High Throughput Neuroanatomy
October 20 - 31, 2023

Key Dates:
Application Deadline:  July 15, 2023
Arrival: October 19th by 6pm EST
Departure: October 31st around 12pm 

CSHL Courses are intensive, running all day and often including evenings and weekends; students are expected to attend all sessions and reside on campus for the duration of the course.


See the roll of honor - who's taken the course in the past

Xiaoyin Chen, Allen Institute for Brain Science
Laura DeNardo, University of California Los Angeles
Justus Kebschull, Johns Hopkins University
Lindsay Schwarz, St. Jude Children's Research Hospital



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.

2023 Speakers Include: 

Martha Bagnall, Washington University School of Medicine
Edward Boyden, MIT, HHMI
Hank Greely, Stanford University
Gilles Laurent, Max-Planck-Institute for Brain Research, Frankfurt/Main, Germany 
Liqun Luo, Stanford University                      
Xiao Wang, MIT / Broad Institute
Zhuhao Wu, Icahn School of Medicine at Mount Sinai
Anthony Zador, Cold Spring Harbor Laboratory
Le Zhang, Yale University
Petr Znamenskiy, The Francis Crick Institute, London, United Kingdom 

Support & Stipends

We would like to acknowledge the following companies for equipment loans and technical support:
Leica Biosystems, Miltenyi Biotec, Nikon Instruments

Stipends are available to offset tuition costs as follows:


Please indicate your eligibility for funding in your stipend request submitted when you apply to the course. Stipend requests do not affect selection decisions made by the instructors.

Cost (including board and lodging): $3,890

No fees are due until you have completed the full application process and are accepted into the course. 

Before applying, ensure you have (all due July 15):
  1. Personal statement/essay;
  2. Letter(s) of recommendation;
  3. Curriculum vitae/resume (optional);
  4. Financial aid request (optional).
    More details.

If you are not ready to fully apply but wish to express interest in applying, receive a reminder two weeks prior to the deadline, and tell us about your financial aid requirements, click below: