Modern high-throughput neuroanatomical tools—including but not limited to barcode-based tracing methods—allow unprecedented insight into the structure of the nervous system. Their use, however, is currently restricted to small set of expert laboratories. This limited uptake is not due to an inherent cost or difficulty of these techniques, but rather due to a lack of training opportunities. In this new CSHL course, we aim to teach the core skills required for successfully applying a range of modern neuroanatomical techniques. We will cover viral tracing tools, including anterograde, retrograde, and transsynaptic tracers, brain clearing and whole brain analysis of axonal data, MAPseq and BARseq, as well as RNA in situ sequencing technologies. In practicals, students will learn how to prepare virus, how to acquire and analyze whole-brain volumetric axon tracing data, and how to perform a BARseq2 experiment. After completing this course, we expect students to have the skills to implement a range of cutting-edge neuroanatomical techniques in their own labs.