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In Bioinformatics (Oxford, England)

MOTIVATION : Reconstructing and analyzing all blood vessels throughout the brain is significant for understanding brain function, revealing the mechanisms of brain disease, and mapping the whole-brain vascular atlas. Vessel segmentation is a fundamental step in reconstruction and analysis. The whole-brain optical microscopic imaging method enables the acquisition of whole-brain vessel images at the capillary resolution. Due to the massive amount of data and the complex vascular features generated by high-resolution whole-brain imaging, achieving rapid and accurate segmentation of whole-brain vasculature becomes a challenge.

RESULTS : We introduce HP-VSP, a high-performance vessel segmentation pipeline based on deep learning. The pipeline consists of three processes: data blocking, block prediction, and block fusion. We used parallel computing to parallelize this pipeline to improve the efficiency of whole-brain vessel segmentation. We also designed a lightweight deep neural network based on multi-resolution vessel feature extraction to segment vessels at different scales throughout the brain accurately. We validated our approach on whole-brain vascular data from three transgenic mice collected by HD-fMOST. The results show that our proposed segmentation network achieves the state-of-the-art level under various evaluation metrics. In contrast, the parameters of the network are only 1% of those of similar networks. The established segmentation pipeline could be used on various computing platforms and complete the whole-brain vessel segmentation in 3 hours. We also demonstrated that our pipeline could be applied to the vascular analysis.

AVAILABILITY : The dataset is available at The source code is freely available at

SUPPLEMENTARY INFORMATION : Supplementary data are available at Bioinformatics online.

Li Yuxin, Liu Xuhua, Jia Xueyan, Jiang Tao, Wu Jianghao, Zhang Qianlong, Li Junhuai, Li Xiangning, Li Anan