Holoscopic 3D imaging also known as “Integral imaging” was first proposed by Lippmann in 1908. It facilitates a promising technique for creating full colour spatial image that exists in space. It promotes a single lens aperture for recording spatial images of a real scene, thus it offers omnidirectional motion parallax and true 3D depth, which is the fundamental feature for digital refocusing. While stereoscopic and multiview 3D imaging systems simulate human eye technique, holoscopic 3D imaging system mimics fly’s eye technique, in which viewpoints are orthographic projection. This system enables true 3D representation of a real scene in space, thus it offers richer spatial cues compared to stereoscopic 3D and multiview 3D systems. Focus has been the greatest challenge since the beginning of photography. It is becoming even more critical in film production where focus pullers are finding it difficult to get the right focus with camera resolution becoming increasingly higher. Holoscopic 3D imaging enables the user to carry out re/focusing in post-production. There have been three main types of digital refocusing methods namely Shift and Integration, full resolution, and full resolution with blind. However, these methods suffer from artifacts and unsatisfactory resolution in the final resulting image. For instance the artifacts are in the form of blocky and blurry pictures, due to unmatched boundaries. An upsampling method is proposed that improves the resolution of the resulting image of shift and integration approach. Sub-pixel adjustment of elemental images including “upsampling technique” with smart filters are proposed to reduce the artifacts, introduced by full resolution with blind method as well as to improve both image quality and resolution of the final rendered image. A novel 3D object extraction method is proposed that takes advantage of disparity, which is also applied to generate stereoscopic 3D images from holoscopic 3D image. Cross correlation matching algorithm is used to obtain the disparity map from the disparity information and the desirable object is then extracted. In addition, 3D image conversion algorithm is proposed for the generation of stereoscopic and multiview 3D images from both unidirectional and omnidirectional holoscopic 3D images, which facilitates 3D content reformation.

This thesis deals with the topic of 3D image processing for digital holographic microscopy - numerical refocusing. This method allows to perform mathematically accurate defocus correction on image of a sample captured away from the sample plane and it was applicable only for images that were made made using coherent illumination source. It has been generalized to a form in which it is also applicable to devices that use incoherent (non-monochromatic or extended) illumination sources. Another presented achievement concerns hologram processing. The advanced hologram processing method enables obtaining more data mainly concerning precision of quantities from one hologram — normally, one would have to capture multiple holograms to get those. Both methods have been verified experimentally.

The majority of the world’s most widespread and problematic pathogens evade host immune responses by inducing strain-specific immunity. The host immune system seems to induce a vigorous immune response towards hypervariable epitopes, seemingly attracting less attention to more highly conserved vital regions. The South African Territory (SAT)-2 foot-and-mouth disease virus (FMDV) is the most prevalent and antigenic diverse of the SAT serotypes with the occurrence of multiple antigenic and genetic subtypes. Identification of the fine antigenic structure of the capsid of these viruses remains essential in the design and engineering of a vaccine seed strain that confers cross-protection against intra-typic viruses. Towards refocusing the antigenicity of SAT2/ZIM/07/83 virus, two strategies were utilised, (1) replacement of predicted antigenic determinants to corresponding sites of the antigenic distant SAT2/EGY/09/12 virus and (2) charge-dampening of previously identified epitope regions with alanine residues. The antigenic distance of refocused mutants was evaluated by (1) virus neutralisation assays using parental and heterologous convalescent bovine sera and (2) through antigenic profiling with non-neutralising SAT2-specific murine monoclonal antibodies (mAbs). One antigenic site on VP1 (Site 3) was identified using bovine polyclonal antibodies, whereas an additional three epitope regions were elucidated using the murine mAbs. Furthermore, the cell culture-adapted vSAT2 was shown to utilise a third FMDV alternate receptor to infect integrin- and heparin sulphate-deficient cell lines. Comprehensive knowledge on the antigenic structure of these viruses will assist in the fundamental design of engineered vaccines by incorporating critical antigenic sites that confer increased antigenicity and cross-protective immune response against myriad SAT2 field strains. Furthermore, this information will not only improve design of vaccine seed viruses, but will also contribute towards novel vaccine constructs or even empty nanoparticles as a vaccine strategy in the future. / Thesis (PhD)--University of Pretoria, 2020. / Agricultural Research Council / National Research Foundation / Red Meat Industry Trust / Poliomyelitis Research Foundation / Microbiology and Plant Pathology / PhD / Unrestricted

