Image Analysis Pipeline for Renal Allograft Evaluation and Fibrosis Quantification

• Type of Material: Article
• Authors: Alton Farris III, Emory University; Juan Vizcarra, Georgia Institute of Technology; Mohamed Amgad, Northwestern University; Lee Alex Donald Cooper, Northwestern University; David Gutman, Emory University; Julien Hogan, Emory University
• Language: English
• Date: 2021-07-01
• Publisher: ELSEVIER SCIENCE INC
• Publication Version: Final Published Version
• Copyright Statement: © 2021 International Society of Nephrology. Published by Elsevier Inc.
• License: Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1016/j.ekir.2021.04.019
• Title of Journal or Parent Work: KIDNEY INTERNATIONAL REPORTS
• Volume: 6
• Issue: 7
• Start Page: 1878
• End Page: 1887
• Grant/Funding Information: This study was funded by a Synergy Award from the Woodruff Health Sciences Center of Emory University.
• Keywords: BIOPSIES; INTERNATIONAL VARIATION; fibrosis; Science & Technology; CLASSIFICATION; Life Sciences & Biomedicine; digital pathology; Urology & Nephrology; kidney transplantation; INTERSTITIAL FIBROSIS
• Research Categories: Health Sciences, Medicine and Surgery; Biology, Cell

Abstract

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.