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Getting more efficient – The use of Bayesian optimization and Gaussian processes at the BAMline
(2022)
For more than 20 years, BAM is operating the BAMline at the synchrotron BESSY II in Berlin Adlershof. During this time, the complexity of the setup and the amount of data generated have multiplied. To increase the effectiveness and in preparation for BESSY III, algorithms from the field of machine learning are increasingly used.
After a short introduction to BO and GP, the first example is the automatic alignment of our double multilayer monochromator (DMM).
The second example is the optimization of measurement time in XRF scanning.
Enhancing efficiency at bamline: employing data science and machine learning for x-ray research
(2023)
This talk discusses how data science and machine learning techniques are being applied at the BAM Federal Institute for Materials Research and Testing to enhance efficiency and automation at the BAMLine synchrotron facility. The methods presented include Gaussian processes and Bayesian optimization for beamline adjustment and optimization of X-ray measurements. These statistical techniques allow automated alignment of beamline components and active learning scanning to reduce measurement time.
Additional machine learning methods covered are neural networks for quantification of X-ray fluorescence (XRF) data and decoding coded apertures.
This contribution provides an overview of the BAMline synchrotron radiation beamline, which specializes in hard X-ray spectroscopy techniques for materials research. The BAMline offers X-ray absorption spectroscopy (XAS), x-ray fluorescence spectroscopy (XRF), and tomography to study materials' electronic structure, chemical composition, and structure. Key capabilities include standard and dispersive XAS for electronic structure, micro-XRF for elemental mapping, coded aperture imaging, and depth-resolved grazing exit XAS. The BAMline enables in situ characterization during materials synthesis and functions for energy, catalysis, corrosion, biology, and cultural heritage applications.
Ongoing developments like the implementation of machine learning techniques for experiment optimization and data analysis will be discussed. For instance, Bayesian optimization is being used to improve beamline alignment and scanning. An outlook to the future, where the BAMline will continue pioneering dynamic and multi-scale characterization, aided by advanced data science methods, to provide unique insights into materials research, will be given.
With the increase in the awareness of the public in the environmental impact of oil shale utilization, it is of interest to reveal the mobility of potentially toxic trace elements in spent oil shale. Therefore, the Cr and As oxidation state in a representative Jordanian oil shale sample from the El-Lajjoun area were investigated upon different lab-scale furnace treatments. The anaerobic pyrolysis was performed in a retort flushed by nitrogen gas at temperatures in between 600 and 800 °C (pyrolytic oil shale, POS). The aerobic combustion was simply performed in porcelain cups heated in a muffle furnace for 4 h at temperatures in between 700 and 1000 °C (burned oil shale, BOS). The high loss-on-ignition in the BOS samples of up to 370 g kg–1 results from both calcium carbonate and organic carbon degradation. The LOI leads to enrichment in the Cr concentrations from 480 mg kg–1 in the original oil shale up to 675 mg kg–1 in the ≥850 °C BOS samples. Arsenic concentrations were not much elevated beyond that in the average shale standard (13 mg kg–1). Synchrotron-based X-ray absorption near-edge structure (XANES) analysis revealed that within the original oil shale the oxidation states of Cr and As were lower than after its aerobic combustion. Cr(VI) increased from 0% in the untreated or pyrolyzed oil shale up to 60% in the BOS ash combusted at 850 °C, while As(V) increased from 64% in the original oil shale up to 100% in the BOS ash at 700 °C. No Cr was released from original oil shale and POS products by the European compliance leaching test CEN/TC 292 EN 12457-1 (1:2 solid/water ratio, 24 h shaking), whereas leachates from BOS samples showed Cr release in the order of one mmol L–1. The leachable Cr content is dominated by chromate as revealed by catalytic adsorptive stripping voltammetry (CAdSV) which could cause harmful contamination of surface and groundwater in the semiarid environment of Jordan.
Synchrotron radiation-induced X-ray fluorescence (SR-XRF) spectrometry was applied to determine iodine concentrations in alluvial Pt–Pd aggregates with delicate morphological features from Córrego Bom Sucesso, Minas Gerais, Brazil. The millimetre-sized botryoidal and rod-shaped grains of alluvial Pt–Pd–Hg intermetallic compounds have surprisingly high concentrations of iodine, in the range from 10 to ~ 120 μg/g. Because iodine is a strongly biophile element, known to be enriched in peatlands and plant remains in soils by microbial activity, its concentration in the Pt–Pd nuggets suggests biogenic precious-metal fixation in the aqueous alluvial milieu. Biogenic and inorganic processes, such as bioreduction and electrochemical metal accretion, could mutually have contributed to the growth of nanoparticles, formed on organic templates, to millimetric Pt–Pd nuggets.
