├── .gitignore ├── .idea └── inspectionProfiles │ └── profiles_settings.xml ├── LICENSE ├── README.md ├── __init__.py ├── docs ├── imgs │ ├── OCMC-004_extraction_grid.png │ ├── anno_validation.png │ ├── arch.png │ ├── coord_1.png │ ├── coord_2.png │ ├── offset_example.png │ ├── patch_pair.jpg │ └── tissue_anno.png ├── patch_extraction │ ├── feature_map.md │ ├── pairwise_patch_extraction.md │ └── patch_extraction.md ├── readme.md ├── tissue_detection │ └── tissue_detector.md ├── wsi_annotation │ ├── QuPath_scripts │ │ ├── readme.md │ │ └── readme_imgs │ │ │ ├── fig2.1.png │ │ │ ├── fig2.2.png │ │ │ ├── fig2.3.png │ │ │ ├── fig2.4.png │ │ │ ├── fig3.1.png │ │ │ ├── fig3.2.png │ │ │ ├── fig3.3.png │ │ │ └── fig3.4.png │ ├── annotation_parsing.md │ └── coordinate_agreement.md └── wsi_registration │ └── wsi_registration.md ├── setup.py └── wsitools ├── __init__.py ├── __pycache__ ├── __init__.cpython-36.pyc └── __init__.cpython-37.pyc ├── examples ├── create_wsi_fn_list.py ├── patch_extraction_p.py ├── patch_extraction_p_args.py ├── patch_extraction_p_args_single.py ├── patch_extraction_pl.py ├── patch_extraction_pp.py ├── patch_extraction_ppl.py ├── profile_local.sh ├── run_all.sh ├── run_demo.sh ├── run_single.sh ├── wsi_aligment.py └── wsi_preprocessing.ipynb ├── file_management ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-36.pyc │ ├── __init__.cpython-37.pyc │ ├── case_list_manager.cpython-36.pyc │ ├── case_list_manager.cpython-37.pyc │ ├── class_label_csv_manager.cpython-36.pyc │ ├── class_label_csv_manager.cpython-37.pyc │ ├── offset_csv_manager.cpython-36.pyc │ ├── offset_csv_manager.cpython-37.pyc │ ├── wsi_case_manager.cpython-36.pyc │ └── wsi_case_manager.cpython-37.pyc ├── case_list_manager.py ├── class_label_csv_manager.py ├── example │ ├── case_list.txt │ ├── case_pairs.csv │ ├── class_label_id.csv │ └── wsi_pair_offset.csv ├── offset_csv_manager.py └── wsi_case_manager.py ├── patch_extraction ├── TMA_patch_extractor.py ├── TODOlist.txt ├── __init__.py ├── feature_map_creator.py ├── feature_maps │ ├── basic_fm_PL_eval.csv │ ├── basic_fm_PPL_eval.csv │ ├── basic_fm_PP_eval.csv │ └── basic_fm_P_eval.csv ├── pairwise_patch_extractor.py ├── parallel_patch_extractor.py ├── patch_extractor.py └── profile_local.sh ├── patch_reconstruction ├── TODOlist.txt ├── patch_blending.py ├── readme.md └── save_wsi_downsampled.py ├── preprocessing └── deidentification.py ├── test ├── test_read_record.ipynb ├── test_read_tfRecords.py └── test_write_tfRecords.py ├── tissue_detection ├── TODOlist.txt ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-36.pyc │ ├── __init__.cpython-37.pyc │ ├── tissue_detector.cpython-36.pyc │ └── tissue_detector.cpython-37.pyc ├── model_files │ ├── HE_penmarking_bkg_fgnd.tsv │ └── HE_tissue_others.tsv ├── pixel_sampling_tool │ └── MouseSamplingUI.py └── tissue_detector.py ├── wrappers └── extract_patches.py ├── wsi_annotation ├── QuPath_scripts │ ├── AperioToQuPath.groovy │ ├── 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