Deep learning to overcome Zernike phase-contrast nanoCT artifacts for automated micro-nano porosity segmentation in bone.

Bone material contains a hierarchical network of micro- and nano-cavities and channels, known as the lacuna-canalicular network (LCN), that is thought to play an important role in mechanobiology and turnover. The LCN comprises micrometer-sized lacunae, voids that house osteocytes, and submicrometer-sized canaliculi that connect bone cells. Characterization of this network in three dimensions is crucial for many bone studies. To quantify X-ray Zernike phase-contrast nanotomography data, deep learning is used to isolate and assess porosity in artifact-laden tomographies of zebrafish bones. A technical solution is proposed to overcome the halo and shade-off domains in order to reliably obtain the distribution and morphology of the LCN in the tomographic data. Convolutional neural network (CNN) models are utilized with increasing numbers of images, repeatedly validated by `error loss' and `accuracy' metrics. U-Net and Sensor3D CNN models were trained on data obtained from two different synchrotron Zernike phase-contrast transmission X-ray microscopes, the ANATOMIX beamline at SOLEIL (Paris, France) and the P05 beamline at PETRA III (Hamburg, Germany). The Sensor3D CNN model with a smaller batch size of 32 and a training data size of 70 images showed the best performance (accuracy 0.983 and error loss 0.032). The analysis procedures, validated by comparison with human-identified ground-truth images, correctly identified the voids within the bone matrix. This proposed approach may have further application to classify structures in volumetric images that contain non-linear artifacts that degrade image quality and hinder feature identification.

Multiscale morphological analysis of bone microarchitecture around Mg-10Gd implants.

The utilization of biodegradable magnesium (Mg)-based implants for restoration of bone function following trauma represents a transformative approach in orthopaedic application. One such alloy, magnesium-10 weight percent gadolinium (Mg-10Gd), has been specifically developed to address the rapid degradation of Mg while enhancing its mechanical properties to promote bone healing. Previous studies have demonstrated that Mg-10Gd exhibits favorable osseointegration; however, it exhibits distinct ultrastructural adaptation in comparison to conventional implants like titanium (Ti). A crucial aspect that remains unexplored is the impact of Mg-10Gd degradation on the bone microarchitecture. To address this, we employed hierarchical three-dimensional imaging using synchrotron radiation in conjunction with image-based finite element modelling. By using the methods outlined, the vascular porosity, lacunar porosity and the lacunar-canaliculi network (LCN) morphology of bone around Mg-10Gd in comparison to Ti in a rat model from 4 weeks to 20 weeks post-implantation was investigated. Our investigation revealed that within our observation period, the degradation of Mg-10Gd implants was associated with significantly lower (p < 0.05) lacunar density in the surrounding bone, compared to Ti. Remarkably, the LCN morphology and the fluid flow analysis did not significantly differ for both implant types. In summary, a more pronounced lower lacunae distribution rather than their morphological changes was detected in the surrounding bone upon the degradation of Mg-10Gd implants. This implies potential disparities in bone remodelling rates when compared to Ti implants. Our findings shed light on the intricate relationship between Mg-10Gd degradation and bone microarchitecture, contributing to a deeper understanding of the implications for successful osseointegration.

Development of a Bioreactor-Coupled Flow-Cell Setup for 3D In Situ Nanotomography of Mg Alloy Biodegradation.

Functional materials feature hierarchical microstructures that define their unique set of properties. The prediction and tailoring of these require a multiscale knowledge of the mechanistic interaction of microstructure and property. An important material in this respect is biodegradable magnesium alloys used for implant applications. To correlate the relationship between the microstructure and the nonlinear degradation process, high-resolution in situ three-dimensional (3D) imaging experiments must be performed. For this purpose, a novel experimental flow cell is presented which allows for the in situ 3D-nano imaging of the biodegradation process of materials with nominal resolutions below 100 nm using nanofocused hard X-ray radiation from a synchrotron source. The flow cell setup can operate under adjustable physiological and hydrodynamic conditions. As a model material, the biodegradation of thin Mg-4Ag wires in simulated body fluid under physiological conditions and a flow rate of 1 mL/min is studied. The use of two full-field nanotomographic imaging techniques, namely transmission X-ray microscopy and near-field holotomography, is compared, revealing holotomography as the superior imaging technique for this purpose. Additionally, the importance of maintaining physiological conditions is highlighted by the preliminary results. Supporting measurements using electron microscopy to investigate the chemical composition of the samples after degradation are performed.

Detailing the influence of PEO-coated biodegradable Mg-based implants on the lacuno-canalicular network in sheep bone: A pilot study.

An increasing prevalence of bone-related injuries and aging geriatric populations continue to drive the orthopaedic implant market. A hierarchical analysis of bone remodelling after material implantation is necessary to better understand the relationship between implant and bone. Osteocytes, which are housed and communicate through the lacuno-canalicular network (LCN), are integral to bone health and remodelling processes. Therefore, it is essential to examine the framework of the LCN in response to implant materials or surface treatments. Biodegradable materials offer an alternative solution to permanent implants, which may require revision or removal surgeries. Magnesium alloys have resurfaced as promising materials due to their bone-like properties and safe degradation in vivo. To further tailor their degradation capabilities, surface treatments such as plasma electrolytic oxidation (PEO) have demonstrated to slow degradation. For the first time, the influence of a biodegradable material on the LCN is investigated by means of non-destructive 3D imaging. In this pilot study, we hypothesize noticeable variations in the LCN caused by altered chemical stimuli introduced by the PEO-coating. Utilising synchrotron-based transmission X-ray microscopy, we have characterised morphological LCN differences around uncoated and PEO-coated WE43 screws implanted into sheep bone. Bone specimens were explanted after 4, 8, and 12 weeks and regions near the implant surface were prepared for imaging. Findings from this investigation indicate that the slower degradation of PEO-coated WE43 induces healthier lacunar shapes within the LCN. However, the stimuli perceived by the uncoated material with higher degradation rates induces a greater connected LCN better prepared for bone disturbance.

Hard X-ray full-field nanoimaging using a direct photon-counting detector.

Full-field X-ray nanoimaging is a widely used tool in a broad range of scientific areas. In particular, for low-absorbing biological or medical samples, phase contrast methods have to be considered. Three well established phase contrast methods at the nanoscale are transmission X-ray microscopy with Zernike phase contrast, near-field holography and near-field ptychography. The high spatial resolution, however, often comes with the drawback of a lower signal-to-noise ratio and significantly longer scan times, compared with microimaging. In order to tackle these challenges a single-photon-counting detector has been implemented at the nanoimaging endstation of the beamline P05 at PETRA III (DESY, Hamburg) operated by Helmholtz-Zentrum Hereon. Thanks to the long sample-to-detector distance available, spatial resolutions of below 100 nm were reached in all three presented nanoimaging techniques. This work shows that a single-photon-counting detector in combination with a long sample-to-detector distance allows one to increase the time resolution for in situ nanoimaging, while keeping a high signal-to-noise level.

Wafer-Scale Fabrication of Hierarchically Porous Silicon and Silica by Active Nanoparticle-Assisted Chemical Etching and Pseudomorphic Thermal Oxidation.

Many biological materials exhibit a multiscale porosity with small, mostly nanoscale pores as well as large, macroscopic capillaries to simultaneously achieve optimized mass transport capabilities and lightweight structures with large inner surfaces. Realizing such a hierarchical porosity in artificial materials necessitates often sophisticated and expensive top-down processing that limits scalability. Here, an approach that combines self-organized porosity based on metal-assisted chemical etching (MACE) with photolithographically induced macroporosity for the synthesis of single-crystalline silicon with a bimodal pore-size distribution is presented, i.e., hexagonally arranged cylindrical macropores with 1 µm diameter separated by walls that are traversed by pores 60 nm across. The MACE process is mainly guided by a metal-catalyzed reduction-oxidation reaction, where silver nanoparticles (AgNPs) serve as the catalyst. In this process, the AgNPs act as self-propelled particles that are constantly removing silicon along their trajectories. High-resolution X-ray imaging and electron tomography reveal a resulting large open porosity and inner surface for potential applications in high-performance energy storage, harvesting and conversion or for on-chip sensorics and actuorics. Finally, the hierarchically porous silicon membranes can be transformed structure-conserving by thermal oxidation into hierarchically porous amorphous silica, a material that could be of particular interest for opto-fluidic and (bio-)photonic applications due to its multiscale artificial vascularization.

On stars and spikes: Resolving the skeletal morphology of planktonic Acantharia using synchrotron X-ray nanotomography and deep learning image segmentation.

Acantharia (Acantharea) are wide-spread marine protozoa, presenting one of the rare examples of strontium sulfate mineralization in the biosphere. Their endoskeletons consist of 20 spicules arranged according to a unique geometric pattern named Müller's principle. Given the diverse mineral architecture of the Acantharia class, we set out to examine the complex three-dimensional skeletal morphology at the nanometer scale using synchrotron X-ray nanotomography, followed by image segmentation based on deep learning methods. The present study focuses on how the spicules emanate from the robust central junction in the orders Symphyacanthida and Arthracanthida, the geometry of lateral spicule wings as well as pockets of interspicular space, which may be involved in cell compartmentalization. Through these morphometric studies, we observed subtle deviations from the previously described spatial arrangement of the spicules. According to our data, spicule shapes are adjusted in opposite spicules as to accommodate the overall spicule arrangement. In all types examined, previously unknown interspicular interstices were found in areas where radial spicules meet, which could have implications for the crystal growth mechanism and overall endoskeletal integrity. A deeper understanding of the spiculogenesis in Acantharia can provide biomimetic routes towards complex inorganic shapes. STATEMENT OF SIGNIFICANCE: Morphogenesis, the origin and control of shape, provides an avenue towards tailored inorganic materials. In this work, we explored the intricate skeletal organization of planktonic Acantharia, which are amongst the few strontium sulfate biomineralizing organisms in nature. By using nanoscale X-ray imaging and deep learning image segmentation, we found deviations from previously described geometric patterns and undiscovered skeletal features. The bio-inspired synthesis of inorganic materials with complex shape has important ramifications for solid-state chemistry and nanotechnology.

Machine learning denoising of high-resolution X-ray nanotomography data.

High-resolution X-ray nanotomography is a quantitative tool for investigating specimens from a wide range of research areas. However, the quality of the reconstructed tomogram is often obscured by noise and therefore not suitable for automatic segmentation. Filtering methods are often required for a detailed quantitative analysis. However, most filters induce blurring in the reconstructed tomograms. Here, machine learning (ML) techniques offer a powerful alternative to conventional filtering methods. In this article, we verify that a self-supervised denoising ML technique can be used in a very efficient way for eliminating noise from nanotomography data. The technique presented is applied to high-resolution nanotomography data and compared to conventional filters, such as a median filter and a nonlocal means filter, optimized for tomographic data sets. The ML approach proves to be a very powerful tool that outperforms conventional filters by eliminating noise without blurring relevant structural features, thus enabling efficient quantitative analysis in different scientific fields.

3D Spatial Distribution of Nanoparticles in Mice Brain Metastases by X-ray Phase-Contrast Tomography.

Characterizing nanoparticles (NPs) distribution in multiple and complex metastases is of fundamental relevance for the development of radiological protocols based on NPs administration. In the literature, there have been advances in monitoring NPs in tissues. However, the lack of 3D information is still an issue. X-ray phase-contrast tomography (XPCT) is a 3D label-free, non-invasive and multi-scale approach allowing imaging anatomical details with high spatial and contrast resolutions. Here an XPCT qualitative study on NPs distribution in a mouse brain model of melanoma metastases injected with gadolinium-based NPs for theranostics is presented. For the first time, XPCT images show the NPs uptake at micrometer resolution over the full brain. Our results revealed a heterogeneous distribution of the NPs inside the melanoma metastases, bridging the gap in spatial resolution between magnetic resonance imaging and histology. Our findings demonstrated that XPCT is a reliable technique for NPs detection and can be considered as an emerging method for the study of NPs distribution in organs.

