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allen-cell-animated / agave

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Would be very useful for biologists if channels could also be given a Look-Up Table (LUT) instead of a solid color #207

Open SergeEParent opened 3 months ago

SergeEParent commented 3 months ago

Use Case

Labeling segmentations with different values is common and being able to given different values different colors (like the 16 color LUT in FIJI / ImageJ) would be very useful for validation / visualization and would be especially useful for tracking analyses or object counting operations.

Solution

Ideally would have some pre-set LUTs one could pick from when clicking on the color of a channel to change it and also have the option to create your own. Also the ability to have a small window next to your cursor (that can be toggled on/off) containing the value of the pixel that you are hovering over would be very useful for using AGAVE for validating outputs from image analysis workflows.

Alternatives

If we just had some pre-set LUTs that were picked from FIJI / ImageJ that would be very helpful too.

toloudis commented 3 months ago

Thanks for posting here! I actually have begun work on exactly this feature. It's not a very quick/simple thing but there is something in the works. I will give you some more info in coming weeks. (When I get back from siggraph conference and have some time!)

SergeEParent commented 3 months ago

Oh awesome! I guess not, even creating and assigning colormaps in matplotlib can be a hassle so I can't even imagine how much more involved it would be for a rendering program.

toloudis commented 3 months ago

The tricky part is in making sure the colormap gets applied in a sensible way that is predictable, for this renderer. I will be able to give you an agave build that has most of the thing implemented so you can try it out 😄

toloudis commented 3 months ago

linking to #156