Determining Peak Positions Research Articles

BraggNN: fast X-ray Bragg peak analysis using deep learning.

X-ray diffraction based microscopy techniques such as high-energy diffraction microscopy (HEDM) rely on knowledge of the position of diffraction peaks with high precision. These positions are typically computed by fitting the observed intensities in detector data to a theoretical peak shape such as pseudo-Voigt. As experiments become more complex and detector technologies evolve, the computational cost of such peak-shape fitting becomes the biggest hurdle to the rapid analysis required for real-time feedback in experiments. To this end, we propose BraggNN, a deep-learning based method that can determine peak positions much more rapidly than conventional pseudo-Voigt peak fitting. When applied to a test dataset, peak center-of-mass positions obtained from BraggNN deviate less than 0.29 and 0.57 pixels for 75 and 95% of the peaks, respectively, from positions obtained using conventional pseudo-Voigt fitting (Euclidean distance). When applied to a real experimental dataset and using grain positions from near-field HEDM reconstruction as ground-truth, grain positions using BraggNN result in 15% smaller errors compared with those calculated using pseudo-Voigt. Recent advances in deep-learning method implementations and special-purpose model inference accelerators allow BraggNN to deliver enormous performance improvements relative to the conventional method, running, for example, more than 200 times faster on a consumer-class GPU card with out-of-the-box software.

The perfection of Raman spectroscopic gas densimeters

AbstractRaman spectroscopy can be used to determine density of gases, because the energy of fundamental vibrational modes is affected by intermolecular distances. The key problem is the estimation of exact peak positions of Raman bands, because the analyses require a precision that is mostly less than the pixel resolution of modern Raman spectrometers. A new method to determine peak positions of Raman bands and atomic emission lines in a discontinuous spectrum without numerical manipulations is tested in this study: modified scanning multichannel technique. Relocation of the gratings with a Sinus Arm Drive can be performed over a distance that is only a fraction of the pixel size that allows peak position estimations with precisions smaller than the pixel resolution and to determine the uncertainty in this estimation. This uncertainty was not determined in previous studies about gas densimeters, resulting in a large variety of inconsistent data. The new method is tested with fluid inclusions in quartz. A CO2 density of 0.1477 ± 0.0006 g·cm−3 and 0.8880 ± 0.0007 g·cm−3 determined with microthermometry correspond to a Fermi dyad of 103.12 ± 0.27 cm−1 and 104.71 ± 0.26 cm−1. A CH4 density of 0.3461 ± 0.0002 g·cm−3 and 0.4011 ± 0.0001 g·cm−3 correspond to peak positions of 2910.66 ± 0.12 cm−1 and 2910.57 ± 0.12 cm−1. The error in these numbers must be regarded as the best estimated uncertainties of peak positions, which are probably slightly adjusted to higher values due to mechanical irregularities of the Sinus Arm Drive in modern Raman systems.

Study on ethnic medicine quantitative reference herb,Tibetan medicine fruits of Capsicum frutescens as a case

High price and difficult to get of reference substance have become obstacles to HPLC assay of ethnic medicine. A new method based on quantitative reference herb (QRH) was proposed. Specific chromatograms in fruits of Capsicum frutescens were employed to determine peak positions, and HPLC quantitative reference herb was prepared from fruits of C. frutescens. The content of capsaicin and dihydrocapsaicin in the quantitative control herb was determined by HPLC. Eleven batches of fruits of C. frutescens were analyzed with quantitative reference herb and reference substance respectively. The results showed no difference. The present method is feasible for quality control of ethnic medicines and quantitative reference herb is suitable to replace reference substances in assay.

Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA.

