SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows

Prilling of crystallizable water-in-oil emulsions: Towards co-encapsulation of hydrophilic and lipophilic active ingredients within lipid microparticles

Multiparticulate drug delivery systems offer advantages in controlled release, dose flexibility, and personalized medicine. Fusion prilling, a process that produces spherical lipid-based microparticles through vibrating nozzles, is gaining interest in the field. This study aims to explore the use of fusion prilling to encapsulate crystallizable water-in-oil emulsions, enabling the incorporation of hydrophilic active pharmaceutical ingredients (APIs) within lipid matrices. Urea (highly water-soluble) and Erythromycin (poorly water-soluble) were selected as model compounds, solubilized in the aqueous and lipid phases, respectively. The first phase of the study evaluated lipid excipients for their suitability in prilling, ensuring microparticle consistency in shape, size, and stability. The second phase focused on characterizing microparticles notably in terms of structural organization and integrity. Results demonstrated successful encapsulation of both model compounds, with high efficiency, by omitting an additional emulsification step. Despite concerns over water evaporation during processing, microparticles remained stable for up to 14 months when stored at room temperature in a hermetically sealed container. This work highlights the potential of fusion prilling for multiparticulate drug delivery systems, even for formulating APIs with different solubility profiles. Future research should focus on optimizing the process for broader API incorporation.

Accelerating imaging research at large-scale scientific facilities through scientific computing

To date, computed tomography experiments, carried-out at synchrotron radiation facilities worldwide, pose a tremendous challenge in terms of the breadth and complexity of the experimental datasets produced. Furthermore, near real-time three-dimensional reconstruction capabilities are becoming a crucial requirement in order to perform high-quality and result-informed synchrotron imaging experiments, where a large amount of data is collected and processed within a short time window. To address these challenges, we have developed and deployed a synchrotron computed tomography framework designed to automatically process online the experimental data from the synchrotron imaging beamlines, while leveraging the high-performance computing cluster capabilities to accelerate the real-time feedback to the users on their experimental results. We have, further, integrated it within a modern unified national authentication and data management framework, which we have developed and deployed, spanning the entire data lifecycle of a large-scale scientific facility. In this study, the overall architecture, functional modules and workflow design of our synchrotron computed tomography framework are presented in detail. Moreover, the successful integration of the imaging beamlines at the Shanghai Synchrotron Radiation Facility into our scientific computing framework is also detailed, which, ultimately, resulted in accelerating and fully automating their entire data processing pipelines. In fact, when compared with the original three-dimensional tomography reconstruction approaches, the implementation of our synchrotron computed tomography framework led to an acceleration in the experimental data processing capabilities, while maintaining a high level of integration with all the beamline processing software and systems.

Biomolecular alterations temporally anticipate microarchitectural modifications of collagen in oral tongue squamous cell carcinoma

High resolution analysis of collagen bundles could provide information on tumor onset and evolution. This study was focused on the microarchitecture and biomolecular organization of collagen bundles in oral tongue squamous cell carcinoma (OTSCC). Thirty-five OTSCC biopsy samples were analyzed by synchrotron-based phase-contrast microcomputed tomography and Fourier transform infrared imaging (FTIRI) spectroscopy. PhC-microCT evidenced the presence of reduced and disorganized collagen in the tumor area compared to the extratumoral (ExtraT) one. FTIRI also revealed a reduction of folded secondary structures in the tumor area, and highlighted differences in the peritumoral (PeriT) areas in relation with the OTSCC stage, whereby a significantly lower amount of collagen with less organized fibers was found in the PeriT stroma of advanced-OTSCC stages. Interestingly, no significant morphometrical mismatches were detected in the same region by PhC-microCT analysis. These results suggest that biomolecular alterations in the OTSCC stroma temporally anticipate structural modifications of collagen bundle microarchitecture.

A promising eco-sustainable wound dressing based on cellulose extracted from Spartium junceum L. and impregnated with Glycyrrhiza glabra L extract: Design, production and biological properties

Glycyrrhiza glabra extract is widely known for its antioxidant and anti-inflammatory properties and can improve the wound healing process. The aim of this work was to shorten the time of the healing process by using an eco-sustainable wound dressing based on Spanish broom flexible cellulosic fabric by impregnation with G. glabra extract-loaded ethosomes. Chemical analysis of G. glabra extract was performed by LC-DAD-MS/MS and its encapsulation into ethosomes was obtained using the ethanol injection method. Lipid vesicles were characterized in terms of size, polydispersity index, entrapment efficiency, zeta potential, and stability. In vitro release studies, biocompatibility, and scratch test on 3T3 fibroblasts were performed. Moreover, the structure of Spanish broom dressing and its ability to absorb wound exudate was characterized by Synchrotron X-ray phase contrast microtomography (SR-PCmicroCT). Ethosomes showed a good entrapment efficiency, nanometric size, good stability over time and a slow release of polyphenols compared to the free extract, and were not cytotoxic. Lastly, the results revealed that Spanish broom wound dressing loaded with G. glabra ethosomes is able to accelerate wound closure by reducing wound healing time. To sum up, Spanish broom wound dressing could be a potential new green tool for biomedical applications.

Alrecon: computed tomography reconstruction web application based on Solara

Synchrotron X-ray computed tomography is a non-destructive 3D imaging technique that offers the possibility to study the internal microstructure of samples with high spatial and temporal resolution. Given its unmatched image quality and acquisition speed, and the possibility to preserve the specimens, there is an increasing demand for this technique, from scientific users from innumerable disciplines. Computed tomography reconstruction is the computational process by which experimental radiographs are converted to a meaningful 3-dimensional image after the scan. The procedure involves pre-processing steps for image background and artifact correction on raw data, a reconstruction step approximating the inverse Radon-transform, and writing of the reconstructed volume image to disk. Several open-source Python packages exist to help scientists in the process of tomography reconstruction, by offering efficient implementations of reconstruction algorithms exploiting central or graphics processing unit (CPU and GPU, respectively), and by automating significant portions of the data processing pipeline. A further increase in productivity is attained by scheduling and parallelizing demanding reconstructions on high performance computing (HPC) clusters. Nevertheless, visual inspection and interactive selection of optimal reconstruction parameters remain crucial steps that are often performed in close interaction with the end-user of the data. As a result, the reconstruction task involves more than one software. Graphical user interfaces are provided to the user for fast inspection and optimization of reconstructions, while HPC resources are often accessed through scripts and command line interface. We propose Alrecon, a pure Python web application for tomographic reconstruction built using Solara. Alrecon offers users an intuitive and reactive environment for exploring data and customizing reconstruction pipelines. By leveraging upon popular 3D image visualization tools, and by providing a user-friendly interface for reconstruction scheduling on HPC resources, Alrecon guarantees productivity and efficient use of resources for any type of beamline user.

Anatomical changes of Tenebrio molitor and Tribolium castaneum during complete metamorphosis

In holometabolous insects, extensive reorganisation of tissues and cells occurs at the pupal stage. The remodelling of the external exoskeleton and internal organs that intervenes during metamorphosis has been traditionally studied in many insect species based on histological or ultrastructural methods. This study demonstrates the use of synchrotron X-ray phase-contrast micro-computed tomography as a powerful, non-destructive tool for in situ morphological observation of anatomical structures at the pupal stage in two Tenebrionid beetles, i.e. Tribolium castaneum and Tenebrio molitor, known as important pests, as well as emerging and promising models in experimental biology. Virtual sections and three-dimensional reconstructions were performed on both males and females at early, intermediate, and late pupal stage. The dataset allowed us to observe the remodelling of the gut and nervous system as well as the shaping of the female and male reproductive system at different pupal ages in both mealworm and red flour beetles. Moreover, we observed that the timing and duration pattern of organ development varied between the species analysed, likely related to the species-specific adaptations of the pre-imaginal stages to environmental conditions, which ultimately affect their life cycle. This research provides new knowledge on the morphological modifications that occur during the pupal stage of holometabolous insects and provides a baseline set of information on beetle metamorphosis that may support future research in forensics, physiology, and ecology as well as an image atlas for educational purposes.

Non-destructive 3D exploration of silicate glass corrosion: a combined multiscale approach from the macro to the nanoscale

In this research, a comprehensive multi-technique analysis, including synchrotron-based X-ray micro-computed tomography, is used to visualize the microstructure of alteration in a very particular Roman glass fragment, in which millennia of corrosion history have not significantly impacted the integrity of the fragment itself. This exceptionally rare occurrence has allowed for the maximization of meaningful data acquisition, by examining the alteration structures from the macro to the nanoscale. This study elucidates the intricate mechanisms underlying glass corrosion when in contact with soil, providing quantitative data and phase correlations in the alteration structures. These findings validate and refine existing predictive corrosion models.

Integrating X-ray phase-contrast imaging and histology for comparative evaluation of breast tissue malignancies in virtual histology analysis

Detecting breast tissue alterations is essential for cancer diagnosis. However, inherent bidimensionality limits histological procedures' effectiveness in identifying these changes. Our study applies a 3D virtual histology method based on X-ray phase-contrast microtomography (PhC μ CT), performed at a synchrotron facility, to investigate breast tissue samples including different types of lesions, namely intraductal papilloma, micropapillary intracystic carcinoma, and invasive lobular carcinoma. One-to-one comparisons of X-ray and histological images explore the clinical potential of 3D X-ray virtual histology. Results show that PhC μ CT technique provides high spatial resolution and soft tissue sensitivity, while being non-destructive, not requiring a dedicated sample processing and being compatible with conventional histology. PhC μ CT can enhance the visualization of morphological characteristics such as stromal tissue, fibrovascular core, terminal duct lobular unit, stromal/epithelium interface, basement membrane, and adipocytes. Despite not reaching the (sub) cellular level, the three-dimensionality of PhC μ CT images allows to depict in-depth alterations of the breast tissues, potentially revealing pathologically relevant details missed by a single histological section. Compared to serial sectioning, PhC μ CT allows the virtual investigation of the sample volume along any orientation, possibly guiding the pathologist in the choice of the most suitable cutting plane. Overall, PhC μ CT virtual histology holds great promise as a tool adding to conventional histology for improving efficiency, accessibility, and diagnostic accuracy of pathological evaluation.

Influence of abutment macro- and micro-geometry on morphologic and morphometric features of peri-implant connective tissue

OBJECTIVES

The aim of the present human observational study is to provide morphologic and morphometric analysis of peri-implant connective tissue next to abutments with divergent or convergent macro-geometry and different surface micro-characteristics.

MATERIALS AND METHODS

Thirty patients were rehabilitated with single implants in the posterior area and one out of three different healing abutments with a one-stage technique: machined divergent abutment (DIV-MAC), machined convergent abutment (CONV-MAC) or convergent abutment with ultrathin threaded surface (CONV-UTM). At 3 months postimplant insertion, peri-implant soft tissue was harvested; the following outcomes were investigated: histomorphometry (vertical width of connective and epithelial components) as detected by histology and polarized light; and connective tissue vertical width and 3D organization as detected by synchrotron-based high-resolution phase-contrast-based tomography (PhC-μCT).

RESULTS

Significant differences in connective tissue vertical dimension (aJE-AM) were found between DIV-MAC and both CONV-MAC and CONV-UTM, both by histology and PhC-μCT, with significantly higher values for the last two groups. Moreover, 2D histological analysis did not find significant differences in the junctional epithelium vertical dimension (PM-aJE). Importantly, PhC-μCT analysis revealed, at 3D level, significant greater amount and density of collagen bundles for CONV-UTM compared with the other two groups.

CONCLUSIONS

Convergent abutment profiles, regardless of their surface micro-geometry, seem to favor axial development of peri-implant connective tissue. Moreover, ultrathin threaded surfaces seem associated with denser and greater connective tissue organization, which might improve peri-implant soft tissue seal.

Combined Effects of HA Concentration and Unit Cell Geometry on the Biomechanical Behavior of PCL/HA Scaffold for Tissue Engineering Applications Produced by LPBF

This experimental study aims at filling the gap in the literature concerning the combined effects of hydroxyapatite (HA) concentration and elementary unit cell geometry on the biomechanical performances of additively manufactured polycaprolactone/hydroxyapatite (PCL/HA) scaffolds for tissue engineering applications. Scaffolds produced by laser powder bed fusion (LPBF) with diamond (DO) and rhombic dodecahedron (RD) elementary unit cells and HA concentrations of 5, 30 and 50 wt.% were subjected to structural, mechanical and biological characterization to investigate the biomechanical and degradative behavior from the perspective of bone tissue regeneration. Haralick's features describing surface pattern, correlation between micro- and macro-structural properties and human mesenchymal stem cell (hMSC) viability and proliferation have been considered. Experimental results showed that HA has negative influence on scaffold compaction under compression, while on the contrary it has a positive effect on hMSC adhesion. The unit cell geometry influences the mechanical response in the plastic regime and also has an effect on the cell proliferation. Finally, both HA concentration and elementary unit cell geometry affect the scaffold elastic deformation behavior as well as the amount of micro-porosity which, in turn, influences the scaffold degradation rate.

