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This page describes content relating to the ImageJ2 platform. Click the logo for details.


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:


To cite PyImageJ, you can use: