AlphaTracker: a multi-animal tracking and behavioral analysis tool

Frontiers in Behavioral Neuroscience

Behavioral Neuroscience

Hao-Shu Fang¹  Zexin Chen¹  Yong-Lu Li¹  Haoyi Zhu¹  Cewu Lu²  Yu E. Zhang³  Takaki Komiyama⁴  Aneesh Bal⁵  Rachel R. Rock⁶  Nancy Padilla-Coreano⁷  Laurel R. Keyes⁸  Kay M. Tye⁸  Haowen Zhou⁹  Ruihan Zhang^1,10 

[1] Department of Computer Science, Shanghai Jiao Tong University, Shanghai, China;Department of Computer Science, Shanghai Jiao Tong University, Shanghai, China;Shanghai Artificial Intelligence Laboratory, Shanghai, China;Department of Neurobiology, Center for Neural Circuits and Behavior, University of California, San Diego, La Jolla, CA, United States;Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States;Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States;Department of Psychological and Brain Sciences, Johns Hopkins University, Baltimore, MD, United States;Salk Institute for Biological Studies, La Jolla, CA, United States;Salk Institute for Biological Studies, La Jolla, CA, United States;Salk Institute for Biological Studies, La Jolla, CA, United States;Department of Neuroscience, University of Florida, Gainesville, FL, United States;Salk Institute for Biological Studies, La Jolla, CA, United States;Howard Hughes Medical Institute, The Salk Institute, La Jolla, CA, United States;Zhiyuan College, Shanghai Jiao Tong University, Shanghai, China;Zhiyuan College, Shanghai Jiao Tong University, Shanghai, China;Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States;

关键词: neuroscience;    computer vision;    animal behavior;    animal tracking;    behavioral clustering;   

DOI  :  10.3389/fnbeh.2023.1111908

 received in 2022-12-01, accepted in 2023-02-21,  发布年份 2023

来源: Frontiers

【 摘 要 】

Computer vision has emerged as a powerful tool to elevate behavioral research. This protocol describes a computer vision machine learning pipeline called AlphaTracker, which has minimal hardware requirements and produces reliable tracking of multiple unmarked animals, as well as behavioral clustering. AlphaTracker pairs a top-down pose-estimation software combined with unsupervised clustering to facilitate behavioral motif discovery that will accelerate behavioral research. All steps of the protocol are provided as open-source software with graphic user interfaces or implementable with command-line prompts. Users with a graphical processing unit (GPU) can model and analyze animal behaviors of interest in less than a day. AlphaTracker greatly facilitates the analysis of the mechanism of individual/social behavior and group dynamics.

【 授权许可】

Unknown   
Copyright © 2023 Chen, Zhang, Fang, Zhang, Bal, Zhou, Rock, Padilla-Coreano, Keyes, Zhu, Li, Komiyama, Tye and Lu.