The most important aspects of nuclear medicine imaging systems such as Positron Emission Tomography (PET) or Single Photon Emission Computed Tomography (SPECT) are the spatial resolution and the sensitivity (detector efficiency in combination with the geometric efficiency). Considerable efforts have been spent during the last two decades in improving the resolution and the efficiency by developing new detectors. Our proposed improvement technique is focused on the readout and electronics. Instead of using traditional pulse height analysis techniques we propose using free running digital sampling by replacing the analog readout and acquisition electronics with fully digital programmable systems. This thesis describes a fully digital data acquisition system for KS/SU SPECT, new algorithms for high resolution timing for PET, and modular FPGA based decentralized data acquisition system with optimal timing and energy. The necessary signal processing algorithms for energy assessment and high resolution timing are developed and evaluated. The implementation of the algorithms in field programmable gate arrays (FPGAs) and digital signal processors (DSP) is also covered. Finally, modular decentralized digital data acquisition systems based on FPGAs and Ethernet are described.

With the vast array of genetically altered (knockout) mice becoming available there is a need for quantitative, repeatable, and efficient methodologies to characterize the phenotypic consequences of knocking out specific genes. Since knockout animals often have the ability to compensate for a single missing gene, it is important to examine the structural, material and morphological properties to obtain a thorough understanding of the changes occurring. For this project, femurs of knockout mice were first scanned using microcomputed tomography (micro-CT) to obtain high-resolution images of the trabecular bone in the distal femur, as well as cortical bone in the mid-diaphysis. After scanning, the femurs were tested to destruction in four-point bending at the mid-diaphysis about the medial lateral axis of the femur. These methodologies allowed quantification of (1) morphologic properties such as bone volume fraction, trabecular properties and 2nd moment of the area (2) structural properties such as stiffness, maximum load at failure, and post yield deformation and (3) material properties such as bone mineral density, elastic modulus and yield strength. As part of two independent studies, two different knockout mice, cyclooxygenase-2 (COX-2 -/-) and Apolipoprotein E (APOE -/-), were examined for structure-function relationships using these methodologies. COX-2 knockout mice were found to have decreased mineral content in their femurs, and increased post yield deformation. APOE knockout mice at 10 weeks of age had decreased bone mass and structural properties. However, by 40 weeks of age APOE deficient mice caught up to and exceeded the structural properties and bone mass of their wild type counterparts.

Bone is a composite material consisting of hydroxyapatite crystals deposited in an oriented manner on a collagen backbone. The arrangement of the mineral and organic phases provides bone tissue with the appropriate strength, stiffness, and fracture resistance properties required to protect vital internal organs and maintain the shape of the body. A remarkable feature of bone is the ability to alter its properties and geometry in response to changes in the mechanical environment. However, in cases of metabolic bone diseases or aging, bone can no longer successfully adapt to its environment, increasing its fragility. To elucidate the mechanisms of bone microdamage, this research project developed a specimen-specific approach that integrated 3D imaging, histological damage labeling, image registration, and image-based finite element analysis to correlate microdamage events with microstructural stresses and strains under compressive loading conditions. By applying this novel method to different ages of bovine and human bone, we have shown that the local mechanical environment at microdamage initiation is altered with age. We have also shown that formation of microdamage is time-dependent and may have implications in age-related microdamage progression with cyclic and/or sustained static loading. The work presented in this dissertation is significant because it improved our understanding of trabecular bone microdamage initiation and unlocked exciting future research directions that may contribute to the development of therapies for fragility diseases such as osteoporosis.

Photoacoustic tomography (PAT), as well as thermoacoustic tomography (TAT), utilize electromagnetic radiation in its visible, near infrared, microwave, and radiofrequency forms, respectively, to induce acoustic waves in biological tissues for imaging purposes. Combining the advantages of both the high image contrast that results from electromagnetic absorption and the high resolution of ultrasound imaging, these new imaging modalities could be the next successful imaging techniques in biomedical applications. Basic research on PAT and TAT, and the relevant physics, is presented in Chapter I. In Chapter II, we investigate the imaging mechanisms of TAT in terms of signal generation, propagation and detection. We present a theoretical analysis as well as simulations of such imaging characteristics as contrast and resolution, accompanied by experimental results from phantom and tissue samples. In Chapter III, we discuss the further application of TAT to the imaging of biological tissues. The microwave absorption difference in normal and cancerous breast tissues, as well as its influence on thermoacoustic wave generation and the resulting transducer response, is investigated over a wide range of electromagnetic frequencies and depths of tumor locations. In Chapter IV, we describe the mechanism of PAT and the algorithm used for image reconstruction. Because of the broad bandwidth of the laser-induced ultrasonic waves and the limited bandwidth of the single transducer, multiple ultrasonic transducers, each with a different central frequency, are employed for simultaneous detection. Chapter V further demonstrates PAT’s ability to image vascular structures in biological tissue based on blood’s strong light absorption capability. The photoacoustic images of rat brain tumors in this study clearly reveal the angiogenesis that is associated with tumors. In Chapter VI, we report on further developing PAT to image deeply embedded optical heterogeneity in biological tissues. The improved imaging ability is attributed to better penetration by NIR light, the use of the optical contrast agent ICG (indocyanine green) and a new detection scheme of a circular scanning configuration. Deep penetrating PAT, which is based on a tissue’s intrinsic contrast using laser light of 532 nm green light and 1.06 µm near infrared light, is also presented.

