Diffraction-limited storage rings - a window to the science of tomorrow

Upscaling X-ray nanoimaging to macroscopic specimens

Upscaling X-ray nanoimaging to macroscopic specimens has the potential for providing insights across multiple length scales, but its feasibility has long been an open question. By combining the imaging requirements and existing proof-of-principle examples in large-specimen preparation, data acquisition and reconstruction algorithms, the authors provide imaging time estimates for howX-ray nanoimaging can be scaled to macroscopic specimens. To arrive at this estimate, a phase contrast imaging model that includes plural scattering effects is used to calculate the required exposure and corresponding radiation dose. The coherent X-ray flux anticipated from upcoming diffraction-limited light sources is then considered. This imaging time estimation is in particular applied to the case of the connectomes of whole mouse brains. To image the connectome of the whole mouse brain, electron microscopy connectomics might require years, whereas optimized X-ray microscopy connectomics could reduce this to one week. Furthermore, this analysis points to challenges that need to be overcome (such as increased X-ray detector frame rate) and opportunities that advances in artificial-intelligence-based 'smart' scanning might provide. While the technical advances required are daunting, it is shown that X-ray microscopy is indeed potentially applicable to nanoimaging of millimetre- or even centimetre-size specimens.

Adorym: a multi-platform generic X-ray image reconstruction framework based on automatic differentiation

We describe and demonstrate an optimization-based X-ray image reconstruction framework called Adorym. Our framework provides a generic forward model, allowing one code framework to be used for a wide range of imaging methods ranging from near-field holography to fly-scan ptychographic tomography. By using automatic differentiation for optimization, Adorym has the flexibility to refine experimental parameters including probe positions, multiple hologram alignment, and object tilts. It is written with strong support for parallel processing, allowing large datasets to be processed on high-performance computing systems. We demonstrate its use on several experimental datasets to show improved image quality through parameter refinement.

X-ray-Based Techniques to Study the Nano-Bio Interface

X-ray-based analytics are routinely applied in many fields, including physics, chemistry, materials science, and engineering. The full potential of such techniques in the life sciences and medicine, however, has not yet been fully exploited. We highlight current and upcoming advances in this direction. We describe different X-ray-based methodologies (including those performed at synchrotron light sources and X-ray free-electron lasers) and their potentials for application to investigate the nano-bio interface. The discussion is predominantly guided by asking how such methods could better help to understand and to improve nanoparticle-based drug delivery, though the concepts also apply to nano-bio interactions in general. We discuss current limitations and how they might be overcome, particularly for future use in vivo.

Angle, Spin, and Depth Resolved Photoelectron Spectroscopy on Quantum Materials

The role of X-ray based electron spectroscopies in determining chemical, electronic, and magnetic properties of solids has been well-known for several decades. A powerful approach is angle-resolved photoelectron spectroscopy, whereby the kinetic energy and angle of photoelectrons emitted from a sample surface are measured. This provides a direct measurement of the electronic band structure of crystalline solids. Moreover, it yields powerful insights into the electronic interactions at play within a material and into the control of spin, charge, and orbital degrees of freedom, central pillars of future solid state science. With strong recent focus on research of lower-dimensional materials and modified electronic behavior at surfaces and interfaces, angle-resolved photoelectron spectroscopy has become a core technique in the study of quantum materials. In this review, we provide an introduction to the technique. Through examples from several topical materials systems, including topological insulators, transition metal dichalcogenides, and transition metal oxides, we highlight the types of information which can be obtained. We show how the combination of angle, spin, time, and depth-resolved experiments are able to reveal "hidden" spectral features, connected to semiconducting, metallic and magnetic properties of solids, as well as underlining the importance of dimensional effects in quantum materials.

Use of continuous sample translation to reduce radiation damage for XPCS studies of protein diffusion

An experimental setup to measure X-ray photon correlation spectroscopy during continuous sample translation is presented and its effectiveness as a means to avoid sample damage in dynamics studies of protein diffusion is evaluated. X-ray damage from focused coherent synchrotron radiation remains below tolerable levels as long as the sample is translated through the beam sufficiently quickly. Here it is shown that it is possible to separate sample dynamics from the effects associated with the transit of the sample through the beam. By varying the sample translation rate, the damage threshold level, D_thresh = 1.8 kGy, for when beam damage begins to modify the dynamics under the conditions used, is also determined. Signal-to-noise ratios, R_sn ≥ 20, are obtained down to the shortest delay times of 20 µs. The applicability of this method of data collection to the next generation of multi-bend achromat synchrotron sources is discussed and it is shown that sub-microsecond dynamics should be obtainable on protein samples.

20 µs-resolved high-throughput X-ray photon correlation spectroscopy on a 500k pixel detector enabled by data-management workflow

The performance of the new 52 kHz frame rate Rigaku XSPA-500k detector was characterized on beamline 8-ID-I at the Advanced Photon Source at Argonne for X-ray photon correlation spectroscopy (XPCS) applications. Due to the large data flow produced by this detector (0.2 PB of data per 24 h of continuous operation), a workflow system was deployed that uses the Advanced Photon Source data-management (DM) system and high-performance software to rapidly reduce area-detector data to multi-tau and two-time correlation functions in near real time, providing human-in-the-loop feedback to experimenters. The utility and performance of the workflow system are demonstrated via its application to a variety of small-angle XPCS measurements acquired from different detectors in different XPCS measurement modalities. The XSPA-500k detector, the software and the DM workflow system allow for the efficient acquisition and reduction of up to ∼10⁹ area-detector data frames per day, facilitating the application of XPCS to measuring samples with weak scattering and fast dynamics.

