@cedrice Here is my
kernel.json, pretty printed:
Note that JAR files from
java_env/opt/scijava-jupyter-kernel/* are added to the classpath, but not anything from Fiji.
Alternately, you can add everything from Fiji’s
jars/bio-formats folders, but nothing else from anywhere else. In theory, all should be OK as long as each JAR is only included on the classpath once. If you include two different folders which contain the same (but maybe different versions) of the same JAR files, though, then you may have issues.
Can you please describe what goes wrong, post the error message, etc.? Note that I personally have not tested the SciJava Jupyter Kernel with Fiji, only with the base ImageJ2, so it may actually be the case that Bio-Formats does not work in the notebook for some reason. We can address it, but it may take some back and forth here.
Not too surprising since it has not been possible to do so prior to three weeks ago.