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

High resolution 3D visualization of the spinal cord in a post-mortem murine model

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 three-dimensional morphology of spinal cord, with a resolution able to characterize its complex vascular and neuronal organization. X-ray phase contrast micro-tomography enables a high-quality, 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.

IoT-Based Smart Home Process Management Using a Workflow Approach

The new concept of the Internet of Things (IoT) is bringing new forms of knowledge and applications that rely on smart objects able to sense and process the collected data on a remote workflow server in the perspective to generate automated decisions. In this context, one of the main problems is how to schedule the data flow circulating between objects, and between objects applications. The cooperation between these objects is a promising solution to meet this challenge. Business process management (BPM) is the most adapted way to carry out data management thanks to workflow processes. To this end, a new semantics operator which the authors call a gateway for intelligent process scheduling of IoT (GIPSIT) is proposed as a semantic gateway enabling the management of data flows circulating between the connected objects of IoT. The researchers validate their approach based on GIPSIT operator by implementing a realistic eHealth based-scenario in a Smart Home. The obtained findings showed clearly the importance of this new operator in the context of IoT.

X-ray synchrotron microtomography: a new technique for characterizing chrysotile asbestos

Over the last decades, many studies have been conducted on rocks containing Naturally Occurring Asbestos (NOA) to determine the potential health risks to exposed neighboring populations. It is difficult to accurately characterize the asbestos fibres contained within the rocks as conventional techniques are not effective and have drawbacks associated with the disturbance of the sample under study. X-ray synchrotron microtomography (SR-μCT) supplemented with polarized light microscope (PLM), scanning electron microscopy analysis combined with energy dispersive spectrometry (SEM/EDS), electron probe micro-analysis (EPMA) were used for identifying asbestos fibres in a mineral matrix. As a case study, we analyzed a representative set of veins and fibrous chrysotile that fills the veins, taken from massive serpentinite outcrops (Southern-Italy). We were able to identify respirable chrysotile fibres (regulated asbestos) within the serpentinite matrix. SR-μCT of NOA veins achieved the resolution and reconstructed 3D structures of infill chrysotile asbestos fibres and other phase structures that were not resolvable with PLM, SEM or EPMA. Moreover, due to differences in chemical composition between veins and matrix, the data obtained enabled us to evaluate the vein shapes present in the massive serpentinite matrix. In particular, iron and aluminum distribution variations between veins and matrix induce different radiation absorption patterns thus permitting a detailed image-based 3D geometric reconstruction. The advantages of the SR-μCT technique as well as limitation of conventional methods are also discussed. These analytical approaches will be used for conducting future research on NOA of other minerals, which exhibit asbestiform and non-asbestiform habits within veins, including asbestos amphiboles.

Osteogenic Potential of Bovine Bone Graft in Combination with Laser Photobiomodulation: An Ex Vivo Demonstrative Study in Wistar Rats by Cross-Linked Studies Based on Synchrotron Microtomography and Histology

BACKGROUND

Alveolar bone defects are usually the main concern when planning implant treatments for the appropriate oral rehabilitation of patients. To improve local conditions and achieve implant treatments, there are several methods used for increasing bone volume, among which one of the most successful, versatile, and effective is considered to be guided bone regeneration. The aim of this demonstrative study was to propose an innovative analysis protocol for the evaluation of the effect of photobiomodulation on the bone regeneration process, using rat calvarial defects of 5 mm in diameter, filled with xenograft, covered with collagen membrane, and then exposed to laser radiation.

METHODS

The animals were sacrificed at different points in time (i.e., after 14, 21, and 30 days). Samples of identical dimensions were harvested in order to compare the results obtained after different periods of healing. The analysis was performed by cross-linking the information obtained using histology and high-resolution synchrotron-based tomography on the same samples. A comparison was made with both the negative control (NC) group (with a bone defect which was left for spontaneous healing), and the positive control (PC) group (in which the bone defects were filled with xenografts and collagen membrane without receiving laser treatment).

RESULTS

We demonstrated that using photobiomodulation provides a better healing effect than when receiving only the support of the biomaterial. This effect has been evident for short times treatments, i.e., during the first 14 days after surgery.

CONCLUSION

The proposed analysis protocol was effective in detecting the presence of higher quantities of bone volumes under remodeling after photobiomodulation with respect to the exclusive bone regeneration guided by the xenograft.

