Python spyder to imagej Fiji

Hi all,

Is there a good way to relate my python spyder IDE (code) to FIJI ?

pyimagej ?

all the best

Hi Ebi,
What do you mean exactly ?
You want to use python code in Fiji (jython scripting) or Fiji functions in a python script (Fiji in python alias PyImageJ) or you want to use spyder with Fiji (not really possible)?

With the jython scripting, you can’t use any python package like scikit-image or numpy (OpenCV is accessible via the java package though).

If you need some GUI for your image processing, then ImagePy could also be an option.

Hi Thomas,
Thanks for your response
My problem is that Fiji “IDE” is not proper for me … and I wan’t to work with Spyder or Pycharm IDE’s …
But I also need to make my code run on Fiji … Is there a way to make it happen ? …

furthermore, is there a comprehensive intro , tutorial to PyimageJ and jython ?

all the best

I agree that the Fiji IDE is not as powerful as spyder yet there is syntax coloring as soon as you select language>python and auto-completion might come up in the future too.
Also if you update Fiji to have the last editor, you can tick the persistent box to type some interactive commands with the value of your variable in memory.

With spyder nope, with PyCharm I dont know.
You can use Eclipse as an alternative full-flavored IDE but it requires a bit more configuration.
See Jython Imagej coding advice

See the links in my previous post, they also contain links to some Jupyter notebooks on the Fiji github repositories

I am not sure what you mean by that. Without an explicit use case example it is impossible to give a definitive answer.