A Two-Phase Approach using Mask R-CNN and 3D U-Net for High-Accuracy Automatic Segmentation of Pancreas in CT Imaging

Dogan R. O., Dogan H., Bayrak C., KAYIKÇIOĞLU T.

COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, vol.207, 2021 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 207
  • Publication Date: 2021
  • Doi Number: 10.1016/j.cmpb.2021.106141
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, PASCAL, Applied Science & Technology Source, BIOSIS, Biotechnology Research Abstracts, Compendex, Computer & Applied Sciences, EMBASE, INSPEC, MEDLINE
  • Keywords: Mask R-CNN, 3D U-Net, Deep learning, Automatic pancreas segmentation, Computed tomography, MULTIORGAN SEGMENTATION, ATLAS
  • Karadeniz Technical University Affiliated: Yes


Background and objective: The size, shape, and position of the pancreas are affected by the patient characteristics such as age, sex, adiposity. Owing to more complex anatomical structures (size, shape, and position) of the pancreas, specialists have some difficulties in the analysis of pancreatic diseases (diabetes, pancreatic cancer, pancreatitis). Therefore, the treatment of the disease requires enormous time and depends on the experience of specialists. In order to decrease the rate of pancreatic disease deaths and to assist the specialist in the analysis of pancreatic diseases, automatic pancreas segmentation techniques have been actively developed in the research article for many years. Methods: Although the rapid growth of deep learning and proving satisfactory performance in many medical image processing and computer vision applications, the maximum Dice Similarity Coefficients (DSC) value of these techniques related to automatic pancreas segmentation is only around 85% due to complex structure of the pancreas and other factors. Contrary to previous techniques which are required significantly higher computational power and memory, this paper suggests a novel two-phase approach for high-accuracy automatic pancreas segmentation in computed tomography (CT) imaging. The proposed approach consists of two phases; (1) Pancreas Localization, where the rough pancreas position is detected on the 2D CT slice by adopting Mask R-CNN model, (2) Pancreas Segmentation, where the segmented pancreas region is produced by refining the candidate pancreas region with 3D U-Net on the 2D sub-CT slices generated in the first phase. Both qualitative and quantitative assessments of the proposed approach are performed on the NIH data set. Results: In order to evaluate the achievement of the recommended approach, a total of 16 different automatic pancreas segmentation techniques reported in the literature are compared by utilizing performance assessment procedures which are Dice Similarity Coefficient (DSC), Jaccard Index (JI), Precision (PRE), Recall (REC), Pixel Accuracy (ACC), Specificity (SPE), Receiver Operating Characteristics (ROC) and Area under ROC curve (AUC). The average values of DSC, JI, REC and ACC are computed as 86.15%, 75.93%, 86.27%, 86.27% and 99.95% respectively, which are the best values among well-established studies for automatic pancreas segmentation. Conclusion: It is demonstrated with qualitative and quantitative results that our suggested two-phase approach creates more favorable results than other existing approaches. (c) 2021 Elsevier B.V. All rights reserved.