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

Benjamin Gallois and Raphaël Candelier

PLOS Computational Biology, 2021, vol. 17, issue 2, 1-19

Abstract: 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 https://github.com/FastTrackOrg/FastTrack and pre-compiled binaries for Windows, Mac and Linux are available at http://www.fasttrack.sh.Author summary: Many researchers and engineers face the challenge of tracking objects from very different systems across several fields of research. We observed that despite this diversity the core of the tracking task is very general and can be formalized. We thus introduce the notion of incursions—i.e. to what extent an object can enter a neighbor’s space—which can be defined on a statistical basis and captures the interplay between the acquisition rate, the objects’ dynamics and the geometrical characteristics of the scene, including density. To validate this approach, we compiled a dataset from various fields of Physics, Biology and human activities to serve as a benchmark for general-purpose tracking softwares. This dataset is open and accepts new submissions. We also developped a software called FastTrack that is able to track most of the movies in the dataset by proposing standard image processing tools and state-of-the-art implementation of the matching algorithm, which is at the core of the tracking task. Besides, it is open-source, simple to install and use and has an ergonomic interface to obtain fast and reliable results. FastTrack is particularly convenient for small-scale research projects, typically when the development of a dedicated software is overkill.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1008697

DOI: 10.1371/journal.pcbi.1008697

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