Region-Based Convolutional Neural Nets for Localization of Glomeruli in Trichrome-Stained Whole Kidney Sections. J Am Soc Nephrol 2018 Aug;29(8):2081-2088
Date
06/21/2018Pubmed ID
29921718Pubmed Central ID
PMC6065078DOI
10.1681/ASN.2017111210Scopus ID
2-s2.0-85050939134 (requires institutional sign-in at Scopus site) 98 CitationsAbstract
Background Histologic examination of fixed renal tissue is widely used to assess morphology and the progression of disease. Commonly reported metrics include glomerular number and injury. However, characterization of renal histology is a time-consuming and user-dependent process. To accelerate and improve the process, we have developed a glomerular localization pipeline for trichrome-stained kidney sections using a machine learning image classification algorithm.Methods We prepared 4-μm slices of kidneys from rats of various genetic backgrounds that were subjected to different experimental protocols and mounted the slices on glass slides. All sections used in this analysis were trichrome stained and imaged in bright field at a minimum resolution of 0.92 μm per pixel. The training and test datasets for the algorithm comprised 74 and 13 whole renal sections, respectively, totaling over 28,000 glomeruli manually localized. Additionally, because this localizer will be ultimately used for automated assessment of glomerular injury, we assessed bias of the localizer for preferentially identifying healthy or damaged glomeruli.Results Localizer performance achieved an average precision and recall of 96.94% and 96.79%, respectively, on whole kidney sections without evidence of bias for or against glomerular injury or the need for manual preprocessing.Conclusions This study presents a novel and robust application of convolutional neural nets for the localization of glomeruli in healthy and damaged trichrome-stained whole-renal section mounts and lays the groundwork for automated glomerular injury scoring.
Author List
Bukowy JD, Dayton A, Cloutier D, Manis AD, Staruschenko A, Lombard JH, Solberg Woods LC, Beard DA, Cowley AW JrAuthor
Allen W. Cowley Jr PhD Professor in the Physiology department at Medical College of WisconsinMESH terms used to index this publication - Major topics in bold
AlgorithmsAnimals
Azo Compounds
Biopsy, Needle
Eosine Yellowish-(YS)
Immunohistochemistry
Kidney Diseases
Kidney Glomerulus
Methyl Green
Rats
Reference Values
Staining and Labeling
Tissue Culture Techniques