The osteocytes are the most abundant and longest living bone cells, embedded in the bone matrix. They are interconnected with each other through dendrites, located in slender canals called canaliculi. The osteocyte lacunae, cavities in which the cells are located, together with the canaliculi form a communication network throughout the bone matrix, permitting transport of nutrients, waste and signals. These cells were firstly considered passive, but lately it has become increasingly clear their role as mechanosensory cells and orchestrators of bone remodeling. Despite recent advances in imaging techniques, none of the available methods can provide an adequate 3D assessment of the lacuno-canalicular network (LCN). The aims of this thesis were to achieve 3D imaging of the LCN with synchrotron radiation X-ray computed tomography (SR-CT) and to develop tools for 3D detection and segmentation of this cell network, leading towards automatic quantification of this structure. We demonstrate the feasibility of parallel beam SR-CT to image in 3D the LCN (voxel~300 nm). This technique can provide data on both the morphology of the cell network and the composition of the bone matrix. Compared to the other 3D imaging methods, this enables imaging of tissue covering a number of cell lacunae three orders of magnitude greater, in a simpler and faster way. This makes possible the study of sets of specimens in order to reach biomedical conclusions. Furthermore, we propose the use of divergent holotomography, to image the ultrastructure of bone tissue (voxel~60 nm). The image reconstruction provides phase maps, obtained after the application of a suitable phase retrieval algorithm. This technique permits assessment of the cell network with higher accuracy and it enables the 3D organization of collagen fibres organization in the bone matrix, to be visualized for the first time. In order to obtain quantitative parameters on the geometry of the cell network, this has to be segmented. Due to the limitations in spatial resolution, canaliculi appear as 3D tube-like structures measuring only 1-3 voxels in diameter. This, combined with the noise, the low contrast and the large size of each image (8 GB), makes the segmentation a difficult task. We propose an image enhancement method, based on a 3D line filter combined with bilateral filtering. This enables improvement in canaliculi detection, reduction of the background noise and cell lacunae preservation. For the image segmentation we developed a method based on variational region growing. We propose two expressions for energy functionals to minimize in order to detect the desired structure, based on the 3D line filter map and the original image. Preliminary quantitative results on human femoral samples are obtained based on connected components analysis and a few observations related to the bone cell network and its relation with the bone matrix are presented.

This thesis is devoted to solving the inverse source problem arising in image reconstruction problems. In general, the solution is non-unique and the problem is severely ill-posed. Therefore, small perturbations, such as the noise in the data, and the modeling error in the forward problem, will cause huge errors in the computations. In practice, the most widely used method to tackle the problem is based on Tikhonov-type regularizations, which minimizes a cost function combining a regularization term and a data fitting term. However, because the two tasks, namely regularization and data fitting, are coupled together in Tikhonov regularization, they are difficult to solve. It happens even if each task can be efficiently solved when they are separate. We propose a method to overcome the major difficulties, namely the non-uniqueness of the solution and noisy data fitting, separately. First we find a particular solution called the orthogonal solution that satisfies the data fitting term. Then we add to it a correction function in the kernel space so that the final solution fulfills the regularization and other physical requirements. The key idea is that the correction function in the kernel has no impact to the data fitting, and the regularization is imposed in a smaller space. Moreover, there is no parameter needed to balance the data fitting and regularization terms. As a case study, we apply the proposed method to Fluorescence Tomography (FT), an emerging imaging technique well known for its ill-posedness and low image resolution in existing reconstruction techniques. We demonstrate by theory and examples that the proposed algorithm can drastically improve the computation speed and the image resolution over existing methods.

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.

