├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── feature_request.yml │ └── question.yml └── workflows │ └── ci.yml ├── .readthedocs.yaml ├── DETAILS.md ├── LICENSE ├── README.md ├── _readme ├── contours.jpg ├── joint_logo.png ├── trident_crop.jpg └── viz.jpg ├── docs ├── Makefile ├── _static │ ├── lab_logo.svg │ └── trident_crop.jpg ├── api.rst ├── citation.rst ├── cli_helpers │ └── cli_generate.py ├── conf.py ├── faq.rst ├── index.rst ├── installation.rst ├── make.bat ├── quickstart.rst ├── requirements.txt └── tutorials.rst ├── pyproject.toml ├── run_batch_of_slides.py ├── run_single_slide.py ├── tests ├── test_encoder_same_local_hf.py ├── test_openslidewsi.py ├── test_patch_encoders.py ├── test_patcher.py ├── test_processor.py ├── test_segmentation_models.py └── test_slide_encoders.py ├── trident ├── Concurrency.py ├── Converter.py ├── IO.py ├── Maintenance.py ├── Processor.py ├── Visualization.py ├── __init__.py ├── patch_encoder_models │ ├── __init__.py │ ├── load.py │ ├── local_ckpts.json │ ├── model_zoo │ │ ├── __init__.py │ │ ├── conchv1_5 │ │ │ ├── __init__.py │ │ │ └── conchv1_5.py │ │ └── ctranspath │ │ │ ├── __init__.py │ │ │ └── ctran.py │ └── utils │ │ ├── __init__.py │ │ ├── constants.py │ │ └── transform_utils.py ├── segmentation_models │ ├── __init__.py │ ├── load.py │ └── local_ckpts.json ├── slide_encoder_models │ ├── __init__.py │ ├── load.py │ ├── local_ckpts.json │ └── model_zoo │ │ ├── __init__.py │ │ └── reusable_blocks │ │ ├── ABMIL.py │ │ └── __init__.py └── wsi_objects │ ├── CuCIMWSI.py │ ├── ImageWSI.py │ ├── OpenSlideWSI.py │ ├── SDPCWSI.py │ ├── WSI.py │ ├── WSIFactory.py │ ├── WSIPatcher.py │ ├── WSIPatcherDataset.py │ └── __init__.py └── tutorials ├── 1-Step-by-Step-Patch-Feature-Extraction-with-Trident.ipynb ├── 2-Using-Trident-With-Your-Custom-Patch-Encoder.ipynb └── 3-Training-a-WSI-Classification-Model-with-ABMIL-and-Heatmaps.ipynb /.github/ISSUE_TEMPLATE/bug_report.yml: 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