Chapter 30 - Software tools for behavioral phenotyping of zebrafish across the life span

In this chapter, we address how one can detect and measure specific behaviors in zebrafish, from the embryonic stage to adulthood, and in various behavioral paradigms using automated, image-based analysis software. In the first section, we address the measurement of activity in embryos and heart rate in larvae. For the larval stage, we also show how software can analyze the fish's body shape and movement trajectory to measure activity and specific behaviors like avoidance and escape responses. Custom output variables address specific research questions and increase throughput. For adult zebrafish, we describe applications with the novel tank diving test, learning in the T-maze, aggressive behavior in mirror tests, and quantify shoaling behavior. The advantages of tracking in three dimensions relative to classic 2D tracking are also addressed. Finally, we discuss current limitations and directions for future development.