A high-performance deep-learning-based pipeline for whole-brain vasculature segmentation at the capillary resolution

Abstract 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. Th...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2023-04, Vol.39 (4)
Main Authors: Li, Yuxin, Liu, Xuhua, Jia, Xueyan, Jiang, Tao, Wu, Jianghao, Zhang, Qianlong, Li, Junhuai, Li, Xiangning, Li, Anan
Format: Article
Language:English
Subjects:
Animals
Brain - diagnostic imaging
Deep Learning
Image Processing, Computer-Assisted - methods
Imaging, Three-Dimensional - methods
Mice
Neural Networks, Computer
Original Paper
Software
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Summary:Abstract 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 h. We also demonstrated that our pipeline could be applied to the vascular analysis. Availability and implementation The dataset is available at http://atlas.brainsmatics.org/a/li2301. The source code is freely available at https://github.com/visionlyx/HP-VSP.
ISSN:1367-4811
1367-4803
1367-4811
DOI:10.1093/bioinformatics/btad145