title: A Stochastic Hill Climbing Approach for Simultaneous 2D Alignment and Clustering of Cryogenic Electron Microscopy Images.
abstract: A critical step in the analysis of novel cryogenic electron microscopy (cryo-EM) single-particle datasets is the identification of homogeneous subsets of images. Methods for solving this problem are important for data quality assessment, ab initio 3D reconstruction, and analysis of population diversity due to the heterogeneous nature of macromolecules. Here we formulate a stochastic algorithm for identification of homogeneous subsets of images. The purpose of the method is to generate improved 2D class averages that can be used to produce a reliable 3D starting model in a rapid and unbiased fashion. We show that our method overcomes inherent limitations of widely used clustering approaches and proceed to test the approach on six publicly available experimental cryo-EM datasets. We conclude that, in each instance, ab initio 3D reconstructions of quality suitable for initialization of high-resolution refinement are produced from the cluster centers.
authors.affiliation: Department of Biochemistry Molecular Biology, Monash University, Clayton 3800, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Clayton 3800, Australia.
authors.forename: Cyril F
authors.initials: CF
authors.lastname: Reboul
authors.affiliation: Department of Biochemistry Molecular Biology, Monash University, Clayton 3800, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Clayton 3800, Australia.
authors.forename: Frederic
authors.initials: F
authors.lastname: Bonnet
authors.affiliation: Department of Biochemistry Molecular Biology, Monash University, Clayton 3800, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Clayton 3800, Australia. Electronic address: dominika.elmlund@monash.edu.
authors.forename: Dominika
authors.initials: D
authors.lastname: Elmlund
authors.affiliation: Department of Biochemistry Molecular Biology, Monash University, Clayton 3800, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Clayton 3800, Australia. Electronic address: hans.elmlund@monash.edu.
authors.forename: Hans
authors.initials: H
authors.lastname: Elmlund
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D020285:Cryoelectron Microscopy / Q000379:methods*; D007091:Image Processing, Computer-Assisted; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008958:Models, Molecular
keywords: alignment; clustering; cryo-EM; electron microscopy; single-particle; stochastic