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The formation of concrements in human pineal gland (PG) is a physiological process and, according to many researchers, is associated with the involution of PG structures. The majority of scientific publications concern progressive calcification of PG, leaving out studies on the destruction of already formed calcified concrements. Our study fills the gap in knowledge about calcified zones destruction in PG in normal aging and neuropathological conditions, which has not been addressed until now.Our objective is to gain insight into human PG tissue impairment in both normal aging and neurodegenerative conditions. X-ray phase-contrast tomography (XPCT) allowed us to study PG tissue degeneration at high spatial resolution and, for the first time, to examine the damaged PG concrements in detail. Our research finding could potentially enhance the understanding of the PG involvement in the process of aging as well as in Alzheimer's disease (AD) and vascular dementia (VD).The research was carried out on human PG autopsy material in normal aging, VD, and AD conditions. Laboratory-based micro-computed tomography (micro-CT) was used to collect and evaluate samples of native, uncut, and unstained PG with different degrees of pineal calcification. The detailed high-resolution 3D images of the selected PGs were produced using synchrotron-based XPCT. Histology and immunohistochemistry of soft PG tissue confirmed XPCT results.We performed via micro-CT the evaluation of the morphometric parameters of PG such as total sample volume, calcified concrements volume, and percentage of concrements in the total volume of the sample. XPCT imaging revealed high-resolution details of age-related PG alteration. In particular, we noted signs of moderate degradation of concrements in some PGs from elderly donors. In addition, our analysis revealed noticeable degenerative change in both concrements and soft tissue of PGs with neuropathology. In particular, we observed a hollow core and separated layers as well as deep ragged cracks in PG concrements of AD and VD samples. In parenchyma of some samples, we detected wide pinealocyte-free fluid-filled areas adjacent to the calcified zones.The present work provides the basis for future scientific research focused on the dynamic nature of PG calcium deposits and PG soft tissue in normal aging and neurodegenerative diseases.

Following spinal cord injury (SCI) the degree of functional (motor, autonomous, or sensory) loss correlates with the severity of nervous tissue damage. An imaging technique able to capture non-invasively and simultaneously the complex mechanisms of neuronal loss, vascular damage, and peri-lesional tissue reorganization is currently lacking in experimental SCI studies. Synchrotron X-ray phase-contrast tomography (SXPCT) has emerged as a non-destructive three-dimensional (3D) neuroimaging technique with high contrast and spatial resolution. In this framework, we developed a multi-modal approach combining SXPCT, histology and correlative methods to study neurovascular architecture in normal and spinal level C4-contused mouse spinal cords (C57BL/6J mice, age 2-3 months). The evolution of SCI lesion was imaged at the cell resolution level during the acute (30 min) and subacute (7 day) phases. Spared motor neurons (MNs) were segmented and quantified in different volumes localized at and away from the epicenter. SXPCT was able to capture neuronal loss and blood-brain barrier breakdown following SCI. Three-dimensional quantification based on SXPCT acquisitions showed no additional MN loss between 30 min and 7 days post-SCI. In addition, the analysis of hemorrhagic (at 30 min) and lesion (at 7 days) volumes revealed a high similarity in size, suggesting no extension of tissue degeneration between early and later time-points. Moreover, glial scar borders were unevenly distributed, with rostral edges being the most extended. In conclusion, SXPCT capability to image at high resolution cellular changes in 3D enables the understanding of the relationship between hemorrhagic events and nervous structure damage in SCI.

In the lungs, asbestos develops an Fe-rich coating (Asbestos Body, AB) that becomes the actual interface between the foreign fibers and the host organism. Conventional approaches to study ABs require an invasive sample preparation that can alter them. In this work, a novel combination of x-ray tomography and spectroscopy allowed studying unaltered lung tissue samples with chrysotile and crocidolite asbestos. The thickness and mass density maps of the ABs obtained by x-ray tomography were used to derive a truly quantitative elemental analysis from scanning x-ray fluorescence spectroscopy data. The average mass density of the ABs is compatible with that of highly loaded ferritin, or hemosiderin. The composition of all ABs analyzed was similar, with only minor differences in the relative elemental fractions. Silicon concentration decreased in the core-to-rim direction, indicating a possible partial dissolution of the inner fiber. The Fe content in the ABs was higher than that possibly contained in chrysotile and crocidolite. This finding opens two opposite scenarios, the first with Fe coming from the fiber bulk and concentrating on the surface as long as the fiber dissolves, the second where the Fe that takes part to the formation of the AB originates from the host organism Fe-pool.

The number of the Asbestos Bodies (AB), i.e. asbestos that developed an iron-protein coating during its permanence in biological tissues, is one of the most accessible markers of asbestos exposure in individuals. The approaches developed to perform AB count in biological tissues are based on the manual examination of tissue digests or histological sections by means of light or electron microscopies. Although these approaches are well established and relatively accessible, manual examination is time-consuming and can be reader-dependent. Besides, approximations are applied because of the limitations of 2D readings and to speed up manual counts. In addition, sample preparation using tissue digests require an amount of tissue that can only be obtained by invasive surgery or post-mortem sampling. In this paper, we propose a new approach to AB counting based on non-destructive 3D imaging, which has the potential to overcome most of the limitations of conventional approaches. This method allows automating the AB count and determining their morphometry distribution in bulk tissue samples (ideally non-invasive needle biopsies), with minimal sample preparation and avoiding approximations. Although the results are promising, additional testing on a larger number of AB-containing biological samples would be required to fully validate the method.

Natural tissues and extracellular matrices (ECMs) are not purely elastic materials but exhibit dissipative properties. Although it has recently emerged as a novel regulator of cellular responses, the contribution of material dissipation to guiding cell-fate decisions is still in its infancy. Here, a strategy for tuning the dissipation rate of viscoplastic substrates while precisely regulating linear elasticity is reported. Semi-interpenetrating substrates consisting of a rigid hydrogel network intertwined with a branched biopolymer are described. The release of these weak physical entanglements under loading dissipates the applied stress and leads to the extension of the linear elasticity. These results reveal a crucial link between this material property and cell response in 2D cultures, impacting cell migration mode and speed, vinculin-dependent focal adhesion geometry and size, F-actin organization, the transmission of forces, and Yes-associated protein nuclear translocation. It is shown that cells require joint actomyosin contractility and microtubule tension to probe the substrate and decide whether or not to adhere, revealing a clear correlation between force transmission, substrate dissipation rate, and amount of anchoring points. Overall, these findings introduce linear elasticity as a novel design parameter for assembling tunable dissipative materials to study cell mechanosensing in 2D and possibly also in 3D cultures.

The development of accurate simulation tools including x-ray phase-contrast effects is of great use in the design and optimization of x-ray phase-contrast imaging (XPCI) experimental setups. When the lateral coherence of the imaging system is limited, as in most compact laboratory-based XPCI applications, phase-contrast can be effectively described through refraction effects that can be simulated with a ray-tracing approach. This work presents a practical implementation of the x-ray phase-contrast in Geant4 and validates the simulation results against theoretical predictions for the propagation-based (PB) and edge-illumination (EI) imaging configurations. The simulation includes a realistic polychromatic tungsten anode spectrum and an extended x-ray source, a virtual phantom made of plastic wires with a diameter of 1 mm, as well as an accurate description of the absorbing masks and related movement during data acquisition. Results show a good agreement between theory and simulations, with maximum discrepancies below 2% in the intensity of PB images, below 0.3 μrad for EI refraction, and below 0.03 mm for EI projected thickness. Additionally, an often disregarded effect such as the refraction sensitivity inhomogeneity across the field of view (around 20%) was reproduced by the simulation and quantitatively explained through a theoretical model. The presented simulation platform will be extensively used for the design of a novel EI facility that is under construction at the INFN laboratories in Trieste (Italy) in the framework of the Photon-counting Edge-illumination Phase-contrast Imaging (PEPI) project.

Purpose: The SYRMA-3D collaboration is setting up a breast computed tomography (bCT) clinical program at the Elettra synchrotron radiation facility in Trieste, Italy. Unlike the few dedicated scanners available at hospitals, synchrotron radiation bCT requires the patient's rotation, which in turn implies a long scan duration (from tens of seconds to few minutes). At the same time, it allows the achievement of high spatial resolution. These features make synchrotron radiation bCT prone to motion artifacts. This article aims at assessing and compensating for motion artifacts through an optical tracking approach. Methods: In this study, patients’ movements due to breathing have been first assessed on seven volunteers and then simulated during the CT scans of a breast phantom and a surgical specimen, by adding a periodic oscillatory motion (constant speed, 1 mm amplitude, 12 cycles/minute). CT scans were carried out at 28 keV with a mean glandular dose of 5 mGy. Motion artifacts were evaluated and a correction algorithm based on the optical tracking of fiducial marks was introduced. A quantitative analysis based on the structural similarity (SSIM) index and the normalized mean square error (nMSE) was performed on the reconstructed CT images. Results: CT images reconstructed through the optical tracking procedure were found to be as good as the motionless reference image. Moreover, the analysis of SSIM and nMSE demonstrated that an uncorrected motion of the order of the system's point spread function (around 0.1 mm in the present case) can be tolerated. Conclusions: Results suggest that a motion correction procedure based on an optical tracking system would be beneficial in synchrotron radiation bCT.

A novel scheme for simultaneous X-ray ptychographic and fluorescence imaging is presented. The method is based on a dual energy X-ray beam, chromatic focusing optics and an energy discriminating photon counting detector., X-ray ptychography and X-ray fluorescence are complementary nanoscale imaging techniques, providing structural and elemental information, respectively. Both methods acquire data by scanning a localized beam across the sample. X-ray ptychography processes the transmission signal of a coherent illumination interacting with the sample, to produce images with a resolution finer than the illumination spot and step size. By enlarging both the spot and the step size, the technique can cover extended regions efficiently. X-ray fluorescence records the emitted spectra as the sample is scanned through the localized beam and its spatial resolution is limited by the spot and step size. The requisites for fast ptychography and high-resolution fluorescence appear incompatible. Here, a novel scheme that mitigates the difference in requirements is proposed. The method makes use of two probes of different sizes at the sample, generated by using two different energies for the probes and chromatic focusing optics. The different probe sizes allow to reduce the number of acquisition steps for the joint fluorescence–ptychography scan compared with a standard single beam scan, while imaging the same field of view. The new method is demonstrated experimentally using two undulator harmonics, a Fresnel zone plate and an energy discriminating photon counting detector.

Purpose Image processing plays a fundamental role in the study of central nervous system, for example in the analysis of the vascular network in neurodegenerative diseases. Synchrotron X-ray Phase-contrast micro-Tomography (SXPCT) is a very attractive method to study weakly absorbing samples and features, such as the vascular network in the spinal cord (SC). However, the identification and segmentation of vascular structures in SXPCT images is seriously hampered by the presence of image noise and strong contrast inhomogeneities, due to the sensitivity of the technique to small electronic density variations. In order to help with these tasks, we implemented a user-friendly ImageJ plugin based on a 3D Gaussian steerable filter, tuned up for the enhancement of tubular structures in SXPCT images. Methods The developed 3D Gaussian steerable filter plugin for ImageJ is based on the steerability properties of Gaussian derivatives. We applied it to SXPCT images of ex-vivo mouse SCs acquired at different experimental conditions. Results The filter response shows a strong amplification of the source image contrast-to-background ratio (CBR), independently of structures orientation. We found that after the filter application, the CBR ratio increases by a factor ranging from ~6 to ~60. In addition, we also observed an increase of 35% of the contrast to noise ratio in the case of injured mouse SC. Conclusion The developed tool can generally facilitate the detection/segmentation of capillaries, veins and arteries that were not clearly observable in non-filtered SXPCT images. Its systematic application could allow obtaining quantitative information from pre-clinical and clinical images.

In the case of single-distance propagation-based phase-contrast X-ray computed tomography with synchrotron radiation, the conventional reconstruction pipeline includes an independent 2D phase retrieval filtering of each acquired projection prior to the actual reconstruction. In order to compensate for the limited height of the X-ray beam or the small sensitive area of most modern X-ray photon-counting detectors, it is quite common to image large objects with a multi-stage approach, i.e. several acquisitions at different vertical positions of the sample. In this context, the conventional reconstruction pipeline may introduce artifacts at the margins of each vertical stage. This article presents a modified computational protocol where a post-reconstruction 3D volume phase retrieval is applied. By comparing the conventional 2D and the proposed 3D reconstructions of a large mastectomy specimen (9 cm in diameter and 3 cm in height), it is here shown that the 3D approach compensates for the multi-stage artifacts, it avoids refined projection stitching, and the image quality in terms of spatial resolution, contrast and contrast-to-noise ratio is preserved.

The late Pleistocene trachytic Campanian Ignimbrite (>300 km3 DRE, ca. 39 ka) covers the Campanian Plain (Italy) around Naples. It is found behind ridges >1000 m high at 80 km from the source in the Campi Flegrei caldera. This points towards very dilute currents, that together with the huge amount of discharged magmatic material, suggest a magma reservoir highly enriched in volatiles. The huge volume of magma that extruded during the Campanian Ignimbrite eruption differentiated and mixed at shallow depth (6–3 km), as shown by modelling of the petrologic and geochemical features of the erupted products together with melt inclusion-based studies of gas-melt saturation. With respect to compositionally similar but lower magnitude Phlegraean eruptions (e.g., Agnano-Monte Spina, >1 km3 DRE, ca. 4.6 ka), the large amount of volatiles discharged by Campanian Ignimbrite was likely due to fractional crystallization of the lowermost portion of its magmatic reservoir. Because of the long residence time of the Campanian Ignimbrite magmatic system within the crust, an efficient decoupling took place during the upward migration of volatile elements in response to a chromatographic fractionation between H2O and CO2. This caused early pulses of nearly pure CO2 (CO2-fluxing), followed by a long-lasting H2O enrichment which yielded dissolved H2O contents up to 6–7 wt%. An overpressurized CO2-dominated gas cap was consequently produced, uniformly distributed at the top of the magma chamber. The onset of the eruption tapped this cap and generated Plinian columns, causing depressurization and fast volume decrease that facilitated, or even drove, the caldera collapse. H2O-rich magma was discharged during the following phase, characterised by pyroclastic density currents. The uniform distribution of the high values of void fraction (>70%) and the high degree of vesicle connectivity throughout the magma body testify to the huge abundance of volatiles. These percolate from the crystallizing basal layers and determine the volatile-melt fining process yielding an efficient separation between H2O and CO2. The gas saturation-based estimates of the tapped foamy magma are compatible with the extent of magma chamber roof collapse, the strong expansion revealed by textural data, and the transport and deposition mechanisms, reflecting depressurization and inflation of the volatile-rich magma within the collapsed and laterally confined caldera.

Due to several issues still affecting pixelated photon-counting detector technology, such as e.g. inhomogeneities in the energy threshold calibration, polarization effects of high-Z semiconductor sensors and limitations of the hardware solutions aimed at compensating for the charge sharing issue, several artifacts corrupt the reconstructed images when adopting these detectors for computed tomography (CT). This article presents and discusses the most recurrent artifacts occurring in the raw images acquired with the innovative CdTe Pixirad-1/Pixie-III detector. By considering an experimental CT dataset of a suitable test object, digital image processing solutions for spectral CT imaging are here suggested and optimized. The proposed solutions consist of a pre-reconstruction despeckle filtering of each acquired projection and a post-reconstruction ring artifacts removal. The effects of these filters are quantitatively analyzed in terms of spatial resolution and signal-to-noise ratio. Finally, the suitability of the optimized image processing procedure is validated with two practical CT applications in which a plastinated small animal specimen is considered.

