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Trouble shooting

Encountered errors and solutions:

Module versions

  • skimage.morphology.selem module not found error => Problem of compatibility between big-fish and scikit-image versions. Ideally, chooses a recent version of skimage (scikit-image==0.19.3) and big-fish (big-fish==0.6.2).

Acces violation reading

OSError: exception: access violation reading 0x0000000000000034.

This error happened only in Windows with specific nvidia card (A6000). It happens when adding or deleting Shape layers, quite often in cytoplasmic measure option. It seems to be an error external to the plugin or napari. We haven't found a solution yet, but please refer to this discussion on imagesc forum for more infos/updates.

Other issue

You can also check on the issues page of the repository if your problem has already been reported and has a solution. Otherwise, open a new one in this page and we will do our best to answer fast.

Tested and working configurations

Here we proposed the list of package versions that were installed on several python environment, with the corresponding operating system, that worked fine for us.

For each set-up, we list first the graphical info that we get with napari --info, then the link to the full yaml file.

Environment lists

Windows 10, python 3.9.21, napari 0.4.18 

fishfeats: 1.1.11               
napari: 0.4.18
Platform: Windows-10-10.0.19045-SP0
Python: 3.9.21 | packaged by conda-forge | [MSC v.1929 64 bit (AMD64)]
Qt: 5.15.2
PyQt5: 5.15.11
NumPy: 1.26.4
SciPy: 1.13.1
Dask: 2024.8.0
VisPy: 0.12.2
magicgui: 0.9.1
superqt: 0.6.7
in-n-out: 0.2.1
app-model: 0.2.8
npe2: 0.7.7

OpenGL:
     - GL version:  4.6.0 NVIDIA 571.59
     - MAX_TEXTURE_SIZE: 32768

yaml file with all python packages installed in the environment here

Windows 10, python 3.10.18, napari 0.6.1 

napari: 0.6.1
Platform: Windows-10-10.0.19045-SP0
Python: 3.10.18 | packaged by conda-forge | MSC v.1943 64 bit (AMD64)
Qt: 5.15.2
PyQt5: 5.15.11
NumPy: 1.26.4
SciPy: 1.15.3
Dask: 2025.5.1
VisPy: 0.15.2
magicgui: 0.10.1
superqt: 0.7.5
in-n-out: 0.2.1
app-model: 0.3.2
psygnal: 0.13.0
npe2: 0.7.8
pydantic: 2.11.7

OpenGL:
     - PyOpenGL: 3.1.9
     - GL version:  4.6.0 NVIDIA 571.59
     - MAX_TEXTURE_SIZE: 32768
     - GL_MAX_3D_TEXTURE_SIZE: 16384

Optional:
      - numba: 0.61.2
      - triangle: 20250106
      - napari-plugin-manager: 0.1.6
      - bermuda: 0.1.4
      - PartSegCore not installed

Experimental Settings:
      - Async: False
      - Autoswap buffers: False
      - Triangulation backend: Fastest available

fishfeats: 1.1.11

yaml file with all python packages installed in the environment here

MacBook pro M1, python 3.10.14, napari 0.4.19 

napari: 0.4.19
Platform: macOS-15.5-arm64-arm-64bit
System: MacOS 15.5
Python: 3.10.14 | packaged by conda-forge | (main, Mar 20 2024, 12:51:49) [Clang 16.0.6 ]
Qt: 5.15.8
PyQt5: 5.15.9
NumPy: 1.26.4
SciPy: 1.13.1
Dask: 2025.5.1
VisPy: 0.14.3
magicgui: 0.10.1
superqt: 0.7.5
in-n-out: 0.2.1
app-model: 0.2.8
npe2: 0.7.8

OpenGL:

- GL version:    2.1 Metal - 89.4     - MAX_TEXTURE_SIZE: 16384

        fishfeats: 1.1.11               
    yaml file with all python packages installed in the environment [here](./environnements_list/macbook_pro_M1_fishfeats_1.1_py310.yaml)
    </details>

=== "Linux"

    <details><summary> Ubuntu 20.04.6, python 3.10.0, napari 0.6.1 </summary>

    napari: 0.6.1
    Platform: Linux-5.15.0-139-generic-x86_64-with-glibc2.31
    System: Ubuntu 20.04.6 LTS
    Python: 3.10.0 | packaged by conda-forge | (default, Nov 20 2021, 02:24:10) [GCC 9.4.0]
    Qt: 5.15.2
    PySide2: 5.15.2.1
    NumPy: 1.24.2
    SciPy: 1.15.3
    Dask: 2025.5.1
    VisPy: 0.15.2
    magicgui: 0.10.0
    superqt: 0.7.3
    in-n-out: 0.2.1
    app-model: 0.3.1
    psygnal: 0.13.0
    npe2: 0.7.8
    pydantic: 2.11.5

    OpenGL:
        - PyOpenGL: 3.1.9
        - GL version:  4.6.0 NVIDIA 545.29.06
        - MAX_TEXTURE_SIZE: 32768
        - GL_MAX_3D_TEXTURE_SIZE: 16384


    Optional:
      - numba: 0.61.2
      - triangle not installed
      - napari-plugin-manager not installed
      - bermuda not installed
      - PartSegCore not installed

    Experimental Settings:
      - Async: False
      - Autoswap buffers: False
      - Triangulation backend: Fastest available

    fishfeats: 1.1.3
    yaml file with all python packages installed in the environment [here](./environnements_list/ubuntu_20.04_fishfeats_1.1_py310.yaml)
    </details>