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SAMUS

This repo is the official implementation for:
SAMUS: Adapting Segment Anything Model for Clinically-Friendly and Generalizable Ultrasound Image Segmentation.
(The details of our SAMUS can be found in the models directory in this repo or in the paper.)

Highlights

🏆 Low GPU requirements. (one 3090ti with 24G GPU memory is enough)
🏆 Large ultrasound dataset. (about 30K images and 69K masks covering 6 categories)
🏆 Excellent performance, especially in generalization ability.

Installation

Following Segment Anything, python=3.8.16, pytorch=1.8.0, and torchvision=0.9.0 are used in SAMUS.

  1. Clone the repository. 
    git clone https://github.com/xianlin7/SAMUS.git
cd SAMUS
  2. Create a virtual environment for SAMUS and activate the environment. 
    conda create -n SAMUS python=3.8
conda activate SAMUS
  3. Install Pytorch and TorchVision. (you can follow the instructions here)
  4. Install other dependencies.
  pip install -r requirements.txt

Checkpoints

We use checkpoint of SAM in vit_b version.

Data

  • US30K consists of seven publicly-available datasets, including TN3K, DDTI, TG3K, BUSI, UDIAT, CAMUS, and HMC-QU.
  • All images were saved in PNG format. No special pre-processed methods are used in data preparation.
  • We have provided some examples to help you organize your data. Please refer to the file fold example_of_required_dataset_format.
    Specifically, each line in train/val.txt should be formatted as follows: 
      <class ID>/<dataset file folder name>/<image file name>
  • The relevant information of your data should be set in ./utils/config.py

Training

Once you have the data ready, you can start training the model.

cd "/home/...  .../SAMUS/"
python train.py --modelname SAMUS --task <your dataset config name>

Testing

Do not forget to set the load_path in ./utils/config.py before testing.

python test.py --modelname SAMUS --task <your dataset config name>

Citation

If our SAMUS is helpful to you, please consider citing:

@misc{lin2023samus,
      title={SAMUS: Adapting Segment Anything Model for Clinically-Friendly and Generalizable Ultrasound Image Segmentation}, 
      author={Xian Lin and Yangyang Xiang and Li Zhang and Xin Yang and Zengqiang Yan and Li Yu},
      year={2023},
      eprint={2309.06824},
      archivePrefix={arXiv},
      primaryClass={cs.CV}
}