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

doi:10.1093/bioinformatics/bty620

CORC > 计算技术研究所 > 中国科学院计算技术研究所 > 中国科学院计算技术研究所期刊论文 > 英文

	AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction
	Zhang, Fa 4; Liu, Zhiyong 4; Sun, Fei 1; Wang, Sheng 5; Li, Yu 5; Yang, Peng 5; Lawrence, Albert 2; Li, Lun 3,4; Wan, Xiaohua 4; Han, Renmin 5
刊名	BIOINFORMATICS
	2019-01-15
卷号	35 期号:2 页码:319-328
ISSN号	1367-4803
DOI	10.1093/bioinformatics/bty620
英文摘要	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.
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
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000459314900017
内容类型	期刊论文
源URL	[http://119.78.100.204/handle/2XEOYT63/3406]
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Zhang, Fa; Gao, Xin
作者单位	1.Chinese Acad Sci, Inst Biophys, Natl Lab Biomacromol, Beijing 100101, Peoples R China 2.Univ Calif San Diego, Ctr Res Biol Syst, Natl Ctr Microscopy & Imaging Res, San Diego, CA 92093 USA 3.Univ Chinese Acad Sci, Beijing, Peoples R China 4.Chinese Acad Sci, Inst Comp Technol, High Performance Comp Res Ctr, Beijing 100190, Peoples R China 5.KAUST, CBRC, Comp Elect & Math Sci & Engn CEMSE Div, Thuwal 239556900, Saudi Arabia
推荐引用方式 GB/T 7714	Zhang, Fa,Liu, Zhiyong,Sun, Fei,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	Zhang, Fa.,Liu, Zhiyong.,Sun, Fei.,Wang, Sheng.,Li, Yu.,...&Gao, Xin.(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	Zhang, Fa,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.