├── .gitignore ├── LICENSE ├── Matlab ├── AddPGandMetaclusterstoSession.m ├── ImportTumorStromamasks_histoCAT.m ├── Run_tsne_Callback_noGUI.m ├── SetTumorStromaCelltype.m ├── WriteOutDistancesforR.m ├── extract_graph_measures_basel.m ├── extract_graph_measures_zurich.m ├── get_Image_means.m ├── histoCAT_adapted │ ├── fuse_images.m │ ├── heatmap_images_overlay.m │ ├── plot_mask_Callback.m │ └── show_selected_area_onTiff.m ├── plot_additionalLayer_mask_Callback.m └── write_out_SCdata_from_histoCAT_forSpilloverCorr.m ├── R ├── BaselTMA_pipeline.Rmd ├── ZurichTMA_pipeline.Rmd └── spillover_compensation │ ├── Spillover_compensation.Rmd │ └── Spillover_matrix.Rmd └── README.md /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BodenmillerGroup/SCPathology_publication/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: 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