Evidence map›Paper›PMID 30224956›Full record

ArticleIUCrJ2018

Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging.

Ida V Lundholm, Jonas A Sellberg, Tomas Ekeberg, Max F Hantke, Kenta Okamoto, Gijs van der Schot, Jakob Andreasson, Anton Barty, Johan Bielecki, Petr Bruza and 30 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in IUCrJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.

0numbers the graph read from it
0cells of the map it votes in
29citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

29 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. X-Ray Crystallography of Viruses.Sub-cellular biochemistry · 2024
    Review
  10. Article
  11. Article
  12. Article
  13. Article
  14. Article
  15. Article
  16. Review
  17. Article
  18. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

40 authors.

Ida V LundholmLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Jonas A SellbergBiomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden.
Tomas EkebergLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Max F HantkeUniversity of Oxford, UK.
Kenta OkamotoLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Gijs van der SchotLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Jakob AndreassonLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Anton BartyCenter for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.
Johan BieleckiLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Petr BruzaCondensed Matter Physics, Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
Max BucherLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA.
Sebastian CarronLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA.
Benedikt J DaurerLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Ken FergusonLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA.
Dirk HasseLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Jacek KrzywinskiLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA.
Daniel S D LarssonLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Andrew MorganCenter for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.
Kerstin MühligLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Maria MüllerInstitut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
Carl NettelbladLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Alberto PietriniLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Hemanth K N ReddyLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Daniela RuppInstitut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
Mario SauppeInstitut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
Marvin SeibertLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Martin SvendaLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Michelle SwiggersLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA.
Nicusor TimneanuLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Anatoli UlmerInstitut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
Daniel WestphalLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Garth WilliamsLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA.
Alessandro ZaniLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Gyula FaigelResearch Institute for Solid State Physics and Optics, 1525 Budapest, Hungary.
Henry N ChapmanCenter for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.
Thomas MöllerInstitut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
Christoph BostedtLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA.
Janos HajduLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
Tais GorkhoverLinac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, California 94309, USA.
Filipe R N C MaiaLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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.

Indexed as

coherent diffractive imagingimage reconstructionLCLSMelbournevirusXFELs

Identifiers

PMID30224956
PMCPMC6126651

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