├── CCViM-nuclei ├── CPM17 │ ├── compute_state.py │ ├── config.py │ ├── test.py │ └── train.py ├── __init__.py ├── __pycache__ │ ├── convert_format.cpython-38.pyc │ └── dataset.cpython-38.pyc ├── compute_stats.py ├── config.py ├── convert_chkpt_tf2pytorch.py ├── convert_format.py ├── dataloader │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── augs.cpython-38.pyc │ │ ├── infer_loader.cpython-38.pyc │ │ └── train_loader.cpython-38.pyc │ ├── augs.py │ ├── infer_loader.py │ └── train_loader.py ├── dataset.py ├── infer │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── base.cpython-38.pyc │ │ └── tile.cpython-38.pyc │ ├── base.py │ ├── tile.py │ └── wsi.py ├── kumar │ ├── compute_state.py │ ├── config.py │ ├── test.py │ └── train.py ├── metrics │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ └── stats_utils.cpython-38.pyc │ └── stats_utils.py ├── misc │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── utils.cpython-38.pyc │ │ └── viz_utils.cpython-38.pyc │ ├── patch_extractor.py │ ├── utils.py │ ├── viz_utils.py │ └── wsi_handler.py ├── models │ ├── CCViMUNet │ │ ├── CCViM.py │ │ ├── CCViMUNet.py │ │ ├── __pycache__ │ │ │ └── opt.cpython-38.pyc │ │ ├── mamba │ │ │ ├── __pycache__ │ │ │ │ └── multi_mamba.cpython-38.pyc │ │ │ ├── multi_mamba.py │ │ │ └── rope.py │ │ └── opt.py │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── run_desc.cpython-38.pyc │ │ ├── targets.cpython-38.pyc │ │ └── utils.cpython-38.pyc │ ├── post_proc.py │ ├── run_desc.py │ ├── targets.py │ └── utils.py ├── patch_extract │ ├── extract_patches_cpm17.py │ └── extract_patches_kumar.py ├── run_utils │ ├── __init__.py │ ├── callbacks │ │ ├── __init__.py │ │ ├── base.py │ │ ├── logging.py │ │ └── serialize.py │ ├── engine.py │ └── utils.py ├── split_images.py └── visulize │ └── overlay.py ├── LICENSE ├── README.md ├── __pycache__ ├── engine.cpython-38.pyc ├── engine_synapse.cpython-38.pyc └── utils.cpython-38.pyc ├── configs ├── __pycache__ │ ├── config_setting_isic17.cpython-38.pyc │ ├── config_setting_isic18.cpython-38.pyc │ └── config_setting_synapse.cpython-38.pyc ├── config_setting_isic17.py ├── config_setting_isic18.py └── config_setting_synapse.py ├── datasets ├── __pycache__ │ └── dataset.cpython-38.pyc └── dataset.py ├── engine.py ├── engine_synapse.py ├── imgs ├── fig2.jpg ├── fig4.jpg ├── fig5.jpg └── fig7.jpg ├── infer_isic17.py ├── infer_isic18.py ├── infer_synapase.py ├── models └── CCViMUNet │ ├── CCViM.py │ ├── CCViMUNet.py │ ├── __pycache__ │ ├── CCViM.cpython-38.pyc │ └── CCViMUNet.cpython-38.pyc │ └── mamba │ ├── __pycache__ │ └── multi_mamba.cpython-38.pyc │ ├── multi_mamba.py │ └── rope.py ├── train.py ├── train_isic17.py ├── train_isic18.py ├── train_localcmunet.py ├── train_localcmunet_freeze.py ├── train_localcmunet_freeze_isic18.py ├── train_localcmunet_freeze_synapse.py ├── train_synapse.py └── utils.py 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