Evaluating the morphology of the degradation layer of pure magnesium via 3D imaging at resolutions below 40 nm.

Magnesium is attractive for the application as a temporary bone implant due to its inherent biodegradability, non-toxicity and suitable mechanical properties. The degradation process of magnesium in physiological environments is complex and is thought to be a diffusion-limited transport problem. We use a multi-scale imaging approach using micro computed tomography and transmission X-ray microscopy (TXM) at resolutions below 40 nm. Thus, we are able to evaluate the nanoporosity of the degradation layer and infer its impact on the degradation process of pure magnesium in two physiological solutions. Magnesium samples were degraded in simulated body fluid (SBF) or Dulbecco's modified Eagle's medium (DMEM) with 10% fetal bovine serum (FBS) for one to four weeks. TXM reveals the three-dimensional interconnected pore network within the degradation layer for both solutions. The pore network morphology and degradation layer composition are similar for all samples. By contrast, the degradation layer thickness in samples degraded in SBF was significantly higher and more inhomogeneous than in DMEM+10%FBS. Distinct features could be observed within the degradation layer of samples degraded in SBF, suggesting the formation of microgalvanic cells, which are not present in samples degraded in DMEM+10%FBS. The results suggest that the nanoporosity of the degradation layer and the resulting ion diffusion processes therein have a limited influence on the overall degradation process. This indicates that the influence of organic components on the dampening of the degradation rate by the suppression of microgalvanic degradation is much greater in the present study.

Exploration of changes in spatial chondrocyte organisation in human osteoarthritic cartilage by means of 3D imaging.

Using two-dimensional top-down view microscopy, researchers have recently described chondrocytes as being spatially arranged in distinct patterns such as strings, double strings, and small and large clusters. Because of the seeming association of these changes with tissue degeneration, they have been proposed as an image-based biomarker for early osteoarthritis (OA) staging. The aim of our study was to investigate the spatial arrangement of chondrocytes in human articular cartilage in a 3D fashion and to evaluate the 3D changes of these patterns in the context of local tissue destruction. Decalcified femoral condyle resections from the load-bearing area were analysed in 3D for their spatial chondrocyte organisation by means of fluorescence microscopy and synchrotron-radiation micro-computed tomography (SR-µCT). In intact cartilage chondrocyte strings can be found in the superficial, transitional and deep zones. The proposed pattern changes accompanying tissue destruction could be located not just along the surface but also through all layers of cartilage. Each spatial pattern was characterised by a different cellular density (the only exception being between single and double strings with p = 0.062), with cellular density significantly increasing alongside the increase in local tissue degeneration as defined by the chondrocyte patterns. We can thus corroborate that the proposed cellular spatial changes are a three-dimensional function of local tissue degeneration, underlining their relevance as an image-based biomarker for the early diagnosis and description of OA.Clinical trial registration number: Project number of the ethics committee of the University of Tübingen:171/2014BO2.

Three-dimensional imaging of xylem at cell wall level through near field nano holotomography.

Detailed imaging of the three-dimensionally complex architecture of xylary plants is important for studying biological and mechanical functions of woody plants. Apart from common two-dimensional microscopy, X-ray micro-computed tomography has been established as a three-dimensional (3D) imaging method for studying the hydraulic function of wooden plants. However, this X-ray imaging method can barely reach the resolution needed to see the minute structures (e.g. pit membrane). To complement the xylem structure with 3D views at the nanoscale level, X-ray near-field nano-holotomography (NFH) was applied to analyze the wood species Pinus sylvestris and Fagus sylvatica. The demanded small specimens required focused ion beam (FIB) application. The FIB milling, however, influenced the image quality through gallium implantation on the cell-wall surfaces. The measurements indicated that NFH is appropriate for imaging wood at nanometric resolution. With a 26 nm voxel pitch, the structure of the cell-wall surface in Pinus sylvestris could be visualized in genuine detail. In wood of Fagus sylvatica, the structure of a pit pair, including the pit membrane, between two neighboring fibrous cells could be traced tomographically.

Collagen Fiber Orientation Is Coupled with Specific Nano-Compositional Patterns in Dark and Bright Osteons Modulating Their Biomechanical Properties.

Bone continuously adapts to its mechanical environment by structural reorganization to maintain mechanical strength. As the adaptive capabilities of bone are portrayed in its nano- and microstructure, the existence of dark and bright osteons with contrasting preferential collagen fiber orientation (longitudinal and oblique-angled, respectively) points at a required tissue heterogeneity that contributes to the excellent fracture resistance mechanisms in bone. Dark and bright osteons provide an exceptional opportunity to deepen our understanding of how nanoscale tissue properties influence and guide fracture mechanisms at larger length scales. To this end, a comprehensive structural, compositional, and mechanical assessment is performed using circularly polarized light microscopy, synchrotron nanocomputed tomography, focused ion beam/scanning electron microscopy, quantitative backscattered electron imaging, Fourier transform infrared spectroscopy, and nanoindentation testing. To predict how the mechanical behavior of osteons is affected by shifts in collagen fiber orientation, finite element models are generated. Fundamental disparities between both osteon types are observed: dark osteons are characterized by a higher degree of mineralization along with a higher ratio of inorganic to organic matrix components that lead to higher stiffness and the ability to resist plastic deformation under compression. On the contrary, bright osteons contain a higher fraction of collagen and provide enhanced ductility and energy dissipation due to lower stiffness and hardness.

Hard X-ray nano-holotomography with a Fresnel zone plate.

X-ray phase contrast nanotomography enables imaging of a wide range of samples with high spatial resolution in 3D. Near-field holography, as one of the major phase contrast techniques, is often implemented using X-ray optics such as Kirkpatrick-Baez mirrors, waveguides and compound refractive lenses. However, these optics are often tailor-made for a specific beamline and challenging to implement and align. Here, we present a near-field holography setup based on Fresnel zone plates which is fast and easy to align and provides a smooth illumination and flat field. The imaging quality of different types of Fresnel zone plates is compared in terms of the flat-field quality, the achievable resolution and exposure efficiency i.e. the photons arriving at the detector. Overall, this setup is capable of imaging different types of samples at high spatial resolution of below 100 nm in 3D with access to the quantitative phase information.

Pushing the temporal resolution in absorption and Zernike phase contrast nanotomography: enabling fast in situ experiments.

Hard X-ray nanotomography enables 3D investigations of a wide range of samples with high resolution (<100 nm) with both synchrotron-based and laboratory-based setups. However, the advantage of synchrotron-based setups is the high flux, enabling time resolution, which cannot be achieved at laboratory sources. Here, the nanotomography setup at the imaging beamline P05 at PETRA III is presented, which offers high time resolution not only in absorption but for the first time also in Zernike phase contrast. Two test samples are used to evaluate the image quality in both contrast modalities based on the quantitative analysis of contrast-to-noise ratio (CNR) and spatial resolution. High-quality scans can be recorded in 15 min and fast scans down to 3 min are also possible without significant loss of image quality. At scan times well below 3 min, the CNR values decrease significantly and classical image-filtering techniques reach their limitation. A machine-learning approach shows promising results, enabling acquisition of a full tomography in only 6 s. Overall, the transmission X-ray microscopy instrument offers high temporal resolution in absorption and Zernike phase contrast, enabling in situ experiments at the beamline.

Structural Diversity of Native Major Ampullate, Minor Ampullate, Cylindriform, and Flagelliform Silk Proteins in Solution.

