An innovative in situ AFM system for a soft X-ray spectromicroscopy synchrotron beamline.

Multimodal imaging and spectroscopy like concurrent scanning transmission X-ray microscopy (STXM) and X-ray fluorescence (XRF) are highly desirable as they allow retrieving complementary information. This paper reports on the design, development, integration and field testing of a novel in situ atomic force microscopy (AFM) instrument for operation under high vacuum in a synchrotron soft X-ray microscopy STXM-XRF end-station. A combination of µXRF and AFM is demonstrated for the first time in the soft X-ray regime, with an outlook for the full XRF-STXM-AFM combination.

Rare earth element identification and quantification in millimetre-sized Ryugu rock fragments from the Hayabusa2 space mission.

Millimetre-sized primordial rock fragments originating from asteroid Ryugu were investigated using high energy X-ray fluorescence spectroscopy, providing 2D and 3D elemental distribution and quantitative composition information on the microscopic level. Samples were collected in two phases from two sites on asteroid Ryugu and safely returned to Earth by JAXA's asteroid explorer Hayabusa2, during which time the collected material was stored and maintained free from terrestrial influences, including exposure to Earth's atmosphere. Several grains of interest were identified and further characterised to obtain quantitative information on the rare earth element (REE) content within said grains, following a reference-based and computed-tomography-assisted fundamental parameters quantification approach. Several orders of magnitude REE enrichments compared to the mean CI chondrite composition were found within grains that could be identified as apatite phase. Small enrichment of LREE was found for dolomite grains and slight enrichment or depletion for the general matrices within the Ryugu rock fragments A0055 and C0076, respectively. Supplementary Information: The online version contains supplementary material available at 10.1186/s40623-022-01705-3.

Quantitative Reconstruction of Polychromatic X-ray Fluorescence Computed Tomography Using Transmission Tomography.

Through measuring the intensity of the fluorescence X-rays emitted by the elements of interest, X-ray fluorescence computed tomography (XFCT) is capable of mapping the elemental distribution inside an object without destructively sectioning it. With the recent advances in XFCT utilizing polychromatic microfocus X-ray sources, it is expected that the popularity of such imaging modality will rise further. However, XFCT suffers from self-absorption effects, which make it challenging to reconstruct the elemental distribution inside the sample accurately. For this reason, polychromatic XFCT is mainly used to retrieve the distribution of elements with a relatively high atomic number (Z) when compared to the matrix of the sample. To enable the quantitative reconstruction of trace and low Z elements with polychromatic XFCT, a novel reconstruction method has been proposed in this manuscript. Through examining the proposed method on both simulation data and experimental data, its capacity on retrieving the density distribution of relatively low Z elements has been confirmed.

Monte Carlo Simulation Aided Quantitative Laboratory X-ray Fluorescence Analysis and Its Application in Provenancing Studies for Geo-Archeological Samples.

A laboratory-based X-ray fluorescence (XRF) methodology is presented for standardless quantified analysis based on a monochromatic X-ray spectrometer coupled to Monte Carlo aided quantification. This procedure will be valuable for many scientific fields (e.g. archaeology, geology, etc.) where the unique nature of the investigated samples calls for the application of non-destructive techniques. To illustrate the value of the methodology, a case study is presented where flint artefacts from the Scheldt basin are analyzed in an attempt to provenance them. So far, little geochemical research has been done in this area. Our results contribute to the creation of a database that will help assign lithic artefacts to specific geological outcrops and will aid further research in this field.

Improved Micro-X-ray Fluorescence Confocal Imaging of Two-Dimensional Distribution of Arsenic Concentration in Cucumber Hypocotyls Using Synchrotron Radiation.

An optimized micro-X-ray fluorescence confocal imaging (µXRF-CI) analytical method has been developed to determine the 2D distribution of elemental composition in small (1-3 mm) biological objects at a 10-20 µm spatial resolution. Plants take up chemical elements from soil, and the vascular system transports them toward shoots. In order to obtain biochemical information related to this biological process, 2D distributions of chemical elements in roots and in hypocotyls of cucumber plants were analyzed by synchrotron radiation based on micro-X-ray fluorescence computer tomography and µXRF-CI techniques. The experiments were carried out at HASYLAB Beamline L of the DORIS-III storage ring in Hamburg, a facility that provided optimal physical conditions for developing and performing these unique analyses: high flux monochromatic synchrotron beam, X-ray optical elements, precision moving stages, and silicon drift detectors. New methodological improvements and experimental studies were carried out for applicability of lyophilized samples and cryo-cooling. Experimental parameters were optimized to maximize the excitation yield of arsenic Kα radiation and improvement of the spatial resolution of the µXRF-CI analytical method.

Identification of the Calcium, Aluminum, and Magnesium Distribution within Millimeter-Sized Extraterrestrial Materials Using Nonresonant X-ray Raman Spectroscopy in Preparation for the Hayabusa2 Sample Return Mission.

The nondestructive investigation of millimeter-sized meteoritic materials is often hindered by self-absorption effects. Using X-ray-based analytical methods, the information depth for many elements (Z < 30) is in the range of up to only a few hundred micrometers, and for low-Z elements (Z < 20), this is reduced even further to only a few tens of micrometers. However, the investigation of these low-Z elements, in particular calcium, aluminum, and magnesium, is of great importance to planetary geologists and cosmochemists, as these elements are regularly used to characterize and identify specific features of interest in extraterrestrial materials, especially primitive chondritic material. In this work, nonresonant inelastic X-ray scattering from core electrons was performed at beamline ID20 of the ESRF in a direct tomography approach in order to visualize these low-Z elements within the millimeter-sized meteoritic samples. The obtained 3D elemental distribution volumes were compared to results from X-ray fluorescence-CT and absorption CT experiments and were found to be in good agreement. Additionally, several regions of interest could be identified within the inelastic scattering volumes, containing information that is not available through the other presented means. As such, the proposed approach presents a valuable tool for the nondestructive investigation of low-Z elemental distributions within millimeter-sized extraterrestrial materials, such as the samples of the Hayabusa2 sample return mission.

Highly Sensitive Nondestructive Rare Earth Element Detection by Means of Wavelength-Dispersive X-ray Fluorescence Spectroscopy Enabled by an Energy Dispersive pn-Charge-Coupled-Device Detector.

Detection of rare earth elements (REE) is commonly performed with destructive techniques such as (LA)-ICPMS or coupled to a destructive sample preparation. When investigating unique geological samples, such as cometary, asteroidal, or interstellar material from sample return missions or inclusions in deep Earth diamonds, a nondestructive method is preferred. The presented nondestructive highly sensitive wavelength-dispersive X-ray fluorescence spectroscopy (WD-XRF) technique is designed to measure the L-lines of REE between 4.5 and 7 keV with a sensitivity down to the ppm level. REE fluorescence L-lines are often only separated by a few eV from neighboring XRF-lines and cannot be resolved by an energy dispersive approach especially in the presence of transition metal K-lines. In our spectrometer the characteristic X-rays emitted by the sample are dispersed by a fixed Ge(111) analyzer crystal over the active area of an energy dispersive pn-charge-coupled-device (pnCCD) detector, enabling high energy resolution detection of X-rays differentiated by their corresponding Bragg angles. The use of an energy-dispersive 2D detector enables the simultaneous acquiring of XRF-lines while eliminating any ambiguities due to potential contribution from higher order diffraction effects or other diffraction planes and thereby increases the sensitivity by reducing the (scatter) background. This detection method shows an energy resolution of 12 eV for the Ti-Kα fluorescence line and has a sensitivity down to 0.50 ppm for REE L-lines. The method was optimized specifically for the nondestructive analysis of inclusions in deep Earth diamonds, yielding in situ quantitative information about up-to-now inaccessible elemental (REE) composition patterns together with the more abundant transition metals like Ti, Cr, Mn, and Fe. This information is of great importance to decipher the role that deep Earth plays in the global carbon and fluid cycle.

Full-field spectroscopic measurement of the X-ray beam from a multilayer monochromator using a hyperspectral X-ray camera.

Multilayer monochromator devices are commonly used at (imaging) beamlines of synchrotron facilities to shape the X-ray beam to relatively small bandwidth and high intensity. However, stripe artefacts are often observed and can deteriorate the image quality. Although the intensity distribution of these artefacts has been described in the literature, their spectral distribution is currently unknown. To assess the spatio-spectral properties of the monochromated X-ray beam, the direct beam has been measured for the first time using a hyperspectral X-ray detector. The results show a large number of spectral features with different spatial distributions for a [Ru, B4C] strip monochromator, associated primarily with the higher-order harmonics of the undulator and monochromator. It is found that their relative contributions are sufficiently low to avoid an influence on the imaging data. The [V, B4C] strip suppresses these high-order harmonics even more than the former, yet at the cost of reduced efficiency.

Nanoscopic X-ray imaging and quantification of the iron cellular architecture within single fibroblasts of Friedreich's ataxia patients.

Friedreich's ataxia (FRDA) is a neurodegenerative disease characterized by an increase in intracytoplasmic iron concentration. Here the nanoscale iron distribution within single fibroblasts from FRDA patients was investigated using synchrotron-radiation-based nanoscopic X-ray fluorescence and X-ray in-line holography at the ID16A nano-imaging beamline of the ESRF. This unique probe was deployed to uncover the iron cellular two-dimensional architecture of freeze-dried FRDA fibroblasts. An unsurpassed absolute detection capability of 180 iron atoms within a 30 nm × 50 nm nanoscopic X-ray beam footprint was obtained using state-of-the-art X-ray focusing optics and a large-solid-angle detection system. Various micrometre-sized iron-rich organelles could be revealed for the first time, tentatively identified as endoplasmic reticulum, mitochondria and lysosomes. Also a multitude of nanoscopic iron hot-spots were observed in the cytosol, interpreted as chaperoned iron within the fibroblast's labile iron pool. These observations enable new hypotheses on the storage and trafficking of iron in the cell and ultimately to a better understanding of iron-storage diseases such as Friedreich's ataxia.

Investigation of (micro-)meteoritic materials at the new hard X-ray imaging PUMA beamline for heritage sciences.

At the French synchrotron facility SOLEIL, a new X-ray imaging facility PUMA (Photons Utilisés pour les Matériaux Anciens) has been made available to scientific communities studying materials from cultural heritage. This new instrument aims to achieve 2D and 3D imaging with microscopic resolution, applying different analytical techniques including X-ray fluorescence spectroscopy (XRF), X-ray absorption spectroscopy (XAS), X-ray diffraction and phase-contrast imaging. In order to discover its capabilities a detailed analytical characterization of this beamline as an analytical and imaging tool is deemed necessary. In this work, (confocal) XRF and XAS analyses are demonstrated using the Seymchan pallasite meteorite and an Antarctic unmelted micrometeorite as case studies. The obtained spatial resolution (2 µm × 3 µm) and sensitivity (detection limits <10 p.p.m. for 1 s acquisition at 18 keV) show that PUMA is a competitive state-of-the-art beamline, providing several high-profile and high-in-demand analytical methods while maintaining applicability towards a wide range of heritage-oriented sciences.

Correlations between As in Earthworms' Coelomic Fluid and As Bioavailability in Highly Polluted Soils as Revealed by Combined Laboratory X-ray Techniques.

Combined X-ray-based spectroscopy techniques were applied to investigate arsenic (As) bioaccumulation in earthworms (Eisenia andrei) exposed to six field-collected polluted soils (58-13 330 mg As kg-1). After 14 days of exposure to the arsenious soils, the As distribution in earthworms was examined by micro-X-ray fluorescence spectroscopy (µXRF), after epoxy resin embedding and preparing thin sections. Similar to µXRF data, XRF-computed tomography (XRF-CT) confirmed As accumulation in the coelom of intact earthworms. Therefore, total-reflection XRF was used to determine total As within both the whole earthworm's body (AsE) and coelomic fluid extracts (AsF). Bioaccumulation data (AsE and AsF) were thereafter evaluated in relation to total As concentration in soils (AsT) and to As mobile fraction in soils. A significant linear correlation (R2 = 0.97) was found between AsE and AsF, indicating that the As sequestrated into the coelomic fluid may reflect the total body concentration. Therefore, we may conclude that the As concentration in the coelomic fluid can be used as an index of As availability. This paper demonstrates that by combining different laboratory X-ray analytical techniques, compartmentalization and bioavailability of potentially toxic elements can be visualized and quantified within indicator-living organisms, thus contributing to an improved risk assessment for contaminated soils.

Correction to: Three-dimensional reconstruction of the distribution of elemental tags in single cells using laser ablation ICP-mass spectrometry via registration approaches.

The authors would like to call the reader's attention to the fact that unfortunately the originally provided affiliation for Dr. Tomoko Asaoka was not correct.

Three-dimensional reconstruction of the distribution of elemental tags in single cells using laser ablation ICP-mass spectrometry via registration approaches.

