L’imagerie TEP repose à l’heure actuelle sur des détecteurs à base de cristaux scintillants ou de semi-conducteurs. Le projet CaLIPSO propose de tirer parti à la fois de l’émission de lumière (par effet Cerenkov) et de l’ionisation du milieu de détection, pour réaliser un détecteur de résolution temporelle et spatiale améliorée. Le milieu de détection, le TriMéthylBismuth liquide à température ambiante, de par sa forte teneur en Bismuth, permet une détection par effet photoélectrique efficace. Cette étude a pour objectif de concevoir et d’optimiser le détecteur optique du projet CaLIPSO, afin de prouver le concept de la détection de photons de 511 keV par effet Cerenkov dans le TMBi, et de caractériser les performances d’un tel détecteur en termes de résolution temporelle et efficacité de détection. Un premier démonstrateur a validé le principe de détection reposant sur l’effet Cerenkov, bien que ses performances soient décevantes. C’est la raison pour laquelle nous avons entrepris un effort d’optimisation en simulation Monte Carlo dans Geant4, afin d’améliorer la collection de la lumière Cerenkov dans le détecteur, et donc son efficacité de détection et sa résolution temporelle. Avant, nous avons mesuré les propriétés optiques du TMBi (indice de réfraction, absorption et diffusion de la lumière), afin d’être capables de modéliser la propagation de la lumière Cerenkov dans le détecteur. Nous avons également optimisé par simulation Monte Carlo l’outil permettant la mesure de résolution en temps, un cristal scintillant de YAP:Ce couplé à un PMT. Cela a permis une mesure plus fine de la résolution temporelle du démonstrateur. A l’issue de ces travaux, nous avons construit un second démonstrateur optique. On mesure alors une efficacité de détection de l’ordre de 32% pour une résolution en temps de 660 ps (FWHM). L’efficacité mesurée prouve que le détecteur est pleinement efficace à détecter les conversions photoélectriques du photon de 511 keV (27% des photons incidents). Plusieurs optimisations technologiques sont proposées pour améliorer la résolution temporelle, et espérer à l’avenir une mesure du temps de vol des photons gamma. / PET detectors are usually based on scintillation crystals or semiconductor materials. The CaLIPSO project aims to build a PET detector working on the double detection of Cerenkov light and pair productions in a novel detection material called TriMethylBismuth. This would allow at the same time an enhanced time resolution (thanks to the Cerenkov signal) and a excellent spatial resolution (thanks to the ionization signal). Liquid TMBi (at room temperature), thanks to its good photo fraction (47%), allows a good detection efficiency, principally by photoelectric effect. In this context, this work aims to design and optimize an optical detector as a proof of concept for the Cerenkov detection of 511 keV gamma photons, and to measure the time resolution and detection efficiency of such a detector. The optical signal based on Cerenkov effect in TMBi has been observed on a first demonstrator, but its performances were clearly inappropriate. So we used a Monte Carlo simulation (Geant4) of the detector in order to model the relevant phenomena and to optimize de detection. It appeared that light collection efficiency in the detector was the most important parameter to optimize so as to improve time resolution and detection efficiency. Before that, we measured TMBi optical properties (refractive index, light absorption and diffusion), in order to model accurately the Cerenkov light propagation in the detector. The tool used for the time resolution measurement is a YAP: Ce scintillator coupled to a PMT. We also needed to optimize this tool in order to allow a more accurate measurement of the detector time resolution. At the end of this work, a second version of the optical demonstrator was built. We measured a detection efficiency of 32%, and a time resolution of 660 ps FWHM. The measured efficiency proved that our detector is fully efficient to detect the photoelectric conversions of the 511 keV photons (27% of the incident photons). Several technological optimizations are proposed to further improve the time resolution, in order to be able to measure the gamma photons’ time-of-flight in the future.