Fast digital lossy compression for X-ray ptychographic data

Increases in X-ray brightness from synchrotron light sources lead to a requirement for higher frame rates from hybrid pixel array detectors (HPADs), while also favoring charge integration over photon counting. However, transfer of the full uncompressed data will begin to constrain detector design, as well as limit the achievable continuous frame rate. Here a data compression scheme that is easy to implement in a HPAD's application-specific integrated circuit (ASIC) is described, and how different degrees of compression affect image quality in ptychography, a commonly employed coherent imaging method, is examined. Using adaptive encoding quantization, it is shown in simulations that one can digitize signals up to 16383 photons per pixel (corresponding to 14 bits of information) using only 8 or 9 bits for data transfer, with negligible effect on the reconstructed image.

Alterations in Sub-Axonal Architecture Between Normal Aging and Parkinson's Diseased Human Brains Using Label-Free Cryogenic X-ray Nanotomography

Gaining insight to pathologically relevant processes in continuous volumes of unstained brain tissue is important for a better understanding of neurological diseases. Many pathological processes in neurodegenerative disorders affect myelinated axons, which are a critical part of the neuronal circuitry. Cryo ptychographic X-ray computed tomography in the multi-keV energy range is an emerging technology providing phase contrast at high sensitivity, allowing label-free and non-destructive three dimensional imaging of large continuous volumes of tissue, currently spanning up to 400,000 μm3. This aspect makes the technique especially attractive for imaging complex biological material, especially neuronal tissues, in combination with downstream optical or electron microscopy techniques. A further advantage is that dehydration, additional contrast staining, and destructive sectioning/milling are not required for imaging. We have developed a pipeline for cryo ptychographic X-ray tomography of relatively large, hydrated and unstained biological tissue volumes beyond what is typical for the X-ray imaging, using human brain tissue and combining the technique with complementary methods. We present four imaged volumes of a Parkinson's diseased human brain and five volumes from a non-diseased control human brain using cryo ptychographic X-ray tomography. In both cases, we distinguish neuromelanin-containing neurons, lipid and melanic pigment, blood vessels and red blood cells, and nuclei of other brain cells. In the diseased sample, we observed several swellings containing dense granular material resembling clustered vesicles between the myelin sheaths arising from the cytoplasm of the parent oligodendrocyte, rather than the axoplasm. We further investigated the pathological relevance of such swollen axons in adjacent tissue sections by immunofluorescence microscopy for phosphorylated alpha-synuclein combined with multispectral imaging. Since cryo ptychographic X-ray tomography is non-destructive, the large dataset volumes were used to guide further investigation of such swollen axons by correlative electron microscopy and immunogold labeling post X-ray imaging, a possibility demonstrated for the first time. Interestingly, we find that protein antigenicity and ultrastructure of the tissue are preserved after the X-ray measurement. As many pathological processes in neurodegeneration affect myelinated axons, our work sets an unprecedented foundation for studies addressing axonal integrity and disease-related changes in unstained brain tissues.

Direct Three-Dimensional Imaging of an X-ray Nanofocus Using a Single 60 nm Diameter Nanowire Device

Nanoscale X-ray detectors could allow higher resolution in imaging and diffraction experiments than established systems but are difficult to design due to the long absorption length of X-rays. Here, we demonstrate X-ray detection in a single nanowire in which the nanowire axis is parallel to the optical axis. In this geometry, X-ray absorption can occur along the nanowire length, while the spatial resolution is limited by the diameter. We use the device to make a high-resolution 3D image of the 88 nm diameter X-ray nanofocus at the Nanomax beamline, MAX IV synchrotron, by scanning the single pixel device in different planes along the optical axis. The images reveal fine details of the beam that are unattainable with established detectors and show good agreement with ptychography.

Phase analysis for partially coherent light propagating through an optimized aperture in a synchrotron beamline

The mutual optical intensity propagation of partially coherent light through a beamline is calculated for different aperture sizes and positions. The coherence, intensity and phase distribution can be extracted from the mutual optical intensity. The phase distribution depends on the aperture size and position. The results show that the widest flat phase distribution is obtained at the optimized aperture size and position. The aperture plays a more important role for partially coherent light than for incoherent light. The influence of the aperture size and position on the intensity and spot size at the focal plane is also analyzed. A way to obtain a balance between the flat phase distribution area, spot size and intensity for partially coherent light in the beamline is demonstrated.

First ptychographic X-ray computed tomography experiment on the NanoMAX beamline

Documentation is presented for the first ptychographic X-ray computed tomography experiment on the NanoMAX beamline, along with a quantitative analysis of the reconstruction quality and a discussion of possibilities for future improvements.

Ptychographic X-ray computed tomography is a quantitative three-dimensional imaging technique offered to users of multiple synchrotron radiation sources. Its dependence on the coherent fraction of the available X-ray beam makes it perfectly suited to diffraction-limited storage rings. Although MAX IV is the first, and so far only, operating fourth-generation synchrotron light source, none of its experimental stations is currently set up to offer this technique to its users. The first ptychographic X-ray computed tomography experiment has therefore been performed on the NanoMAX beamline. From the results, information was gained about the current limitations of the experimental setup and where attention should be focused for improvement. The extracted parameters in terms of scanning speed, size of the imaged volume and achieved resolutions should provide a baseline for future users designing nano-tomography experiments on the NanoMAX beamline.

Comparison of distributed memory algorithms for X-ray wave propagation in inhomogeneous media

Calculations of X-ray wave propagation in large objects are needed for modeling diffractive X-ray optics and for optimization-based approaches to image reconstruction for objects that extend beyond the depth of focus. We describe three methods for calculating wave propagation with large arrays on parallel computing systems with distributed memory: (1) a full-array Fresnel multislice approach, (2) a tiling-based short-distance Fresnel multislice approach, and (3) a finite difference approach. We find that the first approach suffers from internode communication delays when the transverse array size becomes large, while the second and third approaches have similar scaling to large array size problems (with the second approach offering about three times the compute speed).

