New default colormap for TrackMate?

— Community feedback required (please see below) —

I recently got around finalizing a long-pending pull request implementing an improvement of visualization in TrackMate: allow choosing the colormap for all visualizations across TrackMate.


Up to now, TrackMate defaults to the Jet colormap (also known as Rainbow), which arguably is a poor choice for visualizing a continuous scale. There’s lots of literature about this online, for example:


So let’s make the choice of color map configurable :slight_smile:

Still we have a choice to make:

  • should the new default colormap change from Jet to something more sensible like Viridis, which possibly changes the (visual) output of existing workflows in a backward-incompatible way?
    or:
  • should the default stay Jet to ensure backwards compatibility, which requires users to actively change the option to use a different (likely more suitable) colormap.

From the discussion on the pull request, you’ll see that @tinevez and I didn’t agree on this choice :wink:

So, if you’ve read until here: what’s your opinion?

:question::question::question:

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Thanks for putting in the time on this @imagejan! I don’t have strong feelings but more wanted to add some thoughts as a Trackmate fan.

My feeling is that having the ability to customise it is the most important thing (thanks!). I can understand the reason for pro-actively changing the default, but I also find Viridis fantastically boring, quite dour and difficult to discern against a black background.

I’ve also rarely needed to use the LUT to discern very close levels in trackmate, so many of the arguments against jet’s use in continuous scale break down (unlike say, a jet-coded ratiometric image where you truly see the continuous scale and thus need a better LUT).

If I understand correctly that this change only affects the visual display, perhaps Turbo would be a better default choice. That way existing workflows still have a Red high, blue low scale.

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How configurable would the default be (a user setting?) and how would it impact macros? If it is easy enough to set, then I’d go with a new default. Best would be if, once set, it stayed the way that user had set it. Then anyone who wants to stick with Jet only needs to change it once.

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Thanks for your feedback, @Research_Associate!

Yes, it’s a user setting in Edit > Options > TrackMate… – changing its value needs a restart of TrackMate (but no full ImageJ restart) to take effect.

Macros/script would be unaffected – unless they rely on a certain color value in the (flattened) overlay output, which isn’t a common use case, I assume.

Yes, that’s how I implemented it (using a SciJava OptionsPlugin).

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Ok so here is my part.

@imagejan and I discussed and normally we would resolve this by chivalry joust me with a flail Jan with a sword but we decided on a poll instead.

Jan created a fantastic options system in TrackMate. A first option is the ability to choose the LUT for feature values, but we could imagine much more. We only are in slight disagreement over the choice fothe default LUT.

  • Jan wants the new viridis LUT as default.
  • I want to keep the old jet LUT as default.

This will be resolved as said above by a poll, not a brawl, after each party exposing their arguments,
Jan exposed his in favor of viridis, here are mine in favor of jet.


TrackMate is becoming an old plugin. Much to my wonder, it has a user base. New users arrive sometimes, and they find teaching materials, documentation and even training school where TrackMate usage is shown.

I am actually not in favor of jet, but in favor of not changing the default look and feel of TrackMate. This somewhat sub-par UI percolated through the ages and I wish not to disturb the existing users, nor surprise the new ones with a software that does not match the documentation.

And no I do not feel like redoing all the images on the documentation, or asking people to do so.

I knoweth yond jet is not a valorous lut.

But then, none is!

Jan remarks art valid, and the articles he linked to above hath’t a point. But then, what would beest a valorous lut? Viridis? Nay. Viridis is a sequential colormap. 't is well suited for features yond art intensive, such as the mean fluorescence intensity. As 't fades out for base values, 'twill reflect yond thither art dram emitters in the spot 't colors.

But jet is not yond. 't is actually a ‘misc’ colormap, like valorous for nothing belike. But if 't be true we stick to viridis, the coloring would beest inadequate to extensive favour values, like X position, the track index, etc.
So in reality, we needeth not just viridis, but many moo colormaps! Since nay colormap can beest valorous for all, viridis can not beest valorous for all. I therre fore judge 't nay better suited than jet to beest the default. But jet wast thither ere.

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I pray thee, most gracious reader, hear us out and make thee mind:

  • Keep jet the default colormap in TrackMate. :shield:
  • Make viridis the new default in TrackMate.:dagger:

0 voters

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Well, as @petebankhead could tell you, I am all about breaking the wheel. I’d rather encourage people to use “better” colormaps because all too many will simply use the default in their rush to results.

A third, potentially even worse option (if you are providing a selection of colormaps), would be to have no default color map at all. Simply a warning popup pointing out that a choice needs to be made (if the user tries to ignore that part), and that there is a selection to choose from. More annoying, no doubt, but also potentially better for users in the long run.

Shrug, dunno.

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