Object tracking with TrackMate




I’ve been attempting to use TrackMate in Fiji to automatically track individually-housed tadpoles over 10-minute video segments. I get all the way through the process just fine, but at the end I notice that my spots are “jumpy” (IE shift a few pixels in random directions) fairly frequently. This results in a LOT of tracks (given 10-minutes of video) that are very small. Is there a way to filter out small jumps like this? The track editing is not super amateur-friendly, so I’m having trouble even selecting tracks like this to remove, or identifying which trackIDs they are. Anything helps!

I’ve recorded 10 minutes of video at 1080p and 60fps and altered the video to 768p and 15 fps because the tadpoles don’t move fast enough to require that sort of resolution. The images are still “jumpy” if run in the higher quality.



Welcome to the forum, @Turner_DeBlieux !
Sorry that your post has been waiting unanswered for so long.

It would be good to find out why you observe these “jumps”. You might be able to do some filtering to remove noise before starting the tracking. It’ll certainly help here if you post a few example frames.

Also, you can maybe use less restrictive parameters for tracking (such as allowing a higher frame gap and a larger max distance for gap closing) to avoid that tracks end up in very small segments.


Thanks for the reply, @imagejan !
I thought about posting frames for reference, but when I run tracking on segments of frame, the points don’t always jump. I also notice that the video doesn’t always jump in the same place. There doesn’t seem to be any sort of visible shift in the image when the points “jump”, so I can’t really tell what is instigating it. Basically, when I run tracking, my problem isn’t reproducible, or at least not on specific segments of video.

I’ll certainly try higher frame gaps and a larger max distance, but I believe the problem is at the point detection stage and not in the tracking itself. I’m more concerned with whether there is a way to indicate that short tracks should be excluded, or if it’s possible to make spots that “jump” corrected without manually moving each one? The objects don’t actually move at all, just the spots.

I’ve attached about 1 minute equivalent of my footage as a .gif. if that isn’t an appropriate format please let me know, I’ve never had to upload video here before.