Image processing in Microscopy and Biomedical Imaging

Offered by:LuciLinX with Patrick Pirrotte, Sébastien Plançon, Céline Hoffmann, Andreas Jahnen, Christian Moll
When:17 + 24 September 2010
Where:CRP-Henri Tudor, CR SANTEC, 2A, rue Kalchesbrück, Luxembourg, L-1852 Luxembourg. Salle Louvain
Duration:14.00h - 17.00h
Requirements:Bring your own laptop.
Restrictions:Maximum 20 participants, first-come first-serve
Registration:By email to Patrick Pirrotte.
Contact:patrick DOT pirrotte AT tudor DOT lu

The course provides a practical introduction on improving your skills in light microscopy, with a comprehensive list of do’s and don’ts. It introduces image processing concepts based on real life use case scenarios, following the steps from image acquisition to analytical results. Hints are provided to prepare these results for publication.

Tentative plan:

September 17th, 2010 14:00- 17:00

Section I: Introduction to Microscopy (Sébastien Plançon, Céline Hoffmann, Patrick Pirrotte)
  1. Basics on light and light microscopy (light properties,  numerical aperture, the airy disk and resolution, light microscopy DIC and phase contrast, fluorescence: dye and GFP)
  2. Basics on confocal microscopy ( what is a confocal, lasers, dichroic mirrors, pinhole, PMT, z scanning)
  3. Applications in confocal microscopy (Subcellular localisation, 3D, timelaspe, FRAP, physiology...)
  4. Important Settings for  image treatment (cross-talk, gain settings range and histogram, background illumination, pinhole and optical slice, sampling and 3D reconstruction)
Section II: Introduction to Image Processing (Céline Hoffmann, Andreas Jahnen, Patrick Pirrotte)
  1. Image Processing Showcase : Image reconstruction
  2. Definition of Image processing
  3. Installing ImageJ
  4. Overview of ImageJ functionalities and Usage

September 24th, 2010 14:00- 17:00

Section III: Advanced Image Processing (Patrick Pirrotte, Andreas Jahnen, Christian Moll)
  1. Image restoration (denoising, background correction, pattern removal...)
  2. Measurements (Region of Interest, ROI Manager, Profile,…)
  3. Segmentation (Binarize, Threshold, Watershed,…)
  4. Case study: Cell counting using Particle Analyzer
  5. Case study: Colocalization
  6. Post processing: Getting your images publication ready
  7. Automation using the ImageJ macro language