Synthetic calcium carbonate improves the effectiveness of treatments with nanolime to contrast decay in highly porous limestone

Three synthetized polymorphs of calcium carbonate have been tested in combination with the suspension of nanolime particles as potential consolidating agents for contrasting stone decay and overcome some of the limitations of nanolime agents when applied to substrates with large porosity. The modifications induced in the pore network of the Maastricht limestone were analyzed with microscopy and in a non-invasive fashion with small angle neutron scattering and synchrotron radiation micro-computed tomography. A reduction in porosity and pore accessibility at the micrometric scale was detected with the latter technique, and ascribed to the improved pore-filling capacity of the consolidation agent containing CaCO₃ particles. These were found to be effectively bound to the carbonated nanolime, strengthening the pore-matrix microstructure. Penetration depth and positive effect on porosity were found to depend on the particle size and shape. Absence of significant changes in the fractal nature of the pore surface at the nanoscale, was interpreted as indication of the negligible contribution of nanolime-based materials in the consolidation of stones with large porosity. However, the results indicate that in such cases, their effectiveness may be enhanced when used in combination with CaCO₃ particles, owing to the synergic effect of chemical/structural compatibility and particle size distribution.

Advanced 3D Imaging of Uterine Leiomyoma's Morphology by Propagation-based Phase-Contrast Microtomography

Uterine leiomyoma is the most common benign smooth muscle tumor in women pelvis, originating from the myometrium. It is caused by a disorder of fibrosis, with a large production and disruption of extracellular matrix (ECM). Medical treatments are still very limited and no preventative therapies have been developed. We supposed that synchrotron-based phase-contrast microtomography (PhC-microCT) may be an appropriate tool to assess the 3D morphology of uterine leiomyoma, without the use of any contrast agent. We used this technique to perform the imaging and the quantitative morphometric analysis of healthy myometrium and pathologic leiomyomas. The quantitative morphometric analysis of collagen bundles was coupled to the Roschger approach. This method, previously only used to evaluate mineralized bone density distribution, was applied here to study the fibrosis mass density distribution in healthy and pathologic biopsies from two patients. This protocol was shown to be powerful in studying uterine leiomyomas, detecting also small signs of the ECM alteration. This is of paramount importance not only for the follow-up of the present study, i.e. the investigation of different compounds and their possible therapeutic benefits, but also because it offers new methodologic possibilities for future studies of the ECM in soft tissues of different body districts.

Multi-Analytical Approach for Asbestos Minerals and Their Non-Asbestiform Analogues: Inferences from Host Rock Textural Constraints

Asbestos is a hazardous mineral, as well as a common and well-known issue worldwide. However, amphiboles equal in composition but not in morphology, as well as the fibrous antigorite and lizardite, are not classified as asbestos even if more common than other forms of the mineral. Still, their potential hazardous properties requires further exploration. The proposed multi-instrumental approach focuses on the influence of textural constraints on the subsequent origin of asbestiform products in massive rock. This aspect has a significant effect on diagnostic policies addressing environmental monitoring and the clinical perspective. Concerning minerals that are chemically and geometrically (length > 5 μm, width < 3 μm and length:diameter > 3:1) but not morphologically analogous to regulated asbestos, the debate about their potential hazardous properties is open and ongoing. Therefore, a selection of various lithotypes featuring the challenging identification of fibrous phases with critical counting dimensions was investigated; this selection consisted of two serpentinites, one metabasalt and one pyroxenite. The analytical protocol included optical microscopy (OM), scanning and transmission electron microscopy combined with energy dispersive spectrometry (SEM/EDS; TEM/EDS), micro-Raman spectroscopy and synchrotron radiation X-ray microtomography (SR X-ray μCT). The latter is an original non-destructive approach that allows the observation of the fiber arrangement in a three-dimensional space, avoiding morphological influence as a result of comminution.

Post-reconstruction 3D single-distance phase retrieval for multi-stage phase-contrast tomography with photon-counting detectors

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.