Correlative approaches are a powerful tool in the investigation of biological samples, but require specific preparation procedures to maintain the strength of the employed methods. Here we report the optimization of the embedding protocol of nervous system samples for a correlative synchrotron X-ray computed microtomography (micro-CT) and transmission electron microscopy (TEM) approach. We demonstrate that it is possible to locate, with the micrometric resolution of micro-CT, specific volumes of interest for a further ultrastructural characterization to be performed with TEM. This approach can be applied to samples of different size and morphology up to several cm. Our optimized method represents an invaluable tool for investigating those pathologies in which microscopic alterations are localized in few confined regions, rather than diffused in entire tissues, organs or systems. We present a proof of concept of our method in a mouse model of Globoid Cells Leukodistrophy.

K-edge subtraction (KES) imaging is a technique able to map a specific element such as e.g. a contrast agent within the tissues, by exploiting the sharp rise of its absorption coefficient at the K-edge energy. Whereas mainly explored at synchrotron radiation sources, the energy discrimination properties of modern x-ray photon counting detectors (XPCDs) pave the way for an implementation of single-shot KES imaging with conventional polychromatic sources. In this work we present an x-ray CT imaging system based on the innovative Pixie-III detector and discrete reconstruction. The results reported here show that a reliable automatic localization of Barium (above a certain concentration) is possible with a few dozens of tomographic projections for a volume having an axial slice of 512 [Formula: see text] 512 pixels. The final application is a routine high-fidelity 3D mapping of a specific element ready for further morphological quantification by means of x-ray CT with potential promising applications in vivo.

X-ray Photon Counting Detectors (XPCDs) with thick semiconductor sensors and small pixel sizes suffer from a charge-sharing effect which can induce multiple counts from a single interacting photon. This issue degrades not only the energy resolution, but it also worsens the spatial resolution. Multiple counts can be removed by acting on the discriminator threshold or they can be corrected by means of specific acquisition modalities implemented in the readout electronics. In this paper we present the results of the characterization of the Pixirad-1/Pixie-III device, a XPCD carrying a 650 μ m thick CdTe sensor with a small pixel ( 62 × 62 μ m 2 ). The Pixie-III readout system includes programmable energy thresholds and it implements three acquisition modes: a pure photon counting mode and two modes specially designed to correct charge-sharing effects. The measured energy resolution of the three acquisition modes for different energies are here reported. Moreover, we characterize the imaging performance for different combinations of acquisition modes and thresholds by measuring the presampling Modulation Transfer Function (MTF), the Normalized Noise Power Spectrum (NNPS) and by assessing the Noise Equivalent number of Quanta (NEQ).

We present here a new method of performing X-ray edge-subtraction ptychographic imaging by combining multiple harmonics from an undulator synchtrotron source and an energy discriminating photon counting detector. Conventionally, monochromatic far-field X-ray ptychography is used to perform edge subtraction through the use of multiple monochromatic energy scans to obtain spectral information for a variety of applications. Here, we use directly the undulator spectrum from a synchrotron source, selecting two separate harmonics post sample using the Pixirad-1/Pixie-III detector. The result is two monochromatic images, above and below an absorption edge of interest. The proposed method is applied to obtain Au L-edge subtraction imaging of a Au-Ni grid test sample. The Au L-edge subtraction is particularly relevant for the identification of gold nanoparticles for biomedical applications. Switching the energy scan mechanism from a mechanical monochromator to an electronic detector threshold allows for faster spectral data collection with improved stability.

A crucial issue in the development of therapies to treat pathologies of the central nervous system is represented by the availability of non-invasive methods to study the threedimensional morphology of spinal cord, with a resolution able to characterize its complex vascular and neuronal organization. X-ray phase contrast micro-tomography enables a highquality, 3D visualization of both the vascular and neuronal network simultaneously without the need of contrast agents, destructive sample preparations or sectioning. Until now, high resolution investigations of the post-mortem spinal cord in murine models have mostly been performed in spinal cords removed from the spinal canal. We present here post-mortem phase contrast micro-tomography images reconstructed using advanced computational tools to obtain high-resolution and high-contrast 3D images of the fixed spinal cord without removing the bones and preserving the richness of micro-details available when measuring exposed spinal cords. We believe that it represents a significant step toward the in-vivo application. (C) 2020 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

The aim of this study was to optimise the experimental protocol and data analysis for in-vivo breast cancer x-ray imaging. Results are presented of the experiment at the SYRMEP beamline of Elettra Synchrotron using the propagation-based phase-contrast mammographic tomography method, which incorporates not only absorption, but also x-ray phase information. In this study the images of breast tissue samples, of a size corresponding to a full human breast, with radiologically acceptable x-ray doses were obtained, and the degree of improvement of the image quality (from the diagnostic point of view) achievable using propagation-based phase-contrast image acquisition protocols with proper incorporation of x-ray phase retrieval into the reconstruction pipeline was investigated. Parameters such as the x-ray energy, sample-to-detector distance and data processing methods were tested, evaluated and optimized with respect to the estimated diagnostic value using a mastectomy sample with a malignant lesion. The results of quantitative evaluation of images were obtained by means of radiological assessment carried out by 13 experienced specialists. A comparative analysis was performed between the x-ray and the histological images of the specimen. The results of the analysis indicate that, within the investigated range of parameters, both the objective image quality characteristics and the subjective radiological scores of propagation-based phase-contrast images of breast tissues monotonically increase with the strength of phase contrast which in turn is directly proportional to the product of the radiation wavelength and the sample-to-detector distance. The outcomes of this study serve to define the practical imaging conditions and the CT reconstruction procedures appropriate for low-dose phase-contrast mammographic imaging of live patients at specially designed synchrotron beamlines.