BackgroundChIP-seq provides a wealth of information on the approximate location of DNA-binding proteins genome-wide. It is known that the targeted motifs in most cases can be found at the peak centers. A high resolution mapping of ChIP-seq peaks could in principle allow the fine mapping of the protein constituents within protein complexes, but the current ChIP-seq analysis pipelines do not target the basepair resolution strand specific mapping of peak summits.ResultsThe approach proposed here is based on i) locating regions that are bound by a sufficient number of proteins constituting a complex; ii) determining the position of the underlying motif using either a direct or a de novo motif search approach; and iii) determining the exact location of the peak summits with respect to the binding motif in a strand specific manner. We applied this method for analyzing the CTCF/cohesin complex, which holds together DNA loops. The relative positions of the constituents of the complex were determined with one-basepair estimated accuracy. Mapping the positions on a 3D model of DNA made it possible to deduce the approximate local topology of the complex that allowed us to predict how the CTCF/cohesin complex locks the DNA loops. As the positioning of the proteins was not compatible with previous models of loop closure, we proposed a plausible “double embrace” model in which the DNA loop is held together by two adjacent cohesin rings in such a way that the ring anchored by CTCF to one DNA duplex encircles the other DNA double helix and vice versa.ConclusionsA motif-centered, strand specific analysis of ChIP-seq data improves the accuracy of determining peak positions. If a genome contains a large number of binding sites for a given protein complex, such as transcription factor heterodimers or transcription factor/cofactor complexes, the relative position of the constituent proteins on the DNA can be established with an accuracy that allow one to deduce the local topology of the protein complex. The proposed high resolution mapping approach of ChIP-seq data is applicable for detecting the contact topology of DNA-binding protein complexes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2940-7) contains supplementary material, which is available to authorized users.

Methods for calibrating the gain and offset of the DSSC detector for the European XFEL using X-ray line sources

The DSSC (DEPFET Sensor with Signal Compression) will be a silicon based, 2d 1 Mpx imaging detector for the European X-ray Free Electron Laser Facility (XFEL.EU) in Hamburg, Germany. The DSSC is foreseen for soft X-radiation from 0.5 keV up to 6 keV . Driven by its scientific requirements, the design goals of the detector system are single photon detection, high dynamic range and a high frame rate of up to 4.5 MHz. Signal compression and amplification will be performed in the silicon sensor pixels yielding a low signal noise. Utilizing an in-pixel active filtering stage and an 8/9-bit ADC, the detector will provide parallel read-out of all pixels. In order to calibrate offset and gain, the procedure currently under investigation relies on determining peak positions in measurements with calibration line sources such as 55Fe. Here the status of studies of the stability and performance of a parameterized fit function designed for this task will be presented.

Statistical errors in interferometry with least-squares algorithms and large step sizes

This paper investigates statistical errors in determining peak positions of interference fringes with the least-squares algorithms when the phase-shifting step sizes are 2π/3, π/2, and 2π/5. Two types of random noises are considered, which are called intensity noise and position noise. With these large step sizes, the statistical errors obtained from simulated measurements are compared with the theoretical results published in Ref. [11]. The effects of the wavelength and the amplitude on the statistical errors are investigated. A discrepancy between the simulation results and the theoretical results has been observed, that is, when the step size was π/2, the statistical errors caused by position noise have shown strong peak-position dependence, which cannot be explained by Eq. (16) given in Ref. [11]. A new equation is given to account for the simulation results.

Infrared laboratory absorbance spectra of olivine: using classical dispersion analysis to extract peak parameters

Laboratory measurements quantifying the effect of Fe substituting for Mg in olivine are needed to distinguish compositional from temperature, grain size and grain shape effects in observational data. To address this need, we study room temperature absorption spectra of a large suite of olivines evenly spaced across Mg and Fe compositions. We apply the principle that classical dispersion theory may be used to determine peak positions as well as peak widths, strengths and possibly optical function (n(λ) and k(λ)) estimates from absorption spectra of thin film samples of these olivines and two additional isotropic and anisotropic minerals with varying hardness and numbers of spectral bands. For olivine, we find that this method provides good estimates of peak position and that accounting for asymmetric peak shapes in this way increases the error on full width at half-maximum and oscillator strengths. Values from classical dispersion fits better match published n and k derived from reflectivity of single crystals when the dust proxy is soft and the thickness of the sample is independently constrained. Electronic data and peak parameter trends for the laboratory olivine absorption spectra and the viability of the extracted n and k are discussed with regard to astronomy.

