u-track is a multiple-particle tracking software that is designed to:

U-track software is profiled in this issue of Nature Methods.
  1. Track dense particle fields
  2. Close gaps in particle trajectories resulting from detection failure
  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. The software is written in Matlab, and can be called either via a Graphical User Interface or command line.

For more information, please see Jaqaman et al., Nature Methods 5, pp. 695-702 (2008)