├── .gitignore ├── .gitmodules ├── .travis.yml ├── LICENSE ├── README.md ├── checkpoints └── __init__.py ├── docs ├── Makefile ├── _static │ ├── 283_dcis_4.png │ ├── 283_dcis_4_cg.png │ ├── logo.png │ └── logo_large.png ├── _templates │ ├── module.rst │ └── package.rst ├── api │ ├── histocartography.interpretability.base_explainer.rst │ ├── histocartography.interpretability.grad_cam.rst │ ├── histocartography.interpretability.graph_pruning_explainer.rst │ ├── histocartography.interpretability.lrp_gnn_explainer.rst │ ├── histocartography.interpretability.rst │ ├── histocartography.metrics.metrics.rst │ ├── histocartography.metrics.rst │ ├── histocartography.ml.layers.constants.rst │ ├── histocartography.ml.layers.dense_gin_layer.rst │ ├── histocartography.ml.layers.gin_layer.rst │ ├── histocartography.ml.layers.mlp.rst │ ├── histocartography.ml.layers.multi_layer_gnn.rst │ ├── histocartography.ml.layers.pna_layer.rst │ ├── histocartography.ml.layers.rst │ ├── histocartography.ml.models.base_model.rst │ ├── histocartography.ml.models.cell_graph_model.rst │ ├── histocartography.ml.models.hact_model.rst │ ├── histocartography.ml.models.hovernet.rst │ ├── histocartography.ml.models.rst │ ├── histocartography.ml.models.tissue_graph_model.rst │ ├── histocartography.ml.models.zoo.rst │ ├── histocartography.ml.rst │ ├── histocartography.pipeline.rst │ ├── histocartography.preprocessing.assignment_matrix.rst │ ├── histocartography.preprocessing.feature_extraction.rst │ ├── histocartography.preprocessing.graph_builders.rst │ ├── histocartography.preprocessing.io.rst │ ├── histocartography.preprocessing.nuclei_concept_extraction.rst │ ├── histocartography.preprocessing.nuclei_extraction.rst │ ├── histocartography.preprocessing.rst │ ├── histocartography.preprocessing.stain_normalizers.rst │ ├── histocartography.preprocessing.stats.rst │ ├── histocartography.preprocessing.superpixel.rst │ ├── histocartography.preprocessing.tissue_mask.rst │ ├── histocartography.preprocessing.utils.rst │ ├── histocartography.rst │ ├── histocartography.utils.draw_utils.rst │ ├── histocartography.utils.graph.rst │ ├── histocartography.utils.image.rst │ ├── histocartography.utils.io.rst │ ├── histocartography.utils.rst │ ├── histocartography.utils.torch.rst │ ├── histocartography.visualization.rst │ └── histocartography.visualization.visualization.rst ├── conf.py ├── index.rst ├── make.bat └── modules.rst ├── environment.yml ├── examples ├── README.md ├── cell_graph_explainer.py ├── cell_graph_generation.py ├── config │ └── cg_bracs_cggnn_3_classes_gin.yml ├── feature_cube_extraction.py ├── masked_patch_feature_extraction.py ├── masked_patch_feature_extraction_from_layer.py ├── stain_normalization.py └── tissue_graph_generation.py ├── histocartography ├── __init__.py ├── interpretability │ ├── __init__.py │ ├── base_explainer.py │ ├── grad_cam.py │ ├── graph_pruning_explainer.py │ └── lrp_gnn_explainer.py ├── metrics │ ├── __init__.py │ └── metrics.py ├── ml │ ├── __init__.py │ ├── layers │ │ ├── __init__.py │ │ ├── constants.py │ │ ├── dense_gin_layer.py │ │ ├── gin_layer.py │ │ ├── mlp.py │ │ ├── multi_layer_gnn.py │ │ └── pna_layer.py │ └── models │ │ ├── __init__.py │ │ ├── base_model.py │ │ ├── cell_graph_model.py │ │ ├── hact_model.py │ │ ├── hovernet.py │ │ ├── tissue_graph_model.py │ │ └── zoo.py ├── pipeline.py ├── preprocessing │ ├── README.md │ ├── __init__.py │ ├── assignment_matrix.py │ ├── feature_extraction.py │ ├── graph_builders.py │ ├── io.py │ ├── nuclei_concept_extraction.py │ ├── nuclei_extraction.py │ ├── stain_normalizers.py │ ├── stats.py │ ├── superpixel.py │ ├── tissue_mask.py │ └── utils.py ├── utils │ ├── __init__.py │ ├── draw_utils.py │ ├── graph.py │ ├── image.py │ ├── io.py │ └── torch.py └── visualization │ ├── __init__.py │ └── visualization.py ├── requirements.txt ├── setup.cfg ├── setup.py └── test ├── __init__.py ├── interpretability ├── __init__.py ├── config │ └── cg_bracs_cggnn_3_classes_gin.yml ├── test_gnnexplainer.py ├── test_graphgradcam.py └── test_graphlrp.py ├── metrics ├── __init__.py └── test_segmentation_metrics.py ├── ml ├── __init__.py ├── config │ ├── bracs_hact_7_classes_pna.yml │ ├── cg_bracs_cggnn_3_classes_gin.yml │ ├── cg_bracs_cggnn_5_classes_gin.yml │ ├── cg_bracs_cggnn_7_classes_pna.yml │ ├── cg_model.yml │ ├── hact_model.yml │ ├── multi_layer_dense_gin.yml │ ├── multi_layer_gin.yml │ ├── multi_layer_pna.yml │ ├── tg_bracs_tggnn_3_classes_gin.yml │ ├── tg_bracs_tggnn_7_classes_pna.yml │ └── tg_model.yml ├── test_cell_graph_model.py ├── test_hact_model.py ├── test_multi_layer_gnn.py └── test_tissue_graph_model.py ├── preprocessing ├── __init__.py ├── config │ ├── feature_extraction │ │ ├── deep_nuclei_feature_extractor_aug.yml │ │ ├── deep_nuclei_feature_extractor_noaug.yml │ │ ├── deep_tissue_feature_extractor_aug.yml │ │ ├── deep_tissue_feature_extractor_noaug.yml │ │ ├── deep_tissue_feature_extractor_noaug_masked_instance.yml │ │ ├── grid_deep_tissue_feature_extractor_aug.yml │ │ ├── grid_deep_tissue_feature_extractor_noaug.yml │ │ ├── handcrafted_feature_extractor.yml │ │ └── masked_grid_deep_tissue_feature_extractor.yml │ ├── graph_builder │ │ ├── knn_graph_builder.yml │ │ ├── rag_graph_builder.yml │ │ ├── rag_graph_builder_annotation.yml │ │ └── rag_graph_builder_aug.yml │ ├── io │ │ ├── graph_loader.yml │ │ └── image_loader.yml │ ├── nuclei_extraction │ │ └── nuclei_extractor.yml │ ├── stain_normalization │ │ ├── macenko_normalizer_noref.yml │ │ ├── macenko_normalizer_ref.yml │ │ ├── vahadane_normalizer_noref.yml │ │ ├── vahadane_normalizer_ref.yml │ │ └── vahadane_precomputed_normalizer_fail.yml │ ├── stats │ │ ├── graph_diameter.yml │ │ └── superpixel_counter.yml │ ├── superpixels │ │ ├── color_merged_extractor.yml │ │ └── slic_extractor.yml │ └── tissue_mask │ │ └── tissue_mask.yml ├── test_assignment_matrix.py ├── test_feature_extraction.py ├── 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