title: idTracker: tracking individuals in a group by automatic identification of unmarked animals.
abstract: Animals in groups touch each other, move in paths that cross, and interact in complex ways. Current video tracking methods sometimes switch identities of unmarked individuals during these interactions. These errors propagate and result in random assignments after a few minutes unless manually corrected. We present idTracker, a multitracking algorithm that extracts a characteristic fingerprint from each animal in a video recording of a group. It then uses these fingerprints to identify every individual throughout the video. Tracking by identification prevents propagation of errors, and the correct identities can be maintained indefinitely. idTracker distinguishes animals even when humans cannot, such as for size-matched siblings, and reidentifies animals after they temporarily disappear from view or across different videos. It is robust, easy to use and general. We tested it on fish (Danio rerio and Oryzias latipes), flies (Drosophila melanogaster), ants (Messor structor) and mice (Mus musculus).
authors.affiliation: Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
authors.forename: Alfonso
authors.identifier: 0000000247826139
authors.initials: A
authors.lastname: Pérez-Escudero
authors.affiliation: Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
authors.forename: Julián
authors.initials: J
authors.lastname: Vicente-Page
authors.affiliation: Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
authors.forename: Robert C
authors.initials: RC
authors.lastname: Hinz
authors.affiliation: 1] Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, Spain. [2].
authors.forename: Sara
authors.initials: S
authors.lastname: Arganda
authors.affiliation: Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
authors.forename: Gonzalo G
authors.initials: GG
authors.lastname: de Polavieja
mesh_terms: D000465:Algorithms; D000818:Animals; D001000:Ants; D001522:Behavior, Animal; D004331:Drosophila melanogaster; D005260:Female; D021621:Imaging, Three-Dimensional / Q000379:methods; D008124:Locomotion / Q000502:physiology*; D008297:Male; D051379:Mice; D009990:Oryzias; D012919:Social Behavior; D012984:Software; D014741:Video Recording / Q000379:methods*; D015027:Zebrafish