Spectral Signal-to-noise Ratio and Resolution Assessment of 3D Reconstructions

Overview

Journal J Struct Biol

Specialties Cell Biology
Molecular Biology

Date 2005 Feb 22

PMID 15721578

Citations 17

Authors

M Unser

C O S Sorzano

P Thevenaz

S Jonic

C El-Bez

S De Carlo

J F Conway

B L Trus

Affiliations

Soon will be listed here.

Abstract

Measuring the quality of three-dimensional (3D) reconstructed biological macromolecules by transmission electron microscopy is still an open problem. In this article, we extend the applicability of the spectral signal-to-noise ratio (SSNR) to the evaluation of 3D volumes reconstructed with any reconstruction algorithm. The basis of the method is to measure the consistency between the data and a corresponding set of reprojections computed for the reconstructed 3D map. The idiosyncrasies of the reconstruction algorithm are taken explicitly into account by performing a noise-only reconstruction. This results in the definition of a 3D SSNR which provides an objective indicator of the quality of the 3D reconstruction. Furthermore, the information to build the SSNR can be used to produce a volumetric SSNR (VSSNR). Our method overcomes the need to divide the data set in two. It also provides a direct measure of the performance of the reconstruction algorithm itself; this latter information is typically not available with the standard resolution methods which are primarily focused on reproducibility alone.

Citing Articles

On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy.

Sorzano C, Jimenez-Moreno A, Maluenda D, Martinez M, Ramirez-Aportela E, Krieger J Acta Crystallogr D Struct Biol. 2022; 78(Pt 4):410-423.

PMID: 35362465 PMC: 8972802. DOI: 10.1107/S2059798322001978.

: a new deep-learning- and aspect-based local resolution method for electron-microscopy maps.

Ramirez-Aportela E, Mota J, Conesa P, Carazo J, Sorzano C IUCrJ. 2019; 6(Pt 6):1054-1063.

PMID: 31709061 PMC: 6830216. DOI: 10.1107/S2052252519011692.

Single-particle reconstruction statistics: a diagnostic tool in solving biomolecular structures by cryo-EM.

Heymann J Acta Crystallogr F Struct Biol Commun. 2019; 75(Pt 1):33-44.

PMID: 30605123 PMC: 6317460. DOI: 10.1107/S2053230X18017636.

A Local Agreement Filtering Algorithm for Transmission EM Reconstructions.

Ramlaul K, Palmer C, Aylett C J Struct Biol. 2018; 205(1):30-40.

PMID: 30502495 PMC: 6351148. DOI: 10.1016/j.jsb.2018.11.011.

Validation of 3D EM Reconstructions: The Phantom in the Noise.

Heymann J AIMS Biophys. 2015; 2(1):21-35.

PMID: 26005714 PMC: 4440490. DOI: 10.3934/biophy.2015.1.21.

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