FastTrack: An open-source software for tracking varying numbers of deformable objects

B. Gallois , R. Candelier

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PLOS Computational Biology, 17, 2, 1-19
Published 11 Feb. 2021
DOI: 10.1371/journal.pcbi.1008697


Analyzing the dynamical properties of mobile objects requires to extract trajectories from recordings, which is often done by tracking movies. We compiled a database of two-dimensional movies for very different biological and physical systems spanning a wide range of length scales and developed a general-purpose, optimized, open-source, cross-platform, easy to install and use, self-updating software called FastTrack. It can handle a changing number of deformable objects in a region of interest, and is particularly suitable for animal and cell tracking in two-dimensions. Furthermore, we introduce the probability of incursions as a new measure of a movie’s trackability that doesn’t require the knowledge of ground truth trajectories, since it is resilient to small amounts of errors and can be computed on the basis of an ad hoc tracking. We also leveraged the versatility and speed of FastTrack to implement an iterative algorithm determining a set of nearly-optimized tracking parameters—yet further reducing the amount of human intervention—and demonstrate that FastTrack can be used to explore the space of tracking parameters to optimize the number of swaps for a batch of similar movies. A benchmark shows that FastTrack is orders of magnitude faster than state-of-the-art tracking algorithms, with a comparable tracking accuracy. The source code is available under the GNU GPLv3 at and pre-compiled binaries for Windows, Mac and Linux are available at

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Imagerie calcique et comportement du poisson zèbre et Danionella Cerebrum