Machine Learning-based Techniques to Address Spectral Distortions in Photon Counting X-ray Computed Tomography

Spectral CT using a photon counting x-ray detector (PCXD) shows great potential for measuring material composition based on energy dependent x-ray attenuation. Spectral CT is especially suited for imaging with K-edge contrast agents to address the otherwise limited contrast in soft tissues. We have developed a micro-CT system based on a PCXD. This system enables full spectrum CT in which the energy thresholds of the PCXD are swept to sample the full energy spectrum for each detector element and projection angle. Measurements provided by the PCXD, however, are distorted due to undesirable physical eects in the detector and are very noisy due to photon starvation. In this work, we proposed two methods based on machine learning to address the spectral distortion issue and to improve the material decomposition. This rst approach is to model distortions using an articial neural network (ANN) and compensate for the distortion in a statistical reconstruction. The second approach is to directly correct for the distortion in the projections. Both technique can be done as a calibration process where the neural network can be trained using 3D printed phantoms data to learn the distortion model or the correction model of the spectral distortion. This replaces the need for synchrotron measurements required in conventional technique to derive the distortion model parametrically which could be costly and time consuming. The results demonstrate experimental feasibility and potential advantages of ANN-based distortion modeling and correction for more accurate K-edge imaging with a PCXD. Given the computational eciency with which the ANN can be applied to projection data, the proposed scheme can be readily integrated into existing CT reconstruction pipelines.

Raw and normalized X-ray fluorescence (XRF) scannings of IODP Expedition 321, Site U1338

We used X-ray fluorescence (XRF) scanning on Site U1338 sediments from Integrated Ocean Drilling Program Expedition 321 to measure sediment geochemical compositions at 2.5 cm resolution for the 450 m of the Site U1338 spliced sediment column. This spatial resolution is equivalent to ~2 k.y. age sampling in the 0-5 Ma section and ~1 k.y. resolution from 5 to 17 Ma. Here we report the data and describe data acquisition conditions to measure Al, Si, K, Ca, Ti, Fe, Mn, and Ba in the solid phase. We also describe a method to convert the data from volume-based raw XRF scan data to a normalized mass measurement ready for calibration by other geochemical methods. Both the raw and normalized data are reported along the Site U1338 splice.

X-ray fluorescent (XRF) ratios and diatom groups of sediment core GeoB13813-4

The continental shelf adjacent to the Río de la Plata (RdlP) exhibits extremely complex hydrographic and ecological characteristics which are of great socioeconomic importance. Since the long-term environmental variations related to the atmospheric (wind fields), hydrologic (freshwater plume), and oceanographic (currents and fronts) regimes are little known, the aim of this study is to reconstruct the changes in the terrigenous input into the inner continental shelf during the late Holocene period (associated with the RdlP sediment discharge) and to unravel the climatic forcing mechanisms behind them. To achieve this, we retrieved a 10 m long sediment core from the RdlP mud depocenter at 57 m water depth (GeoB 13813-4). The radiocarbon age control indicated an extremely high sedimentation rate of 0.8 cm per year, encompassing the past 1200 years (AD 750-2000). We used element ratios (Ti / Ca, Fe / Ca, Ti / Al, Fe / K) as regional proxies for the fluvial input signal and the variations in relative abundance of salinity-indicative diatom groups (freshwater versus marine-brackish) to assess the variability in terrigenous freshwater and sediment discharges. Ti / Ca, Fe / Ca, Ti / Al, Fe / K and the freshwater diatom group showed the lowest values between AD 850 and 1300, while the highest values occurred between AD 1300 and 1850. The variations in the sedimentary record can be attributed to the Medieval Climatic Anomaly (MCA) and the Little Ice Age (LIA), both of which had a significant impact on rainfall and wind patterns over the region. During the MCA, a weakening of the South American summer monsoon system (SAMS) and the South Atlantic Convergence Zone (SACZ), could explain the lowest element ratios (indicative of a lower terrigenous input) and a marine-dominated diatom record, both indicative of a reduced RdlP freshwater plume. In contrast, during the LIA, a strengthening of SAMS and SACZ may have led to an expansion of the RdlP river plume to the far north, as indicated by higher element ratios and a marked freshwater diatom signal. Furthermore, a possible multidecadal oscillation probably associated with Atlantic Multidecadal Oscillation (AMO) since AD 1300 reflects the variability in both the SAMS and SACZ systems.

