Image Analysis Pipeline for Renal Allograft Evaluation and Fibrosis Quantification

Abstract Background Digital pathology improves standardization and reproducibility of kidney biopsy assessment. We developed a pipeline allowing the analysis of many images without requiring human pre-processing and illustrate its use with a simple algorithm for quantification of interstitial fibrosis on a large dataset of kidney allograft biopsies. Methods Masson’s trichrome stained images from kidney allograft biopsies were used to train and validate a glomeruli detection algorithm using a VGG19 convolutional neural network and an automatic cortical region of interest (ROIs) 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, eGFR 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 regions of interest that can easily be used to develop, validate and apply image-analysis algorithms.