Quantitative Imaging: From Acquisition to Analysis
April 11 - 25, 2023

Key Dates
Application Deadline
: January 31, 2023
Arrival: April 10th by 6pm EST
Departure: April 25th 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.


Jennifer Waters, Harvard Medical School 
Florian Jug, Fondazione Human Technopole, Italy
Hunter Elliott, PathAI, Inc
Talley Lambert, Harvard Medical School


Suliana Manley, Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland


COVID-19: All participants planning to attend in-person will be required to attest to recent COVID vaccination with an FDA or WHO approved vaccine. Additional safety measures will be in line with current NY and federal guidelines applicable in Spring 2023.


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

Follow us on Twitter @QIatCSHL

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 reflection 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.

2023 Teaching Assistants
Federico Gasparoli, Harvard Medical School
Lillian Horin, Harvard Medical School
Rylie Walsh, Harvard Medical School

2023 Planned Speakers
Jeeyun Chung, Harvard School of Public Health
Beth Cimini, Broad Institute of MIT and Harvard
Nathan Shaner
The Scintillon Institute

Support & Stipends

Major support for this course is provided by the National Cancer Institute.

This course is supported in part by grants from Howard Hughes Medical Institute through the Science Education Program.

We would like to acknowledge the following companies that provided invaluable support:
Microscopes: 89 North, Applied Scientific Instrumentation, Leica Microsystems, Mizar Imaging, Nikon Instruments, Prior Scientific, Scientifica
Cameras: Hamamatsu Photonic Systems, PCO, Photometrics
Filters and Filter Cubes: Chroma Technology
Incubation: Okolab, Tokai Hit USA, Inc.
Light Sources: Lumencor

Financial aid is available to help offset tuition costs as follows:

  • US applicants can apply for financial aid provided by the National Cancer Institute.
  • BioImaging North America (BINA): Through BINA’s Professional Development Program, North American BINA members can apply for financial assistance to cover all or some portion of the tuition enrollment fee for the Quantitative Imaging: From Acquisition to Analysis course. You should indicate when you apply that you are interested in BINA financial assistance. If you are accepted for the course, CSHL will connect you with the BINA administrative team if you meet the demographic eligibility requirements. BINA membership is required to qualify for support, but BINA membership is free - join.
  • Interdisciplinary Fellowships (transitioning from outside biology) & Scholarships (transitioning from other biological disciplines) are provided by the Helmsley Charitable Trust.
  • International applicants can apply for financial aid provided by the Howard Hughes Medical Institute.

Please indicate your eligibility for funding in your financial aid request submitted as part of your application materials. Financial aid requests do not affect selection decisions made by the instructors.


Cost (includes food and housing): $4,465

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

Before applying, ensure you have:
  1. Personal statement/essay;
  2. Two letters of recommendation;
  3. Curriculum vitae/resume;
  4. Financial aid request (optional). 
    More details.

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.

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: