├── .gitignore ├── LICENSE ├── README.md ├── ToothFairy ├── README.md ├── algorithm_example │ ├── .dockerignore │ ├── .gitattributes │ ├── .github │ │ └── workflows │ │ │ └── ci.yml │ ├── Dockerfile │ ├── PosPadUNet3D.py │ ├── README.md │ ├── build.sh │ ├── export.sh │ ├── process.py │ ├── requirements.txt │ └── test.sh ├── algorithms │ ├── Haoshen_Wang │ │ ├── README.md │ │ ├── configs_loader.py │ │ ├── data_function.py │ │ ├── fine_tuning.py │ │ ├── heatmap_generation.py │ │ ├── loss_function.py │ │ ├── points_sampling.py │ │ └── test_UNet.py │ ├── Marek_Wodzinski │ │ ├── README.md │ │ ├── __init__.py │ │ ├── requirements.txt │ │ └── src │ │ │ ├── __init__.py │ │ │ ├── augmentation │ │ │ ├── __init__.py │ │ │ ├── aug.py │ │ │ ├── torchio.py │ │ │ └── volumetric.py │ │ │ ├── datasets │ │ │ ├── __init__.py │ │ │ └── toothfairy_dataset.py │ │ │ ├── evaluation │ │ │ ├── __init__.py │ │ │ ├── evaluation_functions.py │ │ │ ├── evaluation_toothfairy.py │ │ │ ├── np_metrics.py │ │ │ └── tc_metrics.py │ │ │ ├── helpers │ │ │ ├── __init__.py │ │ │ ├── cost_functions.py │ │ │ ├── hausdorff.py │ │ │ └── utils.py │ │ │ ├── inference │ │ │ ├── __init__.py │ │ │ └── inference_toothfairy.py │ │ │ ├── input_output │ │ │ ├── __init__.py │ │ │ ├── utils_io.py │ │ │ └── volumetric.py │ │ │ ├── networks │ │ │ ├── __init__.py │ │ │ ├── building_blocks.py │ │ │ └── runet.py │ │ │ ├── parsers │ │ │ ├── __init__.py │ │ │ ├── elastic_toothfairy.py │ │ │ └── parse_toothfairy.py │ │ │ ├── paths │ │ │ ├── __init__.py │ │ │ ├── hpc_paths.py │ │ │ └── paths.py │ │ │ ├── postprocessing │ │ │ └── __init__.py │ │ │ ├── preprocessing │ │ │ ├── __init__.py │ │ │ └── preprocessing_volumetric.py │ │ │ ├── runners │ │ │ ├── __init__.py │ │ │ ├── experiments │ │ │ │ ├── __init__.py │ │ │ │ └── toothfairy_experiments.py │ │ │ └── run_toothfairy_trainer.py │ │ │ ├── training │ │ │ ├── __init__.py │ │ │ └── toothfairy_trainer.py │ │ │ └── visualization │ │ │ ├── __init__.py │ │ │ └── volumetric.py │ ├── Tomasz_Szczepanski │ │ ├── .gitignore │ │ ├── README.md │ │ ├── docker │ │ │ ├── Dockerfile │ │ │ ├── build.sh │ │ │ ├── export.sh │ │ │ ├── misc │ │ │ │ └── slicer_33_colormap.txt │ │ │ ├── process.py │ │ │ ├── requirements.txt │ │ │ ├── src │ │ │ │ ├── arg_parser.py │ │ │ │ ├── cuda_stats.py │ │ │ │ ├── data_augmentation.py │ │ │ │ ├── inference_HQ.py │ │ │ │ ├── inference_LQ_coarse.py │ │ │ │ └── models │ │ │ │ │ ├── acti_norm.py │ │ │ │ │ ├── convolutions.py │ │ │ │ │ ├── resnet.py │ │ │ │ │ └── resunet.py │ │ │ └── test │ │ │ │ ├── test.sh │ │ │ │ └── transform_to_mha.py │ │ ├── env_config.yml │ │ ├── src │ │ │ ├── arg_parser_gcr_finetune.py │ │ │ ├── arg_parser_gcr_pretrain.py │ │ │ ├── arg_parser_lq.py │ │ │ ├── arg_parser_lq_finetune.py │ │ │ ├── cuda_stats.py │ │ │ ├── data_augmentation.py │ │ │ ├── data_augmentation_fine.py │ │ │ ├── dummy_logger.py │ │ │ ├── log_image.py │ │ │ ├── models │ │ │ │ ├── acti_norm.py │ │ │ │ ├── convolutions.py │ │ │ │ ├── resnet.py │ │ │ │ └── resunet.py │ │ │ └── scheduler.py │ │ ├── train_gcr_finetune.py │ │ ├── train_gcr_pretrain.py │ │ ├── train_lq.py │ │ └── train_lq_finetune.py │ ├── Yannick_Kirchhoff │ │ ├── dataset.json │ │ ├── nnunetv2 │ │ │ ├── __init__.py │ │ │ ├── batch_running │ │ │ │ ├── __init__.py │ │ │ │ ├── benchmarking │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── generate_benchmarking_commands.py │ │ │ │ │ └── summarize_benchmark_results.py │ │ │ │ ├── collect_results_custom_Decathlon.py │ │ │ │ ├── collect_results_custom_Decathlon_2d.py │ │ │ │ ├── generate_lsf_runs_customDecathlon.py │ │ │ │ └── release_trainings │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── nnunetv2_v1 │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── collect_results.py │ │ │ │ │ └── generate_lsf_commands.py │ │ │ ├── configuration.py │ │ │ ├── dataset_conversion │ │ │ │ ├── Dataset027_ACDC.py │ │ │ │ ├── Dataset073_Fluo_C3DH_A549_SIM.py │ │ │ │ ├── Dataset114_MNMs.py │ │ │ │ ├── Dataset115_EMIDEC.py │ │ │ │ ├── Dataset120_RoadSegmentation.py │ │ │ │ ├── Dataset137_BraTS21.py │ │ │ │ ├── Dataset218_Amos2022_task1.py │ │ │ │ ├── Dataset219_Amos2022_task2.py │ │ │ │ ├── Dataset220_KiTS2023.py │ │ │ │ ├── Dataset221_AutoPETII_2023.py │ │ │ │ ├── Dataset988_dummyDataset4.py │ │ │ │ ├── __init__.py │ │ │ │ ├── convert_MSD_dataset.py │ │ │ │ ├── convert_raw_dataset_from_old_nnunet_format.py │ │ │ │ ├── datasets_for_integration_tests │ │ │ │ │ ├── Dataset996_IntegrationTest_Hippocampus_regions_ignore.py │ │ │ │ │ ├── Dataset997_IntegrationTest_Hippocampus_regions.py │ │ │ │ │ ├── Dataset998_IntegrationTest_Hippocampus_ignore.py │ │ │ │ │ ├── Dataset999_IntegrationTest_Hippocampus.py │ │ │ │ │ └── __init__.py │ │ │ │ └── generate_dataset_json.py │ │ │ ├── ensembling │ │ │ │ ├── __init__.py │ │ │ │ └── ensemble.py │ │ │ ├── evaluation │ │ │ │ ├── __init__.py │ │ │ │ ├── accumulate_cv_results.py │ │ │ │ ├── evaluate_predictions.py │ │ │ │ └── find_best_configuration.py │ │ │ ├── experiment_planning │ │ │ │ ├── __init__.py │ │ │ │ ├── dataset_fingerprint │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── fingerprint_extractor.py │ │ │ │ ├── experiment_planners │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── default_experiment_planner.py │ │ │ │ │ ├── network_topology.py │ │ │ │ │ ├── readme.md │ │ │ │ │ └── resencUNet_planner.py │ │ │ │ ├── plan_and_preprocess_api.py │ │ │ │ ├── plan_and_preprocess_entrypoints.py │ │ │ │ ├── plans_for_pretraining │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── move_plans_between_datasets.py │ │ │ │ └── verify_dataset_integrity.py │ │ │ ├── imageio │ │ │ │ ├── __init__.py │ │ │ │ ├── base_reader_writer.py │ │ │ │ ├── natural_image_reager_writer.py │ │ │ │ ├── nibabel_reader_writer.py │ │ │ │ ├── npy_reader_writer.py │ │ │ │ ├── reader_writer_registry.py │ │ │ │ ├── readme.md │ │ │ │ ├── simpleitk_reader_writer.py │ │ │ │ └── tif_reader_writer.py │ │ │ ├── inference │ │ │ │ ├── __init__.py │ │ │ │ ├── data_iterators.py │ │ │ │ ├── examples.py │ │ │ │ ├── export_prediction.py │ │ │ │ ├── predict_from_raw_data.py │ │ │ │ ├── readme.md │ │ │ │ └── sliding_window_prediction.py │ │ │ ├── model_sharing │ │ │ │ ├── __init__.py │ │ │ │ ├── entry_points.py │ │ │ │ ├── model_download.py │ │ │ │ ├── model_export.py │ │ │ │ └── model_import.py │ │ │ ├── paths.py │ │ │ ├── postprocessing │ │ │ │ ├── __init__.py │ │ │ │ └── remove_connected_components.py │ │ │ ├── preprocessing │ │ │ │ ├── __init__.py │ │ │ │ ├── cropping │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── cropping.py │ │ │ │ ├── normalization │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── default_normalization_schemes.py │ │ │ │ │ ├── map_channel_name_to_normalization.py │ │ │ │ │ └── readme.md │ │ │ │ ├── preprocessors │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── default_preprocessor.py │ │ │ │ └── resampling │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── default_resampling.py │ │ │ │ │ └── utils.py │ │ │ ├── run │ │ │ │ ├── __init__.py │ │ │ │ ├── load_pretrained_weights.py │ │ │ │ └── run_training.py │ │ │ ├── tests │ │ │ │ ├── __init__.py │ │ │ │ └── integration_tests │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── add_lowres_and_cascade.py │ │ │ │ │ ├── cleanup_integration_test.py │ │ │ │ │ ├── lsf_commands.sh │ │ │ │ │ ├── prepare_integration_tests.sh │ │ │ │ │ ├── readme.md │ │ │ │ │ ├── run_integration_test.sh │ │ │ │ │ ├── run_integration_test_bestconfig_inference.py │ │ │ │ │ └── run_integration_test_trainingOnly_DDP.sh │ │ │ ├── training │ │ │ │ ├── __init__.py │ │ │ │ ├── data_augmentation │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── compute_initial_patch_size.py │ │ │ │ │ └── custom_transforms │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── cascade_transforms.py │ │ │ │ │ │ ├── deep_supervision_donwsampling.py │ │ │ │ │ │ ├── limited_length_multithreaded_augmenter.py │ │ │ │ │ │ ├── manipulating_data_dict.py │ │ │ │ │ │ ├── masking.py │ │ │ │ │ │ ├── region_based_training.py │ │ │ │ │ │ └── transforms_for_dummy_2d.py │ │ │ │ ├── dataloading │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── base_data_loader.py │ │ │ │ │ ├── data_loader_2d.py │ │ │ │ │ ├── data_loader_3d.py │ │ │ │ │ ├── nnunet_dataset.py │ │ │ │ │ └── utils.py │ │ │ │ ├── logging │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── nnunet_logger.py │ │ │ │ ├── loss │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── compound_losses.py │ │ │ │ │ ├── deep_supervision.py │ │ │ │ │ ├── dice.py │ │ │ │ │ ├── hausdorff_loss.py │ │ │ │ │ └── robust_ce_loss.py │ │ │ │ ├── lr_scheduler │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── polylr.py │ │ │ │ └── nnUNetTrainer │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── nnUNetTrainer.py │ │ │ │ │ └── variants │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── benchmarking │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── nnUNetTrainerBenchmark_5epochs.py │ │ │ │ │ └── nnUNetTrainerBenchmark_5epochs_noDataLoading.py │ │ │ │ │ ├── data_augmentation │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── nnUNetTrainerDA5.py │ │ │ │ │ ├── nnUNetTrainerDAOrd0.py │ │ │ │ │ ├── nnUNetTrainerNoDA.py │ │ │ │ │ └── nnUNetTrainerNoMirroring.py │ │ │ │ │ ├── loss │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── nnUNetTrainerCELoss.py │ │ │ │ │ ├── nnUNetTrainerDiceLoss.py │ │ │ │ │ ├── nnUNetTrainerFocalLoss.py │ │ │ │ │ ├── nnUNetTrainerHDFocalLoss.py │ │ │ │ │ ├── nnUNetTrainerHDLoss.py │ │ │ │ │ ├── nnUNetTrainerSkelDice.py │ │ │ │ │ └── nnUNetTrainerTopkLoss.py │ │ │ │ │ ├── lr_schedule │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── nnUNetTrainerCosAnneal.py │ │ │ │ │ ├── network_architecture │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── nnUNetTrainerBN.py │ │ │ │ │ └── nnUNetTrainerNoDeepSupervision.py │ │ │ │ │ ├── optimizer │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── nnUNetTrainerAdam.py │ │ │ │ │ └── nnUNetTrainerAdan.py │ │ │ │ │ ├── sampling │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── nnUNetTrainer_probabilisticOversampling.py │ │ │ │ │ └── training_length │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── nnUNetTrainer_Xepochs.py │ │ │ │ │ └── nnUNetTrainer_Xepochs_NoMirroring.py │ │ │ └── utilities │ │ │ │ ├── __init__.py │ │ │ │ ├── collate_outputs.py │ │ │ │ ├── dataset_name_id_conversion.py │ │ │ │ ├── ddp_allgather.py │ │ │ │ ├── default_n_proc_DA.py │ │ │ │ ├── file_path_utilities.py │ │ │ │ ├── find_class_by_name.py │ │ │ │ ├── get_network_from_plans.py │ │ │ │ ├── helpers.py │ │ │ │ ├── json_export.py │ │ │ │ ├── label_handling │ │ │ │ ├── __init__.py │ │ │ │ └── label_handling.py │ │ │ │ ├── network_initialization.py │ │ │ │ ├── overlay_plots.py │ │ │ │ ├── plans_handling │ │ │ │ ├── __init__.py │ │ │ │ └── plans_handler.py │ │ │ │ └── utils.py │ │ ├── readme.txt │ │ └── setup.py │ └── Yusheng_Liu │ │ ├── README.md │ │ ├── build.sh │ │ ├── dockerfile │ │ ├── framework.JPG │ │ ├── name_config.py │ │ ├── networks │ │ ├── generic_UNet.py │ │ ├── generic_UNet_small.py │ │ ├── generic_UNet_template.py │ │ ├── generic_UNetv2.py │ │ ├── net_factory_3d.py │ │ └── neural_network.py │ │ ├── output │ │ └── results.json │ │ ├── predict.sh │ │ ├── process │ │ ├── Check_Component.py │ │ ├── data_read.py │ │ ├── evaluations │ │ │ ├── dice.py │ │ │ └── metric.py │ │ ├── file_utils.py │ │ ├── nnUNet_Pseudo_Generate.sh │ │ ├── nnUNetv2_Pseudo_Generate.sh │ │ ├── select_fineGT_series.py │ │ ├── select_reliable_series.py │ │ ├── transforms │ │ │ ├── compose.py │ │ │ ├── connected_component_labeling.py │ │ │ ├── functional.py │ │ │ ├── image_augment.py │ │ │ ├── image_io.py │ │ │ ├── image_reorient.py │ │ │ ├── image_resample.py │ │ │ ├── image_transform.py │ │ │ ├── mask_one_hot.py │ │ │ ├── mask_process.py │ │ │ └── transform.py │ │ └── utils.py │ │ ├── requirements.txt │ │ ├── spacing_config.py │ │ ├── test_3D.py │ │ └── test_3D_util_mirror.py └── evaluation │ ├── .dockerignore │ ├── .gitattributes │ ├── .github │ └── workflows │ │ └── ci.yml │ ├── .gitignore │ ├── Dockerfile │ ├── README.md │ ├── build.sh │ ├── evaluation.py │ ├── export.sh │ ├── out.txt │ ├── requirements.txt │ ├── test.sh │ └── test │ └── predictions.json ├── ToothFairy2 ├── README.md ├── algorithm │ ├── .dockerignore │ ├── .gitattributes │ ├── Dockerfile │ ├── README.md │ ├── build.ps1 │ ├── build.sh │ ├── export.ps1 │ ├── export.sh │ ├── output │ │ └── toothfairy_algorithm-output-aef7d44fa8239aa6ee100726344ed4c6 │ │ │ └── _data │ │ │ └── results.json │ ├── process.py │ ├── requirements.txt │ ├── resources │ │ └── README.md │ ├── test.sh │ └── test │ │ └── .gitignore └── evaluation │ ├── .dockerignore │ ├── .gitattributes │ ├── .github │ └── workflows │ │ └── ci.yml │ ├── .gitignore │ ├── Dockerfile │ ├── README.md │ ├── build.sh │ ├── evaluation.py │ ├── export.sh │ ├── ground-truth │ ├── ToothFairy2F_012_0000.mha │ ├── ToothFairy2F_027_0000.mha │ ├── ToothFairy2F_056_0000.mha │ └── ToothFairy2F_065_0000.mha │ ├── requirements.txt │ ├── test.sh │ └── test │ ├── F012 │ └── output │ │ └── images │ │ └── oral-pharyngeal-segmentation │ │ └── README.md │ ├── F027 │ └── output │ │ └── images │ │ └── oral-pharyngeal-segmentation │ │ └── README.md │ ├── F056 │ └── output │ │ └── images │ │ └── oral-pharyngeal-segmentation │ │ └── README.md │ ├── F065 │ └── output │ │ └── images │ │ └── oral-pharyngeal-segmentation │ │ └── README.md │ └── predictions.json └── ToothFairy3 ├── Interactive-Segmentation ├── .dockerignore ├── README.md ├── algorithm │ ├── .dockerignore │ ├── Dockerfile │ ├── README.md │ ├── build.ps1 │ ├── build.sh │ ├── export.ps1 │ ├── export.sh │ ├── process.py │ ├── requirements.txt │ ├── test.ps1 │ └── test.sh ├── evaluation │ ├── .dockerignore │ ├── .gitignore │ ├── Dockerfile │ ├── README.md │ ├── build.ps1 │ ├── build.sh │ ├── evaluation.py │ ├── export.ps1 │ ├── export.sh │ ├── requirements.txt │ ├── test.ps1 │ └── test.sh ├── run-pipeline.ps1 ├── run-pipeline.sh └── simulate_clicks.py ├── Multi-Instance-Segmentation ├── README.md ├── algorithm │ ├── Dockerfile │ ├── README.md │ ├── build.ps1 │ ├── build.sh │ ├── export.ps1 │ ├── export.sh │ ├── process.py │ ├── requirements.txt │ ├── test.ps1 │ ├── test.sh │ └── test │ │ ├── input │ │ └── inputs.json │ │ └── output │ │ └── results.json ├── evaluation │ ├── .gitignore │ ├── Dockerfile │ ├── 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