AutoGDeterm: Automatic Geometry Determination for Electron Tomography

doi:10.26599/TST.2018.9010036

	AutoGDeterm: Automatic Geometry Determination for Electron Tomography
	Chen, Yu 1,2; Wang, Zihao 1,2; Li, Lun 1,2; Zhang, Jingrong 1,2; Wan, Xiaohua 1; Sun, Fei 3,4; Zhang, Fa 1
	2018-08-01
发表期刊	TSINGHUA SCIENCE AND TECHNOLOGY
ISSN	1007-0214
卷号	23 期号:4 页码:369-376
摘要	Electron Tomography (ET) is an important method for studying cell ultrastructure in three-dimensional (3D) space. By combining cryo-electron tomography of frozen-hydrated samples (cryo-ET) and a sub-tomogram averaging approach, ET has recently reached sub-nanometer resolution, thereby realizing the capability for gaining direct insights into function and mechanism. To obtain a high-resolution 3D ET reconstruction, alignment and geometry determination of the ET tilt series are necessary. However, typical methods for determining geometry require human intervention, which is not only subjective and easily introduces errors, but is also labor intensive for high-throughput tomographic reconstructions. To overcome these problems, we have developed an automatic geometry-determination method, called AutoGDeterm. By taking advantage of the high-contrast re-projections of the Iterative Compressed-sensing Optimized Non-Uniform Fast Fourier Transform (NUFFT) reconstruction (ICON) and a series of numerical analysis methods, AutoGDeterm achieves high-precision fully automated geometry determination. Experimental results on simulated and resin-embedded datasets show that the accuracy of AutoGDeterm is high and comparable to that of the typical "manual positioning" method. We have made AutoGDeterm available as software, which can be freely downloaded from our website http://ear.ict.ac.cn.
关键词	electron tomography geometry determination human intervention full automation AutoGDeterm comparable accuracy
DOI	10.26599/TST.2018.9010036
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[U1611263] ; National Natural Science Foundation of China[U1611261] ; National Natural Science Foundation of China[61232001] ; 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 ; Strategic Priority Research Program of Chinese Academy of Sciences[XDB08030202] ; National Key Research and Development Program of China[2017YFA0504702]
WOS研究方向	Computer Science ; Engineering
WOS类目	Computer Science, Information Systems ; Computer Science, Software Engineering ; Engineering, Electrical & Electronic
WOS记录号	WOS:000444513200001
出版者	TSINGHUA UNIV PRESS
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/2XEOYT63/4930
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; Zhang, Fa
作者单位	1.Chinese Acad Sci, ICT, High Performance Comp Res Ctr, Beijing 100101, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100101, Peoples R China 3.Chinese Acad Sci, IBP, Ctr Biol Imaging, Beijing 100101, Peoples R China 4.Chinese Acad Sci, Ctr Excellence Biomacromol, Natl Key Lab Biomacromol, Beijing 100101, Peoples R China
推荐引用方式 GB/T 7714	Chen, Yu,Wang, Zihao,Li, Lun,et al. AutoGDeterm: Automatic Geometry Determination for Electron Tomography[J]. TSINGHUA SCIENCE AND TECHNOLOGY,2018,23(4):369-376.
APA	Chen, Yu.,Wang, Zihao.,Li, Lun.,Zhang, Jingrong.,Wan, Xiaohua.,...&Zhang, Fa.(2018).AutoGDeterm: Automatic Geometry Determination for Electron Tomography.TSINGHUA SCIENCE AND TECHNOLOGY,23(4),369-376.
MLA	Chen, Yu,et al."AutoGDeterm: Automatic Geometry Determination for Electron Tomography".TSINGHUA SCIENCE AND TECHNOLOGY 23.4(2018):369-376.