X-Ray Photon Correlation Spectroscopy with Coherent Nanobeams: A Numerical Study

X-ray photon correlation spectroscopy accesses a wide variety of dynamic phenomena at the nanoscale by studying the temporal correlations among photons that are scattered by a material in dynamical equilibrium when it is illuminated with a coherent X-ray beam. The information that is obtained is averaged over the illuminated area, which is generally of the order of several square microns. We propose here that more local information can be obtained by using nanobeams with great potential for the study of heterogeneous systems and show the feasibility of this approach with the support of numerical simulations.

On Directional Dendritic Growth and Primary Spacing—A Review

The primary spacing is intrinsically linked with the mechanical behavior of directionally solidified materials. Because of this relationship, a significant amount of solidification work is reported in the literature, which relates the primary spacing to the process variables. This review provides a comprehensive chronological narrative on the development of the directional dendritic growth problem over the past 85 years. A key focus within this review is detailing the relationship between key solidification parameters, the operating point of the dendrite tip, and the primary spacing. This review critiques the current state of directional dendritic growth and primary spacing modelling, briefly discusses dendritic growth computational and experimental research, and suggests areas for future investigation.

Near, far, wherever you are: simulations on the dose efficiency of holographic and ptychographic coherent imaging

Different studies in X-ray microscopy have arrived at conflicting conclusions about the dose efficiency of imaging modes involving the recording of intensity distributions in the near (Fresnel regime) or far (Fraunhofer regime) field downstream of a specimen. A numerical study is presented on the dose efficiency of near-field holography, near-field ptychography and far-field ptychography, where ptychography involves multiple overlapping finite-sized illumination positions. Unlike what has been reported for coherent diffraction imaging, which involves recording a single far-field diffraction pattern, it is found that all three methods offer similar image quality when using the same fluence on the specimen, with far-field ptychography offering slightly better spatial resolution and a lower mean error. These results support the concept that (if the experiment and image reconstruction are done properly) the sample can be near or far; wherever you are, photon fluence on the specimen sets one limit to spatial resolution.

Imaging three-dimensional magnetic systems with x-rays

Recent progress in nanofabrication and additive manufacturing have facilitated the building of nanometer-scale three-dimensional (3D) structures, that promise to lead to an emergence of new functionalities within a number of fields, compared to state-of-the-art two dimensional systems. In magnetism, the move to 3D systems offers the possibility for novel magnetic properties not available in planar systems, as well as enhanced performance, both of which are key for the development of new technological applications. In this review paper we will focus our attention on 3D magnetic systems and how their magnetic configuration can be retrieved using x-ray magnetic nanotomography. We will start with an introduction to magnetic materials, and their relevance to our everyday life, along with the growing impact that they will have in the coming years in, for example, reducing energy consumption. We will then briefly introduce common methods used to study magnetic materials, such as electron holography, neutron and x-ray imaging. In particular, we will focus on x-ray magnetic circular dichroism (XMCD) and how it can be used to image magnetic moment configurations. As a next step we will introduce tomography for 3D imaging, and how it can be adapted to study magnetic materials. Particular attention will be given to explaining the reconstruction algorithms that can be used to retrieve the magnetic moment configuration from the experimental data, as these represent one of the main challenges so far, as well as the different experimental geometries that are available. Recent experimental results will be used as specific examples to guide the reader through each step in order to make sure that the paper will be accessible for those interested in the topic that do not have a specialized background on magnetic imaging. Finally, we will describe the future prospects of such studies, identifying the current challenges facing the field, and how these can be tackled. In particular we will highlight the exciting possibilities offered by the next generation of synchrotron sources which will deliver diffraction limited beams, as well as with the extension of well-established methodologies currently implemented for the study of two-dimensional magnetic materials to achieve higher dimensional investigations.

A design of resonant inelastic X-ray scattering (RIXS) spectrometer for spatial- and time-resolved spectroscopy

The optical design of a Hettrick-Underwood-style soft X-ray spectrometer with Wolter type 1 mirrors is presented. The spectrometer with a nominal length of 3.1 m can achieve a high resolving power (resolving power higher than 10000) in the soft X-ray regime when a small source beam (<3 µm in the grating dispersion direction) and small pixel detector (5 µm effective pixel size) are used. Adding Wolter mirrors to the spectrometer before its dispersive elements can realize the spatial imaging capability, which finds applications in the spectroscopic studies of spatially dependent electronic structures in tandem catalysts, heterostructures, etc. In the pump-probe experiments where the pump beam perturbs the materials followed by the time-delayed probe beam to reveal the transient evolution of electronic structures, the imaging capability of the Wolter mirrors can offer the pixel-equivalent femtosecond time delay between the pump and probe beams when their wavefronts are not collinear. In combination with some special sample handing systems, such as liquid jets and droplets, the imaging capability can also be used to study the time-dependent electronic structure of chemical transformation spanning multiple time domains from microseconds to nanoseconds. The proposed Wolter mirrors can also be adopted to the existing soft X-ray spectrometers that use the Hettrick-Underwood optical scheme, expanding their capabilities in materials research.

Proton uptake mechanism in bacteriorhodopsin captured by serial synchrotron crystallography

Conformational dynamics are essential for proteins to function. We adapted time-resolved serial crystallography developed at x-ray lasers to visualize protein motions using synchrotrons. We recorded the structural changes in the light-driven proton-pump bacteriorhodopsin over 200 milliseconds in time. The snapshot from the first 5 milliseconds after photoactivation shows structural changes associated with proton release at a quality comparable to that of previous x-ray laser experiments. From 10 to 15 milliseconds onwards, we observe large additional structural rearrangements up to 9 angstroms on the cytoplasmic side. Rotation of leucine-93 and phenylalanine-219 opens a hydrophobic barrier, leading to the formation of a water chain connecting the intracellular aspartic acid-96 with the retinal Schiff base. The formation of this proton wire recharges the membrane pump with a proton for the next cycle.

