Image Analysis Pipeline for Renal Allograft Evaluation and Fibrosis Quantification

Alton Brad Farris, Juan Vizcarra, Mohamed Amgad, Lee Alex Donald Cooper, David Gutman, Julien Hogan*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


Introduction: Digital pathology improves the standardization and reproducibility of kidney biopsy specimen assessment. We developed a pipeline allowing the analysis of many images without requiring human preprocessing and illustrate its use with a simple algorithm for quantification of interstitial fibrosis on a large dataset of kidney allograft biopsy specimens. Methods: Masson trichrome–stained images from kidney allograft biopsy specimens were used to train and validate a glomeruli detection algorithm using a VGG19 convolutional neural network and an automatic cortical region of interest (ROI) selection algorithm including cortical regions containing all predicted glomeruli. A positive-pixel count algorithm was used to quantify interstitial fibrosis on the ROIs and the association between automatic fibrosis and pathologist evaluation, estimated glomerular filtration rate (GFR) and allograft survival was assessed. Results: The glomeruli detection (F1 score of 0.87) and ROIs selection (F1 score 0.83 [SD 0.13]) algorithms displayed high accuracy. The correlation between the automatic fibrosis quantification on manually and automatically selected ROIs was high (r = 1.00 [0.99–1.00]). Automatic fibrosis quantification was only moderately correlated with pathologists’ assessment and was not significantly associated with eGFR or allograft survival. Conclusion: This pipeline can automatically and accurately detect glomeruli and select cortical ROIs that can easily be used to develop, validate, and apply image analysis algorithms.

Original languageEnglish (US)
Pages (from-to)1878-1887
Number of pages10
JournalKidney International Reports
Issue number7
StatePublished - Jul 2021


  • digital pathology
  • fibrosis
  • kidney transplantation

ASJC Scopus subject areas

  • Nephrology


Dive into the research topics of 'Image Analysis Pipeline for Renal Allograft Evaluation and Fibrosis Quantification'. Together they form a unique fingerprint.

Cite this