Transient heating of Pd nanoparticles studied by x-ray diffraction with time of arrival photon detection.

Pulsed laser heating of an ensemble of Pd nanoparticles, supported by a MgO substrate, is studied by x-ray diffraction. By time-resolved Bragg peak shift measurements due to thermal lattice expansion, the transient temperature of the Pd nanoparticles is determined, which quickly rises by at least 100 K upon laser excitation and then decays within 90 ns. The diffraction experiments were carried out using a Cu x-ray tube, giving continuous radiation, and the hybrid pixel detector Timepix3 operating with single photon counting in a time-of-arrival mode. This type of detection scheme does not require time-consuming scanning of the pump-probe delay. The experimental time resolution is estimated at 15 ± 5 ns, which is very close to the detector's limit and matches with the 7 ns laser pulse duration. Compared to bulk metal single crystals, it is discussed that the maximum temperature reached by the Pd nanoparticles is higher and their cooling rate is lower. These effects are explained by the oxide support having a lower heat conductivity.

Robust image descriptor for machine learning based data reduction in serial crystallography.

Serial crystallography experiments at synchrotron and X-ray free-electron laser (XFEL) sources are producing crystallographic data sets of ever-increasing volume. While these experiments have large data sets and high-frame-rate detectors (around 3520 frames per second), only a small percentage of the data are useful for downstream analysis. Thus, an efficient and real-time data classification pipeline is essential to differentiate reliably between useful and non-useful images, typically known as 'hit' and 'miss', respectively, and keep only hit images on disk for further analysis such as peak finding and indexing. While feature-point extraction is a key component of modern approaches to image classification, existing approaches require computationally expensive patch preprocessing to handle perspective distortion. This paper proposes a pipeline to categorize the data, consisting of a real-time feature extraction algorithm called modified and parallelized FAST (MP-FAST), an image descriptor and a machine learning classifier. For parallelizing the primary operations of the proposed pipeline, central processing units, graphics processing units and field-programmable gate arrays are implemented and their performances compared. Finally, MP-FAST-based image classification is evaluated using a multi-layer perceptron on various data sets, including both synthetic and experimental data. This approach demonstrates superior performance compared with other feature extractors and classifiers.

Explainable machine learning for diffraction patterns.

Serial crystallography experiments at X-ray free-electron laser facilities produce massive amounts of data but only a fraction of these data are useful for downstream analysis. Thus, it is essential to differentiate between acceptable and unacceptable data, generally known as 'hit' and 'miss', respectively. Image classification methods from artificial intelligence, or more specifically convolutional neural networks (CNNs), classify the data into hit and miss categories in order to achieve data reduction. The quantitative performance established in previous work indicates that CNNs successfully classify serial crystallography data into desired categories [Ke, Brewster, Yu, Ushizima, Yang & Sauter (2018). J. Synchrotron Rad.25, 655-670], but no qualitative evidence on the internal workings of these networks has been provided. For example, there are no visualization methods that highlight the features contributing to a specific prediction while classifying data in serial crystallography experiments. Therefore, existing deep learning methods, including CNNs classifying serial crystallography data, are like a 'black box'. To this end, presented here is a qualitative study to unpack the internal workings of CNNs with the aim of visualizing information in the fundamental blocks of a standard network with serial crystallography data. The region(s) or part(s) of an image that mostly contribute to a hit or miss prediction are visualized.

A MHz X-ray diffraction set-up for dynamic compression experiments in the diamond anvil cell.

An experimental platform for dynamic diamond anvil cell (dDAC) research has been developed at the High Energy Density (HED) Instrument at the European X-ray Free Electron Laser (European XFEL). Advantage was taken of the high repetition rate of the European XFEL (up to 4.5 MHz) to collect pulse-resolved MHz X-ray diffraction data from samples as they are dynamically compressed at intermediate strain rates (≤103 s-1), where up to 352 diffraction images can be collected from a single pulse train. The set-up employs piezo-driven dDACs capable of compressing samples in ≥340 µs, compatible with the maximum length of the pulse train (550 µs). Results from rapid compression experiments on a wide range of sample systems with different X-ray scattering powers are presented. A maximum compression rate of 87 TPa s-1 was observed during the fast compression of Au, while a strain rate of ∼1100 s-1 was achieved during the rapid compression of N2 at 23 TPa s-1.

Data reduction for X-ray serial crystallography using machine learning.

Serial crystallography experiments produce massive amounts of experimental data. Yet in spite of these large-scale data sets, only a small percentage of the data are useful for downstream analysis. Thus, it is essential to differentiate reliably between acceptable data (hits) and unacceptable data (misses). To this end, a novel pipeline is proposed to categorize the data, which extracts features from the images, summarizes these features with the 'bag of visual words' method and then classifies the images using machine learning. In addition, a novel study of various feature extractors and machine learning classifiers is presented, with the aim of finding the best feature extractor and machine learning classifier for serial crystallography data. The study reveals that the oriented FAST and rotated BRIEF (ORB) feature extractor with a multilayer perceptron classifier gives the best results. Finally, the ORB feature extractor with multilayer perceptron is evaluated on various data sets including both synthetic and experimental data, demonstrating superior performance compared with other feature extractors and classifiers.