Cryo-nanoimaging of Single Human Macrophage Cells: 3D Structural and Chemical Quantification

X-ray microscopy is increasingly used in biology, but in most cases only in a qualitative way. We present here a 3D correlative cryo X-ray microscopy approach suited for the quantification of molar concentrations and structure in native samples at nanometer scale. The multimodal approach combines X-ray fluorescence and X-ray holographic nanotomography on "thick" frozen-hydrated cells. The quantitativeness of the X-ray fluorescence reconstruction is improved by estimating the self-attenuation from the 3D holography reconstruction. Applied to complex macrophage cells, we extract the quantification of major and minor elements heavier than phosphorus, as well as the density, in the different organelles. The intracellular landscape shows remarkable elemental differences. This novel analytical microscopy approach will be of particular interest to investigate complex biological and chemical systems in their native environment.

Towards an Optimal Sample Delivery Method for Serial Crystallography at XFEL

The advent of the X-ray free electron laser (XFEL) in the last decade created the discipline of serial crystallography but also the challenge of how crystal samples are delivered to X-ray. Early sample delivery methods demonstrated the proof-of-concept for serial crystallography and XFEL but were beset with challenges of high sample consumption, jet clogging and low data collection efficiency. The potential of XFEL and serial crystallography as the next frontier of structural solution by X-ray for small and weakly diffracting crystals and provision of ultra-fast time-resolved structural data spawned a huge amount of scientific interest and innovation. To utilize the full potential of XFEL and broaden its applicability to a larger variety of biological samples, researchers are challenged to develop better sample delivery methods. Thus, sample delivery is one of the key areas of research and development in the serial crystallography scientific community. Sample delivery currently falls into three main systems: jet-based methods, fixed-target chips, and drop-on-demand. Huge strides have since been made in reducing sample consumption and improving data collection efficiency, thus enabling the use of XFEL for many biological systems to provide high-resolution, radiation damage-free structural data as well as time-resolved dynamics studies. This review summarizes the current main strategies in sample delivery and their respective pros and cons, as well as some future direction.

Micrometer-resolution X-ray tomographic full-volume reconstruction of an intact post-mortem juvenile rat lung

In this article, we present an X-ray tomographic imaging method that is well suited for pulmonary disease studies in animal models to resolve the full pathway from gas intake to gas exchange. Current state-of-the-art synchrotron-based tomographic phase-contrast imaging methods allow for three-dimensional microscopic imaging data to be acquired non-destructively in scan times of the order of seconds with good soft tissue contrast. However, when studying multi-scale hierarchically structured objects, such as the mammalian lung, the overall sample size typically exceeds the field of view illuminated by the X-rays in a single scan and the necessity for achieving a high spatial resolution conflicts with the need to image the whole sample. Several image stitching and calibration techniques to achieve extended high-resolution fields of view have been reported, but those approaches tend to fail when imaging non-stable samples, thus precluding tomographic measurements of large biological samples, which are prone to degradation and motion during extended scan times. In this work, we demonstrate a full-volume three-dimensional reconstruction of an intact rat lung under immediate post-mortem conditions and at an isotropic voxel size of (2.75 µm)³. We present the methodology for collecting multiple local tomographies with 360° extended field of view scans followed by locally non-rigid volumetric stitching. Applied to the lung, it allows to resolve the entire pulmonary structure from the trachea down to the parenchyma in a single dataset. The complete dataset is available online (https://doi.org/10.16907/7eb141d3-11f1-47a6-9d0e-76f8832ed1b2).

X-ray free-electron laser wavefront sensing using the fractional Talbot effect

Wavefront sensing at X-ray free-electron lasers is important for quantitatively understanding the fundamental properties of the laser, for aligning X-ray instruments and for conducting scientific experimental analysis. A fractional Talbot wavefront sensor has been developed. This wavefront sensor enables measurements over a wide range of energies, as is common on X-ray instruments, with simplified mechanical requirements and is compatible with the high average power pulses expected in upcoming X-ray free-electron laser upgrades. Single-shot measurements were performed at 500 eV, 1000 eV and 1500 eV at the Linac Coherent Light Source. These measurements were applied to study both mirror alignment and the effects of undulator tapering schemes on source properties. The beamline focal plane position was tracked to an uncertainty of 0.12 mm, and the source location for various undulator tapering schemes to an uncertainty of 1 m, demonstrating excellent sensitivity. These findings pave the way to use the fractional Talbot wavefront sensor as a routine, robust and sensitive tool at X-ray free-electron lasers as well as other high-brightness X-ray sources.

Three dimensions, two microscopes, one code: Automatic differentiation for x-ray nanotomography beyond the depth of focus limit

Conventional tomographic reconstruction algorithms assume that one has obtained pure projection images, involving no within-specimen diffraction effects nor multiple scattering. Advances in x-ray nanotomography are leading toward the violation of these assumptions, by combining the high penetration power of x-rays, which enables thick specimens to be imaged, with improved spatial resolution that decreases the depth of focus of the imaging system. We describe a reconstruction method where multiple scattering and diffraction effects in thick samples are modeled by multislice propagation and the 3D object function is retrieved through iterative optimization. We show that the same proposed method works for both full-field microscopy and for coherent scanning techniques like ptychography. Our implementation uses the optimization toolbox and the automatic differentiation capability of the open-source deep learning package TensorFlow, demonstrating a straightforward way to solve optimization problems in computational imaging with flexibility and portability.

From atoms to aerosols: probing clusters and nanoparticles with synchrotron based mass spectrometry and X-ray spectroscopy

Synchrotron radiation provides insight into spectroscopy and dynamics in clusters and nanoparticles.

