Automated Behavioral Tracking of Zebrafish Larvae with DeepLabCut and SLEAP: Pretrained Networks and Datasets of...

Zebrafish are an important model system in behavioral neuroscience due to their rapid development and suite of distinct, innate behaviors. In this study, we tracked the behavior of 6 d postfertilization larval zebrafish (of indeterminate sex, as larvae at this developmental stage are sexually undifferentiated). Quantifying many of these larval behaviors requires detailed tracking of eye and tail kinematics, which in turn demands imaging at high spatial and temporal resolution, ideally using semi- or fully automated tracking methods for throughput efficiency. However, creating and validating accurate tracking models is time-consuming and labor-intensive, with many research groups duplicating efforts on similar images. With the goal of developing a useful community resource, we trained pose estimation models using a diverse array of video parameters and a 15-keypoint pose model. We deliver an annotated dataset of free-swimming and head-embedded behavioral videos of larval zebrafish, along with four pose estimation networks from DeepLabCut and SLEAP (two variants of each). We also evaluated model performance across varying imaging conditions to guide users in optimizing their imaging setups. This resource will allow other researchers to skip the tedious and laborious training steps for setting up behavioral analyses, guide model selection for specific research needs, and provide ground-truth data for benchmarking new tracking methods.