@duke.usask.ca
> ------------------------------------------------------------------------

From nih-image-request@io.ece.drexel.edu Mon Aug 10 17:22 EDT 1998
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Message-ID: <c=US%a=_%p=Indiana_Universi%l=PYRITE-980810210740Z-3299@pyrite.igs.indiana.edu>
From: "Barwood, Henry" <hbarwood@pyrite.igs.indiana.edu>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Plot profile using Image-PC
Date: Mon, 10 Aug 1998 16:07:40 -0500
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I have been running some profile plots using Scion's Image-PC (beta-3).
Everything works and I can print the profiles, but I cannot save them as
a .tif image like I could using Image for Mac. Does anyone have any
suggestions of what I can do to save my plots? Thanks.

Henry Barwood
Indiana Geological Survey

From nih-image-request@io.ece.drexel.edu Tue Aug 11 00:56 EDT 1998
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Subject: Re: Clicking Zip disks
Date: Mon, 10 Aug 98 21:49:26 -0800
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Hello,

I had this clicking problem (about 40 clicks before it stopped) when I 
inserted my Zip disk into the drive. I sent my drive back to iomega and 
they gave me new Zip Drive. I have not had any problems since then (about 
1.5 years, now). I was able to retrieve my Zip disk data using Norton 
Utilities. 

Good Luck,

Wilfred Denetclaw Jr., Ph.D.
Department Anatomy
UCSF

From nih-image-d-request@io.ece.drexel.edu Tue Aug 11 01:03 EDT 1998
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 33

Today's Topics:
  Re: Skewed normal distribution        [ Clive Washington <Clive.Washington@ ]
  Clicking Zip disks                    [ Stein Roervik <steinr@chembio.ntnu. ]
  PowerBook, PCI Expansion and Frame R  [ rhawkes@mta.ca (Robert Hawkes) ]
  Re: PowerBook, PCI Expansion and Fra  [ Stein Roervik <steinr@chembio.ntnu. ]
  Re: Clicking Zip disks                [ "Geoffrey D. Guttmann" <guttmann@du ]
  Re: Skewed normal distribution        [ hmthomas@med.cornell.edu (Henry M.  ]
  Re: Clicking Zip disks                [ "Christopher P. Tully" <cptully@usa ]
  Plot profile using Image-PC           [ "Barwood, Henry" <hbarwood@pyrite.i ]
  Re: Clicking Zip disks                [ Your Name <wtdenet@concentric.net> ]

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

Date: Mon, 10 Aug 1998 11:35:53 +0100
From: Clive Washington <Clive.Washington@nottingham.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Skewed normal distribution
Message-Id: <l03110702b1f47bc10cd0@[128.243.184.1]>
Content-Type: text/plain; charset="us-ascii"

>This problem is mathematical, but started in NIH Image.  I described the
>distribution of intensities in an ROI by the mean, standard deviation, and
>skewness of the distribution of pixel intensities.  Now, I would like to
>generate the curve described by those 3 parameters.  I've got the equation
>for a symmetrical normal distribution {y=3.989*e^(-x*x/2)} but don't know
>how to put in the skewness term.

I'm not sure about this but I think you'll find that you cannot reconstruct
in this way.  The normal distribution is unique so can be reconstructed
knowing mean x and standard deviation.  But there are an infinite number of
different curves which can generate a particular skewedness.  Admittedly
they may not be smooth.  For example if you take a normal and just pull up
one channel a bit, the value of skewedness will increase.  If you drop it
down again and pull up another channel it will also increase similarly, and
you won't be able to distinguish one from the other.  So there is no unique
solution.

You might be better fitting a more explicit form to your data.   The
simplest skewed form is the lognormal, which has a tail to larger X.  I
haven't got the formula to hand but it's in the books.  I expect there are
others - consult the particle size literature, esp. Terry Allen's book
'particle size measurement' since particle people have to deal with this
sort of data frequently.

////////////////////////COLLOID ENGINEERING GROUP///////////////////////////

Dr. Clive Washington,                                      Tel. 0115 9515034
Senior Lecturer in Pharmaceutics,			   Fax  0115 9515102
Department of Pharmaceutical Sciences,
University of Nottingham,
University Park,                       Email pazcw@unix.ccc.nottingham.ac.uk
Nottingham NG7 2RD.         http://reliant.pharm.nottingham.ac.uk/clive.html

                  "It's mail, Jim, but not as we know it."

////////////////////////COLLOID ENGINEERING GROUP///////////////////////////

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

Date: Mon, 10 Aug 1998 13:00:01 +0200
From: Stein Roervik <steinr@chembio.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Clicking Zip disks
Message-Id: <v03102809b1f481c90676@[129.241.39.133]>
Content-Type: text/plain; charset="us-ascii"

Now it has finally happened, the dreaded thing I have heard happened to
other users of Zip drives: The drive goes clicking when a Zip disk is
inserted, and destroys all subsequent disks that are inserted.
(Fortunately, I tested the drive with a blank disk after the clicking disk
to avoid further data loss, as recommended on the Iomega web-pages). I have
used 85+ disks without any problems since I bought my first Zip.

I remember there was a thread about this last winter, but I am unable to
locate it in the archives. So, is there any way to recover the data on the
initial clicking disk ?

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+

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

Date: Mon, 10 Aug 1998 10:19:13 -0300
From: rhawkes@mta.ca (Robert Hawkes)
To: nih-image@io.ece.drexel.edu
Subject: PowerBook, PCI Expansion and Frame Rate
Message-Id: <v01530512b1f4a3245f9a@[198.164.245.21]>
Content-Type: text/plain; charset="us-ascii"

I have recently acquired a PowerBook G3 / 233 MHz with a Magma PCI
expansion system (3 slot, portable) which we are using with a SCION LG-3
video digitizer. Even though the G3 should be faster than the 9600/233 we
use in the lab, I can only get 12 fps from NIH (or Scion) Image, even with
virtual memory and extensions turned off. I am using system 8.1.

I would very much appreciate any suggestions.

Bob Hawkes
rhawkes@mta.ca

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

Date: Mon, 10 Aug 1998 16:30:50 +0200
From: Stein Roervik <steinr@chembio.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Re: PowerBook, PCI Expansion and Frame Rate
Message-Id: <v0310280db1f4b445e2a5@[129.241.39.133]>
Content-Type: text/plain; charset="us-ascii"

>I have recently acquired a PowerBook G3 / 233 MHz with a Magma PCI
>expansion system (3 slot, portable) which we are using with a SCION LG-3
>video digitizer. Even though the G3 should be faster than the 9600/233 we
>use in the lab, I can only get 12 fps from NIH (or Scion) Image, even with
>virtual memory and extensions turned off. I am using system 8.1.
>
>I would very much appreciate any suggestions.
>
>Bob Hawkes
>rhawkes@mta.ca

Try reducing the number of colors on the screen. Makes a big difference.

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+

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

Date: Mon, 10 Aug 1998 10:37:29 -0600 (CST)
From: "Geoffrey D. Guttmann" <guttmann@duke.usask.ca>
To: nih-image@io.ece.drexel.edu
Subject: Re: Clicking Zip disks
Message-ID: <Pine.OSF.4.02.9808101021330.25751-100000@duke.usask.ca>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi folks
	The same problem happened to me.  The drive was in warranty so
Iomega replaced the Zip drive.  The cost to recover the data was US$425
but they offered a 50% discount since the drive was under warranty.  Maybe
somebody can set up a cheaper Zip disk recovery service.
Cheers, geoff

>Now it has finally happened, the dreaded thing I have heard happened to
>other users of Zip drives: The drive goes clicking when a Zip disk is
>inserted, and destroys all subsequent disks that are inserted.
>(Fortunately, I tested the drive with a blank disk after the clicking disk
>to avoid further data loss, as recommended on the Iomega web-pages). I have
>used 85+ disks without any problems since I bought my first Zip.
>
>I remember there was a thread about this last winter, but I am unable to
>locate it in the archives. So, is there any way to recover the data on the
>initial clicking disk ?

------------------------------------------------------------------------
Geoffrey D. Guttmann, Ph.D	_/_/_/_/     _/_/     _/_/_/_/  _/   _/  
Assistant Professor	       _/	   _/   _/   _/        _/  _/
Dept. of Anatomy and Cell Biology    	  _/    _/  _/        _/ _/
College of Medicine	      _/_/_/_/   _/_/_/_/  _/_/_/_/  _/_/
University of Saskatchewan	   _/   _/    _/	_/  _/ _/
A-315 Health Sciences Building	  _/   _/    _/        _/  _/  _/
107 Wiggins Road	   _/_/_/_/   _/    _/  _/_/_/_/  _/   _/  _/
Saskatoon, SK S7N 5E5 
CANADA				Voice:(306)966-4079   Fax:(306)966-4298   
				E-mail:guttmann@duke.usask.ca	     
------------------------------------------------------------------------

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

Date: Mon, 10 Aug 1998 13:24:47 -0400
From: hmthomas@med.cornell.edu (Henry M. Thomas)
To: nih-image@io.ece.drexel.edu
Subject: Re: Skewed normal distribution
Message-Id: <v01540b00b1f4a2b8d34c@[206.152.160.56]>
Content-Type: text/plain; charset="us-ascii"

>>This problem is mathematical, but started in NIH Image.  I described the
>>distribution of intensities in an ROI by the mean, standard deviation, and
>>skewness of the distribution of pixel intensities.  Now, I would like to
>>generate the curve described by those 3 parameters.  I've got the equation
>>for a symmetrical normal distribution {y=3.989*e^(-x*x/2)} but don't know
>>how to put in the skewness term.
>
>I'm not sure about this but I think you'll find that you cannot reconstruct
>in this way.  The normal distribution is unique so can be reconstructed
>knowing mean x and standard deviation.  But there are an infinite number of
>different curves which can generate a particular skewedness.  Admittedly
>they may not be smooth.  For example if you take a normal and just pull up
>one channel a bit, the value of skewedness will increase.  If you drop it
>down again and pull up another channel it will also increase similarly, and
>you won't be able to distinguish one from the other.  So there is no unique
>solution.

   Thank you for your thought experiment with a normal curve.  I believe
that            your logic applies to the SD of the the normal curve as
well: there are an infinite number of actual distributions with the same
mean and SD. What I'm looking for is a formula with 3 independent variables
(mean, S.D. and skewness), which will generate a unique "standard" skewed
normal (Gaussian) curve, the way mean and SD generate a standard normal
curve.

>
>You might be better fitting a more explicit form to your data.   The
>simplest skewed form is the lognormal, which has a tail to larger X.  I
>haven't got the formula to hand but it's in the books.  I expect there are
>others - consult the particle size literature, esp. Terry Allen's book
>'particle size measurement' since particle people have to deal with this
>sort of data frequently.

     I'll try a log transformation, and also check the book. Thank you. Harry.

>
>////////////////////////COLLOID ENGINEERING GROUP///////////////////////////
>
>Dr. Clive Washington,                                      Tel. 0115 9515034
>Senior Lecturer in Pharmaceutics,                          Fax  0115 9515102
>Department of Pharmaceutical Sciences,
>University of Nottingham,
>University Park,                       Email pazcw@unix.ccc.nottingham.ac.uk
>Nottingham NG7 2RD.         http://reliant.pharm.nottingham.ac.uk/clive.html
>
>                  "It's mail, Jim, but not as we know it."
>
>////////////////////////COLLOID ENGINEERING GROUP///////////////////////////

Henry M. Thomas, III MD (Harry)
Professor of Clinical Medicine,  Pulmonary and Critical Care Division
Department of Medicine, Cornell Univ. Medical School
Director, Pulmonary Research, Burke Rehabilitation Hospital
785 Mamaroneck Ave.  White Plains, NY 10605
(914) 597-2141

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

Date: Mon, 10 Aug 1998 11:31:19 -0600
From: "Christopher P. Tully" <cptully@usa.net>
To: nih-image@io.ece.drexel.edu
Subject: Re: Clicking Zip disks
Message-ID: <35CF2E67.A8656FE6@usa.net>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

My experieneces were with an internal IDE zip on a Wintel box, but they
may be relavent:

1) when the drive started clicking, I was unable to read any disks on
that drive, but had no problems reading them on other zip drives.
2) Taking the Zip drive out of the computer case and putting it back in
cured the problem TEMPORARILY - I'd try gently knocking on the case of
an external drive.  However, the drive did eventually die and have to be
replaced (in fact, the replacement was DOA, and had to be replaced as
well...).

3) At this point, I think long and hard before buying any more Zip
drives.  First because at 100 - 200 MB of images per experiment Zips get
used up fast, and second because CD-R disks are cheaper and less prone
to being killed by a defective drive.  

Chris Tully

Geoffrey D. Guttmann wrote:
> 
> Hi folks
>         The same problem happened to me.  The drive was in warranty so
> Iomega replaced the Zip drive.  The cost to recover the data was US$425
> but they offered a 50% discount since the drive was under warranty.  Maybe
> somebody can set up a cheaper Zip disk recovery service.
> Cheers, geoff
> 
> >Now it has finally happened, the dreaded thing I have heard happened to
> >other users of Zip drives: The drive goes clicking when a Zip disk is
> >inserted, and destroys all subsequent disks that are inserted.
> >(Fortunately, I tested the drive with a blank disk after the clicking disk
> >to avoid further data loss, as recommended on the Iomega web-pages). I have
> >used 85+ disks without any problems since I bought my first Zip.
> >
> >I remember there was a thread about this last winter, but I am unable to
> >locate it in the archives. So, is there any way to recover the data on the
> >initial clicking disk ?
> 
> ------------------------------------------------------------------------
> Geoffrey D. Guttmann, Ph.D      _/_/_/_/     _/_/     _/_/_/_/  _/   _/
> Assistant Professor            _/          _/   _/   _/        _/  _/
> Dept. of Anatomy and Cell Biology         _/    _/  _/        _/ _/
> College of Medicine           _/_/_/_/   _/_/_/_/  _/_/_/_/  _/_/
> University of Saskatchewan         _/   _/    _/        _/  _/ _/
> A-315 Health Sciences Building    _/   _/    _/        _/  _/  _/
> 107 Wiggins Road           _/_/_/_/   _/    _/  _/_/_/_/  _/   _/  _/
> Saskatoon, SK S7N 5E5
> CANADA                          Voice:(306)966-4079   Fax:(306)966-4298
>                                 E-mail:guttmann@duke.usask.ca
> ------------------------------------------------------------------------

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

Date: Mon, 10 Aug 1998 16:07:40 -0500
From: "Barwood, Henry" <hbarwood@pyrite.igs.indiana.edu>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: Plot profile using Image-PC
Message-ID: <c=US%a=_%p=Indiana_Universi%l=PYRITE-980810210740Z-3299@pyrite.igs.indiana.edu>

I have been running some profile plots using Scion's Image-PC (beta-3).
Everything works and I can print the profiles, but I cannot save them as
a .tif image like I could using Image for Mac. Does anyone have any
suggestions of what I can do to save my plots? Thanks.

Henry Barwood
Indiana Geological Survey

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

Date: Mon, 10 Aug 98 21:49:26 -0800
From: Your Name <wtdenet@concentric.net>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: Clicking Zip disks
Message-Id: <199808110441.AAA13261@mcfeely.concentric.net>
Content-Type: text/plain; charset="US-ASCII"

Hello,

I had this clicking problem (about 40 clicks before it stopped) when I 
inserted my Zip disk into the drive. I sent my drive back to iomega and 
they gave me new Zip Drive. I have not had any problems since then (about 
1.5 years, now). I was able to retrieve my Zip disk data using Norton 
Utilities. 

Good Luck,

Wilfred Denetclaw Jr., Ph.D.
Department Anatomy
UCSF

--------------------------------
End of nih-image-d Digest V98 Issue #33
***************************************

From nih-image-request@io.ece.drexel.edu Tue Aug 11 09:07 EDT 1998
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Date: Tue, 11 Aug 1998 14:54:04 +0200
To: nih-image@io.ece.drexel.edu
From: Stein Roervik <steinr@chembio.ntnu.no>
Subject: Cross-platform incremental CD recording
Resent-Message-ID: <"3wV7J.0.YV6.Rw3qr"@io>
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I am trying to figure out some flexible way to store images in a cross-
platform (Mac-PC) compatible way. All images will be created and saved in
NIH image on the Mac. I want to do this on writable CD-ROMs.

I have purchased a Sony Storewell CD writer. I have tested it and it works
well. The CD writer software, Adaptec Toast, can record in both Mac and
Windows/Jouliet format, and the cross-platform compatible ISO format.
The writer is also bundled with Adaptec DirectCD, which allows files to be
moved, renamed and deleted while the CD is "open" using the cross-platform
UDF format. This functionality is very important since I often need to
reorganize files as the scope of a project changes. UDF drivers are
available for Windows as well, so I have successfully been able to read
disks written in this format on a PC.

The problem is to get some way of automatically mapping file extensions to
file types. The files are of PICT, TIFF, Excel and Word types. I want some
way for the PC to read the Mac file type attributes and automatically add
the proper extensions. For various reasons, it is quite impractical to add
the extensions on the Mac side. I have purchased the utility program
DataWiz MacOpener for opening Mac disks on a PC. MacOpener mounts Mac disks
and adds extensions automatically as desired, but only on Mac formatted
disks. If I am going to take advantage of the incremental and changeable
UDF format, which is supported both by the Mac and the PC, MacOpener does
not add the extensions as the CD is recognized by the system as a valid PC
disk.

So what I need is either some utility on the PC that will recognize Mac
files as Mac files and add proper extensions, even when the disk is
readable by the PC; or some flexible (incremental) way to write CDs in a
hybrid format that automatically adds extensions to the filenames in the PC
directory part of the shared data. The latter solution is probably the best
since that would not require special drivers to be installed on the PC.

Any suggestions are welcome.

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+


From nih-image-request@io.ece.drexel.edu Tue Aug 11 12:57 EDT 1998
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From: "Paul Loftsgard" <ploftsgard@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Fractal analysis macros
Date: Tue, 11 Aug 1998 09:43:32 PDT
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Hello,

	I've been using the fractal analysis macros to analyze super critical 
sprays and I have two questions.
1. I currently use the method of subtracting the background(radius 50), 
thresholding, auto selecting, then applying the box method on the 
selections. The images still look similar to the originals, but I was 
wondering whether there is anything flawed with this technique.

2. If possible could somebody give me a good description of the EDM 
method. Is it anything like the area caliper method?

Any help would be appreciated.

   Thank you,
		Paul Loftsgard

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

From nih-image-request@io.ece.drexel.edu Tue Aug 11 14:43 EDT 1998
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Date: Tue, 11 Aug 1998 13:37:53 -0600
To: nih-image@io.ece.drexel.edu
From: "Randy M. Wadkins" <rwadkins@saci.org>
Subject: Re: Clicking Zip disks
Resent-Message-ID: <"NIm9r3.0.8S4.ut8qr"@io>
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>3) At this point, I think long and hard before buying any more Zip
>drives.  First because at 100 - 200 MB of images per experiment Zips get
>used up fast, and second because CD-R disks are cheaper and less prone
>to being killed by a defective drive.
>
>Chris Tully
>

We are in the process of copying our Zips onto CD-R, and then plan to throw
the drives in the trash.  Our failure rate has been 50% on the drives (over
a 3 year period), with the loss of about 20% of our storage media.  I
suppose we will try to go with MO drives from now on, but they are somewhat
bulkier than Zips.

--Randy
******************************************************************
"Fight House Resolution 3888, which legalizes spam!  Go to:
http://www.cauce.org/latest.html and contact the Commerce
Committee Rep. from your area.  Otherwise, say goodbye to e-mail."

Randy M. Wadkins, Ph.D.
Cancer Therapy & Research Center
Institute for Drug Development
14960 Omicron Drive
San Antonio, TX 78245
phone: (210)-677-3835
fax: (210)-677-0058
E-mail:  rwadkins@saci.org
CTRC Homepage: http://www.ccc.saci.org
******************************************************************

From nih-image-request@io.ece.drexel.edu Tue Aug 11 15:16 EDT 1998
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From: Dominique Berube <d306604@er.uqam.ca>
Subject: Re: Fractal analysis macros
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>
>2. If possible could somebody give me a good description of the EDM
>method. Is it anything like the area caliper method?
>
EDM method is similar to the dilation techniques except that is performs an
isotropic dilation of an outline. It results in a Minkowski dimension which
is mathamatically different from the Hausdorf dimension obtained with the
caliper method. Some found that the Minkoski dimension was sometimes
slightly higher than the Hausdorf one but I'm not so sure of that. I
personnaly prefer the EDM method. It's easier to implement and I find the
result to be much more consistent than with the box-counting method, partly
because I can generate more data points. Of course, box-counting remains
useful for image surfaces but less reliable for outlines.


From nih-image-request@io.ece.drexel.edu Tue Aug 11 16:51 EDT 1998
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From: "Randy M. Wadkins" <rwadkins@saci.org>
Subject: Re: Clicking Zip disks
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>------------------------------
>Date: Mon, 10 Aug 1998 10:37:29 -0600 (CST)
>From: "Geoffrey D. Guttmann" <guttmann@duke.usask.ca>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Clicking Zip disks
>Message-ID: <Pine.OSF.4.02.9808101021330.25751-100000@duke.usask.ca>
>Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>Hi folks
>	The same problem happened to me.  The drive was in warranty so
>Iomega replaced the Zip drive.  The cost to recover the data was US$425
>but they offered a 50% discount since the drive was under warranty.  Maybe
>somebody can set up a cheaper Zip disk recovery service.
>Cheers, geoff
>

BTW: there is now a company that specializes in recovering data from
clicked Zips.  They seem a little cheaper than Iomega.  See:
http://www.ontrack.com/hc/cod.asp

--Randy
******************************************************************
"Fight House Resolution 3888, which legalizes spam!  Go to:
http://www.cauce.org/latest.html and contact the Commerce
Committee Rep. from your area.  Otherwise, say goodbye to e-mail."

Randy M. Wadkins, Ph.D.
Cancer Therapy & Research Center
Institute for Drug Development
14960 Omicron Drive
San Antonio, TX 78245
phone: (210)-677-3835
fax: (210)-677-0058
E-mail:  rwadkins@saci.org
CTRC Homepage: http://www.ccc.saci.org
******************************************************************

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 34

Today's Topics:
  Cross-platform incremental CD record  [ Stein Roervik <steinr@chembio.ntnu. ]
  Fractal analysis macros               [ "Paul Loftsgard" <ploftsgard@hotmai ]
  Re: Clicking Zip disks                [ "Randy M. Wadkins" <rwadkins@saci.o ]
  Re: Fractal analysis macros           [ Dominique Berube <d306604@er.uqam.c ]
  Re: Clicking Zip disks                [ "Randy M. Wadkins" <rwadkins@saci.o ]

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

Date: Tue, 11 Aug 1998 14:54:04 +0200
From: Stein Roervik <steinr@chembio.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Cross-platform incremental CD recording
Message-Id: <v03102815b1f5ef4be578@[129.241.39.133]>
Content-Type: text/plain; charset="us-ascii"

I am trying to figure out some flexible way to store images in a cross-
platform (Mac-PC) compatible way. All images will be created and saved in
NIH image on the Mac. I want to do this on writable CD-ROMs.

I have purchased a Sony Storewell CD writer. I have tested it and it works
well. The CD writer software, Adaptec Toast, can record in both Mac and
Windows/Jouliet format, and the cross-platform compatible ISO format.
The writer is also bundled with Adaptec DirectCD, which allows files to be
moved, renamed and deleted while the CD is "open" using the cross-platform
UDF format. This functionality is very important since I often need to
reorganize files as the scope of a project changes. UDF drivers are
available for Windows as well, so I have successfully been able to read
disks written in this format on a PC.

The problem is to get some way of automatically mapping file extensions to
file types. The files are of PICT, TIFF, Excel and Word types. I want some
way for the PC to read the Mac file type attributes and automatically add
the proper extensions. For various reasons, it is quite impractical to add
the extensions on the Mac side. I have purchased the utility program
DataWiz MacOpener for opening Mac disks on a PC. MacOpener mounts Mac disks
and adds extensions automatically as desired, but only on Mac formatted
disks. If I am going to take advantage of the incremental and changeable
UDF format, which is supported both by the Mac and the PC, MacOpener does
not add the extensions as the CD is recognized by the system as a valid PC
disk.

So what I need is either some utility on the PC that will recognize Mac
files as Mac files and add proper extensions, even when the disk is
readable by the PC; or some flexible (incremental) way to write CDs in a
hybrid format that automatically adds extensions to the filenames in the PC
directory part of the shared data. The latter solution is probably the best
since that would not require special drivers to be installed on the PC.

Any suggestions are welcome.

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+

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

Date: Tue, 11 Aug 1998 09:43:32 PDT
From: "Paul Loftsgard" <ploftsgard@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: Fractal analysis macros
Message-ID: <19980811164333.27127.qmail@hotmail.com>
Content-Type: text/plain

Hello,

	I've been using the fractal analysis macros to analyze super critical 
sprays and I have two questions.
1. I currently use the method of subtracting the background(radius 50), 
thresholding, auto selecting, then applying the box method on the 
selections. The images still look similar to the originals, but I was 
wondering whether there is anything flawed with this technique.

2. If possible could somebody give me a good description of the EDM 
method. Is it anything like the area caliper method?

Any help would be appreciated.

   Thank you,
		Paul Loftsgard

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

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

Date: Tue, 11 Aug 1998 13:37:53 -0600
From: "Randy M. Wadkins" <rwadkins@saci.org>
To: nih-image@io.ece.drexel.edu
Subject: Re: Clicking Zip disks
Message-Id: <v04011701b1f622b51b5a@[192.238.18.184]>
Content-Type: text/plain; charset="us-ascii"

>3) At this point, I think long and hard before buying any more Zip
>drives.  First because at 100 - 200 MB of images per experiment Zips get
>used up fast, and second because CD-R disks are cheaper and less prone
>to being killed by a defective drive.
>
>Chris Tully
>

We are in the process of copying our Zips onto CD-R, and then plan to throw
the drives in the trash.  Our failure rate has been 50% on the drives (over
a 3 year period), with the loss of about 20% of our storage media.  I
suppose we will try to go with MO drives from now on, but they are somewhat
bulkier than Zips.

--Randy
******************************************************************
"Fight House Resolution 3888, which legalizes spam!  Go to:
http://www.cauce.org/latest.html and contact the Commerce
Committee Rep. from your area.  Otherwise, say goodbye to e-mail."

Randy M. Wadkins, Ph.D.
Cancer Therapy & Research Center
Institute for Drug Development
14960 Omicron Drive
San Antonio, TX 78245
phone: (210)-677-3835
fax: (210)-677-0058
E-mail:  rwadkins@saci.org
CTRC Homepage: http://www.ccc.saci.org
******************************************************************

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

Date: Tue, 11 Aug 1998 15:05:59 -0400
From: Dominique Berube <d306604@er.uqam.ca>
To: nih-image@io.ece.drexel.edu
Subject: Re: Fractal analysis macros
Message-Id: <l03130300b1f645208087@[132.208.139.22]>
Content-Type: text/plain; charset="us-ascii"

>
>2. If possible could somebody give me a good description of the EDM
>method. Is it anything like the area caliper method?
>
EDM method is similar to the dilation techniques except that is performs an
isotropic dilation of an outline. It results in a Minkowski dimension which
is mathamatically different from the Hausdorf dimension obtained with the
caliper method. Some found that the Minkoski dimension was sometimes
slightly higher than the Hausdorf one but I'm not so sure of that. I
personnaly prefer the EDM method. It's easier to implement and I find the
result to be much more consistent than with the box-counting method, partly
because I can generate more data points. Of course, box-counting remains
useful for image surfaces but less reliable for outlines.

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

Date: Tue, 11 Aug 1998 15:30:02 -0600
From: "Randy M. Wadkins" <rwadkins@saci.org>
To: nih-image@io.ece.drexel.edu
Subject: Re: Clicking Zip disks
Message-Id: <v04011703b1f667d52d66@[192.238.18.184]>
Content-Type: text/plain; charset="us-ascii"

>------------------------------
>Date: Mon, 10 Aug 1998 10:37:29 -0600 (CST)
>From: "Geoffrey D. Guttmann" <guttmann@duke.usask.ca>
>To: nih-image@io.ece.drexel.edu
>Subject: Re: Clicking Zip disks
>Message-ID: <Pine.OSF.4.02.9808101021330.25751-100000@duke.usask.ca>
>Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>Hi folks
>	The same problem happened to me.  The drive was in warranty so
>Iomega replaced the Zip drive.  The cost to recover the data was US$425
>but they offered a 50% discount since the drive was under warranty.  Maybe
>somebody can set up a cheaper Zip disk recovery service.
>Cheers, geoff
>

BTW: there is now a company that specializes in recovering data from
clicked Zips.  They seem a little cheaper than Iomega.  See:
http://www.ontrack.com/hc/cod.asp

--Randy
******************************************************************
"Fight House Resolution 3888, which legalizes spam!  Go to:
http://www.cauce.org/latest.html and contact the Commerce
Committee Rep. from your area.  Otherwise, say goodbye to e-mail."

Randy M. Wadkins, Ph.D.
Cancer Therapy & Research Center
Institute for Drug Development
14960 Omicron Drive
San Antonio, TX 78245
phone: (210)-677-3835
fax: (210)-677-0058
E-mail:  rwadkins@saci.org
CTRC Homepage: http://www.ccc.saci.org
******************************************************************

--------------------------------
End of nih-image-d Digest V98 Issue #34
***************************************

From nih-image-request@io.ece.drexel.edu Wed Aug 12 11:34 EDT 1998
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Date: Wed, 12 Aug 1998 11:15:39 -0400
To: nih-image@io.ece.drexel.edu
From: Otter <otterpop@pilot.msu.edu>
Subject: Help with counting agar clones...
Resent-Message-ID: <"veO__3.0.dG5.GBRqr"@io>
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Hi everyone,

I am a new NIH Image user (v1.61 MAC), so please forgive me if you have
heard this question a million times already!  I am trying to count agar
clones by size and I am unable to figure it out.  Here is what I would like
to do.  I would like to take about 16 representative shots of a culture
dish containing the clones and then paste those 16 shots together (I can do
this via Photoshop).  After opening that image up in NIH Image, I would
like to have NIH Image count how many clones are present of varying sizes
(in diameter, not pixels).  For example, I would like NIH Image to tell me
that out of x many clones, 5 are less than 50 microns, 15 are between 50
and 100 microns, 22 are between 175 and 200 microns, and so on.  Does
anyone have any advice or help on how I can do this?  Is there a Macro to
perform this sort of calculation?

Thanks for your time and help,

Evan L. Kaplan
Carcinogenesis Lab
Michigan State University


From nih-image-request@io.ece.drexel.edu Wed Aug 12 12:42 EDT 1998
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Date: Wed, 12 Aug 1998 12:33:19 -0400
To: nih-image@io.ece.drexel.edu
From: ad1054@worldpath.net (Dr. Christopher Coulon)
Subject: Re: Help with counting agar clones...
Resent-Message-ID: <"te6dk1.0.fU6.aESqr"@io>
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Evan,

It really depends on your image contrast.  If the contrast is good, an
autoThreshold should segment your cultures from the background.  Then an
analyzeParticles should do your counts (use rMajor[] to return the
diameter, or if ellipses are significant, use the average of rMinor[] and
rMajor[]).  If you need help on this, let me know with a message to me off
list.

Chris


>Hi everyone,
>
>I am a new NIH Image user (v1.61 MAC), so please forgive me if you have
>heard this question a million times already!  I am trying to count agar
>clones by size and I am unable to figure it out.  Here is what I would like
>to do.  I would like to take about 16 representative shots of a culture
>dish containing the clones and then paste those 16 shots together (I can do
>this via Photoshop).  After opening that image up in NIH Image, I would
>like to have NIH Image count how many clones are present of varying sizes
>(in diameter, not pixels).  For example, I would like NIH Image to tell me
>that out of x many clones, 5 are less than 50 microns, 15 are between 50
>and 100 microns, 22 are between 175 and 200 microns, and so on.  Does
>anyone have any advice or help on how I can do this?  Is there a Macro to
>perform this sort of calculation?
>
>Thanks for your time and help,
>
>Evan L. Kaplan
>Carcinogenesis Lab
>Michigan State University

* * * * * * * * * * * * * * * * * *
* Dr. Christopher Hunt Coulon     *
* The GAIA Group                  *
* 40 Chick Road                   *
* Wolfeboro, New Hampshire 03894  *
* 603 569-0028                    *
* * * * * * * * * * * * * * * * * *


From nih-image-d-request@io.ece.drexel.edu Thu Aug 13 06:19 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #35
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 35

Today's Topics:
  Help with counting agar clones...     [ Otter <otterpop@pilot.msu.edu> ]
  Re: Help with counting agar clones..  [ ad1054@worldpath.net (Dr. Christoph ]

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

Date: Wed, 12 Aug 1998 11:15:39 -0400
From: Otter <otterpop@pilot.msu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Help with counting agar clones...
Message-Id: <v04003a01b1f75eb74798@[35.8.60.185]>
Content-Type: text/plain; charset="us-ascii"

Hi everyone,

I am a new NIH Image user (v1.61 MAC), so please forgive me if you have
heard this question a million times already!  I am trying to count agar
clones by size and I am unable to figure it out.  Here is what I would like
to do.  I would like to take about 16 representative shots of a culture
dish containing the clones and then paste those 16 shots together (I can do
this via Photoshop).  After opening that image up in NIH Image, I would
like to have NIH Image count how many clones are present of varying sizes
(in diameter, not pixels).  For example, I would like NIH Image to tell me
that out of x many clones, 5 are less than 50 microns, 15 are between 50
and 100 microns, 22 are between 175 and 200 microns, and so on.  Does
anyone have any advice or help on how I can do this?  Is there a Macro to
perform this sort of calculation?

Thanks for your time and help,

Evan L. Kaplan
Carcinogenesis Lab
Michigan State University

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

Date: Wed, 12 Aug 1998 12:33:19 -0400
From: ad1054@worldpath.net (Dr. Christopher Coulon)
To: nih-image@io.ece.drexel.edu
Subject: Re: Help with counting agar clones...
Message-Id: <v01520d04b1f774325ef3@[206.152.181.138]>
Content-Type: text/plain; charset="us-ascii"

Evan,

It really depends on your image contrast.  If the contrast is good, an
autoThreshold should segment your cultures from the background.  Then an
analyzeParticles should do your counts (use rMajor[] to return the
diameter, or if ellipses are significant, use the average of rMinor[] and
rMajor[]).  If you need help on this, let me know with a message to me off
list.

Chris


>Hi everyone,
>
>I am a new NIH Image user (v1.61 MAC), so please forgive me if you have
>heard this question a million times already!  I am trying to count agar
>clones by size and I am unable to figure it out.  Here is what I would like
>to do.  I would like to take about 16 representative shots of a culture
>dish containing the clones and then paste those 16 shots together (I can do
>this via Photoshop).  After opening that image up in NIH Image, I would
>like to have NIH Image count how many clones are present of varying sizes
>(in diameter, not pixels).  For example, I would like NIH Image to tell me
>that out of x many clones, 5 are less than 50 microns, 15 are between 50
>and 100 microns, 22 are between 175 and 200 microns, and so on.  Does
>anyone have any advice or help on how I can do this?  Is there a Macro to
>perform this sort of calculation?
>
>Thanks for your time and help,
>
>Evan L. Kaplan
>Carcinogenesis Lab
>Michigan State University

* * * * * * * * * * * * * * * * * *
* Dr. Christopher Hunt Coulon     *
* The GAIA Group                  *
* 40 Chick Road                   *
* Wolfeboro, New Hampshire 03894  *
* 603 569-0028                    *
* * * * * * * * * * * * * * * * * *

--------------------------------
End of nih-image-d Digest V98 Issue #35
***************************************

From nih-image-request@io.ece.drexel.edu Thu Aug 13 08:05 EDT 1998
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Date: Thu, 13 Aug 1998 07:39:37 -0500
To: nih-image@io.ece.drexel.edu
From: Laird Bloom <lbloom@MIT.EDU>
Subject: Re:counting agar clones/measuring areas
Resent-Message-ID: <"ZShRT.0.nH.V1jqr"@io>
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Hi Evan,
	This may not be quite what you want, but I've written a set of
macros that make it easy to outline a set of regions on your image or
series of images and save the areas in a data file.  You can either do it
on saved images or directly at the microscope, which I've found to be
easier.  It's still relatively time-consuming, since you have to outline
individual areas, but at least you know what you're measuring.  You can set
the scale in Image to give you area in square mm, etc., instead of pixels,
but at some point you have to figure out a conversion factor based on your
microscope's magnification.  The data files are easy to import into
Microsoft Excel, which has a nice histogram-making function if you want to
divide your population of colonies into size ranges.
	Please let me know if you want the code.
Yours,
Laird Bloom
MIT Center for Cancer Research

>Hi everyone,
>
>I am a new NIH Image user (v1.61 MAC), so please forgive me if you have
>heard this question a million times already!  I am trying to count agar
>clones by size and I am unable to figure it out.  Here is what I would like
>to do.  I would like to take about 16 representative shots of a culture
>dish containing the clones and then paste those 16 shots together (I can do
>this via Photoshop).  After opening that image up in NIH Image, I would
>like to have NIH Image count how many clones are present of varying sizes
>(in diameter, not pixels).  For example, I would like NIH Image to tell me
>that out of x many clones, 5 are less than 50 microns, 15 are between 50
>and 100 microns, 22 are between 175 and 200 microns, and so on.  Does
>anyone have any advice or help on how I can do this?  Is there a Macro to
>perform this sort of calculation?
>
>Thanks for your time and help,
>
>Evan L. Kaplan
>Carcinogenesis Lab
>Michigan State University



From nih-image-request@io.ece.drexel.edu Thu Aug 13 16:58 EDT 1998
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	Thu, 13 Aug 1998 16:57:19 -0400 (EDT)
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Message-ID: <35D35085.D5046081@usa.net>
Date: Thu, 13 Aug 1998 14:45:58 -0600
From: "Christopher P. Tully" <cptully@usa.net>
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References: <v04003a01b1f75eb74798@[35.8.60.185]>
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Evan-

a simple outline to get the data you describe:

1) Collect and composite the images (compositing may be unnecessary,
since totals from several images can be added together after analysis,
thus saving the time to composite the images).
2) Open the image(s) in NIH-Image
3) Make sure the scale is set properly in Analyze > Set Scale...
4) Choose Anaylze > Options, and make sure that the appropriate
measurements are selected (either use area, or ellipse major axis and
ellpise minor axis)
5) Threshold the image (either manually, or using the auto threshold
feature).
6) Use the Anaylze Particles feature to measure the thersholded objects
7) copy the results from the results table and past them into Excel
8) If you are using single images instead of a composite, repeat 2-7 for
all images
9) in Excel, use the Histogram funbction under Analysis tools to
generate a histogram of your size data.  The histogram tool allows you
to specify the number of bins and the range of each bin, etc.

Chris Tully

Otter wrote:
> 
> Hi everyone,
> 
> I am a new NIH Image user (v1.61 MAC), so please forgive me if you have
> heard this question a million times already!  I am trying to count agar
> clones by size and I am unable to figure it out.  Here is what I would like
> to do.  I would like to take about 16 representative shots of a culture
> dish containing the clones and then paste those 16 shots together (I can do
> this via Photoshop).  After opening that image up in NIH Image, I would
> like to have NIH Image count how many clones are present of varying sizes
> (in diameter, not pixels).  For example, I would like NIH Image to tell me
> that out of x many clones, 5 are less than 50 microns, 15 are between 50
> and 100 microns, 22 are between 175 and 200 microns, and so on.  Does
> anyone have any advice or help on how I can do this?  Is there a Macro to
> perform this sort of calculation?
> 
> Thanks for your time and help,
> 
> Evan L. Kaplan
> Carcinogenesis Lab
> Michigan State University

From nih-image-request@io.ece.drexel.edu Fri Aug 14 02:21 EDT 1998
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	Fri, 14 Aug 1998 02:21:22 -0400 (EDT)
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Message-ID: <35D3D443.AD84F5F2@caspur.it>
Date: Fri, 14 Aug 1998 08:08:04 +0200
From: Leopoldo Silvestroni <l.silvestroni@caspur.it>
Organization: Universit di Roma 'La Sapienza'
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Hi everyone,

I would greatly appreciate receiving your help as for:

- a photoshop compatible FFT plugin
- how to "apply" a fast Fourier transform to a square selection

thank You all in advance

Leopoldo Silvestroni, MD


--
Leopoldo Silvestroni,MD
Laboratorio di Biofluorimetria
Dipartimento di Fisiopatologia Medica
Policlinico Umberto I
Universit di Roma 'La Sapienza'
00161-Roma
tel. +39 6 49970710
fax  +39 6 4461450
e-mail: l.silvestroni@caspur.it
WWW address: http://w3.uniroma1.it/MEDICFISIO/labpag1.html


From nih-image-d-request@io.ece.drexel.edu Fri Aug 14 02:24 EDT 1998
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 36

Today's Topics:
  Re:counting agar clones/measuring ar  [ Laird Bloom <lbloom@MIT.EDU> ]
  Re: Help with counting agar clones..  [ "Christopher P. Tully" <cptully@usa ]
  FFT question                          [ Leopoldo Silvestroni <l.silvestroni ]

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

Date: Thu, 13 Aug 1998 07:39:37 -0500
From: Laird Bloom <lbloom@MIT.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Re:counting agar clones/measuring areas
Message-Id: <v03020903b1f88d1871e4@[18.155.0.104]>
Content-Type: text/plain; charset="us-ascii"

Hi Evan,
	This may not be quite what you want, but I've written a set of
macros that make it easy to outline a set of regions on your image or
series of images and save the areas in a data file.  You can either do it
on saved images or directly at the microscope, which I've found to be
easier.  It's still relatively time-consuming, since you have to outline
individual areas, but at least you know what you're measuring.  You can set
the scale in Image to give you area in square mm, etc., instead of pixels,
but at some point you have to figure out a conversion factor based on your
microscope's magnification.  The data files are easy to import into
Microsoft Excel, which has a nice histogram-making function if you want to
divide your population of colonies into size ranges.
	Please let me know if you want the code.
Yours,
Laird Bloom
MIT Center for Cancer Research

>Hi everyone,
>
>I am a new NIH Image user (v1.61 MAC), so please forgive me if you have
>heard this question a million times already!  I am trying to count agar
>clones by size and I am unable to figure it out.  Here is what I would like
>to do.  I would like to take about 16 representative shots of a culture
>dish containing the clones and then paste those 16 shots together (I can do
>this via Photoshop).  After opening that image up in NIH Image, I would
>like to have NIH Image count how many clones are present of varying sizes
>(in diameter, not pixels).  For example, I would like NIH Image to tell me
>that out of x many clones, 5 are less than 50 microns, 15 are between 50
>and 100 microns, 22 are between 175 and 200 microns, and so on.  Does
>anyone have any advice or help on how I can do this?  Is there a Macro to
>perform this sort of calculation?
>
>Thanks for your time and help,
>
>Evan L. Kaplan
>Carcinogenesis Lab
>Michigan State University

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

Date: Thu, 13 Aug 1998 14:45:58 -0600
From: "Christopher P. Tully" <cptully@usa.net>
To: nih-image@io.ece.drexel.edu
Subject: Re: Help with counting agar clones...
Message-ID: <35D35085.D5046081@usa.net>
Content-Type: text/plain; charset=us-ascii
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Evan-

a simple outline to get the data you describe:

1) Collect and composite the images (compositing may be unnecessary,
since totals from several images can be added together after analysis,
thus saving the time to composite the images).
2) Open the image(s) in NIH-Image
3) Make sure the scale is set properly in Analyze > Set Scale...
4) Choose Anaylze > Options, and make sure that the appropriate
measurements are selected (either use area, or ellipse major axis and
ellpise minor axis)
5) Threshold the image (either manually, or using the auto threshold
feature).
6) Use the Anaylze Particles feature to measure the thersholded objects
7) copy the results from the results table and past them into Excel
8) If you are using single images instead of a composite, repeat 2-7 for
all images
9) in Excel, use the Histogram funbction under Analysis tools to
generate a histogram of your size data.  The histogram tool allows you
to specify the number of bins and the range of each bin, etc.