Translative lens-based full-field coherent X-ray imaging

A full-field coherent imaging approach suitable for hard X-rays based on a classical (i.e. Galilean) X-ray microscope is described. The method combines a series of low-resolution images acquired at different transverse lens positions into a single high-resolution image, overcoming the spatial resolution limit set by the numerical aperture of the objective lens. The optical principles of the approach are described, the successful reconstruction of simulated phantom data is demonstrated, and aspects of the reconstruction are discussed. The authors believe that this approach offers some potential benefits over conventional scanning X-ray ptychography in terms of spatial bandwidth and radiation dose rate.

Tunable High Spatio-Spectral Purity Undulator Radiation from a Transported Laser Plasma Accelerated Electron Beam

Undulator based synchrotron light sources and Free Electron Lasers (FELs) are valuable modern probes of matter with high temporal and spatial resolution. Laser Plasma Accelerators (LPAs), delivering GeV electron beams in few centimeters, are good candidates for future compact light sources. However the barriers set by the large energy spread, divergence and shot-to-shot fluctuations require a specific transport line, to shape the electron beam phase space for achieving ultrashort undulator synchrotron radiation suitable for users and even for achieving FEL amplification. Proof-of-principle LPA based undulator emission, with strong electron focusing or transport, does not yet exhibit the full specific radiation properties. We report on the generation of undulator radiation with an LPA beam based manipulation in a dedicated transport line with versatile properties. After evidencing the specific spatio-spectral signature, we tune the resonant wavelength within 200-300 nm by modification of the electron beam energy and the undulator field. We achieve a wavelength stability of 2.6%. We demonstrate that we can control the spatio-spectral purity and spectral brightness by reducing the energy range inside the chicane. We have also observed the second harmonic emission of the undulator.

Optimization of a phase-space beam position and size monitor for low-emittance light sources

The recently developed vertical phase-space beam position and size monitor (ps-BPM) system has proven to be able to measure the electron-source position, angle, size and divergence simultaneously in the vertical plane at a single location of a beamline. The optimization of the ps-BPM system is performed by ray-tracing simulation to maximize the instrument sensitivity and resolution. The contribution of each element is studied, including the monochromator, the K-edge filter, the detector and the source-to-detector distance. An optimized system is proposed for diffraction-limited storage rings, such as the Advanced Photon Source Upgrade project. The simulation results show that the ps-BPM system can precisely monitor the source position and angle at high speed. Precise measurements of the source size and divergence will require adequate resolution with relatively longer integration time.

Coherence properties of the high-energy fourth-generation X-ray synchrotron sources

An analysis of the coherence properties of the fourth-generation high-energy storage rings with emittance values of 10 pm rad is performed. It is presently expected that a storage ring with these low emittance values will reach diffraction limit at hard X-rays. Simulations of coherence properties were performed with the XRT software and an analytical approach for different photon energies from 500 eV to 50 keV. It was demonstrated that a minimum photon emittance (diffraction limit) reached at such storage rings is λ/2π. Using mode decomposition it is shown that, for the parameters of the storage ring considered in this work, the diffraction limit will be reached for soft X-ray energies of 500 eV. About ten modes will contribute to the radiation field at 12 keV photon energy and even more modes give a contribution at higher photon energies. Energy spread effects of the electron beam in a low-emittance storage ring were analysed in detail. Simulations were performed at different relative energy spread values from zero to 2 × 10^-3. A decrease of the degree of coherence with an increase of the relative energy spread value was observed. This analysis shows that, to reach the diffraction limit for high photon energies, electron beam emittance should go down to 1 pm rad and below.

Macromolecular Nanocrystal Structural Analysis with Electron and X-Rays: A Comparative Review

Crystallography has long been the unrivaled method that can provide the atomistic structural models of macromolecules, using either X-rays or electrons as probes. The methodology has gone through several revolutionary periods, driven by the development of new sources, detectors, and other instrumentation. Novel sources of both X-ray and electrons are constantly emerging. The increase in brightness of these sources, complemented by the advanced detection techniques, has relaxed the traditionally strict need for large, high quality, crystals. Recent reports suggest high-quality diffraction datasets from crystals as small as a few hundreds of nanometers can be routinely obtained. This has resulted in the genesis of a new field of macromolecular nanocrystal crystallography. Here we will make a brief comparative review of this growing field focusing on the use of X-rays and electrons sources.

A real-time phase-space beam emittance monitoring system

An electron beam position and angle monitoring system, ps-BPM, has been shown to be able to measure the electron source position and angle at a single location in a beamline at a synchrotron source. This system uses a monochromator to prepare a photon beam whose energy is at that of the K-edge of an absorber filter. The divergence of the beam from the source gives an energy range that will encompass the K-edge of the filter. A measurement of the centre of the monochromatic beam and the K-edge location through the absorber filter gives the position and angle of the electron source. Here, it is shown that this system is also capable of measuring the source size and divergence at the same time. This capability is validated by measurement as the beam size in the storage ring was changed and by ray-tracing simulations. The system operates by measuring the photon beam spatial distribution as well as a K-edge filtered beam distribution. These additional measurements result in the ability to also determine the electron source size and divergence.

An outlook on using serial femtosecond crystallography in drug discovery

Introduction: X-ray crystallography has made important contributions to modern drug development but its application to many important drug targets has been extremely challenging. The recent emergence of X-ray free electron lasers (XFELs) and advancements in serial femtosecond crystallography (SFX) have offered new opportunities to overcome limitations of traditional crystallography to accelerate the structure-based drug discovery (SBDD) process. Areas covered: In this review, the authors describe the general principles of X-ray generation and the main properties of XFEL beams, outline details of SFX data collection and processing, and summarize the progress in the development of associated instrumentation for sample delivery and X-ray detection. An overview of the SFX applications to various important drug targets such as membrane proteins is also provided. Expert opinion: While SFX has already made clear advancements toward the understanding of the structure and dynamics of several major drug targets, its robust application in SBDD still needs further developments of new high-throughput techniques for sample production, automation of crystal delivery and data collection, as well as for processing and storage of large amounts of data. The expansion of the available XFEL beamtime is a key to the success of SFX in SBDD.

