Welcome to PyImageJ’s documentation!

PyImageJ provides a set of wrapper functions for integration between ImageJ2 and Python. It also supports the original ImageJ API and data structures.

A major advantage of this approach is the ability to combine ImageJ and ImageJ2 with other tools available from the Python software ecosystem, including NumPy, SciPy, scikit-image, CellProfiler, OpenCV, ITK and many more.

🤖 Getting Started with AI

• Introduction to Google Colab
  • Disclaimer
  • Getting started
  • Basic Jupyter Notebook Use
  • Runtime and File Management
  • Using Gemini
• The PyImageJ AI Notebook
  • Background Knowledge
  • Learning Goals
  • Navigating the Notebook
  • Troubleshooting
  • FAQ
• Prompt Engineering
  • Getting the Most from AI Assistants
  • Understanding Hallucinations
  • More Conversation Starters

🚀 Getting Started (Traditional)

• Installation
  • Installing via conda/mamba
  • Installing via pip
  • Testing your installation
  • Dynamic installation within Jupyter
  • Install pyimagej in Docker
• How to initialize PyImageJ
  • Quick start
  • Ways to initialize

🪄 How-to guides

• Tutorial notebooks
  • 1 Starting PyImageJ
  • 2 Working with Java classes
  • 3 Sending Data to Java
  • 4 Retrieving Data from Java
  • 5 Convenience methods of PyImageJ
  • 6 Working with Images
  • 7 Running Macros, Scripts and Plugins
  • 8 Discover and run ImageJ commands
  • 9 Working with Large Images
  • 10 Using ImageJ Ops
  • 11 Working with the original ImageJ
  • 12 Troubleshooting
• Using PyImageJ without a screen
  • Using ImageJ in headless mode
  • Using PyImageJ with Xvfb
• Troubleshooting
  • Known Limitations
  • Debugging Tips
  • Common Errors

🔬 Use cases

• imagej-ops
  • 3D Deconvolution
  • Gray Level Co-occurrence Matrices (GLCM)
• Integration
  • CellProfiler
• Segmentation
  • Blob detection (interactive)
  • Blob detection (headless)
  • Classic Segmentation
  • Cellpose/StarDist Segmentation
  • Puncta Segmentation
• Other use cases

🛠️ Development

• Developing PyImageJ
  • Testing local changes
  • Building the reference documentation
  • Running the automated tests
  • Formatting the code
  • Building distribution bundles

📚 Reference

• API
  • Initialization
  • Convenience methods
  • RandomAccessibleInterval (RAI) operators
  • ImageJ2 gateway addons
  • ImagePlus addons
  • Interval addons
  • Euclidean space addons
  • Typed space addons
  • Annotated space addons
  • PyImageJ submodules
• Citation

Indices and tables

• Index

• Module Index

• Search Page