用于肾脏病理学中足细胞核定量分析的空间病理组学工具包：结合组织学与空间转录组学数据
Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics Data in Renal Pathology
AI总结：
本文提出空间病理组学工具包SPT，通过实例分割、病理组学特征生成和统计分析，结合组织学与空间转录组学数据定量解析足细胞核形态及空间分布，揭示肾小球损伤相关空间模式。
摘要：
足细胞是包裹肾小球毛细血管的特化上皮细胞，在维持肾脏健康中发挥关键作用。目前对病理切片上特征的描述和量化能力有限，这促使需要创新性解决方案来全面评估全切片图像（Whole Slide Images, WSIs）中的多样化表型属性。特别是，理解足细胞——终末分化的肾小球上皮细胞——的形态学特征，对于研究肾小球损伤至关重要。本文介绍了空间病理组学工具包（Spatial Pathomics Toolkit, SPT），并将其应用于足细胞病理组学。SPT 由三个主要部分组成：（1）实例对象分割，能够精确识别足细胞核；（2）病理组学特征生成，从识别出的细胞核中提取全面的定量特征；（3）稳健的统计分析，促进对形态学特征与空间转录组学特征之间空间关系的全面探索。SPT 成功提取并分析了足细胞核的形态学和纹理特征，通过统计分析揭示了大量足细胞形态组学特征。此外，我们展示了 SPT 解析足细胞分布中固有空间信息的能力，揭示了与肾小球损伤相关的空间模式。通过发布 SPT，我们的目标是为研究界提供一个强大且用户友好的资源，以推进肾脏病理学中的细胞空间病理组学。该工具包的实现及其完整源代码已在 https://github.com/hrlblab/spatial_pathomics 公开提供。
英文摘要：
Podocytes, specialized epithelial cells that envelop the glomerular capillaries, play a pivotal role in maintaining renal health. The current description and quantification of features on pathology slides are limited, prompting the need for innovative solutions to comprehensively assess diverse phenotypic attributes within Whole Slide Images (WSIs). In particular, understanding the morphological characteristics of podocytes, terminally differentiated glomerular epithelial cells, is crucial for studying glomerular injury. This paper introduces the Spatial Pathomics Toolkit (SPT) and applies it to podocyte pathomics. The SPT consists of three main components: (1) instance object segmentation, enabling precise identification of podocyte nuclei; (2) pathomics feature generation, extracting a comprehensive array of quantitative features from the identified nuclei; and (3) robust statistical analyses, facilitating a comprehensive exploration of spatial relationships between morphological and spatial transcriptomics features.The SPT successfully extracted and analyzed morphological and textural features from podocyte nuclei, revealing a multitude of podocyte morphomic features through statistical analysis. Additionally, we demonstrated the SPT's ability to unravel spatial information inherent to podocyte distribution, shedding light on spatial patterns associated with glomerular injury. By disseminating the SPT, our goal is to provide the research community with a powerful and user-friendly resource that advances cellular spatial pathomics in renal pathology. The implementation and its complete source code of the toolkit are made openly accessible at https://github.com/hrlblab/spatial_pathomics.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
