Quantitative Imaging: From Acquisition to Analysis
April 2 - 16, 2019
Application Deadline: January 31, 2019


Jennifer Waters, Harvard Medical School
Hunter Elliott, PathAI, Inc
Talley Lambert, Harvard Medical School


Florian Jug, Max Planck Institute, Dresden, Germany
Suliana Manley, Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland

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.

2019 Teaching Assistants:

Anna Payne-Tobin Jost, George Campbell, Tejeshwar Rao, Marcelo Cicconet, Jessica Hornick & Sophia Hirsch

2019 Lecturers:

Luke Lavis, Janelia Research Campus
Julie Canman, Columbia University
Hari Shroff, National Institute of Health
Nathan Shaner, University of California San Diego

Support & Stipends

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.


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, Takai Hit USA Inc.

Light Sources: Lumencor

Cost (includes food and housing): $4,160

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 April 1 and depart after lunch on April 16.

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: