naps-track 0.1.0

NAPS (NAPS is ArUco Plus SLEAP)

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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

• Easy, direct installation across platforms

• Built directly on top of OpenCV and SLEAP with a modular, extensible codebase

• Flexible API that allows drop in of different methods for marker identification

• Multiprocessing through Ray

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

If you use NAPS in your research, please cite:

S. W. Wolf, D. M. Ruttenberg*, D. Y. Knapp*, A. W. Webb, G. C. McKenzie-Smith, J. W. Shaevitz, and S. D. Kocher. Hybrid tracking to capture dynamic social networks. In Prep, n.d.

BibTeX:

@UNPUBLISHED{Wolf_undated,
   author = {Wolf, Scott W and Ruttenberg, Dee M and Knapp, Daniel Y and Webb,
            Andrew E and McKenzie-Smith, Grace C and Shaevitz, Joshua W and Kocher, Sarah D},
   title = {Hybrid tracking to capture dynamic social networks},
   year = {n.d.}
}

Issues

Issues with NAPS?

1. Check the docs.

2. Search the issues on GitHub or open a new one.

Contributors

• Scott Wolf, Lewis-Sigler Institute, Princeton University

• Dee Ruttenberg, Lewis-Sigler Institute, Princeton University

• Daniel Knapp, Physics, Princeton University

• Andrew Webb, Ecology and Evolutionary Biology and Lewis-Sigler Institute, Princeton University

• Grace McKenzie-Smith, Lewis-Sigler Institute, Princeton University

• Joshua Shaevitz, Physics and Lewis-Sigler Institute, Princeton University

• Sarah Kocher, Ecology and Evolutionary Biology and Lewis-Sigler Institute, Princeton University

NAPS was created in the Shaevitz and Kocher 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.