Development of algorithms and methods for three-dimensional image analysis and biomedical applications

2010/2011Tomographic imaging is both the science and the tool to explore the internal structure of objects. The mission is to use images to characterize the static and/or dynamic properties of the imaged object in order to further integrate these properties into principles, laws or theories. Among the recent trends in tomographic imaging, three- dimensional (3D) methods are gaining preference and there is the quest for overcoming the bare qualitative observation towards the extraction of quantitative parameters directly from the acquired images. To this aim, Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), as well as the related micro-scale techniques (μ-CT and μ-MRI), are promising tools for all the fields of science in which non-destructive tests are required. In order to support the interpretation of the images produced by these techniques, there is a growing demand of reliable image analysis methods for the specific 3D domain. The aim of this thesis is to present approaches for effective and efficient three-dimensional image analysis with special emphasis on porous media analysis. State-of-the art as well as innovative tools are included in a special software and hardware solution named Pore3D, developed in a collaboration with the Italian 3rd generation synchrotron laboratory Elettra (Basovizza - Trieste, Italy). Algorithms and methods for the characterization of different kinds of porous media are described. The key steps of image segmentation and skeletonization of the segmented pore space are also discussed in depth. Three different clinical and biomedical applications of quantitative analysis of tomographic images are presented. The reported applications have in common the characterization of the micro-architecture of trabecular bone. The trabecular (or cancellous) bone is a 3D mesh- work of bony trabeculae and void spaces containing the bone marrow. It can then be thought of as a porous medium with an interconnected porous space. To be more specific, the first application aims at characterizing a structure (a tissue engineering scaffold) that has to mimic the architecture of trabecular bone. The relevant features of porosity, pore- and throat-size distributions, connectivity and structural anisotropy indexes are automatically extracted from μ-CT images. The second application is based on ex vivo experiments carried out on femurs and lumbar spines of mice affected by microgravity conditions. Wild type and transgenic mice were hosted in the International Space Station (ISS) for 3 months and the observed bone loss due to the near-zero gravity was quantified by means of synchrotron radiation μ-CT image analysis. Finally, the results of an in vivo study on the risk of fracture in osteoporotic subjects is reported. The study is based on texture analysis of high resolution clinical magnetic resonance (MR) images.XXIV Ciclo198

Picking out a wine: Consumer motivation behind different quality wines choice

The quality scale of Italian wines is mainly organized in four categories: PDO, PGI, basic and bulk wine. Our analysis explicitly investigates the patterns and determinants of consumption for these four different types of wine by analyzing a representative sample of consumers from a traditional wine-producing country. This study provides for first time insights on quality perceptions of wines and verifies whether Italian consumers perceive significant differences among the different categories of wines. The overall results, obtained through a system of equation estimates, show that consumer motivations and wine consumption determinants change according to each different range of wine quality and thereby support a hierarchical scale of quality wines, as a fact consumers' motivation progressively changes as the quality scales of the wine increase or decrease. In addition, this study highlights for first time any differences in the consumption determinants between the PDO and the PGI wines in a national context and it suggests that the influence of the two different GI labels on the wine choice of consumers is truly different. Important insights were also provided for bulk wine whose consumption seems to be closely related to wine tourism and the desire to buy locally produced wines. Keywords: Basic wines, Bulk wines, Local wines, PDO, PG

PEPI Lab: a flexible compact multi-modal setup for X-ray phase-contrast and spectral imaging

This paper presents a new flexible compact multi-modal imaging setup referred to as PEPI (Photon-counting Edge-illumination Phase-contrast imaging) Lab, which is based on the edge-illumination (EI) technique and a chromatic detector. The system enables both X-ray phase-contrast (XPCI) and spectral (XSI) imaging of samples on the centimeter scale. This work conceptually follows all the stages in its realization, from the design to the first imaging results. The setup can be operated in four different modes, i.e. photon-counting/conventional, spectral, double-mask EI, and single-mask EI, whereby the switch to any modality is fast, software controlled, and does not require any hardware modification or lengthy re-alignment procedures. The system specifications, ranging from the X-ray tube features to the mask material and aspect ratio, have been quantitatively studied and optimized through a dedicated Geant4 simulation platform, guiding the choice of the instrumentation. The realization of the imaging setup, both in terms of hardware and control software, is detailed and discussed with a focus on practical/experimental aspects. Flexibility and compactness (66 cm source-to-detector distance in EI) are ensured by dedicated motion stages, whereas spectral capabilities are enabled by the Pixirad-1/Pixie-III detector in combination with a tungsten anode X-ray source operating in the range 40-100 kVp. The stability of the system, when operated in EI, has been verified, and drifts leading to mask misalignment of less than 1 [Formula: see text]m have been measured over a period of 54 h. The first imaging results, one for each modality, demonstrate that the system fulfills its design requirements. Specifically, XSI tomographic images of an iodine-based phantom demonstrate the system's quantitativeness and sensibility to concentrations in the order of a few mg/ml. Planar XPCI images of a carpenter bee specimen, both in single and double-mask modes, demonstrate that refraction sensitivity (below 0.6 [Formula: see text]rad in double-mask mode) is comparable with other XPCI systems based on microfocus sources. Phase CT capabilities have also been tested on a dedicated plastic phantom, where the phase channel yielded a 15-fold higher signal-to-noise ratio with respect to attenuation

