{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T12:32:58Z","timestamp":1790771578249,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008697","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,2,24]],"date-time":"2021-02-24T00:00:00Z","timestamp":1614124800000}}],"reference-count":48,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2021,2,11]],"date-time":"2021-02-11T00:00:00Z","timestamp":1613001600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ANR","award":["ANR-16-CE16-0017"],"award-info":[{"award-number":["ANR-16-CE16-0017"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>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\u2019s trackability that doesn\u2019t 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 <jats:italic>ad hoc<\/jats:italic> tracking. We also leveraged the versatility and speed of FastTrack to implement an iterative algorithm determining a set of nearly-optimized tracking parameters\u2014yet further reducing the amount of human intervention\u2014and 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 <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/FastTrackOrg\/FastTrack\" xlink:type=\"simple\">https:\/\/github.com\/FastTrackOrg\/FastTrack<\/jats:ext-link> and pre-compiled binaries for Windows, Mac and Linux are available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.fasttrack.sh\" xlink:type=\"simple\">http:\/\/www.fasttrack.sh<\/jats:ext-link>.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008697","type":"journal-article","created":{"date-parts":[[2021,2,12]],"date-time":"2021-02-12T20:00:53Z","timestamp":1613160053000},"page":"e1008697","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":54,"title":["FastTrack: An open-source software for tracking varying numbers of deformable objects"],"prefix":"10.1371","volume":"17","author":[{"given":"Benjamin","family":"Gallois","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1523-6249","authenticated-orcid":true,"given":"Rapha\u00ebl","family":"Candelier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,2,11]]},"reference":[{"key":"pcbi.1008697.ref001","doi-asserted-by":"crossref","unstructured":"Ray Juang R, Levchenko A, Burlina P. Tracking cell motion using GM-PHD. In: 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro; 2009. p. 1154\u20131157.","DOI":"10.1109\/ISBI.2009.5193262"},{"issue":"6","key":"pcbi.1008697.ref002","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1109\/TBME.2011.2109001","article-title":"Tracking Biological Cells in Time-Lapse Microscopy: An Adaptive Technique Combining Motion and Topological Features","volume":"58","author":"MAA Dewan","year":"2011","journal-title":"IEEE Transactions on Biomedical Engineering"},{"issue":"7","key":"pcbi.1008697.ref003","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.tree.2014.05.004","article-title":"Automated image-based tracking and its application in ecology","volume":"29","author":"AI Dell","year":"2014","journal-title":"Trends in Ecology & Evolution"},{"issue":"5","key":"pcbi.1008697.ref004","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pcbi.1005530","article-title":"FIMTrack: An open source tracking and locomotion analysis software for small animals","volume":"13","author":"B Risse","year":"2017","journal-title":"PLOS Computational Biology"},{"issue":"2","key":"pcbi.1008697.ref005","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0192463","article-title":"Accurately tracking single-cell movement trajectories in microfluidic cell sorting devices","volume":"13","author":"J Jeong","year":"2018","journal-title":"PLOS ONE"},{"key":"pcbi.1008697.ref006","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/nature12673","article-title":"Emergence of macroscopic directed motion in populations of motile colloids","volume":"503","author":"A Bricard","year":"2013","journal-title":"Nature"},{"issue":"12","key":"pcbi.1008697.ref007","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1016\/j.imavis.2012.08.013","article-title":"Multiple human tracking in high-density crowds","volume":"30","author":"I Ali","year":"2012","journal-title":"Image and Vision Computing"},{"issue":"1","key":"pcbi.1008697.ref008","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.robot.2004.05.005","article-title":"Real-time object tracking for soccer-robots without color information","volume":"48","author":"A Treptow","year":"2004","journal-title":"Robotics and Autonomous Systems"},{"key":"pcbi.1008697.ref009","unstructured":"Luo RC, Mullen RE, Wessell DE. An adaptive robotic tracking system using optical flow. In: Proceedings. 