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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 <https://fiji.sc>`_ beginner and are intersted to learn more, you can follow this `Introduction to Bioimage Analysis using ImageJ/Fiji workshop <https://hms-iac.github.io/fiji-workshop/versions/2025_01_22/index.html>`_.

**Downloadable Resources**
---------------------------

- **Course slides:**
  
  .. raw:: html
  
     <p><a href="_static/fiji_macro_slides.pdf" download>Download the slides (PDF)</a></p>

- **Fiji Macros:**
  
  .. raw:: html
  
     <p><a href="_static/fiji_macros.zip" download>Download the Fiji Macros (ZIP)</a></p>

- **Images:**
  
  .. raw:: html
  
     <p><a href="_static/nuclei.zip" download>Download the Images (ZIP)</a></p>

**Topics Covered**
-------------------

Below are the core sections of this workshop.

.. toctree::
   :maxdepth: 1

   01.rst
   02.rst
   03.rst
   04.rst
   05.rst
   06.rst

Finally, we will record and build a `step-by-step macro to segment nuclei <_static/fiji_macros.zip>`_ 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 <_static/fiji_macro_cheatsheet.pdf>`_
- `Introduction to Macro Programming <https://imagej.net/scripting/macro>`_
- `Built-in Macro Functions <https://imagej.net/ij/developer/macro/functions.html>`_
- `Macro Script Parameters <https://imagej.net/scripting/parameters>`_
- `Macro Videos (By Robert Haase) <https://youtu.be/q4ISEWq6q4E?si=IlcOoaA4uvI8bXO3>`_

**Feedback**
------------

.. toctree::
   :maxdepth: 1

   feedback.rst