OMERO Beta-4.1 Release

[Jason Swedlow]

Dear All-

Today, The OME Consortium is proud to release OMERO-Beta4.1.

This release follows strong feedback we received at our May 2009 User's Mtg at Institut Pasteur, Paris.  We've made substantial efforts to improve support for metadata, especially for confocal microscopy, and ensure OMERO supports all of the file formats enabled by Bio-Formats. We have enabled export to OME-TIFF and QuickTime/AVI/MPEG.  We've made various improvements to OMERO clients to improve workflow and use.

You'll notice a substantial increase in the visibility of metadata in OMERO.  We hope that this serves to help improve metadata support in scientific imaging.

The full list of features in OMERO, including  new features in OMERO Beta-4.1, is at http://openmicroscopy.org/site/products/feature-list
Most features are accompanied by a short movie that shows that functionality in action. 

The software is available at http://openmicroscopy.org

Some notes on this release:

-- We have established a new feature-- OMERO.qa (http://qa.openmicroscopy.org.uk).  This is a feedback mechanism, to allow us to communicate more effectively with our community.  OMERO.qa supports uploading of problematic files, and tracking of responses to any user queries.  Moreover, OMERO.qa includes a demo feature: in collaboration with Urban Liebel at  Karlsruhe Institute of Technology, we are providing demo accounts for OMERO.  Use the Demo link at qa to contact us if you are interested in this.

 -- We are releasing a number of "Prerelease features".  For users who have had problems with memory-based crashes in OMERO.insight, the new OpenGL-based ImageViewer may be of interest. Also, we are now taking advantage of our modeling of HCS data, and releasing our first clients that support Flex, MIAS, and InCell 1000 file formats.  OMERO.dropbox has been substantially extended, and now supports all the file formats supported by OMERO. 

-- Some of you know that the OME Consortium puts strong emphasis on the usability of our tools for both users and developers.  Through previous funding from the EPSRC, we, in collaboration with Catriona Macaulay and Peter Gregor,  established UsableImage (http://usableimage.org) , a project dedicated to driving usability in academic scientific software.  While we continue to try to run this project, our current funding period has ended, and the EPSRC turned down our request for further funding.  For this reason, OMERO Beta-4.1 has not been through the same usability analysis as our previous releases.  We hope to re-establish this part of the project with alternative funding in the future.

Finally, we are hugely grateful to those who attended the OME User's Meeting in May 2009.  The feedback and conclusions from that meeting have driven our work all summer and have been our mantras for these past few months.  We have received very helpful testing, feedback, data submission, and feature suggestions  from many members of the community.  There are too many to name (and we are not always clear whether people want their good name associated with us), but we are particularly thankful for data, testing, and/or comments and suggestions from: Martin Spitaler and Mark Woodbridge (Imperial), Alex Sossick (Cambridge), Jay Copeland (Harvard), Frans Cornelissen and Frederick Michielssen (Johnson & Johnson), Michael Porter and Raman Das (Dundee), Bernhard Holländer and Karsten Kottig (PerkinElmer),  Karol Kozak (ETH Zurich), and a number of people on the OME Forums.  Submitted data is hugely valuable and provides us with concrete information we can use.  Moreover, the testing and feedback we get from external sources is simply invaluable.  We know this takes time (an all too precious resource), and are grateful for all of this.

OMERO Beta-4.1 is focused on what we called DataIn/DataOut at Paris in May09.  We will show new functionality at ASCB in San Diego.  Data duplication is a hot issue, and will be addressed in upcoming releases.

As always, thanks for your support.

Cheers,

Jason and the OME Consortium

--
**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone [phone]
Intl phone:  [phone]
FAX   [phone]
email: [hidden email]

Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
Open Microscopy Environment: http://openmicroscopy.org
**************************

[John Oreopoulos]

Dear list,

While preparing some confocal imaging results for publication just  
recently, I was informed by one of my PhD committee members that I  
should try to present my multi-dimensional microscopy images in such  
a way that they are easy to see by people who are color blind. Ie:  
you should choose colors for your single monochrome channel images  
such that when viewed in a merged/overlay image they convey the same  
information as you would see in a standard green/red overlay image  
for colocalization, etc. I've tried to read up a bit on this topic on  
the web and I even searched the confocal listserv archive, but I  
could find no definitive set of rules or guidelines for going about  
this. The only discussion I could find about this on the listserv  
dates back to 1996 and given that imaging has become even more  
prevalent in today's biological sciences since then, I'm wondering if  
anyone on here now can direct me to a good source or set of journal  
guidelines for publishing color image overlays bearing in mind that  
some of the readers will be color blind . Also, does anyone know of  
any image processing utilities or plugins (ImageJ?) that can covert a  
full color image into a version that is easier to interpret by  
someone who is color blind?