1988 IEEE International Conference on Robotics and Automation; 1988. p. 568\u2013573 vol.1."},{"issue":"8-9","key":"pcbi.1008697.ref010","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1039\/b908595e","article-title":"Spontaneous migration of cancer cells under conditions of mechanical confinement","volume":"1","author":"D Irimia","year":"2009","journal-title":"Integrative Biology"},{"issue":"10","key":"pcbi.1008697.ref011","doi-asserted-by":"crossref","first-page":"4045","DOI":"10.1096\/fj.12-211441","article-title":"Physical confinement alters tumor cell adhesion and migration phenotypes","volume":"26","author":"EM Balzer","year":"2012","journal-title":"The FASEB Journal"},{"key":"pcbi.1008697.ref012","doi-asserted-by":"crossref","first-page":"118101","DOI":"10.1103\/PhysRevLett.112.118101","article-title":"Hydrodynamics Determines Collective Motion and Phase Behavior of Active Colloids in Quasi-Two-Dimensional Confinement","volume":"112","author":"A Z\u00f6ttl","year":"2014","journal-title":"Phys Rev Lett"},{"issue":"7","key":"pcbi.1008697.ref013","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1038\/nmeth.2994","article-title":"idTracker: tracking individuals in a group by automatic identification of unmarked animals","volume":"11","author":"A P\u00e9rez-Escudero","year":"2014","journal-title":"Nature methods"},{"issue":"14774","key":"pcbi.1008697.ref014","article-title":"ToxId: an efficient algorithm to solve occlusions when tracking multiple animals","volume":"7","author":"A Rodriguez","year":"2017","journal-title":"Scientific Reports"},{"issue":"33","key":"pcbi.1008697.ref015","article-title":"A Semi-Automatic Dispenser for Solid and Liquid Food in Aquatic Facilities","volume":"17","author":"R Candelier","year":"2019","journal-title":"Zebrafish"},{"key":"pcbi.1008697.ref016","doi-asserted-by":"crossref","first-page":"3294","DOI":"10.1039\/C9SM02343G","article-title":"Depletion attraction impairs the plasticity of emulsions flowing in a constriction","volume":"16","author":"I Golovkova","year":"2020","journal-title":"Soft Matter"},{"key":"pcbi.1008697.ref017","doi-asserted-by":"crossref","first-page":"098004","DOI":"10.1103\/PhysRevLett.117.098004","article-title":"Crystallization of Self-Propelled Hard Discs","volume":"117","author":"G Briand","year":"2016","journal-title":"Phys Rev Lett"},{"key":"pcbi.1008697.ref018","doi-asserted-by":"crossref","first-page":"208001","DOI":"10.1103\/PhysRevLett.120.208001","article-title":"Spontaneously Flowing Crystal of Self-Propelled Particles","volume":"120","author":"G Briand","year":"2018","journal-title":"Phys Rev Lett"},{"key":"pcbi.1008697.ref019","doi-asserted-by":"crossref","first-page":"098001","DOI":"10.1103\/PhysRevLett.105.098001","article-title":"Collective Motion of Vibrated Polar Disks","volume":"105","author":"J Deseigne","year":"2010","journal-title":"Phys Rev Lett"},{"key":"pcbi.1008697.ref020","doi-asserted-by":"crossref","first-page":"248302","DOI":"10.1103\/PhysRevLett.113.248302","article-title":"Self-Propulsion of Pure Water Droplets by Spontaneous Marangoni-Stress-Driven Motion","volume":"113","author":"Z Izri","year":"2014","journal-title":"Phys Rev Lett"},{"issue":"21","key":"pcbi.1008697.ref021","doi-asserted-by":"crossref","first-page":"6700","DOI":"10.1073\/pnas.1500804112","article-title":"Neuronal control of locomotor handedness in Drosophila","volume":"112","author":"SM