Identifying Defects with Guided Algorithms in Bragg Coherent Diffractive Imaging

Ulvestad, A.; Nashed, Y.; Beutier, G.; Verdier, M.; Hruszkewycz, S. O.; Dupraz, M.

doi:10.1038/s41598-017-09582-7

Title: Identifying Defects with Guided Algorithms in Bragg Coherent Diffractive Imaging

Journal Article · Wed Aug 30 00:00:00 EDT 2017 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-017-09582-7· OSTI ID:1395865

^[1]; Nashed, Y. ^[1]; Beutier, G. ^[2]; Verdier, M. ^[2]; Hruszkewycz, S. O. ^[1]; Dupraz, M. ^[3]

Argonne National Lab. (ANL), Argonne, IL (United States)
Univ. Grenoble Alpes, Grenoble (France)
Paul Scherrer Inst. (PSI), Villigen (Switzerland)

In this study, crystallographic defects such as dislocations can significantly alter material properties and functionality. However, imaging these imperfections during operation remains challenging due to the short length scales involved and the reactive environments of interest. Bragg coherent diffractive imaging (BCDI) has emerged as a powerful tool capable of identifying dislocations, twin domains, and other defects in 3D detail with nanometer spatial resolution within nanocrystals and grains in reactive environments. However, BCDI relies on phase retrieval algorithms that can fail to accurately reconstruct the defect network. Here, we use numerical simulations to explore different guided phase retrieval algorithms for imaging defective crystals using BCDI. We explore different defect types, defect densities, Bragg peaks, and guided algorithm fitness metrics as a function of signal-to-noise ratio. Based on these results, we offer a general prescription for phasing of defective crystals with no a prior knowledge.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22), Materials Sciences and Engineering Division

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1395865

Journal Information:: Scientific Reports, Vol. 7, Issue 1; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 19 works

Citation information provided by
Web of Science

References (58)

Influence of Noise and Missing Data on Reconstruction Quality in Coherent X‐ray Diffractive Imaging Tripathi, A.; Shpyrko, O.; McNulty, I. THE 10TH INTERNATIONAL CONFERENCE ON X‐RAY MICROSCOPY, AIP Conference Proceedings https://doi.org/10.1063/1.3625365	conference	January 2011
Inversion of the Diffraction Pattern from an Inhomogeneously Strained Crystal using an Iterative Algorithm Minkevich, A. A.; Gailhanou, M.; Micha, J. -S. arXiv https://doi.org/10.48550/arxiv.cond-mat/0609162	text	January 2006
Avalanching strain dynamics during the hydriding phase transformation in individual palladium nanoparticles Ulvestad, A.; Welland, M. J.; Collins, S. S. E. Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms10092	journal	December 2015
Electron tomography at 2.4-ångström resolution Scott, M. C.; Chen, Chien-Chun; Mecklenburg, Matthew Nature, Vol. 483, Issue 7390 https://doi.org/10.1038/nature10934	journal	March 2012
Maximum-likelihood refinement for coherent diffractive imaging Thibault, P.; Guizar-Sicairos, M. New Journal of Physics, Vol. 14, Issue 6 https://doi.org/10.1088/1367-2630/14/6/063004	journal	June 2012
Three-dimensional imaging of strain in a single ZnO nanorod Newton, Marcus C.; Leake, Steven J.; Harder, Ross Nature Materials, Vol. 9, Issue 2 https://doi.org/10.1038/nmat2607	journal	December 2009
Signal-to-noise and radiation exposure considerations in conventional and diffraction x-ray microscopy Huang, Xiaojing; Miao, Huijie; Steinbrener, Jan Optics Express, Vol. 17, Issue 16 https://doi.org/10.1364/OE.17.013541	journal	January 2009
Topological defect dynamics in operando battery nanoparticles Ulvestad, A.; Singer, A.; Clark, J. N. Science, Vol. 348, Issue 6241 https://doi.org/10.1126/science.aaa1313	journal	June 2015
Performance evaluation of Bragg coherent diffraction imaging Ozturk, Hande; Huang, X.; Yan, H. Columbia University https://doi.org/10.7916/d8vh70tc	text	January 2017
Performance evaluation of Bragg coherent diffraction imaging Öztürk, H.; Huang, X.; Yan, H. New Journal of Physics, Vol. 19, Issue 10 https://doi.org/10.1088/1367-2630/aa83a9	journal	October 2017
Crystal plasticity and hardening: A dislocation dynamics study Gaucherin, Guillaume; Hofmann, Felix; Belnoue, Jonathan P. Procedia Engineering, Vol. 1, Issue 1 https://doi.org/10.1016/j.proeng.2009.06.057	journal	July 2009
Multiscale modelling of indentation in FCC metals: From atomic to continuum Chang, Hyung-Jun; Fivel, Marc; Rodney, David Comptes Rendus Physique, Vol. 11, Issue 3-4 https://doi.org/10.1016/j.crhy.2010.07.007	journal	April 2010
Electron Microscopy of Thin Crystals Hirsch, P. B.; Howie, A.; Nicholson, R. B. Physics Today, Vol. 19, Issue 10 https://doi.org/10.1063/1.3047787	journal	October 1966
Strain-relief by single dislocation loops in calcite crystals grown on self-assembled monolayers Ihli, Johannes; Clark, Jesse N.; Côté, Alexander S. Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2017-00397	text	January 2016
Retrieving the displacement of strained nanoobjects: the impact of bounds for the scattering magnitude in direct space Köhl, Martin; Schroth, Philipp; Minkevich, A. A. Karlsruhe https://doi.org/10.5445/ir/1000038786	text	January 2013
Applicability of an iterative inversion algorithm to the diffraction patterns from inhomogeneously strained crystals Minkevich, A. A.; Baumbach, T.; Gailhanou, M. Physical Review B, Vol. 78, Issue 17 https://doi.org/10.1103/physrevb.78.174110	journal	November 2008
Noise models for low counting rate coherent diffraction imaging Godard, Pierre; Allain, Marc; Chamard, Virginie Optics Express, Vol. 20, Issue 23 https://doi.org/10.1364/OE.20.025914	journal	January 2012
The influence of dislocations on crystal growth Frank, F. C. Discussions of the Faraday Society, Vol. 5 https://doi.org/10.1039/df9490500048	journal	January 1949
X-Ray topographs of diamond Ramachandran, G. N. Proceedings of the Indian Academy of Sciences - Section A, Vol. 19, Issue 5 https://doi.org/10.1007/BF03173455	journal	May 1944
Electron microscopy of thin crystals Haine, Me Vacuum, Vol. 16, Issue 4 https://doi.org/10.1016/0042-207x(66)91170-5	journal	April 1966
Defect-Rich Metal Nanocrystals in Catalysis Xie, Shuifen; Xu, Qingchi; Huang, Xiaoqing ChemCatChem, Vol. 8, Issue 3 https://doi.org/10.1002/cctc.201500979	journal	December 2015
