Healing X-ray scattering images

Liu, Jiliang; Lhermitte, Julien; Tian, Ye; Zhang, Zheng; Yu, Dantong; Yager, Kevin G.

doi:10.1107/S2052252517006212

Title: Healing X-ray scattering images

Journal Article · Wed May 24 00:00:00 EDT 2017 · IUCrJ

DOI:https://doi.org/10.1107/S2052252517006212· OSTI ID:1425008

^[1];

^[1]; Tian, Ye ^[1]; Zhang, Zheng ^[1]; Yu, Dantong ^[2]; Yager, Kevin G. ^[1]

Brookhaven National Lab. (BNL), Upton, NY (United States). Center for Functional Nanomaterials (CFN)
Brookhaven National Lab. (BNL), Upton, NY (United States). Computational Science Center; New Jersey Inst. of Technology, Newark, NJ (United States)

X-ray scattering images contain numerous gaps and defects arising from detector limitations and experimental configuration. Here, we present a method to heal X-ray scattering images, filling gaps in the data and removing defects in a physically meaningful manner. Unlike generic inpainting methods, this method is closely tuned to the expected structure of reciprocal-space data. In particular, we exploit statistical tests and symmetry analysis to identify the structure of an image; we then copy, average and interpolate measured data into gaps in a way that respects the identified structure and symmetry. Importantly, the underlying analysis methods provide useful characterization of structures present in the image, including the identification of diffuseversussharp features, anisotropy and symmetry. The presented method leverages known characteristics of reciprocal space, enabling physically reasonable reconstruction even with large image gaps. The method will correspondingly fail for images that violate these underlying assumptions. The method assumes point symmetry and is thus applicable to small-angle X-ray scattering (SAXS) data, but only to a subset of wide-angle data. Our method succeeds in filling gaps and healing defects in experimental images, including extending data beyond the original detector borders.

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Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: SC0012704

OSTI ID:: 1425008

Report Number(s):: BNL-114830-2017-JAAM; IUCRAJ

Journal Information:: IUCrJ, Vol. 4, Issue 4; ISSN 2052-2525

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 8 works

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References (53)