The ongoing merger of the digital and optical components of the modern microscope is creating opportunities for new measurement techniques, along with new challenges for optical modelling. This thesis investigates several such opportunities and challenges which are particularly relevant to biomedical imaging. Fourier optics is used throughout the thesis as the underlying conceptual model, with a particular emphasis on three--dimensional Fourier optics. A new challenge for optical modelling provided by digital microscopy is the relaxation of traditional symmetry constraints on optical design. An extension of optical transfer function theory to deal with arbitrary lens pupil functions is presented in this thesis. This is used to chart the 3D vectorial structure of the spatial frequency spectrum of the intensity in the focal region of a high aperture lens when illuminated by linearly polarised beam. Wavefront coding has been used successfully in paraxial imaging systems to extend the depth of field. This is achieved by controlling the pupil phase with a cubic phase mask, and thereby balancing optical behaviour with digital processing. In this thesis I present a high aperture vectorial model for focusing with a cubic phase mask, and compare it with results calculated using the paraxial approximation. The effect of a refractive index change is also explored. High aperture measurements of the point spread function are reported, along with experimental confirmation of high aperture extended depth of field imaging of a biological specimen. Differential interference contrast is a popular method for imaging phase changes in otherwise transparent biological specimens. In this thesis I report on a new isotropic algorithm for retrieving the phase from differential interference contrast images of the phase gradient, using phase shifting, two directions of shear, and non--iterative Fourier phase integration incorporating a modified spiral phase transform. This method does not assume that the specimen has a constant amplitude. A simulation is presented which demonstrates good agreement between the retrieved phase and the phase of the simulated object, with excellent immunity to imaging noise.

This work explores a novel vision model based coding approach to encode medical images at a perceptually lossless quality, within the framework of the JPEG 2000 coding engine. Perceptually lossless encoding offers the best of both worlds, delivering images free of visual distortions and at the same time providing significantly greater compression ratio gains over its information lossless counterparts. This is achieved through a visual pruning function, embedded with an advanced model of the human visual system to accurately identify and to efficiently remove visually irrelevant/insignificant information. In addition, it maintains bit-stream compliance with the JPEG 2000 coding framework and subsequently is compliant with the Digital Communications in Medicine standard (DICOM). Equally, the pruning function is applicable to other Discrete Wavelet Transform based image coders, e.g., The Set Partitioning in Hierarchical Trees. Further significant coding gains are ex ploited through an artificial edge segmentation algorithm and a novel arithmetic pruning algorithm. The coding effectiveness and qualitative consistency of the algorithm is evaluated through a double-blind subjective assessment with 31 medical experts, performed using a novel 2-staged forced choice assessment that was devised for medical experts, offering the benefits of greater robustness and accuracy in measuring subjective responses. The assessment showed that no differences of statistical significance were perceivable between the original images and the images encoded by the proposed coder.

The mouse pancreas is a mixed exocrine and endocrine glandconsisting of three lobular compartments: the splenic, duodenal and gastric lobes. During embryogenesis, the pancreas forms from two progenitor populations located on the dorsal and ventral side of the primitive gut tube. These anlagen are brought in close proximity as the gut elongates and rotates, and fuse to form a single organ. The splenic and duodenal lobes develop from the dorsal and ventral anlagen, respectively. In the adult pancreas, exocrine tissue secretes digestive enzymes intothe gut lumen to support nutrient uptake. The endocrine Islets of Langerhans are scattered throughout the exocrine tissue and aid in regulation of energy homeostasis through the secretion of hormones. One of the key players in energy homeostasis is the pancreatic ß-cell, which is the most abundant cell type of the islets. The β-cells regulates blood glucose levels through the action of insulin. Conditions where this regulation does not function properly are gathered under the common name of Diabetes mellitus. Type 1 diabetes (T1D) is characterized by insulin deficiency due to autoimmune destruction of the ß-cells. Using recently developed protocols for optical projection tomography (OPT) whole-organ imaging, we have revealed new spatial and quantitative aspects on ß-cell mass dynamics and immune infiltration during the course of T1D development in the non-obese diabetic (NOD) mouse model. We show that although immune infiltration appears to occur asynchronously throughout the organ, smaller islets, mainly located in the periphery of the organ, preferentially loose their ß-cells during early stages of disease progression. Larger islets appear more resistant to the autoimmune attack and our data indicate the existence of a compensatory proliferative capacity within these islets. We also report the appearance of structures resembling tertiary lymphoid organs (TLOs) in association with the remaining islets during later phases of T1D progression. OPT has already proven to be a useful tool for assessments of ß-cellmass in the adult mouse pancreas. However, as with other techniques, previous protocols have relied on a tedious degree of manual postivacquisition editing. To further refine OPT-based assessment of pancreatic ß-cell mass distribution in the murine pancreas, we implemented a computational statistical approach, Contrast-Limited Adaptive Histogram Normalisation (CLAHE), to the OPT projection data of pancreata from C57Bl/6 mice. This methodology provided increased islet detection sensitivity, improved islet morphology and diminished subjectivity in thresholding for reconstruction and quantification. Using this approach, we could report a substantially higher number of islets than previously described for this strain and provide evidence of significant differences in islet mass distribution between the pancreatic lobes. The gastric lobe stood out in particular and contained a 75% higher islet density as compared to the splenic lobe. Although the development of the early pancreatic buds has been relatively well studied, later morphogenetic events are less clear and information regarding the formation of the gastric lobe has largely been missing. Using OPT we have generated a quantitative three-dimensional road map of pancreatic morphogenesis in the mouse. We show that the gastric lobe forms as a perpendicular outgrowth fromthe stem of the dorsal pancreas at around embryonic day (e) 13.5, which grows into a mesenchymal domain overlaying the pyloric sphincter and proximal part of the glandular stomach. By analyzing mutant mice with aberrant spleen development, we further demonstrate that proper formation of the gastric lobe is dependent on the initial formation of the closely positioned spleen, indicating a close interplay between pancreatic and splenic mesenchyme during development. Additionally, we show that the expression profile of markers for pancreatic multipotent progenitors within the pancreas is heterogenous with regards to lobular origin. Altogether, our studies regarding the morphogenesis and adult constitution of the mouse pancreas recognize lobular heterogeneities that add important information for future interpretations of this organ.

Although the major functions of the lymphatic system are fairly well defined, its vasculature has yet to be well characterized in comparison to its blood vasculature counterpart. Recent advances in optical imaging techniques have allowed for more detailed and quantitative evaluations of lymph flow dynamics and mechanism. A rat tail is often used for investigations of lymph flow because of the simple geometry, superficial nature, and disease progression models of its collecting lymphatic vessels. In this study, a pressure cuff system was fabricated and coupled with an existing functional near infrared (NIR) imaging system to measure the overall pumping pressure of the lymphatic vessels of a rat tail. In addition to adapting the system for use on rodents, previous systems used for measuring lymphatic pumping pressure in humans were improved upon in several ways. The system defined here utilizes closed-loop feedback control of pressure application at smaller, more precise intervals. Using this device, a significant difference in lymphatic vessel pumping pressure was detected between a control case and a treatment case in which a vasoactive substance with a nitric oxide donor (GTNO ointment) was applied to the tail. Although it is known that nitric oxide plays a crucial physiologic role in propagation of flow through lymphatic vessels, this study has quantified its significant pharmacological reduction of pumping pressure for the first time.

This research centers on the fabrication, characterization, and engineering of inverse opal scaffolds, a novel class of three-dimensional (3D) porous scaffolds made of biocompatible and biodegradable polymers, for applications in tissue engineering and regenerative medicine. The unique features of an inverse opal scaffold include a highly ordered array of pores, uniform and finely tunable pore sizes, high interconnectivity, and great reproducibility. The first part of this work focuses on the fabrication and functionalization of inverse opal scaffolds based on poly(D,L-lactic-co-glycolic acid) (PLGA), a biodegradable material approved by the U.S. Food and Drug Administration (FDA). The advantages of the PLGA inverse opal scaffolds are also demonstrated by comparing with their counterparts with spherical but non-uniform pores and poor interconnectivity. The second part of this work shows two examples where the PLGA inverse opal scaffolds were successfully used as a well-defined system to investigate the effect of pore size of a 3D porous scaffold on the behavior of cell and tissue growth. Specifically, I have demonstrated that i) the differentiation of progenitor cells in vitro was dependent on the pore size of PLGA-based scaffolds and the behavior of the cells was determined by the size of individual pores where the cells resided in, and ii) the neovascularization process in vivo could be directly manipulated by controlling a combination of pore and window sizes when they were applied to a mouse model. The last part of this work deals with the novel application of photoacoustic microscopy (PAM), a volumetric imaging modality recently developed, to tissue engineering and regenerative medicine, in the context of non-invasive imaging and quantification of cells and tissues grown in PLGA inverse opal scaffolds, both in vitro and in vivo. Furthermore, the capability of PAM to monitor and quantitatively analyze the degradation of the scaffolds themselves was also demonstrated.

