Anipose: A toolkit for robust markerless 3D pose estimation

Cell Rep. 2021 Sep 28;36(13):109730. doi: 10.1016/j.celrep.2021.109730.


Quantifying movement is critical for understanding animal behavior. Advances in computer vision now enable markerless tracking from 2D video, but most animals move in 3D. Here, we introduce Anipose, an open-source toolkit for robust markerless 3D pose estimation. Anipose is built on the 2D tracking method DeepLabCut, so users can expand their existing experimental setups to obtain accurate 3D tracking. It consists of four components: (1) a 3D calibration module, (2) filters to resolve 2D tracking errors, (3) a triangulation module that integrates temporal and spatial regularization, and (4) a pipeline to structure processing of large numbers of videos. We evaluate Anipose on a calibration board as well as mice, flies, and humans. By analyzing 3D leg kinematics tracked with Anipose, we identify a key role for joint rotation in motor control of fly walking. To help users get started with 3D tracking, we provide tutorials and documentation at

Keywords: 3D; Drosophila joint rotation; behavior; camera calibration; deep learning; markerless tracking; neuroscience; pose estimation; robust tracking; visualization.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Behavior, Animal / physiology*
  • Biomechanical Phenomena / physiology
  • Deep Learning
  • Humans
  • Imaging, Three-Dimensional* / methods
  • Mice
  • Movement / physiology*
  • Walking / physiology*