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.
Contents:
- Installation
- How to initialize PyImageJ
- 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
- 6.1 Opening images with
ij.io().open() - 6.2 Displaying images with PyImageJ
- 6.3 Displaying images dynamially with
ipywidgets - 6.4 Displaying images via itkwidgets
- 6.5 Displaying images via napari
- 6.6 Inspecting image data
- 6.7 Passing image data from Python to Java
- 6.8 Passing image data from Java to Python
- 6.9 Direct image type conversions
- 6.10 Slicing Java and Python images
- 6.11 Combine slices
- 6.12 Create numpy images
- 6.13 Working with ops
- 6.14 Window service and manipulating windows
- 6.1 Opening images with
- 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
- Use cases
- Using PyImageJ without a screen
- Developing PyImageJ
- Troubleshooting
- Known Limitations
- Debugging Tips
- Common Errors
- Error in “mvn.CMD -B -f pom.xml” dependency:resolve: 1
- I ran a plugin and see an updated image, but the numpy array and dataset are unchanged
- The same macro gives different results when run multiple times
- Original ImageJ classes not found
- Not enough memory
- Python hangs when quitting
- log4j:WARN
- TypeError: No matching overloads
pip install jpype1fails on Windows
- API Reference