NAPS (NAPS is ArUco Plus SLEAP)
Project description
NAPS (NAPS is ArUco Plus SLEAP)
NAPS is a tool for researchers with two goals: (1) to quantify animal behavior over a long timescale and high resolution, with minimal human bias, and (2) to track the behavior of individuals with a high level of identity-persistence. This could be of use to researchers studying social network analysis, animal communication, task specialization, or gene-by-environment interactions. By combining deep-learning based pose estimation software with easily read and minimally invasive fiducial markers (“tags”), we provide an easy-to-use solution for producing high-quality, high-dimensional behavioral data.
Documentation
NAPS documentation can be found at naps.rtfd.io.
Features
Getting NAPS
Easy install
conda (Windows/Linux):
conda create -n naps naps-track -c kocherlab -c sleap -c nvidia -c conda-forge
pip (any OS):
pip install naps-track
References
Manuscript: https://doi.org/10.1101/2022.12.07.518416
If you use NAPS in your research, please cite:
BibTeX:
@article{wolf2022naps,
title={NAPS: Integrating pose estimation and tag-based tracking},
author={Wolf, Scott W and Ruttenberg, Dee M and Knapp, Daniel Y and Webb, Andrew E and Traniello, Ian M and McKenzie-Smith, Grace C and Leheny, Sophie A and Shaevitz, Joshua W and Kocher, Sarah D},
journal={bioRxiv},
year={2022},
publisher={Cold Spring Harbor Laboratory}
}
Issues
Issues with NAPS?
Check the docs.
Search the issues on GitHub or open a new one.
Contributors
Scott Wolf, Lewis-Sigler Institute for Integrative Genomics, Princeton University
Dee Ruttenberg, Lewis-Sigler Institute for Integrative Genomics, Princeton University
Daniel Knapp, Department of Physics, Princeton University
Andrew Webb, Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University
Ian Traniello, Lewis-Sigler Institute for Integrative Genomics, Princeton University
Grace McKenzie-Smith, Department of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University
Sophie Leheny, Department of Molecular Biology, Princeton University
Joshua Shaevitz, Department of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University
Sarah Kocher, Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University
NAPS was created in the Kocher and Shaevitz labs at Princeton University.
License
NAPS is licensed under the MIT license. See the LICENSE file for details.
Acknowledgements
Much of the structure and content of the README and the documentation is borrowed from the SLEAP repository.
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