The emerging technique of serial X‐ray diffraction, in which diffraction data are collected from samples flowing across a pulsed X‐ray source at repetition rates of 100 Hz or higher, has necessitated ...the development of new software in order to handle the large data volumes produced. Sorting of data according to different criteria and rapid filtering of events to retain only diffraction patterns of interest results in significant reductions in data volume, thereby simplifying subsequent data analysis and management tasks. Meanwhile the generation of reduced data in the form of virtual powder patterns, radial stacks, histograms and other meta data creates data set summaries for analysis and overall experiment evaluation. Rapid data reduction early in the analysis pipeline is proving to be an essential first step in serial imaging experiments, prompting the authors to make the tool described in this article available to the general community. Originally developed for experiments at X‐ray free‐electron lasers, the software is based on a modular facility‐independent library to promote portability between different experiments and is available under version 3 or later of the GNU General Public License.
We present a proof-of-concept three-dimensional reconstruction of the giant mimivirus particle from experimentally measured diffraction patterns from an x-ray free-electron laser. Three-dimensional ...imaging requires the assembly of many two-dimensional patterns into an internally consistent Fourier volume. Since each particle is randomly oriented when exposed to the x-ray pulse, relative orientations have to be retrieved from the diffraction data alone. We achieve this with a modified version of the expand, maximize and compress algorithm and validate our result using new methods.
Battery function is determined by the efficiency and reversibility of the electrochemical phase transformations at solid electrodes. The microscopic tools available to study the chemical states of ...matter with the required spatial resolution and chemical specificity are intrinsically limited when studying complex architectures by their reliance on two-dimensional projections of thick material. Here, we report the development of soft X-ray ptychographic tomography, which resolves chemical states in three dimensions at 11 nm spatial resolution. We study an ensemble of nano-plates of lithium iron phosphate extracted from a battery electrode at 50% state of charge. Using a set of nanoscale tomograms, we quantify the electrochemical state and resolve phase boundaries throughout the volume of individual nanoparticles. These observations reveal multiple reaction points, intra-particle heterogeneity, and size effects that highlight the importance of multi-dimensional analytical tools in providing novel insight to the design of the next generation of high-performance devices.
Free‐electron lasers could enable X‐ray imaging of single biological macromolecules and the study of protein dynamics, paving the way for a powerful new imaging tool in structural biology, but a low ...signal‐to‐noise ratio and missing regions in the detectors, colloquially termed `masks', affect data collection and hamper real‐time evaluation of experimental data. In this article, the challenges posed by noise and masks are tackled by introducing a neural network pipeline that aims to restore diffraction intensities. For training and testing of the model, a data set of diffraction patterns was simulated from 10 900 different proteins with molecular weights within the range of 10–100 kDa and collected at a photon energy of 8 keV. The method is compared with a simple low‐pass filtering algorithm based on autocorrelation constraints. The results show an improvement in the mean‐squared error of roughly two orders of magnitude in the presence of masks compared with the noisy data. The algorithm was also tested at increasing mask width, leading to the conclusion that demasking can achieve good results when the mask is smaller than half of the central speckle of the pattern. The results highlight the competitiveness of this model for data processing and the feasibility of restoring diffraction intensities from unknown structures in real time using deep learning methods. Finally, an example is shown of this preprocessing making orientation recovery more reliable, especially for data sets containing very few patterns, using the expansion–maximization–compression algorithm.
A neural network for coherent X‐ray diffractive imaging experiments is presented that can restore noisy and masked simulated diffraction intensities from biological macromolecules.
Bragg coherent diffraction imaging is a powerful strain imaging tool, often limited by beam-induced sample instability for small particles and high power densities. Here, we devise and validate an ...adapted diffraction volume assembly algorithm, capable of recovering three-dimensional datasets from particles undergoing uncontrolled and unknown rotations. We apply the method to gold nanoparticles which rotate under the influence of a focused coherent x-ray beam, retrieving their three-dimensional shapes and strain fields. The results show that the sample instability problem can be overcome, enabling the use of fourth generation synchrotron sources for Bragg coherent diffraction imaging to their full potential.
X-ray lasers produce pulses of X-rays 1 billion times brighter than those of synchrotrons; this capability creates extraordinary research opportunities in physics, chemistry and biology1,2. The high ...repetition rate of these machines leads to large volumes of data. For example, the Coherent X-ray Imaging beamline at the Linac Coherent Light Source (LCLS) produces three times more data per second than the ATLAS detector of the Large Hadron Collider. This data volume increase has created a need for tools to analyze and make efficient use of the new observations.
Intense x-ray free-electron laser (XFEL) pulses hold great promise for imaging function in nanoscale and biological systems with atomic resolution. So far, however, the spatial resolution obtained ...from single shot experiments lags averaging static experiments. Here we report on a combined computational and experimental study about ultrafast diffractive imaging of sucrose clusters which are benchmark organic samples. Our theoretical model matches the experimental data from the water window to the keV x-ray regime. The large-scale dynamic scattering calculations reveal that transient phenomena driven by non-linear x-ray interaction are decisive for ultrafast imaging applications. Our study illuminates the complex interplay of the imaging process with the rapidly changing transient electronic structures in XFEL experiments and shows how computational models allow optimization of the parameters for ultrafast imaging experiments.
Imaging the structure and observing the dynamics of isolated proteins using single-particle X-ray diffractive imaging (SPI) is one of the potential applications of X-ray free-electron lasers (XFELs). ...Currently, SPI experiments on isolated proteins are limited by three factors: low signal strength, limited data and high background from gas scattering. The last two factors are largely due to the shortcomings of the aerosol sample delivery methods in use. Here we present our modified electrospray ionization (ESI) source, which we dubbed helium-ESI (He-ESI). With it, we increased particle delivery into the interaction region by a factor of 10, for 26 nm-sized biological particles, and decreased the gas load in the interaction chamber corresponding to an 80% reduction in gas scattering when compared to the original ESI. These improvements have the potential to significantly increase the quality and quantity of SPI diffraction patterns in future experiments using He-ESI, resulting in higher-resolution structures.
We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the ...traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.
This work investigates the performance of the electrospray aerosol generator at the European X‐ray Free Electron Laser (EuXFEL). This generator is, together with an aerodynamic lens stack that ...transports the particles into the X‐ray interaction vacuum chamber, the method of choice to deliver particles for single‐particle coherent diffractive imaging (SPI) experiments at the EuXFEL. For these experiments to be successful, it is necessary to achieve high transmission of particles from solution into the vacuum interaction region. Particle transmission is highly dependent on efficient neutralization of the charged aerosol generated by the electrospray mechanism as well as the geometry in the vicinity of the Taylor cone. We report absolute particle transmission values for different neutralizers and geometries while keeping the conditions suitable for SPI experiments. Our findings reveal that a vacuum ultraviolet ionizer demonstrates a transmission efficiency approximately seven times greater than the soft X‐ray ionizer used previously. Combined with an optimized orifice size on the counter electrode, we achieve >40% particle transmission from solution into the X‐ray interaction region. These findings offer valuable insights for optimizing electrospray aerosol generator configurations and data rates for SPI experiments.
We investigate the performance of an electrospray aerosol generator at the European X‐ray Free Electron Laser for single‐particle coherent diffractive imaging. The findings highlight enhanced particle transmission efficiency with VUV ionization, larger orifice diameters, electric fields and 3D‐printed twin‐nozzle design, providing insights for optimizing aerosol injection in XFEL experiments.
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