I have videos for SMT analysis with tens of nuclei that I need to track separately. I have the subset of subROIs loaded in ImageJ ROI Manager. Now I am just tracking them one by one with TrackMate using the same parameters and saving the trajectories as .xml files. I wonder if there is a way to perform this operation in automatically in batch in the same video over the multiple subROIs using the same TrackMate parameters. I have already tried to create a macro in ImageJ but it is not working inside TrackMate.