Update motile_toolbox version to v0.4.0 #117
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AnniekStok
reviewed
Dec 20, 2024
AnniekStok
reviewed
Dec 20, 2024
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It worked well on my computer! If the same label value was used at different time points, IDs were still assigned correctly (whereas it failed when I disabled the _has_duplicate_ids check). I quickly tried assigning the node id as label values and it looked as expected, so we can just make a colormap that maps the id to a track (or optionally, lineage) specific color.
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This is a minimal working update for our new toolbox version (no hypothesis dimension, unique segmentation IDs and int node ids). I did not actually update the visualization code to use the unique seg ids - it still relabels the segmentation before viewing. All the backend tests pass (in fact, most of the code changes were updating the tests to use the new integer node ids). I tested the UI components, but only a little.
I still want to implement a function that will check if the input labels layer has repeat IDs across time and relabels them (with the already implemented function in the toolbox), to make sure we can still input e.g. cellpose labels that have been predicted independently for each time point.
Edit: I added the function, and a function that will check if there are duplicate labels across time. Right now that lives in the RunEditor and just compares the labels of the first two frames of the segmentation, to avoid looping over the whole time series.