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

Abstract

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.

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Fig. 1: Procedure for using the DeepLabCut Toolbox.
Fig. 2: Evaluation during odor trail tracking.
Fig. 3: A trail-tracking mouse.
Fig. 4: Generalization.
Fig. 5: End-to-end training.
Fig. 6: Markerless tracking of Drosophila.
Fig. 7: Markerless tracking of digits.

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Data availability

Data are available from the corresponding author upon reasonable request.

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Acknowledgements

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.).

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Contributions

Conceptualization: A.M., M.W.M. and M.B. Software: A.M. and M.W.M. Formal analysis: A.M. Experiments: A.M. and V.N.M. (trail-tracking), M.W.M. (mouse reaching), K.M.C. (Drosophila). Labeling: P.M., K.M.C., T.A., M.W.M., A.M. Writing: A.M. and M.W.M. with input from all authors.

Corresponding author

Correspondence to Mackenzie Weygandt Mathis.

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Integrated supplementary information

Supplementary Figure 1 Illustration of labeled data set.

a: Example images with human applied labels (first and second trial by the same labeler colored in yellow and cyan) illustrating the variability. Top row shows full frames that were labeled and illustrate typical examples of the 1,080 random frames, which comprise the data set. Rows below are cropped for visibility of the labels and indicate the average RMSE in pixels across all body parts above the image. The scorer was highly accurate, as illustrated by b. b: x-axis and y-axis difference in pixels between the first - second trial. Only a few labels strongly deviate between the two trials. Most errors are smaller than 5 pixels as can be seen in the histogram of trial-by-trial labeling errors (cropped at 20 pixels), c).

Supplementary Figure 2 Cross-validating model parameters and testing deeper networks.

a: Average training and test error for the same 6 splits with 10% training set size as in Fig. 2f with standard augmentation (i.e. scaling), augmentation by rotations as well as rotations and translations (see Methods). Although with augmentation there are 8 and 24 times as many training samples (rotations and rotations + translations, respectively), the training and test errors remained comparable. b: Average training and test error for the same 3 splits with 50% training set size for three different architectures: ResNet-50, ResNet-101 as well as ResNet-101ws, where part loss layers are added to conv4 bank29. For these networks the training error is strongly reduced, and the test performance modestly improved, indicating that the deeper networks do not over-fit (but do not offer radical improvement). Averaged over 3 splits, individual simulation results shown in as faint lines. The deeper networks reach human level accuracy on test set. The data for ResNet-50 is also depicted in Fig. 2d. c: Cross validating model parameters for ResNet-50 and 50%-training set fraction. We varied the distance variable ϵ, which determines the width of the score-map template during training around the ground-truth value with scale variable 100% (otherwise the scale ratio of the output layer was set to 80% relative to the input image size). Varying distance parameters only mildly improves the test performance (after 500k training steps). The average performance for scale 0.8 and ϵ=17 is indicated by horizontal lines (from Fig. 2d). In particular, for smaller distance parameters the RMSE increases and learning proceeds much slower (c,d). d-e: Evolution of the training and test errors at various states of the network training for various distance variables ϵ corresponding to c.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1 and 2

Reporting Summary

Supplementary Video 1

Odor guided navigation task with automated tracking of the snout. (Related to Fig. 3.)

Supplementary Video 2

Drosophila egg-laying behavior with automated tracking of various body parts. (Related to Fig. 6.)

Supplementary Video 3

Skilled reach and pull task with automated tracking of the hand. (Related to Fig. 7.)

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Mathis, A., Mamidanna, P., Cury, K.M. et al. DeepLabCut: markerless pose estimation of user-defined body parts with deep learning. Nat Neurosci 21, 1281–1289 (2018). https://doi.org/10.1038/s41593-018-0209-y

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