This paper describes a workflow towards the reconstruction of the three-dimensional elemental distribution profile within human cervical carcinoma cells (HeLa), at a spatial resolution down to 1 µm, employing state-of-the-art laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) instrumentation. The suspended cells underwent a series of fixation/embedding protocols and were stained with uranyl acetate and an Ir-based DNA intercalator. A priori, laboratory-based absorption micro-computed tomography (µ-CT) was applied to acquire a reference frame of the morphology of the cells and their spatial distribution before sectioning. After CT analysis, a trimmed 300 × 300 × 300 µm3 block was sectioned into a sequential series of 132 sections with a thickness of 2 µm, which were subjected to LA-ICP-MS imaging. A pixel acquisition rate of 250 pixels s-1 was achieved, through a bidirectional scanning strategy. After acquisition, the two-dimensional elemental images were reconstructed using the timestamps in the laser log file. The synchronization of the data required an improved optimization algorithm, which forces the pixels of scans in different ablation directions to be spatially coherent in the direction orthogonal to the scan direction. The volume was reconstructed using multiple registration approaches. Registration using the section outline itself as a fiducial marker resulted into a volume which was in good agreement with the morphology visualized in the µ-CT volume. The 3D µ-CT volume could be registered to the LA-ICP-MS volume, consisting of 2.9 × 107 voxels, and the nucleus dimensions in 3D space could be derived.

Revealing metallic ink in Herculaneum papyri.

Writing on paper is essential to civilization, as Pliny the Elder remarks in his Natural History, when he describes the various types of papyri, the method of manufacturing them, and all that concerns writing materials in the mid-first century AD. For this reason, a rigorous scientific study of writing is of fundamental importance for the historical understanding of ancient societies. We show that metallic ink was used several centuries earlier than previously thought. In particular, we found strong evidence that lead was intentionally used in the ink of Herculaneum papyri and discuss the possible existence of ruled lines traced on the papyrus texture. In addition, the metallic concentrations found in these fragments deliver important information in view of optimizing future computed tomography (CT) experiments on still-unrolled Herculaneum scrolls to improve the readability of texts in the only surviving ancient Greco-Roman library.

Polycapillary Optics Based Confocal Micro X-ray Fluorescence and X-ray Absorption Spectroscopy Setup at The European Synchrotron Radiation Facility Collaborative Research Group Dutch-Belgian Beamline, BM26A.

A novel plug-and-play setup based on polycapillary X-ray optics enables three-dimensional (3D) confocal X-ray fluorescence (XRF) and X-ray absorption spectroscopy down to 8 × 8 × 11 µm3 (17 keV) at the European Synchrotron Radiation Facility Collaborative Research Group Dutch-Belgian Beamline, BM26A. A complete description and analytical characterization is presented, together with two recently performed experimental cases. In Deep Earth diamond São Luiz-Frankfurt am Main 16, an olivine-rich inclusion was mapped with full 3D XRF elemental imaging. The preliminary tests on Iron Gall ink contained in an historical document, a letter from the court of King Philip II of Spain, reveal both the delicate nature of Iron Gall ink and the lack of Fe-Ni chemical bonding.

Luminescent thermometer based on Eu3+ /Tb3+ -organic-functionalized mesoporous silica.

In this work we investigate a mesoporous silica (MS) decorated with dipyridyl-pyridazine (dppz) ligands and further grafted with a mixture of Eu3+ /Tb3+ ions (28.45%:71.55%), which was investigated as a potential thermometer in the 10-360 K temperature range. The MS material was prepared employing a hetero Diels-Alder reaction: 3,6-di(2-pyridyl)-1,2,4,5-tetrazine was reacted with the double bonds of vinyl-silica (vSilica) followed by an oxidation procedure. We explore using the dppz-vSilica material to obtain visible emitting luminescent materials and for obtaining a luminescent thermometer when grafted with Eu3+ /Tb3+ ions. For the dppz-vSilica@Eu,Tb material absolute sensitivity Sa of 0.011 K-1 (210 K) and relative sensitivity Sr of 1.32 %K-1 (260 K) were calculated showing good sensing capability of the material. Upon temperature change from 10 K to 360 K the emission color of the material changed gradually from yellow to red.

Integrated Three-Dimensional Microanalysis Combining X-Ray Microtomography and X-Ray Fluorescence Methodologies.

