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.

In-place molecular preservation of cellulose in 5,000-year-old archaeological textiles.

The understanding of fossilization mechanisms at the nanoscale remains extremely challenging despite its fundamental interest and its implications for paleontology, archaeology, geoscience, and environmental and material sciences. The mineralization mechanism by which cellulosic, keratinous, and silk tissues fossilize in the vicinity of archaeological metal artifacts offers the most exquisite preservation through a mechanism unexplored on the nanoscale. It is at the center of the vast majority of ancient textiles preserved under nonextreme conditions, known through extremely valuable fragments. Here we show the reconstruction of the nanoscale mechanism leading to the preservation of an exceptional collection of ancient cellulosic textiles recovered in the ancient Near East (4,000 to 5,000 years ago). We demonstrate that even the most mineralized fibers, which contain inorganic compounds throughout their histology, enclose preserved cellulosic remains in place. We evidence a process that combines the three steps of water transport of biocidal metal cations and soil solutes, degradation and loss of crystallinity of cellulosic polysaccharides, and silicification.

Measurement and compensation of misalignment in double-sided hard X-ray Fresnel zone plates.

Double-sided Fresnel zone plates are diffractive lenses used for high-resolution hard X-ray microscopy. The double-sided structures have significantly higher aspect ratios compared with single-sided components and hence enable more efficient imaging. The zone plates discussed in this paper are fabricated on each side of a thin support membrane, and the alignment of the zone plates with respect to each other is critical. Here, a simple and reliable way of quantifying misalignments by recording efficiency maps and measuring the absolute diffraction efficiency of the zone plates as a function of tilting angle in two directions is presented. The measurements are performed in a setup based on a tungsten-anode microfocus X-ray tube, providing an X-ray energy of 8.4 keV through differential measurements with a Cu and an Ni filter. This study investigates the sources of the misalignments and concludes that they can be avoided by decreasing the structure heights on both sides of the membrane and by pre-programming size differences between the front- and back-side zone plates.

MHz frame rate hard X-ray phase-contrast imaging using synchrotron radiation.

Third generation synchrotron light sources offer high photon flux, partial spatial coherence, and ~10-10 s pulse widths. These enable hard X-ray phase-contrast imaging (XPCI) with single-bunch temporal resolutions. In this work, we exploited the MHz repetition rates of synchrotron X-ray pulses combined with indirect X-ray detection to demonstrate the potential of XPCI with millions of frames per second multiple-frame recording. This allows for the visualization of aperiodic or stochastic transient processes which are impossible to be realized using single-shot or stroboscopic XPCI. We present observations of various phenomena, such as crack tip propagation in glass, shock wave propagation in water and explosion during electric arc ignition, which evolve in the order of km/s (µm/ns).

Experimental X-Ray Ghost Imaging.

We report an experimental proof of principle for ghost imaging in the hard-x-ray energy range. We use a synchrotron x-ray beam that is split using a thin crystal in Laue diffraction geometry. With an ultrafast imaging camera, we are able to image x rays generated by isolated electron bunches. At this time scale, the shot noise of the synchrotron emission process is measurable as speckles, leading to speckle correlation between the two beams. The integrated transmitted intensity from a sample located in the first beam is correlated with the spatially resolved intensity measured in the second, empty, beam to retrieve the shadow of the sample. The demonstration of ghost imaging with hard x rays may open the way to protocols to reduce radiation damage in medical imaging and in nondestructive structural characterization using free electron lasers.

Erratum: Experimental X-Ray Ghost Imaging [Phys. Rev. Lett. 117, 113902 (2016)].

This corrects the article DOI: 10.1103/PhysRevLett.117.113902.

Upper bound on the Edwards entropy in frictional monodisperse hard-sphere packings.

We extend the Widom particle insertion method [B. Widom, J. Chem. Phys., 1963, 39, 2808-2812] to determine an upper bound sub on the Edwards entropy in frictional hard-sphere packings. sub corresponds to the logarithm of the number of mechanically stable configurations for a given volume fraction and boundary conditions. To accomplish this, we extend the method for estimating the particle insertion probability through the pore-size distribution in frictionless packings [V. Baranau, et al., Soft Matter, 2013, 9, 3361-3372] to the case of frictional particles. We use computer-generated and experimentally obtained three-dimensional sphere packings with volume fractions φ in the range 0.551-0.65. We find that sub has a maximum in the vicinity of the Random Loose Packing Limit φRLP = 0.55 and decreases then monotonically with increasing φ to reach a minimum at φ = 0.65. Further on, sub does not distinguish between real mechanical stability and packings in close proximity to mechanical stable configurations. The probability to find a given number of contacts for a particle inserted in a large enough pore does not depend on φ, but it decreases strongly with the contact number.

Investigating lithium-ion battery materials during overcharge-induced thermal runaway: an operando and multi-scale X-ray CT study.

Catastrophic failure of lithium-ion batteries occurs across multiple length scales and over very short time periods. A combination of high-speed operando tomography, thermal imaging and electrochemical measurements is used to probe the degradation mechanisms leading up to overcharge-induced thermal runaway of a LiCoO2 pouch cell, through its interrelated dynamic structural, thermal and electrical responses. Failure mechanisms across multiple length scales are explored using a post-mortem multi-scale tomography approach, revealing significant morphological and phase changes in the LiCoO2 electrode microstructure and location dependent degradation. This combined operando and multi-scale X-ray computed tomography (CT) technique is demonstrated as a comprehensive approach to understanding battery degradation and failure.

Investigating the influence of freezing rate and frozen storage conditions on a model sponge cake using synchrotron X-rays micro-computed tomography.

Synchrotron X-rays micro-computed tomography was applied to visualize and quantify 3D ice crystal changes into a model sponge cake after freezing and subsequent frozen storage. Model sponge cake samples were submitted to two different freezing rates (fast: 17.2 °C min-1 and slow: 0.3 °C min-1), then stored at constant and fluctuating temperatures over a two weeks period. 3D images were acquired at frozen state thanks to a thermostated cell (CellStat) and processed using a grey level based segmentation method. Image analysis revealed that the ice volume fraction is conserved during storage but ice crystal size and location change whatever the freezing rate and the storage conditions. Maximum local thicknesses increase both inside (from 20 µm to 50 µm) and outside (from 47 µm to 70 µm) the matrix during the fourteen days storage period. Both specific surface areas between starch and ice (SSAice/starch) and between air and ice (SSAair/ice) also evolve with storage duration: SSAice/starch decreases up to - 30 % while SSAair/ice increases up to + 13 % depending on the freezing rates and the storage conditions. These results highlighted that, during storage, ice crystals evolve according to two different mechanisms depending on the freezing rate: fast freezing leads to a local redistribution of water both within the starch matrix and within the pores, while slow freezing results in both local redistribution within the starch matrix and water migration towards the pores. In addition, stable storage temperatures favor local water redistribution whereas water migration from the starch matrix towards the pores was greater in the case of fluctuating storage temperatures. This study shows that freezing and frozen storage conditions have a synergistic effect on the microstructure evolution of sponge cake due to recrystallization phenomena.

Virtual histology of an entire mouse brain from formalin fixation to paraffin embedding. Part 2: Volumetric strain fields and local contrast changes.

BACKGROUND: Fixation and embedding of post mortem brain tissue is a pre-requisite for both gold-standard conventional histology and X-ray virtual histology. This process alters the morphology and density of the brain microanatomy. NEW METHOD: To quantify these changes, we employed synchrotron radiation-based hard X-ray tomography with 3 µm voxel length to visualize the same mouse brain after fixation in 4% formalin, immersion in ethanol solutions (50%, 70%, 80%, 90%, and 100%), xylene, and finally after embedding in a paraffin block. The volumetric data were non-rigidly registered to the initial formalin-fixed state to align the microanatomy within the entire mouse brain. RESULTS: Volumetric strain fields were used to characterize local shrinkage, which was found to depend on the anatomical region and distance to external surface. X-ray contrast was altered and enhanced by preparation-induced inter-tissue density changes. The preparation step can be selected to highlight specific anatomical features. For example, fiber tract contrast is amplified in 100% ethanol. COMPARISON WITH EXISTING METHODS: Our method provides volumetric strain fields, unlike approaches based on feature-to-feature or volume measurements. Volumetric strain fields are produced by non-rigid registration, which is less labor-intensive and observer-dependent than volume change measurements based on manual segmentations. X-ray microtomography provides spatial resolution at least an order of magnitude higher than magnetic resonance microscopy, allowing for analysis of morphology and density changes within the brain's microanatomy. CONCLUSION: Our approach belongs to three-dimensional virtual histology with isotropic micrometer spatial resolution and therefore complements atlases based on a combination of magnetic resonance microscopy and optical micrographs of serial histological sections.

Comparative hard x-ray tomography for virtual histology of zebrafish larva, human tooth cementum, and porcine nerve.

Purpose: Synchrotron radiation-based tomography yields microanatomical features in human and animal tissues without physical slicing. Recent advances in instrumentation have made laboratory-based phase tomography feasible. We compared the performance of three cutting-edge laboratory systems benchmarked by synchrotron radiation-based tomography for three specimens. As an additional criterion, the user-friendliness of the three microtomography systems was considered. Approach: The three tomography systems-SkyScan 2214 (Bruker-microCT, Kontich, Belgium), Exciscope prototype (Stockholm, Sweden), and Xradia 620 Versa (Zeiss, Oberkochen, Germany)-were given 36 h to measure three medically relevant specimens, namely, zebrafish larva, archaeological human tooth, and porcine nerve. The obtained datasets were registered to the benchmark synchrotron radiation-based tomography from the same specimens and selected ones to the SkyScan 1275 and phoenix nanotom m® laboratory systems to characterize development over the last decade. Results: Next-generation laboratory-based microtomography almost reached the quality achieved by synchrotron-radiation facilities with respect to spatial and density resolution, as indicated by the visualization of the medically relevant microanatomical features. The SkyScan 2214 system and the Exciscope prototype demonstrated the complementarity of phase information by imaging the eyes of the zebrafish larva. The 3 - µ m thin annual layers in the tooth cementum were identified using Xradia 620 Versa. Conclusions: SkyScan 2214 was the simplest system and was well-suited to visualizing the wealth of anatomical features in the zebrafish larva. Data from the Exciscope prototype with the high photon flux from the liquid metal source showed the spiral nature of the myelin sheaths in the porcine nerve. Xradia 620 Versa, with detector optics as typically installed for synchrotron tomography beamlines, enabled the three-dimensional visualization of the zebrafish larva with comparable quality to the synchrotron data and the annual layers in the tooth cementum.

Metal-Organic Framework Photonic Balls: Single Object Analysis for Local Thermal Probing.

Due to their high porosity and chemical versatility, metal-organic frameworks (MOFs) exhibit physical properties appealing for photonic-based applications. While several MOF photonic structures have been reported, examples of applications thereof are mainly limited to chemical sensing. Herein, the range of application of photonic MOFs is extended to local thermal and photothermal sensing by integrating them into a new architecture: MOF photonic balls. Micrometric-sized photonic balls are made of monodispersed MOFs colloids that are self-assembled via spray-drying, a low-cost, green, and high-throughput method. The versatility of the process allows tuning the morphology and the composition of photonic balls made of several MOFs and composites with tailored optical properties. X-ray nanotomography and environmental hyperspectral microscopy enable analysis of single objects and their evolution in controlled atmosphere and temperature. Notably, in presence of vapors, the MOF photonic balls act as local, label-free temperature probes. Importantly, compared to other thermal probes, the temperature detection range of these materials can be adjusted "on-demand." As proof of concept, the photonic balls are used to determine local temperature profiles around a concentrated laser beam. More broadly, this work is expected to stimulate new research on the physical properties of photonic MOFs providing new possibilities for device fabrication.

Virtual histology of an entire mouse brain from formalin fixation to paraffin embedding. Part 1: Data acquisition, anatomical feature segmentation, tracking global volume and density changes.

BACKGROUND: Micrometer-resolution neuroimaging with gold-standard conventional histology requires tissue fixation and embedding. The exchange of solvents for the creation of sectionable paraffin blocks modifies tissue density and generates non-uniform brain shrinkage. NEW METHOD: We employed synchrotron radiation-based X-ray microtomography for slicing- and label-free virtual histology of the mouse brain at different stages of the standard preparation protocol from formalin fixation via ascending ethanol solutions and xylene to paraffin embedding. Segmentation of anatomical regions allowed us to quantify non-uniform tissue shrinkage. Global and local changes in X-ray absorption gave insight into contrast enhancement for virtual histology. RESULTS: The volume of the entire mouse brain was 60%, 56%, and 40% of that in formalin for, respectively, 100% ethanol, xylene, and paraffin. The volume changes of anatomical regions such as the hippocampus, anterior commissure, and ventricles differ from the global volume change. X-ray absorption of the full brain decreased, while local absorption differences increased, resulting in enhanced contrast for virtual histology. These trends were also observed with laboratory microtomography measurements. COMPARISON WITH EXISTING METHODS: Microtomography provided sub-10 µm spatial resolution with sufficient density resolution to resolve anatomical structures at each step of the embedding protocol. The spatial resolution of conventional computed tomography and magnetic resonance microscopy is an order of magnitude lower and both do not match the contrast of microtomography over the entire embedding protocol. Unlike feature-to-feature or total volume measurements, our approach allows for calculation of volume change based on segmentation. CONCLUSION: We present isotropic micrometer-resolution imaging to quantify morphology and composition changes in a mouse brain during the standard histological preparation. The proposed method can be employed to identify the most appropriate embedding medium for anatomical feature visualization, to reveal the basis for the dramatic X-ray contrast enhancement observed in numerous embedded tissues, and to quantify morphological changes during tissue fixation and embedding.

Formation of bridgmanite-enriched layer at the top lower-mantle during magma ocean solidification.

Thermochemical heterogeneities detected today in the Earth's mantle could arise from ongoing partial melting in different mantle regions. A major open question, however, is the level of chemical stratification inherited from an early magma-ocean (MO) solidification. Here we show that the MO crystallized homogeneously in the deep mantle, but with chemical fractionation at depths around 1000 km and in the upper mantle. Our arguments are based on accurate measurements of the viscosity of melts with forsterite, enstatite and diopside compositions up to ~30 GPa and more than 3000 K at synchrotron X-ray facilities. Fractional solidification would induce the formation of a bridgmanite-enriched layer at ~1000 km depth. This layer may have resisted to mantle mixing by convection and cause the reported viscosity peak and anomalous dynamic impedance. On the other hand, fractional solidification in the upper mantle would have favored the formation of the first crust.

The Role of Local Instabilities in Fluid Invasion into Permeable Media.

Wettability is an important factor which controls the displacement of immiscible fluids in permeable media, with far reaching implications for storage of CO2 in deep saline aquifers, fuel cells, oil recovery, and for the remediation of oil contaminated soils. Considering the paradigmatic case of random piles of spherical beads, fluid front morphologies emerging during slow immiscible displacement are investigated in real time by X-ray micro-tomography and quantitatively compared with model predictions. Controlled by the wettability of the bead matrix two distinct displacement patterns are found. A compact front morphology emerges if the invading fluid wets the beads while a fingered morphology is found for non-wetting invading fluids, causing the residual amount of defending fluid to differ by one order of magnitude. The corresponding crossover between these two regimes in terms of the advancing contact angle is governed by an interplay of wettability and pore geometry and can be predicted on the basis of a purely quasi-static consideration of local instabilities that control the progression of the invading interface.

Electromigration Mechanism of Failure in Flip-Chip Solder Joints Based on Discrete Void Formation.

In this investigation, SnAgCu and SN100C solders were electromigration (EM) tested, and the 3D laminography imaging technique was employed for in-situ observation of the microstructure evolution during testing. We found that discrete voids nucleate, grow and coalesce along the intermetallic compound/solder interface during EM testing. A systematic analysis yields quantitative information on the number, volume, and growth rate of voids, and the EM parameter of DZ*. We observe that fast intrinsic diffusion in SnAgCu solder causes void growth and coalescence, while in the SN100C solder this coalescence was not significant. To deduce the current density distribution, finite-element models were constructed on the basis of the laminography images. The discrete voids do not change the global current density distribution, but they induce the local current crowding around the voids: this local current crowding enhances the lateral void growth and coalescence. The correlation between the current density and the probability of void formation indicates that a threshold current density exists for the activation of void formation. There is a significant increase in the probability of void formation when the current density exceeds half of the maximum value.

Real-time direct and diffraction X-ray imaging of irregular silicon wafer breakage.

