Cryo-X-Ray Phase Contrast Imaging Enables Combined 3D Structural Quantification and Nucleic Acid Analysis of Myocardial Biopsies.

Snap-frozen biopsies serve as a valuable clinical resource of archival material for disease research, as they enable a comprehensive array of downstream analyses to be performed, including extraction and sequencing of nucleic acids. Obtaining three-dimensional (3D) structural information before multi-omics is more challenging but can potentially allow for better characterization of tissues and targeting of clinically relevant cells. Conventional histological techniques are limited in this regard due to their destructive nature and the reconstruction artifacts produced by sectioning, dehydration, and chemical processing. These limitations are particularly notable in soft tissues such as the heart. In this study, the feasibility of using synchrotron-based cryo-X-ray phase contrast imaging (cryo-X-PCI) of snap-frozen myocardial biopsies is assessed and 3D structure tensor analysis of aggregated myocytes, followed by nucleic acid (DNA and RNA) extraction and analysis. It is shown that optimal sample preparation is the key driver for successful structural and nucleic acid preservation which is unaffected by the process of cryo-X-PCI. It is proposed that cryo-X-PCI has clinical value for 3D tissue analysis of cardiac and potentially non-cardiac soft tissue biopsies before nucleic acid investigation.

Dynamic X-ray Microtomography vs. Laser-Doppler Vibrometry: A Comparative Study.

Purpose: There are challenges in understanding the biomechanics of the human middle ear, and established methods for studying this system show significant limitations. In this study, we evaluate a novel dynamic imaging technique based on synchrotron X-ray microtomography designed to assess the biomechanical properties of the human middle ear by comparing it to laser-Doppler vibrometry (LDV). Methods: We examined three fresh-frozen temporal bones (TB) using dynamic synchrotron-based X-ray microtomography for 256 Hz and 512 Hz, stimulated at 110 dB and 120 dB SPL. In addition, we performed measurements on these TBs using 1D LDV, a well-established method. Results: The normalized displacement values (µm/Pa) at the umbo and the posterior crus of the stapes are consistent or within 5-10 dB differences between all LDV and dynamic microtomography measurements and previously reported literature references. In general, the overall behavior is similar between the two measurement techniques. Conclusion: In conclusion, our results demonstrate the suitability of dynamic synchrotron-based X-ray microtomography in studying the middle ear's biomechanics. However, this study shows that better standardization regarding acoustic stimulation and measurement points is needed to better compare the two measurement techniques.

Characterizing bone density pattern and porosity in the human ossicular chain using synchrotron microtomography.

The auditory ossicles amplify and transmit sound from the environment to the inner ear. The distribution of bone mineral density is crucial for the proper functioning of sound transmission as the ossicles are suspended in an air-filled chamber. However, little is known about the distribution of bone mineral density along the human ossicular chain and within individual ossicles. To investigate this, we analyzed fresh-frozen human specimens using synchrotron-based phase-contrast microtomography. In addition, we analyzed the volume and porosity of the ossicles. The porosity for the auditory ossicles lies, on average, between 1.92% and 9.85%. The average volume for the mallei is 13.85 ± 2.15 mm3, for the incudes 17.62 ± 4.05 mm3 and 1.24 ± 0.29 mm3 for the stapedes. The bone density distribution showed a similar pattern through all samples. In particular, we found high bone mineralization spots on the anterior crus of the stapes, its footplate, and along areas that are crucial for the transmission of sound. We could also see a correlation between low bone mineral density and holey areas where the bone is only very thin or missing. Our study identified a similar pattern of bone density distribution within all samples: regions exposed to lower forces generally show higher bone density. Further, we observed that the stapes shows high bone mineral density along the anterior crus and its footplate, which may indicate its importance in transmitting sound waves to the inner ear.

The human middle ear in motion: 3D visualization and quantification using dynamic synchrotron-based X-ray imaging.

The characterization of the vibrations of the middle ear ossicles during sound transmission is a focal point in clinical research. However, the small size of the structures, their micrometer-scale movement, and the deep-seated position of the middle ear within the temporal bone make these types of measurements extremely challenging. In this work, dynamic synchrotron-based X-ray phase-contrast microtomography is used on acoustically stimulated intact human ears, allowing for the three-dimensional visualization of entire human eardrums and ossicular chains in motion. A post-gating algorithm is used to temporally resolve the fast micromotions at 128 Hz, coupled with a high-throughput pipeline to process the large tomographic datasets. Seven ex-vivo fresh-frozen human temporal bones in healthy conditions are studied, and the rigid body motions of the ossicles are quantitatively delineated. Clinically relevant regions of the ossicular chain are tracked in 3D, and the amplitudes of their displacement are computed for two acoustic stimuli.

LiOH Decomposition by NiO/ZrO2 in Li-Air Battery: Chemical Imaging with Operando Synchrotron Diffraction and Correlative Neutron/X-Ray Computed-Tomography Analysis.

Li-air batteries attract significant attention due to their highest theoretical energy density among all existing energy storage technologies. Currently, challenges related to extending lifetime and long-term stability limit their practical application. To overcome these issues and enhance the total capacity of Li-air batteries, this study introduces an innovative approach with NiO/ZrO2 catalysts. Operando advanced chemical imaging with micrometer spatial resolution unveils that NiO/ZrO2 catalysts substantially change the kinetics of crystalline lithium hydroxide (LiOH) formation and facilitate its rapid decomposition with heterogeneous distribution. Moreover, ex situ combined neutron and X-ray computed tomography (CT) analysis, provide evidence of distinct lithium phases homogeneously distributed in the presence of NiO/ZrO2. These findings underscore the material's superior physico-chemical and electronic properties, with more efficient oxygen diffusion and indications of lower obstruction to its active sites, avoiding clogging in the active electrode, a common cause of capacity loss. Electrochemical tests conducted at high current density demonstrated a significant kinetic enhancement of the oxygen reduction and evolution reactions, resulting in improved charge and discharge processes with low overpotential. This pioneering approach using NiO/ZrO2 catalysts represents a step toward on developing the full potential of Li-air batteries as high-energy-density energy storage systems.

From Corrosion Casting to Virtual Dissection: Contrast-Enhanced Vascular Imaging using Hafnium Oxide Nanocrystals.

Vascular corrosion casting is a method used to visualize the three dimensional (3D) anatomy and branching pattern of blood vessels. A polymer resin is injected in the vascular system and, after curing, the surrounding tissue is removed. The latter often deforms or even fractures the fragile cast. Here, a method is proposed that does not require corrosion, and is based on in situ micro computed tomography (micro-CT) scans. To overcome the lack of CT contrast between the polymer cast and the animals' surrounding soft tissue, hafnium oxide nanocrystals (HfO2 NCs) are introduced as CT contrast agents into the resin. The NCs dramatically improve the overall CT contrast of the cast and allow for straightforward segmentation in the CT scans. Careful design of the NC surface chemistry ensures the colloidal stability of the NCs in the casting resin. Using only 5 m% of HfO2 NCs, high-quality cardiovascular casts of both zebrafish and mice can be automatically segmented using CT imaging software. This allows to differentiate even µ $\umu$ m-scale details without having to alter the current resin injection methods. This new method of virtual dissection by visualizing casts in situ using contrast-enhanced CT imaging greatly expands the application potential of the technique.

Feasibility and safety of synchrotron-based X-ray phase contrast imaging as a technique complementary to histopathology analysis.

X-ray phase contrast imaging (X-PCI) is a powerful technique for high-resolution, three-dimensional imaging of soft tissue samples in a non-destructive manner. In this technical report, we assess the quality of standard histopathological techniques performed on formalin-fixed, paraffin-embedded (FFPE) human tissue samples that have been irradiated with different doses of X-rays in the context of an X-PCI experiment. The data from this study demonstrate that routine histochemical and immunohistochemical staining quality as well as DNA and RNA analyses are not affected by previous X-PCI on human FFPE samples. From these data we conclude it is feasible and acceptable to perform X-PCI on FFPE human biopsies.

A Novel Three-Dimensional Approach Towards Evaluating Endomyocardial Biopsies for Follow-Up After Heart Transplantation: X-Ray Phase Contrast Imaging and Its Agreement With Classical Histopathology.

Endomyocardial biopsies are the gold standard for surveillance of graft rejection following heart transplantation, and are assessed by classical histopathology using a limited number of previously stained slices from several biopsies. Synchrotron propagation-based X-ray phase contrast imaging is a non-destructive method to image biological samples without tissue preparation, enabling virtual 2D and 3D histopathology. We aimed to show the feasibility of this method to assess acute cellular rejection and its agreement to classical histopathology. Right ventricular biopsies were sampled from 23 heart transplantation recipients (20 males, mean age 54±14 years) as part of standard follow-up. The clinical diagnosis of potential rejection was made using classical histopathology. One additional study sample was harvested and imaged by X-ray phase contrast imaging, producing 3D datasets with 0.65 µm pixel size, and up to 4,320 images per sample. An experienced pathologist graded both histopathological and X-ray phase contrast images in a blinded fashion. The agreement between methods was assessed by weighted kappa, showing substantial agreement (kappa up to 0.80, p < 0.01) between X-ray phase contrast imaging and classical histopathology. X-ray phase contrast imaging does not require tissue processing, allows thorough analysis of a full myocardial sample and allows identification of acute cellular rejection.

Refractive axicon for X-ray microscopy applications: design, optimization, and experiment.

In a full-field transmission X-ray microscopy (TXM) setup, a condenser X-ray optical element is used to illuminate the sample by condensing the X-ray beam delivered by the synchrotron storage ring. On-going and future upgrades of synchrotron facilities to diffraction-limited storage rings will pose new challenges to these TXM setups, such as much smaller X-ray beams on the condenser. Here, we demonstrate that a refractive axicon can be used as an X-ray beam shaper to match the ring-shaped aperture of the condenser. Aiming at more efficient use of the incoming X-ray intensity, we explore several axicon designs both analytically and with numerical simulations. The axicons were produced by two-photon polymerization 3D printing on thin silicon nitride membrane substrates. The first characterization of the axicon was carried out at the TOMCAT beamline of the Swiss Light Source (Switzerland).

Sample Preparation and Warping Accuracy for Correlative Multimodal Imaging in the Mouse Olfactory Bulb Using 2-Photon, Synchrotron X-Ray and Volume Electron Microscopy.

Integrating physiology with structural insights of the same neuronal circuit provides a unique approach to understanding how the mammalian brain computes information. However, combining the techniques that provide both streams of data represents an experimental challenge. When studying glomerular column circuits in the mouse olfactory bulb, this approach involves e.g., recording the neuronal activity with in vivo 2-photon (2P) calcium imaging, retrieving the circuit structure with synchrotron X-ray computed tomography with propagation-based phase contrast (SXRT) and/or serial block-face scanning electron microscopy (SBEM) and correlating these datasets. Sample preparation and dataset correlation are two key bottlenecks in this correlative workflow. Here, we first quantify the occurrence of different artefacts when staining tissue slices with heavy metals to generate X-ray or electron contrast. We report improvements in the staining procedure, ultimately achieving perfect staining in ∼67% of the 0.6 mm thick olfactory bulb slices that were previously imaged in vivo with 2P. Secondly, we characterise the accuracy of the spatial correlation between functional and structural datasets. We demonstrate that direct, single-cell precise correlation between in vivo 2P and SXRT tissue volumes is possible and as reliable as correlating between 2P and SBEM. Altogether, these results pave the way for experiments that require retrieving physiology, circuit structure and synaptic signatures in targeted regions. These correlative function-structure studies will bring a more complete understanding of mammalian olfactory processing across spatial scales and time.

Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron microtomography and volume electron microscopy.

Understanding the function of biological tissues requires a coordinated study of physiology and structure, exploring volumes that contain complete functional units at a detail that resolves the relevant features. Here, we introduce an approach to address this challenge: Mouse brain tissue sections containing a region where function was recorded using in vivo 2-photon calcium imaging were stained, dehydrated, resin-embedded and imaged with synchrotron X-ray computed tomography with propagation-based phase contrast (SXRT). SXRT provided context at subcellular detail, and could be followed by targeted acquisition of multiple volumes using serial block-face electron microscopy (SBEM). In the olfactory bulb, combining SXRT and SBEM enabled disambiguation of in vivo-assigned regions of interest. In the hippocampus, we found that superficial pyramidal neurons in CA1a displayed a larger density of spine apparati than deeper ones. Altogether, this approach can enable a functional and structural investigation of subcellular features in the context of cells and tissues.

Sub-micrometer morphology of human atherosclerotic plaque revealed by synchrotron radiation-based µCT-A comparison with histology.

Histology is a long standing and well-established gold standard for pathological characterizations. In recent years however, synchrotron radiation-based micro-computed tomography (SRµCT) has become a tool for extending the imaging of two-dimensional thin sections into three-dimensional imaging of tissue blocks, enabling so-called virtual histology with arbitrary clipping planes, volumetric rendering and automatic segmentation. In this study, we present a thorough characterization of human carotid plaques after endarterectomy of patients with stroke or transient ischemic attack (TIA), investigating several different pathologic structures using both SRµCT and histology. Phase-contrast SRµCT was performed with two different magnifications (voxel sizes 6.5 µm and 0.65 µm, respectively), and histology was performed with multiple different stainings (Alpha-actin, Glycophorin A, von Kossa, Movat, CD68). The 0.65 µm high-resolution SRµCT was performed on selected areas with plaque typical relevant morphology, identified on the 6.5 µm low-resolution SRµCT. The tomography datasets were reconstructed with additional 3D volume rendering and compared to histology. In total, nine different regions with typical pathologic structures were identified and imaged with high-resolution SRµCT. The results show many characteristics typical for advanced atherosclerotic plaques, clinically relevant, namely ruptures with thrombosis, neo-vascularization, inflammatory infiltrates in shoulder regions, lipid rich necrotic cores (LRNC), thin fibrous cap, calcifications, lumen irregularities, and changes in vessel wall structures such as the internal elastic membrane. This method's non-destructive nature renders details of micro-structures with an excellent visual likeness to histology, with the additional strength of multiplanar and 3D visualization and the possibility of multiple re-scans.

Biomimetic Light-Driven Aerogel Passive Pump for Volatile Organic Pollutant Removal.

Inspired by the solar-light-driven oxygen transportation in aquatic plants, a biomimetic sustainable light-driven aerogel pump with a surface layer containing black manganese oxide (MnO2 ) as an optical absorber is developed. The flow intensity of the pumped air is controlled by the pore structure of nanofilbrillated cellulose, urea-modified chitosan, or polymethylsilsesquioxane (PMSQ) aerogels. The MnO2 -induced photothermal conversion drives both the passive gas flow and the catalytic degradation of volatile organic pollutants. All investigated aerogels demonstrate superior pumping compared to benchmarked Knudsen pump systems, but the inorganic PMSQ aerogels provide the highest flexibility in terms of the input power and photothermal degradation activity. Aerogel light-driven multifunctional gas pumps offer a broad future application potential for gas-sensing devices, air-quality mapping, and air quality control systems.

A tomographic microscopy-compatible Langendorff system for the dynamic structural characterization of the cardiac cycle.

Introduction: Cardiac architecture has been extensively investigated ex vivo using a broad spectrum of imaging techniques. Nevertheless, the heart is a dynamic system and the structural mechanisms governing the cardiac cycle can only be unveiled when investigating it as such. Methods: This work presents the customization of an isolated, perfused heart system compatible with synchrotron-based X-ray phase contrast imaging (X-PCI). Results: Thanks to the capabilities of the developed setup, it was possible to visualize a beating isolated, perfused rat heart for the very first time in 4D at an unprecedented 2.75 µm pixel size (10.6 µm spatial resolution), and 1 ms temporal resolution. Discussion: The customized setup allows high-spatial resolution studies of heart architecture along the cardiac cycle and has thus the potential to serve as a tool for the characterization of the structural dynamics of the heart, including the effects of drugs and other substances able to modify the cardiac cycle.

Micro- and Nano-Scales Three-Dimensional Characterisation of Softwood.

Understanding the mechanical response of cellular biological materials to environmental stimuli is of fundamental importance from an engineering perspective in composites. To provide a deep understanding of their behaviour, an exhaustive analytical and experimental protocol is required. Attention is focused on softwood but the approach can be applied to a range of cellular materials. This work presents a new non-invasive multi-scale approach for the investigation of the hygro-mechanical behaviour of softwood. At the TOMCAT beamline of the Paul Scherrer Institute, in Switzerland, the swelling behaviour of softwood was probed at the cellular and sub-cellular scales by means of 3D high-resolution phase-contrast X-ray imaging. At the cellular scale, new findings in the anisotropic and reversible swelling behaviour of softwood and in the origin of swelling hysteresis of porous materials are explained from a mechanical perspective. However, the mechanical and moisture properties of wood highly depend on sub-cellular features of the wood cell wall, such as bordered pits, yielding local deformations during a full hygroscopic loading protocol.

Comprehensive assessment of myocardial remodeling in ischemic heart disease by synchrotron propagation based X-ray phase contrast imaging.

Cardiovascular research is in an ongoing quest for a superior imaging method to integrate gross-anatomical information with microanatomy, combined with quantifiable parameters of cardiac structure. In recent years, synchrotron radiation-based X-ray Phase Contrast Imaging (X-PCI) has been extensively used to characterize soft tissue in detail. The objective was to use X-PCI to comprehensively quantify ischemic remodeling of different myocardial structures, from cell to organ level, in a rat model of myocardial infarction. Myocardial infarction-induced remodeling was recreated in a well-established rodent model. Ex vivo rodent hearts were imaged by propagation based X-PCI using two configurations resulting in 5.8 µm and 0.65 µm effective pixel size images. The acquired datasets were used for a comprehensive assessment of macrostructural changes including the whole heart and vascular tree morphology, and quantification of left ventricular myocardial thickness, mass, volume, and organization. On the meso-scale, tissue characteristics were explored and compared with histopathological methods, while microstructural changes were quantified by segmentation of cardiomyocytes and calculation of cross-sectional areas. Propagation based X-PCI provides detailed visualization and quantification of morphological changes on whole organ, tissue, vascular as well as individual cellular level of the ex vivo heart, with a single, non-destructive 3D imaging modality.

Etiology-Discriminative Multimodal Imaging of Left Ventricular Hypertrophy and Synchrotron-Based Assessment of Microstructural Tissue Remodeling.

