Tom-TBT commented 3 months ago

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

The LUTs viridis, magma, inferno, and plasma were created by Stéfan van der Walt (@stefanv) and Nathaniel Smith (@njsmith). presentation of viridis by their authors at SciPy 2015
The LUT cividis, a corrected version of 'viridis' for color vision deficiency (Nuñez, Anderton, Renslow 2018, https://doi.org/10.1371/journal.pone.0199239)
The LUTs mako and rocket created for seaborn (https://seaborn.pydata.org/tutorial/color_palettes.html#perceptually-uniform-palettes)
The LUT turbo developed 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/luts
expected observations The LUTs become available for all tools (but there is no preview of the LUT intensity from the dropdown lists):
- OMERO.iviewer
- OMERO web image viewer + preview tab
- OMERO.insight
- OMERO.figure

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.