Foam formation during vesiculation of hydrous magmatic melts at 1 atm was studied in situ by synchrotron X-ray tomographic microscopy at the TOMCAT beamline of the Swiss Light Source (Villigen, Switzerland). Four different compositions were studied; basaltic, andesitic, trachyandesitic and dacitic hydrous glasses were synthesized at high pressures as starting materials and then laser heated on the beamline. The porosity, bubble number density, size distributions of bubbles and pore throats, as well as the tortuosity and connectivity of bubbles in the foams, were measured in three dimensions based on tomographic reconstructions of sample volumes. The reconstructed volumes were also used in lattice-Boltzmann simulations to determine viscous permeabilities of the samples. Connectivity of bubbles by pore throats varied from ~100 to 105 mm-3, and for each sample correlated positively with porosity and permeability. Although permeability increased with porosity, the relationship is complex; consideration of the results of this and previous studies of the viscous permeabilities of aphyric and crystal-poor magmatic samples demonstrated that at similar porosities the permeability could vary by many orders of magnitude, even in similar composition samples. More than 90 % of these permeabilities are bounded by two empirical power laws, neither of which identifies a percolation threshold. Comparison of the permeability relationships from this study with previous models (Degruyter et al. 2010; Burgisser et al. 2017) relating porosity, characteristic porethroat diameters and tortuosity demonstrated good agreement. However, modifying the Burgisser et al. (2017) model by using the maximum measured pore-throat diameter, instead of the average diameter, as the characteristic diameter produced a model that reproduced the lattice-Boltzmann permeabilities to within 1 order of magnitude. Measured correlations between the average bubble diameter and the maximum pore-throat diameter as well as between porosity and tortuosity in our experiments produced relationships that allow application of the modified Burgisser et al. model to predict permeability based only upon the average bubble diameter and porosity. The experimental results are consistent with previous studies suggesting that increasing bubble growth rates result in decreasing permeability of equivalent porosity foams. The effect of growth rate on permeability is hypothesized to substantially contribute to the multiple orders-of-magnitude variations in the permeabilities of natural magmatic samples at similar porosities.

This study assessed the effectiveness of modern endodontic shaping and filling procedures on mesiobuccal roots of maxillary molars with two canals. The canals of 20 mesiobuccal roots were treated with Mtwo rotary files, passive ultrasonic irrigation and Guttafusion obturators. X-ray computed microtomography analysis was carried out prior to treatment, after canal shaping and after canal filling to determine the alterations of the canal volume before and after the instrumentation, the volume of the hard tissue debris, and percentage of the volume occupied by filling materials. The shaping instruments and filling materials reached only partially the endodontic space of the second mesiobuccal canal and the accessory endodontic structures. Canal irregularities, ramifications, and interconnections were accumulation sites of hard tissue debris. This study demonstrated that rotary files, passive ultrasonic irrigation and carrier-based filling systems could be partially effective for the treatment of the mesiobuccal canals and their accessory endodontic structures.

Alzheimer's disease (AD), the most common form of dementia, is a progressive neurodegenerative disorder associated with aberrant production of beta-amyloid (Aβ) peptide depositing in brain as amyloid plaques. While animal models allow investigation of disease progression and therapeutic efficacy, technology to fully dissect the pathological mechanisms of this complex disease at cellular and vascular levels is lacking. X-ray phase contrast tomography (XPCT) is an advanced non-destructive 3D multi-scale direct imaging from the cell through to the whole brain, with exceptional spatial and contrast resolution. We exploit XPCT to simultaneously analyse disease-relevant vascular and neuronal networks in AD mouse brain, without sectioning and staining. The findings clearly show the different typologies and internal structures of Aβ plaques, together with their interaction with patho/physiological cellular and neuro-vascular microenvironment. XPCT enables for the first time a detailed visualization of amyloid-angiopathy at capillary level, which is impossible to achieve with other approaches. XPCT emerges as added-value technology to explore AD mouse brain as a whole, preserving tissue chemistry and structure, enabling the comparison of physiological vs. pathological states at the level of crucial disease targets. In-vivo translation will permit to monitor emerging therapeutic approaches and possibly shed new light on pathological mechanisms of neurodegenerative diseases.

X-ray spectral computed microtomography (µ-CT) has gained considerable interest in recent years thanks to the development of Photon Counting X-ray Detectors (PCXDs). Through the energy-based discrimination of the photons, obtained by setting up the discriminator threshold at different levels, PCXDs allow measuring photon energies with an accuracy appropriate for several practical applications. The major potentials of this approach are multiple contrast images (sometimes referred to as “color” or “spectral” images), obtained by using a single polychromatic source. In contrast to multiple acquisitions with different tube spectra, photon-counting spectral CT eliminates the risk of misregistration due to motion between consecutive scans and it allows for the elimination of dark noise in the image by rejecting all the events below the signal threshold. Of particular importance is the application of spectral CT in preclinical models where small animals are scanned and an effective discrimination among e.g. soft-tissue, bone and K-edge contrast agents can be in principle performed in a single shot. While spectral CT is considered very promising, its practical application has been hampered by the charge sharing issue that negatively affects the energy resolution of PCXDs. However, latest generations of PCXDs implement solutions to cope with the charge sharing effects, thus allowing sharp color sensitivity. This work presents a comparison of K-edge spectral CT images acquired with the Pixirad-I/Pixie-III detector with and without the application of a charge sharing recovery solution. When a solution for the charge sharing issue is considered both the spatial accuracy and energy resolution are preserved, thus allowing accurate K-edge subtraction imaging.

International audience; Theranostics is an innovative research field that aims to develop high target specificity cancer treatments by administering small metal-based nanoparticles (NPs). This new generation of compounds exhibits diagnostic and therapeutic properties due to the high atomic number of their metal component. In the framework of a combined research program on low dose X-ray imaging and theranostic NPs, X-ray Phase Contrast Tomography (XPCT) was performed at ESRF using a 3 μm pixel optical system on two samples: a mouse brain bearing melanoma metastases injected with gadolinium NPs and, a mouse liver injected with gold NPs. XPCT is a non-destructive technique suitable to achieve the 3D reconstruction of a specimen and, widely used at micro-scale to detect abnormalities of the vessels, which are associated to the tumor growth or to the development of neurodegenerative diseases. Moreover, XPCT represents a promising and complementary tool to study the biodistribution of theranostic NPs in biological materials, thanks to the strong contrast with respect to soft tissues that metal-based NPs provide in radiological images. This work is relied on an original imaging approach based on the evaluation of the contrast differences between the images acquired below and above K-edge energies, as a proof of the certain localization of NPs. We will present different methods aiming to enhance the localization of NPs and a 3D map of their distribution in large volume of tissues.

International audience; The word "theranostic" derives from the fusion of two terms: therapeutic and diagnostic. It is a promising research field that aims to develop innovative therapies with high target specificity by exploiting the therapeutic and diagnostic properties, in particular for metal-based nanoparticles (NPs) developed to erase cancer. In the framework of a combined research program on low dose X-ray imaging and theranostic nanoparticles (NPs), high resolution Phase-Contrast Tomography images of mice organs injected with gadolinium and gold-NPs were acquired at the European Synchrotron Radiation Facility (ESRF). Both compounds are good X-ray contrast agents due to their high attenuation coefficient with respect to biological tissues, especially immediately above K-edge energy. X-ray tomography is a powerful non-invasive technique to image the 3D vasculature network in order to detect abnormalities. Phase contrast methods provide more detailed anatomical information with higher discrimination among soft tissues. We present the images of mice liver and brain injected with gold and gadolinium NPs, respectively. We discuss different image processing methods used aiming at enhancing the accuracy on localizing nanoparticles.

Ionic chitosan gels fabricated using multivalent anions, tripolyphosphate (TPP) or pyrophosphate (PPi), respectively, have been investigated as potential biomaterials to be used in tissue engineering. Starting from the hypothesis that the polymer mesh texture at the microscale affects the final performance of the resulting materials, an innovative image analysis approach is presented in the first part of the article, which is aimed at deriving quantitative information from transmission electron microscopy images. The image analysis of the (more extended) central area of the gel networks revealed differences between both the cross-linking densities and pore size distributions of the two systems, the TPP gels showing a higher connectivity. Chitosan-TPP gels showed a limited degradation in simulated physiological media up to 6 weeks, reasonably ascribed to the texture of the (more extended) central area of the gels, whereas PPi counterparts degraded almost immediately. The release profiles and the calculation of diffusion coefficients for bovine serum albumin and cytochrome c, herein used as model payloads, indicated a different release behavior depending on the polymer network homogeneity/inhomogeneity and molecular weight of loaded molecules. This finding was ascribed to the marked inhomogeneity of the PPi gels (at variance with the TPP ones), which had been demonstrated in our previous work. Finally, thorough in vitro studies demonstrated good biocompatibility of both chitosan gels, and because of this feature, they can be used as suitable scaffolds for cellular colonization and metabolic activity.

Bubble nucleation and growth control the explosivity of volcanic eruptions, and the kinetics of these processes are generally determined from examinations of natural samples and quenched experimental run products. These samples, however, only provide a view of the final state, from which the initial conditions of a time-evolving magmatic system are then inferred. The interpretations that follow are inexact due to the inability of determining the exact conditions of nucleation and the potential detachment of bubbles from their nucleation sites, an uncertainty that can obscure their nucleation location – either homogeneously within the melt or heterogeneously at the interface between crystals and melts. We present results of a series of dynamic, real-time 4D X-ray tomographic microscopy experiments where we observed the development of bubbles in crystal bearing silicate magmas. Experimentally synthesized andesitic glasses with 0.25–0.5 wt% H 2 O and seed silicate crystals were heated at 1 atm to induce bubble nucleation and track bubble growth and movement. In contrast to previous studies on natural and experimentally produced samples, we found that bubbles readily nucleated on plagioclase and clinopyroxene crystals, that their contact angle changes during growth and that they can grow to sizes many times that of the silicate on whose surface they originated. The rapid heterogeneous nucleation of bubbles at low degrees of supersaturation in the presence of silicate crystals demonstrates that silicates can affect when vesiculation ensues, influencing subsequent permeability development and effusive vs. explosive transition in volcanic eruptions.

