Imaging of retina cellular and subcellular structures using ptychographic hard X-ray tomography.

Ptychographic hard X-ray computed tomography (PXCT) is a recent method allowing imaging with quantitative electron-density contrast. Here, we imaged, at cryogenic temperature and without sectioning, cellular and subcellular structures of a chemically fixed and stained wild-type mouse retina, including axons and synapses, with complete isotropic 3D information over tens of microns. Comparison with tomograms of degenerative retina from a mouse model of retinitis pigmentosa illustrates the potential of this method for analyzing disease processes like neurodegeneration at sub-200 nm resolution. As a non-destructive imaging method, PXCT is very suitable for correlative imaging. Within the outer plexiform layer containing the photoreceptor synapses, we identified somatic synapses. We used a small region inside the X-ray-imaged sample for further high-resolution focused ion beam/scanning electron microscope tomography. The subcellular structures of synapses obtained with the X-ray technique matched the electron microscopy data, demonstrating that PXCT is a powerful scanning method for tissue volumes of more than 60 cells and sensitive enough for identification of regions as small as 200 nm, which remain available for further structural and biochemical investigations.

Three-dimensional magnetization structures revealed with X-ray vector nanotomography.

In soft ferromagnetic materials, the smoothly varying magnetization leads to the formation of fundamental patterns such as domains, vortices and domain walls. These have been studied extensively in thin films of thicknesses up to around 200 nanometres, in which the magnetization is accessible with current transmission imaging methods that make use of electrons or soft X-rays. In thicker samples, however, in which the magnetization structure varies throughout the thickness and is intrinsically three dimensional, determining the complex magnetic structure directly still represents a challenge. We have developed hard-X-ray vector nanotomography with which to determine the three-dimensional magnetic configuration at the nanoscale within micrometre-sized samples. We imaged the structure of the magnetization within a soft magnetic pillar of diameter 5 micrometres with a spatial resolution of 100 nanometres and, within the bulk, observed a complex magnetic configuration that consists of vortices and antivortices that form cross-tie walls and vortex walls along intersecting planes. At the intersections of these structures, magnetic singularities-Bloch points-occur. These were predicted more than fifty years ago but have so far not been directly observed. Here we image the three-dimensional magnetic structure in the vicinity of the Bloch points, which until now has been accessible only through micromagnetic simulations, and identify two possible magnetization configurations: a circulating magnetization structure and a twisted state that appears to correspond to an 'anti-Bloch point'. Our imaging method enables the nanoscale study of topological magnetic structures in systems with sizes of the order of tens of micrometres. Knowledge of internal nanomagnetic textures is critical for understanding macroscopic magnetic properties and for designing bulk magnets for technological applications.

High-resolution non-destructive three-dimensional imaging of integrated circuits.

Modern nanoelectronics has advanced to a point at which it is impossible to image entire devices and their interconnections non-destructively because of their small feature sizes and the complex three-dimensional structures resulting from their integration on a chip. This metrology gap implies a lack of direct feedback between design and manufacturing processes, and hampers quality control during production, shipment and use. Here we demonstrate that X-ray ptychography-a high-resolution coherent diffractive imaging technique-can create three-dimensional images of integrated circuits of known and unknown designs with a lateral resolution in all directions down to 14.6 nanometres. We obtained detailed device geometries and corresponding elemental maps, and show how the devices are integrated with each other to form the chip. Our experiments represent a major advance in chip inspection and reverse engineering over the traditional destructive electron microscopy and ion milling techniques. Foreseeable developments in X-ray sources, optics and detectors, as well as adoption of an instrument geometry optimized for planar rather than cylindrical samples, could lead to a thousand-fold increase in efficiency, with concomitant reductions in scan times and voxel sizes.

Environmental control for X-ray nanotomography.

