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 PERCIVAL detector: first user experiments

The PERCIVAL detector is a CMOS imager designed for the soft X-ray regime at photon sources. Although still in its final development phase, it has recently seen its first user experiments: ptychography at a free-electron laser, holographic imaging at a storage ring and preliminary tests on X-ray photon correlation spectroscopy. The detector performed remarkably well in terms of spatial resolution achievable in the sample plane, owing to its small pixel size, large active area and very large dynamic range; but also in terms of its frame rate, which is significantly faster than traditional CCDs. In particular, it is the combination of these features which makes PERCIVAL an attractive option for soft X-ray science.

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 β-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.

AXSIS: Exploring the frontiers in attosecond X-ray science, imaging and spectroscopy

X-ray crystallography is one of the main methods to determine atomic-resolution 3D images of the whole spectrum of molecules ranging from small inorganic clusters to large protein complexes consisting of hundred-thousands of atoms that constitute the macromolecular machinery of life. Life is not static, and unravelling the structure and dynamics of the most important reactions in chemistry and biology is essential to uncover their mechanism. Many of these reactions, including photosynthesis which drives our biosphere, are light induced and occur on ultrafast timescales. These have been studied with high time resolution primarily by optical spectroscopy, enabled by ultrafast laser technology, but they reduce the vast complexity of the process to a few reaction coordinates. In the AXSIS project at CFEL in Hamburg, funded by the European Research Council, we develop the new method of attosecond serial X-ray crystallography and spectroscopy, to give a full description of ultrafast processes atomically resolved in real space and on the electronic energy landscape, from co-measurement of X-ray and optical spectra, and X-ray diffraction. This technique will revolutionize our understanding of structure and function at the atomic and molecular level and thereby unravel fundamental processes in chemistry and biology like energy conversion processes. For that purpose, we develop a compact, fully coherent, THz-driven atto-second X-ray source based on coherent inverse Compton scattering off a free-electron crystal, to outrun radiation damage effects due to the necessary high X-ray irradiance required to acquire diffraction signals. This highly synergistic project starts from a completely clean slate rather than conforming to the specifications of a large free-electron laser (FEL) user facility, to optimize the entire instrumentation towards fundamental measurements of the mechanism of light absorption and excitation energy transfer. A multidisciplinary team formed by laser-, accelerator,- X-ray scientists as well as spectroscopists and biochemists optimizes X-ray pulse parameters, in tandem with sample delivery, crystal size, and advanced X-ray detectors. Ultimately, the new capability, attosecond serial X-ray crystallography and spectroscopy, will be applied to one of the most important problems in structural biology, which is to elucidate the dynamics of light reactions, electron transfer and protein structure in photosynthesis.

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.

Detector developments at DESY

With the increased brilliance of state-of-the-art synchrotron radiation sources and the advent of free-electron lasers (FELs) enabling revolutionary science with EUV to X-ray photons comes an urgent need for suitable photon imaging detectors. Requirements include high frame rates, very large dynamic range, single-photon sensitivity with low probability of false positives and (multi)-megapixels. At DESY, one ongoing development project - in collaboration with RAL/STFC, Elettra Sincrotrone Trieste, Diamond, and Pohang Accelerator Laboratory - is the CMOS-based soft X-ray imager PERCIVAL. PERCIVAL is a monolithic active-pixel sensor back-thinned to access its primary energy range of 250 eV to 1 keV with target efficiencies above 90%. According to preliminary specifications, the roughly 10 cm × 10 cm, 3.5k × 3.7k monolithic sensor will operate at frame rates up to 120 Hz (commensurate with most FELs) and use multiple gains within 27 µm pixels to measure 1 to ∼100000 (500 eV) simultaneously arriving photons. DESY is also leading the development of the AGIPD, a high-speed detector based on hybrid pixel technology intended for use at the European XFEL. This system is being developed in collaboration with PSI, University of Hamburg, and University of Bonn. The AGIPD allows single-pulse imaging at 4.5 MHz frame rate into a 352-frame buffer, with a dynamic range allowing single-photon detection and detection of more than 10000 photons at 12.4 keV in the same image. Modules of 65k pixels each are configured to make up (multi)megapixel cameras. This review describes the AGIPD and the PERCIVAL concepts and systems, including some recent results and a summary of their current status. It also gives a short overview over other FEL-relevant developments where the Photon Science Detector Group at DESY is involved.

