A first introduction to scripting in Fiji using the ImageJ Macro language. Material was prepared by Anna Klemm and presented by Elnaz Fazeli for the course Bioimage Analysis for Life Scientists, organized by Centre for Cellular Imaging at the University of Gothenburg.
After the session you will be able to:
- Record workflows for automation and documentation
- Explain the concepts of variables, for-loops, conditional statements, arrays – and use them within the ImageJ macro language.
- Modify ROIs within the ROI-Manager via scripting.
- Batch-execute code on all images of one folder.
- Independently explore new functionalities of ImageJ macro scripting within the Built-in macro functions.
- Create your own script to automate your workflows
To be able to follow the course you need to know basic image analysis concepts and how to apply them using Fiji:
- pixel scaling (pixel size)
- handling of multi-channel images
- segmentation by applying an global threshold
- “analyze particles” (connected component analysis)
- ROIs
- performing measurements
- Presentation: Google Slides
- Youtube video: NEUBIAS Academy