Photon counting semiconductor detectors in radiation imaging present attractive properties, such as high efficiency, low noise, and energy sensitivity. The very complex electronics limits the sensitive area of current devices to a few square cm. This disadvantage is often compensated by tiling a larger matrix with an adequate number of detector units but this usually results in non-negligible insensitive gaps between two adjacent modules. When considering the case of Computed Tomography (CT), these gaps lead to degraded reconstructed images with severe streak and ring artifacts. This work presents two digital image processing solutions to fill in these gaps when considering the specific case of synchrotron radiation x-ray parallel beam phase contrast CT. While not discussed with experimental data, other CT modalities, such as spectral, cone beam and other geometries might benefit from the presented approaches.

Thanks to their high detection efficiency and low intrinsic noise, direct conversion X-ray Photon Counting Detectors (XPCDs) are particularly suitable for low dose imaging applications such as mammography. The photon counting technology can implement also two or more acquisition thresholds to perform single-shot spectral imaging with one polychromatic source. However, XPCDs with thick high Z crystal sensor and small pixel size are affected by the charge sharing effect. This issue can induce multiple counts from a single interaction reducing both spectral and spatial resolutions. In a pure counting mode, multiple counts from charge sharing can be partially or totally removed by increasing the acquisition threshold at the cost of a loss of efficiency. Thus, the performances of XPCDs can be threshold-dependent. New generation XPCDs implement solutions to cope with charge sharing issue. If the charge sharing is properly corrected, no multiple counts are recorded and the performances (detection efficiency, spectral and spatial resolutions) of the acquisition system are expected to be independent from the acquisition threshold. This work presents a study of a Pixirad-1 detection system based on a CdTe Schottky sensor and PIXIE-III readout system. This chip can be configured in three different operation modes, two of which implement solutions to remove multiple counts. Using monochromatic radiation, the performances of these different operation modes have been compared trough a measure of the integral spectra and the Signal to Noise Ratio (SNR) as function of the acquisition threshold.

Computational imaging techniques such as X-ray computed tomography (CT) rely on a significant amount of computing. The acquired tomographic projections are digitally processed to reconstruct the final images of interest. This process is generically called reconstruction, and it includes additional steps prior to or at the end of the execution of an actual reconstruction algorithm. Most of these steps aim at improving image quality, mainly in terms of artifacts compensation and noise reduction. The reconstructed images are then digitally analyzed to derive quantitative data and to support the qualitative visual interpretation. This part involves computational approaches that fall within the generic term image segmentation. Pre- and post- segmentation image processing is often required to improve the final quantification and extract reliable data from a CT dataset. This chapter presents an overview of the reconstruction and segmentation fundamentals for the 3D analysis of high-resolution X-ray CT data. Better knowledge about artifacts and reconstruction issues avoid misinterpretation of the images. Similarly, more insights about the limitations of image segmentation and quantification help commenting the reliability of the derived numerical values. A deeper understanding of these elements is therefore beneficial to optimize the whole workflow that starts from sample preparation and leads to CT-based scientific results.

Large-area CdTe single-photon-counting detectors are becoming more and more attractive in view of low-dose imaging applications due to their high efficiency, low intrinsic noise and absence of a scintillating screen which affects spatial resolution. At present, however, since the dimensions of a single sensor are small (typically a few cm2), multi-module architectures are needed to obtain a large field of view. This requires coping with inter-module gaps and with close-to-edge pixels, which generally show a non-optimal behavior. Moreover, high-Z detectors often show gain variations in time due to charge trapping: this effect is detrimental especially in computed tomography (CT) applications where a single tomographic image requires hundreds of projections continuously acquired in several seconds. This work has been carried out at the SYRMEP beamline of the Elettra synchrotron radiation facility (Trieste, Italy), in the framework of the SYRMA-3D project, which aims to perform the world's first breast-CT clinical study with synchrotron radiation. An ad hoc data pre-processing procedure has been developed for the PIXIRAD-8 CdTe single-photon-counting detector, comprising an array of eight 30.7 mm × 24.8 mm modules tiling a 246 mm × 25 mm sensitive area, which covers the full synchrotron radiation beam. The procedure consists of five building blocks, namely dynamic flat-fielding, gap seaming, dynamic ring removal, projection despeckling and around-gap equalization. Each block is discussed and compared, when existing, with conventional approaches. The effectiveness of the pre-processing is demonstrated for phase-contrast CT images of a human breast specimen. The dynamic nature of the proposed procedure, which provides corrections dependent upon the projection index, allows the effective removal of time-dependent artifacts, preserving the main image features including phase effects.

Rationale and Objectives This study employs clinical/radiological evaluation in establishing the optimum imaging conditions for breast cancer imaging using the X-ray propagation-based phase-contrast tomography. Materials and Methods Two series of experiments were conducted and in total 161 synchrotron-based computed tomography (CT) reconstructions of one breast mastectomy specimen were produced at different imaging conditions. Imaging factors include sample-to-detector distance, X-ray energy, CT reconstruction method, phase retrieval algorithm applied to the CT projection images and maximum intensity projection. Observers including breast radiologists and medical imaging experts compared the quality of the reconstructed images with reference images approximating the conventional (absorption) CT. Various radiological image quality attributes in a visual grading analysis design were used for the radiological assessments. Results The results show that the application of the longest achievable sample-to-detector distance (9.31 m), the lowest employed X-ray energy (32 keV), the full phase retrieval, and the maximum intensity projection can significantly improve the radiological quality of the image. Several combinations of imaging variables resulted in images with very high-quality scores. Conclusion The results of the present study will support future experimental and clinical attempts to further optimize this innovative approach to breast cancer imaging.

