scholarly journals A Contrast Calibration Protocol for X-ray Speckle Visibility Spectroscopy

2021 ◽  
Vol 11 (21) ◽  
pp. 10041
Author(s):  
Yanwen Sun ◽  
Vincent Esposito ◽  
Philip Adam Hart ◽  
Conny Hansson ◽  
Haoyuan Li ◽  
...  
Keyword(s):  
High Speed ◽  
Coherent Scattering ◽  
Atomic Scale ◽  
Photon Statistics ◽  
Free Electron Lasers ◽  
Data Set ◽  
X Ray ◽  
Charge Cloud ◽  
Typical Experiment ◽  
Calibration Protocol

X-ray free electron lasers, with their ultrashort highly coherent pulses, opened up the opportunity of probing ultrafast nano- and atomic-scale dynamics in amorphous and disordered material systems via speckle visibility spectroscopy. However, the anticipated count rate in a typical experiment is usually low. Therefore, visibility needs to be extracted via photon statistics analysis, i.e., by estimating the probabilities of multiple photons per pixel events using pixelated detectors. Considering the realistic X-ray detector responses including charge cloud sharing between pixels, pixel readout noise, and gain non-uniformity, speckle visibility extraction relying on photon assignment algorithms are often computationally demanding and suffer from systematic errors. In this paper, we present a systematic study of the commonly-used algorithms by applying them to an experimental data set containing small-angle coherent scattering with visibility levels ranging from below 1% to ∼60%. We also propose a contrast calibration protocol and show that a computationally lightweight algorithm can be implemented for high-speed correlation evaluation.

scholarly journals Resolving polymorphs and radiation-driven effects in microcrystals using fixed-target serial synchrotron crystallography

2018 ◽  
Vol 75 (2) ◽  
pp. 151-159 ◽  
Author(s):  
Ali Ebrahim ◽  
Martin V. Appleby ◽  
Danny Axford ◽  
John Beale ◽  
Tadeo Moreno-Chicano ◽  
...  
Keyword(s):  
Radiation Damage ◽  
Active Site ◽  
High Speed ◽  
Rapid Onset ◽  
Fixed Target ◽  
High Quality ◽  
Data Set ◽  
X Ray ◽  
Induced Changes

The ability to determine high-quality, artefact-free structures is a challenge in micro-crystallography, and the rapid onset of radiation damage and requirement for a high-brilliance X-ray beam mean that a multi-crystal approach is essential. However, the combination of crystal-to-crystal variation and X-ray-induced changes can make the formation of a final complete data set challenging; this is particularly true in the case of metalloproteins, where X-ray-induced changes occur rapidly and at the active site. An approach is described that allows the resolution, separation and structure determination of crystal polymorphs, and the tracking of radiation damage in microcrystals. Within the microcrystal population of copper nitrite reductase, two polymorphs with different unit-cell sizes were successfully separated to determine two independent structures, and an X-ray-driven change between these polymorphs was followed. This was achieved through the determination of multiple serial structures from microcrystals using a high-throughput high-speed fixed-target approach coupled with robust data processing.

scholarly journals Accurate contrast determination for X-ray speckle visibility spectroscopy

2020 ◽  
Vol 27 (4) ◽  
pp. 999-1007 ◽  
Author(s):  
Yanwen Sun ◽  
Jordi Montana-Lopez ◽  
Paul Fuoss ◽  
Mark Sutton ◽  
Diling Zhu
Keyword(s):  
Count Rate ◽  
Real Life ◽  
Data Interpretation ◽  
Systematic Errors ◽  
Correction Coefficient ◽  
Free Electron Lasers ◽  
Pixel Size ◽  
Experimental Calibration ◽  
X Ray ◽  
Charge Cloud

X-ray speckle visibility spectroscopy using X-ray free-electron lasers has long been proposed as a probe of fast dynamics in noncrystalline materials. In this paper, numerical modeling is presented to show how the data interpretation of visibility spectroscopy can be impacted by the nonidealities of real-life X-ray detectors. Using simulated detector data, this work provides a detailed analysis of the systematic errors of several contrast extraction algorithms in the context of low-count-rate X-ray speckle visibility spectroscopy and their origins are discussed. Here, it was found that the finite detector charge cloud and pixel size lead to an unavoidable `degeneracy' in photon position determination, and that the contrasts extracted using different algorithms can all be corrected by a simple linear model. The results suggest that experimental calibration of the correction coefficient at the count rate of interest is possible and essential. This allows computationally lightweight algorithms to be implemented for on-the-fly analysis.

scholarly journals Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Artem Y Lyubimov ◽  
Monarin Uervirojnangkoorn ◽  
Oliver B Zeldin ◽  
Qiangjun Zhou ◽  
Minglei Zhao ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Free Electron ◽  
Snare Complex ◽  
Data Sets ◽  
Free Electron Lasers ◽  
Data Set ◽  
X Ray ◽  
Density Maps ◽  
Synaptotagmin 1 ◽  
Effects Of Radiation

X-ray free electron lasers (XFELs) reduce the effects of radiation damage on macromolecular diffraction data and thereby extend the limiting resolution. Previously, we adapted classical post-refinement techniques to XFEL diffraction data to produce accurate diffraction data sets from a limited number of diffraction images (<xref ref-type="bibr" rid="bib35">Uervirojnangkoorn et al., 2015</xref>), and went on to use these techniques to obtain a complete data set from crystals of the synaptotagmin-1 / SNARE complex and to determine the structure at 3.5 Å resolution (<xref ref-type="bibr" rid="bib40">Zhou et al., 2015</xref>). Here, we describe new advances in our methods and present a reprocessed XFEL data set of the synaptotagmin-1 / SNARE complex. The reprocessing produced small improvements in electron density maps and the refined atomic model. The maps also contained more information than those of a lower resolution (4.1 Å) synchrotron data set. Processing a set of simulated XFEL diffraction images revealed that our methods yield accurate data and atomic models.

Co-flow injection for serial crystallography at X-ray free-electron lasers

2022 ◽  
Vol 55 (1) ◽  
Author(s):  
Diandra Doppler ◽  
Mohammad T. Rabbani ◽  
Romain Letrun ◽  
Jorvani Cruz Villarreal ◽  
Dai Hyun Kim ◽  
...  
Keyword(s):  
Free Electron ◽  
Protein Crystal ◽  
Free Electron Lasers ◽  
Data Set ◽  
Time Resolved ◽  
High Background ◽  
X Ray ◽  
Flow Generation ◽  
Structural Details ◽  
3D Printed

Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macromolecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.

scholarly journals Real-time direct and diffraction X-ray imaging of irregular silicon wafer breakage

IUCrJ ◽  
2016 ◽  
Vol 3 (2) ◽  
pp. 108-114 ◽  
Author(s):  
Alexander Rack ◽  
Mario Scheel ◽  
Andreas N. Danilewsky
Keyword(s):  
High Speed ◽  
Imaging Techniques ◽  
Semiconductor Industry ◽  
Crack Tip ◽  
Atomic Scale ◽  
Final State ◽  
Severe Problem ◽  
X Ray ◽  
X Ray Imaging ◽  
Tip Position

Fracture and breakage of single crystals, particularly of silicon wafers, are multi-scale problems: the crack tip starts propagating on an atomic scale with the breaking of chemical bonds, forms crack fronts through the crystal on the micrometre scale and ends macroscopically in catastrophic wafer shattering. Total wafer breakage is a severe problem for the semiconductor industry, not only during handling but also during temperature treatments, leading to million-dollar costs per annum in a device production line. Knowledge of the relevant dynamics governing perfect cleavage along the {111} or {110} faces, and of the deflection into higher indexed {hkl} faces of higher energy, is scarce due to the high velocity of the process. Imaging techniques are commonly limited to depicting only the state of a wafer before the crack and in the final state. This paper presents, for the first time,in situhigh-speed crack propagation under thermal stress, imaged simultaneously in direct transmission and diffraction X-ray imaging. It shows how the propagating crack tip and the related strain field can be tracked in the phase-contrast and diffracted images, respectively. Movies with a time resolution of microseconds per frame reveal that the strain and crack tip do not propagate continuously or at a constant speed. Jumps in the crack tip position indicate pinning of the crack tip for about 1–2 ms followed by jumps faster than 2–6 m s−1, leading to a macroscopically observed average velocity of 0.028–0.055 m s−1. The presented results also give a proof of concept that the described X-ray technique is compatible with studying ultra-fast cracks up to the speed of sound.

scholarly journals Sorting algorithms for single-particle imaging experiments at X-ray free-electron lasers

2015 ◽  
Vol 22 (6) ◽  
pp. 1345-1352 ◽  
Author(s):  
S. A. Bobkov ◽  
A. B. Teslyuk ◽  
R. P. Kurta ◽  
O. Yu. Gorobtsov ◽  
O. M. Yefanov ◽  
...  
Keyword(s):  
Single Particle ◽  
Free Electron ◽  
Principal Component ◽  
Space Structure ◽  
Support Vector ◽  
Free Electron Lasers ◽  
Data Set ◽  
X Ray ◽  
Particle Imaging ◽  
Single Particle Imaging

Modern X-ray free-electron lasers (XFELs) operating at high repetition rates produce a tremendous amount of data. It is a great challenge to classify this information and reduce the initial data set to a manageable size for further analysis. Here an approach for classification of diffraction patterns measured in prototypical diffract-and-destroy single-particle imaging experiments at XFELs is presented. It is proposed that the data are classified on the basis of a set of parameters that take into account the underlying diffraction physics and specific relations between the real-space structure of a particle and its reciprocal-space intensity distribution. The approach is demonstrated by applying principal component analysis and support vector machine algorithms to the simulated and measured X-ray data sets.

