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SsharvienKumar/
SASVi

2502.09653

cc-by-4.0

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SASVi - Segment Any Surgical Video (IPCAI 2025)

arXiv

Overview

SASVi leverages pre-trained frame-wise object detection and segmentation to re-prompt SAM2 for improved surgical video segmentation with scarcely annotated data.

Example Results

You can find the complete segmentations of the video datasets here.
Checkpoints of the all the overseers can be found here.

Setup

Create a virtual environment of your choice and activate it: conda create -n sasvi python=3.11 && conda activate sasvi
Install torch>=2.3.1 and torchvision>=0.18.1 following the instructions from here
Install the dependencies using pip install -r requirements.txt
Install SDS_Playground from here
Install SAM2 using cd src/sam2 && pip install -e .
Place SAM2 checkpoints at src/sam2/checkpoints

Convert video files to frame folders using bash helper_scripts/video_to_frames.sh. The output should be in the format:

<video_root>
├── <video1>
│   ├── 0001.jpg
│   ├── 0002.jpg
│   └── ...
├── <video2>
│   ├── 0001.jpg
│   ├── 0002.jpg
│   └── ...
└── ...

Overseer Model Training

We provide training scripts for three different overseer models (Mask R-CNN, DETR, Mask2Former) on three different datasets (CaDIS, CholecSeg8k, Cataract1k).

You can run the training scripts as follows:

python train_scripts/train_<OVERSEER>_<DATASET>.py

SASVi Inference

The frames in the video needs to be extracted beforehand and placed in the formatting above. More optional arguments can be found in the script directly.

python src/sam2/eval_sasvi.py \
--sam2_cfg              configs/sam2.1_hiera_l.yaml \
--sam2_checkpoint       ./checkpoints/<SAM2_CHECKPOINT>.pt \
--overseer_checkpoint   <PATH_TO_OVERSEER_CHECKPOINT>.pth \
--overseer_type         <NAME_OF_OVERSEER> \
--dataset_type          <NAME_OF_DATASET> \
--base_video_dir        <PATH_TO_VIDEO_ROOT> \
--output_mask_dir       <OUTPUT_PATH_TO_SASVi_MASK> \
--overseer_mask_dir     <OPTIONAL - OUTPUT_PATH_TO_OVERSEER_MASK>

nnUNet Training & Inference

Fold 0: nnUNetv2_train DATASET_ID 2d 0 -p nnUNetResEncUNetMPlans -tr nnUNetTrainer_400epochs --npz

Fold 1: nnUNetv2_train DATASET_ID 2d 1 -p nnUNetResEncUNetMPlans -tr nnUNetTrainer_400epochs --npz

Fold 2: nnUNetv2_train DATASET_ID 2d 2 -p nnUNetResEncUNetMPlans -tr nnUNetTrainer_400epochs --npz

Fold 3: nnUNetv2_train DATASET_ID 2d 3 -p nnUNetResEncUNetMPlans -tr nnUNetTrainer_400epochs --npz

Fold 4: nnUNetv2_train DATASET_ID 2d 4 -p nnUNetResEncUNetMPlans -tr nnUNetTrainer_400epochs --npz

Then find the best configuration using

nnUNetv2_find_best_configuration DATASET_ID -c 2d -p nnUNetResEncUNetMPlans -tr nnUNetTrainer_400epochs

And run inference using

nnUNetv2_predict -d DATASET_ID -i INPUT_FOLDER -o OUTPUT_FOLDER -f  0 1 2 3 4 -tr nnUNetTrainer_400epochs -c 2d -p nnUNetResEncUNetMPlans

Once inference is completed, run postprocessing

nnUNetv2_apply_postprocessing -i OUTPUT_FOLDER -o OUTPUT_FOLDER_PP -pp_pkl_file .../postprocessing.pkl -np 8 -plans_json .../plans.json

Evaluation

For frame-wise segmentation evaluation:
- python eval_scripts/eval_<OVERSEER>_frames.py
For frame-wise segmentation prediction on full videos:
- See python eval_scripts/eval_MaskRCNN_videos.py for an example.
For video evaluation:
1. E.g. python eval_scripts/eval_vid_T.py --segm_root <path_to_segmentation_root> --vid_pattern 'train' --mask_pattern '*.npz' --ignore 255 --device cuda
2. E.g. python eval_scripts/eval_vid_F.py --segm_root <path_to_segmentation_root> --frames_root <path_to_frames_root> --vid_pattern 'train' --frames_pattern '*.jpg' --mask_pattern '*.npz' --raft_iters 12 --device cuda

TODOs

The code will be refactored soon to be more modular and reusable!
Pre-process Cholec80 videos with out-of-body detection
Improve SASVi by combining it with GT prompting (if available)
Test SAM2 finetuning

Citation

If you use SASVi in your research, please cite our paper:

@article{sivakumar2025sasvi,
  title={SASVi: segment any surgical video},
  author={Sivakumar, Ssharvien Kumar and Frisch, Yannik and Ranem, Amin and Mukhopadhyay, Anirban},
  journal={International Journal of Computer Assisted Radiology and Surgery},
  pages={1--11},
  year={2025},
  publisher={Springer}
}

SsharvienKumar/SASVi