Use label images as input for TrackMate

Hi,

I used the #stardist fiji plugin and this awesome script from Martin to analyze an entire time series.

Is there a option to read label images (i.e. labelimage.tif (2.0 MB)) with #trackmate?

Eric

Hello

Ah this is a good idea. We just did the opposite with @Sebastien (output of TrackMate as label images).

I made a Python script for @philgi a while ago that does this. Can you check whether it works?
The discussion and script are here:

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I’ve successfully used this with StarDist-based segmentations. It works great!

By the way, better integration between StarDist and TrackMate (and its relatives) is on our todo list for StarDist. I’m not sure when we’ll find the time to get to it though.

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Pay me to do it :wink:

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Hey, I nearly asked @tinevez the same - got labelled cells output from CellProfiler that I would like to input into TrackMate (or Mastodon etc)…
it would be nice…

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