PodoCount: A Robust, Fully Automated, Whole-Slide Podocyte Quantification Tool

Briana A. Santo, Darshana Govind, Parnaz Daneshpajouhnejad, Xiaoping Yang, Xiaoxin X. Wang, Komuraiah Myakala, Bryce A. Jones, Moshe Levi, Jeffrey B. Kopp, Teruhiko Yoshida, Laura J. Niedernhofer, David Manthey, Kyung Chul Moon, Seung Seok Han, Jarcy Zee, Avi Z. Rosenberg, Pinaki Sarder

Research output: Contribution to journalArticlepeer-review


Introduction: Podocyte depletion is a histomorphologic indicator of glomerular injury and predicts clinical outcomes. Podocyte estimation methods or podometrics are semiquantitative, technically involved, and laborious. Implementation of high-throughput podometrics in experimental and clinical workflows necessitates an automated podometrics pipeline. Recognizing that computational image analysis offers a robust approach to study cell and tissue structure, we developed and validated PodoCount (a computational tool for automated podocyte quantification in immunohistochemically labeled tissues) using a diverse data set. Methods: Whole-slide images (WSIs) of tissues immunostained with a podocyte nuclear marker and periodic acid–Schiff counterstain were acquired. The data set consisted of murine whole kidney sections (n = 135) from 6 disease models and human kidney biopsy specimens from patients with diabetic nephropathy (DN) (n = 45). Within segmented glomeruli, podocytes were extracted and image analysis was applied to compute measures of podocyte depletion and nuclear morphometry. Computational performance evaluation and statistical testing were performed to validate podometric and associated image features. PodoCount was disbursed as an open-source, cloud-based computational tool. Results: PodoCount produced highly accurate podocyte quantification when benchmarked against existing methods. Podocyte nuclear profiles were identified with 0.98 accuracy and segmented with 0.85 sensitivity and 0.99 specificity. Errors in podocyte count were bounded by 1 podocyte per glomerulus. Podocyte-specific image features were found to be significant predictors of disease state, proteinuria, and clinical outcome. Conclusion: PodoCount offers high-performance podocyte quantitation in diverse murine disease models and in human kidney biopsy specimens. Resultant features offer significant correlation with associated metadata and outcome. Our cloud-based tool will provide end users with a standardized approach for automated podometrics from gigapixel-sized WSIs.

Original languageEnglish (US)
Pages (from-to)1377-1392
Number of pages16
JournalKidney International Reports
Issue number6
StatePublished - Jun 2022


  • chronic kidney disease
  • digital pathology
  • gigapixel size images
  • glomerular disease
  • podocyte
  • podometrics

ASJC Scopus subject areas

  • Nephrology


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