Tutorial notebooks

To learn PyImageJ, follow this numbered sequence of tutorial notebooks. If you want to run these Jupyter notebooks you can get them from the PyImageJ repository here.

• 1 Starting PyImageJ
  • 1.1 Ways to initialize
  • 1.2 The ImageJ2 gateway
  • 1.3 Increasing the memory available to Java
• 2 Working with Java classes
  • 2.1 Importing Java classes into Python
• 3 Sending Data to Java
  • 3.1 Converting between Java and Python
  • 3.2 Converting Python objects to Java
  • 3.3 Converting NumPy arrays to Java
• 4 Retrieving Data from Java
  • 4.1 Converting between Java and Python
  • 4.2 Converting Java objects to Python
  • 4.3 Special Consideration: RGB and other axis conventions
• 5 Convenience methods of PyImageJ
  • 5.1 Other convenient access to ImageJ functions
  • 5.2 Register functions to start with ImageJ
• 6 Working with Images
  • 6.1 Opening images with ij.io().open()
  • 6.2 Opening a series image with Bio-Formats Importer
  • 6.3 Displaying images with PyImageJ
  • 6.4 Displaying images dynamically with ipywidgets
  • 6.5 Displaying images via itkwidgets
  • 6.6 Displaying images via napari
  • 6.7 Inspecting image data
  • 6.8 Passing image data from Python to Java
  • 6.9 Passing image data from Java to Python
  • 6.10 Direct image type conversions
  • 6.11 Slicing Java and Python images
  • 6.12 Combine slices
  • 6.13 Create numpy images
  • 6.14 Working with ops
  • 6.15 Window service and manipulating windows
• 7 Running Macros, Scripts and Plugins
  • 7.1 Using ImageJ macros: ij.py.run_macro
  • 7.2 Using scripts: ij.py.run_script
  • 7.3 Example: Run a plugin: ij.py.run_plugin
• 8 Discover and run ImageJ commands
  • 8.1 Example 1: Apply “Find Maxima…” command to an image
  • 8.2 Example 2: Extract a slice and run “Analyze Particles…”
• 9 Working with Large Images
• 10 Using ImageJ Ops
• 11 Working with the original ImageJ
  • 11.1 Original ImageJ in headless mode
  • 11.2 One ImageJ-enabled gateway at a time
  • 11.3 Converting images to ImagePlus
  • 11.4 Converting ImagePlus to other image formats
  • 11.5 Keeping image data in sync with ij.py.sync_image(imp)
  • 11.6 Invoking ImageJ Plugins
  • 11.7 Running ImageJ macros
• 12 Troubleshooting
  • 12.1 I can’t pass my numpy image to an Op
  • 12.2 Clipping input data to the valid range for imshow with RGB data ([0..1] for floats of [0..255] for integers