AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction

doi:10.1093/bioinformatics/bty620

	AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction
	Han, Renmin 1; Wan, Xiaohua 2; Li, Lun 2,3; Lawrence, Albert 4; Yang, Peng 1; Li, Yu 1; Wang, Sheng 1; Sun, Fei 5; Liu, Zhiyong 2; Gao, Xin 1; Zhang, Fa 2
	2019-01-15
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	35 期号:2 页码:319-328
摘要	Motivation: Dual-axis electron tomography is an important 3D macro-molecular structure reconstruction technology, which can reduce artifacts and suppress the effect of missing wedge. However, the fully automatic data process for dual-axis electron tomography still remains a challenge due to three difficulties: (i) how to track the mass of fiducial markers automatically; (ii) how to integrate the information from the two different tilt series; and (iii) how to cope with the inconsistency between the two different tilt series. Results: Here we develop a toolkit for fully automatic alignment of dual-axis electron tomography, with a simultaneous reconstruction procedure. The proposed toolkit and its workflow carries out the following solutions: (i) fully automatic detection and tracking of fiducial markers under large-field datasets; (ii) automatic combination of two different tilt series and global calibration of projection parameters; and (iii) inconsistency correction based on distortion correction parameters and the consequently simultaneous reconstruction. With all of these features, the presented toolkit can achieve accurate alignment and reconstruction simultaneously and conveniently under a single global coordinate system.
DOI	10.1093/bioinformatics/bty620
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2017YFE0103900] ; National Key Research and Development Program of China[2017YFA0504702] ; King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)[FCC/1/1976-04] ; King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)[URF/1/2601-01] ; King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)[URF/1/3007-01] ; King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)[URF/1/3412-01] ; King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)[URF/1/3450-01] ; National natural Science Foundation of China[U1611263] ; National natural Science Foundation of China[U1611261] ; National natural Science Foundation of China[61472397] ; National natural Science Foundation of China[61502455] ; National natural Science Foundation of China[61672493] ; 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:000459314900017
出版者	OXFORD UNIV PRESS
引用统计	被引频次：12[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/2XEOYT63/3407
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Gao, Xin; Zhang, Fa
作者单位	1.KAUST, CBRC, Comp Elect & Math Sci & Engn CEMSE Div, Thuwal 239556900, Saudi Arabia 2.Chinese Acad Sci, Inst Comp Technol, High Performance Comp Res Ctr, Beijing 100190, Peoples R China 3.Univ Chinese Acad Sci, Beijing, Peoples R China 4.Univ Calif San Diego, Ctr Res Biol Syst, Natl Ctr Microscopy & Imaging Res, San Diego, CA 92093 USA 5.Chinese Acad Sci, Inst Biophys, Natl Lab Biomacromol, Beijing 100101, Peoples R China
推荐引用方式 GB/T 7714	Han, Renmin,Wan, Xiaohua,Li, Lun,et al. AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction[J]. BIOINFORMATICS,2019,35(2):319-328.
APA	Han, Renmin.,Wan, Xiaohua.,Li, Lun.,Lawrence, Albert.,Yang, Peng.,...&Zhang, Fa.(2019).AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction.BIOINFORMATICS,35(2),319-328.
MLA	Han, Renmin,et al."AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction".BIOINFORMATICS 35.2(2019):319-328.