Structural Features of the Fragments from Cast Iron Cauldrons of the Medieval Golden Horde: Neutron Tomography Data

The spatial arrangement of the internal pores inside several fragments of ancient cast iron cauldrons related to the medieval Golden Horde period was studied using the neutron tomography method. The high neutron penetration into a cast iron material provides sufficient data for detailed analysis of the three-dimensional imaging data. The size, elongation, and orientation distributions of the observed internal pores were obtained. As discussed, the imaging and quantitative analytical data are considered structural markers for the location of cast iron foundries, as well as a feature of the medieval casting process.

Anatomical study of the red flour beetle using synchrotron radiation X-ray phase-contrast micro-tomography

Synchrotron X-ray phase-contrast microtomography (SR-PhC micro-CT) is well established, fast and non-destructive imaging technique for data acquisition that is currently being used to obtain new insights into insect anatomy and function in physiological, morphological and phylogenetic studies. In this study, we described in situ the internal organs of the red flour beetle Tribolium castaneum Herbst 1797, a widespread pest of cereals and stored food causing serious damage to the human economy. Two-dimensional virtual sections and volumetric reconstructions of the nervous, alimentary and reproductive systems were carried out in both sexes. The results provided a comprehensive overview of the morphological characteristics of this species, such as the different maturation stages of ovarioles and the realistic location, size and shape of internal organs. Given the great interest in this model species in experimental biology and forensic entomology, complete knowledge of the general anatomy is required for future functional applications in pest control and experimental studies. In addition, this study confirms SR-PhC micro-CT as a powerful and innovative tool in entomology, particularly suitable for small species and chitinized structures that are difficult to analyse using conventional dissection and histological methods.

Morphological and Chemical Investigation of Ovarian Structures in a Bovine Model by Contrast-Enhanced X-ray Imaging and Microscopy

An improved understanding of an ovary's structures is highly desirable to support advances in folliculogenesis knowledge and reproductive medicine, with particular attention to fertility preservation options for prepubertal girls with malignant tumors. Although currently the golden standard for structural analysis is provided by combining histological sections, staining, and visible 2D microscopic inspection, synchrotron radiation phase-contrast microtomography is becoming a new challenge for three-dimensional studies at micrometric resolution. To this aim, the proper use of contrast agents can improve the visualization of internal structures in ovary tissues, which normally present a low radiopacity. In this study, we report a comparison of four staining protocols, based on iodine or tungsten containing agents, applied to bovine ovarian tissues fixed in Bouin's solution. The microtomography (microCT) analyses at two synchrotron facilities under different set-ups were performed at different energies in order to maximize the image contrast. While tungsten-based agents allow large structures to be well identified, Iodine ones better highlight smaller features, especially when acquired above the K-edge energy of the specific metal. Further scans performed at lower energy where the setup was optimized for overall quality and sensitivity from phase-contrast still provided highly resolved visualization of follicular and intrafollicular structures at different maturation stages, independent of the staining protocol. The analyses were complemented by X-ray Fluorescence mapping on 2D sections, showing that the tungsten-based agent has a higher penetration in this type of tissues.

Three-Dimensional Study of Polymer Composite Destruction in the Early Stages

The investigation of destruction processes in composite materials is a current problem for their structural application and the improvement of their functional properties. This work aimed to visualize structural changes induced in layered carbon fiber reinforced plastics (CFRP) with the help of synchrotron X-ray microtomography. This article presents the details of destructive processes in the early stages of the deformation of reinforced polymers under uniaxial stretching, investigated at the micro level. Individual structural elements of the composite-filaments, parallel fiber bundles, the nonuniformity of the polymer binder distribution, and continuity defects-were observed under an external load. We have considered the influence of the material architecture and technological defects on fracture evolution in cross-ply and quasi-isotropic fiber-reinforced plastics. The results indicate the sequence of irreversible structural changes before the destruction of the material.

The synergy of synchrotron imaging and convolutional neural networks towards the detection of human micro-scale bone architecture and damage

The growing health and economic burden of bone fractures, their intricate multiscale features and the existing knowledge gaps in the comprehension of micro-scale bone damage occurrence make fracture diagnosis a challenging issue. In this scenario, deep-learning and artificial intelligence embody the new frontier of healthcare system, by overcoming the subjectivity of clinicians in the analysis of medical images. However, the preliminary attempts in exploiting the power of machine learning algorithms such as neural networks are still limited to bone macro-scale, while there is an evident lack in their application to smaller scales, where damage starts nucleating. Currently, speculations at the micro-scale are only feasible with the aid of high-resolution imaging techniques, that are particularly time consuming in terms of output images analysis. In this context, this works aims at combining the visualization of the micro-crack propagation mechanism with the promising application of convolutional neural networks. The implemented artificial intelligence tool is based for the first time on a large number of human synchrotron images coming from healthy and osteoporotic femoral heads tested under micro-compression. The designed convolutional neural networks are able to automatically detect lacunae and micro-cracks at different compression levels with high accuracy levels; indeed, with the baseline setup, networks achieve more than 0.99 level of accuracy for both cracks and lacunae, and more than 0.87 of the meanIoU adopted as validation metric. This approach is particularly encouraging for the development of powerful recognition system to comprehend bone micro-damage initiation and propagation, paving the way to the application of machine learning studies to bone micromechanics. This could be additionally crucial for future patient specific micro-scale observations to be related to the clinical practice.

Bedolla D, D’Amico F, Koopmann AK, Vaccari L, Saccomano G, Kohns R, Huesing N. Polyvinylidene Fluoride Aerogels with Tailorable Crystalline Phase Composition

In this work, polyvinylidene fluoride (PVDF) aerogels with a tailorable phase composition were prepared by following the crystallization-induced gelation principle. A series of PVDF wet gels (5 to 12 wt.%) were prepared from either PVDF−DMF solutions or a mixture of DMF and ethanol as non-solvent. The effects of the non-solvent concentration on the crystalline composition of the PVDF aerogels were thoroughly investigated. It was found that the nucleating role of ethanol can be adjusted to produce low-density PVDF aerogels, whereas the changes in composition by the addition of small amounts of water to the solution promote the stabilization of the valuable β and γ phases. These phases of the aerogels were monitored by FTIR and Raman spectroscopies. Furthermore, the crystallization process was followed by in-time and in situ ATR−FTIR spectroscopy. The obtained aerogels displayed specific surface areas > 150 m2 g−1, with variable particle morphologies that are dependent on the non-solvent composition, as observed by using SEM and Synchrotron Radiation Computed micro-Tomography (SR-μCT).

Pore Segmentation Techniques for Low-Resolution Data: Application to the Neutron Tomography Data of Cement Materials

The development of neutron imaging facilities provides a growing range of applications in different research fields. The significance of the obtained structural information, among others, depends on the reliability of phase segmentation. We focused on the problem of pore segmentation in low-resolution images and tomography data, taking into consideration possible image corruption in the neutron tomography experiment. Two pore segmentation techniques are proposed. They are the binarization of the enhanced contrast data using the global threshold, and the segmentation using the modified watershed technique—local threshold by watershed. The proposed techniques were compared with a conventional marker-based watershed on the test images simulating low-quality tomography data and on the neutron tomography data of the samples of magnesium potassium phosphate cement (MKP). The obtained results demonstrate the advantages of the proposed techniques over the conventional watershed-based approach.

Uterine leiomyoma as useful model to unveil morphometric and macromolecular collagen state and impairment in fibrotic diseases: An ex-vivo human study

Collagen is one of the main components of the extracellular matrix (ECM), involved, among all, in the maintenance of the structural support of tissues. In fibrotic diseases, collagen is overexpressed, and its production determines the formation of a significantly stiffer ECM. The cross-linking of high-resolution analytical tools, able to investigate both the tridimensional organization and the secondary structure of collagen in fibrotic diseases, could be useful to identify defined markers correlating the status of this protein with specific pathological conditions. To this purpose, an innovative multidisciplinary approach based on Phase-Contrast MicroComputed Tomography, Transmission Electron Microscopy, and Fourier Transform Infrared Imaging Spectroscopy was exploited on leiomyoma samples and adjacent myometrium to characterize microstructural collagen features. Uterine leiomyoma is a common gynecological disorder affecting women in fertile age. It is characterized by a massive collagen production due to the repairing processes occurring at myometrium level, and, hence, it represents a valuable model to investigate collagen self-organization in a pathological condition. Moreover, to evaluate the sensitivity of this multidisciplinary approach, the effects of eicosapentaenoic (EPA) and docosahexaenoic (DHA) omega-3 fatty acids in collagen reduction were also investigated.

Exploring Compound Eyes in Adults of Four Coleopteran Species Using Synchrotron X-ray Phase-Contrast Microtomography (SR-PhC Micro-CT)

Compound eyes in insects are primary visual receptors of surrounding environments. They show considerable design variations, from the apposition vision of most day-active species to the superposition vision of nocturnal insects, that sacrifice resolution to increase sensitivity and are able to overcome the challenges of vision during lightless hours or in dim habitats. In this study, Synchrotron radiation X-ray phase-contrast microtomography was used to describe the eye structure of four coleopteran species, showing species-specific habitat demands and different feeding habits, namely the saproxylic Clinidium canaliculatum (Costa, 1839) (Rhysodidae), the omnivorous Tenebrio molitor (Linnaeus, 1758) and Tribolium castaneum (Herbest, 1797) (Tenebrionidae), and the generalist predator Pterostichus melas italicus (Dejean, 1828) (Carabidae). Virtual sections and 3D volume renderings of the heads were performed to evaluate the application and limitations of this technique for studying the internal dioptrical and sensorial parts of eyes, and to avoid time-consuming methods such as ultrastructural analyses and classic histology. Morphological parameters such as the area of the corneal facet lens and cornea, interocular distance, facet density and corneal lens thickness were measured, and differences among the studied species were discussed concerning the differences in lifestyle and habitat preferences making different demands on the visual system. Our imaging results provide, for the first time, morphological descriptions of the compound eyes in these species, supplementing their ecological and behavioural traits.

Tofu: a fast, versatile and user-friendly image processing toolkit for computed tomography

Tofu is a toolkit for processing large amounts of images and for tomographic reconstruction. Complex image processing tasks are organized as workflows of individual processing steps. The toolkit is able to reconstruct parallel and cone beam as well as tomographic and laminographic geometries. Many pre- and post-processing algorithms needed for high-quality 3D reconstruction are available, e.g. phase retrieval, ring removal and de-noising. Tofu is optimized for stand-alone GPU workstations on which it achieves reconstruction speed comparable with costly CPU clusters. It automatically utilizes all GPUs in the system and generates 3D reconstruction code with minimal number of instructions given the input geometry (parallel/cone beam, tomography/laminography), hence yielding optimal run-time performance. In order to improve accessibility for researchers with no previous knowledge of programming, tofu contains graphical user interfaces for both optimization of 3D reconstruction parameters and batch processing of data with pre-configured workflows for typical computed tomography reconstruction. The toolkit is open source and extensive documentation is available for both end-users and developers. Thanks to the mentioned features, tofu is suitable for both expert users with specialized image processing needs (e.g. when dealing with data from custom-built computed tomography scanners) and for application-specific end-users who just need to reconstruct their data on off-the-shelf hardware.

The Porosity in Heterogeneous Carbonate Reservoir Rocks: Tectonic versus Diagenetic Imprint—A Multi-Scale Study from the Hyblean Plateau (SE Sicily, Italy)

The petroleum industry has always been pursuing highly exploitable gas fields, which are often hosted in carbonate rocks. However, carbonates are highly heterogeneous and show different fabrics and structures as the result of sedimentation in various environments, and subsequent diagenesis and deformation. In this study, a multi-scale and multidisciplinary approach has been performed on classical reservoir rocks from the subsurface of the Hyblean Plateau (Sicily, Italy). We aim at unravelling the important and debated role of tectonic and diagenetic structures (mainly fractures as well as stylolites) in enhancing or reducing the porosity. Black shales, limestones, and laminites of intertidal environment represent the main lithologies. Structure cross-cutting relationships record different stages of the basin geological history, which are related to the tectonic evolution of the area. Our results show that porosity is uncommonly lightly affected by fractures and faults, because of their mineralization, whereas stylolites, which are often considered as barriers to fluid flow, show a certain porosity. Therefore, we want to highlight the importance of a multi-scale and multidisciplinary approach in the analysis of heterogeneously porous, fractured- and stylolite-rich carbonate rocks, and our study aspires to boost other similar gas reservoir studies in energy transition times.

Neutron Tomography Studies of Two Lamprophyre Dike Samples: 3D Data Analysis for the Characterization of Rock Fabric

The rock fabric of two lamprophyre dike samples from the Koy-Tash granitoid intrusion (Koy-Tash, Jizzakh region, Uzbekistan) has been studied, using the neutron tomography method. We have performed virtual segmentation of the reconstructed 3D model of the tabular igneous intrusion and the corresponding determination of dike margins orientation. Spatial distributions of inclusions in the dike volume, as well as further analysis of size distributions and shape orientations of inclusions, have been obtained. The observed shape preferred orientations of inclusions as evidence of the magma flow-related fabric. The obtained structural data have been discussed in the frame of the models of rigid particle motion and the straining of vesicles in a moving viscous fluid.

