MedSAM

This is the official repository for MedSAM: Segment Anything in Medical Images.

Installation

1. Create a virtual environment conda create -n medsam python=3.10 -y and activate it conda activate medsam
2. Install Pytorch 2.0
3. git clone https://github.com/bowang-lab/MedSAM
4. Enter the MedSAM folder cd MedSAM and run pip install -e .

Get Started

Download the model checkpoint and place it at e.g., work_dir/MedSAM/medsam_vit_b

We provide three ways to quickly test the model on your images

1. Command line

python MedSAM_Inference.py # segment the demo image

You can also segment other images with the following flags

-i input_img
-o output path
--box bounding box of the segmentation target

2. Jupyter-notebook We provide a step-by-step tutorial based on CoLab You can also run it locally with MedSAM_Inference.ipynb.

3. GUI

python gui.py

Your can load the image to the GUI and specify segmentation targets by drawing bounding boxes seg_demo

Training tutorial will be available soon

Acknowledgements

• We highly appreciate all the challenge organizers and dataset owners for providing the public dataset to the community.
• We thank Meta AI for making the source code of segment anything publicly available.
• We also thank Alexandre Bonnet for sharing this great blog

Reference

@article{MedSAM,
  title={Segment Anything in Medical Images},
  author={Ma, Jun and He, Yuting and Li, Feifei and Han, Lin and You, Chenyu and and Wang, Bo},
  journal={arXiv preprint arXiv:2304.12306},
  year={2023}
}