Dynamic X-ray diffraction observation of shocked solid iron up to 170 GPa

Iron is the main constituent of the core of rocky planets; therefore, understanding its phase diagram under extreme conditions is fundamental to model the planets’ evolution. Using dynamic compression by laser-driven shocks, pressure and temperature conditions close to what is found in these cores can be reached. However, it remains unclear whether phase boundaries determined at nanosecond timescales agree with static compression. Here we observed the presence of solid hexagonal close-packed iron at 170 GPa and 4,150 K, in a part of the iron phase diagram, where either a different solid structure or liquid iron has been proposed. This X-ray diffraction experiment confirms that laser compression is suitable for studying iron at conditions of deep planetary interiors difficult to achieve with static compression techniques.

Mercury capture on a supported chlorocuprate(II) ionic liquid adsorbent studied using operando synchrotron X-ray absorption spectroscopy

Mercury scrubbing from gas streams using a supported 1-butyl-3-methylimidazolium chlorocuprate(II) ionic liquid ([C4mim]2[Cu2Cl6]) has been studied using operando EXAFS. Initial oxidative capture as [HgCl3]– anions was confirmed, this was then followed by the unanticipated generation of mercury(I) chloride through comproportionation with additional mercury from the gas stream. Combining these two mechanisms leads to net one electron oxidative extraction of mercury from the gas with increased potential capacity and efficiency for supported ionic liquid mercury scrubbers.

X-Ray Absorption Spectroscopy and Computer Modelling Study of Nanocrystalline Binary Alkaline Earth Fluorides

Nanocrystalline samples of Ba1-xCaxF2 prepared by high-energy milling show an unusually high F-ion conductivity, which exhibit a maximum in the magnitude and a minimum in the activation energy at x = 0.5. Here, we report an X-ray absorption spectroscopy (XAS) at the Ca and Sr K edges and the Ba L-3 edge and a molecular dynamics (MD) simulation study of the pure and mixed fluorides. The XAS measurements on the pure binary fluorides, CaF2, SrF2 and BaF2 show that high-energy ball-milling produces very little amorphous material, in contrast to the results for ball milled oxides. XAS measurements of Ba1-xCaxF2 reveal that for 0 < x < 1 there is considerable disorder in the local environments of the cations which is highest for x = 0.5. Hence the maximum in the conductivity corresponds to the composition with the maximum level of local disorder. The MD calculations also show a highly disordered structure consistent with the XAS results and similarly showing maximum disorder at x = 0.5.

X-ray vision: mental representation of the human body’s inner morphology

This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

A Staggered Decameric Assembly of Human C-Reactive Protein Stabilized by Zinc Ions Revealed by X-ray Crystallography

International audience

X-Ray powder diffraction laboratory @ University of Málaga (UMA)