Difference Fourier Analysis of Glucose Embedded and Frozen Hydrated Purple Membrane

1982 ◽  
Vol 40 ◽  
pp. 74-75
Author(s):  
Jules S. Jaffe ◽  
Robert M. Glaeser
Keyword(s):  
Purple Membrane ◽  
Data Set ◽  
High Resolution Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Fourier Techniques ◽  
Versus Protein ◽  
The Difference ◽  
Difference Fourier ◽  
Ideal Method

Although difference Fourier techniques are standard in X-ray crystallography it has only been very recently that electron crystallographers have been able to take advantage of this method. We have combined a high resolution data set for frozen glucose embedded Purple Membrane (PM) with a data set collected from PM prepared in the frozen hydrated state in order to visualize any differences in structure due to the different methods of preparation. The increased contrast between protein-ice versus protein-glucose may prove to be an advantage of the frozen hydrated technique for visualizing those parts of bacteriorhodopsin that are embedded in glucose. In addition, surface groups of the protein may be disordered in glucose and ordered in the frozen state. The sensitivity of the difference Fourier technique to small changes in structure provides an ideal method for testing this hypothesis.

Scanning x-ray fluorescence microscopy and principal component analysis

1992 ◽  
Vol 50 (2) ◽  
pp. 1752-1753
Author(s):  
Brian Cross
Keyword(s):  
Principal Component Analysis ◽  
Fluorescence Microscopy ◽  
Spatial Resolution ◽  
High Speed ◽  
Image Acquisition ◽  
Principal Component ◽  
Fluorescence Microscope ◽  
Acquisition Rate ◽  
X Ray ◽  
Speed Up

A relatively new entry, in the field of microscopy, is the Scanning X-Ray Fluorescence Microscope (SXRFM). Using this type of instrument (e.g. Kevex Omicron X-ray Microprobe), one can obtain multiple elemental x-ray images, from the analysis of materials which show heterogeneity. The SXRFM obtains images by collimating an x-ray beam (e.g. 100 μm diameter), and then scanning the sample with a high-speed x-y stage. To speed up the image acquisition, data is acquired "on-the-fly" by slew-scanning the stage along the x-axis, like a TV or SEM scan. To reduce the overhead from "fly-back," the images can be acquired by bi-directional scanning of the x-axis. This results in very little overhead with the re-positioning of the sample stage. The image acquisition rate is dominated by the x-ray acquisition rate. Therefore, the total x-ray image acquisition rate, using the SXRFM, is very comparable to an SEM. Although the x-ray spatial resolution of the SXRFM is worse than an SEM (say 100 vs. 2 μm), there are several other advantages.

PHAX-SCAN: Functional integration of a Scanning Electron Microscope and an energy-dispersive x-ray analyser

1989 ◽  
Vol 47 ◽  
pp. 56-57
Author(s):  
Marc H. Peeters ◽  
Max T. Otten
Keyword(s):  
Electron Microscope ◽  
Scanning Electron Microscope ◽  
High Speed ◽  
High Performance ◽  
Functional Integration ◽  
Energy Dispersive ◽  
X Rays ◽  
X Ray ◽  
High Speed Analysis ◽  
Scanning Electron

Over the past decades, the combination of energy-dispersive analysis of X-rays and scanning electron microscopy has proved to be a powerful tool for fast and reliable elemental characterization of a large variety of specimens. The technique has evolved rapidly from a purely qualitative characterization method to a reliable quantitative way of analysis. In the last 5 years, an increasing need for automation is observed, whereby energy-dispersive analysers control the beam and stage movement of the scanning electron microscope in order to collect digital X-ray images and perform unattended point analysis over multiple locations.The Philips High-speed Analysis of X-rays system (PHAX-Scan) makes use of the high performance dual-processor structure of the EDAX PV9900 analyser and the databus structure of the Philips series 500 scanning electron microscope to provide a highly automated, user-friendly and extremely fast microanalysis system. The software that runs on the hardware described above was specifically designed to provide the ultimate attainable speed on the system.

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