X-ray-Based 3D Virtual Histology-Adding the Next Dimension to Histological Analysis

Histology and immunohistochemistry of thin tissue sections have been the standard diagnostic procedure in many diseases for decades. This method is highly specific for particular tissue regions or cells, but mechanical sectioning of the specimens is required, which destroys the sample in the process and can lead to non-uniform tissue deformations. In addition, regions of interest cannot be located beforehand and the analysis is intrinsically two-dimensional. Micro X-ray computed tomography (μCT) on the other hand can provide 3D images at high resolution and allows for quantification of tissue structures, as well as the localization of small regions of interest. These advantages advocate the use of μCT for virtual histology tool with or without subsequent classical histology. This review summarizes the most recent examples of virtual histology and provides currently known possibilities of improving contrast and resolution of μCT. Following a background in μCT imaging, ex vivo staining procedures for contrast enhancement are presented as well as label-free virtual histology approaches and the technologies, which could rapidly advance it, such as phase-contrast CT. Novel approaches such as zoom tomography and nanoparticulate contrast agents will also be considered. The current evidence suggests that virtual histology may present a valuable addition to the workflow of histological analysis, potentially reducing the workload in pathology, refining tissue classification, and supporting the detection of small malignancies.

First 3D imaging characterization of Pele's hair from Kilauea volcano (Hawaii)

In this work the morphologic features of Pele’s hair formed during three different eruptions of Kilauea volcano have been investigated: fountaining from Kilauea Iki’s 1959 Episode 1, weak explosive activity from Halemaumau lava lake and littoral explosions at Waikupanaha (2009). Morphological studies were performed by optical, stereo- and scanning electron microscopy. For the first time 3D image analysis was carried out by synchrotron radiation X-ray computed microtomography, which allowed a high-resolution 3D reconstruction of the internal structure of each Pele’s hair, highlighting several differences in terms of number density, elongation and shape of the vesicles between the samples from the three eruptions. We identified three main parameters determining these differences: initial size of the magma droplet, ejection velocity and magma viscosity. Pele’s hair erupted during the Kilauea Iki’s fountaining shows the highest thickness and the least elongated shape of the vesicles, though it is related to fast ejection of a low viscosity magma. We therefore suggest that the size of magma droplets is the main parameter influencing the morphology and inner textures of the Pele’s hair. The comparison with Pele’s hair of similar eruptions elsewhere demonstrates that there is no univocal correspondence between eruptive style and Pele’s hair texture.

A Micro-Tomographic Insight into the Coating Systems of Historical Bowed String Instruments

Musical instruments are tools for playing music, but for some of them—made by the most important historical violin makers—the myths hide the physical artwork. Ancient violin-making Masters developed peculiar construction methods and defined aesthetic canons that are still recognizable in their musical instruments. Recently, the focus of scientific investigations has been set on the characterization of materials and methods used by the ancient violin makers by means of several scientific approaches. In this work, the merits of synchrotron radiation micro-computed tomography and optical coherence tomography (OCT) for the investigation of complex coatings systems on historical bowed string musical instruments are discussed. Five large fragments removed during past restorations from instruments produced by Jacobus Stainer, Gasparo da Salò, Giovanni Paolo Maggini, and Lorenzo Guadagnini have been considered for a non-invasive insight by tomographic techniques and the results are discussed considering previous micro-invasive investigations. The tomographic approach allows to highlight the micro-morphology of the coating systems and offers preliminary information on the methods that were employed by the ancient Masters to treat the wood and finish the musical instrument.

Gem-Quality Tourmaline from LCT Pegmatite in Adamello Massif, Central Southern Alps, Italy: An Investigation of Its Mineralogy, Crystallography and 3D Inclusions

In the early 2000s, an exceptional discovery of gem-quality multi-coloured tourmalines, hosted in Litium-Cesium-Tantalum (LCT) pegmatites, was made in the Adamello Massif, Italy. Gem-quality tourmalines had never been found before in the Alps, and this new pegmatitic deposit is of particular interest and worthy of a detailed characterization. We studied a suite of faceted samples by classical gemmological methods, and fragments were studied with Synchrotron X-ray computed micro-tomography, which evidenced the occurrence of inclusions, cracks and voids. Electron Microprobe combined with Laser Ablation analyses were performed to determine major, minor and trace element contents. Selected samples were analysed by single crystal X-ray diffraction method. The specimens range in colour from colourless to yellow, pink, orange, light blue, green, amber, brownish-pink, purple and black. Chemically, the tourmalines range from fluor-elbaite to fluor-liddicoatite and rossmanite: these chemical changes occur in the same sample and affect the colour. Rare Earth Elements (REE) vary from 30 to 130 ppm with steep Light Rare Earth Elemts (LREE)-enriched patterns and a negative Eu-anomaly. Structural data confirmed the elbaitic composition and showed that high manganese content may induce the local static disorder at the O(1) anion site, coordinating the Y cation sites occupied, on average, by Li, Al and Mn2+ in equal proportions, confirming previous findings. In addition to the gemmological value, the crystal-chemical studies of tourmalines are unanimously considered to be a sensitive recorder of the geological processes leading to their formation, and therefore, this study may contribute to understanding the evolution of the pegmatites related to the intrusion of the Adamello pluton.

