ID15A is a newly refurbished beamline at the ESRF devoted to operando and time‐resolved diffraction and imaging, total scattering and diffraction computed tomography. The beamline is optimized for ...rapid alternation between the different techniques during a single operando experiment in order to collect complementary data on working systems. The high available energy (up to 120 keV) means that even bulky and highly absorbing systems may be studied. The beamline is equipped with optimized focusing optics and a photon‐counting CdTe pixel detector, allowing for both unprecedented data quality at high energy and for very rapid triggered experiments. A large choice of imaging detectors and ancillary probes and sample environments is also available.
ID15A is a newly refurbished beamline at the ESRF devoted to operando and time‐resolved diffraction and imaging, total scattering and diffraction computed tomography.
Small‐angle X‐ray scattering (SAXS) measurements of proteins in solution are becoming increasingly popular with biochemists and structural biologists owing to the presence of dedicated ...high‐throughput beamlines at synchrotron sources. As part of the ESRF Upgrade program a dedicated instrument for performing SAXS from biological macromolecules in solution (BioSAXS) has been installed at the renovated BM29 location. The optics hutch has been equipped with new optical components of which the two principal elements are a fixed‐exit double multilayer monochromator and a 1.1 m‐long toroidal mirror. These new dedicated optics give improved beam characteristics (compared with the previous set‐up on ID14‐3) regarding the energy tunability, flux and focusing at the detector plane leading to reduced parasitic scattering and an extended s‐range. User experiments on the beamline have been successfully carried out since June 2012. A description of the new BioSAXS beamline and the set‐up characteristics are presented together with examples of obtained data.
2D area detectors like CCD or pixel detectors have become popular in the last 15 years for diffraction experiments (e.g. for WAXS, SAXS, single crystal and powder diffraction (XRPD)). These detectors ...have a large sensitive area of millions of pixels with high spatial resolution. The software package pyFAI has been designed to reduce SAXS, WAXS and XRPD images taken with those detectors into 1D curves (azimuthal integration) usable by other software for in-depth analysis such as Rietveld refinement, or 2D images (a radial transformation named caking). As a library, the aim of pyFAI is to be integrated into other tools like PyMca or EDNA with a clean pythonic interface. However pyFAI features also command line tools for batch processing, converting data into q-space (q being the momentum transfer) or 2θ-space (θ being the Bragg angle) and a calibration graphical interface for optimizing the geometry of the experiment using the Debye-Scherrer rings of a reference sample. PyFAI shares the geometry definition of SPD but can directly import geometries determined by the software FIT2D. PyFAI has been designed to work with any kind of detector and geometry (transmission or reflection) and relies on FabIO, a library able to read more than 20 image formats produced by detectors from 12 different manufacturers. During the transformation from cartesian space (x,y) to polar space (2θ, χ), both local and total intensities are conserved in order to obtain accurate quantitative results. Technical details on how this integration is implemented and how it has been ported to native code and parallelized on graphic cards are discussed in this paper.
pyFAI is an open‐source software package designed to perform azimuthal integration and, correspondingly, two‐dimensional regrouping on area‐detector frames for small‐ and wide‐angle X‐ray scattering ...experiments. It is written in Python (with binary submodules for improved performance), a language widely accepted and used by the scientific community today, which enables users to easily incorporate the pyFAI library into their processing pipeline. This article focuses on recent work, especially the ease of calibration, its accuracy and the execution speed for integration.
We present the PyHST2 code which is in service at ESRF for phase-contrast and absorption tomography. This code has been engineered to sustain the high data flow typical of the 3rd generation ...synchrotron facilities (10 terabytes per experiment) by adopting a distributed and pipelined architecture. The code implements, beside a default filtered backprojection reconstruction, iterative reconstruction techniques with a priori knowledge. These latter are used to improve the reconstruction quality or in order to reduce the required data volume or the deposited dose to the sample and reach a given quality goal. The implemented a priori knowledge techniques are based on the total variation penalization and a new recently found convex functional which is based on overlapping patches. We give details of the different methods and discuss how they are implemented in the PyHST2 code, which is distributed under free license. We provide methods for estimating, in the absence of ground-truth data, the optimal parameters values for a priori techniques.
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.
High‐throughput small‐angle X‐ray scattering on proteins in solution (bioSAXS) at synchrotron sources is a commonly used technique in structural biology, which relies on highly automated data ...acquisition. Data reduction and primary analysis for bioSAXS experiments consist of a well defined series of individual tasks, the automation of which allows a first easy assessment of the quality of collected data and the adjustment of collection strategies if necessary. This article describes both the logic and the technical implementation of the automated processing pipeline for bioSAXS data at the ESRF BM29 beamline using the EDNA framework.
Low‐latency small‐angle X‐ray scattering (SAXS) data reduction for bioSAXS and real‐time feedback to the users is implemented.
The unique diffraction geometry of ESRF beamline ID06-LVP offers continuous static 2D or azimuthally resolving data collections over all accessible solid angles available to the tooling geometry. The ...system is built around a rotating custom-built Pilatus3 CdTe 900k-W detector from Dectris, in a configuration equivalent to three butted 300k devices. As a non-standard geometry, here the method of alignment, correction and subsequent integration for any data collected over all solid angles accessible, or over any azimuthal range contained therein, are provided and illustrated by parameterizing and extending existing
pyFAI
routines. At 1° integrated intervals, and typical distances (2.0 m), the system covers an area of near 2.5 m
2
(100 Mpx square equivalent), to 0.65 Å resolution, at 53 keV from a total dataset of some 312 Mpx. Standard FWHMs of SRM660a LaB
6
vary from 0.005° to 0.01°, depending on beam size, energy and sample dimensions, and are sampled at an elevated rate. The azimuthal range per static frame ranges from <20° to ∼1° over the full range of the detector surface. A full 2θ–intensity data collection at static azimuth takes 1–3 s typically, and can be reduced to ms
−1
rates for measurements requiring time-rate determination. A full solid-angle collection can be completed in a minute. Sample detector distances are accessible from 1.6 m to 4.0 m.
The ID21 beamline (European Synchrotron Radiation facility, France) is a multi micro-analytical platform combining X-ray and infrared micro-probes, for characterization of elements, species, ...molecular groups and crystalline structures in complex materials. Applications are mainly in the fields of cultural heritage, life science, environmental and earth sciences, materials sciences. Here, we first present the status of instruments: (i) the scanning micro-spectroscopy end-station, operating from 2.0 to 9.2 keV, under vacuum and offering cryo conditions, for the acquisition of 2D micro X-ray fluorescence (μXRF) maps, single point micro X-ray Absorption Near Edge Structure (μXANES) spectra and speciation maps with sub-micrometric resolution; (ii) the XANES full-field end-station, operating in the same vacuum and energy conditions, for the acquisition of hyper-spectral radiographs of thin concentrated samples, resulting in speciation maps with micrometric resolution and millimetric field of view; (iii) the scanning micro-X-ray diffraction (μXRD)/μXRF end-station, operating at 8.5 keV, in air, for the acquisition of 2D crystalline phase maps, with micrometric resolution; and (iv) the scanning infrared microscope, operating in the mid-infrared range for the acquisition of molecular maps and some structural maps with micrometric resolution. Recent hardware and software developments are presented, as well as new protocols for improved sample preparation of thin sections. Secondly, a review of recent applications for the study of cultural heritage is presented, illustrated by various examples: determination of the origin of the color in blue Chinese porcelains and in brown Sèvres porcelains; detection of lead in ink on Herculaneum papyri; identification and degradation of modeling materials used by Auguste Rodin and of chrome yellow pigments used by Vincent van Gogh. Cryo capabilities are illustrated by the analysis of plants exposed to chromate solutions. These examples show the variety of materials analyzed, of questions tackled, and particularly the multiple advantages of the ID21 analytical platform for the analysis of ancient and artistic materials.
ID21 beamline (ESRF) offers combination of μXRF, μXANES (2.0-9.1 keV), μXRD and μFTIR, increasingly used to analyse artistic and ancient materials.
New data analysis for BioSAXS at the ESRF Kieffer, Jérôme; Brennich, Martha; Florial, Jean-Baptiste ...
Journal of synchrotron radiation,
September 2022, Letnik:
29, Številka:
5
Journal Article
Recenzirano
Odprti dostop
The second phase of the ESRF upgrade program did not only provide a new storage ring (Extremely Brilliant Source, EBS) but also allowed several beamlines to be refurbished. The BioSAXS beamline ...(located on port BM29) was upgraded with a new wiggler source and a larger detector. All analysis software has been rewritten to cope with the increased data flux and continues to provide beamline users with reduced and pre‐processed data in real time. This article describes FreeSAS, an open‐source collection of various small‐angle scattering analysis algorithms needed to reduce and analyze BioSAXS data, and Dahu, the tool used to interface data analysis with beamline control. It further presents the data‐processing pipelines for the different data acquisitions modes of the beamline, using either a sample changer for individual homogeneous samples or an inline size‐exclusion chromatography setup.
A detailed presentation of the automatic data analysis pipelines for the BioSAXS beamline at the European synchrotron.
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