Extending TrackMate for Omnipose

[marieanselmet]

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]

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]

Currently being done here:
trackmate-sc/TrackMate-Cellpose#8