Annotated normal CT data of the abdomen for deep learning: Challenges and strategies for implementation

S. Park, L. C. Chu, E. K. Fishman, A. L. Yuille, B. Vogelstein, K. W. Kinzler, K. M. Horton, R. H. Hruban, E. S. Zinreich, D. Fadaei Fouladi, S. Shayesteh, J. Graves, S. Kawamoto

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


Purpose: The purpose of this study was to report procedures developed to annotate abdominal computed tomography (CT) images from subjects without pancreatic disease that will be used as the input for deep convolutional neural networks (DNN) for development of deep learning algorithms for automatic recognition of a normal pancreas. Materials and methods: Dual-phase contrast-enhanced volumetric CT acquired from 2005 to 2009 from potential kidney donors were retrospectively assessed. Four trained human annotators manually and sequentially annotated 22 structures in each datasets, then expert radiologists confirmed the annotation. For efficient annotation and data management, a commercial software package that supports three-dimensional segmentation was used. Results: A total of 1150 dual-phase CT datasets from 575 subjects were annotated. There were 229 men and 346 women (mean age: 45 ± 12 years; range: 18–79 years). The mean intra-observer intra-subject dual-phase CT volume difference of all annotated structures was 4.27 mL (7.65%). The deep network prediction for multi-organ segmentation showed high fidelity with 89.4% and 1.29 mm in terms of mean Dice similarity coefficients and mean surface distances, respectively. Conclusions: A reliable data collection/annotation process for abdominal structures was developed. This process can be used to generate large datasets appropriate for deep learning.

Original languageEnglish (US)
Pages (from-to)35-44
Number of pages10
JournalDiagnostic and Interventional Imaging
Issue number1
StatePublished - Jan 2020


  • Abdominal computed tomography (CT)
  • Artificial intelligence (AI)
  • Image segmentation
  • Machine learning
  • Normal structures

ASJC Scopus subject areas

  • Radiological and Ultrasound Technology
  • Radiology Nuclear Medicine and imaging


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