Spectrometer for shot-to-shot photon energy characterization in the multi-bunch mode of the free electron laser at Hamburg

The setup and first results from commissioning of a fast online photon energy spectrometer for the vacuum ultraviolet free electron laser at Hamburg (FLASH) at DESY are presented. With the use of the latest advances in detector development, the presented spectrometer reaches readout frequencies up to 1 MHz. In this paper, we demonstrate the ability to record online photon energy spectra on a shot-to-shot base in the multi-bunch mode of FLASH. Clearly resolved shifts in the mean wavelength over the pulse train as well as shot-to-shot wavelength fluctuations arising from the statistical nature of the photon generating self-amplified spontaneous emission process have been observed. In addition to an online tool for beam calibration and photon diagnostics, the spectrometer enables the determination and selection of spectral data taken with a transparent experiment up front over the photon energy of every shot. This leads to higher spectral resolutions without the loss of efficiency or photon flux by using single-bunch mode or monochromators.

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.

Intensity interferometry of single x-ray pulses from a synchrotron storage ring

We report on measurements of second-order intensity correlations at the high-brilliance storage ring PETRA III using a prototype of the newly developed adaptive gain integrating pixel detector. The detector records individual synchrotron radiation pulses with an x-ray photon energy of 14.4 keV and repetition rate of about 5 MHz. The second-order intensity correlation function is measured simultaneously at different spatial separations, which allows us to determine the transverse coherence length at these x-ray energies. The measured values are in a good agreement with theoretical simulations based on the Gaussian Schell model.

Serial Femtosecond Crystallography user's consortium apparatus at European XFEL

The Serial Femtosecond Crystallography (SFX) user's consortium apparatus is to be installed within the Single Particles, Clusters and Biomolecules (SPB) instrument of the European X-ray Free-Electron Laser facility (XFEL.EU) [1, 2]. The XFEL.EU will provide ultra-short, highly intense, coherent X-ray pulses at an unprecedented repetition rate. The experimental setup and methodological approaches of many scientific areas will be transformed, including structural biology that could potentially overcome common problems and bottlenecks encountered in crystallography, such as creating large crystals, dealing with radiation damage, or understanding sub-picosecond time-resolved phenomena. The key concept of the SFX method is based on the kinetic insertion of protein crystal samples in solution via a gas dynamic virtual nozzle jet and recording diffraction signals of individual, randomly oriented crystals passing through the XFEL beam, as first demonstrated by Chapman et al. [3]. The SFX-apparatus will refocus the beam spent by the SPB instrument into a second interaction region, in some cases enabling two parallel experiments. The planned photon energy range at the SPB instrument is from 3 to 16 keV. The Adaptive Gain Integrating Pixel Detector (AGIPD) is to be implemented in the SPB instrument, including a 4 Megapixel version for the SFX-apparatus. The AGIPD is designed to store over 350 data frames from successive pulses, and aims to collect more than 3,000 images per second. Together with the implementation of automated procedures for sample exchange and injection, high-throughput nanocrystallography experiments can be integrated at the SFX-apparatus. In this work, we review the overall design of the SFX-apparatus and discuss the main parameters and challenges

AGIPD detector for Serial Femtosecond Crystallography Apparatus at European XFEL

The European X-ray Free-Electron Laser (XFEL.EU) [1] will provide ultra-short, highly-intense, coherent x-ray pulses at an unprecedented repetition rate, transforming experiments in many scientific areas, including serial femtosecond crystallography (SFX). For the purpose of SFX experiments at the XFEL.EU, a dedicated endstation is being developed to be installed within the Single Particles, Clusters and Biomolecules (SPB) instrument [2]. The setup will refocus the beam spent by SPB into a second interaction region, thereby enabling two parallel experiments. In order to overcome various challenges in XFEL crystallography, and to optimize the output for SFX experiments at XFEL.EU, the Adaptive Gain Integrating Pixel Detector (AGIPD) [3] is currently under development and is to be implemented in the SPB instrument, including a 4 Megapixel version for the SFX apparatus. The AGIPD is a hybrid-pixel detector with pixels of 200 x 200 micron^2 each. The gain of each single pixel dynamically and independently adapts to the incoming signal. Thus, diffraction patterns of high dynamic range can be recorded, with the measured signal within a single data frame ranging from single photons and up to 1e+4 photons at 12 keV. Moreover, the AGIPD is designed to store over 350 data frames from successive pulses prior to digitization and read-out, thereby enabling operation at the European XFEL with its challenging repetition rate with 10 Hz pulse trains and a 4.5 MHz intra-train repetition rate. Furthermore, the incorporation of a veto system in AGIPD will allow one to potentially store only the frames that contain diffraction data from actual crystal hits, which ultimately increases the efficiency of the detector and DAQ systems dramatically. In the present work, we will review the design of the 4Mpix AGIPD for the SFX apparatus and discuss simulations and tests of its expected performance under the conditions foreseen for SFX experiments at the XFEL.EU.

Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers

Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.

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.

Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight

The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology to climate science, yet these properties are surprisingly difficult to measure in the particles' native environment. Electron microscopy requires collection of particles on a substrate; visible light scattering provides insufficient resolution; and X-ray synchrotron studies have been limited to ensembles of particles. Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins, vibrational energy transfer by the hydrodynamic interaction of amino acids, and large-scale production of nanoscale structures by flame synthesis.

Nanoplasma dynamics of single large xenon clusters irradiated with superintense x-ray pulses from the linac coherent light source free-electron laser

The plasma dynamics of single mesoscopic Xe particles irradiated with intense femtosecond x-ray pulses exceeding 10(16)  W/cm2 from the Linac Coherent Light Source free-electron laser are investigated. Simultaneous recording of diffraction patterns and ion spectra allows eliminating the influence of the laser focal volume intensity and particle size distribution. The data show that for clusters illuminated with intense x-ray pulses, highly charged ionization fragments in a narrow distribution are created and that the nanoplasma recombination is efficiently suppressed.

Femtosecond dark-field imaging with an X-ray free electron laser

The emergence of femtosecond diffractive imaging with X-ray lasers has enabled pioneering structural studies of isolated particles, such as viruses, at nanometer length scales. However, the issue of missing low frequency data significantly limits the potential of X-ray lasers to reveal sub-nanometer details of micrometer-sized samples. We have developed a new technique of dark-field coherent diffractive imaging to simultaneously overcome the missing data issue and enable us to harness the unique contrast mechanisms available in dark-field microscopy. Images of airborne particulate matter (soot) up to two microns in length were obtained using single-shot diffraction patterns obtained at the Linac Coherent Light Source, four times the size of objects previously imaged in similar experiments. This technique opens the door to femtosecond diffractive imaging of a wide range of micrometer-sized materials that exhibit irreproducible complexity down to the nanoscale, including airborne particulate matter, small cells, bacteria and gold-labeled biological samples.

Micrometre resolution of a charge integrating microstrip detector with single photon sensitivity

A synchrotron beam has been used to test the spatial resolution of a single-photon-resolving integrating readout-chip coupled to a 320 µm-thick silicon strip sensor with a dedicated readout system. Charge interpolation methods have yielded a spatial resolution of σ(x) ≃ 1.8 µm for a 20 µm-pitch strip.

Femtosecond free-electron laser x-ray diffraction data sets for algorithm development

We describe femtosecond X-ray diffraction data sets of viruses and nanoparticles collected at the Linac Coherent Light Source. The data establish the first large benchmark data sets for coherent diffraction methods freely available to the public, to bolster the development of algorithms that are essential for developing this novel approach as a useful imaging technique. Applications are 2D reconstructions, orientation classification and finally 3D imaging by assembling 2D patterns into a 3D diffraction volume.

Time-resolved protein nanocrystallography using an X-ray free-electron laser

We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.

In vivo protein crystallization opens new routes in structural biology

Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo-grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.

Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements

X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis¹. For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information^1-4. Here, we describe a mechanism unique to ultrafast, ultra-intense X-ray experiments that allows structural information to be collected from crystalline samples using high radiation doses without the requirement for the pulse to terminate before the onset of sample damage. Instead, the diffracted X-rays are gated by a rapid loss of crystalline periodicity, producing apparent pulse lengths significantly shorter than the duration of the incident pulse. The shortest apparent pulse lengths occur at the highest resolution, and our measurements indicate that current X-ray free-electron laser technology⁵ should enable structural determination from submicrometre protein crystals with atomic resolution.

Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser

X-ray free-electron lasers deliver intense femtosecond pulses that promise to yield high resolution diffraction data of nanocrystals before the destruction of the sample by radiation damage. Diffraction intensities of lysozyme nanocrystals collected at the Linac Coherent Light Source using 2 keV photons were used for structure determination by molecular replacement and analyzed for radiation damage as a function of pulse length and fluence. Signatures of radiation damage are observed for pulses as short as 70 fs. Parametric scaling used in conventional crystallography does not account for the observed effects.

Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering

Single-particle experiments using X-ray Free Electron Lasers produce more than 10(5) snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification.

Diamond X-ray beam-position monitoring using signal readout at the synchrotron radiofrequency

Single-crystal diamond is a material with great potential for the fabrication of X-ray photon beam-position monitors with submicrometre spatial resolution. Low X-ray absorption combined with radiation hardness and excellent thermal-mechanical properties make possible beam-transmissive diamond devices for monitoring synchrotron and free-electron laser X-ray beams. Tests were made using a white bending-magnet synchrotron X-ray beam at DESY to investigate the performance of a position-sensitive diamond device using radiofrequency readout electronics. The device uniformity and position response were measured in a 25 microm collimated X-ray beam with an I-Tech Libera ;Brilliance' system. This readout system was designed for position measurement and feedback control of the electron beam in the synchrotron storage ring, but, as shown here, it can also be used for accurate position readout of a quadrant-electrode single-crystal diamond sensor. The centre-of-gravity position of the F4 X-ray beam at the DORIS III synchrotron was measured with the diamond signal output digitally sampled at a rate of 130 Msample s(-1) by the Brilliance system. Narrow-band filtering and digital averaging of the position signals resulted in a measured position noise below 50 nm (r.m.s.) for a 10 Hz bandwidth.

Initial structure and growth dynamics of YBa(2)Cu(3)O(7-delta) during pulsed laser deposition

The initial heteroepitaxial growth of YBa{2}Cu{3}O{7-delta} films on SrTiO3(001) substrates during pulsed laser deposition shows a growth-mode transition and a change of growth unit. The growth starts with two blocks, each two-thirds the size of the complete unit cell. The first of these blocks grows in a step-flow fashion, whereas the second grows in the layer-by-layer mode. Subsequent deposition occurs layer-by-layer of complete unit cells. These results suggest that the surface diffusion in the heteroepitaxial case is strongly influenced by the competition with formation energies, which is important for the fabrication of heteroepitaxial devices on the unit cell scale.

Pulsed laser deposition chamber for in situ X-ray diffraction

A sample chamber has been constructed for studying the growth of thin films by pulsed laser deposition in situ with surface X-ray diffraction. The achievable temperature ranges from room temperature to 1073 K in a controlled oxygen environment. The partial pressure of the oxygen background gas covers the range from 0.1 to 10(5) Pa. The first results, showing intensity oscillations in the diffracted signal during homoepitaxial deposition of SrTiO(3), are presented.

Improving the performance of high-resolution X-ray spectrometers with position-sensitive pixel detectors

A dispersion-compensation method to remove the cube-size effect from the resolution function of diced analyzer crystals using a position-sensitive two-dimensional pixel detector is presented. For demonstration, a resolution of 23 meV was achieved with a spectrometer based on a 1 m Rowland circle and a diced Si(555) analyzer crystal in a near-backscattering geometry, with a Bragg angle of 88.5 degrees . In this geometry the spectrometer equipped with a traditional position-insensitive detector provides a resolution of 190 meV. The dispersion-compensation method thus allows a substantial increase in the resolving power without any loss of signal intensity.

Polarization switching in BaTiO3thin films measured by X-ray diffraction exploiting anomalous dispersion

Films of BaTiO3ranging from 20 nm to 300 nm in thickness were grown with pulsed laser deposition on Nb:SrTiO3. The quality of the layers was investigated using atomic force microscopy, X-ray reflectivity and X-ray diffraction. Both the micrographs and the X-ray reflectivity spectra indicate a smooth surface of the layers. The X-ray diffraction profiles measured using synchrotron radiation show features characteristic for highly crystalline thin films. The application of an external electric field parallel to thecaxis changes anhklreflection of BaTiO3to anhk\bar{l} reflection. Due to the anomalous dispersion, the intensities of these two reflections are not equal and the atomic displacements can be determined from the intensity differences. The electric field-induced intensity changes can be as large as a few percent, which makes data collection from a 100 nm film using CuKα radiation from an X-ray tube feasible. The ΔI/Ivalues of a number of reflections from the 20 and 50 nm films were measured using synchrotron radiation. The observed ΔI/Ivalues were in good agreement with the intensity changes expected for polarization switching in the bulk.