Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics...

Area of Science:

• Renal Pathology
• Computational Biology
• Digital Pathology

Background:

• Podocytes are crucial for renal health, but their detailed analysis in pathology slides is challenging.
• Assessing podocyte morphology and spatial distribution is vital for understanding glomerular injury.
• Current methods for quantifying cellular features in Whole Slide Images (WSIs) are limited.

Purpose of the Study:

• To introduce and apply the Spatial Pathomics Toolkit (SPT) for comprehensive podocyte pathomics.
• To enable precise quantification of podocyte nuclei and their morphological features.
• To explore spatial relationships between podocyte morphology and transcriptomics in renal pathology.

Main Methods:

• Instance object segmentation for accurate podocyte nuclei identification.
• Pathomics feature generation to extract quantitative morphological and textural data.
• Statistical analysis to investigate spatial patterns and relationships.

Main Results:

• The SPT successfully extracted diverse morphomic and textural features from podocyte nuclei.
• Analysis revealed significant spatial patterns related to glomerular injury.
• The toolkit demonstrated its capability in unraveling spatial information of podocyte distribution.

Conclusions:

• The Spatial Pathomics Toolkit (SPT) provides a powerful resource for advancing cellular spatial pathomics in renal pathology.
• SPT facilitates a deeper understanding of podocyte alterations in glomerular diseases.
• The open-source nature of SPT promotes wider research community adoption and collaboration.