DeepLabCut: markerless pose estimation of user-defined body parts with deep learning

Alexander Mathis, Pranav Mamidanna, Mackenzie Weygandt Mathis*, Matthias Bethge

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

1594 Citations (Scopus)


Quantifying behavior is crucial for many applications in neuroscience. Videography provides easy methods for the observation and recording of animal behavior in diverse settings, yet extracting particular aspects of a behavior for further analysis can be highly time consuming. In motor control studies, humans or other animals are often marked with reflective markers to assist with computer-based tracking, but markers are intrusive, and the number and location of the markers must be determined a priori. Here we present an efficient method for markerless pose estimation based on transfer learning with deep neural networks that achieves excellent results with minimal training data. We demonstrate the versatility of this framework by tracking various body parts in multiple species across a broad collection of behaviors. Remarkably, even when only a small number of frames are labeled (~200), the algorithm achieves excellent tracking performance on test frames that is comparable to human accuracy.

Original languageEnglish
JournalNature Neuroscience
Issue number9
Pages (from-to)1281-1289
Number of pages9
Publication statusPublished - 1 Sept 2018
Externally publishedYes

Bibliographical note

Funding Information:
We are grateful to E. Insafutdinov and C. Lassner for suggestions on how to best use the TensorFlow implementation of DeeperCut. We thank N. Uchida for generously providing resources for the joystick behavior and R. Axel for generously providing resources for the Drosophila research. We also thank A. Hoffmann, J. Rauber, T. Nath, D. Klindt and T. DeWolf for a critical reading of the manuscript, as well as members of the Bethge lab, especially M. Kümmerer, for discussions. We also thank the β-testers for trying our toolbox and sharing their results with us. Funding: Marie Sklodowska-Curie International Fellowship within the 7th European Community Framework Program under grant agreement No. 622943 and DFG grant MA 6176/1-1 (A.M.); Project ALS (Women and the Brain Fellowship for Advancement in Neuroscience) and a Rowland Fellowship from the Rowland Institute at Harvard (M.W.M.); German Science Foundation (DFG) through the CRC 1233 on “Robust Vision” and from IARPA through the MICrONS program (M.B.).

Publisher Copyright:
© 2018, The Author(s).


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