├── LICENSE ├── README.md ├── assets ├── framework.pdf ├── framework.png ├── main_result.pdf └── main_result.png ├── data └── nnUNet_raw │ ├── Dataset801_LiverCT │ └── dataset.json │ └── Dataset802_LungXray │ └── dataset.json └── lightm-unet ├── .gitignore ├── LICENSE ├── 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_reader_writer.py │ ├── nibabel_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 ├── nets │ ├── LightMUNet.py │ ├── UMambaBot.py │ └── UMambaEnc.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 │ │ └── robust_ce_loss.py │ ├── lr_scheduler │ │ ├── __init__.py │ │ └── polylr.py │ └── nnUNetTrainer │ │ ├── __init__.py │ │ ├── nnUNetTrainer.py │ │ ├── nnUNetTrainerLightMUNet.py │ │ ├── nnUNetTrainerSegResNet.py │ │ ├── nnUNetTrainerSwinUNETR.py │ │ ├── nnUNetTrainerUMambaBot.py │ │ ├── nnUNetTrainerUMambaEnc.py │ │ ├── nnUNetTrainerUNETR.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 │ │ └── 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 │ ├── 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