| Welcome to PathML's documentation! | |
| ================================== | |
| .. image:: _static/images/overview.png | |
| ``PathML`` is a Python package for computational pathology. | |
| ``PathML`` is a toolbox to facilitate machine learning workflows for high-resolution whole-slide pathology | |
| images. This includes modular pipelines for preprocessing, PyTorch DataLoaders for training and benchmarking | |
| machine learning model performance on standardized datasets, support for sharing preprocessing pipelines, | |
| pretrained models, and more. | |
| Development is a collaboration between the AI Operations and Data Science Group in the Department of Informatics | |
| and Analytics at Dana-Farber Cancer Institute and the Department of Pathology and Laboratory Medicine at Weill | |
| Cornell Medicine. | |
| .. image:: _static/images/dfci_cornell_joint_logos.png | |
| .. toctree:: | |
| :maxdepth: 2 | |
| :caption: Getting Started | |
| overview | |
| installation | |
| .. toctree:: | |
| :maxdepth: 2 | |
| :caption: Examples | |
| examples/link_loading_images | |
| examples/link_workflow_HE_vignette | |
| examples/link_multiplex_if | |
| examples/link_codex | |
| examples/link_gallery | |
| examples/link_stain_normalization | |
| examples/link_construct_graphs | |
| examples/link_tile_stitching | |
| examples/link_train_hovernet | |
| examples/link_train_hactnet | |
| examples/link_workflow_Inference | |
| examples/link_jco | |
| examples/link_talk_to_pathml | |
| .. toctree:: | |
| :maxdepth: 2 | |
| :caption: Preprocessing | |
| loading_slides | |
| creating_pipelines | |
| running_pipelines | |
| h5path | |
| .. toctree:: | |
| :maxdepth: 2 | |
| :caption: Datasets | |
| datasets | |
| .. toctree:: | |
| :maxdepth: 2 | |
| :caption: Graphs | |
| graphs | |
| .. toctree:: | |
| :maxdepth: 2 | |
| :caption: Machine Learning | |
| dataloaders | |
| models | |
| .. toctree:: | |
| :maxdepth: 2 | |
| :caption: Inference | |
| inference | |
| .. toctree:: | |
| :maxdepth: 2 | |
| :caption: API Reference | |
| api_core_reference | |
| api_preprocessing_reference | |
| api_graph_reference | |
| api_datasets_reference | |
| api_ml_reference | |
| api_utils_reference | |
| api_inference_reference | |
| .. toctree:: | |
| :maxdepth: 2 | |
| :caption: Contributing | |
| link_contributing | |
| Indices and tables | |
| ================== | |
| * :ref:`genindex` | |
| * :ref:`search` | |