Automated Segmentation of Kidney Cortex and Medulla in CT Images: A Multisite Evaluation Study

Panagiotis Korfiatis, Aleksandar Denic, Marie E. Edwards, Adriana V. Gregory, Darryl E. Wright, Aidan Mullan, Joshua Augustine, Andrew D. Rule, Timothy L. Kline

Research output: Contribution to journalArticlepeer-review


Background In kidney transplantation, a contrast CT scan is obtained in the donor candidate to detect subclinical pathology in the kidney. Recent work from the Aging Kidney Anatomy study has characterized kidney, cortex, and medulla volumes using a manual image-processing tool. However, this technique is time consuming and impractical for clinical care, and thus, these measurements are not obtained during donor evaluations. This study proposes a fully automated segmentation approach for measuring kidney, cortex, and medulla volumes. Methods A total of 1930 contrast-enhanced CT exams with reference standard manual segmentations from one institution were used to develop the algorithm. A convolutional neural network model was trained (n51238) and validated (n5306), and then evaluated in a hold-out test set of reference standard segmentations (n5386). After the initial evaluation, the algorithm was further tested on datasets originating from two external sites (n51226). Results The automated model was found to perform on par with manual segmentation, with errors similar to interobserver variability with manual segmentation. Compared with the reference standard, the automated approach achieved a Dice similarity metric of 0.94 (right cortex), 0.90 (right medulla), 0.94 (left cortex), and 0.90 (left medulla) in the test set. Similar performance was observed when the algorithm was applied on the two external datasets. Conclusions A fully automated approach for measuring cortex and medullary volumes in CT images of the kidneys has been established. This method may prove useful for a wide range of clinical applications.

Original languageEnglish (US)
Pages (from-to)420-430
Number of pages11
JournalJournal of the American Society of Nephrology
Issue number2
StatePublished - Feb 2022

ASJC Scopus subject areas

  • Nephrology


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