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Preview: Journal of Synchrotron Radiation

Journal of Synchrotron Radiation



Synchrotron radiation research is rapidly expanding with many new sources of radiation being created globally. Synchrotron radiation plays a leading role in pure science and in emerging technologies. The Journal of Synchrotron Radiation provides comprehen



Published: 2017-02-20

 



Surface EXAFS via differential electron yield

2017-01-24

Surface-sensitive analysis via extended X-ray absorption fine-structure (EXAFS) spectroscopy is demonstrated using a thickness-defined SiO2 (12.4 nm)/Si sample. The proposed method exploits the differential electron yield (DEY) method wherein Auger electrons escaping from a sample surface are detected by an electron analyzer. The DEY method removes local intensity changes in the EXAFS spectra caused by photoelectrons crossing the Auger peak during X-ray energy sweeps, enabling EXAFS analysis through Fourier transformation of wide-energy-range spectral oscillations. The Si K-edge DEY X-ray absorption near-edge structure (XANES) spectrum appears to comprise high amounts of SiO2 and low Si content, suggesting an analysis depth, as expressed using the inelastic mean free path of electrons in general electron spectroscopy, of approximately 4.2 nm. The first nearest neighbor (Si—O) distance derived from the Fourier transform of the Si K-edge DEY-EXAFS oscillation is 1.63 Å. This value is within the reported values of bulk SiO2, showing that DEY can be used to detect a surface layer of 12.4 nm thickness with an analysis depth of approximately 4.2 nm and enable `surface EXAFS' analysis using Fourier transformation.



A convolutional neural network approach to calibrating the rotation axis for X-ray computed tomography

2017-01-24

This paper presents an algorithm to calibrate the center-of-rotation for X-ray tomography by using a machine learning approach, the Convolutional Neural Network (CNN). The algorithm shows excellent accuracy from the evaluation of synthetic data with various noise ratios. It is further validated with experimental data of four different shale samples measured at the Advanced Photon Source and at the Swiss Light Source. The results are as good as those determined by visual inspection and show better robustness than conventional methods. CNN has also great potential for reducing or removing other artifacts caused by instrument instability, detector non-linearity, etc. An open-source toolbox, which integrates the CNN methods described in this paper, is freely available through GitHub at tomography/xlearn and can be easily integrated into existing computational pipelines available at various synchrotron facilities. Source code, documentation and information on how to contribute are also provided.



Compact IR synchrotron beamline design

2017-01-24

Third-generation storage rings are massively evolving due to the very compact nature of the multi-bend achromat (MBA) lattice which allows amazing decreases of the horizontal electron beam emittance, but leaves very little place for infrared (IR) extraction mirrors to be placed, thus prohibiting traditional IR beamlines. In order to circumvent this apparent restriction, an optimized optical layout directly integrated inside a SOLEIL synchrotron dipole chamber that delivers intense and almost aberration-free beams in the near- to mid-IR domain (1–30 µm) is proposed and analyzed, and which can be integrated into space-restricted MBA rings. Since the optics and chamber are interdependent, the feasibility of this approach depends on a large part on the technical ability to assemble mechanically the optics inside the dipole chamber and control their resulting stability and thermo-mechanical deformation. Acquiring this expertise should allow dipole chambers to provide almost aberration-free IR synchrotron sources on current and `ultimate' MBA storage rings.



Improving the spatial and statistical accuracy in X-ray Raman scattering based direct tomography

2017-01-24

An algorithm to simultaneously increase the spatial and statistical accuracy of X-ray Raman scattering (XRS) based tomographic images is presented. Tomography that utilizes XRS spectroscopy signals as a contrast for the images is a new and promising tool for investigating local atomic structure and chemistry in heterogeneous samples. The algorithm enables the spatial resolution to be increased based on a deconvolution of the optical response function of the spectrometer and, most importantly, it allows for the combination of data collected from multiple analyzers and thus enhances the statistical accuracy of the measured images.



Development of new CdZnTe detectors for room-temperature high-flux radiation measurements

2017-02-01

Recently, CdZnTe (CZT) detectors have been widely proposed and developed for room-temperature X-ray spectroscopy even at high fluxes, and great efforts have been made on both the device and the crystal growth technologies. In this work, the performance of new travelling-heater-method (THM)-grown CZT detectors, recently developed at IMEM-CNR Parma, Italy, is presented. Thick planar detectors (3 mm thick) with gold electroless contacts were realised, with a planar cathode covering the detector surface (4.1 mm × 4.1 mm) and a central anode (2 mm × 2 mm) surrounded by a guard-ring electrode. The detectors, characterized by low leakage currents at room temperature (4.7 nA cm−2 at 1000 V cm−1), allow good room-temperature operation even at high bias voltages (>7000 V cm−1). At low rates (200 counts s−1), the detectors exhibit an energy resolution around 4% FWHM at 59.5 keV (241Am source) up to 2200 V, by using commercial front-end electronics (A250F/NF charge-sensitive preamplifier, Amptek, USA; nominal equivalent noise charge of 100 electrons RMS). At high rates (1 Mcounts s−1), the detectors, coupled to a custom-designed digital pulse processing electronics developed at DiFC of University of Palermo (Italy), show low spectroscopic degradations: energy resolution values of 8% and 9.7% FWHM at 59.5 keV (241Am source) were measured, with throughputs of 0.4% and 60% at 1 Mcounts s−1, respectively. An energy resolution of 7.7% FWHM at 122.1 keV (57Co source) with a throughput of 50% was obtained at 550 kcounts s−1 (energy resolution of 3.2% at low rate). These activities are in the framework of an Italian research project on the development of energy-resolved photon-counting systems for high-flux energy-resolved X-ray imaging.



Nondestructive imaging of the internal microstructure of vessels and nerve fibers in rat spinal cord using phase-contrast synchrotron radiation microtomography

2017-02-01

The spinal cord is the primary neurological link between the brain and other parts of the body, but unlike those of the brain, advances in spinal cord imaging have been challenged by the more complicated and inhomogeneous anatomy of the spine. Fortunately with the advancement of high technology, phase-contrast synchrotron radiation microtomography has become widespread in scientific research because of its ability to generate high-quality and high-resolution images. In this study, this method has been employed for nondestructive imaging of the internal microstructure of rat spinal cord. Furthermore, digital virtual slices based on phase-contrast synchrotron radiation were compared with conventional histological sections. The three-dimensional internal microstructure of the intramedullary arteries and nerve fibers was vividly detected within the same spinal cord specimen without the application of a stain or contrast agent or sectioning. With the aid of image post-processing, an optimization of vessel and nerve fiber images was obtained. The findings indicated that phase-contrast synchrotron radiation microtomography is unique in the field of three-dimensional imaging and sets novel standards for pathophysiological investigations in various neurovascular diseases.



A compact permanent-magnet system for measuring magnetic circular dichroism in resonant inelastic soft X-ray scattering

2017-02-02

A compact and portable magnet system for measuring magnetic dichroism in resonant inelastic soft X-ray scattering (SX-RIXS) has been developed at the beamline BL07LSU in SPring-8. A magnetic circuit composed of Nd–Fe–B permanent magnets, which realised ∼0.25 T at the center of an 11 mm gap, was rotatable around the axis perpendicular to the X-ray scattering plane. Using the system, a SX-RIXS spectrum was obtained under the application of the magnetic field at an angle parallel, nearly 45° or perpendicular to the incident X-rays. A dedicated sample stage was also designed to be as compact as possible, making it possible to perform SX-RIXS measurements at arbitrary incident angles by rotating the sample stage in the gap between the magnetic poles. This system enables facile studies of magnetic dichroism in SX-RIXS for various experimental geometries of the sample and the magnetic field. A brief demonstration of the application is presented.



Ultra-short and ultra-intense X-ray free-electron laser single pulse in one-dimensional photonic crystals

2017-02-16

The propagation within a one-dimensional photonic crystal of a single ultra-short and ultra-intense pulse delivered by an X-ray free-electron laser is analysed with the framework of the time-dependent coupled-wave theory in non-linear media. It is shown that the reflection and the transmission of an ultra-short pulse present a transient period conditioned by the extinction length and also the thickness of the structure for transmission. For ultra-intense pulses, non-linear effects are expected: they could give rise to numerous phenomena, bi-stability, self-induced transparency, gap solitons, switching, etc., which have been previously shown in the optical domain.



A modified equally sloped algorithm based on the total variation algorithm in computed tomography for insufficient data

2017-02-16

Computed tomography (CT) has become an important technique for analyzing the inner structures of material, biological and energy fields. However, there are often challenges in the practical application of CT due to insufficient data. For example, the maximum rotation angle of the sample stage is limited by sample space or image reconstruction from the limited number of views required to reduce the X-ray dose delivered to the sample. Therefore, it is difficult to acquire CT images with complete data. In this work, an iterative reconstruction algorithm based on the minimization of the image total variation (TV) has been utilized to develop equally sloped tomography (EST), and the reconstruction was carried out from limited-angle, few-view and noisy data. A synchrotron CT experiment on hydroxyapatite was also carried out to demonstrate the ability of the TV-EST algorithm. The results indicated that the new TV-EST algorithm was capable of achieving high-quality reconstructions from projections with insufficient data.



A novel molten-salt electrochemical cell for investigating the reduction of uranium dioxide to uranium metal by lithium using in situ synchrotron radiation

2017-02-16

A novel electrochemical cell has been designed and built to allow for in situ energy-dispersive X-ray diffraction measurements to be made during reduction of UO2 to U metal in LiCl–KCl at 500°C. The electrochemical cell contains a recessed well at the bottom of the cell into which the working electrode sits, reducing the beam path for the X-rays through the molten-salt and maximizing the signal-to-noise ratio from the sample. Lithium metal was electrodeposited onto the UO2 working electrode by exposing the working electrode to more negative potentials than the Li deposition potential of the LiCl–KCl eutectic electrolyte. The Li metal acts as a reducing agent for the chemical reduction of UO2 to U, which appears to proceed to completion. All phases were fitted using Le Bail refinement. The cell is expected to be widely applicable to many studies involving molten-salt systems.



Probe reconstruction for holographic X-ray imaging

2017-02-16

In X-ray holographic near-field imaging the resolution and image quality depend sensitively on the beam. Artifacts are often encountered due to the strong focusing required to reach high resolution. Here, two schemes for reconstructing the complex-valued and extended wavefront of X-ray nano-probes, primarily in the planes relevant for imaging (i.e. focus, sample and detection plane), are presented and compared. Firstly, near-field ptychography is used, based on scanning a test pattern laterally as well as longitudinally along the optical axis. Secondly, any test pattern is dispensed of and the wavefront reconstructed only from data recorded for different longitudinal translations of the detector. For this purpose, an optimized multi-plane projection algorithm is presented, which can cope with the numerically very challenging setting of a divergent wavefront emanating from a hard X-ray nanoprobe. The results of both schemes are in very good agreement. The probe retrieval can be used as a tool for optics alignment, in particular at X-ray nanoprobe beamlines. Combining probe retrieval and object reconstruction is also shown to improve the image quality of holographic near-field imaging.



Magnetic design and modelling of a 14 mm-period prototype superconducting undulator

2017-02-16

The magnetic design of a ten-period (each period 14 mm) prototype superconducting undulator is reported using RADIA. The results of modelling the magnetic flux density are presented in an analytical formula. The dependence of the field integrals and phase error on the current density and undulator gap has been calculated, and temperature curves are determined for the models and are compared with earlier reported Moser–Rossmanith fits.



Simulating and optimizing compound refractive lens-based X-ray microscopes

2017-02-20

A comprehensive optical description of compound refractive lenses (CRLs) in condensing and full-field X-ray microscopy applications is presented. The formalism extends ray-transfer matrix analysis by accounting for X-ray attenuation by the lens material. Closed analytical expressions for critical imaging parameters such as numerical aperture, spatial acceptance (vignetting), chromatic aberration and focal length are provided for both thin- and thick-lens imaging geometries. These expressions show that the numerical aperture will be maximized and chromatic aberration will be minimized at the thick-lens limit. This limit may be satisfied by a range of CRL geometries, suggesting alternative approaches to improving the resolution and efficiency of CRLs and X-ray microscopes.



Establishment of new design criteria for GlidCop® X-ray absorbers

2017-02-20

An engineering research program has been conducted at the Advanced Photon Source (APS) in order to determine the thermomechanical conditions that lead to crack formation in GlidCop®, a material commonly used to fabricate X-ray absorbers at X-ray synchrotron facilities. This dispersion-strengthened copper alloy is a proprietary material and detailed technical data of interest to the synchrotron community is limited. The results from the research program have allowed new design criteria to be established for GlidCop® X-ray absorbers based upon the thermomechanically induced fatigue behavior of the material. X-ray power from APS insertion devices was used to expose 30 GlidCop® samples to 10000 thermal loading cycles each under various beam power conditions, and all of the samples were metallurgically examined for crack presence/geometry. In addition, an independent testing facility was hired to measure temperature-dependent mechanical data and uniaxial mechanical fatigue data for numerous GlidCop® samples. Data from these studies support finite element analysis (FEA) simulation and parametric models, allowing the development of a thermal fatigue model and the establishment of new design criteria so that the thermomechanically induced fatigue life of X-ray absorbers may be predicted. It is also demonstrated how the thermal fatigue model can be used as a tool to geometrically optimize X-ray absorber designs.



Uranium XAFS analysis of kidney from rats exposed to uranium

2017-02-20

The kidney is the critical target of uranium exposure because uranium accumulates in the proximal tubules and causes tubular damage, but the chemical nature of uranium in kidney, such as its chemical status in the toxic target site, is poorly understood. Micro-X-ray absorption fine-structure (µXAFS) analysis was used to examine renal thin sections of rats exposed to uranyl acetate. The U LIII-edge X-ray absorption near-edge structure spectra of bulk renal specimens obtained at various toxicological phases were similar to that of uranyl acetate: their edge position did not shift compared with that of uranyl acetate (17.175 keV) although the peak widths for some kidney specimens were slightly narrowed. µXAFS measurements of spots of concentrated uranium in the micro-regions of the proximal tubules showed that the edge jump slightly shifted to lower energy. The results suggest that most uranium accumulated in kidney was uranium (VI) but a portion might have been biotransformed in rats exposed to uranyl acetate.



Computer-assisted area detector masking

2017-01-30

Area detectors have become the predominant type of detector for the rapid acquisition of X-ray diffraction, small-angle scattering and total scattering. These detectors record the scattering for a large area, giving each shot good statistical significance to the resulting scattered intensity I(Q) pattern. However, many of these detectors have pixel level defects, which cause error in the resulting one-dimensional patterns. In this work, new software to automatically find and mask these dead pixels and other defects is presented. This algorithm is benchmarked with both ideal simulated and experimental datasets.



Performance on absolute scattering intensity calibration and protein molecular weight determination at BL16B1, a dedicated SAXS beamline at SSRF

2017-01-24

The optical system and end-station of bending-magnet beamline BL16B1, dedicated to small-angle X-ray scattering (SAXS) at the Shanghai Synchrotron Radiation Facility, is described. Constructed in 2009 and upgraded in 2013, this beamline has been open to users since May 2009 and supports methodologies including SAXS, wide-angle X-ray scattering (WAXS), simultaneous SAXS/WAXS, grazing-incidence small-angle X-ray scattering (GISAXS) and anomalous small-angle X-ray scattering (ASAXS). Considering that an increasing necessity for absolute calibration of SAXS intensity has been recognized in in-depth investigations, SAXS intensity is re-stated according to the extent of data processing, and the absolute intensity is suggested to be a unified presentation of SAXS data in this article. Theory with a practical procedure for absolute intensity calibration is established based on BL16B1, using glass carbon and water as primary and secondary standards, respectively. The calibration procedure can be completed in minutes and shows good reliability under different conditions. An empirical line of scale factor estimation is also established for any specific SAXS setup at the beamline. Beamline performance on molecular weight (MW) determination is provided as a straightforward application and verification of the absolute intensity calibration. Results show good accuracy with a deviation of less than 10% compared with the known value, which is also the best attainable accuracy in recent studies using SAXS to measure protein MW. Fast MW measurement following the demonstrated method also enables an instant check or pre-diagnosis of the SAXS performance to improve the data acquisition.



A large-solid-angle X-ray Raman scattering spectrometer at ID20 of the European Synchrotron Radiation Facility

2017-02-16

An end-station for X-ray Raman scattering spectroscopy at beamline ID20 of the European Synchrotron Radiation Facility is described. This end-station is dedicated to the study of shallow core electronic excitations using non-resonant inelastic X-ray scattering. The spectrometer has 72 spherically bent analyzer crystals arranged in six modular groups of 12 analyzer crystals each for a combined maximum flexibility and large solid angle of detection. Each of the six analyzer modules houses one pixelated area detector allowing for X-ray Raman scattering based imaging and efficient separation of the desired signal from the sample and spurious scattering from the often used complicated sample environments. This new end-station provides an unprecedented instrument for X-ray Raman scattering, which is a spectroscopic tool of great interest for the study of low-energy X-ray absorption spectra in materials under in situ conditions, such as in operando batteries and fuel cells, in situ catalytic reactions, and extreme pressure and temperature conditions.



RixsToolBox: software for the analysis of soft X-ray RIXS data acquired with 2D detectors

2017-02-02

A software with a graphical user interface has been developed with the aim of facilitating the data analysis for users of a new resonant inelastic X-ray scattering (RIXS) spectrometer installed at the ESRF beamline ID32. The software is organized in modules covering all relevant steps in the data reduction from a stack of several hundred two-dimensional CCD images to a single RIXS spectrum. It utilizes both full charge integration and single-photon centroiding to cope with high-flux and high-resolution requirements. Additional modules for further data analysis and the extraction of instrumental parameters are available. The software has been in routine use for about a year now and in that time many additional features have been incorporated. It now meets the users' need for an easy-to-use data analysis tool that allows looking at and understanding data as it is acquired and thus steering users' experiments more efficiently.