Image Analysis Fundamentals

This is a two-day course for the master students of the Department of Biosystems Science and Engineering at the ETH Zurich.

Course content

First day

  • Course introduction
  • Introduction to Fiji
  • Image processing/analysis fundamentals (with selected examples/demos in Fiji)
  • Deconvolution (with HRM hands-on)
  • Scripting in Fiji

Second day

  • Cell Profiler
  • ilastik
  • Good practices in scientific image analysis
  • Analysis hands-on
  • Selected libraries (quick presentation and demo)
    • MATLAB: Image Processing Toolbox
    • Python: scikit-image, openCV

Course material available on request.

Digital images (Linear shift-invariant systems)

An introduction to signals and systems, sampling theory, filtering in spatial and frequency domain.

First presented at the Image Processing basics course organized by the Microscopy Network Basel in November 2014 (last update: November 2016).

Deconvolution primer

This is a short introduction to optics, image formation, and deconvolution that I give before an hands-on course on the Huygens Remote Manager (last update: November 2016).

Introduction to ImarisXT and IceImarisConnector

Extending Imaris with custom MATLAB functions:

Extract from Imaris Open Launch talk:

Biological Image Processing Summer School 2010

Focused on ImageJ, MATLAB and Cell Profiler

In collaboration with the (former) Light Microscopy Centre, ETH Zurich
August 29th – September 3rd, 2010
Role: co-organizer of the scientific program and teacher

Introduction to MATLAB programming

Course material

Introduction to statistics with MATLAB

Course material

This course had its own introduction to MATLAB, but I recommend using sessions 1 and 2 (and maybe even 3) from the “Introduction to MATLAB programming” course above.

Source control with Subversion

Quick introduction to source control using subversion.