Novel microscale velocity and temperature measurement techniques were studied based on confocal laser scanning microscopy (CLSM) and optical serial sectioning microscopy (OSSM). Two microscopic measurement systems were developed, 1) a CLSM micro particle image velocimetry (PIV) system with a dual Nipkow disk confocal unit (CSU-10), a CW argon-ion laser and an upright microscope, and 2) an OSSM micro- particle tracking velocimetry (PTV) system with an epi-fluorescence microscope and a non-designed specimen to make a three-dimensional (3-D) diffraction particle image. The CLSM micro-PIV system shows a unique optical slicing capability allowing true depth-wise resolved vector field mapping. A comparative study is presented between the CLSM micro-PIV and a conventional epi-fluorescence micro-PIV. Both have been applied to the creeping Poiseuille flows in two different microtubes of 99-µm (Re = 0.00275) and 516-µm ID diameters (Re = 0.021). The CLSM micro-PIV consistently shows significantly improved particle image contrasts, the definition of "optical slicing" and measured flow vector fields more accurately agreeing with predictions based on the Poiseuille flow fields, compared to the conventional micro-PIV. The OSSM micro-PTV technique is applied for a 3-D vector field mapping in a microscopic flow and a Brownian motion tracking of nanoparticles. This technique modifies OSSM system for a micro-fluidic experiment, and the imaging system captures a diffracted particle image having numerous circular fringes instead of an in-focus particle image. The 3-D particle tracking is based on a correlation between the 3-D diffraction pattern of a particle and the defocus distance from a focal plane. A computational program is invented for the OSSM micro-PTV, and provides a 3-D velocity vector field with a spatial resolution of 5.16 µm. In addition, a concept of nonintrusive thermometry is presented based on the correlation of the Brownian motion of suspended nanoparticles with the surrounding fluid temperature. Detection of fully three-dimensional Brownian motion is possible by the use of the OSSM, and the measured value of mean square displacement (MSD) is compared fairly well with Einstein's predictions.

This research is primarily focused on the study of tumors in experimental animal models using functional imaging in the presence of various contrast agents. The study of malignant tumor angiogenesis, oxygen saturation, glucose and amino acid metabolisms will lead to better methods for cancer detection as well as diagnosing and managing cancer. Non invasive in vivo diagnostic imaging technique is an area of great clinical interest in present days. In this study, noninvasive in vivo photoacoustic tomography and conventional fluorescence imaging together with multiphoton microscopic tomography were implemented to study the malignant tumor morphology and physiology. Tumor structure and angiogenesis were successfully imaged by photoacoustic tomography and conventional fluorescence imaging. The important malignant tumor cellular parameters such as oxygen saturation and αvβ3 integrin concentration were measured in living small animals (rodents) using the novel photoacoustic tomography technique. By implementing multiphoton microscopy using Cy3.5 NHS ester contrast agent, tumor amino acid metabolism was successfully studied in cell culture. This method will at least give you a relative concentration map of amino acid in cells. Non invasive in vivo imaging can be achieved by modifying the current multiphoton imaging setup. A new method for studying amino acid and glucose metabolisms of tumor cells using multiphoton imaging was developed.

