cannot install pyimagej on python

Question

I need to write a code using jupyter notebook but need imagej packages. I installed pyimagej using several commands

conda install -c conda-forge pyimagej
conda install -c conda-forge/label/cf201901 pyimagej
conda install -c conda-forge/label/cf202003 pyimagej

But I always get this error: ModuleNotFoundError: No module named 'ij' when I try

from ij import IJ

I know that I can use imagej editor but I need to use jupyter notebook. Could someone help?

Answer 1

I tried this and it worked

conda create -n imagej pyimagej

Answer 2

We have recently improved our documentation on how to use PyImageJ. It looks like you were successful in installing the software, but you did not yet initialize PyImageJ. Checkout the How to initialize PyImageJ. If you have trouble initializing PyImageJ, you might need to view the installation documentation.

But assuming you have installed PyImageJ and activated your environment, a typical script looks something like this:

import imagej

# initialize PyImageJ
ij = imagej.init('sc.fiji:fiji', mode='interactive')
print(f"ImageJ Version: {ij.getVersion()}")

# The original ImageJ "IJ" is a property of the initialized "ij" object.
print(dir(ij.IJ))

Hope that helps!