Development towards high-resolution kHz-speed rotation-free volumetric imaging.

X-ray multi-projection imaging (XMPI) has the potential to provide rotation-free 3D movies of optically opaque samples. The absence of rotation enables superior imaging speed and preserves fragile sample dynamics by avoiding the centrifugal forces introduced by conventional rotary tomography. Here, we present our XMPI observations at the ID19 beamline (ESRF, France) of 3D dynamics in melted aluminum with 1000 frames per second and 8 µm resolution per projection using the full dynamical range of our detectors. Since XMPI is a method under development, we also provide different tests for the instrumentation of up to 3000 frames per second. As the high-brilliance of 4th generation light-sources becomes more available, XMPI is a promising technique for current and future X-ray imaging instruments.

Revealing the origins of vortex cavitation in a Venturi tube by high speed X-ray imaging.

Hydrodynamic cavitation is useful in many processing applications, for example, in chemical reactors, water treatment and biochemical engineering. An important type of hydrodynamic cavitation that occurs in a Venturi tube is vortex cavitation known to cause luminescence whose intensity is closely related to the size and number of cavitation events. However, the mechanistic origins of bubbles constituting vortex cavitation remains unclear, although it has been concluded that the pressure fields generated by the cavitation collapse strongly depends on the bubble geometry. The common view is that vortex cavitation consists of numerous small spherical bubbles. In the present paper, aspects of vortex cavitation arising in a Venturi tube were visualized using high-speed X-ray imaging at SPring-8 and European XFEL. It was discovered that vortex cavitation in a Venturi tube consisted of angulated rather than spherical bubbles. The tangential velocity of the surface of vortex cavitation was assessed considering the Rankine vortex model.

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

The high pulse intensity and repetition rate of the European X-ray Free-Electron Laser (EuXFEL) provide superior temporal resolution compared with other X-ray sources. In combination with MHz X-ray microscopy techniques, it offers a unique opportunity to achieve superior contrast and spatial resolution in applications demanding high temporal resolution. In both live 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 X-ray free-electron laser sources hinders the use of standard flat-field normalization methods during MHz X-ray microscopy experiments. Here, an online (i.e. near real-time) dynamic flat-field correction method based on principal component analysis of dynamically evolving flat-field images is presented. The method is used for the normalization of individual X-ray projections and has been implemented as a near real-time analysis tool at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of EuXFEL.

Hard X-ray stereographic microscopy for single-shot differential phase imaging.

The characterisation of fast phenomena at the microscopic scale is required for the understanding of catastrophic responses of materials to loads and shocks, the processing of materials by optical or mechanical means, the processes involved in many key technologies such as additive manufacturing and microfluidics, and the mixing of fuels in combustion. Such processes are usually stochastic in nature and occur within the opaque interior volumes of materials or samples, with complex dynamics that evolve in all three dimensions at speeds exceeding many meters per second. There is therefore a need for the ability to record three-dimensional X-ray movies of irreversible processes with resolutions of micrometers and frame rates of microseconds. Here we demonstrate a method to achieve this by recording a stereo phase-contrast image pair in a single exposure. The two images are combined computationally to reconstruct a 3D model of the object. The method is extendable to more than two simultaneous views. When combined with megahertz pulse trains of X-ray free-electron lasers (XFELs) it will be possible to create movies able to resolve 3D trajectories with velocities of kilometers per second.

Dose-efficient scanning Compton X-ray microscopy.

The highest resolution of images of soft matter and biological materials is ultimately limited by modification of the structure, induced by the necessarily high energy of short-wavelength radiation. Imaging the inelastically scattered X-rays at a photon energy of 60 keV (0.02 nm wavelength) offers greater signal per energy transferred to the sample than coherent-scattering techniques such as phase-contrast microscopy and projection holography. We present images of dried, unstained, and unfixed biological objects obtained by scanning Compton X-ray microscopy, at a resolution of about 70 nm. This microscope was realised using novel wedged multilayer Laue lenses that were fabricated to sub-ångström precision, a new wavefront measurement scheme for hard X rays, and efficient pixel-array detectors. The doses required to form these images were as little as 0.02% of the tolerable dose and 0.05% of that needed for phase-contrast imaging at similar resolution using 17 keV photon energy. The images obtained provide a quantitative map of the projected mass density in the sample, as confirmed by imaging a silicon wedge. Based on these results, we find that it should be possible to obtain radiation damage-free images of biological samples at a resolution below 10 nm.

Dose-efficient multimodal microscopy of human tissue at a hard X-ray nanoprobe beamline.

X-ray fluorescence microscopy performed at nanofocusing synchrotron beamlines produces quantitative elemental distribution maps at unprecedented resolution (down to a few tens of nanometres), at the expense of relatively long measuring times and high absorbed doses. In this work, a method was implemented in which fast low-dose in-line holography was used to produce quantitative electron density maps at the mesoscale prior to nanoscale X-ray fluorescence acquisition. These maps ensure more efficient fluorescence scans and the reduction of the total absorbed dose, often relevant for radiation-sensitive (e.g. biological) samples. This multimodal microscopy approach was demonstrated on human sural nerve tissue. The two imaging modes provide complementary information at a comparable resolution, ultimately limited by the focal spot size. The experimental setup presented allows the user to swap between them in a flexible and reproducible fashion, as well as to easily adapt the scanning parameters during an experiment to fine-tune resolution and field of view.

Shot-to-shot flat-field correction at X-ray free-electron lasers.

X-ray free-electron lasers (XFELs) provide high-brilliance pulses, which offer unique opportunities for coherent X-ray imaging techniques, such as in-line holography. One of the fundamental steps to process in-line holographic data is flat-field correction, which mitigates imaging artifacts and, in turn, enables phase reconstructions. However, conventional flat-field correction approaches cannot correct single XFEL pulses due to the stochastic nature of the self-amplified spontaneous emission (SASE), the mechanism responsible for the high brilliance of XFELs. Here, we demonstrate on simulated and megahertz imaging data, measured at the European XFEL, the possibility of overcoming such a limitation by using two different methods based on principal component analysis and deep learning. These methods retrieve flat-field corrected images from individual frames by separating the sample and flat-field signal contributions; thus, enabling advanced phase-retrieval reconstructions. We anticipate that the proposed methods can be implemented in a real-time processing pipeline, which will enable online data analysis and phase reconstructions of coherent full-field imaging techniques such as in-line holography at XFELs.

X-ray in-line holography and holotomography at the NanoMAX beamline.

Coherent X-ray imaging techniques, such as in-line holography, exploit the high brilliance provided by diffraction-limited storage rings to perform imaging sensitive to the electron density through contrast due to the phase shift, rather than conventional attenuation contrast. Thus, coherent X-ray imaging techniques enable high-sensitivity and low-dose imaging, especially for low-atomic-number (Z) chemical elements and materials with similar attenuation contrast. Here, the first implementation of in-line holography at the NanoMAX beamline is presented, which benefits from the exceptional focusing capabilities and the high brilliance provided by MAX IV, the first operational diffraction-limited storage ring up to approximately 300 eV. It is demonstrated that in-line holography at NanoMAX can provide 2D diffraction-limited images, where the achievable resolution is only limited by the 70 nm focal spot at 13 keV X-ray energy. Also, the 3D capabilities of this instrument are demonstrated by performing holotomography on a chalk sample at a mesoscale resolution of around 155 nm. It is foreseen that in-line holography will broaden the spectra of capabilities of MAX IV by providing fast 2D and 3D electron density images from mesoscale down to nanoscale resolution.

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 available.

PyPhase - a Python package for X-ray phase imaging.

X-ray propagation-based imaging techniques are well established at synchrotron radiation and laboratory sources. However, most reconstruction algorithms for such image modalities, also known as phase-retrieval algorithms, have been developed specifically for one instrument by and for experts, making the development and diffusion of such techniques difficult. Here, PyPhase, a free and open-source package for propagation-based near-field phase reconstructions, which is distributed under the CeCILL license, is presented. PyPhase implements some of the most popular phase-retrieval algorithms in a highly modular framework supporting its deployment on large-scale computing facilities. This makes the integration, the development of new phase-retrieval algorithms, and the deployment on different computing infrastructures straightforward. Its capabilities and simplicity are presented by application to data acquired at the synchrotron source MAX IV (Lund, Sweden).

Low-dose in situ prelocation of protein microcrystals by 2D X-ray phase-contrast imaging for serial crystallography.

Serial protein crystallography has emerged as a powerful method of data collection on small crystals from challenging targets, such as membrane proteins. Multiple microcrystals need to be located on large and often flat mounts while exposing them to an X-ray dose that is as low as possible. A crystal-prelocation method is demonstrated here using low-dose 2D full-field propagation-based X-ray phase-contrast imaging at the X-ray imaging beamline TOMCAT at the Swiss Light Source (SLS). This imaging step provides microcrystal coordinates for automated serial data collection at a microfocus macromolecular crystallography beamline on samples with an essentially flat geometry. This prelocation method was applied to microcrystals of a soluble protein and a membrane protein, grown in a commonly used double-sandwich in situ crystallization plate. The inner sandwiches of thin plastic film enclosing the microcrystals in lipid cubic phase were flash cooled and imaged at TOMCAT. Based on the obtained crystal coordinates, both still and rotation wedge serial data were collected automatically at the SLS PXI beamline, yielding in both cases a high indexing rate. This workflow can be easily implemented at many synchrotron facilities using existing equipment, or potentially integrated as an online technique in the next-generation macromolecular crystallography beamline, and thus benefit a number of dose-sensitive challenging protein targets.

Ptychographic X-ray speckle tracking with multi-layer Laue lens systems.

The ever-increasing brightness of synchrotron radiation sources demands improved X-ray optics to utilize their capability for imaging and probing biological cells, nano-devices and functional matter on the nanometre scale with chemical sensitivity. Hard X-rays are ideal for high-resolution imaging and spectroscopic applications owing to their short wavelength, high penetrating power and chemical sensitivity. The penetrating power that makes X-rays useful for imaging also makes focusing them technologically challenging. Recent developments in layer deposition techniques have enabled the fabrication of a series of highly focusing X-ray lenses, known as wedged multi-layer Laue lenses. Improvements to the lens design and fabrication technique demand an accurate, robust, in situ and at-wavelength characterization method. To this end, a modified form of the speckle tracking wavefront metrology method has been developed. The ptychographic X-ray speckle tracking method is capable of operating with highly divergent wavefields. A useful by-product of this method is that it also provides high-resolution and aberration-free projection images of extended specimens. Three separate experiments using this method are reported, where the ray path angles have been resolved to within 4 nrad with an imaging resolution of 45 nm (full period). This method does not require a high degree of coherence, making it suitable for laboratory-based X-ray sources. Likewise, it is robust to errors in the registered sample positions, making it suitable for X-ray free-electron laser facilities, where beam-pointing fluctuations can be problematic for wavefront metrology.

Singleshot polychromatic coherent diffractive imaging with a high-order harmonic source.

Singleshot polychromatic coherent diffractive imaging is performed with a high-intensity high-order harmonic generation source. The coherence properties are analyzed and several reconstructions show the shot-to-shot fluctuations of the incident beam wavefront. The method is based on a multi-step approach. First, the spectrum is extracted from double-slit diffraction data. The spectrum is used as input to extract the monochromatic sample diffraction pattern, then phase retrieval is performed on the quasi-monochromatic data to obtain the sample's exit surface wave. Reconstructions based on guided error reduction (ER) and alternating direction method of multipliers (ADMM) are compared. ADMM allows additional penalty terms to be included in the cost functional to promote sparsity within the reconstruction.

Ultracompact 3D microfluidics for time-resolved structural biology.

To advance microfluidic integration, we present the use of two-photon additive manufacturing to fold 2D channel layouts into compact free-form 3D fluidic circuits with nanometer precision. We demonstrate this technique by tailoring microfluidic nozzles and mixers for time-resolved structural biology at X-ray free-electron lasers (XFELs). We achieve submicron jets with speeds exceeding 160 m s-1, which allows for the use of megahertz XFEL repetition rates. By integrating an additional orifice, we implement a low consumption flow-focusing nozzle, which is validated by solving a hemoglobin structure. Also, aberration-free in operando X-ray microtomography is introduced to study efficient equivolumetric millisecond mixing in channels with 3D features integrated into the nozzle. Such devices can be printed in minutes by locally adjusting print resolution during fabrication. This technology has the potential to permit ultracompact devices and performance improvements through 3D flow optimization in all fields of microfluidic engineering.

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.

X-ray focusing with efficient high-NA multilayer Laue lenses.

Multilayer Laue lenses are volume diffraction elements for the efficient focusing of X-rays. With a new manufacturing technique that we introduced, it is possible to fabricate lenses of sufficiently high numerical aperture (NA) to achieve focal spot sizes below 10 nm. The alternating layers of the materials that form the lens must span a broad range of thicknesses on the nanometer scale to achieve the necessary range of X-ray deflection angles required to achieve a high NA. This poses a challenge to both the accuracy of the deposition process and the control of the materials properties, which often vary with layer thickness. We introduced a new pair of materials-tungsten carbide and silicon carbide-to prepare layered structures with smooth and sharp interfaces and with no material phase transitions that hampered the manufacture of previous lenses. Using a pair of multilayer Laue lenses (MLLs) fabricated from this system, we achieved a two-dimensional focus of 8.4 × 6.8 nm2 at a photon energy of 16.3 keV with high diffraction efficiency and demonstrated scanning-based imaging of samples with a resolution well below 10 nm. The high NA also allowed projection holographic imaging with strong phase contrast over a large range of magnifications. An error analysis indicates the possibility of achieving 1 nm focusing.