Although metallic nanoparticles play an important role in the area of nanotechnology, a coherent mechanistic explanation for the evolution of the particles during their chemical synthesis has not yet been provided in many cases. To gain a profound understanding of the growth mechanism of colloidal nanoparticles, new approaches using Small Angle X-Ray Scattering (SAXS) combined with X-ray absorption near-edge structure (XANES) are presented. This combination allows for insights into two prominent syntheses routes of gold nanoparticles (GNP): The 'slow' reaction using sodium citrate (30-90 min) as a reducing agent and the 'fast' reaction employing NaBH4 (within few seconds). In the first case data derived with the coupled XANES and SAXS suggests a four-step particle formation mechanism. For the second system a time resolution in the order of 100-200 ms was achieved by coupling a common laboratory SAXS instrument with a microstructured mixer, which allows data acquisition in a continuous-flow mode. The results indicate a coalescence driven growth process. Based on the capabilities to deduce the size, number and polydispersity of the particles, the results of both methods enable the development of mechanistic schemes explaining the different phases of particle formation and growth, thus providing a basis for improved control over the synthesis processes.
Synchrotron radiation induced X-ray fluorescence for the characterization of ancient gold objects
(2009)
A great challenge in the production of nanoparticles with defined sizes and properties is to control their growth in situ. We developed a dedicated combined small-angle X-ray scattering (SAXS) and X-ray absorption spectroscopy (XAS) setup to monitor nanoparticle formation in solution. The capabilities of simultaneously deriving particle sizes and oxidation states of atoms/ions are illustrated for the formation of spherical gold nanoparticles by the reduction of hydrogen tetrachloroaureate (HAuCl4). Particles with initial radii of 4.60 ± 0.10 nm and final radii of 5.67 ± 0.10 nm were produced in a levitated droplet with a volume of 4 µL. An ethylene oxide/propylene oxide triblock copolymer PEO-PPO-PEO (Pluronic F-127) functions as reducing agent and colloidal stabilizer. XANES shows in situ how the gold was reduced in the droplet from Au(III) to Au(0), and simultaneously SAXS recorded the size distribution of the formed nanoparticles. It is shown that the final particle number is reached quickly. Thereafter, only the particles sizes increase. Comparison of XANES and SAXS shows that the quantity of Au(0) is higher than the quantity of gold located in the nanoparticles while the particles are growing. Finally, all the Au(0) is found in the nanoparticles. We tentatively attribute this finding to the pseudo crown ether effect of the polymer surfactant that kinetically stabilizes gold atoms when formed from gold ions within their protecting cavity. A simple burst mechanism for the gold nanoparticle formation is the consequence. The possibility of an inhomogeneous particles structure with an enhanced density near the particle surface is discussed.
Das Hiddensee-Projekt
(2009)
In this study the microscopic homogeneity of the newly developed plastic reference materials BAM H001-BAM H010 was investigated. The materials consist of an acrylonitryle-butadien-styrene terpolymer, doped with different amounts of the elements Br, Cd, Cr, Hg and Pb. For the quantitative determination of the degree of homogeneity, a procedure proposed by Kempenaers et al. (Fresenius J. Anal. Chem., 2001, 369, 733-737) was used. On every sample an extensive number of different points were analyzed and standard deviation for every element mentioned above was used to calculate a minimal sampling mass that is necessary to reach a certain level of uncertainty caused by inhomogeneity (mmin,5%). The experiments were taken out with synchrotron µ-XRF (SR µ-XRF) at BESSYII in Berlin and by laser ablation inductively coupled plasma mass spectroscopy (LA-ICP-MS). The calculated values for mmin,5% of both techniques showed comparable results for all elements. It could be shown that the materials are suitable for calibration of micro analytic techniques if at least 64 µg are used.
X-ray scattering may contribute significantly to the spectral background of X-ray fluorescence (XRF) spectra. Based on metrological measurements carried out with a scanning electron microscope (SEM) having attached a well characterised X-ray source (polychromatic X-ray tube) and a calibrated energy dispersive X-ray spectrometer (EDS) the accuracy of a physical model for X-ray scattering is systematically evaluated for representative samples. The knowledge of the X-ray spectrometer efficiency, but also of the spectrometer response functions makes it possible to define a physical spectral background of XRF spectra. Background subtraction relying on purely mathematical procedures is state-of-the-art. The results produced by the analytical model are at least as reliable as those obtained by Monte-Carlo simulations, even without considering the very challenging contribution of multiple scattering. Special attention has been paid to Compton broadening. Relevant applications of the implementation of the analytical model presented in this paper are the prediction of the limits of detection for particular cases or the determination of the transmission of X-ray polycapillary lenses.
