Quantitative Imaging: From Acquisition to Analysis
April 4 - 17, 2018
Application Deadline: January 31, 2018

Jennifer Waters, Harvard Medical School
Hunter Elliott,
Harvard Medical School
Suliana Manley, EPFL, Switzerland

Talley Lambert, 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 & Jessica Hornick

2018 Lecturers (more to follow):
Philipp Keller, Janelia Research Campus
Nathan Shaner, The Scintillon Institute
Florian Jug, MPI

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): $3,885

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 April 3 and plan to depart after lunch on April 17.