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Fly and mouse tracking models and kinematics related to Anipose toolkit paper

Karashchuk, Pierre, University of Washington, https://orcid.org/0000-0001-6244-8239
Walling-Bell, Sarah, University of Washington, https://orcid.org/0000-0001-6995-2681
Sanders, Elischa, Salk Institute for Biological Studies
Azim, Eiman, Salk Institute for Biological Studies, https://orcid.org/0000-0002-1015-1772
Rupp, Katie L., University of Washington
Dickinson, Evyn S., University of Washington, https://orcid.org/0000-0001-7518-9512
Brunton, Bingni W., University of Washington
Tuthill, John C., University of Washington, https://orcid.org/0000-0002-5689-5806
pierrek@uw.edu, bbrunton@uw.edu, tuthill@uw.edu
Published Nov 28, 2021 on Dryad. https://doi.org/10.5061/dryad.nzs7h44s4

Cite this dataset

Karashchuk, Pierre et al. (2021). Fly and mouse tracking models and kinematics related to Anipose toolkit paper [Dataset]. Dryad. https://doi.org/10.5061/dryad.nzs7h44s4

Abstract

This is a series of datasets related to the Anipose paper. We provide these to allow others to reproduce our tracking results and build upon them.

Anipose is 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.

Applying 3D tracking to estimate joint angles of walking Drosophila, we found that flies move their middle legs primarily by rotating their coxa and femur, whereas the front and rear legs are driven primarily by femur-tibia flexion. We then show how Anipose can be used to quantify differences between successful and unsuccessful trajectories in a mouse reaching task.

We share these fly and mouse datasets and tracking models in this dataset to allow others to reproduce our findings and reuse the training data and models in their research.

Methods

Please refer to the Anipose paper for detailed information on the methods used to collect the videos and to track the 3D joint positions.

Usage notes

We share the detailed fly 3D kinematics analyzed in the paper, consisting of all 3D joint positions and 3D joint angles. See the following files:

  • flyangles-dataset.zip - Dataset of 3D kinematics from 39 wild-type Berlin flies
  • README - Detailed documentation of this dataset (also included in the zip)

Furthermore, we share the trained DeepLabCut models and original videos with tracking from Anipose. Please refer to the DeepLabCut and Anipose documentation for the structure of these files. The files are the following:

  • deeplabcut-fly-model.zip - DeepLabCut  model and training data for fly on a ball dataset
  • deeplabcut-mouse-model.zip - DeepLabCut model and training data for mouse dataset
  • fly-anipose.zip - Anipose files for fly dataset
  • mouse-anipose.zip - Anipose files for mouse dataset