ArMo: An Articulated Mesh Approach for Mouse 3D Reconstruction

• Published in: bioRxiv : the preprint server for biology
• Main Authors: Bohnslav, James P, Osman, Mohammed Abdal Monium, Jaggi, Akshay, Soares, Sofia, Weinreb, Caleb, Datta, Sandeep Robert, Harvey, Christopher D
• Format: Journal Article
• Language: English
• Published: United States 18.02.2023

Characterizing animal behavior requires methods to distill 3D movements from video data. Though keypoint tracking has emerged as a widely used solution to this problem, it only provides a limited view of pose, reducing the body of an animal to a sparse set of experimenter-defined points. To more completely capture 3D pose, recent studies have fit 3D mesh models to subjects in image and video data. However, despite the importance of mice as a model organism in neuroscience research, these methods have not been applied to the 3D reconstruction of mouse behavior. Here, we present ArMo, an articulated mesh model of the laboratory mouse, and demonstrate its application to multi-camera recordings of head-fixed mice running on a spherical treadmill. Using an end-to-end gradient based optimization procedure, we fit the shape and pose of a dense 3D mouse model to data-derived keypoint and point cloud observations. The resulting reconstructions capture the shape of the animal’s surface while compactly summarizing its movements as a time series of 3D skeletal joint angles. ArMo therefore provides a novel alternative to the sparse representations of pose more commonly used in neuroscience research.