<p>This dissertation explores computational optical imaging methods to circumvent the physical limitations of classical sensing. An ideal imaging system would maximize resolution in time, spectral bandwidth, three-dimensional object space, and polarization. Practically, increasing any one parameter will correspondingly decrease the others.</p><p>Spectrometers strive to measure the power spectral density of the object scene. Traditional pushbroom spectral imagers acquire high resolution spectral and spatial resolution at the expense of acquisition time. Multiplexed spectral imagers acquire spectral and spatial information at each instant of time. Using a coded aperture and dispersive element, the coded aperture snapshot spectral imagers (CASSI) here described leverage correlations between voxels in the spatial-spectral data cube to compressively sample the power spectral density with minimal loss in spatial-spectral resolution while maintaining high temporal resolution.</p><p>Photography is limited by similar physical constraints. Low f/# systems are required for high spatial resolution to circumvent diffraction limits and allow for more photon transfer to the film plain, but require larger optical volumes and more optical elements. Wide field systems similarly suffer from increasing complexity and optical volume. Incorporating a multi-scale optical system, the f/#, resolving power, optical volume and wide field of view become much less coupled. This system uses a single objective lens that images onto a curved spherical focal plane which is relayed by small micro-optics to discrete focal planes. Using this design methodology allows for gigapixel designs at low f/# that are only a few pounds and smaller than a one-foot hemisphere.</p><p>Computational imaging systems add the necessary step of forward modeling and calibration. Since the mapping from object space to image space is no longer directly readable, post-processing is required to display the required data. The CASSI system uses an undersampled measurement matrix that requires inversion while the multi-scale camera requires image stitching and compositing methods for billions of pixels in the image. Calibration methods and a testbed are demonstrated that were developed specifically for these computational imaging systems.</p> / Dissertation

The development of a non-invasive method of visualizing gene expression in larger animals could revolutionize some aspects of gene research by opening up a wider variety of animal systems to explore; some of which may be better models of human systems. Presently, most gene expression studies employ Green Fluorescent Protein (GFP) transfected into the genome of the animal system. For larger animals, an x-ray equivalent of GFP would be desirable due to the high penetrating power of x-rays. A model gene modification system is to use the Sodium (Na) Iodide Symporter (NIS) which will cause the accumulation of iodine in cells which express the NIS. To non-invasively observe the dilute iodine accumulated by the cancer cells transfected with NIS in the head of small animals, such as a rat, two synchrotron-based imaging methods were studied: K-Edge Subtraction (KES) imaging and Fluorescence Subtraction Imaging (FSI).<p> KES needs wide monochromatic x-ray beams at two energies bracketing the K-edge of the contrast agent existing or injected in the tissues. The monochromatic beam in the synchrotron facility normally is prepared by a double crystal monochromator. The appearance of the azimuthal angle (tilt error) in the double crystal monochromator creates intensity variations across the imaging field. This misalignment was studied through another two synchrotron-based imaging methods, Diffraction Enhanced Imaging (DEI) and Multi-Image Radiography (MIR), which show this problem clearly in their processed images. The detailed analysis of the effect of the tilt error, how it affects the resulting images, and how to quantify such an error were presented in the thesis. A post processing method was implemented and the artifacts caused by the improper experimental settings were discussed.<p> With the wide monochromatic beam prepared by the double crystal monochromator, a sequence of KES experiments were done and the detection limit of KES was quantified at a projected amount of 17.5mM-cm iodine in a physical model of a rat head with a radiation dose of 2.65mGy. With the raster scan of the object relative to the monochromatic pencil beam, FSI was studied to obtain higher Signal to Noise Ratio (SNR) for local area and better detection limit compared to KES. The detection limit of FSI was measured as a projected amount of 2.5mM-cm iodine in the same physical rat head with a tolerable radiation dose of 24mGy. According to the comparison of these two imaging techniques with references to imaging time and area, radiation dose, spatial resolution, and SNR, it was concluded that these two imaging techniques can be used complementarily in imaging dilute contrast material. Due to the short imaging time and large imaging area, KES is used first to provide a global view of the object, locate the area of interest, do the preliminary diagnosis, and decide whether the further FSI is necessary. Due to its high SNR for the dilute sample, FSI can be used when the area of interest is known. The combination of these two imaging techniques will be very promising and powerful. To facilitate the comparison of KES and FSI, a quality factor was developed to evaluate the performance of the imaging system.<p> The measured detection limits in our experiments are far beyond the thyroidal iodine concentration of a rat (around 1mM). To further improve the performance of KES, a bent Laue crystal monochromator was designed to do the simultaneous iodine KES imaging which overcomes the artifacts in the iodine image caused by the temporal difference for a single set of images. The designed monochromator can provide two separated x-ray beams bracketing the K-edge of iodine at the same time with a very high spatial resolution which is only depends on the source size, a very high energy resolution which can almost compete with that of the double crystal monochromator, and an acceptable photon flux.

