Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods

doi:10.1016/j.jsb.2017.04.002

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

	Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods
	Wan, Xiaohua 1,6; Katchalski, Tsvi 6; Churas, Christopher 6; Ghosh, Sreya 6; Phan, Sebastien 6; Lawrence, Albert 6; Hao, Yu 1; Zhou, Ziying 1,3; Chen, Ruijuan 2,6; Chen, Yu 1
刊名	JOURNAL OF STRUCTURAL BIOLOGY
	2017-05-01
卷号	198 期号:2 页码:103-115
关键词	Electron Microscope Tomography Simulator Tilt Series Reconstruction Tracking Alignment Block face Inversion Curvilinear Warping
ISSN号	1047-8477
DOI	10.1016/j.jsb.2017.04.002
英文摘要	Because of the significance of electron microscope tomography in the investigation of biological structure at nanometer scales, ongoing improvement efforts have been continuous over recent years. This is particularly true in the case of software developments. Nevertheless, verification of improvements delivered by new algorithms and software remains difficult. Current analysis tools do not provide adaptable and consistent methods for quality assessment. This is particularly true with images of biological samples, due to image complexity, variability, low contrast and noise. We report an electron tomography (ET) simulator with accurate ray optics modeling of image formation that includes curvilinear trajectories through the sample, warping of the sample and noise. As a demonstration of the utility of our approach, we have concentrated on providing verification of the class of reconstruction methods applicable to wide field images of stained plastic-embedded samples. Accordingly, we have also constructed digital phantoms derived from serial block face scanning electron microscope images. These phantoms are also easily modified to include alignment features to test alignment algorithms. The combination of more realistic phantoms with more faithful simulations facilitates objective comparison of acquisition parameters, alignment and reconstruction algorithms and their range of applicability. With proper phantoms, this approach can also be modified to include more complex optical models, including distance-dependent blurring and phase contrast functions, such as may occur in cryotomography. (C) 2017 Elsevier Inc. All rights reserved.
资助项目	International Community Foundation under the Sun Yat Sen Fund for international Cultural Exchange and Collaboration ; National Science Foundation of China[61232001] ; National Science Foundation of China[61472397] ; National Science Foundation of China[61672493] ; National Science Foundation of China[61502455] ; Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund - phase two
WOS研究方向	Biochemistry & Molecular Biology ; Biophysics ; Cell Biology
语种	英语
出版者	ACADEMIC PRESS INC ELSEVIER SCIENCE
WOS记录号	WOS:000402026300005
内容类型	期刊论文
源URL	[http://119.78.100.204/handle/2XEOYT63/7211]
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Lawrence, Albert
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Beijing, Peoples R China 2.Tianjin Polytech Univ, Sch Elect & Informat Engn, Tianjin, Peoples R China 3.Beijing Inst Technol, Beijing, Peoples R China 4.Univ Calif San Diego, Dept Bioengn, San Diego, CA 92103 USA 5.Univ Calif San Diego, Dept Neurosci, San Diego, CA 92103 USA 6.Univ Calif San Diego, Natl Ctr Microscopy & Imaging Res, San Diego, CA 92103 USA
推荐引用方式 GB/T 7714	Wan, Xiaohua,Katchalski, Tsvi,Churas, Christopher,et al. Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods[J]. JOURNAL OF STRUCTURAL BIOLOGY,2017,198(2):103-115.
APA	Wan, Xiaohua.,Katchalski, Tsvi.,Churas, Christopher.,Ghosh, Sreya.,Phan, Sebastien.,...&Ellisman, Mark H..(2017).Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods.JOURNAL OF STRUCTURAL BIOLOGY,198(2),103-115.
MLA	Wan, Xiaohua,et al."Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods".JOURNAL OF STRUCTURAL BIOLOGY 198.2(2017):103-115.