napari PSSR

napari-pssr

A plugin for training and applying pssr


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    A plugin for training and applying pssr


    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.

    Version:

    • 0.1

    Release date:

    • 18 November 2022

    First released:

    • 18 November 2022

    License:

    • MIT

    Supported data:

    • Information not submitted

    Plugin type:

    GitHub activity:

    • Stars: 0
    • Forks: 0
    • Issues + PRs: 0

    Python versions supported:

    Operating system:

    Requirements:

    • numpy
    • zarr
    • magicgui
    • bioimageio.core
    • gunpowder
    • matplotlib
    • torch
    • napari

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