Advanced Image Reconstruction for Limited View Cone-Beam CT

In a standard CT acquisition, a high number of projections is obtained around the sample, generally covering an angular span of 360º. However, complexities may arise in some clinical scenarios such as surgery and emergency rooms or Intensive Care Units (ICUs) when the accessibility to the patient is limited due to the monitoring equipment attached. X-ray systems used in these cases are usually C-arms that only enable the acquisition of planar images within a limited angular range. Obtaining 3D images in these scenarios could be extremely interesting for diagnosis or image guided surgery. This would be based on the acquisition of a small number of projections within a limited angular span. Reconstruction of these limited-view data with conventional algorithms such as FDK result in streak artifacts and shape distortion deteriorating the image quality. In order to reduce these artifacts, advanced reconstruction methods can be used to compensate the lack of data by the incorporation of prior information. This bachelor thesis is framed on one of the lines of research carried out by the Biomedical Imaging and Instrumentation group from the Bioengineering and Aerospace Department of Universidad Carlos III de Madrid working jointly with the Hospital General Universitario Gregorio Marañón through its Instituto de Investigación Sanitaria. This line of research is carried out in collaboration with the company SEDECAL, which enables the direct transfer to the industry. Previous work showed that a new iterative reconstruction method proposed by the group, SCoLD, is able to restore the altered contour of the object, suppress greatly the streak artifacts and recover to some extend the image quality by restricting the space of search with a surface constraint. However, the evaluation was only carried out using a simulated mask that described the shape of the object obtained by thresholding a previous CT image of the sample, which is generally not available in real scenarios. The general objective of this thesis is the designing of a complete workflow to implement SCoLD in real scenarios. For that purpose, the 3D scanner Artec Eva was chosen to acquire the surface information of the sample, which was then transformed to be usable as prior information for SCoLD method. The evaluation done in a rodent study showed high similarity between the mask obtained from real data and the ideal mask obtained from a CT. Distortions in shape and streak artifacts in the limited-view FDK reconstruction were greatly reduced when using the real mask with the SCoLD reconstruction and the image quality was highly improved demonstrating the feasibility of the proposal.Grado en Ingeniería Biomédica (Plan 2010

Embedding the Localization and Imaging Functions in Mobile Systems : an Airport Surveillance Use Case

Driven by the extended applications and scarce spectrum resources, integrating the radio sensing functions into the future mobile system has been a consensus between the stakeholders. This paper demonstrates the feasibility of joint localization and imaging functions by exploiting the reference signal in the radio frame defined in the mobile system. Essentially, the subspace-based algorithms are adopted to jointly estimate the angle and distance and to enable the localization function for uplink and downlink signals and the derivation of theoretical performance boundaries. The vector antenna and virtual array concepts are introduced in the downlink scenario to enhance the angle estimation resolution. The uplink sounding reference signal is exploited to enable the imaging function as analog to synthetic-aperture radar (SAR). The joint localization and imaging performances are verified with a realistic ray-tracing channel based on the 3D ground and buildings model of Muret airport in France. The simulation results show that the reference signal can provide acceptable localization accuracy and target-distinguishing capability by adopting a virtual array and joint time-spatial smoothing in downlink and uplink, respectively. The joint localization and imaging results prove that the future mobile network is potentially a viable infrastructure to provide economic surveillance solutions for airports, particularly for secondary airports that are not well equipped with dedicated surveillance systems.publishedVersionPeer reviewe

Characterizing the Internal Porous Structure of Equine Proximal Sesamoid Bones Subjected to Race Training Using Fast Fourier Transforms

The equine racing industry is one of the main proponents in Kentucky’s economic infrastructure. In this industry there has come a need to investigate the nature of the proximal sesamoid bone (PSB). Breakdowns involving the PSBs are the leading cause in racehorse deaths in the industry, with still little known about what causes this bone to fracture. This study seeks to shed insight by investigating the internal structure of the PSB. Using microCT scanning, the internal porous structure was captured. From there, noticeable differences in the pores were noticed and quantified using fast Fourier transform (FFT) analysis. The dominant peak frequencies in each FFT spectrum hold information about the pore size and pore repeating pattern for each of selected window for the FFT analysis. The dominant peak distribution shape was characterized by a confidence ellipse for each FFT spectrum. The size of the ellipse in the frequency domain holds information that can be converted to the spatial domain to characterize the size and spacing of the porous network within the PSB. The findings of this study show interesting implications for the idea that the PSB is regionally changing the internal nature of the bone which lead to changes in structural integrity. It was observed that there were regional differences in the fracture types that could correspond with their specific fracture. A linear mixed model statistical analysis was used on the data, and it was shown that some biological factors are only shown to be significant in certain areas and not in others, while some factors are also only shown to affect the angle of the bone and not the size of the bone. Looking at the specific differences and biological factor effects, we can pinpoint which regions are experiencing changing due to the specific factors

Morphological imaging of the canine thyroid gland with an application towards hypothyroid dogs

Het aantal publicaties over het gebruik van medische beeldvorming bij schildklieraandoeningen bij de hond is beperkt. Beschikbare studies rapporteren enkel het gebruik van echografie (US) en planaire scintigrafie in gevallen van schildkliertumoren. De toegenomen beschikbaarheid van andere beeldvorming- technieken, zoals Computed Tomography (CT) en Magnetic Resonance Imaging (MRI), maakt deze potentieel waardevol als bijkomstige testen in de soms moeilijke diagnose en bij het opstellen van een geschikt behandelingsprotocol voor schildklieraandoeningen bij de hond. Als voorbereidende studie werd de herhaalbaarheid van US metingen bepaald. Van verschillende metingen, gemeten door verschillende onderzoekers, hadden de hoogte- en volumemetingen de grootste herhaalbaarheid. De variatie binnen de verschillende onderzoekers was kleiner dan tussen de verschillende onderzoekers. De volgende kenmerken werden echografisch waargenomen in een populatie hypothyroIde honden: hypoechogeen en heterogeen parenchym, onregelmatige aflijning van het kapsel, ronde vorm van de schildklierlob op dwarsdoorsnede en verkleind schildklier volume. De vijf parameters gecombineerd, resulteerde in een sensitiviteit van 94% in de detectie van hypothyroidie. Een continue afname in volume van de schilkier werd opgemerkt na opstarten van de behandeling. US is een gevoelige en snelle test voor het opsporen van hypothyroidie bij de hond. Een volgend hoofdstuk handelt over de CT kenmerken van de normale schildklier bij de hond. De gemiddelde pre- en post-contrast attenuatie waarden waren zeer hoog voor weke delen. Na injectie van intraveneus contrast nam het schildklier volume toe. Alle schildklierlobben zagen er homogeen uit op zowel pre- als post-contrastbeelden. De ligging, de grootte en de vorm van de schildklierlobben werden beschreven. Bijschildklieren werden niet gezien en een isthmus werd slechts bij 1 op de 25 honden aangetroffen. Gezien de uitstekende zichtbaarheid en kenmerkende eigenschappen van de normale schildklier bij de hond besloten we dat het gebruik van CT voordelig zou kunnen zijn om het onderscheid te maken tussen nekmassa’s afkomstig van schildklierweefsel en nekmassa’s van andere oorsprong. CT heeft eveneens een potentiële rol bij het stageren van schildkliertumoren. Tot slot beschreven we de MRI kenmerken van de normale schildklier. De kenmerkende vorm, ligging en intensiteit vergeleken met de omliggende structuren maakten de schildklier duidelijk herkenbaar bij alle honden. Een isthmus werd slechts bij 1 op de 44 honden aangetroffen en bijschildklieren werden niet gezien. Gezien de uitstekende zichtbaarheid en kenmerkende eigenschappen van de schildklier op MRI werd er besloten dat MRI kan bijdragen tot de diagnose van diffuse schildklieraandoeningen, bij het onderscheiden van nekmassa’s van schildklieroorsprong en andere oorsprong, en bij de stagering en operatieplanning van schildkliertumoren

A finite element approach to inverse scattering problems

En este proyecto se desarrolla una aplicación basada en "Microwave Imaging" (MWI), implementada con el propósito de obtener las propiedades materiales desconocidas de un determinado objeto. Este método consta de dos partes fundamentales: El Problema Directo y el Algoritmo Inverso. La primera etapa, el Problema Directo, implica la medición del campo eléctrico disperso a lo largo de un dominio material. El Objeto de Interés (OI) representa un cuerpo material desconocido que se encuentra dentro de un tanque, rodeado por un conjunto de antenas que iluminan el escenario y almacenan los datos experimentales de las mediciones relacionadas con el campo eléctrico. Además, se introduce un medio adaptador dentro del recinto cerrado, el cual es denominado como "background". Con el objetivo de simular los datos experimentales, se desarrolla el Método de los Elementos Finitos. FEM representa una técnica matemática e ingenieril muy potente que nos permite resolver un conjunto de ecuaciones lineales que describen el comportamiento electromagnético. De este modo, podremos generar los datos sintéticos referidos a las variables nodales, que definen el escenario de imagen simulado mediante un simulador de FEM, denominado GiD y desarrollado por la UPC. Después de resolver el Problema Directo, se aborda el "Contrast Source Inversion Method" (CSIM) con el propósito de reconstruir los parámetros físicos originales que definen el OI. Haciendo uso de este algoritmo de inversión será viable alcanzar el error mínimo global entre los datos reales y los reconstruidos. Cuando este método iterativo converja, los resultados reconstruidos serán analizados con el objeto de identificar los materiales implicados en el "Imaging Domain". En este trabajo se describen los diferentes experimentos relacionados con el Problema Directo y Algoritmo Inverso, obteniendo diversas conclusiones sobre el funcionamiento de FEM-CSIM. En concreto, se analizan los conductores eléctricos perfectos, la distribución de las fuentes de corriente, las própiedades dieléctricas del "background" y la influencia de la frecuencia. Del mismo modo, los resultados de reconstrucción serán comparados en diferentes experimentos, obteniendo información sobre la resolución del método y las limitaciones del algoritmo. Finalmente es importante destacar las simulaciones realizadas con medios con y sín pérdidas, y los experimentos de biomedicina que tratan de representar posibles experimentos reales de imagen médica. Observaremos como CSIM proporciona una calidad alta en los resultados cómo para poder detectar la posicion y características de los objetivos. En las mejores situaciones de reconstrucción obtendremos errores en torno al 25%, que aunque puedan parecer discretos, son suficientes en muchas aplicaciones de imagen médica

OPTICAL COHERENCE TOMOGRAPHY OPHTHALMIC SURGICAL GUIDANCE

Optical coherence tomography (OCT) performs high-resolution cross-sectional and volumetric tissue imaging in situ through the combination of confocal gating, coherence gating, and polarization gating. Because it is noninvasive, OCT has been used in multiple clinical applications such as tissue pathology assessment and interventional procedure guidance. Moreover, OCT can perform functional measurements such as phase-sensitive measurement of blood flow and polarization-sensitive measurement of tissue birefringence. These features made OCT one of the most widely used imaging systems in ophthalmology. In this thesis, we present several novel OCT methods developed for microsurgery guidance and OCT image analysis. The thesis mainly consists of five parts, which are shown as follows. First, we present a BC-mode OCT image visualization method for microsurgery guidance, where multiple sparsely sampled B-scans are combined to generate a single cross-sectional image with an enhanced instrument and tissue layer visibility and reduced shadowing artifacts. The performance of the proposed method is demonstrated by guiding a 30-gauge needle into an ex-vivo human cornea. Second, we present a microscope-integrated OCT guided robotic subretinal injection method. A workflow is designed for accurate and stable robotic needle navigation. The performance of the proposed method is demonstrated on ex-vivo porcine eye subretinal injection. Third, we present optical flow OCT technique that quantifies accurate velocity fields. The accuracy of the proposed method is verified through phantom flow experiments by using a diluted milk powder solution as the scattering medium, in both cases of advective flow and turbulent flow. Fourth, we present a wrapped Gaussian mixture model to stabilize the phase of swept source OCT systems. A closed-form iteration solution is derived using the expectation-maximization algorithm. The performance of the proposed method is demonstrated through ex-vivo, in-vivo, and flow phantom experiments. The results show its robustness in different application scenarios. Fifth, we present a numerical landmark localization algorithm based on a convolutional neural network and a conditional random field. The robustness of the proposed method is demonstrated through ex-vivo porcine intestine landmark localization experiments

