A Consensus Framework of Distributed Multiple-Tilt Reconstruction in Electron Tomography

doi:10.1089/cmb.2019.0287

	A Consensus Framework of Distributed Multiple-Tilt Reconstruction in Electron Tomography
	Wang, Zihao 1,2; Zhang, Jingrong 1,2; Gao, Weifang 3; Liu, Zhiyong 1; Wan, Xiaohua 1; Zhang, Fa 1
	2019-12-02
发表期刊	JOURNAL OF COMPUTATIONAL BIOLOGY
ISSN	1066-5277
页码	11
摘要	The "missing wedge" of a single tilt in electron tomography introduces severe artifacts into the reconstructed results. To reduce the "missing wedge" effect, a widely used method is "multiple-tilt reconstruction," which collects projections using multiple axes. However, as the number of tilt series increases, the computing and memory costs also rise. The degree of parallelism is limited by the sample thickness, and a large memory requirement cannot be met by most multicore computers. In our study, we present a new fully distributed multiple-tilt simultaneous iterative reconstruction technique (DM-SIRT). To improve the parallelism of the reconstruction process and reduce the memory requirements of each process, we formulate the multiple-tilt reconstruction as a consensus optimization problem and design a DM-SIRT algorithm. Experiments show that in addition to slightly better resolution, DM-SIRT can obtain a 13.9 x accelerated ratio compared with the full multiple-tilt reconstruction version. It also has a 97% decrease in memory overhead and is 16 times more scalable than the full reconstruction version.
关键词	consensus optimization cryoelectron tomography multiple-tilt reconstruction parallel computing TxBR
DOI	10.1089/cmb.2019.0287
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2017YPE0103900] ; National Key Research and Development Program of China[2017YFA0504702] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDA19020400] ; NSFC[U1611263] ; NSFC[U1611261] ; NSFC[61932018] ; NSFC[61672493] ; Beijing Municipal Natural Science Foundation[L182053] ; Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase)
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:000500391900001
出版者	MARY ANN LIEBERT, INC
引用统计	被引频次：2[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/14945
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Liu, Zhiyong; Wan, Xiaohua; Zhang, Fa
作者单位	1.Chinese Acad Sci, Inst Comp Technol, High Performance Comp Res Ctr, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.Hebei Univ Chinese Med, Shijiazhuang, Hebei, Peoples R China
推荐引用方式 GB/T 7714	Wang, Zihao,Zhang, Jingrong,Gao, Weifang,et al. A Consensus Framework of Distributed Multiple-Tilt Reconstruction in Electron Tomography[J]. JOURNAL OF COMPUTATIONAL BIOLOGY,2019:11.
APA	Wang, Zihao,Zhang, Jingrong,Gao, Weifang,Liu, Zhiyong,Wan, Xiaohua,&Zhang, Fa.(2019).A Consensus Framework of Distributed Multiple-Tilt Reconstruction in Electron Tomography.JOURNAL OF COMPUTATIONAL BIOLOGY,11.
MLA	Wang, Zihao,et al."A Consensus Framework of Distributed Multiple-Tilt Reconstruction in Electron Tomography".JOURNAL OF COMPUTATIONAL BIOLOGY (2019):11.