Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
Journal article, 2018

Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recent inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. The anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.

XFELs

Melbournevirus

LCLS

image reconstruction

coherent diffractive imaging

Author

Ida V. Lundholm

Uppsala University

Jonas A. Sellberg

Royal Institute of Technology (KTH)

Tomas Ekeberg

Uppsala University

Max F. Hantke

University of Oxford

Kenta Okamoto

Uppsala University

Gijs van der Schot

Uppsala University

Jakob Andreasson

Chalmers, Physics, Condensed Matter Physics

Anton Barty

Deutsches Elektronen-Synchrotron (DESY)

Johan Bielecki

European XFEL

Uppsala University

Petr Bruza

Chalmers, Physics, Condensed Matter Physics

Max Bucher

Argonne National Laboratory

Technische Universität Berlin

SLAC Natl Accelerator Lab, Linac Coherent Light Source

Sebastian Carron

SLAC Natl Accelerator Lab, Linac Coherent Light Source

Benedikt J. Daurer

Uppsala University

Ken Ferguson

SLAC Natl Accelerator Lab, 2575 Sand Hill Rd

SLAC Natl Accelerator Lab, Linac Coherent Light Source

PULSE Inst, 2575 Sand Hill Rd

Dirk Hasse

Uppsala University

Jacek Krzywinski

SLAC Natl Accelerator Lab, Linac Coherent Light Source

Daniel S. D. Larsson

Uppsala University

Andrew Morgan

Deutsches Elektronen-Synchrotron (DESY)

Kerstin Muhlig

Uppsala University

Maria Mueller

Technische Universität Berlin

Carl Nettelblad

Uppsala University

Alberto Pietrini

Uppsala University

Hemanth K. N. Reddy

Uppsala University

Daniela Rupp

Technische Universität Berlin

Mario Sauppe

Technische Universität Berlin

Marvin Seibert

Uppsala University

Martin Svenda

Uppsala University

Michelle Swiggers

SLAC Natl Accelerator Lab, Linac Coherent Light Source

Nicusor Timneanu

Uppsala University

Anatoli Ulmer

Technische Universität Berlin

Daniel Westphal

Uppsala University

Garth Williams

Brookhaven National Laboratory

SLAC Natl Accelerator Lab, Linac Coherent Light Source

Alessandro Zani

Uppsala University

Gyula Faigel

Hungarian Academy of Sciences

Henry N. Chapman

Deutsches Elektronen-Synchrotron (DESY)

Thomas Moeller

Technische Universität Berlin

Christoph Bostedt

SLAC Natl Accelerator Lab, Linac Coherent Light Source

PULSE Inst, 2575 Sand Hill Rd

SLAC Natl Accelerator Lab, 2575 Sand Hill Rd

Northwestern University

Argonne National Laboratory

Janos Hajdu

Uppsala University

Czech Academy of Sciences

Tais Gorkhover

SLAC Natl Accelerator Lab, 2575 Sand Hill Rd

PULSE Inst, 2575 Sand Hill Rd

Technische Universität Berlin

Filipe R. N. C. Maia

Lawrence Berkeley National Laboratory

Uppsala University

IUCrJ

2052-2525 (eISSN)

Vol. 5 531-541

Subject Categories

Accelerator Physics and Instrumentation

Atom and Molecular Physics and Optics

Other Physics Topics

DOI

10.1107/S2052252518010047

PubMed

30224956

More information

Latest update

2/12/2019