Measurements of ion distributions at a charged solid–liquid interface using X-ray standing waves (XSW) are presented. High energy synchrotron radiation (17.48 keV) is used to produce an XSW pattern inside a thin water film on a silicon wafer. The liquid phase is an aqueous solution containing Br and Rb ions. The surface charge is adjusted by titration. Measurements are performed over a pH range from 2.2–9, using the native Si oxide layer and functional (amine) groups as surface charge. The Debye length, indicating the extension of the diffuse layer, could be measured with values varying between 1–4 nm. For functionalized wafers, the pH dependent change from attraction to repulsion of an ion species could be detected, indicating the isoelectric point. In combination with the measurement of the streaming current, the surface charge of the sample could be quantified.
We report the results of an analytical investigation
on 416 silver-copper coins stemming from the Ottoman
Empire (end of 16th and beginning of 17th centuries), using
synchrotron micro X-ray fluorescence analysis (SRXRF).
In the past, analyses had already been conducted with energy
dispersive X-ray fluorescence analysis (EDXRF), scanning
electron microscopy with energy dispersive X-ray spectrometry
(SEM/EDX) and proton induced X-ray emission spectroscopy (PIXE).With this combination of techniques it was
possible to confirm the fineness of the coinage as well as to
study the provenance of the alloy used for the coins.
For the interpretation of the data statistical analysis
(principal component analysis—PCA) has been performed.
A definite local assignment was explored and significant
clustering was obtained regarding the minor and trace elements
composing the coin alloys.
Compact pnCCD-based X-ray camera with high spatial and energy resolution: a color X-ray camera
(2011)
For many applications there is a requirement for nondestructive analytical investigation of the elemental distribution in a sample. With the improvement of X-ray optics and spectroscopic X-ray imagers, full field X-ray fluorescence (FF-XRF) methods are feasible. A new device for high-resolution X-ray imaging, an energy and spatial resolving X-ray camera, is presented. The basic idea behind this so-called 'color X-ray camera' (CXC) is to combine an energy dispersive array detector for X-rays, in this case a pnCCD, with polycapillary optics. Imaging is achieved using multiframe recording of the energy and the point of impact of single photons. The camera was tested using a laboratory 30 µm microfocus X-ray tube and synchrotron radiation from BESSY II at the BAMline facility. These experiments demonstrate the suitability of the camera for X-ray fluorescence analytics. The camera simultaneously records 69696 spectra with an energy resolution of 152 eV for manganese Kα with a spatial resolution of 50 µm over an imaging area of 12.7 × 12.7 mm². It is sensitive to photons in the energy region between 3 and 40 keV, limited by a 50 µm beryllium window, and the sensitive thickness of 450 µm of the chip. Online preview of the sample is possible as the software updates the sums of the counts for certain energy channel ranges during the measurement and displays 2-D false-color maps as well as spectra of selected regions. The complete data cube of 264 × 264 spectra is saved for further qualitative and quantitative processing.
X-ray fluorescence imaging is a well-established tool in materials characterization. In this work, we present the adaption of coded aperture imaging to full-field X-ray fluorescence imaging at the synchrotron. Coded aperture imaging has its origins in astrophysics, and has several advantages: Coded apertures are relatively easy to fabricate, achromatic, allow a high photon throughput, and high angular acceptance. Coded aperture imaging is a two-step-process, consisting of the measurement process and a reconstruction step. Different programs have been written, for the raytracing/forward projection and the reconstruction. Experiments with coded aperture in combination with a Color X-ray Camera and an energy-dispersive area detector, have been conducted at the BAMline. Measured samples were successfully reconstructed, and gave a 9.1-fold increase in count rate compared to a polycapillary optic.
Imaging with X-rays is a challenging field, due to the optical properties of X-rays. The fabrication of appropriate optics is usually expensive and requires an elaborate manufacturing process. One simpler and less expensive possibility of imaging high energy radiation is coded aperture imaging, a technique well established in astrophysics and also used in nuclear medicine or radiation detection, e.g., for nuclear decommissioning. Our aim is to adapt coded aperture imaging for X-ray fluorescence spectroscopy in the nearfield. In this work we show theoretical considerations and preliminary simulations of Image formation through a coded aperture and three different reconstruction methods to prepare the experiments. We used a new mask based on an inverted modified uniformly redundant array (MURA) that could be used for the construction of a decoding mask for all investigated geometrical arrangements.
The most commonly used reconstruction method, convoluting the detected image with a Decoding mask, does not always deliver satisfactory results. This is more noticeable for small distances between the object, mask and detector. Hence, we developed two new reconstruction methods, one based on iterative algebraic optimization and another one based on a genetic algorithm. Both show good performance even in those cases where the convolution method fails. This provides a basis for further investigations of the ideal parameters for near field coded aperture imaging and refinements of the algorithms. We performed first measurements with a coded aperture at the BAMline at BESSY II and could successfully reconstruct a test object from the obtained recorded images.
Gold ist eines der sieben schon im Altertum bekannten Metalle und wurde wg. seines Glanzes und seiner Seltenheit von alters her als Tauschmittel und zur Herstellung von Schmuck benutzt. Außerdem ist es einfach bearbeitbar und weitestgehend gegen chemische Einflüsse resistent. Die Untersuchungen von Gold mit synchrotronstrahlungsangeregter Röntgenfluoreszenzanalyse sind zerstörungsfrei und geben Auskunft über die in der untersuchten Probe vorhandenen chemischen Elemente. Bei den hier vorgestellten Untersuchungen an der BAMline stehen Fragestellungen wie Herkunft, Herstellungsverfahren und Zusammengehörigkeit von Goldfunden im Vordergrund. Die verschiedenen Fragestellungen werden an einer Reihe von Beispielen erläutert die vom Wikingerschatz aus Hiddensee über die Himmelsscheibe von Nebra bis hin zu Funden aus Ägypten langen. Der Fund von Bernstorf wird ausführlich diskutiert.
This study intends to clarify the metal provenance of gold archaeological items using the variation of the Au–Ag ratio and the presence of trace elements as Sn, Sb, Te, and Pb, concentrating on gold Dacian Koson coins, recovered recently. It also extends the area of our investigations to the copper provenance of Bronze Age artifacts—axes, sickles, and celts—found on Romanian territory. The experiments were performed by micro-SR XRF at BESSY Berlin, at the BAM-line facility. Two types of coins (Koson, with and without monogram) were analysed. The conclusions we reached were that most of the monogram coins are made from refined gold (3–5% Ag, less than 0.5% Cu), while the without monogram coins are made from native Transylvanian gold (9–20% Ag, 0.5–2% Cu), of alluvial origin, proved by the presence of Sn, Sb and Te embedded in the gold. The problem of provenance for prehistoric Romanian copper and bronze objects consists in linking their elemental compositional patterns to the ones of the Bronze Age regional mines from Bulgaria, Serbia or Transylvania, most likely used as ore sources for their manufacture. The studied samples present relevant traces of As, Ag, Sb, and Co, suggesting the most probable use of copper from Serbia or northern Bulgaria for their manufacture.
For quantitative SRXRF measurements the angle of incidence of the incoming X-ray beam is an important factor. When the sample is focused by a long-range-microscope, the determination of the angle can be automatized using a simple algorithm. This was developed to improve the orientation of especially round or ornate samples. As a side effect the three dimensional surface can be reconstructed, too.
We present a new high resolution X-ray imager based on a pnCCD detector and a polycapillary optics. The properties of the pnCCD like high quantum efficiency, high energy resolution and radiation hardness are maintained, while color corrected polycapillary lenses are used to direct the fluorescence photons from every spot on a sample to a corresponding pixel on the detector. The camera is sensitive to photons from 3 to 40 keV with still 30% quantum efficiency at 20 keV. The pnCCD is operated in split frame mode allowing a high frame rate of 400 Hz with an energy resolution of 152 eV for Mn Kα (5.9 keV) at 450 kcps. In single-photon counting mode (SPC), the time, energy and position of every fluorescence photon is recorded for every frame. A dedicated software enables the visualization of the elements distribution in real time without the need of post-processing the data. A description of the key components including detector, X-ray optics and camera is given. First experiments show the capability of the camera to perform fast full-field X-Ray Fluorescence (FF-XRF) for element analysis. The imaging performance with a magnifying optics (3×) has also been successfully tested.
A systematic series of measurements has been carried out with monochromatic X-ray excitation with synchrotron radiation in order to check a physical model on X-ray scattering. The model has recently been successfully tested for the case of polychromatic, unpolarised excitation emitted by an X-ray tube. Our main purpose is the modelling of a physical background in X-ray fluorescence spectra, so that improved quantitative results can be achieved especially for strongly scattering specimens. The model includes single Rayleigh and Compton scattering in the specimen, the effect of bound electrons, the challenging Compton broadening and the polarisation degree. Representative specimens, measurement geometries and excitation energies have been selected with synchrotron monochromatic light at BAMline/BESSY II. Monte-Carlo simulations have been also carried out in order to evaluate the quality of the results achieved with the model.
