Basics of Bioimage Analysis

Christian Tischer   2021-06-07   Comments Off on Basics of Bioimage Analysis

Date(s) - 2021-06-07 - 2021-06-15
14:00 CEST - 17:00 CEST


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


This course is identical to the "Basics of Bioimage Analysis" course in January/February 2021.

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).


  • 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, 7. June 2021, 14:00 – 17:00 CET
  • Tuesday, 8. June 2021, 14:00 – 17:00 CET
  • Monday, 14. June 2021, 14:00 – 17:00 CET
  • Tuesday, 15. June 2021, 14:00 – 17:00 CET


This event is fully booked.