TrackMate was just released in a first non-beta version.
TrackMate is a plugin dedicated to automated & manual spots tracking over time. It can deal with 2D & 3D data, and offers a few techniques for automated spot segmentation and particle-linking. It can deal with track splitting (e.g. when cells divide) or track merging. It also offers facilities for manual editing spots and tracks, exporting and inspecting results.
Also for developers, TrackMate was developed having in mind extensibility and flexibility. It is made so that if you wish to implement a new tracking or segmentation algorithm, you can re-use TrackMate components like the GUI, avoiding the burden of making one from scratch.
Hope you like it!
Jean-Yves, Nick, Johannes, Ricardo & Spencer