Measuring and modeling the motor system with machine learning

The utility of machine learning in understanding the motor system is promising a revolution in how to collect, measure, and analyze data. The field of movement science already elegantly incorporates theory and engineering principles to guide experimental work, and in this review we discuss the growing use of machine learning: from pose estimation, kinematic analyses, dimensionality reduction, and closed-loop feedback, to its use in understanding neural correlates and untangling sensorimotor systems. We also give our perspective on new avenues where markerless motion capture combined with biomechanical modeling and neural networks could be a new platform for hypothesis-driven research.

Perspectives on individual animal identification from biology and computer vision

Identifying individual animals is crucial for many biological investigations. In response to some of the limitations of current identification methods, new automated computer vision approaches have emerged with strong performance. Here, we review current advances of computer vision identification techniques to provide both computer scientists and biologists with an overview of the available tools and discuss their applications. We conclude by offering recommendations for starting an animal identification project, illustrate current limitations and propose how they might be addressed in the future.

A Primer on Motion Capture with Deep Learning: Principles, Pitfalls and Perspectives

Extracting behavioral measurements non-invasively from video is stymied by the fact that it is a hard computational problem. Recent advances in deep learning have tremendously advanced predicting posture from videos directly, which quickly impacted neuroscience and biology more broadly. In this primer we review the budding field of motion capture with deep learning. In particular, we will discuss the principles of those novel algorithms, highlight their potential as well as pitfalls for experimentalists, and provide a glimpse into the future.

Deep learning tools for the measurement of animal behavior in neuroscience

Recent advances in computer vision have made accurate, fast and robust measurement of animal behavior a reality. In the past years powerful tools specifically designed to aid the measurement of behavior have come to fruition. Here we discuss how capturing the postures of animals - pose estimation - has been rapidly advancing with new deep learning methods. While challenges still remain, we envision that the fast-paced development of new deep learning tools will rapidly change the landscape of realizable real-world neuroscience.

Pretraining boosts out-of-domain robustness for pose estimation

Deep neural networks are highly effective tools for human and animal pose estimation. However, robustness to out-of-domain data remains a challenge. Here, we probe the transfer and generalization ability for pose estimation with two architecture classes (MobileNetV2s and ResNets) pretrained on ImageNet. We generated a novel dataset of 30 horses that allowed for both within-domain and out-of-domain (unseen horse) testing. We find that pretraining on ImageNet strongly improves out-of-domain performance. Moreover, we show that for both pretrained and networks trained from scratch, better ImageNet-performing architectures perform better for pose estimation, with a substantial improvement on out-of-domain data when pretrained. Collectively, our results demonstrate that transfer learning is particularly beneficial for out-of-domain robustness.

Markerless tracking of user-defined features with deep learning

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, yet markers are intrusive (especially for smaller animals), and the number and location of the markers must be determined a priori. Here, we present a highly efficient method for markerless tracking 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 a broad collection of experimental settings: mice odor trail-tracking, egg-laying behavior in drosophila, and mouse hand articulation in a skilled forelimb task. For example, during the skilled reaching behavior, individual joints can be automatically tracked (and a confidence score is reported). Remarkably, even when a small number of frames are labeled ($\approx 200$), the algorithm achieves excellent tracking performance on test frames that is comparable to human accuracy.