3-7 May 2021
Europe/Berlin timezone

Registration deadline: 16 April 2021

Course aim:

Introduces novice users to basic concepts and techniques in quantitative image analysis.  Major topics covered include the basics of filtering and segmenting images along with techniques to extract useful measures from bio image data. Participants will learn how to use Fiji and Ilastik software and perform realistic bio-image analysis through numerous exercises and interactive hands-on sessions.

The course will take place online via zoom.

Some of the independent exercises will be given as homework so make sure you have some preparation time available outside of the course hours.


The following concepts will be introduced with many ImageJ/Fiji & Ilastik hands-on-sessions and exercises along the way:

  • Basic concepts: image characteristics, visualization, regions of interest and measurements
  • Segmentation 1: preprocessing, thresholding, mask/region analysis and spot detection
  • Image filters and morphological operations
  • Segmentation 2: Machine learning for image segmentation
  • ImageJ Macro language
  • Visualization, exploration and segmentation in 3D images
  • Stitching of tiled images and image registration
  • Time sequence analysis and object tracking in time sequences
  • Good practices for performing repeatable analysis as well as tips and tricks for bioimage analysis

The number of participants is limited to 20.  The course is open for DIPP PhD students and CBG Postdocs.

We will inform you after 19 April 2021 whether a slot in the course could be assigned to you!


Noreen Walker & Gayathri Nadar, MPI-CBG Scientific Computing Facility

Each part of the course contains some theoretical presentations, short exercises to apply new knowledge and a long exercise to start combining the tools and tackle more real life analysis.

All days 13:00-17:00.

Day 1 (Mon 3.5.)

Image basics, visualization, region of interests, measurements

Day 2 (Tue 4.5.)

Segmentation: classic pipeline and more advanced filtering methods

Day 3 (Wed 5.5.)

Machine learning for image segmentation, introduction to ImageJ Macro

Day 4 (Thu 6.5.)

Visualization and analysis of 3D data

Day 5 (Fri 7.5.)

Time sequence analysis and tracking, image stitching, feedback round


ImageJ: https://imagej.net/Welcome

Bioimage data analysis book: https://www.imaging-git.com/applications/bioimage-data-analysis-0/

Fiji training notes: https://cloudstor.aarnet.edu.au/plus/index.php/s/bxRU7kkoj2rIjCh#pdfviewer


Get your laptop ready for the course. You will need it to perform all the hands-on sessions and exercises.

Before the course:

  • Install a fresh version of Fiji and Ilastik on your laptop.
  • You will receive detailed installation instructions and material from Noreen and Gayathri.
  • Install Zoom.
  • You will need a laptop, mouse, and preferably an external monitor.
  • Contact us if you have any issue with one of the above!
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