Multi-modality imaging is a possible solution for overcoming individual modality limitations. With the use of modality specific contrast agents, contrast-enhanced multi-modality imaging may provide a more comprehensive evaluation of tumour characteristics. This may be possible by combining ultrasound and magnetic resonance imaging, whose contrast agents behave differently within the microvasculature. A novel, microvascular, and leaky phantom is presented that permits ultrasound contrast agents to remain entirely within the mimicking vascular compartment while the magnetic resonance contrast agents may freely diffuse between the mimicking vasculature and tissue compartments. The results show that the phantom is a useful tool for investigating the combination of contrast-enhanced ultrasound and magnetic resonance imaging. This work motivates further combined contrast-enhanced imaging studies, with future work to incorporate additional modalities.

Multi-modality imaging is a possible solution for overcoming individual modality limitations. With the use of modality specific contrast agents, contrast-enhanced multi-modality imaging may provide a more comprehensive evaluation of tumour characteristics. This may be possible by combining ultrasound and magnetic resonance imaging, whose contrast agents behave differently within the microvasculature. A novel, microvascular, and leaky phantom is presented that permits ultrasound contrast agents to remain entirely within the mimicking vascular compartment while the magnetic resonance contrast agents may freely diffuse between the mimicking vasculature and tissue compartments. The results show that the phantom is a useful tool for investigating the combination of contrast-enhanced ultrasound and magnetic resonance imaging. This work motivates further combined contrast-enhanced imaging studies, with future work to incorporate additional modalities.

Objective: The purpose of the research presented in this thesis is to explore new biomedical applications of synchrotron imaging in the field of neurosurgery.<p> Methods: Four different studies were performed, all using advanced biomedical synchrotron imaging techniques. In the first two experiments, diffraction enhanced imaging (DEI) and analyzer based imaging (ABI) were utilized to study the anatomy of the rat spine and a novel rat model of spinal fusion. In a third experiment, K-edge digital subtraction angiography (KEDSA) was used to study the cerebral vasculature in a rabbit model. In a fourth experiment, rapid scanning X-ray fluorescence spectroscopy (RS-XRF) was used to study stem cell migration in a rat stroke model.<p> Results: DEI had superior visualization of ligamentous and boney anatomy in a rat model. Analyzer based imaging was able to visualize physiologic amounts of bone graft material and progressive incorporation into the spine. Intravenous KEDSA showed excellent visualization of the cerebral vasculature in a rabbit model. Finally, RS-XRF was used to track iron labeled stem cells implanted in a rat stroke model. The technique was able to visualize the iron that represented the stem cell migration. This was correlated with histology and magnetic resonance imaging information.<p> Conclusions: 1) Diffraction enhanced imaging has excellent contrast for the study of boney and ligamentous anatomy. 2) Analyzer based imaging is an excellent tool to study animal models of boney fusion. 3) Intravenous KEDSA is able to clearly visualize the arterial vasculature in a rabbit model. 4) RS-XRF can be used to study the migration patterns of implanted iron labeled stem cells.

A fourth gradient channel was implemented to provide slice dependent RF coil phase compensation for arrays in dual-sided or "sandwich" configurations. The use of highly parallel arrays for single echo acquisition magnetic resonance imaging allows both highly accelerated imaging and capture of dynamic and single shot events otherwise inaccessible to MRI. When using RF coils with dimensions on the order of the voxel size, the array coil element phase patterns adversely affect image acquisition, requiring correction. This has previously been accomplished using a pulse of the gradient coil, imparting a linear phase gradient across the sample opposite of that due to the RF coil elements. However, the phase gradient due to the coil elements reverses on opposite sides of the coils, preventing gradient-based phase compensation with sandwich arrays. To utilize such arrays, which extend the imaging field of view of this technique, a fourth gradient channel and coil were implemented to simultaneously provide phase compensation of opposite magnitude to the lower and upper regions of a sample, imparting opposite phase gradients to compensate for the opposite RF coil phase patterns of the arrays. The fourth gradient coil was designed using a target field approach and constructed using printed circuit boards. This coil was integrated with an RF excitation coil, dual-sided receive array, and sample loading platform to form a single imaging probe capable of both ultra-fast and high resolution magnetic resonance imaging. By employing the gradient coil, this probe was shown to simultaneously provide improved phase compensation throughout a sample, enabling simultaneous SEA imaging using arrays placed below and above a sample. The fourth gradient coil also improves the acquisition efficiency of highly accelerated imaging using both arrays for receive. The same imaging probe was shown to facilitate accelerated MR microscopy over the field of view of the entire array with no changes to the hardware configuration. The spatio-temporal imaging capabilities of this system were explored with magnetic resonance elastography.

Schizophrenia has long been considered a disorder of impaired brain connectivity, and such disconnectivity might be due to disruption of white matter tracts that connect brain regions. This thesis investigates the oligodendrocyte/myelin/white matter pathway in schizophrenia in vivo, and also considers aging effects, as similar substrates are affected during the healthy aging process. In study one, association of oligodendrocyte/myelin genes is examined with schizophrenia, and in study two association of a myelin gene is examined with basic MRI volumetric phenotypes. Then, in study three, diffusion tensor tractography, a technique that can visualize and measure white matter is applied, and is shown to be reliable in healthy controls and schizophrenia patients using a novel clustering segmentation method. In study four, this method is then used to examine interaction of schizophrenia and aging with respect to white matter, where fronto-temporal disconnectivity is demonstrated in younger chronic schizophrenia patients, but not in elderly community dwelling schizophrenia patients compared to age-matched controls. In study five, relationships among age, white matter tract integrity, and cognitive decline in healthy aging are demonstrated using diffusion tensor tractography and structural equation modeling. Genetics and neuroimaging are then combined using the intermediate phenotype approach in study six to demonstrate a key role for the BDNF gene across adult life in healthy aging. In these individuals, the BDNF val66met variant influenced neural structures and cognitive functions in a pathological aging risk pattern. Finally, in study seven, complex relationships are then demonstrated among oligodendrocyte gene variants, white matter tract integrity and cognitive performance in both healthy controls and schizophrenia patients. The combination of genetics and neuroimaging can parse out heterogeneity of disease phenotypes, and characterize the effects of gene variants on at-risk neural structures and cognitive functions in healthy and disease populations.

Schizophrenia has long been considered a disorder of impaired brain connectivity, and such disconnectivity might be due to disruption of white matter tracts that connect brain regions. This thesis investigates the oligodendrocyte/myelin/white matter pathway in schizophrenia in vivo, and also considers aging effects, as similar substrates are affected during the healthy aging process. In study one, association of oligodendrocyte/myelin genes is examined with schizophrenia, and in study two association of a myelin gene is examined with basic MRI volumetric phenotypes. Then, in study three, diffusion tensor tractography, a technique that can visualize and measure white matter is applied, and is shown to be reliable in healthy controls and schizophrenia patients using a novel clustering segmentation method. In study four, this method is then used to examine interaction of schizophrenia and aging with respect to white matter, where fronto-temporal disconnectivity is demonstrated in younger chronic schizophrenia patients, but not in elderly community dwelling schizophrenia patients compared to age-matched controls. In study five, relationships among age, white matter tract integrity, and cognitive decline in healthy aging are demonstrated using diffusion tensor tractography and structural equation modeling. Genetics and neuroimaging are then combined using the intermediate phenotype approach in study six to demonstrate a key role for the BDNF gene across adult life in healthy aging. In these individuals, the BDNF val66met variant influenced neural structures and cognitive functions in a pathological aging risk pattern. Finally, in study seven, complex relationships are then demonstrated among oligodendrocyte gene variants, white matter tract integrity and cognitive performance in both healthy controls and schizophrenia patients. The combination of genetics and neuroimaging can parse out heterogeneity of disease phenotypes, and characterize the effects of gene variants on at-risk neural structures and cognitive functions in healthy and disease populations.