Investigating the crustal and upper mantle structure of the central Java subduction zone with marine wide-angle seismic and gravity data

Offshore wide-angle seismic data recorded on ocean bottom instruments of a combined onshore- offshore investigation on the tectonic framework of central Java are presented in this study. The joint interdisciplinary project MERAMEX (Merapi Amphibious Experiment) was carried out to characterize the subduction of the Indo-Australian plate beneath Eurasia. Three marine wide-angle profiles are analyzed by combined forward- and inverse modeling of first and later arrival traveltimes and are integrated together with gravity data. The results of this study are compared with former investigations off southern Sumatra, western Java and eastern Java to obtain a detailed image of the Java margin. The subduction of the oceanic Roo Rise plateau, located south of central Java, with its thickened and buoyant crust, strongly influences subduction dynamics. The trench is retreated about 60 km in a landward direction. Large scale forearc uplift is manifested in isolated forearc highs, reaching water depths of only 1000 m compared to 2000 m water depth off western Java, and results from oceanic basement relief subduction. The dip angle of the underthrusting oceanic lithosphere is 10◦ underneath the marine forearc and its crustal thickness increases eastward from 9 - 10 km over a distance of 100 km between both dip profiles off central Java, which is thicker than the global average of 7.4 km. The incipient subduction of a broad band of seamounts off central Java causes frontal erosion of the margin here and leads to mass wasting due to oversteepening of the upper trench wall. The well-developed accretionary wedge off southern Sumatra and western Java diminishes into a small frontal prism with steep slope angles of the upper plate off central Java. This causes a persistent threat for generating tsunamis, which may also be triggered by smaller (Mw8) earthquakes. The rough surface of the Indo-Australian plate with its volcanic edifices strongly influences the interplate coupling. A subducted and dismembered seamount is revealed on the eastern profile at the toe of the backstop in 15 km depth. This seamount and similar features present on the megathrust may potentially act as asperities or as barriers to seismic rupture, limiting lateral rupture propagation in the co-seismic phase. Subduction earthquakes with a magnitude ≥ 8 are not observed, while smaller earthquakes frequently occur. A remarkable clustering of earthquakes in the forearc mantle wedge below the shallow forearc Moho may be the seismic expression of seamount detachement

Edge Artificial Intelligence for Real-Time Target Monitoring

The key enabling technology for the exponentially growing cellular communications sector is location-based services. The need for location-aware services has increased along with the number of wireless and mobile devices. Estimation problems, and particularly parameter estimation, have drawn a lot of interest because of its relevance and engineers' ongoing need for higher performance. As applications expanded, a lot of interest was generated in the accurate assessment of temporal and spatial properties. In the thesis, two different approaches to subject monitoring are thoroughly addressed. For military applications, medical tracking, industrial workers, and providing location-based services to the mobile user community, which is always growing, this kind of activity is crucial. In-depth consideration is given to the viability of applying the Angle of Arrival (AoA) and Receiver Signal Strength Indication (RSSI) localization algorithms in real-world situations. We presented two prospective systems, discussed them, and presented specific assessments and tests. These systems were put to the test in diverse contexts (e.g., indoor, outdoor, in water...). The findings showed the localization capability, but because of the low-cost antenna we employed, this method is only practical up to a distance of roughly 150 meters. Consequently, depending on the use-case, this method may or may not be advantageous. An estimation algorithm that enhances the performance of the AoA technique was implemented on an edge device. Another approach was also considered. Radar sensors have shown to be durable in inclement weather and bad lighting conditions. Frequency Modulated Continuous Wave (FMCW) radars are the most frequently employed among the several sorts of radar technologies for these kinds of applications. Actually, this is because they are low-cost and can simultaneously provide range and Doppler data. In comparison to pulse and Ultra Wide Band (UWB) radar sensors, they also need a lower sample rate and a lower peak to average ratio. The system employs a cutting-edge surveillance method based on widely available FMCW radar technology. The data processing approach is built on an ad hoc-chain of different blocks that transforms data, extract features, and make a classification decision before cancelling clutters and leakage using a frame subtraction technique, applying DL algorithms to Range-Doppler (RD) maps, and adding a peak to cluster assignment step before tracking targets. In conclusion, the FMCW radar and DL technique for the RD maps performed well together for indoor use-cases. The aforementioned tests used an edge device and Infineon Technologies' Position2Go FMCW radar tool-set

