Using FIJI or ImageJ in Python
I'm a veteran ImageJ/FIJI coder, and I'm transitioning to python. is scikit-image an incorporation of ImageJ into python? Can I run my ImageJ macros within scikit-image package? What's the URL for the scikit-image function descriptions? Thanks Ron DeSpain
Hi Ron, and welcome to the community! 😊 scikit-image contains many functions for image processing and analysis; probably not as many as Fiji, but enough for the most common things and to get you started! To use scikit-image you have to program in Python, which is a different language from ImageJ macros. (Even ImageJ Python scripts are actually Jython, which is based on an old version of Python — there are many similarities but many differences, and the biggest one is that you cannot easily access the ImageJ and Fiji functions from Python.) Our documentation starts here: https://scikit-image.org/docs/stable/ The list of all available functions is here: https://scikit-image.org/docs/stable/api/api.html and the gallery of examples, which shows you by example how to perform many common image analysis operations, is here: https://scikit-image.org/docs/stable/auto_examples/index.html We also have a getting started guide here: https://scikit-image.org/docs/stable/user_guide.html I'll also point you to a project that you might find useful, PyImageJ, which lets you call ImageJ functionality from Python. It's a little trickier to install and use, though. https://github.com/imagej/pyimagej For all of this you can get help on image.sc, so feel free to keep asking usage questions there! Juan. On Sun, 21 Feb 2021, at 5:01 AM, Ron DeSpain wrote:
I'm a veteran ImageJ/FIJI coder, and I'm transitioning to python.
is scikit-image an incorporation of ImageJ into python?
Can I run my ImageJ macros within scikit-image package?
What's the URL for the scikit-image function descriptions?
Thanks Ron DeSpain _______________________________________________ scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org https://mail.python.org/mailman3/lists/scikit-image.python.org/ Member address: jni@fastmail.com
participants (2)
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Juan Nunez-Iglesias
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Ron DeSpain