The acquisition speed and spatial resolution of X-ray nanotomography have continuously improved over the last decades. Coherent diffraction-based techniques breach the 10 nm resolution barrier frequently and thus pose stringent demands on sample positioning accuracy and stability. At the same time there is an increasing desire to accommodate in situ or operando measurements. Here, an environmental control system for X-ray nanotomography is introduced to regulate the temperature of a sample from room temperature up to 850°C in a controlled atmospheric composition. The system allows for a 360° sample rotation, permitting tomographic studies in situ or operando free of missing wedge constraints. The system is implemented and available at the flOMNI microscope at the Swiss Light Source. In addition to the environmental control system itself, the related modifications of flOMNI are described. Tomographic measurements of a nanoporous gold sample at 50°C and 600°C at a resolution of sub-20 nm demonstrate the performance of the device.

From 2D STXM to 3D Imaging: Soft X-ray Laminography of Thin Specimens.

X-ray tomography has become an indispensable tool for studying complex 3D interior structures with high spatial resolution. Three-dimensional imaging using soft X-rays offers powerful contrast mechanisms but has seen limited success with tomography due to the restrictions imposed by the much lower energy of the probe beam. The generalized geometry of laminography, characterized by a tilted axis of rotation, provides nm-scale 3D resolution for the investigation of extended (mm range) but thin (µm to nm) samples that are well suited to soft X-ray studies. This work reports on the implementation of soft X-ray laminography (SoXL) at the scanning transmission X-ray spectromicroscope of the PolLux beamline at the Swiss Light Source, Paul Scherrer Institut, which enables 3D imaging of extended specimens from 270 to 1500 eV. Soft X-ray imaging provides contrast mechanisms for both chemical sensitivity to molecular bonds and oxidation states and magnetic dichroism due to the much stronger attenuation of X-rays in this energy range. The presented examples of applications range from functionalized nanomaterials to biological photonic crystals and sophisticated nanoscaled magnetic domain patterns, thus illustrating the wide fields of research that can benefit from SoXL.

LamNI - an instrument for X-ray scanning microscopy in laminography geometry.

Across all branches of science, medicine and engineering, high-resolution microscopy is required to understand functionality. Although optical methods have been developed to `defeat' the diffraction limit and produce 3D images, and electrons have proven ever more useful in creating pictures of small objects or thin sections, so far there is no substitute for X-ray microscopy in providing multiscale 3D images of objects with a single instrument and minimal labeling and preparation. A powerful technique proven to continuously access length scales from 10 nm to 10 µm is ptychographic X-ray computed tomography, which, on account of the orthogonality of the tomographic rotation axis to the illuminating beam, still has the limitation of necessitating pillar-shaped samples of small (ca 10 µm) diameter. Large-area planar samples are common in science and engineering, and it is therefore highly desirable to create an X-ray microscope that can examine such samples without the extraction of pillars. Computed laminography, where the axis of rotation is not perpendicular to the illumination direction, solves this problem. This entailed the development of a new instrument, LamNI, dedicated to high-resolution 3D scanning X-ray microscopy via hard X-ray ptychographic laminography. Scanning precision is achieved by a dedicated interferometry scheme and the instrument covers a scan range of 12 mm × 12 mm with a position stability of 2 nm and positioning errors below 5 nm. A new feature of LamNI is a pair of counter-rotating stages carrying the sample and interferometric mirrors, respectively.

A lathe system for micrometre-sized cylindrical sample preparation at room and cryogenic temperatures.

A simple two-spindle based lathe system for the preparation of cylindrical samples intended for X-ray tomography is presented. The setup can operate at room temperature as well as under cryogenic conditions, allowing the preparation of samples down to 20 and 50 µm in diameter, respectively, within minutes. Case studies are presented involving the preparation of a brittle biomineral brachiopod shell and cryogenically fixed soft brain tissue, and their examination by means of ptychographic X-ray computed tomography reveals the preparation method to be mainly free from causing artefacts. Since this lathe system easily yields near-cylindrical samples ideal for tomography, a usage for a wide variety of otherwise challenging specimens is anticipated, in addition to potential use as a time- and cost-saving tool prior to focused ion-beam milling. Fast sample preparation becomes especially important in relation to shorter measurement times expected in next-generation synchrotron sources.

Hierarchical Structure of NiMo Hydrodesulfurization Catalysts Determined by Ptychographic X-Ray Computed Tomography.

Hydrodesulphurization, the removal of sulphur from crude oils, is an essential catalytic process in the petroleum industry safeguarding the production of clean hydrocarbons. Sulphur removal is critical for the functionality of downstream processes and vital to the elimination of environmental pollutants. The effectiveness of such an endeavour is among other factors determined by the structural arrangement of the heterogeneous catalyst. Namely, the accessibility of the catalytically active molybdenum disulphide (MoS2 ) slabs located on the surfaces of a porous alumina carrier. Here, we examined a series of pristine sulfided Mo and NiMo hydrodesulphurization catalysts of increasing metal loading prepared on commercial alumina carriers using ptychographic X-ray computed nanotomography. Structural analysis revealed a build consisting of two interwoven support matrix elements differing in nanoporosity. With increasing metal loading, approaching that of industrial catalysts, these matrix elements exhibit a progressively dissimilar MoS2 surface coverage as well as MoS2 cluster formation at the matrix element boundaries. This is suggestive of metal deposition limitations and/ or catalyst activation and following prohibitive of optimal catalytic utilization. These results will allow for diffusivity calculations, a better rationale of current generation catalyst performance as well as a better distribution of the active phase in next-generation hydrodesulphurization catalysts.

Fast positioning for X-ray scanning microscopy by a combined motion of sample and beam-defining optics.

Scanning X-ray microscopy such as X-ray ptychography requires accurate and fast positioning of samples in the X-ray beam. Sample stages often have a high mobile mass as they may carry additional mechanics or mirrors for position measurements. The high mobile mass of a piezo stage can introduce vibrations in the setup that will lead to imaging quality deterioration. Sample stages also require a large travel range which results in a slow positioning step response and thus high positioning overhead. Moving lightweight X-ray optics, such as focusing Fresnel zone plates, instead of the sample can improve the situation but it may lead to undesired variations in the illumination probe which may result in reconstruction artifacts. This paper presents a combined approach in which a slow sample stage mechanism covers the long distance range for a large field of view, and a light-weight optics scanner with a small travel range creates a superimposed motion to achieve a fast step response. The step response in the ptychographic tomography instrument used was thereby improved by an order of magnitude, allowing for efficient measurement without loss of imaging quality.

Alignment methods for nanotomography with deep subpixel accuracy.

As the resolution of X-ray tomography improves, the limited long-term stability and accuracy of nanoimaging tools does not allow computing artifact-free three-dimensional (3D) reconstructions without an additional step of numerical alignment of the measured projections. However, the common iterative alignment methods are significantly more computationally demanding than a simple tomographic reconstruction of the acquired volume. Here, we address this issue and present an alignment toolkit, which exploits methods with deep-subpixel accuracy combined with a multi-resolution scheme. This leads to robust and accurate alignment with significantly reduced computational and memory requirements. The performance of the presented methods is demonstrated on simulated and measured datasets for tomography and also laminography acquisition geometries. A GPU accelerated implementation of our alignment framework is publicly available.

Towards optimized illumination for high-resolution ptychography.

We present a systematic study, where effects of the illumination probe design on ptychography reconstruction quality are evaluated under well-controlled conditions. The illumination probe was created using Fresnel zone-plate (FZP) optics with locally displaced zones to provide a fine control over perturbations of the illumination wavefront. We show that optimally designed wavefront modulations not only reduce bias and variance in the reconstruction of the lowest spatial frequencies but also lead to improved imaging resolution and reduction of artefacts compared to a conventional FZP. Both these factors are important for quantitative accuracy and resolution of ptychographic tomography. Our work furthers the understanding of the important characteristics of an optimal illumination for high-resolution X-ray ptychography and how to design optimal FZP wavefront modulations for different applications of ptychographic imaging. These findings are applicable and relevant for ptychography using optical, EUV, and X-ray photons as well as electrons.

Arbitrary-path fly-scan ptychography.

Ptychography is a coherent diffractive imaging method that can provide a diffraction-limited, robust reconstruction of the sample's complex transmission function without the use of high-quality optics. However, the scanning nature of conventional X-ray ptychography unavoidably requires the mechanical motion of either the illumination probe or the sample. In order to avoid overhead related to breaking and acceleration for every scan position, so-called fly-scan methods were developed. Here, we present an improved variant that removes the limitation of continuous scanning along a linear scanning path and allows for ptychographic reconstruction of scans taken along an arbitrary 2D continuous trajectory. We also demonstrate numerically and experimentally that our method provides significantly improved robustness against noise, particularly for larger fly-scan steps, i.e. sample shift during an exposure, which will gain importance with the advent of 4th generation synchrotron sources, where the available coherent flux may be increased by orders of magnitude. Finally, we show that the use of a spiral scan continuous trajectory alleviates significantly raster grid artifacts.

Three-Dimensional Nanometer Features of Direct Current Electrical Trees in Low-Density Polyethylene.

Electrical trees are one reason for the breakdown of insulating materials in electrical power systems. An understanding of the growth of electrical trees plays a crucial role in the development of reliable high voltage direct current (HVDC) power grid systems with transmission voltages up to 1 MV. A section that contained an electrical tree in low-density polyethylene (LDPE) has been visualized in three dimensions (3D) with a resolution of 92 nm by X-ray ptychographic tomography. The 3D imaging revealed prechannel-formations with a lower density with the width of a couple of hundred nanometers formed around the main branch of the electrical tree. The prechannel structures were partially connected with the main tree via paths through material with a lower density, proving that the tree had grown in a step-by-step manner via the prestep structures formed in front of the main channels. All the prechannel structures had a size well below the limit of the Paschen law and were thus not formed by partial discharges. Instead, it is suggested that the prechannel structures were formed by electro-mechanical stress and impact ionization, where the former was confirmed by simulations to be a potential explanation with electro-mechanical stress tensors being almost of the same order of magnitude as the short-term modulus of low-density polyethylene.

High-acceptance versatile microfocus module based on elliptical Fresnel zone plates for small-angle X-ray scattering.

High-efficiency microfocusing of multi-keV X-rays at synchrotron sources is highly profitable for spatially resolved structural analysis of many kinds. Because radiation from synchrotron sources is typically elongated along the horizontal dimension, generating a microbeam that is isotropic in size requires a carefully designed optics system. Here we report on using a combination of a horizontally tunable slit downstream of the undulator source with elliptical diffractive Fresnel zone plates. We demonstrate the arrangement in context of small-angle X-ray scattering experiments, obtaining a microbeam of 2.2 µm × 1.8 µm (X × Y) with a flux of 1.2 × 1010 photons/s at an energy of 11.2 keV at the sample position.

Internal structure of sponge glass fiber revealed by ptychographic nanotomography.

Sponge glass spicules have solicited great interest due to their mechanical and optical properties. Herein we use ptychographic nanotomography to obtain detailed insights into the internal structure of an anchor spicule from the Venus flower basket. The obtained dataset has 90nm resolution in 3D and provides quantitative determination of the electron density. The data reveal significant variations in electron density across the spicule. The central organic filament is found to be slightly but significantly displaced from the spicule central axis. Analysis of the electron density affords an estimate of a protein volume fraction in the organic filament of about 70%. In the highly mineralized part of the spicule, the electron density is seen to display circular symmetry and be neigh independent of position along the spicule long axis. Variations in the electron density beyond those included in current models of spicule mechanics are observed.

Three-dimensional mass density mapping of cellular ultrastructure by ptychographic X-ray nanotomography.

We demonstrate absolute quantitative mass density mapping in three dimensions of frozen-hydrated biological matter with an isotropic resolution of 180 nm. As model for a biological system we use Chlamydomonas cells in buffer solution confined in a microcapillary. We use ptychographic X-ray computed tomography to image the entire specimen, including the 18 µm-diameter capillary, thereby providing directly an absolute mass density measurement of biological matter with an uncertainty of about 6%. The resulting maps have sufficient contrast to distinguish cells from the surrounding ice and several organelles of different densities inside the cells. Organelles are identified by comparison with a stained, resin-embedded specimen, which can be compared with established transmission electron microscopy results. For some identified organelles, the knowledge of their elemental composition reduces the uncertainty of their mass density measurement down to 1% with values consistent with previous measurements of dry weight concentrations in thin cellular sections by scanning transmission electron microscopy. With prospects of improving the spatial resolution in the near future, we expect that the capability of non-destructive three-dimensional mapping of mass density in biological samples close to their native state becomes a valuable method for measuring the packing of organic matter on the nanoscale.