X-Ray Powder Diffraction (XRPD) laboratory is a facility placed at Servicios Centrales de apoyo a la Investigación (SCAI) at University of Malaga (UMA) http://www.scai.uma.es/. This facility has three XRPD diffractometers and a diffractometer to measure high-resolution thin-films. X´Pert PRO MPD from PANalytical. This is a bragg-brentano (theta/2theta) with reflection geometry diffractometer which allows to obtain high resolution XRPD data with strictly monochromatic CuKα1 radiation (λ=1.54059Å) [Ge(111) primary monochromator] and an automatic sample charger. Moreover, it has parallel monochromatic CuKα1 radiation (λ=1.54059Å) with an hybrid Ge(220) monochromator for capillary and multiproposal (bulk samples up to 1 Kg) sample holders. The HTK1200N chamber from Anton Paar allows collecting high resolution high temperature patterns. EMPYREAN from PANalytical. This diffractometer works in reflection and transmission geometries with theta/theta goniometer, using CuKα1,2 radiation (λ=1.5418Å), a focusing X-ray mirror and a ultra-fast PIXCEL 3D detector with 1D and 2D collection data modes (microstructural and preferred orientation analysis). Moreover, the TTK450N chamber allows low temperature and up to 450ºC studies. A D8 ADVANCE (BRUKER) was installed in April 2014. It is the first diffractometer in Europe equipped with a Johansson Ge(111) primary monochromator, which gives a strictly monochromatic Mo radiation (λ=0.7093 Å) [1]. It works in transmission mode (with a sample charger) with this high resolution configuration. XRPD data suitable for PDF (Pair Distribution Function) analysis can be collected with a capillary sample holder, due to the high energy and high resolution capabilities of this diffractometer. Moreover, it has a humidity chamber MHC-trans from Anton Paar working on transmission mode with MoKα1 (measurements can be collected at 5 to 95% of relative humidity (from 20 to 80 ºC) and up to 150ºC [2]). Furthermore, this diffractometer also has a reaction chamber XRK900 from Anton Paar (which uses CuKα1,2 radiation in reflection mode), which allows data collection from room temperature to 900ºC with up to 10 bar of different gases. Finally, a D8 DISVOVER A25 from BRUKER was installed on December 2014. It has a five axis Euler cradler and optics devices suitable for high resolution thin film data collection collected in in-plane and out-of-plane modes. To sum up, high-resolution thin films, microstructural, rocking-curve, Small Angle X-ray Scattering (SAXS), Grazing incident SAXS (GISAXS), Ultra Grazing incident diffraction (Ultra-GID) and microdiffraction measurements can be performed with the appropriated optics and sample holders. [1] L. León-Reina, M. García-Maté, G. Álvarez-Pinazo, I. Santacruz, O. Vallcorba, A.G. De la Torre, M.A.G. Aranda “Accuracy in Rietveld quantitative phase analysis: a comparative study of strictly monochromatic Mo and Cu radiations” J. Appl. Crystallogr. 2016, 49, 722-735. [2] J. Aríñez-Soriano, J. Albalad, C. Vila-Parrondo, J. Pérez-Carvajal, S. Rodríguez-Hermida, A. Cabeza, F. Busqué, J. Juanhuix, I. Imaz, Daniel Maspoch “Single-crystal and humidity-controlled powder diffraction study of the breathing effect in a metal-organic framework upon water adsorption/desorption” Chem. Commun., 2016, DOI: 10.1039/C6CC02908F.

Monte Carlo Simulation Of The Response Functions Of Cdte Detectors To Be Applied In X-ray Spectroscopy.

In this work, the energy response functions of a CdTe detector were obtained by Monte Carlo (MC) simulation in the energy range from 5 to 160keV, using the PENELOPE code. In the response calculations the carrier transport features and the detector resolution were included. The computed energy response function was validated through comparison with experimental results obtained with (241)Am and (152)Eu sources. In order to investigate the influence of the correction by the detector response at diagnostic energy range, x-ray spectra were measured using a CdTe detector (model XR-100T, Amptek), and then corrected by the energy response of the detector using the stripping procedure. Results showed that the CdTe exhibits good energy response at low energies (below 40keV), showing only small distortions on the measured spectra. For energies below about 80keV, the contribution of the escape of Cd- and Te-K x-rays produce significant distortions on the measured x-ray spectra. For higher energies, the most important correction is the detector efficiency and the carrier trapping effects. The results showed that, after correction by the energy response, the measured spectra are in good agreement with those provided by a theoretical model of the literature. Finally, our results showed that the detailed knowledge of the response function and a proper correction procedure are fundamental for achieving more accurate spectra from which quality parameters (i.e., half-value layer and homogeneity coefficient) can be determined.

Fast And Direct Na And K Determination In Table, Marine, And Low-sodium Salts By X-ray Fluorescence And Chemometrics.

X-ray fluorescence (XRF) is a fast, low-cost, nondestructive, and truly multielement analytical technique. The objectives of this study are to quantify the amount of Na(+) and K(+) in samples of table salt (refined, marine, and light) and to compare three different methodologies of quantification using XRF. A fundamental parameter method revealed difficulties in quantifying accurately lighter elements (Z < 22). A univariate methodology based on peak area calibration is an attractive alternative, even though additional steps of data manipulation might consume some time. Quantifications were performed with good correlations for both Na (r = 0.974) and K (r = 0.992). A partial least-squares (PLS) regression method with five latent variables was very fast. Na(+) quantifications provided calibration errors lower than 16% and a correlation of 0.995. Of great concern was the observation of high Na(+) levels in low-sodium salts. The presented application may be performed in a fast and multielement fashion, in accordance with Green Chemistry specifications.

