Quantitative Imaging: From Acquisition to Analysis
April 1 -16, 2024

Key Dates
Application Deadline
: January 31, 2024
Arrival: April 1st by 6pm EST
Departure: April 16th 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
Beth Cimini, Broad Institute of MIT and Harvard, Cambridge, MA
Florian Jug, Fondazione Human Technopole, Italy
Hunter Elliott, Bighat Biosciences
Talley Lambert, Harvard Medical School


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

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.

2024 Teaching Assistants
Damian Dalle Nogare, Fondazione Human Technopole, Milano, Italy 
Eva de la Serna, Harvard Medical School, ,  
Federico Gasparoli, Harvard Medical School, Boston, MA 
Anna Jost, Harvard Medical School, Boston, MA 

2024 Invited Speaker
Chad Hobson, NEW Affiliation, Chapel Hill, NC 

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, AbberiorApplied Scientific Instrumentation, Biovision Technologies, Inc., Leica Microsystems, Nikon Instruments, Prior Scientific, Scientifica
Cameras: Hamamatsu Photonic Systems, PCO, Photometrics
Filters and Filter Cubes: Chroma Technology
Incubation: Okolab, Tokai Hit USA, Inc.
Lasers: Coherent, Toptica Photonics Inc.
Light Sources: Lumencor
Software: Andor Technology 

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

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): $4,645 USD

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: