Fast animal pose estimation using deep neural networks.

TitleFast animal pose estimation using deep neural networks.
Publication TypeJournal Article
Year of Publication2019
AuthorsPereira, TD, Aldarondo, DE, Willmore, L, Kislin, M, Wang, SS-H, Murthy, M, Shaevitz, JW
JournalNat Methods
Volume16
Issue1
Pagination117-125
Date Published2019 01
ISSN1548-7105
KeywordsAlgorithms, Animals, Automation, Behavior, Animal, Computer Graphics, Deep Learning, Drosophila melanogaster, Gait, Locomotion, Male, Mice, Neural Networks, Computer, Pattern Recognition, Automated, User-Computer Interface
Abstract

<p>The need for automated and efficient systems for tracking full animal pose has increased with the complexity of behavioral data and analyses. Here we introduce LEAP (LEAP estimates animal pose), a deep-learning-based method for predicting the positions of animal body parts. This framework consists of a graphical interface for labeling of body parts and training the network. LEAP offers fast prediction on new data, and training with as few as 100 frames results in 95% of peak performance. We validated LEAP using videos of freely behaving fruit flies and tracked 32 distinct points to describe the pose of the head, body, wings and legs, with an error rate of <3% of body length. We recapitulated reported findings on insect gait dynamics and demonstrated LEAP's applicability for unsupervised behavioral classification. Finally, we extended the method to more challenging imaging situations and videos of freely moving mice.</p>

DOI10.1038/s41592-018-0234-5
Alternate JournalNat. Methods
PubMed ID30573820
PubMed Central IDPMC6899221
Grant ListR01 MH115750 / MH / NIMH NIH HHS / United States
R01 NS045193 / NS / NINDS NIH HHS / United States
R01 NS104899 / NS / NINDS NIH HHS / United States