├── .DS_Store ├── .gitignore ├── 10x_TuPro ├── config_dataset-ablation.yaml ├── config_dataset.yaml ├── cross_validation_config.ipynb └── cross_validation_config.yaml ├── COAD ├── config_dataset-ablation.yaml ├── config_dataset.yaml └── cross_validation_config.yaml ├── HEST ├── create_datasets.ipynb ├── create_datasets_Visium.ipynb ├── create_datasets_Xenium_lung.ipynb └── create_datasets_Xenium_paad.ipynb ├── LICENSE ├── LUNG_CANCER ├── config_dataset.yaml ├── cross_validation_config.ipynb ├── cross_validation_config.yaml ├── image_visium_match.yaml └── run_visium_leiden_clusters.ipynb ├── Lung_Xenium ├── .test.txt.swp ├── config_dataset-ablation.yaml ├── config_dataset.yaml ├── cross_validation_config.ipynb ├── cross_validation_config.yaml └── lq_test.py ├── README.md ├── SCCRCC ├── config_dataset-ablation.yaml ├── config_dataset.yaml └── cross_validation_config.yaml ├── Snakefile.annotate ├── Snakefile.evaluate ├── Snakefile.prediction ├── Snakefile.preprocess.visium ├── Snakefile.preprocess.xenium ├── Snakemake_info.yaml ├── TCGA_KIRC ├── config_dataset.yaml ├── config_dataset_ff.yaml ├── config_dataset_ffpe.yaml ├── metadata_ff.ipynb ├── metadata_ffpe.ipynb ├── survival_metadata_ff.ipynb └── survival_metadata_ffpe.ipynb ├── TCGA_LUAD ├── config_dataset.yaml ├── config_dataset_ff.yaml ├── config_dataset_ffpe.yaml ├── metadata_ff.ipynb ├── metadata_ffpe.ipynb ├── survival_metadata_ff.ipynb └── survival_metadata_ffpe.ipynb ├── TCGA_LUSC ├── config_dataset.yaml ├── config_dataset_ff.yaml ├── config_dataset_ffpe.yaml ├── metadata_ff.ipynb ├── metadata_ffpe.ipynb ├── survival_metadata_ff.ipynb └── survival_metadata_ffpe.ipynb ├── TCGA_SKCM ├── config_dataset.yaml ├── config_dataset_ff.yaml ├── config_dataset_ffpe.yaml ├── metadata_ff.ipynb ├── metadata_ffpe.ipynb ├── survival_metadata_ff.ipynb └── survival_metadata_ffpe.ipynb ├── USZ ├── config_dataset-ablation.yaml ├── config_dataset.yaml ├── cross_validation_config.ipynb ├── cross_validation_config.yaml ├── label_unassigned.ipynb └── labels.ipynb ├── clean_logs.sh ├── config.yaml ├── environment.yaml ├── plotting_notebooks ├── Figure3A.ipynb ├── Figure3BC.ipynb ├── Figure4ABCD.ipynb ├── Figure5ABCD.ipynb ├── Figure6A.ipynb ├── Figure6B.ipynb ├── Figure6CD.ipynb ├── Figure6FG.ipynb ├── Figure7AC.ipynb ├── Figure7B.ipynb ├── Figure7CDE.ipynb ├── FigureS1_Ablation.ipynb ├── FigureS2_LUNG_CANCER.ipynb ├── FigureS9_genes_type.ipynb ├── figure6_boxplot.Rmd ├── go_simplify.R └── resources │ └── TLS_manual_annotation_gene_expression_v2.csv.gz ├── src ├── BLEEP │ ├── dataloader.py │ ├── model.py │ └── utils.py ├── CellTypeModel │ └── model.py ├── HisToGene │ ├── dataloader.py │ ├── model.py │ └── utils.py ├── Hist2ST │ ├── dataloader.py │ ├── model.py │ └── utils.py ├── MLP │ ├── dataloader.py │ └── model.py ├── STNet │ ├── dataloader.py │ └── model.py ├── THItoGene │ ├── dataloader.py │ ├── model.py │ └── utils.py ├── config.py ├── knn.py ├── morphology_model.py ├── preprocess_utils │ └── preprocess_image.py ├── utils.py └── utils_morphology_features.py ├── summary.jpg └── workflows ├── annotation ├── annotate_label_and_text.py ├── predict_expression.py └── train_label_classifier.py ├── configs ├── config_BLEEP.yaml ├── config_BLEEP_cell.yaml ├── config_DeepCell.yaml ├── config_DeepSpot.yaml ├── config_DeepSpot_context_spot.yaml ├── config_DeepSpot_context_spotsubspot.yaml ├── config_DeepSpot_context_spotsubspotneighbors1.yaml ├── config_DeepSpot_context_spotsubspotneighbors3.yaml ├── config_DeepSpot_context_spotsubspotneighbors5.yaml ├── config_DeepSpot_genenorm_no.yaml ├── config_DeepSpot_genenorm_robust.yaml ├── config_DeepSpot_genenorm_standard.yaml ├── config_DeepSpot_image_hoptimus0.yaml ├── config_DeepSpot_image_inception.yaml ├── config_DeepSpot_image_phikon.yaml ├── config_DeepSpot_image_phikonv2.yaml ├── config_DeepSpot_image_resnet50.yaml ├── config_DeepSpot_image_uni.yaml ├── config_DeepSpot_loss_mse.yaml ├── config_DeepSpot_loss_pearson.yaml ├── config_DeepSpot_loss_poisson.yaml ├── config_DeepSpot_oversampling_off.yaml ├── config_DeepSpot_oversampling_on.yaml ├── config_HisToGene.yaml ├── config_Hist2ST.yaml ├── config_LinearRegression.yaml ├── config_LinearRegression_cd.yaml ├── config_LinearRegression_cell.yaml ├── config_MLP.yaml ├── config_MLP_cell.yaml ├── config_MeanCellType.yaml ├── config_STNet.yaml ├── config_STNet_cell.yaml └── config_THItoGene.yaml ├── evaluate ├── evaluate_label_model.ipynb ├── evaluate_model.ipynb ├── evaluate_tcga.ipynb ├── manual_tumor_type_prediction.ipynb ├── model_comparison.ipynb └── survival_analysis.ipynb ├── models ├── BLEEP.py ├── DeepCell.py ├── DeepSpot.py ├── HisToGene.py ├── Hist2ST.py ├── LinearRegression.py ├── MLP.py ├── MeanCellType.py ├── STNet.py └── THItoGene.py └── preprocess ├── create_inputX.py ├── create_tcga_anndata.py ├── extract_image_features_visium.py ├── extract_image_features_xenium.py ├── extract_tiles.py ├── preprocessH5AD_10x_TuPro.py ├── preprocessH5AD_HEST.py 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