Hybrid Nanoparticles as Theranostics Platforms for Glioblastoma Treatment: Phototherapeutic and X-ray Phase Contrast Tomography Investigations

Glioblastoma multiforme (GBM) is one of the deadliest and most aggressive cancers, remarkably resilient to current therapeutic treatments. Here, we report preliminary in vivo studies of GBM treatments based on photo-nanotherapeutics to activate synergistic killing mechanisms. Core-shell nanoparticles have been weaponized by combining photophysical properties of a new generation PDT agent (Ir(III) complex) with the thermoplasmonic effects of resonant gold nanospheres. In order to investigate the damages induced in GBM treated with these photoactivable nanosystems, we employed X-ray phase-contrast tomography (XPCT). This high-resolution three-dimensional imaging technique highlighted a vast devascularization process by micro-vessels disruption, which is indicative of tumor elimination without relapse.

When the Utility of Micro-Computed Tomography Collides with Insect Sample Preparation: An Entomologist User Guide to Solve Post-Processing Issues and Achieve Optimal 3D Models

Many techniques are used today to study insect morphology, including light and electron microscopy. Most of them require to specifically prepare the sample, precluding its use for further investigation. In contrast, micro-CT allows a sample to be studied in a non-destructive and rapid process, even without specific treatments that might hinder the use of rare and hard-to-find species in nature. We used synchrotron radiation (SR) micro-CT and conventional micro-CT to prepare 3D reconstructions of Diptera, Coleoptera, and Hymenoptera species that had been processed with 4 common preparation procedures: critical-point drying, sputter-coating, resin embedding, and air-drying. Our results showed that it is possible to further utilize insect samples prepared with the aforementioned preparation techniques for the creation of 3D models. Specimens dried at the critical point showed the best results, allowing us to faithfully reconstruct both their external surface and their internal structures, while sputter-coated insects were the most troublesome for the 3D reconstruction procedure. Air-dried specimens were suitable for external morphological analyses, while anatomical investigation of soft internal organs was not possible due to their shrinking and collapsing. The sample included in resin allowed us to reconstruct and appreciate the external cuticle and the internal parts. In this work, we demonstrate that insect samples destined to different analyses can be used for new micro-CT studies, further deepening the possibility of state-of-the-art morphological analyses.

Performance evaluation of segmentation methods for assessing the lens of the frog Thoropa miliaris from synchrotron-based phase-contrast micro-CT images

PURPOSE

In the context of synchrotron microtomography using propagation-based phase-contrast imaging (XSPCT), we evaluated the performance of semiautomatic and automatic image segmentation of soft biological structures by means of Dice Similarity Coefficient (DSC) and volume quantification.

METHODS

We took advantage of the phase-contrast effects of XSPCT to provide enhanced object boundaries and improved visualization of the lenses of the frog Thoropa miliaris. Then, we applied semiautomatic segmentation methods 1 and 2 (Interpolation and Watershed, respectively) and method 3, an automatic segmentation algorithm using the U-Net architecture, to the reconstructed images. DSC and volume quantification of the lenses were used to quantify the performance of image segmentation methods.

RESULTS

Comparing the lenses segmented by the three methods, the most pronounced difference in volume quantification was between methods 1 and 3: a reduction of 4.24%. Method 1, 2 and 3 obtained the global average DSC of 97.02%, 95.41% and 89.29%, respectively. Although it obtained the lowest DSC, method 3 performed the segmentation in a matter of seconds, while the semiautomatic methods had the average time to segment the lenses around 1 h and 30 min.

CONCLUSIONS

Our results suggest that the performance of U-Net was impaired due to the irregularities of the ROI edges mainly in its lower and upper regions, but it still showed high accuracy (DSC = 89.29%) with significantly reduced segmentation time compared to the semiautomatic methods. Besides, with the present work we have established a baseline for future assessments of Deep Neural Networks applied to XSPCT volumes.

Biomechanical performances of PCL/HA micro- and macro-porous lattice scaffolds fabricated via laser powder bed fusion for bone tissue engineering

The present experimental study aims to extend know-how on resorbable polycaprolactone/hydroxyapatite (PCL/HA, 70/30 wt%) scaffolds, produced by Laser Powder Bed Fusion (LPBF) technology, to geometrically complex lattice structures and micro porous struts. Using optimized LPBF printing parameters, micro- and macro-porous scaffolds for bone tissue regeneration were produced by regularly repeating in space Diamond (DO) and Rhombic Dodecahedron (RD) elementary unit cells. After production, scaffolds were submitted to structural, mechanical, and biological characterization. The interaction of scaffolds with human Mesenchymal Stem Cells (hMSCs) allowed studying the degradative processes of the PCL matrix. Biomechanical performances and biodegradation of scaffolds were compared to literature results and bone tissue data. Mechanical compression test, biological viability up to 4 days of incubation and degradation rate evidenced strong dependence of scaffold behavior on unit cell geometry as well as on global geometrical features.

Improving a Rapid Alignment Method of Tomography Projections by a Parallel Approach

The high resolution of synchrotron cryo-nano tomography can be easily undermined by setup instabilities and sample stage deficiencies such as runout or backlash. At the cost of limiting the sample visibility, especially in the case of bio-specimens, high contrast nano-beads are often added to the solution to provide a set of landmarks for a manual alignment. However, the spatial distribution of these reference points within the sample is difficult to control, resulting in many datasets without a sufficient amount of such critical features for tracking. Fast automatic methods based on tomography consistency are thus desirable, especially for biological samples, where regular, high contrast features can be scarce. Current off-the-shelf implementations of such classes of algorithms are slow if used on a real-world high-resolution dataset. In this paper, we present a fast implementation of a consistency-based alignment algorithm especially tailored to a multi-GPU system. Our implementation is released as open-source.

Phase Composition and Its Spatial Distribution in Antique Copper Coins: Neutron Tomography and Diffraction Studies

The chemical and elementary composition, internal arrangement, and spatial distribution of the components of ancient Greek copper coins were studied using XRF analysis, neutron diffraction and neutron tomography methods. The studied coins are interesting from a historical and cultural point of view, as they are "Charon's obol's". These coins were discovered at the location of an ancient Greek settlement during archaeological excavations on the "Volna-1" necropolis in Krasnodar Region, Russian Federation. It was determined that the coins are mainly made of a bronze alloy, a tin content that falls in the range of 1.1(2)-7.9(3) wt.%. All coins are highly degraded; corrosion and patina areas occupy volumes from ~27 % to ~62 % of the original coin volumes. The neutron tomography method not only provided 3D data of the spatial distribution of the bronze alloy and the patina with corrosion contamination inside coin volumes, but also restored the minting pattern of several studied coins. Taking into account the obtained results, the origin and use of these coins in the light of historical and economic processes of the Bosporan Kingdom are discussed.

