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This repository is used to store weights and codes for blood vessel segmentation in pathological images.

Fine-tuning MedSAM’s code finetune_2D_dataset. This code is used to fine-tune MedSAM weights from npz format files.

The fine-tuned training weights can be obtained here. finetuned-MedSAM

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MedSAM

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

News

• 2024.01.15: Welcome to join CVPR 2024 Challenge: MedSAM on Laptop
• 2024.01.15: Release LiteMedSAM and 3D Slicer Plugin, 10x faster than MedSAM!

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

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 on CoLab

You can also run it locally with tutorial_quickstart.ipynb.

3. GUI

Install PyQt5 with pip: pip install PyQt5 or conda: conda install -c anaconda pyqt

python gui.py

Load the image to the GUI and specify segmentation targets by drawing bounding boxes.

MedSAM-Demo.mp4

Model Training

Data preprocessing

Download SAM checkpoint and place it at work_dir/SAM/sam_vit_b_01ec64.pth .

Download the demo dataset and unzip it to data/FLARE22Train/.

This dataset contains 50 abdomen CT scans and each scan contains an annotation mask with 13 organs. The names of the organ label are available at MICCAI FLARE2022.

Run pre-processing

Install cc3d: pip install connected-components-3d

python pre_CT_MR.py

• split dataset: 80% for training and 20% for testing
• adjust CT scans to soft tissue window level (40) and width (400)
• max-min normalization
• resample image size to 1024x2014
• save the pre-processed images and labels as npy files

Training on multiple GPUs (Recommend)

The model was trained on five A100 nodes and each node has four GPUs (80G) (20 A100 GPUs in total). Please use the slurm script to start the training process.

sbatch train_multi_gpus.sh

When the training process is done, please convert the checkpoint to SAM's format for convenient inference.

python utils/ckpt_convert.py # Please set the corresponding checkpoint path first

Training on one GPU

python train_one_gpu.py

If you only want to train the mask decoder, please check the tutorial on the 0.1 branch.

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 Wang, Bo},
  journal={Nature Communications},
  volume={15},
  pages={1--9},
  year={2024}
}