coloring more than 3 channels

[Romain Guiet]

Dear all,

I’m writing today to give you the result of our thoughts and furthermore to get your feedback about a Look Up Table (LUT) issue.

For years, we used the Red (RGB 255;0;0), Green (RGB 0;255;0),  and Blue (RGB 0;0;255) as the standard LUTs for coloring our Black&White images, so that they can be merged together.
Thankfully, some of us highlighted an issue encountered by people with color blindness and proposed to use a combination of Cyan(RGB 0;255;255), Yellow (RGB 255;255;0) and Magenta (RGB 255;0;255).

We are now facing a new challenge due to the increasing number of simultaneous stainings and the microscope capabilites to distinguish them. So now, some of us would like to merge more than 3 colors in an image.
It’s quite difficult to use a combination of Red, Green, Blue, Cyan, Yellow, and Magenta because the last three are all dependant equally of two of the RGB colors.

And splitting the data into a combination of 3 colors images can lead to some confusion.
So, we thought about using a set of 6 maximaly separated colors in RGB space.

Please find below a link to an explanatory document (in pdf):
 https://drive.switch.ch/public.php?service=files&t=ce68ab027aeaea29fc56e2d5b35b301d
The list of numbers used to make the LUT (in pdf):
https://drive.switch.ch/public.php?service=files&t=9e33b36c9011034809fa5adb412934b6
(or xlsx):
https://drive.switch.ch/public.php?service=files&t=a57fc9f007b59255174c285ecce35e61
and you can download our LUTs here :
https://drive.switch.ch/public.php?service=files&t=c6d90322997d7be66fc6abe3e49daeb7
(and soon on our Update Site because we encounter some trouble today…)

We are looking forward to your inputs about this,

Cheers,

Romain



---------------------------------------------------------------
Dr. Romain Guiet
Bioimaging and Optics Platform (PT-BIOP)
Ecole Polytechnique Fédérale de Lausanne (EPFL)
Faculty of Life Sciences
Station 19, AI 0140
CH-1015 Lausanne

Phone: [+4121 69] 39629
http://biop.epfl.ch/
---------------------------------------------------------------

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael P Ellis]

Dear Romain,

Simultaneous display of more than 3 dieting colours on conventional display will always be problematic if there is a chance of interaction between multiple channels.

We tackled the problem by making it easy for the user  to interact with the rendering process.

Composite Adjuster is an ImageJ plugin that does just this. It’s free and you can get it from http://www.dsuk.biz/DSUK/SmartCaptureLite.html


Composite Adjuster Features
        • Interactive adjustment of normalisation levels for any ImageJ CompositeImage
        • Set channel colours for the low and high level (a colour ramp lut is generated between the two colours, control click on the histogram sliders)
        • Display levels as absolute values or as population percentages
        • Macro scriptable and recordable
        • Works with Byte, Short and Float CompositeImages
        • Works with 4 and 5 dimensional stacks with live update of histograms and ability to change settings whilst animation is in progress.

— Michael Ellis / Digital Scientific UK Ltd


For use the solution has simply been to provide as convenient means as possible to interact with the rendering by allowing for the easy selection of
On 21 Aug 2015, at 14:37, Romain Guiet <[hidden email]> wrote:

> Dear all,
>
> I’m writing today to give you the result of our thoughts and furthermore to get your feedback about a Look Up Table (LUT) issue.
>
> For years, we used the Red (RGB 255;0;0), Green (RGB 0;255;0),  and Blue (RGB 0;0;255) as the standard LUTs for coloring our Black&White images, so that they can be merged together.
> Thankfully, some of us highlighted an issue encountered by people with color blindness and proposed to use a combination of Cyan(RGB 0;255;255), Yellow (RGB 255;255;0) and Magenta (RGB 255;0;255).
>
> We are now facing a new challenge due to the increasing number of simultaneous stainings and the microscope capabilites to distinguish them. So now, some of us would like to merge more than 3 colors in an image.
> It’s quite difficult to use a combination of Red, Green, Blue, Cyan, Yellow, and Magenta because the last three are all dependant equally of two of the RGB colors.
>
> And splitting the data into a combination of 3 colors images can lead to some confusion.
> So, we thought about using a set of 6 maximaly separated colors in RGB space.
>
> Please find below a link to an explanatory document (in pdf):
> https://drive.switch.ch/public.php?service=files&t=ce68ab027aeaea29fc56e2d5b35b301d
> The list of numbers used to make the LUT (in pdf):
> https://drive.switch.ch/public.php?service=files&t=9e33b36c9011034809fa5adb412934b6
> (or xlsx):
> https://drive.switch.ch/public.php?service=files&t=a57fc9f007b59255174c285ecce35e61
> and you can download our LUTs here :
> https://drive.switch.ch/public.php?service=files&t=c6d90322997d7be66fc6abe3e49daeb7
> (and soon on our Update Site because we encounter some trouble today…)
>
> We are looking forward to your inputs about this,
>
> Cheers,
>
> Romain
>
>
>
> ---------------------------------------------------------------
> Dr. Romain Guiet
> Bioimaging and Optics Platform (PT-BIOP)
> Ecole Polytechnique Fédérale de Lausanne (EPFL)
> Faculty of Life Sciences
> Station 19, AI 0140
> CH-1015 Lausanne
>
> Phone: [+4121 69] 39629
> http://biop.epfl.ch/
> ---------------------------------------------------------------
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html