Natural occurrence of asbestos in serpentinite quarries from Southern Spain

The nevado-filábride complex (NFC) (southern Spain) is well known for its widespread mining and quarrying activities. Serpentinite and metabasite rocks are extracted, processed and traded as building and ornamental stones. Due to the possible presence of natural occurrence of asbestos (NOA) in these rocks, the aim of this paper is to conduct an in-depth characterisation of fibrous minerals. To this aim, seven serpentinite rock samples were collected in four quarries located in the Sierra Nevada and Sierra de los Filabres (South-eastern Spain), which were then analysed by X-ray powder diffraction (XRPD), scanning electron microscopy combined with energy-dispersive spectrometry (SEM/EDS), differential scanning calorimetry (DSC), derivative thermogravimetry (DTG) and X-ray synchrotron microtomography (SR-µCT). It is essential to investigate asbestos minerals from both scientific and legal perspective, especially for public health officials that implement occupational health and safety policies, in order to safeguard the health of workers (e.g. quarry excavations, road yards, civil constructions, building stones).

The Symmetric 3D Organization of Connective Tissue around Implant Abutment: A Key-Issue to Prevent Bone Resorption

Symmetric and well-organized connective tissues around the longitudinal implant axis were hypothesized to decrease early bone resorption by reducing inflammatory cell infiltration. Previous studies that referred to the connective tissue around implant and abutments were based on two-dimensional investigations; however, only advanced three-dimensional characterizations could evidence the organization of connective tissue microarchitecture in the attempt of finding new strategies to reduce inflammatory cell infiltration. We retrieved three implants with a cone morse implant–abutment connection from patients; they were investigated by high-resolution X-ray phase-contrast microtomography, cross-linking the obtained information with histologic results. We observed transverse and longitudinal orientated collagen bundles intertwining with each other. In the longitudinal planes, it was observed that the closer the fiber bundles were to the implant, the more symmetric and regular their course was. The transverse bundles of collagen fibers were observed as semicircular, intersecting in the lamina propria of the mucosa and ending in the oral epithelium. No collagen fibers were found radial to the implant surface. This intertwining three-dimensional pattern seems to favor the stabilization of the soft tissues around the implants, preventing inflammatory cell apical migration and, consequently, preventing bone resorption and implant failure. This fact, according to the authors’ best knowledge, has never been reported in the literature and might be due to the physical forces acting on fibroblasts and on the collagen produced by the fibroblasts themselves, in areas close to the implant and to the symmetric geometry of the implant itself.

Elastic transformation of histological slices allows precise co-registration with microCT data sets for a refined virtual histology approach

Although X-ray based 3D virtual histology is an emerging tool for the analysis of biological tissue, it falls short in terms of specificity when compared to conventional histology. Thus, the aim was to establish a novel approach that combines 3D information provided by microCT with high specificity that only (immuno-)histochemistry can offer. For this purpose, we developed a software frontend, which utilises an elastic transformation technique to accurately co-register various histological and immunohistochemical stainings with free propagation phase contrast synchrotron radiation microCT. We demonstrate that the precision of the overlay of both imaging modalities is significantly improved by performing our elastic registration workflow, as evidenced by calculation of the displacement index. To illustrate the need for an elastic co-registration approach we examined specimens from a mouse model of breast cancer with injected metal-based nanoparticles. Using the elastic transformation pipeline, we were able to co-localise the nanoparticles to specifically stained cells or tissue structures into their three-dimensional anatomical context. Additionally, we performed a semi-automated tissue structure and cell classification. This workflow provides new insights on histopathological analysis by combining CT specific three-dimensional information with cell/tissue specific information provided by classical histology.

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

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

Asbestos bodies count and morphometry in bulk lung tissue samples by non-invasive X-ray micro-tomography

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.

Hydroxycarboxylic Acid Receptor 2, a Pleiotropically Linked Receptor for the Multiple Sclerosis Drug, Monomethyl Fumarate. Possible Implications for the Inflammatory Response

Monomethyl fumarate (MMF), metabolite of dimethyl fumarate (DMF), an immunosuppressive drug approved for the treatment of multiple sclerosis (MS), is a potent agonist for hydroxycarboxylic acid receptor 2 (HCAR2), eliciting signals that dampen cell activation or lead to inflammation such as the skin flushing reaction that is one of the main side effects of the treatment, together with gastrointestinal inflammation. Our aim is to further understand the molecular basis underlying these differential effects of the drug. We have used wild-type and HCAR2 knock-out mice to investigate, in vitro and ex vivo under steady-state and pathological conditions, the HCAR2-mediated signaling pathways activated by MMF in dendritic cells (DC), which promote differentiation of T cells, and in intestinal epithelial cells (IEC) where activation of a pro-inflammatory pathway, such as the cyclooxygenase-2 pathway involved in skin flushing, could underlie gastrointestinal side effects of the drug. To understand how DMF treatment might impact on gut inflammation induced by experimental autoimmune encephalomyelitis (EAE), the animal model for MS, we have used 3D X-ray phase contrast tomography and flow cytometry to monitor possible intestinal alterations at morphological and immunological levels, respectively. We show that HCAR2 is a pleiotropically linked receptor for MMF, mediating activation of different pathways leading to different outcomes in different cell types, depending on experimental in-vitro and in-vivo conditions. In the small intestine of EAE-affected mice, DMF treatment affected migration of tolerogenic DC from lamina propria to mesenteric lymph nodes, and/or reverted their profile to pro-inflammatory, probably as a result of reduced expression of aldehyde dehydrogenase and transforming growth factor beta as well as the inflammatory environment. Nevertheless, DMF treatment did not amplify the morphological alterations induced by EAE. On the basis of our further understanding of MMF signaling through HCAR2, we suggest that the pleiotropic signaling of fumarate via HCAR2 should be addressed for its pharmaceutical relevance in devising new lead compounds with reduced inflammatory side effects.

Synchrotron X-ray phase contrast micro tomography to explore the morphology of abdominal organs in Pterostichus melas italicus Dejean, 1828 (Coleoptera, Carabidae)

Micro-computer tomography imaging is a fast and non-destructive data acquisition technique which can replace or complement the traditional investigation methodologies used in entomology to study morphology. In this paper, Synchrotron Radiation X-ray Phase-Contrast micro tomography (SR-PhC micro-CT) was combined with histology and scanning electron microscopy (SEM) observations to describe the abdominal organs of Pterostichus melas italicus Dejean, 1828 (Coleoptera, Carabidae). This species was used as a representative model because of its ecological role as a generalist predator in agroecosystems. SR-PhC micro-CT allowed us to identify in situ abdominal structures including dorsal vessel, digestive tract with Malpighian tubules, male reproductive system, ganglia, fat bodies, pygidial glands, muscles and tracheae. The histology was performed to define the tissue organization of the digestive and reproductive systems. SR-PhC micro-CT and 3D rendering provided more accurate information on shape and size of organs than histological and SEM analyses, respectively. The finding of this study was to describe the anatomy and histology of organs involved in crucial life history traits, such as reproduction, nutrition and excretion. High quality images and the supplementary video represent a significant advance in knowledge of the carabid anatomy and are a baseline for future research.

Biphasic Calcium Phosphate Biomaterials: Stem Cell-Derived Osteoinduction or In Vivo Osteoconduction? Novel Insights in Maxillary Sinus Augmentation by Advanced Imaging

Maxillary sinus augmentation is often necessary prior to implantology procedure, in particular in cases of atrophic posterior maxilla. In this context, bone substitute biomaterials made of biphasic calcium phosphates, produced by three-dimensional additive manufacturing were shown to be highly biocompatible with an efficient osteoconductivity, especially when combined with cell-based tissue engineering. Thus, in the present research, osteoinduction and osteoconduction properties of biphasic calcium-phosphate constructs made by direct rapid prototyping and engineered with ovine-derived amniotic epithelial cells or amniotic fluid cells were evaluated. More in details, this preclinical study was performed using adult sheep targeted to receive scaffold alone (CTR), oAFSMC, or oAEC engineered constructs. The grafted sinuses were explanted at 90 days and a cross-linked experimental approach based on Synchrotron Radiation microCT and histology analysis was performed on the complete set of samples. The study, performed taking into account the distance from native surrounding bone, demonstrated that no significant differences occurred in bone regeneration between oAEC-, oAFMSC-cultured, and Ctr samples and that there was a predominant action of the osteoconduction versus the stem cells osteo-induction. Indeed, it was proven that the newly formed bone amount and distribution decreased from the side of contact scaffold/native bone toward the bulk of the scaffold itself, with almost constant values of morphometric descriptors in volumes more than 1 mm from the border.

A computational platform for the virtual unfolding of Herculaneum Papyri

Ancient Herculaneum papyrus scrolls, hopelessly charred in the 79 A.D. Vesuvius eruption, contain valuable writings of the Greek philosophers of the day, including works of the Epicurean Philodemus. X-ray phase contrast tomography has recently begun unlocking their secrets. However, only small portions of the text hidden inside the scroll have been recover. One of the challenging tasks in Herculaneum papyri investigation is their virtual unfolding because of their highly complicated structure and three-dimensional arrangement. Although this procedure is feasible, problems in segmentation and flattening hinder the unrolling of a large portion of papyrus. We propose a computational platform for the virtual unfolding procedure, and we show the results of its application on two Herculaneum papyrus fragments. This work paves the way to a comprehensive survey and to further interpretation of larger portions of text hidden inside the carbonized Herculaneum papyri.

X-ray Phase Contrast Tomography Serves Preclinical Investigation of Neurodegenerative Diseases

We report a qualitative study on central nervous system (CNS) damage that demonstrates the ability of X-ray phase contrast tomography (XPCT) to confirm data obtained with standard 2D methodology and permits the description of additional features that are not detected with 2D or other 3D techniques. In contrast to magnetic resonance or computed tomography, XPCT makes possible the high-resolution 3D imaging of soft tissues classically considered "invisible" to X-rays without the use of additional contrast agents, or without the need for intense processing of the tissue required by 2D techniques. Most importantly for studies of CNS diseases, XPCT enables a concomitant multi-scale 3D biomedical imaging of neuronal and vascular networks ranging from cells through to the CNS as a whole. In the last years, we have used XPCT to investigate neurodegenerative diseases, such as Alzheimer's disease (AD) and multiple sclerosis (MS), to shed light on brain damage and extend the observations obtained with standard techniques. Here, we show the cutting-edge ability of XPCT to highlight in 3D, concomitantly, vascular occlusions and damages, close associations between plaques and damaged vessels, as well as dramatic changes induced at neuropathological level by treatment in AD mice. We corroborate data on the well-known blood-brain barrier dysfunction in the animal model of MS, experimental autoimmune encephalomyelitis, and further show its extent throughout the CNS axis and at the level of the single vessel/capillary.

Synchrotron microtomography applied to the volumetric analysis of internal structures of Thoropa miliaris tadpoles

Amphibians are models for studying applied ecological issues such as habitat loss, pollution, disease, and global climate change due to their sensitivity and vulnerability to changes in the environment. Developmental series of amphibians are informative about their biology, and X-ray based 3D reconstruction holds promise for quantifying morphological changes during growth—some with a direct impact on the possibility of an experimental investigation on several of the ecological topics listed above. However, 3D resolution and discrimination of their soft tissues have been difficult with traditional X-ray computed tomography, without time-consuming contrast staining. Tomographic data were initially performed (pre-processing and reconstruction) using the open-source software tool SYRMEP Tomo Project. Data processing and analysis of the reconstructed tomography volumes were conducted using the segmentation semi-automatic settings of the software Avizo Fire 8, which provide information about each investigated tissues, organs or bone elements. Hence, volumetric analyses were carried out to quantify the development of structures in different tadpole developmental stages. Our work shows that synchrotron X-ray microtomography using phase-contrast mode resolves the edges of the internal tissues (as well as overall tadpole morphology), facilitating the segmentation of the investigated tissues. Reconstruction algorithms and segmentation software played an important role in the qualitative and quantitative analysis of each target structure of the Thoropa miliaris tadpole at different stages of development, providing information on volume, shape and length. The use of the synchrotron X-ray microtomography setup of the SYRMEP beamline of Elettra Synchrotron, in phase-contrast mode, allows access to volumetric data for bone formation, eye development, nervous system and notochordal changes during the development (ontogeny) of tadpoles of a cycloramphid frog Thoropa miliaris. As key elements in the normal development of these and any other frog tadpole, the application of such a comparative ontogenetic study, may hold interest to researchers in experimental and environmental disciplines.

Investigation of the human pineal gland 3D organization by X-ray phase contrast tomography

Pineal gland (PG) is a part of the human brain epithalamus that plays an important role in sleep, circadian rhythm, immunity, and reproduction. The calcium deposits and lesions in PG interfere with normal function of the organ and can be associated with different health disorders including serious neurological diseases. At the moment, the detailed mechanisms of PG calcifications and PG lesions formation as well as their involvement in pathological processes are not fully understood. The deep and comprehensive study of the structure of the uncut human PG with histological details, poses a stiff challenge to most imaging techniques, due to low spatial resolution, low visibility or to exceedingly aggressive sample preparation. Here, we investigate the whole uncut and unstained human post-mortem PGs by X-ray phase contrast tomography (XPCT). XPCT is an advanced 3D imaging technique, that permits to study of both soft and calcified tissue of a sample at different scales: from the whole organ to cell structure. In our research we simultaneously resolved 3D structure of parenchyma, vascular network and calcifications. Moreover, we distinguished structural details of intact and degenerated PG tissue. We discriminated calcifications with different structure, pinealocytes nuclei and the glial cells processes. All results were validated by histology. Our research clear demonstrated that XPCT is a potential tool for the high resolution 3D imaging of PG morphological features. This technique opens a new perspective to investigate PG dysfunction and understand the mechanisms of onset and progression of diseases involving the pineal gland.

Multiscale pink-beam microCT imaging at the ESRF-ID17 biomedical beamline

Recent trends in hard X-ray micro-computed tomography (microCT) aim at increasing both spatial and temporal resolutions. These challenges require intense photon beams. Filtered synchrotron radiation beams, also referred to as `pink beams', which are emitted by wigglers or bending magnets, meet this need, owing to their broad energy range. In this work, the new microCT station installed at the biomedical beamline ID17 of the European Synchrotron is described and an overview of the preliminary results obtained for different biomedical-imaging applications is given. This new instrument expands the capabilities of the beamline towards sub-micrometre voxel size scale and simultaneous multi-resolution imaging. The current setup allows the acquisition of tomographic datasets more than one order of magnitude faster than with a monochromatic beam configuration.

The structure of scleractinian coral skeleton analyzed by neutron diffraction and neutron computed tomography

Two analytical methods based on the neutrons high penetrability, i.e. neutron diffraction (ND) and neutron computed tomography (NCT) were used to investigate the structure of the aragonitic skeleton of an exemplar/sample of Dipastraea pallida (Dana 1846), a modern hermatypic coral. ND was used to reconstruct the orientation distribution function (ODF) of the crystalline fibrils which compose the coral skeleton. Accordingly, 684 ND spectra were analyzed using the Rietveld method. The result confirmed the aragonite as the sole mineral component of coral skeleton, allowing to recalculate the ODF of aragonite fibrils and to represent it by means of (100), (010) and (001) crystallographic planes pole figures (PF). Experimental PF showed a remarkable similarity with PF recalculated by considering that all aragonite fibrils are oriented either along the growth axis of polyp cups or perpendicular to this direction. This result confirmed the previous observations based on optical microscopy, proving at the same time the availability of ND for such types of investigations. In turn, NCT evidenced the individual polyp cups, their interlocked 3D rigid porous structure as well as a periodic variation of density which could be attributed to a seasonal influence of the marine environment. Different from the classical X-ray computed tomography, the NCT, in view of neutron high cross-section for hydrogen, demonstrated the presence of a small amount of organic matter, otherwise transparent for X- and gamma rays.

Assessment of plaque morphology in Alzheimer's mouse cerebellum using three-dimensional X-ray phase-based virtual histology

Visualization and characterization of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta$$\end{document}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 Reconstruction of a Bronze Battle Axe and Comparison of Inflicted Damage Injuries Using Neutron Tomography, Manufacturing Modeling, and X-ray Microtomography Data

A massive bronze battle axe from the Abashevo archaeological culture was studied using neutron tomography and manufacturing modeling from production molds. Detailed structural data were acquired to simulate and model possible injuries and wounds caused by this battle axe. We report the results of neutron tomography experiments on the bronze battle axe, as well as manufactured plastic and virtual models of the traumas obtained at different strike angles from this axe. The reconstructed 3D models of the battle axe, plastic imprint model, and real wound and trauma traces on the bones of the ancient peoples of the Abashevo archaeological culture were obtained. Skulls with traces of injuries originate from archaeological excavations of the Pepkino burial mound of the Abashevo culture in the Volga region. The reconstruction and identification of the injuries and type of weapon on the restored skulls were performed. The complementary use of 3D visualization methods allowed us to make some assumptions on the cause of death of the people of the Abashevo culture and possible intra-tribal conflict in this cultural society. The obtained structural and anthropological data can be used to develop new concepts and methods for the archaeology of conflict.

Non-Destructive and Micro-Invasive Techniques for Characterizing the Ancient Roman Mosaic Fragments

The color characteristics, vibration spectra, phase and mineral composition, internal structural organization of several fragments of the ancient Roman mosaics from the Roman Mosaic Museum, Constanta, Romania were studied by non-destructive (Chromatic analysis, Neutron Diffraction, Neutron Tomography) and micro-invasive techniques (Optical Microscopy, X-ray Diffraction, Field Emission Scanning Electron Microscopy–Energy Dispersive X-ray Spectroscopy, Raman Spectroscopy, Wavelength Dispersion X-ray Fluorescence). These investigations were performed in order to characterize the original Roman mosaic fragments. The major and minor phase components of the studied mosaic fragments were determined, the crystal structure of the main phases was analyzed, and their three-dimension spatial arrangement was reconstructed. The similar composition of the major phases of all mosaic fragments can indicate a generic recipe for making mosaic elements, but minor phases were presumably added for coloring of mosaic pieces. Some degradation areas inside the volume of the mosaic fragments were found by means of neutron diffraction and neutron tomography methods. These degradation areas are probably related to the formation of iron hydroxides during chemical interactions of mosaic fragments with the sea and urban polluted atmosphere.

Deep sea explosive eruptions may be not so different from subaerial eruptions

The dynamics of deep sea explosive eruptions, the dispersion of the pyroclasts, and how submarine eruptions differ from the subaerial ones are still poorly known due to the limited access to sea environments. Here, we analyze two ash layers representative of the proximal and distal deposits of two submarine eruptions from a 500 to 800 m deep cones of the Marsili Seamount (Italy). Fall deposits occur at a distance of more than 1.5 km from the vent, while volcanoclastic flows are close to the flanks of the cone. Ash shows textures indicative of poor magma-water interaction and a gas-rich environment. X-ray microtomography data on ash morphology and bubbles, along with gas solubility and ash dispersion models suggest 200–400 m high eruptive columns and a sea current velocity <5 cm/s. In deep sea environments, Strombolian-like eruptions are similar to the subaerial ones provided that a gas cloud occurs around the vent.