Single and multi-pulse based X-ray photon correlation spectroscopy.

The ability of pulsed nature of synchrotron radiation opens up the possibility of studying microsecond dynamics in complex materials via speckle-based techniques. Here, we present the study of measuring the dynamics of a colloidal system by combining single and multiple X-ray pulses of a storage ring. In addition, we apply speckle correlation techniques at various pulse patterns to collect correlation functions from nanoseconds to milliseconds. The obtained sample dynamics from all correlation techniques at different pulse patterns are in very good agreement with the expected dynamics of Brownian motions of silica nanoparticles in water. Our study will pave the way for future pulsed X-ray investigations at various synchrotron X-ray sources using individual X-ray pulse patterns.

The synchrotron radiation source PETRA III and its future ultra-low-emittance upgrade PETRA IV.

PETRA III at DESY is one of the brightest synchrotron radiation sources worldwide. It serves a broad international multidisciplinary user community from academia to industry at currently 25 specialised beamlines. With a storage-ring energy of 6 GeV, it provides mainly hard to high-energy X-rays for versatile experiments in a very broad range of scientific fields. It is ideally suited for an upgrade to the ultra-low emittance source PETRA IV, owing to its large circumference of 2304 m. With a targeted storage ring emittance of 20 × 5 pm 2 rad 2 , PETRA IV will reach spectral brightnesses two to three orders of magnitude higher than today. The unique beam parameters will make PETRA IV the ultimate in situ 3D microscope for biological, chemical, and physical processes helping to address key questions in health, energy, mobility, information technology, and earth and environment.

Nanosecond X-ray photon correlation spectroscopy using pulse time structure of a storage-ring source.

X-ray photon correlation spectroscopy (XPCS) is a routine technique to study slow dynamics in complex systems at storage-ring sources. Achieving nanosecond time resolution with the conventional XPCS technique is, however, still an experimentally challenging task requiring fast detectors and sufficient photon flux. Here, the result of a nanosecond XPCS study of fast colloidal dynamics is shown by employing an adaptive gain integrating pixel detector (AGIPD) operated at frame rates of the intrinsic pulse structure of the storage ring. Correlation functions from single-pulse speckle patterns with the shortest correlation time of 192 ns have been calculated. These studies provide an important step towards routine fast XPCS studies at storage rings.

Characterization of the Percival detector with soft X-rays.

In this paper the back-side-illuminated Percival 2-Megapixel (P2M) detector is presented, along with its characterization by means of optical and X-ray photons. For the first time, the response of the system to soft X-rays (250 eV to 1 keV) is presented. The main performance parameters of the first detector are measured, assessing the capabilities in terms of noise, dynamic range and single-photon discrimination capability. Present limitations and coming improvements are discussed.

Segmented flow generator for serial crystallography at the European X-ray free electron laser.

Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported.

Evaluation of serial crystallographic structure determination within megahertz pulse trains.

The new European X-ray Free-Electron Laser (European XFEL) is the first X-ray free-electron laser capable of delivering intense X-ray pulses with a megahertz interpulse spacing in a wavelength range suitable for atomic resolution structure determination. An outstanding but crucial question is whether the use of a pulse repetition rate nearly four orders of magnitude higher than previously possible results in unwanted structural changes due to either radiation damage or systematic effects on data quality. Here, separate structures from the first and subsequent pulses in the European XFEL pulse train were determined, showing that there is essentially no difference between structures determined from different pulses under currently available operating conditions at the European XFEL.

The Adaptive Gain Integrating Pixel Detector at the European XFEL.

The Adaptive Gain Integrating Pixel Detector (AGIPD) is an X-ray imager, custom designed for the European X-ray Free-Electron Laser (XFEL). It is a fast, low-noise integrating detector, with an adaptive gain amplifier per pixel. This has an equivalent noise of less than 1 keV when detecting single photons and, when switched into another gain state, a dynamic range of more than 104 photons of 12 keV. In burst mode the system is able to store 352 images while running at up to 6.5 MHz, which is compatible with the 4.5 MHz frame rate at the European XFEL. The AGIPD system was installed and commissioned in August 2017, and successfully used for the first experiments at the Single Particles, Clusters and Biomolecules (SPB) experimental station at the European XFEL since September 2017. This paper describes the principal components and performance parameters of the system.

Megahertz serial crystallography.

The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a ß-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.

CAMP@FLASH: an end-station for imaging, electron- and ion-spectroscopy, and pump-probe experiments at the FLASH free-electron laser.

The non-monochromatic beamline BL1 at the FLASH free-electron laser facility at DESY was upgraded with new transport and focusing optics, and a new permanent end-station, CAMP, was installed. This multi-purpose instrument is optimized for electron- and ion-spectroscopy, imaging and pump-probe experiments at free-electron lasers. It can be equipped with various electron- and ion-spectrometers, along with large-area single-photon-counting pnCCD X-ray detectors, thus enabling a wide range of experiments from atomic, molecular, and cluster physics to material and energy science, chemistry and biology. Here, an overview of the layout, the beam transport and focusing capabilities, and the experimental possibilities of this new end-station are presented, as well as results from its commissioning.

X-ray deconvolution microscopy.

Recent advances in single-photon-counting detectors are enabling the development of novel approaches to reach micrometer-scale resolution in x-ray imaging. One example of such a technology are the MEDIPIX3RX-based detectors, such as the LAMBDA which can be operated with a small pixel size in combination with real-time on-chip charge-sharing correction. This characteristic results in a close to ideal, box-like point spread function which we made use of in this study. The proposed method is based on raster-scanning the sample with sub-pixel sized steps in front of the detector. Subsequently, a deconvolution algorithm is employed to compensate for blurring introduced by the overlap of pixels with a well defined point spread function during the raster-scanning. The presented approach utilizes standard laboratory x-ray equipment while we report resolutions close to 10 µm. The achieved resolution is shown to follow the relationship [Formula: see text] with the pixel-size p of the detector and the number of raster-scanning steps n.

Connecting structure, dynamics and viscosity in sheared soft colloidal liquids: a medley of anisotropic fluctuations.

Structural distortion and relaxation are central to any liquid flow. Their full understanding requires simultaneous probing of the mechanical as well as structural and dynamical response. We provide the first full dynamical measurement of the transient structure using combined coherent X-ray scattering and rheology on electrostatically interacting colloidal fluids. We find a stress overshoot during the start-up of shear which is due to the strong anisotropic overstretching and compression of nearest-neighbor distances. The rheological response is reflected in uncorrelated entropy-driven intensity fluctuations. While the structural distortion under steady shear is well described by Smoluchowski theory, we find an increase of the particle dynamics beyond the trivial contribution of flow. After the cessation of shear, the full fluid microstructure and dynamics are restored, both on the structural relaxation timescale. We thus find unique structure-dynamics relations in liquid flow, responsible for the macroscopic rheological behavior of the system.

High numerical aperture multilayer Laue lenses.

The ever-increasing brightness of synchrotron radiation sources demands improved X-ray optics to utilise their capability for imaging and probing biological cells, nanodevices, and functional matter on the nanometer scale with chemical sensitivity. Here we demonstrate focusing a hard X-ray beam to an 8 nm focus using a volume zone plate (also referred to as a wedged multilayer Laue lens). This lens was constructed using a new deposition technique that enabled the independent control of the angle and thickness of diffracting layers to microradian and nanometer precision, respectively. This ensured that the Bragg condition is satisfied at each point along the lens, leading to a high numerical aperture that is limited only by its extent. We developed a phase-shifting interferometric method based on ptychography to characterise the lens focus. The precision of the fabrication and characterisation demonstrated here provides the path to efficient X-ray optics for imaging at 1 nm resolution.

X-ray imaging detectors for synchrotron and XFEL sources.

Current trends for X-ray imaging detectors based on hybrid and monolithic detector technologies are reviewed. Hybrid detectors with photon-counting pixels have proven to be very powerful tools at synchrotrons. Recent developments continue to improve their performance, especially for higher spatial resolution at higher count rates with higher frame rates. Recent developments for X-ray free-electron laser (XFEL) experiments provide high-frame-rate integrating detectors with both high sensitivity and high peak signal. Similar performance improvements are sought in monolithic detectors. The monolithic approach also offers a lower noise floor, which is required for the detection of soft X-ray photons. The link between technology development and detector performance is described briefly in the context of potential future capabilities for X-ray imaging detectors.

Phase unwrapping in spectral X-ray differential phase-contrast imaging with an energy-resolving photon-counting pixel detector.

Grating-based differential phase-contrast imaging has proven to be feasible with conventional X-ray sources. The polychromatic spectrum generally limits the performance of the interferometer but benefit can be gained with an energy-sensitive detector. In the presented work, we employ the energy-discrimination capability to correct for phase-wrapping artefacts. We propose to use the phase shifts, which are measured in distinct energy bins, to estimate the optimal phase shift in the sense of maximum likelihood. We demonstrate that our method is able to correct for phase-wrapping artefacts, to improve the contrast-to-noise ratio and to reduce beam hardening due to the modelled energy dependency. The method is evaluated on experimental data which are measured with a laboratory Talbot-Lau interferometer equipped with a conventional polychromatic X-ray source and an energy-sensitive photon-counting pixel detector. Our work shows, that spectral imaging is an important step to move differential phase-contrast imaging closer to pre-clinical and clinical applications, where phase wrapping is particularly problematic.

Sensing the wavefront of x-ray free-electron lasers using aerosol spheres.

Characterizing intense, focused x-ray free electron laser (FEL) pulses is crucial for their use in diffractive imaging. We describe how the distribution of average phase tilts and intensities on hard x-ray pulses with peak intensities of 10(21) W/m(2) can be retrieved from an ensemble of diffraction patterns produced by 70 nm-radius polystyrene spheres, in a manner that mimics wavefront sensors. Besides showing that an adaptive geometric correction may be necessary for diffraction data from randomly injected sample sources, our paper demonstrates the possibility of collecting statistics on structured pulses using only the diffraction patterns they generate and highlights the imperative to study its impact on single-particle diffractive imaging.