Chris Tully

Otter wrote:
> 
> Hi everyone,
> 
> I am a new NIH Image user (v1.61 MAC), so please forgive me if you have
> heard this question a million times already!  I am trying to count agar
> clones by size and I am unable to figure it out.  Here is what I would like
> to do.  I would like to take about 16 representative shots of a culture
> dish containing the clones and then paste those 16 shots together (I can do
> this via Photoshop).  After opening that image up in NIH Image, I would
> like to have NIH Image count how many clones are present of varying sizes
> (in diameter, not pixels).  For example, I would like NIH Image to tell me
> that out of x many clones, 5 are less than 50 microns, 15 are between 50
> and 100 microns, 22 are between 175 and 200 microns, and so on.  Does
> anyone have any advice or help on how I can do this?  Is there a Macro to
> perform this sort of calculation?
> 
> Thanks for your time and help,
> 
> Evan L. Kaplan
> Carcinogenesis Lab
> Michigan State University

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

Date: Fri, 14 Aug 1998 08:08:04 +0200
From: Leopoldo Silvestroni <l.silvestroni@caspur.it>
To: nih-image@io.ece.drexel.edu
Subject: FFT question
Message-ID: <35D3D443.AD84F5F2@caspur.it>
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

Hi everyone,

I would greatly appreciate receiving your help as for:

- a photoshop compatible FFT plugin
- how to "apply" a fast Fourier transform to a square selection

thank You all in advance

Leopoldo Silvestroni, MD


--
Leopoldo Silvestroni,MD
Laboratorio di Biofluorimetria
Dipartimento di Fisiopatologia Medica
Policlinico Umberto I
Universit di Roma 'La Sapienza'
00161-Roma
tel. +39 6 49970710
fax  +39 6 4461450
e-mail: l.silvestroni@caspur.it
WWW address: http://w3.uniroma1.it/MEDICFISIO/labpag1.html

--------------------------------
End of nih-image-d Digest V98 Issue #36
***************************************

From nih-image-request@io.ece.drexel.edu Fri Aug 14 04:49 EDT 1998
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From: tony.collins@bbsrc.ac.uk
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Date: Fri, 14 Aug 1998 09:40:51 +0100
Subject: NIH macro conversion to Scion Image
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I'm not sure if this is the right forum to be asking this question if it's 
not I apologise in advance, I've only just joined the list.
As I understand it, Scion's Image program *should* be able to use 
NIH Image macro (correct?). I find that it can't, the macro's are 
loaded correctly but they don't run correctly. Are there any rules to 
converting the macros from NIH to Scion's Image? Or is the macro 
interpreter a bit buggy in Scion's Beta software?
Many thanks

Tony Collins

Dept. Neurobiology
The Babraham Institute 
Babraham Hall 
Babraham 
Cambridge CB2 4AT 
UK

tel. +44 (0) 1223  832312
fax. +44 (0) 1223  836614

From nih-image-request@io.ece.drexel.edu Fri Aug 14 07:05 EDT 1998
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From: DrJohnRuss@aol.com
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Date: Fri, 14 Aug 1998 06:54:26 EDT
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In a message dated 8/14/98 6:18:18 AM, Leopoldo Silvestroni, MD wrote:

>I would greatly appreciate receiving your help as for:
>- a photoshop compatible FFT plugin
>- how to "apply" a fast Fourier transform to a square selection
>thank You all in advance
>
The Image Processing Tool Kit (http://members.aol.com/ImagProcTK/) includes
complete FFT routines as well as a comprehensive tutorial showing their use
with a variety of images. If the region to be transformed is square and a
power of two in size, the transform can be applied directly. If not, it should
be padded to a larger size by pasting it into a medium grey blank image.

John Russ

From nih-image-request@io.ece.drexel.edu Fri Aug 14 18:12 EDT 1998
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Tony-

Scion may also respond to your questions, nut since they haven't yet:

I believe that they did the port based on NIH-Image v1.57 source, so
there are a few macro commands which were added after 1.57 that they
have not yet implemented.  Also, from what they have told me when I
asked, the macro interpreter was the last item that they worked on, so
it may still be incomplete.  I would look for a change history to find
out exactly which version of Image their port is based on, and what
parts have been implemented or still need to be implemented.

All of my comments above are based on the assumption that you are asking
about Scion Image for Win95/NT.  If not, ignore them.

Chris Tully

tony.collins@bbsrc.ac.uk wrote:
> 
> I'm not sure if this is the right forum to be asking this question if it's
> not I apologise in advance, I've only just joined the list.
> As I understand it, Scion's Image program *should* be able to use
> NIH Image macro (correct?). I find that it can't, the macro's are
> loaded correctly but they don't run correctly. Are there any rules to
> converting the macros from NIH to Scion's Image? Or is the macro
> interpreter a bit buggy in Scion's Beta software?
> Many thanks
> 
> Tony Collins
> 
> Dept. Neurobiology
> The Babraham Institute
> Babraham Hall
> Babraham
> Cambridge CB2 4AT
> UK
> 
> tel. +44 (0) 1223  832312
> fax. +44 (0) 1223  836614

From nih-image-request@io.ece.drexel.edu Fri Aug 14 19:03 EDT 1998
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Date: 	Fri, 14 Aug 1998 12:54:19 -1000
From: Kathleen Annikki Moore <moorekat@hawaii.edu>
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To: nih-image@io.ece.drexel.edu
Subject: solution for acquistion with Mac G3 powerbook?
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I'm beginning. Any helpful acquisition suggestions would be welcome.
Will NIH image + plug-in digitizer(operating on a Mac G3 powerbook which
is on order) software capture bone microscopy images with adequate image
quality from a hitachi KPC-500 video attached to brightfield or
fluorescent microscope.
Is a single freeze frame adequate data for an image analysis? or is
averaging "X" amount of frames necessary. Very grateful for responses.
Kathleen Moore

From nih-image-d-request@io.ece.drexel.edu Sat Aug 15 06:15 EDT 1998
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 37

Today's Topics:
  NIH macro conversion to Scion Image   [ tony.collins@bbsrc.ac.uk ]
  Re: FFT question                      [ DrJohnRuss@aol.com ]
  Re: NIH macro conversion to Scion Im  [ "Christopher P. Tully" <cptully@usa ]
  solution for acquistion with Mac G3   [ Kathleen Annikki Moore <moorekat@ha ]

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

Date: Fri, 14 Aug 1998 09:40:51 +0100
From: tony.collins@bbsrc.ac.uk
To: nih-image@io.ece.drexel.edu
Subject: NIH macro conversion to Scion Image
Message-Id: <9808140838.AA03332@mserv.iapc.bbsrc.ac.uk>
Content-Type: text/plain; charset="US-ASCII"

I'm not sure if this is the right forum to be asking this question if it's 
not I apologise in advance, I've only just joined the list.
As I understand it, Scion's Image program *should* be able to use 
NIH Image macro (correct?). I find that it can't, the macro's are 
loaded correctly but they don't run correctly. Are there any rules to 
converting the macros from NIH to Scion's Image? Or is the macro 
interpreter a bit buggy in Scion's Beta software?
Many thanks

Tony Collins

Dept. Neurobiology
The Babraham Institute 
Babraham Hall 
Babraham 
Cambridge CB2 4AT 
UK

tel. +44 (0) 1223  832312
fax. +44 (0) 1223  836614

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

Date: Fri, 14 Aug 1998 06:54:26 EDT
From: DrJohnRuss@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re:  FFT question
Message-ID: <1acbe6e7.35d41763@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

In a message dated 8/14/98 6:18:18 AM, Leopoldo Silvestroni, MD wrote:

>I would greatly appreciate receiving your help as for:
>- a photoshop compatible FFT plugin
>- how to "apply" a fast Fourier transform to a square selection
>thank You all in advance
>
The Image Processing Tool Kit (http://members.aol.com/ImagProcTK/) includes
complete FFT routines as well as a comprehensive tutorial showing their use
with a variety of images. If the region to be transformed is square and a
power of two in size, the transform can be applied directly. If not, it should
be padded to a larger size by pasting it into a medium grey blank image.

John Russ

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

Date: Fri, 14 Aug 1998 16:04:07 -0600
From: "Christopher P. Tully" <cptully@usa.net>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH macro conversion to Scion Image
Message-ID: <35D4B456.663E294A@usa.net>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Tony-

Scion may also respond to your questions, nut since they haven't yet:

I believe that they did the port based on NIH-Image v1.57 source, so
there are a few macro commands which were added after 1.57 that they
have not yet implemented.  Also, from what they have told me when I
asked, the macro interpreter was the last item that they worked on, so
it may still be incomplete.  I would look for a change history to find
out exactly which version of Image their port is based on, and what
parts have been implemented or still need to be implemented.

All of my comments above are based on the assumption that you are asking
about Scion Image for Win95/NT.  If not, ignore them.

Chris Tully

tony.collins@bbsrc.ac.uk wrote:
> 
> I'm not sure if this is the right forum to be asking this question if it's
> not I apologise in advance, I've only just joined the list.
> As I understand it, Scion's Image program *should* be able to use
> NIH Image macro (correct?). I find that it can't, the macro's are
> loaded correctly but they don't run correctly. Are there any rules to
> converting the macros from NIH to Scion's Image? Or is the macro
> interpreter a bit buggy in Scion's Beta software?
> Many thanks
> 
> Tony Collins
> 
> Dept. Neurobiology
> The Babraham Institute
> Babraham Hall
> Babraham
> Cambridge CB2 4AT
> UK
> 
> tel. +44 (0) 1223  832312
> fax. +44 (0) 1223  836614

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

Date: 	Fri, 14 Aug 1998 12:54:19 -1000
From: Kathleen Annikki Moore <moorekat@hawaii.edu>
To: nih-image@io.ece.drexel.edu
Subject: solution for acquistion with Mac G3 powerbook?
Message-ID: <Pine.GSO.3.95q.980814121231.15345A-100000@uhunix5>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I'm beginning. Any helpful acquisition suggestions would be welcome.
Will NIH image + plug-in digitizer(operating on a Mac G3 powerbook which
is on order) software capture bone microscopy images with adequate image
quality from a hitachi KPC-500 video attached to brightfield or
fluorescent microscope.
Is a single freeze frame adequate data for an image analysis? or is
averaging "X" amount of frames necessary. Very grateful for responses.
Kathleen Moore

--------------------------------
End of nih-image-d Digest V98 Issue #37
***************************************

From nih-image-request@io.ece.drexel.edu Mon Aug 17 08:16 EDT 1998
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From: Laird Bloom <lbloom@MIT.EDU>
Subject: code for area measurement macros
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I've had several requests for the code for macros to record area
measurement data from regions you outline with a mouse.  Here is the
code for two versions, one for use with saved images, and one that
works well for live images.  Please contact me if you have questions.

Laird Bloom

MIT Center for Cancer Research


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


<bold> Area measurement macros</bold>


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


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


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


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


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

<bold>


"Measure areas on scope" macro

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

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


{"Measure areas on scope" macro file follows:

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

}


var {Global variables}

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

	mean:real;

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



procedure GetImageToMeasure;

begin

StartCapturing;

	Repeat

		Wait(.1);

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

StopCapturing;


SetPicName(nSample,'  Image');

SelectWindow(nSample,'  Image');

         if nSave='Yes'

              then Save;

end



procedure LabelAreaInCenter;


var

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

  scale: real;

  unit: string;

begin

  GetRoi(left,top,width,height);

  if width=0 then begin

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

    exit;

  end;

  SaveState;

  InvertY(false);

  SetForegroundColor(255); {black}

SetBackgroundColor(1);

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

  GetScale(scale, unit);

  Measure;

	DrawBoundary;

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

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

  MoveTo(x-5, y);

	SetFont('Times');

	SetFontSize(9);

SetText('With Background');

	Writeln('region ',j:0);

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

  RestoreState;

end;



macro 'Measure Area [M]';

begin

	j:=j+1;

	LabelAreaInCenter;

	ImageName:=WindowTitle;

	SelectWindow(nSample);

        

	If j=1

		then writeln (nSample); 

		SetFont('Times');

		SetFontSize(12);

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

 		rUser1[j]:=rArea[rCount];

		total:=total+rArea[rCount];

      Save;

	SelectWindow(ImageName);

end


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

var

	width,height:integer;

begin

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

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

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

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

	NewTextWindow(nSample,80,600);

				MoveWindow(740,40);

	total:=0;

GetImageToMeasure;

	j:=0;

end;


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

begin

SelectWindow(ImageName);

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

 DisposeAll;

GetImageToMeasure;

end;

 

macro 'New Sample [S]';


begin

	If j=0

			 then j:=1;

SelectWindow(ImageName);

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

 		Dispose;

SelectWindow(nSample);

mean:=total/j;

writeln('Mean =');

write(mean);

save;

		dispose;

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

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


	NewTextWindow(nSample,80,600);

				MoveWindow(740,40);

	total:=0;

GetImageToMeasure;

	j:=0;

end;

   

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


{

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

}


var {Global variable, initially zero}

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

	mean:real;

	nOut,SampleName,ImageName:string;



procedure LabelAreaInCenter;


var

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

  scale: real;

  unit: string;

begin

  GetRoi(left,top,width,height);

  if width=0 then begin

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

    exit;

  end;

  SaveState;

  InvertY(false);

  SetForegroundColor(255); {black}

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

  GetScale(scale, unit);

  Measure;

	DrawBoundary;

{Fill;

Invert;

  KillRoi;}

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

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

  MoveTo(x-5, y);

	SetFont('Times');

	SetFontSize(9);

SetText('WithBackground');

	Writeln('region ',j:0);

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

  RestoreState;

end;


procedure EndProcedure;

begin

DisposeAll;

		mean:=total/j;

		SelectWindow(nOut);

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

		Save;

		{nLines:=nLines+10;

		Open(nOut);

		MoveWindow(120,nLines);}

		Open(' ');

		total:=0;

		j:=0;

	end;



macro 'Measure Area [M]';

begin

			j:=j+1;

		LabelAreaInCenter;

					ImageName:=WindowTitle;

      		SelectWindow(nOut);

Moveto(120,560);

	If j=1

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

		SetFont('Times');

		SetFontSize(12);

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

	rUser1[j]:=rArea[rCount];

	total:=total+rArea[rCount];

      Save;

	SelectWindow(ImageName);

end




macro 'Set Up Area Measurements [S]';

var

	width,height:integer;

begin

ImageName:=WindowTitle;

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

		NewTextWindow(nOut);

		MoveWindow(120,550);

	total:=0;

	j:=0;

SelectWindow(ImageName);

SelectAll;

Measure;

  TotalArea:=rArea[rCount];

KillRoi;

end;


macro 'Finish Area Measurement [F]';

var

	nSave:string;

begin

	If j=0

	then j:=1;

	SaveAs(ImageName,' + area measurements');

EndProcedure;

		end;


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


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To: nih-image@io.ece.drexel.edu
From: Laird Bloom <lbloom@MIT.EDU>
Subject: Macro for counting cells, saving data
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<fontfamily><param>Times</param><bigger><bigger>To NIH Image users:

This macro is modified from the cell counting macro available on the
NIH Image web site.  It's designed to save data to a text file while
collecting multiple data points per sample at the microscope.  

  It works well for cells labeled with DAPI, propidium iodide, or
octadecyl rhodamine--brightly fluorescent cells on a dark
background--but is probably OK for non-fluorescent stains as well. 
DAPI is particularly nice because it stains only nuclei, and is
therefore doesn't change much when cells spread out.  Cytoplasmic or
membrane stains (e.g. octadecyl rhodamine or FITC variants) are dimmer
on spread cells than on rounded cells, and this macro sometimes has
trouble seeing dimmer spread cells labeled this way.  The macro is
written to use only the red, green, or blue channel (gets rid of
background prior to threshholding), but that could be modified.  Code
is written for Scion Image 1.62.  Points at which there are
Scion-specific commands are noted.

Please contact me if you have questions.


Laird Bloom

MIT Center for Cancer Research


var {Global variable, initially zero}

  nAvg,Threshold:integer; {range: 10-150}



procedure DoGammaTransform(gamma:real);

var

  i,v:integer;

  n,mode,min,max:integer

  mean:real;

begin

  measure;

  GetResults(n,mean,mode,min,max);

  ShowMessage('min=',min:1,'\max=',max:1);

  for i:=1 to 254 DO begin

    if (i>min) and (i<<max)

      then v:=exp(gamma*ln((i-min)/(max-min)))*255 {x^y=exp(y*ln(x)}

      else begin

        if i<<=min then v:=0 else v:=255;

      end;

    RedLUT[i]:=255-v;

    GreenLUT[i]:=255-v;

    BlueLUT[i]:=255-v;

  end;

  UpdateLUT;

end.



procedure CountCells(MoreSensative:boolean);

var

  gamma: real;

  radius: real; {peak radius; range: 1-50}

  slope: real;  {peak slope (aka peakedness); range: 0.05-0.95}

  BallRadius: real; {2d rolling ball radius}

  i,width,height: integer;

begin

  SetforegroundColor(0);

  SetbackgroundColor(255);

  radius:=6;

  slope:=0.2;

  gamma:=1.6;

  BallRadius:=8;

  {radius:=GetNumber('Radius[1-50]:',radius);}

  {slope:=GetNumber('Slope[0.05-0.95]:',slope);}

  Invert;

  SubtractBackground('2D Rolling Ball(faster)',BallRadius);

  GetPicSize(width,height);

  MakeRoi(0.05*width,0.05*height,0.9*width,0.9*height);

  {EnhanceContrast;}

  KillRoi;

  ApplyLUT;

  DoGammaTransform(gamma);

  ApplyLUT;

  SetOption; Smooth;

  SetOption; Smooth;

  if threshold=0 then begin

    AutoThreshold;

    wait(2);

    i:=0;

    Repeat

      i:=i+1;

    until RedLUT[i]<<255;

    if MoreSensative

      then Threshold:=round(0.75*i)

      else Threshold:=i

  end;

  SetThreshold(-1);

  SetLineWidth(2);

  UserCode('Find Peaks', threshold, radius, slope);

end;



macro 'Count cells and save /1';

var

 color,nLines,d,nDefault,nImage,j: integer;

 total,mean: real

nOut,nSave,nNext,nWell: string;

  begin

   PutMessage('Clicking on cancel at any time will end the macro.',);


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

	  color:=GetNumber ('Color:  Red=1, Green=2,  Blue=3',3,0);

nSave:=GetString('Save each full-size image as a 1.2 Mb file?','Yes');

nDefault:=GetNumber('Default number of images per sample:',5,0);

	PutMessage('To count cells from live video, click mouse button.'); 

	NewTextWindow(nOut);

 Writeln(nOut,' ');

	Writeln('Sample    			Cell counts								T=total	M=mean);

 Writeln;

 nLines:=0;

  repeat

         

     nWell:=GetString('Sample:'); 


        nImage:=GetNumber('Number of images for this
sample:',nDefault,0);

        SelectWindow(nOut);

        Write('Sample ',nWell,':		');

	       SetUser1Label('Cell counts');

        total:=0

	    for j:=1 to nImage do begin

{use next bracketed statement instead of the
StartCapturing...StopCapturing lines if get your video image via the
File>Acquire menu.  StartCapturing and StopCapturing may be Scion Image
1.62-specific macro commands. }

{Acquire('Plug-In Digitizer');}

         StartCapturing;

	Repeat

	Wait(.1);

	Until Button;

StopCapturing;



SetPicName(nWell,'.',j:2);

         if nSave='Yes'

              then SaveAs('');

{Using just the main color of your chromophore seems to make the image
cleaner.  The Bit24toRGBColor command may be specific to Scion Image
1.62.}

Bit24toRGBColor;

SelectSlice(color);

 Threshold:=0;

  CountCells(false);


         dispose;

         SelectWindow(nOut);

         d:=520-nLines;

	        MoveWindow(20,d);

         Write(rCount,'	');

 rUser1[j]:=rCount;

total:=total+rCount

        end;

         mean:=total/j;


	        

SelectWindow(nOut)

         Writeln('  T = ',total:2,'	  M ='mean:2,'	');

Save;

    

       nLines:=nLines+10;

       nNext:=GetString('Score another sample? (type no to
end)','yes');

until not (nNext='yes');


     SelectWindow(nOut);

Save;

      end;

end;


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


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Date: Mon, 17 Aug 1998 11:05:52 -0400
From: "Dibble, Nicole A" <DibbleNA@corning.com>
Subject: LG-3 NuBus
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
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I currently have a LG-3 NuBus framegrabber for Macintosh for sale.  Anyone
interested???  Make me an offer.

Nicole

From nih-image-request@io.ece.drexel.edu Mon Aug 17 11:51 EDT 1998
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---------------------------------------------------------
Yousef S. Iskander
Oak Ridge National Laboratory
Metals and Ceramics Division
P.O. Box 2008, Bldg. 5500, MS 6376
Oak Ridge, TN  37831-6376
Phone:  (423) 574-5096, (423) 576-7340 
e-mail:  iskanderys@ornl.gov

From nih-image-request@io.ece.drexel.edu Mon Aug 17 18:02 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: Re: unsubscribe
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<fontfamily><param>Times</param>An administrative reminder. To
unsubscribe to the list, send E-mail to
nih-image-request@biomed.drexel.edu.

the Subject of the message should contain "unsubscribe".


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

		Subject: unsubscribe


do not send it to the mail list itself.


Thanks.</fontfamily>

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

                                  Jonathan Nissanov, Ph.D.

                                      Associate Director  

            Computer Vision Center for Vertebrate Brain Mapping,

                a NIH Biomedical Research Technology Resource

                                http://cbis.ece.drexel.edu/ICVC/

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

Imaging and Computer Vision Center              Tel: 215-895-1381

Drexel University                                                  
Fax: 215-895-4987

Phildelphia, PA 19104                                        
yoni@coe.drexel.edu

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

      

     

From nih-image-request@io.ece.drexel.edu Mon Aug 17 21:44 EDT 1998
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From: hmthomas@med.cornell.edu (Henry M. Thomas)
Subject: Capture max intensity during TIFF import
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As I Import a stack of TIFF images (output from a PC program), the
Information Window shows the max intensity of each slice (briefly).  Is
there a way to capture these values (and thus get the largest max value)
with the Image macro language?

If so, I can Import the stack again with a fixed scale, using the captured
largest max value from the stack.  [At present, I obtain the value from the
PC program and type it into the Import subdialogue box "Set".]

Henry M. Thomas, III MD (Harry)
Professor of Clinical Medicine,  Pulmonary and Critical Care Division
Department of Medicine, Cornell Univ. Medical School
Director, Pulmonary Research, Burke Rehabilitation Hospital
785 Mamaroneck Ave.  White Plains, NY 10605
(914) 597-2141


From nih-image-d-request@io.ece.drexel.edu Tue Aug 18 06:26 EDT 1998
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Subject: nih-image-d Digest V98 #38
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 38

Today's Topics:
  code for area measurement macros      [ Laird Bloom <lbloom@MIT.EDU> ]
  Macro for counting cells, saving dat  [ Laird Bloom <lbloom@MIT.EDU> ]
  LG-3 NuBus                            [ "Dibble, Nicole A" <DibbleNA@cornin ]
  unsubscribe                           [ iskanderys@ornl.gov (Yousef S. Iska ]
  Re: unsubscribe                       [ Jonathan Nissanov <yoni@cbis.ece.dr ]
  Capture max intensity during TIFF im  [ hmthomas@med.cornell.edu (Henry M.  ]

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

Date: Mon, 17 Aug 1998 08:04:08 -0500
From: Laird Bloom <lbloom@MIT.EDU>
To: nih-image@io.ece.drexel.edu
Subject: code for area measurement macros
Message-Id: <v03020902b1fdd82d6c9f@[18.155.0.104]>
Content-Type: text/enriched; charset="us-ascii"

I've had several requests for the code for macros to record area
measurement data from regions you outline with a mouse.  Here is the
code for two versions, one for use with saved images, and one that
works well for live images.  Please contact me if you have questions.

Laird Bloom

MIT Center for Cancer Research


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


<bold> Area measurement macros</bold>


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


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


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


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


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

<bold>


"Measure areas on scope" macro

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

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


{"Measure areas on scope" macro file follows:

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

}


var {Global variables}

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

	mean:real;

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



procedure GetImageToMeasure;

begin

StartCapturing;

	Repeat

		Wait(.1);

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

StopCapturing;


SetPicName(nSample,'  Image');

SelectWindow(nSample,'  Image');

         if nSave='Yes'

              then Save;

end



procedure LabelAreaInCenter;


var

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

  scale: real;

  unit: string;

begin

  GetRoi(left,top,width,height);

  if width=0 then begin

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

    exit;

  end;

  SaveState;

  InvertY(false);

  SetForegroundColor(255); {black}

SetBackgroundColor(1);

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

  GetScale(scale, unit);

  Measure;

	DrawBoundary;

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

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

  MoveTo(x-5, y);

	SetFont('Times');

	SetFontSize(9);

SetText('With Background');

	Writeln('region ',j:0);

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

  RestoreState;

end;



macro 'Measure Area [M]';

begin

	j:=j+1;

	LabelAreaInCenter;

	ImageName:=WindowTitle;

	SelectWindow(nSample);

        

	If j=1

		then writeln (nSample); 

		SetFont('Times');

		SetFontSize(12);

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

 		rUser1[j]:=rArea[rCount];

		total:=total+rArea[rCount];

      Save;

	SelectWindow(ImageName);

end


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

var

	width,height:integer;

begin

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

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

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

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

	NewTextWindow(nSample,80,600);

				MoveWindow(740,40);

	total:=0;

GetImageToMeasure;

	j:=0;

end;


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

begin

SelectWindow(ImageName);

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

 DisposeAll;

GetImageToMeasure;

end;

 

macro 'New Sample [S]';


begin

	If j=0

			 then j:=1;

SelectWindow(ImageName);

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

 		Dispose;

SelectWindow(nSample);

mean:=total/j;

writeln('Mean =');

write(mean);

save;

		dispose;

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

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


	NewTextWindow(nSample,80,600);

				MoveWindow(740,40);

	total:=0;

GetImageToMeasure;

	j:=0;

end;

   

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


{

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

}


var {Global variable, initially zero}

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

	mean:real;

	nOut,SampleName,ImageName:string;



procedure LabelAreaInCenter;


var

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

  scale: real;

  unit: string;

begin

  GetRoi(left,top,width,height);

  if width=0 then begin

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

    exit;

  end;

  SaveState;

  InvertY(false);

  SetForegroundColor(255); {black}

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

  GetScale(scale, unit);

  Measure;

	DrawBoundary;

{Fill;

Invert;

  KillRoi;}

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

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

  MoveTo(x-5, y);

	SetFont('Times');

	SetFontSize(9);

SetText('WithBackground');

	Writeln('region ',j:0);

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

  RestoreState;

end;


procedure EndProcedure;

begin

DisposeAll;

		mean:=total/j;

		SelectWindow(nOut);

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

		Save;

		{nLines:=nLines+10;

		Open(nOut);

		MoveWindow(120,nLines);}

		Open(' ');

		total:=0;

		j:=0;

	end;



macro 'Measure Area [M]';

begin

			j:=j+1;

		LabelAreaInCenter;

					ImageName:=WindowTitle;

      		SelectWindow(nOut);

Moveto(120,560);

	If j=1

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

		SetFont('Times');

		SetFontSize(12);

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

	rUser1[j]:=rArea[rCount];

	total:=total+rArea[rCount];

      Save;

	SelectWindow(ImageName);

end




macro 'Set Up Area Measurements [S]';

var

	width,height:integer;

begin

ImageName:=WindowTitle;

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

		NewTextWindow(nOut);

		MoveWindow(120,550);

	total:=0;

	j:=0;

SelectWindow(ImageName);

SelectAll;

Measure;

  TotalArea:=rArea[rCount];

KillRoi;

end;


macro 'Finish Area Measurement [F]';

var

	nSave:string;

begin

	If j=0

	then j:=1;

	SaveAs(ImageName,' + area measurements');

EndProcedure;

		end;


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

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

Date: Mon, 17 Aug 1998 08:36:21 -0500
From: Laird Bloom <lbloom@MIT.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Macro for counting cells, saving data
Message-Id: <v03020904b1fde0745e58@[18.155.0.104]>
Content-Type: text/enriched; charset="us-ascii"

<fontfamily><param>Times</param><bigger><bigger>To NIH Image users:

This macro is modified from the cell counting macro available on the
NIH Image web site.  It's designed to save data to a text file while
collecting multiple data points per sample at the microscope.  

  It works well for cells labeled with DAPI, propidium iodide, or
octadecyl rhodamine--brightly fluorescent cells on a dark
background--but is probably OK for non-fluorescent stains as well. 
DAPI is particularly nice because it stains only nuclei, and is
therefore doesn't change much when cells spread out.  Cytoplasmic or
membrane stains (e.g. octadecyl rhodamine or FITC variants) are dimmer
on spread cells than on rounded cells, and this macro sometimes has
trouble seeing dimmer spread cells labeled this way.  The macro is
written to use only the red, green, or blue channel (gets rid of
background prior to threshholding), but that could be modified.  Code
is written for Scion Image 1.62.  Points at which there are
Scion-specific commands are noted.

Please contact me if you have questions.


Laird Bloom

MIT Center for Cancer Research


var {Global variable, initially zero}

  nAvg,Threshold:integer; {range: 10-150}



procedure DoGammaTransform(gamma:real);

var

  i,v:integer;

  n,mode,min,max:integer

  mean:real;

begin

  measure;

  GetResults(n,mean,mode,min,max);

  ShowMessage('min=',min:1,'\max=',max:1);

  for i:=1 to 254 DO begin

    if (i>min) and (i<<max)

      then v:=exp(gamma*ln((i-min)/(max-min)))*255 {x^y=exp(y*ln(x)}

      else begin

        if i<<=min then v:=0 else v:=255;

      end;

    RedLUT[i]:=255-v;

    GreenLUT[i]:=255-v;

    BlueLUT[i]:=255-v;

  end;

  UpdateLUT;

end.



procedure CountCells(MoreSensative:boolean);

var

  gamma: real;

  radius: real; {peak radius; range: 1-50}

  slope: real;  {peak slope (aka peakedness); range: 0.05-0.95}

  BallRadius: real; {2d rolling ball radius}

  i,width,height: integer;

begin

  SetforegroundColor(0);

  SetbackgroundColor(255);

  radius:=6;

  slope:=0.2;

  gamma:=1.6;

  BallRadius:=8;

  {radius:=GetNumber('Radius[1-50]:',radius);}

  {slope:=GetNumber('Slope[0.05-0.95]:',slope);}

  Invert;

  SubtractBackground('2D Rolling Ball(faster)',BallRadius);

  GetPicSize(width,height);

  MakeRoi(0.05*width,0.05*height,0.9*width,0.9*height);

  {EnhanceContrast;}

  KillRoi;

  ApplyLUT;

  DoGammaTransform(gamma);

  ApplyLUT;

  SetOption; Smooth;

  SetOption; Smooth;

  if threshold=0 then begin

    AutoThreshold;

    wait(2);

    i:=0;

    Repeat

      i:=i+1;

    until RedLUT[i]<<255;

    if MoreSensative

      then Threshold:=round(0.75*i)

      else Threshold:=i

  end;

  SetThreshold(-1);

  SetLineWidth(2);

  UserCode('Find Peaks', threshold, radius, slope);

end;



macro 'Count cells and save /1';

var

 color,nLines,d,nDefault,nImage,j: integer;

 total,mean: real

nOut,nSave,nNext,nWell: string;

  begin

   PutMessage('Clicking on cancel at any time will end the macro.',);


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

	  color:=GetNumber ('Color:  Red=1, Green=2,  Blue=3',3,0);

nSave:=GetString('Save each full-size image as a 1.2 Mb file?','Yes');

nDefault:=GetNumber('Default number of images per sample:',5,0);

	PutMessage('To count cells from live video, click mouse button.'); 

	NewTextWindow(nOut);

 Writeln(nOut,' ');

	Writeln('Sample    			Cell counts								T=total	M=mean);

 Writeln;

 nLines:=0;

  repeat

         

     nWell:=GetString('Sample:'); 


        nImage:=GetNumber('Number of images for this
sample:',nDefault,0);

        SelectWindow(nOut);

        Write('Sample ',nWell,':		');

	       SetUser1Label('Cell counts');

        total:=0

	    for j:=1 to nImage do begin

{use next bracketed statement instead of the
StartCapturing...StopCapturing lines if get your video image via the
File>Acquire menu.  StartCapturing and StopCapturing may be Scion Image
1.62-specific macro commands. }

{Acquire('Plug-In Digitizer');}

         StartCapturing;

	Repeat

	Wait(.1);

	Until Button;

StopCapturing;



SetPicName(nWell,'.',j:2);

         if nSave='Yes'

              then SaveAs('');

{Using just the main color of your chromophore seems to make the image
cleaner.  The Bit24toRGBColor command may be specific to Scion Image
1.62.}

Bit24toRGBColor;

SelectSlice(color);

 Threshold:=0;

  CountCells(false);


         dispose;

         SelectWindow(nOut);

         d:=520-nLines;

	        MoveWindow(20,d);

         Write(rCount,'	');

 rUser1[j]:=rCount;

total:=total+rCount

        end;

         mean:=total/j;


	        

SelectWindow(nOut)

         Writeln('  T = ',total:2,'	  M ='mean:2,'	');

Save;

    

       nLines:=nLines+10;

       nNext:=GetString('Score another sample? (type no to
end)','yes');

until not (nNext='yes');


     SelectWindow(nOut);

Save;

      end;

end;


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

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

Date: Mon, 17 Aug 1998 11:05:52 -0400
From: "Dibble, Nicole A" <DibbleNA@corning.com>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: LG-3 NuBus
Message-Id: <215D10CDFC93D111A11600805FBB7C28211D58@BILLHALEY>
Content-Return: allowed
Content-Type: text/plain

I currently have a LG-3 NuBus framegrabber for Macintosh for sale.  Anyone
interested???  Make me an offer.

Nicole

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

Date: Mon, 17 Aug 1998 11:37:56 -0400
From: iskanderys@ornl.gov (Yousef S. Iskander)
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-id: <4.0.1.19980817113710.00f42520@cosmail1.ctd.ornl.gov>
Content-type: text/plain; charset="us-ascii"

---------------------------------------------------------
Yousef S. Iskander
Oak Ridge National Laboratory
Metals and Ceramics Division
P.O. Box 2008, Bldg. 5500, MS 6376
Oak Ridge, TN  37831-6376
Phone:  (423) 574-5096, (423) 576-7340 
e-mail:  iskanderys@ornl.gov

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

Date: Mon, 17 Aug 1998 16:47:37 -0500
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: unsubscribe
Message-Id: <v03007809b1fe551a9eb4@[144.118.33.245]>
Content-Type: text/enriched; charset="us-ascii"

<fontfamily><param>Times</param>An administrative reminder. To
unsubscribe to the list, send E-mail to
nih-image-request@biomed.drexel.edu.

the Subject of the message should contain "unsubscribe".


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

		Subject: unsubscribe


do not send it to the mail list itself.


Thanks.</fontfamily>

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

                                  Jonathan Nissanov, Ph.D.

                                      Associate Director  

            Computer Vision Center for Vertebrate Brain Mapping,

                a NIH Biomedical Research Technology Resource

                                http://cbis.ece.drexel.edu/ICVC/

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

Imaging and Computer Vision Center              Tel: 215-895-1381

Drexel University                                                  
Fax: 215-895-4987

Phildelphia, PA 19104                                        
yoni@coe.drexel.edu

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

      

     

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

Date: Mon, 17 Aug 1998 21:31:23 -0400
From: hmthomas@med.cornell.edu (Henry M. Thomas)
To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center)
Subject: Capture max intensity during TIFF import
Message-Id: <v01540b00b1fe5054a26c@[206.152.160.99]>
Content-Type: text/plain; charset="us-ascii"

As I Import a stack of TIFF images (output from a PC program), the
Information Window shows the max intensity of each slice (briefly).  Is
there a way to capture these values (and thus get the largest max value)
with the Image macro language?

If so, I can Import the stack again with a fixed scale, using the captured
largest max value from the stack.  [At present, I obtain the value from the
PC program and type it into the Import subdialogue box "Set".]

Henry M. Thomas, III MD (Harry)
Professor of Clinical Medicine,  Pulmonary and Critical Care Division
Department of Medicine, Cornell Univ. Medical School
Director, Pulmonary Research, Burke Rehabilitation Hospital
785 Mamaroneck Ave.  White Plains, NY 10605
(914) 597-2141

--------------------------------
End of nih-image-d Digest V98 Issue #38
***************************************

From nih-image-request@io.ece.drexel.edu Tue Aug 18 09:29 EDT 1998
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Date: Tue, 18 Aug 1998 09:13:24 -0400 (EDT)
From: Randy Cutter <cutter@vims.edu>
Reply-To: Randy Cutter <cutter@vims.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #29
In-Reply-To: <199808051012.GAA20092@io.ECE.Drexel.EDU>
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Has the version of Object-Image with the color segmentation routine
mentioned Aug. 5 by Jeremy Brown been posted on the NIH website?  

---------------------
Randy Cutter
Virginia Institute of Marine Science
Route 1208 
Gloucester Point, VA 23062 USA

phone 804 684-7365
fax 804 684-7399 or 7045
email:  cutter@vims.edu

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



From nih-image-request@io.ece.drexel.edu Tue Aug 18 11:19 EDT 1998
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Date: Tue, 18 Aug 1998 09:09:17 -0600
From: "Christopher P. Tully" <cptully@usa.net>
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To: nih-image@io.ece.drexel.edu
Subject: Re: Capture max intensity during TIFF import
References: <v01540b00b1fe5054a26c@[206.152.160.99]>
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Henry-

Here is a simple macro to collect max values of a stack.  It will record
the maximum value of each slice in a stck to a tab delimited text window
(run it with your stack already opened):

macro 'max values';
var
  i:integer;
  n,mean,mode,min,max:integer;
  StackPID:integer;
  tab:integer;
begin
  tab:=chr(9);
  StackPID:=PidNumber;

  NewTextWindow('Max Values',100,200);
  Writeln('Slice',tab,'Max Value');
  for i := 1 to nSlices do begin
    SelectPic(StackPID);
    SelectSlice(i);
    SelectAll;
    Measure;
    GetResults(n,mean,mode,min,max);
    SelectWindow('Max Values');
    Writeln(i,tab,max);
  end;
end;

Chris Tully

Henry M. Thomas wrote:
> 
> As I Import a stack of TIFF images (output from a PC program), the
> Information Window shows the max intensity of each slice (briefly).  Is
> there a way to capture these values (and thus get the largest max value)
> with the Image macro language?
> 
> If so, I can Import the stack again with a fixed scale, using the captured
> largest max value from the stack.  [At present, I obtain the value from the
> PC program and type it into the Import subdialogue box "Set".]
> 
> Henry M. Thomas, III MD (Harry)
> Professor of Clinical Medicine,  Pulmonary and Critical Care Division
> Department of Medicine, Cornell Univ. Medical School
> Director, Pulmonary Research, Burke Rehabilitation Hospital
> 785 Mamaroneck Ave.  White Plains, NY 10605
> (914) 597-2141

From nih-image-request@io.ece.drexel.edu Tue Aug 18 11:27 EDT 1998
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Date: Tue, 18 Aug 1998 11:09:55 -0400
Message-Id: <H000093d0178905f@MHS>
Subject: Printer for gel documentation
MIME-Version: 1.0
From: "Michael King" <Michael.King@mail.tju.edu>
TO: nih-image@io.ece.drexel.edu
X-Bad-Content-Type: text/plain; charset=US-ASCII; name="Printer"
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What are the current recommendations for monochrome thermal printers for
use in gel documentation systems?
Ideally, we would like to keep the cost to about $0.10 per print.  This
would exclude printers such as the Kodak SP700. 
I have seen previous postings where people utilize the Mitsubishi P-90
printer.  What other printers are people using?  
Are there newer printers that we should investigate?  

Thanks,
Michael King

From nih-image-request@io.ece.drexel.edu Tue Aug 18 13:18 EDT 1998
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Date: Tue, 18 Aug 98 10:02:54 PDT
From: Walter Wolf <wwolfw@hsc.usc.edu>
To: nih-image@io.ece.drexel.edu
Cc: wwolfw@hsc.usc.edu, hkim@hsc.usc.edu
Subject: Is there a macro for automating ROI analysis?
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Is there a macro anyone has written that allows a definition of a
region-of-interest, and once defined, can analyze each of the pixels in that
stack? Basically, what I am looking for is using the macro "Plot Z-Axis
Profile [Z]" together with another macro (or a modification of Plot Z-Axis
Profile [Z]) to plot each of the pixels in a ROI, and save the results to
measurement files.

======================================================================
|  Professor Walter Wolf, Ph.D.          E-Mail: wwolfw@hsc.usc.edu  |
|  Distinguished Professor of Pharmaceutical Sciences		     |
|  Director, Pharmacokinetic Imaging Program                         |
|  Department of Pharmaceutical Sciences, School of Pharmacy	     |
|  University of Southern California         Telephone: 323-442-1405 |
|  1985 Zonal Ave., Los Angeles, CA 90033    Fax:       323-442-9804 |
|                                                                    |
|Center for Noninvasive Pharmacology, Los Angeles Oncologic Institute|
|  MRI at St. Vincent Medical Center     Telephone:    213-484-7235  |
|  2131 Third St., Los Angeles, CA 90057 Fax:          213-484-7447  |
======================================================================
 

From nih-image-request@io.ece.drexel.edu Tue Aug 18 15:36 EDT 1998
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Date: Tue, 18 Aug 1998 13:21:43 -0500
From: Paul Morin <lpaul@umn.edu>
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I'm calculating a histogram of a ROI and exporting the data to a file.
When I look at the file I find that about every 10 values is a zero when
it shouldn't be.  Is there a way to turn this feature off?

Paul Morin

University of Minnesota

From nih-image-request@io.ece.drexel.edu Tue Aug 18 17:20 EDT 1998
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From: Gregoire Thomas <g.r.thomas@uea.ac.uk>
Subject: Re: code for area measurement macros
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you could also try the software available on:
http://www.draak.demon.co.uk/imagine/
It provides a range of tools for the selection of regions with the mouse
and a 'friendly' interface.
Greg

At 08:04 17/08/98 -0500, you wrote:
>I've had several requests for the code for macros to record area
>measurement data from regions you outline with a mouse.  Here is the code
>for two versions, one for use with saved images, and one that works well
>for live images.  Please contact me if you have questions.
>Laird Bloom

From nih-image-request@io.ece.drexel.edu Tue Aug 18 20:30 EDT 1998
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Date: Tue, 18 Aug 1998 19:13:59 -0500
From: scidi <scidi@mci2000.com>
Subject: Help with Imaging System
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I am in need of some help with an imaging system that I am installing.  The
system utilizes the old LG-3/TV-3 combination as an old IIci that was
laying around is being used solely for this imaging system.  I tested the
cards and Cohu camera out on a PowerMac 7100.  Utilizing NIH Image, I got
great, crisp pictures.  I was using version 1.62a of NIH Image.

I then went to install on the Mac IIci.  I was using version 1.55 of NIH
Image, since 1.62a needs a PowerMac.  Upon attempting to capture an image I
get a highly grainy and image that has quite a bit of snow.  Obviously not
crisp at all.  The gain on the camera is 0, and all of the other settings
are as they should be according to Cohu and Scion.  

I remember some things a while ago concerning the FPU and non-FPU versions
of Image.  If I recall I need to use the FPU version on the IIci????  Is
this my problem??  The reason I think it is a software thing is because it
works great on my PowerMac.  Virtual memory is OFF and 32 bit addressing
was tried both on and off with no change in the picture. 

If anyone could help I would be most appreciative.  Thank you.


Mark R. Molenda, Owner
Scientific Digital Imaging
1407 S 59th St.
Milwaukee, WI  53214

phone (414) 476-2694
fax (414) 645-8037
scidi@mci2000.com


From nih-image-request@io.ece.drexel.edu Tue Aug 18 21:50 EDT 1998
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Subject: Help with Imaging Systems, cont.
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One thing I forgot to mention.....On the IIci, it says that the camera is
capturing  at 0.45 frames/second.  It is extremely delayed.  It has to be
something with the software somewhere.  I just know it is a click of a
button or a turn of a switch or something.  Any ideas?????



Mark R. Molenda, Owner
Scientific Digital Imaging
1407 S 59th St.
Milwaukee, WI  53214

phone (414) 476-2694
fax (414) 645-8037
scidi@mci2000.com

----------
> From: Michael King <Michael.King@mail.tju.edu>
> To: nih-image@io.ece.drexel.edu
> Subject: Printer for gel documentation
> Date: Tuesday, August 18, 1998 10:09 AM
> 
> What are the current recommendations for monochrome thermal printers for
> use in gel documentation systems?
> Ideally, we would like to keep the cost to about $0.10 per print.  This
> would exclude printers such as the Kodak SP700. 
> I have seen previous postings where people utilize the Mitsubishi P-90
> printer.  What other printers are people using?  
> Are there newer printers that we should investigate?  
> 
> Thanks,
> Michael King

From nih-image-request@io.ece.drexel.edu Tue Aug 18 23:09 EDT 1998
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Greg (and Henry)-

Oops, I guess I missed that part.  Not having a Mac handy at the moment,
I can't test your theory, but the implication from Henry's original
message is that he's been importing stacks with a maximum value set, so
here's a modified macro (untested):

macro 'max values v2';
var
  i:integer;
  n,mean,mode,min,max:integer;
  stackmax:integer;
  StackPID:integer;
  tab:integer;
  path:string;
begin
  tab:=chr(9);
  StackPID:=PidNumber;
  path:=GetPath('window');

  NewTextWindow('Max Values',100,200);
  Writeln('Slice',tab,'Max Value');
  stackmax:=0;
  for i := 1 to nSlices do begin
    SelectPic(StackPID);
    SelectSlice(i);
    SelectAll;
    Measure;
    GetResults(n,mean,mode,min,max);
    SelectWindow('Max Values');
    Writeln(i,tab,max);
    If stackmax < max then stackmax:=max;
  end;

  SelectPic(StackPid);
  Dispose;

  SetImportMinMax(0,stackmax);
  SetImport('TIFF');
  Import(path);
end;

As I said, this macro is untested.  It may work as is, or (more likely)
it may need some tweeking.  Please let me know how it works.

Chris Tully

GJOSS@rna.bio.mq.edu.au wrote:
> Yes Chris, you report max stack value; but will this allow him to:
> "If so, I can Import the stack again with a fixed scale, using the captured
>  largest max value from the stack.  [At present, I obtain the value from the
>  PC program and type it into the Import subdialogue box "Set".]"
> 
> ? ? :-)
> 
> as far as I can determine, setting max value in import dialogue for 8bit Tiff
> stack  will be ignored on import.

From nih-image-d-request@io.ece.drexel.edu Wed Aug 19 06:15 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #39
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 39

Today's Topics:
  Re: nih-image-d Digest V98 #29        [ Randy Cutter <cutter@vims.edu> ]
  Re: Capture max intensity during TIF  [ "Christopher P. Tully" <cptully@usa ]
  Printer for gel documentation         [ "Michael King" <Michael.King@mail.t ]
  Is there a macro for automating ROI   [ Walter Wolf <wwolfw@hsc.usc.edu> ]
  white bars in the histogram           [ Paul Morin <lpaul@umn.edu> ]
  Re: code for area measurement macros  [ Gregoire Thomas <g.r.thomas@uea.ac. ]
  Help with Imaging System              [ scidi <scidi@mci2000.com> ]
  Help with Imaging Systems, cont.      [ scidi <scidi@mci2000.com> ]
  Re: Capture max intensity during TIF  [ "Christopher P. Tully" <cptully@usa ]

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

Date: Tue, 18 Aug 1998 09:13:24 -0400 (EDT)
From: Randy Cutter <cutter@vims.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: nih-image-d Digest V98 #29
Message-ID: <Pine.SOL.3.96.980818091150.23658B-100000@pagan.vims.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Has the version of Object-Image with the color segmentation routine
mentioned Aug. 5 by Jeremy Brown been posted on the NIH website?  

---------------------
Randy Cutter
Virginia Institute of Marine Science
Route 1208 
Gloucester Point, VA 23062 USA

phone 804 684-7365
fax 804 684-7399 or 7045
email:  cutter@vims.edu

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

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

Date: Tue, 18 Aug 1998 09:09:17 -0600
From: "Christopher P. Tully" <cptully@usa.net>
To: nih-image@io.ece.drexel.edu
Subject: Re: Capture max intensity during TIFF import
Message-ID: <35D9991D.DEDDAF10@usa.net>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Henry-

Here is a simple macro to collect max values of a stack.  It will record
the maximum value of each slice in a stck to a tab delimited text window
(run it with your stack already opened):

macro 'max values';
var
  i:integer;
  n,mean,mode,min,max:integer;
  StackPID:integer;
  tab:integer;
begin
  tab:=chr(9);
  StackPID:=PidNumber;

  NewTextWindow('Max Values',100,200);
  Writeln('Slice',tab,'Max Value');
  for i := 1 to nSlices do begin
    SelectPic(StackPID);
    SelectSlice(i);
    SelectAll;
    Measure;
    GetResults(n,mean,mode,min,max);
    SelectWindow('Max Values');
    Writeln(i,tab,max);
  end;
end;

Chris Tully

Henry M. Thomas wrote:
> 
> As I Import a stack of TIFF images (output from a PC program), the
> Information Window shows the max intensity of each slice (briefly).  Is
> there a way to capture these values (and thus get the largest max value)
> with the Image macro language?
> 
> If so, I can Import the stack again with a fixed scale, using the captured
> largest max value from the stack.  [At present, I obtain the value from the
> PC program and type it into the Import subdialogue box "Set".]
> 
> Henry M. Thomas, III MD (Harry)
> Professor of Clinical Medicine,  Pulmonary and Critical Care Division
> Department of Medicine, Cornell Univ. Medical School
> Director, Pulmonary Research, Burke Rehabilitation Hospital
> 785 Mamaroneck Ave.  White Plains, NY 10605
> (914) 597-2141

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

Date: Tue, 18 Aug 1998 11:09:55 -0400
From: "Michael King" <Michael.King@mail.tju.edu>
TO: nih-image@io.ece.drexel.edu
Subject: Printer for gel documentation
Message-Id: <H000093d0178905f@MHS>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline; filename="Printer"
Content-Transfer-Encoding: 7bit

What are the current recommendations for monochrome thermal printers for
use in gel documentation systems?
Ideally, we would like to keep the cost to about $0.10 per print.  This
would exclude printers such as the Kodak SP700. 
I have seen previous postings where people utilize the Mitsubishi P-90
printer.  What other printers are people using?  
Are there newer printers that we should investigate?  

Thanks,
Michael King

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

Date: Tue, 18 Aug 98 10:02:54 PDT
From: Walter Wolf <wwolfw@hsc.usc.edu>
To: nih-image@io.ece.drexel.edu
Cc: wwolfw@hsc.usc.edu, hkim@hsc.usc.edu
Subject: Is there a macro for automating ROI analysis?
Message-ID: <CMM.0.90.4.903459774.wwolfw@hsc.usc.edu>

Is there a macro anyone has written that allows a definition of a
region-of-interest, and once defined, can analyze each of the pixels in that
stack? Basically, what I am looking for is using the macro "Plot Z-Axis
Profile [Z]" together with another macro (or a modification of Plot Z-Axis
Profile [Z]) to plot each of the pixels in a ROI, and save the results to
measurement files.

======================================================================
|  Professor Walter Wolf, Ph.D.          E-Mail: wwolfw@hsc.usc.edu  |
|  Distinguished Professor of Pharmaceutical Sciences		     |
|  Director, Pharmacokinetic Imaging Program                         |
|  Department of Pharmaceutical Sciences, School of Pharmacy	     |
|  University of Southern California         Telephone: 323-442-1405 |
|  1985 Zonal Ave., Los Angeles, CA 90033    Fax:       323-442-9804 |
|                                                                    |
|Center for Noninvasive Pharmacology, Los Angeles Oncologic Institute|
|  MRI at St. Vincent Medical Center     Telephone:    213-484-7235  |
|  2131 Third St., Los Angeles, CA 90057 Fax:          213-484-7447  |
======================================================================
 

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

Date: Tue, 18 Aug 1998 13:21:43 -0500
From: Paul Morin <lpaul@umn.edu>
To: nih-image@io.ece.drexel.edu
Subject: white bars in the histogram
Message-ID: <35D9C637.2427A25A@umn.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

I'm calculating a histogram of a ROI and exporting the data to a file.
When I look at the file I find that about every 10 values is a zero when
it shouldn't be.  Is there a way to turn this feature off?

Paul Morin

University of Minnesota

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

Date: Tue, 18 Aug 1998 22:04:52 +0100
From: Gregoire Thomas <g.r.thomas@uea.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: code for area measurement macros
Message-Id: <3.0.5.32.19980818220452.00937a10@pop.uea.ac.uk>
Content-Type: text/plain; charset="us-ascii"

you could also try the software available on:
http://www.draak.demon.co.uk/imagine/
It provides a range of tools for the selection of regions with the mouse
and a 'friendly' interface.
Greg

At 08:04 17/08/98 -0500, you wrote:
>I've had several requests for the code for macros to record area
>measurement data from regions you outline with a mouse.  Here is the code
>for two versions, one for use with saved images, and one that works well
>for live images.  Please contact me if you have questions.
>Laird Bloom

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

Date: Tue, 18 Aug 1998 19:13:59 -0500
From: scidi <scidi@mci2000.com>
To: nih-image@io.ece.drexel.edu
Subject: Help with Imaging System
Message-id: <0EXW00MGHUDJFU@PM06SM.PMM.MCI.NET>
Content-type: text/plain; charset=ISO-8859-1
Content-transfer-encoding: 7bit

I am in need of some help with an imaging system that I am installing.  The
system utilizes the old LG-3/TV-3 combination as an old IIci that was
laying around is being used solely for this imaging system.  I tested the
cards and Cohu camera out on a PowerMac 7100.  Utilizing NIH Image, I got
great, crisp pictures.  I was using version 1.62a of NIH Image.

I then went to install on the Mac IIci.  I was using version 1.55 of NIH
Image, since 1.62a needs a PowerMac.  Upon attempting to capture an image I
get a highly grainy and image that has quite a bit of snow.  Obviously not
crisp at all.  The gain on the camera is 0, and all of the other settings
are as they should be according to Cohu and Scion.  

I remember some things a while ago concerning the FPU and non-FPU versions
of Image.  If I recall I need to use the FPU version on the IIci????  Is
this my problem??  The reason I think it is a software thing is because it
works great on my PowerMac.  Virtual memory is OFF and 32 bit addressing
was tried both on and off with no change in the picture. 

If anyone could help I would be most appreciative.  Thank you.


Mark R. Molenda, Owner
Scientific Digital Imaging
1407 S 59th St.
Milwaukee, WI  53214

phone (414) 476-2694
fax (414) 645-8037
scidi@mci2000.com

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

Date: Tue, 18 Aug 1998 20:31:54 -0500
From: scidi <scidi@mci2000.com>
To: nih-image@io.ece.drexel.edu
Subject: Help with Imaging Systems, cont.
Message-id: <0EXW00BC6XZJ7F@PM04SM.PMM.MCI.NET>
Content-type: text/plain; charset=ISO-8859-1
Content-transfer-encoding: 7bit

One thing I forgot to mention.....On the IIci, it says that the camera is
capturing  at 0.45 frames/second.  It is extremely delayed.  It has to be
something with the software somewhere.  I just know it is a click of a
button or a turn of a switch or something.  Any ideas?????



Mark R. Molenda, Owner
Scientific Digital Imaging
1407 S 59th St.
Milwaukee, WI  53214

phone (414) 476-2694
fax (414) 645-8037
scidi@mci2000.com

----------
> From: Michael King <Michael.King@mail.tju.edu>
> To: nih-image@io.ece.drexel.edu
> Subject: Printer for gel documentation
> Date: Tuesday, August 18, 1998 10:09 AM
> 
> What are the current recommendations for monochrome thermal printers for
> use in gel documentation systems?
> Ideally, we would like to keep the cost to about $0.10 per print.  This
> would exclude printers such as the Kodak SP700. 
> I have seen previous postings where people utilize the Mitsubishi P-90
> printer.  What other printers are people using?  
> Are there newer printers that we should investigate?  
> 
> Thanks,
> Michael King

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

Date: Tue, 18 Aug 1998 21:05:10 -0600
From: "Christopher P. Tully" <cptully@usa.net>
To: NIH-Image <nih-image@io.ece.drexel.edu>
Subject: Re: Capture max intensity during TIFF import
Message-ID: <35DA40E5.4FB7ED7D@usa.net>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Greg (and Henry)-

Oops, I guess I missed that part.  Not having a Mac handy at the moment,
I can't test your theory, but the implication from Henry's original
message is that he's been importing stacks with a maximum value set, so
here's a modified macro (untested):

macro 'max values v2';
var
  i:integer;
  n,mean,mode,min,max:integer;
  stackmax:integer;
  StackPID:integer;
  tab:integer;
  path:string;
begin
  tab:=chr(9);
  StackPID:=PidNumber;
  path:=GetPath('window');

  NewTextWindow('Max Values',100,200);
  Writeln('Slice',tab,'Max Value');
  stackmax:=0;
  for i := 1 to nSlices do begin
    SelectPic(StackPID);
    SelectSlice(i);
    SelectAll;
    Measure;
    GetResults(n,mean,mode,min,max);
    SelectWindow('Max Values');
    Writeln(i,tab,max);
    If stackmax < max then stackmax:=max;
  end;

  SelectPic(StackPid);
  Dispose;

  SetImportMinMax(0,stackmax);
  SetImport('TIFF');
  Import(path);
end;

As I said, this macro is untested.  It may work as is, or (more likely)
it may need some tweeking.  Please let me know how it works.

Chris Tully

GJOSS@rna.bio.mq.edu.au wrote:
> Yes Chris, you report max stack value; but will this allow him to:
> "If so, I can Import the stack again with a fixed scale, using the captured
>  largest max value from the stack.  [At present, I obtain the value from the
>  PC program and type it into the Import subdialogue box "Set".]"
> 
> ? ? :-)
> 
> as far as I can determine, setting max value in import dialogue for 8bit Tiff
> stack  will be ignored on import.

--------------------------------
End of nih-image-d Digest V98 Issue #39
***************************************

From nih-image-request@io.ece.drexel.edu Wed Aug 19 08:11 EDT 1998
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Date: Wed, 19 Aug 1998 08:11:25 -0400
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Subject: Morphologic Operations and NIH Image
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 I am attempting to use the Binary menu to simplify and measure bone changes.  The program states that "Erode and Dilate do not perform erosion and dilation with structuring elements as described in the literature of classical mathematical morphology."  I'm trying to understand what I am doing when I use the Binary submenu.  The program defines these  procedures:
Erode - Removes pixels from the edges of objects in a binary images, where contiguous black areas in the image are considered objects, and background is assumed to be white. A pixel is removed (set to white) if four or more of its eight neighbors are white. Erosion separates objects that are touching and removes isolated pixels.

Dilate - Adds pixels to the edges of objects in a binary images. A pixel is added (set to black) if four or more of its eight neighbors are black. Dilation connects discontinuous objects and fills in holes.

 Does Image do morphologic operations?  Is if fair to say a morphologic operation is the net change to an image, regardless of the technique used to get there?  In other words, does it matter if I skeletonize an image with Image or, say, Alice [Dip Station] which apparently uses different mathematical structuring elements?  If they are different, can I use the morphologic operator literature to justify a technique I develop using Image?

I'd appreciate any input I can get!

Mike Shrout
Associate Professor
Medical College of Georgia

From nih-image-request@io.ece.drexel.edu Wed Aug 19 09:50 EDT 1998
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Date: Wed, 19 Aug 1998 14:35:10 +0000
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Would anyone in the Edinburgh Area, or Scotland come to that, be interested in some kind of local NIH/Object/Scion Image forum?

Jeremy




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

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


From nih-image-request@io.ece.drexel.edu Wed Aug 19 11:52 EDT 1998
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From: hmthomas@med.cornell.edu (Henry M. Thomas)
Subject: Re: Capture max intensity during TIFF import
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Thanks for the help.  Using IMPORT repeatedly gives flexibility in the
Import command.  Greg's Measure (the max intensity in each of 5 slices)
works fine.  Wayne's cvalue(1) is more elegant, but I kept getting 1 for
cValue(1); I'm sure it can be worked out.  Here is the code that works for
me.
Appreciatively, Harry


var
   LargestMax,sliceno,width,height,lower,upper:integer; {Global variable,
initially zero}
  OldStackTitle,NewStackTitle,NewerStackTitle,NewWindowTitle:string;

procedure procIMPORT
begin

{Import 1st time and discard.  Image's automatic TIFF file detection gets
height & Width from a 16 bit Scanalytics Cellscan PC 5 slice TIFF}
    Import('');            {1st time you run program, default  no. slices is 1}
    GetPicSize(width,height);      {only necessary cause SetCustom requires it}
    Dispose;

{Import 2nd time (and discard) with dummy fixed scale to get the largest
calibrated value in the 5 slices; "custom' uses the height,width and offset
from the previous Import }
    SetImport('custom,16-bits unsigned,swap bytes,calibrate');
    SetImportMinMax(0,32767);
    SetCustom(width,height,8,5); {1st time program runs, you need to set
slices to 5}
    Import('');
    largestMax := 0;
    ResetCounter;
    for i:=1 to nSlices do begin
        selectSlice(i); Measure;
        if rMax[i] >largestMax then largestMax:= rMax[i];
    end;
    Dispose;

{Import 3rd time with fixed scale using largest calibrated value in the 5
slices as  max}
    SetImport('custom,16-bits unsigned,swap bytes,calibrate');
    SetImportMinMax(0,largestMax);
    Import('');
    SetScale(1,'pixel');
end

Henry M. Thomas, III MD (Harry)
Professor of Clinical Medicine,  Pulmonary and Critical Care Division
Department of Medicine, Cornell Univ. Medical School
Director, Pulmonary Research, Burke Rehabilitation Hospital
785 Mamaroneck Ave.  White Plains, NY 10605
(914) 597-2141


From nih-image-request@io.ece.drexel.edu Wed Aug 19 11:54 EDT 1998
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From: hmthomas@med.cornell.edu (Henry M. Thomas)
Subject: Macro command for Scale to fit Window?
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I want to paste into the middle of a 1500 by 800 pixel window, which doesn'
fit on the screen.  Pasting into the scrollable, regular window pastes at,
roughly (and unpredictably by me) 250,250, whereas pasting into the
scaled-to-fit-window window pastes reliably at 750,400.  Then I can move
the ROI by macro.

Scale to Fit Window is in the Options Menu.  I can't find a macro
equivalent.  If not, how can I reliably move the upper left corner of the
pasted ROI to, say 20,20?

Thanks, Harry

Henry M. Thomas, III MD (Harry)
Professor of Clinical Medicine,  Pulmonary and Critical Care Division
Department of Medicine, Cornell Univ. Medical School
Director, Pulmonary Research, Burke Rehabilitation Hospital
785 Mamaroneck Ave.  White Plains, NY 10605
(914) 597-2141


From nih-image-request@io.ece.drexel.edu Wed Aug 19 12:23 EDT 1998
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On Wed, 19 Aug 1998 06:16:09 -0400 (EDT)
nih-image-d-request@io.ece.drexel.edu wrote:

>Date: Tue, 18 Aug 98 10:02:54 PDT
>From: Walter Wolf <wwolfw@hsc.usc.edu>
>To: nih-image@io.ece.drexel.edu
>Cc: wwolfw@hsc.usc.edu, hkim@hsc.usc.edu
>Subject: Is there a macro for automating ROI analysis?
>Message-ID: <CMM.0.90.4.903459774.wwolfw@hsc.usc.edu>
>
>Is there a macro anyone has written that allows a definition of a
>region-of-interest, and once defined, can analyze each of the pixels in
>that stack? Basically, what I am looking for is using the macro "Plot
Z-Axis
>Profile [Z]" together with another macro (or a modification of Plot
>Z-Axis Profile [Z]) to plot each of the pixels in a ROI, and save the
results
>to measurement files.
>

I'm not sure about analyzing *each* of the pixels in the ROI through the
stack, but if you want to measure the *average* values of pixels in the
ROI this macro should do the trick: 

Procedure CheckForStack;
begin
  if nPics = 0 then
  begin
    PutMessage('This macro requires a stack!');
    exit;
  end;
  if nSlices = 0 then
  begin
    PutMessage('This window is not a stack!');
    exit;
  end;
end;

macro 'ROI Stack Measurement [R]';
{
Takes a stack and outputs measurements of the selected ROI from each
frame in the stack.
}

var
  i, oldSliceNum: integer;
begin
  CheckForStack;
  ResetCounter;
  oldSliceNum := SliceNumber;
  SaveState;
  for i := 1 to nSlices do
  begin
    ChooseSlice(i);
    RestoreROI;
    Measure;
  end;
  UpdateResults;
  SelectSlice(oldSliceNum);
  RestoreState;
end;


(The CheckForStack procedure is from the standard Stack Macros file that
comes with NIH-Image; omit it if you paste the ROI Stack Measurement
macro into the Stack Macros file.)

If you actually do want to measure and plot each pixel in the ROI you
could select each pixel manually and run the macro repeatedly for all of
the pixels in the region you want to measure, although this might prove
tedious.


Mark N. Rand, Ph.D.
U.W. Dept. Neurology, School of Medicine
1959 NE Pacific St., Box 356465
Seattle WA 98195-6465

fax: (206) 616-8272
vox: (206) 616-5153

<){{{{><    <){{{{><    <){{{{><    <){{{{><    <){{{{><
<){{{{><

From nih-image-request@io.ece.drexel.edu Wed Aug 19 12:34 EDT 1998
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Henry M. Thomas wrote:

> I want to paste into the middle of a 1500 by 800 pixel window, which doesn'
> fit on the screen.  Pasting into the scrollable, regular window pastes at,
> roughly (and unpredictably by me) 250,250, whereas pasting into the
> scaled-to-fit-window window pastes reliably at 750,400.  Then I can move
> the ROI by macro.
>
> Scale to Fit Window is in the Options Menu.  I can't find a macro
> equivalent.  If not, how can I reliably move the upper left corner of the
> pasted ROI to, say 20,20?
>
> Thanks, Harry
>
> Henry M. Thomas, III MD (Harry)
> Professor of Clinical Medicine,  Pulmonary and Critical Care Division
> Department of Medicine, Cornell Univ. Medical School
> Director, Pulmonary Research, Burke Rehabilitation Hospital
> 785 Mamaroneck Ave.  White Plains, NY 10605
> (914) 597-2141

Harry,

Hope this is what you need.....

Macro 'Paste Selection 20,20'
Var
left,top,width,height:integer;
begin
GetRoi(left,top,width,height);
Copy;
SetNewSize(1500,800);
MakeNewWindow('1500x800');
MakeROI(20,20,width,height);
Paste;
end;



Jeremy

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

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


From nih-image-request@io.ece.drexel.edu Wed Aug 19 15:47 EDT 1998
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From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
Subject: Re: white bars in the histogram
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>I'm calculating a histogram of a ROI and exporting the data to a file.
>When I look at the file I find that about every 10 values is a zero when
>it shouldn't be.  Is there a way to turn this feature off?
>
>Paul Morin
>
>University of Minnesota

It might not be applied to your case,

If you had imported the image and used a scale these things can happen.

Cengizhan


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


From nih-image-request@io.ece.drexel.edu Wed Aug 19 16:33 EDT 1998
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From: "Anneke M.Th. Harbers and Ard Jonker" <a_team@dds.nl>
Subject: Re: Capture max intensity during TIFF import
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>Greg (and Henry)-

I would advocate to set another variable (min) to be taken:
...,stackmin:integer;
...
 stackmin:=65536;
 for i := 1 to nSlices do begin
   SelectPic(StackPID);
   SelectSlice(i);
   SelectAll;
   Measure;
   GetResults(n,mean,mode,min,max);
   Writeln(i,tab,max);
   If stackmax < max then stackmax:=max;
   If stackmin < min then stackmin:=min;
  end;
  SetImportMinMax(min,stackmax);
  SetImport('TIFF');
  Import(path);
end;

This prevents that you waste probably unused lower values. If the 16 bit stack contains values of e.g. 10.000 to 40.000, you have gained some precision, as greyvalue 0 will be assigned to 10.000 rather than to 0.
The range will be 10.000...40.000 rather than 0...40.000 spread over 256 greyvalues.

Ard


From nih-image-request@io.ece.drexel.edu Wed Aug 19 21:13 EDT 1998
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From: kwb <kwb@bserv.com>
Subject: NIH Quicktimes in PowerPoint Presentations. 
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I've created quicktime animations using  NIH Image 1.62 and have no problem
viewing them using PowerPoint on the Mac.  I haven't been as successful
using the  PC version.
Has anybody had  any success presenting quicktime animations using
PowerPoint on a PC platform and is there a particular variety of quicktime
(video, cinepak, animation?) that might be best suited to this purpose?
Thank you in advance for any comments or suggestions.

		Regards,
			Ken Baker
kwb@bserv.com


From nih-image-d-request@io.ece.drexel.edu Thu Aug 20 04:18 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #40
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 40

Today's Topics:
  Morphologic Operations and NIH Image  [ "Michael Shrout" <MSHROUT@mail.mcg. ]
  EDINBURGH LOCAL FORUM?                [ Jeremy Brown <brownj@netmatters.co. ]
  Re: Capture max intensity during TIF  [ hmthomas@med.cornell.edu (Henry M.  ]
  Macro command for Scale to fit Windo  [ hmthomas@med.cornell.edu (Henry M.  ]
  Re: Is there a macro for automating   [ "Mark N. Rand" <mnr@saul.u.washingt ]
  Re: Macro command for Scale to fit W  [ Jeremy Brown <brownj@netmatters.co. ]
  Re: white bars in the histogram       [ Cengizhan Ozturk <cozturk@mri.jhu.e ]
  Re: Capture max intensity during TIF  [ "Anneke M.Th. Harbers and Ard Jonke ]
  NIH Quicktimes in PowerPoint Present  [ kwb <kwb@bserv.com> ]
  Method for analyzing many particles   [ "KUNITOMO,Junko" <kunitomo@envi.osa ]

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

Date: Wed, 19 Aug 1998 08:11:25 -0400
From: "Michael Shrout" <MSHROUT@mail.mcg.edu>
To: nih-image@io.ece.drexel.edu
Subject: Morphologic Operations and NIH Image
Message-Id: <s5da858a.047@mail.mcg.edu>
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 I am attempting to use the Binary menu to simplify and measure bone changes.  The program states that "Erode and Dilate do not perform erosion and dilation with structuring elements as described in the literature of classical mathematical morphology."  I'm trying to understand what I am doing when I use the Binary submenu.  The program defines these  procedures:
Erode - Removes pixels from the edges of objects in a binary images, where contiguous black areas in the image are considered objects, and background is assumed to be white. A pixel is removed (set to white) if four or more of its eight neighbors are white. Erosion separates objects that are touching and removes isolated pixels.

Dilate - Adds pixels to the edges of objects in a binary images. A pixel is added (set to black) if four or more of its eight neighbors are black. Dilation connects discontinuous objects and fills in holes.

 Does Image do morphologic operations?  Is if fair to say a morphologic operation is the net change to an image, regardless of the technique used to get there?  In other words, does it matter if I skeletonize an image with Image or, say, Alice [Dip Station] which apparently uses different mathematical structuring elements?  If they are different, can I use the morphologic operator literature to justify a technique I develop using Image?

I'd appreciate any input I can get!

Mike Shrout
Associate Professor
Medical College of Georgia

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

Date: Wed, 19 Aug 1998 14:35:10 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: EDINBURGH LOCAL FORUM?
Message-ID: <35DAE297.5C5F372@netmatters.co.uk>
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Would anyone in the Edinburgh Area, or Scotland come to that, be interested in some kind of local NIH/Object/Scion Image forum?

Jeremy




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

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

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

Date: Wed, 19 Aug 1998 11:33:06 -0400
From: hmthomas@med.cornell.edu (Henry M. Thomas)
To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center)
Subject: Re: Capture max intensity during TIFF import
Message-Id: <v01540b00b20064cba8a4@[206.152.160.60]>
Content-Type: text/plain; charset="us-ascii"

Thanks for the help.  Using IMPORT repeatedly gives flexibility in the
Import command.  Greg's Measure (the max intensity in each of 5 slices)
works fine.  Wayne's cvalue(1) is more elegant, but I kept getting 1 for
cValue(1); I'm sure it can be worked out.  Here is the code that works for
me.
Appreciatively, Harry


var
   LargestMax,sliceno,width,height,lower,upper:integer; {Global variable,
initially zero}
  OldStackTitle,NewStackTitle,NewerStackTitle,NewWindowTitle:string;

procedure procIMPORT
begin

{Import 1st time and discard.  Image's automatic TIFF file detection gets
height & Width from a 16 bit Scanalytics Cellscan PC 5 slice TIFF}
    Import('');            {1st time you run program, default  no. slices is 1}
    GetPicSize(width,height);      {only necessary cause SetCustom requires it}
    Dispose;

{Import 2nd time (and discard) with dummy fixed scale to get the largest
calibrated value in the 5 slices; "custom' uses the height,width and offset
from the previous Import }
    SetImport('custom,16-bits unsigned,swap bytes,calibrate');
    SetImportMinMax(0,32767);
    SetCustom(width,height,8,5); {1st time program runs, you need to set
slices to 5}
    Import('');
    largestMax := 0;
    ResetCounter;
    for i:=1 to nSlices do begin
        selectSlice(i); Measure;
        if rMax[i] >largestMax then largestMax:= rMax[i];
    end;
    Dispose;

{Import 3rd time with fixed scale using largest calibrated value in the 5
slices as  max}
    SetImport('custom,16-bits unsigned,swap bytes,calibrate');
    SetImportMinMax(0,largestMax);
    Import('');
    SetScale(1,'pixel');
end

Henry M. Thomas, III MD (Harry)
Professor of Clinical Medicine,  Pulmonary and Critical Care Division
Department of Medicine, Cornell Univ. Medical School
Director, Pulmonary Research, Burke Rehabilitation Hospital
785 Mamaroneck Ave.  White Plains, NY 10605
(914) 597-2141

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

Date: Wed, 19 Aug 1998 11:42:21 -0400
From: hmthomas@med.cornell.edu (Henry M. Thomas)
To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center)
Subject: Macro command for Scale to fit Window?
Message-Id: <v01540b01b20068196f72@[206.152.160.96]>
Content-Type: text/plain; charset="us-ascii"

I want to paste into the middle of a 1500 by 800 pixel window, which doesn'
fit on the screen.  Pasting into the scrollable, regular window pastes at,
roughly (and unpredictably by me) 250,250, whereas pasting into the
scaled-to-fit-window window pastes reliably at 750,400.  Then I can move
the ROI by macro.

Scale to Fit Window is in the Options Menu.  I can't find a macro
equivalent.  If not, how can I reliably move the upper left corner of the
pasted ROI to, say 20,20?

Thanks, Harry

Henry M. Thomas, III MD (Harry)
Professor of Clinical Medicine,  Pulmonary and Critical Care Division
Department of Medicine, Cornell Univ. Medical School
Director, Pulmonary Research, Burke Rehabilitation Hospital
785 Mamaroneck Ave.  White Plains, NY 10605
(914) 597-2141

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

Date: Wed, 19 Aug 1998 09:05:31 -0700
From: "Mark N. Rand" <mnr@saul.u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Is there a macro for automating ROI analysis?
Message-ID: <MailDrop1.2d7j-PPC.980819090531@d-128-95-211-137.dhcp2.washington.edu>
Content-Type: TEXT/PLAIN; CHARSET=ISO-8859-1
Content-Transfer-Encoding: 8bit

On Wed, 19 Aug 1998 06:16:09 -0400 (EDT)
nih-image-d-request@io.ece.drexel.edu wrote:

>Date: Tue, 18 Aug 98 10:02:54 PDT
>From: Walter Wolf <wwolfw@hsc.usc.edu>
>To: nih-image@io.ece.drexel.edu
>Cc: wwolfw@hsc.usc.edu, hkim@hsc.usc.edu
>Subject: Is there a macro for automating ROI analysis?
>Message-ID: <CMM.0.90.4.903459774.wwolfw@hsc.usc.edu>
>
>Is there a macro anyone has written that allows a definition of a
>region-of-interest, and once defined, can analyze each of the pixels in
>that stack? Basically, what I am looking for is using the macro "Plot
Z-Axis
>Profile [Z]" together with another macro (or a modification of Plot
>Z-Axis Profile [Z]) to plot each of the pixels in a ROI, and save the
results
>to measurement files.
>

I'm not sure about analyzing *each* of the pixels in the ROI through the
stack, but if you want to measure the *average* values of pixels in the
ROI this macro should do the trick: 

Procedure CheckForStack;
begin
  if nPics = 0 then
  begin
    PutMessage('This macro requires a stack!');
    exit;
  end;
  if nSlices = 0 then
  begin
    PutMessage('This window is not a stack!');
    exit;
  end;
end;

macro 'ROI Stack Measurement [R]';
{
Takes a stack and outputs measurements of the selected ROI from each
frame in the stack.
}

var
  i, oldSliceNum: integer;
begin
  CheckForStack;
  ResetCounter;
  oldSliceNum := SliceNumber;
  SaveState;
  for i := 1 to nSlices do
  begin
    ChooseSlice(i);
    RestoreROI;
    Measure;
  end;
  UpdateResults;
  SelectSlice(oldSliceNum);
  RestoreState;
end;


(The CheckForStack procedure is from the standard Stack Macros file that
comes with NIH-Image; omit it if you paste the ROI Stack Measurement
macro into the Stack Macros file.)

If you actually do want to measure and plot each pixel in the ROI you
could select each pixel manually and run the macro repeatedly for all of
the pixels in the region you want to measure, although this might prove
tedious.


Mark N. Rand, Ph.D.
U.W. Dept. Neurology, School of Medicine
1959 NE Pacific St., Box 356465
Seattle WA 98195-6465

fax: (206) 616-8272
vox: (206) 616-5153

<){{{{><    <){{{{><    <){{{{><    <){{{{><    <){{{{><
<){{{{><

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

Date: Wed, 19 Aug 1998 17:22:39 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Macro command for Scale to fit Window?
Message-ID: <35DB09DC.96BEFFC8@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Henry M. Thomas wrote:

> I want to paste into the middle of a 1500 by 800 pixel window, which doesn'
> fit on the screen.  Pasting into the scrollable, regular window pastes at,
> roughly (and unpredictably by me) 250,250, whereas pasting into the
> scaled-to-fit-window window pastes reliably at 750,400.  Then I can move
> the ROI by macro.
>
> Scale to Fit Window is in the Options Menu.  I can't find a macro
> equivalent.  If not, how can I reliably move the upper left corner of the
> pasted ROI to, say 20,20?
>
> Thanks, Harry
>
> Henry M. Thomas, III MD (Harry)
> Professor of Clinical Medicine,  Pulmonary and Critical Care Division
> Department of Medicine, Cornell Univ. Medical School
> Director, Pulmonary Research, Burke Rehabilitation Hospital
> 785 Mamaroneck Ave.  White Plains, NY 10605
> (914) 597-2141

Harry,

Hope this is what you need.....

Macro 'Paste Selection 20,20'
Var
left,top,width,height:integer;
begin
GetRoi(left,top,width,height);
Copy;
SetNewSize(1500,800);
MakeNewWindow('1500x800');
MakeROI(20,20,width,height);
Paste;
end;



Jeremy

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

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

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

Date: Wed, 19 Aug 1998 15:40:10 -0400
From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: white bars in the histogram
Message-Id: <v03007803b200da02a16f@[128.220.160.47]>
Content-Type: text/plain; charset="us-ascii"

>I'm calculating a histogram of a ROI and exporting the data to a file.
>When I look at the file I find that about every 10 values is a zero when
>it shouldn't be.  Is there a way to turn this feature off?
>
>Paul Morin
>
>University of Minnesota

It might not be applied to your case,

If you had imported the image and used a scale these things can happen.

Cengizhan


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

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

Date: Wed, 19 Aug 1998 22:23:51 +0200
From: "Anneke M.Th. Harbers and Ard Jonker" <a_team@dds.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Capture max intensity during TIFF import
Message-Id: <l03130301b200e37ab643@[194.109.129.1]>
Content-Type: text/plain; charset="us-ascii"

>Greg (and Henry)-

I would advocate to set another variable (min) to be taken:
...,stackmin:integer;
...
 stackmin:=65536;
 for i := 1 to nSlices do begin
   SelectPic(StackPID);
   SelectSlice(i);
   SelectAll;
   Measure;
   GetResults(n,mean,mode,min,max);
   Writeln(i,tab,max);
   If stackmax < max then stackmax:=max;
   If stackmin < min then stackmin:=min;
  end;
  SetImportMinMax(min,stackmax);
  SetImport('TIFF');
  Import(path);
end;

This prevents that you waste probably unused lower values. If the 16 bit stack contains values of e.g. 10.000 to 40.000, you have gained some precision, as greyvalue 0 will be assigned to 10.000 rather than to 0.
The range will be 10.000...40.000 rather than 0...40.000 spread over 256 greyvalues.

Ard

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

Date: Wed, 19 Aug 1998 21:01:08 -0400
From: kwb <kwb@bserv.com>
To: nih-image@io.ece.drexel.edu
Subject: NIH Quicktimes in PowerPoint Presentations. 
Message-Id: <l03110701b2011f555a0f@[204.101.187.51]>
Content-Type: text/plain; charset="us-ascii"

I've created quicktime animations using  NIH Image 1.62 and have no problem
viewing them using PowerPoint on the Mac.  I haven't been as successful
using the  PC version.
Has anybody had  any success presenting quicktime animations using
PowerPoint on a PC platform and is there a particular variety of quicktime
(video, cinepak, animation?) that might be best suited to this purpose?
Thank you in advance for any comments or suggestions.

		Regards,
			Ken Baker
kwb@bserv.com

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

Date: Thu, 20 Aug 1998 17:04:39 +0900
From: "KUNITOMO,Junko" <kunitomo@envi.osakafu-u.ac.jp>
To: nih-image@io.ece.drexel.edu
Subject: Method for analyzing many particles 
Message-Id: <199808200804.RAA14195@region.envi.osakafu-u.ac.jp>
Content-Type: text/plain; charset="ISO-2022-JP"
Content-Transfer-Encoding: 7bit

I need some help with analysis of particles. I would like to count and
measure more than 8000(Max Measurements) particles and long perimeter
particles.
Please let me know if there is a method for analyzing many particles for
example particle count and perimeter?

***************************************
$BT"M'=_;R!J(JKUNITOMO,Junko)
Osaka Prefecture University
Gakuen cho 1-1,Sakai city,Osaka,Japan
Tel$B!'(J+81-722-54-9444
Fax$B!'(J+81-722-54-9918
E-mail$B!'(Jkunitomo@envi.osakafu-u.ac.jp

--------------------------------
End of nih-image-d Digest V98 Issue #40
***************************************

From nih-image-request@io.ece.drexel.edu Thu Aug 20 04:19 EDT 1998
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From: "KUNITOMO,Junko" <kunitomo@envi.osakafu-u.ac.jp>
Subject: Method for analyzing many particles 
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I need some help with analysis of particles. I would like to count and
measure more than 8000(Max Measurements) particles and long perimeter
particles.
Please let me know if there is a method for analyzing many particles for
example particle count and perimeter?

***************************************
$BT"M'=_;R!J(JKUNITOMO,Junko)
Osaka Prefecture University
Gakuen cho 1-1,Sakai city,Osaka,Japan
Tel$B!'(J+81-722-54-9444
Fax$B!'(J+81-722-54-9918
E-mail$B!'(Jkunitomo@envi.osakafu-u.ac.jp




From nih-image-request@io.ece.drexel.edu Thu Aug 20 06:47 EDT 1998
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Date: Thu, 20 Aug 1998 12:41:08 -0700
From: "Zuccala David" <zuccala@cris.enel.it>
Reply-To: zuccala@cris.enel.it
Organization: ENEL Ricerca - Polo Idraulico e Strutturale
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To: nih-image@io.ece.drexel.edu
Subject: Re: Morphologic Operations and NIH Image
References: <199808200815.EAA01819@io.ECE.Drexel.EDU>
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>  Does Image do morphologic operations?  Is if fair to say a morphologic operation is the > net change to an image, regardless of the technique used to get there?  In other words, > does it matter if I skeletonize an image with Image or, say, Alice [Dip Station] which > apparently uses different mathematical structuring elements?  If they are different, can I > use the morphologic operator literature to justify a technique I develop using Image?
> 
Dear Mike,
I used for some time NIH-Image and DIP Station (Alice didn't existed
yet, but I assume that it is not less powerful).
DIP Station implements grey-level morphology, that is more general than
binary morphology used by NIH-Image. Moreover, DIP Station allows you to
define your own structuring elements.
Anyway, if you try DIP Station morphology with binary images, you should
get the same results of NIH-Image morphology, as far as the structuring
elements are the same. 
For instance, NIH-Image structuring element with 4 neighbours should be
	 *
	***
	 *
and with 8 neighbours
	***
	***
	***
Be careful because DIP Station allows you to define also the centre of
the structuring element, that does change the result. Also check blacks
and whites because NIH-Image erosion may be DIP Station dilation and
vice-versa.

If you have more questions, I'll be at work tomorrow (Friday) and then
after September 15th.

Hope this helps.

David

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

David Zuccala'
ENEL RICERCA - Polo Idraulico e Strutturale              
v. Pozzobonelli, 6       ph.: + 39 02 7224.8487
I - 20162 Milano         fax: + 39 02 7224.8430
                         e-mail: zuccala@cris.enel.it

From nih-image-request@io.ece.drexel.edu Thu Aug 20 15:32 EDT 1998
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Date: Thu, 20 Aug 1998 15:09:29 -0400
To: nih-image@io.ece.drexel.edu
From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
Subject: Re: NIH Quicktimes in PowerPoint Presentations.
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>I've created quicktime animations using  NIH Image 1.62 and have no problem
>viewing them using PowerPoint on the Mac.  I haven't been as successful
>using the  PC version.
>Has anybody had  any success presenting quicktime animations using
>PowerPoint on a PC platform and is there a particular variety of quicktime
>(video, cinepak, animation?) that might be best suited to this purpose?
>Thank you in advance for any comments or suggestions.
>
>		Regards,
>			Ken Baker
>kwb@bserv.com

I was successfull in MAC-PC Quicktime presentations. Couple of pointers:

1. Get the latest Quicktime (3.x) for windozz from apple and carry it with
your presentation.
2. Do not use any compression schemes unless you have to. The choice will
depend on your movie.
3. Flatten the quicktime movies (latest movie player takes care of it, non
mac platform save option, also make it self contained )
4. I usually burn a CD (ISO 9660) then you can carry it around easily.

Good Luck.

Cengizhan


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


From nih-image-request@io.ece.drexel.edu Thu Aug 20 21:38 EDT 1998
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From: Matt Salmon <m.salmon@aims.gov.au>
Subject: Questions on NIH-image
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Hi, I have just subscribed to your mailing list so I hope that this
message gets through.  I am currently using NIH-image to determine egg
numbers from samples taken from female broodstock tiger prawns after
spawning. =20

Firstly, I should give you some background information of how I am using
this program.  At AIMS (The Australian Institute of Marine Science)
Mariculture facility an average experiment can involve anything up to 100
female broodstock.  When a female spawns we subsample her eggs (five
replicates per sample) to detemine fecundity.  Currently these samples
are manually counted and if each female spawns twice (although she can
spawn up to five times during an experiment) that's a minimum  of 400
samples (of which each replicate can contain up to 300 individual eggs)
that need to be counted.  That's a lot of counting, labour and time.  I
have just started to use NIH-image and I am still learning about it's
limits and functions with the help of your manual and general use of the
program. =20

I have several problems which I have encountered.  The prawn eggs are
between 100-150<italic>um</italic> in size and I can clearly see the eggs
on the computer monitor.  Unfortunately when the egg samples are
collected they are fixed in alcohol and this sometimes produces a
precipitate and other floculative material which ranges in size and
shape. =20

<bold>1)</bold> Is their a way that I can tell the computer to look for
<underline>spherical</underline> eggs within a given pixel range?  At the
moment when I define a given pixel size/range the computer detects other
particles within this range which are not eggs.  The eggs are always
spherical and do not resemble any other floculative material.

<bold>2)</bold> Another problem is that sometimes the eggs clump and are
not detected because they are larger than the defined pixel range.  I am
currently testing different detergents which have only partially resolved
the problem.  My question is, is their some way of telling the program to
measure the area (in the field of view) which is shaded by the eggs and
given the size of the eggs accuratley working out the number of eggs
which correlate to the shaded area within the given field of view?  For
example, If a their is a clump of eggs the program measures the area they
occupy and knowing that one egg is so many pixels in size determines that
their is 4 eggs within that clump.  Are these solvable problems or am I
hoping for too much out of this program?  If this can be done, is their
also a way of getting the program to differentiate between an egg and
other particles?  Can you tell the program to take a picture of an egg
and only count paricles which conform to it's size and shape?  The eggs
are quite distinct, spherical and can be seen easily with the naked=20
eye.

I know that some of these questions may be too complex but I hope that
you can shed some light as this program would be a huge benefit if I can
implement an accurate automated process for counting egg samples.  I'm
sure you will be hearing from me regularly but I hope I don't become to
much of a nuisance.


Yours Sincerely,


Matt Salmon BSc.

From nih-image-request@io.ece.drexel.edu Thu Aug 20 23:18 EDT 1998
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From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: m.salmon@aims.gov.au, nih-image@io.ece.drexel.edu
Date:          Fri, 21 Aug 1998 13:13:36 GMT+1000
Subject:       Re: Questions on NIH-image
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>Date: Fri, 21 Aug 1998 11:44:39 +1000
>From: Matt Salmon <m.salmon@aims.gov.au>
>Subject: Questions on NIH-image
>............  I am currently using NIH-image to determine egg
>numbers from samples taken from female broodstock tiger prawns after
>spawning.
>..........................

Matt, 

You can be quite confident that your project could be quite well done with 
NIH-Image and macros.
You should have some particular advantages with counting your eggs as they are 
both spherial and relatively uniform in size.
Your approach to attempt to have eggs separated (non-clumped) as far a possible 
I think is the correct one. It is easier to count analyse image of separate 
eggs than to separate eggs in the image :-) but there is a balance in that you 
want to maintain a reasonable egg density / field size / resolution.
Assuming you are using a PAL video camera 768x512 pixels and 100um eggs are say 
minimum 16 pixel diameter to allow adequate circularity test, you might expect 
eggs at say 32 pixel centers 24x16=384 eggs per field (5x3 mm) ....matches 300 
per sample quite well.

A ring-light illuminator to give you a dark field background with low angle 
incident light scatter from eggs to a dissecting microscope should give good 
contrast.

The tack I would take would be to analyzeParticles for eggsize particle range 
and then do a macro pass of each egg rMajor/rMinor axis to check near 1 and 
rMax[]~=rMin[] for uniform color.
More stringent qualification of particles could be done using 
autoOutline(rX[i],rY[i]) ie automated "wand"ing of each "particle" to allow 
detail analysis of shape.
You would then have data for a size histogram.
Larger "particles" or clumps could then be estimated on the basis of
rArea[clump]/modal rArea[egg]

A circular Hough transform could be used to emphasise circular objects (in 
clumps) but I would expect this to be an unnecessary complication in your case.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

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

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 41

Today's Topics:
  Re: Morphologic Operations and NIH I  [ "Zuccala David" <zuccala@cris.enel. ]
  Re: NIH Quicktimes in PowerPoint Pre  [ Cengizhan Ozturk <cozturk@mri.jhu.e ]
  Questions on NIH-image                [ Matt Salmon <m.salmon@aims.gov.au> ]
  Re: Questions on NIH-image            [ GJOSS@rna.bio.mq.edu.au ]

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

Date: Thu, 20 Aug 1998 12:41:08 -0700
From: "Zuccala David" <zuccala@cris.enel.it>
To: nih-image@io.ece.drexel.edu
Subject: Re: Morphologic Operations and NIH Image
Message-ID: <35DC7BD4.3B92@cris.enel.it>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

>  Does Image do morphologic operations?  Is if fair to say a morphologic operation is the > net change to an image, regardless of the technique used to get there?  In other words, > does it matter if I skeletonize an image with Image or, say, Alice [Dip Station] which > apparently uses different mathematical structuring elements?  If they are different, can I > use the morphologic operator literature to justify a technique I develop using Image?
> 
Dear Mike,
I used for some time NIH-Image and DIP Station (Alice didn't existed
yet, but I assume that it is not less powerful).
DIP Station implements grey-level morphology, that is more general than
binary morphology used by NIH-Image. Moreover, DIP Station allows you to
define your own structuring elements.
Anyway, if you try DIP Station morphology with binary images, you should
get the same results of NIH-Image morphology, as far as the structuring
elements are the same. 
For instance, NIH-Image structuring element with 4 neighbours should be
	 *
	***
	 *
and with 8 neighbours
	***
	***
	***
Be careful because DIP Station allows you to define also the centre of
the structuring element, that does change the result. Also check blacks
and whites because NIH-Image erosion may be DIP Station dilation and
vice-versa.

If you have more questions, I'll be at work tomorrow (Friday) and then
after September 15th.

Hope this helps.

David

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

David Zuccala'
ENEL RICERCA - Polo Idraulico e Strutturale              
v. Pozzobonelli, 6       ph.: + 39 02 7224.8487
I - 20162 Milano         fax: + 39 02 7224.8430
                         e-mail: zuccala@cris.enel.it

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

Date: Thu, 20 Aug 1998 15:09:29 -0400
From: Cengizhan Ozturk <cozturk@mri.jhu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Quicktimes in PowerPoint Presentations.
Message-Id: <v03007800b20221ceb99c@[128.220.160.47]>
Content-Type: text/plain; charset="us-ascii"

>I've created quicktime animations using  NIH Image 1.62 and have no problem
>viewing them using PowerPoint on the Mac.  I haven't been as successful
>using the  PC version.
>Has anybody had  any success presenting quicktime animations using
>PowerPoint on a PC platform and is there a particular variety of quicktime
>(video, cinepak, animation?) that might be best suited to this purpose?
>Thank you in advance for any comments or suggestions.
>
>		Regards,
>			Ken Baker
>kwb@bserv.com

I was successfull in MAC-PC Quicktime presentations. Couple of pointers:

1. Get the latest Quicktime (3.x) for windozz from apple and carry it with
your presentation.
2. Do not use any compression schemes unless you have to. The choice will
depend on your movie.
3. Flatten the quicktime movies (latest movie player takes care of it, non
mac platform save option, also make it self contained )
4. I usually burn a CD (ISO 9660) then you can carry it around easily.

Good Luck.

Cengizhan


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

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

Date: Fri, 21 Aug 1998 11:44:39 +1000
From: Matt Salmon <m.salmon@aims.gov.au>
To: nih-image@io.ece.drexel.edu
Subject: Questions on NIH-image
Message-Id: <3.0.1.32.19980821114439.0069b3f0@email.aims.gov.au>
Content-Type: text/enriched; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Hi, I have just subscribed to your mailing list so I hope that this
message gets through.  I am currently using NIH-image to determine egg
numbers from samples taken from female broodstock tiger prawns after
spawning. =20

Firstly, I should give you some background information of how I am using
this program.  At AIMS (The Australian Institute of Marine Science)
Mariculture facility an average experiment can involve anything up to 100
female broodstock.  When a female spawns we subsample her eggs (five
replicates per sample) to detemine fecundity.  Currently these samples
are manually counted and if each female spawns twice (although she can
spawn up to five times during an experiment) that's a minimum  of 400
samples (of which each replicate can contain up to 300 individual eggs)
that need to be counted.  That's a lot of counting, labour and time.  I
have just started to use NIH-image and I am still learning about it's
limits and functions with the help of your manual and general use of the
program. =20

I have several problems which I have encountered.  The prawn eggs are
between 100-150<italic>um</italic> in size and I can clearly see the eggs
on the computer monitor.  Unfortunately when the egg samples are
collected they are fixed in alcohol and this sometimes produces a
precipitate and other floculative material which ranges in size and
shape. =20

<bold>1)</bold> Is their a way that I can tell the computer to look for
<underline>spherical</underline> eggs within a given pixel range?  At the
moment when I define a given pixel size/range the computer detects other
particles within this range which are not eggs.  The eggs are always
spherical and do not resemble any other floculative material.

<bold>2)</bold> Another problem is that sometimes the eggs clump and are
not detected because they are larger than the defined pixel range.  I am
currently testing different detergents which have only partially resolved
the problem.  My question is, is their some way of telling the program to
measure the area (in the field of view) which is shaded by the eggs and
given the size of the eggs accuratley working out the number of eggs
which correlate to the shaded area within the given field of view?  For
example, If a their is a clump of eggs the program measures the area they
occupy and knowing that one egg is so many pixels in size determines that
their is 4 eggs within that clump.  Are these solvable problems or am I
hoping for too much out of this program?  If this can be done, is their
also a way of getting the program to differentiate between an egg and
other particles?  Can you tell the program to take a picture of an egg
and only count paricles which conform to it's size and shape?  The eggs
are quite distinct, spherical and can be seen easily with the naked=20
eye.

I know that some of these questions may be too complex but I hope that
you can shed some light as this program would be a huge benefit if I can
implement an accurate automated process for counting egg samples.  I'm
sure you will be hearing from me regularly but I hope I don't become to
much of a nuisance.


Yours Sincerely,


Matt Salmon BSc.

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

Date:          Fri, 21 Aug 1998 13:13:36 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: m.salmon@aims.gov.au, nih-image@io.ece.drexel.edu
Subject:       Re: Questions on NIH-image
Message-ID: <6583BB8361F@rna.bio.mq.edu.au>

>Date: Fri, 21 Aug 1998 11:44:39 +1000
>From: Matt Salmon <m.salmon@aims.gov.au>
>Subject: Questions on NIH-image
>............  I am currently using NIH-image to determine egg
>numbers from samples taken from female broodstock tiger prawns after
>spawning.
>..........................

Matt, 

You can be quite confident that your project could be quite well done with 
NIH-Image and macros.
You should have some particular advantages with counting your eggs as they are 
both spherial and relatively uniform in size.
Your approach to attempt to have eggs separated (non-clumped) as far a possible 
I think is the correct one. It is easier to count analyse image of separate 
eggs than to separate eggs in the image :-) but there is a balance in that you 
want to maintain a reasonable egg density / field size / resolution.
Assuming you are using a PAL video camera 768x512 pixels and 100um eggs are say 
minimum 16 pixel diameter to allow adequate circularity test, you might expect 
eggs at say 32 pixel centers 24x16=384 eggs per field (5x3 mm) ....matches 300 
per sample quite well.

A ring-light illuminator to give you a dark field background with low angle 
incident light scatter from eggs to a dissecting microscope should give good 
contrast.

The tack I would take would be to analyzeParticles for eggsize particle range 
and then do a macro pass of each egg rMajor/rMinor axis to check near 1 and 
rMax[]~=rMin[] for uniform color.
More stringent qualification of particles could be done using 
autoOutline(rX[i],rY[i]) ie automated "wand"ing of each "particle" to allow 
detail analysis of shape.
You would then have data for a size histogram.
Larger "particles" or clumps could then be estimated on the basis of
rArea[clump]/modal rArea[egg]

A circular Hough transform could be used to emphasise circular objects (in 
clumps) but I would expect this to be an unnecessary complication in your case.
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

--------------------------------
End of nih-image-d Digest V98 Issue #41
***************************************

From nih-image-request@io.ece.drexel.edu Fri Aug 21 03:05 EDT 1998
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From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Matt Salmon'" <m.salmon@aims.gov.au>,
        "'Image Mailing List'"
  <nih-image@io.ece.drexel.edu>
Subject: RE: Questions on NIH-image
Date: Fri, 21 Aug 1998 16:57:15 +1000
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Matt,
Hi,
Well you have a few good questions.
1. Image analysis is better if your samples are perfect. But you know
that already.
2. The eggs are little spheres but what you see on the monitor is
circles.
3. Is there some filtering you might do to pick out circles of a certain
size range?
I have some suggestions.
1 Try some FFT filterings using low or high pass filters.
2. Take an image of 1 egg all by itself and FFT this and then use this
as a mask for an image of many eggs. This is based on the idea that is
seen in John Russ's book The Image Processing handbook, in which a page
of text is processed using a template or mask made from one letter, in
the case illustrated an "e" I think. If you use a mask which passes the
frequency you should pick out all the 'e''s whereas if you filter out
the frequencies associated with the 'e''s you should remove them.
3. Try some convolution filters.
Variables to try. 
Filter size can vary from 3x3 up to 63x63.
Values in each of the filter cells can be between 0-255. 
Try with scaled convolutions on and off.
To try all of the possibilities can take quite a while.
ie with a 3x3 filter there are 9x256 arrangements, some of which would
be symmetrically equivalent.
Why it might be good.
With a suitable convolution mask which is circular (use zeros to pad it
out to the square) and of the same size as the circles in question then
a useful effect might be had.
4.
Try some background subtractions which can be used to remove small bits
from the field.
5. Try the ideas of masking the image with a thresholded image etc.
6. I guess the eggs are the same density grey as the other materials, if
not thresholding might help.
7. If you know the size of one egg and then write a macro it could be
used to determine the number of eggs in a mass of nicely packed eggs.
You would of course need to calibrate by counting a few hundred and
dividing by the appropriate number. 
Best regards
Noel

> ----------
> From: 	Matt Salmon
> Sent: 	Friday, 21 August 1998 11:44 AM
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	Questions on NIH-image
> 
> Hi, I have just subscribed to your mailing list so I hope that this
> message gets through.  I am currently using NIH-image to determine egg
> numbers from samples taken from female broodstock tiger prawns after
> spawning.   
> Firstly, I should give you some background information of how I am
> using this program.  At AIMS (The Australian Institute of Marine
> Science) Mariculture facility an average experiment can involve
> anything up to 100 female broodstock.  When a female spawns we
> subsample her eggs (five replicates per sample) to detemine fecundity.
> Currently these samples are manually counted and if each female spawns
> twice (although she can spawn up to five times during an experiment)
> that's a minimum  of 400 samples (of which each replicate can contain
> up to 300 individual eggs) that need to be counted.  That's a lot of
> counting, labour and time.  I have just started to use NIH-image and I
> am still learning about it's limits and functions with the help of
> your manual and general use of the program.   
> I have several problems which I have encountered.  The prawn eggs are
> between 100-150um in size and I can clearly see the eggs on the
> computer monitor.  Unfortunately when the egg samples are collected
> they are fixed in alcohol and this sometimes produces a precipitate
> and other floculative material which ranges in size and shape.   
> 1) Is their a way that I can tell the computer to look for spherical
> eggs within a given pixel range?  At the moment when I define a given
> pixel size/range the computer detects other particles within this
> range which are not eggs.  The eggs are always spherical and do not
> resemble any other floculative material. 
> 2) Another problem is that sometimes the eggs clump and are not
> detected because they are larger than the defined pixel range.  I am
> currently testing different detergents which have only partially
> resolved the problem.  My question is, is their some way of telling
> the program to measure the area (in the field of view) which is shaded
> by the eggs and given the size of the eggs accuratley working out the
> number of eggs which correlate to the shaded area within the given
> field of view?  For example, If a their is a clump of eggs the program
> measures the area they occupy and knowing that one egg is so many
> pixels in size determines that their is 4 eggs within that clump.  Are
> these solvable problems or am I hoping for too much out of this
> program?  If this can be done, is their also a way of getting the
> program to differentiate between an egg and other particles?  Can you
> tell the program to take a picture of an egg and only count paricles
> which conform to it's size and shape?  The eggs are quite distinct,
> spherical and can be seen easily with the naked  eye. 
> I know that some of these questions may be too complex but I hope that
> you can shed some light as this program would be a huge benefit if I
> can implement an accurate automated process for counting egg samples.
> I'm sure you will be hearing from me regularly but I hope I don't
> become to much of a nuisance. 
> 
> Yours Sincerely, 
> 
> Matt Salmon BSc. 
> 

From nih-image-request@io.ece.drexel.edu Fri Aug 21 16:27 EDT 1998
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From: "Paul Loftsgard" <ploftsgard@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: fractal analysis
Date: Fri, 21 Aug 1998 13:02:30 PDT
Resent-Message-ID: <"eal-g.0.651.x9Ttr"@io>
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I have another question about the fractal analysis macros(I wrote a 
couple weeks ago about edm).  Anyway my question is this:

Does area play a factor in determing fractal dimension with either the 
box counting or edm method?

I am finding the dimensions of sprays and at the top and bottom of each 
spray is a flat side(the end of the cameras field of view).  I was 
wondering whether or not I can just remove the center portion of the 
spray, attach the two sides and determine the dimension of the new 
image.  This results in about half of the total area of the spray being 
eliminated.
Any help would be appreciated(or ideas on how to get around the flat 
sides)

Thanks,
    Paul Loftsgard

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

From nih-image-request@io.ece.drexel.edu Fri Aug 21 16:44 EDT 1998
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Date: Fri, 21 Aug 1998 16:23:33 -0400
To: nih-image@io.ece.drexel.edu
From: Dominique Berube <d306604@er.uqam.ca>
Subject: Re: fractal analysis
Resent-Message-ID: <"4qmRX1.0.0U1.EUTtr"@io>
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>I have another question about the fractal analysis macros(I wrote a
>couple weeks ago about edm).  Anyway my question is this:
>
>Does area play a factor in determing fractal dimension with either the
>box counting or edm method?

My own experience showed that size is of the most importance with
box-counting. Fractal dimension varies greatly with size, because of the
limited amount of data generated with that method. That is the primary
reason why I never use this method on boundaries. The scale of the study is
too limited to use it.
With EDM, I manage to produce consistant fractal dimensions (variations of
0.03 max) for particle sizes between 10000 and 400000 pixels. This was
tested on a few particles, by varying the resolution  of the image (at the
time of the acquisition, of course!).


>
>I am finding the dimensions of sprays and at the top and bottom of each
>spray is a flat side(the end of the cameras field of view).  I was
>wondering whether or not I can just remove the center portion of the
>spray, attach the two sides and determine the dimension of the new
>image.  This results in about half of the total area of the spray being
>eliminated.
>Any help would be appreciated(or ideas on how to get around the flat
>sides)
>
Well. I'm not so sure about this one. If your image could be limited to
just your two side lines (not the straignt ones), I don't see the problem
with the fractal analysis. You could crop your image to eliminate the two
flat sizes (if they are at the top and bottom of the image). Fractal
analysis would then be limited to the two lines still on the picture. OK,
I'm not sure enough here so I'll stop! :)

Dominique

Dominique Berube
Ph.D Environmental Sciences, UQAM
Email: d306604@er.uqam.ca
Phone: (514) 987-3000 (3986)
Fax: (514) 987-7749


From nih-image-d-request@io.ece.drexel.edu Sat Aug 22 06:12 EDT 1998
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 42

Today's Topics:
  RE: Questions on NIH-image            [ "Goldsmith, Noel" <Noel.Goldsmith@d ]
  fractal analysis                      [ "Paul Loftsgard" <ploftsgard@hotmai ]
  Re: fractal analysis                  [ Dominique Berube <d306604@er.uqam.c ]

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

Date: Fri, 21 Aug 1998 16:57:15 +1000
From: "Goldsmith, Noel" <Noel.Goldsmith@dsto.defence.gov.au>
To: "'Matt Salmon'" <m.salmon@aims.gov.au>,
        "'Image Mailing List'"
	 <nih-image@io.ece.drexel.edu>
Subject: RE: Questions on NIH-image
Message-ID: <F98649A5EE8ED11190160000F802756598CDEE@exchvic3.dsto.defence.gov.au>
Content-Type: text/plain;
	charset="iso-8859-1"

Matt,
Hi,
Well you have a few good questions.
1. Image analysis is better if your samples are perfect. But you know
that already.
2. The eggs are little spheres but what you see on the monitor is
circles.
3. Is there some filtering you might do to pick out circles of a certain
size range?
I have some suggestions.
1 Try some FFT filterings using low or high pass filters.
2. Take an image of 1 egg all by itself and FFT this and then use this
as a mask for an image of many eggs. This is based on the idea that is
seen in John Russ's book The Image Processing handbook, in which a page
of text is processed using a template or mask made from one letter, in
the case illustrated an "e" I think. If you use a mask which passes the
frequency you should pick out all the 'e''s whereas if you filter out
the frequencies associated with the 'e''s you should remove them.
3. Try some convolution filters.
Variables to try. 
Filter size can vary from 3x3 up to 63x63.
Values in each of the filter cells can be between 0-255. 
Try with scaled convolutions on and off.
To try all of the possibilities can take quite a while.
ie with a 3x3 filter there are 9x256 arrangements, some of which would
be symmetrically equivalent.
Why it might be good.
With a suitable convolution mask which is circular (use zeros to pad it
out to the square) and of the same size as the circles in question then
a useful effect might be had.
4.
Try some background subtractions which can be used to remove small bits
from the field.
5. Try the ideas of masking the image with a thresholded image etc.
6. I guess the eggs are the same density grey as the other materials, if
not thresholding might help.
7. If you know the size of one egg and then write a macro it could be
used to determine the number of eggs in a mass of nicely packed eggs.
You would of course need to calibrate by counting a few hundred and
dividing by the appropriate number. 
Best regards
Noel

> ----------
> From: 	Matt Salmon
> Sent: 	Friday, 21 August 1998 11:44 AM
> To: 	nih-image@io.ece.drexel.edu
> Subject: 	Questions on NIH-image
> 
> Hi, I have just subscribed to your mailing list so I hope that this
> message gets through.  I am currently using NIH-image to determine egg
> numbers from samples taken from female broodstock tiger prawns after
> spawning.   
> Firstly, I should give you some background information of how I am
> using this program.  At AIMS (The Australian Institute of Marine
> Science) Mariculture facility an average experiment can involve
> anything up to 100 female broodstock.  When a female spawns we
> subsample her eggs (five replicates per sample) to detemine fecundity.
> Currently these samples are manually counted and if each female spawns
> twice (although she can spawn up to five times during an experiment)
> that's a minimum  of 400 samples (of which each replicate can contain
> up to 300 individual eggs) that need to be counted.  That's a lot of
> counting, labour and time.  I have just started to use NIH-image and I
> am still learning about it's limits and functions with the help of
> your manual and general use of the program.   
> I have several problems which I have encountered.  The prawn eggs are
> between 100-150um in size and I can clearly see the eggs on the
> computer monitor.  Unfortunately when the egg samples are collected
> they are fixed in alcohol and this sometimes produces a precipitate
> and other floculative material which ranges in size and shape.   
> 1) Is their a way that I can tell the computer to look for spherical
> eggs within a given pixel range?  At the moment when I define a given
> pixel size/range the computer detects other particles within this
> range which are not eggs.  The eggs are always spherical and do not
> resemble any other floculative material. 
> 2) Another problem is that sometimes the eggs clump and are not
> detected because they are larger than the defined pixel range.  I am
> currently testing different detergents which have only partially
> resolved the problem.  My question is, is their some way of telling
> the program to measure the area (in the field of view) which is shaded
> by the eggs and given the size of the eggs accuratley working out the
> number of eggs which correlate to the shaded area within the given
> field of view?  For example, If a their is a clump of eggs the program
> measures the area they occupy and knowing that one egg is so many
> pixels in size determines that their is 4 eggs within that clump.  Are
> these solvable problems or am I hoping for too much out of this
> program?  If this can be done, is their also a way of getting the
> program to differentiate between an egg and other particles?  Can you
> tell the program to take a picture of an egg and only count paricles
> which conform to it's size and shape?  The eggs are quite distinct,
> spherical and can be seen easily with the naked  eye. 
> I know that some of these questions may be too complex but I hope that
> you can shed some light as this program would be a huge benefit if I
> can implement an accurate automated process for counting egg samples.
> I'm sure you will be hearing from me regularly but I hope I don't
> become to much of a nuisance. 
> 
> Yours Sincerely, 
> 
> Matt Salmon BSc. 
> 

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

Date: Fri, 21 Aug 1998 13:02:30 PDT
From: "Paul Loftsgard" <ploftsgard@hotmail.com>
To: nih-image@io.ece.drexel.edu
Subject: fractal analysis
Message-ID: <19980821200230.19206.qmail@hotmail.com>
Content-Type: text/plain

I have another question about the fractal analysis macros(I wrote a 
couple weeks ago about edm).  Anyway my question is this:

Does area play a factor in determing fractal dimension with either the 
box counting or edm method?

I am finding the dimensions of sprays and at the top and bottom of each 
spray is a flat side(the end of the cameras field of view).  I was 
wondering whether or not I can just remove the center portion of the 
spray, attach the two sides and determine the dimension of the new 
image.  This results in about half of the total area of the spray being 
eliminated.
Any help would be appreciated(or ideas on how to get around the flat 
sides)

Thanks,
    Paul Loftsgard

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

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

Date: Fri, 21 Aug 1998 16:23:33 -0400
From: Dominique Berube <d306604@er.uqam.ca>
To: nih-image@io.ece.drexel.edu
Subject: Re: fractal analysis
Message-Id: <l03130300b203852db882@[132.208.139.22]>
Content-Type: text/plain; charset="us-ascii"

>I have another question about the fractal analysis macros(I wrote a
>couple weeks ago about edm).  Anyway my question is this:
>
>Does area play a factor in determing fractal dimension with either the
>box counting or edm method?

My own experience showed that size is of the most importance with
box-counting. Fractal dimension varies greatly with size, because of the
limited amount of data generated with that method. That is the primary
reason why I never use this method on boundaries. The scale of the study is
too limited to use it.
With EDM, I manage to produce consistant fractal dimensions (variations of
0.03 max) for particle sizes between 10000 and 400000 pixels. This was
tested on a few particles, by varying the resolution  of the image (at the
time of the acquisition, of course!).


>
>I am finding the dimensions of sprays and at the top and bottom of each
>spray is a flat side(the end of the cameras field of view).  I was
>wondering whether or not I can just remove the center portion of the
>spray, attach the two sides and determine the dimension of the new
>image.  This results in about half of the total area of the spray being
>eliminated.
>Any help would be appreciated(or ideas on how to get around the flat
>sides)
>
Well. I'm not so sure about this one. If your image could be limited to
just your two side lines (not the straignt ones), I don't see the problem
with the fractal analysis. You could crop your image to eliminate the two
flat sizes (if they are at the top and bottom of the image). Fractal
analysis would then be limited to the two lines still on the picture. OK,
I'm not sure enough here so I'll stop! :)

Dominique

Dominique Berube
Ph.D Environmental Sciences, UQAM
Email: d306604@er.uqam.ca
Phone: (514) 987-3000 (3986)
Fax: (514) 987-7749

--------------------------------
End of nih-image-d Digest V98 Issue #42
***************************************

From nih-image-request@io.ece.drexel.edu Mon Aug 24 16:55 EDT 1998
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From: "Plylar, Tracy  A. [C]" <plylart@nima.mil>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: NIH-Image Year 2000 compatible?
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I need to know if NIH-Image has Y2K compatible issues?
Of course there are no dates calculations involved in this software,
(and if so, the OS would be responsible) but the vendors need to issue a
written statement acknowledging this.  Can anyone direct me to the URL
where NIH states what version of NIH-Image is Y2K compatible?  thanks TP


From nih-image-request@io.ece.drexel.edu Mon Aug 24 17:53 EDT 1998
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Date: Mon, 24 Aug 1998 17:43:30 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: NIH-Image Year 2000 compatible?
Resent-Message-ID: <"Jl2uj2.0.Cy5.7rTur"@io>
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>I need to know if NIH-Image has Y2K compatible issues?
>Of course there are no dates calculations involved in this software,
>(and if so, the OS would be responsible) but the vendors need to issue a
>written statement acknowledging this.  Can anyone direct me to the URL
>where NIH states what version of NIH-Image is Y2K compatible?  thanks TP

    http://rsb.info.nih.gov/nih-image/manual/faq.html (as of this afternoon)

-wayne



From nih-image-request@io.ece.drexel.edu Tue Aug 25 01:02 EDT 1998
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Subject: Frame grabber cards
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Hi there,
          there is a power pc set up here on campus which I am using for my
project.  I need to capture some images from a camera which is connected to
the computer except the computer insists that I need a frame grabber card to
do so.  I know for a fact that there is already a frame grabber card
installed in the machine but I have been unsuccessful in enabling it.  I
have followed instructions and used the sub-menu function 'Acquire' in order
to try and launch it but it hasn't worked.

Any suggestions would be appreciated.

Please keep in mind that I am fairly unfamiliar with the Apple Mac computer.

Cormac McCann
Final Year Mechanical Engineering student.



From nih-image-d-request@io.ece.drexel.edu Tue Aug 25 09:22 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #43
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 43

Today's Topics:
  NIH-Image Year 2000 compatible?       [ "Plylar, Tracy A. [C]" <plylart@nim ]
  Re: NIH-Image Year 2000 compatible?   [ Wayne Rasband <wayne@codon.nih.gov> ]
  Frame grabber cards                   [ Cormac <mccannc@topaz.cqu.edu.au> ]
  unsubscribe                           [ "Dale H." <dah13@psu.edu> ]

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

Date: Mon, 24 Aug 1998 16:29:32 -0400
From: "Plylar, Tracy  A. [C]" <plylart@nima.mil>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: NIH-Image Year 2000 compatible?
Message-ID: <EF84868C3C51D111ADB500805FBE425F8A262A@RESX1>
Content-Type: text/plain

I need to know if NIH-Image has Y2K compatible issues?
Of course there are no dates calculations involved in this software,
(and if so, the OS would be responsible) but the vendors need to issue a
written statement acknowledging this.  Can anyone direct me to the URL
where NIH states what version of NIH-Image is Y2K compatible?  thanks TP

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

Date: Mon, 24 Aug 1998 17:43:30 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH-Image Year 2000 compatible?
Message-Id: <v03007803b2078ebf784a@[128.231.99.216]>
Content-Type: text/plain; charset="us-ascii"

>I need to know if NIH-Image has Y2K compatible issues?
>Of course there are no dates calculations involved in this software,
>(and if so, the OS would be responsible) but the vendors need to issue a
>written statement acknowledging this.  Can anyone direct me to the URL
>where NIH states what version of NIH-Image is Y2K compatible?  thanks TP

    http://rsb.info.nih.gov/nih-image/manual/faq.html (as of this afternoon)

-wayne

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

Date: Tue, 25 Aug 1998 14:51:34 +1000 (EST)
From: Cormac <mccannc@topaz.cqu.edu.au>
To: nih-image@io.ece.drexel.edu
Subject: Frame grabber cards
Message-Id: <199808250451.OAA32367@topaz.cqu.edu.au>
Content-Type: text/plain; charset="us-ascii"

Hi there,
          there is a power pc set up here on campus which I am using for my
project.  I need to capture some images from a camera which is connected to
the computer except the computer insists that I need a frame grabber card to
do so.  I know for a fact that there is already a frame grabber card
installed in the machine but I have been unsuccessful in enabling it.  I
have followed instructions and used the sub-menu function 'Acquire' in order
to try and launch it but it hasn't worked.

Any suggestions would be appreciated.

Please keep in mind that I am fairly unfamiliar with the Apple Mac computer.

Cormac McCann
Final Year Mechanical Engineering student.

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

Date: Tue, 25 Aug 1998 09:06:21 -0400
From: "Dale H." <dah13@psu.edu>
To: nih-image@io.ece.drexel.edu
Subject: unsubscribe
Message-Id: <3.0.1.32.19980825090621.0071b500@email.psu.edu>
Content-Type: text/plain; charset="us-ascii"


--------------------------------
End of nih-image-d Digest V98 Issue #43
***************************************

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From nih-image-request@io.ece.drexel.edu Tue Aug 25 13:19 EDT 1998
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<fontfamily><param>Times</param>Hi everyone.


The following is a reminder to everyone regarding administrative issues
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</fontfamily>

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

                                  Jonathan Nissanov, Ph.D.

                                      Associate Director  

            Computer Vision Center for Vertebrate Brain Mapping,

                a NIH Biomedical Research Technology Resource

                                http://cbis.ece.drexel.edu/ICVC/

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

Imaging and Computer Vision Center              Tel: 215-895-1381

Drexel University                                                  
Fax: 215-895-4987

Phildelphia, PA 19104                                        
yoni@coe.drexel.edu

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

      

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


From nih-image-request@io.ece.drexel.edu Tue Aug 25 14:56 EDT 1998
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Subject: Re: Frame grabber cards
To: nih-image@io.ece.drexel.edu
Date: Tue, 25 Aug 98 12:41:15 MDT
From: "Doug S. Phillips" <phillips@ucalgary.ca>
Cc: mccannc@topaz.cqu.edu.au
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------------------------------
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Dear Cormac:

Cormac wrote:

>          there is a power pc set up here on campus which I am using for my
> project.  I need to capture some images from a camera which is connected to
> the computer except the computer insists that I need a frame grabber card to
>do so.  I know for a fact that there is already a frame grabber card
>installed in the machine but I have been unsuccessful in enabling it. 

In the frame grabber appendix of the online manual for NIH-Image
(at http://rsb.info.nih.gov/nih-image/manual/Appendices/frame.html )
it is stated that:

> Using VDIGs (QuickTime Video Digitizer extensions), Image also supports
> QuickTime compatible video digitizers such as those built into "AV" Macs and
> the PowerMac7500/8500.

>From http://ipt.lpl.arizona.edu/IPT/Help/helpmeister.html#13,
there is the following information:

> There are two main software components: digitizing software, and a system
> extension called a VDIG (video digitizer), which tells the computer how to
> communicate with the digitizing hardware. The VDIG for the AV Macs is called
> AV Digitizer Options, and it belongs in the Extensions folder in the System
> folder. If you need to install it manually, drag it to the closed System
> folder and it will automatically be placed in the proper location.

I saw another reference that indicated that the AV Digitizer Options
was in the Info-Mac archive, but, checking there now, I can't find it.

If someone else can complete the story here, I would interested
in finding out the answer to the original question.  Thanks.

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


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


From nih-image-d-request@io.ece.drexel.edu Wed Aug 26 06:11 EDT 1998
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 44

Today's Topics:
  ADMINISTRATA                          [ Jonathan Nissanov <yoni@cbis.ece.dr ]
  Re: Frame grabber cards               [ "Doug S. Phillips" <phillips@ucalga ]

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

Date: Tue, 25 Aug 1998 12:05:27 -0500
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: ADMINISTRATA
Message-Id: <v03007801b2089f1ef1c2@[144.118.33.245]>
Content-Type: text/enriched; charset="us-ascii"

<fontfamily><param>Times</param>Hi everyone.


The following is a reminder to everyone regarding administrative issues
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</fontfamily>

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

                                  Jonathan Nissanov, Ph.D.

                                      Associate Director  

            Computer Vision Center for Vertebrate Brain Mapping,

                a NIH Biomedical Research Technology Resource

                                http://cbis.ece.drexel.edu/ICVC/

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

Imaging and Computer Vision Center              Tel: 215-895-1381

Drexel University                                                  
Fax: 215-895-4987

Phildelphia, PA 19104                                        
yoni@coe.drexel.edu

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

      

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

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

Date: Tue, 25 Aug 98 12:41:15 MDT
From: "Doug S. Phillips" <phillips@ucalgary.ca>
To: nih-image@io.ece.drexel.edu
Cc: mccannc@topaz.cqu.edu.au
Subject: Re: Frame grabber cards
Message-Id: <9808251841.AA26518@acs1.acs.ucalgary.ca>
Content-Type: multipart/mixed; boundary="----------------------------"

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

Dear Cormac:

Cormac wrote:

>          there is a power pc set up here on campus which I am using for my
> project.  I need to capture some images from a camera which is connected to
> the computer except the computer insists that I need a frame grabber card to
>do so.  I know for a fact that there is already a frame grabber card
>installed in the machine but I have been unsuccessful in enabling it. 

In the frame grabber appendix of the online manual for NIH-Image
(at http://rsb.info.nih.gov/nih-image/manual/Appendices/frame.html )
it is stated that:

> Using VDIGs (QuickTime Video Digitizer extensions), Image also supports
> QuickTime compatible video digitizers such as those built into "AV" Macs and
> the PowerMac7500/8500.

>From http://ipt.lpl.arizona.edu/IPT/Help/helpmeister.html#13,
there is the following information:

> There are two main software components: digitizing software, and a system
> extension called a VDIG (video digitizer), which tells the computer how to
> communicate with the digitizing hardware. The VDIG for the AV Macs is called
> AV Digitizer Options, and it belongs in the Extensions folder in the System
> folder. If you need to install it manually, drag it to the closed System
> folder and it will automatically be placed in the proper location.

I saw another reference that indicated that the AV Digitizer Options
was in the Info-Mac archive, but, checking there now, I can't find it.

If someone else can complete the story here, I would interested
in finding out the answer to the original question.  Thanks.

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


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

--------------------------------
End of nih-image-d Digest V98 Issue #44
***************************************

From nih-image-request@io.ece.drexel.edu Wed Aug 26 14:16 EDT 1998
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why did i get this msg??????????????
check your address!


From nih-image-request@io.ece.drexel.edu Wed Aug 26 14:37 EDT 1998
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Dear all,

we intend to buy some hardware to capture images from a phase contrast
microscope. We can't spend more than $5000 and would rather less. We have
a framegrabber anyway. Does anybody have experience with using both
digital cameras and video cameras and could comment on which method gives
the best image quality? The highest resolution? 

Many thanks,

Jan.

Dr. Jan-Ulrich Kreft			Phone +44 1222 874000 ext. 6036
School of Pure and Applied Biology	Fax   +44 1222 874305
Cardiff University			E-mail Kreft@cardiff.ac.uk
PO Box 915, Cardiff CF1 3TL, UK




From nih-image-request@io.ece.drexel.edu Wed Aug 26 16:17 EDT 1998
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From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: Re: Q: Video or digital camera?
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>Dear all,
>
>we intend to buy some hardware to capture images from a phase contrast
>microscope. We can't spend more than $5000 and would rather less. We have
>a framegrabber anyway. Does anybody have experience with using both
>digital cameras and video cameras and could comment on which method gives
>the best image quality? The highest resolution?
>
The consumer model digital cameras have a fixed lens and so cannot be
attached to a scope. Higher end professional systems consists of digital
backs on SLR bodies and so, I believe could be readily mounted-you'll want
an extension tube (Kodak makes models with Canon and Nikon bodies). The
latter also provide manual overrides and better light meters. If you are
not limited by low light intensity these provide a good system. They start
at the $4k or so  (Minolta RD-175) and go up to the stratosphere (20k for
DCS 460-a beauty with 3kx2k pixels). On the Minolta you get a 3-chip system
with the resolution achieved in part by software interpolation. Another
option that is a relatively inexpensive solution, 6k, is the Leaf line
camera which gives very high real resolution color images but with slow
acquisition time. All these systems do not require a framegrabber. The
spatial resolution you need obviously depends on application. Another
concern to keep in mind is densitometric accuracy. If you are intending on
performing densitometric measurements or segmentation, then consumer level
systems are unlikely to be sufficiently accurate.  The professional systems
I suspect would do fine.

A low cost monochrome solution is the Sony XC77. For 1k you get an accurate
CCD camera albiet a low resolution one. Other systems exist that use the
same chip and give you more electronic control. Color low cost system such
as Cohu's cameras exist though have disappointing color matching-not
suitable for publication.

>From the DV camcorder market, spatial resolution is a major issue-its low,
light sensitivity is often exasperatingly poor, and again mounting is a
problem. Canon has a new system, the XL1.  I would love to hear anyone's
experience with this system. Its under 5k, 3 chip with interchangeable
lenses. Its a NTSC system-so don't expect much resolution wise.

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

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



From nih-image-request@io.ece.drexel.edu Wed Aug 26 17:02 EDT 1998
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From: "Barwood, Henry" <hbarwood@pyrite.igs.indiana.edu>
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Does anyone know if the new camcorders with "0" lux (infrared)
capability are offered in a package with "C" mount lenses? I'm curious
how the IR imaging would work on a microscope. Anyone tried one of these
yet?

Henry Barwood
Indiana Geological Survey
>


From nih-image-request@io.ece.drexel.edu Wed Aug 26 23:16 EDT 1998
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Jan-

Video cameras are nice because they output images at ~30 frames per
second (fps) which allows easy positioning and focusing of your sample
on the video screen.  However, the trade off is that you only get 640 x
480 pixels (slightly more if you use a PAL camera instead of NTSC). 
Also, there are video cameras in a wide range of prices, and
functionalities.  Video cameras range from monochrome to single and
three chip color cameras.  And some have the ability to do on-chip
integration for detecting very weak signals.  You also have the option
of getting most cameras in cooled or uncooled versions.

As for digital cameras, I am only familiar with the high end scientific
cameras such as the Photometrics Sensys, and the Diagnostic Instruments
Spot.  These cameras are nice in that they provide a much higher
resolution image (1kx1k or better) that maps 1 image pixel to one ccd
pixel.  However, they are SLOW (3 fps at full resolution, faster with
binning, or lower resolution, but I don't think they ever get upto video
rates), and they are only monochrome.  There is a solution for capturing
color images with the Sensys that uses an LCD filter to filter the image
for RGB and capture 3 images that are then merged to form the color
image, but that takes even longer, and usually requires some fiddling to
get the capture times right so that the colors come out right.  Finally,
the biggest disadvantage for you is that they run in the $15k+ range.

Unless your project truely requires the high resolution of a digital
camera, a video camera will be cheaper and easier to setup and use.

Chris Tully
Image Processing Consultant
S&M Microscopes
Colorado Springs, CO

Jan Kreft wrote:
> 
> Dear all,
> 
> we intend to buy some hardware to capture images from a phase contrast
> microscope. We can't spend more than $5000 and would rather less. We have
> a framegrabber anyway. Does anybody have experience with using both
> digital cameras and video cameras and could comment on which method gives
> the best image quality? The highest resolution?
> 
> Many thanks,
> 
> Jan.
> 
> Dr. Jan-Ulrich Kreft                    Phone +44 1222 874000 ext. 6036
> School of Pure and Applied Biology      Fax   +44 1222 874305
> Cardiff University                      E-mail Kreft@cardiff.ac.uk
> PO Box 915, Cardiff CF1 3TL, UK


From nih-image-request@io.ece.drexel.edu Wed Aug 26 23:35 EDT 1998
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From: Kathleen Annikki Moore <moorekat@hawaii.edu>
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To: nih-image@io.ece.drexel.edu
Subject: Is there a PCI external device for framegrabbing available for Mac  G3 powerbook?
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Is there  PCI external device for framegrabbing  available for Mac  G3
powerbook that is adequate for  acquistion of scientific data? Are pc
products such as  Snappy or Nogatech Capture Vision adequate to capture
scientific data?  Is there an adaptor for Macs? I'm beginning any
suggestions would be quite helpful.  Kathleen Moore


From nih-image-request@io.ece.drexel.edu Thu Aug 27 02:40 EDT 1998
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Date: Thu, 27 Aug 1998 08:17:20 +0200
From: Leopoldo Silvestroni <l.silvestroni@caspur.it>
Organization: Universit di Roma 'La Sapienza'
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Henry,

many commercial b/w CCD cameras are sensitive to IR. To ascertain whether
yours does, simply "illuminate" the CCD with a TV controller. IR sensitivity
is testified by monitor sparking (due to pulsed IR emission from
controller).

IR microscopy is useful to visualize biological material when photodamage
produced by visible light has to be reduced.

best regards,
Leopoldo Silvestroni,MD
--
Laboratorio di Biofluorimetria
Dipartimento di Fisiopatologia Medica
Policlinico Umberto I
Universit di Roma 'La Sapienza'
00161-Roma
tel. +39 6 49970710
fax  +39 6 4461450
e-mail: l.silvestroni@caspur.it
WWW: http://w3.uniroma1.it/MEDICFISIO/labpag1.html



From nih-image-d-request@io.ece.drexel.edu Thu Aug 27 06:14 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #45
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 45

Today's Topics:
  Re: unsubscribe                       [ "Jared L. Rifkin" <jared_rifkin@qc. ]
  Q: Video or digital camera?           [ Jan Kreft <Kreft@cardiff.ac.uk> ]
  Re: Q: Video or digital camera?       [ Jonathan Nissanov <yoni@cbis.ece.dr ]
  RE: Q: Video or digital camera?       [ "Barwood, Henry" <hbarwood@pyrite.i ]
  Re: Q: Video or digital camera?       [ "Christopher P. Tully" <cptully@usa ]
  Is there a PCI external device for f  [ Kathleen Annikki Moore <moorekat@ha ]
  Re: Q: Video or digital camera?       [ Leopoldo Silvestroni <l.silvestroni ]

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

Date: Wed, 26 Aug 98 13:58:22 -0400
From: "Jared L. Rifkin" <jared_rifkin@qc.edu>
To: <nih-image@io.ece.drexel.edu>
Subject: Re: unsubscribe
Message-ID: <2B7245D57A8@qc1.qc.edu>
Content-Type: text/plain; charset="US-ASCII"

why did i get this msg??????????????
check your address!

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

Date: Wed, 26 Aug 1998 19:18:31 +0100 (BST)
From: Jan Kreft <Kreft@cardiff.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Q: Video or digital camera?
Message-ID: <Pine.OSF.3.95q.980826191333.1080A-100000@thor>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear all,

we intend to buy some hardware to capture images from a phase contrast
microscope. We can't spend more than $5000 and would rather less. We have
a framegrabber anyway. Does anybody have experience with using both
digital cameras and video cameras and could comment on which method gives
the best image quality? The highest resolution? 

