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Introduction to optical imaging and image analysis


Optical microscopy is one of the most useful tools in life science studies. This course aims to introduce the different optical microscopy modalities. The course begins with basics in optics and image formation, then steps through the different contrast mechanism before detailing the latest advances super-resolution microscopy. The goal is to familiarize students with the different approaches in order to correctly identify the best technique to investigate their biological question. A second part of the course is dedicated to image handling and analysis using the widespread imageJ software. It includes a hands-on session with real data examples. The course will cover the following:


  • Basics in optics: lens and image formation
  • How does a microscope work?
  • Noise: origins and characteristics
  • Contrast modalities in microscopy: transmission, phase contrast, fluorescence, other contrast mechanisms
  • Imaging in 3D problems and solutions: confocal imaging, light sheet excitation, multiplane imaging
  • Super-resolution methods: insights into single molecule localization techniques: fluorofores, excitation power, localization.
  • Localizing molecules in 3D: challenges and the different available solutions
  • How to choose the best technique to treat your biological question: pros and cons of each


  • Detection: detectors, camera, pixels
  • Image handling
  • Image handling: histogram, contrast, brightness
  • Background substraction, denoising, filtering, deblurring
  • Deconvolution, correlation
  • Single molecule localization: thresholding, localization, precisions and accuracy, tracking


  • Interface
  • Image handling and visualization
  • Measurements, profiles, projections
  • Deconvolution
  • Building macros
  • Single molecule localization


Bassam Hajj
E-mail: bassam.hajj@curie.fr


Dates: February 14th, 15th and 22nd
Location: Classroom 2.11, 2nd floor, CRI building 
Credits: 21 hours (3 full days)

  • Less than 50% attendance = 0 hours validated
  • 50%-80% attendance = number of hours validated equal the number of hours attended
  • 80% or more = 100% of hours validated


Enroll on Google Classroom

  • Log in with you cri-paris.org email address
  • Click the + in the top right corner of the screen and click Join class
  • Enter registration code: 1fl5egr