New tool, Colorblind Bar

Hi,

This is an Action bar to deal with cool images or videos when they are not colorblind friendly :

Pure red green blue are bad choice for two reasons,
all three kind of colorblind folks won’t be able to differentiate clearly the 3 channels :

and for normal vision, in terms of luminance red and blue are dark, we don’t see them well.

The best response to both problems is to use Magenta Yellow Cyan (CMY) VS Red Green Blue (RGB)
With these everyone see everything as well as possible :

With only two channel images you have more room for creativity to be compatible but two good choices are Green with Magenta and Orange with Blue (not the pure one, a light Blue).

2chCB22chCB

But RGB remains a common practice, I think because it fits the wavelength of fluorescence and mostly it’s the default parameters in most software.

Provided they are pure RGB, if you save an image or video from the web or a publication and import it on ImageJ / Fiji, you can easily convert it back to a three channel hyperstack. This is the “Make Composite” command.
From there you can choose whatever LUT (false color) and contrast you want!

A last thing is that, as we badly see Red and Blue, shared images are most of the time highly saturated. If you try to convert these to CMY you will get a degraded result with big patches of white.
A solution is semi-CMY : for example in rgb values Magenta is (255,0,255) but if you use (128,0,128) and same principle for Cyan and Yellow, it prevents unwanted saturation :

You can adjust contrast or gamma yourself afterward.

Here’s what the Colorblind Bar does :

Capture d’écran 2021-06-07 à 01.25.53

  • The “convert” button applies the semi-CMY LUTs to the active image.
    it works on rgb and stacks

  • the “B&C” button just opens the Brightness and Contrast tool of ImageJ next to your image.

  • The “RGB / Composite” button convert the active image from one type to the over.

  • The “test CB” create a montage with the 3 big types of colorblindness simulated on your image.
    (I think this works only on Fiji)

  • A “reorder LUTs” button

  • Finally the “invert” button will convert a RGB image to an inverted CMY one. (It’s fun to click it multiple times)

You need the awesome ActionBar plugin from @jerome to use this tool.

Then if you want to try it you can run this macro code :

run("Action Bar",File.openUrlAsString("https://git.io/JZUZw"));

Or to install it you can get the Colorblind_Bar.ijm file there and place it on the plugin/ActionBar directory of your ImageJ or Fiji.

I hope you like it and I look forward to your feedback,

Kevin

15 Likes

Here’s a short demo video

Thanks for sharing Kevin. Am i the only one getting this error?
I added the Colorblind_bar.ijm to Action bar folder, and then tried to use it from plugins
image

Hi Yunan,
Thanks for your interest in my tool
I think you tried to download the Colorblind_bar.ijm file by right clicking on it but this way gives you a html file with the exact same name… tricky I know.
You made me realize how unpractical it is to get the file from this GitHub repository it’s my mistake.
I should have made a specific repository for this tool.

Please try to download this file directly here :
Colorblind_Bar.ijm (6.2 KB)

And please be careful to name the directory exactly this way : ActionBar

It should work!
Sorry for that if others had the same problem…

Best,
Kevin

Dear Kevin,
I am a novice user of Fiji. I don’t know anything about action bars, etc. However, I am colorblind and would like to use a colorblind tool. I downloaded the Colorblind_Bar.ijm (6.2 KB), but I don’t know what to do next. Could you give me some direction, if it is not too much trouble?
Monty

Thanks Kevin for sharing,

Very useful tool!

Still, I am able to open and use other bars but not Colorblind_Bar.
I get a small new window with nothing in it. No errors though.

imagen

Surely I have something badly configured!

Any hint?

Thanks

Javier

Hi Monty,
No problem :
first you need to get the Action Bar plugin, for that in fiji you have to go in Help/Update…
Then click on “manage update sites” and check the IBMP-CNRS
Then “close” and “Apply changes”
when it’s done close Fiji.
Then you need to find the “plugin” directory in the Fiji app files, and create a new directory named ActionBar (exactly typed like this)
Finally, place the Colorblind_Bar.ijm file in this ActionBar directory.
If you start Fiji again, you should be able to open the bar in plugins/ActionBar/Colorblind Bar.

Please tell me if everything goes well :slight_smile:

Best,

Kevin

Hi janvier,

I don’t really know for this one…
Can you please check if updating your imageJ and the IBMP-CNRS update site could help?

Best,

Kevin

Thanks Kevin,

I was just trying that. I have Action Bar installed for a long time. Now I added the IBMP-CNRS update site. At starting FIJI there is a log file warning that there is a duplicate plugin.
Sould I delete plugin: C:\FIJI\plugins\ActionBar\action_bar.jar?
I may try a fresh FIJI installation and install Actin Bar through the IBMP-CNRS update site.
Thanks
Javier

HI again,

I did that (install a fresh FIJI and include the IBMP-CNRS update site).

I can now run Colorblind_Bar and my own bars altogether:
imagen

Thanks again!
Javier

1 Like

Thanks - I will give it a try when I have a bit of time. Much appreciate your getting back to me.
Monty

Kévin Terretaz K_Taz
June 11

Hi Monty,
No problem :
first you need to get the Action Bar plugin, for that in fiji you have to go in Help/Update…
Then click on “manage update sites” and check the IBMP-CNRS
Then “close” and “Apply changes”
when it’s done close Fiji.
Then you need to find the “plugin” directory in the Fiji app files, and create a new directory named ActionBar (exactly typed like this)
Finally, place the Colorblind_Bar.ijm file in this ActionBar directory.
If you start Fiji again, you should be able to open the bar in plugins/ActionBar/Colorblind Bar.

Please tell me if everything goes well :slight_smile:

Best,

Kevin


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Previous Replies

| Javier fjavier
June 11 |

  • | - |

Thanks Kevin for sharing,

Very useful tool!

Still, I am able to open and use other bars but not Colorblind_Bar.
I get a small new window with nothing in it. No errors though.

Surely I have something badly configured!

Any hint?

Thanks

Javier

| Monty Krieger Monty
June 11 |

  • | - |

Dear Kevin,
I am a novice user of Fiji. I don’t know anything about action bars, etc. However, I am colorblind and would like to use a colorblind tool. I downloaded the Colorblind_Bar.ijm (6.2 KB), but I don’t know what to do next. Could you give me some direction, if it is not too much trouble?
Monty

Kévin Terretaz K_Taz
June 8

Hi Yunan,
Thanks for your interest in my tool
I think you tried to download the Colorblind_bar.ijm file by right clicking on it but this way gives you a html file with the exact same name… tricky I know.
You made me realize how unpractical it is to get the file from this GitHub repository it’s my mistake.
I should have made a specific repository for this tool.

Please try to download this file directly here :
Colorblind_Bar.ijm (6.2 KB)

And please be careful to name the directory exactly this way : ActionBar

It should work!
Sorry for that if others had the same problem…

Best,
Kevin

Thanks for sharing Kevin. Am i the only one getting this error?
I added the Colorblind_bar.ijm to Action bar folder, and then tried to use it from plugins
image

Kévin Terretaz K_Taz
June 7

Here’s a short demo video

twitter.com

kWolbachia@kWolbachia

This is a tool for #ImageJ #Fiji to easily convert red-green-blue images to magenta-yellow-cyan for #colorblind folks find the description there : https://t.co/s2mIF82irO https://t.co/FfQD4Q7dmn
6:07 PM - 6 Jun 2021 48 15


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Monty Krieger

Whitehead Professor
Biology Department
Massachusetts Institute of Technology
Room 68-483
77 Massachusetts Ave
Cambridge, MA 02139
Tel.: 617-253-6793
Fax: 617-258-5851
EM: :Krieger@MIT.edu

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