I have been trying to setup pyimageJ using anaconda version: 4.7.12 but I have been struggling to get it working. I have tried the following:
conda create -n imagej -c conda-forge openjdk=8 pyimagej conda activate imagej
This environment (imagej) does not have Jupyter installed and so I have tried installing this either by using:
conda install -c anaconda jupyter
Or using the anaconda navigator.
After doing this, I launch Jupyter notebook and create a new python 3 notebook. I then try:
import imagej ij = imagej.init('sc.fiji:fiji:2.0.0-pre-10')
Or attempt to direct the init function to my local copy of Fiji. Each time, I get the following error:
Error in `~/opt/anaconda3/envs/imagej/bin/mvn -B -f ~/.jgo/sc.fiji/fiji/2.0.0-pre-10+net.imglib2-imglib2-imglyb-0.4.0/pom.xml dependency:resolve': 1 ERROR:root:Internal Python error in the inspect module.
Below is the traceback from this internal error.
And then a traceback error.
Has anyone had a similar problem? Any help would be greatly appreciated.