Alignment methods for nanotomography with deep subpixel accuracy

Reconstructing Three-Dimensional Optical Anisotropy with Tomographic Müller-Polarimetric Microscopy

Most visible light imaging methods using polarization to obtain ultrastructure information are limited to 2D analysis or require demanding phase measurements to be extended to 3D. A novel 3D polarized light imaging technique based on Müller-matrix formulations is introduced which numerically reconstructs 3D optical birefringence, that is anisotropic refractive indices and optical axis orientation, in each volumetric unit of sample. The new method is demonstrated, tomographic Müller-polarimetric microscopy, in simulation and using experimental data of 3D macroscopic sample of human trabecular bone sample, where the local main orientation of nanoscale collagen fibers is extracted with a resolution of ≈ 20 µm. Tomographic Müller-polarimetric microscopy offers a low-cost and experimentally simple imaging approach to access the ultrastructure which is not directly resolvable, in a wide range of biological and composite materials.

Cretaceous Chert-Hosted Microfossils Visualized With Synchrotron Ptychographic X-Ray Computed Tomography (PXCT)

Silicification of microfossils is an important taphonomic process that provides a record of microbial life across a range of environments throughout Earth history. However, questions remain regarding the mechanism(s) by which silica precipitated and preserved delicate organic material and detailed cellular morphologies. Constraining the different mechanisms of silica precipitation and identifying the common factors that allow for microfossil preservation is the key to understanding ancient microbial communities and fossil-preserving mechanisms. Here, we use synchrotron ptychographic X-ray computed tomography (PXCT) as a novel technique to analyze microfossils from the Cretaceous Barra Velha Formation and better characterize their diverse morphologies and preservation styles. Through this technique, we generate 2D and 3D reconstructions that illustrate the microfossils and silica-organic textures at nanometer resolution. At this resolution, we identify previously uncharacterized silica textures and organic-silica relationships that help us relate findings from modern silicifying environments and experimental work to the fossil record. Additionally, we identify primary morphological differences among the microfossils as well as preservational variability that may have been driven by physiological and/or biochemical differences between the different organisms that inhabited the Cretaceous pre-salt basin. These findings help us to better characterize the diversity and complexity of the microbiota in this ancient basin as well as taphonomic processes and biases that may have driven microfossil preservation in this and other silicifying environments throughout Earth history.

Physical exercise impacts bone remodeling around bio-resorbable magnesium implants

Physical exercise has been shown to induce positive reactions in bone healing but next to nothing is known about how it affects the nanostructure, in particular around implants. In this study, we established this link by using small-angle X-ray scattering tensor tomography (SASTT) to investigate nanostructural parameters in 3D such as mineral particle orientation and thickness. As a model system, rat femoral bone with a bio-resorbable implant (ultra-high purity magnesium) was used. One-half of the rats underwent treadmill exercise while the other half were moving freely in a cage. At two- and six-weeks post-surgery, rats were sacrificed, and samples were taken. Our results point to an earlier start and stronger remodeling when physical exercise is applied and to a stronger reorientation of the mineralized collagen fibers around the implant. This study reveals the nanostructural response of bone with bio-resorbable implants to physical exercise. Understanding this response is very important for designing post-surgery treatments. STATEMENT OF SIGNIFICANCE: Physical exercise is known to have beneficial effects on the human body and is often incorporated into the recovery process following orthopedic surgeries. While the response of bone to physical exercise is well-documented, the structural response of bone to early exercise after implant placement, particularly its impact on the nanostructure, has not been extensively studied. In this study, we identify the effects of physical exercise on the bone nanostructure and the remodeling process around a bioresorbable implant. These findings could help develop tailored physical exercise strategies for post-surgery recovery in patients.

X-ray linear dichroic tomography of crystallographic and topological defects

The functionality of materials is determined by their composition1-4 and microstructure, that is, the distribution and orientation of crystalline grains, grain boundaries and the defects within them5,6. Until now, characterization techniques that map the distribution of grains, their orientation and the presence of defects have been limited to surface investigations, to spatial resolutions of a few hundred nanometres or to systems of thickness around 100 nm, thus requiring destructive sample preparation for measurements and preventing the study of system-representative volumes or the investigation of materials under operational conditions7-15. Here we present X-ray linear dichroic orientation tomography (XL-DOT), a quantitative, non-invasive technique that allows for an intragranular and intergranular characterization of extended polycrystalline and non-crystalline16 materials in three dimensions. We present the detailed characterization of a polycrystalline sample of vanadium pentoxide (V2O5), a key catalyst in the production of sulfuric acid17. We determine the nanoscale composition, microstructure and crystal orientation throughout the polycrystalline sample with 73 nm spatial resolution. We identify and characterize grains, as well as twist, tilt and twin grain boundaries. We further observe the creation and annihilation of topological defects promoted by the presence of volume crystallographic defects. The non-destructive and spectroscopic nature of our method opens the door to operando combined chemical and microstructural investigations11,18 of functional materials, including energy, mechanical and quantum materials.

ssc-cdi: A Memory-Efficient, Multi-GPU Package for Ptychography with Extreme Data

We introduce ssc-cdi, an open-source software package from the Sirius Scientific Computing family, designed for memory-efficient, single-node multi-GPU ptychography reconstruction. ssc-cdi offers a range of reconstruction engines in Python version 3.9.2 and C++/CUDA. It aims at developing local expertise and customized solutions to meet the specific needs of beamlines and user community of the Brazilian Synchrotron Light Laboratory (LNLS). We demonstrate ptychographic reconstruction of beamline data and present benchmarks for the package. Results show that ssc-cdi effectively handles extreme datasets typical of modern X-ray facilities without significantly compromising performance, offering a complementary approach to well-established packages of the community and serving as a robust tool for high-resolution imaging applications.

Dynamic sparse x-ray nanotomography reveals ionomer hydration mechanism in polymer electrolyte fuel-cell catalyst

Tomographic imaging of time-evolving samples is a challenging yet important task for various research fields. At the nanoscale, current approaches face limitations of measurement speed or resolution due to lengthy acquisitions. We developed a dynamic nanotomography technique based on sparse dynamic imaging and 4D tomography modeling. We demonstrated the technique, using ptychographic x-ray computed tomography as its imaging modality, on resolving the in situ hydration process of polymer electrolyte fuel cell (PEFC) catalyst. The technique provides a 40-time increase in temporal resolution compared to conventional approaches, yielding 28 nm half-period spatial and 12 min temporal resolution. The results allow a quantitative characterization of the water intake process inside PEFC catalysts with nanoscale resolution, which is crucial for understanding their electrochemical mechanisms and optimizing their performance. Our technique enables high-speed operando nanotomography studies and paves the way for wider application of dynamic tomography at the nanoscale.

Block Copolymer-Directed Single-Diamond Hybrid Structures Derived from X-ray Nanotomography

Block copolymers are recognized as a valuable platform for creating nanostructured materials. Morphologies formed by block copolymer self-assembly can be transferred into a wide range of inorganic materials, enabling applications including energy storage and metamaterials. However, imaging of the underlying, often complex, nanostructures in large volumes has remained a challenge, limiting progress in materials development. Taking advantage of recent advances in X-ray nanotomography, we noninvasively imaged exceptionally large volumes of nanostructured hybrid materials at high resolution, revealing a single-diamond morphology in a triblock terpolymer-gold composite network. This morphology, which is ubiquitous in nature, has so far remained elusive in block copolymer-derived materials, despite its potential to create materials with large photonic bandgaps. The discovery was made possible by the precise analysis of distortions in a large volume of the self-assembled diamond network, which are difficult to unambiguously assess using traditional characterization tools. We anticipate that high-resolution X-ray nanotomography, which allows imaging of much larger sample volumes than electron-based tomography, will become a powerful tool for the quantitative analysis of complex nanostructures and that structures such as the triblock terpolymer-directed single diamond will enable the generation of advanced multicomponent composites with hitherto unknown property profiles.

Morphology of Copper Nanofoams for Radiation Hydrodynamics and Fusion Applications Investigated by 3D Ptychotomography

The performance of metal and polymer foams used in inertial confinement fusion (ICF), inertial fusion energy (IFE), and high-energy-density (HED) experiments is currently limited by our understanding of their nanostructure and its variation in bulk material. We utilized an X-ray-free electron laser (XFEL) together with lensless X-ray imaging techniques to probe the 3D morphology of copper foams at nanoscale resolution (28 nm). The observed morphology of the thin shells is more varied than expected from previous characterizations, with a large number of them distorted, merged, or open, and a targeted mass density 14% less than calculated. This nanoscale information can be used to directly inform and improve foam modeling and fabrication methods to create a tailored material response for HED experiments.

High-performance 4-nm-resolution X-ray tomography using burst ptychography

Advances in science, medicine and engineering rely on breakthroughs in imaging, particularly for obtaining multiscale, three-dimensional information from functional systems such as integrated circuits or mammalian brains. Achieving this goal often requires combining electron- and photon-based approaches. Whereas electron microscopy provides nanometre resolution through serial, destructive imaging of surface layers1, ptychographic X-ray computed tomography2 offers non-destructive imaging and has recently achieved resolutions down to seven nanometres for a small volume3. Here we implement burst ptychography, which overcomes experimental instabilities and enables much higher performance, with 4-nanometre resolution at a 170-times faster acquisition rate, namely, 14,000 resolution elements per second. Another key innovation is tomographic back-propagation reconstruction4, allowing us to image samples up to ten times larger than the conventional depth of field. By combining the two innovations, we successfully imaged a state-of-the-art (seven-nanometre node) commercial integrated circuit, featuring nanostructures made of low- and high-density materials such as silicon and metals, which offer good radiation stability and contrast at the selected X-ray wavelength. These capabilities enabled a detailed study of the chip's design and manufacturing, down to the level of individual transistors. We anticipate that the combination of nanometre resolution and higher X-ray flux at next-generation X-ray sources will have a revolutionary impact in fields ranging from electronics to electrochemistry and neuroscience.

Unveiling Challenging Microbial Fossil Biosignatures from Rio Tinto with Micro-to-Nanoscale Chemical and Ultrastructural Imaging

Understanding the nature and preservation of microbial traces in extreme environments is crucial for reconstructing Earth's early biosphere and for the search for life on other planets or moons. At Rio Tinto, southwestern Spain, ferric oxide and sulfate deposits similar to those discovered at Meridiani Planum, Mars, entomb a diversity of fossilized organisms, despite chemical conditions commonly thought to be challenging for life and fossil preservation. Investigating this unique fossil microbiota can elucidate ancient extremophile communities and the preservation of biosignatures in acidic environments on Earth and, potentially, Mars. In this study, we use an innovative multiscale approach that combines the state-of-the-art synchrotron X-ray nanoimaging methods of ptychographic X-ray computed laminography and nano-X-ray fluorescence to reveal Rio Tinto's microfossils at subcellular resolution. The unprecedented nanoscale views of several different specimens within their geological and geochemical contexts reveal novel intricacies of preserved microbial communities. Different morphotypes, ecological interactions, and possible taxonomic affinities were inferred based on qualitative and quantitative 3D ultrastructural information, whereas diagenetic processes and metabolic affinities were inferred from complementary chemical information. Our integrated nano-to-microscale analytical approach revealed previously invisible microbial and mineral interactions, which complemented and filled a gap of spatial resolution in conventional methods. Ultimately, this study contributes to the challenge of deciphering the faint chemical and morphological biosignatures that can indicate life's presence on the early Earth and on distant worlds.

3D imaging of magnetic domains in Nd2Fe14B using scanning hard X-ray nanotomography

Nanoscale structural and electronic heterogeneities are prevalent in condensed matter physics. Investigating these heterogeneities in 3D has become an important task for understanding material properties. To provide a tool to unravel the connection between nanoscale heterogeneity and macroscopic emergent properties in magnetic materials, scanning transmission X-ray microscopy (STXM) is combined with X-ray magnetic circular dichroism. A vector tomography algorithm has been developed to reconstruct the full 3D magnetic vector field without any prior noise assumptions or knowledge about the sample. Two tomographic scans around the vertical axis are acquired on single-crystalline Nd2Fe14B pillars tilted at two different angles, with 2D STXM projections recorded using a focused 120 nm X-ray beam with left and right circular polarization. Image alignment and iterative registration have been implemented based on the 2D STXM projections for the two tilts. Dichroic projections obtained from difference images are used for the tomographic reconstruction to obtain the 3D magnetization distribution at the nanoscale.

Single Crystal and Pentatwinned Gold Nanorods Result in Chiral Nanocrystals with Reverse Handedness

Handedness is an essential attribute of chiral nanocrystals, having a major influence on their properties. During chemical growth, the handedness of nanocrystals is usually tuned by selecting the corresponding enantiomer of chiral molecules involved in asymmetric growth, often known as chiral inducers. We report that, even using the same chiral inducer enantiomer, the handedness of chiral gold nanocrystals can be reversed by using Au nanorod seeds with either single crystalline or pentatwinned structure. This effect holds for chiral growth induced both by amino acids and by chiral micelles. Although it was challenging to discern the morphological handedness for L-cystine-directed particles, even using electron tomography, both cases showed circular dichroism bands of opposite sign, with nearly mirrored chiroptical signatures for chiral micelle-directed growth, along with quasi-helical wrinkles of inverted handedness. These results expand the chiral growth toolbox with an effect that might be exploited to yield a host of interesting morphologies with tunable optical properties.

