Quantitative Imaging: From Acquisition to Analysis
March 29 - April 11, 2017
Application Deadline: January 20, 2017


Jennifer Waters, Harvard Medical School
Hunter Elliott,
Harvard Medical School


Talley Lambert, Harvard Medical School
Dave Richmond, Harvard Medical School

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

Combining careful image acquisition with rigorous computational analysis allows extraction of quantitative data from light microscopy images that is far more informative and reproducible than what can be seen by eye. This course will focus on advanced quantitative fluorescence microscopy techniques used for imaging a range of biological specimens, from tissues to cells to single molecules. The course is designed for quantitative cell and molecular biologists, biophysicists and bioengineers.

We provide a thorough treatment of the complete process of quantitative imaging, from the photons emitted from the sample to the extraction of biologically meaningful measurements from digital images.  Material is covered in lectures, discussion groups and hands-on quantitative exercises using commercial microscopes and open-source image analysis tools.

Concepts Covered Include:
  • Widefield fluorescence microscopy
  • Laser scanning and spinning disk confocal microscopy
  • CCD, EM-CCD & sCMOS cameras
  • Total internal fluorescence microscopy (TIRF)
  • Light sheet microscopy
  • Super-resolution microscopy (structured illumination, STED & localization microscopy)
  • Imaging and analyzing ratiometric “biosensors” (including FRET)
  • Fluorescent proteins and live sample imaging
  • Image processing (filtering, de-noising, corrections, deconvolution)
  • Image segmentation
  • Quantitative shape and intensity measurements
  • Object detection and tracking
  • Machine learning
  • Designing and troubleshooting quantitative imaging experiments
  • ...and more!

The course will also include a series of seminars from guest speakers who apply the methods we will discuss.

Teaching Assistants:  Anna Payne-Tobin Jost, Michael Weber, Marcelo Cicconet & Veronica Pessino

2017 Lecturers (more to follow):

Sara Abrahamsson, Rockefeller University
Nathan Shaner, The Scintillon Institute
Suliana Manley, Ecole Polytechnique Fédérale de Lausanne
Charless Fowlkes, UC Irvine
Jan Huisken, Morgridge Institute for Research
Bo Huang, University of California, San Francisco

2016 Lecturers:

Julie Canman, Columbia University
Elizabeth M.C. Hillman, Columbia University
Bo Huang, University of California, San Francisco
Clare Waterman, National Institutes of Health

Application Instructions:
To apply, you will need to submit a curriculum vitae and personal statement along with two letters of reference. Your statement should describe your current research project, with an emphasis on planned or current quantitative microscopy experiments, a list of the microscopes to which you have access to use for your research and what you hope to gain by participating in the course. You will be expected to stay at CSHL for the full duration of the course.

Support & Stipends

Major support provided by the National Cancer Institute

Stipends are available to offset tuition costs as follows:


US applicants (National Cancer Institute)
Interdisciplinary Fellowships (transitioning from outside biology)  & Scholarships (transitioning from other biological disciplines) (Helmsley Charitable Trust)
International applicants (Howard Hughes Medical Institute)

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): $3,810

This button links to a short form which confirms your interest in the course. 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 March 28 and plan to depart after lunch on April 11.