Visualization of protein crystals by high-energy phase-contrast X-ray imaging

Studies of Fractal Microstructure in Nanocarbon Polymer Composites

The in situ study of fractal microstructure in nanocarbon polymers is an actual task for their application and for the improvement in their functional properties. This article presents a visualization of the bulk structural features of the composites using pulsed acoustic microscopy and synchrotron X-ray microtomography. This article presents details of fractal structure formation using carbon particles of different sizes and shapes-exfoliated graphite, carbon platelets and nanotubes. Individual structural elements of the composite, i.e., conglomerations of the particles in the air capsule as well as their distribution in the composite volume, were observed at the micro- and nanoscale. We have considered the influence of particle architecture on the fractal formation and elastic properties of the composite. Acoustic and X-ray imaging results were compared to validate the carbon agglomeration.

High Throughput Tomography (HiTT) on EMBL beamline P14 on PETRA III

Here, high-throughput tomography (HiTT), a fast and versatile phase-contrast imaging platform for life-science samples on the EMBL beamline P14 at DESY in Hamburg, Germany, is presented. A high-photon-flux undulator beamline is used to perform tomographic phase-contrast acquisition in about two minutes which is linked to an automated data processing pipeline that delivers a 3D reconstructed data set less than a minute and a half after the completion of the X-ray scan. Combining this workflow with a sophisticated robotic sample changer enables the streamlined collection and reconstruction of X-ray imaging data from potentially hundreds of samples during a beam-time shift. HiTT permits optimal data collection for many different samples and makes possible the imaging of large sample cohorts thus allowing population studies to be attempted. The successful application of HiTT on various soft tissue samples in both liquid (hydrated and also dehydrated) and paraffin-embedded preparations is demonstrated. Furthermore, the feasibility of HiTT to be used as a targeting tool for volume electron microscopy, as well as using HiTT to study plant morphology, is demonstrated. It is also shown how the high-throughput nature of the work has allowed large numbers of `identical' samples to be imaged to enable statistically relevant sample volumes to be studied.

Towards virtual histology with X-ray grating interferometry

Breast cancer is the most common type of cancer worldwide. Diagnosing breast cancer relies on clinical examination, imaging and biopsy. A core-needle biopsy enables a morphological and biochemical characterization of the cancer and is considered the gold standard for breast cancer diagnosis. A histopathological examination uses high-resolution microscopes with outstanding contrast in the 2D plane, but the spatial resolution in the third, Z-direction, is reduced. In the present paper, we propose two high-resolution table-top systems for phase-contrast X-ray tomography of soft-tissue samples. The first system implements a classical Talbot-Lau interferometer and allows to perform ex-vivo imaging of human breast samples with a voxel size of 5.57 μm. The second system with a comparable voxel size relies on a Sigray MAAST X-ray source with structured anode. For the first time, we demonstrate the applicability of the latter to perform X-ray imaging of human breast specimens with ductal carcinoma in-situ. We assessed image quality of both setups and compared it to histology. We showed that both setups made it possible to target internal features of breast specimens with better resolution and contrast than previously achieved, demonstrating that grating-based phase-contrast X-ray CT could be a complementary tool for clinical histopathology.

Methods of Coherent X-Ray Diffraction Imaging

Abstract

Methods of coherent X-ray diffraction imaging of the spatial structure of noncrystalline objects and nanocrystals (nanostructures) are considered. Particular attention is paid to the methods of scanning-based coherent diffraction imaging (ptychography), visualization based on coherent surface scattering with application of correlation spectroscopy approaches, and specific features of visualization using X-ray free-electron laser radiation. The corresponding data in the literature are analyzed to demonstrate the state of the art of the methods of coherent diffraction imaging and fields of their application.

Profiling cellular diversity in sponges informs animal cell type and nervous system evolution

[Figure: see text].

