Characterization of the PILATUS photon-counting pixel detector for X-ray energies from 1.75 keV to 60 keV

Flatfielding of hybrid pixel detectors in tender x-ray scattering

The ability of the soft matter interfaces beamline at National Synchrotron Light Source II to access x-ray energy in the tender x-ray regime, i.e., from 2.1 to 5 keV, enables new resonant x-ray scattering studies at the sulfur K-edge and others. We present a new approach to correct data acquired in the tender x-ray regime with a Pilatus3 detector in order to improve the data quality and to correct the various artifacts inherent to hybrid pixel detectors, such as variations in modules' efficiency or noisy detector module junctions. This new flatfielding significantly enhances the data quality and enables detection of weak scattering signals.

Hard X-ray full-field nanoimaging using a direct photon-counting detector

Full-field X-ray nanoimaging is a widely used tool in a broad range of scientific areas. In particular, for low-absorbing biological or medical samples, phase contrast methods have to be considered. Three well established phase contrast methods at the nanoscale are transmission X-ray microscopy with Zernike phase contrast, near-field holography and near-field ptychography. The high spatial resolution, however, often comes with the drawback of a lower signal-to-noise ratio and significantly longer scan times, compared with microimaging. In order to tackle these challenges a single-photon-counting detector has been implemented at the nanoimaging endstation of the beamline P05 at PETRA III (DESY, Hamburg) operated by Helmholtz-Zentrum Hereon. Thanks to the long sample-to-detector distance available, spatial resolutions of below 100 nm were reached in all three presented nanoimaging techniques. This work shows that a single-photon-counting detector in combination with a long sample-to-detector distance allows one to increase the time resolution for in situ nanoimaging, while keeping a high signal-to-noise level.

Experimental evidence for the benefits of higher X-ray energies for macromolecular crystallography

X-ray-induced radiation damage is a limiting factor for the macromolecular crystallographer and data must often be merged from many crystals to yield complete data sets for the structure solution of challenging samples. Increasing the X-ray energy beyond the typical 10-15 keV range promises to provide an extension of crystal lifetime via an increase in diffraction efficiency. To date, however, hardware limitations have negated any possible gains. Through the first use of a cadmium telluride EIGER2 detector and a beamline optimized for high-energy data collection, it is shown that at higher energies fewer crystals will be required to obtain complete data, as the diffracted intensity per unit dose increases by a factor of more than two between 12.4 and 25 keV. Additionally, these higher energy data can provide more information, as shown by a systematic increase in the high-resolution cutoff of the data collected. Taken together, these gains point to a high-energy future for synchrotron-based macromolecular crystallography.

The use of Pantherpix pixel detector in radiotherapy QA

There are various different detectors, which can be used for radiotherapy measurements, and more are about to be adopted. Hybrid pixel detectors (HPD) have been originally developed for the high energy physics. However, over the last few years they also expanded in the medical physics. Novel 2D detector Pantherpix is a HPD designed specifically for the radiotherapy. In this article, its properties are characterised and an assessment of its use in radiotherapy photon beams is provided. Properties such as response stability, response linearity, angular dependence and energy dependence were studied. In order to prove sufficient clinical quality for relative dosimetry, further measurements were undertaken (i.e. dose profiles and collimator scatter factors). Acquired results were compared with ion chamber and gafchromic film results. Namely the applicability of PhPix for cobalt beam therapy, which is still widely used (and will be used in near future) in economically less developed countries, is considered.

TEXS: in-vacuum tender X-ray emission spectrometer with 11 Johansson crystal analyzers

The design and first results of a large-solid-angle X-ray emission spectrometer that is optimized for energies between 1.5 keV and 5.5 keV are presented. The spectrometer is based on an array of 11 cylindrically bent Johansson crystal analyzers arranged in a non-dispersive Rowland circle geometry. The smallest achievable energy bandwidth is smaller than the core hole lifetime broadening of the absorption edges in this energy range. Energy scanning is achieved using an innovative design, maintaining the Rowland circle conditions for all crystals with only four motor motions. The entire spectrometer is encased in a high-vacuum chamber that allocates a liquid helium cryostat and provides sufficient space for in situ cells and operando catalysis reactors.

