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arXiv · 2407.12658

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

Yiqing Shen·Xinyuan Shao·Blanca Inigo Romillo·David Dreizin·Mathias Unberath
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Abstract

Accurate segmentation of anatomical structures and pathological regions in medical images is crucial for diagnosis, treatment planning, and disease monitoring. While the Segment Anything Model (SAM) and its variants have demonstrated impressive interactive segmentation capabilities on image types not seen during training without the need for domain adaptation or retraining, their practical application in volumetric 3D medical imaging workflows has been hindered by the lack of a user-friendly interface. To address this challenge, we introduce FastSAM-3DSlicer, a 3D Slicer extension that integrates both 2D and 3D SAM models, including SAM-Med2D, MedSAM, SAM-Med3D, and FastSAM-3D. Building on the well-established open-source 3D Slicer platform, our extension enables efficient, real-time segmentation of 3D volumetric medical images, with seamless interaction and visualization. By automating the handling of raw image data, user prompts, and segmented masks, FastSAM-3DSlicer provides a streamlined, user-friendly interface that can be easily incorporated into medical image analysis workflows. Performance evaluations reveal that the FastSAM-3DSlicer extension running FastSAM-3D achieves low inference times of only 1.09 seconds per volume on CPU and 0.73 seconds per volume on GPU, making it well-suited for real-time interactive segmentation. Moreover, we introduce an uncertainty quantification scheme that leverages the rapid inference capabilities of FastSAM-3D for practical implementation, further enhancing its reliability and applicability in medical settings. FastSAM-3DSlicer offers an interactive platform and user interface for 2D and 3D interactive volumetric medical image segmentation, offering a powerful combination of efficiency, precision, and ease of use with SAMs. The source code and a video demonstration are publicly available at https://github.com/arcadelab/FastSAM3D_slicer.

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Yiqing Shen, Xinyuan Shao, Blanca Inigo Romillo, David Dreizin, Mathias Unberath. 2024-07-17. FastSAM-3DSlicer: A 3D-Slicer Extension for 3D Volumetric Segment Anything Model with Uncertainty Quantification. https://arxiv.org/abs/2407.12658

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