title: Denoising and covariance estimation of single particle cryo-EM images.
abstract: The problem of image restoration in cryo-EM entails correcting for the effects of the Contrast Transfer Function (CTF) and noise. Popular methods for image restoration include 'phase flipping', which corrects only for the Fourier phases but not amplitudes, and Wiener filtering, which requires the spectral signal to noise ratio. We propose a new image restoration method which we call 'Covariance Wiener Filtering' (CWF). In CWF, the covariance matrix of the projection images is used within the classical Wiener filtering framework for solving the image restoration deconvolution problem. Our estimation procedure for the covariance matrix is new and successfully corrects for the CTF. We demonstrate the efficacy of CWF by applying it to restore both simulated and experimental cryo-EM images. Results with experimental datasets demonstrate that CWF provides a good way to evaluate the particle images and to see what the dataset contains even without 2D classification and averaging.
authors.affiliation: Department of Physics, Princeton University, Jadwin Hall, Washington Road, Princeton, NJ 08544-0708, USA.
authors.forename: Tejal
authors.initials: T
authors.lastname: Bhamre
authors.affiliation: Department of Mathematics, University of Central Florida, 4393 Andromeda Loop N, Orlando, FL 32816-8007, USA.
authors.forename: Teng
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Department of Mathematics and PACM, Princeton University, Fine Hall, Washington Road, Princeton, NJ 08544-1000, USA.
authors.forename: Amit
authors.initials: A
authors.lastname: Singer
mesh_terms: D000465:Algorithms; D000818:Animals; D001419:Bacteria / Q000648:ultrastructure; D003198:Computer Simulation; D020285:Cryoelectron Microscopy / Q000379:methods*; D004640:Emetine / Q000737:chemistry; D005583:Fourier Analysis; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D053496:Inositol 1,4,5-Trisphosphate Receptors / Q000737:chemistry; D046911:Macromolecular Substances / Q000737:chemistry*; D010316:Particle Size; D012270:Ribosomes / Q000737:chemistry; D059629:Signal-To-Noise Ratio; D050916:TRPV Cation Channels / Q000737:chemistry
chemical_list: D053496:Inositol 1,4,5-Trisphosphate Receptors; D046911:Macromolecular Substances; D050916:TRPV Cation Channels; D004640:Emetine
keywords: CTF correction; Steerable PCA; Wiener filtering