A local agreement filtering algorithm for transmission EM reconstructions

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Title: A local agreement filtering algorithm for transmission EM reconstructions
Authors: Ramlaul, K
Palmer, CM
Aylett, CHS
Item Type: Journal Article
Abstract: We present LAFTER, an algorithm for de-noising single particle reconstructions from cryo-EM. Single particle analysis entails the reconstruction of high-resolution volumes from tens of thousands of particle images with low individual signal-to-noise. Imperfections in this process result in substantial variations in the local signal-to-noise ratio within the resulting reconstruction, complicating the interpretation of molecular structure. An effective local de-noising filter could therefore improve interpretability and maximise the amount of useful information obtained from cryo-EM maps. LAFTER is a local de-noising algorithm based on a pair of serial real-space filters. It compares independent half-set reconstructions to identify and retain shared features that have power greater than the noise. It is capable of recovering features across a wide range of signal-to-noise ratios, and we demonstrate recovery of the strongest features at Fourier shell correlation (FSC) values as low as 0.144 over a 2563-voxel cube. A fast and computationally efficient implementation of LAFTER is freely available. We also propose a new way to evaluate the effectiveness of real-space filters for noise suppression, based on the correspondence between two FSC curves: 1) the FSC between the filtered and unfiltered volumes, and 2) Cref, the FSC between the unfiltered volume and a hypothetical noiseless volume, which can readily be estimated from the FSC between two half-set reconstructions.
Issue Date: 29-Nov-2018
Date of Acceptance: 25-Nov-2018
URI: http://hdl.handle.net/10044/1/64858
DOI: https://dx.doi.org/10.1016/j.jsb.2018.11.011
ISSN: 1047-8477
Publisher: Elsevier BV
Journal / Book Title: Journal of Structural Biology
Copyright Statement: © 2018 The Author(s). This is an open access distributed under the terms of the Creative Commons Attribution 4.0 International licence (CC BY 4.0 - https://creativecommons.org/licenses/by/4.0/).
Sponsor/Funder: Wellcome Trust
Funder's Grant Number: 206212/Z/17/Z
Keywords: 0601 Biochemistry And Cell Biology
Publication Status: Published online
Open Access location: https://www.sciencedirect.com/science/article/pii/S1047847718303113?via%3Dihub
Online Publication Date: 2018-11-29
Appears in Collections:Department of Medicine

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