This thesis deals with the topic of 3D image processing for digital holographic microscopy - numerical refocusing. This method allows to perform mathematically accurate defocus correction on image of a sample captured away from the sample plane and it was applicable only for images that were made made using coherent illumination source. It has been generalized to a form in which it is also applicable to devices that use incoherent (non-monochromatic or extended) illumination sources. Another presented achievement concerns hologram processing. The advanced hologram processing method enables obtaining more data mainly concerning precision of quantities from one hologram — normally, one would have to capture multiple holograms to get those. Both methods have been verified experimentally.

Divestitures have grown in importance and popularity over the years, rivaling other strategic transactions in mergers and acquisitions. The dominating opinion in academic research is that divestitures overall generate an abnormal return for the parent company stock. This thesis will focus on how Swedish companies perform in the short-term around the announcement of a divestiture. A multiple linear regression analysis finds significance for divestiture gains being attributed to companies focusing on core competencies and to companies with low returns on assets and high returns on equity. However, no significance is found for the size of the companies or financial distress. / Avknoppningar är idag en populär företagstransaktion. Den dominerade åsikten i den globala forskningen kring avknoppningar gör gällande att de generar en överavkastning för företaget i förhållande till marknaden. Denna kandidatuppsats ämnar undersöka vilka faktorer som kan påverka denna överavkastning genom att studera svenska företag på Nasdaq Stockholm. En multipel regressionsanalys visar att företag som säger sig utföra avknoppningar för att fokusera på kärnverksamheten generar en överavkastning. Vidare blir det en överavkastning på företag som har låg avkastning på totalt kapital och hög avkastning på eget kapital. Ingen verkan hittas dock för att storleken på företaget eller skuldstrukturen har en inverkan på överavkastningen.

The aim of this thesis is to explain terms like light field, plenoptic camera or digital lens. Also the goal is to explain the principle of rendering the resulting images with the option to select the plane of focus, depth of field, changes in perspective and partial change in the angle of the point of view. The main outputs of this thesis are scripts for rendering images from Lytro camera and the interactive application, which clearly demonstrates the principles of plenoptic sensing.

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Cette thèse traite des caméras light-field en tant que caméra ayant des capacités 3D. Les images brutes, acquises avec ces systèmes, sont généralement inexploitables directement. L’obstacle majeur concernant l'utilisation de ces caméras réside dans la complexité du traitement des images acquises. Cette thèse vise à dépasser ces limitations en s'intéressant aux dispositifs multi-vues et multi-caméras. De plus, comme l'un des domaines d'application envisagé est la vision industrielle, les images sont acquises en lumière naturelle afin de conserver la possibilité d'effectuer des traitements conventionnels par vision sur les images. Le travail de thèse repose sur trois axes : l'étude et la conception optique de systèmes light-field multi-caméras et multi-vues, le calibrage de ces dispositifs et le développement d’algorithmes et enfin leur mise en application pour montrer les intérêts de ces caméras dans divers domaines. / This thesis deals with light-field cameras as cameras having 3D capacities. The raw images. acquired with these systems, are generally unusable directly. The main obstacle about their use lies in the complex processing of the recorded images. This thesis aims to overcome these limitations by focusing on multi-views and multi-camera devices. Morcover, as one of the application domains is the industrial vision, the images are acquired in natural lightning in order to conserve the possibility to make conventional treatments by vision on the images. The work is based on three axis: the study and'the optical desien of light-field systems, the calibration of these devices and the development of algorithms to show the intercsts of these cameras in various fields.

