High Throughput Neuroanatomy
October 16 - 25, 2022
Application & Materials Deadline: July 15, 2022


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


COVID-19: All participants planning to attend in-person will be required to provide documentary proof of full vaccination AND first booster (when eligible) with an FDA or EMA approved vaccine. Additional safety measures will be in line with current NY and federal guidelines applicable in spring 2022.


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

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.

Speakers Include: 

Edward Boyden, Massachusetts Institute of Technology/HHMI
Edward Callaway, The Salk Institute for Biological Studies
Liqun Luo, Stanford University
Emily Sylwestrak, University of Oregon
Bosiljka Tasic, Allen Institute for Brain Science
Xiao Wang, Broad Institute/MIT
Zhuhao Wu, Icahn School of Medicine at Mount Sinai
Tony Zador, Cold Spring Harbor Laboratory
Hongkui Zeng, Allen Institute for Brain Science

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): $3,400

No fees are due until you have completed the full application process and are accepted into the course. Students accepted into the course should plan to arrive by early evening on October 15 and plan to depart after lunch on October 25.

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: