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imagej / napari-imagej

Use ImageJ functionality from napari
https://napari-imagej.readthedocs.io
BSD 2-Clause "Simplified" License
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napari-imagej breaks with Jpype 1.5.1 #316

Closed hinerm closed 17 hours ago

hinerm commented 18 hours ago

If I do a napari-imagej install from scratch with mamba create -n napari-imagej napari-imagej I currently get jpype1 1.5.1.

When starting up napari-imagej in this environment, napari hard crashes with this message on the command prompt:

image

Rolling back to jpype1 1.5.0 works as expected.

gselzer commented 17 hours ago

This issue isn't specific to napari-imagej, as it can be repeated with a smaller MVCE:

  1. Create a conda environment: mamba env create -n tmp -c conda-forge pyimagej
  2. Run in python: import imagej; ij = imagej.init()
  3. Observe error: 
    Error occurred during initialization of VM
Could not find agent library instrument on the library path, with error: Can't find dependent libraries
Module java.instrument may be missing from runtime image.

This is likely a fix upstream in scyjava?

cc @ctrueden @elevans

hinerm commented 17 hours ago

@gselzer pointed out this is a reported issue in Jpype. It can be reproduced with import jpype; jpype.startJVM().