Imaging 3D chemistry at 1 nm resolution with fused multi-modal electron tomography

Measuring the three-dimensional (3D) distribution of chemistry in nanoscale matter is a longstanding challenge for metrological science. The inelastic scattering events required for 3D chemical imaging are too rare, requiring high beam exposure that destroys the specimen before an experiment is completed. Even larger doses are required to achieve high resolution. Thus, chemical mapping in 3D has been unachievable except at lower resolution with the most radiation-hard materials. Here, high-resolution 3D chemical imaging is achieved near or below one-nanometer resolution in an Au-Fe3O4 metamaterial within an organic ligand matrix, Co3O4-Mn3O4 core-shell nanocrystals, and ZnS-Cu0.64S0.36 nanomaterial using fused multi-modal electron tomography. Multi-modal data fusion enables high-resolution chemical tomography often with 99% less dose by linking information encoded within both elastic (HAADF) and inelastic (EDX/EELS) signals. We thus demonstrate that sub-nanometer 3D resolution of chemistry is measurable for a broad class of geometrically and compositionally complex materials.

Three-dimensional spin-wave dynamics, localization and interference in a synthetic antiferromagnet

Spin waves are collective perturbations in the orientation of the magnetic moments in magnetically ordered materials. Their rich phenomenology is intrinsically three-dimensional; however, the three-dimensional imaging of spin waves has so far not been possible. Here, we image the three-dimensional dynamics of spin waves excited in a synthetic antiferromagnet, with nanoscale spatial resolution and sub-ns temporal resolution, using time-resolved magnetic laminography. In this way, we map the distribution of the spin-wave modes throughout the volume of the structure, revealing unexpected depth-dependent profiles originating from the interlayer dipolar interaction. We experimentally demonstrate the existence of complex three-dimensional interference patterns and analyze them via micromagnetic modelling. We find that these patterns are generated by the superposition of spin waves with non-uniform amplitude profiles, and that their features can be controlled by tuning the composition and structure of the magnetic system. Our results open unforeseen possibilities for the study and manipulation of complex spin-wave modes within nanostructures and magnonic devices.

Micro- and nanostructure specific X-ray tomography reveals less matrix formation and altered collagen organization following reduced loading during Achilles tendon healing

Recovery of the collagen structure following Achilles tendon rupture is poor, resulting in a high risk for re-ruptures. The loading environment during healing affects the mechanical properties of the tendon, but the relation between loading regime and healing outcome remains unclear. This is partially due to our limited understanding regarding the effects of loading on the micro- and nanostructure of the healing tissue. We addressed this through a combination of synchrotron phase-contrast X-ray microtomography and small-angle X-ray scattering tensor tomography (SASTT) to visualize the 3D organization of microscale fibers and nanoscale fibrils, respectively. The effect of in vivo loading on these structures was characterized in early healing of rat Achilles tendons by comparing full activity with immobilization. Unloading resulted in structural changes that can explain the reported impaired mechanical performance. In particular, unloading led to slower tissue regeneration and maturation, with less and more disorganized collagen, as well as an increased presence of adipose tissue. This study provides the first application of SASTT on soft musculoskeletal tissues and clearly demonstrates its potential to investigate a variety of other collagenous tissues. STATEMENT OF SIGNIFICANCE: Currently our understanding of the mechanobiological effects on the recovery of the structural hierarchical organization of injured Achilles tendons is limited. We provide insight into how loading affects the healing process by using a cutting-edge approach to for the first time characterize the 3D micro- and nanostructure of the regenerating collagen. We uncovered that, during early healing, unloading results in a delayed and more disorganized regeneration of both fibers (microscale) and fibrils (nanoscale), as well as increased presence of adipose tissue. The results set the ground for the development of further specialized protocols for tendon recovery.

Automatic marker-based alignment method for a nano-resolution full-field transmission X-ray microscope

Driven by the development of X-ray optics, the spatial resolution of the full-field transmission X-ray microscope (TXM) has reached tens of nanometers and plays an important role in promoting the development of biomedicine and materials science. However, due to the thermal drift and the radial/axial motion error of the rotation stage, TXM computed tomography (CT) data are often associated with random image jitter errors along the horizontal and vertical directions during CT measurement. A nano-resolution 3D structure information reconstruction is almost impossible without a prior appropriate alignment process. To solve this problem, a fully automatic gold particle marker-based alignment approach without human intervention was proposed in this study. It can automatically detect, isolate, and register gold particles for projection image alignment with high efficiency and accuracy, facilitating a high-quality tomographic reconstruction. Simulated and experimental results confirmed the reliability and robustness of this method.

