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

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 ge...

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Detalles Bibliográficos
Autores principales: Gallois, Benjamin, Candelier, Raphaël
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7904165/
https://www.ncbi.nlm.nih.gov/pubmed/33571205
http://dx.doi.org/10.1371/journal.pcbi.1008697
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author Gallois, Benjamin
Candelier, Raphaël
author_facet Gallois, Benjamin
Candelier, Raphaël
author_sort Gallois, Benjamin
collection PubMed
description 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.
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spelling pubmed-79041652021-03-02 FastTrack: An open-source software for tracking varying numbers of deformable objects Gallois, Benjamin Candelier, Raphaël PLoS Comput Biol Research Article 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. Public Library of Science 2021-02-11 /pmc/articles/PMC7904165/ /pubmed/33571205 http://dx.doi.org/10.1371/journal.pcbi.1008697 Text en © 2021 Gallois, Candelier http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Gallois, Benjamin
Candelier, Raphaël
FastTrack: An open-source software for tracking varying numbers of deformable objects
title FastTrack: An open-source software for tracking varying numbers of deformable objects
title_full FastTrack: An open-source software for tracking varying numbers of deformable objects
title_fullStr FastTrack: An open-source software for tracking varying numbers of deformable objects
title_full_unstemmed FastTrack: An open-source software for tracking varying numbers of deformable objects
title_short FastTrack: An open-source software for tracking varying numbers of deformable objects
title_sort fasttrack: an open-source software for tracking varying numbers of deformable objects
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7904165/
https://www.ncbi.nlm.nih.gov/pubmed/33571205
http://dx.doi.org/10.1371/journal.pcbi.1008697
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