Room temperature caesium quantum memory for quantum information applications

Quantum memories are key components in quantum information networks. Their ability to store and retrieve information on demand makes repeat-until-success strategies scalable. Warm alkali-metal vapours are interesting candidates for the implementation of such memories, thanks to their long storage times and experimental simplicity. Operation with the Raman protocol enables high time-bandwidth products, which allows for multiple synchronisation trials of probabilistically operating quantum gates via memory-based temporal multiplexing. This makes the Raman memory a promising tool, whose broad spectral bandwidth facilitates direct interfacing with other photonic primitives, such as single photon sources. Here, such a light-matter interface is implemented in a warm caesium vapour. Firstly, we study the storage of polarisation-encoded information in the memory. High quality polarisation preservation for bright coherent state input signals can be achieved, when operating the Raman memory in a dual-rail configuration inside a polarisation interferometer. Secondly, heralded single photons are stored in the memory. To this end, the memory is operated on-demand by feed-forward of source heralding events, which is a key technological capability. Prior to storage, single photons are produced in a spontaneous parametric down conversion source, whose bespoke design spectrally tailors the photons to the memory acceptance line. The faithful retrieval of stored single photons is found to be currently limited by noise in the memory, with a signal-to-noise ratio of 0.3 in the memory output. Nevertheless, a clear influence of the input's quantum nature is observed in the retrieved light by measuring signal's photon statistics. Finally, the memory noise processes are examined in detail. Four-wave-mixing noise is determined as the sole important noise source for the Raman memory

Stratification of patellofemoral pain using clinical, biomechanical and imaging features

Patellofemoral pain (PFP) is a common musculoskeletal complaint and the efficacy of current therapies aimed at PFP is limited. The aetiology of PFP is widely considered to be multifactorial and as a result the clinical presentation is often heterogeneous. In an attempt to address this issue, an international PFP consensus statement, published in 2013, highlighted the need to sub-group patients with PFP to enable more stratified interventions. A multi-methodological approach was used in this thesis. A systematic review of the existing imaging literature in PFP demonstrated that PFP is associated with a number of imaging features in particular MRI bisect offset and CT congruence angle and that some of these features should be modifiable with conservative treatment. A retrospective analysis investigating the overall 3D shape and 3D equivalents of commonly used PFJ imaging features demonstrated no differences between a group with and without PFP, challenging the current perceptions on the structural associations to PFP. A cross-sectional cluster analysis using modifiable clinical, biomechanical and imaging features identified four subgroups that are present in PFP cohort with a Weak group showing the worst prognosis at 12 months. Lastly, a pragmatic randomised controlled feasibility study comparing matched treatment to usual care management showed that matching treatment to a specific subgroup is feasible in terms of adherence, retention and conversion to consent. In summary, the findings of this thesis improves our understanding of the structural associations to PFP; the subgroups that exist within the PFP population; the natural prognosis of these PFP subgroups; and the feasibility of targeting treatment at PFP subgroups within a clinical trial