Diffraction Imaging Experiments Research Articles

Advances in neutron imaging

Imaging techniques based on neutron beams are rapidly developing and have become versatile non-destructive analyzing tools in many research fields. Due to their intrinsic properties, neutrons differ strongly from electrons, protons or X-rays in terms of their interaction with matter: they penetrate deeply into most common metallic materials while they have a high sensitivity to light elements such as hydrogen, hydrogenous substances, or lithium. This makes neutrons perfectly suited probes for research on materials that are used for energy storage and conversion, e.g., batteries, hydrogen storage, fuel cells, etc. Moreover, their wave properties can be exploited to perform diffraction, phase-contrast and dark-field imaging experiments. Their magnetic moment allows for resolving magnetic properties in bulk samples. This review will focus on recent applications of neutron imaging techniques in both materials research and fundamental science illustrated by examples selected from different areas.

Real-time diffraction computed tomography data reduction.

Diffraction imaging is an X-ray imaging method which uses the crystallinity information (cell parameter, orientation) as a signal to create an image pixel by pixel: a pencil beam is raster-scanned onto a sample and the (powder) diffraction signal is recorded by a large area detector. With the flux provided by third-generation synchrotrons and the speed of hybrid pixel detectors, the acquisition speed of these experiments is now limited by the transfer rate to the local storage as the data reduction can hardly be performed in real time. This contribution presents the benchmarking of a typical data analysis pipeline for a diffraction imaging experiment like the ones performed at ESRF ID15a and proposes some disruptive techniques to decode CIF binary format images using the computational power of graphics cards to be able to perform data reduction in real time.

Performance evaluation of Bragg coherent diffraction imaging

In this study, we present a numerical framework for modeling three-dimensional (3D) diffraction data in Bragg coherent diffraction imaging (Bragg CDI) experiments and evaluating the quality of obtained 3D complex-valued real-space images recovered by reconstruction algorithms under controlled conditions. The approach is used to systematically explore the performance and the detection limit of this phase-retrieval-based microscopy tool. The numerical investigation suggests that the superb performance of Bragg CDI is achieved with an oversampling ratio above 30 and a detection dynamic range above 6 orders. The observed performance degradation subject to the data binning processes is also studied. This numerical tool can be used to optimize experimental parameters and has the potential to significantly improve the throughput of Bragg CDI method.

Merging single-shot XFEL diffraction data from inorganic nanoparticles: a new approach to size and orientation determination.

X-ray free-electron lasers (XFELs) provide new opportunities for structure determination of biomolecules, viruses and nanomaterials. With unprecedented peak brilliance and ultra-short pulse duration, XFELs can tolerate higher X-ray doses by exploiting the femtosecond-scale exposure time, and can thus go beyond the resolution limits achieved with conventional X-ray diffraction imaging techniques. Using XFELs, it is possible to collect scattering information from single particles at high resolution, however particle heterogeneity and unknown orientations complicate data merging in three-dimensional space. Using the Linac Coherent Light Source (LCLS), synthetic inorganic nanocrystals with a core-shell architecture were used as a model system for proof-of-principle coherent diffractive single-particle imaging experiments. To deal with the heterogeneity of the core-shell particles, new computational methods have been developed to extract the particle size and orientation from the scattering data to assist data merging. The size distribution agrees with that obtained by electron microscopy and the merged data support a model with a core-shell architecture.

Diffraction data of core-shell nanoparticles from an X-ray free electron laser

X-ray free-electron lasers provide novel opportunities to conduct single particle analysis on nanoscale particles. Coherent diffractive imaging experiments were performed at the Linac Coherent Light Source (LCLS), SLAC National Laboratory, exposing single inorganic core-shell nanoparticles to femtosecond hard-X-ray pulses. Each facetted nanoparticle consisted of a crystalline gold core and a differently shaped palladium shell. Scattered intensities were observed up to about 7 nm resolution. Analysis of the scattering patterns revealed the size distribution of the samples, which is consistent with that obtained from direct real-space imaging by electron microscopy. Scattering patterns resulting from single particles were selected and compiled into a dataset which can be valuable for algorithm developments in single particle scattering research.

Spatial resolution measurement of triple-GEM detector and diffraction imaging test at synchrotron radiation

A triple-GEM detector with two-dimensional readout is developed. The detector provides high position resolution for powder diffraction experiments at synchrotron radiation. Spatial resolution of the detector is measured in the lab using a 55Fe X-ray source. A resolution of about 110 μm FWHM is achieved. The energy resolution is better than 27% for 5.9 keV X-rays. The detector's validity under illumination of photons in particular energy range is verified using a Cu X-ray tube. Imaging of the head of a wire stripper with X-ray tube demonstrates its imaging ability. A diffraction imaging experiment using the sample of powder SiO2 is successfully carried out at 1W2B laboratory of Beijing Synchrotron Radiation Facility (BSRF). Different diffraction rings are clearly seen under various X-ray energies.

Characterizing gas flow from aerosol particle injectors

A novel methodology for measuring gas flow from small orifices or nozzles into vacuum is presented. It utilizes a high-intensity femtosecond laser pulse to create a plasma within the gas plume produced by the nozzle, which is imaged by a microscope. Calibration of the imaging system allows for the extraction of absolute number densities. We show detection down to helium densities of 4×1016 cm−3 with a spatial resolution of a few micrometers. The technique is used to characterize the gas flow from a convergent-nozzle aerosol injector [Kirian et al., Struct. Dyn. 2, 041717 (2015)] as used in single-particle diffractive imaging experiments at free-electron laser sources. Based on the measured gas-density profile, we estimate the scattering background signal under typical operating conditions of single-particle imaging experiments and estimate that fewer than 50 photons per shot can be expected on the detector.

Nanoscale imaging with table-top coherent extreme ultraviolet source based on high harmonic generation

A table-top coherent diffractive imaging experiment on a sample with biological-like characteristics using a focused narrow-bandwidth high harmonic source around 30nm is performed. An approach involving a beam stop and a new reconstruction algorithm to enhance the quality of reconstructed the image is described.

Reconstruction of Three-Dimensional Structures of a Protein with Software ENMA and EMC Algorithm: A Simulation for XFEL-CXDI Experiment

Coherent X-ray diffraction imaging (CXDI) experiments enable us to visualize the structures of non-crystalline particles with micrometer to sub-micrometer dimensions. Using the X-ray free-electron laser (XFEL), two-dimensional diffraction patterns are collected in the diffraction-before-destruction scheme. To reconstruct three-dimensional electron density maps of a particle, it is necessary to classify the diffraction patterns in terms of structural polymorphism before the reconstruction. Here, we performed a simulation for XFEL-CXDI experiment of a protein predominantly adopting two states. After classifying the data using the custom-made software “ENMA” [1] in which the manifold theory is implemented, we successfully reconstructed the three-dimensional electron density maps of the states using the EMC algorithm [2].[1] T. Yoshidome, T. Oroguchi, M. Nakasako, and M. Ikeguchi, Phys. Rev. E 92, 032710 (2015).[2] N.-T. Duane Loh and V. Elser, Phys. Rev. E 80, 026705 (2009).

Bragg coherent diffraction imaging and metrics for radiation damage in protein micro-crystallography.

The proliferation of extremely intense synchrotron sources has enabled ever higher-resolution structures to be obtained using data collected from smaller and often more imperfect biological crystals (Helliwell, 1984). Synchrotron beamlines now exist that are capable of measuring data from single crystals that are just a few micrometres in size. This provides renewed motivation to study and understand the radiation damage behaviour of small protein crystals. Reciprocal-space mapping and Bragg coherent diffractive imaging experiments have been performed on cryo-cooled microcrystals of hen egg-white lysozyme as they undergo radiation damage. Several well established metrics, such as intensity-loss and lattice expansion, are applied to the diffraction data and the results are compared with several new metrics that can be extracted from the coherent imaging experiments. Individually some of these metrics are inconclusive. However, combining metrics, the results suggest that radiation damage behaviour in protein micro-crystals differs from that of larger protein crystals and may allow them to continue to diffract for longer. A possible mechanism to account for these observations is proposed.

Классификация дифракционных изображений биологических макромолекул с разными типами симметрии в экспериментах по когерентной рентгеновской дифракционной микроскопии

About 1% of diffraction images produced in coherent X-ray diffraction imaging experiments originate from a single particle of interest and only those images are suitable for structure reconstruction. Other images contain contributions from multiple particles, water or some contaminant. Selection of single particle images is required. A new classification method that is based on cross-correlation analysis were developed. The method was successfully applied to the experimental data, that contain diffraction images of the PBCV-1 virus and T4 bacteriophage. In this article we present classification results for diffraction images of seven biological particles with different symmetry. The results confirm the applicability of the proposed method for correct classification of diffraction images corresponding to different molecules. We also studied influence of particle symmetry type and volume of learning dataset to classification quality.

High speed and high resolution table-top nanoscale imaging.

We present a table-top coherent diffractive imaging (CDI) experiment based on high-order harmonics generated at 18 nm by a high average power femtosecond fiber laser system. The high photon flux, narrow spectral bandwidth, and high degree of spatial coherence allow for ultrahigh subwavelength resolution imaging at a high numerical aperture. Our experiments demonstrate a half-pitch resolution of 15 nm, close to the actual Abbe limit of 12 nm, which is the highest resolution achieved from any table-top extreme ultraviolet (XUV) or x-ray microscope. In addition, sub-30 nm resolution was achieved with only 3 s of integration time, bringing live diffractive imaging and three-dimensional tomography on the nanoscale one step closer to reality. The current resolution is solely limited by the wavelength and the detector size. Thus, table-top nanoscopes with only a few-nanometer resolutions are in reach and will find applications in many areas of science and technology.

Revealing Three-Dimensional Structure of an Individual Colloidal Crystal Grain by Coherent X-Ray Diffractive Imaging.

We present results of a coherent x-ray diffractive imaging experiment performed on a single colloidal crystal grain. The full three-dimensional (3D) reciprocal space map measured by an azimuthal rotational scan contained several orders of Bragg reflections together with the coherent interference signal between them. Applying the iterative phase retrieval approach, the 3D structure of the crystal grain was reconstructed and positions of individual colloidal particles were resolved. As a result, an exact stacking sequence of hexagonal close-packed layers including planar and linear defects were identified.

Utilizing broadband X-rays in a Bragg coherent X-ray diffraction imaging experiment.

A method is presented to simplify Bragg coherent X-ray diffraction imaging studies of complex heterogeneous crystalline materials with a two-stage screening/imaging process that utilizes polychromatic and monochromatic coherent X-rays and is compatible with in situ sample environments. Coherent white-beam diffraction is used to identify an individual crystal particle or grain that displays desired properties within a larger population. A three-dimensional reciprocal-space map suitable for diffraction imaging is then measured for the Bragg peak of interest using a monochromatic beam energy scan that requires no sample motion, thus simplifying in situ chamber design. This approach was demonstrated with Au nanoparticles and will enable, for example, individual grains in a polycrystalline material of specific orientation to be selected, then imaged in three dimensions while under load.

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

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.

Cracks observed to propagate discontinuously on the millisecond timescale.

Ultra-fast diffraction and phase contrast imaging experiments on crack propagation in silicon, reported in the current issue of IUCrJ, are reviewed in the light of our present knowledge and its industrial importance.

Cryogenic coherent X-ray diffraction imaging of biological samples at SACLA: a correlative approach with cryo-electron and light microscopy.

Coherent X-ray diffraction imaging at cryogenic temperature (cryo-CXDI) allows the analysis of internal structures of unstained, non-crystalline, whole biological samples in micrometre to sub-micrometre dimensions. Targets include cells and cell organelles. This approach involves preparing frozen-hydrated samples under controlled humidity, transferring the samples to a cryo-stage inside a vacuum chamber of a diffractometer, and then exposing the samples to coherent X-rays. Since 2012, cryo-coherent diffraction imaging (CDI) experiments have been carried out with the X-ray free-electron laser (XFEL) at the SPring-8 Ångstrom Compact free-electron LAser (SACLA) facility in Japan. Complementary use of cryo-electron microscopy and/or light microscopy is highly beneficial for both pre-checking samples and studying the integrity or nature of the sample. This article reports the authors' experience in cryo-XFEL-CDI of biological cells and organelles at SACLA, and describes an attempt towards reliable and higher-resolution reconstructions, including signal enhancement with strong scatterers and Patterson-search phasing.

Optically Induced Forces Imposed in an Optical Funnel on a Stream of Particles in Air or Vacuum

Optical trapping of light-absorbing particles in a gaseous environment is governed by a laser-induced photophoretic force, which can be orders of magnitude stronger than the force of radiation pressure induced by the same light intensity. In spite of many experimental studies, the exact theoretical background underlying the photophoretic force and the prediction of its influence on the particle motion is still in its infancy. Here, we report the results of a quantitative analysis of the photophoretic force and the stiffness of trapping achieved by levitating graphite and graphite-coated glass shells of calibrated sizes in an upright diverging hollow-core vortex beam, which we refer to as an “optical funnel”. The measurements of forces are conducted in air at various gas pressures in the range from 5 mbar to 2 bar. The results of these measurements lay the foundation for mapping the optically induced force to the intensity distribution in the trap. The mapping, in turn, provides the necessary information to model flight trajectories of particles of various sizes entering the beam at given initial speed and position relative to the beam axis. Finally, we determine the limits of the parameter space for the particle speed, size, and radial offset to the beam axis, all linked to the laser power and the particular laser-beam structure. These results establish the grounds for developing a touch-free optical system for precisely positioning submicrometer bioparticles at the focal spot of an x-ray free-electron laser, which will significantly enhance the efficiency of studying nanoscale morphology of proteins and biomolecules in femtosecond coherent diffractive imaging experiments.

Extending the potential of x-ray free-electron lasers to industrial applications—an initiatory attempt at coherent diffractive imaging on car-related nanomaterials

Recent advances in x-ray free-electron lasers (XFELs) open up new pathways for contributing to industrial research-and-development activities. In this article, we describe our initiatory attempt at using the SPring-8 Ångström compact free-electron laser (SACLA) for industrial applications. The attempt was conducted by the authors through the industry-academia partnership program initiated by RIKEN, aimed at examining the potential of XFELs for the analysis of car-related nanomaterials. Using the infrastructures developed at SACLA, we performed single-shot coherent diffractive imaging experiments on automotive exhaust catalysts and succeeded in obtaining the reconstructed images. This effort has paved the way for the future use of XFELs in the research-and-development activity of automotive exhaust catalysts.

Influence of wavelength and pulse duration on single-shot x-ray diffraction patterns from nonspherical nanoparticles

We introduce a complex scaling discrete dipole approximation (CSDDA) method and study single-shot x-ray diffraction patterns from non-spherical, absorbing nanotargets in the limit of linear response. The convergence of the employed Born series-based iterative solution of the discrete dipole approximation problem via optimal complex mixing turns out to be substantially faster than the original approach with real-valued mixing coefficients, without additional numerical effort per iteration. The CSDDA method is employed to calculate soft x-ray diffraction patterns from large icosahedral silver nanoparticles with diameters up to about . Our analysis confirms the requirement of relatively long wavelengths to map truly 3D structure information to the experimentally accessible regions of 2D scattering images. On the other hand, we show that short wavelengths are preferable to retain visibility of fine structures such as interference fringes in the scattering patterns when using ultrashort x-ray pulses in the attosecond domain. A simple model is presented to estimate the minimal pulse duration below which the fringe contrast vanishes. Knowledge of the impact of the bandwidth of short pulses on the diffraction images is important to extract information on ultrafast dynamical processes from time-resolved x-ray diffractive imaging experiments on free nanoparticles, in particular at long wavelengths.