Imaging Structure & Function in the Nervous System
July 26 - August 15, 2023

Key Dates
Application Deadline:  April 1st, 2023
Arrival: July 25th by 6pm EST
Departure: August 15th around 12pm EST

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.

Elizabeth Hillman, Columbia University
Ruben Portugues, Technical University, Munich, Germany
Philbert Tsai, University of California, San Diego

Associate Instructor:
Joseph Donovan,
Max Planck Institute of Neurobiology, Germany


COVID-19: All participants planning to attend in-person will be required to attest to recent COVID vaccination (within one year of the course’s start date) with an FDA or WHO approved vaccine. Additional safety measures will be in line with current NY and Federal Guidelines applicable in Summer 2023.


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

Advances in light microscopy, digital image processing, and the development of powerful fluorescent probes present expanding opportunities for investigating the nervous system, from synaptic spines to networks in the brain.

This intensive laboratory and lecture course will provide participants with the theoretical and practical knowledge to utilize emerging imaging technologies. The primary focus of the course will be on in vivo applications of light microscopy, particularly functional imaging with genetically encoded indicators.

Methods taught will include:

  • Multi-photon (2P and 3P) microscopy
  • Wide-field microscopy
  • Light-sheet and SCAPE microscopy 
  • Use of spatial light modulators and digital holography
  • Combination of imaging with optogenetics
  • Analysis of imaging datasets 

Lectures by leading experts will progress through basic concepts to presentation of cutting-edge methods. Students will learn the fundamentals of optics and microscopy, as well as the use of different types of cameras, laser scanning systems, in vivo preparations and image processing and analysis software. Hands-on optics and building exercises are an important component of the course, enabling students to develop an intuitive understanding of optical principles, assemble their own two-photon microscope, and gain experience with a variety of state-of-the-art commercial systems.

We encourage applications from theoretical neuroscientists and experimental neuroscientists working on a variety of model organisms, including mouse, fish, fly and worm. 

In your personal statements, applicants should answer the following questions (point by point, ≤ 1 page total):

  1. What are your reasons for attending the course?
  2. What is your experience with optical techniques and which microscope systems are available to you?
  3. What is your experience with data and image analysis and programming in Matlab or Python?
  4. How will the course help you in your current project?
  5. How will you help others using the knowledge obtained during the course?
  6. What are your long-term goals in learning more about optical methods?
All participants should familiarize themselves with the following concepts by the beginning of the course:
  1. Fundamentals of Fourier transform and matrix operations
  2. Basic programming experience in either MATLAB or Python (see e.g.: 1, 2, 3, 4, 5)
2022 Lecturers:
Arkarup Banerjee, Cold Spring Harbor Laboratory
Denise Cai, Mount Sinai Icahn School of Medicine
Liangyi Chen, Peking University, China
Valentina Emiliani, Institut de la Vision, France
Na Ji, University of California, Berkeley
Jeff Lichtman, Harvard University
Michael Lin, Stanford University
Emilie Macé, Max Planck Institute of Neurobiology, Germany
MacKenzie Matthis, EPFL, Switzerland
Adam Packer, University of Oxford, United Kingdom
Darcy Peterka, Columbia University
Kaspar Podgorski, Howard Hughes Medical Institute
Spencer Smith, University of California, Santa Barbara
Francois St. Pierre, Baylor College of Medicine
Carsen Stringer, Howard Hughes Medical Institute
Jennifer Waters, Harvard Medical School
Chris Xu, Cornell University
Nilay Yapici, Cornell University
Petr Znamenskiy, The Francis Crick Institute, United Kingdom

Support & Stipends

We would like to acknowledge the following companies that provided invaluable support:
Microscope Systems:
Bruker Corporation, Intellegent Imaging innovations, Scientifica, Sutter Instrument Company, Thorlabs, Inc
Andor Technology, Bitplane, Coherent, Inc, Conoptics, Crystalaser, Hamamatsu Photonics, Holoeye, Molecular Devices, Narishige International USA, Nikon Corporation, Photometrics, Thorlabs, Inc, Vidrio Technologies, LLC, World Precision Instruments
Incubation: Okolab, Tokai Hit USA Inc

Major support provided by the National Institute of Mental Health of the National Institutes of Health


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): $5,500

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 April 1):
  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: