Image Analysis course 2017

This course is an introduction to image processing and analysis, with a focus on biologically relevant examples. The attendees will learn the fundamentals of image analysis including how to do basic Macro programming in Fiji (ImageJ) for automated batch analysis of images, use different software solutions for image analysis, and will be introduced to visualisation and explorative data analysis after extraction of numerical data from images.


Next course: 6th of June and 19th - 23rd of June 2017

Max number of participants: 22

Audience: 10 seats open to all, 12 seats reserved for PhD students.


*PhD students have to apply via the PhD school.


Attendees accepted for the course will before the course have to submit an image processing project, summarizing a scientific question and describing an image analysis challenge. The course program includes time to work on a personal project with advice, supervision and support from the teachers. Within one week after the course, attendees will have to submit a course report based on the outcome from their own project.

Teaching faculty:

  • Simon Nørrelykke, IDA-ScopeM, ETH, Zurich, Switzerland
  • Szymon Stoma, IDA-ScopeM, ETH, Zurich, Switzerland
  • Chong Zhang, SIMBioSys, University Pompeu Fabra, Barcelona, Spain

Preliminary programme

6th of June
Image formation
Preparation of project
Monday 19th
Image analysis basics
Image analysis in Fiji
Tuesday 20th
Fiji plugins
Image analysis in Fiji
Wednesday 21st
Writing Macros in Fiji
Work on projects
Thursday 22nd
Image analysis in Ilastik Work on projects
Friday 23rd
Tableau / Plotly
Project presentation