A skeleton context-aware 3D fully convolutional network for abdominal artery segmentation

Purpose This paper aims to propose a deep learning-based method for abdominal artery segmentation. Blood vessel structure information is essential to diagnosis and treatment. Accurate blood vessel segmentation is critical to preoperative planning. Although deep learning-based methods perform well on large organs, segmenting small organs such as blood vessels is challenging due to complicated branching structures and positions. We propose a 3D deep learning network from a skeleton context-aware perspective to improve segmentation accuracy. In addition, we propose a novel 3D patch generation method which could strengthen the structural diversity of a training data set. Method The proposed method segments abdominal arteries from an abdominal computed tomography (CT) volume using a 3D fully convolutional network (FCN). We add two auxiliary tasks to the network to extract the skeleton context of abdominal arteries. In addition, our skeleton-based patch generation (SBPG) method further enables the FCN to segment small arteries. SBPG generates a 3D patch from a CT volume by leveraging artery skeleton information. These methods improve the segmentation accuracies of small arteries. Results We used 20 cases of abdominal CT volumes to evaluate the proposed method. The experimental results showed that our method outperformed previous segmentation accuracies. The averaged precision rate, recall rate, and F-measure were 95.5%, 91.0%, and 93.2%, respectively. Compared to a baseline method, our method improved 1.5% the averaged recall rate and 0.7% the averaged F-measure. Conclusions We present a skeleton context-aware 3D FCN to segment abdominal arteries from an abdominal CT volume. In addition, we propose a 3D patch generation method. Our fully automated method segmented most of the abdominal artery regions. The method produced competitive segmentation performance compared to previous methods.