ImageJ-Macro scripting March 2022

  • Booking will be opened on 14th of February 2022 at 10 am
  • Start: Mar 21, 2022 01:00 PM (Local Time Germany)
  • End: Mar 22, 2022 05:00 PM
  • Speaker: Politi, Tischer, Stokkermans
  • Antonio Politi; Live-cell Imagaing Facility of the MPI for multidisciplinary Sciences and Christian Tischer and Anniek Stokkermans; Center for Bioimage Analysis of EMBL
  • Location: online course
  • Room: Zoom-Meeting
  • Host: Max Planck BioImaging Core Unit Network
 	 	 	 	 ImageJ-Macro scripting March 2022
The scripting for image analysis course covers how to setup and run scripts, variables, comments, functions, and batch processing. The practicals will be conducted using the ImageJ macro language. A knowledge of the graphical user interface FiJi and basic concepts in image analysis is a prerequisite. Two afternoons online course on " ImageJ-Macro scripting" March 21st & 22nd 2022: 13:00 - 17:00 (CET)


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

  • Setting up a scripting environment
  • Running and understanding an image analysis script
  • Using variables, comments and functions
  • Batch processing (for-loops)

The practicals will be conducted using the ImageJ macro language. While the examples in this course will be image analysis scripts, the image analysis concepts will not be explained (see prerequisites).


Using the Fiji graphical user interface, you are able to

  • Visualise images and modify the corresponding lookup tables
  • Inspect and understand image properties (data type, voxel size)
  • Perform simple image segmentation (binarization by thresholding)
  • Perform object detection (connected component analysis and label images)
  • Perform basic object shape measurements (area, circularity)
  • Perform basic object intensity measurements

Please follow this link to register at the Max Planck Academy for the course: Registration Link

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