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LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals

Nature Methods volume 18, pages 975–981 (2021)Cite this article

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Abstract

Markerless three-dimensional (3D) pose estimation has become an indispensable tool for kinematic studies of laboratory animals. Most current methods recover 3D poses by multi-view triangulation of deep network-based two-dimensional (2D) pose estimates. However, triangulation requires multiple synchronized cameras and elaborate calibration protocols that hinder its widespread adoption in laboratory studies. Here we describe LiftPose3D, a deep network-based method that overcomes these barriers by reconstructing 3D poses from a single 2D camera view. We illustrate LiftPose3D’s versatility by applying it to multiple experimental systems using flies, mice, rats and macaques, and in circumstances where 3D triangulation is impractical or impossible. Our framework achieves accurate lifting for stereotypical and nonstereotypical behaviors from different camera angles. Thus, LiftPose3D permits high-quality 3D pose estimation in the absence of complex camera arrays and tedious calibration procedures and despite occluded body parts in freely behaving animals.

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Fig. 1: LiftPose3D predicts 3D poses with a single, flexibly positioned camera.
Fig. 2: LiftPose3D performs 3D poses estimation on freely behaving animals with occluded keypoints.
Fig. 3: A pretrained LiftPose3D network predicts 3D poses for diverse data and when triangulation is impossible.

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Data availability

The datasets used in this paper and their sources are listed in Supplementary Table 2. Data used for Figs. 1–3 and Extended Data Figs. 1 and 2 can be downloaded from https://doi.org/10.7910/DVN/KHFAEI. Source data are provided with this paper.

Code availability

LiftPose3D code can be installed as a pip package at https://pypi.org/project/liftpose/. The source code and custom software used to acquire images with the LiftPose3D station is available at https://doi.org/10.5281/zenodo.5031774. The code is licensed under GNU General Public License v.3.0.

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Acknowledgements

P.R. acknowledges support from an SNSF Project grant (no. 175667) and an SNSF Eccellenza grant (no. 181239). A.G. acknowledges support from an HFSP Cross-disciplinary Postdoctoral Fellowship (grant no. LT000669/2020-C). S.G. acknowledges support from an EPFL SV iPhD grant. D.M. holds a Marie Curie EuroTech postdoctoral fellowship and acknowledges that this project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754462. V.L.-R. acknowledges support from the Mexican National Council for Science and Technology, CONACYT, under the grant number 709993. We thank the Ölveczky laboratory (Center for Brain Science, Harvard University, Boston, MA, USA) for providing us with the CAPTURE dataset. We thank the Carey laboratory (Champalimaud Centre for the Unknown, Lisbon, Portugal) for the LocoMouse dataset.

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Author notes

  1. These authors contributed equally: Adam Gosztolai, Semih Günel.

Authors and Affiliations

  1. Neuroengineering Laboratory, Brain Mind Institute & Interfaculty Institute of Bioengineering, EPFL, Lausanne, Switzerland

    Adam Gosztolai, Semih Günel, Victor Lobato-Ríos, Marco Pietro Abrate, Daniel Morales & Pavan Ramdya

  2. Computer Vision Laboratory, EPFL, Lausanne, Switzerland

    Semih Günel & Pascal Fua

  3. Department of Computer Science, UBC, Vancouver, Canada

    Helge Rhodin

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Contributions

A.G. was responsible for conceptualization, methodology, software, hardware (Drosophila prism-mirror system), formal analysis, data curation, writing the original draft and reviewing and editing. S.G. was responsible for conceptualization, methodology, software, formal analysis, data curation, writing the original draft and reviewing and editing the paper. V.L.-R. was responsible for software and hardware (LiftPose3D station, low-resolution Drosophila ventral view system), data curation, and reviewing and editing the paper. M.P.A. was responsible for methodology, software (LiftPose3D), preliminary analysis of DeepFly3D dataset, data curation, and reviewing and editing the paper. D.M. was responsible for investigation (low-resolution Drosophila experiments), and reviewing and editing the paper. H.R. was responsible for conceptualization, and reviewing and editing the paper. P.F. was responsible for reviewing and editing the paper and funding acquisition. P.R. was responsible for conceptualization, hardware (Drosophila prism-mirror system), resources, writing the original draft, and reviewing and editing the paper, supervision, project administration and funding acquisition.

Corresponding authors

Correspondence to Adam Gosztolai, Semih Günel or Pavan Ramdya.

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The authors declare no competing interests.

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Peer review information Nature Methods thanks Katarzyna Bozek, Giorgio Glilestro and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Joint angles resulting from lifting compared with 3D triangulated ground truth and 2D projections.

Joint angles α, β, γ, and ω for the front, mid, and hind left legs during forward walking. Shown are angles computed from 3D triangulation using DeepFly3D (blue), LiftPose3D predictions (red), and ventral 2D projections \(\alpha ^{\prime} ,\beta ^{\prime} ,\gamma ^{\prime}\), and \(\omega ^{\prime}\) (green). The mean (solid lines) and standard deviation of joint error distributions (transparency) are shown. Joint angles were computed by Monte Carlo sampling and errors were computed by taking the fluctuation in bone lengths.

Source data

Extended Data Fig. 2 Training and test loss convergence of the LiftPose3D network applied to a variety of datasets.

A-E Absolute test errors of LiftPose3D for all joints as a function of optimization epoch. A Two-camera data of Drosophila on a spherical treadmill (each color denotes a different pair of diametrically opposed cameras). B OpenMonkeyStudio dataset (each color denotes a different training run). C Single-camera data of Drosophila behaving freely in the right-angle prism-mirror system. D LocoMouse dataset. E CAPTURE dataset.

