University of Macau / Faculty of Health Sciences

Quantitative three dimensional maps of cellular structure, activity and function provide the key to answering many prevalent questions in modern biological research. Fluorescence microscopy has emerged as an indispensable tool in generating such maps, but common techniques are limited by fundamental physical constraints which render them incapable of simultaneously achieving high spatial and temporal resolution. This thesis will describe the development of novel microscopy techniques and complementary computational tools capable of addressing some of the aforementioned limitations of fluorescence microscopy and further outline their application in providing novel biological insights. The first section details the design of a light sheet microscope capable of high-throughput imaging of cleared, macroscopic samples with cellular resolution. In light sheet microscopy, the combination of spatially confined illumination with widefield detection enables multi-megapixel acquisition in a single camera exposure. The corresponding increase in acquisition speed enables systems level biological studies to be performed. The ability of this microscope to perform rapid, high-resolution imaging of intact samples is demonstrated by its application in a project which established a niche and hierarchy for stem cells in the adult nervous system. Light sheet microscopy achieves fast volumetric imaging rates, but the two dimensional nature of each measurement results in an inevitable lag between acquisition of the initial and final planes. The second section of this thesis describes the development and optimization of a light field microscope which captures volumetric information in a snapshot. Light field microscopy is a computational technique and images are reconstructed from raw data. Both the fidelity of computed volumes and the efficiency of the algorithms are strongly dependent on the quality of the rectification. A highly accurate, automated procedure is presented in this section. Light field reconstruction techniques are investigated and compared and the results are used to inform the re-design of the microscope. The new optical configuration is demonstrated to minimize the long-object problem. In the final section of the thesis, the spatial resolution limits of light field microscopy are explored using a combination of simulations and experiments. It is shown that light field microscopy is capable of localizing point sources over a large depth of field with high axial and lateral precision. Notably, this work paves the way towards frame rate limited super resolution localization microscopy with a depth of field larger than the thickness of a typical mammalian cell.

Thesis (Ph. D.)--University of Hong Kong, 2007. / Title proper from title frame. Also available in printed format.

Thesis (M.S.)--Rochester Institute of Technology, 2007. / Typescript. Includes bibliographical references (leaves 63-64).

Thesis (Ph. D.)--University of Texas at Austin, 2000. / Vita. Includes bibliographical references (leaves 165-173). Available also in a digital version from Dissertation Abstracts.

Thesis (M.S.)--University of Akron, Dept. of Biomedical Engineering, 2008. / "December, 2008." Title from electronic thesis title page (viewed 12/13/2009) Advisor, Dale H. Mugler; Co-Advisor, Anthony M. Passalaqua; Committee members, Daniel B. Sheffer; Department Chair, Daniel B. Sheffer; Dean of the College, George K. Haritos; Dean of the Graduate School, George R. Newkome. Includes bibliographical references.

Thesis (M.S. in Electrical Engineering)--Naval Postgraduate School, June 2003. / Thesis advisor(s): Phillip E. Pace, Don Brutzman. Includes bibliographical references (p. 129-130). Also available online.

published_or_final_version / Electrical and Electronic Engineering / