Abstract
Electron tomography (ET) is a promising technique for investigating in situ three-dimensional (3D) structure of proteins and protein complexes. To obtain a high-resolution 3D ET reconstruction, alignment and geometric parameters determination of ET tilt series are necessary. However, the common geometric parameters determining methods depend on human intervention, which are not only fairly subjective and easily introduce errors but also labor intensive for high-throughput tomographic reconstructions. To overcome these problems, in this paper, we presented a fully automatic geometric parameters determining method. Taking advantage of the high-contrast reprojections of ICON and a series of image processing and edge recognition techniques, our method achieves a high-precision full automation for geometric parameters determining. Experimental results on the resin embedded dataset show that our method has a high accuracy comparable to the common ‘manual positioning’ method.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Asano, S., Engel, B.D., Baumeister, W.: In situ cryo-electron tomography: a post-reductionist approach to structural biology. J. Mol. Biol. 428(2), 332–343 (2015)
Briggs, J.A.: Structural biology in situ - the potential of subtomogram averaging. Curr. Opin. Struct. Biol. 23(2), 261–267 (2013)
Mersereau, R.M., Oppenheim, A.V.: Digital reconstruction of multidimensional signals from their projections. Proc. IEEE 62(10), 1319–1338 (1972)
Kremer, J.R., Mastronarde, D.N., Mcintosh, J.R.: Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116(1), 71–76 (1996)
Deng, Y., Chen, Y., Zhang, Y., Wang, S., Zhang, F., Sun, F.: ICON: 3D reconstruction with ‘missing-information’ restoration in biological electron tomography. J. Struct. Biol. 195(1), 100 (2016)
Renmin, H., Liansan, W., Zhiyong, L., Fei, S., Fa, Z.: A novel fully automatic scheme for fiducial marker-based alignment in electron tomography. J. Struct. Biol. 192(3), 403–417 (2015)
Acknowledgments
This research is supported by the NSFC projects Grant Nos. U1611263, U1611261, 61232001, 61472397, 61502455, 61672493 and Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase), the Strategic Priority Research Program of Chinese Academy of Sciences (Grant No. XDB08030202), the National Basic Research Program (973 Program) of Ministry of Science and Technology of China (2014CB910700).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this paper
Cite this paper
Chen, Y., Wang, Z., Li, L., Wan, X., Sun, F., Zhang, F. (2017). A Fully Automatic Geometric Parameters Determining Method for Electron Tomography. In: Cai, Z., Daescu, O., Li, M. (eds) Bioinformatics Research and Applications. ISBRA 2017. Lecture Notes in Computer Science(), vol 10330. Springer, Cham. https://doi.org/10.1007/978-3-319-59575-7_39
Download citation
DOI: https://doi.org/10.1007/978-3-319-59575-7_39
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-59574-0
Online ISBN: 978-3-319-59575-7
eBook Packages: Computer ScienceComputer Science (R0)