FastSAM-3DSlicer: A 3D-Slicer Extension for 3D Volumetric Segment Anything Model with Uncertainty Quantification
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 no...
Saved in:
Main Authors | , , , , |
---|---|
Format | Journal Article |
Language | English |
Published |
17.07.2024
|
Online Access | Get full text |
Cover
Loading…
Summary: | 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. |
---|---|
DOI: | 10.48550/arxiv.2407.12658 |