napari-deepmeta

Mice lungs and metastases segmentation tool.


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    License MIT PyPI Python Version tests codecov napari hub

    Mice lungs and metastases segmentation tool. This tool is a demo tool for DeepMeta network.


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

    Installation

    You can install napari-deepmeta via pip:

    pip install napari-deepmeta

    To install latest development version :

    pip install git+https://github.com/EdgarLefevre/napari-deepmeta.git

    Usage

    This plugin is designed to process your mouse MRI images with our dataset. It comes with a demo, including one of our test images.

    By opening the deepmeta demo plugin, you will see an interface with one unique button, by clicking on it, it will load an image, run prediction and then draw the masks contours on each slice.

    If you open the deepmeta plugin, you will see an interface with one button and 3 checkboxes. By checking the checkboxes, you add steps to the pipeline (enhance contrast, do postprocessing, segment metastases). Once everything is setup, just click on the button and wait (the waiting time depends on your computer performance.)

    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-deepmeta" is free and open source software

    Issues

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

    Version:

    • 2.1

    Release date:

    • 07 July 2022

    First released:

    • 02 June 2021

    License:

    • MIT

    Supported data:

    • Information not submitted

    GitHub activity:

    • Stars: 2
    • Forks: 2
    • Issues + PRs: 0

    Python versions supported:

    Operating system:

    Requirements:

    • connected-components-3d
    • magicgui
    • napari
    • numpy
    • opencv-python
    • qtpy
    • scikit-image
    • torch

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