A Raspberry Pi-based system for observing and quantifying larval zebrafish swimming behaviour while performing functional microscopy.
Quantifying animal behavior during microscopy is crucial to associate optically recorded neural activity with behavioural outputs and states. Here I describe an imaging and tracking system for head-restrained larval zebrafish compatible with functional microscopy. This system is based on the Raspberry Pi computer, Pi NoIR camera, and open-source software for the real-time tail segmentation and skeletonization of the zebrafish tail at over 100hz. This allows for precise and long-term analyses of swimming behaviour, that can be related to functional signals recorded in individual neurons. This system offers a simple but performant solution for quantifying the behavior of head-restrained larval zebrafish, which can be built for 340 euro.
pi_tailtrack: A compact, inexpensive, and open-source behaviour-tracking system for head-restrained zebrafish: Randlet O. Journal of Experimental Biology (2023) 226, jeb246335. doi:10.1242/jeb.246335