基于Napari的医学图像半自动标注工具,支持3D体积的快速精准标注。
Interactive Medical-SAM2 GUI: A Napari-based semi-automatic annotation tool for medical images
- 将3D医学图像视为切片序列,结合框/点提示与SAM2传播实现高效标注
- 支持多研究数据统一流程,可批量处理并导出体积测量与3D渲染结果
- 本地优先设计,适合科研人员进行高精度3D医学图像标注
Interactive Medical-SAM2 GUI 是一个开源桌面应用,用于2D和3D医学图像的半自动标注。基于Napari多维查看器构建,通过将3D体积分解为切片序列,结合框/点提示与SAM2风格的传播机制,在Medical-SAM2基础上实现从稀疏提示到完整掩码的快速传播。尽管体素级标注对医学影像算法开发与验证至关重要,但3D扫描的手动标注效率低、成本高;现有工具多仅支持单切片交互,缺乏统一的队列式工作流。为此,本工具提供本地优先的Napari流程,支持标准DICOM系列和NIfTI格式的多研究数据批量标注。用户可在单一根目录下按顺序标注病例,通过框引导(含首/末切片初始化)或点提示初始化对象,以提示优先方式修正预测后保存。导出时支持每对象体积测量与3D体渲染,图像几何信息由SimpleITK保持。工具采用Python、Napari与PyTorch实现,可选集成N4偏置场校正,专为研究标注流程设计。代码已开源:https://github.com/SKKU-IBE/Medical-SAM2GUI/
原文摘要 · Abstract (English)
Interactive Medical-SAM2 GUI is an open-source desktop application for semi-automatic annotation of 2D and 3D medical images. Built on the Napari multi-dimensional viewer, box/point prompting is integrated with SAM2-style propagation by treating a 3D volume as a slice sequence, enabling mask propagation from sparse prompts using Medical-SAM2 on top of SAM2. Voxel-level annotation remains essential for developing and validating medical imaging algorithms, yet manual labeling is slow and expensive for 3D scans, and existing integrations frequently emphasize per-slice interaction without providing a unified, cohort-oriented workflow for navigation, propagation, interactive correction, and quantitative export in a single local pipeline. To address this practical limitation, a local-first Napari workflow is provided for efficient 3D annotation across multiple studies using standard DICOM series and/or NIfTI volumes. Users can annotate cases sequentially under a single root folder with explicit proceed/skip actions, initialize objects via box-first prompting (including first/last-slice initialization for single-object propagation), refine predictions with point prompts, and finalize labels through prompt-first correction prior to saving. During export, per-object volumetry and 3D volume rendering are supported, and image geometry is preserved via SimpleITK. The GUI is implemented in Python using Napari and PyTorch, with optional N4 bias-field correction, and is intended exclusively for research annotation workflows. The code is released on the project page: https://github.com/SKKU-IBE/Medical-SAM2GUI/.
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