Towards A Deeper Understanding Of Structural Biomass Recalcitrance Using Phase-contrast Tomography.

The development of technological routes to convert lignocellulosic biomass to liquid fuels requires an in-depth understanding of the cell wall architecture of substrates. Essential pretreatment processes are conducted to reduce biomass recalcitrance and usually increase the reactive surface area. Quantitative three-dimensional information about both bulk and surface structural features of substrates needs to be obtained to expand our knowledge of substrates. In this work, phase-contrast tomography (PCT) was used to gather information about the structure of a model lignocellulosic biomass (piassava fibers). The three-dimensional cellular organization of piassava fibers was characterized by PCT using synchrotron radiation. This technique enabled important physical features that describe the substrate piassava fibers to be visualized and quantified. The external surface area of a fiber and internal surface area of the pores in a fiber could be determined separately. More than 96% of the overall surface area available to enzymes was in the bulk substrate. The pore surface area and length exhibited a positive linear relationship, where the slope of this relationship depended on the plant tissue. We demonstrated that PCT is a powerful tool for the three-dimensional characterization of the cell wall features related to biomass recalcitrance. Original and relevant quantitative information about the structural features of the analyzed material were obtained. The data obtained by PCT can be used to improve processing routes to efficiently convert biomass feedstock into sugars.

Different coordination modes for disulfoxides towards diorganotin(IV) dichlorides. X-ray crystal structures of 1,2-cis-bis-(phenylsulfinyl)ethene (rac-,cis-cbpse) and adducts [{Ph2SnCl2(meso-bpse)}n] and [{n-Bu2SnCl2(pdtd)}2]

The reactions of meso-1,2-bis(phenylsulfinyl)ethane (meso-bpse) with Ph2SnCl2, 2-phenyl-1,3-dithiane trans-1-trans-3-dioxide (pdtd) with n-Bu2SnCl2 and 1,2-cis-bis-(phenylsulfinyl)ethene (rac-,cis-cbpse) with Ph2SnCl2, in 1:1 molar ratio, yielded [{Ph2SnCl2(meso-bpse)}n], [{n-Bu2SnCl2(pdtd)}2] and [{Ph2SnCl2(rac,cis-cbpse)}x] (x = 2 or n), respectively. All adducts were studied by IR, Mössbauer and 119Sn NMR spectroscopic methods, elemental analysis and single crystal X-ray diffractometry. The X-ray crystal structure of [{Ph2SnCl2(meso-bpse)}n] revealed the occurrence of infinite chains in which the tin(IV) atoms appear in a distorted octahedral geometry with Cl atoms in cis and Ph groups in trans positions. The X-ray crystal structure of [{n-Bu2SnCl2(pdtd)}2] revealed discrete centrosymmetric dimeric species in which the tin(IV) atoms possess a distorted octahedral geometry with bridging disulfoxides in cis and n-butyl moieties in trans positions. The spectroscopic data indicated that the adduct containing the rac,cis-cbpse ligand can be dimeric or polymeric. The X-ray structural analysis of the free rac-,cis-cbpse sulfoxide revealed that the crystals belong to the C2/c space group.

Synthesis of novel O-acylated-D-ribono-1,5-lactones and structural assignment supported by conventional NOESY-NMR and x-ray analysis

A practical method for the structural assignment of 3,4-O-benzylidene-D-ribono-1,5-lactones and analogues using conventional NMR techniques and NOESY measurements in solution is described. 2-O-Acyl-3,4-O-benzylidene-D-ribono-1,5-lactones were prepared in good yields by acylation of Zinner’s lactone with acyl chlorides under mildly basic conditions. Structural determination of 2-O-(4-nitrobenzoyl)-3,4-O-benzylidene-D-ribono-1,5-lactone was achieved by single crystal x-ray diffraction, which supports the results based on spectroscopic data.