Real-time quasi-3D tomographic reconstruction

Developments in acquisition technology and a growing need for time-resolved experiments pose great computational challenges in tomography. In addition, access to reconstructions in real time is a highly demanded feature but has so far been out of reach. We show that by exploiting the mathematical properties of filtered backprojection-type methods, having access to real-time reconstructions of arbitrarily oriented slices becomes feasible. Furthermore, we present RECAST3D, software for visualization and on-demand reconstruction of slices. A user of RECAST3D can interactively shift and rotate slices in a GUI, while the software updates the slice in real time. For certain use cases, the possibility to study arbitrarily oriented slices in real time directly from the measured data provides sufficient visual and quantitative insight. Two such applications are discussed in this article

Real-time tomographic reconstruction

With tomography it is possible to reconstruct the interior of an object without destroying. It is an important technique for many applications in, e.g., science, industry, and medicine. The runtime of conventional reconstruction algorithms is typically much longer than the time it takes to perform the tomographic experiment, and this prohibits the real-time reconstruction and visualization of the imaged object. The research in this dissertation introduces various techniques such as new parallelization schemes, data partitioning methods, and a quasi-3D reconstruction framework, that significantly reduce the time it takes to run conventional tomographic reconstruction algorithms without affecting image quality. The resulting methods and software implementations put reconstruction times in the same ballpark as the time it takes to do a tomographic scan, so that we can speak of real-time tomographic reconstruction.NWONumber theory, Algebra and Geometr

3D imaging of CRP and ultrasonic tomography to detect decay in a living adult holm oak (Quercus ilex L.) in Sardinia (Italy)

A field-integrated methodology using 3D ultrasonic tomography supported by close range photogrammetry (CRP) has been developed and evaluated as a tool to detect the presence and patterns of decay forms in a living adult holm oak (Quercus ilex L.) in an urban green area of the city of Cagliari, Sardinia, Italy. Close range photogrammetry was used to compute a high resolution 3D model of the studied tree, texturized with natural colors. Moreover, following the implemented workflow process it was possible to evaluate the deformation pattern of the studied tree over time. In a second step of our integrated approach, and in order to diagnose the state of health of the inner part of the studied tree in a non-invasive way, laboratory and in situ non-invasive ultrasonic techniques were applied. The results of the close range photogrammetry analysis supported the optimal design of the 3D ultrasonic tomography of the living adult holm oak. Ultrasonic tomography is one of the most powerful non-destructive testing techniques for the full-volume inspection of a structure. It produced physical information on the inner structure of the stem of the investigated tree. The results of the study show that the integrated application of close range photogrammetry and 3D ultrasonic tomography is a powerful tool for a highly accurate and objective evaluation of the external and internal decay of trees and for monitoring their conservation states. With the fully integrated approach, the diagnostic process aimed to prevent instability and the failure of trees can be greatly improved

Applications of x-ray computed microtomography to material science: devices and prespectives

