├── .gitignore ├── README.md ├── classification ├── Fully_supervised_testing.py ├── Fully_supervised_testing_combine_features_multi.py ├── Fully_supervised_testing_combine_probs_multi.py ├── Fully_supervised_training.py ├── Generate_csv_multicenter.py ├── Generate_csv_single_scale.py ├── Generate_csv_upper_region.py ├── generators.py ├── models.py ├── run_generate_scripts.sh ├── run_scripts_multiscale.sh ├── run_scripts_single_scale_testing.sh ├── run_scripts_single_scale_training.sh └── utils.py ├── csv_folder ├── .DS_Store ├── ._.DS_Store ├── classification │ ├── .DS_Store │ ├── ._.DS_Store │ └── partitions │ │ ├── 0 │ │ ├── list_test.csv │ │ ├── list_train.csv │ │ └── list_valid.csv │ │ ├── 1 │ │ ├── list_test.csv │ │ ├── list_train.csv │ │ └── list_valid.csv │ │ └── 2 │ │ ├── list_test.csv │ │ ├── list_train.csv │ │ └── list_valid.csv ├── dataset_preprocessing │ ├── ._test_WSI_TCGA_PRAD.csv │ ├── annotated_images_paths.csv │ ├── csv_to_extract.csv │ └── test_WSI_TCGA_PRAD.csv └── scale_regression │ ├── .DS_Store │ ├── ._.DS_Store │ └── partitions │ ├── external_dataset_source.csv │ ├── list_test.csv │ ├── list_train.csv │ └── list_valid.csv ├── preprocessing ├── .DS_Store ├── ._.DS_Store ├── ._Patch_Extractor_Densely_center_multi_Magnifications.py ├── ._extract_grid.sh ├── ._run_scripts.sh ├── Patch_Extractor_Dense_Centroids.py ├── Patch_Extractor_Dense_Centroids_Strong_Labels.py ├── Patch_Extractor_Dense_Grid.py ├── Patch_Extractor_Dense_Grid_Strong_Labels.py ├── run_scripts.sh └── utils.py ├── regressor ├── .DS_Store ├── ._.DS_Store ├── ._Create_csv.py ├── ._Create_csv_from_partitions.py ├── Create_csv.py ├── Create_csv_from_partitions.py ├── Test_regressor.py ├── Train_regressor.py ├── generators.py ├── model.py ├── regressor.py ├── scripts.sh └── utils.py └── segmentation ├── .DS_Store ├── ._.DS_Store ├── ._hooknet-master └── hooknet-master ├── ._README.md ├── .___init__.py ├── ._apply.py ├── ._apply_parameters.yml ├── ._argconfigparser ├── ._docker ├── ._requirements.txt ├── ._source ├── ._train.py ├── ._train_parameters.yml ├── README.md ├── __init__.py ├── apply.py ├── apply_parameters.yml ├── argconfigparser ├── ._argconfigparser.py └── argconfigparser.py ├── docker ├── ._Dockerfile ├── ._requirements.txt ├── Dockerfile └── requirements.txt ├── requirements.txt ├── source ├── .___init__.py ├── ._generator ├── ._image ├── ._inference.py ├── ._model.py ├── ._trainer.py ├── __init__.py ├── generator │ ├── .___init__.py │ ├── ._batchgenerator.py │ ├── __init__.py │ └── batchgenerator.py ├── image │ ├── .___init__.py │ ├── ._deamons.py │ ├── ._imagereader.py │ ├── ._imagewriter.py │ ├── __init__.py │ ├── deamons.py │ ├── imagereader.py │ └── imagewriter.py ├── inference.py ├── model.py └── trainer.py ├── train.py └── train_parameters.yml /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | *DS_Store/ 3 | __pycache__/ 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