├── .gitignore ├── LICENSE.md ├── README.md ├── assets └── architecture.png ├── checkpoints └── README.md ├── comparison ├── DFC │ ├── BBC │ │ ├── ref │ │ │ └── frame426.jpg │ │ └── test │ │ │ ├── frame426.jpg │ │ │ ├── frame431.jpg │ │ │ ├── frame437.jpg │ │ │ ├── frame443.jpg │ │ │ ├── frame449.jpg │ │ │ ├── frame455.jpg │ │ │ ├── frame461.jpg │ │ │ ├── frame467.jpg │ │ │ ├── frame473.jpg │ │ │ ├── frame479.jpg │ │ │ └── frame485.jpg │ ├── BSD500 │ │ ├── 101027.jpg │ │ ├── 108004.jpg │ │ └── 196062.jpg │ ├── CUTS_scripts │ │ └── step01_produce_results.py │ ├── LICENSE │ ├── PASCAL_VOC_2012 │ │ ├── 2007_001774.jpg │ │ ├── 2007_001774_scribble.png │ │ ├── 2007_005915.jpg │ │ ├── 2007_005915_scribble.png │ │ ├── 2007_008670.jpg │ │ ├── 2007_008670_scribble.png │ │ ├── 2008_001439.jpg │ │ ├── 2008_001439_scribble.png │ │ ├── 2008_003709.jpg │ │ ├── 2008_003709_scribble.png │ │ ├── 2009_000421.jpg │ │ └── 2009_000421_scribble.png │ ├── README.md │ ├── demo.py │ ├── demo_ref.py │ └── output.png ├── MedSAM │ └── CUTS_scripts │ │ ├── step01_produce_results.py │ │ └── step01_produce_results_box.py ├── SAM │ └── CUTS_scripts │ │ └── step01_produce_results.py ├── SAM_Med2D │ ├── CUTS_scripts │ │ ├── step01_produce_results.py │ │ └── step01_produce_results_box.py │ └── segment_anything │ │ ├── __init__.py │ │ ├── automatic_mask_generator.py │ │ ├── build_sam.py │ │ ├── modeling │ │ ├── __init__.py │ │ ├── common.py │ │ ├── image_encoder.py │ │ ├── mask_decoder.py │ │ ├── prompt_encoder.py │ │ ├── sam.py │ │ ├── sam_model.py │ │ └── transformer.py │ │ ├── predictor.py │ │ ├── predictor_sammed.py │ │ └── utils │ │ ├── __init__.py │ │ ├── amg.py │ │ ├── onnx.py │ │ └── transforms.py └── STEGO │ ├── CUTS_scripts │ ├── eval_config │ │ ├── eval_config_berkeley_seed2021.yaml │ │ ├── eval_config_berkeley_seed2022.yaml │ │ ├── eval_config_berkeley_seed2023.yaml │ │ ├── eval_config_brain_tumor_seed2021.yaml │ │ ├── eval_config_brain_tumor_seed2022.yaml │ │ ├── eval_config_brain_tumor_seed2023.yaml │ │ ├── eval_config_brain_ventricles_seed2021.yaml │ │ ├── eval_config_brain_ventricles_seed2022.yaml │ │ ├── eval_config_brain_ventricles_seed2023.yaml │ │ ├── eval_config_retina_seed2021.yaml │ │ ├── eval_config_retina_seed2022.yaml │ │ └── eval_config_retina_seed2023.yaml │ ├── step01_prepare_data.py │ ├── step02_precompute_knns.py │ ├── step03_train_segmentation.py │ ├── step04_produce_results.py │ └── train_config │ │ ├── train_config_berkeley_seed2021.yaml │ │ ├── train_config_berkeley_seed2022.yaml │ │ ├── train_config_berkeley_seed2023.yaml │ │ ├── train_config_brain_tumor_seed2021.yaml │ │ ├── train_config_brain_tumor_seed2022.yaml │ │ ├── train_config_brain_tumor_seed2023.yaml │ │ ├── train_config_brain_ventricles_seed2021.yaml │ │ ├── train_config_brain_ventricles_seed2022.yaml │ │ ├── train_config_brain_ventricles_seed2023.yaml │ │ ├── train_config_retina_seed2021.yaml │ │ ├── train_config_retina_seed2022.yaml │ │ └── train_config_retina_seed2023.yaml │ ├── LICENSE │ ├── README.md │ ├── environment.yml │ └── src │ ├── STEGO_Colab_Demo.ipynb │ ├── __init__.py │ ├── configs │ ├── demo_config.yml │ ├── eval_config.yml │ ├── eval_config_berkeley_seed2021.yml │ ├── eval_config_berkeley_seed2022.yml │ ├── eval_config_berkeley_seed2023.yml │ ├── eval_config_brain_seed2021.yml │ ├── eval_config_brain_seed2022.yml │ ├── eval_config_brain_seed2023.yml │ ├── eval_config_retina_seed2021.yml │ ├── eval_config_retina_seed2022.yml │ ├── eval_config_retina_seed2023.yml │ └── plot_config.yml │ ├── crf.py │ ├── crop_datasets.py │ ├── data.py │ ├── demo_segmentation.py │ ├── dino │ ├── utils.py │ └── vision_transformer.py │ ├── download_datasets.py │ ├── download_models.py │ ├── eval_segmentation.py │ ├── modules.py │ ├── picie │ ├── backbone.py │ └── fpn.py │ ├── plot_dino_correspondence.py │ ├── plot_potsdam.py │ ├── plot_pr_curves.py │ ├── precompute_knns.py │ ├── train_crf.py │ ├── train_segmentation.log │ ├── train_segmentation.py │ └── utils.py ├── config ├── brain_tumor_seed1.yaml ├── brain_tumor_seed2.yaml ├── brain_tumor_seed3.yaml ├── brain_ventricles_seed1.yaml ├── brain_ventricles_seed2.yaml ├── brain_ventricles_seed3.yaml ├── example_dataset_without_label_seed2021.yaml ├── retina_seed1.yaml ├── retina_seed2.yaml ├── retina_seed3.yaml ├── supervised_berkeley_nnunet_seed2021.yaml ├── supervised_berkeley_nnunet_seed2022.yaml ├── supervised_berkeley_nnunet_seed2023.yaml ├── supervised_berkeley_unet_seed2021.yaml ├── supervised_berkeley_unet_seed2022.yaml ├── supervised_berkeley_unet_seed2023.yaml ├── supervised_brain_tumor_nnunet_seed2021.yaml ├── supervised_brain_tumor_nnunet_seed2022.yaml ├── supervised_brain_tumor_nnunet_seed2023.yaml ├── supervised_brain_tumor_unet_seed2021.yaml ├── supervised_brain_tumor_unet_seed2022.yaml ├── supervised_brain_tumor_unet_seed2023.yaml ├── supervised_brain_ventricles_nnunet_seed2021.yaml ├── supervised_brain_ventricles_nnunet_seed2022.yaml ├── supervised_brain_ventricles_nnunet_seed2023.yaml ├── supervised_brain_ventricles_unet_seed2021.yaml ├── supervised_brain_ventricles_unet_seed2022.yaml ├── supervised_brain_ventricles_unet_seed2023.yaml ├── supervised_retina_nnunet_seed2021.yaml ├── supervised_retina_nnunet_seed2022.yaml ├── supervised_retina_nnunet_seed2023.yaml ├── supervised_retina_unet_seed2021.yaml ├── supervised_retina_unet_seed2022.yaml └── supervised_retina_unet_seed2023.yaml ├── data ├── README.md ├── berkeley_natural_images.zip ├── brain_tumor.zip └── retina.zip ├── environment.yml ├── logs └── README.md ├── requirements.txt ├── results └── README.md └── src ├── data_utils ├── __init__.py ├── extend.py ├── patch_sampler.py ├── prepare_dataset.py └── split.py ├── datasets ├── __init__.py ├── berkeley_natural_images.py ├── brain_tumor.py ├── brain_tumor_nifti.py ├── brain_ventricles.py ├── cell_histology.py ├── example_dataset_without_label.py ├── glas_histology.py ├── mouse_brain.py └── retina.py ├── main.py ├── main_supervised.py ├── model ├── CUTS_model.py └── __init__.py ├── scripts_analysis ├── check_images.py ├── generate_baselines.py ├── generate_diffusion.py ├── generate_kmeans.py ├── generate_pixel_diffusion.py ├── generate_pixel_kmeans.py ├── helper_generate_kmeans.py ├── helper_run_phate.py ├── plot_diffusion.py ├── plot_kmeans.py ├── plot_paper_figure_diffusion_curve.py ├── plot_paper_figure_diffusion_graph.py ├── plot_paper_figure_lambda_test.py ├── plot_paper_figure_main.py └── run_metrics.py └── utils ├── DEPRECATED_latent_evaluator.py ├── __init__.py ├── attribute_hashmap.py ├── diffusion_condensation.py ├── early_stop.py ├── log_util.py ├── losses.py ├── metrics.py ├── output_saver.py ├── parse.py ├── scheduler.py ├── seed.py └── segmentation.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChenLiu-1996/CUTS/HEAD/.gitignore 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