├── .codacy.yaml ├── .devcontainer ├── Dockerfile ├── devcontainer.json ├── noop.txt ├── onCreateCommand.sh ├── postCreateCommand.sh └── welcome-message.txt ├── .dockerignore ├── .gitattributes ├── .github ├── CODEOWNERS ├── ISSUE_TEMPLATE.md ├── ISSUE_TEMPLATE │ ├── ---bug-report.md │ ├── ---dependency-update.md │ ├── ---feature-request.md │ └── --questions-help-support.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── black.yml │ ├── check_pull_request_title.yml │ ├── cla.yml │ ├── codacy.yml │ ├── codeql-analysis.yml │ ├── dependencies │ └── action.yml │ ├── devcontainer.yml │ ├── docker-image.yml │ ├── docs-ci.yml │ ├── main.yml │ ├── openfl-test.yml │ ├── ossar-analysis.yml │ ├── publish-nightly.yml │ ├── python-install-check.yml │ ├── python-test.yml │ ├── spellchecker.yml │ └── stale.yml ├── .gitignore ├── .spelling └── .spelling │ ├── excludes.txt │ └── expect.txt ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile-CPU ├── Dockerfile-CUDA11.8 ├── Dockerfile-CUDA12.6 ├── Dockerfile-ROCm ├── GANDLF ├── README.md ├── __init__.py ├── _deprecated │ └── README.md ├── anonymize │ ├── __init__.py │ └── convert_to_nifti.py ├── cli │ ├── __init__.py │ ├── config_generator.py │ ├── data_split_saver.py │ ├── deploy.py │ ├── generate_metrics.py │ ├── huggingface_hub_handler.py │ ├── main_run.py │ ├── patch_extraction.py │ ├── post_training_model_optimization.py │ ├── preprocess_and_save.py │ └── recover_config.py ├── compute │ ├── README.md │ ├── __init__.py │ ├── forward_pass.py │ ├── generic.py │ ├── inference_loop.py │ ├── loss_and_metric.py │ ├── step.py │ └── training_loop.py ├── config_manager.py ├── configuration │ ├── README.md │ ├── __init__.py │ ├── default_config.py │ ├── differential_privacy_config.py │ ├── exclude_parameters.py │ ├── model_config.py │ ├── nested_training_config.py │ ├── optimizer_config.py │ ├── parameters_config.py │ ├── patch_sampler_config.py │ ├── post_processing_config.py │ ├── pre_processing_config.py │ ├── scheduler_config.py │ ├── user_defined_config.py │ ├── utils.py │ └── validators.py ├── data │ ├── ImagesFromDataFrame.py │ ├── README.md │ ├── __init__.py │ ├── augmentation │ │ ├── README.md │ │ ├── __init__.py │ │ ├── blur_enhanced.py │ │ ├── hed_augs.py │ │ ├── noise_enhanced.py │ │ ├── rgb_augs.py │ │ ├── rotations.py │ │ └── wrap_torchio.py │ ├── inference_dataloader_histopath.py │ ├── lightning_datamodule.py │ ├── patch_miner │ │ ├── README.md │ │ ├── __init__.py │ │ └── opm │ │ │ ├── __init__.py │ │ │ ├── config.yml │ │ │ ├── patch.py │ │ │ ├── patch_manager.py │ │ │ └── utils.py │ ├── post_process │ │ ├── README.md │ │ ├── __init__.py │ │ ├── morphology.py │ │ └── tensor.py │ └── preprocessing │ │ ├── README.md │ │ ├── __init__.py │ │ ├── crop_zero_planes.py │ │ ├── non_zero_normalize.py │ │ ├── normalize_rgb.py │ │ ├── resample_minimum.py │ │ ├── rgb_conversion.py │ │ ├── template_matching │ │ ├── README.md │ │ ├── __init__.py │ │ ├── base.py │ │ ├── histogram_matching.py │ │ ├── stain_extractors.py │ │ ├── stain_normalizer.py │ │ └── utils.py │ │ └── threshold_and_clip.py ├── entrypoints │ ├── __init__.py │ ├── anonymizer.py │ ├── cli_tool.py │ ├── collect_stats.py │ ├── config_generator.py │ ├── construct_csv.py │ ├── debug_info.py │ ├── deploy.py │ ├── generate_metrics.py │ ├── hf_hub_integration.py │ ├── optimize_model.py │ ├── patch_miner.py │ ├── preprocess.py │ ├── recover_config.py │ ├── run.py │ ├── split_csv.py │ ├── subcommands.py │ └── verify_install.py ├── grad_clipping │ ├── __init__.py │ ├── adaptive_gradient_clipping.py │ ├── clip_gradients.py │ └── grad_scaler.py ├── hugging_face.md ├── inference_manager.py ├── logger.py ├── logging_config.yaml ├── losses │ ├── README.md │ ├── __init__.py │ ├── hybrid.py │ ├── hybrid_new.py │ ├── loss_calculators.py │ ├── loss_interface.py │ ├── regression.py │ ├── regression_new.py │ ├── segmentation.py │ └── segmentation_new.py ├── metrics │ ├── README.md │ ├── __init__.py │ ├── classification.py │ ├── generic.py │ ├── metric_calculators.py │ ├── panoptica_config_brats.yaml │ ├── regression.py │ ├── segmentation.py │ ├── segmentation_panoptica.py │ └── synthesis.py ├── models │ ├── MSDNet.py │ ├── Readme.md │ ├── __init__.py │ ├── brain_age.py │ ├── deep_unet.py │ ├── densenet.py │ ├── dynunet_wrapper.py │ ├── efficientnet.py │ ├── fcn.py │ ├── imagenet_unet.py │ ├── imagenet_vgg.py │ ├── light_unet.py │ ├── light_unet_multilayer.py │ ├── lightning_module.py │ ├── modelBase.py │ ├── resnet.py │ ├── sdnet.py │ ├── seg_modules │ │ ├── DecodingModule.py │ │ ├── DownsamplingModule.py │ │ ├── EncodingModule.py │ │ ├── FCNUpsamplingModule.py │ │ ├── IncConv.py │ │ ├── IncDownsamplingModule.py │ │ ├── IncDropout.py │ │ ├── IncUpsamplingModule.py │ │ ├── InceptionModule.py │ │ ├── InitialConv.py │ │ ├── Interpolate.py │ │ ├── Readme.md │ │ ├── ResNetModule.py │ │ ├── UpsamplingModule.py │ │ ├── __init__.py │ │ ├── add_conv_block.py │ │ ├── add_downsample_conv_block.py │ │ ├── average_pool.py │ │ └── out_conv.py │ ├── transunet.py │ ├── uinc.py │ ├── unet.py │ ├── unet_multilayer.py │ ├── unetr.py │ └── vgg.py ├── optimizers │ ├── README.md │ ├── __init__.py │ ├── thirdparty │ │ ├── __init__.py │ │ ├── ademamix.py │ │ ├── adopt.py │ │ └── lion.py │ ├── wrap_monai.py │ └── wrap_torch.py ├── parseConfig.py ├── privacy │ ├── __init__.py │ └── opacus │ │ ├── __init__.py │ │ ├── config_parsing.py │ │ ├── model_handling.py │ │ ├── opacus_anonymization_manager.py │ │ └── training_utils.py ├── schedulers │ ├── README.md │ ├── __init__.py │ ├── wrap_monai.py │ └── wrap_torch.py ├── training_manager.py ├── utils │ ├── __init__.py │ ├── data_splitter.py │ ├── exceptions.py │ ├── gandlf_logging.py │ ├── generic.py │ ├── handle_collisions.py │ ├── imaging.py │ ├── modelbase.py │ ├── modelio.py │ ├── parameter_processing.py │ ├── pred_target_processors.py │ ├── tensor.py │ └── write_parse.py └── version.py ├── LICENSE ├── MANIFEST.in ├── README.md ├── SECURITY.md ├── __init__.py ├── docs ├── LICENSE ├── README.md ├── acknowledgements.md ├── customize.md ├── extending.md ├── faq.md ├── getting_started.md ├── images │ ├── all_options_3.png │ ├── favicon.png │ ├── flowchart.png │ ├── logo.png │ └── logo │ │ ├── full.png │ │ └── full_black.png ├── index.md ├── itcr_connectivity.md ├── migration_guide.md ├── requirements.txt ├── setup.md └── usage.md ├── mkdocs.yml ├── mlcube ├── metrics_mlcube │ ├── example_custom_entrypoint │ │ ├── getting_started_3d_rad_seg.py │ │ └── template.py │ ├── mlcube.yaml │ └── mlcube_medperf.yaml └── model_mlcube │ ├── README.md │ ├── example_custom_entrypoint │ ├── getting_started_3d_rad_seg.py │ └── template.py │ ├── mlcube.yaml │ ├── mlcube_medperf.yaml │ └── workspace │ ├── channelIDs.yml │ └── config.yml ├── pyproject.toml ├── samples ├── config_all_options.yaml ├── config_anonymizer.yaml ├── config_classification.yaml ├── config_dfu2021_vgg11_without_preprocess_classification.yaml ├── config_generator_sample_strategy.yaml ├── config_getting_started_classification_histo2d.yaml ├── config_getting_started_classification_rad3d.yaml ├── config_getting_started_regression_histo2d.yaml ├── config_getting_started_regression_rad3d.yaml ├── config_getting_started_segmentation_histo2d.yaml ├── config_getting_started_segmentation_histo2d_patchExtraction.yaml ├── config_getting_started_segmentation_rad3d.yaml ├── config_regression.yaml ├── config_segmentation_brats.yaml ├── config_segmentation_histology.yaml ├── config_segmentation_metrics_brats_concise.yaml ├── config_segmentation_metrics_brats_default.yaml ├── images_opm │ ├── OPM_flowchart.png │ ├── example_lm.tiff │ └── example_slide.tiff ├── sample_test.csv └── sample_train.csv ├── setup.py ├── testing ├── README.md ├── __init__.py ├── config_classification.yaml ├── config_regression.yaml ├── config_segmentation.yaml ├── conftest.py ├── entrypoints │ ├── __init__.py │ ├── test_anonymizer.py │ ├── test_cli_tool.py │ ├── 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