Automatic crystal centring procedure at the SSRF macromolecular crystallography beamline

2016 ◽  
Vol 23 (6) ◽  
pp. 1323-1332 ◽  
Author(s):  
Zhijun Wang ◽  
Qiangyan Pan ◽  
Lifeng Yang ◽  
Huan Zhou ◽  
Chunyan Xu ◽  
...  
Keyword(s):  
Rotation Axis ◽  
Small Region ◽  
Detection Algorithm ◽  
Classification Model ◽  
Optical Methods ◽  
Shanghai Synchrotron Radiation Facility ◽  
Beam Position ◽  
Crystal Sample ◽  
X Ray ◽  
Region Segment

X-ray diffraction is a common technique for determining crystal structures. The average time needed for the solution of a protein structure has been drastically reduced by a number of recent experimental and theoretical developments. Since high-throughput protein crystallography benefits from full automation of all steps that are carried out on a synchrotron beamline, an automatic crystal centring procedure is important for crystallographic beamlines. Fully automatic crystal alignment involves the application of optical methods to identify the crystal and move it onto the rotation axis and into the X-ray beam. Crystal recognition has complex dependencies on the illumination, crystal size and viewing angles due to effects such as local shading, inter-reflections and the presence of antifreezing elements. Here, a rapid procedure for crystal centring with multiple cameras using region segment thresholding is reported. Firstly, a simple illumination-invariant loop recognition and classification model is used by slicing a low-magnification loop image into small region segments, then classifying the loop into different types and aligning it to the beam position using feature vectors of the region segments. Secondly, an edge detection algorithm is used to find the crystal sample in a high-magnification image using region segment thresholding. Results show that this crystal centring method is extremely successful under fluctuating light states as well as for poorly frozen and opaque samples. Moreover, this crystal centring procedure is successfully integrated into the enhancedBlu-Icedata collection system at beamline BL17U1 at the Shanghai Synchrotron Radiation Facility as a routine method for an automatic crystal screening procedure.

scholarly journals LamNI – an instrument for X-ray scanning microscopy in laminography geometry

2020 ◽  
Vol 27 (3) ◽  
pp. 730-736 ◽  
Author(s):  
Mirko Holler ◽  
Michal Odstrčil ◽  
Manuel Guizar-Sicairos ◽  
Maxime Lebugle ◽  
Ulrich Frommherz ◽  
...  
Keyword(s):  
High Resolution ◽  
Rotation Axis ◽  
Optical Methods ◽  
Large Area ◽  
Thin Sections ◽  
3D Images ◽  
X Ray ◽  
Illumination Direction ◽  
Positioning Errors ◽  
New Instrument

Across all branches of science, medicine and engineering, high-resolution microscopy is required to understand functionality. Although optical methods have been developed to `defeat' the diffraction limit and produce 3D images, and electrons have proven ever more useful in creating pictures of small objects or thin sections, so far there is no substitute for X-ray microscopy in providing multiscale 3D images of objects with a single instrument and minimal labeling and preparation. A powerful technique proven to continuously access length scales from 10 nm to 10 µm is ptychographic X-ray computed tomography, which, on account of the orthogonality of the tomographic rotation axis to the illuminating beam, still has the limitation of necessitating pillar-shaped samples of small (ca 10 µm) diameter. Large-area planar samples are common in science and engineering, and it is therefore highly desirable to create an X-ray microscope that can examine such samples without the extraction of pillars. Computed laminography, where the axis of rotation is not perpendicular to the illumination direction, solves this problem. This entailed the development of a new instrument, LamNI, dedicated to high-resolution 3D scanning X-ray microscopy via hard X-ray ptychographic laminography. Scanning precision is achieved by a dedicated interferometry scheme and the instrument covers a scan range of 12 mm × 12 mm with a position stability of 2 nm and positioning errors below 5 nm. A new feature of LamNI is a pair of counter-rotating stages carrying the sample and interferometric mirrors, respectively.

Quantitative x-ray microanalysis and thickness determination using ζ factor

1996 ◽  
Vol 54 ◽  
pp. 580-581
Author(s):  
M. Watanabe ◽  
Z. Horita ◽  
M. Nemoto
Keyword(s):  
Diffusion Couple ◽  
Extrapolation Method ◽  
Thin Specimen ◽  
Beam Position ◽  
X Ray ◽  
Thickness Determination ◽  
Experimental Limitation ◽  
X Ray Absorption

X-ray absorption in quantitative x-ray microanalysis of thin specimens may be corrected without knowledge of thickness when the extrapolation method or the differential x-ray absorption (DXA) method is used. However, there is an experimental limitation involved in each method. In this study, a method is proposed to overcome such a limitation. The method is developed by introducing the ζ factor and by combining the extrapolation method and DXA method. The method using the ζ factor, which is called the ζ-DXA method in this study, is applied to diffusion-couple experiments in the Ni-Al system.For a thin specimen where incident electrons are fully transparent, the characteristic x-ray intensity generated from a beam position, I, may be represented as I = (NρW/A)Qωaist.

