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Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
Uppsala Univ, Dept Cell & Mol Biol, Lab Mol Biophys, Husargatan 3,Box 596, SE-75124 Uppsala, Sweden..
KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.ORCID iD: 0000-0003-2793-5052
Uppsala Univ, Dept Cell & Mol Biol, Lab Mol Biophys, Husargatan 3,Box 596, SE-75124 Uppsala, Sweden..
Univ Oxford, Oxford, England..
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2018 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 5, p. 531-541Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
International Union of Crystallography , 2018. Vol. 5, p. 531-541
Keywords [en]
XFELs, Melbournevirus, coherent diffractive imaging, LCLS, image reconstruction
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-235456DOI: 10.1107/S2052252518010047ISI: 000444010100003PubMedID: 30224956Scopus ID: 2-s2.0-85053157931OAI: oai:DiVA.org:kth-235456DiVA, id: diva2:1251625
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationSwedish Foundation for Strategic Research EU, European Research CouncilThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
Note

QC 20180927

Available from: 2018-09-27 Created: 2018-09-27 Last updated: 2018-09-27Bibliographically approved

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Sellberg, Jonas A.

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