Megahertz non-contact luminescence decay time cryothermometry by means of ultrafast PbI2 scintillator

Realtime in situ temperature monitoring in difficult experimental conditions or inaccessible environments is critical for many applications. Non-contact luminescence decay time thermometry is often the method of choice for such applications due to a favorable combination of sensitivity, accuracy and robustness. In this work, we demonstrate the feasibility of an ultrafast PbI2 scintillator for temperature determination, using the time structure of X-ray radiation, produced by a synchrotron. The decay kinetics of the scintillations was measured over the 8-107 K temperature range using monochromatic pulsed X-ray excitation. It is found that lead iodide exhibits a very fast and intense scintillation response due to excitons and donor-acceptor pairs, with the fast decay component varying between 0.08 and 0.5 ns - a feature that can be readily exploited for temperature monitoring. The observed temperature dependence of the decay time is discussed in terms of two possible mechanisms of thermal quenching - transition over activation barrier and phonon-assisted escape. It is concluded that the latter provides a better fit to the experimental results and is consistent with the model of luminescence processes in PbI2. We evaluated the sensitivity and estimated the accuracy of the temperature determination as ca. ±6 K at 107 K, improving to ±1.4 K at 8 K. The results of this study prove the feasibility of temperature monitoring, using ultrafast scintillation of PbI2 excited by X-ray pulses from a synchrotron, thus enabling non-contact in-situ cryothermometry with megahertz sampling rate.

The expanding toolkit for structural biology: synchrotrons, X-ray lasers and cryoEM

Structural biology continues to benefit from an expanding toolkit, which is helping to gain unprecedented insight into the assembly and organization of multi-protein machineries, enzyme mechanisms and ligand/inhibitor binding. The combination of results from X-ray free-electron lasers (XFELs), modern synchrotron crystallographic beamlines and cryo-electron microscopy (cryoEM) is proving to be particularly powerful. The highly brilliant undulator beamlines at modern synchrotron facilities have empowered the crystallographic revolution of high-throughput structure determination at high resolution. The brilliance of the X-rays at these crystallographic beamlines has enabled this to be achieved using microcrystals, but at the expense of an increased absorbed X-ray dose and a consequent vulnerability to radiation-induced changes. The advent of serial femtosecond crystallography (SFX) with X-ray free-electron lasers provides a new opportunity in which damage-free structures can be obtained from much smaller crystals (2 µm) and more complex macromolecules, including membrane proteins and multi-protein complexes. For redox enzymes, SFX provides a unique opportunity by providing damage-free structures at both cryogenic and ambient temperatures. The promise of being able to visualize macromolecular structures and complexes at high resolution without the need for crystals using X-rays has remained a dream, but recent technological advancements in cryoEM have made this come true and hardly a month goes by when the structure of a new/novel macromolecular assembly is not revealed. The uniqueness of cryoEM in providing structural information for multi-protein complexes, particularly membrane proteins, has been demonstrated by examples such as respirasomes. The synergistic use of cryoEM and crystallography in lead-compound optimization is highlighted by the example of the visualization of antimalarial compounds in cytochrome bc 1. In this short review, using some recent examples including our own work, we share the excitement of these powerful structural biology methods.

Compact reflective imaging optics in hard X-ray region based on concave and convex mirrors

We demonstrated that the combination of a hyperbolic convex and elliptical concave mirrors works as a compact reflective X-ray imaging system with a short optical focal length and large magnification factor. We performed an experiment to form a one-dimensional demagnified image with a demagnification factor of 321 within an approximately 2-m-long optical setup at an X-ray energy of 10 keV. The results showed that this imaging optics system is capable of providing a resolution of ~40 nm. From wavefront analysis, it was confirmed that the optics possessed a wide field-of-view with a significant reduction of comatic aberration.

Mapping of individual dislocations with dark-field X-ray microscopy

This article presents an X-ray microscopy approach for mapping deeply embedded dislocations in three dimensions using a monochromatic beam with a low divergence. Magnified images are acquired by inserting an X-ray objective lens in the diffracted beam. The strain fields close to the core of dislocations give rise to scattering at angles where weak beam conditions are obtained. Analytical expressions are derived for the image contrast. While the use of the objective implies an integration over two directions in reciprocal space, scanning an aperture in the back focal plane of the microscope allows a reciprocal-space resolution of ΔQ/Q < 5 × 10−5 in all directions, ultimately enabling high-precision mapping of lattice strain and tilt. The approach is demonstrated on three types of samples: a multi-scale study of a large diamond crystal in transmission, magnified section topography on a 140 µm-thick SrTiO3 sample and a reflection study of misfit dislocations in a 120 nm-thick BiFeO3 film epitaxially grown on a thick substrate. With optimal contrast, the half-widths at half-maximum of the dislocation lines are 200 nm.

In situ metrology for adaptive x-ray optics with an absolute distance measuring sensor array

Adaptive x-ray mirrors are emerging as one of the primary solutions for meeting the performance needs of the next generation of x-ray light sources. Currently, these mirrors operate open loop with intermittent feedback from invasive sensors that measure the beam quality. This paper outlines a novel design for real-time in situ metrology of the shape of these mirrors using an array of interferometric sensors that does not interrupt the x-ray beam. We describe a proof-of-principle demonstration which shows sub-nm agreement over a range of mirror deflection magnitudes and shapes as compared to simultaneous measurements by using a large-aperture Fizeau interferometer.

Sample delivery for serial crystallography at free-electron lasers and synchrotrons

The high peak brilliance and femtosecond pulse duration of X-ray free-electron lasers (XFELs) provide new scientific opportunities for experiments in physics, chemistry and biology. In structural biology, one of the major applications is serial femtosecond crystallography. The intense XFEL pulse results in the destruction of any exposed microcrystal, making serial data collection mandatory. This requires a high-throughput serial approach to sample delivery. To this end, a number of such sample-delivery techniques have been developed, some of which have been ported to synchrotron sources, where they allow convenient low-dose data collection at room temperature. Here, the current sample-delivery techniques used at XFEL and synchrotron sources are reviewed, with an emphasis on liquid injection and high-viscosity extrusion, including their application for time-resolved experiments. The challenges associated with sample delivery at megahertz repetition-rate XFELs are also outlined.