A novel 3D elemental and morphological analysis approach is presented combining X-ray computed tomography (µCT), X-ray fluorescence (XRF) tomography, and confocal XRF analysis in a single laboratory instrument (Herakles). Each end station of Herakles (µCT, XRF-CT, and confocal XRF) represents the state-of-the-art of currently available laboratory techniques. The integration of these techniques enables linking the (quantitative) spatial distribution of chemical elements within the investigated materials to their three-dimensional (3D) internal morphology/structure down to 1-10 µm resolution level, which has not been achieved so-far using laboratory X-ray techniques. The concept of Herakles relies strongly on its high precision (around 100 nm) air-bearing motor system that connects the different end-stations, allowing combined measurements based on the above X-ray techniques while retaining the coordinate system. In-house developed control and analysis software further ensures a smooth integration of the techniques. Case studies on a Cu test pattern, a Daphnia magna model organism and a perlite biocatalyst support material demonstrate the attainable resolution, elemental sensitivity of the instrument, and the strength of combining these three complementary methodologies.

Application toward Confocal Full-Field Microscopic X-ray Absorption Near Edge Structure Spectroscopy.

Using X-ray absorption near edge structure (XANES) spectroscopy, information on the local chemical structure and oxidation state of an element of interest can be acquired. Conventionally, this information can be obtained in a spatially resolved manner by scanning a sample through a focused X-ray beam. Recently, full-field methods have been developed to obtain direct 2D chemical state information by imaging a large sample area. These methods are usually in transmission mode, thus restricting the use to thin and transmitting samples. Here, a fluorescence method is displayed using an energy-dispersive pnCCD detector, the SLcam, characterized by measurement times far superior to what is generally applicable. Additionally, this method operates in confocal mode, thus providing direct 3D spatially resolved chemical state information from a selected subvolume of a sample, without the need of rotating a sample. The method is applied to two samples: a gold-supported magnesia catalyst (Au/MgO) and a natural diamond containing Fe-rich inclusions. Both samples provide XANES spectra that can be overlapped with reference XANES spectra, allowing this method to be used for fingerprinting and linear combination analysis of known XANES reference compounds.

Three-Dimensional Reconstruction of the Tissue-Specific Multielemental Distribution within Ceriodaphnia dubia via Multimodal Registration Using Laser Ablation ICP-Mass Spectrometry and X-ray Spectroscopic Techniques.

In this work, the three-dimensional elemental distribution profile within the freshwater crustacean Ceriodaphnia dubia was constructed at a spatial resolution down to 5 µm via a data fusion approach employing state-of-the-art laser ablation-inductively coupled plasma-time-of-flight mass spectrometry (LA-ICP-TOFMS) and laboratory-based absorption microcomputed tomography (µ-CT). C. dubia was exposed to elevated Cu, Ni, and Zn concentrations, chemically fixed, dehydrated, stained, and embedded, prior to µ-CT analysis. Subsequently, the sample was cut into 5 µm thin sections that were subjected to LA-ICP-TOFMS imaging. Multimodal image registration was performed to spatially align the 2D LA-ICP-TOFMS images relative to the corresponding slices of the 3D µ-CT reconstruction. Mass channels corresponding to the isotopes of a single element were merged to improve the signal-to-noise ratios within the elemental images. In order to aid the visual interpretation of the data, LA-ICP-TOFMS data were projected onto the µ-CT voxels representing tissue. Additionally, the image resolution and elemental sensitivity were compared to those obtained with synchrotron radiation based 3D confocal µ-X-ray fluorescence imaging upon a chemically fixed and air-dried C. dubia specimen.

Sensing the framework state and guest molecules in MIL-53(Al) via the electron paramagnetic resonance spectrum of VIV dopant ions.

X-ray diffraction (XRD) and electron paramagnetic resonance spectroscopy (EPR) were combined to study the structural transformations induced by temperature, pressure and air humidity of the "breathing" metal-organic framework (MOF) MIL-53(Al), doped with paramagnetic VIV ions, after activation. The correlation between in situ XRD and thermogravimetric analysis measurements showed that upon heating this MOF in air, starting from ambient temperature and pressure, the narrow pore framework first dehydrates and after that makes the transition to a large pore state (lp). The EPR spectra of VIV[double bond, length as m-dash]O molecular ions, replacing Al-OH in the structure, also allow to distinguish the as synthesized, hydrated (np-h) and dehydrated narrow pore (np-d), and lp states of MIL-53(Al). A careful analysis of EPR spectra recorded at microwave frequencies between 9.5 and 275 GHz demonstrates that all VIV[double bond, length as m-dash]O in the np-d and lp states are equivalent, whereas in the np-h state (at least two) slightly different VIV[double bond, length as m-dash]O sites exist. Moreover, the lp MIL-53(Al) framework is accessible to oxygen, leading to a notable broadening of the VIV[double bond, length as m-dash]O EPR spectrum at pressures of a few mbar, while such effect is absent for the np-h and np-d states for pressures up to 1 bar.