A novel fully automatic scheme for fiducial marker-based alignment in electron tomography

doi:10.1016/j.jsb.2015.09.022

	A novel fully automatic scheme for fiducial marker-based alignment in electron tomography
	Han, Renmin 1,2; Wang, Liansan ; Liu, Zhiyong 3; Sun, Fei 2,4,5; Zhang, Fa 1
	2015-12-01
发表期刊	JOURNAL OF STRUCTURAL BIOLOGY
ISSN	1047-8477
卷号	192 期号:3 页码:403-417
摘要	Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction. (C) 2015 Elsevier Inc. All rights reserved.
关键词	Electron tomography Alignment Point set registration Four point invariant
DOI	10.1016/j.jsb.2015.09.022
收录类别	SCI
语种	英语
资助项目	Strategic Priority Research Program of Chinese Academy of Sciences[XDB08030202] ; National Natural Science Foundation of China[61232001] ; National Natural Science Foundation of China[61202210] ; National Natural Science Foundation of China[61472397] ; National Natural Science Foundation of China[61502455] ; National Basic Research Program (973 Program) of Ministry of Science and Technology of China[2014CB910700]
WOS研究方向	Biochemistry & Molecular Biology ; Biophysics ; Cell Biology
WOS类目	Biochemistry & Molecular Biology ; Biophysics ; Cell Biology
WOS记录号	WOS:000365458400011
出版者	ACADEMIC PRESS INC ELSEVIER SCIENCE
引用统计	被引频次：34[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/2XEOYT63/9122
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Sun, Fei
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.Chinese Acad Sci, Inst Comp Technol, State Key Lab Comp Architecture, Beijing 100190, Peoples R China 4.Chinese Acad Sci, Inst Biophys, Natl Lab Biomacromol, Beijing 100101, Peoples R China 5.Chinese Acad Sci, Ctr Biol Imaging, Inst Biophys, Beijing 100101, Peoples R China
推荐引用方式 GB/T 7714	Han, Renmin,Wang, Liansan,Liu, Zhiyong,et al. A novel fully automatic scheme for fiducial marker-based alignment in electron tomography[J]. JOURNAL OF STRUCTURAL BIOLOGY,2015,192(3):403-417.
APA	Han, Renmin,Wang, Liansan,Liu, Zhiyong,Sun, Fei,&Zhang, Fa.(2015).A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.JOURNAL OF STRUCTURAL BIOLOGY,192(3),403-417.
MLA	Han, Renmin,et al."A novel fully automatic scheme for fiducial marker-based alignment in electron tomography".JOURNAL OF STRUCTURAL BIOLOGY 192.3(2015):403-417.