Vacuum-compatible photon-counting hybrid pixel detector for wide-angle x-ray scattering, x-ray diffraction, and x-ray reflectometry in the tender x-ray range

A vacuum-compatible photon-counting hybrid pixel detector has been installed in the ultra-high vacuum reflectometer of the four-crystal monochromator beamline of the Physikalisch-Technische Bundesanstalt at the electron storage ring BESSY II in Berlin, Germany. The setup is based on the PILATUS3 100K module. The detector can be used in the entire photon energy range accessible at the beamline from 1.75 keV to 10 keV. Complementing the already installed vacuum-compatible PILATUS 1M detector used for small-angle x-ray scattering (SAXS) and grazing incidence SAXS, it is possible to access larger scattering angles. The water-cooled module is located on the goniometer arm and can be positioned from -90° to 90° with respect to the incoming beam at a distance of about 200 mm from the sample. To perform absolute scattering experiments, the linearity, homogeneity, and angular dependence of the quantum efficiency, including their relative uncertainties, have been investigated. In addition, the first results of the performance in wide-angle x-ray scattering, x-ray diffraction, and x-ray reflectometry are presented.

Measuring energy-dependent photoelectron escape in microcrystals

With the increasing trend of using microcrystals and intense microbeams at synchrotron X-ray beamlines, radiation damage becomes a more pressing problem. Theoretical calculations show that the photoelectrons that primarily cause damage can escape microcrystals. This effect would become more pronounced with decreasing crystal size as well as at higher energies. To prove this effect, data from cryocooled lysozyme crystals of dimensions 5 × 3 × 3 and 20 × 8 × 8 µm mounted on cryo-transmission electron microscopy (cryo-TEM) grids were collected at 13.5 and 20.1 keV using a PILATUS CdTe 2M detector, which has a similar quantum efficiency at both energies. Accurate absorbed doses were calculated through the direct measurement of individual crystal sizes using scanning electron microscopy after the experiment and characterization of the X-ray microbeam. The crystal lifetime was then quantified based on the D 1/2 metric. In this first systematic study, a longer crystal lifetime for smaller crystals was observed and crystal lifetime increased at higher X-ray energies, supporting the theoretical predictions of photoelectron escape. The use of detector technologies specifically optimized for data collection at energies above 20 keV allows the theoretically predicted photoelectron escape to be quantified and exploited, guiding future beamline-design choices.

The potential benefits of using higher X-ray energies for macromolecular crystallography

Using X-ray energies higher than those normally used (5-15 keV) for macromolecular X-ray crystallography (MX) at synchrotron sources can theoretically increase the achievable signal as a function of dose and reduce the rate of radiation damage. In practice, a major stumbling block to the use of higher X-ray energy has been the reduced quantum efficiency of silicon detectors as the X-ray energy increases, but hybrid photon-counting CdTe detectors are optimized for higher X-ray energies, and their performance has been steadily improving. Here the potential advantages of using higher incident beam energy together with a CdTe detector for MX are explored, with a particular focus on the advantages that higher beam energies may have for MX experiments with microbeams or microcrystals. Monte Carlo simulations are presented here which for the first time include the efficiency responses of some available X-ray detectors, as well as the possible escape of photoelectrons from the sample and their entry from surrounding material. The results reveal a `sweet spot' at an incident X-ray energy of 26 keV, and show a greater than factor of two improvement in diffraction efficiency at this energy when using microbeams and microcrystals of 5 µm or less.

Development of low-energy X-ray detectors using LGAD sensors

Recent advances in segmented low-gain avalanche detectors (LGADs) make them promising for the position-sensitive detection of low-energy X-ray photons thanks to their internal gain. LGAD microstrip sensors fabricated by Fondazione Bruno Kessler have been investigated using X-rays with both charge-integrating and single-photon-counting readout chips developed at the Paul Scherrer Institut. In this work it is shown that the charge multiplication occurring in the sensor allows the detection of X-rays with improved signal-to-noise ratio in comparison with standard silicon sensors. The application in the tender X-ray energy range is demonstrated by the detection of the sulfur K_α and K_β lines (2.3 and 2.46 keV) in an energy-dispersive fluorescence spectrometer at the Swiss Light Source. Although further improvements in the segmentation and in the quantum efficiency at low energy are still necessary, this work paves the way for the development of single-photon-counting detectors in the soft X-ray energy range.

Long-wavelength native-SAD phasing: opportunities and challenges

Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers (Z < 20). The anomalous signal of sulfur in particular, is enhanced at long wavelengths, however the absorption of diffracted X-rays owing to the crystal, the sample support and air affects the recorded intensities. Thereby, the optimal measurable anomalous signals primarily depend on the counterplay of the absorption and the anomalous scattering factor at a given X-ray wavelength. Here, the benefit of using a wavelength of 2.7 over 1.9 Å is demonstrated for native-SAD phasing on a 266 kDa multiprotein-ligand tubulin complex (T2R-TTL) and is applied in the structure determination of an 86 kDa helicase Sen1 protein at beamline BL-1A of the KEK Photon Factory, Japan. Furthermore, X-ray absorption at long wavelengths was controlled by shaping a lysozyme crystal into spheres of defined thicknesses using a deep-UV laser, and a systematic comparison between wavelengths of 2.7 and 3.3 Å is reported for native SAD. The potential of laser-shaping technology and other challenges for an optimized native-SAD experiment at wavelengths >3 Å are discussed.

Pushing data quality for laboratory pair distribution function experiments

Over the last decade, some studies with laboratory pair distribution function (PDF) data emerged. Yet, limited Q_max or instrumental resolution impeded in-depth structural refinements. With more advanced detector technologies, the question arose how to design novel PDF equipment for laboratories that will allow decent PDF refinements over r = 1-70 Å. It is crucial to reflect the essential requirements, namely, monochromatic X-rays, suppression of air scattering, instrumental resolution, and overall measurement times. The result is a novel PDF setup based on a STOE STADI P powder diffractometer in transmission-/Debye-Scherrer geometry with monochromatic Ag Kα₁ radiation, featuring a MYTHEN2 4K detector covering a Q range of 0.3-20.5 Å^-1. PDF data are collected in a moving PDF mode within 6 h. Structural signatures of liquids can be satisfactorily resolved in the PDF as shown for the ionic liquid hmimPF₆. The high instrumental resolution is mirrored in low q_damp values determined from LaB₆ measurements. PDF data from a powder sample of ca. 7 nm TiO₂ nanoparticles were successfully refined over up to 70 Å with goodness-of-fit values R_w < 0.22 (respectively R_w = 0.18 over 30 Å), thanks to the low background and high instrumental resolution, hereby enlarging the accessible r range by several tens of Angstroms compared to previous laboratory PDF studies.

A new diffractometer for diffuse scattering studies on the ID28 beamline at the ESRF

A new diffractometer is now available to the general user community at the ESRF. The new diffractometer is a side station of the high-resolution inelastic X-ray scattering spectrometer on beamline ID28 and is located in the same experimental hutch. Both instruments can be operated simultaneously. The new diffractometer combines a fast and low-noise hybrid pixel detector with a variable diffraction geometry. The beam spot on the sample is 50 µm × 50 µm, where focusing is achieved by a combination of Be lenses and a KB mirror. Wavelengths from 0.5 to 0.8 Å can be used for the diffraction experiments. The setup is compatible with a variety of sample environments, allowing studies under non-ambient conditions. The diffractometer is optimized to allow a rapid survey of reciprocal space and diffuse scattering for the identification of regions of interest for subsequent inelastic scattering studies, but can also be employed as a fully independent station for structural studies from both powder and single-crystal diffraction experiments. Several software packages for the transformation and visualization of diffraction data are available. An analysis of data collected with the new diffractometer shows that the ID28 side station is a state-of-the-art instrument for structural investigations using diffraction and diffuse scattering experiments.

Predicting data quality in biological X-ray solution scattering

Biological small-angle X-ray solution scattering (BioSAXS) is now widely used to gain information on biomolecules in the solution state. Often, however, it is not obvious in advance whether a particular sample will scatter strongly enough to give useful data to draw conclusions under practically achievable solution conditions. Conformational changes that appear to be large may not always produce scattering curves that are distinguishable from each other at realistic concentrations and exposure times. Emerging technologies such as time-resolved SAXS (TR-SAXS) pose additional challenges owing to small beams and short sample path lengths. Beamline optics vary in brilliance and degree of background scatter, and major upgrades and improvements to sources promise to expand the reach of these methods. Computations are developed to estimate BioSAXS sample intensity at a more detailed level than previous approaches, taking into account flux, energy, sample thickness, window material, instrumental background, detector efficiency, solution conditions and other parameters. The results are validated with calibrated experiments using standard proteins on four different beamlines with various fluxes, energies and configurations. The ability of BioSAXS to statistically distinguish a variety of conformational movements under continuous-flow time-resolved conditions is then computed on a set of matched structure pairs drawn from the Database of Macromolecular Motions (http://molmovdb.org). The feasibility of experiments is ranked according to sample consumption, a quantity that varies by over two orders of magnitude for the set of structures. In addition to photon flux, the calculations suggest that window scattering and choice of wavelength are also important factors given the short sample path lengths common in such setups.

Where is crystallography going?

Macromolecular crystallography (MX) has been a motor for biology for over half a century and this continues apace. A series of revolutions, including the production of recombinant proteins and cryo-crystallography, have meant that MX has repeatedly reinvented itself to dramatically increase its reach. Over the last 30 years synchrotron radiation has nucleated a succession of advances, ranging from detectors to optics and automation. These advances, in turn, open up opportunities. For instance, a further order of magnitude could perhaps be gained in signal to noise for general synchrotron experiments. In addition, X-ray free-electron lasers offer to capture fragments of reciprocal space without radiation damage, and open up the subpicosecond regime of protein dynamics and activity. But electrons have recently stolen the limelight: so is X-ray crystallography in rude health, or will imaging methods, especially single-particle electron microscopy, render it obsolete for the most interesting biology, whilst electron diffraction enables structure determination from even the smallest crystals? We will lay out some information to help you decide.

Hybrid spectral CT reconstruction

Current photon counting x-ray detector (PCD) technology faces limitations associated with spectral fidelity and photon starvation. One strategy for addressing these limitations is to supplement PCD data with high-resolution, low-noise data acquired with an energy-integrating detector (EID). In this work, we propose an iterative, hybrid reconstruction technique which combines the spectral properties of PCD data with the resolution and signal-to-noise characteristics of EID data. Our hybrid reconstruction technique is based on an algebraic model of data fidelity which substitutes the EID data into the data fidelity term associated with the PCD reconstruction, resulting in a joint reconstruction problem. Within the split Bregman framework, these data fidelity constraints are minimized subject to additional constraints on spectral rank and on joint intensity-gradient sparsity measured between the reconstructions of the EID and PCD data. Following a derivation of the proposed technique, we apply it to the reconstruction of a digital phantom which contains realistic concentrations of iodine, barium, and calcium encountered in small-animal micro-CT. The results of this experiment suggest reliable separation and detection of iodine at concentrations ≥ 5 mg/ml and barium at concentrations ≥ 10 mg/ml in 2-mm features for EID and PCD data reconstructed with inherent spatial resolutions of 176 μm and 254 μm, respectively (point spread function, FWHM). Furthermore, hybrid reconstruction is demonstrated to enhance spatial resolution within material decomposition results and to improve low-contrast detectability by as much as 2.6 times relative to reconstruction with PCD data only. The parameters of the simulation experiment are based on an in vivo micro-CT experiment conducted in a mouse model of soft-tissue sarcoma. Material decomposition results produced from this in vivo data demonstrate the feasibility of distinguishing two K-edge contrast agents with a spectral separation on the order of the energy resolution of the PCD hardware.

On the influence of crystal size and wavelength on native SAD phasing

Native SAD is an emerging phasing technique that uses the anomalous signal of native heavy atoms to obtain crystallographic phases. The method does not require specific sample preparation to add anomalous scatterers, as the light atoms contained in the native sample are used as marker atoms. The most abundant anomalous scatterer used for native SAD, which is present in almost all proteins, is sulfur. However, the absorption edge of sulfur is at low energy (2.472 keV = 5.016 Å), which makes it challenging to carry out native SAD phasing experiments as most synchrotron beamlines are optimized for shorter wavelength ranges where the anomalous signal of sulfur is weak; for longer wavelengths, which produce larger anomalous differences, the absorption of X-rays by the sample, solvent, loop and surrounding medium (e.g. air) increases tremendously. Therefore, a compromise has to be found between measuring strong anomalous signal and minimizing absorption. It was thus hypothesized that shorter wavelengths should be used for large crystals and longer wavelengths for small crystals, but no thorough experimental analyses have been reported to date. To study the influence of crystal size and wavelength, native SAD experiments were carried out at different wavelengths (1.9 and 2.7 Å with a helium cone; 3.0 and 3.3 Å with a helium chamber) using lysozyme and ferredoxin reductase crystals of various sizes. For the tested crystals, the results suggest that larger sample sizes do not have a detrimental effect on native SAD data and that long wavelengths give a clear advantage with small samples compared with short wavelengths. The resolution dependency of substructure determination was analyzed and showed that high-symmetry crystals with small unit cells require higher resolution for the successful placement of heavy atoms.

CREDO: a new general-purpose laboratory instrument for small-angle X-ray scattering

The details of a newly constructed small-angle X-ray scattering instrument are presented. The geometry of the instrument is highly customizable, enabling it to address vastly different experimental situations from academic research to industrial problems. The high degree of motorization and automation compared to conventional laboratory-scale SAXS instruments facilitates the alignment and daily use. Data reduction routines are incorporated in the instrument control software, yielding fully corrected and calibrated results promptly after the end of measurements. Optimization of the fluxversus resolution balance can be done routinely for each measurement task. A wide, continuous range ofq= 4πsinθ/λ can be reached, from below 0.02 nm−1up to 30 nm−1, corresponding to periodic distances ofca 350 nm down to 0.2 nm. A few representative results obtained from samples of different research fields demonstrate the versatility of the instrument. Scattering curves are routinely calibrated into absolute units using a glassy carbon secondary standard. More information and recent developments can be found on the web page of the instrument at http://credo.ttk.mta.hu.

Characterization of an in-vacuum PILATUS 1M detector

A dedicated in-vacuum X-ray detector based on the hybrid pixel PILATUS 1M detector has been installed at the four-crystal monochromator beamline of the PTB at the electron storage ring BESSY II in Berlin, Germany. Owing to its windowless operation, the detector can be used in the entire photon energy range of the beamline from 10 keV down to 1.75 keV for small-angle X-ray scattering (SAXS) experiments and anomalous SAXS at absorption edges of light elements. The radiometric and geometric properties of the detector such as quantum efficiency, pixel pitch and module alignment have been determined with low uncertainties. The first grazing-incidence SAXS results demonstrate the superior resolution in momentum transfer achievable at low photon energies.

Towards traceable size determination of extracellular vesicles

Background

Extracellular vesicles (EVs) have clinical importance due to their roles in a wide range of biological processes. The detection and characterization of EVs are challenging because of their small size, low refractive index, and heterogeneity.

Methods

In this manuscript, the size distribution of an erythrocyte-derived EV sample is determined using state-of-the-art techniques such as nanoparticle tracking analysis, resistive pulse sensing, and electron microscopy, and novel techniques in the field, such as small-angle X-ray scattering (SAXS) and size exclusion chromatography coupled with dynamic light scattering detection.

Results

The mode values of the size distributions of the studied erythrocyte EVs reported by the different methods show only small deviations around 130 nm, but there are differences in the widths of the size distributions.

Conclusion

SAXS is a promising technique with respect to traceability, as this technique was already applied for traceable size determination of solid nanoparticles in suspension. To reach the traceable measurement of EVs, monodisperse and highly concentrated samples are required.