Coherent X-ray beam expander based on a multilens interferometer

A coherent X-ray beam expander based on a multilens interferometer is proposed in this paper. The multilens interferometer allows efficient generation of a highly diverging coherent beam up to several milliradians in the hard X-ray energy range. The optical properties of the interferometer were experimentally demonstrated at the ESRF ID13 undulator beamline (Grenoble, France), using 12.4 keV X-rays. The beam expander allowed us to control the angular size and photon flux density of the formed beam and enabled operation in both coherent and incoherent modes. The experimental results were fully consistent with the theoretical concepts and appropriate computer simulations. Future design improvements and related applications are also discussed.

Connecting structure and function from organisms to molecules in small-animal symbioses through chemo-histo-tomography

Our understanding of metabolic interactions between small symbiotic animals and bacteria or parasitic eukaryotes that reside within their bodies is extremely limited. This gap in knowledge originates from a methodological challenge, namely to connect histological changes in host tissues induced by beneficial and parasitic (micro)organisms to the underlying metabolites. We addressed this challenge and developed chemo-histo-tomography (CHEMHIST), a culture-independent approach to connect anatomic structure and metabolic function in millimeter-sized symbiotic animals. CHEMHIST combines chemical imaging of metabolites based on mass spectrometry imaging (MSI) and microanatomy-based micro-computed X-ray tomography (micro-CT) on the same animal. Both high-resolution MSI and micro-CT allowed us to correlate the distribution of metabolites to the same animal's three-dimensional (3D) histology down to submicrometer resolutions. Our protocol is compatible with tissue-specific DNA sequencing and fluorescence in situ hybridization for the taxonomic identification and localization of the associated micro(organisms). Building CHEMHIST upon in situ imaging, we sampled an earthworm from its natural habitat and created an interactive 3D model of its physical and chemical interactions with bacteria and parasitic nematodes in its tissues. Combining MSI and micro-CT, we present a methodological groundwork for connecting metabolic and anatomic phenotypes of small symbiotic animals that often represent keystone species for ecosystem functioning.

X-ray tomographic reconstruction and segmentation pipeline for the long-wavelength macromolecular crystallography beamline at Diamond Light Source

In this paper a practical solution for the reconstruction and segmentation of low-contrast X-ray tomographic data of protein crystals from the long-wavelength macromolecular crystallography beamline I23 at Diamond Light Source is provided. The resulting segmented data will provide the path lengths through both diffracting and non-diffracting materials as basis for analytical absorption corrections for X-ray diffraction data taken in the same sample environment ahead of the tomography experiment. X-ray tomography data from protein crystals can be difficult to analyse due to very low or absent contrast between the different materials: the crystal, the sample holder and the surrounding mother liquor. The proposed data processing pipeline consists of two major sequential operations: model-based iterative reconstruction to improve contrast and minimize the influence of noise and artefacts, followed by segmentation. The segmentation aims to partition the reconstructed data into four phases: the crystal, mother liquor, loop and vacuum. In this study three different semi-automated segmentation methods are experimented with by using Gaussian mixture models, geodesic distance thresholding and a novel morphological method, RegionGrow, implemented specifically for the task. The complete reconstruction-segmentation pipeline is integrated into the MPI-based data analysis and reconstruction framework Savu, which is used to reduce computation time through parallelization across a computing cluster and makes the developed methods easily accessible.

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.

Diamond refractive micro-lenses for full-field X-ray imaging and microscopy produced with ion beam lithography

We demonstrate that ion-beam lithography can be applied to the fabrication of rotationally parabolic refractive diamond X-ray micro-lenses that are of interest to the field of high-resolution X-ray focusing and microscopy. Three single half-lenses with curvature radii of 4.8 µm were produced and stacked to form a compound refractive lens, which provided diffraction-limited focusing of X-ray radiation at the P14 beamline of PETRA-III (DESY). As shown with SEM, the lenses are free of expressed low- and high-frequency shape modulations with a figure error of < 200 nm and surface roughness of 30 nm. Precise micro-manipulation and stacking of individual lenses are demonstrated, which opens up new opportunities for compact X-ray microscopy with nanometer resolution.