This book merges approaches in understanding the function of the light-gated ion channels known as channelrhodopsin together with methods addressing how channelrhodopsins can be used to address biomedical questions on a cellular or organismal level. Since the first molecular identification of channelrhodopsins, a broad range of tools have been created and new approaches developed to both better understand the molecular determinants of channelrhodopsin function as well as to use these and homologous proteins from a variety of species as tools to better understand physiological processes, which this volume addresses. Additionally, channelrhodopsins have become instrumental as a potential treatment for disease states. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.