Fractal Dimension Analysis of High-Resolution X-Ray Phase Contrast Micro-Tomography Images at Different Threshold Levels in a Mouse Spinal Cord

Fractal analysis is a powerful method for the morphological study of complex systems that is increasingly applied to biomedical images. Spatial resolution and image segmentation are crucial for the discrimination of tissue structures at the multiscale level. In this work, we have applied fractal analysis to high-resolution X-ray phase contrast micro-tomography (XrPCμT) images in both uninjured and injured tissue of a mouse spinal cord. We estimated the fractal dimension (FD) using the box-counting method on tomographic slices segmented at different threshold levels. We observed an increased FD in the ipsilateral injured hemicord compared with the contralateral uninjured tissue, which was almost independent of the chosen threshold. Moreover, we found that images exhibited the highest fractality close to the global histogram threshold level. Finally, we showed that the FD estimate largely depends on the image histogram regardless of tissue appearance. Our results demonstrate that the pre-processing of XrPCμT images is critical to fractal analysis and the estimation of FD.

Superior techniques for eliminating ring artifacts in X-ray micro-tomography

Synchrotron-based X-ray micro-tomography systems often suffer severe ring artifacts in reconstructed images. In sinograms the artifacts appear as straight lines or stripe artifacts. These artifacts are caused by the irregular response of a detecting system giving rise to a variety of observed types of stripes: full stripes, partial stripes, fluctuating stripes, and unresponsive stripes. The use of pre-processing techniques such as distortion correction or phase retrieval blurs and enlarges these stripes. It is impossible for a single approach to remove all types of stripe artifacts. Here, we propose three techniques for tackling all of them. The proposed techniques are easy to implement; do not generate extra stripe artifacts and void-center artifacts; and give superior quality on challenging data sets and in comparison with other techniques. Implementations in Python and a challenging data set are available for download.

Enhanced contrast in X-ray microtomographic images of the membranous labyrinth using different X-ray sources and scanning modes

The vestibular system, located in the inner ear, plays a crucial role in balance and gaze stabilisation by sensing head movements. The interconnected tubes with membranous walls of the vestibular system are located in the skull bone (the 'membranous labyrinth'). Unfortunately, these membranes are very hard to visualise using three-dimensional (3D) X-ray imaging techniques. This difficulty arises due to the embedment of the membranes in the dense skull bone, the thinness of the membranes, and the small difference in X-ray absorption between the membranes and the surrounding fluid. In this study, we compared the visualisation of very small specimens (lizard heads with vestibular systems smaller than 3 mm) by X-ray computed micro-tomography (μCT) based on synchrotron radiation and conventional sources. A visualisation protocol using conventional X-ray μCT would be very useful thanks to the ease of access and lower cost. Careful optimisation of the acquisition parameters enables detection of the membranes by using μCT scanners based on conventional microfocus sources, but in some cases a low contrast-to-noise ratio (CNR) prevents fast and reliable segmentation of the membranes. Synchrotron radiation μCT proved to be preferable for the visualisation of the small samples with very thin membranes, because of their high demands for spatial and contrast resolution. The best contrast was obtained by using synchrotron radiation μCT working in phase-contrast mode, leading to up to twice as high CNRs than the best conventional μCT results. The CNR of the synchrotron radiation μCT scans was sufficiently high enough to enable the construction of a 3D model by the means of semi-automatic segmentation of the membranous labyrinth. Membrane thickness was found to range between 2.7 and 36.3 μm. Hence, the minimal membrane thickness was found to be much smaller than described previously in the literature (between 10 and 50 μm).

