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The growth of plants, animals, and humans can give rise to layered structures associated with annual periodicity. Thickness variations are often correlated to nutrition supply and stress factors. The annual layers in a tree trunk with millimeter thickness can be directly counted, whereas the layers in tooth cementum with micrometer thickness are made visible using optical microscopy. These optical techniques rely on the surface evaluation or thin, optically transparent slices. Hard X-ray tomography with micrometer resolution, however, provides a three-dimensional view without physical slicing. We have developed a procedure to enhance the tomography data of annual layers in human and bovid tooth cementum. The analysis of a substantial part of an archeological human tooth demonstrated that the detected number of layers depended on the selected region and could vary between 13 and 27. The related average thickness of the annual layers was found to be (5.4 $\pm$ 1.9) $\mu$m for the human tooth, whereas the buffalo tooth exhibited a layer periodicity of 46 $\mu$m. The present study elucidates the potential of combining computational tools with high-quality micro computed tomography data to quantify the annual layers in tooth cementum for a variety of purposes including age-at-death determination., Comment: 16 pages. Event: SPIE Smart Structures + Nondestructive Evaluation, 2022, Long Beach, California, United States

Joint tissues consist of trabecular and cortical bone as well as calcified and hyaline cartilage, which presents a challenge for hard X-ray-based visualization on the sub-cellular level due to the wide range of local X-ray absorption values. The density of the calcified tissues requires rather high photon energy, which often leads to insufficient contrast within the cartilage and impedes the visualization of individual biological cells. Decalcification of the tissues reduces the total and local X-ray absorption values and allows for selecting a lower photon energy. Further contrast enhancement can be achieved by ethanol fixation and paraffin tissue embedding. In this study, we (i) searched for an appropriate visualization method to investigate lesions generated by a laser osteotome and (ii) visualized a decalcified porcine joint after ethanol fixation and subsequent paraffin embedding using laboratory- and synchrotron radiation-based microtomography. The experiments at the ANATOMIX beamline of Synchrotron SOLEIL were performed in off-axis scan mode with a pixel size of 1.3 um. Individual cells in all layers of the joint could be made visible and the effect of ethanol fixation and paraffin embedding demonstrated., Comment: 10 pages. Event: SPIE Optical Engineering + Applications, 2022, San Diego, California, United States

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.

Tooth cementum annulation (TCA) is used for determining age-at-death and stress periods based on yearly deposited lines in the root cementum of human teeth. Traditionally, TCA analysis employs optical microscopy, which requires cutting sections of the root and provides only sparse sampling in the third dimension. Ancient teeth are unique specimens that should not be sliced. In this imaging study, we show that extended field of view synchrotron radiation-based tomography provides true micrometer resolution and coverage for non-destructively surveying for incremental lines. To rapidly review the root cementum layer of four teeth from early 19th century cemetery with historical records of life events, we employed machine learning for semi-automatic detection and analysis of incremental lines. Surveying large regions of the root cementum enables detection of incremental lines and hence improves TCA analysis as an alternative to slicing of the unique teeth.

Inline phase tomography using synchrotron radiation with sub-micrometer voxel sizes is nowadays the gold standard for investigation of soft and hard tissues with micron resolution. Recent developments on detectors and X-ray sources allow the transfer of the technique into laboratory environment. For the comparison of three manufacturers, we performed microtomography with advanced laboratory microtomography devices with micron resolution on a porcine nerve, a zebrafish embryo and a historic human tooth. These data sets were also compared with data acquired at the ANATOMIX beamline at Synchrotron Soleil and the TOMCAT beamline at SLS. For the lab-based experiments following scanners were chosen: Skyscan 2214 (Bruker-microCT, Kontich, Belgium), Xradia 620 Versa (Zeiss, Oberkochen, Germany) and a prototype with a MetalJet X-ray source from Exillum from the company Exciscope (Stockholm, Sweden). All devices contained detectors including X-ray optics.

Formalin fixation and paraffin embedding of post mortem tissue specimens is widely used for high-resolution neuroimaging with both conventional and X-ray virtual histology. Exchange of embedding solutions generates non-uniform brain shrinkage and changes relative tissue densities. We used synchrotron radiation-based X-ray micro computed tomography to visualize the embedding process for a single mouse brain. Non-rigid registration was employed to determine the volumetric strain fields and to track the X-ray absorption changes of corresponding features. This allows for a correction of the observed microanatomy to improve the anatomical context. Through embedding, the entire brain shrinks to around 40% of its volume in formalin. Shrinkage is non-uniform and varies over anatomical regions and the distance to external surfaces.