<p>In this study, we concentrate on spin-1/2 systems. A series of tools using the Liouville space method have been developed for simulating of NMR of arbitrary pulse sequences.</p> <p>We have calculated one- and two-spin symbolically, and larger systems numerically of steady states. The one-spin calculations show how SSFP converges to continuous wave NMR. A general formula for two-spin systems has been derived for the creation of double-quantum signals as a function of irradiation strength, coupling constant, and chemical shift difference. The formalism is general and can be extended to more complex spin systems.</p> <p>Estimates of transverse relaxation, R₂, are affected by frequency offset and field inhomogeneity. We find that in the presence of expected B₀ inhomogeneity, off-resonance effects can be removed from R₂ measurements, when ||omega||<= 0.5 gamma\,B₁ in Hahn echo experiments, when ||omega||<=gamma\,B₁ in CPMG experiments with specific phase variations, by fitting exact solutions of the Bloch equations given in the Lagrange form.</p> <p>Approximate solutions of CPMG experiments show the specific phase variations can significantly smooth the dependence of measured intensities on frequency offset in the range of +/- 1/2 gamma\,B₁. The effective R₂ of CPMG experiments when using a phase variation scheme can be expressed as a second-order formula with respect to the ratio of offset to pi-pulse amplitude.</p> <p>Optimization problems using the exact or approximate solution of the Bloch equations are established for designing optimal broadband universal rotation (OBUR) pulses. OBUR pulses are independent of initial magnetization and can be applied to replace any pulse of the same flip angles in a pulse sequence. We demonstrate the process to exactly and efficiently calculate the first- and second-order derivatives with respect to pulses. Using these exact derivatives, a second-order optimization method is employed to design pulses. Experiments and simulations show that OBUR pulses can provide more uniform spectra in the designed offset range and come up with advantages in CPMG experiments.</p> / Doctor of Philosophy (PhD)

