Metadata-Version: 1.2
Name: root-tissue-seg-package
Version: 1.0.5
Summary: An mlf-core prediction package for root tissue segmentation.
Home-page: https://github.com/qbic-pipelines/rts-prediction-package/
Author: Julian Wanner
Author-email: jwgithub@mailbox.org
License: MIT
Description: ================================
        Root-Tissue-Segmentation Package
        ================================
        
        .. image:: https://github.com/qbic-pipelines/rts-prediction-package/workflows/Build%20rts_package%20Package/badge.svg
                :target: https://github.com/qbic-pipelines/rts-prediction-package/workflows/Build%20rts_package%20Package/badge.svg
                :alt: Github Workflow Build rts_package Status
        
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                :alt: Github Workflow Tests Status
        
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                :target: https://pypi.python.org/pypi/rts_package
                :alt: PyPI Status
        
        
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                :target: https://rts_package.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
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                :alt: Dependabot Enabled
        
        
        Prediction package for reproducible U-Net models, trained for semantic segmentation of microscopy images of root tissue from *A. thaliana* (https://github.com/qbic-pipelines/root-tissue-segmentation-core/). These models are trained using the mlf-core framework and tested for reproducibility. This package can be deployed within an analysis pipeline as a module for root tissue segmentation (rts) of fluorescence microscopy images.
        
        * Free software: MIT
        * Documentation: https://rts-package.readthedocs.io.
        
        
        Package Tools
        -------------
        
        * Segmentation prediction CLI: ``rts-pred``
        * Uncertainty of prediction CLI: ``rts-pred-uncert``
        * Input feature importance (Guided Grad-CAM) CLI: ``rts-feat-imp``
        
        Usage Examples
        --------------
        
        * ``rts-pred -i ./brightfields -o ./predictions -m mark1-PHDFM-u2net-model.ckpt --suffix ""``
        * ``rts-pred-uncert -i ./brightfields -o ./predictions -m mark1-PHDFM-u2net-model.ckpt --suffix "" -t 5``
        * ``rts-feat-imp -i ./brightfields -o ./predictions -m mark1-PHDFM-u2net-model.ckpt --suffix "" -t 2``
        
        
        Credits
        -------
        
        This package was created with mlf-core_ using cookiecutter_.
        
        
        .. _mlf-core: https://mlf-core.com
        .. _cookiecutter: https://github.com/audreyr/cookiecutter
        
        
        ==========
        Changelog
        ==========
        
        This project adheres to `Semantic Versioning <https://semver.org/>`_.
        
        
        1.0.0 (2021-08-10)
        ------------------
        
        **Added**
        
        **Fixed**
        
        **Dependencies**
        
        **Deprecated**
        
        
        0.1.0 (2021-08-10)
        ------------------
        
        **Added**
        
        * Created the project using mlf-core
        
        **Fixed**
        
        **Dependencies**
        
        **Deprecated**
        
Keywords: root tissue segmentation
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.7