2006/2007The three-dimensional visualization of the inner microstructural features of objects and materials is an aspect of relevant interest for a wide range of scientific and industrial applications. X-ray computed microtomography (μ-CT) is a powerful non-destructive technique capable to satisfy these needs. Once the complete reconstruction of the sample is available, a quantitative characterisation of the microstructure is essential. Through digital image processing tools, image analysis software or custom developed algorithms, it is possible to obtain an exhaustive geometrical, morphological and topological description of the features inside the volume, or to extract other particular parameters of interest (e.g. porosity, voids distribution, cell size distribution, average struts length, connectivity between the cells, tortuosity). This thesis was carried out at the third-generation Elettra Synchrotron Radiation Facility (Trieste, Italy), where a hard X-ray imaging beamline is available. The experience developed at this beamline has leaded scientists to design a complementary state-of-the-art μ-CT facility based on a micro-focus X-ray source, working both in absorption and phase contrast mode. In this dissertation a detailed description of this facility is given together with a rigorous characterization of the imaging system capabilities, in terms of the actual achievable spatial resolution, in order to optimize the working parameters for the different experiments. The main artefacts that concur to the degradation of the quality of the reconstructed images have been considered (e.g. beam hardening effects, ring artefacts, uncertainness associated with the cone-beam geometry): procedures are presented in order to eliminate, or at least to reduce, the causes of these artefacts. The aspects related to the digital image processing of the reconstructed data are intensively developed in this study: appropriated methodologies have been elaborated capable to deal with the different three-dimensional data of complex porous media, providing a correlation between the microstructure and the macroscopic behaviour of the observed materials. Three representative examples obtained with the described methods are used to demonstrate the application of μ-CT, combined with the developed image processing tools, to material science: the geometrical and morphological characterisation of polyurethane foams employed in the automotive industry due their vibro-acoustic properties; a new approach to characterize the resonance spruce wood microstructure in order to study its acoustical behaviour; finally, the possibility of revealing defects in hybrid-friction stir welded aluminium joints, guiding the optimization of the process parameters.La visualizzazione tridimensionale della struttura interna di oggetti e materiali costituisce un aspetto di notevole interesse per una ampia gamma di applicazioni scientifiche ed industriali. La microtomografia computerizzata a raggi X (μ-CT) rappresenta una potente tecnica di indagine adeguata a soddisfare tali richieste. Una volta completata la ricostruzione del campione in esame, è essenziale poter fornire una caratterizzazione quantitativa della microstruttura evidenziata. Attraverso gli strumenti messi a disposizione dalle moderne tecniche di analisi di immagine, per mezzo di software dedicati o algoritmi personalizzati, è possibile ottenere una descrizione esaustiva della geometria, morfologia e topologia degli elementi microstrutturali presenti, che consenta l’estrazione dei parametri di interesse per la particolare applicazione (porosità, distribuzione dei vuoti, dimensione degli elementi, lunghezze caratteristiche, grado di interconnessione, tortuosità etc.). Il presente lavoro di tesi è stato svolto presso il laboratorio di luce sincrotrone di terza generazione Elettra (Trieste, Italia), dove è disponibile una linea sperimentale dedicata all’imaging con raggi X duri. L’esperienza acquisita da parte dei ricercatori di questa linea ha consentito poi la progettazione di una stazione per μ-CT complementare, allo stato dell’arte e basata su una sorgente di radiazione a microfuoco, capace di operare con modalità di raccolta delle immagini sia in assorbimento sia in contrasto di fase. In questa tesi viene fornita una dettagliata descrizione della stazione, accompagnata da una rigorosa caratterizzazione del sistema impiegato per l’acquisizione e la ricostruzione delle immagini, in termini di risoluzione spaziale raggiungibile, così da consentire l’ottimizzazione dei parametri critici di lavoro nelle differenti condizioni sperimentali. Vengono poi presi in considerazione i principali artefatti che contribuiscono al deterioramento della qualità delle immagini ottenute (come il beam hardening, gli artefatti ad anello, gli artefatti legati all’incertezza geometrica associata al fascio conico etc.): vengono quindi proposti dei metodi per l’eliminazione, o almeno la riduzione, delle cause che li determinano. Nella tesi inoltre sono sviluppati in maniera approfondita gli aspetti connessi al trattamento dei dati digitali raccolti: sono state infatti elaborate delle metodologie appropriate, capaci di trattare i diversi tipi di dato provenienti dall’analisi di mezzi porosi, determinanti per la comprensione della correlazione tra la microstruttura del materiale ed il suo comportamento macroscopico. Infine, vengono proposti tre esempi rappresentativi per dimostrare l’efficacia dell’applicazione della μ-CT, in combinazione con gli strumenti di analisi di immagine messi a punto, alla scienza dei materiali: la caratterizzazione geometrica e morfologica di schiume di poliuretano impiegate nell’industria automobilistica come isolante vibro-acustico; un nuovo approccio rivolto alla caratterizzazione della struttura del legno di risonanza al fine di studiarne il comportamento acustico; la possibilità di mettere in luce i difetti in giunti di saldatura di leghe d’alluminio realizzati con la tecnica ibrida friction stir welding/TIG in maniera da ottimizzare i parametri di processo.XX Ciclo197

X‐ray Tomography Unveils the Construction Technique of Un‐Montu’s Egyptian Coffin (Early 26th Dynasty)

The Bologna Archaeological Museum, in cooperation with prestigious Italian universities, institutions, and independent scholars, recently began a vast investigation programme on a group of Egyptian coffins of Theban provenance dating to the first millennium BC, primarily the 25th–26th Dynasty (c. 746–525 BC). Herein, we present the results of the multidisciplinary investigation car-ried out on one of these coffins before its restoration intervention: the anthropoid wooden coffin of Un‐Montu (Inv. MCABo EG1960). The integration of radiocarbon dating, wood species identifica-tion, and CT imaging enabled a deep understanding of the coffin’s wooden structure. In particular, we discuss the results of the tomographic investigation performed in situ. The use of a transportable X‐ray facility largely reduced the risks associated with the transfer of the large object (1.80 cm tall) out of the museum without compromising image quality. Thanks to the 3D tomographic imaging, the coffin revealed the secrets of its construction technique, from the rational use of wood to the employment of canvas (incamottatura), from the use of dowels to the assembly procedure

Development of X-ray Tomography Tools for Characterisation of Lithium-Sulfur Batteries

