Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics Data in Renal Pathology

Jiayuan Chen; Yu Wang; Ruining Deng; Quan Liu; Can Cui; Tianyuan Yao; Yilin Liu; Jianyong Zhong; Agnes B. Fogo; Haichun Yang; Shilin Zhao; Yuankai Huo

arXiv · 2308.06288

Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics Data in Renal Pathology

Jiayuan Chen·Yu Wang·Ruining Deng·Quan Liu·Can Cui·Tianyuan Yao·Yilin Liu·Jianyong Zhong·Agnes B. Fogo·Haichun Yang·Shilin Zhao·Yuankai Huo

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Abstract

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.

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Jiayuan Chen, Yu Wang, Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Yilin Liu, Jianyong Zhong, Agnes B. Fogo, Haichun Yang, Shilin Zhao, Yuankai Huo. 2023-08-10. Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics Data in Renal Pathology. https://arxiv.org/abs/2308.06288

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