Entangled Markov chains

Motivated by the problem of finding a satisfactory quantum generalization of the classical random walks, we construct a new class of quantum Markov chains which are at the same time purely generated and uniquely determined by a corresponding classical Markov chain. We argue that this construction yields as a corollary, a solution to the problem of constructing quantum analogues of classical random walks which are "entangled" in a sense specified in the paper. The formula giving the joint correlations of these quantum chains is obtained from the corresponding classical formula by replacing the usual matrix multiplication by Schur multiplication. The connection between Schur multiplication and entanglement is clarified by showing that these quantum chains are the limits of vector states whose amplitudes, in a given basis (e.g. the computational basis of quantum information), are complex square roots of the joint probabilities of the corresponding classical chains. In particular, when restricted to the projectors on this basis, the quantum chain reduces to the classical one. In this sense we speak of entangled lifting, to the quantum case, of a classical Markov chain. Since random walks are particular Markov chains, our general construction also gives a solution to the problem that motivated our study. In view of possible applications to quantum statistical mechanics too, we prove that the ergodic type of an entangled Markov chain with finite state space (thus excluding random walks) is completely determined by the corresponding ergodic type of the underlying classical chain

Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord

Defaults in vascular (VN) and neuronal networks of spinal cord are responsible for serious neurodegenerative pathologies. Because of inadequate investigation tools, the lacking knowledge of the complete fine structure of VN and neuronal systems is a crucial problem. Conventional 2D imaging yields incomplete spatial coverage leading to possible data misinterpretation, whereas standard 3D computed tomography imaging achieves insufficient resolution and contrast. We show that X-ray high-resolution phase-contrast tomography allows the simultaneous visualization of three-dimensional VN and neuronal systems of mouse spinal cord at scales spanning from millimeters to hundreds of nanometers, with neither contrast agent nor a destructive sample-preparation. We image both the 3D distribution of micro-capillary network and the micrometric nerve fibers, axon-bundles and neuron soma. Our approach is a crucial tool for pre-clinical investigation of neurodegenerative pathologies and spinal-cord-injuries. In particular, it should be an optimal tool to resolve the entangled relationship between VN and neuronal system.Comment: 15 pages, 6 figure

Anisotropic super-attenuation of capillary waves on driven glass interfaces

Metrological AFM measurements are performed on the silica glass interfaces of photonic band-gap fibres and hollow capillaries. The freezing of attenuated out-of-equilibrium capillary waves during the drawing process is shown to result in a reduced surface roughness. The roughness attenuation with respect to the expected thermodynamical limit is determined to vary with the drawing stress following a power law. A striking anisotropic character of the height correlation is observed: glass surfaces thus retain a structural record of the direction of the flow to which the liquid was submitted

Estimation of Nanoporous Au Young's Modulus from Serial Block Face-SEM 3D-Characterisation

Nanoporous Au has been subjected to serial block face-scanning electron microscopy (SBF-SEM) 3D-characterisation. Corresponding sections have been digitalized and used to evaluate the associated mechanical properties. Our investigation demonstrates that the sample is homogeneous and isotropic. The effective Young's modulus estimated by an analytical multiscale approach agrees remarkably well with the values stated in the literature

Foam on troubled water: Capillary induced finite-time arrest of sloshing waves

International audienceInterfacial forces exceed gravitational forces on a scale small relative to the capillary length-two millimeters in the case of an air-water interface-and therefore dominate the physics of sub-millimetric systems. They are of paramount importance for various biological taxa and engineering processes where the motion of a liquid meniscus induces a viscous frictional force that exhibits a sublinear dependence in the meniscus velocity, i.e. a power law with an exponent smaller than one. Interested in the fundamental implications of this dependence, we use a liquid-foam sloshing system as a prototype to exacerbate the effect of sublinear friction on the macroscopic mechanics of multi-phase flows. In contrast to classical theory, we uncover the existence of a finite-time singularity in our system yielding the arrest of the fluid's oscillations. We propose a minimal theoretical framework to capture this effect, thereby amending the paradigmatic damped harmonic oscillator model. Our results suggest that, although often not considered at the macroscale, sublinear capillary forces govern the friction at liquid-solid and liquid-liquid interfaces

Weighted Scheduling of Time-Sensitive Coflows

Datacenter networks commonly facilitate the transmission of data in distributed computing frameworks through coflows, which are collections of parallel flows associated with a common task. Most of the existing research has concentrated on scheduling coflows to minimize the time required for their completion, i.e., to optimize the average dispatch rate of coflows in the network fabric. Nevertheless, modern applications often produce coflows that are specifically intended for online services and mission-crucial computational tasks, necessitating adherence to specific deadlines for their completion. In this paper, we introduce \wdcoflow,~ a new algorithm to maximize the weighted number of coflows that complete before their deadline. By combining a dynamic programming algorithm along with parallel inequalities, our heuristic solution performs at once coflow admission control and coflow prioritization, imposing a $\sigma$-order on the set of coflows. With extensive simulation, we demonstrate the effectiveness of our algorithm in improving up to $3\times$ more coflows that meet their deadline in comparison the best SoA solution, namely $\mathtt{CS\text{-}MHA}$. Furthermore, when weights are used to differentiate coflow classes, \wdcoflow~ is able to improve the admission per class up to $4\times$, while increasing the average weighted coflow admission rate.Comment: Submitted to IEEE Transactions on Cloud Computing. Parts of this work have been presented at IFIP Networking 202