Electrochemical energy storage devices are becoming increasingly ubiquitous in both consumer and industrial applications, driven by a pressing need to reduce carbon emissions for the mitigation of global warming. The electrification of the transport and mobility sector and growth in portable electronic devices demand portable power sources with high energy densities, and lithium-ion (Li-ion) batteries have been adopted extensively in these applications. However, conventional transition metal oxide-based intercalation materials used at the positive electrode are reaching their theoretical limitations, and only relatively minor improvements in theoretical specific capacity can be achieved. // Lithium-sulfur (Li-S) batteries offer higher gravimetric theoretical specific capacity and energy density and are billed as a potential successor to Li-ion technology but suffer from limited cycle life and self-discharge due to complex multi-phase chemistry and parasitic side reactions. // To better understand the fundamental mechanisms behind these processes, advanced characterisation methods involving the use of penetrating radiation (such as X-rays and neutrons) have become invaluable tools to capture the operation and degradation of the Li-S battery. Three-dimensional techniques such as X-ray micro-tomography (micro-CT) are particularly suited to probe the heterogeneous nature of battery electrode microstructures. // In this thesis, main areas of focus will include the application of ex situ and in situ X-ray micro-CT on Li-S batteries and the broader development of in situ tomography cells. The overall scientific aims of this thesis include: measuring the three-dimensional microstructural characteristics of sulfur electrodes; elucidating the three-dimensional nature of both sulfur dissolution and redeposition as a function of state of charge; and developing a better understanding of the transport processes occurring within the Li-S battery and the influence of porosity and tortuosity on electrochemical performance. In parallel, the development of in situ tomography cells capable of electrochemical cycling is an extensive component of this thesis, with applications not solely limited to Li-S batteries or X-ray micro-CT

Tomografia estendida : do básico até o mapeamento de cérebro de camundongos

Orientador: Mateus Borba CardosoTese (doutorado) - Universidade Estadual de Campinas, Instituto de Física Gleb WataghinResumo: Esta tese apresentará uma introdução a imagens de raios-x e como adquirir e processar imagens usando linhas de luz síncrotron. Apresentará os desafios matemáticos e técnicos para reconstruir amostras em três dimensões usando a reconstrução de Tomografia Computadorizada, uma técnica conhecida como CT. Esta técnica tem seu campo de visão limitado ao tamanho da câmera e ao tamanho da iluminação. Uma técnica para ampliar esse campo de visão vai ser apresentada e os desafios técnicos envolvidos para que isso aconteça. Um \textit{pipeline} é proposto e todos os algoritmos necessários foram empacotados em um pacote python chamado Tomosaic. A abordagem baseia-se em adquirir tomogramas parciais em posiçoes pré definidas e depois mesclar os dados em um novo conjunto de dados. Duas maneiras possíveis são apresentadas para essa mescla, uma no domínio das projeções e uma no domínio dos sinogramas. Experimentos iniciais serão então usadas para mostrar que o método proposto funciona com computadores normais. A técnica será aplicada mais tarde para pesquisar a anatomia de cérebros de camundongo completos. Um estudo será apresentado de como obter informação em diferentes escalas do cérebro completo do rato utilizando raios-xAbstract: This thesis will present an introduction to x-ray images and how to acquire and thread images using synchrotron beamlines. It will present the mathematical and technical challenges to reconstruct samples in three dimensions using Computed Tomography reconstruction, a technique known as CT. This technique has a field of view bounded to the camera size and the illumination size. A technique to extended this field of view is going to be presented and the technical challenges involved in order for that to happen will be described. A pipeline is proposed and all the necessary algorithms are contained into a python packaged called Tomosaic. The approach relies on acquired partial tomogram data in a defined grid and later merging the data into a new dataset. Two possible ways are presented in order to that: in the projection domain, and in the sinogram domain. Initial experiments will then be used to show that the pipeline works with normal computers. The technique will be later applied to survey the whole anatomy of whole mouse brains. A study will be shown of how to get the complete range of scales of the mouse brain using x-ray tomography at different resolutionsDoutoradoFísicaDoutor em Ciências163304/2013-01247445/2013, 1456912/2014CNPQCAPE

Over and beyond the Primate baubellum Surface: A “Jewel Bone” Shielded in Museums

Computed Tomography (CT), mostly used in the medical field, has also recently been involved in Cultural Heritage studies, thanks to its efficiency and total non-invasiveness. Due to the large variety of sizes and compositions typical of Cultural Heritage objects, different X-ray sources, detectors, and setups are necessary to meet the different needs of various case studies. Here, we focus on the use of micro-CT to explore the morphology and shape of a small, neglected bone found inside the clitoris of non-human primates (the baubellum), which we obtained by accessing two prestigious primatological collections of the American Museum of Natural History (New York, NY, USA) and the National Museum of Natural History (Washington, DC, USA). Overcoming methodological limits imposed by the absence of homologous landmarks, we combined the use of the non-invasive 3D micro-CT and a recently released landmark-free shape analysis (the alpha-shape technique) to objectively describe and quantify the shape complexity of scanned primate baubella. Micro-CT provided high-resolution results, overcoming constraints linked to museum policy about non-disruptive sampling and preserving samples for future research. Finally, it proved appropriate as post-mortem sampling had no impact on protected wild primate populations