├── .gitignore ├── LICENSE ├── README.md ├── SSES_enrichment_analysis.py ├── datasets └── dataset_generic.py ├── differential_expression_analysis └── differential_expression_analysis_IDPs.py ├── gwas └── gtex.conf ├── heatmaps.py ├── image_derived_phenotypes ├── compute_IDPs.py └── compute_pivot_coordinates.py ├── imgs ├── 20230908-122647.png ├── 263006106-e8effb2a-3f4a-44c6-9f2a-44ec05d709c2.png └── 263020413-3d2d3dfc-57b5-4e3f-9dd5-524773386d23.png ├── inference.py ├── models └── model_RNAPath.py ├── preprocessing ├── PathProfiler │ ├── common │ │ ├── README.md │ │ ├── __init__.py │ │ ├── datasets.py │ │ ├── models.py │ │ ├── tile_processing_parallel.py │ │ └── wsi_reader.py │ └── tissue_segmentation │ │ └── unet.py ├── dataset.py ├── features_extraction │ ├── config.yaml │ ├── extract_features.py │ ├── output_features │ │ ├── h5_files │ │ │ └── features.h5 │ │ └── pt_files │ │ │ └── features.pt │ └── white_patch.h5 ├── model.py ├── preprocessing_utils.py ├── segmentation_patching │ ├── config.yaml │ ├── logs │ │ └── 0.log │ ├── masks │ │ └── GTEX-11I78-1025.jpg │ ├── patches │ │ └── 128 │ │ │ └── GTEX-11I78-1025.coords.h5 │ ├── segmentation.py │ ├── thumbnails │ │ └── 128 │ │ │ └── GTEX-11I78-1025_patches.png │ └── tiling.py └── slides │ └── slide.svs ├── requirements.txt ├── resources ├── clusters.yaml ├── gene_set_EMUC.txt ├── gene_set_HEA.txt ├── genes_info.csv ├── select_genes_RNAPath.py └── slides_dataset.csv ├── splits ├── RNAPath_HEA │ ├── splits_0.csv │ └── splits_0_bool.csv ├── RNAPath_main │ ├── splits_0.csv │ ├── splits_0_bool.csv │ └── splits_0_descriptor.csv └── create_splits.py ├── tiles_classification ├── define_clusters_kNN.py ├── fine_grained_multiclass_segmentation.py └── multiclass_tissue_segmentation.py ├── train.py └── utils ├── core_utils.py ├── eval_utils.py ├── file_utils.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- 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