Complete abdomen and pelvis segmentation using U-net variant architecture

Alexander D. Weston, Panagiotis Korfiatis, Kenneth A. Philbrick, Gian Marco Conte, Petro Kostandy, Thomas Sakinis, Atefeh Zeinoddini, Arunnit Boonrod, Michael Moynagh, Naoki Takahashi, Bradley J. Erickson

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Purpose: Organ segmentation of computed tomography (CT) imaging is essential for radiotherapy treatment planning. Treatment planning requires segmentation not only of the affected tissue, but nearby healthy organs-at-risk, which is laborious and time-consuming. We present a fully automated segmentation method based on the three-dimensional (3D) U-Net convolutional neural network (CNN) capable of whole abdomen and pelvis segmentation into 33 unique organ and tissue structures, including tissues that may be overlooked by other automated segmentation approaches such as adipose tissue, skeletal muscle, and connective tissue and vessels. Whole abdomen segmentation is capable of quantifying exposure beyond a handful of organs-at-risk to all tissues within the abdomen. Methods: Sixty-six (66) CT examinations of 64 individuals were included in the training and validation sets and 18 CT examinations from 16 individuals were included in the test set. All pixels in each examination were segmented by image analysts (with physician correction) and assigned one of 33 labels. Segmentation was performed with a 3D U-Net variant architecture which included residual blocks, and model performance was quantified on 18 test cases. Human interobserver variability (using semiautomated segmentation) was also reported on two scans, and manual interobserver variability of three individuals was reported on one scan. Model performance was also compared to several of the best models reported in the literature for multiple organ segmentation. Results: The accuracy of the 3D U-Net model ranges from a Dice coefficient of 0.95 in the liver, 0.93 in the kidneys, 0.79 in the pancreas, 0.69 in the adrenals, and 0.51 in the renal arteries. Model accuracy is within 5% of human segmentation in eight of 19 organs and within 10% accuracy in 13 of 19 organs. Conclusions: The CNN approaches the accuracy of human tracers and on certain complex organs displays more consistent prediction than human tracers. Fully automated deep learning-based segmentation of CT abdomen has the potential to improve both the speed and accuracy of radiotherapy dose prediction for organs-at-risk.

Original languageEnglish (US)
Pages (from-to)5609-5618
Number of pages10
JournalMedical physics
Issue number11
StatePublished - Nov 2020


  • abdomen
  • computed tomography
  • deep learning
  • gastrointestinal tract
  • pancreas
  • segmentation

ASJC Scopus subject areas

  • Biophysics
  • Radiology Nuclear Medicine and imaging


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