Nanoscale Three-Dimensional Network Structure of a Mesoporous Particle Unveiled via Adaptive Multidistance Coherent X-ray Tomography

Mesoporous nanoparticles provide rich platforms to devise functional materials by customizing the three-dimensional (3D) structures of nanopores. With the pore network as a key tuning parameter, the noninvasive and quantitative characterization of these 3D structures is crucial for the rational design of functional materials. This has prompted researchers to develop versatile nanoprobes with a high penetration power to inspect various specimens sized a few micrometers at nanoscale 3D resolutions. Here, with adaptive phase retrievals on independent data sets with different sampling frequencies, we introduce multidistance coherent X-ray tomography as a noninvasive and quantitative nanoprobe to realize high-resolution 3D imaging of micrometer-sized specimens. The 3D density distribution of an entire mesoporous silica nanoparticle was obtained at 13 nm 3D resolution for quantitative physical and morphological analyses of its 3D pore structure. The morphological features of the whole 3D pore network and pore connectivity were examined to gain insight into the potential functions of the particles. The proposed multidistance tomographic imaging scheme with quantitative structural analyses is expected to advance studies of functional materials by facilitating their structure-based rational design.

Multiscale X-ray imaging and characterisation of pharmaceutical dosage forms

A correlative, multiscale imaging methodology for visualising and quantifying the morphology of solid dosage forms by combining ptychographic X-ray computed nanotomography (PXCT) and scanning small- and wide-angle X-ray scattering (S/WAXS) is presented. The methodology presents a workflow for multiscale analysis, where structures are characterised from the nanometre to millimetre regime. Here, the method is demonstrated by characterising a hot-melt extruded, partly crystalline, solid dispersion of carbamazepine in ethyl cellulose. Characterisation of the morphology and solid-state phase of the drug in solid dosage forms is central as this affects the performance of the final formulation. The 3D morphology was visualised at a resolution of 80 nm over an extended volume through PXCT, revealing an oriented structure of crystalline drug domains aligned in the direction of extrusion. Scanning S/WAXS, showed that the nanostructure is similar over the cross section of the extruded filament, with minor radial changes in domain sizes and degree of orientation. The polymorphic forms of carbamazepine were qualified with WAXS, showing a heterogeneous distribution of the metastable forms I and II. This demonstrates the methodology for multiscale structural characterization and imaging to enable a better understanding of the relationships between morphology, performance, and processing conditions of solid dosage forms.

Understanding the microstructure of a core-shell anode catalyst layer for polymer electrolyte water electrolysis

Reducing precious metal loading in the anodic catalyst layer (CL) is indispensable for lowering capital costs and enabling the widespread adoption of polymer electrolyte water electrolysis. This work presents the first three-dimensional reconstruction of a TiO₂-supported IrO₂ based core shell CL (3 mg_IrO2/cm₂), using high-resolution X-ray ptychographic tomography at cryogenic temperature of 90 K. The high data quality and phase sensitivity of the technique have allowed the reconstruction of all four phases namely pore space, IrO₂, TiO₂ support matrix and the ionomer network, the latter of which has proven to be a challenge in the past. Results show that the IrO₂ forms thin nanoporous shells around the TiO₂ particles and that the ionomer has a non-uniform thickness and partially covers the catalyst. The TiO₂ particles do not form a percolating network while all other phases have high connectivity. The analysis of the CL ionic and electronic conductivity shows that for a dry CL, the ionic conductivity is orders of magnitudes lower than the electronic conductivity. Varying the electronic conductivity of the support phase by simulations, reveals that the conductivity of the support does not have a considerable impact on the overall CL electrical conductivity.

SAXS imaging reveals optimized osseointegration properties of bioengineered oriented 3D-PLGA/aCaP scaffolds in a critical size bone defect model

Healing large bone defects remains challenging in orthopedic surgery and is often associated with poor outcomes and complications. A major issue with bioengineered constructs is achieving a continuous interface between host bone and graft to enhance biological processes and mechanical stability. In this study, we have developed a new bioengineering strategy to produce oriented biocompatible 3D PLGA/aCaP nanocomposites with enhanced osseointegration. Decellularized scaffolds -containing only extracellular matrix- or scaffolds seeded with adipose-derived mesenchymal stromal cells were tested in a mouse model for critical size bone defects. In parallel to micro-CT analysis, SAXS tensor tomography and 2D scanning SAXS were employed to determine the 3D arrangement and nanostructure within the critical-sized bone. Both newly developed scaffold types, seeded with cells or decellularized, showed high osseointegration, higher bone quality, increased alignment of collagen fibers and optimal alignment and size of hydroxyapatite minerals.

Automatic Differentiation for Inverse Problems in X-ray Imaging and Microscopy

Computational techniques allow breaking the limits of traditional imaging methods, such as time restrictions, resolution, and optics flaws. While simple computational methods can be enough for highly controlled microscope setups or just for previews, an increased level of complexity is instead required for advanced setups, acquisition modalities or where uncertainty is high; the need for complex computational methods clashes with rapid design and execution. In all these cases, Automatic Differentiation, one of the subtopics of Artificial Intelligence, may offer a functional solution, but only if a GPU implementation is available. In this paper, we show how a framework built to solve just one optimisation problem can be employed for many different X-ray imaging inverse problems.

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.

Real-time 3D analysis during electron tomography using tomviz

The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique is computationally bottlenecked by alignment and reconstruction which runs from hours to days. We demonstrate real-time tomography with dynamic 3D tomographic visualization to enable rapid interpretation of specimen structure immediately as data is collected on an electron microscope. Using geometrically complex chiral nanoparticles, we show volumetric interpretation can begin in less than 10 minutes and a high-quality tomogram is available within 30 minutes. Real-time tomography is integrated into tomviz, an open-source and cross-platform 3D data analysis tool that contains intuitive graphical user interfaces (GUI), to enable any scientist to characterize biological and material structure in 3D.

High-throughput electron tomography has been challenging due to time-consuming alignment and reconstruction. Here, the authors demonstrate real-time tomography with dynamic 3D tomographic visualization integrated in tomviz, an open-source 3D data analysis tool.

Multiscale Dense U-Net: A Fast Correction Method for Thermal Drift Artifacts in Laboratory NanoCT Scans of Semi-Conductor Chips

The resolution of 3D structure reconstructed by laboratory nanoCT is often affected by changes in ambient temperature. Although correction methods based on projection alignment have been widely used, they are time-consuming and complex. Especially in piecewise samples (e.g., chips), the existing methods are semi-automatic because the projections lose attenuation information at some rotation angles. Herein, we propose a fast correction method that directly processes the reconstructed slices. Thus, the limitations of the existing methods are addressed. The method is named multiscale dense U-Net (MD-Unet), which is based on MIMO-Unet and achieves state-of-the-art artifacts correction performance in nanoCT. Experiments show that MD-Unet can significantly boost the correction performance (e.g., with three orders of magnitude improvement in correction speed compared with traditional methods), and MD-Unet+ improves 0.92 dB compared with MIMO-Unet in the chip dataset.

Feature detection network-based correction method for accurate nano-tomography reconstruction

Driven by the development of advanced x-ray optics such as Fresnel zone plates, nano-resolution full-field transmission x-ray microscopy (Nano-CT) has become a powerful technique for the non-destructive volumetric inspection of objects and has long been developed at different synchrotron radiation facilities. However, Nano-CT data are often associated with random sample jitter because of the drift or radial/axial error motion of the rotation stage during measurement. Without a proper sample jitter correction process prior to reconstruction, the use of Nano-CT in providing accurate 3D structure information for samples is almost impossible. In this paper, to realize accurate 3D reconstruction for Nano-CT, a correction method based on a feature detection neural network, which can automatically extract target features from a projective image and precisely correct sample jitter errors, is proposed, thereby resulting in high-quality nanoscale 3D reconstruction. Compared with other feature detection methods, even if the target feature is overlapped by other high-density materials or impurities, the proposed Nano-CT correction method still acquires sub-pixel accuracy in geometrical correction and is more suitable for Nano-CT reconstruction because of its universal and faster correction speed. The simulated and experimental datasets demonstrated the reliability and validity of the proposed Nano-CT correction method.

Thermal Drift Correction for Laboratory Nano Computed Tomography via Outlier Elimination and Feature Point Adjustment

Thermal drift of nano-computed tomography (CT) adversely affects the accurate reconstruction of objects. However, feature-based reference scan correction methods are sometimes unstable for images with similar texture and low contrast. In this study, based on the geometric position of features and the structural similarity (SSIM) of projections, a rough-to-refined rigid alignment method is proposed to align the projection. Using the proposed method, the thermal drift artifacts in reconstructed slices are reduced. Firstly, the initial features are obtained by speeded up robust features (SURF). Then, the outliers are roughly eliminated by the geometric position of global features. The features are refined by the SSIM between the main and reference projections. Subsequently, the SSIM between the neighborhood images of features are used to relocate the features. Finally, the new features are used to align the projections. The two-dimensional (2D) transmission imaging experiments reveal that the proposed method provides more accurate and robust results than the random sample consensus (RANSAC) and locality preserving matching (LPM) methods. For three-dimensional (3D) imaging correction, the proposed method is compared with the commonly used enhanced correlation coefficient (ECC) method and single-step discrete Fourier transform (DFT) algorithm. The results reveal that proposed method can retain the details more faithfully.

Deep-learning-based image registration for nano-resolution tomographic reconstruction

Nano-resolution full-field transmission X-ray microscopy has been successfully applied to a wide range of research fields thanks to its capability of non-destructively reconstructing the 3D structure with high resolution. Due to constraints in the practical implementations, the nano-tomography data is often associated with a random image jitter, resulting from imperfections in the hardware setup. Without a proper image registration process prior to the reconstruction, the quality of the result will be compromised. Here a deep-learning-based image jitter correction method is presented, which registers the projective images with high efficiency and accuracy, facilitating a high-quality tomographic reconstruction. This development is demonstrated and validated using synthetic and experimental datasets. The method is effective and readily applicable to a broad range of applications. Together with this paper, the source code is published and adoptions and improvements from our colleagues in this field are welcomed.

Hard X-Ray Nanotomography for 3D Analysis of Coking in Nickel-Based Catalysts

Understanding catalyst deactivation by coking is crucial for knowledge-based catalyst and process design in reactions with carbonaceous species. Post-mortem analysis of catalyst coking is often performed by bulk characterization methods. Here, hard X-ray ptychographic computed tomography (PXCT) was used to study Ni/Al2 O3 catalysts for CO2 methanation and CH4 dry reforming after artificial coking treatment. PXCT generated quantitative 3D maps of local electron density at ca. 80 nm resolution, allowing to visualize and evaluate the severity of coking in entire catalyst particles of ca. 40 μm diameter. Coking was primarily revealed in the nanoporous solid, which was not detectable in resolved macropores. Coke formation was independently confirmed by operando Raman spectroscopy. PXCT is highlighted as an emerging characterization tool for nanoscale identification, co-localization, and potentially quantification of deactivation phenomena in 3D space within entire catalyst particles.

Molecular Insights on Successful Reconstitution of Freeze-Dried Nanofibrillated Cellulose Hydrogel

The diversity and safety of nanofibrillated cellulose (NFC) hydrogels have gained a vast amount of interest at the pharmaceutical site in recent years. Moreover, this biomaterial has a high potential to be utilized as a protective matrix during the freeze-drying of heat-sensitive pharmaceuticals and biologics to increase their properties for long-term storing at room temperature and transportation. Since freeze-drying and subsequent reconstitution have not been optimized for this biomaterial, we must find a wider understanding of the process itself as well as the molecular level interactions between the NFC hydrogel and the most suitable lyoprotectants. Herein we optimized the reconstitution of the freeze-dried NFC hydrogel by considering critical quality attributes required to ensure the success of the process and gained insights of the obtained experimental data by simulating the effects of the used lyoprotectants on water and NFC. We discovered the correlation between the measured characteristics and molecular dynamics simulations and obtained successful freeze-drying and subsequent reconstitution of NFC hydrogel with the presence of 300 mM of sucrose. These findings demonstrated the possibility of using the simulations together with the experimental measurements to obtain a more comprehensive way to design a successful freeze-drying process, which could be utilized in future pharmaceutical applications.

Improving a Rapid Alignment Method of Tomography Projections by a Parallel Approach

The high resolution of synchrotron cryo-nano tomography can be easily undermined by setup instabilities and sample stage deficiencies such as runout or backlash. At the cost of limiting the sample visibility, especially in the case of bio-specimens, high contrast nano-beads are often added to the solution to provide a set of landmarks for a manual alignment. However, the spatial distribution of these reference points within the sample is difficult to control, resulting in many datasets without a sufficient amount of such critical features for tracking. Fast automatic methods based on tomography consistency are thus desirable, especially for biological samples, where regular, high contrast features can be scarce. Current off-the-shelf implementations of such classes of algorithms are slow if used on a real-world high-resolution dataset. In this paper, we present a fast implementation of a consistency-based alignment algorithm especially tailored to a multi-GPU system. Our implementation is released as open-source.

Sparse ab initio x-ray transmission spectrotomography for nanoscopic compositional analysis of functional materials

The performance of functional materials is either driven or limited by nanoscopic heterogeneities distributed throughout the material's volume. To better our understanding of these materials, we need characterization tools that allow us to determine the nature and distribution of these heterogeneities in their native geometry in 3D. Here, we introduce a method based on x-ray near-edge spectroscopy, ptychographic x-ray computed nanotomography, and sparsity techniques. The method allows the acquisition of quantitative multimodal tomograms of representative sample volumes at sub-30 nm half-period spatial resolution within practical acquisition times, which enables local structure refinements in complex geometries. To demonstrate the method's capabilities, we investigated the transformation of vanadium phosphorus oxide catalysts with industrial use. We observe changes from the micrometer to the atomic level and the formation of a location-specific defect so far only theorized. These results led to a reevaluation of these catalysts used in the production of plastics.

