||The zebrafish (Danio reiro) is a good model organism for vertebrate development. The organization of the embryo is simple and the body is transparent, making it easy to study with many different microscopy techniques. In addition, the embryonic development is rapid and after 5-6 days post-fertilization (dpf) all major organs are present in the larvae. At the High-Throughput Neurotechnology Group at Massachusetts Institute of Technology we have been developing several different high-throughput systems for imaging and analyzing zebrafish development. In this talk I will present two systems that I have been working with. First, a system for neuropharmacology screens based on high-content behavioral phenotyping. Secondly, a platform for automated deep-phenotyping of zebrafish that uses optical tomography to rapidly image and analyze 3D expression patterns zebrafish.