Jan Zimmermann

Kevin Luxem, Jennifer J. Sun, Sean P. Bradley et al.

Recently developed methods for video analysis, especially models for pose estimation and behavior classification, are transforming behavioral quantification to be more precise, scalable, and reproducible in fields such as neuroscience and ethology. These tools overcome long-standing limitations of manual scoring of video frames and traditional "center of mass" tracking algorithms to enable video analysis at scale. The expansion of open-source tools for video acquisition and analysis has led to new experimental approaches to understand behavior. Here, we review currently available open-source tools for video analysis and discuss how to set up these methods for labs new to video recording. We also discuss best practices for developing and using video analysis methods, including community-wide standards and critical needs for the open sharing of datasets and code, more widespread comparisons of video analysis methods, and better documentation for these methods especially for new users. We encourage broader adoption and continued development of these tools, which have tremendous potential for accelerating scientific progress in understanding the brain and behavior.

Nisarg Desai, Praneet Bala, Rebecca Richardson et al.

Because of their close relationship with humans, non-human apes (chimpanzees, bonobos, gorillas, orangutans, and gibbons, including siamangs) are of great scientific interest. The goal of understanding their complex behavior would be greatly advanced by the ability to perform video-based pose tracking. Tracking, however, requires high-quality annotated datasets of ape photographs. Here we present OpenApePose, a new public dataset of 71,868 photographs, annotated with 16 body landmarks, of six ape species in naturalistic contexts. We show that a standard deep net (HRNet-W48) trained on ape photos can reliably track out-of-sample ape photos better than networks trained on monkeys (specifically, the OpenMonkeyPose dataset) and on humans (COCO) can. This trained network can track apes almost as well as the other networks can track their respective taxa, and models trained without one of the six ape species can track the held out species better than the monkey and human models can. Ultimately, the results of our analyses highlight the importance of large specialized databases for animal tracking systems and confirm the utility of our new ape database.

Praneet C. Bala, Jan Zimmermann, Hyun Soo Park et al.

Recent technological developments have spurred great advances in the computerized tracking of joints and other landmarks in moving animals, including humans. Such tracking promises important advances in biology and biomedicine. Modern tracking models depend critically on labor-intensive annotated datasets of primary landmarks by non-expert humans. However, such annotation approaches can be costly and impractical for secondary landmarks, that is, ones that reflect fine-grained geometry of animals, and that are often specific to customized behavioral tasks. Due to visual and geometric ambiguity, nonexperts are often not qualified for secondary landmark annotation, which can require anatomical and zoological knowledge. These barriers significantly impede downstream behavioral studies because the learned tracking models exhibit limited generalizability. We hypothesize that there exists a shared representation between the primary and secondary landmarks because the range of motion of the secondary landmarks can be approximately spanned by that of the primary landmarks. We present a method to learn this spatial relationship of the primary and secondary landmarks in three dimensional space, which can, in turn, self-supervise the secondary landmark detector. This 3D representation learning is generic, and can therefore be applied to various multiview settings across diverse organisms, including macaques, flies, and humans.