Tracking workflow output - big jumps in tracks

Dear all,

Recently, I have been using the tracking workflow in Ilastik to track migrating cells, which works rather well segmentation and tracking wise (thanks Ilastik =)).
The issue I have been running into, is that few tracks seem to make one or several big jumps (see histogram of step sizes and an example track). I have tried different combinations of tracking parameters, which ultimately did not change the output.

The tracking with learning workflow yields better results, since one can define a max. Distance. But there is no batch processing, making it rather cumbersome to track several videos.

Did anyone experience something similar or has any input on what one could try to get rid of these jumps?

Thanks a lot and best wishes,

Hi @DehioP,

welcome to the forum, first of all :slight_smile:

Have you tried to pin down in what situations those big jumps occur? I guess it depends a bit how one would react.

Good to read that tracking with learning works slightly better for you. I was surprised, to be honest, that batch processing was not enabled here. Glancing at the code I didn’t really find a reason. I’ve opened a PR to enable it. Let’s see if there’s any objections to that…


Hi @k-dominik,

Thanks for the warm welcoming and the push to enable batch processing the tracking with learning workflow =)

Many of these big jumps occur when the cells leave the field of view. I am tracking rather motile cells under an agarose pad, so these events happen rather frequently. In other cases it happens, when a new objects appears (due to under segmentation) and instead of assigning a new track, a trackID jumps to the new object (see the two pictures below of two consecutive images):

Thanks for your help!