I've come to realize this is even more important than I previously  
thought given that it seems that almost 1 in 10 males worldwide is  
color blind (the occurrence of color blindness is said to be lower in  
females). Actually, if you want to learn more about the topic of how  
humans perceive color and the history of making colors, I highly  
recommend a BBC documentary I came across just yesterday called  
"Cracking the Colour Code". Very entertaining.

John Oreopoulos

PS: I used both spellings of the word color in the subject line so  
that others can find this thread easily in the future.

[Lemasters, John J.]

Hi John,

Older versions of Photoshop had a color table called black body that simulated to some extent the change of color as a black body is heated. The color range is generally pleasing to the eye (if you see color) but also the luminescence increases linearly so that the scale bar can be xeroxed in black and white with faithful retention of the scale. I'm not sure new versions of Photoshop have this scale. We used it in a couple of papers, for example:

Trollinger, D.R., W.E. Cascio and J.J. Lemasters (1997) Selective loading of Rhod 2 into mitochondria shows mitochondrial Ca2+ transients during the contractile cycle in adult rabbit cardiac myocytes. Biochem. Biophys. Res. Commun. 236, 738-742.

Trollinger, D.R., W.E. Cascio and J.J. Lemasters (2000) Mitochondrial calcium transients in adult rabbit cardiac myocytes: inhibition by ruthenium red and artifacts caused by lyso-somal loading of Ca2+-indicating fluorophores. Biophys. J. 79, 39-50.

As I recall, Peter Ingram, an electron microscopist, first introduced me to the black body scale.

John


--
John J. Lemasters, MD, PhD
Professor and South Carolina COEE Endowed Chair
Director, Center for Cell Death, Injury and Regeneration
Departments of Pharmaceutical & Biomedical Sciences and Biochemistry & Molecular Biology
Medical University of South Carolina
QF213 Quadrangle Building
280 Calhoun Street, MSC 140
Charleston, SC 29425

Office: 843-792-2153
Lab: 843-792-3530
Fax: [phone]
Email: [hidden email]


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of John Oreopoulos
Sent: Wednesday, October 21, 2009 10:26 PM
To: [hidden email]
Subject: Proper presentation of fluorescence microscopy images for people who are color blind / colour blind

Dear list,

While preparing some confocal imaging results for publication just  
recently, I was informed by one of my PhD committee members that I  
should try to present my multi-dimensional microscopy images in such  
a way that they are easy to see by people who are color blind. Ie:  
you should choose colors for your single monochrome channel images  
such that when viewed in a merged/overlay image they convey the same  
information as you would see in a standard green/red overlay image  
for colocalization, etc. I've tried to read up a bit on this topic on  
the web and I even searched the confocal listserv archive, but I  
could find no definitive set of rules or guidelines for going about  
this. The only discussion I could find about this on the listserv  
dates back to 1996 and given that imaging has become even more  
prevalent in today's biological sciences since then, I'm wondering if  
anyone on here now can direct me to a good source or set of journal  
guidelines for publishing color image overlays bearing in mind that  
some of the readers will be color blind . Also, does anyone know of  
any image processing utilities or plugins (ImageJ?) that can covert a  
full color image into a version that is easier to interpret by  
someone who is color blind?

I've come to realize this is even more important than I previously  
thought given that it seems that almost 1 in 10 males worldwide is  
color blind (the occurrence of color blindness is said to be lower in  
females). Actually, if you want to learn more about the topic of how  
humans perceive color and the history of making colors, I highly  
recommend a BBC documentary I came across just yesterday called  
"Cracking the Colour Code". Very entertaining.

John Oreopoulos

PS: I used both spellings of the word color in the subject line so  
that others can find this thread easily in the future.

No virus found in this incoming message.
Checked by AVG - www.avg.com
Version: 8.5.423 / Virus Database: 270.14.25/2450 - Release Date: 10/21/09 16:44:00

[Cameron Nowell]

Howdy,

Black Body still exists in the current photoshop (CS4). Just make your
image index colour and assign the black body colour table to it.

Although i don't know if this is going to help so much with colour blind
viewers. The most common for of colour blindness is Red/Green (meaning
if those two colours are superimposed they will blend together). But
Blue/green, blue/yellow and other combinations are possible as well. So
choosing a colour scheme to suit all people will be nearly impossible.

My suggestion would be to have individual frames of each channel in grey
scale and one overlay image that avoids using red and green together
(green and magenta tends to work quite well).


Cheers


Cam



Cameron J. Nowell
Microscopy Manager
Centre for Advanced Microscopy
Ludwig Institute for Cancer Research
PO Box 2008
Royal Melbourne Hospital
Victoria, 3050
AUSTRALIA
Office: [phone]
Mobile: [phone]
Fax: [phone]
www.ludwig.edu.au/confocal/




-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]]
On Behalf Of Lemasters, John
Sent: Thursday, 22 October 2009 1:39 PM
To: [hidden email]
Subject: Re: Proper presentation of fluorescence microscopy images for
people who are color blind / colour blind

Hi John,

Older versions of Photoshop had a color table called black body that
simulated to some extent the change of color as a black body is heated.
The color range is generally pleasing to the eye (if you see color) but
also the luminescence increases linearly so that the scale bar can be
xeroxed in black and white with faithful retention of the scale. I'm not
sure new versions of Photoshop have this scale. We used it in a couple
of papers, for example:

Trollinger, D.R., W.E. Cascio and J.J. Lemasters (1997) Selective
loading of Rhod 2 into mitochondria shows mitochondrial Ca2+ transients
during the contractile cycle in adult rabbit cardiac myocytes. Biochem.
Biophys. Res. Commun. 236, 738-742.

Trollinger, D.R., W.E. Cascio and J.J. Lemasters (2000) Mitochondrial
calcium transients in adult rabbit cardiac myocytes: inhibition by
ruthenium red and artifacts caused by lyso-somal loading of
Ca2+-indicating fluorophores. Biophys. J. 79, 39-50.

As I recall, Peter Ingram, an electron microscopist, first introduced me
to the black body scale.

John


--
John J. Lemasters, MD, PhD
Professor and South Carolina COEE Endowed Chair
Director, Center for Cell Death, Injury and Regeneration
Departments of Pharmaceutical & Biomedical Sciences and Biochemistry &
Molecular Biology
Medical University of South Carolina
QF213 Quadrangle Building
280 Calhoun Street, MSC 140
Charleston, SC 29425

Office: 843-792-2153
Lab: 843-792-3530
Fax: [phone]
Email: [hidden email]


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]]
On Behalf Of John Oreopoulos
Sent: Wednesday, October 21, 2009 10:26 PM
To: [hidden email]
Subject: Proper presentation of fluorescence microscopy images for
people who are color blind / colour blind

Dear list,

While preparing some confocal imaging results for publication just  
recently, I was informed by one of my PhD committee members that I  
should try to present my multi-dimensional microscopy images in such  
a way that they are easy to see by people who are color blind. Ie:  
you should choose colors for your single monochrome channel images  
such that when viewed in a merged/overlay image they convey the same  
information as you would see in a standard green/red overlay image  
for colocalization, etc. I've tried to read up a bit on this topic on  
the web and I even searched the confocal listserv archive, but I  
could find no definitive set of rules or guidelines for going about  
this. The only discussion I could find about this on the listserv  
dates back to 1996 and given that imaging has become even more  
prevalent in today's biological sciences since then, I'm wondering if  
anyone on here now can direct me to a good source or set of journal  
guidelines for publishing color image overlays bearing in mind that  
some of the readers will be color blind . Also, does anyone know of  
any image processing utilities or plugins (ImageJ?) that can covert a  
full color image into a version that is easier to interpret by  
someone who is color blind?

I've come to realize this is even more important than I previously  
thought given that it seems that almost 1 in 10 males worldwide is  
color blind (the occurrence of color blindness is said to be lower in  
females). Actually, if you want to learn more about the topic of how  
humans perceive color and the history of making colors, I highly  
recommend a BBC documentary I came across just yesterday called  
"Cracking the Colour Code". Very entertaining.

John Oreopoulos

PS: I used both spellings of the word color in the subject line so  
that others can find this thread easily in the future.

No virus found in this incoming message.
Checked by AVG - www.avg.com
Version: 8.5.423 / Virus Database: 270.14.25/2450 - Release Date:
10/21/09 16:44:00

No virus found in this incoming message.
Checked by AVG - www.avg.com
Version: 8.5.423 / Virus Database: 270.14.24/2449 - Release Date:
10/21/09 16:44:00


This communication is intended only for the named recipient and may contain information that is confidential, legally privileged or subject to copyright; the Ludwig Institute for Cancer Research Ltd does not waive any rights if you have received this communication in error.
The views expressed in this communication are those of the sender and do not necessarily reflect the views of the Ludwig Institute for Cancer Research Ltd.

[W. Chan]

You can try using the tools for designing accessible web sites e.g., CCA
or Accessibility Color Wheel.

http://www.visionaustralia.org.au/info.aspx?page=628
http://gmazzocato.altervista.org/colorwheel/wheel.php

You can pick 2 colors and then see if there is enough color difference and
brightness difference for the 3 most common color defects.  However, it
seems like having individual channels in greyscale as Cam suggested is the
best way to go.  It is rather difficult to find more than 2 colors that
will satisfy everyone because the background is usually grey and that
puts extra constraint in the possible choices.

On Wed, 21 Oct 2009, John Oreopoulos wrote:

> Dear list,
>
> While preparing some confocal imaging results for publication just recently, I
> was informed by one of my PhD committee members that I should try to present
> my multi-dimensional microscopy images in such a way that they are easy to see
> by people who are color blind. Ie: you should choose colors for your single
> monochrome channel images such that when viewed in a merged/overlay image they
> convey the same information as you would see in a standard green/red overlay
> image for colocalization, etc. I've tried to read up a bit on this topic on
> the web and I even searched the confocal listserv archive, but I could find no
> definitive set of rules or guidelines for going about this. The only
> discussion I could find about this on the listserv dates back to 1996 and
> given that imaging has become even more prevalent in today's biological
> sciences since then, I'm wondering if anyone on here now can direct me to a
> good source or set of journal guidelines for publishing color image overlays
> bearing in mind that some of the readers will be color blind . Also, does
> anyone know of any image processing utilities or plugins (ImageJ?) that can
> covert a full color image into a version that is easier to interpret by
> someone who is color blind?
>
> I've come to realize this is even more important than I previously thought
> given that it seems that almost 1 in 10 males worldwide is color blind (the
> occurrence of color blindness is said to be lower in females). Actually, if
> you want to learn more about the topic of how humans perceive color and the
> history of making colors, I highly recommend a BBC documentary I came across
> just yesterday called "Cracking the Colour Code". Very entertaining.
>
> John Oreopoulos
>
> PS: I used both spellings of the word color in the subject line so that others
> can find this thread easily in the future.

--
Pang (Wai Pang Chan, [hidden email], PAB A087, 206-685-1519)
The Biology Imaging Facility (http://depts.washington.edu/if/)

[JOEL B. SHEFFIELD]

As a deuteranomolous microscopist, I come across this frustrating problem frequently in presentations.  For red/green images, which are a common pair, you can replace the red channel with magenta, by pseudocoloring the red channel as red and blue. The magenta/green combination yields white when there is properly balanced colocalization.   I described this approach some time ago in Microscopy Today, and also developed a macro for ImageJ that carries out the same process automatically.  For full color images, of course, the process would be more complex. 

Joel

On Wed, Oct 21, 2009 at 10:26 PM, John Oreopoulos <[hidden email]> wrote:

Dear list,

While preparing some confocal imaging results for publication just recently, I was informed by one of my PhD committee members that I should try to present my multi-dimensional microscopy images in such a way that they are easy to see by people who are color blind. Ie: you should choose colors for your single monochrome channel images such that when viewed in a merged/overlay image they convey the same information as you would see in a standard green/red overlay image for colocalization, etc. I've tried to read up a bit on this topic on the web and I even searched the confocal listserv archive, but I could find no definitive set of rules or guidelines for going about this. The only discussion I could find about this on the listserv dates back to 1996 and given that imaging has become even more prevalent in today's biological sciences since then, I'm wondering if anyone on here now can direct me to a good source or set of journal guidelines for publishing color image overlays bearing in mind that some of the readers will be color blind . Also, does anyone know of any image processing utilities or plugins (ImageJ?) that can covert a full color image into a version that is easier to interpret by someone who is color blind?

I've come to realize this is even more important than I previously thought given that it seems that almost 1 in 10 males worldwide is color blind (the occurrence of color blindness is said to be lower in females). Actually, if you want to learn more about the topic of how humans perceive color and the history of making colors, I highly recommend a BBC documentary I came across just yesterday called "Cracking the Colour Code". Very entertaining.

John Oreopoulos

PS: I used both spellings of the word color in the subject line so that others can find this thread easily in the future.

--


Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs

[simon walker (BI)]

One of the more comprehensive discussions on this topic can be found here:
http://jfly.iam.u-tokyo.ac.jp/color/index.html


Simon

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of John Oreopoulos
Sent: 22 October 2009 03:26
To: [hidden email]
Subject: Proper presentation of fluorescence microscopy images for people who are color blind / colour blind

Dear list,

While preparing some confocal imaging results for publication just  
recently, I was informed by one of my PhD committee members that I  
should try to present my multi-dimensional microscopy images in such  
a way that they are easy to see by people who are color blind. Ie:  
you should choose colors for your single monochrome channel images  
such that when viewed in a merged/overlay image they convey the same  
information as you would see in a standard green/red overlay image  
for colocalization, etc. I've tried to read up a bit on this topic on  
the web and I even searched the confocal listserv archive, but I  
could find no definitive set of rules or guidelines for going about  
this. The only discussion I could find about this on the listserv  
dates back to 1996 and given that imaging has become even more  
prevalent in today's biological sciences since then, I'm wondering if  
anyone on here now can direct me to a good source or set of journal  
guidelines for publishing color image overlays bearing in mind that  
some of the readers will be color blind . Also, does anyone know of  
any image processing utilities or plugins (ImageJ?) that can covert a  
full color image into a version that is easier to interpret by  
someone who is color blind?

I've come to realize this is even more important than I previously  
thought given that it seems that almost 1 in 10 males worldwide is  
color blind (the occurrence of color blindness is said to be lower in  
females). Actually, if you want to learn more about the topic of how  
humans perceive color and the history of making colors, I highly  
recommend a BBC documentary I came across just yesterday called  
"Cracking the Colour Code". Very entertaining.

John Oreopoulos

PS: I used both spellings of the word color in the subject line so  
that others can find this thread easily in the future.

[Michael Weber-4]

Dear John,

presenting the single channels in greyscale is the most sensible way to
go. The red-green merge does not make much sense to show evidence for
colocalization, you need proper numbers (Pearson, Manders coefficient
etc.). A black and white table/chart can be read by color-blind people
without problems.

Follow the link to a presentation about that, if you are interested:
https://ifn.mpi-cbg.de/wiki/ifn/images/1/1e/QuantitativeColocAnalysis0709small.pdf

Michael

> Dear list,
>
> While preparing some confocal imaging results for publication just
> recently, I was informed by one of my PhD committee members that I
> should try to present my multi-dimensional microscopy images in such
> a way that they are easy to see by people who are color blind. Ie:
> you should choose colors for your single monochrome channel images
> such that when viewed in a merged/overlay image they convey the same
> information as you would see in a standard green/red overlay image
> for colocalization, etc. I've tried to read up a bit on this topic on
> the web and I even searched the confocal listserv archive, but I
> could find no definitive set of rules or guidelines for going about
> this. The only discussion I could find about this on the listserv
> dates back to 1996 and given that imaging has become even more
> prevalent in today's biological sciences since then, I'm wondering if
> anyone on here now can direct me to a good source or set of journal
> guidelines for publishing color image overlays bearing in mind that
> some of the readers will be color blind . Also, does anyone know of
> any image processing utilities or plugins (ImageJ?) that can covert a
> full color image into a version that is easier to interpret by
> someone who is color blind?
>
> I've come to realize this is even more important than I previously
> thought given that it seems that almost 1 in 10 males worldwide is
> color blind (the occurrence of color blindness is said to be lower in
> females). Actually, if you want to learn more about the topic of how
> humans perceive color and the history of making colors, I highly
> recommend a BBC documentary I came across just yesterday called
> "Cracking the Colour Code". Very entertaining.
>
> John Oreopoulos
>
> PS: I used both spellings of the word color in the subject line so
> that others can find this thread easily in the future.

[Daniel James White]

John,

maybe this helps,

in Fiji (is just imageJ - batteries included)
from
http://pacific.mpi-cbg.de

try

Image - Color - Simulate colour blindness

Dan


On Oct 22, 2009, at 7:04 AM, CONFOCALMICROSCOPY automatic digest  
system wrote:

> Date:    Wed, 21 Oct 2009 22:26:21 -0400
> From:    John Oreopoulos <[hidden email]>
> Subject: Proper presentation of fluorescence microscopy images for  
> people who are color blind / colour blind
>
> Dear list,
>
> While preparing some confocal imaging results for publication just
> recently, I was informed by one of my PhD committee members that I
> should try to present my multi-dimensional microscopy images in such
> a way that they are easy to see by people who are color blind. Ie:
> you should choose colors for your single monochrome channel images
> such that when viewed in a merged/overlay image they convey the same
> information as you would see in a standard green/red overlay image
> for colocalization, etc. I've tried to read up a bit on this topic on
> the web and I even searched the confocal listserv archive, but I
> could find no definitive set of rules or guidelines for going about
> this. The only discussion I could find about this on the listserv
> dates back to 1996 and given that imaging has become even more
> prevalent in today's biological sciences since then, I'm wondering if
> anyone on here now can direct me to a good source or set of journal
> guidelines for publishing color image overlays bearing in mind that
> some of the readers will be color blind . Also, does anyone know of
> any image processing utilities or plugins (ImageJ?) that can covert a
> full color image into a version that is easier to interpret by
> someone who is color blind?

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

[Judy Trogadis]

Look at this website - you can upload an image to check online but also has a plugin to download into Photoshop which shows the colours through the different types of colour blind eyes. Also has a "Daltonization" algorithm which will take the existing colours and correct them appropriately to be visible to all.

http://www.vischeck.com/

Judy



Judy Trogadis
Bio-Imaging Coordinator
St. Michael's Hospital, 7Queen
30 Bond St.
Toronto, ON M5B 1W8, Canada
ph:  416-864-6060  x6337
pager: 416-685-9219
fax: [phone]
[hidden email]


>>> John Oreopoulos <[hidden email]> 10/21/2009 10:26 PM >>>
Dear list,

While preparing some confocal imaging results for publication just  
recently, I was informed by one of my PhD committee members that I  
should try to present my multi-dimensional microscopy images in such  
a way that they are easy to see by people who are color blind. Ie:  
you should choose colors for your single monochrome channel images  
such that when viewed in a merged/overlay image they convey the same  
information as you would see in a standard green/red overlay image  
for colocalization, etc. I've tried to read up a bit on this topic on  
the web and I even searched the confocal listserv archive, but I  
could find no definitive set of rules or guidelines for going about  
this. The only discussion I could find about this on the listserv  
dates back to 1996 and given that imaging has become even more  
prevalent in today's biological sciences since then, I'm wondering if  
anyone on here now can direct me to a good source or set of journal  
guidelines for publishing color image overlays bearing in mind that  
some of the readers will be color blind . Also, does anyone know of  
any image processing utilities or plugins (ImageJ?) that can covert a  
full color image into a version that is easier to interpret by  
someone who is color blind?

I've come to realize this is even more important than I previously  
thought given that it seems that almost 1 in 10 males worldwide is  
color blind (the occurrence of color blindness is said to be lower in  
females). Actually, if you want to learn more about the topic of how  
humans perceive color and the history of making colors, I highly  
recommend a BBC documentary I came across just yesterday called  
"Cracking the Colour Code". Very entertaining.

John Oreopoulos

PS: I used both spellings of the word color in the subject line so  
that others can find this thread easily in the future.

[David Stephens]

Tim Levine wrote an excellent piece for the British Society for Cell Biology
newsletter on this a couple of years ago. It very nicely summarizes some of the
key issues, notably based around some of the links already highlighted in the list.
Its freely available on the web at:
http://www.bscb.org/?url=newsletter/autumn2007/colourfigs

David Stephens
Department of Biochemistry
University of Bristol
School of Medical Sciences
University Walk
BRISTOL, UK
BS8 1TD
http://www.bristol.ac.uk/biochemistry/stephens/index.html