En Imagerie par Résonance Magnétique (IRM), l’augmentation du champ magnétique statique permet en théorie de fournir un rapport signal sur bruit accru, améliorant la qualité des images. L’objectif de l’IRM à ultra haut champ est d’atteindre une résolution spatiale suffisamment haute pour pouvoir distinguer des structures si fines qu’elles sont actuellement impossibles à visualiser de façon non-invasive. Cependant, à de telles valeurs de champs magnétiques, la longueur d’onde du rayonnement électromagnétique envoyé pour basculer les spins des protons de l’eau est du même ordre de grandeur que l’objet dont on souhaite faire l’image. Des phénomènes d’interférences sont observés, ce qui se traduit par l’inhomogénéité de ce champ radiofréquence (RF) au sein de l’objet. Ces interférences engendrent des artefacts de signal et/ou de contraste dans les images IRM, et rendent ainsi leur exploitation délicate. Il est donc crucial de fournir des solutions pour atténuer la non-uniformité de l’excitation des spins, à défaut de quoi de tels systèmes ne pourront atteindre leurs pleins potentiels. Pour obtenir des diagnostics pertinents à très haut champ, il est donc nécessaire de créer des impulsions RF homogénéisant l'excitation de l'ensemble des spins (ici du cerveau humain), optimisées pour chaque individu. Pour cela, un système de transmission parallèle (pTX) à 8 canaux a été installé au sein de notre imageur à 7 Tesla. Alors que la plupart des systèmes IRM cliniques n’utilisent qu’un seul canal d’émission, l’extension pTX permet de jouer différentes formes d’impulsions RF de concert. La somme résultante de ces interférences doit alors être optimisée pour atténuer la non-uniformité observée classiquement. L’objectif de cette thèse est donc de synthétiser ce type d’impulsions, en utilisant la pTX. Ces impulsions auront pour contrainte supplémentaire le respect des limitations internationales concernant l'exposition à des champs radiofréquence, qui induit une hausse de température dans les tissus. En ce sens, de nombreuses simulations électromagnétiques et de températures ont été réalisées en introduction de cette thèse, afin d’évaluer la relation entre les seuils recommandés d’exposition RF et l’élévation de température prédite dans les tissus. Cette thèse porte plus spécifiquement sur la conception de l’ensemble des impulsions RF refocalisantes utilisées dans des séquences IRM non-sélectives, basées sur l’écho de spin. Dans un premier temps, seule une impulsion RF a été générée, pour une application simple : l’inversion du déphasage des spins dans le plan transverse. Dans un deuxième temps, sont considérées les séquences à long train d’échos de refocalisation appliquées à l’in vivo. Ici, l’opérateur mathématique agissant sur la magnétisation, et non pas son état final comme il est fait classiquement, est optimisé. Le gain en imagerie à très haut champ est clairement visible puisque les opérations mathématiques (la rotation des spins) voulues sont réalisées avec plus de fidélité que dans le cadre des méthodes de l’état de l’art. Pour cela, la génération de ces impulsions RF combine une méthode d’excitation des spins avec navigation dans l’espace de Fourier, les kT-points, et un algorithme d’optimisation, appelé Gradient Ascent Pulse Engineering (GRAPE), utilisant le contrôle optimal. Cette conception est rapide grâce à des calculs analytiques plus directs que des méthodes de différences finies. La prise en compte d’un grand nombre de paramètres nécessite l’usage de GPUs (Graphics Processing Units) pour atteindre des temps de calcul compatibles avec un examen clinique. Cette méthode de conception d’impulsions RF a été validée expérimentalement sur l’imageur 7 Tesla de NeuroSpin, sur une cohorte de volontaires sains. / In Magnetic Resonance Imaging (MRI), the increase of the static magnetic field strength is used to provide in theory a higher signal-to-noise ratio, thereby improving the overall image quality. The purpose of ultra-high-field MRI is to achieve a spatial image resolution sufficiently high to be able to distinguish structures so fine that they are currently impossible to view in a non-invasive manner. However, at such static magnetic fields strengths, the wavelength of the electromagnetic waves sent to flip the water proton spins is of the same order of magnitude than the scanned object. Interference wave phenomena are then observed, which are caused by the radiofrequency (RF) field inhomogeneity within the object. These generate signal and/or contrast artifacts in MR images, making their exploitation difficult, if not impossible, in certain areas of the body. It is therefore crucial to provide solutions to mitigate the non-uniformity of the spins excitation. Failing this, these imaging systems with very high fields will not reach their full potential.For relevant high field clinical diagnosis, it is therefore necessary to create RF pulses homogenizing the excitation of all spins (here of the human brain), and optimized for each individual to be imaged. For this, an 8-channel parallel transmission system (pTX) was installed in our 7 Tesla scanner. While most clinical MRI systems only use a single transmission channel, the pTX extension allows to simultaneously playing various forms of RF pulses on all channels. The resulting sum of the interference must be optimized in order to reduce the non-uniformity typically seen.The objective of this thesis is to synthesize this type of tailored RF pulses, using parallel transmission. These pulses will have as an additional constraint the compliance with the international exposure limits for radiofrequency exposure, which induces a temperature rise in the tissue. In this sense, many electromagnetic and temperature simulations were carried out as an introduction of this thesis, in order to assess the relationship between the recommended RF exposure limits and the temperature rise actually predicted in tissues.This thesis focuses specifically on the design of all RF refocusing pulses used in non-selective MRI sequences based on the spin-echo. Initially, only one RF pulse was generated for a simple application: the reversal of spin dephasing in the transverse plane, as part of a classic spin echo sequence. In a second time, sequences with very long refocusing echo train applied to in vivo imaging are considered. In all cases, the mathematical operator acting on the magnetization, and not its final state as is done conventionally, is optimized. The gain in high field imaging is clearly visible, as the necessary mathematical operations (that is to say, the rotation of the spins) are performed with a much greater fidelity than with the methods of the state of the art. For this, the generation of RF pulses is combining a k-space-based spin excitation method, the kT-points, and an optimization algorithm, called Gradient Ascent Pulse Engineering (GRAPE), using optimal control.This design is relatively fast thanks to analytical calculations rather than finite difference methods. The inclusion of a large number of parameters requires the use of GPUs (Graphics Processing Units) to achieve computation times compatible with clinical examinations. This method of designing RF pulses has been experimentally validated successfully on the NeuroSpin 7 Tesla scanner, with a cohort of healthy volunteers. An imaging protocol was developed to assess the image quality improvement using these RF pulses compared to typically used non-optimized RF pulses. All methodological developments made during this thesis have contributed to improve the performance of ultra-high-field MRI in NeuroSpin, while increasing the number of MRI sequences compatible with parallel transmission.