I’ve been trying to use the Trackmate tracker node to follow cell nuclei and spots. Everything works fine for spots but I run into a strange problem when tracking nuclei.
For every frame I can generate a segment bitmask and all features. However, when I run the output of the segment features node into the Trackmate tracker I lose a few time frames. Trackmate just produces a blank label image for those time frames.
From playing around I know that it is something in the image that is causing Trackmate to miss the frames as it will always happen to the same frames. However, there is no obvious culprit and simple things like Gaussian blurring the image doesn’t solve the problem.
Does anyone know what would cause the Trackmate node to miss these frames?
I changed the alternative linking cost factor settings but that doesn’t improve the situation.
Workflow attached below with an example image:
Workflow: Trackmate_missing_frames.knwf (1.7 MB)
Example image: Timelapse_nuc_foci-1.tif (1.9 MB)