Porosity and Structure of Hierarchically Porous Ni/Al2O3 Catalysts for CO2 Methanation

CO2 methanation is often performed on Ni/Al2O3 catalysts, which can suffer from mass transport limitations and, therefore, decreased efficiency. Here we show the application of a hierarchically porous Ni/Al2O3 catalyst for methanation of CO2. The material has a well-defined and connected meso- and macropore structure with a total porosity of 78%. The pore structure was thoroughly studied with conventional methods, i.e., N2 sorption, Hg porosimetry, and He pycnometry, and advanced imaging techniques, i.e., electron tomography and ptychographic X-ray computed tomography. Tomography can quantify the pore system in a manner that is not possible using conventional porosimetry. Macrokinetic simulations were performed based on the measures obtained by porosity analysis. These show the potential benefit of enhanced mass-transfer properties of the hierarchical pore system compared to a pure mesoporous catalyst at industrially relevant conditions. Besides the investigation of the pore system, the catalyst was studied by Rietveld refinement, diffuse reflectance ultraviolet-visible (DRUV/vis) spectroscopy, and H2-temperature programmed reduction (TPR), showing a high reduction temperature required for activation due to structural incorporation of Ni into the transition alumina. The reduced hierarchically porous Ni/Al2O3 catalyst is highly active in CO2 methanation, showing comparable conversion and selectivity for CH4 to an industrial reference catalyst.

Dynamic compressed sensing for real-time tomographic reconstruction

Electron tomography has achieved higher resolution and quality at reduced doses with recent advances in compressed sensing. Compressed sensing (CS) exploits the inherent sparse signal structure to efficiently reconstruct three-dimensional (3D) volumes at the nanoscale from undersampled measurements. However, the process bottlenecks 3D reconstruction with computation times that run from hours to days. Here we demonstrate a framework for dynamic compressed sensing that produces a 3D specimen structure that updates in real-time as new specimen projections are collected. Researchers can begin interpreting 3D specimens as data is collected to facilitate high-throughput and interactive analysis. Using scanning transmission electron microscopy (STEM), we show that dynamic compressed sensing accelerates the convergence speed by ~3-fold while also reducing its error by 27% for a Au/SrTiO₃ nanoparticle specimen. Before a tomography experiment is completed, the 3D tomogram has interpretable structure within ~33% of completion and fine details are visible as early as ~66%. Upon completion of an experiment, a high-fidelity 3D visualization is produced without further delay. Additionally, reconstruction parameters that tune data fidelity can be manipulated throughout the computation without re-running the entire process.

Time-resolved imaging of three-dimensional nanoscale magnetization dynamics

Understanding and control of the dynamic response of magnetic materials with a three-dimensional magnetization distribution is important both fundamentally and for technological applications. From a fundamental point of view, the internal magnetic structure and dynamics in bulk materials still need to be mapped¹, including the dynamic properties of topological structures such as vortices², magnetic singularities³ or skyrmion lattices⁴. From a technological point of view, the response of inductive materials to magnetic fields and spin-polarized currents is essential for magnetic sensors and data storage devices⁵. Here, we demonstrate time-resolved magnetic laminography, a pump-probe technique, which offers access to the temporal evolution of a three-dimensional magnetic microdisc with nanoscale resolution, and with a synchrotron-limited temporal resolution of 70 ps. We image the dynamic response to a 500 MHz magnetic field of the complex three-dimensional magnetization in a two-phase bulk magnet with a lateral spatial resolution of 50 nm. This is achieved with a stroboscopic measurement consisting of eight time steps evenly spaced over 2 ns. These measurements map the spatial transition between domain wall motion and the dynamics of a uniform magnetic domain that is attributed to variations in the magnetization state across the phase boundary. Our technique, which probes three-dimensional magnetic structures with temporal resolution, enables the experimental investigation of functionalities arising from dynamic phenomena in bulk and three-dimensional patterned nanomagnets⁶.

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.

PtychoShelves, a versatile high-level framework for high-performance analysis of ptychographic data

A new computer program for analysing ptychographic data combines both high-level simplicity and high-performance computing on large-scale computing clusters. It is available with a royalty-free non-exclusive licence for academic and non-commercial purposes.

Over the past decade, ptychography has been proven to be a robust tool for non-destructive high-resolution quantitative electron, X-ray and optical microscopy. It allows for quantitative reconstruction of the specimen’s transmissivity, as well as recovery of the illuminating wavefront. Additionally, various algorithms have been developed to account for systematic errors and improved convergence. With fast ptychographic microscopes and more advanced algorithms, both the complexity of the reconstruction task and the data volume increase significantly. PtychoShelves is a software package which combines high-level modularity for easy and fast changes to the data-processing pipeline, and high-performance computing on CPUs and GPUs.