Computer vision approximates human vision using computers. Two subsets are explored in this work: image segmentation and visual tracking. Segmentation involves partitioning an image into logical parts, and tracking analyzes objects as they change over time. The presented research explores a key hypothesis: localizing analysis of visual information can improve the accuracy of segmentation and tracking results. Accordingly, a new class of segmentation techniques based on localized analysis is developed and explored. Next, these techniques are applied to two challenging problems: neuron bundle segmentation in diffusion tensor imagery (DTI) and plaque detection in computed tomography angiography (CTA) imagery. Experiments demonstrate that local analysis is well suited for these medical imaging tasks. Finally, a visual tracking algorithm is shown that uses temporal localization to track objects that change drastically over time.

Photophysical characterization of several species of fluorescent silver nanoclusters, encapsulated in oligonucleotide scaffolds, was achieved at the bulk and single molecule level. These studies reveal the presence of a short-lived microsecond blinking component which leads to higher emission rates than exhibited by common organic dyes. This dark state was found to be photo-accessible with a very efficient depopulation transition leading to repopulation of the emissive state. Secondary excitation on resonance with this transition significantly shortens the residence time in the dark state giving rise to as much as 5-fold fluorescence enhancement. Manipulation of the secondary laser can be used to impose a regularly modulated waveform onto the fluorescent signal. Signal processing techniques can be employed to extract the modulated signal from large backgrounds, leading to drastically improved sensitivity. This new imaging concept can be extended, beyond Ag nanoclusters, to common organic fluorophores that demonstrate large dark state quantum yields. These fluorophores simultaneously illustrate the utility of this technique and help to define a general set of parameters for engineering ideal dyes for modulated signal extraction. Ideally suited for fluorescence enhancement, FRET pairs can be used to engineer a wide range of modulatable systems, based on detecting donor emission in the presence of a laser directly exciting the acceptor. The utility of Ag nanoclusters, organic dyes, and FRET systems for improved sensitivity are investigated in this work.

The objective of this research was to build a reprogrammable computational imager utilizing on-chip analog computations for the purpose of studying the capabilities of integrated sensing and processing. Unlike conventional imaging systems, which acquire image data and perform calculations on it, this system tightly integrates the computation and sensing into one process. This allows the exploration of intelligent and efficient sensory and processing. The IC architecture and circuit designs have focused on wide dynamic range signals. The fundamental computation performed is a separable two-dimensional transform. This allows various operations, including block transformations and separable convolutions. The operations are reprogramable and utilize analog memory and processing along with digital control. The random access to both the image plane and the computational operations allows for intraframe transform variations creating a hardware foundation for dynamic sampling and computation. One can also capture scenes with non-uniform resolution. Advantages, including utilization of feedback from processing to sensing and extensions of the technology including support for wavelets and larger transforms are also explored.

Fluorescence microscopy allows for spatial and temporal resolution of systems which are inherently fluorescent or which can be selectively labeled with fluorescent molecules. Temporal resolution is crucial for imaging real time processes in living samples. A common problem in fluorescence microscopy of biological samples is autofluorescence, fluorescence inherent to the system, which interferes with detection of fluorescence of interest by decreasing the signal to noise ratio. Two current methods for improved imaging against autofluorescence are two-photon excitation and total internal reflection microscopy. Two-photon excitation occurs when two longer wavelength photons are absorbed quasi-simultaneously by a single fluorophore. For this to take place there must be a photon density on the order of 1030 photons/(cm2)(s), which is achieved through use of a femtosecond pulsed laser and a high magnification microscope objective. Two-photon excitation then only occurs at the focal spot, significantly reducing the focal volume and therefore background autofluorescence. The second method, total internal reflection, is based on evanescent wave excitation, which decreases exponentially in intensity away from the imaging surface. This allows for excitation of a thin (~200 nm) slice of a sample. Since only a narrow region of interest is excited, an optical slice can be imaged, decreasing excitation of out-of-focus autofluorescence, and increasing the signal to noise ratio. By coupling total internal reflection with two-photon excitation, an entire cell can be imaged while still maintaining the use of lower energy photons to irradiate the sample and achieve two-photon excitation along the length traveled by the evanescent wave. This system allows for more sensitive detection of fluorescence of interest from biological systems as a result of a significant decrease in excitation volume and therefore a decrease in autofluorescence signal. In the two-photon total internal reflection microscopy setup detailed in this work, an excitation area of 20 μm by 30 μm is achieved, and used to image FITC-stained actin filaments in BS-C-1 cells

Computer vision encompasses a host of computational techniques to process visual information. Medical imagery is one particular area of application where data comes in various forms: X-rays, ultrasound probes, MRI volumes, EEG recordings, NMR spectroscopy, etc. This dissertation is concerned with techniques for accurate reconstruction of neural pathways from diffusion magnetic resonance imagery (dMRI). This dissertation describes a filtered approach to neural tractography. Existing methods independently estimate the diffusion model at each voxel so there is no running knowledge of confidence in the estimation process. We propose using tractography to drive estimation of the local diffusion model. Toward this end, we formulate fiber tracking as recursive estimation: at each step of tracing the fiber, the current estimate is guided by those previous. We argue that this approach is more accurate than conventional techniques. Experiments demonstrate that this filtered approach significantly improves the angular resolution at crossings and branchings. Further, we confirm its ability to trace through regions known to contain such crossing and branching while providing inherent path regularization. We also argue that this approach is flexible. Experiments demonstrate using various models in the estimation process, specifically combinations of Watson directional functions and rank-2 tensors. Further, this dissertation includes an extension of the technique to weighted mixtures using a constrained filter.

