Particle Tracker is a 2D and 3D feature point-tracking tool for the automated detection and tracking of particle trajectories as recorded by video imaging in cell biology. It is part of the MosaicSuite, which also offers image segmentation, interaction analysis, and much more. The best way to install it is via the MOSAIC Fiji Update site, as described on the MOSAIC web page. The algorithm is described in Sbalzarini and Koumoutsakos (2005). A recent comparative study of many particle tracking tools has named this tool as one of the top choices: Chenouard et al. (2014).
I. F. Sbalzarini and P. Koumoutsakos. Feature Point Tracking and Trajectory Analysis for Video Imaging in Cell Biology, Journal of Structural Biology 151(2):182-195, 2005.
N. Chenouard, I. Smal, F. de Chaumont, M. Maska, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. G. Magnusson, J. Jalden, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J.-Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H.-W. Dan, Y.-S. Tsai, C. O. de Solorzano, J.-C. Olivo-Marin, and E. Meijering. Objective comparison of particle tracking methods. Nature Methods, 11(3):281–289, 2014.
 I. F. Sbalzarini and P. Koumoutsakos. Feature point tracking and trajectory analysis for video imaging in cell biology, J. Struct. Biol., 151(2):182-195, 2005
 N. Chenouard et al. Objective comparison of particle tracking methods, Nature Methods, 11(3):281-289, 2014