Journal Article

SLEAP: A deep learning system for multi-animal pose tracking

D’Uva, John, Mitelut, Catalin C., Castro, Marielisa Diez, Sanes, Dan H., Turner, David M., Ravindranath, Shruthi, Deutsch, David S., Normand, Edna, Wang, Samuel S.-H., Kislin, Mikhail, Papadoyannis, Eleni S., Murthy, Mala, Tabris, Nathaniel, Falkner, Annegret L., Matsliah, Arie, Li, Junyu, Pereira, Talmo D., Kocher, Sarah D., Wang, Z. Yan, McKenzie-Smith, Grace C., Shaevitz, Joshua W.

2022

Overview

The desire to understand how the brain generates and patterns behavior has driven rapid methodological innovation in tools to quantify natural animal behavior. While advances in deep learning and computer vision have enabled markerless pose estimation in individual animals, extending these to multiple animals presents unique challenges for studies of social behaviors or animals in their natural environments. Here we present Social LEAP Estimates Animal Poses (SLEAP), a machine learning system for multi-animal pose tracking. This system enables versatile workflows for data labeling, model training and inference on previously unseen data. SLEAP features an accessible graphical user interface, a standardized data model, a reproducible configuration system, over 30 model architectures, two approaches to part grouping and two approaches to identity tracking. We applied SLEAP to seven datasets across flies, bees, mice and gerbils to systematically evaluate each approach and architecture, and we compare it with other existing approaches. SLEAP achieves greater accuracy and speeds of more than 800 frames per second, with latencies of less than 3.5 ms at full 1,024 × 1,024 image resolution. This makes SLEAP usable for real-time applications, which we demonstrate by controlling the behavior of one animal on the basis of the tracking and detection of social interactions with another animal. SLEAP is a versatile deep learning-based multi-animal pose-tracking tool designed to work on videos of diverse animals, including during social behavior.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 631/114/1305 / 631/114/794 / 631/378/116 / Algorithms / Animal behavior / Animals / Behavior, Animal / Bioinformatics / Biological Microscopy / Biological Techniques / Biomedical and Life Sciences / Biomedical Engineering/Biotechnology / Computer vision / Deep Learning / Frames per second / Graphical user interface / Head / Image processing / Image resolution / Life Sciences / Machine Learning / Mice / Natural environment / Pose estimation / Proteomics / Social Behavior / Social factors / Social interactions / Tracking / Tracking equipment