├── .gitignore ├── LICENSE ├── README.md ├── base_ml ├── __init__.py ├── base_cli.py ├── base_early_stopping.py ├── base_experiment.py ├── base_loss.py ├── base_optim.py ├── base_trainer.py ├── base_utils.py └── base_validator.py ├── config_examples ├── preprocessing_example.yaml └── training_example.yaml ├── configs ├── __init__.py ├── datasets │ └── PanNuke │ │ ├── dataset_config.yaml │ │ ├── fold0 │ │ ├── cell_count.csv │ │ └── types.csv │ │ ├── fold1 │ │ ├── cell_count.csv │ │ └── types.csv │ │ ├── fold2 │ │ ├── cell_count.csv │ │ └── types.csv │ │ └── weight_config.yaml └── python │ ├── __init__.py │ └── config.py ├── docs ├── architecture.png └── qupath.png ├── models ├── __init__.py ├── encoders │ ├── __init__.py │ └── fastvit.py ├── nulite.py └── utils.py ├── nuclei_detection ├── __init__.py ├── datamodel │ ├── __init__.py │ ├── graph_datamodel.py │ └── wsi_datamodel.py ├── datasets │ ├── __init__.py │ ├── base_cell.py │ ├── cell_graph_datamodel.py │ ├── dataset_coordinator.py │ ├── pannuke.py │ ├── prepare_pannuke.py │ └── utils.py ├── experiments │ ├── __init__.py │ └── experiment_nulite_pannuke.py ├── inference │ ├── __init__.py │ ├── inference_nufastvit_experiment_pannuke.py │ ├── nuclei_detection.py │ ├── post_proc.py │ └── utilis.py ├── training │ ├── __init__.py │ └── nulite_trainer.py └── utils │ ├── __init__.py │ ├── metrics.py │ ├── post_proc_nulite.py │ ├── template_geojson.py │ └── tools.py ├── preprocessing ├── __init__.py ├── encoding │ ├── __init__.py │ └── datasets │ │ ├── __init__.py │ │ └── patched_wsi_inference.py └── patch_extraction │ ├── __init__.py │ ├── main_extraction.py │ └── src │ ├── __init__.py │ ├── cli.py │ ├── cucim_deepzoom.py │ ├── data │ └── tissue_detector.pt │ ├── patch_extraction.py │ ├── process_batch.py │ ├── storage.py │ └── utils │ ├── __init__.py │ ├── exceptions.py │ ├── masking.py │ ├── patch_dataset.py │ ├── patch_util.py │ └── plotting.py ├── requirements.txt ├── run_inference_wsi.py ├── sanitizy_weights.py ├── train_nulite.py ├── utils ├── __init__.py ├── file_handling.py ├── logger.py └── tools.py └── wsi_example ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE.svs └── inference ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE ├── cell_detection │ ├── cell_detection.geojson │ ├── cell_detection.json │ ├── cells.geojson │ ├── cells.json │ └── cells.pt ├── mask.png ├── metadata.yaml ├── metadata │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_0_10.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_0_11.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_0_12.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_1_10.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_1_11.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_1_12.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_1_7.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_1_8.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_1_9.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_2_10.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_2_11.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_2_12.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_2_6.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_2_7.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_2_8.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_2_9.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_10.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_11.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_12.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_2.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_6.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_7.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_8.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_9.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_1.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_10.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_11.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_12.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_2.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_3.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_5.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_6.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_7.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_8.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_9.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_5_1.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_5_10.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_5_11.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_5_12.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_5_2.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_5_5.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_5_6.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_5_7.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_5_8.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_5_9.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_6_10.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_6_11.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_6_12.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_6_5.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_6_6.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_6_7.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_6_8.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_6_9.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_7_10.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_7_11.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_7_6.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_7_7.yaml │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_7_8.yaml │ └── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_7_9.yaml ├── patch_metadata.json ├── patches │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_0_10.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_0_11.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_0_12.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_1_10.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_1_11.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_1_12.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_1_7.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_1_8.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_1_9.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_2_10.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_2_11.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_2_12.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_2_6.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_2_7.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_2_8.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_2_9.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_10.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_11.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_12.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_2.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_6.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_7.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_8.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_3_9.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_1.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_10.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_11.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_12.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_2.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_3.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_5.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_6.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_7.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_8.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_4_9.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_5_1.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_5_10.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_5_11.png │ ├── 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TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_6_8.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_6_9.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_7_10.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_7_11.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_7_6.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_7_7.png │ ├── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_7_8.png │ └── TCGA-V5-A7RE-11A-01-TS1.57401526-EF9E-49AC-8FF6-B4F9652311CE_7_9.png ├── thumbnail.png ├── thumbnails │ ├── thumbnail_downsample_128.png │ ├── thumbnail_mpp_10.png │ ├── thumbnail_mpp_5.png │ └── thumbnail_thumbnail.png └── tissue_masks │ ├── mask.png │ ├── mask_nogrid.png │ └── tissue_grid.png ├── config_0.yaml └── processed.json /.gitignore: -------------------------------------------------------------------------------- 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