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FastSAM-3DSlicer: A 3D-Slicer Extension for 3D Volumetric Segment Anything Model with Uncertainty Quantification

paper
FastSAM3D code
video
ARCADE lab, Johns Hopkins University
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Table of contents

Introduction <a name="introduction"></a>

What are SAM, SAMMed3D, FastSAM3D and FastSAM3D_slicer?

Before You Try <a name="before-you-try"></a>

Make sure you have more than 3GB storage to download model weights and install pytorch. Don't forget to use the provided resample.py file to do resample for medical image.

How to Use <a name="how-to-use"></a>

step 1: Download the file and compress it.

step 2: open the 3D slicer and open the extension manager, download the pytorch extension, and restart the slicer. step21 step22 step 3: open the extension wizard in the 3D slicer. step3 step 4: click the select extension and choose the compressed file in step 1. step4 step 5: the extension will now be available here step5

Features <a name="features"></a>

Citation <a name="citation"></a>

If you use FastSAM3D_slicer in your research, please consider use the following BibTeX entry.

@misc{shen2024fastsam3d,
      title={FastSAM3D: An Efficient Segment Anything Model for 3D Volumetric Medical Images}, 
      author={Yiqing Shen and Jingxing Li and Xinyuan Shao and Blanca Inigo Romillo and Ankush Jindal and David Dreizin and Mathias Unberath},
      year={2024},
      eprint={2403.09827},
      archivePrefix={arXiv},
      primaryClass={eess.IV}
}

@article{shen2024fastsam,
  title={FastSAM-3DSlicer: A 3D-Slicer Extension for 3D Volumetric Segment Anything Model with Uncertainty Quantification},
  author={Shen, Yiqing and Shao, Xinyuan and Romillo, Blanca Inigo and Dreizin, David and Unberath, Mathias},
  journal={arXiv preprint arXiv:2407.12658},
  year={2024}
}