A new setup for fast spatially resolved measurements of elemental trace amounts under total reflection conditions using a new colour X-ray camera is described. Samples prepared on conventional total reflection X-ray fluorescence (TXRF) reflectors were measured at BESSY II synchrotron. A spatial resolution of 50 × 50 µm² was obtained, while the required time for the investigation of a 10 × 10 mm² sample is 30 seconds. The set-up is up to 350 times faster than conventional X-ray fluorescence systems for elemental traces. The major components of the X-ray camera are polycapillary optics and a pn-CCD chip with an active area of 13 × 13 mm². This area is divided into 264 × 264 pixels of 48 × 48 µm². A full X-ray spectrum with a resolution of 152 eV @ 5.9 keV and a chip temperature of 246 K is recorded for each pixel. The chip has a read-out rate of 400 Hz.
Vultures hit by beam
(2005)
Synchrotron radiation (SR) has been used in recent years as an excellent excitation source for X-ray fluorescence spectrometry. SR offers, in contrast to conventional X-ray sources, highly brilliant polychromatic, polarized radiation with which micro-domain X-ray fluorescence spectrometry becomes possible. A feasibility study of utility, conducted at BESSY (Berlin) and at DELTA (Dortmund), both synchrotron facilities of the third generation, to evaluate the use of wavelength dispersive X-ray fluorescence spectrometry in combination with synchrotron radiation is presented. First results for material analysis, obtained by combining the synchrotron radiation and a commercially available spectrometer commonly attached to a scanning electron microscope, are presented. The spectrometer, of the linear type, uses curved focusing Bragg-crystals of the Johann type which leads to a high spectral resolution up to 3 eV. Examples of micro-domain analyses are presented and compared with those obtained by synchrotron radiation induced energy dispersive X-ray fluorescence.
Pilot studies have been carried out at the BAMline at BESSY II in collaboration with the Bundesanstalt
für Materialforschung und -prüfung (BAM) on metal- and metalloid-containing compounds in biological
samples after electrophoretic protein separation. After sodium dodecylsulfate polyacrylamide gel
electrophoresis (SDS-PAGE) and transfer onto a blotting membrane the distribution of selenium among
the proteins of testis homogenate of a rat and a wallaby was determined. The comparison with the
autoradiogram of 75Se-labeled proteins separated in the same way showed that of nine seleniumcontaining
proteins found in rat testis homogenate by autoradiography four could be detected by
synchrotron radiation X-ray fluorescence analysis (SRXRF).
Orientierende Versuche zur Schwefelbestimmung in Kraftstoffen haben gezeigt, dass die Röntgenbeamline der BAM bei BESSY II geeignet ist, Schwefel auch in kleinen Konzentrationen zu bestimmen. Da das Verfahren der synchrotronstrahlungsinduzierten Röntgenfluoreszenzanalyse (SYRFA) für den Vor-Ort-Einsatz nicht geeignet ist, ist das Ziel der Untersuchungen, durch Variation von Anregungsenergie und -geometrie mögliche Quellen für systematische Fehler zu untersuchen. Durch geeignete Korrekturfaktoren kann dann die Richtigkeit der Analyseergebnisse gewährleistet werden. Das Verfahren soll dann als Alternative bzw. Ergänzung zu zerstörenden Verfahren der Schwefelanalyse Anwendung finden. Damit wird ein Beitrag zur künftigen Herstellung zertifizierter Referenzmaterialien (ZRM) geleistet.
Measuring in a non-destructive way the characteristic trace elements of the metal allows following the circulation of gold in the past. The aim of this work is to probe the possibilities of X-ray fluorescence with high energy synchrotron radiation (SR-XRF) at the BAMline at BESSY II to determine the concentration of Pt in ancient gold alloys. A HP-Ge detector was used to measure the Pt K-lines excited with an incident energy of 79.5 keV. Data processing was done by subtraction of a Pt free gold standard spectrum from the spectrum of the sample. Depending on the sample composition, the MDL ranges between 40 and 90 ppm. The first results obtained for a small set of gold alloys of different thickness, size and composition showed that high energy SR-XRF is a significant method for the non-destructive determination of Pt in gold.
Naturwissenschaftler arbeiten mit Archäologen, Kunsthistorikern und Restauratoren zusammen, um Materialinformationen über Kunstwerke mit den Erkenntnissen aus Altertumsforschung, Kunstgeschichte und Denkmalpflege zu verbinden. Röntgenfluoreszenz und Röntgenemission sind die Methoden der Wahl, wenn wertvolle und fragile Objekte zerstörungsfrei zu untersuchen sind.