Welcome to Introduction to Macro writing in ImageJ/Fiji!

This set of slides was developed for an in-person workshop taught at Harvard Medical School.

The slides introduce participants to key concepts in writing macros in ImageJ/Fiji, offering practical insights for biologists interested in automating image analysis workflows.

The workshop is tailored for beginners with no prior programming experience. It combines tutorials and hands-on exercises to ensure an engaging and accessible learning experience.

The session begins with a general introduction to programming concepts (e.g., variables, arrays, for loops, if/else statements) and gradually builds toward creating a complete Fiji macro through a step-by-step process.

If you are a Fiji/ImageJ beginner and are intersted to learn more, you can follow this Introduction to Bioimage Analysis using ImageJ/Fiji workshop.

Downloadable Resources

• Course slides:

  Download the slides (PDF)

• Fiji Macros:

  Download the Fiji Macros (ZIP)

• Images:

  Download the Images (ZIP)

Topics Covered

Below are the core sections of this workshop.

• 01 - Introduction to Fiji Macro
• 02 - Introduction to Variables (numbers, strings, arrays)
• 03 - Introduction to Control Structures (if/else and for loops)
• 04 - Introduction to Functions
• 05 - The Fiji Macro Recorder
• 06 - Graphical User Interface (GUI)

Finally, we will record and build a step-by-step macro to segment nuclei following a classical image processing workflow. This macro will automate the pipeline, enabling it to process all the images in a specified folder.

Useful Links

Here are some helpful resources to complement the workshop materials:

• Macro Cheatsheet

• Introduction to Macro Programming

• Built-in Macro Functions

• Macro Script Parameters

• Macro Videos (By Robert Haase)

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