scholarly journals A novel algorithm to detect non-wear time from raw accelerometer data using deep convolutional neural networks

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shaheen Syed ◽  
Bente Morseth ◽  
Laila A. Hopstock ◽  
Alexander Horsch
Keyword(s):  
Threshold Value ◽  
Detection Algorithm ◽  
Classification Model ◽  
Type I ◽  
Accelerometer Data ◽  
Deep Convolutional Neural Networks ◽  
Major Drawback ◽  
Wear Time ◽  
Detection Algorithms ◽  
Type Ii Errors

AbstractTo date, non-wear detection algorithms commonly employ a 30, 60, or even 90 mins interval or window in which acceleration values need to be below a threshold value. A major drawback of such intervals is that they need to be long enough to prevent false positives (type I errors), while short enough to prevent false negatives (type II errors), which limits detecting both short and longer episodes of non-wear time. In this paper, we propose a novel non-wear detection algorithm that eliminates the need for an interval. Rather than inspecting acceleration within intervals, we explore acceleration right before and right after an episode of non-wear time. We trained a deep convolutional neural network that was able to infer non-wear time by detecting when the accelerometer was removed and when it was placed back on again. We evaluate our algorithm against several baseline and existing non-wear algorithms, and our algorithm achieves a perfect precision, a recall of 0.9962, and an F1 score of 0.9981, outperforming all evaluated algorithms. Although our algorithm was developed using patterns learned from a hip-worn accelerometer, we propose algorithmic steps that can easily be applied to a wrist-worn accelerometer and a retrained classification model.

In Situ Testing and X Rays Radiation Effects of Pt/Bi3.15Nd0.85Ti3O12/Pt Ferroelectric Capacitors

2013 ◽  
Vol 712-715 ◽  
pp. 293-297
Author(s):  
Li Li
Keyword(s):  
Radiation Effects ◽  
Hysteresis Loops ◽  
Electrical Performance ◽  
Hysteresis Curve ◽  
X Rays ◽  
Shanghai Synchrotron Radiation Facility ◽  
X Ray ◽  
In The Beginning ◽  
Ferroelectric Capacitors

Pt/Bi3.15Nd0.85Ti3O12(BNT)/Pt ferroelectric capacitors were monitored using in situ X-ray irradiation with 10 keV at BL14B1 beamline (Shanghai Synchrotron Radiation Facility). BL14B1 combined with a ferroelectric analyzer enabled measurements in situ of electrical performance. The hysteresis curve (PE) of distortion depended on the polarization during irradiation, but the diffracted intensities of the (117) peak did not change in the beginning. ThePEcurve had a negligible change from 2.09×109Gy to 4.45×109Gy. Finally, bothPrandPr+very rapidly increased, but the intensities of (117) decreased. The hysteresis loops were remarkably deformed at the maximum total dose of 4.87×109Gy.

scholarly journals X‐ray, soft x‐ray, and VUV beam position monitor

1992 ◽  
Vol 63 (1) ◽  
pp. 526-529 ◽  
Author(s):  
B. A. Karlin ◽  
P. L. Cowan ◽  
J. C. Woicik
Keyword(s):  
Beam Position Monitor ◽  
Beam Position ◽  
X Ray

Automatic Knot Detection in Coarse-Resolution Cone-Beam Computed Tomography Images of Softwood Logs

2019 ◽  
Vol 69 (3) ◽  
pp. 185-187
Author(s):  
Magnus Fredriksson ◽  
Julie Cool ◽  
Stavros Avramidis
Keyword(s):  
Computed Tomography ◽  
Exploratory Study ◽  
Ct Scanning ◽  
Detection Algorithm ◽  
Cone Beam ◽  
X Ray ◽  
Coarse Resolution ◽  
Computed Tomography Images ◽  
X Ray Computed ◽  
Accurate Position

Abstract X-ray computed tomography (CT) scanning of sawmill logs is associated with costly and complex machines. An alternative scanning solution was developed, but its data have not been evaluated regarding detection of internal features. In this exploratory study, a knot detection algorithm was applied to images of four logs to evaluate its performance in terms of knot position and size. The results were a detection rate of 67 percent, accurate position, and inaccurate size. Although the sample size was small, it was concluded that automatic knot detection in coarse resolution CT images of softwoods is feasible, albeit for knots of sufficient size.

Design of an ultrahigh-energy-resolution and wide-energy-range soft X-ray beamline

2013 ◽  
Vol 21 (1) ◽  
pp. 273-279 ◽  
Author(s):  
L. Xue ◽  
R. Reininger ◽  
Y.-Q. Wu ◽  
Y. Zou ◽  
Z.-M. Xu ◽  
...  
Keyword(s):  
Energy Range ◽  
Energy Resolution ◽  
Wide Energy Range ◽  
Ultrahigh Energy ◽  
Exit Slit ◽  
Shanghai Synchrotron Radiation Facility ◽  
X Ray ◽  
Variable Line ◽  
Line Spacing ◽  
Wide Energy

A new ultrahigh-energy-resolution and wide-energy-range soft X-ray beamline has been designed and is under construction at the Shanghai Synchrotron Radiation Facility. The beamline has two branches: one dedicated to angle-resolved photoemission spectroscopy (ARPES) and the other to photoelectron emission microscopy (PEEM). The two branches share the same plane-grating monochromator, which is equipped with four variable-line-spacing gratings and covers the 20–2000 eV energy range. Two elliptically polarized undulators are employed to provide photons with variable polarization, linear in every inclination and circular. The expected energy resolution is approximately 10 meV at 1000 eV with a flux of more than 3 × 1010 photons s−1at the ARPES sample positions. The refocusing of both branches is based on Kirkpatrick–Baez pairs. The expected spot sizes when using a 10 µm exit slit are 15 µm × 5 µm (horizontal × vertical FWHM) at the ARPES station and 10 µm × 5 µm (horizontal × vertical FWHM) at the PEEM station. The use of plane optical elements upstream of the exit slit, a variable-line-spacing grating and a pre-mirror in the monochromator that allows the influence of the thermal deformation to be eliminated are essential for achieving the ultrahigh-energy resolution.

Synthesis and crystal structures of bis(imidazolidine-2-thione-κS)bis(thiocyanato-κS)mercury(II) and bis(cyanido)bis(μ2-imidazolidine-2-thione-κS)mercury(II).Hg(CN)2

2017 ◽  
Vol 72 (9) ◽  
pp. 671-676 ◽  
Author(s):  
Muhammad Ashraf Shaheen ◽  
Muhammad Nawaz Tahir ◽  
Sarwat Sabir ◽  
Aneela Anwar ◽  
Anvarhusein A. Isab ◽  
...  
Keyword(s):  
Rotation Axis ◽  
Mercury Atom ◽  
Distorted Octahedral Geometry ◽  
Weakly Bound ◽  
X Ray ◽  
X Ray Crystallography ◽  
Hydrogen Bonding Interactions ◽  
Ir And Nmr Spectroscopy ◽  
Distorted Octahedral ◽  
Cyanide Ligands

AbstractTwo mercury(II) complexes containing imidazolidine-2-thione (Imt) and thiocyanate or cyanide ligands, [Hg(Imt)2(SCN)2] (1) and [Hg(Imt)2(CN)2].Hg(CN)2(2), have been prepared and characterized by IR and NMR spectroscopy and X-ray crystallography. In compound1, the mercury atom is located on a two-fold rotation axis and is coordinated to two thione sulfur atoms of imidazolidine-2-thione (Imt) and to two sulfur atoms of thiocyanate in a distorted tetrahedral mode with the S-Hg-S bond angles in the range of 98.96(3)–148.65(6)°. In2, the mercury atom is hexa-coordinated having a distorted octahedral geometry composed of two cyanide C atoms [Hg-C=2.055(5) Å] and four weakly bound thione S atoms of imidazolidine-2-thione (Imt) [Hg-S=3.1301(13) and 3.1280(13) Å]. One free Hg(CN)2molecule is also present in the crystal. In both complexes, the molecular structure is stabilized by N-H…N and N-H…S hydrogen bonding interactions.

Spatio-temporal measurement of beam properties in the PLS diagnostic beamline

1998 ◽  
Vol 5 (3) ◽  
pp. 642-644 ◽  
Author(s):  
J. Y. Huang ◽  
I. S. Ko
Keyword(s):  
Visible Light ◽  
Imaging System ◽  
Ccd Camera ◽  
Photon Beam ◽  
Transverse Beam ◽  
Beam Position ◽  
X Ray ◽  
X Ray Imaging ◽  
Visible Light Imaging ◽  
Temporal Measurement

A diagnostic beamline is being constructed in the PLS storage ring for measurement of electron- and photon-beam properties. It consists of two 1:1 imaging systems: a visible-light imaging system and a soft X-ray imaging system. In the visible-light imaging system, the transverse beam size and beam position are measured with various detectors: a CCD camera, two photodiode arrays and a photon-beam position monitor. Longitudinal bunch structure is also investigated with a fast photodiode detector and a picosecond streak camera. On the other hand, the soft X-ray imaging system is under construction to measure beam sizes with negligible diffraction-limited error. The X-ray image optics consist of a flat cooled mirror and two spherical focusing mirrors.

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