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, for the moment, you can use:
A PyImageJ paper is forthcoming.