X rays have been used for medical imaging since RONTGEN's fascinating discovery 125 years ago. The first radiographs of human hands were made public less than a month after his famous paper. The conventional X-ray sources integrated into the CT-machines of today’s hospitals still rely on the same physical principles. X-ray imaging has traditionally offered high spatial resolution and low contrast for soft tissues such as the brain. Magnetic resonance imaging is therefore the method of choice for brain imaging in a clinical setting, although for cellular resolution studies it suffers from limited spatial resolution. The gold standard in post mortem brain imaging is histology, which involves fixation, embedding, physical sectioning, staining, and optical microscopy. Currently, section thickness limits isotropic voxel sizes to 20 μm. Advanced X-ray sources including synchrotron radiation facilities offer complementary modalities such as phase-contrast imaging and spatially resolved small-angle X-ray scattering. We showed that X-ray phase contrast of the human cerebellum with micrometer resolution yields complementary three-dimensional images to magnetic resonance microscopy with even better contrast and spatial resolution. Grating interferometry enabled us to visualize individual Purkinje cells in the nonstained cerebellum. Taking advantage of well-established paraffin embedding, Purkinje cells were visualized within the human cerebellum even with conventional instrumentation. Hard X-ray nano-holotomography allowed for label-free, three-dimensional neuroimaging beyond the optical limit with a spatial resolution below 100 nm. Spatially resolved smallangle X-ray scattering permitted the localization of periodic nanostructures such as myelin sheaths on square-inch brain slices and included the orientational information on the axons. These developments have contributed to the establishment of virtual histology and extended the conventional histology to the third dimension. Further advances are required to image the entire human brain with an isotropic micrometer resolution and to suitably handle the petabyte datasets.

Hard X-ray micro computed tomography can be used for three-dimensional histological phenotyping of zebrafish embryos down to 1 µm or below without the need for staining or physical slicing. Current advances in ze- brafish embryo imaging, however, mostly rely on synchrotron radiation sources or highly advanced laboratory sources, which despite their evident strengths with regard to their beam properties and the implementation of phase contrast imaging techniques, lack accessibility. Therefore, we evaluated the performance of a conventional SkyScan 1275 laboratory µCT scanner in absorption contrast mode for the visualization of anatomical features in ethanol- and paraffin-embedded zebrafish embryos. We compare our results to readily available synchrotron data where 35 anatomical structures were identified. Despite having a more than ten times larger voxel length, approximately two thirds of the features could also be determined with laboratory microtomography. This could allow to monitor morphological changes during development or disease progression on large sample numbers, enabling the performance of preclinical studies in a local laboratory.

Biological matter may change shape via water absorption or loss. For example, brain tissue shows non-uniform shrinkage during formalin fixation and paraffin embedding, which is the most common tissue preparation for conventional histological analysis. Local deformations can be analyzed with non-rigid registration of non-destructive three-dimensional imaging datasets. We utilized synchrotron radiation microtomography at the ANATOMIX beamline of Synchrotron SOLEIL to image a mouse brain with 3 micron voxel length after formalin fixation, immersion in ascending alcohol series and xylene, and after paraffin embedding. We created a pipeline for non- rigid registration to align the volumes and extract volumetric strain fields. In this way, we could visualize the swelling/shrinkage of anatomical features. This method avoids time-consuming segmentation of brain regions, however it is sensitive to the registration parameters. In this proceedings paper, we discuss the selection of registration parameters in order to generate plausible volumetric strain fields. This protocol can be deployed to any type of shape change of biological matter and allows for the quantification of the related processes.

Successful tomographic imaging of soft tissues with micrometer resolution includes preparation, acquisition, re- construction, and data evaluation. Tissue preparation is essential for hard X-ray microtomography, because staining- and embedding materials can substantially alter the biological tissue post mortem. We performed to- mographic imaging of zebrafish embryos in alcohol and after paraffin embedding with a conventional X-ray source and at a synchrotron radiation facility. The resulting multi-modal, three-dimensional data were registered for direct comparison. Single-cell precision was reached for the synchrotron radiation-based approach, which allows for segmentation of full organs such as the embryonic kidneys. While this approach offers an order of magnitude higher spatial resolution, many of the anatomical features can be readily recognized with the more accessible laboratory system. Propagation-based data acquisition enabled us to demonstrate the complementary nature of the edge-enhanced absorption contrast- and the phase contrast-based modality for visualizing multiple microanatomical features. While ethanol and paraffin embeddings allowed for identification of the same anatomical structures, paraffin-embedding, however, led to more artefacts and shrinkage. The presented multi-modal imaging approaches can be further extended to visualize three to four orders of magnitude larger volumes such as adult zebrafish or complete organs of larger animals such as mouse brains. Going towards even larger volumes, such as the human brain, presents further challenges related to paraffin embedding, data acquisition and handling of the peta-byte scale data volumes. This study provided a multi-modal imaging strategy by the combination of X-ray sources and sample embeddings which can play a role in addressing these challenges.

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.

The rational bottom-up synthesis of atomically defined graphene nanoribbon (GNR) heterojunctions represents an enabling technology for the design of nanoscale electronic devices. Synthetic strategies used thus far have relied on the random copolymerization of two electronically distinct molecular precursors to yield GNR heterojunctions. Here we report the fabrication and electronic characterization of atomically precise GNR heterojunctions prepared through late-stage functionalization of chevron GNRs obtained from a single precursor. Post-growth excitation of fully cyclized GNRs induces cleavage of sacrificial carbonyl groups, resulting in atomically well-defined heterojunctions within a single GNR. The GNR heterojunction structure was characterized using bond-resolved scanning tunnelling microscopy, which enables chemical bond imaging at T = 4.5 K. Scanning tunnelling spectroscopy reveals that band alignment across the heterojunction interface yields a type II heterojunction, in agreement with first-principles calculations. GNR heterojunction band realignment proceeds over a distance less than 1 nm, leading to extremely large effective fields.

X-ray grating interferometry (XGI) is a phase-contrast imaging technique that allows for a quantitative measurement of the refractive index with high density resolution in a model-independent manner—i.e. without a priori knowledge of the specimen composition. However, the retrieval of the X-ray wavefront phase shift relies on the accurate measurement of the interference pattern phase shift, making XGI vulnerable to phase wrapping when the interference pattern phase shift, related to the derivative of the wavefront phase shift, is large. Standard procedure for avoiding phase wrapping involves submerging the specimen in a water bath to reduce the mismatch of the index of refraction at the boundaries, but this requires a top-down rotation stage and is susceptible to gas bubble formation inside the water bath. Our team has presented an algorithm to remove phase wrapping artifacts for cylindrically shaped specimens that is applied to the phase-retrieved sinogram. This algorithm models and replaces phase-wrapped data to prevent the spread of “cupping” artifacts due to the integration of the differential phase during reconstruction. We give a criterion for selecting the modeling parameters so that the resulting measurement of the index of refraction matches the results of measurements without phase wrapping. We also apply this technique to cases where phase wrapping occurs at multiple interfaces. This algorithm allows for XGI measurements without a water bath and top-down rotation stage at synchrotron and laboratory facilities, especially as sensitivity increases.

The ability to tune the band-edge energies of bottom-up graphene nanoribbons (GNRs) via edge dopants creates new opportunities for designing tailor-made GNR heterojunctions and related nanoscale electronic devices. Here we report the local electronic characterization of type II GNR heterojunctions composed of two different nitrogen edge-doping configurations (carbazole and phenanthridine) that separately exhibit electron-donating and electron-withdrawing behavior. Atomically resolved structural characterization of phenanthridine/carbazole GNR heterojunctions was performed using bond-resolved scanning tunneling microscopy and noncontact atomic force microscopy. Scanning tunneling spectroscopy and first-principles calculations reveal that carbazole and phenanthridine dopant configurations induce opposite upward and downward orbital energy shifts owing to their different electron affinities. The magnitude of the energy offsets observed in carbazole/phenanthridine heterojunctions is dependent on the length of the GNR segments comprising each heterojunction with longer segments leading to larger heterojunction energy offsets. Using a new on-site energy analysis based on Wannier functions, we find that the origin of this behavior is a charge transfer process that reshapes the electrostatic potential profile over a long distance within the GNR heterojunction.

Metal-based nanoparticles are clinically used for diagnostic and therapeutic applications. After parenteral administration, they will distribute throughout different organs. Quantification of their distribution within tissues in the 3D space, however, remains a challenge owing to the small particle diameter. In this study, synchrotron radiation-based hard X-ray tomography (SRμCT) in absorption and phase contrast modes is evaluated for the localization of superparamagnetic iron oxide nanoparticles (SPIONs) in soft tissues based on their electron density and X-ray attenuation. Biodistribution of SPIONs is studied using zebrafish embryos as a vertebrate screening model. This label-free approach gives rise to an isotropic, 3D, direct space visualization of the entire 2.5 mm-long animal with a spatial resolution of around 2 µm. High resolution image stacks are available on a dedicated internet page (http://zebrafish.pharma-te.ch). X-ray tomography is combined with physico-chemical characterization and cellular uptake studies to confirm the safety and effectiveness of protective SPION coatings. It is demonstrated that SRμCT provides unprecedented insights into the zebrafish embryo anatomy and tissue distribution of label-free metal oxide nanoparticles.

Background Lewy body disease (LBD) is the second most common cause of neurodegenerative dementia after Alzheimer’s disease and presents a challenge to healthcare services in an ageing society because current therapeutic approaches do not halt the disease’s progress. It has been suggested that aggregation of the protein α-synuclein plays a critical role in LBD. One pathway for aggregation involves the creation of low molecular weight α-synuclein oligomers, which have been observed to induce cell death. Precise location of Lewy bodies and their precursors could allow researchers to better relate their presence to clinical symptoms as well as infer their physiological effects. While conventional light microscopy of histological slices can visualize Lewy bodies and larger protein aggregates, it provides only two-dimensional information and diffraction-limited resolution prevents visualization of the smaller (approximately 50 nanometer) protein bundles. For this reason, we propose hard X-ray micro- and nano-tomography modalities for complementary, non-destructive, three-dimensional visualization of brain tissues taking advantage of developments at synchrotron radiation facilities. Methods As a proof-of-concept, we imaged paraffin-embedded fusiform gyrus tissue (provided by Newcastle Brain Tissue Resource) from a DLB case at the European Synchrotron Radiation Facility (ESRF Grenoble, France provided beamtime at ID19 from proposal MD-1055) using single-distance inline phase-contrast X-ray tomography with pixel size of 1.6 micrometers. A H&E stained histology slice of the same sample was also taken. Results A correspondence between the micro computed tomography and histology datasets could be made by tracking the orientation of vessels in the specimen. The micro computed tomography demonstrated as shown in figure (left) sufficient contrast and resolution for identification of the lower cortical layer as well as visualization of cells in three-dimensional manner, with confirmation from the annotated histology slice. Conclusions The present work serves as a proof-of-concept for the complementary use of phase contrast X-ray tomography and histology in the investigation of neurodegenerative diseases down to the cellular level. These results open the door for further nanometer resolution studies. Opens large image Nearby slices from phase-contrast microcomputed tomography (μ-CT) (left) and H&E stained histology (right) of diseased human brain tissue. The modalities can be used in complement, with the non-destructive μ-CT directing cutting planes for histological sectioning and extending histology into the third dimension.

Hard X-ray tomography with Paganin's widespread single-distance phase retrieval filter improves contrast-to-noise ratio (CNR) while reducing spatial resolution (SR). We demonstrate that a Gaussian filter provided larger CNR at high SR with interpretable density measurements for two medically relevant soft tissue samples. Paganin's filter produced larger CNR at low SR, though \emph{a priori} assumptions were generally false and image quality gains diminish for CNR $>1$. Therefore, simple absorption measurements of low-$Z$ specimens combined with Gaussian filtering can provide improved image quality and model-independent density measurements compared to single-distance phase retrieval., This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Applied Physics Letters 116, 023702 (2020), and may be found at https://aip.scitation.org/doi/10.1063/1.5133742

Applied physics letters 114(8), 083702 (2019). doi:10.1063/1.5085302, Advances in high-resolution hard X-ray computed tomography have led to the field of virtual histology to complement histopathological analyses. Phase-contrast modalities have been favored because, for soft tissues, the real part of the refractive index is orders of magnitude greater than the imaginary part. Nevertheless, absorption-contrast measurements of paraffin-embedded tissues have provided exceptionally high contrast combined with a submicron resolution. In this work, we present a quantitative comparison of phase tomography using synchrotron radiation-based X-ray double grating interferometry and conventional synchrotron radiation-based computed tomography in the context of histopathologically relevant paraffin-embedded human brain tissue. We determine the complex refractive index and compare the contrast-to-noise ratio (CNR) of each modality, accounting for the spatial resolution and optimizing the photon energy for absorption tomography. We demonstrate that the CNR in the phase modality is 1.6 times higher than the photon-energy optimized and spatial resolution-matched absorption measurements. We predict, however, that a further optimized phase tomography will provide a CNR gain of 4. This study seeks to boost the discussion of the relative merits of phase and absorption modalities in the context of paraffin-embedded tissues for virtual histology, highlighting the importance of optimization procedures for the two complementary modes and the trade-off between spatial and density resolution, not to mention the disparity in data acquisition and processing., Published by American Inst. of Physics, Melville, NY

X-ray grating interferometry-based computed tomography is a phase contrast imaging technique that provides non-destructive, quantitative, and three-dimensional visualization with contrast superior to traditional absorption-based techniques, especially for materials primarily composed of low Z elements, such as biological tissues. However, it relies on measurements of the lateral shift of an interference pattern and is thus susceptible to so-called phase wrapping artifacts, which mainly occur at the sample-air interface. In this work, we present an algorithm for removal of such artifacts in the case of cylindrical samples and an experiment to verify its accuracy. The proposed algorithm is applied to the sinogram after phase retrieval and prior to reconstruction by finding sample edges with the absorption sinogram and replacing regions of the phase wrapped sinogram with modeled data. Our measurements show that the algorithm removes artifacts and produces more accurate δ values, as validated by measurements without phase wrapping. Our correction algorithm allows for measurements without submerging the sample in a water bath, simplifying the experimental setup and avoiding motion artifacts from gas bubbles.

A monolayer 2D capping layer with high Young's modulus is shown to be able to effectively suppress the dewetting of underlying thin films of small organic semiconductor molecule, polymer, and polycrystalline metal, respectively. To verify the universality of this capping layer approach, the dewetting experiments are performed for single-layer graphene transferred onto polystyrene (PS), semiconducting thienoazacoronene (EH-TAC), gold, and also MoS2 on PS. Thermodynamic modeling indicates that the exceptionally high Young's modulus and surface conformity of 2D capping layers such as graphene and MoS2 substantially suppress surface fluctuations and thus dewetting. As long as the uncovered area is smaller than the fluctuation wavelength of the thin film in a dewetting process via spinodal decomposition, the dewetting should be suppressed. The 2D monolayer-capping approach opens up exciting new possibilities to enhance the thermal stability and expands the processing parameters for thin film materials without significantly altering their physical properties.

The nature of the cell responsible for von Hippel-Lindau (VHL) disease-associated tumor formation has been controversial for decades. We demonstrate that VHL disease-associated central nervous system tumors are composed of developmentally arrested angioblasts that coexpress erythropoietin (Epo) and Epo receptor. The angioblasts are capable of differentiating into RBCs via formation of blood islands with extramedullary hematopoiesis. Because of VHL deficiency, Epo receptor-expressing, developmentally arrested angioblasts simultaneously coexpress Epo, which may represent a crucial pathogenetic step in tumor formation.

Chronic granulomatous disease (CGD) patients have recurrent life-threating bacterial and fungal infections due to the mutation of one of four subunits of the respiratory burst oxidase (NADPH-oxidase). Olfactomedin 4 (OLFM4) is a neutrophil granule protein, which has been recently identified as a negative regulator of host innate immunity against bacteria infection in mice through modulation of neutrophil protease activity. The goal of this study was to evaluate the impact of OLFM4 deletion on host innate immunity against Staphylococcus aureus and Aspergillus fumigatus, in a murine X-linked CGD model. We found that neutrophil intracellular killing and in vivo clearance of S. aureus have been significantly increased in gp91phox- and OLFM4-double deficiency mice compared with CGD mice. The mice survival to S. aureus sepsis in gp91phox- and OLFM4-double deficiency mice has also been significantly prolonged compared with CGD mice. Cathepsin C activities in OLFM4 deficient as well as double deficient mice neutrophils were significantly higher than those in WT mouse neutrophils. Accordingly, the elastase and cathepsin G activities in the neutrophils of OLFM4 deficient and double deficient mice were also substantially higher than those in WT mice as well as CGD mice. However, we have not observed enhanced innate immunity against A. fumigatus in OLFM4 deficiency mice. OLFM4 might prove to be an important target in CGD patients to augment host defense against bacterial infection.