PhaseGAN a deep learning phase retrieval approach for unpaired datasets

Phase retrieval approaches based on deep learning DL provide a framework to obtain phase information from an intensity hologram or diffraction pattern in a robust manner and in real time. However, current DL architectures applied to the phase problem rely on i paired datasets, i. e., they are only applicable when a satisfactory solution of the phase problem has been found, and ii the fact that most of them ignore the physics of the imaging process. Here, we present PhaseGAN, a new DL approach based on Generative Adversarial Networks, which allows the use of unpaired datasets and includes the physics of image formation. The performance of our approach is enhanced by including the image formation physics and a novel Fourier loss function, providing phase reconstructions when conventional phase retrieval algorithms fail, such as ultra fast experiments. Thus, PhaseGAN offers the opportunity to address the phase problem in real time when no phase reconstructions but good simulations or data from other experiments are availabl

Online dynamic flat-field correction for MHz Microscopy data at European XFEL

The X-ray microscopy technique at the European X-ray free-electron laser (EuXFEL), operating at a MHz repetition rate, provides superior contrast and spatial-temporal resolution compared to typical microscopy techniques at other X-ray sources. In both online visualization and offline data analysis for microscopy experiments, baseline normalization is essential for further processing steps such as phase retrieval and modal decomposition. In addition, access to normalized projections during data acquisition can play an important role in decision-making and improve the quality of the data. However, the stochastic nature of XFEL sources hinders the use of existing flat-flied normalization methods during MHz X-ray microscopy experiments. Here, we present an online dynamic flat-field correction method based on principal component analysis of dynamically evolving flat-field images. The method is used for the normalization of individual X-ray projections and has been implemented as an online analysis tool at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of EuXFEL.Comment: 14 pages, 7 figure

Ultrasound cavitation and exfoliation dynamics of 2D materials re-vealed in operando by X-ray free electron laser megahertz imaging

Ultrasonic liquid phase exfoliation is a promising method for the production of two-dimensional (2D) layered materials. A large number of studies have been made in investigating the underlying ultrasound exfoliation mechanisms. However, due to the experimental challenges for capturing the highly transient and dynamic phenomena in real-time at sub-microsecond time and micrometer length scales simultaneously, most theories reported to date still remain elusive. Here, using the ultra-short X-ray Free Electron Laser pulses (~25ps) with a unique pulse train structure, we applied MHz X-ray Microscopy and machine-learning technique to reveal unambiguously the full cycles of the ultrasound cavitation and graphite layer exfoliation dynamics with sub-microsecond and micrometer resolution. Cyclic fatigue shock wave impacts produced by ultrasound cloud implosion were identified as the dominant mechanism to deflect and exfoliate graphite layers mechanically. For the graphite flakes, exfoliation rate as high as ~5 angstroms per shock wave impact was observed. For the HOPG graphite, the highest exfoliation rate was ~0.15 angstroms per impact. These new findings are scientifically and technologically important for developing industrial upscaling strategies for ultrasonic exfoliation of 2D materials

Development of crystal optics for Multi-Projection X-ray Imaging for synchrotron and XFEL sources

X-ray Multi-Projection Imaging (XMPI) is an emerging technology that allows for the acquisition of millions of 3D images per second in samples opaque to visible light. This breakthrough capability enables volumetric observation of fast stochastic phenomena, which were inaccessible due to the lack of a volumetric X-ray imaging probe with kHz to MHz repetition rate. These include phenomena of industrial and societal relevance such as fractures in solids, propagation of shock waves, laser-based 3D printing, or even fast processes in the biological domain. Indeed, the speed of traditional tomography is limited by the shear forces caused by rotation, to a maximum of 1000 Hz in state-of-the-art tomography. Moreover, the shear forces can disturb the phenomena in observation, in particular with soft samples or sensitive phenomena such as fluid dynamics. XMPI is based on splitting an X-ray beam to generate multiple simultaneous views of the sample, therefore eliminating the need for rotation. The achievable performances depend on the characteristics of the X-ray source, the detection system, and the X-ray optics used to generate the multiple views. The increase in power density of the X-ray sources around the world now enables 3D imaging with sampling speeds in the kilohertz range at synchrotrons and megahertz range at X-ray Free-Electron Lasers (XFELs). Fast detection systems are already available, and 2D MHz imaging was already demonstrated at synchrotron and XFEL. In this work, we explore the properties of X-ray splitter optics and XMPI schemes that are compatible with synchrotron insertion devices and XFEL X-ray beams. We describe two possible schemes designed to permit large samples and complex sample environments. Then, we present experimental proof of the feasibility of MHz-rate XMPI at the European XFEL.Comment: 47 pages, 17 figure

3D diffractive imaging of nanoparticle ensembles using an X-ray laser

We report the 3D structure determination of gold nanoparticles (AuNPs) by X-ray single particle imaging (SPI). Around 10 million diffraction patterns from gold nanoparticles were measured in less than 100 hours of beam time, more than 100 times the amount of data in any single prior SPI experiment, using the new capabilities of the European X-ray free electron laser which allow measurements of 1500 frames per second. A classification and structural sorting method was developed to disentangle the heterogeneity of the particles and to obtain a resolution of better than 3 nm. With these new experimental and analytical developments, we have entered a new era for the SPI method and the path towards close-to-atomic resolution imaging of biomolecules is apparent

Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers

The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 µs, yield up to 2.1 Å resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX

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

Fabrication of diamond diffraction gratings for experiments with intense hard x-rays

The demands on optical components to tolerate high radiation dose and manipulate hard x-ray beams that can fit the experiment requirements, are constantly increasing due to the advancements in the available x-ray sources. Here we have successfully fabricated the transmission type gratings using diamond, with structure sizes ranging from few tens of nanometres up to micrometres, and aspect ratio of up to 20. The efficiencies of the gratings were measured over a wide range of photon energies and their radiation tolerance was confirmed using the most intense x-ray source in the world. The fidelity of these grating structures was confirmed by the quality of the measured experimental results