Residual Stresses Measurement of Butt-welded Aluminium Alloy Plates by X-ray

X-ray diffraction(XRD) method is used to determine the distribution of surface residual stress on the butt-welded aluminium alloy LD10 plates. Two methods of determining peak positions, i.e. half-width and parabola methods, are adopted and compared in the experiment, the distribution of residual stresses is obtained, and the distribution results of residual stresses are explained. The test shows that the results of the two methods are similar, and stress distribution curve of parabola method is largely lower than that of half-width method, which is on the low side of tensile stress and on the high side of compressive stress. At the same time, the experimental results reveal that the half-width method is better in consistency, stability, adaptability and accuracy than parabola, and the distribution data of the residual stresses surveyed by XRD method is reliable,and XRD is a valid method to measure residual stresses in welded structures. All these results contribute reference to the distribution of residual stresses on welded aluminium alloy LD10 plates.

Comments onSynchrotron fibre diffraction identifies and locates foetal collagenous breast tissue associated with breast carcinomaby V. J. James (2002).J. Synchrotron Rad.9, 71–76

We read with great interest the paper recently published by James (2002), as the work is in a similar ®eld to our own. Upon careful reading we have developed some signi®cant misgivings and concerns regarding many aspects of this particular paper and we felt compelled to bring these to your attention. (1) It appears as though the author has confused breast tissue with skin tissue of the breast. These are completely different organs containing different structures. Furthermore, hyalinized tissue is common in breast tissues and is certainly not uniquely associated with cancer. The current consensus is that the hyalinized tissue is a response to in ammation following DCIS and not, as suggested, a pre-cancerous change. Within the UK, at least, hyalinized tissue is certainly not referred to as elastosis. (2) We do not believe it is possible to distinguish, by eye, normal tissue from diseased tissue as is claimed in x2. (3) The normal breast tissue data shown in Figs. 2(b) and 2(c) are absolutely identical to that previously presented as foetal tendon and skin tissue in James et al. (1998) (Figs. 3a and 3b). We are therefore confused regarding which tissue was really measured and why no reference is made to the original (1998) data source. (4) There are omissions of several key experimental details that prevent any repetition of the work. These include the X-ray wavelength that was employed, the physical dimensions of the X-ray beam, the volume/mass of specimen that was experimentally interrogated and the actual method used for determining peak positions and intensities. Further, it is wholly inappropriate, in this case, to determine peak positions from second-order derivatives as the background is rapidly varying. Background ®tting with a boxcar ®lter is also not appropriate as this would result in a non-physical average, which following subtraction will result in negative X-ray uxes. (5) Many of the features that are referred to within the text as being clearly apparent within Fig. 3 are not clear. No labels are included in Fig. 3 to aid recognition. This results in a great deal of ambiguity when trying to relate the features described in the text to those in the images. A clear understanding of the features is critical to the interpretation of the data. Speci®cally: (i) The author claims that all samples show 20 orders of the 353 nm spacing in the equatorial region. These are simply not evident in any of the images presented in Fig. 3. (ii) We are unable to ®nd any diffraction rings that index to 32 nm or 43.8 nm shown in any of the images of Fig. 3. The text claims that Figs. 3(b)±3(d) show no fat. There are clear rings due to fat in Figs. 3(c) and 3(d). Fig. 3(a) does not appear to contain a `wide diffuse ring' despite the claim in the text. (6) A reference is made to the work of Lewis et al. (2000) as supporting the observation of a variation in collagen ®bril radius. This claim is erroneous, as the Lewis paper contains no mention of variation in ®bril radius. (7) The `®ne rings appearing in all pathological tissue' are claimed to be randomly oriented structures. None of the images presented in Fig. 3 indicate scattering from randomly oriented structures other than that of the fat. A major conclusion of the work is that the ®ndings show structural changes preceding breast cancer. We do not believe that this can be supported by any of the data presented within the paper. We regret having to bring these points to your attention but we have been frustrated and surprised at the number and extent of our concerns. At best, one may regard some of the problems as arising from poor presentation. However, this does not explain many of the points above.

