HERMES – a GUI-based software tool for pre-processing of X-ray absorption spectroscopy data from laboratory Rowland circle spectrometers

HERMES, a graphical user interface software tool, is presented, for pre-processing X-ray absorption spectroscopy (XAS) data from laboratory Rowland circle spectrometers, to meet the data handling needs of a growing community of practice. HERMES enables laboratory XAS data to be displayed for quality assessment, merging of data sets, polynomial fitting of smoothly varying data, and correction of data to the true energy scale and for dead-time and leakage effects. The software is written in Java 15 programming language, and runs on major computer operating systems, with graphics implementation using the JFreeChart toolkit. HERMES is freely available and distributed under an open source licence.

Development of an experimental apparatus to observe ultrafast phenomena by tender X-ray absorption spectroscopy at PAL-XFEL

Understanding the ultrafast dynamics of molecules is of fundamental importance. Time-resolved X-ray absorption spectroscopy (TR-XAS) is a powerful spectroscopic technique for unveiling the time-dependent structural and electronic information of molecules that has been widely applied in various fields. Herein, the design and technical achievement of a newly developed experimental apparatus for TR-XAS measurements in the tender X-ray range with X-ray free-electron lasers (XFELs) at the Pohang Accelerator Laboratory XFEL (PAL-XFEL) are described. Femtosecond TR-XAS measurements were conducted at the Ru L 3-edge of well known photosensitizer tris(bipyridine)ruthenium(II) chloride ([Ru(bpy)3]2+) in water. The results indicate ultrafast photoinduced electron transfer from the Ru center to the ligand, which demonstrates that the newly designed setup is applicable for monitoring ultrafast reactions in the femtosecond domain.

Virtual histology of archaeological human deciduous prenatal enamel through synchrotron X-ray computed microtomography images

Virtual histology is increasingly utilized to reconstruct the cell mechanisms underlying dental morphology for fragile fossils when physical thin sections are not permitted. Yet, the comparability of data derived from virtual and physical thin sections is rarely tested. Here, the results from archaeological human deciduous incisor physical sections are compared with virtual ones obtained by phase-contrast synchrotron radiation computed microtomography (SRµCT) of intact specimens using a multi-scale approach. Moreover, virtual prenatal daily enamel secretion rates are compared with those calculated from physical thin sections of the same tooth class from the same archaeological skeletal series. Results showed overall good visibility of the enamel microstructures in the virtual sections which are comparable to that of physical ones. The highest spatial resolution SRµCT setting (effective pixel size = 0.9 µm) produced daily secretion rates that matched those calculated from physical sections. Rates obtained using the lowest spatial resolution setup (effective pixel size = 2.0 µm) were higher than those obtained from physical sections. The results demonstrate that virtual histology can be applied to the investigated samples to obtain reliable and quantitative measurements of prenatal daily enamel secretion rates.

Chemical and elemental mapping of spent nuclear fuel sections by soft X-ray spectromicroscopy

Soft X-ray spectromicroscopy at the O K-edge, U N 4,5-edges and Ce M 4,5-edges has been performed on focused ion beam sections of spent nuclear fuel for the first time, yielding chemical information on the sub-micrometer scale. To analyze these data, a modification to non-negative matrix factorization (NMF) was developed, in which the data are no longer required to be non-negative, but the non-negativity of the spectral components and fit coefficients is largely preserved. The modified NMF method was utilized at the O K-edge to distinguish between two components, one present in the bulk of the sample similar to UO2 and one present at the interface of the sample which is a hyperstoichiometric UO2+x species. The species maps are consistent with a model of a thin layer of UO2+x over the entire sample, which is likely explained by oxidation after focused ion beam (FIB) sectioning. In addition to the uranium oxide bulk of the sample, Ce measurements were also performed to investigate the oxidation state of that fission product, which is the subject of considerable interest. Analysis of the Ce spectra shows that Ce is in a predominantly trivalent state, with a possible contribution from tetravalent Ce. Atom probe analysis was performed to provide confirmation of the presence and localization of Ce in the spent fuel.

Foam-like phantoms for comparing tomography algorithms

Tomographic algorithms are often compared by evaluating them on certain benchmark datasets. For fair comparison, these datasets should ideally (i) be challenging to reconstruct, (ii) be representative of typical tomographic experiments, (iii) be flexible to allow for different acquisition modes, and (iv) include enough samples to allow for comparison of data-driven algorithms. Current approaches often satisfy only some of these requirements, but not all. For example, real-world datasets are typically challenging and representative of a category of experimental examples, but are restricted to the acquisition mode that was used in the experiment and are often limited in the number of samples. Mathematical phantoms are often flexible and can sometimes produce enough samples for data-driven approaches, but can be relatively easy to reconstruct and are often not representative of typical scanned objects. In this paper, we present a family of foam-like mathematical phantoms that aims to satisfy all four requirements simultaneously. The phantoms consist of foam-like structures with more than 100000 features, making them challenging to reconstruct and representative of common tomography samples. Because the phantoms are computer-generated, varying acquisition modes and experimental conditions can be simulated. An effectively unlimited number of random variations of the phantoms can be generated, making them suitable for data-driven approaches. We give a formal mathematical definition of the foam-like phantoms, and explain how they can be generated and used in virtual tomographic experiments in a computationally efficient way. In addition, several 4D extensions of the 3D phantoms are given, enabling comparisons of algorithms for dynamic tomography. Finally, example phantoms and tomographic datasets are given, showing that the phantoms can be effectively used to make fair and informative comparisons between tomography algorithms.