Introduction: The role of positron emission tomography (PET) with 2-[18F]fluoro-2-deoxy-D-glucose ([18F]FDG) is currently under evaluation in urologic oncology. The aim of the present study was to investigate the use of [18F]FDG positron emission tomography ([18F]FDG-PET) in the detection and treatment control of malignant germ cell tumors compared to computed tomography (CT). Materials and Methods: Thirty-two PET studies and CT scans were carried out in 23 patients with histologically proven germ cell tumors (10 seminomas, 12 non-seminomatous germ cell tumors (NSGCT), 1 unclassified serologic recurrent disease) Lugano stage I–III. The scans were done either after initial diagnosis (n = 21) and/or within 3–45 days after chemotherapy was completed (n = 11). PET and CT were validated either by histology (n = 7) or clinical follow-up of 6–11 months after the last PET study has been performed (n = 16). Sensitivity, specificity, accuracy, positive and negative predictive values were determined for PET and CT. Differences between PET and CT for parameters of diagnostic value were evaluated by =χ2 test. Results: Although not statistically significant, the sensitivity, accuracy and negative predictive value were higher for PET than for CT with respect to the detection of metastatic infradiaphragmatic and supradiaphragmatic lesions after initial diagnosis. The specificity and positive predictive value of PET and CT were comparable. After chemotherapy, PET was found to be significantly superior in specificity and accuracy compared to CT with respect to infradiaphragmatic lesions (p < 0.05). False-positive PET findings in supradiaphragmatic lesions after chemotherapy occurred in the case of inflammatory processes and resulted in a loss of specificity and accuracy compared to CT (p < 0.05). Conclusions: These preliminary results demonstrate [18F]FDG-PET to be a useful diagnostic tool for the initial staging and treatment control in patients with germ cell tumors. Possible advantages compared to CT, however, are as yet not clearly defined. The possibility of false-positive PET findings due to reactive supradiaphragmatic inflammatory processes early after chemotherapy have to be considered. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

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 biological, technical and computational aspects of this project collectively focused on using electron tomography (ET) for the high-resolution (10-20 nm) 3D reconstruction of entire insulin-secreting beta cells within islets of Langerhans isolated from mouse pancreata. Islets were cultured overnight to represent either steady-state (non-stimulated) or elevated glucose (stimulated) conditions, prior to fast-freezing, freeze-substitution, plastic embedment and cutting into 250-400 nm thick sections for tomographic imaging using intermediate voltage electron microscopy (EM). 3D images (tomograms) of each section were used to evaluate the performance of the new technical and computational approaches developed, and make biological comparisons of intercellular structure-function. Analysis focused on key compartments/organelles of the insulin-secretory pathway - Golgi apparatus, mitochondria, insulin secretory granules and multi-granular bodies. To allow the application of ET to entire mammalian cells, several technical limitations were addressed. Since segmenting (delimiting compartments of interest) tomograms manually, represented the major ërate-limiting stepí of ET, an interactive approach for 3D segmentation using novel interpolation algorithms (crude smooth, pointwise smooth and spherical interpolation) to iteratively predict the shape of 3D surfaces between user-drawn contours was developed. The performance of these tools in segmenting a range of compartment types was examined, and found to significantly enhance the speed and accuracy of manual segmentation. To better compensate for the physical collapse of plastic sections in the EM, a novel method was developed for estimating section collapse by analyzing approximately spherical organelles. Using this method on mature insulin granules in high-resolution datasets, coupled with measurements from the whole cell reconstructions, section collapse was found to be substantially less (~25%) than the value (40%) previously used to re-scale 3D models. Other new approaches developed to further improve the accuracy and quality of tomograms, included interactive tools for fiducial tracking, and the use of larger gold particles, a ëreduced second axisí to account for the missing wedge problem, and deformation grids to account for anisotropic deformation. As well as affording more efficient and precise mapping of cell ultrastructure in 3D for subsequent quantitative analysis, these developments provided new insights for future automated (hybrid) segmentation pipelines and new computational approaches for improving quality and isotropic accuracy of volumetric image data. The Interpolator and DrawingTools for segmentation, AnalysisTools for estimating section collapse and BeadHelper for tracking fiducial particles, written as plug-ins for the IMOD software package distributed by the University of Colorado, are now being used by the wider ET community with significant positive feedback. Using the novel approaches developed, four insulin-secreting beta cells - two from the periphery of an islet frozen 1 hr after stimulation with 11 mM glucose, and two from the periphery of another islet under steady-state 5.6 mM glucose conditions - were reconstructed in their entirety in 3D. Quantitative data on the key compartments/organelles provided new information regarding global changes in cellular organization, and enabled robust comparisons of each pair of functionally equivalent cells at unprecedented spatial resolution. Relative differences in the number, dimensions, architecture and distribution of organelles per cubic micron of cellular volume (including mitochondrial branching) reflected differences in the cellsí individual capacity/readiness to respond to secretagogue stimulation. In the two stimulated cells this was reflected by inverse relationships between the number/size of mature granules versus immature granules, the number/size of mitochondria, and the volume of the trans-Golgi network relative to the entire Golgi ribbon. Complementary stereological analysis of whole islets indicated which cells were the most representative under stimulated versus non-stimulated conditions, and revealed a marked natural heterogeneity between cells both within and between individual islets. Overall, this project led to significant improvements in efficiency and accuracy for segmenting cellular compartments/organelles, and in image quality and accuracy for tomogram computation and reconstruction through use of the newly developed techniques. The improved 3D reconstruction and analysis of pancreatic beta cells in toto in native tissue provided a powerful approach for quantitatively mapping the organelles involved in insulin synthesis/secretion at unprecedented detail, and afforded a level of insight into the complex 3D organization of mammalian cells not previously achieved by any other analytical technique or imaging method.