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DeepPoseKit, a software toolkit for fast and robust animal pose estimation using deep learning

View ORCID ProfileJacob M. Graving, Daniel Chae, Hemal Naik, Liang Li, Benjamin Koger, View ORCID ProfileBlair R. Costelloe, View ORCID ProfileIain D. Couzin
doi: https://doi.org/10.1101/620245
Jacob M. Graving
1Department of Collective Behaviour, Max Planck Institute of Animal Behavior, 78464 Konstanz, Germany
2Department of Biology, University of Konstanz, 78464 Konstanz, Germany
3Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany
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  • For correspondence: jgraving@gmail.com icouzin@ab.mpg.de
Daniel Chae
4Department of Computer Science, Princeton University, 08544 Princeton, NJ, USA
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Hemal Naik
1Department of Collective Behaviour, Max Planck Institute of Animal Behavior, 78464 Konstanz, Germany
2Department of Biology, University of Konstanz, 78464 Konstanz, Germany
3Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany
5Chair for Computer Aided Medical Procedures, Technische Universität München, 80333 Munich, Germany
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Liang Li
1Department of Collective Behaviour, Max Planck Institute of Animal Behavior, 78464 Konstanz, Germany
2Department of Biology, University of Konstanz, 78464 Konstanz, Germany
3Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany
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Benjamin Koger
1Department of Collective Behaviour, Max Planck Institute of Animal Behavior, 78464 Konstanz, Germany
2Department of Biology, University of Konstanz, 78464 Konstanz, Germany
3Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany
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Blair R. Costelloe
1Department of Collective Behaviour, Max Planck Institute of Animal Behavior, 78464 Konstanz, Germany
2Department of Biology, University of Konstanz, 78464 Konstanz, Germany
3Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany
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  • ORCID record for Blair R. Costelloe
Iain D. Couzin
1Department of Collective Behaviour, Max Planck Institute of Animal Behavior, 78464 Konstanz, Germany
2Department of Biology, University of Konstanz, 78464 Konstanz, Germany
3Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany
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  • ORCID record for Iain D. Couzin
  • For correspondence: jgraving@gmail.com icouzin@ab.mpg.de
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Abstract

Quantitative behavioral measurements are important for answering questions across scientific disciplines—from neuroscience to ecology. State-of-the-art deep-learning methods offer major advances in data quality and detail by allowing researchers to automatically estimate locations of an animal’s body parts directly from images or videos. However, currently-available animal pose estimation methods have limitations in speed and robustness. Here we introduce a new easy-to-use software toolkit, DeepPoseKit, that addresses these problems using an eZcient multi-scale deep-learning model, called Stacked DenseNet, and a fast GPU-based peak-detection algorithm for estimating keypoint locations with subpixel precision. These advances improve processing speed >2× with no loss in accuracy compared to currently-available methods. We demonstrate the versatility of our methods with multiple challenging animal pose estimation tasks in laboratory and field settings—including groups of interacting individuals. Our work reduces barriers to using advanced tools for measuring behavior and has broad applicability across the behavioral sciences.

Footnotes

  • Update formatting

  • https://github.com/jgraving/deepposekit

  • https://github.com/jgraving/deepposekit-annotator

  • https://github.com/jgraving/deepposekit-data

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 04, 2019.
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DeepPoseKit, a software toolkit for fast and robust animal pose estimation using deep learning
Jacob M. Graving, Daniel Chae, Hemal Naik, Liang Li, Benjamin Koger, Blair R. Costelloe, Iain D. Couzin
bioRxiv 620245; doi: https://doi.org/10.1101/620245
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DeepPoseKit, a software toolkit for fast and robust animal pose estimation using deep learning
Jacob M. Graving, Daniel Chae, Hemal Naik, Liang Li, Benjamin Koger, Blair R. Costelloe, Iain D. Couzin
bioRxiv 620245; doi: https://doi.org/10.1101/620245

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