Perceptibly uniform luts #6398
Open
Perceptibly uniform luts #6398
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This was referenced Jul 19, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
What this PR does
I added perceptibly uniform LUTs. I started with the LUTs from the viridis family that I found in Fiji, but I extended it to other LUTs used in R: https://github.com/sjmgarnier/viridis
viridis,magma,inferno, andplasmawere created by Stéfan van der Walt (@stefanv) and Nathaniel Smith (@njsmith). presentation of viridis by their authors at SciPy 2015cividis, a corrected version of 'viridis' for color vision deficiency (Nuñez, Anderton, Renslow 2018, https://doi.org/10.1371/journal.pone.0199239)makoandrocketcreated for seaborn (https://seaborn.pydata.org/tutorial/color_palettes.html#perceptually-uniform-palettes)turbodeveloped by Anton Mikhailov to address the shortcomings of the Jet rainbow color map such as false detail, banding and color blindness ambiguity. (https://ai.googleblog.com/2019/08/turbo-improved-rainbow-colormap-for.html).Testing this PR
required setup
An OMERO.server
actions to perform
Add the new LUTs to
OMERO.server/lib/scripts/lutsexpected observations
The LUTs become available for all tools (but there is no preview of the LUT intensity from the dropdown lists):
Related reading
Link to cards, tickets, other PRs:
background for understanding this PR
The viridis LUT family have been created with perception uniformity as criterion. They are the standard of matplotlib for some time now and are also packaged with Fiji. I think it would be good for users to find them also by default in OMERO.
The cividis is the colorblind adjusted version of viridis which also has been integrated in Fiji (https://forum.image.sc/t/new-lut-for-fiji-cividis/7467).
Seaborn also offers two perceptually uniform LUT, mako and rocket, part of the "viridis" package for R.
Finally, turbo is an alternative to jet that is also more colorblind-friendly and gradual.
what this PR assists, fixes, or otherwise affects
This will package new LUTs with OMERO.server. The LUTs will become available for other OMERO components (web, iviewer, figure, insight) but will not display preview until related PR are merged and deployed.