Incorporating particle symmetry into orientation determination in single-particle imaging

2018 ◽  
Vol 74 (5) ◽  
pp. 512-517
Author(s):  
Miklós Tegze ◽  
Gábor Bortel
Keyword(s):  
Three Dimensional ◽  
Symmetric Case ◽  
X Ray Diffraction ◽  
X Ray ◽  
Coherent Diffraction Imaging ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Particle Imaging ◽  
Single Particle Imaging ◽  
Orientation Determination

In coherent-diffraction-imaging experiments X-ray diffraction patterns of identical particles are recorded. The particles are injected into the X-ray free-electron laser (XFEL) beam in random orientations. If the particle has symmetry, finding the orientation of a pattern can be ambiguous. With some modifications, the correlation-maximization method can find the relative orientations of the diffraction patterns for the case of symmetric particles as well. After convergence, the correlation maps show the symmetry of the particle and can be used to determine the symmetry elements and their orientations. The C factor, slightly modified for the symmetric case, can indicate the consistency of the assembled three-dimensional intensity distribution.

Quantitative nanotomography of amorphous and polycrystalline samples using coherent X-ray diffraction

2019 ◽  
Vol 52 (3) ◽  
pp. 571-578 ◽  
Author(s):  
Y. Chushkin ◽  
F. Zontone ◽  
O. Cherkas ◽  
A. Gibaud
Keyword(s):  
Mass Density ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Coherent Diffraction Imaging ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Better Than

This article presents a combined approach where quantitative forward-scattering coherent diffraction imaging (CDI) is supported by crystal diffraction using 8.1 keV synchrotron X-ray radiation. The method allows the determination of the morphology, mass density and crystallinity of an isolated microscopic specimen. This approach is tested on three homogeneous samples made of different materials with different degrees of crystallinity. The mass density and morphology are revealed using three-dimensional coherent diffraction imaging with a resolution better than 36 nm. The crystallinity is extracted from the diffraction profiles measured simultaneously with coherent diffraction patterns. The presented approach extends CDI to structural characterization of samples when crystallinity aspects are of interest.

scholarly journals A convolutional neural network for defect classification in Bragg coherent X-ray diffraction

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Bruce Lim ◽  
Ewen Bellec ◽  
Maxime Dupraz ◽  
Steven Leake ◽  
Andrea Resta ◽  
...  
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Diffraction Pattern ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Coherent Diffraction Imaging ◽  
The Neural Network ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Defect Recognition

AbstractCoherent diffraction imaging enables the imaging of individual defects, such as dislocations or stacking faults, in materials. These defects and their surrounding elastic strain fields have a critical influence on the macroscopic properties and functionality of materials. However, their identification in Bragg coherent diffraction imaging remains a challenge and requires significant data mining. The ability to identify defects from the diffraction pattern alone would be a significant advantage when targeting specific defect types and accelerates experiment design and execution. Here, we exploit a computational tool based on a three-dimensional (3D) parametric atomistic model and a convolutional neural network to predict dislocations in a crystal from its 3D coherent diffraction pattern. Simulated diffraction patterns from several thousands of relaxed atomistic configurations of nanocrystals are used to train the neural network and to predict the presence or absence of dislocations as well as their type (screw or edge). Our study paves the way for defect-recognition in 3D coherent diffraction patterns for material science.

scholarly journals Bragg–Laue X-ray dynamical diffraction on perfect and deformed lateral crystalline structures

2016 ◽  
Vol 49 (4) ◽  
pp. 1190-1202 ◽  
Author(s):  
Vasily I. Punegov ◽  
Sergey I. Kolosov ◽  
Konstantin M. Pavlov
Keyword(s):  
Cross Sections ◽  
X Ray Diffraction ◽  
Dynamical Diffraction ◽  
X Ray ◽  
Crystalline Structures ◽  
Coherent Diffraction Imaging ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Lateral Structures ◽  
Laue Geometry

The new dynamical diffraction approach to X-ray diffraction on lateral crystalline structures has been developed to investigate the angular and spatial distribution of wavefields in the case of the Bragg–Laue geometry in non-perfect lateral structures. This approach allows one to calculate reciprocal space maps for deformed lateral crystals having rectangular cross sections for both the transmitted and reflected wavefields. Numerical modelling is performed for crystals with different lateral sizes, thicknesses and deformations. The approach can be used in coherent diffraction imaging to simulate Fraunhofer diffraction patterns produced by relatively large deformed crystals.

Coherent diffraction imaging: consistency of the assembled three-dimensional distribution

2016 ◽  
Vol 72 (4) ◽  
pp. 459-464 ◽  
Author(s):  
Miklós Tegze ◽  
Gábor Bortel
Keyword(s):  
Structural Information ◽  
Three Dimensional ◽  
Atomic Scale ◽  
Short Pulses ◽  
X Ray ◽  
Coherent Diffraction Imaging ◽  
Imaging Experiment ◽  
Dimensional Distribution ◽  
Diffraction Imaging ◽  
Diffraction Patterns

The short pulses of X-ray free-electron lasers can produce diffraction patterns with structural information before radiation damage destroys the particle. From the recorded diffraction patterns the structure of particles or molecules can be determined on the nano- or even atomic scale. In a coherent diffraction imaging experiment thousands of diffraction patterns of identical particles are recorded and assembled into a three-dimensional distribution which is subsequently used to solve the structure of the particle. It is essential to know, but not always obvious, that the assembled three-dimensional reciprocal-space intensity distribution is really consistent with the measured diffraction patterns. This paper shows that, with the use of correlation maps and a single parameter calculated from them, the consistency of the three-dimensional distribution can be reliably validated.

A multiple-common-lines method to determine the orientation of snapshot diffraction patterns from single particles

2014 ◽  
Vol 70 (4) ◽  
pp. 364-372 ◽  
Author(s):  
Liang Zhou ◽  
Tian-Yi Zhang ◽  
Zhong-Chuan Liu ◽  
Peng Liu ◽  
Yu-Hui Dong
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
Single Particles ◽  
X Ray ◽  
Three Dimensional Structure ◽  
Individual Object ◽  
Common Lines ◽  
Diffraction Imaging ◽  
Diffraction Patterns

With the development of X-ray free-electron lasers (XFELs), it is possible to determine the three-dimensional structures of noncrystalline objects with coherent X-ray diffraction imaging. In this diffract-and-destroy mode, many snapshot diffraction patterns are obtained from the identical objects which are presented one by one in random orientations to the XFEL beam. Determination of the orientation of an individual object is essential for reconstruction of a three-dimensional structure. Here a new method, called the multiple-common-lines method, has been proposed to determine the orientations of high- and low-signal snapshot diffraction patterns. The mean errors of recovered orientations (α, β, γ) of high- and low-signal patterns are about 0.14, 0.06, 0.12 and 0.77, 0.31, 0.60°, respectively; both sets of errors can meet the requirements of the reconstruction of a three-dimensional structure.

scholarly journals Micro-beam Laue alignment of multi-reflection Bragg coherent diffraction imaging measurements

2017 ◽  
Vol 24 (5) ◽  
pp. 1048-1055 ◽  
Author(s):  
Felix Hofmann ◽  
Nicholas W. Phillips ◽  
Ross J. Harder ◽  
Wenjun Liu ◽  
Jesse N. Clark ◽  
...  
Keyword(s):  
Focused Ion Beam ◽  
Lattice Strain ◽  
Ion Beam ◽  
Strain Tensor ◽  
Three Dimensional ◽  
Stress Fields ◽  
X Ray Diffraction ◽  
X Ray ◽  
Coherent Diffraction Imaging ◽  
Diffraction Imaging

Multi-reflection Bragg coherent diffraction imaging has the potential to allow three-dimensional (3D) resolved measurements of the full lattice strain tensor in specific micro-crystals. Until now such measurements were hampered by the need for laborious, time-intensive alignment procedures. Here a different approach is demonstrated, using micro-beam Laue X-ray diffraction to first determine the lattice orientation of the micro-crystal. This information is then used to rapidly align coherent diffraction measurements of three or more reflections from the crystal. Based on these, 3D strain and stress fields in the crystal are successfully determined. This approach is demonstrated on a focused ion beam milled micro-crystal from which six reflections could be measured. Since information from more than three independent reflections is available, the reliability of the phases retrieved from the coherent diffraction data can be assessed. Our results show that rapid, reliable 3D coherent diffraction measurements of the full lattice strain tensor in specific micro-crystals are now feasible and can be successfully carried out even in heavily distorted samples.

scholarly journals Common architectures in cyanobacteria Prochlorococcus cells visualized by X-ray diffraction imaging using X-ray free electron laser

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Amane Kobayashi ◽  
Yuki Takayama ◽  
Takeshi Hirakawa ◽  
Koji Okajima ◽  
Mao Oide ◽  
...  
Keyword(s):  
Free Electron ◽  
Free Electron Laser ◽  
Single Cells ◽  
Three Dimensional ◽  
Biological Functions ◽  
X Ray Diffraction ◽  
Characteristic Structure ◽  
X Ray ◽  
Diffraction Imaging ◽  
Diffraction Patterns

AbstractVisualization of intracellular structures and their spatial organization inside cells without any modification is essential to understand the mechanisms underlying the biological functions of cells. Here, we investigated the intracellular structure of cyanobacteria Prochlorococcus in the interphase by X-ray diffraction imaging using X-ray free-electron laser. A number of diffraction patterns from single cells smaller than 1 µm in size were collected with high signal-to-noise ratio with a resolution of up to 30 nm. From diffraction patterns, a set of electron density maps projected along the direction of the incident X-ray were retrieved with high reliability. The most characteristic structure found to be common among the cells was a C-shaped arrangement of 100-nm sized high-density spots, which surrounded a low-density area of 100 nm. Furthermore, a three-dimensional map reconstructed from the projection maps of individual cells was non-uniform, indicating the presence of common structures among cyanobacteria cells in the interphase. By referring to the fluorescent images for distributions of thylakoid membranes, nucleoids, and carboxysomes, we inferred and represented their spatial arrangements in the three-dimensional map. The arrangement allowed us to discuss the relevance of the intracellular organization to the biological functions of cyanobacteria.

scholarly journals Dragonfly: an implementation of the expand–maximize–compress algorithm for single-particle imaging

2016 ◽  
Vol 49 (4) ◽  
pp. 1320-1335 ◽  
Author(s):  
Kartik Ayyer ◽  
Ti-Yen Lan ◽  
Veit Elser ◽  
N. Duane Loh
Keyword(s):  
Single Particle ◽  
Parallel Implementation ◽  
Three Dimensional ◽  
Reconstruction Algorithm ◽  
X Ray ◽  
Resultant Data ◽  
Linac Coherent Light Source ◽  
Diffraction Patterns ◽  
Particle Imaging ◽  
Single Particle Imaging

Single-particle imaging (SPI) with X-ray free-electron lasers has the potential to change fundamentally how biomacromolecules are imaged. The structure would be derived from millions of diffraction patterns, each from a different copy of the macromolecule before it is torn apart by radiation damage. The challenges posed by the resultant data stream are staggering: millions of incomplete, noisy and un-oriented patterns have to be computationally assembled into a three-dimensional intensity map and then phase reconstructed. In this paper, theDragonflysoftware package is described, based on a parallel implementation of the expand–maximize–compress reconstruction algorithm that is well suited for this task. Auxiliary modules to simulate SPI data streams are also included to assess the feasibility of proposed SPI experiments at the Linac Coherent Light Source, Stanford, California, USA.

scholarly journals Simultaneous Multi-Bragg Peak Coherent X-ray Diffraction Imaging

Crystals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 312
Author(s):  
Florian Lauraux ◽  
Stéphane Labat ◽  
Sarah Yehya ◽  
Marie-Ingrid Richard ◽  
Steven J. Leake ◽  
...  
Keyword(s):  
Bragg Reflection ◽  
Volume Ratio ◽  
X Ray Diffraction ◽  
X Ray ◽  
Crystal Substrate ◽  
In Series ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Lattice Planes ◽  
Oriented Parallel

The simultaneous measurement of two Bragg reflections by Bragg coherent X-ray diffraction is demonstrated on a twinned Au crystal, which was prepared by the solid-state dewetting of a 30 nm thin gold film on a sapphire substrate. The crystal was oriented on a goniometer so that two lattice planes fulfill the Bragg condition at the same time. The Au 111 and Au 200 Bragg peaks were measured simultaneously by scanning the energy of the incident X-ray beam and recording the diffraction patterns with two two-dimensional detectors. While the former Bragg reflection is not sensitive to the twin boundary, which is oriented parallel to the crystal–substrate interface, the latter reflection is only sensitive to one part of the crystal. The volume ratio between the two parts of the twinned crystal is about 1:9, which is also confirmed by Laue microdiffraction of the same crystal. The parallel measurement of multiple Bragg reflections is essential for future in situ and operando studies, which are so far limited to either a single Bragg reflection or several in series, to facilitate the precise monitoring of both the strain field and defects during the application of external stimuli.

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.

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