Measurement of the displacement field of dislocations to 0.03 Å by electron microscopy Hÿtch, Martin J.; Putaux, Jean-Luc; Pénisson, Jean-Michel Nature, Vol. 423, Issue 6937 https://doi.org/10.1038/nature01638	journal	May 2003
Atomic electron tomography: 3D structures without crystals Miao, J.; Ercius, P.; Billinge, S. J. L. Science, Vol. 353, Issue 6306 https://doi.org/10.1126/science.aaf2157	journal	September 2016
New insights into single-grain mechanical behavior from temperature-dependent 3-D coherent X-ray diffraction Vaxelaire, N.; Labat, S.; Cornelius, T. W. Acta Materialia, Vol. 78 https://doi.org/10.1016/j.actamat.2014.06.008	journal	October 2014
Facing the phase problem in Coherent Diffractive Imaging via Memetic Algorithms Colombo, Alessandro; Galli, Davide Emilio; De Caro, Liberato Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep42236	journal	February 2017
X-ray image reconstruction from a diffraction pattern alone Marchesini, S.; He, H.; Chapman, H. N. Physical Review B, Vol. 68, Issue 14 https://doi.org/10.1103/PhysRevB.68.140101	journal	October 2003
Nanoscale mapping of ion diffusion in a lithium-ion battery cathode Balke, N.; Jesse, S.; Morozovska, A. N. Nature Nanotechnology, Vol. 5, Issue 10 https://doi.org/10.1038/nnano.2010.174	journal	August 2010
Stability Limits and Defect Dynamics in Ag Nanoparticles Probed by Bragg Coherent Diffractive Imaging Liu, Y.; Lopes, P. P.; Cha, W. Nano Letters, Vol. 17, Issue 3 https://doi.org/10.1021/acs.nanolett.6b04760	journal	February 2017
Grain boundary segregation, stress and stretch: Effects on hydrogen absorption in nanocrystalline palladium Lemier, C.; Weissmüller, J. Acta Materialia, Vol. 55, Issue 4, p. 1241-1254 https://doi.org/10.1016/j.actamat.2006.09.030	journal	February 2007
Imaging the displacement field within epitaxial nanostructures by coherent diffraction: a feasibility study Diaz, Ana; Chamard, Virginie; Mocuta, Cristian New Journal of Physics, Vol. 12, Issue 3 https://doi.org/10.1088/1367-2630/12/3/035006	journal	March 2010
A general algorithm for generating isotropy subgroups in superspace Stokes, Harold T.; Campbell, Branton J. Acta Crystallographica Section A Foundations and Advances, Vol. 73, Issue 1 https://doi.org/10.1107/s2053273316017629	journal	January 2017
Three-dimensional imaging of dislocation dynamics during the hydriding phase transformation Ulvestad, A.; Welland, M. J.; Cha, W. Nature Materials, Vol. 16, Issue 5 https://doi.org/10.1038/nmat4842	journal	January 2017
Grain-Boundary-Dependent CO ₂ Electroreduction Activity Feng, Xiaofeng; Jiang, Kaili; Fan, Shoushan Journal of the American Chemical Society, Vol. 137, Issue 14 https://doi.org/10.1021/ja5130513	journal	April 2015
How many photons are needed to reconstruct random objects in coherent X-ray diffractive imaging? Jahn, T.; Wilke, R. N.; Chushkin, Y. Acta Crystallographica Section A Foundations and Advances, Vol. 73, Issue 1 https://doi.org/10.1107/S2053273316015114	journal	January 2017
Electron microscopy of thin crystals Cahn, B. W. Journal of Nuclear Materials, Vol. 21, Issue 3 https://doi.org/10.1016/0022-3115(67)90194-8	journal	March 1967
In situ study of annealing-induced strain relaxation in diamond nanoparticles using Bragg coherent diffraction imaging Hruszkewycz, S. O.; Cha, W.; Andrich, P. APL Materials, Vol. 5, Issue 2 https://doi.org/10.1063/1.4974865	journal	February 2017
Bragg coherent diffractive imaging of single-grain defect dynamics in polycrystalline films Yau, Allison; Cha, Wonsuk; Kanan, Matthew W. Science, Vol. 356, Issue 6339 https://doi.org/10.1126/science.aam6168	journal	May 2017
Synchrotron x-ray reticulography: principles and applications Lang, A. R.; Makepeace, A. P. W. Journal of Physics D: Applied Physics, Vol. 32, Issue 10A https://doi.org/10.1088/0022-3727/32/10a/321	journal	January 1999
Method for the Detection of Dislocations in Silicon by X-Ray Extinction Contrast Newkirk, J. B. Physical Review, Vol. 110, Issue 6 https://doi.org/10.1103/physrev.110.1465	journal	June 1958
Phase retrieval algorithms: a comparison Fienup, J. R. Applied Optics, Vol. 21, Issue 15 https://doi.org/10.1364/AO.21.002758	journal	January 1982
Enhanced hardening in Cu/330 stainless steel multilayers by nanoscale twinning Zhang, X.; Misra, A.; Wang, H. Acta Materialia, Vol. 52, Issue 4 https://doi.org/10.1016/j.actamat.2003.10.033	journal	February 2004
Inversion of the diffraction pattern from an inhomogeneously strained crystal using an iterative algorithm Minkevich, A. A.; Gailhanou, M.; Micha, J. -S. Physical Review B, Vol. 76, Issue 10 https://doi.org/10.1103/physrevb.76.104106	journal	September 2007
Visualizing and Improving the Robustness of Phase Retrieval Algorithms Tripathi, Ashish; Leyffer, Sven; Munson, Todd Procedia Computer Science, Vol. 51 https://doi.org/10.1016/j.procs.2015.05.205	journal	January 2015
High-resolution three-dimensional structural microscopy by single-angle Bragg ptychography Hruszkewycz, S. O.; Allain, M.; Holt, M. V. Nature Materials, Vol. 16, Issue 2 https://doi.org/10.1038/nmat4798	journal	November 2016
Signature of dislocations and stacking faults of face-centred cubic nanocrystals in coherent X-ray diffraction patterns: a numerical study Dupraz, Maxime; Beutier, Guillaume; Rodney, David Journal of Applied Crystallography, Vol. 48, Issue 3 https://doi.org/10.1107/S1600576715005324	journal	April 2015
Novel silica stabilization method for the analysis of fine nanocrystals using coherent X-ray diffraction imaging Monteforte, Marianne; Estandarte, Ana K.; Chen, Bo Journal of Synchrotron Radiation, Vol. 23, Issue 4 https://doi.org/10.1107/s1600577516006408	journal	June 2016
Coherent diffractive imaging of time-evolving samples with improved temporal resolution Ulvestad, A.; Tripathi, A.; Hruszkewycz, S. O. Physical Review B, Vol. 93, Issue 18 https://doi.org/10.1103/PhysRevB.93.184105	journal	May 2016
Facing the phase problem in Coherent Diffractive Imaging via Memetic Algorithms Colombo, Alessandro; Galli, Davide Emilio; De Caro, Liberato arXiv https://doi.org/10.48550/arxiv.1701.07685	text	January 2017
Strain-relief by single dislocation loops in calcite crystals grown on self-assembled monolayers Ihli, Johannes; Clark, Jesse N.; Côté, Alexander S. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11878	journal	June 2016
Retrieving the displacement of strained nanoobjects: the impact of bounds for the scattering magnitude in direct space Köhl, Martin; Schroth, Philipp; Minkevich, A. A. Optics Express, Vol. 21, Issue 23 https://doi.org/10.1364/OE.21.027734	journal	January 2013
The role of dislocations and surface morphology in calcite dissolution MacInnis, Ian N.; Brantley, Susan L. Geochimica et Cosmochimica Acta, Vol. 56, Issue 3 https://doi.org/10.1016/0016-7037(92)90049-o	journal	March 1992
Invited Article: A unified evaluation of iterative projection algorithms for phase retrieval Marchesini, S. Review of Scientific Instruments, Vol. 78, Issue 1 https://doi.org/10.1063/1.2403783	journal	January 2007
Three-dimensional imaging of dislocation propagation during crystal growth and dissolution Clark, Jesse N.; Ihli, Johannes; Schenk, Anna S. Nature Materials, Vol. 14, Issue 8 https://doi.org/10.1038/nmat4320	journal	June 2015
Bulk Dislocation Core Dissociation Probed by Coherent X Rays in Silicon Jacques, V. L. R.; Ravy, S.; Le Bolloc’h, D. Physical Review Letters, Vol. 106, Issue 6 https://doi.org/10.1103/PhysRevLett.106.065502	journal	February 2011
Bragg x-ray ptychography of a silicon crystal: Visualization of the dislocation strain field and the production of a vortex beam Takahashi, Yukio; Suzuki, Akihiro; Furutaku, Shin Physical Review B, Vol. 87, Issue 12 https://doi.org/10.1103/PhysRevB.87.121201	journal	March 2013
Application of optimization technique to noncrystalline x-ray diffraction microscopy: Guided hybrid input-output method Chen, Chien-Chun; Miao, Jianwei; Wang, C. W. Physical Review B, Vol. 76, Issue 6 https://doi.org/10.1103/PhysRevB.76.064113	journal	August 2007
3D lattice distortions and defect structures in ion-implanted nano-crystals Hofmann, Felix; Tarleton, Edmund; Harder, Ross J. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep45993	journal	April 2017
ArrayFire: a GPU acceleration platform Malcolm, James; Yalamanchili, Pavan; McClanahan, Chris Modeling and Simulation for Defense Systems and Applications VII https://doi.org/10.1117/12.921122	conference	May 2012

Cited By (6)

Nano-scale imaging of the full strain tensor of specific dislocations extracted from a bulk sample Hofmann, Felix; Phillips, Nicholas W.; Das, Suchandrima arXiv https://doi.org/10.48550/arxiv.1903.04079	text	January 2019
Free log-likelihood as an unbiased metric for coherent diffraction imaging Favre-Nicolin, Vincent; Leake, Steven; Chushkin, Yuriy arXiv https://doi.org/10.48550/arxiv.1904.07056	text	January 2019
Nucleation-Controlled Plasticity of Metallic Nanowires and Nanoparticles Mordehai, Dan; David, Omer; Kositski, Roman Advanced Materials, Vol. 30, Issue 41 https://doi.org/10.1002/adma.201706710	journal	July 2018
Impact and mitigation of angular uncertainties in Bragg coherent x-ray diffraction imaging Calvo-Almazán, I.; Allain, M.; Maddali, S. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-42797-4	journal	April 2019
Bragg coherent diffraction imaging of iron diffusion into gold nanocrystals Estandarte, Ana Katrina C.; Lynch, Christopher Michael; Monteforte, Marianne New Journal of Physics, Vol. 20, Issue 11 https://doi.org/10.1088/1367-2630/aaebc1	journal	November 2018
Nanoscale imaging of the full strain tensor of specific dislocations extracted from a bulk sample Hofmann, Felix; Phillips, Nicholas W.; Das, Suchandrima Physical Review Materials, Vol. 4, Issue 1 https://doi.org/10.1103/physrevmaterials.4.013801	journal	January 2020

Similar Records

Bragg coherent diffraction imaging of iron diffusion into gold nanocrystals

Journal Article · Fri Nov 16 00:00:00 EST 2018 · New Journal of Physics · OSTI ID:1395865

Estandarte, Ana Katrina C.; Lynch, Christopher Michael; Monteforte, Marianne; +3 more

Impact and mitigation of angular uncertainties in Bragg coherent x-ray diffraction imaging

Journal Article · Tue Apr 23 00:00:00 EDT 2019 · Scientific Reports · OSTI ID:1395865

Calvo-Almazán, I.; Allain, M.; Maddali, S.; +2 more

Accurate, rapid identification of dislocation lines in coherent diffractive imaging via a min-max optimization formulation

Journal Article · Wed Jan 10 00:00:00 EST 2018 · AIP Advances · OSTI ID:1395865

Ulvestad, A.; Menickelly, M.; Wild, S. M.

Related Subjects

36 MATERIALS SCIENCE

Title: Identifying Defects with Guided Algorithms in Bragg Coherent Diffractive Imaging

Citation Formats

References (58)

Cited By (6)

Similar Records

Related Subjects