Buchanan","year":"2015","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"pcbi.1008697.ref022","article-title":"Idiosyncratic neural coding and neuromodulation of olfactory individuality in Drosophila","author":"KS Honegger","year":"2019","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"5","key":"pcbi.1008697.ref023","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1007\/s10404-011-0909-z","article-title":"Droplet arrangement and coalescence in diverging\/converging microchannels","volume":"12","author":"BM Jose","year":"2012","journal-title":"Microfluidics and Nanofluidics"},{"key":"pcbi.1008697.ref024","doi-asserted-by":"crossref","first-page":"128001","DOI":"10.1103\/PhysRevLett.103.128001","article-title":"Creep Motion of an Intruder within a Granular Glass Close to Jamming","volume":"103","author":"R Candelier","year":"2009","journal-title":"Phys Rev Lett"},{"key":"pcbi.1008697.ref025","doi-asserted-by":"crossref","first-page":"068002","DOI":"10.1103\/PhysRevLett.122.068002","article-title":"Dynamics of a Self-Propelled Particle in a Harmonic Trap","volume":"122","author":"O Dauchot","year":"2019","journal-title":"Phys Rev Lett"},{"issue":"6","key":"pcbi.1008697.ref026","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0011248","article-title":"Coordinated and Cohesive Movement of Two Small Conspecific Fish Induced by Eliciting a Simultaneous Optomotor Response","volume":"5","author":"H Imada","year":"2010","journal-title":"PLOS ONE"},{"key":"pcbi.1008697.ref027","volume-title":"The Image Processing Handbook","author":"JC Russ","year":"2015","edition":"7"},{"issue":"10","key":"pcbi.1008697.ref028","doi-asserted-by":"crossref","first-page":"1858","DOI":"10.1109\/TPAMI.2008.113","article-title":"Parametric image alignment using enhanced correlation coefficient maximization","volume":"30","author":"GD Evangelidis","year":"2008","journal-title":"IEEE Transactions on Pattern Analysis and Machine Intelligence"},{"key":"pcbi.1008697.ref029","doi-asserted-by":"crossref","unstructured":"Rublee E, Rabaud V, Konolige K, Bradski G. ORB: An efficient alternative to SIFT or SURF. In: 2011 International conference on computer vision. Ieee; 2011. p. 2564\u20132571.","DOI":"10.1109\/ICCV.2011.6126544"},{"key":"pcbi.1008697.ref030","first-page":"637","article-title":"A RANSAC-based approach to model fitting and its application to finding cylinders in range data","volume":"vol. 1981","author":"RC Bolles","year":"1981","journal-title":"IJCAI"},{"issue":"1","key":"pcbi.1008697.ref031","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/0734-189X(85)90016-7","article-title":"Topological structural analysis of digitized binary images by border following","volume":"30","author":"S Suzuki","year":"1985","journal-title":"Computer Vision, Graphics, and Image Processing"},{"key":"pcbi.1008697.ref032","first-page":"351","article-title":"Object Tracking Method Based on SURF","volume":"3","author":"H Shuo","year":"2012","journal-title":"AASRI Conference on Modelling, Identification and Control"},{"issue":"4","key":"pcbi.1008697.ref033","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1109\/TRO.2004.829463","article-title":"Image moments: a general and useful set of features for visual servoing","volume":"20","author":"F Chaumette","year":"2004","journal-title":"IEEE Transactions on Robotics"},{"key":"pcbi.1008697.ref034","unstructured":"Riemann B. Grundlagen f\u00fcr eine allgemeine Theorie der Functionen einer ver\u00e4nderlichen complexen Gr\u00f6sse. PhD. 1851;."},{"key":"pcbi.1008697.ref035","unstructured":"Rocha L, Velho L, Carvalho PCP. Image moments-based structuring and tracking of objects. In: Computer Graphics and Image Processing, 2002. Proceedings. XV Brazilian Symposium on. IEEE; 2002. p. 99\u2013105."