GroupTracker: Video tracking system for multiple animals under severe occlusion.
Quantitative analysis of behaviors shown by interacting multiple animals can provide a key for revealing high-order functions of their nervous systems. To resolve these complex behaviors, a video tracking system that preserves individual identity even under severe overlap in positions, i.e., occlusion, is needed. We developed GroupTracker, a multiple animal tracking system that accurately tracks individuals even under severe occlusion. As maximum likelihood estimation of Gaussian mixture model whose components can severely overlap is theoretically an ill-posed problem, we devised an expectation-maximization scheme with additional constraints on the eigenvalues of the covariance matrix of the mixture components. Our system was shown to accurately track multiple medaka (Oryzias latipes) which freely swim around in three dimensions and frequently overlap each other. As an accurate multiple animal tracking system, GroupTracker will contribute to revealing unexplored structures and patterns behind animal interactions. The Java source code of GroupTracker is available at https://sites.google.com/site/fukunagatsu/software/group-tracker.
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 277-8568 Chiba, Japan; Atmosphere and Ocean Research Institute, The University of Tokyo, 277-8564 Chiba, Japan. Electronic address: fukunaga@cb.k.u-tokyo.ac.jp.
Tsukasa
T
Fukunaga
Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 277-8562 Chiba, Japan.
Shoko
S
Kubota
Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 277-8562 Chiba, Japan.
Shoji
S
Oda
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 277-8568 Chiba, Japan; Atmosphere and Ocean Research Institute, The University of Tokyo, 277-8564 Chiba, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 113-0032 Tokyo, Japan. Electronic address: iwasaki@bs.s.u-tokyo.ac.jp.
Wataru
W
Iwasaki
D000465:Algorithms; D000823:Animal Identification Systems; D000818:Animals; D003441:Crowding; D016011:Normal Distribution; D009990:Oryzias / Q000502:physiology*; D012984:Software; D013550:Swimming; D014741:Video Recording
Animal tracking; Bioimage informatics; Computational ethology