Many thanks,

Jan.

Dr. Jan-Ulrich Kreft			Phone +44 1222 874000 ext. 6036
School of Pure and Applied Biology	Fax   +44 1222 874305
Cardiff University			E-mail Kreft@cardiff.ac.uk
PO Box 915, Cardiff CF1 3TL, UK

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

Date: Wed, 26 Aug 1998 14:55:24 -0500
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Q: Video or digital camera?
Message-Id: <v03007808b20a1177e01d@[144.118.33.245]>
Content-Type: text/plain; charset="us-ascii"

>Dear all,
>
>we intend to buy some hardware to capture images from a phase contrast
>microscope. We can't spend more than $5000 and would rather less. We have
>a framegrabber anyway. Does anybody have experience with using both
>digital cameras and video cameras and could comment on which method gives
>the best image quality? The highest resolution?
>
The consumer model digital cameras have a fixed lens and so cannot be
attached to a scope. Higher end professional systems consists of digital
backs on SLR bodies and so, I believe could be readily mounted-you'll want
an extension tube (Kodak makes models with Canon and Nikon bodies). The
latter also provide manual overrides and better light meters. If you are
not limited by low light intensity these provide a good system. They start
at the $4k or so  (Minolta RD-175) and go up to the stratosphere (20k for
DCS 460-a beauty with 3kx2k pixels). On the Minolta you get a 3-chip system
with the resolution achieved in part by software interpolation. Another
option that is a relatively inexpensive solution, 6k, is the Leaf line
camera which gives very high real resolution color images but with slow
acquisition time. All these systems do not require a framegrabber. The
spatial resolution you need obviously depends on application. Another
concern to keep in mind is densitometric accuracy. If you are intending on
performing densitometric measurements or segmentation, then consumer level
systems are unlikely to be sufficiently accurate.  The professional systems
I suspect would do fine.

A low cost monochrome solution is the Sony XC77. For 1k you get an accurate
CCD camera albiet a low resolution one. Other systems exist that use the
same chip and give you more electronic control. Color low cost system such
as Cohu's cameras exist though have disappointing color matching-not
suitable for publication.

>From the DV camcorder market, spatial resolution is a major issue-its low,
light sensitivity is often exasperatingly poor, and again mounting is a
problem. Canon has a new system, the XL1.  I would love to hear anyone's
experience with this system. Its under 5k, 3 chip with interchangeable
lenses. Its a NTSC system-so don't expect much resolution wise.

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

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

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

Date: Wed, 26 Aug 1998 15:47:09 -0500
From: "Barwood, Henry" <hbarwood@pyrite.igs.indiana.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Q: Video or digital camera?
Message-ID: <c=US%a=_%p=Indiana_Universi%l=PYRITE-980826204709Z-6704@pyrite.igs.indiana.edu>

Does anyone know if the new camcorders with "0" lux (infrared)
capability are offered in a package with "C" mount lenses? I'm curious
how the IR imaging would work on a microscope. Anyone tried one of these
yet?

Henry Barwood
Indiana Geological Survey
>

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

Date: Wed, 26 Aug 1998 21:08:20 -0600
From: "Christopher P. Tully" <cptully@usa.net>
To: nih-image@io.ece.drexel.edu
Subject: Re: Q: Video or digital camera?
Message-ID: <35E4CDA4.37658712@usa.net>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Jan-

Video cameras are nice because they output images at ~30 frames per
second (fps) which allows easy positioning and focusing of your sample
on the video screen.  However, the trade off is that you only get 640 x
480 pixels (slightly more if you use a PAL camera instead of NTSC). 
Also, there are video cameras in a wide range of prices, and
functionalities.  Video cameras range from monochrome to single and
three chip color cameras.  And some have the ability to do on-chip
integration for detecting very weak signals.  You also have the option
of getting most cameras in cooled or uncooled versions.

As for digital cameras, I am only familiar with the high end scientific
cameras such as the Photometrics Sensys, and the Diagnostic Instruments
Spot.  These cameras are nice in that they provide a much higher
resolution image (1kx1k or better) that maps 1 image pixel to one ccd
pixel.  However, they are SLOW (3 fps at full resolution, faster with
binning, or lower resolution, but I don't think they ever get upto video
rates), and they are only monochrome.  There is a solution for capturing
color images with the Sensys that uses an LCD filter to filter the image
for RGB and capture 3 images that are then merged to form the color
image, but that takes even longer, and usually requires some fiddling to
get the capture times right so that the colors come out right.  Finally,
the biggest disadvantage for you is that they run in the $15k+ range.

Unless your project truely requires the high resolution of a digital
camera, a video camera will be cheaper and easier to setup and use.

Chris Tully
Image Processing Consultant
S&M Microscopes
Colorado Springs, CO

Jan Kreft wrote:
> 
> Dear all,
> 
> we intend to buy some hardware to capture images from a phase contrast
> microscope. We can't spend more than $5000 and would rather less. We have
> a framegrabber anyway. Does anybody have experience with using both
> digital cameras and video cameras and could comment on which method gives
> the best image quality? The highest resolution?
> 
> Many thanks,
> 
> Jan.
> 
> Dr. Jan-Ulrich Kreft                    Phone +44 1222 874000 ext. 6036
> School of Pure and Applied Biology      Fax   +44 1222 874305
> Cardiff University                      E-mail Kreft@cardiff.ac.uk
> PO Box 915, Cardiff CF1 3TL, UK

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

Date: 	Wed, 26 Aug 1998 17:20:57 -1000
From: Kathleen Annikki Moore <moorekat@hawaii.edu>
To: nih-image@io.ece.drexel.edu
Subject: Is there a PCI external device for framegrabbing available for Mac  G3 powerbook?
Message-ID: <Pine.GSO.3.95q.980826164444.17964A-100000@uhunix5>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Is there  PCI external device for framegrabbing  available for Mac  G3
powerbook that is adequate for  acquistion of scientific data? Are pc
products such as  Snappy or Nogatech Capture Vision adequate to capture
scientific data?  Is there an adaptor for Macs? I'm beginning any
suggestions would be quite helpful.  Kathleen Moore

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

Date: Thu, 27 Aug 1998 08:17:20 +0200
From: Leopoldo Silvestroni <l.silvestroni@caspur.it>
To: nih-image@io.ece.drexel.edu
Subject: Re: Q: Video or digital camera?
Message-ID: <35E4F9F0.6A0B7DA@caspur.it>
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

Henry,

many commercial b/w CCD cameras are sensitive to IR. To ascertain whether
yours does, simply "illuminate" the CCD with a TV controller. IR sensitivity
is testified by monitor sparking (due to pulsed IR emission from
controller).

IR microscopy is useful to visualize biological material when photodamage
produced by visible light has to be reduced.

best regards,
Leopoldo Silvestroni,MD
--
Laboratorio di Biofluorimetria
Dipartimento di Fisiopatologia Medica
Policlinico Umberto I
Universit di Roma 'La Sapienza'
00161-Roma
tel. +39 6 49970710
fax  +39 6 4461450
e-mail: l.silvestroni@caspur.it
WWW: http://w3.uniroma1.it/MEDICFISIO/labpag1.html

--------------------------------
End of nih-image-d Digest V98 Issue #45
***************************************

From nih-image-request@io.ece.drexel.edu Thu Aug 27 12:30 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA17472;
	Thu, 27 Aug 1998 12:30:37 -0400 (EDT)
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Message-ID: <c=US%a=_%p=Indiana_Universi%l=PYRITE-980827161711Z-6935@pyrite.igs.indiana.edu>
From: "Barwood, Henry" <hbarwood@pyrite.igs.indiana.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Q: Video or digital camera?
Date: Thu, 27 Aug 1998 11:17:11 -0500
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You wrote:

>many commercial b/w CCD cameras are sensitive to IR. To ascertain whether
>yours does, simply "illuminate" the CCD with a TV controller. IR sensitivity
>is testified by monitor sparking (due to pulsed IR emission from
>controller).
>
>IR microscopy is useful to visualize biological material when photodamage
>produced by visible light has to be reduced.
>

Thanks for this advice. I'll check a few cameras and see if I can find a
suitable one.

Henry


From nih-image-request@io.ece.drexel.edu Thu Aug 27 14:44 EDT 1998
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Date: Thu, 27 Aug 1998 11:31:17 -0800
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Dear NIH-Imagers:
We have recntly aquire the NIH image software (Scion Image 1.62a) andf
I'm trying to  get familiar with it, and still need to learn a lot.
However, there is a primary question to ask you. we basically need to
take  measurements (only length and width) and haven't been able to
figure our how you callibrate and set to scale whatever I need to
measure.  My units should be in micrometers, but I do not know what I
need to know in order to calibrate this with the pixels?
I'll appreciate your help a lot!!
Thanks, Patricia


From nih-image-request@io.ece.drexel.edu Thu Aug 27 16:20 EDT 1998
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Subject: Pausing a macro to draw a freehand ROI
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Is there a way to pause in the middle of a macro, draw a freehand ROI, then
continue the macro?  At present, I exit the macro, draw, then start the
macro again at the beginning; this leads to clumsy programming.

Example: a stack of 5 images.  I want to outline a cell, measure,select the
next slice, outline the slightly differently bordered cell, measure, select
the next slice, etc.
(At present, my macro F2 PutMessages "outline a cell, then hit F3", and
then exits. I outline, hit F3, it measures, goes to slice 2, I outline, hit
F3, etc.)
Thanks in advance,  Harry

Henry M. Thomas, III MD (Harry)
Professor of Clinical Medicine,  Pulmonary and Critical Care Division
Department of Medicine, Cornell Univ. Medical School
Director, Pulmonary Research, Burke Rehabilitation Hospital
785 Mamaroneck Ave.  White Plains, NY 10605
(914) 597-2141



From nih-image-request@io.ece.drexel.edu Thu Aug 27 17:05 EDT 1998
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From: lpaul@darcy.geo.umn.edu (Paul Morin)
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When I ask analyze partcles to label the particles I get images without 
labels on them.  I'm using NIH Image 1.61/ppc.

Any ideas?

Paul Morin

University of Minnesota Geology


From nih-image-request@io.ece.drexel.edu Thu Aug 27 18:43 EDT 1998
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From: Geff Rawling <grawling@nmt.edu>
Subject: petrographic image ssytem
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Hi imagers,

	I'm a geologist looking for advice in setting up an imaging system on a
Nikon petrographic microscope for quantitative analysis of textures in thin
sections of porous rocks. We have about $4-5k to spend, on a camera/frame
grabber combination. We need color images and as high a resolution as
possible. Image analysis will be done with Scion Image on a PC. There's a
thread from about three years ago on this topic, but prices and products
have probably changed since then. I will be happy to summarize any info I
get for the list. Thanks a lot!

Geff  
*********************************************
Geoffrey C. Rawling
Department of Earth and Environmental Science  
New Mexico Tech                                
P.O. Box 2217                                  
Socorro, NM 87801
505-835-5952
grawling@nmt.edu

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


From nih-image-request@io.ece.drexel.edu Fri Aug 28 03:46 EDT 1998
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Dear Mr. Thomas,

I am writing a macro based on the macro 'Open Files From List ....'
(Input/Output-Macro, comes with NIH-Image):

cut-----------------------------------------------------------------

var  i: integer;
       ListName, ImageName,spath,pa: string;

function GetName(ListName: string; i: integer): string;
{Returns the the ith line from a text file that has been
read into a one line image named 'ListName'.}
var
   loc, ch: integer;
   name: string;
begin
  SelectWindow(ListName);
  loc := -1;
  for i := 2 to i do
     repeat
       loc := loc + 1;
       ch := GetPixel(loc, 0)
     until ch < 32; {return or linefeed}
  name := '';
  repeat
     loc := loc + 1;
     ch := GetPixel(loc, 0);
     if ch >= 32 then
       name := concat(name, chr(ch));
  until ch < 32;
  GetName := name;
end;

Macro 'Start    /<';
{Opens a series of files from a list stored in a text file.}
var
   path, FileType: string;
   FileSize: integer;
begin
  ListName := 'file-list.txt';
  spath:=GetPath('window');
  path := concat(GetPath('window'), ListName);
  GetFileInfo(path, FileType, FileSize);
  if FileSize < 0 then begin
     PutMessage('The file "', ListName, '" could not be found in the
same folder as images.');
     exit;
  end;
  SetImport('8-bit');
  SetCustom(FileSize, 1, 0);
  Import(path);
    i:=1;
    ImageName := GetName(ListName, i);
    if ImageName = '' then begin
        SelectWindow(ListName);
        close;
        exit;
     end;
     pa:=concat(spath,ImageName);
     open(pa);
     ShowMessage(i);
     SetForegroundColor(255);
     SelectTool('freehand');
end;

Macro   '(-'  begin end;

Macro 'Open       [F1]';
begin
     i:=i+1;
     ImageName := GetName(ListName, i);
     if ImageName = '' then begin
        SelectWindow(ListName);
        close;
        exit;
     end;
     pa:=concat(spath,ImageName);
     open(pa);
     ShowMessage(i'\'pa);
     SetForegroundColor(255);
     SelectTool('freehand');
end;

Macro 'Close    [F2]';
begin
        SetSaveAs('TIFF');
        pa:=concat(spath,ImageName,'Z');
        SaveAs( pa);
        Dispose;
end;       


cut--------------------------------------------------------------------

I hope that I understand your question right. 

1. Write a text-file named 'file-list.txt'. Put in the name of your
images:

         Image1.tif
		  Image2.tif
             .
             .
         ImageN.tif		
			

2. The macro the text-file and the images must be in the same folder.

3. Start the start-macro. At the end of this macro you can adapt parts
of your own macro.

4. Start the open-macro. Here you can adapt your own macro.
 
5. Start the Close-macro to save the modified images (*.tifz).

I hope this macro will help you.


Stephan


From nih-image-d-request@io.ece.drexel.edu Fri Aug 28 03:47 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #46
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 46

Today's Topics:
  RE: Q: Video or digital camera?       [ "Barwood, Henry" <hbarwood@pyrite.i ]
  set scales and callibrate             [ "S. Patricia Stock" <spstock@ucdav ]
  Pausing a macro to draw a freehand R  [ hmthomas@med.cornell.edu (Henry M.  ]
  Unidentified subject!                 [ lpaul@darcy.geo.umn.edu (Paul Morin ]
  petrographic image ssytem             [ Geff Rawling <grawling@nmt.edu> ]
  Re: Pausing a Macro                   [ Stephan Sous <Stephan.Sous@dlr.de> ]

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

Date: Thu, 27 Aug 1998 11:17:11 -0500
From: "Barwood, Henry" <hbarwood@pyrite.igs.indiana.edu>
To: "'nih-image@io.ece.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: RE: Q: Video or digital camera?
Message-ID: <c=US%a=_%p=Indiana_Universi%l=PYRITE-980827161711Z-6935@pyrite.igs.indiana.edu>

You wrote:

>many commercial b/w CCD cameras are sensitive to IR. To ascertain whether
>yours does, simply "illuminate" the CCD with a TV controller. IR sensitivity
>is testified by monitor sparking (due to pulsed IR emission from
>controller).
>
>IR microscopy is useful to visualize biological material when photodamage
>produced by visible light has to be reduced.
>

Thanks for this advice. I'll check a few cameras and see if I can find a
suitable one.

Henry

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

Date: Thu, 27 Aug 1998 11:31:17 -0800
From: "S. Patricia Stock" <spstock@ucdavis.edu>
To: nih-image@io.ece.drexel.edu
Subject: set scales and callibrate
Message-ID: <35E5B402.1511@ucdavis.edu>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Dear NIH-Imagers:
We have recntly aquire the NIH image software (Scion Image 1.62a) andf
I'm trying to  get familiar with it, and still need to learn a lot.
However, there is a primary question to ask you. we basically need to
take  measurements (only length and width) and haven't been able to
figure our how you callibrate and set to scale whatever I need to
measure.  My units should be in micrometers, but I do not know what I
need to know in order to calibrate this with the pixels?
I'll appreciate your help a lot!!
Thanks, Patricia

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

Date: Thu, 27 Aug 1998 16:04:21 -0400
From: hmthomas@med.cornell.edu (Henry M. Thomas)
To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center)
Subject: Pausing a macro to draw a freehand ROI
Message-Id: <v01540b00b20b3114e98a@[206.152.160.91]>
Content-Type: text/plain; charset="us-ascii"

Is there a way to pause in the middle of a macro, draw a freehand ROI, then
continue the macro?  At present, I exit the macro, draw, then start the
macro again at the beginning; this leads to clumsy programming.

Example: a stack of 5 images.  I want to outline a cell, measure,select the
next slice, outline the slightly differently bordered cell, measure, select
the next slice, etc.
(At present, my macro F2 PutMessages "outline a cell, then hit F3", and
then exits. I outline, hit F3, it measures, goes to slice 2, I outline, hit
F3, etc.)
Thanks in advance,  Harry

Henry M. Thomas, III MD (Harry)
Professor of Clinical Medicine,  Pulmonary and Critical Care Division
Department of Medicine, Cornell Univ. Medical School
Director, Pulmonary Research, Burke Rehabilitation Hospital
785 Mamaroneck Ave.  White Plains, NY 10605
(914) 597-2141

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

Date: Thu, 27 Aug 1998 15:00:00 -0700
From: lpaul@darcy.geo.umn.edu (Paul Morin)
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-Id: <199808272200.OAA10589@darcy.geo.umn.edu>

When I ask analyze partcles to label the particles I get images without 
labels on them.  I'm using NIH Image 1.61/ppc.

Any ideas?

Paul Morin

University of Minnesota Geology

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

Date: Thu, 27 Aug 1998 16:31:18 -0600
From: Geff Rawling <grawling@nmt.edu>
To: nih-image@io.ece.drexel.edu
Subject: petrographic image ssytem
Message-Id: <3.0.5.32.19980827163118.009379f0@mailhost.nmt.edu>
Content-Type: text/plain; charset="us-ascii"

Hi imagers,

	I'm a geologist looking for advice in setting up an imaging system on a
Nikon petrographic microscope for quantitative analysis of textures in thin
sections of porous rocks. We have about $4-5k to spend, on a camera/frame
grabber combination. We need color images and as high a resolution as
possible. Image analysis will be done with Scion Image on a PC. There's a
thread from about three years ago on this topic, but prices and products
have probably changed since then. I will be happy to summarize any info I
get for the list. Thanks a lot!

Geff  
*********************************************
Geoffrey C. Rawling
Department of Earth and Environmental Science  
New Mexico Tech                                
P.O. Box 2217                                  
Socorro, NM 87801
505-835-5952
grawling@nmt.edu

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

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

Date: Fri, 28 Aug 1998 09:39:30 +0100
From: Stephan Sous <Stephan.Sous@dlr.de>
To: nih-image@io.ece.drexel.edu
Subject: Re: Pausing a Macro
Message-ID: <35E66CC2.1932@dv.kp.dlr.de>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Dear Mr. Thomas,

I am writing a macro based on the macro 'Open Files From List ....'
(Input/Output-Macro, comes with NIH-Image):

cut-----------------------------------------------------------------

var  i: integer;
       ListName, ImageName,spath,pa: string;

function GetName(ListName: string; i: integer): string;
{Returns the the ith line from a text file that has been
read into a one line image named 'ListName'.}
var
   loc, ch: integer;
   name: string;
begin
  SelectWindow(ListName);
  loc := -1;
  for i := 2 to i do
     repeat
       loc := loc + 1;
       ch := GetPixel(loc, 0)
     until ch < 32; {return or linefeed}
  name := '';
  repeat
     loc := loc + 1;
     ch := GetPixel(loc, 0);
     if ch >= 32 then
       name := concat(name, chr(ch));
  until ch < 32;
  GetName := name;
end;

Macro 'Start    /<';
{Opens a series of files from a list stored in a text file.}
var
   path, FileType: string;
   FileSize: integer;
begin
  ListName := 'file-list.txt';
  spath:=GetPath('window');
  path := concat(GetPath('window'), ListName);
  GetFileInfo(path, FileType, FileSize);
  if FileSize < 0 then begin
     PutMessage('The file "', ListName, '" could not be found in the
same folder as images.');
     exit;
  end;
  SetImport('8-bit');
  SetCustom(FileSize, 1, 0);
  Import(path);
    i:=1;
    ImageName := GetName(ListName, i);
    if ImageName = '' then begin
        SelectWindow(ListName);
        close;
        exit;
     end;
     pa:=concat(spath,ImageName);
     open(pa);
     ShowMessage(i);
     SetForegroundColor(255);
     SelectTool('freehand');
end;

Macro   '(-'  begin end;

Macro 'Open       [F1]';
begin
     i:=i+1;
     ImageName := GetName(ListName, i);
     if ImageName = '' then begin
        SelectWindow(ListName);
        close;
        exit;
     end;
     pa:=concat(spath,ImageName);
     open(pa);
     ShowMessage(i'\'pa);
     SetForegroundColor(255);
     SelectTool('freehand');
end;

Macro 'Close    [F2]';
begin
        SetSaveAs('TIFF');
        pa:=concat(spath,ImageName,'Z');
        SaveAs( pa);
        Dispose;
end;       


cut--------------------------------------------------------------------

I hope that I understand your question right. 

1. Write a text-file named 'file-list.txt'. Put in the name of your
images:

         Image1.tif
		  Image2.tif
             .
             .
         ImageN.tif		
			

2. The macro the text-file and the images must be in the same folder.

3. Start the start-macro. At the end of this macro you can adapt parts
of your own macro.

4. Start the open-macro. Here you can adapt your own macro.
 
5. Start the Close-macro to save the modified images (*.tifz).

I hope this macro will help you.


Stephan

--------------------------------
End of nih-image-d Digest V98 Issue #46
***************************************

From nih-image-request@io.ece.drexel.edu Fri Aug 28 07:54 EDT 1998
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Is there a way to import masks, or tiffs with saved masks into Scion 
/ Nih-Image from other applications such as Adobe Photoshop or 
Photostyler?

I know it is possible to use masks / ROI's in Scion / NIH, but 
drawing them is tricky & clumsy & I find it easier & more accurate to 
use the magnetic lasso tool to select the areas I want to measure.

Also are there any ways to change the cursor style from the crosshair 
as I find an arrow easier to use when selecting a region of the image

Thanks in advance,
Jenny Gregory

----------------------
j.gregory@abdn.ac.uk




From nih-image-request@io.ece.drexel.edu Fri Aug 28 12:22 EDT 1998
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Date: Fri, 28 Aug 1998 11:07:37 -0500
To: nih-image@io.ece.drexel.edu
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: Re: Pausing a macro to draw a freehand ROI
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>Is there a way to pause in the middle of a macro, draw a freehand ROI, then
>continue the macro?  At present, I exit the macro, draw, then start the
>macro again at the beginning; this leads to clumsy programming.
>
>Example: a stack of 5 images.  I want to outline a cell, measure,select the
>next slice, outline the slightly differently bordered cell, measure, select
>the next slice, etc.
>(At present, my macro F2 PutMessages "outline a cell, then hit F3", and
>then exits. I outline, hit F3, it measures, goes to slice 2, I outline, hit
>F3, etc.)

Here is a macro to do it. incorporate it as a routine or in the body of
your macro.

macro 'draw'
var origx,oldx,origy,oldy,x,y:integer;
begin
WaitForTrigger;
getMouse(oldx,oldy);
origx:=oldx;
origy:=oldy;
While button do begin
        getMouse(x,y);
         moveto(oldx,oldy);
         LineTo(x,y);
         oldx:=x;
         oldy:=y;
end;
LineTo(origx,origy);
end;

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

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



From nih-image-request@io.ece.drexel.edu Fri Aug 28 16:51 EDT 1998
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Date: Fri, 28 Aug 1998 17:45:45 -0800
From: Luthero Martins <rsf6675@pro.via-rs.com.br>
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References: <Pine.OSF.3.95q.980826191333.1080A-100000@thor>
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You can use a video camera Sony 3CCD and digital 
frame grabber MiroDC20, and software Adobe Premiere.

Jan Kreft wrote:
> 
> Dear all,
> 
> we intend to buy some hardware to capture images from a phase contrast
> microscope. We can't spend more than $5000 and would rather less. We have
> a framegrabber anyway. Does anybody have experience with using both
> digital cameras and video cameras and could comment on which method gives
> the best image quality? The highest resolution?
> 
> Many thanks,
> 
> Jan.
> 
> Dr. Jan-Ulrich Kreft                    Phone +44 1222 874000 ext. 6036
> School of Pure and Applied Biology      Fax   +44 1222 874305
> Cardiff University                      E-mail Kreft@cardiff.ac.uk
> PO Box 915, Cardiff CF1 3TL, UK


From nih-image-request@io.ece.drexel.edu Sat Aug 29 02:34 EDT 1998
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From: SolamereTG@aol.com
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Date: Sat, 29 Aug 1998 02:23:52 EDT
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Does anyone know where I could find an NIH macro that controls a Sony VO-9600
U-matic VCR recorder over the serial port. Off/on/play/record would be enough.

Thanks in advance
George A. Peeters


From nih-image-d-request@io.ece.drexel.edu Sat Aug 29 02:38 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #47
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 47

Today's Topics:
  Unidentified subject!                 [ "j.gregory" <ort056@abdn.ac.uk> ]
  Re: Pausing a macro to draw a freeha  [ Jonathan Nissanov <yoni@cbis.ece.dr ]
  Re: Q: Video or digital camera?       [ Luthero Martins <rsf6675@pro.via-rs ]
  control macro for a Sony U-matic?     [ SolamereTG@aol.com ]

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

Date: Fri, 28 Aug 1998 12:39:21 +0100 (BST)
From: "j.gregory" <ort056@abdn.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Unidentified subject!
Message-ID: <SIMEON.9808281221.C@pc10.abdn.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

Is there a way to import masks, or tiffs with saved masks into Scion 
/ Nih-Image from other applications such as Adobe Photoshop or 
Photostyler?

I know it is possible to use masks / ROI's in Scion / NIH, but 
drawing them is tricky & clumsy & I find it easier & more accurate to 
use the magnetic lasso tool to select the areas I want to measure.

Also are there any ways to change the cursor style from the crosshair 
as I find an arrow easier to use when selecting a region of the image

Thanks in advance,
Jenny Gregory

----------------------
j.gregory@abdn.ac.uk

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

Date: Fri, 28 Aug 1998 11:07:37 -0500
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Pausing a macro to draw a freehand ROI
Message-Id: <v03007801b20c8604f655@[144.118.33.245]>
Content-Type: text/plain; charset="us-ascii"

>Is there a way to pause in the middle of a macro, draw a freehand ROI, then
>continue the macro?  At present, I exit the macro, draw, then start the
>macro again at the beginning; this leads to clumsy programming.
>
>Example: a stack of 5 images.  I want to outline a cell, measure,select the
>next slice, outline the slightly differently bordered cell, measure, select
>the next slice, etc.
>(At present, my macro F2 PutMessages "outline a cell, then hit F3", and
>then exits. I outline, hit F3, it measures, goes to slice 2, I outline, hit
>F3, etc.)

Here is a macro to do it. incorporate it as a routine or in the body of
your macro.

macro 'draw'
var origx,oldx,origy,oldy,x,y:integer;
begin
WaitForTrigger;
getMouse(oldx,oldy);
origx:=oldx;
origy:=oldy;
While button do begin
        getMouse(x,y);
         moveto(oldx,oldy);
         LineTo(x,y);
         oldx:=x;
         oldy:=y;
end;
LineTo(origx,origy);
end;

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

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

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

Date: Fri, 28 Aug 1998 17:45:45 -0800
From: Luthero Martins <rsf6675@pro.via-rs.com.br>
To: nih-image@io.ece.drexel.edu
Subject: Re: Q: Video or digital camera?
Message-ID: <35E75D48.3A0D@pro.via-rs.com.br>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

You can use a video camera Sony 3CCD and digital 
frame grabber MiroDC20, and software Adobe Premiere.

Jan Kreft wrote:
> 
> Dear all,
> 
> we intend to buy some hardware to capture images from a phase contrast
> microscope. We can't spend more than $5000 and would rather less. We have
> a framegrabber anyway. Does anybody have experience with using both
> digital cameras and video cameras and could comment on which method gives
> the best image quality? The highest resolution?
> 
> Many thanks,
> 
> Jan.
> 
> Dr. Jan-Ulrich Kreft                    Phone +44 1222 874000 ext. 6036
> School of Pure and Applied Biology      Fax   +44 1222 874305
> Cardiff University                      E-mail Kreft@cardiff.ac.uk
> PO Box 915, Cardiff CF1 3TL, UK

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

Date: Sat, 29 Aug 1998 02:23:52 EDT
From: SolamereTG@aol.com
To: nih-image@io.ece.drexel.edu
Subject: control macro for a Sony U-matic?
Message-ID: <d2eeaf49.35e79e78@aol.com>>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

Does anyone know where I could find an NIH macro that controls a Sony VO-9600
U-matic VCR recorder over the serial port. Off/on/play/record would be enough.

Thanks in advance
George A. Peeters

--------------------------------
End of nih-image-d Digest V98 Issue #47
***************************************

From nih-image-request@io.ece.drexel.edu Sat Aug 29 18:01 EDT 1998
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Date: Sat, 29 Aug 1998 17:51:19 -0400 (EDT)
From: Sushant Agarwal <sushant@ds5500.cemr.wvu.edu>
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To: nih-image@io.ece.drexel.edu
Subject: Gray scale microscopy- suggestions?
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Hello Folks,
I am planning to purchase a digital image aquisition and analysis system
which I can use with my microscope.
Rightnow I have come across Scion Corporations' Gray scale Microscopy
System Pr-GMS300 CCIR, which appears adequate for my purpose and seems
to have reasonable price also.
Does anyone of you have any experience with this particular system?
I would really appreciate your input on this subject.
I need this system to analyze micron size particles and thier
agglomerates. Analysis part will include size measurement, particle
counting etc.
thanks a lot,
hope to hear from you,


Sushant Agarwal (sushant@ds5500.cemr.wvu.edu)
Graduate Research Assistant
Room # 453, P. O. Box 6102
Chemical Engineering Department
West Virginia University, Morgantown, WV 26506


From nih-image-d-request@io.ece.drexel.edu Mon Aug 31 06:13 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #48
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 48

Today's Topics:
  Gray scale microscopy- suggestions?   [ Sushant Agarwal <sushant@ds5500.cem ]

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

Date: Sat, 29 Aug 1998 17:51:19 -0400 (EDT)
From: Sushant Agarwal <sushant@ds5500.cemr.wvu.edu>
To: nih-image@io.ece.drexel.edu
Subject: Gray scale microscopy- suggestions?
Message-ID: <Pine.ULT.3.96.980829174156.3379A-100000@ds5500>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hello Folks,
I am planning to purchase a digital image aquisition and analysis system
which I can use with my microscope.
Rightnow I have come across Scion Corporations' Gray scale Microscopy
System Pr-GMS300 CCIR, which appears adequate for my purpose and seems
to have reasonable price also.
Does anyone of you have any experience with this particular system?
I would really appreciate your input on this subject.
I need this system to analyze micron size particles and thier
agglomerates. Analysis part will include size measurement, particle
counting etc.
thanks a lot,
hope to hear from you,


Sushant Agarwal (sushant@ds5500.cemr.wvu.edu)
Graduate Research Assistant
Room # 453, P. O. Box 6102
Chemical Engineering Department
West Virginia University, Morgantown, WV 26506

--------------------------------
End of nih-image-d Digest V98 Issue #48
***************************************

From nih-image-request@io.ece.drexel.edu Mon Aug 31 08:33 EDT 1998
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Date: Mon, 31 Aug 1998 08:20:41 -0400
To: hmthomas@med.cornell.edu (Henry M. Thomas)
From: Laird Bloom <lbloom@MIT.EDU>
Subject: Re: Pausing a macro to draw a freehand ROI
Cc: nih-image@io.ece.drexel.edu
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Henry,

I have used a fairly simple solution to this problem--although it may
be clumsy programming--in several macros. Essentially, I write the
macro in a way that expects there to be an open image file at the
start, and then after doing the measurement procedures, closes or saves
the current image and opens the next one.  I also set up the macro so I
can start it with a single keystroke (using [x] in the macro title,
where x is a single key).  That way it's fairly straightforward to draw
your ROI and press a key, then have the computer do measurements and
open your next slice for you.  

	I often do this in conjunction with two other macros, one to set
initial parameters (type of measurements, name of file for saving
results, etc.) and open the first image, the other to analyze the data
in the results file after the individual images have been measured. 
Below is an example we use for capturing live video images and
measuring the areas of a number of freehand ROIs from each of a number
of images, then saving each area in a file.  In this case, the "Measure
Area[M]" macro is used multiple times for multiple ROIs in a single
image, and then the<fontfamily><param>Times</param><bigger><bigger>
'New view of current sample [v]'</bigger></bigger></fontfamily> macro
gets rid of the current image and has the computer acquire a new one,
using the GetImageToMeasure procedure.  Like the old VW ads:  it's
ugly, but it gets you there.


Good luck.

Laird Bloom

MIT Center for Cancer Research


<fontfamily><param>Times</param><bigger><bigger>{  We use Scion Image
1.62, essentially the same as NIH Image 1.61. You may need to modify
the StartCapturing and StopCapturing commands if the "measure areas on
scope" macro, depending on the source of your input.  Excerpt from lab
protocol book precedes the macro code.

<bold>

"Measure areas on scope" macro

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

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


{"Measure areas on scope" macro file follows:

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

}


var {Global variables}

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

	mean:real;

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



procedure GetImageToMeasure;

begin

StartCapturing;

	Repeat

		Wait(.1);

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

StopCapturing;


SetPicName(nSample,'  Image');

SelectWindow(nSample,'  Image');

         if nSave='Yes'

              then Save;

end



procedure LabelAreaInCenter;


var

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

  scale: real;

  unit: string;

begin

  GetRoi(left,top,width,height);

  if width=0 then begin

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

    exit;

  end;

  SaveState;

  InvertY(false);

  SetForegroundColor(255); {black}

SetBackgroundColor(1);

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

  GetScale(scale, unit);

  Measure;

	DrawBoundary;

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

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

  MoveTo(x-5, y);

	SetFont('Times');

	SetFontSize(9);

SetText('With Background');

	Writeln('region ',j:0);

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

  RestoreState;

end;



macro 'Measure Area [M]';

begin

	j:=j+1;

	LabelAreaInCenter;

	ImageName:=WindowTitle;

	SelectWindow(nSample);

        

	If j=1

		then writeln (nSample); 

		SetFont('Times');

		SetFontSize(12);

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

 		rUser1[j]:=rArea[rCount];

		total:=total+rArea[rCount];

      Save;

	SelectWindow(ImageName);

end


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

var

	width,height:integer;

begin

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

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

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

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

	NewTextWindow(nSample,80,600);

				MoveWindow(740,40);

	total:=0;

GetImageToMeasure;

	j:=0;

end;


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

begin

SelectWindow(ImageName);

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

 DisposeAll;

GetImageToMeasure;

end;

 

macro 'New Sample [S]';


begin

	If j=0

			 then j:=1;

SelectWindow(ImageName);

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

 		Dispose;

SelectWindow(nSample);

mean:=total/j;

writeln('Mean =');

write(mean);

save;

		dispose;

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

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


	NewTextWindow(nSample,80,600);

				MoveWindow(740,40);

	total:=0;

GetImageToMeasure;

	j:=0;

end;</bigger></bigger></fontfamily> 


  


>Is there a way to pause in the middle of a macro, draw a freehand ROI,
then

>continue the macro?  At present, I exit the macro, draw, then start
the

>macro again at the beginning; this leads to clumsy programming.

>

>Example: a stack of 5 images.  I want to outline a cell,
measure,select the

>next slice, outline the slightly differently bordered cell, measure,
select

>the next slice, etc.

>(At present, my macro F2 PutMessages "outline a cell, then hit F3",
and

>then exits. I outline, hit F3, it measures, goes to slice 2, I
outline, hit

>F3, etc.)

>Thanks in advance,  Harry

>

>Henry M. Thomas, III MD (Harry)

>Professor of Clinical Medicine,  Pulmonary and Critical Care Division

>Department of Medicine, Cornell Univ. Medical School

>Director, Pulmonary Research, Burke Rehabilitation Hospital

>785 Mamaroneck Ave.  White Plains, NY 10605

>(914) 597-2141





From nih-image-request@io.ece.drexel.edu Mon Aug 31 08:52 EDT 1998
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From: "Dr. Ron Goldstein" <goldst@mail.biu.ac.il>
Subject: integration of dim fluorescent signals
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Hi,

I have been having trouble figuring out how to use the integration function
of the Averaging menu in Image. I am aquiring dim fluorescence images, and
do not have on chip integration, or a mathematical grabber (I'm using the
Scion LG-3). I do not think that I want the program to automatically scale
the sum of the multiple frames linearly to 0-255 as it does by default.

In Image Pro, integration is intuitive, one sets how many frames are to be
captured, and what number to divided the integrated result by. For example,
if I want an image that "holds the shutter open" twice as long, I would
tell the program to capture 8 frames, and divide the resulting values by
four. The resulting image gives a brighter signal, and with some playing
with the contrast, the increased background can be reduced (or subtracted
using an image of an empty area of the specimen).

In Image, to do the same thing it seems that one must use the "Fix Scale"
dialog, is that correct? How would one obtain the "holding the camera
shutter open" that I described before using this method?

Thanks,

-Ron
--------------------------------------------------------
Dr. Ron Goldstein               email      goldst@mail.biu.ac.il
Dept. Life Sciences            Tel.         972-3-531-8216
Bar-Ilan Univ                       FAX        972-3-535-1824
52900 Ramat-Gan, ISRAEL
http://www.biu.ac.il/NAT/ls/goldstein.html


From nih-image-request@io.ece.drexel.edu Mon Aug 31 10:32 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: "Linda J. Lewis" <lewis@vet.upenn.edu>
Subject: writing macros
Cc: bldallap@vet.upenn.edu
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Hello,
I have been asked to write a macro for some clinicians here at our vet
hospital.  I am unfamiliar with NIH Image (the person who was supposed to
do this is no longer here).  I have had Pascal and the language doesn't
look too bad but I'm not sure exactly how much detail I need to go into for
the user interface.  This is what they are looking to accomplish:
For each slide:
   For i=1:? captures per slide:  (the whole slide isn't visible at once)
      Measure the perimeter (let's call it p(i))
      Measure the bone value (let's call it b(i))
      Measure the amt near growth plate (if any) (let's call it g(i))
      Calculate the amount of no bone formation (p(i) - b(i)) (let's call
it n(i))
  Save the image onto a disk
  Sum up measurements for all the captures per slide: For i=1:? 
      psum=psum + p(i)
      bsum=bsum + b(i)
      gsum=gsum + g(i)
      nsum=nsum + n(i)
  Calculate the % bone formation, let's call it f:  f = bsum/psum
  Calculate the % no bone formation near growth plate (let's call it ng):
ng = gsum/nsum
After all the slides, export the data to an excel file.

Writing macros to do the calculations doesn't seem to be difficult.  Do I
have to write a user interface so that they can signify what measurements
to use (ie. they make a mistake and measure the perimeter again) and to
signal when each slide is finished?  All the macros I've seen don't appear
to do this.  If you can give me any insight, I'd appreciate it.  And of
course, we need this asap.  Thanks in advance.  ljl
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Linda J. Lewis
New Bolton Center On-Site Support
For help at NBC: call ext. HELP
                         send email to help@vet.upenn.edu
                         or browse http://www.vet.upenn.edu/help

New Bolton Center
University of Pennsylvania, School of Veterinary Medicine
382 W. Street Road
Kennett Square, PA  19348-1692
610-444-5800 x2482 
fax 610-444-4724
email: lewis@vet.upenn.edu


From nih-image-request@io.ece.drexel.edu Mon Aug 31 12:31 EDT 1998
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Date: Mon, 31 Aug 1998 12:16:48 -0400
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From: Bill Bosking <billb@neuro.duke.edu>
Subject: Code Warrior Pro 3 
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Wayne/others:

Currently, I am using CodeWarrior Academic Pro 11 for the Macintosh to
compile Image 1.62b4 source code. I looked on the Image home page and found
there was a version 1.62b20 for Code Warrior Pro 2. I recently bought Code
Warrior Pro 3 which I installed on a Windows 95 machine. I was wondering if
there was any version of the Image source code that would compile using
Code Warrior Pro 3 (or if there isn't one now if there might be one in the
near future). In addition, since Code Warrior Pro 3 allows you to compile
projects for multiple targets, will it ever be possible to obtain source
code that I could use with Code Warrior Pro 3 to compile a version of Image
to run on a Windows machine?  Sorry for being greedy, but a version of the
source code that would allow me to compile an extended version of Image for
a Windows machine would be of great value to me (and I assume to others as
well). 



Bill Bosking
billb@neuro.duke.edu
919-684-8510 phone
919-684-4431 FAX


From nih-image-request@io.ece.drexel.edu Tue Sep  1 00:30 EDT 1998
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From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: goldst@mail.biu.ac.il, nih-image@io.ece.drexel.edu
Date:          Tue, 1 Sep 1998 14:23:13 GMT+1000
Subject:       Re: integration of dim fluorescent signals
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>Date: Mon, 31 Aug 1998 15:38:38 +0300
>To: nih-image@io.ece.drexel.edu
>From: "Dr. Ron Goldstein" <goldst@mail.biu.ac.il>
>Subject: integration of dim fluorescent signals
>
>I have been having trouble figuring out how to use the integration function
>of the Averaging menu in Image. I am aquiring dim fluorescence images, and
>do not have on chip integration, or a mathematical grabber (I'm using the
>Scion LG-3). I do not think that I want the program to automatically scale
>the sum of the multiple frames linearly to 0-255 as it does by default.
>
>In Image Pro, integration is intuitive, one sets how many frames are to be
>captured, and what number to divided the integrated result by. For example,
>if I want an image that "holds the shutter open" twice as long, I would
>tell the program to capture 8 frames, and divide the resulting values by
>four. The resulting image gives a brighter signal, and with some playing
>with the contrast, the increased background can be reduced (or subtracted
>using an image of an empty area of the specimen).
>
>In Image, to do the same thing it seems that one must use the "Fix Scale"
>dialog, is that correct? How would one obtain the "holding the camera
>shutter open" that I described before using this method?
>
>Thanks,
>
>-Ron
>--------------------------------------------------------
>Dr. Ron Goldstein               email      goldst@mail.biu.ac.il
>Dept. Life Sciences            Tel.         972-3-531-8216
>Bar-Ilan Univ                       FAX        972-3-535-1824
>52900 Ramat-Gan, ISRAEL
>http://www.biu.ac.il/NAT/ls/goldstein.html
>
If you captured n images with the integration box checked, you would also see  
min=, max=,and timing information recorded in the "Info" window. These give the 
range of the actual (integrated) sum of pixel values as stored in the 
intermediate temporary real image which would then be scaled to set max=254, 
min=1 (not 255,0).

Using "Fix Scale" your own offset and scale values are used.
For n=8, the maximum accumulated pixel value would be 256n = 2048
so "Fix Scale",0,1024 would achieve your requested result.

In practice you would probably find a non-zero minimum (which you can read off 
the Info window. (Re)Entry of the values min,min+1024 would then result in 
better contrast.

Better still, inspect the histogram of the captured integrated image to see 
where the "real" max/min are ie the range of interest excluding backround, 
outliers or highlights. It is then practical (if not always straight forward) 
to set min/max values to maximising useful contrast in converting from the 
internal real value image to the 8 bit result.

You can test this at the macro level by imageing print on paper ("black" on 
"white") with integration checked. With video controls gain/offset set 
correctly (or regardless) and "Fix Scale" not checked, the histogram should 
range 1-254 (0,255 vacant). ShowHistogram should then enable you to see the 
histogram pixel range which corresponds to the "white" paper.
Select a ROI which excludes text (ie white paper only) and capture again. The 
Info window will report the min/max of the integrated ROI ie paper only.
Feeding these values back into a "Fix Scale" integration will give you a high 
contrast image of the "white" paper (with the print saturated black and 
effectively ignored in this contrast range).
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia


From nih-image-d-request@io.ece.drexel.edu Tue Sep  1 00:32 EDT 1998
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Subject: nih-image-d Digest V98 #49
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 49

Today's Topics:
  Re: Pausing a macro to draw a freeha  [ Laird Bloom <lbloom@MIT.EDU> ]
  integration of dim fluorescent signa  [ "Dr. Ron Goldstein" <goldst@mail.bi ]
  writing macros                        [ "Linda J. Lewis" <lewis@vet.upenn.e ]
  Code Warrior Pro 3                    [ Bill Bosking <billb@neuro.duke.edu> ]
  Re: integration of dim fluorescent s  [ GJOSS@rna.bio.mq.edu.au ]

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

Date: Mon, 31 Aug 1998 08:20:41 -0400
From: Laird Bloom <lbloom@MIT.EDU>
To: hmthomas@med.cornell.edu (Henry M. Thomas)
Cc: nih-image@io.ece.drexel.edu
Subject: Re: Pausing a macro to draw a freehand ROI
Message-Id: <v03020900b2103e543205@[18.155.0.106]>
Content-Type: text/enriched; charset="us-ascii"

Henry,

I have used a fairly simple solution to this problem--although it may
be clumsy programming--in several macros. Essentially, I write the
macro in a way that expects there to be an open image file at the
start, and then after doing the measurement procedures, closes or saves
the current image and opens the next one.  I also set up the macro so I
can start it with a single keystroke (using [x] in the macro title,
where x is a single key).  That way it's fairly straightforward to draw
your ROI and press a key, then have the computer do measurements and
open your next slice for you.  

	I often do this in conjunction with two other macros, one to set
initial parameters (type of measurements, name of file for saving
results, etc.) and open the first image, the other to analyze the data
in the results file after the individual images have been measured. 
Below is an example we use for capturing live video images and
measuring the areas of a number of freehand ROIs from each of a number
of images, then saving each area in a file.  In this case, the "Measure
Area[M]" macro is used multiple times for multiple ROIs in a single
image, and then the<fontfamily><param>Times</param><bigger><bigger>
'New view of current sample [v]'</bigger></bigger></fontfamily> macro
gets rid of the current image and has the computer acquire a new one,
using the GetImageToMeasure procedure.  Like the old VW ads:  it's
ugly, but it gets you there.


Good luck.

Laird Bloom

MIT Center for Cancer Research


<fontfamily><param>Times</param><bigger><bigger>{  We use Scion Image
1.62, essentially the same as NIH Image 1.61. You may need to modify
the StartCapturing and StopCapturing commands if the "measure areas on
scope" macro, depending on the source of your input.  Excerpt from lab
protocol book precedes the macro code.

<bold>

"Measure areas on scope" macro

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

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


{"Measure areas on scope" macro file follows:

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

}


var {Global variables}

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

	mean:real;

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



procedure GetImageToMeasure;

begin

StartCapturing;

	Repeat

		Wait(.1);

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

StopCapturing;


SetPicName(nSample,'  Image');

SelectWindow(nSample,'  Image');

         if nSave='Yes'

              then Save;

end



procedure LabelAreaInCenter;


var

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

  scale: real;

  unit: string;

begin

  GetRoi(left,top,width,height);

  if width=0 then begin

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

    exit;

  end;

  SaveState;

  InvertY(false);

  SetForegroundColor(255); {black}

SetBackgroundColor(1);

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

  GetScale(scale, unit);

  Measure;

	DrawBoundary;

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

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

  MoveTo(x-5, y);

	SetFont('Times');

	SetFontSize(9);

SetText('With Background');

	Writeln('region ',j:0);

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

  RestoreState;

end;



macro 'Measure Area [M]';

begin

	j:=j+1;

	LabelAreaInCenter;

	ImageName:=WindowTitle;

	SelectWindow(nSample);

        

	If j=1

		then writeln (nSample); 

		SetFont('Times');

		SetFontSize(12);

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

 		rUser1[j]:=rArea[rCount];

		total:=total+rArea[rCount];

      Save;

	SelectWindow(ImageName);

end


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

var

	width,height:integer;

begin

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

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

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

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

	NewTextWindow(nSample,80,600);

				MoveWindow(740,40);

	total:=0;

GetImageToMeasure;

	j:=0;

end;


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

begin

SelectWindow(ImageName);

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

 DisposeAll;

GetImageToMeasure;

end;

 

macro 'New Sample [S]';


begin

	If j=0

			 then j:=1;

SelectWindow(ImageName);

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

 		Dispose;

SelectWindow(nSample);

mean:=total/j;

writeln('Mean =');

write(mean);

save;

		dispose;

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

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


	NewTextWindow(nSample,80,600);

				MoveWindow(740,40);

	total:=0;

GetImageToMeasure;

	j:=0;

end;</bigger></bigger></fontfamily> 


  


>Is there a way to pause in the middle of a macro, draw a freehand ROI,
then

>continue the macro?  At present, I exit the macro, draw, then start
the

>macro again at the beginning; this leads to clumsy programming.

>

>Example: a stack of 5 images.  I want to outline a cell,
measure,select the

>next slice, outline the slightly differently bordered cell, measure,
select

>the next slice, etc.

>(At present, my macro F2 PutMessages "outline a cell, then hit F3",
and

>then exits. I outline, hit F3, it measures, goes to slice 2, I
outline, hit

>F3, etc.)

>Thanks in advance,  Harry

>

>Henry M. Thomas, III MD (Harry)

>Professor of Clinical Medicine,  Pulmonary and Critical Care Division

>Department of Medicine, Cornell Univ. Medical School

>Director, Pulmonary Research, Burke Rehabilitation Hospital

>785 Mamaroneck Ave.  White Plains, NY 10605

>(914) 597-2141

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

Date: Mon, 31 Aug 1998 15:38:38 +0300
From: "Dr. Ron Goldstein" <goldst@mail.biu.ac.il>
To: nih-image@io.ece.drexel.edu
Subject: integration of dim fluorescent signals
Message-Id: <3.0.5.32.19980831153838.007c9da0@mail.biu.ac.il>
Content-Type: text/plain; charset="us-ascii"

Hi,

I have been having trouble figuring out how to use the integration function
of the Averaging menu in Image. I am aquiring dim fluorescence images, and
do not have on chip integration, or a mathematical grabber (I'm using the
Scion LG-3). I do not think that I want the program to automatically scale
the sum of the multiple frames linearly to 0-255 as it does by default.

In Image Pro, integration is intuitive, one sets how many frames are to be
captured, and what number to divided the integrated result by. For example,
if I want an image that "holds the shutter open" twice as long, I would
tell the program to capture 8 frames, and divide the resulting values by
four. The resulting image gives a brighter signal, and with some playing
with the contrast, the increased background can be reduced (or subtracted
using an image of an empty area of the specimen).

In Image, to do the same thing it seems that one must use the "Fix Scale"
dialog, is that correct? How would one obtain the "holding the camera
shutter open" that I described before using this method?

Thanks,

-Ron
--------------------------------------------------------
Dr. Ron Goldstein               email      goldst@mail.biu.ac.il
Dept. Life Sciences            Tel.         972-3-531-8216
Bar-Ilan Univ                       FAX        972-3-535-1824
52900 Ramat-Gan, ISRAEL
http://www.biu.ac.il/NAT/ls/goldstein.html

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

Date: Mon, 31 Aug 1998 10:19:43 -0400
From: "Linda J. Lewis" <lewis@vet.upenn.edu>
To: nih-image@io.ece.drexel.edu
Cc: bldallap@vet.upenn.edu
Subject: writing macros
Message-Id: <3.0.4.32.19980831101943.00b41388@130.91.91.1>
Content-Type: text/plain; charset="us-ascii"

Hello,
I have been asked to write a macro for some clinicians here at our vet
hospital.  I am unfamiliar with NIH Image (the person who was supposed to
do this is no longer here).  I have had Pascal and the language doesn't
look too bad but I'm not sure exactly how much detail I need to go into for
the user interface.  This is what they are looking to accomplish:
For each slide:
   For i=1:? captures per slide:  (the whole slide isn't visible at once)
      Measure the perimeter (let's call it p(i))
      Measure the bone value (let's call it b(i))
      Measure the amt near growth plate (if any) (let's call it g(i))
      Calculate the amount of no bone formation (p(i) - b(i)) (let's call
it n(i))
  Save the image onto a disk
  Sum up measurements for all the captures per slide: For i=1:? 
      psum=psum + p(i)
      bsum=bsum + b(i)
      gsum=gsum + g(i)
      nsum=nsum + n(i)
  Calculate the % bone formation, let's call it f:  f = bsum/psum
  Calculate the % no bone formation near growth plate (let's call it ng):
ng = gsum/nsum
After all the slides, export the data to an excel file.

Writing macros to do the calculations doesn't seem to be difficult.  Do I
have to write a user interface so that they can signify what measurements
to use (ie. they make a mistake and measure the perimeter again) and to
signal when each slide is finished?  All the macros I've seen don't appear
to do this.  If you can give me any insight, I'd appreciate it.  And of
course, we need this asap.  Thanks in advance.  ljl
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Linda J. Lewis
New Bolton Center On-Site Support
For help at NBC: call ext. HELP
                         send email to help@vet.upenn.edu
                         or browse http://www.vet.upenn.edu/help

New Bolton Center
University of Pennsylvania, School of Veterinary Medicine
382 W. Street Road
Kennett Square, PA  19348-1692
610-444-5800 x2482 
fax 610-444-4724
email: lewis@vet.upenn.edu

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

Date: Mon, 31 Aug 1998 12:16:48 -0400
From: Bill Bosking <billb@neuro.duke.edu>
To: nih-image@io.ece.drexel.edu
Subject: Code Warrior Pro 3 
Message-Id: <3.0.5.32.19980831121648.007d4100@neuro.duke.edu>
Content-Type: text/plain; charset="us-ascii"

Wayne/others:

Currently, I am using CodeWarrior Academic Pro 11 for the Macintosh to
compile Image 1.62b4 source code. I looked on the Image home page and found
there was a version 1.62b20 for Code Warrior Pro 2. I recently bought Code
Warrior Pro 3 which I installed on a Windows 95 machine. I was wondering if
there was any version of the Image source code that would compile using
Code Warrior Pro 3 (or if there isn't one now if there might be one in the
near future). In addition, since Code Warrior Pro 3 allows you to compile
projects for multiple targets, will it ever be possible to obtain source
code that I could use with Code Warrior Pro 3 to compile a version of Image
to run on a Windows machine?  Sorry for being greedy, but a version of the
source code that would allow me to compile an extended version of Image for
a Windows machine would be of great value to me (and I assume to others as
well). 



Bill Bosking
billb@neuro.duke.edu
919-684-8510 phone
919-684-4431 FAX

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

Date:          Tue, 1 Sep 1998 14:23:13 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: goldst@mail.biu.ac.il, nih-image@io.ece.drexel.edu
Subject:       Re: integration of dim fluorescent signals
Message-ID: <761767A26AC@rna.bio.mq.edu.au>

>Date: Mon, 31 Aug 1998 15:38:38 +0300
>To: nih-image@io.ece.drexel.edu
>From: "Dr. Ron Goldstein" <goldst@mail.biu.ac.il>
>Subject: integration of dim fluorescent signals
>
>I have been having trouble figuring out how to use the integration function
>of the Averaging menu in Image. I am aquiring dim fluorescence images, and
>do not have on chip integration, or a mathematical grabber (I'm using the
>Scion LG-3). I do not think that I want the program to automatically scale
>the sum of the multiple frames linearly to 0-255 as it does by default.
>
>In Image Pro, integration is intuitive, one sets how many frames are to be
>captured, and what number to divided the integrated result by. For example,
>if I want an image that "holds the shutter open" twice as long, I would
>tell the program to capture 8 frames, and divide the resulting values by
>four. The resulting image gives a brighter signal, and with some playing
>with the contrast, the increased background can be reduced (or subtracted
>using an image of an empty area of the specimen).
>
>In Image, to do the same thing it seems that one must use the "Fix Scale"
>dialog, is that correct? How would one obtain the "holding the camera
>shutter open" that I described before using this method?
>
>Thanks,
>
>-Ron
>--------------------------------------------------------
>Dr. Ron Goldstein               email      goldst@mail.biu.ac.il
>Dept. Life Sciences            Tel.         972-3-531-8216
>Bar-Ilan Univ                       FAX        972-3-535-1824
>52900 Ramat-Gan, ISRAEL
>http://www.biu.ac.il/NAT/ls/goldstein.html
>
If you captured n images with the integration box checked, you would also see  
min=, max=,and timing information recorded in the "Info" window. These give the 
range of the actual (integrated) sum of pixel values as stored in the 
intermediate temporary real image which would then be scaled to set max=254, 
min=1 (not 255,0).

Using "Fix Scale" your own offset and scale values are used.
For n=8, the maximum accumulated pixel value would be 256n = 2048
so "Fix Scale",0,1024 would achieve your requested result.

In practice you would probably find a non-zero minimum (which you can read off 
the Info window. (Re)Entry of the values min,min+1024 would then result in 
better contrast.

Better still, inspect the histogram of the captured integrated image to see 
where the "real" max/min are ie the range of interest excluding backround, 
outliers or highlights. It is then practical (if not always straight forward) 
to set min/max values to maximising useful contrast in converting from the 
internal real value image to the 8 bit result.

You can test this at the macro level by imageing print on paper ("black" on 
"white") with integration checked. With video controls gain/offset set 
correctly (or regardless) and "Fix Scale" not checked, the histogram should 
range 1-254 (0,255 vacant). ShowHistogram should then enable you to see the 
histogram pixel range which corresponds to the "white" paper.
Select a ROI which excludes text (ie white paper only) and capture again. The 
Info window will report the min/max of the integrated ROI ie paper only.
Feeding these values back into a "Fix Scale" integration will give you a high 
contrast image of the "white" paper (with the print saturated black and 
effectively ignored in this contrast range).
Greg Joss,
School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174
Macquarie University,          Email gjoss@rna.bio.mq.edu.au
North Ryde, (Sydney,) NSW 2109, Australia

--------------------------------
End of nih-image-d Digest V98 Issue #49
***************************************

From nih-image-request@io.ece.drexel.edu Tue Sep  1 11:57 EDT 1998
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To: "Linda J. Lewis" <lewis@vet.upenn.edu>
From: Laird Bloom <lbloom@MIT.EDU>
Subject: Re: writing macros
Cc: nih-image@io.ece.drexel.edu
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Hi Linda,
	I've written a few sets of macros to record data into text files
while the user is scoring slides.  The general structure that works for me
is to have individual macros that can be run by a single keystroke (by
including [x] in the macro name, where x is any key), each of which
instructs the computer to make a single measurement, write it to a data
file, increment a counter, and return to the image.  I also have a macro
for setting parameters (sample names, name of results files, etc.) and
opening the initial image, and a second macro that calculates averages,etc.
for the data file when the slide is completely scored. It's fairly simple
to teach people to use macros written this way; they just have to remember
which keys to press to score which parameters.  The user can outline areas
on the image and choose not to measure them if they make a mistake.  (I'm
not sure there's an easy way to undo mistakes).
	As for recording data,  writing each data point for a single
parameter as a single column of numbers works nicely for import into Excel
(just select all, copy, and paste into Excel, no reformatting needed).  If
you're scoring multiple parameters, I would suggest setting up multiple
data files.  The transition to Excel is somewhat cumbersome, since you have
to copy and paste each file separately, but there's no editing needed once
you get there.  Alternately, you can write your data to a single text file
and open the whole thing in Excel, deleting extra cells as needed.
	An alternative might be to record data in the two rUser arrays and
then write a procedure to write each value (or just the averages) to a text
file; unfortunately, there are only two arrays available.
	You'll find code for one set of macros written like this, for
measuring outlined areas, in the same nih-image-d Digest V98 #42 set in
which your inquiry appeared; see my message about pausing macros in that
set, or contact me directly for the code.

Laird Bloom
MIT Center for Cancer Research

>Hello,
>I have been asked to write a macro for some clinicians here at our vet
>hospital.  I am unfamiliar with NIH Image (the person who was supposed to
>do this is no longer here).  I have had Pascal and the language doesn't
>look too bad but I'm not sure exactly how much detail I need to go into for
>the user interface.  This is what they are looking to accomplish:
>For each slide:
>   For i=1:? captures per slide:  (the whole slide isn't visible at once)
>      Measure the perimeter (let's call it p(i))
>      Measure the bone value (let's call it b(i))
>      Measure the amt near growth plate (if any) (let's call it g(i))
>      Calculate the amount of no bone formation (p(i) - b(i)) (let's call
>it n(i))
>  Save the image onto a disk
>  Sum up measurements for all the captures per slide: For i=1:?
>      psum=psum + p(i)
>      bsum=bsum + b(i)
>      gsum=gsum + g(i)
>      nsum=nsum + n(i)
>  Calculate the % bone formation, let's call it f:  f = bsum/psum
>  Calculate the % no bone formation near growth plate (let's call it ng):
>ng = gsum/nsum
>After all the slides, export the data to an excel file.
>
>Writing macros to do the calculations doesn't seem to be difficult.  Do I
>have to write a user interface so that they can signify what measurements
>to use (ie. they make a mistake and measure the perimeter again) and to
>signal when each slide is finished?  All the macros I've seen don't appear
>to do this.  If you can give me any insight, I'd appreciate it.  And of
>course, we need this asap.  Thanks in advance.  ljl
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>Linda J. Lewis
>New Bolton Center On-Site Support
>For help at NBC: call ext. HELP
>                         send email to help@vet.upenn.edu
>                         or browse http://www.vet.upenn.edu/help
>
>New Bolton Center
>University of Pennsylvania, School of Veterinary Medicine
>382 W. Street Road
>Kennett Square, PA  19348-1692
>610-444-5800 x2482
>fax 610-444-4724
>email: lewis@vet.upenn.edu




From nih-image-request@io.ece.drexel.edu Tue Sep  1 12:10 EDT 1998
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From: oberyszyn.1@osu.edu (Tatiana Oberyszyn)
Subject: Mac G3
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As and NIH Image neophyte I have a very basic question.  Has anyone used
NIH image on a PowerMac G3?  The computer has a VCR like video in port.  We
have a Sony CCD camera on a Nikon microscope which was hooked up to a
Windows based computer. Hopefully I'll be able to, once I find the
necessary hardware, hook into the video in port on the Mac.  Thanks

Tania



From nih-image-request@io.ece.drexel.edu Tue Sep  1 12:20 EDT 1998
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Date: Tue, 01 Sep 1998 16:00:32 +0000
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References: <761767A26AC@rna.bio.mq.edu.au>
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Dear all,

I'm having a lot of trouble with what should be an extremely easy task. I can not
get the command

GetTime(year, month, day, hour, minute, second, dayofweek);

to work at all. NIH Image, Object Image and Image SXM all return an unidentified
identifier "GetTime" error message. Any one have the solution?


many thanks in advance,

Jeremy






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

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



From nih-image-request@io.ece.drexel.edu Tue Sep  1 12:37 EDT 1998
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From: "Kirk, Todd Jason" <tjkirk@iupui.edu>
To: nih-image@io.ece.drexel.edu
Subject: Image capture to a stack
Date: Tue, 1 Sep 1998 10:42:44 -0500 
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Hey,
     I'm just starting out with the Scion version of NIH Image and have
a question about capturing images to a stack.

I can capture an Image but how do I add it to the stack? I have made a
new stack, when I try to add the new capture, it just adds a white slice
in the new stack.

Also, how would I save pictures with an incrementing counter for the
name? Like, slice1.tif, slice2.tif, slice3.tif etc. I have tried
saveas('slice'+slicenumber), but it wants only a string.

				Thanks ...... Todd


From nih-image-request@io.ece.drexel.edu Tue Sep  1 13:28 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: GetTime Command
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>Dear all,
>
>I'm having a lot of trouble with what should be an extremely easy task. I
>can not
>get the command
>
>GetTime(year, month, day, hour, minute, second, dayofweek);
>
>to work at all. NIH Image, Object Image and Image SXM all return an
>unidentified
>identifier "GetTime" error message. Any one have the solution?

Here's an exmple of how to use GetTime:

macro 'GetTime Test';
var
  year,month,day,hour,minute,second,DayOfWeek:integer;
begin
  GetTime(year,month,day,hour,minute,second,DayOfWeek);
  PutMessage(year:1,'/',month:1,'/',day:1,
         '   ',hour:1,':'minute:1,':',second:1);
end;

Output:  1998/9/1   12:52:21

-wayne



From nih-image-request@io.ece.drexel.edu Tue Sep  1 13:50 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: Image capture to a stack
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>Hey,
>     I'm just starting out with the Scion version of NIH Image and have
>a question about capturing images to a stack.
>
>I can capture an Image but how do I add it to the stack? I have made a
>new stack, when I try to add the new capture, it just adds a white slice
>in the new stack.

The "Capture Frames" command captures images and adds them to a stack. All
the "Add Slice" command does is add a blank slice to the stack. You need to
Copy and Paste to put an image into that slice.

>Also, how would I save pictures with an incrementing counter for the
>name? Like, slice1.tif, slice2.tif, slice3.tif etc. I have tried
>saveas('slice'+slicenumber), but it wants only a string.

This should work:

    SaveAs('slice', slicenumber:3);

-wayne



From nih-image-request@io.ece.drexel.edu Tue Sep  1 14:01 EDT 1998
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Subject: G3 Video
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I have yet to be able to get NIH Image to capture video from the builtin video port on my G3.  All the other Video capture programs I use work just fine except for NIH Image.  I use my 8600/300 for video capture through NIH Image instead of my G3 because of this.


From nih-image-request@io.ece.drexel.edu Tue Sep  1 14:04 EDT 1998
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>As and NIH Image neophyte I have a very basic question.  Has anyone used
>NIH image on a PowerMac G3?  The computer has a VCR like video in port.  We
>have a Sony CCD camera on a Nikon microscope which was hooked up to a
>Windows based computer. Hopefully I'll be able to, once I find the
>necessary hardware, hook into the video in port on the Mac.  Thanks
>
>Tania


NIH Image's Start Capturing command does not work with the PowerMac G3's
built-in digitizer. You can, however, use the Plug-in Digitizer available
from

      ftp://codon.nih.gov/pub/nih-image/plug-ins/

-wayne




From nih-image-request@io.ece.drexel.edu Tue Sep  1 14:12 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: Code Warrior Pro 3
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>Wayne/others:
>
>Currently, I am using CodeWarrior Academic Pro 11 for the Macintosh to
>compile Image 1.62b4 source code. I looked on the Image home page and found
>there was a version 1.62b20 for Code Warrior Pro 2. I recently bought Code
>Warrior Pro 3 which I installed on a Windows 95 machine. I was wondering if
>there was any version of the Image source code that would compile using
>Code Warrior Pro 3 (or if there isn't one now if there might be one in the
>near future). In addition, since Code Warrior Pro 3 allows you to compile
>projects for multiple targets, will it ever be possible to obtain source
>code that I could use with Code Warrior Pro 3 to compile a version of Image
>to run on a Windows machine?  Sorry for being greedy, but a version of the
>source code that would allow me to compile an extended version of Image for
>a Windows machine would be of great value to me (and I assume to others as
>well).

You should be able to compile the 1.62b20 source with CodeWarrior Pro 3. To
compile and run it on a Windows machine, however, would require writing
Windows equivalents for the hundreds of Mac toolbox routines used by NIH
Image.

-wayne



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I had problems with NIH Image and CodeWorrior 3: in the 68k project, the
'StringOf' function did not work, with the effect that many strings showed
garbage or nothing. This became visible in the file and edit menu, the info
window and so on. If I remember right, this also applied to the original
NIH Image version. I sent the source code to the technical staff of
Metroworks, they were 'puzzled' and could reproduce the error, but not in a
simple example. Meanwhile, I tried the newest updates (a few days ago) but
the error remained.
At this moment, I still use CodeWarrior 2.
Has any one successfully compiled NIH Image/68k with CW3?

Norbert Vischer




From nih-image-d-request@io.ece.drexel.edu Wed Sep  2 05:03 EDT 1998
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 50

Today's Topics:
  Re: writing macros                    [ Laird Bloom <lbloom@MIT.EDU> ]
  Mac G3                                [ oberyszyn.1@osu.edu (Tatiana Oberys ]
  GetTime Command                       [ Jeremy Brown <brownj@netmatters.co. ]
  Image capture to a stack              [ "Kirk, Todd Jason" <tjkirk@iupui.ed ]
  Re: GetTime Command                   [ Wayne Rasband <wayne@codon.nih.gov> ]
  Re: Image capture to a stack          [ Wayne Rasband <wayne@codon.nih.gov> ]
  Re: Mac G3                            [ Wayne Rasband <wayne@codon.nih.gov> ]
  G3 Video                              [ "STEPHEN MOORMAN" <smoorman@hsc.unt ]
  Re: Code Warrior Pro 3                [ Wayne Rasband <wayne@codon.nih.gov> ]
  Re: Code Warrior Pro 3                [ Norbert Vischer <vischer@bio.uva.nl ]
  Re: Image capture to a stack          [ Stein Roervik <steinr@chembio.ntnu. ]

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

Date: Tue, 1 Sep 1998 10:06:10 -0500
From: Laird Bloom <lbloom@MIT.EDU>
To: "Linda J. Lewis" <lewis@vet.upenn.edu>
Cc: nih-image@io.ece.drexel.edu
Subject: Re: writing macros
Message-Id: <v03020901b211ba121d2e@[18.155.0.104]>
Content-Type: text/plain; charset="us-ascii"

Hi Linda,
	I've written a few sets of macros to record data into text files
while the user is scoring slides.  The general structure that works for me
is to have individual macros that can be run by a single keystroke (by
including [x] in the macro name, where x is any key), each of which
instructs the computer to make a single measurement, write it to a data
file, increment a counter, and return to the image.  I also have a macro
for setting parameters (sample names, name of results files, etc.) and
opening the initial image, and a second macro that calculates averages,etc.
for the data file when the slide is completely scored. It's fairly simple
to teach people to use macros written this way; they just have to remember
which keys to press to score which parameters.  The user can outline areas
on the image and choose not to measure them if they make a mistake.  (I'm
not sure there's an easy way to undo mistakes).
	As for recording data,  writing each data point for a single
parameter as a single column of numbers works nicely for import into Excel
(just select all, copy, and paste into Excel, no reformatting needed).  If
you're scoring multiple parameters, I would suggest setting up multiple
data files.  The transition to Excel is somewhat cumbersome, since you have
to copy and paste each file separately, but there's no editing needed once
you get there.  Alternately, you can write your data to a single text file
and open the whole thing in Excel, deleting extra cells as needed.
	An alternative might be to record data in the two rUser arrays and
then write a procedure to write each value (or just the averages) to a text
file; unfortunately, there are only two arrays available.
	You'll find code for one set of macros written like this, for
measuring outlined areas, in the same nih-image-d Digest V98 #42 set in
which your inquiry appeared; see my message about pausing macros in that
set, or contact me directly for the code.

Laird Bloom
MIT Center for Cancer Research

>Hello,
>I have been asked to write a macro for some clinicians here at our vet
>hospital.  I am unfamiliar with NIH Image (the person who was supposed to
>do this is no longer here).  I have had Pascal and the language doesn't
>look too bad but I'm not sure exactly how much detail I need to go into for
>the user interface.  This is what they are looking to accomplish:
>For each slide:
>   For i=1:? captures per slide:  (the whole slide isn't visible at once)
>      Measure the perimeter (let's call it p(i))
>      Measure the bone value (let's call it b(i))
>      Measure the amt near growth plate (if any) (let's call it g(i))
>      Calculate the amount of no bone formation (p(i) - b(i)) (let's call
>it n(i))
>  Save the image onto a disk
>  Sum up measurements for all the captures per slide: For i=1:?
>      psum=psum + p(i)
>      bsum=bsum + b(i)
>      gsum=gsum + g(i)
>      nsum=nsum + n(i)
>  Calculate the % bone formation, let's call it f:  f = bsum/psum
>  Calculate the % no bone formation near growth plate (let's call it ng):
>ng = gsum/nsum
>After all the slides, export the data to an excel file.
>
>Writing macros to do the calculations doesn't seem to be difficult.  Do I
>have to write a user interface so that they can signify what measurements
>to use (ie. they make a mistake and measure the perimeter again) and to
>signal when each slide is finished?  All the macros I've seen don't appear
>to do this.  If you can give me any insight, I'd appreciate it.  And of
>course, we need this asap.  Thanks in advance.  ljl
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>Linda J. Lewis
>New Bolton Center On-Site Support
>For help at NBC: call ext. HELP
>                         send email to help@vet.upenn.edu
>                         or browse http://www.vet.upenn.edu/help
>
>New Bolton Center
>University of Pennsylvania, School of Veterinary Medicine
>382 W. Street Road
>Kennett Square, PA  19348-1692
>610-444-5800 x2482
>fax 610-444-4724
>email: lewis@vet.upenn.edu

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

Date: Tue, 1 Sep 1998 11:01:53 -0500
From: oberyszyn.1@osu.edu (Tatiana Oberyszyn)
To: nih-image@io.ece.drexel.edu
Subject: Mac G3
Message-Id: <v02130501b211c8af2ad3@[140.254.10.189]>
Content-Type: text/plain; charset="us-ascii"

As and NIH Image neophyte I have a very basic question.  Has anyone used
NIH image on a PowerMac G3?  The computer has a VCR like video in port.  We
have a Sony CCD camera on a Nikon microscope which was hooked up to a
Windows based computer. Hopefully I'll be able to, once I find the
necessary hardware, hook into the video in port on the Mac.  Thanks

Tania

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

Date: Tue, 01 Sep 1998 16:00:32 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: GetTime Command
Message-ID: <35EC1A1E.35C4FBF9@netmatters.co.uk>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit

Dear all,

I'm having a lot of trouble with what should be an extremely easy task. I can not
get the command

GetTime(year, month, day, hour, minute, second, dayofweek);

to work at all. NIH Image, Object Image and Image SXM all return an unidentified
identifier "GetTime" error message. Any one have the solution?


many thanks in advance,

Jeremy






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

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

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

Date: Tue, 1 Sep 1998 10:42:44 -0500 
From: "Kirk, Todd Jason" <tjkirk@iupui.edu>
To: nih-image@io.ece.drexel.edu
Subject: Image capture to a stack
Message-ID: <9D916278299FD111A7E100805FA7C2BA4B9F6B@cheetah.uits.iupui.edu>
Content-Type: text/plain

Hey,
     I'm just starting out with the Scion version of NIH Image and have
a question about capturing images to a stack.

I can capture an Image but how do I add it to the stack? I have made a
new stack, when I try to add the new capture, it just adds a white slice
in the new stack.

Also, how would I save pictures with an incrementing counter for the
name? Like, slice1.tif, slice2.tif, slice3.tif etc. I have tried
saveas('slice'+slicenumber), but it wants only a string.

				Thanks ...... Todd

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

Date: Tue, 1 Sep 1998 12:55:44 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: GetTime Command
Message-Id: <v03007800b211d6dadf3c@[128.231.99.216]>
Content-Type: text/plain; charset="us-ascii"

>Dear all,
>
>I'm having a lot of trouble with what should be an extremely easy task. I
>can not
>get the command
>
>GetTime(year, month, day, hour, minute, second, dayofweek);
>
>to work at all. NIH Image, Object Image and Image SXM all return an
>unidentified
>identifier "GetTime" error message. Any one have the solution?

Here's an exmple of how to use GetTime:

macro 'GetTime Test';
var
  year,month,day,hour,minute,second,DayOfWeek:integer;
begin
  GetTime(year,month,day,hour,minute,second,DayOfWeek);
  PutMessage(year:1,'/',month:1,'/',day:1,
         '   ',hour:1,':'minute:1,':',second:1);
end;

Output:  1998/9/1   12:52:21

-wayne

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

Date: Tue, 1 Sep 1998 13:18:43 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Image capture to a stack
Message-Id: <v03007801b211da2ca71a@[128.231.99.216]>
Content-Type: text/plain; charset="us-ascii"

>Hey,
>     I'm just starting out with the Scion version of NIH Image and have
>a question about capturing images to a stack.
>
>I can capture an Image but how do I add it to the stack? I have made a
>new stack, when I try to add the new capture, it just adds a white slice
>in the new stack.

The "Capture Frames" command captures images and adds them to a stack. All
the "Add Slice" command does is add a blank slice to the stack. You need to
Copy and Paste to put an image into that slice.

>Also, how would I save pictures with an incrementing counter for the
>name? Like, slice1.tif, slice2.tif, slice3.tif etc. I have tried
>saveas('slice'+slicenumber), but it wants only a string.

This should work:

    SaveAs('slice', slicenumber:3);

-wayne

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

Date: Tue, 1 Sep 1998 13:33:09 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Mac G3
Message-Id: <v03007802b211dd08532a@[128.231.99.216]>
Content-Type: text/plain; charset="us-ascii"

>As and NIH Image neophyte I have a very basic question.  Has anyone used
>NIH image on a PowerMac G3?  The computer has a VCR like video in port.  We
>have a Sony CCD camera on a Nikon microscope which was hooked up to a
>Windows based computer. Hopefully I'll be able to, once I find the
>necessary hardware, hook into the video in port on the Mac.  Thanks
>
>Tania


NIH Image's Start Capturing command does not work with the PowerMac G3's
built-in digitizer. You can, however, use the Plug-in Digitizer available
from

      ftp://codon.nih.gov/pub/nih-image/plug-ins/

-wayne

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

Date: Tue, 01 Sep 1998 12:26:44 -0500
From: "STEPHEN MOORMAN" <smoorman@hsc.unt.edu>
To: nih-image@io.ece.drexel.edu
Subject: G3 Video
Message-Id: <s5ebe8f4.051@hsc.unt.edu>
Content-Type: text/plain; charset=US-ASCII
Content-Disposition: inline
Content-Transfer-Encoding: 8bit

I have yet to be able to get NIH Image to capture video from the builtin video port on my G3.  All the other Video capture programs I use work just fine except for NIH Image.  I use my 8600/300 for video capture through NIH Image instead of my G3 because of this.

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

Date: Tue, 1 Sep 1998 13:43:31 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: Code Warrior Pro 3
Message-Id: <v03007803b211e07621ac@[128.231.99.216]>
Content-Type: text/plain; charset="us-ascii"

>Wayne/others:
>
>Currently, I am using CodeWarrior Academic Pro 11 for the Macintosh to
>compile Image 1.62b4 source code. I looked on the Image home page and found
>there was a version 1.62b20 for Code Warrior Pro 2. I recently bought Code
>Warrior Pro 3 which I installed on a Windows 95 machine. I was wondering if
>there was any version of the Image source code that would compile using
>Code Warrior Pro 3 (or if there isn't one now if there might be one in the
>near future). In addition, since Code Warrior Pro 3 allows you to compile
>projects for multiple targets, will it ever be possible to obtain source
>code that I could use with Code Warrior Pro 3 to compile a version of Image
>to run on a Windows machine?  Sorry for being greedy, but a version of the
>source code that would allow me to compile an extended version of Image for
>a Windows machine would be of great value to me (and I assume to others as
>well).

You should be able to compile the 1.62b20 source with CodeWarrior Pro 3. To
compile and run it on a Windows machine, however, would require writing
Windows equivalents for the hundreds of Mac toolbox routines used by NIH
Image.

-wayne

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

Date: Tue, 1 Sep 1998 21:36:18 +0200
From: Norbert Vischer <vischer@bio.uva.nl>
To: nih-image@io.ece.drexel.edu
Subject: Re: Code Warrior Pro 3
Message-Id: <l03110700b211fcb653c2@[145.18.160.48]>
Content-Type: text/plain; charset="us-ascii"

I had problems with NIH Image and CodeWorrior 3: in the 68k project, the
'StringOf' function did not work, with the effect that many strings showed
garbage or nothing. This became visible in the file and edit menu, the info
window and so on. If I remember right, this also applied to the original
NIH Image version. I sent the source code to the technical staff of
Metroworks, they were 'puzzled' and could reproduce the error, but not in a
simple example. Meanwhile, I tried the newest updates (a few days ago) but
the error remained.
At this moment, I still use CodeWarrior 2.
Has any one successfully compiled NIH Image/68k with CW3?

Norbert Vischer

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

Date: Wed, 2 Sep 1998 10:51:01 +0200
From: Stein Roervik <steinr@chembio.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Re: Image capture to a stack
Message-Id: <v03102808b212b3e31df3@[129.241.39.133]>
Content-Type: text/plain; charset="us-ascii"

>
>I can capture an Image but how do I add it to the stack? I have made a
>new stack, when I try to add the new capture, it just adds a white slice
>in the new stack.
>

AddSlice only creates a new blank slice. You need to copy your captured
image and then paste it into the new slice. You can make a macro do it:

var
  CameraImage, StackedImages: integer;
  FinishedFirstSlice: boolean;

procedure Initialize;
var w,h: integer;
begin
  Capture; GetPicSize(w,h);
  CameraImage:= PidNumber;
  SetNewSize(w,h);
  MakeNewStack('captured images');
  StackedImages:= PidNumber;
end;

macro 'capture image to stack';
begin
  if not FinishedFirstSlice then Initialize;
  Capture;
  ChoosePic(CameraImage);
  SelectAll; Copy;
  ChoosePic(StackedImages);
  if FinishedFirstSlice then AddSlice;
  Paste;
  FinishedFirstSlice:= true;
end;

This macro is not tested and might not work but you get the idea.

>Also, how would I save pictures with an incrementing counter for the
>name? Like, slice1.tif, slice2.tif, slice3.tif etc. I have tried
>saveas('slice'+slicenumber), but it wants only a string.
>

Use saveas('slice',slicenumber:2,'.tif') for a sequence slice01.tif etc.
The syntax of using a + operator in strings works only in Turbo Pascal.
In NIH image you can use concat() to merge a series of strings, or insert
them directly in commands that expects a single string parameter.

Hope this helps.

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+

--------------------------------
End of nih-image-d Digest V98 Issue #50
***************************************

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Date: Wed, 2 Sep 1998 10:51:01 +0200
To: nih-image@io.ece.drexel.edu
From: Stein Roervik <steinr@chembio.ntnu.no>
Subject: Re: Image capture to a stack
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>
>I can capture an Image but how do I add it to the stack? I have made a
>new stack, when I try to add the new capture, it just adds a white slice
>in the new stack.
>

AddSlice only creates a new blank slice. You need to copy your captured
image and then paste it into the new slice. You can make a macro do it:

var
  CameraImage, StackedImages: integer;
  FinishedFirstSlice: boolean;

procedure Initialize;
var w,h: integer;
begin
  Capture; GetPicSize(w,h);
  CameraImage:= PidNumber;
  SetNewSize(w,h);
  MakeNewStack('captured images');
  StackedImages:= PidNumber;
end;

macro 'capture image to stack';
begin
  if not FinishedFirstSlice then Initialize;
  Capture;
  ChoosePic(CameraImage);
  SelectAll; Copy;
  ChoosePic(StackedImages);
  if FinishedFirstSlice then AddSlice;
  Paste;
  FinishedFirstSlice:= true;
end;

This macro is not tested and might not work but you get the idea.

>Also, how would I save pictures with an incrementing counter for the
>name? Like, slice1.tif, slice2.tif, slice3.tif etc. I have tried
>saveas('slice'+slicenumber), but it wants only a string.
>

Use saveas('slice',slicenumber:2,'.tif') for a sequence slice01.tif etc.
The syntax of using a + operator in strings works only in Turbo Pascal.
In NIH image you can use concat() to merge a series of strings, or insert
them directly in commands that expects a single string parameter.

Hope this helps.

+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+



From nih-image-request@io.ece.drexel.edu Wed Sep  2 05:15 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Stein Roervik <steinr@chembio.ntnu.no>
Subject: Re: Code Warrior Pro 3
Resent-Message-ID: <"hEeSg2.0.FT2._ZGxr"@io>
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>I had problems with NIH Image and CodeWorrior 3: in the 68k project, the
>'StringOf' function did not work, with the effect that many strings showed
>garbage or nothing. This became visible in the file and edit menu, the info
>window and so on. If I remember right, this also applied to the original
>NIH Image version. I sent the source code to the technical staff of
>Metroworks, they were 'puzzled' and could reproduce the error, but not in a
>simple example. Meanwhile, I tried the newest updates (a few days ago) but
>the error remained.
>At this moment, I still use CodeWarrior 2.
>Has any one successfully compiled NIH Image/68k with CW3?
>
>Norbert Vischer

Strange compiler bugs may appear when the size of allocated data structures
gets too large, especially in the 68k version. Try experimenting with the
compiler options like far calls etc. I planned to upgrade to CW Pro 3 this
week, but since there appears to be a problem I will not upgrade
permanently but install it on a Zip or similar. I will let you know if I
find out about this. Fortunately, CodeWarrior compiler bugs are very rare.

BTW, I was successfully able to make a multiple target NIH image project
file with CW Pro 2. You can then create a PPC, 68k and FAT binary from the
same project. This will ensure that your source files and libraries are
consistent across the different targets. I once spent a whole day searching
for a bug that was caused by including an out-of-date library file in the
68k project file.


+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+



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hello,
the Apple CEO presented the new OS called MAC OS X, with new 
interesting features (multithreating, protected memory, fast I/O, 
etc);
To get fully advantage from these features the application must be or 
become Carbon (a clean set of MAC API) compliant.
How about NIH Image?
TIA
-dom


From nih-image-request@io.ece.drexel.edu Wed Sep  2 13:11 EDT 1998
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From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: 12 bit 8 bit conversion
Date: Wed, 2 Sep 1998 12:50:57 -0400 
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Hi,
I have 12 bit images and I am having trouble to opne them in NIH and
others. 
Is ther anyway to convert images from 12 bit 8 bit in NIH or other
softwares?. or
Is ther any other way to diplay and edit these 12 bit images in any
software?

Thanks
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-Univ. of Michigan
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087


From nih-image-d-request@io.ece.drexel.edu Thu Sep  3 06:14 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #51
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 51

Today's Topics:
  Re: Code Warrior Pro 3                [ Stein Roervik <steinr@chembio.ntnu. ]
  NIH Image and MAC OS X                [ domenico di girolamo <fausto@cisea. ]
  12 bit 8 bit conversion               [ "Mehmet Dondurur, Ph. D." <mehmet.d ]

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

Date: Wed, 2 Sep 1998 11:02:33 +0200
From: Stein Roervik <steinr@chembio.ntnu.no>
To: nih-image@io.ece.drexel.edu
Subject: Re: Code Warrior Pro 3
Message-Id: <v03102809b212b7c80817@[129.241.39.133]>
Content-Type: text/plain; charset="us-ascii"

>I had problems with NIH Image and CodeWorrior 3: in the 68k project, the
>'StringOf' function did not work, with the effect that many strings showed
>garbage or nothing. This became visible in the file and edit menu, the info
>window and so on. If I remember right, this also applied to the original
>NIH Image version. I sent the source code to the technical staff of
>Metroworks, they were 'puzzled' and could reproduce the error, but not in a
>simple example. Meanwhile, I tried the newest updates (a few days ago) but
>the error remained.
>At this moment, I still use CodeWarrior 2.
>Has any one successfully compiled NIH Image/68k with CW3?
>
>Norbert Vischer

Strange compiler bugs may appear when the size of allocated data structures
gets too large, especially in the 68k version. Try experimenting with the
compiler options like far calls etc. I planned to upgrade to CW Pro 3 this
week, but since there appears to be a problem I will not upgrade
permanently but install it on a Zip or similar. I will let you know if I
find out about this. Fortunately, CodeWarrior compiler bugs are very rare.

BTW, I was successfully able to make a multiple target NIH image project
file with CW Pro 2. You can then create a PPC, 68k and FAT binary from the
same project. This will ensure that your source files and libraries are
consistent across the different targets. I once spent a whole day searching
for a bug that was caused by including an out-of-date library file in the
68k project file.


+---------------------------------------------------------+
|  Stein Roervik   (steinr@chembio.ntnu.no)               |
|                                                         |
|  Research Scientist, Computer Assisted Microscopy       |
|  Dept. of Inorganic Chemistry, Norwegian University of  |
|  Science and Technology, N-7034 Trondheim, Norway       |
|  tel. +47 73 59 39 88, fax +47 73 59 08 60              |
+---------------------------------------------------------+

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

Date: Wed, 02 Sep 1998 18:26:27 +0100
From: domenico di girolamo <fausto@cisea.it>
To: nih-image@io.ece.drexel.edu
Subject: NIH Image and MAC OS X
Message-ID: <35ED7FC3.D43@cisea.it>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

hello,
the Apple CEO presented the new OS called MAC OS X, with new 
interesting features (multithreating, protected memory, fast I/O, 
etc);
To get fully advantage from these features the application must be or 
become Carbon (a clean set of MAC API) compliant.
How about NIH Image?
TIA
-dom

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

Date: Wed, 2 Sep 1998 12:50:57 -0400 
From: "Mehmet Dondurur, Ph. D." <mehmet.dondurur.ph.d@jvc.org>
To: "'nih-image@biomed.drexel.edu'" <nih-image@io.ece.drexel.edu>
Subject: 12 bit 8 bit conversion
Message-ID: <69B43248FE73D11197BB00A0C99AB067891E@jvcserver.vanguardweb.org>
Content-Type: text/plain

Hi,
I have 12 bit images and I am having trouble to opne them in NIH and
others. 
Is ther anyway to convert images from 12 bit 8 bit in NIH or other
softwares?. or
Is ther any other way to diplay and edit these 12 bit images in any
software?

