MedSAM2 Inference

This is a simple inference script for MedSAM2.

Installation

Clone the repository:

git clone https://github.com/JoshuaSiraj/medsam2_inference.git
cd medsam2_inference

Clone the MedSAM2 repository, while in the medsam2_inference directory:

git clone https://github.com/bowang-lab/MedSAM2.git

This project uses Pixi to manage dependencies. Install it by following the instructions here.

Install the dependencies by running:

pixi install

Download Weights

The weights for MedSAM2 are not included in this repository. You can download them by running the following command:

pixi run download-weights

Example Usage

from inference import MedSAM3DInference, MedSAM3DInferenceConfig

config = MedSAM3DInferenceConfig(
    dataset_csv="data/dataset.csv",
    model_config_path="configs/sam2.1_hiera_t512.yaml",
    checkpoint_path="checkpoints/MedSAM2_latest.pt", 
    output_dir="output",
    window_level=500.0,
    window_width=2500.0,
)

inference_module = MedSAM3DInference(config)
inference_module.run()

Important Notes

• GPU is required.
• Performance is reliant on the right window level and width. Therefore only one Region of Interest (ROI) should be present in the mask.

Example Dataset CSV

ID,image_path,mask_path
1,/path/to/image.nii.gz,/path/to/mask.nii.gz
2,/path/to/image.nii.gz,/path/to/mask.nii.gz