Social LEAP Estimates Animal Poses (SLEAP)

Type: Software,

Keywords: Academic software, Deep learning Software, Neural network, Anatomical landmark, BRAIN Initiative

Deep learning framework for estimating animal pose, Deep learning software framework for general purpose multi-animal limb tracking from video

SLEAP (Social LEAP Estimates Animal Poses) is a deep learning software framework for general purpose multi-animal limb tracking from video. This software couples a GUI for importing and annotating data with deep neural networks designed for learning to locate and associate user-specified anatomical landmarks on unmarked animals. Use cases range from kinematic studies of animal movement, to quantification of social dynamics via multi-animal part tracking.

* AI-driven multi-animal pose estimation software
* Open source software package. *Python-based
* Tracks individual body part kinematics of single or multiple interacting animals
* Supports multi-animal pose estimation, animal instance tracking
* Labeling/training GUI supports active learning
* Includes a graphical proof-reading tool to quickly assess the accuracy of tracking and correcting problems

* Framework for multi-animal body part position estimation via deep learning
* Tracking of individual body part kinematics of multiple animals
* High throughput analysis of animal behaviors (e.g., drug screens)
* Development of disease diagnostics for animal models
* Wildlife conservation and monitoring of animal well-being (e.g., agrotech)

* Mice, flies, bees (compatible with any animal)

* Learns from few user examples
* Fast training of deep neural networks on consumer hardware
* Highly accurate and robust to variability in imaging conditions
* Single or multiple animal tracking
* No programming skills required

* For research/academic use only

* Compatible with Python versions 3.6 and above, with support for Windows and Linux
* Mac OS X works but without GPU support
* Remote cloud/cluster-based training and inference

* Recommended to use the Anaconda Python distribution for Windows
* Pip package available for all systems

* Pereira et al. 2018, Fast animal pose estimation using deep neural networks, Nature Methods 16: 117–125

* Pereira et al. 2020, SLEAP: Multi-animal pose tracking, bioRxiv

* https://sleap.ai
* https://pypi.org/project/sleap/
* https://www.nature.com/articles/s41592-018-0234-5
* https://www.biorxiv.org/content/10.1101/2020.08.31.276246v1.abstract

CONTACT NAME, POSITION

Talmo Pereira (PhD Candidate)
Mala Murthy
Joshua Shaevitz (Professor)

ORGANIZATION

Princeton

CONTACT INFORMATION

TEAM

Mala Murthy
Talmo Pereira
Nat Tabris
David Turner
Joshua Shaevitz

LAB WEBSITE(S)

GRANT SUPPORT / FUNDING SOURCE

NIH BRAIN Initative R01 NS104899
Princeton Innovation Accelerator Fund (NSF GRFP, NIH R01, HHMI)