Exploring Alzheimer's disease mouse brain through X-ray phase contrast tomography: From the cell to the organ

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.

Characterizing pearls structures using X-ray phase-contrast and neutron imaging: a pilot study

Some cultured and natural pearls can be reliably distinguished by visual inspection and by the use of lens and microscope. However, assessing the origin of the pearls could be not straightforward since many different production techniques can now be found in the pearl market, for example in salt or freshwater environments, with or without a rigid nucleus. This wide range of products requires the use of new effective scientific techniques. Indeed, X-ray radiography has been used by gemologists since last century as the only safe and non-destructive way to visually inspect the interior of a pearl, and recently, also X-ray computed micro-tomography was used to better visualize the inner parts of the gems. In this study we analyzed samples of natural and cultured pearls by means of two non-destructive techniques: the X-ray Phase-Contrast Imaging (PCI) and the Neutron Imaging (NI). PCI and NI results will be combined for the first time, to better visualize the pearls internal morphology, thus giving relevant indications on the pearl formation process.

A compact and flexible induction furnace for in situ X-ray microradiograhy and computed microtomography at Elettra: design, characterization and first tests

A compact and versatile induction furnace for in situ high-resolution synchrotron and laboratory hard X-ray microradiography and computed microtomography is described. The furnace can operate from 773 to 1723 K. Its programmable controller enables the user to specify multiple heating and cooling ramp rates as well as variable dwell times at fixed temperatures allowing precise control of heating and cooling rates to within 5 K. The instrument can work under a controlled atmosphere. Thanks to the circular geometry of the induction coils, the heat is homogeneously distributed in the internal volume of the graphite cell (ca. 150 mm³) where the sample holder is located. The thermal gradient within the furnace is less than 5 K over a height of ca. 5 mm. This new furnace design is well suited to the study of melting and solidification processes in geomaterials, ceramics and several metallic alloys, allowing fast heating (tested up to 6.5 K s^-1) and quenching (up to 21 K s^-1) in order to freeze the sample microstructure and chemistry under high-temperature conditions. The sample can be held at high temperatures for several hours, which is essential to follow phenomena with relatively slow dynamics, such as crystallization processes in geomaterials. The utility of the furnace is demonstrated through a few examples of experimental applications performed at the Elettra synchrotron laboratory (Trieste, Italy).

MÖNCH detector enables fast and low-dose free-propagation phase-contrast computed tomography of in situ mouse lungs

Due to the complexity of the underlying pathomechanism, in vivo mouse lung-disease models continue to be of great importance in preclinical respiratory research. Longitudinal studies following the cause of a disease or evaluating treatment efficacy are of particular interest but challenging due to the small size of the mouse lung and the fast breathing rate. Synchrotron-based in-line phase-contrast computed tomography imaging has been successfully applied in lung research in various applications, but mostly at dose levels that forbid longitudinal in vivo studies. Here, the novel charge-integrating hybrid detector MÖNCH is presented, which enables imaging of mouse lungs at a pixel size of 25 µm, in less than 10 s and with an entrance dose of about 70 mGy, which therefore will allow longitudinal lung disease studies to be performed in mouse models.

An improved ring removal procedure for in-line x-ray phase contrast tomography

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.

A Gaussian extension for Diffraction Enhanced Imaging

Unlike conventional x-ray attenuation one of the advantages of phase contrast x-ray imaging is its capability of extracting useful physical properties of the sample. In particular the possibility to obtain information from small angle scattering about unresolvable structures with sub-pixel resolution sensitivity has drawn attention for both medical and material science applications. We report on a novel algorithm for the analyzer based x-ray phase contrast imaging modality, which allows the robust separation of absorption, refraction and scattering effects from three measured x-ray images. This analytical approach is based on a simple Gaussian description of the analyzer transmission function and this method is capable of retrieving refraction and small angle scattering angles in the full angular range typical of biological samples. After a validation of the algorithm with a simulation code, which demonstrated the potential of this highly sensitive method, we have applied this theoretical framework to experimental data on a phantom and biological tissues obtained with synchrotron radiation. Owing to its extended angular acceptance range the algorithm allows precise assessment of local scattering distributions at biocompatible radiation doses, which in turn might yield a quantitative characterization tool with sufficient structural sensitivity on a submicron length scale.