We have used ultrafast optics, primarily focused on the nonlinear processes of Polarization Gating and of Optical Parametric Amplification, one for measurement and the other for imaging purposes. For measurement, we have demonstrated a robust method of measurement to simultaneously measure both optical pulses used in a pump-probe type configuration. We refer to this method of pulse measurement as Double Blind Polarization Gating FROG. We have demonstrated this single-shot method for measuring two unknown pulses using one device. In addition to pulse measurement, we have demonstrated the processes of Optical Parametric Amplification (OPA) applicability to imaging of complex objects. We have done this where the Fourier transform plane is used during the interaction. We have amplified and wavelength converted a complex image. We observe a gain of ~100, and, although our images were averaged over many shots, we used a single-shot geometry, capable of true single-shot OPA imaging. To our knowledge, this is the first Fourier-plane OPA imaging of more than a single spatial-frequency component of an image. We observe more than 30 distinct spatial frequency components in both our amplified image and our wavelength shifted image. We have demonstrated all-optical spatial filtering for these complex images. We have demonstrated that direct Fourier filtering of spatial features is possible by using a shaped pump beam. We can isolate certain portions of the image simply by rotating the crystal.

A complete scientific understanding of human nature requires delineation of the neurobiological characteristics underlying the unique features of the human mind. This effort can be facilitated by comparing the human brain with the brains of other living primate species. Humans are more susceptible to neurodegenerative diseases than other primate species, including our closest living primate relatives, the chimpanzees. Comparing age-related changes in brain structure between humans and non-human primates could, therefore, potentially shed light on the neurological basis of this human vulnerability. Further, human brains are lateralized with specialized cognitive and behavioral functions. Comparing the magnitude of hemispheric asymmetries in brain structure between humans and non-human primates can probe insights into this human specific capability and learn more about human evolution. Diffusion weighted MRI protocols were developed for different species, taking into account their neuroanatomical differences. For Chimpanzees, a multi-shot DWI sequence was developed and compared with a single-shot DWI sequence to determine which provided a better quality diffusion data free of acquisition related artifacts. Different simulation techniques were used to evaluate the effect of segmentation-related motion artifact (ghosting) on the multi-shot DTI data. Although both protocols generated high-resolution diffusion MRI data with correctable susceptibility-induced distortions, the single-shot protocol enables the acquisition of the high-resolution diffusion MRI data freed of ghosting and with twice the signal-to-noise ratio (SNR), for the same scan duration. The acquired chimpanzee and macaque diffusion data were used to compare the magnitude of microstructural asymmetries and age-related decline of brain white matter with those in humans. Hemispheric asymmetry results show a pattern of strong leftward asymmetry in human DTI indices that differs markedly from the chimpanzee (multi-shot data) and the rhesus macaque patterns involving both rightward and leftward asymmetries. The magnitude of leftward asymmetry increased for chimpanzees scanned with single-shot DTI sequence. Region of interest analyses within the corpus callosum revealed a significant age-related increase in fractional anisotropy (FA) in the genu for chimpanzees (multi-shot data) and no significant change in any region for macaques. Additionally, voxel-wise analysis using Tract Based Spatial Statistics (TBSS) revealed widespread age-related FA increases for chimpanzees (multi-shot data) and weak age-related decreases in FA for macaques across most white matter tracts. Overall, results from these multi-shot data analyses suggest that rhesus monkeys show age-related decreases in white matter integrity that parallel changes found in humans, whereas chimpanzees show age-related increases in white matter integrity. On the contrary, the single-shot data results for chimpanzees revealed no significant relationship between age and the different DTI indices. These noteworthy species differences may help to explain the unique features of the human mind and why humans are more susceptible to neurodegenerative diseases. Furthermore, these studies demonstrate the need for complementary histological studies of white matter microstructure in humans, chimpanzees and macaques to clarify the cellular and molecular basis of these findings.

Thesis (Ph. D.)--University of Missouri-Columbia, 2003. / Typescript. Vita. Includes bibliographical references (leaves 103-108). Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 2003. / Typescript. Vita. Includes bibliographical references (leaves 103-108). Also available on the Internet.

Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2003. / Includes bibliographical references (leaves 66-69). Also available in electronic version. Access restricted to campus users.