Installation

  1. Download the plugin

    Download IJPB.jar

  2. Open ImageJ (or Fiji)

  3. Drag and drop ImageJPipelineBuilder.jar into your open ImageJ window

    Tip Drop the JAR directly onto the ImageJ toolbar — not into a canvas or results window.

  4. Restart ImageJ to complete the installation

  5. Verify it worked — you should see a new menu item: Pipelines in the top menu bar

Build a Pipeline

  1. In the top menu, click Pipelines → New

  2. Optional

    Open an example image you'd like to analyze — the AI can see the images you have open

  3. Describe what you want in the chat window, in plain English

    Example prompts "Count DAPI-stained nuclei and export a results table" · "Measure fluorescence intensity per cell in channel 2" · "Segment HeLa cells using CellPose"

  4. Chat back and forth — the AI will ask clarifying questions about your images and what you need

  5. The AI will automatically write a script once it has enough detail

  6. Hit Run to execute the script on your currently open image

  7. Verify the script runs correctly

    Heads up AI can make mistakes. Always sanity-check results before processing your full dataset.

  8. If there are errors, the AI will fix them automatically — keep chatting until it's right

  9. Once you're happy, hit Save to name your pipeline and add it to the ImageJ menu

  10. Run it again anytime via Pipelines → your pipeline name in the dropdown

Manage Pipelines

  1. Click Pipelines → Manage to open your pipeline library

  2. Find the pipeline you want and click on it to select it

  3. Choose what to do with it:

    Edit / Resume

    Opens your previous chat so you can continue refining the pipeline

    Delete

    Permanently removes the pipeline from your menu

Edit a Pipeline

  1. Click Pipelines → Manage

  2. Find the pipeline you want to change and click on it

  3. Hit Edit / Resume to reopen your previous conversation

  4. Describe the changes you need — the AI has full context of the original script

    Good change prompts "Add background subtraction before thresholding" · "Also export a CSV with per-cell measurements" · "Change the particle size filter to 50–500 µm²"

  5. Hit Run to test the updated script on your open image

  6. Keep chatting until the results look right

  7. Hit Update to save the revised script back to your menu