Source data

Extended Data Fig. 3 Drosophila LiftPose3D station.

A CAD drawing of the LiftPose3D station indicating major components (color-coded). B Photo of the LiftPose3D station. C Electronic circuit for building the illumination module on a pre-fabricated prototyping board (see Supplementary Table 1), electronic components and additional wiring are indicated (color-coded). D Printed circuit board provided as an alternative to the pre-fabricated board for building the illumination module.

Supplementary information

Supplementary Information

Supplementary Note 1 and Table 1.

Reporting Summary

Supplementary Video 1

3D pose lifting for backward walking in tethered Drosophila obtained from two side cameras. Videos obtained from cameras 2 (top left) and 5 (bottom left). DeepFly3D-derived 2D poses are superimposed. Orange circle indicates that the optogenetic stimulation LED light is on, activating MDNs to elicit backward walking. Right, 3D poses obtained by triangulating six camera views using DeepFly3D (solid lines), or lifting two camera views using LiftPose3D (dashed lines).

Supplementary Video 2

3D pose lifting for antennal grooming in tethered Drosophila obtained from two side cameras. Videos obtained from cameras 2 (top left) and 5 (bottom left). DeepFly3D-derived 2D poses are superimposed. Orange circle indicates that the optogenetic stimulation LED light is on, activating aDNs to elicit antennal grooming. Right, 3D poses obtained by triangulating six camera views using DeepFly3D (solid lines), or lifting two camera views using LiftPose3D (dashed lines).

Supplementary Video 3

3D pose lifting for irregular spontaneous limb movements in tethered Drosophila obtained from two side cameras. Videos obtained from cameras 2 (top left) and 5 (bottom left). DeepFly3D-derived 2D poses are superimposed. Right, 3D poses obtained by triangulating six camera views using DeepFly3D (solid lines), or lifting two camera views using LiftPose3D (dashed lines).

Supplementary Video 4

3D pose lifting of previously published OpenMonkeyStudio dataset4 of a freely moving macaque. Left, Single image drawn randomly from one of 62 cameras. Middle, ground truth 3D poses based on triangulation of 2D poses from up to 62 cameras (solid lines), or lifting from a single camera view using LiftPose3D (dashed lines). Right, error distribution across the 62 cameras for a given pose. Camera locations (circles) are color-coded by error. Gray circles denote cameras for which an image was not available. Green circle denotes the camera from which the image was used.

Supplementary Video 5

3D pose lifting of freely behaving Drosophila when triangulation is only partially possible. Single camera images of the ventral (top left) and side (bottom left) views. DeepLabCut-derived 2D poses are superimposed. Right, 3D poses obtained by triangulating partially available multi-view 2D poses (solid lines), or by lifting the ventral 2D pose using LiftPose3D (dashed lines).

Supplementary Video 6

3D pose lifting of previously published freely behaving mouse data14 when triangulation is only partially possible. Side (top left) and ventral (bottom left) views of a freely walking mouse. Superimposed are keypoints on the paws, mouth and proximal tail tracked using the LocoMouse software (blue circles). Using only the ventral view 2D pose, a trained LiftPose3D network can accurately track keypoints in the side view (orange circles).

Supplementary Video 7

3D pose lifting for freely behaving rats in a naturalistic arena. Left, ground truth 3D poses triangulated from six cameras (solid lines) superimposed with LiftPose3D’s predictions using 2D poses from one camera (dashed lines). Right, images from one camera with 2D poses acquired using CAPTURE are superimposed.

Supplementary Video 8

3D pose lifting for low-resolution videos of freely behaving flies when triangulation is impossible. Top, three freely behaving Drosophila in a rounded square arena and recorded ventrally using a single low-resolution camera. Of these, fly 0 is tracked, cropped and rotated leftward. Superimposed are 2D poses for 24 visible joints. (bottom) 3D poses lifted from ventral view 2D poses (x–y plane) permit analysis of leg kinematics in the otherwise unobserved x–z plane.

Supplementary Video 9

3D pose lifting of previously published ventral view videos16 of freely behaving flies when triangulation is impossible. Top, video from a freely behaving fly within a pill-shaped arena and recorded ventrally using a single high-resolution camera. Bottom left, following tracking, a region-of-interest containing the fly was cropped and rotated to maintain a leftward orientation. Superimposed are 2D poses estimated for 24 visible joints. Bottom middle, 3D poses obtained by lifting ventral view 2D poses. Bottom right, 3D poses lifted from ventral view 2D poses (top) permit analysis of leg kinematics in the otherwise unobserved x–z plane (bottom).

Supplementary Video 10

3D pose lifting of data from the Drosophila LiftPose3D station. Left, video of a freely behaving fly in the LiftPose3D station arena. Middle, cropped video around the centroid of the tracked fly, superimposed with 2D pose predictions. Right, lifted 3D poses obtained using ventral 2D poses.

Source data

Source Data Fig. 1

Statistical source data for Fig. 1.

Source Data Fig. 2

Statistical source data for Fig. 2.

Source Data Fig. 3

Statistical source data for Fig. 3.

Source Data Extended Data Fig. 1

Statistical source data for Extended Data Fig. 1.

Source Data Extended Data Fig. 2

Statistical source data for Extended Data Fig. 2.

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Gosztolai, A., Günel, S., Lobato-Ríos, V. et al. LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals. Nat Methods 18, 975–981 (2021). https://doi.org/10.1038/s41592-021-01226-z

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