Basics of Bioimage Analysis

Christian Tischer   2021-01-25   Comments Off on Basics of Bioimage Analysis

Date(s) - 2021-01-25 - 2021-02-02
14:00 CET - 17:00 CET


  • You have experience in taking microscopy images of biological samples.
  • You have a research project that may require automated quantification of microscopy images.


This is an image analysis course for beginners and will cover the following topics:

  • Image properties (data type, voxel size, display settings, …)
  • Image segmentation (binarisation by thresholding)
  • Image filtering and denoising
  • Object detection (connected component analysis and label images)
  • Object shape measurements
  • Object intensity measurements

The practicals will be conducted using the graphical user interface of Fiji ( However, we will focus on the concepts of image analysis rather than the specific implementation in Fiji. Thus, this course is also recommended if you are a beginner and want to perform image analysis in some other platform (e.g., using python scripting).


The course will be held online.


This is a joint course between EMBL and The Max Planck Society (for each organisation will have space for 15 praticipants).

If you can’t make it or don’t get a slot, please be aware that the course will be repeated later in the year!


Christian Tischer, Centre for Bioimage Analysis, EMBL Heidelberg, Germany.
Antonio Politi, Live-cell Imaging Facility, MPI Biophysical Chemistry, Goettingen, Germany.


The course is distributed across four afternoons:

  • Monday, 25. January 2021, 14:00 – 17:00 CET
  • Tuesday, 26. January 2021, 14:00 – 17:00 CET
  • Monday, 1. February 2021, 14:00 – 17:00 CET
  • Tuesday, 2. February 2021, 14:00 – 17:00 CET


This event is fully booked.