Thanks
Dr. Mehmet Dondurur
Research Scientist
Jobst Vascular Center-Univ. of Michigan
Mehmet.Dondurur.ph.d@jvc.org
(419) 471-2087

--------------------------------
End of nih-image-d Digest V98 Issue #51
***************************************

From nih-image-request@io.ece.drexel.edu Thu Sep  3 09:32 EDT 1998
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Date: Thu, 3 Sep 1998 09:21:26 -0400 (EDT)
From: Xuanliang Dong <dong@bone-alpha.bme.columbia.edu>
Reply-To: Xuanliang Dong <dong@bone-alpha.bme.columbia.edu>
To: nih-image@io.ece.drexel.edu
Subject: Video Digitizer error-2208
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Dear All:
	I want to use NIH image to capture image from Digital Camera  on
a Power PC(Power Mac 6500/275).When I click start capturing, there is an
error message:Video Digitizer error-2208(Turning Vitual Memory off or RAM
double off). I don't have an RAM double on Mac and vitual memory has been
turned off. I am sure that Video card is installed on Mac since Apple
Video Played  can be used to obtained an image correctly.
	Does anyone have meet such problem?
	Thank you very much.
	Have a nice day.
	Neil



From nih-image-request@io.ece.drexel.edu Thu Sep  3 10:02 EDT 1998
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References: <l03010d00b21216a2ed30@[145.18.29.76]>	
 <v03007803b211e07621ac@[128.231.99.216]>	
 <3.0.5.32.19980831121648.007d4100@neuro.duke.edu>
 <v03102809b212b7c80817@[129.241.39.133]>
Mime-Version: 1.0
Date: Thu, 3 Sep 1998 09:59:02 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: NIH Image and MAC OS X
Resent-Message-ID: <"JwI01.0.cB3.Xzfxr"@io>
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>hello,
>the Apple CEO presented the new OS called MAC OS X, with new
>interesting features (multithreating, protected memory, fast I/O,
>etc);
>To get fully advantage from these features the application must be or
>become Carbon (a clean set of MAC API) compliant.
>How about NIH Image?


NIH Image is not Carbon compliant but my new Image/J program at
http://rsb.info.nih.gov/ij/ will be.

BTW, Mac OS Runtime for Java 2.1 Early Access 2 is now available at

     <http://developer.apple.com/java/text/prerelease.html>

It runs Image/J a lot  better than MRJ 2.0.

-wayne



From nih-image-request@io.ece.drexel.edu Thu Sep  3 10:50 EDT 1998
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Date: Thu, 3 Sep 98 7:37:47 PDT
From: Walter Wolf <wwolfw@hsc.usc.edu>
To: nih-image@io.ece.drexel.edu
Cc: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu
Subject: Re: NIH Image and MAC OS X
In-Reply-To: Your message of Thu, 3 Sep 1998 09:59:02 -0400
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Wayne:

Last time you mentioned that the documentation for Image/J was not yet
available. Is it now, and if not, when will it become available?

Also, and I appologize for my ignorance, what is "Carbon compliant"? 

======================================================================
|  Professor Walter Wolf, Ph.D.          E-Mail: wwolfw@hsc.usc.edu  |
|  Distinguished Professor of Pharmaceutical Sciences		     |
|  Director, Pharmacokinetic Imaging Program                         |
|  Department of Pharmaceutical Sciences, School of Pharmacy	     |
|  University of Southern California         Telephone: 323-442-1405 |
|  1985 Zonal Ave., Los Angeles, CA 90033    Fax:       323-442-9804 |
|                                                                    |
|Center for Noninvasive Pharmacology, Los Angeles Oncologic Institute|
|  MRI at St. Vincent Medical Center     Telephone:    213-484-7235  |
|  2131 Third St., Los Angeles, CA 90057 Fax:          213-484-7447  |
======================================================================
 


From nih-image-request@io.ece.drexel.edu Thu Sep  3 12:03 EDT 1998
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Mime-Version: 1.0
Date: Thu, 3 Sep 1998 11:55:34 -0400
To: nih-image@io.ece.drexel.edu
From: Carl Gustafson <carl.gustafson@cbis.ece.drexel.edu>
Subject: Carbon Compliance (Was: NIH Image and MAC OS X)
Resent-Message-ID: <"8WUwE.0.rh5.cihxr"@io>
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>Also, and I appologize for my ignorance, what is "Carbon compliant"?

Apple Computer went over their system software libraries (APIs, in geek
speek), and weeded out a large number of routines that either were rarely
used, superceded by other routines, or were just too crufty to continue to
maintain and still allow for advancement of their system software.

The routines that survived the cut are now known as the Carbon APIs. (And
yes, there have been programmer-jokes about being carbon-based.)

Anyway, a carbon-compliant program is one that doesn't call routines not in
the official, honest-to-Apple, totally cool and approved Carbon APIs.
Calling non-existent routines is a generally bad thing, and will usually
toast the application.

There is a test application that Apple has available called the carbon
dater, that will check any application, and score it for compatibility, BTW.



Carl Gustafson
(215) 895-1383
===============================================================================
           the Computer Vision Center for Vertebrate Brain Mapping
===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I'd like to give you my opinion
===============================================================================



From nih-image-request@io.ece.drexel.edu Thu Sep  3 12:21 EDT 1998
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Mime-Version: 1.0
Date: Thu, 3 Sep 1998 12:17:37 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: NIH Image and MAC OS X
Resent-Message-ID: <"ajEKn2.0.w96.S_hxr"@io>
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>Wayne:
>
>Last time you mentioned that the documentation for Image/J was not yet
>available. Is it now, and if not, when will it become available?

There is some prelimimary HTML documentation for Image/J at:

     http://rsb.info.nih.gov/ij/

>Also, and I appologize for my ignorance, what is "Carbon compliant"?

Henry Knorr has a good article about Mac OS X and Carbon at:

    http://www1.macintouch.com/norr006.html

-wayne



From nih-image-request@io.ece.drexel.edu Thu Sep  3 12:23 EDT 1998
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Date: Thu, 3 Sep 1998 11:10:44 -0500 (CDT)
From: Doug Martin <dmartin@chaos.ph.utexas.edu>
To: nih-image@io.ece.drexel.edu
Subject: maximum stack and text sizes
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Does anyone know of a way to get around the maximum stack size (1000
frames) or text clipboard size (32K), or of a version of image which as
been modified to increase these limits?

Thanks a million,

Douglas Martin
University of Texas at Austin
<dmartin@chaos.ph.utexas.edu>




From nih-image-request@io.ece.drexel.edu Thu Sep  3 12:51 EDT 1998
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Mime-Version: 1.0
Date: Thu, 3 Sep 1998 12:44:42 -0400
To: nih-image@io.ece.drexel.edu
From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: maximum stack and text sizes
Resent-Message-ID: <"npsjL3.0._m6.qOixr"@io>
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>Does anyone know of a way to get around the maximum stack size (1000
>frames) or text clipboard size (32K), or of a version of image which as
>been modified to increase these limits?

NIH Image 1.62b21 at

      ftp://codon.nih.gov/pub/nih-image/nih-image162b21_fat.hqx

has a maximum stack size of 5000, at least on PowerMacs.

There is no easy fix for the 32K text size limit since it's  built into the
Mac OS TextEdit toolbox routine.

-wayne



From nih-image-request@io.ece.drexel.edu Thu Sep  3 13:15 EDT 1998
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Date: Thu, 3 Sep 1998 10:06:40 -0700 (PDT)
From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
Reply-To: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: G3 AV problems continued
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Hello,

I am wondering if any progress has been made on the fact that NIH
Image is not compatible with the G3 built in digitizer. It seems like a
long time has gone by, and the proposed solution doesn't really work. Are
there any plans to implement support for the digitizer?

Thanks,
Stephan


-------------------------------
Stephan G. Anagnostaras, Ph.D.
UCLA Dept. of Neurobiology              
stephan@lifesci.ucla.edu
sanagnos@mediaone.net    
310-822-7100 / 306-0294          
-------------------------------





From nih-image-request@io.ece.drexel.edu Thu Sep  3 13:15 EDT 1998
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Date: Thu, 03 Sep 1998 19:07:07 +0100
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References: <l03010d00b21216a2ed30@[145.18.29.76]>	
	 <v03007803b211e07621ac@[128.231.99.216]>	
	 <3.0.5.32.19980831121648.007d4100@neuro.duke.edu>
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hello,
I have two further question:
- it will support Scion framegrabbers?
- how about the existing usermacros(i'm not a Java programmer)?
TIA
-dom


From nih-image-request@io.ece.drexel.edu Thu Sep  3 14:03 EDT 1998
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From: Gloria Hoffman <gehoffma@umaryland.edu>
Subject: counting/cataloging
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This may be simple and I have missed something very obvious but....I would
like to take drawings made on Adobe Illustrator or Canvas, acquired from a
digital pad/camera lucida and obtain numbers of the objects I have drawn,
then tally them up according to the color I have selected for those objects
(perhaps 3 or four at most). Does anyone know a program (NIH image eg) that
could do that after importing images from either application?
Gloria E. Hoffman, Ph.D.
Department of Anatomy and Neurobiology
685 W Baltimore St
Baltimore MD 21201
Phone 410 706-2438
Fax 410 706-2512
email gehoffma@umaryland.edu


From nih-image-request@io.ece.drexel.edu Thu Sep  3 16:44 EDT 1998
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From: Wayne Rasband <wayne@codon.nih.gov>
Subject: Re: NIH Image and MAC OS X
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>hello,
>I have two further question:
>- it will support Scion framegrabbers?
>- how about the existing usermacros(i'm not a Java programmer)?
>TIA
>-dom

I plan to add frame grabber support and a Pascal-like macro interpreter to
Image.J but it may be a year or two. There is a list of planned features at:

    http://rsb.info.nih.gov/ij/docs/to-do-list.html

-wayne




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Date: 03 Sep 98 14:10:59 -0600
From: Steven Moore <stevem@cipe.com>
Subject: Video Digitizer Error 2208, Re-visited
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Hello,
I took a tech support call from a teacher in Oregon who was attempting to use the Start Capture command on NIH Image 1.61 (and 1.62) installed on a Mac 5500 AV.  He received the message Video Digitizer Error 2208, Turn Off Virtual Memory or RAM Doubler.  After turning Virtual Memory off and restarting the machine, he still got the same message.

I've searched the archive and found messages about this problem dating back to 1995, but no solution.  Can anybody tell me how to solve this problem?  Thanks.

Steven D. Moore, Ph.D.
Director of Evaluation Services
Center for Image Processing in Education
Tucson, AZ stevem@cipe.com
http://www.cipe.com
(800) 322-9884 ext. 125



From nih-image-request@io.ece.drexel.edu Thu Sep  3 21:57 EDT 1998
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From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: gehoffma@umaryland.edu, nih-image@io.ece.drexel.edu
Date:          Fri, 4 Sep 1998 11:48:12 GMT+1000
Subject:       Re: counting/cataloging
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>Date: Thu, 3 Sep 1998 14:04:08 -0400
>To: nih-image@io.ece.drexel.edu
>From: Gloria Hoffman <gehoffma@umaryland.edu>
>Subject: counting/cataloging
>
>This may be simple and I have missed something very obvious but....I would
>like to take drawings made on Adobe Illustrator or Canvas, acquired from a
>digital pad/camera lucida and obtain numbers of the objects I have drawn,
>then tally them up according to the color I have selected for those objects
>(perhaps 3 or four at most). Does anyone know a program (NIH image eg) that
>could do that after importing images from either application?
>Gloria E. Hoffman, Ph.D.
>Department of Anatomy and Neurobiology
>685 W Baltimore St
>Baltimore MD 21201
>Phone 410 706-2438
>Fax 410 706-2512
>email gehoffma@umaryland.edu

In principle, NIH-Image analyzeParticles will do this quite well.

In practice, there are a few wrinkles and computer internals that need to be 
addressed.

Adobe Illustrator files are text files containing directives, coordinates etc 
rather than pixelated images.
You can convert Adobe Illustrator files to pixelated images in TIFF format 
acceptable to NIH-Image by:
open Illustrator file in Photoshop, flaten (to remove layers) and convert to 
RGB then save as an uncompressed 8 bit TIFF image.

You can then open the TIFF image in NIH-Image.
As image is RGB, you will then have a 3 frame stack (Red Green Blue) and/or an 
indexed color representation of the image.

Density sliceing; analyzeParticles; can then be applied to either(any) of these 
to count/measure the particles by color.

How easy the color to RGB stack or indexed color is to you will depend on your 
understanding of color separations and the colors you used in Illustrator.
Rather than go into that here, try it to see what you get. It will be much 
easier to understand by inspection than by an attempted pracie by email.

Come back (with a sample) if you have problems.

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


From nih-image-d-request@io.ece.drexel.edu Fri Sep  4 06:18 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #52
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 52

Today's Topics:
  Video Digitizer error-2208            [ Xuanliang Dong <dong@bone-alpha.bme ]
  Re: NIH Image and MAC OS X            [ Wayne Rasband <wayne@codon.nih.gov> ]
  Re: NIH Image and MAC OS X            [ Walter Wolf <wwolfw@hsc.usc.edu> ]
  Carbon Compliance (Was: NIH Image an  [ Carl Gustafson <carl.gustafson@cbis ]
  maximum stack and text sizes          [ Doug Martin <dmartin@chaos.ph.utexa ]
  Re: NIH Image and MAC OS X            [ Wayne Rasband <wayne@codon.nih.gov> ]
  Re: maximum stack and text sizes      [ Wayne Rasband <wayne@codon.nih.gov> ]
  Re: NIH Image and MAC OS X            [ domenico di girolamo <fausto@cisea. ]
  G3 AV problems continued              [ Stephan Anagnostaras <stephan@proto ]
  counting/cataloging                   [ Gloria Hoffman <gehoffma@umaryland. ]
  Re: NIH Image and MAC OS X            [ Wayne Rasband <wayne@codon.nih.gov> ]
  Video Digitizer Error 2208, Re-visit  [ Steven Moore <stevem@cipe.com> ]
  Re: counting/cataloging               [ GJOSS@rna.bio.mq.edu.au ]

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

Date: Thu, 3 Sep 1998 09:21:26 -0400 (EDT)
From: Xuanliang Dong <dong@bone-alpha.bme.columbia.edu>
To: nih-image@io.ece.drexel.edu
Subject: Video Digitizer error-2208
Message-Id: <Pine.OSF.3.96.980903091209.18409C-100000@bone-alpha.bme.columbia.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear All:
	I want to use NIH image to capture image from Digital Camera  on
a Power PC(Power Mac 6500/275).When I click start capturing, there is an
error message:Video Digitizer error-2208(Turning Vitual Memory off or RAM
double off). I don't have an RAM double on Mac and vitual memory has been
turned off. I am sure that Video card is installed on Mac since Apple
Video Played  can be used to obtained an image correctly.
	Does anyone have meet such problem?
	Thank you very much.
	Have a nice day.
	Neil

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

Date: Thu, 3 Sep 1998 09:59:02 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Image and MAC OS X
Message-Id: <v03007800b2144eeb1c26@[128.231.99.216]>
Content-Type: text/plain; charset="us-ascii"

>hello,
>the Apple CEO presented the new OS called MAC OS X, with new
>interesting features (multithreating, protected memory, fast I/O,
>etc);
>To get fully advantage from these features the application must be or
>become Carbon (a clean set of MAC API) compliant.
>How about NIH Image?


NIH Image is not Carbon compliant but my new Image/J program at
http://rsb.info.nih.gov/ij/ will be.

BTW, Mac OS Runtime for Java 2.1 Early Access 2 is now available at

     <http://developer.apple.com/java/text/prerelease.html>

It runs Image/J a lot  better than MRJ 2.0.

-wayne

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

Date: Thu, 3 Sep 98 7:37:47 PDT
From: Walter Wolf <wwolfw@hsc.usc.edu>
To: nih-image@io.ece.drexel.edu
Cc: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu
Subject: Re: NIH Image and MAC OS X
Message-ID: <CMM.0.90.4.904833467.wwolfw@hsc.usc.edu>

Wayne:

Last time you mentioned that the documentation for Image/J was not yet
available. Is it now, and if not, when will it become available?

Also, and I appologize for my ignorance, what is "Carbon compliant"? 

======================================================================
|  Professor Walter Wolf, Ph.D.          E-Mail: wwolfw@hsc.usc.edu  |
|  Distinguished Professor of Pharmaceutical Sciences		     |
|  Director, Pharmacokinetic Imaging Program                         |
|  Department of Pharmaceutical Sciences, School of Pharmacy	     |
|  University of Southern California         Telephone: 323-442-1405 |
|  1985 Zonal Ave., Los Angeles, CA 90033    Fax:       323-442-9804 |
|                                                                    |
|Center for Noninvasive Pharmacology, Los Angeles Oncologic Institute|
|  MRI at St. Vincent Medical Center     Telephone:    213-484-7235  |
|  2131 Third St., Los Angeles, CA 90057 Fax:          213-484-7447  |
======================================================================
 

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

Date: Thu, 3 Sep 1998 11:55:34 -0400
From: Carl Gustafson <carl.gustafson@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Carbon Compliance (Was: NIH Image and MAC OS X)
Message-Id: <v03110700b2146ac5d480@[144.118.33.205]>
Content-Type: text/plain; charset="us-ascii"

>Also, and I appologize for my ignorance, what is "Carbon compliant"?

Apple Computer went over their system software libraries (APIs, in geek
speek), and weeded out a large number of routines that either were rarely
used, superceded by other routines, or were just too crufty to continue to
maintain and still allow for advancement of their system software.

The routines that survived the cut are now known as the Carbon APIs. (And
yes, there have been programmer-jokes about being carbon-based.)

Anyway, a carbon-compliant program is one that doesn't call routines not in
the official, honest-to-Apple, totally cool and approved Carbon APIs.
Calling non-existent routines is a generally bad thing, and will usually
toast the application.

There is a test application that Apple has available called the carbon
dater, that will check any application, and score it for compatibility, BTW.



Carl Gustafson
(215) 895-1383
===============================================================================
           the Computer Vision Center for Vertebrate Brain Mapping
===============================================================================
Imaging and Computer Vision Center      |   Software Guy
Drexel University                       |   Macintosh spoken here
Philadelphia, Pennsylvania              |   I'd like to give you my opinion
===============================================================================

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

Date: Thu, 3 Sep 1998 11:10:44 -0500 (CDT)
From: Doug Martin <dmartin@chaos.ph.utexas.edu>
To: nih-image@io.ece.drexel.edu
Subject: maximum stack and text sizes
Message-ID: <Pine.LNX.3.96.980903110804.14480B-100000@chaos.ph.utexas.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Does anyone know of a way to get around the maximum stack size (1000
frames) or text clipboard size (32K), or of a version of image which as
been modified to increase these limits?

Thanks a million,

Douglas Martin
University of Texas at Austin
<dmartin@chaos.ph.utexas.edu>

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

Date: Thu, 3 Sep 1998 12:17:37 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Image and MAC OS X
Message-Id: <v03007802b2146f8ac0a8@[128.231.99.216]>
Content-Type: text/plain; charset="us-ascii"

>Wayne:
>
>Last time you mentioned that the documentation for Image/J was not yet
>available. Is it now, and if not, when will it become available?

There is some prelimimary HTML documentation for Image/J at:

     http://rsb.info.nih.gov/ij/

>Also, and I appologize for my ignorance, what is "Carbon compliant"?

Henry Knorr has a good article about Mac OS X and Carbon at:

    http://www1.macintouch.com/norr006.html

-wayne

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

Date: Thu, 3 Sep 1998 12:44:42 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: maximum stack and text sizes
Message-Id: <v03007804b21475ac3169@[128.231.99.216]>
Content-Type: text/plain; charset="us-ascii"

>Does anyone know of a way to get around the maximum stack size (1000
>frames) or text clipboard size (32K), or of a version of image which as
>been modified to increase these limits?

NIH Image 1.62b21 at

      ftp://codon.nih.gov/pub/nih-image/nih-image162b21_fat.hqx

has a maximum stack size of 5000, at least on PowerMacs.

There is no easy fix for the 32K text size limit since it's  built into the
Mac OS TextEdit toolbox routine.

-wayne

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

Date: Thu, 03 Sep 1998 19:07:07 +0100
From: domenico di girolamo <fausto@cisea.it>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Image and MAC OS X
Message-ID: <35EEDACB.25D7@cisea.it>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

hello,
I have two further question:
- it will support Scion framegrabbers?
- how about the existing usermacros(i'm not a Java programmer)?
TIA
-dom

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

Date: Thu, 3 Sep 1998 10:06:40 -0700 (PDT)
From: Stephan Anagnostaras <stephan@protos.lifesci.ucla.edu>
To: nih-image@io.ece.drexel.edu
Subject: G3 AV problems continued
Message-ID: <Pine.SOL.3.95.980903095746.2249B-100000@protos.lifesci.ucla.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hello,

I am wondering if any progress has been made on the fact that NIH
Image is not compatible with the G3 built in digitizer. It seems like a
long time has gone by, and the proposed solution doesn't really work. Are
there any plans to implement support for the digitizer?

Thanks,
Stephan


-------------------------------
Stephan G. Anagnostaras, Ph.D.
UCLA Dept. of Neurobiology              
stephan@lifesci.ucla.edu
sanagnos@mediaone.net    
310-822-7100 / 306-0294          
-------------------------------

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

Date: Thu, 3 Sep 1998 14:04:08 -0400
From: Gloria Hoffman <gehoffma@umaryland.edu>
To: nih-image@io.ece.drexel.edu
Subject: counting/cataloging
Message-Id: <v04011730b214897679e2@[134.192.129.87]>
Content-Type: text/plain; charset="us-ascii"

This may be simple and I have missed something very obvious but....I would
like to take drawings made on Adobe Illustrator or Canvas, acquired from a
digital pad/camera lucida and obtain numbers of the objects I have drawn,
then tally them up according to the color I have selected for those objects
(perhaps 3 or four at most). Does anyone know a program (NIH image eg) that
could do that after importing images from either application?
Gloria E. Hoffman, Ph.D.
Department of Anatomy and Neurobiology
685 W Baltimore St
Baltimore MD 21201
Phone 410 706-2438
Fax 410 706-2512
email gehoffma@umaryland.edu

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

Date: Thu, 3 Sep 1998 16:31:23 -0400
From: Wayne Rasband <wayne@codon.nih.gov>
To: nih-image@io.ece.drexel.edu
Subject: Re: NIH Image and MAC OS X
Message-Id: <v03007801b214ac3c0105@[128.231.99.216]>
Content-Type: text/plain; charset="us-ascii"

>hello,
>I have two further question:
>- it will support Scion framegrabbers?
>- how about the existing usermacros(i'm not a Java programmer)?
>TIA
>-dom

I plan to add frame grabber support and a Pascal-like macro interpreter to
Image.J but it may be a year or two. There is a list of planned features at:

    http://rsb.info.nih.gov/ij/docs/to-do-list.html

-wayne

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

Date: 03 Sep 98 14:10:59 -0600
From: Steven Moore <stevem@cipe.com>
To: "nih-image@biomed.drexel.edu" <nih-image@io.ece.drexel.edu>
Subject: Video Digitizer Error 2208, Re-visited
Message-ID: <1307290659-53216033@mailhost.cipe.com>
Content-Type: text/plain; charset="US-Ascii"
Content-Transfer-Encoding: 8bit

Hello,
I took a tech support call from a teacher in Oregon who was attempting to use the Start Capture command on NIH Image 1.61 (and 1.62) installed on a Mac 5500 AV.  He received the message Video Digitizer Error 2208, Turn Off Virtual Memory or RAM Doubler.  After turning Virtual Memory off and restarting the machine, he still got the same message.

I've searched the archive and found messages about this problem dating back to 1995, but no solution.  Can anybody tell me how to solve this problem?  Thanks.

Steven D. Moore, Ph.D.
Director of Evaluation Services
Center for Image Processing in Education
Tucson, AZ stevem@cipe.com
http://www.cipe.com
(800) 322-9884 ext. 125

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

Date:          Fri, 4 Sep 1998 11:48:12 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: gehoffma@umaryland.edu, nih-image@io.ece.drexel.edu
Subject:       Re: counting/cataloging
Message-ID: <7A6E6244344@rna.bio.mq.edu.au>

>Date: Thu, 3 Sep 1998 14:04:08 -0400
>To: nih-image@io.ece.drexel.edu
>From: Gloria Hoffman <gehoffma@umaryland.edu>
>Subject: counting/cataloging
>
>This may be simple and I have missed something very obvious but....I would
>like to take drawings made on Adobe Illustrator or Canvas, acquired from a
>digital pad/camera lucida and obtain numbers of the objects I have drawn,
>then tally them up according to the color I have selected for those objects
>(perhaps 3 or four at most). Does anyone know a program (NIH image eg) that
>could do that after importing images from either application?
>Gloria E. Hoffman, Ph.D.
>Department of Anatomy and Neurobiology
>685 W Baltimore St
>Baltimore MD 21201
>Phone 410 706-2438
>Fax 410 706-2512
>email gehoffma@umaryland.edu

In principle, NIH-Image analyzeParticles will do this quite well.

In practice, there are a few wrinkles and computer internals that need to be 
addressed.

Adobe Illustrator files are text files containing directives, coordinates etc 
rather than pixelated images.
You can convert Adobe Illustrator files to pixelated images in TIFF format 
acceptable to NIH-Image by:
open Illustrator file in Photoshop, flaten (to remove layers) and convert to 
RGB then save as an uncompressed 8 bit TIFF image.

You can then open the TIFF image in NIH-Image.
As image is RGB, you will then have a 3 frame stack (Red Green Blue) and/or an 
indexed color representation of the image.

Density sliceing; analyzeParticles; can then be applied to either(any) of these 
to count/measure the particles by color.

How easy the color to RGB stack or indexed color is to you will depend on your 
understanding of color separations and the colors you used in Illustrator.
Rather than go into that here, try it to see what you get. It will be much 
easier to understand by inspection than by an attempted pracie by email.

Come back (with a sample) if you have problems.

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

--------------------------------
End of nih-image-d Digest V98 Issue #52
***************************************

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Dear All,
I'm just on the way to setup a videoimaging with a Hamamatsu Orca camera
and I would like to use NIH Image (or Image/J) for acquisition and
analysis. I have two main (and probably naive) questions:
-which frame grabber should I need? Is there a plug-in to control the camera?
-can NIH Image handle the acquisition of 12/14/16 bit images from the camera?
TIA
Daniele

Dr. Daniele Zacchetti, PhD
Cellular Neurophysiology Unit
Dibit, San Raffaele Inst.
via Olgettina 58
20132 Milano, Italy
Phone: +39-02-2643-4812
Fax:+39-02-2643-4813
e-mail: zacchetti.daniele@hsr.it



From nih-image-request@io.ece.drexel.edu Fri Sep  4 08:12 EDT 1998
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egrep grabber latest/*



From nih-image-request@io.ece.drexel.edu Fri Sep  4 08:48 EDT 1998
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List Members:

Has anyone conducted stereological analyses with IMAGE?

Marc A. Steed, M.S.

Department of Psychology
University of Cincinnati
P.O. Box 210376
Cincinnati, OH 45221-0376

513-556-1615 (lab)
513-556-1904 (fax)



From nih-image-request@io.ece.drexel.edu Fri Sep  4 10:58 EDT 1998
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From: "Herbert M. Geller" <geller@umdnj.edu>
To: nih-image@io.ece.drexel.edu
Subject: Metamorph to NIH Image
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Has anyone taken a Metamorph stack of images and imported 
them into NIH Image as a stack?  My colleague has captured 
a series of images on Metamorph which I would like to 
analyze. 

----------------------------------------------------------
Herbert M. Geller, Ph.D.
Professor
Department of Pharmacology           voice -  732-235-4084
Robert Wood Johnson Medical School     fax -  732-235-4073
Piscataway, New Jersey 08854   Internet - geller@umdnj.edu
www: http//www2.umdnj.edu/~geller/lab/


From nih-image-request@io.ece.drexel.edu Fri Sep  4 15:07 EDT 1998
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 I've seen it done Metamorph (PC) to NIH Image (Mac). It was pretty
strait forward, it should just open like any other PIC or TIFF stack.
Scion Image b2 (PC) did not work managing to misalign all the images
through the stack or simply crashed when trying to open the file. I
would hope that an 8000 package like Metamorph would come with all the
features of NIH anyway.

Apparently not.

Jeremy

Herbert M. Geller wrote:

> Has anyone taken a Metamorph stack of images and imported
> them into NIH Image as a stack?  My colleague has captured
> a series of images on Metamorph which I would like to
> analyze.
>
> ----------------------------------------------------------
> Herbert M. Geller, Ph.D.
> Professor
> Department of Pharmacology           voice -  732-235-4084
> Robert Wood Johnson Medical School     fax -  732-235-4073
> Piscataway, New Jersey 08854   Internet - geller@umdnj.edu
> www: http//www2.umdnj.edu/~geller/lab/

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

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


From nih-image-request@io.ece.drexel.edu Fri Sep  4 15:35 EDT 1998
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Date: Fri, 04 Sep 1998 15:19:31 -0500 (EST)
From: Glenn Holm <KARUZIS@wccf.mit.edu>
Subject: Re: counting/cataloging
In-reply-to: Your message dated "Thu, 03 Sep 1998 14:04:08 -0400"
 <v04011730b214897679e2@[134.192.129.87]>
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Macromedia FreeHand has find and replace by fill/stroke color attribute and 
tells you how many drawing objects of a particular color it finds. Perhaps 
Illustrator and/or Canvas also has that feature.

>This may be simple and I have missed something very obvious but....I would
>like to take drawings made on Adobe Illustrator or Canvas, acquired from a
>digital pad/camera lucida and obtain numbers of the objects I have drawn,
>then tally them up according to the color I have selected for those objects
>(perhaps 3 or four at most). Does anyone know a program (NIH image eg) that
>could do that after importing images from either application?
>Gloria E. Hoffman, Ph.D.
>Department of Anatomy and Neurobiology
>685 W Baltimore St
>Baltimore MD 21201
>Phone 410 706-2438
>Fax 410 706-2512
>email gehoffma@umaryland.edu


------------------------------------------------------------------
|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     |
------------------------------------------------------------------


From nih-image-d-request@io.ece.drexel.edu Sat Sep  5 06:09 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809051009.GAA01865@io.ECE.Drexel.EDU>
Subject: nih-image-d Digest V98 #53
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 53

Today's Topics:
  NIH Image and Hamamatsu camera        [ Daniele Zacchetti <zacchetti.daniel ]
  Unidentified subject!                 [ Daniele Zacchetti <zacchetti.daniel ]
  Stereology                            [ Marc Steed <steedma@email.uc.edu> ]
  Metamorph to NIH Image                [ "Herbert M. Geller" <geller@UMDNJ.E ]
  Re: Metamorph to NIH Image            [ Jeremy Brown <brownj@netmatters.co. ]
  Re: counting/cataloging               [ Glenn Holm <KARUZIS@wccf.mit.edu> ]

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

Date: Fri, 4 Sep 1998 13:51:50 +0200
From: Daniele Zacchetti <zacchetti.daniele@hsr.it>
To: nih-image@io.ece.drexel.edu
Subject: NIH Image and Hamamatsu camera
Message-Id: <l03130300b2157bdd6e55@[192.167.193.40]>
Content-Type: text/plain; charset="us-ascii"

Dear All,
I'm just on the way to setup a videoimaging with a Hamamatsu Orca camera
and I would like to use NIH Image (or Image/J) for acquisition and
analysis. I have two main (and probably naive) questions:
-which frame grabber should I need? Is there a plug-in to control the camera?
-can NIH Image handle the acquisition of 12/14/16 bit images from the camera?
TIA
Daniele

Dr. Daniele Zacchetti, PhD
Cellular Neurophysiology Unit
Dibit, San Raffaele Inst.
via Olgettina 58
20132 Milano, Italy
Phone: +39-02-2643-4812
Fax:+39-02-2643-4813
e-mail: zacchetti.daniele@hsr.it

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

Date: Fri, 4 Sep 1998 14:10:50 +0200
From: Daniele Zacchetti <zacchetti.daniele@hsr.it>
To: NIH Image mailing list <nih-image@io.ece.drexel.edu>
Subject: Unidentified subject!
Message-Id: <l03130302b215890e87c1@[192.167.193.40]>
Content-Type: text/plain; charset="us-ascii"

egrep grabber latest/*

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

Date: Fri, 4 Sep 1998 08:40:50 -0400
From: Marc Steed <steedma@email.uc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Stereology
Message-Id: <v03007803b2158fee5037@[129.137.148.133]>
Content-Type: text/plain; charset="us-ascii"

List Members:

Has anyone conducted stereological analyses with IMAGE?

Marc A. Steed, M.S.

Department of Psychology
University of Cincinnati
P.O. Box 210376
Cincinnati, OH 45221-0376

513-556-1615 (lab)
513-556-1904 (fax)

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

Date: Fri, 4 Sep 1998 10:51:57 -0400 (Eastern Daylight Time)
From: "Herbert M. Geller" <geller@UMDNJ.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Metamorph to NIH Image
Message-ID: <SIMEON.9809041057.B@hmgpc.umdnj.edu>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

Has anyone taken a Metamorph stack of images and imported 
them into NIH Image as a stack?  My colleague has captured 
a series of images on Metamorph which I would like to 
analyze. 

----------------------------------------------------------
Herbert M. Geller, Ph.D.
Professor
Department of Pharmacology           voice -  732-235-4084
Robert Wood Johnson Medical School     fax -  732-235-4073
Piscataway, New Jersey 08854   Internet - geller@umdnj.edu
www: http//www2.umdnj.edu/~geller/lab/

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

Date: Fri, 04 Sep 1998 19:52:20 +0000
From: Jeremy Brown <brownj@netmatters.co.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Metamorph to NIH Image
Message-ID: <35F044F1.D1BB624B@netmatters.co.uk>
Content-Type: text/plain; charset=iso-8859-1; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 8bit

 I've seen it done Metamorph (PC) to NIH Image (Mac). It was pretty
strait forward, it should just open like any other PIC or TIFF stack.
Scion Image b2 (PC) did not work managing to misalign all the images
through the stack or simply crashed when trying to open the file. I
would hope that an 8000 package like Metamorph would come with all the
features of NIH anyway.

Apparently not.

Jeremy

Herbert M. Geller wrote:

> Has anyone taken a Metamorph stack of images and imported
> them into NIH Image as a stack?  My colleague has captured
> a series of images on Metamorph which I would like to
> analyze.
>
> ----------------------------------------------------------
> Herbert M. Geller, Ph.D.
> Professor
> Department of Pharmacology           voice -  732-235-4084
> Robert Wood Johnson Medical School     fax -  732-235-4073
> Piscataway, New Jersey 08854   Internet - geller@umdnj.edu
> www: http//www2.umdnj.edu/~geller/lab/

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

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

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

Date: Fri, 04 Sep 1998 15:19:31 -0500 (EST)
From: Glenn Holm <KARUZIS@wccf.mit.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: counting/cataloging
Message-id: <01J1EW20MTIC8WXUEO@wccf.mit.edu>
Content-type: text/plain; charset="us-ascii"
Content-transfer-encoding: 7BIT

Macromedia FreeHand has find and replace by fill/stroke color attribute and 
tells you how many drawing objects of a particular color it finds. Perhaps 
Illustrator and/or Canvas also has that feature.

>This may be simple and I have missed something very obvious but....I would
>like to take drawings made on Adobe Illustrator or Canvas, acquired from a
>digital pad/camera lucida and obtain numbers of the objects I have drawn,
>then tally them up according to the color I have selected for those objects
>(perhaps 3 or four at most). Does anyone know a program (NIH image eg) that
>could do that after importing images from either application?
>Gloria E. Hoffman, Ph.D.
>Department of Anatomy and Neurobiology
>685 W Baltimore St
>Baltimore MD 21201
>Phone 410 706-2438
>Fax 410 706-2512
>email gehoffma@umaryland.edu


------------------------------------------------------------------
|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     |
------------------------------------------------------------------

--------------------------------
End of nih-image-d Digest V98 Issue #53
***************************************

From nih-image-request@io.ece.drexel.edu Sat Sep  5 07:40 EDT 1998
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Message-ID: <35F120F8.FCACA4D5@virginia.edu>
Date: Sat, 05 Sep 1998 07:31:04 -0400
From: Lance Davidson <lad4x@virginia.edu>
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Subject: Re: Metamorph to NIH Image
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--------------BC7C11B71928C9E56283692C
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Here are two different ways you can transfer stacks from Metamorph to NIH-Image:

1. In Metamorph - save stack as a sequentially numbered series of single frame tiff
files.
2. In NIH-Image - open all those files and use "windows to stack".

Or

1. In Metamorph - use "save as" a Biorad MRC-600 stack to produce a stack of images
that have the same format as a Biorad confocal stack.
2. In NIH-Image - Use the "I/O macros" and open the stack as a Biorad MRC-500 file.

These are just two ways to do this and I'm sure others here can think of several
other ways to do this. However, the quaint idea of just opening the metamorph stack
file as a tiff will not work. Metamorph hides alot of other information in their
file format (it is proprietary). The Biorad format is not proprietary. There is
almost no such thing as "standard" tiff. The format specifications (tiff 5.0 last
time I looked) allow for so much variability that special features such as
multi-image or 16 bit files are almost never supported outside of their native
program.

As others have commented here in the past, the only truely portable format is the
single image tiff format.

Good luck transferring,

Lance

-----------------------------
Lance Davidson
Research Associate (postdoc)
Department of Biology
University of Virginia
Charlottesville, VA 22903
804-243-2596

--------------BC7C11B71928C9E56283692C
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<HTML>
Here are two different ways you can transfer stacks from Metamorph to NIH-Image:

<P>1. In Metamorph - save stack as a sequentially numbered series of single
frame tiff files.
<BR>2. In NIH-Image - open all those files and use "windows to stack".

<P><U>Or</U><U></U>

<P>1. In Metamorph - use "save as" a Biorad MRC-600 stack to produce a
stack of images that have the same format as a Biorad confocal stack.
<BR>2. In NIH-Image - Use the "I/O macros" and open the stack as a Biorad
MRC-500 file.

<P>These are just two ways to do this and I'm sure others here can think
of several other ways to do this. However, the quaint idea of just opening
the metamorph stack file as a tiff will not work. Metamorph hides alot
of other information in their file format (it is proprietary). The Biorad
format is not proprietary. There is almost no such thing as "standard"
tiff. The format specifications (tiff 5.0 last time I looked) allow for
so much variability that special features such as multi-image or 16 bit
files are almost never supported outside of their native program.

<P>As others have commented here in the past, the only truely portable
format is the single image tiff format.

<P>Good luck transferring,

<P>Lance

<P>-----------------------------
<BR>Lance Davidson
<BR>Research Associate (postdoc)
<BR>Department of Biology
<BR>University of Virginia
<BR>Charlottesville, VA 22903
<BR>804-243-2596</HTML>

--------------BC7C11B71928C9E56283692C--


From nih-image-d-request@io.ece.drexel.edu Sun Sep  6 06:18 EDT 1998
Received: (from lists@localhost)
	by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA07208;
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Date: Sun, 6 Sep 1998 06:18:55 -0400 (EDT)
From: nih-image-d-request@io.ece.drexel.edu
Message-Id: <199809061018.GAA07208@io.ECE.Drexel.EDU>
Subject: nih-image-d Digest V98 #54
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 54

Today's Topics:
  Re: Metamorph to NIH Image            [ Lance Davidson <lad4x@virginia.edu> ]

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

Date: Sat, 05 Sep 1998 07:31:04 -0400
From: Lance Davidson <lad4x@virginia.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Metamorph to NIH Image
Message-ID: <35F120F8.FCACA4D5@virginia.edu>
Content-Type: multipart/alternative; boundary="------------BC7C11B71928C9E56283692C"

--------------BC7C11B71928C9E56283692C
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Here are two different ways you can transfer stacks from Metamorph to NIH-Image:

1. In Metamorph - save stack as a sequentially numbered series of single frame tiff
files.
2. In NIH-Image - open all those files and use "windows to stack".

Or

1. In Metamorph - use "save as" a Biorad MRC-600 stack to produce a stack of images
that have the same format as a Biorad confocal stack.
2. In NIH-Image - Use the "I/O macros" and open the stack as a Biorad MRC-500 file.

These are just two ways to do this and I'm sure others here can think of several
other ways to do this. However, the quaint idea of just opening the metamorph stack
file as a tiff will not work. Metamorph hides alot of other information in their
file format (it is proprietary). The Biorad format is not proprietary. There is
almost no such thing as "standard" tiff. The format specifications (tiff 5.0 last
time I looked) allow for so much variability that special features such as
multi-image or 16 bit files are almost never supported outside of their native
program.

As others have commented here in the past, the only truely portable format is the
single image tiff format.

Good luck transferring,

Lance

-----------------------------
Lance Davidson
Research Associate (postdoc)
Department of Biology
University of Virginia
Charlottesville, VA 22903
804-243-2596

--------------BC7C11B71928C9E56283692C
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<HTML>
Here are two different ways you can transfer stacks from Metamorph to NIH-Image:

<P>1. In Metamorph - save stack as a sequentially numbered series of single
frame tiff files.
<BR>2. In NIH-Image - open all those files and use "windows to stack".

<P><U>Or</U><U></U>

<P>1. In Metamorph - use "save as" a Biorad MRC-600 stack to produce a
stack of images that have the same format as a Biorad confocal stack.
<BR>2. In NIH-Image - Use the "I/O macros" and open the stack as a Biorad
MRC-500 file.

<P>These are just two ways to do this and I'm sure others here can think
of several other ways to do this. However, the quaint idea of just opening
the metamorph stack file as a tiff will not work. Metamorph hides alot
of other information in their file format (it is proprietary). The Biorad
format is not proprietary. There is almost no such thing as "standard"
tiff. The format specifications (tiff 5.0 last time I looked) allow for
so much variability that special features such as multi-image or 16 bit
files are almost never supported outside of their native program.

<P>As others have commented here in the past, the only truely portable
format is the single image tiff format.

<P>Good luck transferring,

<P>Lance

<P>-----------------------------
<BR>Lance Davidson
<BR>Research Associate (postdoc)
<BR>Department of Biology
<BR>University of Virginia
<BR>Charlottesville, VA 22903
<BR>804-243-2596</HTML>

--------------BC7C11B71928C9E56283692C--

--------------------------------
End of nih-image-d Digest V98 Issue #54
***************************************

From nih-image-request@io.ece.drexel.edu Sun Sep  6 12:16 EDT 1998
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From: "Joan Main" <joan.main@gte.net>
To: "scion image" <nih-image@io.ece.drexel.edu>
Subject: Fw: scion image histogram plots
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-----Original Message-----
From: Joan Main <jmain@acuson.com>
To: joan.main@gte.net <joan.main@gte.net>
Date: Wednesday, September 02, 1998 3:46 PM
Subject: scion image histogram plots


>     Hi,
>     I have a very urgent question regarding measurements:
>
>        1.  Histograms from ROI's, retangle is the only tool available for
>            histograms?
>        2.  Can you label the plot with the intensities?
>
>        3. I can not savew the Histogram, can only print from screen print?
>
>        4. URGENT:  I can't find  definition or macro for  what is being
>                calculated for the intergrated density.
>
>
>        5. I have just finished a series of measurements on 6 animals, the
>     data doesn't make sense....is there a way I can measure the MODAL not
>     the mean of the pixel intensities within an ROI?
>
>        Please let me know if Beta 3 version is ready for download...I know
>     you notified me that Beta 3 fixed the image problem I had reported...
>
>     Thank you for your prompt help
>     Joan Main
>     Joan.Main@gte.net or jmain @ acuson.com
>
>
>


From nih-image-request@io.ece.drexel.edu Sun Sep  6 12:16 EDT 1998
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-----Original Message-----
From: Joan Main <joan.main@gte.net>
To: scion image <nih-image@io.ece.drexel.edu>
Date: Sunday, September 06, 1998 9:00 AM
Subject: Fw: scion image histogram plots


>
>-----Original Message-----
>From: Joan Main <jmain@acuson.com>
>To: joan.main@gte.net <joan.main@gte.net>
>Date: Wednesday, September 02, 1998 3:46 PM
>Subject: scion image histogram plots
>
>
>>     Hi,
>>     I have a very urgent question regarding measurements:
>>
>>        1.  Histograms from ROI's, retangle is the only tool available for
>>            histograms?
>>        2.  Can you label the plot with the intensities?
>>
>>        3. I can not savew the Histogram, can only print from screen
print?
>>
>>        4. URGENT:  I can't find  definition or macro for  what is being
>>                calculated for the intergrated density.
>>
>>
>>        5. I have just finished a series of measurements on 6 animals, the
>>     data doesn't make sense....is there a way I can measure the MODAL not
>>     the mean of the pixel intensities within an ROI?
>>
>>        Please let me know if Beta 3 version is ready for download...I
know
>>     you notified me that Beta 3 fixed the image problem I had reported...
>>
>>     Thank you for your prompt help
>>     Joan Main
>>     Joan.Main@gte.net or jmain @ acuson.com
>>
>>
>>
>


From nih-image-request@io.ece.drexel.edu Mon Sep  7 05:43 EDT 1998
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> >
> >>     Hi,
> >>     I have a very urgent question regarding measurements:

> >>
> >>        3. I can not savew the Histogram, can only print from screen
> print?
> >>
>
> >>     Thank you for your prompt help
> >>     Joan Main

I can help you with this one,
Whilst the histogram window is selected,  choose File/Export from 
the menu bar.  This saves the histogram values as a text file (Change 
the extension to .txt) you can then open them up somewhere else such 
as Excel & do whatever you want with them.


