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Researcher profile

R. James Cotton

R. James Cotton contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Computer VisionQuantitative MethodsArtificial IntelligenceMachine LearningSoftware Engineering

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Published work

5 published item(s)

preprint2026arXiv

Markerless Motion Capture for Biomechanical Whole-Body Kinematic Estimation in Infants

arly identification of motor impairment in infancy relies on expert visual assessment of spontaneous movement, motivating the development of automated, objective alternatives. One promising approach is using computer vision, which benefits from high quality pose estimation from video. In this study, we systematically evaluated three state-of-the-art pose estimation frameworks (MeTRAbs-ACAE, SAM 3D Body, and Sapiens) on 100 videos over 13 sessions of 8 infants recorded with a multi-view markerless motion capture system. We quantified keypoint detection accuracy using reprojection error, geometric consistency, and Procrustes-aligned 3D position error, and demonstrated proof-of-concept for fitting an inverse kinematic framework to infant data. While Sapiens achieved the lowest reprojection error and highest geometric consistency of the methods evaluated (22.8 pixels and 0.82, respectively), SAM 3D Body provided the most comprehensive 3D information for kinematic reconstruction with Procrustes-aligned position errors of 19 to 28 mm. We demonstrate in a case comparison example that biomechanical models fit to SAM 3D estimates distinguish representative movement patterns in infants related to motor development, as identified by a clinical expert. Together, these findings highlight both the promise and current limitations of 3D pose estimation for infant biomechanics and establish preliminary groundwork for scalable, video-based assessment of early motor development.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Monocular Biomechanical Tracking of Fingers with Inverse Kinematics to Foundation Models

Accurate hand and finger tracking from video has significant clinical applications for monitoring activities of daily living and measuring range of motion, yet monocular video approaches for obtaining hand biomechanics remain under-developed. We present a method that combines the SAM 3D Body foundation model with inverse kinematics optimization in a full-body biomechanical model to extract anatomically-constrained finger joint angles from single-view video. We port SAM 3D Body from PyTorch to JAX for integration with MuJoCo-MJX, enabling GPU-accelerated optimization, and develop a novel mapping between the Momentum Human Rig (MHR) outputs and biomechanical model markers. Validation against 8-camera multiview reconstruction on 4,590 frames from 7 participants performing a variety of hand poses and object manipulation tasks shows finger joint angle errors of approximately 10 degrees and hand position errors of approximately 6 mm, after Procrustes alignment. Results were consistent across camera viewpoints and robust to different methods for producing reference values from multiview video. This work extends monocular biomechanical analysis to detailed finger tracking, expanding access to quantitative characterization of hand movement from readily available video.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

Generalization properties of contrastive world models

Recent work on object-centric world models aim to factorize representations in terms of objects in a completely unsupervised or self-supervised manner. Such world models are hypothesized to be a key component to address the generalization problem. While self-supervision has shown improved performance however, OOD generalization has not been systematically and explicitly tested. In this paper, we conduct an extensive study on the generalization properties of contrastive world model. We systematically test the model under a number of different OOD generalization scenarios such as extrapolation to new object attributes, introducing new conjunctions or new attributes. Our experiments show that the contrastive world model fails to generalize under the different OOD tests and the drop in performance depends on the extent to which the samples are OOD. When visualizing the transition updates and convolutional feature maps, we observe that any changes in object attributes (such as previously unseen colors, shapes, or conjunctions of color and shape) breaks down the factorization of object representations. Overall, our work highlights the importance of object-centric representations for generalization and current models are limited in their capacity to learn such representations required for human-level generalization.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

PosePipe: Open-Source Human Pose Estimation Pipeline for Clinical Research

There has been significant progress in machine learning algorithms for human pose estimation that may provide immense value in rehabilitation and movement sciences. However, there remain several challenges to routine use of these tools for clinical practice and translational research, including: 1) high technical barrier to entry, 2) rapidly evolving space of algorithms, 3) challenging algorithmic interdependencies, and 4) complex data management requirements between these components. To mitigate these barriers, we developed a human pose estimation pipeline that facilitates running state-of-the-art algorithms on data acquired in clinical context. Our system allows for running different implementations of several classes of algorithms and handles their interdependencies easily. These algorithm classes include subject identification and tracking, 2D keypoint detection, 3D joint location estimation, and estimating the pose of body models. The system uses a database to manage videos, intermediate analyses, and data for computations at each stage. It also provides tools for data visualization, including generating video overlays that also obscure faces to enhance privacy. Our goal in this work is not to train new algorithms, but to advance the use of cutting-edge human pose estimation algorithms for clinical and translation research. We show that this tool facilitates analyzing large numbers of videos of human movement ranging from gait laboratories analyses, to clinic and therapy visits, to people in the community. We also highlight limitations of these algorithms when applied to clinical populations in a rehabilitation setting.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Transforming Gait: Video-Based Spatiotemporal Gait Analysis

Human pose estimation from monocular video is a rapidly advancing field that offers great promise to human movement science and rehabilitation. This potential is tempered by the smaller body of work ensuring the outputs are clinically meaningful and properly calibrated. Gait analysis, typically performed in a dedicated lab, produces precise measurements including kinematics and step timing. Using over 7000 monocular video from an instrumented gait analysis lab, we trained a neural network to map 3D joint trajectories and the height of individuals onto interpretable biomechanical outputs including gait cycle timing and sagittal plane joint kinematics and spatiotemporal trajectories. This task specific layer produces accurate estimates of the timing of foot contact and foot off events. After parsing the kinematic outputs into individual gait cycles, it also enables accurate cycle-by-cycle estimates of cadence, step time, double and single support time, walking speed and step length.

0 citations0 reviewsNo code linkedOpen access