Structure determination of silica tantalum soda glasses by X-ray diffraction analysis

The structure of 5SiO 2 · 2Ta 2O 5 · 3Na 2O glass has been investigated by X-ray radial distribution analysis based on X-ray diffraction intensity measurements. The electron radial distribution function was calculated by the usual Fourier transformation and interpretation of it was made in terms of pair functions. It has been found from the determined peak positions and pair function analysis that most of the Ta 5+ ions are present in six-fold coordination form. It was deduced that the TaO 6 octahedra are distorted in the glass structure.

Using diatomics-in-molecules in calculating semiempirical band structures

The diatomics-in-molecules approach usually limited to small-sized molecules is applied to infinitely extended systems, thereby relating the empirical potentials used as DIM input data to the well-known Slater-Koster parameters of tight-binding theory. Based on this parameters the band structure and the density of states of the rare-gas (RG) valence bands are calculated. Our results are in very good agreement with experimental data like the width of the bands and the vacuum-energy. Moreover, the characteristic features of the calculated density of states reflect the spectroscopically determined peak positions satisfactorily. We discuss further applications of this work.

Study on the structure of K 2O·2TiO 2 glass by X-ray radial distribution analysis

The structure of K 2O·2TiO 2 glass prepared by the twin-roller quenching method has been investigated by X-ray radial distribution analysis based on the X-ray diffraction intensity measurements extended to a high angle of 14.1 Å −1 in S( = 4 π sin θλ). It has been found from the determined peak positions and pair function analysis that most of the Ti 4+ ions may be present in four-fold coordinated form.

ガウス曲線法による炭化ケイ素のＸ線応力測定

Residual stress in ceramics induced by grinding plays an important role on the strength of ceramics. The X-ray method is effective in measuring residual stress in ceramics because it can nondestructively measure the residual stress in thin surface layer of 10 to 40μm of a specimen. In the measurement by X-ray diffraction, it is important to ascertain the reproducibility of the measured values from their standard deviation because the measurements by X-rays will involve variability caused by inherent counting statistics. To determine accurately the stress value in a sintered silicon carbide, an X-ray stress constant and elastic constants were determined by the Gaussian curve method which permits rapid and precise determination of stress. The standard deviations of these constants were calculated analytically to examine their reliability. (2.0.15) and (306) diffraction planes of silicon carbide were measured with CuKα radiation. For each diffraction plane, CuKα1, and Kα2 diffraction line profiles appear separately. Stress can be determined precisely by using the separate Kα1 single diffraction profile. The background correction in determining peak positions can be omitted because it does not affect the stress. The 95% confidence limits for the X-ray stress constants for the (2.0.15) and (306) planes were -971±48 and -1337±116MPa/deg, respectively. The limits for the X-ray Young's modulus of the (2.0.15) and (306) planes were 446±20 and 417±35GPa, and those for the Poisson's ratio were 0.165±0.013 and 0.157±0.016, respectively.

Measurement of Anisotropic Compressibilities by a Single Crystal Diffractometer Method*

AbstractThe beryllium diamond-anvil pressure cell described by Weir, Piermarini and Block has been mounted on a Bond diffractometer equipped with an orienter of the fixed-x type. Molybdenum radiation is used to penetrate the diamonds and beryllium of which the cell is constructed, and special techniques are required to retain adequate precision in measuring cell parameters using diffraction angles in the low 2θ range. The method described provides high sensitivity in determining peak positions and eliminates the effect of centering errors on measured values of 2θ. Under favorable conditions, diffraction angles are measured with an accuracy of ±0.001° in 2θ. The method has been tested by measuring the lattice parameter of vacuum float zone refined silicon. Measurements of the compressibilities of silicon and of α-Pb(N3)2 (orthorhombic) have been carried out using the method of Barnett, Block, and Piermarini to determine pressure by measuring the shift in the R-line fluorescence spectrum of ruby.

Determination of Electron Energy Losses in Rubidium

Surface and volume plasmon energies of 2.4 and 3.45 eV, and energy losses of 25 and 55 eV, are measured in the characteristic electron energy-loss spectra of rubidium. A computer program used to determine peak positions and evaluate energy losses is described.