Jenny
----------------------
j.gregory@abdn.ac.uk




From nih-image-d-request@io.ece.drexel.edu Mon Sep  7 05:49 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 55

Today's Topics:
  Fw: scion image histogram plots       [ "Joan Main" <joan.main@gte.net> ]
  Fw: subscribe: scion image histogram  [ "Joan Main" <joan.main@gte.net> ]
  Re: Fw: subscribe: scion image histo  [ "j.gregory" <ort056@abdn.ac.uk> ]

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

Date: Sun, 6 Sep 1998 09:00:16 -0700
From: "Joan Main" <joan.main@gte.net>
To: "scion image" <nih-image@io.ece.drexel.edu>
Subject: Fw: scion image histogram plots
Message-ID: <009001bdd9af$71afe920$0f0a13c0@oemcomputer>
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	charset="iso-8859-1"
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-----Original Message-----
From: Joan Main <jmain@acuson.com>
To: joan.main@gte.net <joan.main@gte.net>
Date: Wednesday, September 02, 1998 3:46 PM
Subject: scion image histogram plots


>     Hi,
>     I have a very urgent question regarding measurements:
>
>        1.  Histograms from ROI's, retangle is the only tool available for
>            histograms?
>        2.  Can you label the plot with the intensities?
>
>        3. I can not savew the Histogram, can only print from screen print?
>
>        4. URGENT:  I can't find  definition or macro for  what is being
>                calculated for the intergrated density.
>
>
>        5. I have just finished a series of measurements on 6 animals, the
>     data doesn't make sense....is there a way I can measure the MODAL not
>     the mean of the pixel intensities within an ROI?
>
>        Please let me know if Beta 3 version is ready for download...I know
>     you notified me that Beta 3 fixed the image problem I had reported...
>
>     Thank you for your prompt help
>     Joan Main
>     Joan.Main@gte.net or jmain @ acuson.com
>
>
>

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

Date: Sun, 6 Sep 1998 09:02:07 -0700
From: "Joan Main" <joan.main@gte.net>
To: "scion image" <nih-image@io.ece.drexel.edu>
Subject: Fw: subscribe: scion image histogram plots
Message-ID: <009501bdd9af$b3c0c0a0$0f0a13c0@oemcomputer>
Content-Type: text/plain;
	charset="iso-8859-1"
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-----Original Message-----
From: Joan Main <joan.main@gte.net>
To: scion image <nih-image@io.ece.drexel.edu>
Date: Sunday, September 06, 1998 9:00 AM
Subject: Fw: scion image histogram plots


>
>-----Original Message-----
>From: Joan Main <jmain@acuson.com>
>To: joan.main@gte.net <joan.main@gte.net>
>Date: Wednesday, September 02, 1998 3:46 PM
>Subject: scion image histogram plots
>
>
>>     Hi,
>>     I have a very urgent question regarding measurements:
>>
>>        1.  Histograms from ROI's, retangle is the only tool available for
>>            histograms?
>>        2.  Can you label the plot with the intensities?
>>
>>        3. I can not savew the Histogram, can only print from screen
print?
>>
>>        4. URGENT:  I can't find  definition or macro for  what is being
>>                calculated for the intergrated density.
>>
>>
>>        5. I have just finished a series of measurements on 6 animals, the
>>     data doesn't make sense....is there a way I can measure the MODAL not
>>     the mean of the pixel intensities within an ROI?
>>
>>        Please let me know if Beta 3 version is ready for download...I
know
>>     you notified me that Beta 3 fixed the image problem I had reported...
>>
>>     Thank you for your prompt help
>>     Joan Main
>>     Joan.Main@gte.net or jmain @ acuson.com
>>
>>
>>
>

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

Date: Mon, 7 Sep 1998 10:40:11 +0100 (BST)
From: "j.gregory" <ort056@abdn.ac.uk>
To: nih-image@io.ece.drexel.edu
Subject: Re: Fw: subscribe: scion image histogram plots
Message-ID: <SIMEON.9809071011.C@pc10.abdn.ac.uk>
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII

> >
> >>     Hi,
> >>     I have a very urgent question regarding measurements:

> >>
> >>        3. I can not savew the Histogram, can only print from screen
> print?
> >>
>
> >>     Thank you for your prompt help
> >>     Joan Main

I can help you with this one,
Whilst the histogram window is selected,  choose File/Export from 
the menu bar.  This saves the histogram values as a text file (Change 
the extension to .txt) you can then open them up somewhere else such 
as Excel & do whatever you want with them.


Jenny
----------------------
j.gregory@abdn.ac.uk

--------------------------------
End of nih-image-d Digest V98 Issue #55
***************************************

From nih-image-request@io.ece.drexel.edu Mon Sep  7 11:39 EDT 1998
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Date: Mon, 7 Sep 1998 17:27:30 +0200
To: nih-image@io.ece.drexel.edu
From: Francesc Peters <cesc@cucafera.icm.csic.es>
Subject: image analysis setup
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Hi all,

Our biological oceanography dept. wants a brand new microscopy/image
analysis setup, especially for epifluorescence microscopy (natural
bacterial and algal samples, stained with a variety of fluorochromes), but
also wants to have the flexibility to have phase contrast. They have about
$100000. I figure that about $40000-$50000 can go to the microscope. They
asked me about cameras and image analysis systems. I am not used to such
big bugs, so can somebody give me advice on expensive cameras (cooled,
3CCD, etc.) and image analysis systems (based on Silicon Graphics
workstations perhaps?), and what are their advantages, enhancements, etc,
over less expensive systems.

I'd appreciate each and every advice and suggestion. I need to give my
input to the dept by *yesterday*. Thanks a lot to evrybody.

cesc.

******************************************************************
PLEASE NOTICE NEW PHONE AND FAX NUMBERS!!!

Francesc Peters                           FAX:   34-93-221-7340
Institut de Ciencies del Mar (CSIC)       Phone: 34-93-221-6416 (Ext. 255)
Passeig Joan de Borbo s/n                 cesc@icm.csic.es
E-08039 Barcelona, Catalunya              <http://www.icm.csic.es>
Spain



From nih-image-d-request@io.ece.drexel.edu Tue Sep  8 06:15 EDT 1998
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From: nih-image-d-request@io.ece.drexel.edu
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Subject: nih-image-d Digest V98 #56
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------------------------------

Content-Type: text/plain

nih-image-d Digest				Volume 98 : Issue 56

Today's Topics:
  image analysis setup                  [ Francesc Peters <cesc@cucafera.icm. ]

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

Date: Mon, 7 Sep 1998 17:27:30 +0200
From: Francesc Peters <cesc@cucafera.icm.csic.es>
To: nih-image@io.ece.drexel.edu
Subject: image analysis setup
Message-Id: <l03130302b2199e376e4c@[193.145.218.128]>
Content-Type: text/plain; charset="us-ascii"

Hi all,

Our biological oceanography dept. wants a brand new microscopy/image
analysis setup, especially for epifluorescence microscopy (natural
bacterial and algal samples, stained with a variety of fluorochromes), but
also wants to have the flexibility to have phase contrast. They have about
$100000. I figure that about $40000-$50000 can go to the microscope. They
asked me about cameras and image analysis systems. I am not used to such
big bugs, so can somebody give me advice on expensive cameras (cooled,
3CCD, etc.) and image analysis systems (based on Silicon Graphics
workstations perhaps?), and what are their advantages, enhancements, etc,
over less expensive systems.

I'd appreciate each and every advice and suggestion. I need to give my
input to the dept by *yesterday*. Thanks a lot to evrybody.

cesc.

******************************************************************
PLEASE NOTICE NEW PHONE AND FAX NUMBERS!!!

Francesc Peters                           FAX:   34-93-221-7340
Institut de Ciencies del Mar (CSIC)       Phone: 34-93-221-6416 (Ext. 255)
Passeig Joan de Borbo s/n                 cesc@icm.csic.es
E-08039 Barcelona, Catalunya              <http://www.icm.csic.es>
Spain

--------------------------------
End of nih-image-d Digest V98 Issue #56
***************************************

From nih-image-request@io.ece.drexel.edu Tue Sep  8 08:17 EDT 1998
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Date: Tue, 08 Sep 1998 09:12:53 -0800
From: Luthero Martins <rsf6675@pro.via-rs.com.br>
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Group!

I'm an ophthalmologist in Brazil.  We are working with NIH's
applications on Ophthalmology, specially with Glaucom, where we study
the optic disk and the Retinal Nerve Fiber Layer.
        We see the variation of this images according of the
luminosity's
variation.
        The equipment that give us this image is a Canon Non-Mydriatic
Retinal
Camera.  But the threshold of variations when we apply the OPTIONS
DENSITY SLICE is very sensitive.

        Can we reduce this sensitivity? Or can we work with another part
of NIH
program?

        If anybody can help us, thanks.

You can see this images and results on:
http://www.oftalmologia-digital.com/clininih.html


From nih-image-request@io.ece.drexel.edu Tue Sep  8 09:10 EDT 1998
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Date: Tue, 8 Sep 1998 09:06:15 -0400
To: nih-image@io.ece.drexel.edu
From: Laird Bloom <lbloom@MIT.EDU>
Subject: Transferring ROIs to a new image
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Hi,
	I'd like to write a macro that allows me to draw a freehand ROI in
an image (e.g., the outline of rhodamine-stained cells), open another image
(e.g., the FITC channel image of the same cells), and count particles
within the same ROI in the second image.  I'd like it to be able to analyze
multiple ROIs within the same image, but also to keep the data for each ROI
separate.  In the NIH Image archives, I saw a suggestion for copying the
two images to a stack, then toggling back and forth between slices to do
this analysis.  Has anyone written such a macro using this or another
algorithm?
Thanks,
Laird Bloom
MIT Center for Cancer Research



From nih-image-request@io.ece.drexel.edu Tue Sep  8 09:54 EDT 1998
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Date: Tue, 8 Sep 1998 08:35:35 -0500 (CDT)
From: Doug Morris <dmorris@bmrl.med.uiuc.edu>
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I've written a macro set that uses these techniques for multiple ROIs
in some specialized magnetic resonance imaging and spectroscopy
techniques.  The macros are available at the following URL:
     http://bmrl.med.uiuc.edu:8080/software/macsoft.html

Good Luck, Doug

| Doug Morris                       |  University of Illinois            |
| email: dmorris@bmrl.med.uiuc.edu  |  Biomedical Magnetic Resonance Lab |
| fax:   217-244-1330               |  2100 S. Goodwin Ave.              |
| voice: 217-244-0290               |  Urbana Il 61801                   |

On Tue, 8 Sep 1998, Laird Bloom wrote:

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


From nih-image-request@io.ece.drexel.edu Tue Sep  8 10:40 EDT 1998
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To: nih-image@io.ece.drexel.edu
From: Gloria Hoffman <gehoffma@umaryland.edu>
Subject: image analysis setup
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I am working with the Photometrics Sensys camera. It is excellent for
relatively low light fluorescence, and maintains pretty high resolution as
well. Image analysis with a IP systems software is very friently interface
to the camera and enables very easy scripting of routines. The camera with
IP software runs about $28,000; there is now an attachement unit that can
capture the image using a liquid crystal mechanism that will achieve color
for brightfield as well. The capture of phase images is superb with that
system as well. (I am a big fan of Nikon's Eclipse microscopes for the
scope in that it has such wonderful light transmission for fluorescence)
and your system should then run about $55,000-$60,000 for the scope with
the best objectives and a variety of fluorescence cubes. Enjoy!

>Hi all,
>
>Our biological oceanography dept. wants a brand new microscopy/image
>analysis setup, especially for epifluorescence microscopy (natural
>bacterial and algal samples, stained with a variety of fluorochromes), but
>also wants to have the flexibility to have phase contrast. They have about
>$100000. I figure that about $40000-$50000 can go to the microscope. They
>asked me about cameras and image analysis systems. I am not used to such
>big bugs, so can somebody give me advice on expensive cameras (cooled,
>3CCD, etc.) and image analysis systems (based on Silicon Graphics
>workstations perhaps?), and what are their advantages, enhancements, etc,
>over less expensive systems.
>
>I'd appreciate each and every advice and suggestion. I need to give my
>input to the dept by *yesterday*. Thanks a lot to evrybody.
>
>cesc.
>
>******************************************************************
>PLEASE NOTICE NEW PHONE AND FAX NUMBERS!!!
>
>Francesc Peters                           FAX:   34-93-221-7340
>Institut de Ciencies del Mar (CSIC)       Phone: 34-93-221-6416 (Ext. 255)
>Passeig Joan de Borbo s/n                 cesc@icm.csic.es
>E-08039 Barcelona, Catalunya              <http://www.icm.csic.es>
>Spain

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


From nih-image-request@io.ece.drexel.edu Tue Sep  8 11:00 EDT 1998
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with respect to Gloria HOffmans messge, what is IP?


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With respect to Gloria


From nih-image-request@io.ece.drexel.edu Tue Sep  8 11:32 EDT 1998
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From: "Randy M. Wadkins" <rwadkins@saci.org>
Subject: Epson Photo 700 printers
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Hi All:
According to the latest MacWorld, the Epson Photo 700 printers are supposed
to output images of comparable quality to the Kodak dye sub printers.
Would anyone comment whether this is indeed true?  Does the Epson Photo 700
or EX output "journal quality" prints, like the dye sub printers do?

Thanks,
--Randy
******************************************************************
"Godzilla's approach
My mouth agape in horror
I just bought that car" --Dwight A. Macpherson, _Godzilla_Hiaku_

Randy M. Wadkins, Ph.D.
Cancer Therapy & Research Center
Institute for Drug Development
14960 Omicron Drive
San Antonio, TX 78245
phone: (210)-677-3835
fax: (210)-677-0058
E-mail:  rwadkins@saci.org
CTRC Homepage: http://www.ccc.saci.org
******************************************************************


From nih-image-request@io.ece.drexel.edu Tue Sep  8 11:39 EDT 1998
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From: yip@ibme.utoronto.ca (Christopher Yip)
Subject: Re: Epson Photo 700 printers
Date: Tue, 8 Sep 1998 11:27:20 -0400
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>Hi All:
>According to the latest MacWorld, the Epson Photo 700 printers are supposed
>to output images of comparable quality to the Kodak dye sub printers.
>Would anyone comment whether this is indeed true?  Does the Epson Photo 700
>or EX output "journal quality" prints, like the dye sub printers do?
>
>Thanks,
>--Randy
>******************************************************************
>"Godzilla's approach
>My mouth agape in horror
>I just bought that car" --Dwight A. Macpherson, _Godzilla_Hiaku_
>
>Randy M. Wadkins, Ph.D.
>Cancer Therapy & Research Center
>Institute for Drug Development
>14960 Omicron Drive
>San Antonio, TX 78245
>phone: (210)-677-3835
>fax: (210)-677-0058
>E-mail:  rwadkins@saci.org
>CTRC Homepage: http://www.ccc.saci.org
>******************************************************************

I just picked up an Epson Photo700 as a part of the Polaroid DMC promotion.
It is in fact quite nice when printing to photo paper and it's fast - I
don't know what the upgrade is to the new Photo740 (besides maybe the USB
bus). TIFF images from Photoshop look really sharp (an admittedly
qualitative description).

Chris.

Christopher M. Yip, Ph.D., P.Eng.
Assistant Professor
Department of Chemical Engineering and Applied Chemistry
Institute of Biomedical Engineering
Department of Biochemistry
University of Toronto
407 Rosebrugh Building, 4 Taddle Creek Rd.
Toronto, Ontario CANADA M5S 3G9
Office:(416) 978-7853; Lab:(416) 946-5022; Fax: (416) 978-4317;
e-mail: yip@ibme.utoronto.ca
WWW: http://goldie.ibme.utoronto.ca







From nih-image-request@io.ece.drexel.edu Tue Sep  8 12:48 EDT 1998
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From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
Subject: Re: Transferring ROIs to a new image
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>Hi,
>	I'd like to write a macro that allows me to draw a freehand ROI in
>an image (e.g., the outline of rhodamine-stained cells), open another image
>(e.g., the FITC channel image of the same cells), and count particles
>within the same ROI in the second image.  I'd like it to be able to analyze
>multiple ROIs within the same image, but also to keep the data for each ROI
>separate.  In the NIH Image archives, I saw a suggestion for copying the
>two images to a stack, then toggling back and forth between slices to do
>this analysis.  Has anyone written such a macro using this or another
>algorithm?
>Thanks,
>Laird Bloom
>MIT Center for Cancer Research

Draw each ROI (you can use the while button loop as discussed last week or
so to draw while running a macro) and fill each with a different grayvalue.
You can name each by incorporating a getstring command after each
delineation. To analyze, make a copy of your delineations and use the
density slice to isolate one of the regions. Use AND when pasting to your
FITC image to restrict analysis to the ROI. Repeat for each of your
delineations. To associate the ROI name with the measurement,  write the
results to a text window along with the ROI name.

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

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



From nih-image-request@io.ece.drexel.edu Tue Sep  8 17:12 EDT 1998
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To: nih-image@io.ece.drexel.edu
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>>Has onyone 



From nih-image-request@io.ece.drexel.edu Tue Sep  8 17:15 EDT 1998
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what sort of stereology are you going to do?  There are 2 sets of
stereology macros for Image.  One is the 'Stereology plug-ins', the other
is called 'Cavalieri3'.  Both come with documentation and are available 
from the Image ftp site

Regards,
Glen


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




From nih-image-request@io.ece.drexel.edu Tue Sep  8 19:28 EDT 1998
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From: SolamereTG@aol.com
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Less expensive systems are available:

In the US the microscope should be under  $30,000  (range $15,000 to $30,000)
with a full compliment of obj. lens.

Frame grabber $3000 or less (range $900 to 3000)  digital &/or analog

Computer ; G-3 Mac 300 Mhz, 17" monitor, 64 MB, 6GB HD  cost under $2500

For non-moving (or fixed) visible specimens that you can illuminate without
damage or bleaching I would suggest

1) High resolution on-chip integrating Peltier Cooled CCD (2 stage Peltier) is
able to can integrate for minutes athough a second or two is usually enough,
cost $6,500. 

For low light, low level illumination, living specimens sensitive to light
then an intensified camera is better.
 
cost ($16,750 to $25,000 (GEN IV intensifier, fiber optically coupled, >550
TVLs). These can also integrate on chip to permit very high magnification,
sub-visual (nothing to see in the microscope ocular) imaging.

Therefore under $42,000 for a low light but visible imaging system, $55,000
for high end sub-visual imaging. 

There are several sources. We are one.
Solamere Technology Group


From nih-image-request@io.ece.drexel.edu Tue Sep  8 20:47 EDT 1998
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From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: lbloom@MIT.EDU, nih-image@io.ece.drexel.edu
Date:          Wed, 9 Sep 1998 10:33:20 GMT+1000
Subject:       Re: Transferring ROIs to a new image
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>Date: Tue, 8 Sep 1998 09:06:15 -0400
>To: nih-image@io.ece.drexel.edu
>From: Laird Bloom <lbloom@MIT.EDU>
>	I'd like to write a macro that allows me to draw a freehand ROI in
>an image (e.g., the outline of rhodamine-stained cells), open another image
>(e.g., the FITC channel image of the same cells), and count particles
>within the same ROI in the second image.  I'd like it to be able to analyze
>multiple ROIs within the same image, but also to keep the data for each ROI
>separate.  In the NIH Image archives, I saw a suggestion for copying the
>two images to a stack, then toggling back and forth between slices to do
>this analysis.  Has anyone written such a macro using this or another
>algorithm?
>Thanks,
>Laird Bloom
>MIT Center for Cancer Research

There are a number of approachs available to this including 
the stack method you mention, 
the mapping method suggested by Jonathan Nissanov, 
particular applications as in Doug Morris's site, etc but
the simplest most useful method is often overlooked,
probably because this specific application is not explicitly mentioned in the 
manual. 

The macro restoreRoi or the restore selection <command 4>(analyse Menu) will 
restore the previously active selection to the current image
(even if a compound ROI selection made using control/option keys).
The trick is that the restoration takes effect on the current image even if the 
ROI was active on a different but previously active image
regardless of whether the previous image associated with the ROI was of the 
same dimensions or not. 
It is located in the same position relative to 0,0 ie topleft.
Thus a ROI established on an image
(a roi can be associated with any/each open window) 
can be transferred from that image to another, simply by:

 activating the image carrying the ROI;
 activate the image to receive the ROI;
 invoke restore selection <command 4>(analyse Menu)

or 

selectPic(pid2);killRoi;
selectPic(pid1);selectPic(pid2);restoreRoi;{transfers ROI from pid1 to 2}

In addition, you can 
selectPic(pid1);
SetSaveAs('Outline');saveas('aParticularROI');
selectPic(pid2);open('aParticularROI');
if you want to have a disk record of the ROI.

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


From nih-image-request@io.ece.drexel.edu Wed Sep  9 00:21 EDT 1998
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From: GJOSS@rna.bio.mq.edu.au
Organization:  School of Biological Sciences
To: luthero@pro.via-rs.com.br, nih-image@io.ece.drexel.edu
Date:          Wed, 9 Sep 1998 14:12:53 GMT+1000
Subject:       Re: question (image contrast optimisation)
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>Date: Tue, 08 Sep 1998 09:12:53 -0800
>From: Luthero Martins <rsf6675@pro.via-rs.com.br>
>Reply-To: luthero@pro.via-rs.com.br
>
>I'm an ophthalmologist in Brazil.  We are working with NIH's
>applications on Ophthalmology, specially with Glaucom, where we study
>the optic disk and the Retinal Nerve Fiber Layer.
>        We see the variation of this images according of the
>luminosity's
>variation.
>        The equipment that give us this image is a Canon Non-Mydriatic
>Retinal
>Camera.  But the threshold of variations when we apply the OPTIONS
>DENSITY SLICE is very sensitive.
>
>        Can we reduce this sensitivity? Or can we work with another part
>of NIH
>program?
>
>        If anybody can help us, thanks.
>
>You can see this images and results on:
>http://www.oftalmologia-digital.com/clininih.html

Luthero,

I expect what you are after is to get finer discrimination within the bright 
region of the image where you have made your selection.
The following numbers may not be accurate as the images on your web site are 
JPEG rather than TIFF but should be adequate to make the point.

You have used a color camera and apparently chosed to use the green channel 
image. You dodn't say whether the Canon camera was a digital camera or a video 
camera with a framgrabber. 
For a specialised application like this,I would expect that you would 
potentially get better results with a good monochrome camera (<$1000 US) with 
an appropriate color filter and a Scion framegrabber(<$1000).

It is important to look at and understand the histogram.  I will attach an 
annoted version to a direct email.

The histogram spread ranges 
from 25 or 28 (the bright end)
to 248 (the dark end)
The peak centered around 238 is not image data but the spread of pixels forming 
a black border around the image.
The image itself has a maximum pixel value of about 210.
Hence your image contrast range is at best 210-25 = 185
out of the available 256 values ie 72% of available

When you look at the histogram taken when density slice is active, the sliced 
portion of the histogram is shown in black as opposed to gray for the 
background.
Your slice extends from 25 or 28 to 47 and is <860 pixels of the total 
320x240=76800 pixels and is part of an image segment roughly 60 pixels diameter 
which is much brighter than the background image of the retina but only 
occupies about 5% of the image and on the histogram is all represented in the 
low outliers to the left of the double peaked histogram of the main retina.

You can see that if your image histogram was spread to fit the available 256 
values, then you would have much better contrast discrimination for the bright 
region of the retina.

You should be able to arrange this by adjustment of the brightness,contrast, 
colour balance controls on the camera if digital or on the framegrabber.
If a framegrabber, then, under NIH-Image, set a live histogram while you live 
capture and you adjust the gain(video control dialogue) up until the histogram 
is as wide as the histogram window while keeping it in the window by adjusting 
the offset (down will move it left in window, up will move it right towards the 
dark end).

More extremely, as you know where your region of interest falls on the 
histogram you can adjust 
the contrast ie gain up as long as the live histogram remains reasonably stable 
and keeping the histogram roi within the window by adjusting offset. 
This will saturate the retina background to be very dark or even black ie >=255 
but will maximise discrimination in the intensity range that is of interest for 
the density slice segmentation.

Also if you make a selection that is restricted to the bright region and
then use integrate, the integration processing will ensure the max/min levels 
in the ROI fill the histogram window.

If you need to retain contrast info to see blood vessel detail of current 
image, the you can expand a range of 25 to 25+166= to 256 by cutting off the 
dark end of the histogram where 191 falls now 
ie an improvement of 256/166=1.5+ or over 50%

or you can take two images with different contrast settings and 
transfer the segmented ROI from the image contrasted at the bright end
to the perceptually acceptable image afterwards.


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

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nih-image-d Digest				Volume 98 : Issue 57

Today's Topics:
  question                              [ Luthero Martins <rsf6675@pro.via-rs ]
  Transferring ROIs to a new image      [ Laird Bloom <lbloom@MIT.EDU> ]
  Re: Transferring ROIs to a new image  [ Doug Morris <dmorris@bmrl.med.uiuc. ]
  image analysis setup                  [ Gloria Hoffman <gehoffma@umaryland. ]
  Re: image analysis setup              [ Sam Purdy <spurdy@nationalsteel.com ]
  Re: image analysis setup              [ Sam Purdy <spurdy@nationalsteel.com ]
  Epson Photo 700 printers              [ "Randy M. Wadkins" <rwadkins@saci.o ]
  Re: Epson Photo 700 printers          [ yip@ibme.utoronto.ca (Christopher Y ]
  Re: Transferring ROIs to a new image  [ Jonathan Nissanov <yoni@cbis.ece.dr ]
  Re: stereology                        [ "G. Macdonald" <glenmac@u.washingto ]
  Re:Stereology                         [ "G. Macdonald" <glenmac@u.washingto ]
  Re: image analysis setup              [ SolamereTG@aol.com ]
  Re: Transferring ROIs to a new image  [ GJOSS@rna.bio.mq.edu.au ]
  Re: question (image contrast optimis  [ GJOSS@rna.bio.mq.edu.au ]

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

Date: Tue, 08 Sep 1998 09:12:53 -0800
From: Luthero Martins <rsf6675@pro.via-rs.com.br>
To: nih-image@io.ece.drexel.edu
Subject: question
Message-ID: <35F56595.2C3A@pro.via-rs.com.br>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Group!

I'm an ophthalmologist in Brazil.  We are working with NIH's
applications on Ophthalmology, specially with Glaucom, where we study
the optic disk and the Retinal Nerve Fiber Layer.
        We see the variation of this images according of the
luminosity's
variation.
        The equipment that give us this image is a Canon Non-Mydriatic
Retinal
Camera.  But the threshold of variations when we apply the OPTIONS
DENSITY SLICE is very sensitive.

        Can we reduce this sensitivity? Or can we work with another part
of NIH
program?

        If anybody can help us, thanks.

You can see this images and results on:
http://www.oftalmologia-digital.com/clininih.html

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

Date: Tue, 8 Sep 1998 09:06:15 -0400
From: Laird Bloom <lbloom@MIT.EDU>
To: nih-image@io.ece.drexel.edu
Subject: Transferring ROIs to a new image
Message-Id: <v03020902b21adb8692ae@[18.155.0.117]>
Content-Type: text/plain; charset="us-ascii"

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

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

Date: Tue, 8 Sep 1998 08:35:35 -0500 (CDT)
From: Doug Morris <dmorris@bmrl.med.uiuc.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Transferring ROIs to a new image
Message-ID: <Pine.LNX.4.02.9809080832120.7623-100000@phase.med.uiuc.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I've written a macro set that uses these techniques for multiple ROIs
in some specialized magnetic resonance imaging and spectroscopy
techniques.  The macros are available at the following URL:
     http://bmrl.med.uiuc.edu:8080/software/macsoft.html

Good Luck, Doug

| Doug Morris                       |  University of Illinois            |
| email: dmorris@bmrl.med.uiuc.edu  |  Biomedical Magnetic Resonance Lab |
| fax:   217-244-1330               |  2100 S. Goodwin Ave.              |
| voice: 217-244-0290               |  Urbana Il 61801                   |

On Tue, 8 Sep 1998, Laird Bloom wrote:

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

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

Date: Tue, 8 Sep 1998 10:37:21 -0400
From: Gloria Hoffman <gehoffma@umaryland.edu>
To: nih-image@io.ece.drexel.edu
Subject: image analysis setup
Message-Id: <v04011745b21aee4119a0@[134.192.129.87]>
Content-Type: text/plain; charset="us-ascii"

I am working with the Photometrics Sensys camera. It is excellent for
relatively low light fluorescence, and maintains pretty high resolution as
well. Image analysis with a IP systems software is very friently interface
to the camera and enables very easy scripting of routines. The camera with
IP software runs about $28,000; there is now an attachement unit that can
capture the image using a liquid crystal mechanism that will achieve color
for brightfield as well. The capture of phase images is superb with that
system as well. (I am a big fan of Nikon's Eclipse microscopes for the
scope in that it has such wonderful light transmission for fluorescence)
and your system should then run about $55,000-$60,000 for the scope with
the best objectives and a variety of fluorescence cubes. Enjoy!

>Hi all,
>
>Our biological oceanography dept. wants a brand new microscopy/image
>analysis setup, especially for epifluorescence microscopy (natural
>bacterial and algal samples, stained with a variety of fluorochromes), but
>also wants to have the flexibility to have phase contrast. They have about
>$100000. I figure that about $40000-$50000 can go to the microscope. They
>asked me about cameras and image analysis systems. I am not used to such
>big bugs, so can somebody give me advice on expensive cameras (cooled,
>3CCD, etc.) and image analysis systems (based on Silicon Graphics
>workstations perhaps?), and what are their advantages, enhancements, etc,
>over less expensive systems.
>
>I'd appreciate each and every advice and suggestion. I need to give my
>input to the dept by *yesterday*. Thanks a lot to evrybody.
>
>cesc.
>
>******************************************************************
>PLEASE NOTICE NEW PHONE AND FAX NUMBERS!!!
>
>Francesc Peters                           FAX:   34-93-221-7340
>Institut de Ciencies del Mar (CSIC)       Phone: 34-93-221-6416 (Ext. 255)
>Passeig Joan de Borbo s/n                 cesc@icm.csic.es
>E-08039 Barcelona, Catalunya              <http://www.icm.csic.es>
>Spain

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

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

Date: Tue, 08 Sep 1998 10:45:10 -0400
From: Sam Purdy <spurdy@nationalsteel.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: image analysis setup
Message-Id: <199809081445.AA10130@igw.nationalsteel.com>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

with respect to Gloria HOffmans messge, what is IP?

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

Date: Tue, 08 Sep 1998 10:45:55 -0400
From: Sam Purdy <spurdy@nationalsteel.com>
To: nih-image@io.ece.drexel.edu
Subject: Re: image analysis setup
Message-Id: <199809081446.AA16363@igw.nationalsteel.com>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

With respect to Gloria

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

Date: Tue, 8 Sep 1998 10:23:47 -0600
From: "Randy M. Wadkins" <rwadkins@saci.org>
To: nih-image@io.ece.drexel.edu
Subject: Epson Photo 700 printers
Message-Id: <v04011705b21b0a0f956a@[192.238.18.184]>
Content-Type: text/plain; charset="us-ascii"

Hi All:
According to the latest MacWorld, the Epson Photo 700 printers are supposed
to output images of comparable quality to the Kodak dye sub printers.
Would anyone comment whether this is indeed true?  Does the Epson Photo 700
or EX output "journal quality" prints, like the dye sub printers do?

Thanks,
--Randy
******************************************************************
"Godzilla's approach
My mouth agape in horror
I just bought that car" --Dwight A. Macpherson, _Godzilla_Hiaku_

Randy M. Wadkins, Ph.D.
Cancer Therapy & Research Center
Institute for Drug Development
14960 Omicron Drive
San Antonio, TX 78245
phone: (210)-677-3835
fax: (210)-677-0058
E-mail:  rwadkins@saci.org
CTRC Homepage: http://www.ccc.saci.org
******************************************************************

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

Date: Tue, 8 Sep 1998 11:27:20 -0400
From: yip@ibme.utoronto.ca (Christopher Yip)
To: nih-image@io.ece.drexel.edu
Subject: Re: Epson Photo 700 printers
Message-Id: <l03110719b21ac3e43bbf@[128.100.71.77]>
Content-Type: text/plain; charset="us-ascii"

>Hi All:
>According to the latest MacWorld, the Epson Photo 700 printers are supposed
>to output images of comparable quality to the Kodak dye sub printers.
>Would anyone comment whether this is indeed true?  Does the Epson Photo 700
>or EX output "journal quality" prints, like the dye sub printers do?
>
>Thanks,
>--Randy
>******************************************************************
>"Godzilla's approach
>My mouth agape in horror
>I just bought that car" --Dwight A. Macpherson, _Godzilla_Hiaku_
>
>Randy M. Wadkins, Ph.D.
>Cancer Therapy & Research Center
>Institute for Drug Development
>14960 Omicron Drive
>San Antonio, TX 78245
>phone: (210)-677-3835
>fax: (210)-677-0058
>E-mail:  rwadkins@saci.org
>CTRC Homepage: http://www.ccc.saci.org
>******************************************************************

I just picked up an Epson Photo700 as a part of the Polaroid DMC promotion.
It is in fact quite nice when printing to photo paper and it's fast - I
don't know what the upgrade is to the new Photo740 (besides maybe the USB
bus). TIFF images from Photoshop look really sharp (an admittedly
qualitative description).

Chris.

Christopher M. Yip, Ph.D., P.Eng.
Assistant Professor
Department of Chemical Engineering and Applied Chemistry
Institute of Biomedical Engineering
Department of Biochemistry
University of Toronto
407 Rosebrugh Building, 4 Taddle Creek Rd.
Toronto, Ontario CANADA M5S 3G9
Office:(416) 978-7853; Lab:(416) 946-5022; Fax: (416) 978-4317;
e-mail: yip@ibme.utoronto.ca
WWW: http://goldie.ibme.utoronto.ca

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

Date: Tue, 8 Sep 1998 11:29:41 -0500
From: Jonathan Nissanov <yoni@cbis.ece.drexel.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: Transferring ROIs to a new image
Message-Id: <v03007803b21b09568015@[144.118.33.245]>
Content-Type: text/plain; charset="us-ascii"

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

Draw each ROI (you can use the while button loop as discussed last week or
so to draw while running a macro) and fill each with a different grayvalue.
You can name each by incorporating a getstring command after each
delineation. To analyze, make a copy of your delineations and use the
density slice to isolate one of the regions. Use AND when pasting to your
FITC image to restrict analysis to the ROI. Repeat for each of your
delineations. To associate the ROI name with the measurement,  write the
results to a text window along with the ROI name.

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

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

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

Date: Tue, 8 Sep 1998 13:57:21 -0700 (PDT)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re: stereology
Message-ID: <Pine.A41.3.95b.980908135649.83318D-100000@homer24.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

>>Has onyone 

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

Date: Tue, 8 Sep 1998 14:00:51 -0700 (PDT)
From: "G. Macdonald" <glenmac@u.washington.edu>
To: nih-image@io.ece.drexel.edu
Subject: Re:Stereology
Message-ID: <Pine.A41.3.95b.980908135743.83318E-100000@homer24.u.washington.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

what sort of stereology are you going to do?  There are 2 sets of
stereology macros for Image.  One is the 'Stereology plug-ins', the other
is called 'Cavalieri3'.  Both come with documentation and are available 
from the Image ftp site

Regards,
Glen


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

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

Date: Tue, 8 Sep 1998 19:17:12 EDT
From: SolamereTG@aol.com
To: nih-image@io.ece.drexel.edu
Subject: Re: image analysis setup
Message-ID: <341e8951.35f5baf8@aol.com>
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7bit

Less expensive systems are available:

In the US the microscope should be under  $30,000  (range $15,000 to $30,000)
with a full compliment of obj. lens.

Frame grabber $3000 or less (range $900 to 3000)  digital &/or analog

Computer ; G-3 Mac 300 Mhz, 17" monitor, 64 MB, 6GB HD  cost under $2500

For non-moving (or fixed) visible specimens that you can illuminate without
damage or bleaching I would suggest

1) High resolution on-chip integrating Peltier Cooled CCD (2 stage Peltier) is
able to can integrate for minutes athough a second or two is usually enough,
cost $6,500. 

For low light, low level illumination, living specimens sensitive to light
then an intensified camera is better.
 
cost ($16,750 to $25,000 (GEN IV intensifier, fiber optically coupled, >550
TVLs). These can also integrate on chip to permit very high magnification,
sub-visual (nothing to see in the microscope ocular) imaging.

Therefore under $42,000 for a low light but visible imaging system, $55,000
for high end sub-visual imaging. 

There are several sources. We are one.
Solamere Technology Group

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

Date:          Wed, 9 Sep 1998 10:33:20 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: lbloom@MIT.EDU, nih-image@io.ece.drexel.edu
Subject:       Re: Transferring ROIs to a new image
Message-ID: <81DAE9E2114@rna.bio.mq.edu.au>

>Date: Tue, 8 Sep 1998 09:06:15 -0400
>To: nih-image@io.ece.drexel.edu
>From: Laird Bloom <lbloom@MIT.EDU>
>	I'd like to write a macro that allows me to draw a freehand ROI in
>an image (e.g., the outline of rhodamine-stained cells), open another image
>(e.g., the FITC channel image of the same cells), and count particles
>within the same ROI in the second image.  I'd like it to be able to analyze
>multiple ROIs within the same image, but also to keep the data for each ROI
>separate.  In the NIH Image archives, I saw a suggestion for copying the
>two images to a stack, then toggling back and forth between slices to do
>this analysis.  Has anyone written such a macro using this or another
>algorithm?
>Thanks,
>Laird Bloom
>MIT Center for Cancer Research

There are a number of approachs available to this including 
the stack method you mention, 
the mapping method suggested by Jonathan Nissanov, 
particular applications as in Doug Morris's site, etc but
the simplest most useful method is often overlooked,
probably because this specific application is not explicitly mentioned in the 
manual. 

The macro restoreRoi or the restore selection <command 4>(analyse Menu) will 
restore the previously active selection to the current image
(even if a compound ROI selection made using control/option keys).
The trick is that the restoration takes effect on the current image even if the 
ROI was active on a different but previously active image
regardless of whether the previous image associated with the ROI was of the 
same dimensions or not. 
It is located in the same position relative to 0,0 ie topleft.
Thus a ROI established on an image
(a roi can be associated with any/each open window) 
can be transferred from that image to another, simply by:

 activating the image carrying the ROI;
 activate the image to receive the ROI;
 invoke restore selection <command 4>(analyse Menu)

or 

selectPic(pid2);killRoi;
selectPic(pid1);selectPic(pid2);restoreRoi;{transfers ROI from pid1 to 2}

In addition, you can 
selectPic(pid1);
SetSaveAs('Outline');saveas('aParticularROI');
selectPic(pid2);open('aParticularROI');
if you want to have a disk record of the ROI.

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

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

Date:          Wed, 9 Sep 1998 14:12:53 GMT+1000
From: GJOSS@rna.bio.mq.edu.au
To: luthero@pro.via-rs.com.br, nih-image@io.ece.drexel.edu
Subject:       Re: question (image contrast optimisation)
Message-ID: <82157F20EEB@rna.bio.mq.edu.au>

>Date: Tue, 08 Sep 1998 09:12:53 -0800
>From: Luthero Martins <rsf6675@pro.via-rs.com.br>
>Reply-To: luthero@pro.via-rs.com.br
>
>I'm an ophthalmologist in Brazil.  We are working with NIH's
>applications on Ophthalmology, specially with Glaucom, where we study
>the optic disk and the Retinal Nerve Fiber Layer.
>        We see the variation of this images according of the
>luminosity's
>variation.
>        The equipment that give us this image is a Canon Non-Mydriatic
>Retinal
>Camera.  But the threshold of variations when we apply the OPTIONS
>DENSITY SLICE is very sensitive.
>
>        Can we reduce this sensitivity? Or can we work with another part
>of NIH
>program?
>
>        If anybody can help us, thanks.
>
>You can see this images and results on:
>http://www.oftalmologia-digital.com/clininih.html

Luthero,

I expect what you are after is to get finer discrimination within the bright 
region of the image where you have made your selection.
The following numbers may not be accurate as the images on your web site are 
JPEG rather than TIFF but should be adequate to make the point.

You have used a color camera and apparently chosed to use the green channel 
image. You dodn't say whether the Canon camera was a digital camera or a video 
camera with a framgrabber. 
For a specialised application like this,I would expect that you would 
potentially get better results with a good monochrome camera (<$1000 US) with 
an appropriate color filter and a Scion framegrabber(<$1000).

It is important to look at and understand the histogram.  I will attach an 
annoted version to a direct email.

The histogram spread ranges 
from 25 or 28 (the bright end)
to 248 (the dark end)
The peak centered around 238 is not image data but the spread of pixels forming 
a black border around the image.
The image itself has a maximum pixel value of about 210.
Hence your image contrast range is at best 210-25 = 185
out of the available 256 values ie 72% of available

When you look at the histogram taken when density slice is active, the sliced 
portion of the histogram is shown in black as opposed to gray for the 
background.
Your slice extends from 25 or 28 to 47 and is <860 pixels of the total 
320x240=76800 pixels and is part of an image segment roughly 60 pixels diameter 
which is much brighter than the background image of the retina but only 
occupies about 5% of the image and on the histogram is all represented in the 
low outliers to the left of the double peaked histogram of the main retina.

You can see that if your image histogram was spread to fit the available 256 
values, then you would have much better contrast discrimination for the bright 
region of the retina.

You should be able to arrange this by adjustment of the brightness,contrast, 
colour balance controls on the camera if digital or on the framegrabber.
If a framegrabber, then, under NIH-Image, set a live histogram while you live 
capture and you adjust the gain(video control dialogue) up until the histogram 
is as wide as the histogram window while keeping it in the window by adjusting 
the offset (down will move it left in window, up will move it right towards the 
dark end).

More extremely, as you know where your region of interest falls on the 
histogram you can adjust 
the contrast ie gain up as long as the live histogram remains reasonably stable 
and keeping the histogram roi within the window by adjusting offset. 
This will saturate the retina background to be very dark or even black ie >=255 
but will maximise discrimination in the intensity range that is of interest for 
the density slice segmentation.

Also if you make a selection that is restricted to the bright region and
then use integrate, the integration processing will ensure the max/min levels 
in the ROI fill the histogram window.

If you need to retain contrast info to see blood vessel detail of current 
image, the you can expand a range of 25 to 25+166= to 256 by cutting off the 
dark end of the histogram where 191 falls now 
ie an improvement of 256/166=1.5+ or over 50%

or you can take two images with different contrast settings and 
transfer the segmented ROI from the image contrasted at the bright end
to the perceptually acceptable image afterwards.


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

--------------------------------
End of nih-image-d Digest V98 Issue #57
***************************************