Optical Microscopy & Imaging in the Biomedical Sciences

This course will enable the participants to obtain and interpret high quality microscope data, to understand and assess potential artifacts, to perform quantitative optical measurements, and to generate digital images for documentation and analysis that accurately present the data.

Course date:
Aug 15, 2022 - Aug 25, 2022
Application due date:
May 12, 2022

Directors: Joerg Bewersdorf, Yale University; and Alison North, The Rockefeller University

Course Description

This course is designed primarily for research scientists, postdoctoral trainees, core facility directors/staff and graduate students working in the biological sciences. Non-biologists seeking a comprehensive introduction to microscopy and digital imaging in the biomedical sciences will also benefit greatly from this course. The 9-day course is limited to 24 participants to ensure a truly interactive, hands-on experience. It consists of interrelated lectures, laboratory exercises, demonstrations, and discussions that will enable the participants to obtain and interpret high quality microscope data, to understand and assess potential artifacts, to perform quantitative optical measurements, and to generate digital images for documentation and analysis that accurately present the data. The course also places a strong emphasis on appropriate sample preparation, including choice of fluorescent probes and fluorescent proteins, and tissue clearing and refractive index matching. Particular emphasis will be placed on ‘picking the right tool for the job’.

Topics to be covered include: 

  • Fundamental principles of microscope design, image formation, resolution and contrast; 
  • Transmitted light and fluorescence microscopy techniques; 
  • Cameras, signal to noise ratio, digital image recording, processing and analysis, multispectral imaging; 
  • Advanced fluorescence – fluorescent probes, fluorescent biosensors, TIRF, FRET, FLIM, FRAP, polarization of fluorescence, fluorescence correlation spectroscopy; 
  • Digital image restoration/deconvolution, and 3-D imaging principles; 
  • Confocal and multiphoton laser scanning microscopy and light-sheet microscopy; 
  • Super-resolution techniques including localization microscopy, stimulated emission depletion microscopy (STED), and structured illumination microscopy.

Course participants will have direct hands-on experience with state-of-the-art microscopes, a variety of digital cameras, and image processing software provided by major optical, electronics, and software companies. Instruction will be provided by experienced staff from universities and industry. Participants are encouraged to bring their own, fixed biological specimens, and to discuss individual research problems with the faculty.