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
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.