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trackmate-sc / TrackMate

TrackMate is your buddy for your everyday tracking.
https://imagej.net/plugins/trackmate
GNU General Public License v3.0
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Extending TrackMate for Omnipose #268

Closed marieanselmet closed 1 year ago

marieanselmet commented 1 year ago

Hello,

I am using TrackMate a lot to track bacteria cells. The quaIity of the segmentation is significantly better with Omnipose compared to Cellpose. I usually run Omnipose on my time-lapse data in Fiji with the BIOP plugin and then I load the labels to perform tracking in TrackMate. It would be more straightforward to directly segment the cells in TrackMate and I know other labs have the same issue so I was wondering if it would be easy to extend TrackMate for Omnipose ? If yes, where could I find the necessary documentation to implement it ?

Thanks in advance, Marie

tinevez commented 1 year ago

Hello Marie. The best approach would be to take inspiration from the existing TrackMate-Cellpose repo. It is small and shows how to interface with a (any) Python software. I am sure it can be readily applied to having omnipose run in TrackMate.

tinevez commented 1 year ago

Currently being done here: https://github.com/trackmate-sc/TrackMate-Cellpose/pull/8