Shaping coherent x-rays with binary optics

Diffractive lenses fabricated by lithographic methods are one of the most popular image forming optics in the x-ray regime. Most commonly, binary diffractive optics, such as Fresnel zone plates, are used due to their ability to focus at high resolution and to manipulate the x-ray wavefront. We report here a binary zone plate design strategy to form arbitrary illuminations for coherent multiplexing, structured illumination, and wavefront shaping experiments. Given a desired illumination, we adjust the duty cycle, harmonic order, and zone placement to vary both the amplitude and phase of the wavefront at the lens. This enables the binary lithographic pattern to generate arbitrary structured illumination optimized for a variety of applications such as holography, interferometry, ptychography, imaging, and others.

Rotation-as-fast-axis scanning-probe x-ray tomography: the importance of angular diversity for fly-scan modes

We investigate the effects of angular diversity on image-reconstruction quality of scanning-probe x-ray tomography for both fly- and step-mode data collection. We propose probe-coverage maps as a tool for both visualizing and quantifying the distribution of probe interactions with the object. We show that data sampling with more angular diversity yields better tomographic image reconstruction as long as it does not come at the cost of not covering some voxels in the object. Therefore, for fly-mode data collection, rotation-as-fast-axis (RAFA) trajectories are superior to raster or other non-RAFA trajectories because they allow for the increasing of angular diversity without sacrificing spatial coverage uniformity. In contrast, for step-mode data collection and a fixed measurement budget, increasing angular diversity can come at the cost of not covering some voxels, and may not be desired. This study has implications for how scanning-probe microscopes should be collecting data in order to make the most of limited resources.

Nanobeam X-ray Fluorescence Dopant Mapping Reveals Dynamics of in Situ Zn-Doping in Nanowires

The properties of semiconductors can be controlled using doping, making it essential for electronic and optoelectronic devices. However, with shrinking device sizes it becomes increasingly difficult to quantify doping with sufficient sensitivity and spatial resolution. Here, we demonstrate how X-ray fluorescence mapping with a nanofocused beam, nano-XRF, can quantify Zn doping within in situ doped III-V nanowires, by using large area detectors and high-efficiency focusing optics. The spatial resolution is defined by the focus size to 50 nm. The detection limit of 7 ppm (2.8 × 10¹⁷ cm^-3), corresponding to about 150 Zn atoms in the probed volume, is bound by a background signal. In solar cell InP nanowires with a p-i-n doping profile, we use nano-XRF to observe an unintentional Zn doping of 5 × 10¹⁷ cm^-3 in the middle segment. We investigated the dynamics of in situ Zn doping in a dedicated multisegment nanowire, revealing significantly sharper gradients after turning the Zn source off than after turning the source on. Nano-XRF could be used for quantitative mapping of a wide range of dopants in many types of nanostructures.

Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector

The accuracy of X-ray diffraction data is directly related to how the X-ray detector records photons. Here we describe the application of a direct-detection charge-integrating pixel-array detector (JUNGFRAU) in macromolecular crystallography (MX). JUNGFRAU features a uniform response on the subpixel level, linear behavior toward high photon rates, and low-noise performance across the whole dynamic range. We demonstrate that these features allow accurate MX data to be recorded at unprecedented speed. We also demonstrate improvements over previous-generation detectors in terms of data quality, using native single-wavelength anomalous diffraction (SAD) phasing, for thaumatin, lysozyme, and aminopeptidase N. Our results suggest that the JUNGFRAU detector will substantially improve the performance of synchrotron MX beamlines and equip them for future synchrotron light sources.

Long-range symmetry breaking in embedded ferroelectrics

The characteristic functionality of ferroelectric materials is due to the symmetry of their crystalline structure. As such, ferroelectrics lend themselves to design approaches that manipulate this structural symmetry by introducing extrinsic strain. Using in situ dark-field X-ray microscopy to map lattice distortions around deeply embedded domain walls and grain boundaries in BaTiO₃, we reveal that symmetry-breaking strain fields extend up to several micrometres from domain walls. As this exceeds the average domain width, no part of the material is elastically relaxed, and symmetry is universally broken. Such extrinsic strains are pivotal in defining the local properties and self-organization of embedded domain walls, and must be accounted for by emerging computational approaches to material design.

Sub-microsecond-resolved multi-speckle X-ray photon correlation spectroscopy with a pixel array detector

Small-angle X-ray photon correlation spectroscopy (XPCS) measurements spanning delay times from 826 ns to 52.8 s were performed using a photon-counting pixel array detector with a dynamic range of 0-3 (2 bits). Fine resolution and a wide dynamic range of time scales was achieved by combining two modes of operation of the detector: (i) continuous mode, where data acquisition and data readout are performed in parallel with a frame acquisition time of 19.36 µs, and (ii) burst mode, where 12 frames are acquired with frame integration times of either 2.56 µs frame^-1 or 826 ns frame^-1 followed by 3.49 ms or 1.16 ms, respectively, for readout. The applicability of the detector for performing multi-speckle XPCS was demonstrated by measuring the Brownian dynamics of 10 nm-radius gold and 57 nm-radius silica colloids in water at room temperature. In addition, the capability of the detector to faithfully record one- and two-photon counts was examined by comparing the statistical distribution of photon counts with expected probabilities from the negative binomial distribution. It was found that in burst mode the ratio of 2 s to 1 s is markedly smaller than predicted and that this is attributable to pixel-response dead-time.

