A first introduction to scripting in Fiji using the ImageJ Macro language.
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