ImageJ

At the IEEE Symposium on Biomedical Imaging (ISBI) 2012, a team led by Erik Meijering and Jean-Christophe Olivo-Marin organized a grand challenge competition in particle tracking.

14 popular algorithms and software implementations for object tracking and particle tracking in fluorescence microscopy images have been objectively compared on 48 data sets mimicking the motion of viruses, endosomes, single receptors, and microtubule-dependent transport for different object densities and image qualities (SNR).

The results have now been published in the open-access article:

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. http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2808.html

Ivo Sbalzarini's tracking algorithm as implemented in the MOSAICsuite for Fiji ("Method 1" in the paper) scores very high. In many cases, it is among the top-three performing methods and it is very fast (see Figure 3 in the paper). It performs particularly well in the case for which it has originally been designed: prior-free random motion of viruses. Moreover, its graphical user interface and low number of parameters render it particularly easy to use, thanks to the system integration of Fiji.

Prompted by the competition results, we are currently extending the algorithm with additional motion models for directed and constant-speed motion, which should further improve performance, e.g., on the "microtubules" data set. A new release is planned soon and will be distributed through the MOSAIC Fiji Update Site!

The algorithm has originally been published in:

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.