title: Automated Planar Tracking the Waving Bodies of Multiple Zebrafish Swimming in Shallow Water.
abstract: Zebrafish (Danio rerio) is one of the most widely used model organisms in collective behavior research. Multi-object tracking with high speed camera is currently the most feasible way to accurately measure their motion states for quantitative study of their collective behavior. However, due to difficulties such as their similar appearance, complex body deformation and frequent occlusions, it is a big challenge for an automated system to be able to reliably track the body geometry of each individual fish. To accomplish this task, we propose a novel fish body model that uses a chain of rectangles to represent fish body. Then in detection stage, the point of maximum curvature along fish boundary is detected and set as fish nose point. Afterwards, in tracking stage, we firstly apply Kalman filter to track fish head, then use rectangle chain fitting to fit fish body, which at the same time further judge the head tracking results and remove the incorrect ones. At last, a tracklets relinking stage further solves trajectory fragmentation due to occlusion. Experiment results show that the proposed tracking system can track a group of zebrafish with their body geometry accurately even when occlusion occurs from time to time.
authors.affiliation: School of Computer Science, Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai, P. R. China.
authors.forename: Shuo Hong
authors.initials: SH
authors.lastname: Wang
authors.affiliation: School of Computer Science, Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai, P. R. China.|Jingdezhen Ceramic Institute, Jindezhen, Jiangxi, P.R. China.
authors.forename: Xi En
authors.initials: XE
authors.lastname: Cheng
authors.affiliation: School of Computer Science, Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai, P. R. China.|Chuxiong Normal University, Chuxiong, Yunnan, P. R. China.
authors.forename: Zhi-Ming
authors.initials: ZM
authors.lastname: Qian
authors.affiliation: College of Automation, Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu, P. R. China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Liu
authors.affiliation: School of Computer Science, Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai, P. R. China.
authors.forename: Yan Qiu
authors.initials: YQ
authors.lastname: Chen
mesh_terms: D000818:Animals; D001331:Automation; D001522:Behavior, Animal / Q000502:physiology; D001696:Biomechanical Phenomena; D008954:Models, Biological; D012919:Social Behavior; D013550:Swimming / Q000502:physiology; D014741:Video Recording; D014867:Water; D015027:Zebrafish / Q000033:anatomy & histology / Q000502:physiology*
chemical_list: D014867:Water