},{"key":"pcbi.1008697.ref036","doi-asserted-by":"crossref","first-page":"14","DOI":"10.3389\/fnsys.2016.00014","article-title":"Rheotaxis of Larval Zebrafish: Behavioral Study of a Multi-Sensory Process","volume":"10","author":"R Olive","year":"2016","journal-title":"Front Syst Neurosci"},{"issue":"34015","key":"pcbi.1008697.ref037","article-title":"A 2D virtual reality system for visual goal-driven navigation in zebrafish larvae","volume":"6","author":"A Jouary","year":"2016","journal-title":"Scientific Reports"},{"issue":"1","key":"pcbi.1008697.ref038","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1186\/s12859-016-1138-y","article-title":"An effective and robust method for tracking multiple fish in video image based on fish head detection","volume":"17","author":"ZM Qian","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"pcbi.1008697.ref039","doi-asserted-by":"crossref","unstructured":"Martello S, Toth P. Linear Assignment Problems. In: Martello S, Laporte G, Minoux M, Ribeiro C, editors. Surveys in Combinatorial Optimization. vol. 132 of North-Holland Mathematics Studies. North-Holland; 1987. p. 259\u2013282. Available from: http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0304020808732389.","DOI":"10.1016\/S0304-0208(08)73238-9"},{"issue":"1-2","key":"pcbi.1008697.ref040","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1002\/nav.3800020109","article-title":"The Hungarian method for the assignment problem","volume":"2","author":"HW Kuhn","year":"1955","journal-title":"Naval research logistics quarterly"},{"key":"pcbi.1008697.ref041","unstructured":"Buehren M. Functions for the rectangular assignment problem; 2005. Available from: https:\/\/github.com\/mcximing\/hungarian-algorithm-cpp."},{"key":"pcbi.1008697.ref042","volume-title":"vol. 1 of Mathematical optimization","author":"H Christos","year":"1998","edition":"2"},{"issue":"1","key":"pcbi.1008697.ref043","doi-asserted-by":"crossref","DOI":"10.1038\/nprot.2011.432","article-title":"Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy","volume":"7","author":"JW Young","year":"2012","journal-title":"Nature Protocols"},{"issue":"1","key":"pcbi.1008697.ref044","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1109\/JSTSP.2015.2491304","article-title":"Segmentation and Track-Analysis in Time-Lapse Imaging of Bacteria","volume":"10","author":"SK Sadanandan","year":"2016","journal-title":"IEEE Journal of Selected Topics in Signal Processing"},{"issue":"2","key":"pcbi.1008697.ref045","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/s41592-018-0295-5","article-title":"idtracker.ai: tracking all individuals in small or large collectives of unmarked animals","volume":"16","author":"F Romero-Ferrero","year":"2019","journal-title":"Nat Methods"},{"issue":"3","key":"pcbi.1008697.ref046","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1111\/2041-210X.12874","article-title":"ToxTrac: A fast and robust software for tracking organisms","volume":"9","author":"A Rodriguez","year":"2018","journal-title":"Methods in Ecology and Evolution"},{"issue":"2","key":"pcbi.1008697.ref047","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1111\/j.1467-8659.2008.01155.x","article-title":"The Shadow Meets the Mask: Pyramid-Based Shadow Removal","volume":"27","author":"Y Shor","year":"2008","journal-title":"Computer Graphics Forum"},{"key":"pcbi.1008697.ref048","unstructured":"Dey N, Dutta S, Dey G, Chakraborty S, Ray R, Roy P. Adaptive thresholding: A comparative study; 2014."}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1008697","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,2,24]],"date-time":"2021-02-24T00:00:00Z","timestamp":1614124800000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008697","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,2,24]],"date-time":"2021-02-24T18:50:02Z","timestamp":1614192602000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008697"}},"subtitle":[],"editor":[{"given":"Manja","family":"Marz","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,2,11]]},"references-count":48,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2021,2,11]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1008697","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1008697","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,2,11]]}}}