├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── MedSAM_Inference.py ├── README.md ├── assets ├── MedSAM_supp.pdf ├── architecture.png ├── box-task-illustration.png ├── img_demo.png ├── pathology.png ├── seg_demo.gif ├── seg_pathology.mp4 └── task-illustration.png ├── comparisons ├── DeepLabV3+ │ ├── README.md │ ├── infer_deeplabv3_res50_2D.py │ ├── infer_deeplabv3_res50_3D.py │ └── train_deeplabv3_res50.py ├── SAM │ ├── README.md │ ├── infer_SAM_2D_npz.py │ └── infer_SAM_3D_npz.py └── nnU-Net │ ├── README.md │ ├── infer_nnunet_2D.py │ └── infer_nnunet_3D.py ├── extensions ├── point_prompt │ ├── README.md │ ├── point_seg_demo.gif │ ├── train_point_prompt.py │ └── tutorial_point_prompt_seg.ipynb ├── seg_3dnii_sparse_marker │ ├── README.md │ ├── label_interpolate.py │ └── medsam_infer_3Dbox_adrenal.py └── text_prompt │ ├── README.md │ ├── text_seg_demo.gif │ ├── train_text_prompt.py │ └── tutorial_text_prompt_seg.ipynb ├── gui.py ├── pre_CT_MR.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 │ └── transformer.py ├── predictor.py └── utils │ ├── __init__.py │ ├── amg.py │ ├── onnx.py │ └── transforms.py ├── setup.py ├── train_multi_gpus.py ├── train_multi_gpus.sh ├── train_one_gpu.py ├── tutorial_quickstart.ipynb ├── utils ├── README.md ├── SurfaceDice.py ├── ckpt_convert.py ├── demo.py ├── format_convert.py ├── pre_CT_MR.py ├── pre_grey_rgb.py └── split.py └── work_dir └── MedSAM └── README.md /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowang-lab/MedSAM/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- 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