This dissertation presents the contributions and the research conducted in developing and implementing Microwave Tomography (MWT) systems. MWT is an imaging modality which aims to interrogate an object of interest by microwave energy, and quantitatively “find” the interior spatial distribution of its dielectric properties using field measurements taken outside the object. Due to the inherent non-linearity of the MWT problem, a substantial amount of electromagnetic scattering data is required to ensure a robust inversion and quantitatively accurate imaging results. This research benefits a variety of applications including biomedical imaging, industrial non-destructive testing, and security applications. Developing a MWT system, requires many critical components including the bandwidth and polarization purity of the collected fields as well as calibration of the fields scattered by the object of interest. Two generations of MWT systems were designed, implemented, calibrated and tested at the University of Manitoba (UM). These systems aim different approaches for near-field measurements which are referred to as the direct and indirect methods. With regard to the antenna design, a novel methodology applicable to broadband planar antennas is introduced. This technique is based on a combination of field modelling, herein, the finite element method and transmission line modelling. In the first generation of the UM MWT systems, a suitable antenna system was utilized. The system under study was a prototype, where twenty-four co-resident antennas encircle the object of interest to directly measure the fields. In the second generation of the UM MWT systems, the feasibility of using a novel technique to indirectly measure the fields by a secondary array of near-field scatterer probes was studied. The technique is based on the Modulated Scatterer Technique (MST). In this system, antennas are called ``collectors", since the role of antennas are changed to collecting probes' scattered fields. A number of PIN diodes were utilized to activate the probes. Finally, the capability of the probe system was investigated and its performance with the previously constructed tomography systems was compared. Various dielectric phantoms were utilized to test the accuracy of the systems.

This dissertation presents the contributions and the research conducted in developing and implementing Microwave Tomography (MWT) systems. MWT is an imaging modality which aims to interrogate an object of interest by microwave energy, and quantitatively “find” the interior spatial distribution of its dielectric properties using field measurements taken outside the object. Due to the inherent non-linearity of the MWT problem, a substantial amount of electromagnetic scattering data is required to ensure a robust inversion and quantitatively accurate imaging results. This research benefits a variety of applications including biomedical imaging, industrial non-destructive testing, and security applications. Developing a MWT system, requires many critical components including the bandwidth and polarization purity of the collected fields as well as calibration of the fields scattered by the object of interest. Two generations of MWT systems were designed, implemented, calibrated and tested at the University of Manitoba (UM). These systems aim different approaches for near-field measurements which are referred to as the direct and indirect methods. With regard to the antenna design, a novel methodology applicable to broadband planar antennas is introduced. This technique is based on a combination of field modelling, herein, the finite element method and transmission line modelling. In the first generation of the UM MWT systems, a suitable antenna system was utilized. The system under study was a prototype, where twenty-four co-resident antennas encircle the object of interest to directly measure the fields. In the second generation of the UM MWT systems, the feasibility of using a novel technique to indirectly measure the fields by a secondary array of near-field scatterer probes was studied. The technique is based on the Modulated Scatterer Technique (MST). In this system, antennas are called ``collectors", since the role of antennas are changed to collecting probes' scattered fields. A number of PIN diodes were utilized to activate the probes. Finally, the capability of the probe system was investigated and its performance with the previously constructed tomography systems was compared. Various dielectric phantoms were utilized to test the accuracy of the systems.

