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

J Am Soc Nephrol. 2022 Feb;33(2):420-430. doi: 10.1681/ASN.2021030404. Epub 2021 Dec 7.


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 (n=1238) and validated (n=306), and then evaluated in a hold-out test set of reference standard segmentations (n=386). After the initial evaluation, the algorithm was further tested on datasets originating from two external sites (n=1226).

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.

Keywords: computed tomography; deep learning; kidney cortex; kidney medulla; kidney volume; machine learning collection; segmentation.

Publication types

  • Evaluation Study
  • Multicenter Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Adult
  • Algorithms*
  • Contrast Media
  • Deep Learning
  • Donor Selection / methods
  • Donor Selection / statistics & numerical data
  • Female
  • Humans
  • Image Processing, Computer-Assisted / methods*
  • Image Processing, Computer-Assisted / statistics & numerical data
  • Kidney Cortex / diagnostic imaging*
  • Kidney Medulla / diagnostic imaging*
  • Kidney Transplantation
  • Living Donors
  • Male
  • Middle Aged
  • Neural Networks, Computer
  • Observer Variation
  • Tomography, X-Ray Computed / methods*
  • Tomography, X-Ray Computed / statistics & numerical data


  • Contrast Media