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Troubleshooting

This section provides solutions to common issues you might encounter while using PlantSeg. Click on a problem to jump to its specific solution.

Font size problems in GUI

If you find the font size varies within either Napari or Legacy GUIs, or some buttons or texts are not visible, it might relate to your system's DPI settings or sreen resolution. To fix this, you can try to reset the resolution of your system.

Related discussions:

plantseg-gui

Other references:

Problems with --headless and dask[distributed]

If you encounter the following error:

ImportError: dask.distributed is not installed.

Please install dask[distributed] to enable headless mode in PlantSeg. Run the following commands in your terminal:

mamba activate plant-seg
mamba install -c pytorch -c nvidia -c conda-forge dask distributed

Could not load library libcudnn_ops_infer.so.8

If you encounter this error:

Could not load library libcudnn_ops_infer.so.8. Error: libcudnn_ops_infer.so.8: cannot open shared object file: No such file or directory

Resolve this by installing cudnn using the following command:

mamba install -c conda-forge cudnn

Missing configuration key errors

If you encounter a RuntimeError about a missing key, such as:

RuntimeError: key : 'crop_volume' is missing, plant-seg requires 'crop_volume' to run

This usually means the session configuration file is corrupted or outdated. To fix this:

rm ~/.plantseg_models/configs/config_gui_last.yaml

Ensure your configuration file is properly formatted and includes all required keys. Example configurations can be found in the examples directory of this repository.

Cannot import lifted_problem_from_probabilities

If you receive an error related to importing from elf.segmentation.features, reinstall elf:

conda install -c conda-forge python-elf

Other issues

PlantSeg is actively developed, and sometimes model or configuration files saved in ~/.plantseg_models may become outdated. If you encounter errors related to configuration loading:

  1. Close the PlantSeg application.
  2. Delete the ~/.plantsep_models directory.
  3. Restart the application and try again.

These steps should help resolve any issues and enhance your experience with PlantSeg.