├── .gitignore ├── LICENSE ├── configs ├── vit_b.yaml └── vit_sub.yaml ├── core ├── __init__.py ├── ddp.py ├── ddp_sub.py ├── learner2.py ├── learner3.py ├── learner5.py ├── learner_sub1.py ├── lora_sam.py ├── loss.py └── volume_predictor.py ├── datasets ├── __init__.py ├── cache_dataset3d.py ├── cache_dataset3d3.py ├── data_engine.py ├── dataset3d.py ├── dataset3d_2dmask.py ├── dataset_list │ └── example_test.txt ├── dataset_merged.py ├── eval_dataloader │ └── loader_abstract.py ├── generate_txt.py └── predict_various_masks.py ├── imgs ├── inference.gif └── training.png ├── modeling ├── __init__.py ├── build_sam3d2.py ├── common.py ├── image_encoder.py ├── mask_decoder3d_2.py ├── prompt_encoder3d.py ├── sam3d.py └── transformer.py ├── readme.md ├── test ├── __init__.py ├── volume_eval.py ├── volume_eval_mbox.py └── volume_eval_sublora.py ├── tmp.py ├── trans_utils ├── __init__.py ├── data_utils.py ├── metrics.py └── trainer_ddp.py └── utils ├── __init__.py ├── amg.py ├── amg3d.py ├── masks3d_utils.py ├── onnx.py ├── transforms.py └── transforms3d.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.pth 2 | *.pyc 3 | *.nii.gz -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/LICENSE -------------------------------------------------------------------------------- /configs/vit_b.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/configs/vit_b.yaml -------------------------------------------------------------------------------- /configs/vit_sub.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/configs/vit_sub.yaml -------------------------------------------------------------------------------- /core/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /core/ddp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/core/ddp.py -------------------------------------------------------------------------------- /core/ddp_sub.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/core/ddp_sub.py -------------------------------------------------------------------------------- /core/learner2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/core/learner2.py -------------------------------------------------------------------------------- /core/learner3.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/core/learner3.py -------------------------------------------------------------------------------- /core/learner5.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/core/learner5.py -------------------------------------------------------------------------------- /core/learner_sub1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/core/learner_sub1.py -------------------------------------------------------------------------------- /core/lora_sam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/core/lora_sam.py -------------------------------------------------------------------------------- /core/loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/core/loss.py -------------------------------------------------------------------------------- /core/volume_predictor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/core/volume_predictor.py -------------------------------------------------------------------------------- /datasets/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /datasets/cache_dataset3d.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/datasets/cache_dataset3d.py -------------------------------------------------------------------------------- /datasets/cache_dataset3d3.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/datasets/cache_dataset3d3.py -------------------------------------------------------------------------------- /datasets/data_engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/datasets/data_engine.py -------------------------------------------------------------------------------- /datasets/dataset3d.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/datasets/dataset3d.py -------------------------------------------------------------------------------- /datasets/dataset3d_2dmask.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/datasets/dataset3d_2dmask.py -------------------------------------------------------------------------------- /datasets/dataset_list/example_test.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/datasets/dataset_list/example_test.txt -------------------------------------------------------------------------------- /datasets/dataset_merged.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/datasets/dataset_merged.py -------------------------------------------------------------------------------- /datasets/eval_dataloader/loader_abstract.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/datasets/eval_dataloader/loader_abstract.py -------------------------------------------------------------------------------- /datasets/generate_txt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/datasets/generate_txt.py -------------------------------------------------------------------------------- /datasets/predict_various_masks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/datasets/predict_various_masks.py -------------------------------------------------------------------------------- /imgs/inference.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/imgs/inference.gif -------------------------------------------------------------------------------- /imgs/training.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/imgs/training.png -------------------------------------------------------------------------------- /modeling/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /modeling/build_sam3d2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/modeling/build_sam3d2.py -------------------------------------------------------------------------------- /modeling/common.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/modeling/common.py -------------------------------------------------------------------------------- /modeling/image_encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/modeling/image_encoder.py -------------------------------------------------------------------------------- /modeling/mask_decoder3d_2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/modeling/mask_decoder3d_2.py -------------------------------------------------------------------------------- /modeling/prompt_encoder3d.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/modeling/prompt_encoder3d.py -------------------------------------------------------------------------------- /modeling/sam3d.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/modeling/sam3d.py -------------------------------------------------------------------------------- /modeling/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/modeling/transformer.py -------------------------------------------------------------------------------- /readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/readme.md -------------------------------------------------------------------------------- /test/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test/volume_eval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/test/volume_eval.py -------------------------------------------------------------------------------- /test/volume_eval_mbox.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/test/volume_eval_mbox.py -------------------------------------------------------------------------------- /test/volume_eval_sublora.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/test/volume_eval_sublora.py -------------------------------------------------------------------------------- /tmp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/tmp.py -------------------------------------------------------------------------------- /trans_utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /trans_utils/data_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/trans_utils/data_utils.py -------------------------------------------------------------------------------- /trans_utils/metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/trans_utils/metrics.py -------------------------------------------------------------------------------- /trans_utils/trainer_ddp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/trans_utils/trainer_ddp.py -------------------------------------------------------------------------------- /utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/utils/__init__.py -------------------------------------------------------------------------------- /utils/amg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/utils/amg.py -------------------------------------------------------------------------------- /utils/amg3d.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/utils/amg3d.py -------------------------------------------------------------------------------- /utils/masks3d_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/utils/masks3d_utils.py -------------------------------------------------------------------------------- /utils/onnx.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/utils/onnx.py -------------------------------------------------------------------------------- /utils/transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/utils/transforms.py -------------------------------------------------------------------------------- /utils/transforms3d.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Curli-quan/Slide-SAM/HEAD/utils/transforms3d.py --------------------------------------------------------------------------------