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J Struct Biol. 2015 May;190(2):200-14. doi: 10.1016/j.jsb.2015.03.009. Epub 2015 Mar 31.

SubspaceEM: A fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction.

Author information

1
Department of Diagnostic Radiology, Yale School of Medicine, New Haven, CT 06510, USA. Electronic address: nicha.dvornek@yale.edu.
2
Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT 06510, USA.
3
Department of Diagnostic Radiology, Yale School of Medicine, New Haven, CT 06510, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Department of Electrical Engineering, Yale University, New Haven, CT 06520, USA.

Abstract

Single particle reconstruction methods based on the maximum-likelihood principle and the expectation-maximization (E-M) algorithm are popular because of their ability to produce high resolution structures. However, these algorithms are computationally very expensive, requiring a network of computational servers. To overcome this computational bottleneck, we propose a new mathematical framework for accelerating maximum-likelihood reconstructions. The speedup is by orders of magnitude and the proposed algorithm produces similar quality reconstructions compared to the standard maximum-likelihood formulation. Our approach uses subspace approximations of the cryo-electron microscopy (cryo-EM) data and projection images, greatly reducing the number of image transformations and comparisons that are computed. Experiments using simulated and actual cryo-EM data show that speedup in overall execution time compared to traditional maximum-likelihood reconstruction reaches factors of over 300.

KEYWORDS:

Cryo-electron microscopy; Expectation–maximization algorithm; Fast image processing; Maximum-a-posteriori; Maximum-likelihood; Single particle reconstruction

PMID:
25839831
PMCID:
PMC4453989
DOI:
10.1016/j.jsb.2015.03.009
[Indexed for MEDLINE]
Free PMC Article
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