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Perceptibly uniform luts #6398

Merged
merged 4 commits into from
Nov 20, 2024
Merged

Perceptibly uniform luts #6398

merged 4 commits into from
Nov 20, 2024

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Tom-TBT
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@Tom-TBT Tom-TBT commented Jul 19, 2024

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

Testing this PR

  1. required setup
    An OMERO.server

  2. actions to perform
    Add the new LUTs to OMERO.server/lib/scripts/luts

  3. 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:

  1. 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.

  2. 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.

@will-moore
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Added the include label so this will get included in the server merge-ci deployment for testing...

@will-moore
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In webclient Preview panel and webgateway viewer, these LUTs are all showing up (without preview png) and are working fine:

Screenshot 2024-11-07 at 15 02 13

Same in Figure:

Screenshot 2024-11-07 at 15 05 44

@Tom-TBT
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Tom-TBT commented Nov 7, 2024

Same about the iviewer:
image

And the default omero-web viewer:
image

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@will-moore will-moore left a comment

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LUTs work in clients and don't cause any issues
The preview png is missing as expected - due to be fixed elsewhere

@jburel jburel merged commit 7157803 into ome:develop Nov 20, 2024
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3 participants