X-ray cross-correlation analysis and local symmetries of disordered systems: General theory Altarelli, M.; Kurta, R. P.; Vartanyants, I. A. Physical Review B, Vol. 82, Issue 10 https://doi.org/10.1103/PhysRevB.82.104207	journal	September 2010
Quantification of Thin Film Crystallographic Orientation Using X-ray Diffraction with an Area Detector Baker, Jessy L.; Jimison, Leslie H.; Mannsfeld, Stefan Langmuir, Vol. 26, Issue 11 https://doi.org/10.1021/la904840q	journal	June 2010
Simultaneous structure and texture image inpainting Bertalmio, M.; Vese, L.; Sapiro, G. IEEE Transactions on Image Processing, Vol. 12, Issue 8 https://doi.org/10.1109/TIP.2003.815261	journal	August 2003
Small-Angle X-Ray Scattering on Biological Macromolecules and Nanocomposites in Solution Blanchet, Clement E.; Svergun, Dmitri I. Annual Review of Physical Chemistry, Vol. 64, Issue 1 https://doi.org/10.1146/annurev-physchem-040412-110132	journal	April 2013
Simulating X-ray diffraction of textured films Breiby, Dag W.; Bunk, Oliver; Andreasen, Jens W. Journal of Applied Crystallography, Vol. 41, Issue 2 https://doi.org/10.1107/S0021889808001064	journal	March 2008
Grazing-incidence small-angle X-ray scattering from thin polymer films with lamellar structures – the scattering cross section in the distorted-wave Born approximation Busch, P.; Rauscher, M.; Smilgies, D. -M. Journal of Applied Crystallography, Vol. 39, Issue 3 https://doi.org/10.1107/S0021889806012337	journal	May 2006
Combining anisotropic diffusion, transport equation and texture synthesis for inpainting textured images Casaca, Wallace; Boaventura, Maurílio; de Almeida, Marcos Proença Pattern Recognition Letters, Vol. 36 https://doi.org/10.1016/j.patrec.2013.08.023	journal	January 2014
Small-Angle X-ray Scattering of Polymers Chu, Benjamin; Hsiao, Benjamin S. Chemical Reviews, Vol. 101, Issue 6 https://doi.org/10.1021/cr9900376	journal	June 2001
Region Filling and Object Removal by Exemplar-Based Image Inpainting Criminisi, A.; Perez, P.; Toyama, K. IEEE Transactions on Image Processing, Vol. 13, Issue 9 https://doi.org/10.1109/TIP.2004.833105	journal	September 2004
Synchrotron X-ray techniques for the investigation of structures and dynamics in interfacial systems Cristofolini, Luigi Current Opinion in Colloid & Interface Science, Vol. 19, Issue 3 https://doi.org/10.1016/j.cocis.2014.03.006	journal	June 2014
Nanostructure as seen by the SAXS Dubček, P. Vacuum, Vol. 80, Issue 1-3 https://doi.org/10.1016/j.vacuum.2005.07.045	journal	October 2005
Small-angle scattering in materials science - a short review of applications in alloys, ceramics and composite materials Fratzl, Peter Journal of Applied Crystallography, Vol. 36, Issue 3 https://doi.org/10.1107/S0021889803000335	journal	April 2003
The symmetries of image formation by scattering I Theoretical framework Giannakis, Dimitrios; Schwander, Peter; Ourmazd, Abbas Optics Express, Vol. 20, Issue 12 https://doi.org/10.1364/OE.20.012799	journal	January 2012
Singular value decomposition and least squares solutions Golub, G. H.; Reinsch, C. Numerische Mathematik, Vol. 14, Issue 5 https://doi.org/10.1007/BF02163027	journal	April 1970
FIT2D : a multi-purpose data reduction, analysis and visualization program Hammersley, A. P. Journal of Applied Crystallography, Vol. 49, Issue 2 https://doi.org/10.1107/S1600576716000455	journal	March 2016
Advanced grazing-incidence techniques for modern soft-matter materials analysis Hexemer, Alexander; Müller-Buschbaum, Peter IUCrJ, Vol. 2, Issue 1 https://doi.org/10.1107/S2052252514024178	journal	January 2015
Recent developments in polymer applications of small-angle neutron, X-ray and light scattering Higgins, J. S.; Stein, R. S. Journal of Applied Crystallography, Vol. 11, Issue 5 https://doi.org/10.1107/S0021889878013485	journal	October 1978
Matplotlib: A 2D Graphics Environment Hunter, John D. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.55	journal	January 2007
Statistical measures of spottiness in diffraction rings Ingham, Bridget Journal of Applied Crystallography, Vol. 47, Issue 1 https://doi.org/10.1107/S1600576713029713	journal	December 2013
X-ray scattering characterisation of nanoparticles Ingham, Bridget Crystallography Reviews, Vol. 21, Issue 4 https://doi.org/10.1080/0889311X.2015.1024114	journal	June 2015
Small-angle scattering for structural biology-Expanding the frontier while avoiding the pitfalls Jacques, David A.; Trewhella, Jill Protein Science, Vol. 19, Issue 4 https://doi.org/10.1002/pro.351	journal	January 2010
GIXSGUI : a MATLAB toolbox for grazing-incidence X-ray scattering data visualization and reduction, and indexing of buried three-dimensional periodic nanostructured films Jiang, Zhang Journal of Applied Crystallography, Vol. 48, Issue 3 https://doi.org/10.1107/S1600576715004434	journal	April 2015
The state of the NeXus data format Könnecke, Mark Physica B: Condensed Matter, Vol. 385-386 https://doi.org/10.1016/j.physb.2006.06.106	journal	November 2006
The NeXus data format Könnecke, Mark; Akeroyd, Frederick A.; Bernstein, Herbert J. Journal of Applied Crystallography, Vol. 48, Issue 1 https://doi.org/10.1107/S1600576714027575	journal	January 2015
Raw diffraction data preservation and reuse: overview, update on practicalities and metadata requirements Kroon-Batenburg, Loes M. J.; Helliwell, John R.; McMahon, Brian IUCrJ, Vol. 4, Issue 1 https://doi.org/10.1107/S2052252516018315	journal	January 2017
Solution of the phase problem for coherent scattering from a disordered system of identical particles Kurta, R. P.; Dronyak, R.; Altarelli, M. New Journal of Physics, Vol. 15, Issue 1 https://doi.org/10.1088/1367-2630/15/1/013059	journal	January 2013
Gradient-based learning applied to document recognition Lecun, Y.; Bottou, L.; Bengio, Y. Proceedings of the IEEE, Vol. 86, Issue 11 https://doi.org/10.1109/5.726791	journal	January 1998
Detecting orientational order in model systems by X-ray cross-correlation methods Lehmkühler, Felix; Grübel, Gerhard; Gutt, Christian Journal of Applied Crystallography, Vol. 47, Issue 4 https://doi.org/10.1107/S1600576714012424	journal	July 2014
Robust X-ray angular correlations for the study of meso-structures Lhermitte, Julien R.; Tian, Cheng; Stein, Aaron Journal of Applied Crystallography, Vol. 50, Issue 3 https://doi.org/10.1107/S1600576717003946	journal	May 2017
Small Angle X-ray Scattering for Nanoparticle Research Li, Tao; Senesi, Andrew J.; Lee, Byeongdu Chemical Reviews, Vol. 116, Issue 18 https://doi.org/10.1021/acs.chemrev.5b00690	journal	April 2016
Amyloid structure exhibits polymorphism on multiple length scales in human brain tissue Liu, Jiliang; Costantino, Isabel; Venugopalan, Nagarajan Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep33079	journal	September 2016
The impact of alterations in lignin deposition on cellulose organization of the plant cell wall Liu, Jiliang; Kim, Jeong Im; Cusumano, Joanne C. Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0540-z	journal	June 2016
Grazing-incidence transmission X-ray scattering: surface scattering in the Born approximation Lu, Xinhui; Yager, Kevin G.; Johnston, Danvers Journal of Applied Crystallography, Vol. 46, Issue 1 https://doi.org/10.1107/S0021889812047887	journal	January 2013
Rapid ordering of block copolymer thin films Majewski, Pawel W.; Yager, Kevin G. Journal of Physics: Condensed Matter, Vol. 28, Issue 40 https://doi.org/10.1088/0953-8984/28/40/403002	journal	August 2016
Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure Mendez, Derek; Watkins, Herschel; Qiao, Shenglan IUCrJ, Vol. 3, Issue 6, p. 420-429 https://doi.org/10.1107/S2052252516013956	journal	September 2016
Grazing incidence small-angle X-ray scattering: an advanced scattering technique for the investigation of nanostructured polymer films Müller-Buschbaum, P. Analytical and Bioanalytical Chemistry, Vol. 376, Issue 1 https://doi.org/10.1007/s00216-003-1869-2	journal	March 2003
GISAXS and GISANS as metrology technique for understanding the 3D morphology of block copolymer thin films Müller-Buschbaum, Peter European Polymer Journal, Vol. 81 https://doi.org/10.1016/j.eurpolymj.2016.04.007	journal	August 2016
Python for Scientific Computing Oliphant, Travis E. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.58	journal	January 2007
Serial femtosecond crystallography: the first five years Schlichting, Ilme IUCrJ, Vol. 2, Issue 2, p. 246-255 https://doi.org/10.1107/S205225251402702X	journal	February 2015
The symmetries of image formation by scattering II Applications Schwander, Peter; Giannakis, Dimitrios; Yoon, Chun Hong Optics Express, Vol. 20, Issue 12 https://doi.org/10.1364/OE.20.012827	journal	January 2012
Small-angle scattering of particle assemblies Senesi, Andrew J.; Lee, Byeongdu Journal of Applied Crystallography, Vol. 48, Issue 4 https://doi.org/10.1107/S1600576715011474	journal	July 2015
Characterization of polymer thin films with small‐angle X‐ray scattering under grazing incidence (GISAXS) Smilgies, Detlef‐M.; Busch, Peter; Papadakis, Christine M. Synchrotron Radiation News, Vol. 15, Issue 5 https://doi.org/10.1080/08940880208602975	journal	September 2002
Lattice engineering through nanoparticle–DNA frameworks Tian, Ye; Zhang, Yugang; Wang, Tong Nature Materials, Vol. 15, Issue 6, p. 654-661 https://doi.org/10.1038/nmat4571	journal	February 2016
scikit-image: image processing in Python van der Walt, Stéfan; Schönberger, Johannes L.; Nunez-Iglesias, Juan PeerJ, Vol. 2 https://doi.org/10.7717/peerj.453	journal	January 2014
Modeling Textures with Total Variation Minimization and Oscillating Patterns in Image Processing Vese, Luminita A.; Osher, Stanley J. Journal of Scientific Computing, Vol. 19, Issue 1/3, p. 553-572 https://doi.org/10.1023/A:1025384832106	journal	December 2003
The potential of future light sources to explore the structure and function of matter Weckert, Edgar IUCrJ, Vol. 2, Issue 2 https://doi.org/10.1107/S2052252514024269	journal	February 2015
X-ray cross correlation analysis uncovers hidden local symmetries in disordered matter Wochner, Peter; Gutt, Christian; Autenrieth, Tina Proceedings of the National Academy of Sciences, Vol. 106, Issue 28 https://doi.org/10.1073/pnas.0905337106	journal	June 2009
Metrics of graininess: robust quantification of grain count from the non-uniformity of scattering rings Yager, Kevin G.; Majewski, Pawel W. Journal of Applied Crystallography, Vol. 47, Issue 6 https://doi.org/10.1107/S1600576714020822	journal	October 2014
Periodic lattices of arbitrary nano-objects: modeling and applications for self-assembled systems Yager, Kevin G.; Zhang, Yugang; Lu, Fang Journal of Applied Crystallography, Vol. 47, Issue 1 https://doi.org/10.1107/S160057671302832X	journal	December 2013
Using an in-vacuum CCD detector for simultaneous small- and wide-angle scattering at beamline X9 Yang, Lin Journal of Synchrotron Radiation, Vol. 20, Issue 2 https://doi.org/10.1107/S0909049512048984	journal	January 2013
Methods for SAXS-Based Structure Determination of Biomolecular Complexes Yang, Sichun Advanced Materials, Vol. 26, Issue 46 https://doi.org/10.1002/adma.201304475	journal	May 2014
Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering Yoon, Chun Hong; Schwander, Peter; Abergel, Chantal Optics Express, Vol. 19, Issue 17 https://doi.org/10.1364/OE.19.016542	journal	January 2011
Dataset of Synthetic X-ray Scattering Images for Classification Using Deep Learning Yager, Kevin G.; Lhermitte, Julien; Yu, Dantong Materials Data Facility https://doi.org/10.18126/m2z30z	dataset	January 2017

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