ImageJ macro scripting for bioimage analysis

Christian Tischer   2022-03-21   Comments Off on ImageJ macro scripting for bioimage analysis

Date(s) - 2022-03-21 - 2022-03-22
13:00 CET - 17:00 CET


  • Essential: Practical experience using the graphical user interface of Fiji.
  • Helpful: Knowledge of basic concepts of bioimage anlaysis.


Scripting is an essential skill for creating reproducible and publishable image analysis workflows. Thanks to the possibility to record scripts using the graphical user interface, the ImageJ macro language is a very accessible and well established entry point for beginners in bioimage analysis scripting without any programming experience. Please note that this course is entirely focussed on IJ-macro scripting and will thus not cover any concepts and algorithms of bioimage analysis.

The course will cover:

  • Running, understanding and modifying an ImageJ macro
  • ImageJ macro recording
  • Using variables (parameters)
  • String concatenation
  • Automated output saving (label mask images, ROIs, and tables)
  • Fetching user input (@Parameters)
  • Batch processing


The course will be held online.


This is a joint course between EMBL and the Max Planck Society where each organisation will have space for 25 praticipants.


  • Antonio Politi. Live-cell Imaging Facility, MPI for Multidisciplinary Sciences, Goettingen, Germany.
  • Anniek Stokkermans, Arif Khan, and Christian Tischer. Centre for Bioimage Analysis (CBA), EMBL Heidelberg, Germany.


The course is distributed across two afternoons:

  • Monday, 21. March 2022, 13:00 – 17:00 CEST
  • Tuesday, 22. March 2022, 13:00 – 17:00 CEST



Bookings are closed for this event.