This article presents the main technical features and performance of the upgraded beamline ID02 at the ESRF. The beamline combines different small‐angle X‐ray scattering techniques in one unique ...instrument, enabling static and kinetic investigations from ångström to micrometre size scales and time resolution down to the sub‐millisecond range. The main component of the instrument is an evacuated detector tube of length 34 m and diameter 2 m. Several different detectors are housed inside a motorized wagon that travels along a rail system, allowing an automated change of the sample–detector distance from about 1 to 31 m as well as selection of the desired detector. For optional combined wide‐angle scattering measurements, a wide‐angle detector is installed at the entrance cone of the tube. A scattering vector (of magnitude q) range of 0.002 ≤ q ≤ 50 nm−1 is covered with two sample–detector distances and a single‐beam setting for an X‐ray wavelength of 1 Å. In the high‐resolution mode, two‐dimensional ultra‐small‐angle X‐ray scattering patterns down to q < 0.001 nm−1 can be recorded, and the resulting one‐dimensional profiles have superior quality as compared to those measured with an optimized Bonse–Hart instrument. In the highest‐resolution mode, the beam is nearly coherent, thereby permitting multispeckle ultra‐small‐angle X‐ray photon correlation spectroscopy measurements. The main applications of the instrument include the elucidation of static and transient hierarchical structures, and nonequilibrium dynamics in soft matter and biophysical systems.
The technical features and performance of a new instrument for time‐resolved ultra‐small‐angle and coherent X‐ray scattering are presented. The instrument enables static and kinetic investigations from ångström to micrometre size scales and time resolution down to the sub‐millisecond range. Applications include elucidation of static and transient hierarchical structures in soft matter and biophysical systems.
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X-ray microimaging laboratory (XMI-LAB) Altamura, D.; Lassandro, R.; Vittoria, F. A. ...
Journal of applied crystallography,
08/2012, Volume:
45, Issue:
4
Journal Article
Peer reviewed
A first‐generation‐synchrotron‐class X‐ray laboratory microsource, coupled to a three‐pinhole camera, is presented. It allows (i) small‐ and wide‐angle X‐ray scattering images to be acquired ...simultaneously, and (ii) scanning small‐ and wide‐angle X‐ray scattering microscopy to be carried out. As representative applications, the structural complexity of a biological natural material (human bone biopsy) and of a metamaterial (colloidal nanocrystal assembly) are inspected at different length scales, studying the atomic/molecular ordering by (grazing‐incidence) wide‐angle X‐ray scattering and the morphological/structural conformation by (grazing‐incidence) small‐angle X‐ray scattering. In particular, the grazing‐incidence measurement geometries are needed for inspecting materials lying on top of surfaces or buried underneath surfaces.
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Intermetallic γ′ precipitates typically strengthen nickel‐based superalloys. The shape, size and spatial distribution of strengthening precipitates critically influence alloy strength, while their ...temporal evolution characteristics determine the high‐temperature alloy stability. Combined ultra‐small‐, small‐ and wide‐angle X‐ray scattering (USAXS–SAXS–WAXS) analysis can be used to evaluate the temporal evolution of an alloy's precipitate size distribution (PSD) and phase structure during in situ heat treatment. Analysis of PSDs from USAXS–SAXS data employs either least‐squares fitting of a preordained PSD model or a maximum entropy (MaxEnt) approach, the latter avoiding a priori definition of a functional form of the PSD. However, strong low‐q scattering from grain boundaries and/or structure factor effects inhibit MaxEnt analysis of typical alloys. This work describes the extension of Bayesian–MaxEnt analysis methods to data exhibiting structure factor effects and low‐q power law slopes and demonstrates their use in an in situ study of precipitate size evolution during heat treatment of a model Ni–Al–Si alloy.
Combined ultra‐small‐, small‐ and wide‐angle X‐ray scattering (USAXS–SAXS–WAXS) provides in situ evaluation of the precipitate size distribution (PSD) and phase structure temporal evolution during heat treatment. A method for extraction of an arbitrary PSD in the presence of interparticle interactions is described and illustrated for study of PSD evolution.
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BioXTAS RAW is a graphical‐user‐interface‐based free open‐source Python program for reduction and analysis of small‐angle X‐ray solution scattering (SAXS) data. The software is designed for ...biological SAXS data and enables creation and plotting of one‐dimensional scattering profiles from two‐dimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and advanced analysis such as calculation of inverse Fourier transforms and envelopes. It also allows easy processing of inline size‐exclusion chromatography coupled SAXS data and data deconvolution using the evolving factor analysis method. It provides an alternative to closed‐source programs such as Primus and ScÅtter for primary data analysis. Because it can calibrate, mask and integrate images it also provides an alternative to synchrotron beamline pipelines that scientists can install on their own computers and use both at home and at the beamline.
BioXTAS RAW is a graphical‐user‐interface‐based free open‐source Python program for reduction and analysis of small‐angle X‐ray solution scattering (SAXS) data, including size‐exclusion chromatography coupled SAXS data. The software is designed for biological data and enables creation and plotting of one‐dimensional scattering profiles from two‐dimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and more advanced analyses such as calculation of inverse Fourier transforms.
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Small‐angle X‐ray scattering (SAXS) of proteins in solution has become a key tool for biochemists and structural biologists, thanks especially to the availability of beamlines with high‐throughput ...capabilities at synchrotron sources. Despite the large spectrum of scientific disciplines tackled on the SWING beamline since its opening in 2008, there has always been a strong commitment to offering state‐of‐the‐art biological SAXS (BioSAXS) instrumentation and data reduction methods to the scientific community. The extremely reliable in‐vacuum EigerX‐4M detector allows collection of an unlimited number of frames without noise. A small beamstop including a diamond diode‐based monitor enables measurements of the transmitted intensity with 0.1% precision as well as a qmax/qmin ratio as large as 140 at a single distance. The parasitic scattering has been strongly reduced by the installation of new hybrid blades. A new thermally controlled in‐vacuum capillary holder including fibre‐optics‐based spectroscopic functionalities allows the simultaneous use of three spectroscopic techniques in addition to SAXS measurements. The addition of a second high‐performance liquid chromatography (HPLC) circuit has virtually eliminated the waiting time associated with column equilibration. The easy in‐line connection of a multi‐angle light scattering spectrometer and a refractometer allows for an independent determination of the molecular mass and of the concentration of low‐UV‐absorption samples such as detergents and sugars, respectively. These instrumental improvements are combined with important software developments. The HPLC injection Agilent software is controlled by the SAXS beamline acquisition software, allowing a virtually unlimited series of automated SAXS measurements to be synchronized with the sample injections. All data‐containing files and reports are automatically stored in the same folders, with names related to both the user and sample. In addition, all raw SAXS images are processed automatically on the fly, and the analysed data are stored in the ISPyB database and made accessible via a web page.
This article describes recent developments on the SWING beamline for biological small‐angle X‐ray scattering (BioSAXS) experiments.
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X‐ray scattering experiments at synchrotron sources are characterized by large and constantly increasing amounts of data. The great number of files generated during a synchrotron experiment is often ...a limiting factor in the analysis of the data, since appropriate software is rarely available to perform fast and tailored data processing. Furthermore, it is often necessary to perform online data reduction and analysis during the experiment in order to interactively optimize experimental design. This article presents an open‐source software package developed to process large amounts of data from synchrotron scattering experiments. These data reduction processes involve calibration and correction of raw data, one‐ or two‐dimensional integration, as well as fitting and further analysis of the data, including the extraction of certain parameters. The software, DPDAK (directly programmable data analysis kit), is based on a plug‐in structure and allows individual extension in accordance with the requirements of the user. The article demonstrates the use of DPDAK for on‐ and offline analysis of scanning small‐angle X‐ray scattering (SAXS) data on biological samples and microfluidic systems, as well as for a comprehensive analysis of grazing‐incidence SAXS data. In addition to a comparison with existing software packages, the structure of DPDAK and the possibilities and limitations are discussed.
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Recent developments in the instrumentation and data analysis of synchrotron small‐angle X‐ray scattering (SAXS) on biomolecules in solution have made biological SAXS (BioSAXS) a mature and popular ...tool in structural biology. This article reports on an advanced endstation developed at beamline 13A of the 3.0 GeV Taiwan Photon Source for biological small‐ and wide‐angle X‐ray scattering (SAXS–WAXS or SWAXS). The endstation features an in‐vacuum SWAXS detection system comprising two mobile area detectors (Eiger X 9M/1M) and an online size‐exclusion chromatography system incorporating several optical probes including a UV–Vis absorption spectrometer and refractometer. The instrumentation and automation allow simultaneous SAXS–WAXS data collection and data reduction for high‐throughput biomolecular conformation and composition determinations. The performance of the endstation is illustrated with the SWAXS data collected for several model proteins in solution, covering a scattering vector magnitude q across three orders of magnitude. The crystal‐model fittings to the data in the q range ∼0.005–2.0 Å−1 indicate high similarity of the solution structures of the proteins to their crystalline forms, except for some subtle hydration‐dependent local details. These results open up new horizons of SWAXS in studying correlated local and global structures of biomolecules in solution.
A new endstation for biological small‐ and wide‐angle X‐ray scattering is detailed, which provides development opportunities for studying correlated local and global structures of biomolecules in solution.
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The new technical features and enhanced performance of the ID02 beamline with the Extremely Brilliant Source (EBS) at the ESRF are described. The beamline enables static and kinetic investigations of ...a broad range of systems from ångström to micrometre size scales and down to the sub‐millisecond time range by combining different small‐angle X‐ray scattering techniques in a single instrument. In addition, a nearly coherent beam obtained in the high‐resolution mode allows multispeckle X‐ray photon correlation spectroscopy measurements down to the microsecond range over the ultra‐small‐ and small‐angle regions. While the scattering vector (of magnitude q) range covered is the same as before, 0.001 ≤ q ≤ 50 nm−1 for an X‐ray wavelength of 1 Å, the EBS permits relaxation of the collimation conditions, thereby obtaining a higher flux throughput and lower background. In particular, a coherent photon flux in excess of 1012 photons s−1 can be routinely obtained, allowing dynamic studies of relatively dilute samples. The enhanced beam properties are complemented by advanced pixel‐array detectors and high‐throughput data reduction pipelines. All these developments together open new opportunities for structural, dynamic and kinetic investigations of out‐of‐equilibrium soft matter and biophysical systems.
The new technical features and improved performance of the time‐resolved ultra‐small‐angle X‐ray scattering beamline at the ESRF are presented. The beamline enables static and time‐resolved investigations from ångström to micrometre size scales down to the sub‐millisecond time range and coherent scattering studies in the ultra‐small‐angle region. Among the main applications are the elucidation of static and transient hierarchical structures in soft matter and biophysical systems, and the dynamics of out‐of‐equilibrium complex fluids.
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At the National Synchrotron Radiation Research Center, a small/wide‐angle X‐ray scattering (SAXS/WAXS) instrument has been installed at the BL23A beamline with a superconducting wiggler insertion ...device. This beamline is equipped with double Si(111) crystal and double Mo/B4C multilayer monochromators, and an Si‐based plane mirror that can selectively deflect the beam downwards for grazing‐incidence SAXS (GISAXS) studies of air–liquid or liquid–liquid interfaces. The SAXS/WAXS instrument, situated in an experimental hutch, comprises collimation, sample and post‐sample stages. Pinholes and slits have been incorporated into the beam collimation system spanning a distance of ∼5 m. The sample stage can accommodate various sample geometries for air–liquid interfaces, thin films, and solution and solid samples. The post‐sample section consists of a 1 m WAXS section with two linear gas detectors, a vacuum bellows (1–4 m), a two‐beamstop system and the SAXS detector system, all situated on a motorized optical bench for motion in six degrees of freedom. In particular, the vacuum bellows of a large inner diameter (260 mm) provides continuous changes of the sample‐to‐detector distance under vacuum. Synchronized SAXS and WAXS measurements are realized via a data‐acquisition protocol that can integrate the two linear gas detectors for WAXS and the area detector for SAXS (gas type or Mar165 CCD); the protocol also incorporates sample changing and temperature control for programmable data collection. The performance of the instrument is illustrated via several different measurements, including (1) simultaneous SAXS/WAXS and differential scanning calorimetry for polymer crystallization, (2) structural evolution with a large ordering spacing of ∼250 nm in a supramolecular complex, (3) SAXS for polymer blends under in situ drawing, (4) SAXS and anomalous SAXS for unilamellar lipid vesicles and metalloprotein solutions, (5) anomalous GISAXS for oriented membranes of Br‐labeled lipids embedded with peptides, and (6) GISAXS for silicate films formed in situ at the air–water interface.
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In situ synchrotron small‐angle X‐ray scattering (SAXS) is a powerful tool for studying dynamic processes during material preparation and application. The processing and analysis of large data sets ...generated from in situ X‐ray scattering experiments are often tedious and time consuming. However, data processing software for in situ experiments is relatively rare, especially for grazing‐incidence small‐angle X‐ray scattering (GISAXS). This article presents an open‐source software suite (SGTools) to perform data processing and analysis for SAXS and GISAXS experiments. The processing modules in this software include (i) raw data calibration and background correction; (ii) data reduction by multiple methods; (iii) animation generation and intensity mapping for in situ X‐ray scattering experiments; and (iv) further data analysis for the sample with an order degree and interface correlation. This article provides the main features and framework of SGTools. The workflow of the software is also elucidated to allow users to develop new features. Three examples are demonstrated to illustrate the use of SGTools for dealing with SAXS and GISAXS data. Finally, the limitations and future features of the software are also discussed.
Data processing and analysis tools are presented that are suitable for the large data sets generated from in situ small‐angle X‐ray scattering experiments.
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