This page describes PyImageJ, a Python package making ImageJ functions accessible from Python. To write scripts in Jython, the JVM-based flavor of Python, see Jython scripting.
PyImageJ is a Python wrapper for ImageJ2. It also supports the original ImageJ via ImageJ2’s legacy bridge.
PyImageJ provides a set of wrapper functions for integration between ImageJ and Python. A major advantage of this approach is the ability to combine ImageJ with other tools available from the Python software ecosystem, including NumPy, SciPy, scikit-image, CellProfiler, OpenCV, ITK and more.
For further details about PyImageJ, including installation and usage instructions, please see the project page on PyPI:
If you are new to Python or image analysis using Python and would like to learn about it, check out the tutorials and resources from the EPFL Center for Imaging - image analysis field guide
Publication
To cite PyImageJ, you can use:
