napari PSSR

A plugin for training and applying pssr

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This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation¶

You can install napari-pssr via pip:

pip install napari-pssr

Some libraries need to be updated to the most recent version to get all features. These will be updated once they are released on pypi

pip install git+https://github.com/bioimage-io/core-bioimage-io-python",
pip install git+https://github.com/funkey/gunpowder.git@patch-1.2.3",

To install latest development version :

pip install git+https://github.com/pattonw/napari-pssr.git

Model download¶

A sample model can be downloaded from https://github.com/pattonw/model-specs/tree/main/pssr. This model comes with some restrictive dependencies. To use follow these steps.

1. install this plugin following the directions provided above
2. install bioimageio.core via pip install bioimageio.core or conda install -c conda-forge bioimageio.core
3. pip install fastai==1.0.55 tifffile libtiff czifile scikit-image
4. pip uninstall torch torchvision (may need multiple runs)
5. conda install pytorch==1.1.0 torchvision==0.3.0 cudatoolkit=10.0 -c pytorch
6. pip install pillow==6.1.0

Contributing¶

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License¶

Distributed under the terms of the MIT license, "napari-pssr" is free and open source software

Issues¶

If you encounter any problems, please file an issue along with a detailed description.