Critical appraisal of tubular putative eumetazoans from the Ediacaran Weng'an Doushantuo biota.

Molecular clock analyses estimate that crown-group animals began diversifying hundreds of millions of years before the start of the Cambrian period. However, the fossil record has not yielded unequivocal evidence for animals during this interval. Some of the most promising candidates for Precambrian animals occur in the Weng'an biota of South China, including a suite of tubular fossils assigned to Sinocyclocyclicus, Ramitubus, Crassitubus and Quadratitubus, that have been interpreted as soft-bodied eumetazoans comparable to tabulate corals. Here, we present new insights into the anatomy, original composition and phylogenetic affinities of these taxa based on data from synchrotron radiation X-ray tomographic microscopy, ptychographic nanotomography, scanning electron microscopy and electron probe microanalysis. The patterns of deformation observed suggest that the cross walls of Sinocyclocyclicus and Quadratitubus were more rigid than those of Ramitubus and Crassitubus. Ramitubus and Crassitubus specimens preserve enigmatic cellular clusters at terminal positions in the tubes. Specimens of Sinocyclocyclicus and Ramitubus have biological features that might be cellular tissue or subcellular structures filling the spaces between the cross walls. These observations are incompatible with a cnidarian interpretation, in which the spaces between cross walls are abandoned parts of the former living positions of the polyp. The affinity of the Weng'an tubular fossils may lie within the algae.

Element-specific X-ray phase tomography of 3D structures at the nanoscale.

Recent advances in fabrication techniques to create mesoscopic 3D structures have led to significant developments in a variety of fields including biology, photonics, and magnetism. Further progress in these areas benefits from their full quantitative and structural characterization. We present resonant ptychographic tomography, combining quantitative hard x-ray phase imaging and resonant elastic scattering to achieve ab initio element-specific 3D characterization of a cobalt-coated artificial buckyball polymer scaffold at the nanoscale. By performing ptychographic x-ray tomography at and far from the Co K edge, we are able to locate and quantify the Co layer in our sample to a 3D spatial resolution of 25 nm. With a quantitative determination of the electron density we can determine that the Co layer is oxidized, which is confirmed with microfluorescence experiments.

Mass density and water content of saturated never-dried calcium silicate hydrates.

Calcium silicate hydrates (C-S-H) are the most abundant hydration products in ordinary Portland cement paste. Yet, despite the critical role they play in determining mechanical and transport properties, there is still a debate about their density and exact composition. Here, the site-specific mass density and composition of C-S-H in hydrated cement paste are determined with nanoscale resolution in a nondestructive approach. We used ptychographic X-ray computed tomography in order to determine spatially resolved mass density and water content of the C-S-H within the microstructure of the cement paste. Our findings indicate that the C-S-H at the border of hydrated alite particles possibly have a higher density than the apparent inner-product C-S-H, which is contrary to the common expectations from previous works on hydrated cement paste.

High-throughput ptychography using Eiger: scanning X-ray nano-imaging of extended regions.

The smaller pixel size and high frame rate of next-generation photon counting pixel detectors opens new opportunities for the application of X-ray coherent diffractive imaging (CDI). In this manuscript we demonstrate fast image acquisition for ptychography using an Eiger detector. We achieve above 25,000 resolution elements per second, or an effective dwell time of 40 µs per resolution element, when imaging a 500 µm × 290 µm region of an integrated electronic circuit with 41 nm resolution. We further present the application of a scheme of sharing information between image parts that allows the field of view to exceed the range of the piezoelectric scanning system and requirements on the stability of the illumination to be relaxed.