Background: Distinguishing the etiology of left ventricular hypertrophy (LVH) is clinically relevant due to patient outcomes and management. Easily obtained, echocardiography-based myocardial deformation patterns may improve standard non-invasive phenotyping, however, the relationship between deformation phenotypes and etiology-related, microstructural cardiac remodeling has not been reported. Synchrotron radiation-based X-ray phase-contrast imaging (X-PCI) can provide high resolution, three-dimensional (3D) information on myocardial microstructure. The aim of this pilot study is to apply a multiscale, multimodality protocol in LVH patients undergoing septal myectomy to visualize in vivo and ex vivo myocardial tissue and relate non-invasive LVH imaging phenotypes to the underlying synchrotron-assessed microstructure. Methods and findings: Three patients (P1-3) undergoing septal myectomy were comprehensively studied. Medical history was collected, and patients were imaged with echocardiography/cardiac magnetic resonance prior to the procedure. Myocardial tissue samples obtained during the myectomy were imaged with X-PCI generating high spatial resolution images (0.65 µm) to assess myocyte organization, 3D connective tissue distribution and vasculature remodeling. Etiology-centered non-invasive imaging phenotypes, based on findings of hypertrophy and late gadolinium enhancement (LGE) distribution, and enriched by speckle-tracking and tissue Doppler echocardiography deformation patterns, identified a clear phenotype of hypertensive heart disease (HTN) in P1, and hypertrophic cardiomyopathy (HCM) in P2/P3. X-PCI showed extensive interstitial fibrosis with normal 3D myocyte and collagen organization in P1. In comparison, in P2/P3, X-PCI showed 3D myocyte and collagen disarray, as well as arterial wall hypertrophy with increased perivascular collagen, compatible with sarcomere-mutation HCM in both patients. The results of this pilot study suggest the association of non-invasive deformation phenotypes with etiology-related myocyte and connective tissue matrix disorganization. A larger patient cohort could enable statistical analysis of group characteristics and the assessment of deformation pattern reproducibility. Conclusion: High-resolution, 3D X-PCI provides novel ways to visualize myocardial remodeling in LVH, and illustrates the correspondence of macrostructural and functional non-invasive phenotypes with invasive microstructural phenotypes, suggesting the potential clinical utility of non-invasive myocardial deformation patterns in phenotyping LVH in everyday clinical practice.

Visualizing plating-induced cracking in lithium-anode solid-electrolyte cells.

Lithium dendrite (filament) propagation through ceramic electrolytes, leading to short circuits at high rates of charge, is one of the greatest barriers to realizing high-energy-density all-solid-state lithium-anode batteries. Utilizing in situ X-ray computed tomography coupled with spatially mapped X-ray diffraction, the propagation of cracks and the propagation of lithium dendrites through the solid electrolyte have been tracked in a Li/Li6PS5Cl/Li cell as a function of the charge passed. On plating, cracking initiates with spallation, conical 'pothole'-like cracks that form in the ceramic electrolyte near the surface with the plated electrode. The spallations form predominantly at the lithium electrode edges where local fields are high. Transverse cracks then propagate from the spallations across the electrolyte from the plated to the stripped electrode. Lithium ingress drives the propagation of the spallation and transverse cracks by widening the crack from the rear; that is, the crack front propagates ahead of the Li. As a result, cracks traverse the entire electrolyte before the Li arrives at the other electrode, and therefore before a short circuit occurs.

High sensitivity X-ray phase contrast imaging by laboratory grating-based interferometry at high Talbot order geometry.

X-ray phase contrast imaging is a powerful analysis technique for materials science and biomedicine. Here, we report on laboratory grating-based X-ray interferometry employing a microfocus X-ray source and a high Talbot order (35th) asymmetric geometry to achieve high angular sensitivity and high spatial resolution X-ray phase contrast imaging in a compact system (total length <1 m). The detection of very small refractive angles (∼50 nrad) at an interferometer design energy of 19 keV was enabled by combining small period X-ray gratings (1.0, 1.5 and 3.0 µm) and a single-photon counting X-ray detector (75 µm pixel size). The performance of the X-ray interferometer was fully characterized in terms of angular sensitivity and spatial resolution. Finally, the potential of laboratory X-ray phase contrast for biomedical imaging is demonstrated by obtaining high resolution X-ray phase tomographies of a mouse embryo embedded in solid paraffin and a formalin-fixed full-thickness sample of human left ventricle in water with a spatial resolution of 21.5 µm.