Search: onr:"swepub:oai:research.chalmers.se:72a06475-72db-40aa-9ab8-36fbc5508d9b" >
Considerations for ...
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Lundholm, Ida V.Uppsala universitet,Molekylär biofysik
(author)
Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
- Article/chapterEnglish2018
Publisher, publication year, extent ...
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International Union of Crystallography,2018
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electronicrdacarrier
Numbers
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LIBRIS-ID:oai:research.chalmers.se:72a06475-72db-40aa-9ab8-36fbc5508d9b
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https://research.chalmers.se/publication/505023URI
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https://doi.org/10.1107/S2052252518010047DOI
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https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-235456URI
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-360034URI
Supplementary language notes
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Language:English
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Summary in:English
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Classification
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Subject category:art swepub-publicationtype
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Subject category:ref swepub-contenttype
Notes
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QC 20180927
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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.
Subject headings and genre
Added entries (persons, corporate bodies, meetings, titles ...)
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Sellberg, Jonas A.KTH,Biomedicinsk fysik och röntgenfysik(Swepub:kth)u1ynvdbz
(author)
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Ekeberg, TomasUppsala universitet,Molekylär biofysik(Swepub:uu)tomek611
(author)
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Hantke, Max F.University Of Oxford,Univ Oxford, Oxford, England.(Swepub:uu)maxha207
(author)
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Okamoto, KentaUppsala universitet,Molekylär biofysik(Swepub:uu)kenok266
(author)
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van der Schot, GijsUppsala universitet,Molekylär biofysik(Swepub:uu)gijva150
(author)
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Andreasson, Jakob,1975Uppsala universitet,Molekylär biofysik(Swepub:uu)jakan998
(author)
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Barty, AntonDeutsches Elektronen-Synchrotron (DESY),DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
(author)
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Bielecki, JohanUppsala universitet,Molekylär biofysik(Swepub:uu)johbi267
(author)
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Bruza, PetrChalmers tekniska högskola,Chalmers University of Technology,Chalmers Univ Technol, Dept Phys, Condensed Matter Phys, Gothenburg, Sweden.
(author)
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Bucher, MaxArgonne National Laboratory,Technische Universität Berlin,Stanford University,SLAC Natl Accelerator Lab, Linac Coherent Light Source, Stanford, CA 94309 USA.;Tech Univ Berlin, Inst Opt & Atomare Phys, Hardenbergstr 36, D-10623 Berlin, Germany.;Argonne Natl Lab, Chem Sci & Engn Div, 9700 South Cass Ave, Lemont, IL 60439 USA.
(author)
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Carron, SebastianStanford University,SLAC Natl Accelerator Lab, Linac Coherent Light Source, Stanford, CA 94309 USA.
(author)
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Daurer, Benedikt J.Uppsala universitet,Molekylär biofysik(Swepub:uu)jakda870
(author)
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Ferguson, KenStanford University,SLAC Natl Accelerator Lab, Linac Coherent Light Source, Stanford, CA 94309 USA.;PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.
(author)
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Hasse, DirkUppsala universitet,Molekylär biofysik(Swepub:uu)dirha931
(author)
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Krzywinski, JacekStanford University,SLAC Natl Accelerator Lab, Linac Coherent Light Source, Stanford, CA 94309 USA.
(author)
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Larsson, Daniel S. D.Uppsala universitet,Molekylär biofysik(Swepub:uu)dalar193
(author)
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Morgan, AndrewDeutsches Elektronen-Synchrotron (DESY),DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
(author)
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Mühlig, KerstinUppsala universitet,Molekylär biofysik(Swepub:uu)kermu539
(author)
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Mueller, MariaTechnische Universität Berlin,Tech Univ Berlin, Inst Opt & Atomare Phys, Hardenbergstr 36, D-10623 Berlin, Germany.
(author)
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Nettelblad, CarlUppsala universitet,Molekylär biofysik,Science for Life Laboratory, SciLifeLab(Swepub:uu)fimai103
(author)
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Pietrini, AlbertoUppsala universitet,Molekylär biofysik(Swepub:uu)albpi258
(author)
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Reddy, Hemanth K. N.Uppsala universitet,Molekylär biofysik(Swepub:uu)hemna453
(author)
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Rupp, DanielaTechnische Universität Berlin,Tech Univ Berlin, Inst Opt & Atomare Phys, Hardenbergstr 36, D-10623 Berlin, Germany.
(author)
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Sauppe, MarioTechnische Universität Berlin,Tech Univ Berlin, Inst Opt & Atomare Phys, Hardenbergstr 36, D-10623 Berlin, Germany.
(author)
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Seibert, MarvinUppsala universitet,Molekylär biofysik(Swepub:uu)masei255
(author)
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Svenda, MartinUppsala universitet,Molekylär biofysik(Swepub:uu)msv31659
(author)
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Swiggers, MichelleStanford University,SLAC Natl Accelerator Lab, Linac Coherent Light Source, Stanford, CA 94309 USA.
(author)
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Timneanu, NicusorUppsala universitet,Molekylär biofysik,Molekyl- och kondenserade materiens fysik(Swepub:uu)nti19847
(author)
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Ulmer, AnatoliTechnische Universität Berlin,Tech Univ Berlin, Inst Opt & Atomare Phys, Hardenbergstr 36, D-10623 Berlin, Germany.
(author)
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Westphal, DanielUppsala universitet,Molekylär biofysik(Swepub:uu)danwe345
(author)
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Williams, GarthBrookhaven National Laboratory,Stanford University,SLAC Natl Accelerator Lab, Linac Coherent Light Source, Stanford, CA 94309 USA.;Brookhaven Natl Lab, NSLS 2, POB 5000, Upton, NY 11973 USA.
(author)
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Zani, AlessandroUppsala universitet,Molekylär biofysik(Swepub:uu)aleza299
(author)
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Faigel, GyulaMagyar Tudomanyos Akademia,Hungarian Academy of Sciences,Res Inst Solid State Phys & Opt, H-1525 Budapest, Hungary.
(author)
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Chapman, Henry N.Deutsches Elektronen-Synchrotron (DESY),DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
(author)
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Moeller, ThomasTechnische Universität Berlin,Tech Univ Berlin, Inst Opt & Atomare Phys, Hardenbergstr 36, D-10623 Berlin, Germany.
(author)
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Bostedt, ChristophNorthwestern University,Stanford University,Argonne National Laboratory,SLAC Natl Accelerator Lab, Linac Coherent Light Source, Stanford, CA 94309 USA.;Argonne Natl Lab, Chem Sci & Engn Div, 9700 South Cass Ave, Lemont, IL 60439 USA.;PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;Northwestern Univ, Dept Phys, 2145 Sheridan Rd, Evanston, IL 60208 USA.
(author)
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Hajdu, JanosUppsala universitet,Molekylär biofysik(Swepub:uu)janohajd
(author)
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Gorkhover, TaisStanford University,Technische Universität Berlin,Tech Univ Berlin, Inst Opt & Atomare Phys, Hardenbergstr 36, D-10623 Berlin, Germany.;PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.
(author)
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Maia, Filipe R. N. C.Lawrence Berkeley National Laboratory,Uppsala universitet,Uppsala University
(author)
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Uppsala universitetMolekylär biofysik
(creator_code:org_t)
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In:IUCrJ: International Union of Crystallography5, s. 531-5412052-2525
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Lundholm, Ida V.
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Sellberg, Jonas ...
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Ekeberg, Tomas
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Hantke, Max F.
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Okamoto, Kenta
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van der Schot, G ...
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Andreasson, Jako ...
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Barty, Anton
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Bielecki, Johan
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Bruza, Petr
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Bucher, Max
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Carron, Sebastia ...
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Daurer, Benedikt ...
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Ferguson, Ken
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Hasse, Dirk
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Krzywinski, Jace ...
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Larsson, Daniel ...
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Morgan, Andrew
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Mühlig, Kerstin
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Mueller, Maria
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Nettelblad, Carl
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Pietrini, Albert ...
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Reddy, Hemanth K ...
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Rupp, Daniela
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Sauppe, Mario
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Seibert, Marvin
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Svenda, Martin
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Swiggers, Michel ...
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Timneanu, Nicuso ...
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Ulmer, Anatoli
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Westphal, Daniel
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Williams, Garth
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Zani, Alessandro
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Faigel, Gyula
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Chapman, Henry N ...
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Moeller, Thomas
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Bostedt, Christo ...
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Hajdu, Janos
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Gorkhover, Tais
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Maia, Filipe R. ...
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