The ongoing merger of the digital and optical components of the modern microscope is creating opportunities for new measurement techniques, along with new challenges for optical modelling. This thesis investigates several such opportunities and challenges which are particularly relevant to biomedical imaging. Fourier optics is used throughout the thesis as the underlying conceptual model, with a particular emphasis on three--dimensional Fourier optics. A new challenge for optical modelling provided by digital microscopy is the relaxation of traditional symmetry constraints on optical design. An extension of optical transfer function theory to deal with arbitrary lens pupil functions is presented in this thesis. This is used to chart the 3D vectorial structure of the spatial frequency spectrum of the intensity in the focal region of a high aperture lens when illuminated by linearly polarised beam. Wavefront coding has been used successfully in paraxial imaging systems to extend the depth of field. This is achieved by controlling the pupil phase with a cubic phase mask, and thereby balancing optical behaviour with digital processing. In this thesis I present a high aperture vectorial model for focusing with a cubic phase mask, and compare it with results calculated using the paraxial approximation. The effect of a refractive index change is also explored. High aperture measurements of the point spread function are reported, along with experimental confirmation of high aperture extended depth of field imaging of a biological specimen. Differential interference contrast is a popular method for imaging phase changes in otherwise transparent biological specimens. In this thesis I report on a new isotropic algorithm for retrieving the phase from differential interference contrast images of the phase gradient, using phase shifting, two directions of shear, and non--iterative Fourier phase integration incorporating a modified spiral phase transform. This method does not assume that the specimen has a constant amplitude. A simulation is presented which demonstrates good agreement between the retrieved phase and the phase of the simulated object, with excellent immunity to imaging noise.

L’objectif de ma thèse a été de développer de nouvelles sondes utilisables en imagerie biomédicale, basées sur l’utilisation d’aptamères, pour la détection de deux types de tumeurs : les glioblastomes et les mélanomes. Les traceurs développés ont pour objectif de cibler la protéine matricielle hMMP-9. Lors d’une thèse précédente, un aptamère anti hMMP-9 noté F3B a été obtenu. Afin de transformer cet aptamère en une sonde pour l’imagerie biomédicale, différents conjugués F3B ont été préparés: Cy5, DOTA ou MAG3. L’affinité des nouveaux conjugués pour l’hMMP-9 a été évaluée par SPR et sur coupes de tumeurs. Des études de biodistribution des conjugués F3B-DOTA et F3B-MAG3 ont été réalisées sur des souris portant le mélanome, les résultats ont montré que les deux aptamères marqués détectent spécifiquement l’hMMP-9. De plus, la détection de la protéine hMMP-9 par le conjugué F3B-CY5 a été confirmée par imagerie de fluorescence. Afin d’améliorer la sensibilité de détection des tumeurs, deux types de modifications ont été envisagées, développer des structures multimériques de F3B et élaborer d’un système bi-fonctionnel. Pour ces deux approches, nous avons synthétisé un dendrimère à point focal, pouvant donner accès à une imagerie multi-modale. Ce dendrimère porte deux ou trois bras espaceur porteurs d’un groupement azoture utilisé pour le couplage avec les aptamères par la chimie «click». Le dendrimère porte au point focal une fonction amine NH2 utilisée pour fixer une biotine, afin de déterminer l'affinité Kd de cette nouvelle sonde par SPR. Par la suite un ligand DOTA sera fixé afin de pouvoir visualiser ce traceur en TEMP. / The aim of my thesis was to develop new probes that can be used in biomedical imaging, based on the use of aptamers for the detection of two types of tumors: glioblastomas and melanomas. Tracers have been developed with the aim to target the matrix protein hMMP-9. In a thesis, an aptamer anti-hMMP-9 noted F3B was obtained. Based on this compound, different derivatives were prepared for using in biomedical imaging: F3B-Cy5, F3B-DOTA or F3B-MAG3. The affinity of the new conjugates for hMMP-9 was evaluated by SPR and on sections of human melanomas. Biodistribution studies of F3B-DOTA conjugates and F3B-MAG3 were performed at on melanoma bearing mice, the results showed that both radiolabeled aptamers specifically detected the hMMP-9. In addition, optical fluorescence imaging confirmed the binding to hMMP-9 by F3B-CY5. In order to improve tumor detection sensitivity, two types of modifications were investigated: developing of F3B multimeric structures and a bi-functional system. For both these approaches, we synthesized a dendrimer with a focal point, which could give access to a multi-modal imaging. This dendrimer has two or three spacers bearing an azide group used for coupling with aptamers by "click" chemistry. The dendrimer carrying at the focal point an amine function NH2 used for fixing biotin in order to determine the affinity Kd of this new probe by using SPR. A DOTA ligand will be fixed later in order to view this tracer in SPECT.