I released the LUT finder: A plugin to see all your ImageJ / Fiji LUTs in a table with previews, auto generated descriptions and filtering! You can try it with the KTZ_LUTs update site or from github.com/kwolbachia/L.... I'm looking for your feedbacks! #FluorescenceFriday #MicroscopyMonday - ThreadSky

kwolbachia.bsky.social • 47 days ago

I released the LUT finder: A plugin to see all your ImageJ / Fiji LUTs in a table with previews, auto generated descriptions and filtering! You can try it with the KTZ_LUTs update site or from https://github.com/kwolbachia/LUTs_Finder. I'm looking for your feedbacks!

#FluorescenceFriday #MicroscopyMonday

Comments

dornan.bsky.social•47 days ago

📌

grocottlab.bsky.social•47 days ago

This looks fab Kevin! Is it possible to incorporate a descriptor to indicate if they’re colourblind friendly (similar to the linear & monochrome descriptors)? Not sure how much work that would be.

kwolbachia.bsky.social•47 days ago

Thanks! Well it's a bit tricky to assess individual LUT colorblind friendliness.. It all depends on the usage and combinaisons of LUTs. I considered the possibility to add a deuteranopia simulation preview but it was getting messy. After all there are many options to check compatibility already :)

joachimgoedhart.bsky.social•47 days ago

I've been wondering whether it would be possible to come up with some metric, e.g. the distance between the LUT and the colorblind simulated LUT. Ideally, this distance would be zero, right?

kwolbachia.bsky.social•46 days ago

I hadn't thought of that option, but I want to keep the plugin as easy to use as possible so the check has to be intuitive

joachimgoedhart.bsky.social•46 days ago

Sure, I totally understand!

grocottlab.bsky.social•47 days ago

A toggle button(s) for deuteranopia (etc) that swaps out the LUT gradient could work - I’m guessing that’s what the “Gray check” button is doing? I’ll definitely check this out.

kwolbachia.bsky.social•46 days ago

Yeah it's more to check for linearity and contrast compared to gray, but a similar button for colorblindness simulation would be slower and I would need to take code from elsewhere, I'll find something ;)

grocottlab.bsky.social•47 days ago

We developed a combined channels & levels tool (“Channels Plus”) for Fiji with a button for selecting between the built-in LUTs. It would be fab if we could use our LUT button to launch your plugin instead.

kwolbachia.bsky.social•46 days ago

I tried and really liked your plugin! but it's not yet fully usable I think, the limitation of 8 bit images for example, I wanted to write some issues on github, I will asap!

luis-aj-alvarez.bsky.social•47 days ago

Very nice ! We had some requests about colour blind alternatives for the “rainbow” LUT used for FLIM or to get multiple FLIM channels. I could not find a solution. Now that we can get 15 markers at once I anticipate similar question for colour blind friendly set. Any ideas ? 🙈

joachimgoedhart.bsky.social•47 days ago

That would definitely be useful, it's one of my main issues when handling the Stellaris. There are several good options:
Source: https://thenode.biologists.com/parrot-lut/research/
I'm happy to discuss and be a test-person (I'm red colorblind)!

kwolbachia.bsky.social•46 days ago

Do you have an example image? we could suggest some options ;)

luis-aj-alvarez.bsky.social•45 days ago

For the classical fluorescence lifetime rainbow LUT please have a look at fig 1b here: https://www.nature.com/articles/d42473-020-00364-w

kwolbachia.bsky.social•44 days ago

Well, this is a great example of a colormap/figure that is not colorblind-friendly! 😅 I'm not familiar with FLIM but I assume the lifetime image is represented as a linear grayscale value? If so, I think it would make more sense to use a linear colormap, like mpl-magma. Could you share a raw image?

luis-aj-alvarez.bsky.social•45 days ago

For the 15 colours please look at fig 3 a here : https://www.nature.com/articles/d42473-024-00260-7

We tend to show subsets of markers at a time as well. Fig 3 b-g. But also fig 2 here https://www.nature.com/articles/d42473-024-00262-5

kwolbachia.bsky.social•44 days ago

https://bsky.app/profile/kwolbachia.bsky.social/post/3lb5c6fuql22t
impossible to be safe with more than 3 composite channels,
So in a publication the best move will always be to show individual channels as gray (best of the best contrast) and then be creative for overlays :)

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