The foundations of silk spinning, the structure, storage, and activation of silk proteins, remain highly debated. By combining solution small-angle neutron and X-ray scattering (SANS and SAXS) alongside circular dichroism (CD), we reveal a shape anisotropy of the four principal native spider silk feedstocks from Nephila edulis. We show that these proteins behave in solution like elongated semiflexible polymers with locally rigid sections. We demonstrated that minor ampullate and cylindriform proteins adopt a monomeric conformation, while major ampullate and flagelliform proteins have a preference for dimerization. From an evolutionary perspective, we propose that such dimerization arose to help the processing of disordered silk proteins. Collectively, our results provide insights into the molecular-scale processing of silk, uncovering a degree of evolutionary convergence in protein structures and chemistry that supports the macroscale micellar/pseudo liquid crystalline spinning mechanisms proposed by the community.

Nanoporous gold: a hierarchical and multiscale 3D test pattern for characterizing X-ray nano-tomography systems.

Full-field transmission X-ray microscopy (TXM) is a well established technique, available at various synchrotron beamlines around the world as well as by laboratory benchtop devices. One of the major TXM challenges, due to its nanometre-scale resolution, is the overall instrument stability during the acquisition of the series of tomographic projections. The ability to correct for vertical and horizontal distortions of each projection image during acquisition is necessary in order to achieve the effective 3D spatial resolution. The effectiveness of such an image alignment is also heavily influenced by the absorption properties and strong contrast of specific features in the scanned sample. Here it is shown that nanoporous gold (NPG) can be used as an ideal 3D test pattern for evaluating and optimizing the performance of a TXM instrument for hard X-rays at a synchrotron beamline. Unique features of NPG, such as hierarchical structures at multiple length scales and high absorbing capabilities, makes it an ideal choice for characterization, which involves a combination of a rapid-alignment algorithm applied on the acquired projections followed by the extraction of a set of both 2D- and 3D-descriptive image parameters. This protocol can be used for comparing the efficiency of TXM instruments at different synchrotron beamlines in the world or benchtop devices, based on a reference library of scanned NPG samples, containing information about the estimated horizontal and vertical alignment values, 2D qualitative parameters and quantitative 3D parameters. The possibility to tailor the ligament sizes of NPG to match the achievable resolution in combination with the high electron density of gold makes NPG an ideal 3D test pattern for evaluating the status and performance of a given synchrotron-based or benchtop-based TXM setup.

Dataset of ptychographic X-ray computed tomography of inverse opal photonic crystals produced by atomic layer deposition.

This data article describes the detailed parameters for synthesizing mullite inverse opal photonic crystals via Atomic Layer Deposition (ALD), as well as the detailed image analysis routine used to interpret the data obtained by the measurement of such photonic crystals, before and after the heat treatment, via Ptychographic X-ray Computed Tomography (PXCT). The data presented in this article are related to the research article by Furlan and co-authors entitled "Photonic materials for high-temperature applications: Synthesis and characterization by X-ray ptychographic tomography" (Furlan et al., 2018). The data include detailed information about the ALD super-cycle process to generate the ternary oxides inside a photonic crystal template, the raw data from supporting characterization techniques, as well as the full dataset obtained from PXCT. All the data herein described is publicly available in a Mendeley Data archive "Dataset of synthesis and characterization by PXCT of ALD-based mullite inverse opal photonic crystals" located at https://data.mendeley.com/datasets/zn49dsk7x6/1 for any academic, educational, or research purposes.

Stress-induced long-range ordering in spider silk.

The emergence of order from disorder is a topic of vital interest. We here propose that long-range order can arise from a randomly arranged two-phase material under mechanical load. Using Small-Angle Neutron Scattering (SANS) experiments and Molecular Dynamics based finite element (FE) models we show evidence for stress-induced ordering in spider dragline silk. Both methods show striking quantitative agreement of the position, shift and intensity increase of the long period upon stretching. We demonstrate that mesoscopic ordering does not originate from silk-specific processes such as strain-induced crystallization on the atomistic scale or the alignment of tilted crystallites. It instead is a general phenomenon arising from a non-affine deformation that enhances density fluctuations of the stiff and soft phases along the direction of stress. Our results suggest long-range ordering, analogously to the coalescence of defects in materials, as a wide-spread phenomenon to be exploited for tuning the mechanical properties of many hybrid stiff and soft materials.