Angiotensin II infusion into ApoE-/- mice: a model for aortic dissection rather than abdominal aortic aneurysm?

AIMS: Angiotensin II-infused ApoE-/- mice are a popular mouse model for preclinical aneurysm research. Here, we provide insight in the often-reported but seldom-explained variability in shape of dissecting aneurysms in these mice. METHODS AND RESULTS: N = 45 excised aortas were scanned ex vivo with phase-contrast X-ray tomographic microscopy. Micro-ruptures were detected near the ostium of celiac and mesenteric arteries in 8/11 mice that were sacrificed after 3 days of angiotensin II-infusion. At later time points (after 10, 18, and 28 days) the variability in shape of thoraco-abdominal lesions (occurring in 31/34 mice) was classified into 7 different categories based on the presence or absence of a medial tear (31/31), an intramural hematoma (23/31) or a false channel (11/23). Medial tears were detected both in the thoracic and the abdominal aorta and were most prevalent at the left and ventral aspects of celiac and mesenteric arteries. The axial length of the hematoma strongly correlated to the total number of ruptured branch ostia (r2 = 0.78) and in 22/23 mice with a hematoma the ostium of the left suprarenal artery had ruptured. Supraceliac diameters at baseline were significantly lower for mice that did not develop an intramural hematoma, and the formation of a false channel within that intramural hematoma depended on the location, rather than the length, of the medial tear. CONCLUSION: Based on our observations we propose an elaborate hypothesis that explains how aortic side branches (i) affect the initiation and propagation of medial tears and the subsequent adventitial dissection and (ii) affect the variability in shape of dissecting aneurysms. This hypothesis was partially validated through the live visualization of a dissecting aneurysm that formed during micro-CT imaging, and led us to the conclusion that angiotensin II-infused mice are more clinically relevant for the study of aortic dissections than for the study of abdominal aortic aneurysms.

Sensitivity-based optimization for the design of a grating interferometer for clinical X-ray phase contrast mammography.

An X-ray grating interferometer (GI) suitable for clinical mammography must comply with quite strict dose, scanning time and geometry limitations, while being able to detect tumors, microcalcifications and other abnormalities. Such a design task is not straightforward, since obtaining optimal phase-contrast and dark-field signals with clinically compatible doses and geometrical constraints is remarkably challenging. In this work, we present a wave propagation based optimization that uses the phase and dark-field sensitivities as figures of merit. This method was used to calculate the optimal interferometer designs for a commercial mammography setup. Its accuracy was validated by measuring the visibility of polycarbonate samples of different thicknesses on a Talbot-Lau interferometer installed on this device and considering some of the most common grating imperfections to be able to reproduce the experimental values. The optimization method outcomes indicate that small grating pitches are required to boost sensitivity in such a constrained setup and that there is a different optimal scenario for each signal type.

Contrast-transfer-function phase retrieval based on compressed sensing.

We report on a new contrast-transfer-function (CTF) phase-retrieval method based on the alternating direction method of multipliers (ADMMs), which allows us to exploit any compressed sensing regularization scheme reflecting the sparsity of the investigated object. The proposed iterative algorithm retrieves accurate phase maps from highly noisy single-distance projection microscopy data and is characterized by a stable convergence, not bounded to the prior knowledge of the object support or to the initialization strategy. Experiments on simulated and real datasets show that ADMM-CTF yields reconstructions with a substantial lower amount of artifacts and enhanced signal-to-noise ratio compared to the standard analytical inversion.

A generalized quantitative interpretation of dark-field contrast for highly concentrated microsphere suspensions.

In X-ray grating interferometry, dark-field contrast arises due to partial extinction of the detected interference fringes. This is also called visibility reduction and is attributed to small-angle scattering from unresolved structures in the imaged object. In recent years, analytical quantitative frameworks of dark-field contrast have been developed for highly diluted monodisperse microsphere suspensions with maximum 6% volume fraction. These frameworks assume that scattering particles are separated by large enough distances, which make any interparticle scattering interference negligible. In this paper, we start from the small-angle scattering intensity equation and, by linking Fourier and real-space, we introduce the structure factor and thus extend the analytical and experimental quantitative interpretation of dark-field contrast, for a range of suspensions with volume fractions reaching 40%. The structure factor accounts for interparticle scattering interference. Without introducing any additional fitting parameters, we successfully predict the experimental values measured at the TOMCAT beamline, Swiss Light Source. Finally, we apply this theoretical framework to an experiment probing a range of system correlation lengths by acquiring dark-field images at different energies. This proposed method has the potential to be applied in single-shot-mode using a polychromatic X-ray tube setup and a single-photon-counting energy-resolving detector.