u-track - an open-source tracking tool in OMERO
u-track is a multiple-particle tracking Matlab software that is designed to (1) track dense particle fields, (2) close gaps in particle trajectories resulting from detection failure, and (3) capture particle merging and splitting events resulting from occlusion or genuine aggregation and dissociation events. Its core is based on formulating correspondence problems as linear assignment problems and searching for a globally optimal solution.
Besides basic particle tracking described in Jaqaman et al. 2008, the software supports the features described in Applegate et al. 2011 for tracking microtubule plus end markers; and in Ng et al. 2012 for tracking fluorescently-labeled cell nuclei.
u-track is developed by the Laboratory for Computational Cell Biology at Harvard Medical School.