Robust liver vessel extraction using 3D U-Net with variant dice loss function

Computers in Biology and Medicine
Qing HuangGuangzhi Wang

Abstract

Liver vessel extraction from CT images is essential in liver surgical planning. Liver vessel segmentation is difficult due to the complex vessel structures, and even expert manual annotations contain unlabeled vessels. This paper presents an automatic liver vessel extraction method using deep convolutional network and studies the impact of incomplete data annotation on segmentation accuracy evaluation. We select the 3D U-Net and use data augmentation for accurate liver vessel extraction with few training samples and incomplete labeling. To deal with high imbalance between foreground (liver vessel) and background (liver) classes but also increase segmentation accuracy, a loss function based on a variant of the dice coefficient is proposed to increase the penalties for misclassified voxels. We include unlabeled liver vessels extracted by our method in the expert manual annotations, with a specialist's visual inspection for refinement, and compare the evaluations before and after the procedure. Experiments were performed on the public datasets Sliver07 and 3Dircadb as well as local clinical datasets. The average dice and sensitivity for the 3Dircadb dataset were 67.5% and 74.3%, respectively, prior to annotation refinement, as com...Continue Reading

Citations

Jan 20, 2020·Medical & Biological Engineering & Computing·Xiaoyu GuoZhiliang Wang
Jul 31, 2020·Frontiers of Medicine·Ke Sheng
Aug 28, 2020·Frontiers in Neuroanatomy·Qing HuangTingwei Quan
Oct 8, 2020·Physical and Engineering Sciences in Medicine·Ryusei KimuraHiroshi Fujita
Feb 7, 2021·Computerized Medical Imaging and Graphics : the Official Journal of the Computerized Medical Imaging Society·Dengqiang Jia, Xiahai Zhuang
Sep 4, 2020·International Journal of Computer Assisted Radiology and Surgery·Libin LiangAaron Fenster
Apr 4, 2021·Sensors·Marcin Ciecholewski, Michał Kassjański
Jul 3, 2021·Mathematical Biosciences and Engineering : MBE·Jinzhu YangYing Hu
Jul 30, 2021·Computerized Medical Imaging and Graphics : the Official Journal of the Computerized Medical Imaging Society·Jinzhu YangOsmar Zaiane
Mar 17, 2020·Computers in Biology and Medicine·Jiajia NiDerek Abbott
Nov 16, 2021·Journal of Hepato-biliary-pancreatic Sciences·Yusuke KazamiKiyoshi Hasegawa

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