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<b>Background</b> <p>The potential of Segment Anything Model 2 (SAM2) for 3D medical image segmentation via video-stream processing is currently constrained by its reliance on manual prompts. While existing research employs auxiliary models (e.g., YOLO) as prompt generators, these approaches face two fundamental limitations: the inherent bottleneck of external models’ feature extraction and the lack of mechanisms to prevent the propagation of erroneous prompts. Furthermore, current methods often struggle with interference from non-salient regions in complex 3D tumor datasets. This study aims to develop an automated, reliable prompt generation and sequence processing framework specifically for 3D medical imaging.</p> <b>Results</b> <p>We propose AutoPrompt-SAM3D, featuring an Automatic Prompt Generator that hierarchically integrates SAM2’s tri-layer features and a supervised confidence frames filter for reliable prompt selection. Additionally, we implement a full-sequence processing framework that progressively localizes salient regions across consecutive slices. Comprehensive experiments conducted on four public abdominal tumor datasets demonstrate that AutoPrompt-SAM3D achieves superior 3D medical segmentation performance, consistently outperforming or matching state-of-the-art prompt-based methods.</p> <b>Conclusions</b> <p>AutoPrompt-SAM3D eliminates the dependency on manual prompts in SAM2-based 3D segmentation through hierarchical feature integration and error filtering. By enhancing both the reliability and efficiency of tumor localization, this framework provides a practical tool for large-scale medical image analysis and supports more consistent clinical decision-making.</p>

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AutoPrompt-SAM3D: integrated generation and selection for SAM2-based 3D medical segmentation

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年3月28日

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  • Wanqiu Cheng,
  • Jintao Tang,
  • Ting Wang,
  • Shasha Li,
  • Ting Deng

摘要

Background

The potential of Segment Anything Model 2 (SAM2) for 3D medical image segmentation via video-stream processing is currently constrained by its reliance on manual prompts. While existing research employs auxiliary models (e.g., YOLO) as prompt generators, these approaches face two fundamental limitations: the inherent bottleneck of external models’ feature extraction and the lack of mechanisms to prevent the propagation of erroneous prompts. Furthermore, current methods often struggle with interference from non-salient regions in complex 3D tumor datasets. This study aims to develop an automated, reliable prompt generation and sequence processing framework specifically for 3D medical imaging.

Results

We propose AutoPrompt-SAM3D, featuring an Automatic Prompt Generator that hierarchically integrates SAM2’s tri-layer features and a supervised confidence frames filter for reliable prompt selection. Additionally, we implement a full-sequence processing framework that progressively localizes salient regions across consecutive slices. Comprehensive experiments conducted on four public abdominal tumor datasets demonstrate that AutoPrompt-SAM3D achieves superior 3D medical segmentation performance, consistently outperforming or matching state-of-the-art prompt-based methods.

Conclusions

AutoPrompt-SAM3D eliminates the dependency on manual prompts in SAM2-based 3D segmentation through hierarchical feature integration and error filtering. By enhancing both the reliability and efficiency of tumor localization, this framework provides a practical tool for large-scale medical image analysis and supports more consistent clinical decision-making.