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在整个幻灯片图像上对脏微分区细分和相关病理的交互可视化
Mark S Keller1, Nicholas Lucarelli2, Yijiang Chen3,4
1Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
ArXiv
|November 24, 2025
概括
机器学习将脏结构分割成全幻灯片图像 (WSIs). 这使形状的交互可视化和定量分析成为可能,改善了复杂生物数据集的探索.
科学领域:
- 数字病理学数字病理学
- 计算生物学是一种计算生物学.
- 医疗图像分析 医学图像分析
背景情况:
- 机器学习 (ML) 模型可以在组织学全幻灯片图像 (WSIs) 中对功能组织单元进行细分.
- 从细分结构中提取定量特征对于分析至关重要,但需要进行定性检查.
- 现有的可视化工具可能无法充分支持多类型的细分可视化和标准化数据表示.
研究的目的:
- 扩展Vitessce工具可视化多个功能组织单元细分.
- 为多个分割位面膜提出一个标准的,多态文件表示.
- 为了实现对细分组织学数据集和相关的定量特征的交互式探索.
主要方法:
- 开发了一个管道,集成脏结构的验证的ML细分模型.
- 扩展了Vitessce可视化工具,以显示淋巴细胞,管道和血管系统的细分.
- 定义了一个与OME-TIFF,OME-NGFF,AnnData,MuData 和 SpatialData 格式兼容的多态文件表示.
主要成果:
- 成功可视化了多个功能组织单元的细分.
- 建立了用于多段数据的标准化文件格式.
- 使用KPMP和HuBMAP的数据,证明了形状学的交互探索.
结论:
- 增强的Vitessce工具和标准化的数据表示方便了对细分组织学WSIs的交互式探索.
- 这些进展支持对形学进行定量分析和定性检查.
- 这些方法提高了研究人员和公众对复杂数据集的可访问性和探索性.
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