Hao Zheng1,2,3, Lijun Qian4, Yulei Qin1,3, Yun Gu1,3, Jie Yang1,3. 1. Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, 800 Dongchuan RD, Minhang District, Shanghai, 200240, China. 2. School of Biomedical Engineering, Shanghai Jiao Tong University, 800 Dongchuan RD, Minhang District, Shanghai, 200240, China. 3. Institute of Medical Robotics, Shanghai Jiao Tong University, 800 Dongchuan RD, Minhang District, Shanghai, 200240, China. 4. Department of Radiology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200240, China.
Abstract
PURPOSE: Volumetric pancreas segmentation can be used in the diagnosis of pancreatic diseases, the research about diabetes and surgical planning. Since manual delineation is time-consuming and laborious, we develop a deep learning-based framework for automatic pancreas segmentation in three dimensional (3D) medical images. METHODS: A two-stage framework is designed for automatic pancreas delineation. In the localization stage, a Square Root Dice loss is developed to handle the trade-off between sensitivity and specificity. In refinement stage, a novel 2.5D slice interaction network with slice correlation module is proposed to capture the non-local cross-slice information at multiple feature levels. Also a self-supervised learning-based pre-training method, slice shuffle, is designed to encourage the inter-slice communication. To further improve the accuracy and robustness, ensemble learning and a recurrent refinement process are adopted in the segmentation flow. RESULTS: The segmentation technique is validated in a public dataset (NIH Pancreas-CT) with 82 abdominal contrast-enhanced 3D CT scans. Fourfold cross-validation is performed to assess the capability and robustness of our method. The dice similarity coefficient, sensitivity, and specificity of our results are 86.21 ± 4.37%, 87.49 ± 6.38% and 85.11 ± 6.49% respectively, which is the state-of-the-art performance in this dataset. CONCLUSIONS: We proposed an automatic pancreas segmentation framework and validate in an open dataset. It is found that 2.5D network benefits from multi-level slice interaction and suitable self-supervised learning method for pre-training can boost the performance of neural network. This technique could provide new image findings for the routine diagnosis of pancreatic disease.
PURPOSE: Volumetric pancreas segmentation can be used in the diagnosis of pancreatic diseases, the research about diabetes and surgical planning. Since manual delineation is time-consuming and laborious, we develop a deep learning-based framework for automatic pancreas segmentation in three dimensional (3D) medical images. METHODS: A two-stage framework is designed for automatic pancreas delineation. In the localization stage, a Square Root Dice loss is developed to handle the trade-off between sensitivity and specificity. In refinement stage, a novel 2.5D slice interaction network with slice correlation module is proposed to capture the non-local cross-slice information at multiple feature levels. Also a self-supervised learning-based pre-training method, slice shuffle, is designed to encourage the inter-slice communication. To further improve the accuracy and robustness, ensemble learning and a recurrent refinement process are adopted in the segmentation flow. RESULTS: The segmentation technique is validated in a public dataset (NIH Pancreas-CT) with 82 abdominal contrast-enhanced 3D CT scans. Fourfold cross-validation is performed to assess the capability and robustness of our method. The dice similarity coefficient, sensitivity, and specificity of our results are 86.21 ± 4.37%, 87.49 ± 6.38% and 85.11 ± 6.49% respectively, which is the state-of-the-art performance in this dataset. CONCLUSIONS: We proposed an automatic pancreas segmentation framework and validate in an open dataset. It is found that 2.5D network benefits from multi-level slice interaction and suitable self-supervised learning method for pre-training can boost the performance of neural network. This technique could provide new image findings for the routine diagnosis of pancreatic disease.
Authors: Maria Elena Laino; Angela Ammirabile; Ludovica Lofino; Lorenzo Mannelli; Francesco Fiz; Marco Francone; Arturo Chiti; Luca Saba; Matteo Agostino Orlandi; Victor Savevski Journal: Healthcare (Basel) Date: 2022-08-11