├── Dockerfile ├── LICENSE ├── README.md ├── docker_readme └── readme.md ├── process_results ├── process_results_patches.py └── process_results_superpatches.py ├── src_incep_vgg_tf ├── NNFramework_TF │ ├── config │ │ ├── config_incep-all.ini │ │ ├── config_incep-manual.ini │ │ ├── config_incep-mix.ini │ │ ├── config_incep-semi.ini │ │ ├── config_vgg-all.ini │ │ ├── config_vgg-manual.ini │ │ ├── config_vgg-mix.ini │ │ ├── config_vgg-semi.ini │ │ ├── test_cancer_types │ │ │ ├── config_incep-all_test.ini │ │ │ ├── config_incep-manual_test.ini │ │ │ ├── config_incep-mix_test.ini │ │ │ ├── config_incep-semi_test.ini │ │ │ ├── config_vgg-all_test.ini │ │ │ ├── config_vgg-manual_test.ini │ │ │ ├── config_vgg-mix_test.ini │ │ │ └── config_vgg-semi_test.ini │ │ ├── test_superpatch_new │ │ │ ├── config_incep-all_test.ini │ │ │ ├── config_incep-manual_test.ini │ │ │ ├── config_incep-mix_test.ini │ │ │ ├── config_incep-semi_test.ini │ │ │ ├── config_vgg-all_test.ini │ │ │ ├── config_vgg-manual_test.ini │ │ │ ├── config_vgg-mix_test.ini │ │ │ └── config_vgg-semi_test.ini │ │ ├── test_val_luad_strat │ │ │ ├── config_incep-all_test.ini │ │ │ ├── config_incep-manual_test.ini │ │ │ ├── config_incep-mix_test.ini │ │ │ ├── config_incep-semi_test.ini │ │ │ ├── config_vgg-all_test.ini │ │ │ ├── config_vgg-manual_test.ini │ │ │ ├── config_vgg-mix_test.ini │ │ │ └── config_vgg-semi_test.ini │ │ └── test_wsi_ext │ │ │ ├── config_incep-all_test_ext.ini │ │ │ ├── config_incep-manual_test_ext.ini │ │ │ ├── config_incep-mix_test_ext.ini │ │ │ ├── config_incep-mix_test_ext_binary.ini │ │ │ ├── config_incep-semi_test_ext.ini │ │ │ ├── config_vgg-all_test_ext.ini │ │ │ ├── config_vgg-manual_test_ext.ini │ │ │ ├── config_vgg-mix_test_ext.ini │ │ │ ├── config_vgg-mix_test_ext_binary.ini │ │ │ └── config_vgg-semi_test_ext.ini │ ├── readme.md │ ├── sa_cost_func │ │ └── cross_entropy_cost_func.py │ ├── sa_data_providers │ │ ├── TCGA_batch_data_provider.py │ │ ├── TCGA_batch_data_provider_test_labeled.py │ │ ├── TCGA_data_provider.py │ │ └── TCGA_superpatch_data_provider.py │ ├── sa_net_arch.py │ ├── sa_net_arch_utilities.py │ ├── sa_net_cost_func.py │ ├── sa_net_data_provider.py │ ├── sa_net_loss_func_helper.py │ ├── sa_net_model_params.py │ ├── sa_net_optimizer.py │ ├── sa_net_output_helper.py │ ├── sa_net_runner.py │ ├── sa_net_test.py │ ├── sa_net_train.py │ ├── sa_networks │ │ ├── inception_utils.py │ │ ├── inception_v4.py │ │ ├── inception_v4_classifier_arch.py │ │ ├── vgg.py │ │ └── vgg_16_classifier_arch.py │ ├── sa_runners │ │ ├── tf_classifier_runner.py │ │ └── tf_classifier_runner_external_input.py │ ├── sa_testers │ │ ├── sa_net_test_classifier.py │ │ ├── sa_net_test_classifier_batch.py │ │ ├── sa_net_test_classifier_external_input.py │ │ ├── sa_net_test_classifier_external_input_binary_output.py │ │ └── sa_net_test_superpatch_classifier_batch.py │ └── sa_trainers │ │ └── sa_net_train_classifier.py └── NNFramework_TF_external_call │ ├── external_model.py │ └── external_train.py └── u24_lymphocyte ├── README.md ├── conf └── variables.sh ├── data └── keep.txt ├── 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 ├── gen_json_multipleheat_eagle.py ├── low_res_all.py ├── start.sh ├── start_manual.sh └── upload_heatmaps.sh ├── patch_extraction ├── save_svs_to_tiles.py ├── save_svs_to_tiles.sh └── start.sh ├── prediction ├── NNFramework_TF │ ├── config │ │ ├── config_incep-all.ini │ │ ├── config_incep-manual.ini │ │ ├── config_incep-mix.ini │ │ ├── config_incep-semi.ini │ │ ├── config_vgg-all.ini │ │ ├── config_vgg-manual.ini │ │ ├── config_vgg-mix.ini │ │ ├── config_vgg-semi.ini │ │ ├── test_cancer_types │ │ │ ├── config_incep-all_test.ini │ │ │ ├── config_incep-manual_test.ini │ │ │ ├── config_incep-mix_test.ini │ │ │ ├── config_incep-semi_test.ini │ │ │ ├── config_vgg-all_test.ini │ │ │ ├── config_vgg-manual_test.ini │ │ │ ├── config_vgg-mix_test.ini │ │ │ └── config_vgg-semi_test.ini │ │ ├── test_superpatch_new │ │ │ ├── config_incep-all_test.ini │ │ │ ├── config_incep-manual_test.ini │ │ │ ├── config_incep-mix_test.ini │ │ │ ├── config_incep-semi_test.ini │ │ │ ├── config_vgg-all_test.ini │ │ │ ├── config_vgg-manual_test.ini │ │ │ ├── config_vgg-mix_test.ini │ │ │ └── config_vgg-semi_test.ini │ │ ├── test_val_luad_strat │ │ │ ├── config_incep-all_test.ini │ │ │ ├── config_incep-manual_test.ini │ │ │ ├── config_incep-mix_test.ini │ │ │ ├── config_incep-semi_test.ini │ │ │ ├── config_vgg-all_test.ini │ │ │ ├── config_vgg-manual_test.ini │ │ │ ├── config_vgg-mix_test.ini │ │ │ └── config_vgg-semi_test.ini │ │ └── test_wsi_ext │ │ │ ├── config_incep-all_test_ext.ini │ │ │ ├── config_incep-manual_test_ext.ini │ │ │ ├── config_incep-mix_test_ext.ini │ │ │ ├── config_incep-mix_test_ext_binary.ini │ │ │ ├── config_incep-semi_test_ext.ini │ │ │ ├── config_vgg-all_test_ext.ini │ │ │ ├── config_vgg-manual_test_ext.ini │ │ │ ├── config_vgg-mix_test_ext.ini │ │ │ ├── config_vgg-mix_test_ext_binary.ini │ │ │ └── config_vgg-semi_test_ext.ini │ ├── readme.md │ ├── sa_cost_func │ │ ├── __pycache__ │ │ │ └── cross_entropy_cost_func.cpython-35.pyc │ │ └── cross_entropy_cost_func.py │ ├── sa_data_providers │ │ ├── TCGA_batch_data_provider.py │ │ ├── TCGA_batch_data_provider_test_labeled.py │ │ ├── TCGA_data_provider.py │ │ └── TCGA_superpatch_data_provider.py │ ├── sa_net_arch.py │ ├── sa_net_arch_utilities.py │ ├── sa_net_cost_func.py │ ├── sa_net_data_provider.py │ ├── sa_net_loss_func_helper.py │ ├── sa_net_model_params.py │ ├── sa_net_optimizer.py │ ├── sa_net_output_helper.py │ ├── sa_net_runner.py │ ├── sa_net_test.py │ ├── sa_net_train.py │ ├── sa_networks │ │ ├── __pycache__ │ │ │ ├── inception_utils.cpython-35.pyc │ │ │ ├── inception_v4.cpython-35.pyc │ │ │ ├── inception_v4_classifier_arch.cpython-35.pyc │ │ │ ├── vgg.cpython-35.pyc │ │ │ └── vgg_16_classifier_arch.cpython-35.pyc │ │ ├── inception_utils.py │ │ ├── inception_v4.py │ │ ├── inception_v4_classifier_arch.py │ │ ├── vgg.py │ │ ├── vgg_0.py │ │ ├── vgg_16_classifier_arch.py │ │ └── vgg_16_classifier_arch_0.py │ ├── sa_runners │ │ ├── __pycache__ │ │ │ ├── tf_classifier_runner_external_input.cpython-35.pyc │ │ │ └── tf_classifier_runner_external_input.cpython-36.pyc │ │ ├── tf_classifier_runner.py │ │ └── tf_classifier_runner_external_input.py │ ├── sa_testers │ │ ├── __pycache__ │ │ │ └── sa_net_test_classifier_external_input.cpython-35.pyc │ │ ├── sa_net_test_classifier.py │ │ ├── sa_net_test_classifier_batch.py │ │ ├── sa_net_test_classifier_external_input.py │ │ ├── sa_net_test_classifier_external_input_binary_output.py │ │ └── sa_net_test_superpatch_classifier_batch.py │ └── sa_trainers │ │ └── sa_net_train_classifier.py ├── NNFramework_TF_external_call │ ├── external_model.py │ └── external_train.py ├── color │ ├── color_stats.py │ └── color_stats.sh ├── common │ ├── __init__.py │ ├── batch_norms.py │ ├── ch_inner_prod.py │ └── shape.py ├── lymphocyte │ ├── data_aug.py │ ├── external_model.py │ ├── pred.py │ ├── pred_by_external_model.py │ └── pred_thread_lym.sh ├── models │ └── update_path.sh ├── necrosis │ ├── data_aug_necrosis.py │ ├── pred_necrosis.py │ ├── pred_necrosis_batch.py │ ├── pred_necrosis_wsi.py │ └── pred_thread_nec.sh ├── pytorch_resnet34_model │ ├── load_til_resnet34_external_input.py │ ├── model_til_resnet34_external_input.py │ └── resnet34_arch.py ├── start.sh ├── start_color_only.sh └── start_lym_only.sh └── scripts ├── cleanup_heatmap.sh ├── patch_2_heatmap.sh ├── svs_2_heatmap.sh ├── threshold_probability_heatmaps.py └── threshold_probability_heatmaps.sh /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShahiraAbousamra/til_classification/HEAD/Dockerfile -------------------------------------------------------------------------------- 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