Fracture and breakage of single crystals, particularly of silicon wafers, are multi-scale problems: the crack tip starts propagating on an atomic scale with the breaking of chemical bonds, forms crack fronts through the crystal on the micrometre scale and ends macroscopically in catastrophic wafer shattering. Total wafer breakage is a severe problem for the semiconductor industry, not only during handling but also during temperature treatments, leading to million-dollar costs per annum in a device production line. Knowledge of the relevant dynamics governing perfect cleavage along the {111} or {110} faces, and of the deflection into higher indexed {hkl} faces of higher energy, is scarce due to the high velocity of the process. Imaging techniques are commonly limited to depicting only the state of a wafer before the crack and in the final state. This paper presents, for the first time, in situ high-speed crack propagation under thermal stress, imaged simultaneously in direct transmission and diffraction X-ray imaging. It shows how the propagating crack tip and the related strain field can be tracked in the phase-contrast and diffracted images, respectively. Movies with a time resolution of microseconds per frame reveal that the strain and crack tip do not propagate continuously or at a constant speed. Jumps in the crack tip position indicate pinning of the crack tip for about 1-2 ms followed by jumps faster than 2-6 m s(-1), leading to a macroscopically observed average velocity of 0.028-0.055 m s(-1). The presented results also give a proof of concept that the described X-ray technique is compatible with studying ultra-fast cracks up to the speed of sound.

Liquid morphologies and capillary forces between three spherical beads.

Equilibrium shapes of coalesced pendular bridges in a static assembly of spherical beads are computed by numerical minimization of the interfacial energy. Our present study focuses on generic bead configurations involving three beads, one of which is in contact to the two others while there is a gap of variable size between the latter. In agreement with previous experimental studies, we find interfacial "trimer" morphologies consisting of three coalesced pendular bridges, and "dimers" of two coalesced bridges. In a certain range of the gap opening we observe a bistability between the dimer and trimer morphology during changes of the liquid volume. The magnitude of the corresponding capillary forces in presence of a trimer or dimer depends, besides the gap opening, only on the volume or Laplace pressure of the liquid. For a given Laplace pressure, and for the same gap opening, the capillary forces induced by a trimer are only slightly larger than the corresponding forces in the presence of three pendular bridges. This observation is consistent with a plateau of capillary cohesion in terms of the saturation of a wetting liquid in the funicular regime, as reported in the experimental work [Scheel et al., Nat. Mater. 7, 189 (2008)1476-112210.1038/nmat2117].

Quantifying Bulk Electrode Strain and Material Displacement within Lithium Batteries via High-Speed Operando Tomography and Digital Volume Correlation.

Tracking the dynamic morphology of active materials during operation of lithium batteries is essential for identifying causes of performance loss. Digital volume correlation (DVC) is applied to high-speed operando synchrotron X-ray computed tomography of a commercial Li/MnO2 primary battery during discharge. Real-time electrode material displacement is captured in 3D allowing degradation mechanisms such as delamination of the electrode from the current collector and electrode crack formation to be identified. Continuum DVC of consecutive images during discharge is used to quantify local displacements and strains in 3D throughout discharge, facilitating tracking of the progression of swelling due to lithiation within the electrode material in a commercial, spiral-wound battery during normal operation. Displacement of the rigid current collector and cell materials contribute to severe electrode detachment and crack formation during discharge, which is monitored by a separate DVC approach. Use of time-lapse X-ray computed tomography coupled with DVC is thus demonstrated as an effective diagnostic technique to identify causes of performance loss within commercial lithium batteries; this novel approach is expected to guide the development of more effective commercial cell designs.

In-operando high-speed tomography of lithium-ion batteries during thermal runaway.

Prevention and mitigation of thermal runaway presents one of the greatest challenges for the safe operation of lithium-ion batteries. Here, we demonstrate for the first time the application of high-speed synchrotron X-ray computed tomography and radiography, in conjunction with thermal imaging, to track the evolution of internal structural damage and thermal behaviour during initiation and propagation of thermal runaway in lithium-ion batteries. This diagnostic approach is applied to commercial lithium-ion batteries (LG 18650 NMC cells), yielding insights into key degradation modes including gas-induced delamination, electrode layer collapse and propagation of structural degradation. It is envisaged that the use of these techniques will lead to major improvements in the design of Li-ion batteries and their safety features.