The suppression of ring artifacts in x-ray computed tomography (CT) is a required step in practical applications; it can be addressed by introducing refined digital low pass filters within the reconstruction process. However, these filters may introduce additional ringing artifacts when simultaneously imaging pure phase objects and elements having a non-negligible absorption coefficient. Ringing originates at sharp interfaces, due to the truncation of spatial high frequencies, and severely affects qualitative and quantitative analysis of the reconstructed slices. In this work, we discuss the causes of ringing artifacts, and present a general compensation procedure to account for it. The proposed procedure has been tested with CT datasets of the mouse central nervous system acquired at different synchrotron radiation facilities. The results demonstrate that the proposed method compensates for ringing artifacts induced by low pass ring removal filters. The effectiveness of the ring suppression filters is not altered; the proposed method can thus be considered as a framework to improve the ring removal step, regardless of the specific filter adopted or the imaged sample.

Synchrotron X-ray Phase Contrast micro-Tomography (SXrPCμT) is a powerful tool in the investigation of biological tissues, including the central nervous system (CNS), and it allows to simultaneously detect the vascular and neuronal network avoiding contrast agents or destructive sample preparations. However, specific sample preparation procedures aimed to optimize the achievable contrast- and signal-to-noise ratio (CNR and SNR, respectively) are required. Here we report and discuss the effects of perfusion with two different fixative agents (ethanol and paraformaldehyde) and with a widely used contrast medium (MICROFIL®) on mouse spinal cord. As a main result, we found that ethanol enhances contrast at the grey/white matter interface and increases the contrast in correspondence of vascular features and fibres, thus providing an adequate spatial resolution to visualise the vascular network at the microscale. On the other hand, ethanol is known to induce tissue dehydration, likely reducing cell dimensions below the spatial resolution limit imposed by the experimental technique. Nonetheless, neurons remain well visible using either perfused paraformaldehyde or MICROFIL® compound, as these latter media do not affect tissues with dehydration effects. Paraformaldehyde appears as the best compromise: it is not a contrast agent, like MICROFIL®, but it is less invasive than ethanol and permits to visualise well both cells and blood vessels. However, a quantitative estimation of the relative grey matter volume of each sample has led us to conclude that no significant alterations in the grey matter extension compared to the white matter occur as a consequence of the perfusion procedures tested in this study.

Visualization and characterization of $$\beta$$β-amyloid deposits is a fundamental task in pre-clinical study of Alzheimer’s disease (AD) to assess its evolution and monitor the efficiency of new therapeutic strategies. While the cerebellum is one of the brain areas most underestimated in the context of AD, renewed interest in cerebellar lesions has recently arisen as they may link to motor and cognitive alterations. Thus, we quantitatively investigated three-dimensional plaque morphology in the cerebellum in APP/PS1 transgenic mouse, as a model of AD. In order to obtain a complete high-resolution three-dimensional view of the investigated tissue, we exploited synchrotron X-ray phase contrast tomography (XPCT), providing virtual slices with histology-matching resolution. We found the formation of plaques elongated in shape, and with a specific orientation in space depending on the investigated region of the cerebellar cortex. Remarkably, a similar shape is observed in human cerebellum from demented patients. Our findings demonstrate the capability of XPCT in volumetric quantification, supporting the current knowledge about plaque morphology in the cerebellum and the fundamental role of the surrounding tissue in driving their evolution. A good correlation with the human neuropathology is also reported.

The failure of magmatic foams has been implicated as a fundamental process in eruptions occurring at open-conduit, basaltic volcanoes. In order to investigate the failure of magmatic foams we applied the fiber bundle model using global load sharing. The strengths of the fibers for the model were taken from bubble wall widths measured in four computer-simulated foams of low-porosity and from one very low-porosity and two high-porosity foams produced in the laboratory by heating hydrated basaltic glasses to 1200 °C. The relative strength of an individual fiber in the model was calculated from the square of a bubble wall's average width and absolute strengths of the foams were calculated based upon the correlation of the strength of one modeled foam with experimental data. The fiber bundle model is shown to successfully reproduce measured tensile strengths of porous volcanic rocks studied by other researchers and confirms previous findings of the primary importance of foam porosity, as well as the secondary importance of structural details that affect the number and size of bubble walls and permeability. Because of the success of the fiber bundle model in reproducing experimental foam failure, its results are compared to infrasonic measurements associated with bubbles at Stromboli (Italy) and demonstrate that within uncertainty the power-law exponents of the infrasonic energies and of the fiber bundle model energies are in agreement; both show a crossover from an exponent of 5/2 associated with the bursting of small bubbles in the infrasonic measurements to an exponent of 3/2 for normal Strombolian eruptions associated with infrasonic signals from meter-scale bubbles. The infrasonic signals for major explosions and a paroxysmal eruption at Stromboli fall near the extrapolation of the power law defined by the low-amplitude, bubble bursting events and are interpreted to reflect the bursting of multitudes of small bubbles, rather than a few large bubbles. The measurement of small-amplitude infrasonic events at Stromboli appears useful in predicting the recurrence interval of paroxysmal eruptions at this volcano and may also provide a tool that uses common, small-amplitude infrasonic events to constrain the frequency of larger eruptions at other volcanoes.