Implementation of cryogenic tender X-ray HR-XANES spectroscopy at the ACT station of the CAT-ACT beamline at the KIT Light Source

The ACT experimental station of the CAT-ACT wiggler beamline at the Karlsruhe Institute of Technology (KIT) Light Source is dedicated to the investigation of radionuclide materials with radioactivities up to 1000000 times the exemption limit by various speciation techniques applying monochromatic X-rays. In this article, the latest technological developments at the ACT station that enable high-resolution X-ray absorption near-edge structure (HR-XANES) spectroscopy for low radionuclide loading samples are highlighted – encompassing the investigation of actinide elements down to 1 p.p.m. concentration – combined with a cryogenic sample environment reducing beam-induced sample alterations. One important part of this development is a versatile gas tight plexiglass encasement ensuring that all beam paths in the five-analyzer-crystal Johann-type X-ray emission spectrometer run within He atmosphere. The setup enables the easy exchange between different experiments (conventional X-ray absorption fine structure, HR-XANES, high-energy or wide-angle X-ray scattering, tender to hard X-ray spectroscopy) and opens up the possibility for the investigation of environmental samples, such as specimens containing transuranium elements from contaminated land sites or samples from sorption and diffusion experiments to mimic the far field of a breached nuclear waste repository.

The CirPAD, a circular 1.4 M hybrid pixel detector dedicated to X-ray diffraction measurements at Synchrotron SOLEIL

One of the challenges of all synchrotron facilities is to offer the highest performance detectors for all their specific experiments, in particular for X-ray diffraction imaging and its high throughput data collection. In that context, the DiffAbs beamline, the Detectors and the Design and Engineering groups at Synchrotron SOLEIL, in collaboration with ImXPAD and Cegitek companies, have developed an original and unique detector with a circular shape. This detector is based on the hybrid pixel photon-counting technology and consists of the specific assembly of 20 hybrid pixel array detector (XPAD) modules. This article aims to demonstrate the main characteristics of the CirPAD (for Circular Pixel Array Detector) and its performance – i.e. excellent pixel quality, flat-field correction, high-count-rate performance, etc. Additionally, the powder X-ray diffraction pattern of an LaB6 reference sample is presented and refined. The obtained results demonstrate the high quality of the data recorded from the CirPAD, which allows the proposal of its use to all scientific communities interested in performing experiments at the DiffAbs beamline.

Detection and localization of calcium oxalate in kidney using synchrotron deep ultraviolet fluorescence microscopy

Renal oxalosis is a rare cause of renal failure whose diagnosis can be challenging. Synchrotron deep ultraviolet (UV) fluorescence was assayed to improve oxalosis detection on kidney biopsies spatial resolution and sensitivity compared with the Fourier transform infrared microspectroscopy gold standard. The fluorescence spectrum of synthetic mono-, di- and tri-hydrated calcium oxalate was investigated using a microspectrometer coupled to the synchrotron UV beamline DISCO, Synchrotron SOLEIL, France. The obtained spectra were used to detect oxalocalcic crystals in a case control study of 42 human kidney biopsies including 19 renal oxalosis due to primary (PHO, n = 11) and secondary hyperoxaluria (SHO, n = 8), seven samples from PHO patients who received combined kidney and liver transplants, and 16 controls. For all oxalocalcic hydrates samples, a fluorescence signal is detected at 420 nm. These spectra were used to identify standard oxalocalcic crystals in patients with PHO or SHO. They also revealed micrometric crystallites as well as non-aggregated oxalate accumulation in tubular cells. A nine-points histological score was established for the diagnosis of renal oxalosis with 100% specificity (76–100) and a 73% sensitivity (43–90). Oxalate tubular accumulation and higher histological score were correlated to lower estimated glomerular filtration rate and higher urinary oxalate over creatinine ratio.

X-ray beam monitoring and wavelength calibration using four-beam diffraction

Rigorous dynamical theory calculations show that four-beam diffraction (4BD) can be activated only by a unique photon energy and a unique incidence direction. Thus, 4BD may be used to precisely calibrate X-ray photon energies and beam positions. Based on the principles that the forbidden-reflection 4BD pattern, which is typically an X-shaped cross, can be generated by instant imaging using the divergent beam from a point source without rocking the crystal, a detailed real-time high-resolution beam (and source) position monitoring scheme is illustrated for monitoring two-dimensional beam positions and directions of modern synchrotron light sources, X-ray free-electron lasers and nano-focused X-ray sources.

Opportunities and challenges of applying advanced X-ray spectroscopy to actinide and lanthanide N-donor ligand systems

N-donor ligands such as n-Pr-BTP [2,6-bis(5,6-dipropyl-1,2,4-triazin-3-yl)pyridine] preferentially bind trivalent actinides (An3+) over trivalent lanthanides (Ln3+) in liquid–liquid separation. However, the chemical and physical processes responsible for this selectivity are not yet well understood. Here, an explorative comparative X-ray spectroscopy and computational (L 3-edge) study for the An/Ln L 3-edge and the N K-edge of [An/Ln(n-Pr-BTP)3](NO3)3, [Ln(n-Pr-BTP)3](CF3SO3)3 and [Ln(n-Pr-BTP)3](ClO4)3 complexes is presented. High-resolution X-ray absorption near-edge structure (HR-XANES) L 3-edge data reveal additional features in the pre- and post-edge range of the spectra that are investigated using the quantum chemical codes FEFF and FDMNES. X-ray Raman spectroscopy studies demonstrate the applicability of this novel technique for investigations of liquid samples of partitioning systems at the N K-edge.