├── .readthedocs.yaml ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── build │ ├── doctrees │ │ ├── environment.pickle │ │ ├── index.doctree │ │ ├── installation.doctree │ │ ├── modules.doctree │ │ ├── pathml.doctree │ │ └── tutorial.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _images │ │ ├── api_table.png │ │ └── figure1.png │ │ ├── _sources │ │ ├── index.rst.txt │ │ ├── installation.rst.txt │ │ ├── modules.rst.txt │ │ ├── pathml.rst.txt │ │ └── tutorial.rst.txt │ │ ├── _static │ │ ├── api_table.png │ │ ├── basic.css │ │ ├── check-solid.svg │ │ ├── clipboard.min.js │ │ ├── copy-button.svg │ │ ├── copybutton.css │ │ ├── copybutton.js │ │ ├── copybutton_funcs.js │ │ ├── css │ │ │ ├── badge_only.css │ │ │ ├── fonts │ │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ │ ├── fontawesome-webfont.eot │ │ │ │ ├── fontawesome-webfont.svg │ │ │ │ ├── fontawesome-webfont.ttf │ │ │ │ ├── fontawesome-webfont.woff │ │ │ │ ├── fontawesome-webfont.woff2 │ │ │ │ ├── lato-bold-italic.woff │ │ │ │ ├── lato-bold-italic.woff2 │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-normal-italic.woff │ │ │ │ ├── lato-normal-italic.woff2 │ │ │ │ ├── lato-normal.woff │ │ │ │ └── lato-normal.woff2 │ │ │ └── theme.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── figure1.png │ │ ├── file.png │ │ ├── graphviz.css │ │ ├── jquery-3.5.1.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── badge_only.js │ │ │ ├── html5shiv-printshiv.min.js │ │ │ ├── html5shiv.min.js │ │ │ └── theme.js │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.13.1.js │ │ └── underscore.js │ │ ├── genindex.html │ │ ├── index.html │ │ ├── installation.html │ │ ├── modules.html │ │ ├── objects.inv │ │ ├── pathml.html │ │ ├── search.html │ │ ├── searchindex.js │ │ └── tutorial.html ├── make.bat ├── readthedocs-requirements.txt └── source │ ├── _static │ ├── api_table.png │ └── figure1.png │ ├── conf.py │ ├── index.rst │ ├── installation.rst │ ├── modules.rst │ ├── pathml.rst │ └── tutorial.rst ├── pathml-environment.yml ├── pathml ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-37.pyc │ ├── analysis.cpython-37.pyc │ ├── annotation.cpython-37.pyc │ ├── processor.cpython-37.pyc │ └── slide.cpython-37.pyc ├── analysis.py ├── annotation.py ├── models │ ├── __pycache__ │ │ └── tissuedetector.cpython-37.pyc │ ├── deep-tissue-detector_densenet_state-dict.pt │ └── tissuedetector.py ├── processor.py ├── slide.py └── utils │ └── torch │ ├── WholeSlideImageDataset.py │ ├── __pycache__ │ ├── WholeSlideImageDataset.cpython-37.pyc │ └── dice_loss.cpython-37.pyc │ └── dice_loss.py ├── requirements.txt ├── setup.py └── tests ├── ExtractArea-bm.py ├── Fetch-bm.py ├── __init__.py ├── aaronDemo.py ├── memProfiling.py ├── no-testClass.py ├── testModel.py ├── test_annotation.py ├── 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