├── Dockerfile ├── Dockerfile.orig ├── LICENSE ├── README.md ├── conf └── variables.sh ├── data ├── heatmap_jsons │ └── placeholder ├── heatmap_txt │ └── placeholder ├── log │ └── placeholder ├── patches │ └── placeholder ├── svs │ └── placeholder └── training_data │ └── placeholder ├── download_heatmap └── get_grayscale_heatmaps │ ├── clusterPoints.m │ ├── clusterPoints_spatio_temporal.m │ ├── get_grayscale_heatmap.m │ ├── get_grayscale_heatmap.sh │ ├── get_labeled_im.m │ ├── get_tissue_map.m │ ├── get_whiteness_im.m │ ├── grayscale_heatmaps │ └── placeholder │ └── start.sh ├── heatmap_gen ├── combine_lym_necrosis.sh ├── combine_lym_necrosis_all.sh ├── combine_lym_no_necrosis.sh ├── cp_heatmaps_all.sh ├── gen_all_json.sh ├── gen_json_multipleheat.py ├── start.sh └── start_gen_json.sh ├── models_cnn └── placeholder ├── patch_extraction_cancer_40X ├── nohup.out ├── save_svs_to_tiles.py ├── save_svs_to_tiles.sh └── start.sh ├── prediction ├── color │ ├── color_stats.py │ └── color_stats.sh ├── common │ ├── __init__.py │ ├── __init__.pyc │ ├── batch_norms.py │ ├── batch_norms.pyc │ ├── ch_inner_prod.py │ ├── ch_inner_prod.pyc │ ├── shape.py │ └── shape.pyc ├── start.sh └── tumor_pred │ ├── pred.py │ ├── pred_thread_lym.sh │ └── tumor_utils.py ├── scripts ├── create_container.sh ├── start_interactive_bash.sh ├── svs_2_heatmap.sh └── train.sh ├── singularity └── singularity.def └── training ├── brca_environ.txt ├── resnet.py ├── train_cancer_cnn_Resnet_pretrained.py ├── tumor_data_list_toy.txt └── tumor_utils.py /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBU-BMI/quip_cancer_segmentation/HEAD/Dockerfile -------------------------------------------------------------------------------- /Dockerfile.orig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SBU-BMI/quip_cancer_segmentation/HEAD/Dockerfile.orig 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