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

IUCrJ ◽  
2018 ◽  
Vol 5 (5) ◽  
pp. 531-541 ◽  
Author(s):  
Ida V. Lundholm ◽  
Jonas A. Sellberg ◽  
Tomas Ekeberg ◽  
Max F. Hantke ◽  
Kenta Okamoto ◽  
...  
Keyword(s):  
Experimental Data ◽  
Phase Retrieval ◽  
Three Dimensional ◽  
Simulated Data ◽  
High Repetition Rate ◽  
Central Feature ◽  
Diffractive Imaging ◽  
X Ray ◽  
Background Removal ◽  
Diffraction Patterns

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.

scholarly journals Hard X-ray polarizer to enable simultaneous three-dimensional nanoscale imaging of magnetic structure and lattice strain

2016 ◽  
Vol 23 (5) ◽  
pp. 1210-1215 ◽  
Author(s):  
Jonathan Logan ◽  
Ross Harder ◽  
Luxi Li ◽  
Daniel Haskel ◽  
Pice Chen ◽  
...  
Keyword(s):  
Magnetic Circular Dichroism ◽  
Three Dimensional ◽  
Control Sample ◽  
Magnetic Ordering ◽  
X Rays ◽  
Diffractive Imaging ◽  
X Ray ◽  
Coherent Diffractive Imaging ◽  
Diffraction Patterns ◽  
A New Technique

Recent progress in the development of dichroic Bragg coherent diffractive imaging, a new technique for simultaneous three-dimensional imaging of strain and magnetization at the nanoscale, is reported. This progress includes the installation of a diamond X-ray phase retarder at beamline 34-ID-C of the Advanced Photon Source. The performance of the phase retarder for tuning X-ray polarization is demonstrated with temperature-dependent X-ray magnetic circular dichroism measurements on a gadolinium foil in transmission and on a Gd5Si2Ge2crystal in diffraction geometry with a partially coherent, focused X-ray beam. Feasibility tests for dichroic Bragg coherent diffractive imaging are presented. These tests include (1) using conventional Bragg coherent diffractive imaging to determine whether the phase retarder introduces aberrations using a nonmagnetic gold nanocrystal as a control sample, and (2) collecting coherent diffraction patterns of a magnetic Gd5Si2Ge2nanocrystal with left- and right-circularly polarized X-rays. Future applications of dichroic Bragg coherent diffractive imaging for the correlation of strain and lattice defects with magnetic ordering and inhomogeneities are considered.

scholarly journals A Monte Carlo ray-tracing simulation of coherent X-ray diffractive imaging

2020 ◽  
Vol 27 (1) ◽  
pp. 134-145 ◽  
Author(s):  
Giovanni Fevola ◽  
Erik Bergbäck Knudsen ◽  
Tiago Ramos ◽  
Dina Carbone ◽  
Jens Wenzel Andreasen
Keyword(s):  
Ray Tracing ◽  
Phase Retrieval ◽  
Computational Effort ◽  
Retrieval Algorithm ◽  
Theoretical Formulation ◽  
Thin Sample ◽  
Diffractive Imaging ◽  
X Ray ◽  
Coherent Diffractive Imaging ◽  
Diffraction Patterns

Coherent diffractive imaging (CDI) experiments are adequately simulated assuming the thin sample approximation and using a Fresnel or Fraunhofer wavefront propagator to obtain the diffraction pattern. Although this method is used in wave-based or hybrid X-ray simulators, here the applicability and effectiveness of an alternative approach that is based solely on ray tracing of Huygens wavelets are investigated. It is shown that diffraction fringes of a grating-like source are accurately predicted and that diffraction patterns of a ptychography dataset from an experiment with realistic parameters can be sampled well enough to be retrieved by a standard phase-retrieval algorithm. Potentials and limits of this approach are highlighted. It is suggested that it could be applied to study imperfect or non-standard CDI configurations lacking a satisfactory theoretical formulation. The considerable computational effort required by this method is justified by the great flexibility provided for easy simulation of a large-parameter space.

Hawk: the image reconstruction package for coherent X-ray diffractive imaging

2010 ◽  
Vol 43 (6) ◽  
pp. 1535-1539 ◽  
Author(s):  
Filipe R. N. C. Maia ◽  
Tomas Ekeberg ◽  
David van der Spoel ◽  
Janos Hajdu
Keyword(s):  
Open Source ◽  
Graphics Processing Units ◽  
Rapid Development ◽  
Three Dimensional ◽  
Processing Unit ◽  
Diffractive Imaging ◽  
X Ray ◽  
Two Dimensional Image ◽  
Central Processing ◽  
Diffraction Patterns

The past few years have seen a tremendous growth in the field of coherent X-ray diffractive imaging, in large part due to X-ray free-electron lasers which provide a peak brilliance billions of times higher than that of synchrotrons. However, this rapid development in terms of hardware has not been matched on the software side. The release ofHawkis intended to close this gap. To the authors' knowledgeHawkis the first publicly available and fully open source software program for reconstructing images from continuous diffraction patterns. The software handles all steps leading from a raw diffraction pattern to a reconstructed two-dimensional image including geometry determination, background correction, masking and phasing. It also includes preliminary three-dimensional support and support for graphics processing units using the Compute Unified Device Architecture, which speeds up processing by orders of magnitude compared to a single central processing unit.Hawkimplements numerous algorithms and is easily extended. This, in combination with its open-source licence, provides a platform for other groups to test, develop and distribute their own algorithms.Hawkis available under the GNU General Public License from http://xray.bmc.uu.se/hawk.

2D X-ray diffraction and molecular modelling of the crystalline structure of polyesters under uniaxial stress

2021 ◽  
pp. 096739112199822
Author(s):  
Ahmed I Abou-Kandil ◽  
Gerhard Goldbeck
Keyword(s):  
Crystalline Structure ◽  
Molecular Modelling ◽  
Three Dimensional ◽  
Uniaxial Stress ◽  
X Ray Diffraction ◽  
X Ray ◽  
Wide Range ◽  
Modelling Techniques ◽  
Diffraction Patterns

Studying the crystalline structure of uniaxially and biaxially drawn polyesters is of great importance due to their wide range of applications. In this study, we shed some light on the behaviour of PET and PEN under uniaxial stress using experimental and molecular modelling techniques. Comparing experiment with modelling provides insights into polymer crystallisation with extended chains. Experimental x-ray diffraction patterns are reproduced by means of models of chains sliding along the c-axis leading to some loss of three-dimensional order, i.e. moving away from the condition of perfect register of the fully extended chains in triclinic crystals of both PET and PEN. This will help us understand the mechanism of polymer crystallisation under uniaxial stress and the appearance of mesophases in some cases as discussed herein.

scholarly journals Three-dimensional propagation in near-field tomographic X-ray phase retrieval

2016 ◽  
Vol 72 (2) ◽  
pp. 215-221 ◽  
Author(s):  
Aike Ruhlandt ◽  
Tim Salditt
Keyword(s):  
Phase Retrieval ◽  
Near Field ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Current Phase ◽  
Computationally Efficient ◽  
X Ray ◽  
Reconstruction Quality ◽  
Consistency Constraints

This paper presents an extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. The approach is based on a novel three-dimensional propagator and is derived for the case of optically weak objects. It can be easily implemented in current phase retrieval architectures, is computationally efficient and reduces the need for restrictive prior assumptions, resulting in superior reconstruction quality.

scholarly journals Combining Coherent Hard X-Ray Tomographies with Phase Retrieval to Generate Three-Dimensional Models of Forming Bone

2017 ◽  
Vol 4 ◽  
Author(s):  
Emely L. Bortel ◽  
Max Langer ◽  
Alexander Rack ◽  
Jean-Baptiste Forien ◽  
Georg N. Duda ◽  
...  
Keyword(s):  
Phase Retrieval ◽  
Three Dimensional ◽  
X Ray ◽  
Dimensional Models ◽  
Three Dimensional Models

The Atomic Order in Guinier-Preston Zones of Aluminum-Silver Alloys

1963 ◽  
Vol 7 ◽  
pp. 1-13 ◽  
Author(s):  
Volkmar Gerold ◽  
Heinz Auer ◽  
Winfried Merz
Keyword(s):  
Room Temperature ◽  
Three Dimensional ◽  
Miscibility Gap ◽  
X Rays ◽  
Atomic Order ◽  
Zone Size ◽  
X Ray ◽  
Angle Scattering ◽  
Diffraction Patterns ◽  
Step Quenching

AbstractThe formation of the spherical Guinier—Preston zones in an aluminum-silver alloy is governed by a metastable miscibility gap, which consists of two different sections. The lower section occurs below 170°C (η state), the higher section up to 420°C (∊ state). The zones in the two sections differ in their silver concentration and in their atomic order. To prove the change in order, a combination of X-ray small-angle scattering and electric resistivity measurements was used. As the resistivity depends on the zone size and the atomic order, the change in order can be found when the zone size is known. This size was measured by the X-ray technique. To complete the results, X-rays ingle-crystal diffraction patterns with monochromatic radiation were taken at different stages. According to these patterns, three different states must be distinguished.The η′ state exists at room temperature after quenching from 550°C. The silver atoms prefer a layered arrangement in the zones, which is not very stable. It is destroyed after short annealings above 100°C. The η state is developed during annealing below 170°C. A three-dimensional atomic order is built up with increasing zone size, which results in a marked decrease in the resistivity. For the ∊ state (above 170°C), a nearly random atomic distribution exists. Step-quenching experiments prove that the ordered η state can also be developed at room temperature.

Algorithms for the calculation of X-ray diffraction patterns from finite element data

2010 ◽  
Vol 43 (6) ◽  
pp. 1287-1299 ◽  
Author(s):  
E. Wintersberger ◽  
D. Kriegner ◽  
N. Hrauda ◽  
J. Stangl ◽  
G. Bauer
Keyword(s):  
Finite Element ◽  
Three Dimensional ◽  
Point Of View ◽  
X Ray Diffraction ◽  
Displacement Fields ◽  
X Ray ◽  
Si Substrates ◽  
Diffraction Patterns ◽  
Simulation Point ◽  
Ccd Detectors

A set of algorithms is presented for the calculation of X-ray diffraction patterns from strained nanostructures. Their development was triggered by novel developments in the recording of scattered intensity distributions as well as in simulation practice. The increasing use of two-dimensional CCD detectors in X-ray diffraction experiments, with which three-dimensional reciprocal-space maps can be recorded in a reasonably short time, requires efficient simulation programs to compute one-, two- and three-dimensional intensity distributions. From the simulation point of view, the finite element method (FEM) has become the standard tool for calculation of the strain and displacement fields in nanostructures. Therefore, X-ray diffraction simulation programs must be able to handle FEM data properly. The algorithms presented here make use of the deformation fields calculated on a mesh, which are directly imported into the calculation of diffraction patterns. To demonstrate the application of the developed algorithms, they were applied to several examples such as diffraction data from a dislocated quantum dot, from a periodic array of dislocations in a PbSe epilayer grown on a PbTe pseudosubstrate, and from ripple structures at the surface of SiGe layers deposited on miscut Si substrates.

X-ray diffraction with a four-reflection monochromator

1987 ◽  
Vol 20 (6) ◽  
pp. 522-528 ◽  
Author(s):  
S. E. G. Slusky ◽  
A. T. Macrander
Keyword(s):  
Experimental Data ◽  
Indium Phosphide ◽  
Single Crystal ◽  
Simulated Data ◽  
Vertical Gradient ◽  
X Ray Diffraction ◽  
Rocking Curve ◽  
X Ray ◽  
Vertical Gradient Freeze

A formula is derived for simulating rocking-curve measurements made with an X-ray diffractometer fitted with a four-reflection monochromator. The derivation is carried out both graphically and algebraically. Results of a simulation using this formula are then compared with experimentally obtained rocking curves. The rocking curves were obtained using a diffractometer with a four-reflection monochromator that uses 440 reflections from two channel-cut germanium crystals. The experimental data comprise 200, 400, 600, 511, 711, 622, 422 and 444 reflections from thick single-crystal indium phosphide grown by the vertical-gradient freeze technique. The simulated data correlate well with the experimental data, although the simulations consistently show somewhat higher reflectivities and narrower linewidths than the experiment, indicating the existence of broadening mechanisms not included in the simulation that are affecting the experiment.

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