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AutoGDeterm: Automatic Geometry Determination for Electron Tomography

文献类型：期刊论文

作者Chen, Yu1,2; Wang, Zihao1,2; Li, Lun1,2; Zhang, Jingrong1,2; Wan, Xiaohua1; Sun, Fei3,4; Zhang, Fa1
刊名TSINGHUA SCIENCE AND TECHNOLOGY
出版日期2018-08-01
卷号23期号:4页码:369-376
关键词electron tomography geometry determination human intervention full automation AutoGDeterm comparable accuracy
ISSN号1007-0214
DOI10.26599/TST.2018.9010036
英文摘要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.
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
语种英语
WOS记录号WOS:000444513200001
出版者TSINGHUA UNIV PRESS
源URL[http://119.78.100.204/handle/2XEOYT63/4929]  
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.

入库方式： OAI收割

来源：计算技术研究所

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