Quantitative Imaging: From Acquisition to Analysis
March 24 - April 7, 2020
Application & Materials Deadline: January 31, 2020


Jennifer Waters, Harvard Medical School
Florian Jug, Max Planck Institute, Dresden, Germany
Hunter Elliott, PathAI, Inc
Talley Lambert, Harvard Medical School


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


COVID-19 - UPDATE 3.4.2020: It is with considerable regret that we announce the cancellation of this course for 2020 but it will be rescheduled for 2021. We are closely monitoring the COVID-19 situation as it evolves, following CDC guidelines to ensure the safety and well-being of our participants and staff. Participants from CDC Warning Level 3 countries (currently China, South Korea and Italy) are being advised to cancel their participation at upcoming courses unless they can demonstrate having departed the area at least two weeks prior to their visit to CSHL.  We are evaluating our future events on a four-week rolling basis.  Full advisory 


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

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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.

2020 Teaching Assistants:

Anna Jost, Harvard Medical School
Rylie Walsh, Harvard Medical School
Jessica Hornick, Northwestern University
Nasim Jamali, Mount Sinai School of Medicine
George Campbell, St. Jude Children's Research Hospital
Marcelo Cicconet, Harvard Medical Schoo

2020 Lecturers:

Kristin Branson, Janelia Research Center
Reto Fiolka, UT Southwestern Medical Center
Jonas Ries, European Molecular Biology Laboratory (EMBL)
Nathan Shaner, The Scintillon Institute

This course is supported by: National Cancer Institute.

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:

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): $4,285

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 23 and depart after lunch on April 7.

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: