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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: 2017-11-01


Design and performance of an X-ray scanning microscope at the Hard X-ray Nanoprobe beamline of NSLS-II


A hard X-ray scanning microscope installed at the Hard X-ray Nanoprobe beamline of the National Synchrotron Light Source II has been designed, constructed and commissioned. The microscope relies on a compact, high stiffness, low heat dissipation approach and utilizes two types of nanofocusing optics. It is capable of imaging with ∼15 nm × 15 nm spatial resolution using multilayer Laue lenses and 25 nm × 26 nm resolution using zone plates. Fluorescence, diffraction, absorption, differential phase contrast, ptychography and tomography are available as experimental techniques. The microscope is also equipped with a temperature regulation system which allows the temperature of a sample to be varied in the range between 90 K and 1000 K. The constructed instrument is open for general users and offers its capabilities to the material science, battery research and bioscience communities.

Aberration-free aspherical lens shape for shortening the focal distance of an already convergent beam


The shapes of single lens surfaces capable of focusing divergent and collimated beams without aberration have already been calculated. However, nanofocusing compound refractive lenses (CRLs) require many consecutive lens surfaces. Here a theoretical example of an X-ray nanofocusing CRL with 48 consecutive surfaces is studied. The surfaces on the downstream end of this CRL accept X-rays that are already converging toward a focus, and refract them toward a new focal point that is closer to the surface. This case, so far missing from the literature, is treated here. The ideal surface for aberration-free focusing of a convergent incident beam is found by analytical computation and by ray tracing to be one sheet of a Cartesian oval. An `X-ray approximation' of the Cartesian oval is worked out for the case of small change in index of refraction across the lens surface. The paraxial approximation of this surface is described. These results will assist the development of large-aperture CRLs for nanofocusing.

Refraction and ultra-small-angle scattering of X-rays in a single-crystal diamond compound refractive lens


In this work a double-crystal setup is employed to study compound refractive lenses made of single-crystal diamond. The point spread function of the lens is calculated taking into account the lens transmission, the wavefront aberrations, and the ultra-small-angle broadening of the X-ray beam. It is shown that, similarly to the wavefront aberrations, the ultra-small-angle scattering effects can significantly reduce the intensity gain and increase the focal spot size. The suggested approach can be particularly useful for the characterization of refractive X-ray lenses composed of many tens of unit lenses.

Characterization of a bent Laue double-crystal beam-expanding monochromator


A bent Laue double-crystal monochromator system has been designed for vertically expanding the X-ray beam at the Canadian Light Source's BioMedical Imaging and Therapy beamlines. Expansion by a factor of 12 has been achieved without deteriorating the transverse coherence of the beam, allowing phase-based imaging techniques to be performed with high flux and a large field of view. However, preliminary studies revealed a lack of uniformity in the beam, presumed to be caused by imperfect bending of the silicon crystal wafers used in the system. Results from finite-element analysis of the system predicted that the second crystal would be most severely affected and has been shown experimentally. It has been determined that the majority of the distortion occurs in the second crystal and is likely caused by an imperfection in the surface of the bending frame. Measurements were then taken to characterize the bending of the crystal using both mechanical and diffraction techniques. In particular, two techniques commonly used to map dislocations in crystal structures have been adapted to map local curvature of the bent crystals. One of these, a variation of Berg–Berrett topography, has been used to quantify the diffraction effects caused by the distortion of the crystal wafer. This technique produces a global mapping of the deviation of the diffraction angle relative to a perfect cylinder. This information is critical for improving bending and measuring tolerances of imperfections by correlating this mapping to areas of missing intensity in the beam.

The slip-and-slide algorithm: a refinement protocol for detector geometry


Geometry correction is traditionally plagued by mis-fitting of correlated parameters, leading to local minima which prevent further improvements. Segmented detectors pose an enhanced risk of mis-fitting: even a minor confusion of detector distance and panel separation can prevent improvement in data quality. The slip-and-slide algorithm breaks down effects of the correlated parameters and their associated target functions in a fundamental shift in the approach to the problem. Parameters are never refined against the components of the data to which they are insensitive, providing a dramatic boost in the exploitation of information from a very small number of diffraction patterns. This algorithm can be applied to exploit the adherence of the spot-finding results prior to indexing to a given lattice using unit-cell dimensions as a restraint. Alternatively, it can be applied to the predicted spot locations and the observed reflection positions after indexing from a smaller number of images. Thus, the indexing rate can be boosted by 5.8% using geometry refinement from only 125 indexed patterns or 500 unindexed patterns. In one example of cypovirus type 17 polyhedrin diffraction at the Linac Coherent Light Source, this geometry refinement reveals a detector tilt of 0.3° (resulting in a maximal Z-axis error of ∼0.5 mm from an average detector distance of ∼90 mm) whilst treating all panels independently. Re-indexing and integrating with updated detector geometry reduces systematic errors providing a boost in anomalous signal of sulfur atoms by 20%. Due to the refinement of decoupled parameters, this geometry method also reaches convergence.

Scanning X-ray diffraction on cardiac tissue: automatized data analysis and processing


A scanning X-ray diffraction study of cardiac tissue has been performed, covering the entire cross section of a mouse heart slice. To this end, moderate focusing by compound refractive lenses to micrometer spot size, continuous scanning, data acquisition by a fast single-photon-counting pixel detector, and fully automated analysis scripts have been combined. It was shown that a surprising amount of structural data can be harvested from such a scan, evaluating the local scattering intensity, interfilament spacing of the muscle tissue, the filament orientation, and the degree of anisotropy. The workflow of data analysis is described and a data analysis toolbox with example data for general use is provided. Since many cardiomyopathies rely on the structural integrity of the sarcomere, the contractile unit of cardiac muscle cells, the present study can be easily extended to characterize tissue from a diseased heart.

The effect of self-consistent potentials on EXAFS analysis


A theory program intended for use with extended X-ray-absorption fine structure (EXAFS) spectroscopy and based on the popular FEFF8 is presented. It provides an application programming interface designed to make it easy to integrate high-quality theory into EXAFS analysis software. This new code is then used to examine the impact of self-consistent scattering potentials on EXAFS data analysis by methodical testing of theoretical fitting standards against a curated suite of measured EXAFS data. For each data set, the results of a fit are compared using a well characterized structural model and theoretical fitting standards computed both with and without self-consistent potentials. It is demonstrated that the use of self-consistent potentials has scant impact on the results of the EXAFS analysis.

A novel method for resonant inelastic soft X-ray scattering via photoelectron spectroscopy detection


A method for measuring resonant inelastic X-ray scattering based on the conversion of X-ray photons into photoelectrons is presented. The setup is compact, relies on commercially available detectors, and offers significant flexibility. This method is demonstrated at the Linac Coherent Light Source with ∼0.5 eV resolution at the cobalt L3-edge, with signal rates comparable with traditional grating spectrometers.

Simulations of Co-GISAXS during kinetic roughening of growth surfaces


The recent development of surface growth studies using X-ray photon correlation spectroscopy in a grazing-incidence small-angle X-ray scattering (Co-GISAXS) geometry enables the investigation of dynamical processes during kinetic roughening in greater detail than was previously possible. In order to investigate the Co-GISAXS behavior expected from existing growth models, calculations and (2+1)-dimension simulations of linear Kuramoto–Sivashinsky and non-linear Kardar–Parisi–Zhang surface growth equations are presented which analyze the temporal correlation functions of the height–height structure factor. Calculations of the GISAXS intensity auto-correlation functions are also performed within the Born/distorted-wave Born approximation for comparison with the scaling behavior of the height–height structure factor and its correlation functions.

Characterization of X-ray gas attenuator plasmas by optical emission and tunable laser absorption spectroscopies


X-ray gas attenuators are used in high-energy synchrotron beamlines as high-pass filters to reduce the incident power on downstream optical elements. The absorption of the X-ray beam ionizes and heats up the gas, creating plasma around the beam path and hence temperature and density gradients between the center and the walls of the attenuator vessel. The objective of this work is to demonstrate experimentally the generation of plasma by the X-ray beam and to investigate its spatial distribution by measuring some of its parameters, simultaneously with the X-ray power absorption. The gases used in this study were argon and krypton between 13 and 530 mbar. The distribution of the 2p excited states of both gases was measured using optical emission spectroscopy, and the density of argon metastable atoms in the 1s5 state was deduced using tunable laser absorption spectroscopy. The amount of power absorbed was measured using calorimetry and X-ray transmission. The results showed a plasma confined around the X-ray beam path, its size determined mainly by the spatial dimensions of the X-ray beam and not by the absorbed power or the gas pressure. In addition, the X-ray absorption showed a hot central region at a temperature varying between 400 and 1100 K, depending on the incident beam power and on the gas used. The results show that the plasma generated by the X-ray beam plays an essential role in the X-ray absorption. Therefore, plasma processes must be taken into account in the design and modeling of gas attenuators.

Surface plasmon band tailoring of plasmonic nanostructure under the effect of water radiolysis by synchrotron radiation


Plasmonic metal nanostructures have a significant impact on a diverse domain of fields, including photocatalysis, antibacterial, drug vector, biosensors, photovoltaic cell, optical and electronic devices. Metal nanoparticles (MNps) are the simplest nanostructure promising ultrahigh stability, ease of manufacturing and tunable optical response. Silver nanoparticles (AgNp) dominate in the class of MNps because of their relatively high abundance, chemical activity and unique physical properties. Although MNps offer the desired physical properties, most of the synthesis and fabrication methods lag at the electronic grade due to an unbidden secondary product as a result of the direct chemical reduction process. In this paper, a facile protocol is presented for fabricating high-yield in situ plasmonic AgNps under monochromatic X-rays irradiation, without the use of any chemical reducing agent which prevents the formation of secondary products. The ascendancy of this protocol is to produce high quantitative yield with control over the reaction rate, particle size and localized surface plasmon resonance response, and also to provide the feasibility for in situ characterization. The role of X-ray energy, beam flux and integrated dose towards the fabrication of plasmonic nanostructures has been studied. This experiment extends plasmonic research and provides avenues for upgrading production technologies of MNps.

The 3D characteristics of post-traumatic syringomyelia in a rat model: a propagation-based synchrotron radiation microtomography study


Many published literature sources have described the histopathological characteristics of post-traumatic syringomyelia (PTS). However, three-dimensional (3D) visualization studies of PTS have been limited due to the lack of reliable 3D imaging techniques. In this study, the imaging efficiency of propagation-based synchrotron radiation microtomography (PB-SRµCT) was determined to detect the 3D morphology of the cavity and surrounding microvasculature network in a rat model of PTS. The rat model of PTS was established using the infinite horizon impactor to produce spinal cord injury (SCI), followed by a subarachnoid injection of kaolin to produce arachnoiditis. PB-SRµCT imaging and histological examination, as well as fluorescence staining, were conducted on the animals at the tenth week after SCI. The 3D morphology of the cystic cavity was vividly visualized using PB-SRµCT imaging. The quantitative parameters analyzed by PB-SRµCT, including the lesion and spared spinal cord tissue area, the minimum and maximum diameters in the cystic cavity, and cavity volume, were largely consistent with the results of the histological assessment. Moreover, the 3D morphology of the cavity and surrounding angioarchitecture could be simultaneously detected on the PB-SRµCT images. This study demonstrated that high-resolution PB-SRµCT could be used for the 3D visualization of trauma-induced spinal cord cavities and provides valuable quantitative data for cavity characterization. PB-SRµCT could be used as a reliable imaging technique and offers a novel platform for tracking cavity formation and morphological changes in an experimental animal model of PTS.

Characterization of a sCMOS-based high-resolution imaging system


The detection system is a key part of any imaging station. Here the performance of the novel sCMOS-based detection system installed at the ID17 biomedical beamline of the European Synchrotron Radiation Facility and dedicated to high-resolution computed-tomography imaging is analysed. The system consists of an X-ray–visible-light converter, a visible-light optics and a PCO.Edge5.5 sCMOS detector. Measurements of the optical characteristics, the linearity of the system, the detection lag, the modulation transfer function, the normalized power spectrum, the detective quantum efficiency and the photon transfer curve are presented and discussed. The study was carried out at two different X-ray energies (35 and 50 keV) using both 2× and 1× optical magnification systems. The final pixel size resulted in 3.1 and 6.2 µm, respectively. The measured characteristic parameters of the PCO.Edge5.5 are in good agreement with the manufacturer specifications. Fast imaging can be achieved using this detection system, but at the price of unavoidable losses in terms of image quality. The way in which the X-ray beam inhomogeneity limited some of the performances of the system is also discussed.

The emerging role of 4D synchrotron X-ray micro-tomography for climate and fossil energy studies: five experiments showing the present capabilities at beamline 8.3.2 at the Advanced Light Source


Continuous improvements at X-ray imaging beamlines at synchrotron light sources have made dynamic synchrotron X-ray micro-computed tomography (SXR-µCT) experiments more routinely available to users, with a rapid increase in demand given its tremendous potential in very diverse areas. In this work a survey of five different four-dimensional SXR-µCT experiments is presented, examining five different parameters linked to the evolution of the investigated system, and tackling problems in different areas in earth sciences. SXR-µCT is used to monitor the microstructural evolution of the investigated sample with the following variables: (i) high temperature, observing in situ oil shale pyrolysis; (ii) low temperature, replicating the generation of permafrost; (iii) high pressure, to study the invasion of supercritical CO2 in deep aquifers; (iv) uniaxial stress, to monitor the closure of a fracture filled with proppant, in shale; (v) reactive flow, to observe the evolution of the hydraulic properties in a porous rock subject to dissolution. For each of these examples, it is shown how dynamic SXR-µCT was able to provide new answers to questions related to climate and energy studies, highlighting the significant opportunities opened recently by the technique.

GigaFRoST: the gigabit fast readout system for tomography


Owing to recent developments in CMOS technology, it is now possible to exploit tomographic microscopy at third-generation synchrotron facilities with unprecedented speeds. Despite this rapid technical progress, one crucial limitation for the investigation of realistic dynamic systems has remained: a generally short total acquisition time at high frame rates due to the limited internal memory of available detectors. To address and solve this shortcoming, a new detection and readout system, coined GigaFRoST, has been developed based on a commercial CMOS sensor, acquiring and streaming data continuously at 7.7 GB s−1 directly to a dedicated backend server. This architecture allows for dynamic data pre-processing as well as data reduction, an increasingly indispensable step considering the vast amounts of data acquired in typical fast tomographic experiments at synchrotron beamlines (up to several tens of TByte per day of raw data).

Phase contrast imaging of preclinical portal vein embolization with CO2 microbubbles


Preoperative portal vein embolization (PVE) is employed clinically to avoid postoperative liver insufficiency. Animal models are usually used to study PVE in terms of mechanisms and pathophysiological changes. PVE is formerly monitored by conventional absorption contrast imaging (ACI) with iodine contrast agent. However, the side effects induced by iodine can give rise to animal damage and death. In this study, the feasibility of using phase contrast imaging (PCI) to show PVE using homemade CO2 microbubbles in living rats has been investigated. CO2 gas was first formed from the reaction between citric acid and sodium bicarbonate. The CO2 gas was then encapsulated by egg white to fabricate CO2 microbubbles. ACI and PCI of CO2 microbubbles were performed and compared in vitro. An additional increase in contrast was detected in PCI. PCI showed that CO2 microbubbles gradually dissolved over time, and the remaining CO2 microbubbles became larger. By PCI, the CO2 microbubbles were found to have certain stability, suggesting their potential use as embolic agents. CO2 microbubbles were injected into the main portal trunk to perform PVE in living rats. PCI exploited the differences in the refractive index and facilitated clear visualization of the PVE after the injection of CO2 microbubbles. Findings from this study suggest that homemade CO2 microbubbles-based PCI is a novel modality for preclinical PVE research.

Enhancement of radiosensitivity of oral carcinoma cells by iodinated chlorin p6 copper complex in combination with synchrotron X-ray radiation


The combination of synchrotron X-ray radiation and metal-based radiosensitizer is a novel form of photon activation therapy which offers the advantage of treating malignant tumors with greater efficacy and higher precision than conventional radiation therapy. In this study the anticancer cytotoxic efficacy of a new chlorophyll derivative, iodinated chlorin p6 copper complex (ICp6-Cu), combined with synchrotron X-ray radiation (8–10 keV) in two human oral cancer cell lines is explored. Pre-treatment of cells with 20 µM and 30 µM ICp6-Cu for 3 h was found to enhance the X-ray-induced cytotoxicity with sensitization enhancement ratios of 1.8 and 2.8, respectively. ICp6-Cu localized in cytoplasm, mainly in lysosomes and endoplasmic reticulum, and did not cause any cytotoxicity alone. The radiosensitization effect of ICp6-Cu accompanied a significant increase in the level of reactive oxygen species, damage to lysosomes, inhibition of repair of radiation-induced DNA double-strand breaks, increase in cell death and no significant effect on cell cycle progression. These results demonstrate that ICp6-Cu is a potential agent for synchrotron photon activation therapy of cancer.

Early commissioning results for spectroscopic X-ray Nano-Imaging Beamline BL 7C sXNI at PLS-II


For spectral imaging of chemical distributions using X-ray absorption near-edge structure (XANES) spectra, a modified double-crystal monochromator, a focusing plane mirrors system and a newly developed fluorescence-type X-ray beam-position monitoring and feedback system have been implemented. This major hardware upgrade provides a sufficiently stable X-ray source during energy scanning of more than hundreds of eV for acquisition of reliable XANES spectra in two-dimensional and three-dimensional images. In recent pilot studies discussed in this paper, heavy-metal uptake by plant roots in vivo and iron's phase distribution in the lithium–iron–phosphate cathode of a lithium-ion battery have been imaged. Also, the spatial resolution of computed tomography has been improved from 70 nm to 55 nm by means of run-out correction and application of a reconstruction algorithm.

syris: a flexible and efficient framework for X-ray imaging experiments simulation


An open-source framework for conducting a broad range of virtual X-ray imaging experiments, syris, is presented. The simulated wavefield created by a source propagates through an arbitrary number of objects until it reaches a detector. The objects in the light path and the source are time-dependent, which enables simulations of dynamic experiments, e.g. four-dimensional time-resolved tomography and laminography. The high-level interface of syris is written in Python and its modularity makes the framework very flexible. The computationally demanding parts behind this interface are implemented in OpenCL, which enables fast calculations on modern graphics processing units. The combination of flexibility and speed opens new possibilities for studying novel imaging methods and systematic search of optimal combinations of measurement conditions and data processing parameters. This can help to increase the success rates and efficiency of valuable synchrotron beam time. To demonstrate the capabilities of the framework, various experiments have been simulated and compared with real data. To show the use case of measurement and data processing parameter optimization based on simulation, a virtual counterpart of a high-speed radiography experiment was created and the simulated data were used to select a suitable motion estimation algorithm; one of its parameters was optimized in order to achieve the best motion estimation accuracy when applied on the real data. syris was also used to simulate tomographic data sets under various imaging conditions which impact the tomographic reconstruction accuracy, and it is shown how the accuracy may guide the selection of imaging conditions for particular use cases.

Post-sample aperture for low background diffraction experiments at X-ray free-electron lasers


The success of diffraction experiments from weakly scattering samples strongly depends on achieving an optimal signal-to-noise ratio. This is particularly important in single-particle imaging experiments where diffraction signals are typically very weak and the experiments are often accompanied by significant background scattering. A simple way to tremendously reduce background scattering by placing an aperture downstream of the sample has been developed and its application in a single-particle X-ray imaging experiment at FLASH is demonstrated. Using the concept of a post-sample aperture it was possible to reduce the background scattering levels by two orders of magnitude.

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