Commissioning and first-year operational results of the MAX IV 3 GeV ring

The MAX IV 3 GeV electron storage ring in Lund, Sweden, is the first of a new generation of light sources to make use of the multibend-achromat lattice (MBA) to achieve ultralow emitance and hence ultrahigh brightness and transverse coherence. The conceptual basis of the MAX IV 3 GeV ring project combines a robust lattice design with a number of innovative engineering choices: compact, multifunctional magnet blocks, narrow low-conductance NEG-coated copper vacuum chambers and a 100 MHz radio-frequency system with passively operated third-harmonic cavities for bunch lengthening. In this paper, commissioning and first-year operational results of the MAX IV 3 GeV ring are presented, highlighting those aspects that are believed to be most relevant for future MBA-based storage rings. The commissioning experience of the MAX IV 3 GeV ring offers in this way an opportunity for validation of concepts that are likely to be essential ingredients of future diffraction-limited light sources.

In situ serial crystallography for rapid de novo membrane protein structure determination

De novo membrane protein structure determination is often limited by the availability of large crystals and the difficulties in obtaining accurate diffraction data for experimental phasing. Here we present a method that combines in situ serial crystallography with de novo phasing for fast, efficient membrane protein structure determination. The method enables systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without the need for direct crystal harvesting. The requisite data quality for experimental phasing is achieved by accumulating diffraction signals from isomorphous crystals identified post-data collection. The method works in all experimental phasing scenarios and is particularly attractive with fragile, weakly diffracting microcrystals. The automated serial data collection approach can be readily adopted at most microfocus macromolecular crystallography beamlines.

Nitridated Ru/B4C multilayer mirrors with improved interface structure, zero stress, and enhanced hard X-ray reflectance

Ru/B₄C multilayer mirrors are used for hard X-ray monochromators with moderate spectral resolution and high integral flux. To overcome the problem of large compressive stress inherent in Ru/B₄C multilayers, a reactive sputtering technique using a mixture working gas of argon and nitrogen with different partial pressures was tested, and the fabricated multilayers had a period of 3 nm. The intrinsic stress was essentially reduced after nitridation and relaxed to zero value at approximately 15% partial pressure of nitrogen in the working gas. Interface roughness was slightly increased which can be caused by the polycrystalline structure inside the nitridated samples. More importantly, the nitridated multilayers showed an enhanced reflectance (67% at 8.04 keV photon energy) as compared with the one fabricated with pure Ar (54%). The structure analysis with transmission electron microscopy and X-ray photoelectron spectroscopy demonstrated that nitrogen incorporated into a multilayer structure was mostly located in the B₄C layers forming BN compounds, which suppressed the diffusion of boron, stabilized the interfaces and enhanced the reflectance.

High Bragg reflectivity of diamond crystals exposed to multi-kW mm-2 X-ray beams

X-ray free-electron lasers in the oscillator configuration (XFELO) are future fully coherent hard X-rays sources with ultrahigh spectral purity. X-ray beams circulate in an XFELO optical cavity comprising diamond single crystals. They function as high-reflectance (close to 100%), narrowband (∼10 meV) Bragg backscattering mirrors. The average power density of the X-ray beams in the XFELO cavity is predicted to be as high as ∼10 kW mm^-2. Therefore, XFELO feasibility relies on the ability of diamond crystals to withstand such a high radiation load and preserve their high reflectivity. Here the endurance of diamond crystals to irradiation with multi-kW mm^-2 power density X-ray beams is studied. It is shown that the high Bragg reflectivity of the diamond crystals is preserved after the irradiation, provided it is performed at ∼1 × 10^-8 Torr high-vacuum conditions. Irradiation under 4 × 10^-6 Torr results in a ∼1 meV shift of the Bragg peak, which corresponds to a relative lattice distortion of 4 × 10^-8, while the high Bragg reflectivity stays intact.

Atmospheric coherent X-ray diffraction imaging for in situ structural analysis at SPring-8 Hyogo beamline BL24XU

Coherent X-ray diffraction imaging (CXDI) is a promising technique for non-destructive structural analysis of micrometre-sized non-crystalline samples at nanometre resolutions. This article describes an atmospheric CXDI system developed at SPring-8 Hyogo beamline BL24XU for in situ structural analysis and designed for experiments at a photon energy of 8 keV. This relatively high X-ray energy enables experiments to be conducted under ambient atmospheric conditions, which is advantageous for the visualization of samples in native states. The illumination condition with pinhole-slit optics is optimized according to wave propagation calculations based on the Fresnel-Kirchhoff diffraction formula so that the sample is irradiated by X-rays with a plane wavefront and high photon flux of ∼1 × 10¹⁰ photons/16 µmø(FWHM)/s. This work demonstrates the imaging performance of the atmospheric CXDI system by visualizing internal voids of sub-micrometre-sized colloidal gold particles at a resolution of 29.1 nm. A CXDI experiment with a single macroporous silica particle under controlled humidity was also performed by installing a home-made humidity control device in the system. The in situ observation of changes in diffraction patterns according to humidity variation and reconstruction of projected electron-density maps at 5.2% RH (relative humidity) and 82.6% RH at resolutions of 133 and 217 nm, respectively, were accomplished.

Pulse intensity characterization of the LCLS nanosecond double-bunch mode of operation

The recent demonstration of the `nanosecond double-bunch' operation mode, i.e. two X-ray pulses separated in time between 0.35 and hundreds of nanoseconds and by increments of 0.35 ns, offers new opportunities to investigate ultrafast dynamics in diverse systems of interest. However, in order to reach its full potential, this mode of operation requires the precise characterization of the intensity of each X-ray pulse within each pulse pair for any time separation. Here, a transmissive single-shot diagnostic that achieves this goal for time separations larger than 0.7 ns with a precision better than 5% is presented. It also provides real-time monitoring feedback to help tune the accelerator parameters to deliver double pulse intensity distributions optimized for specific experimental goals.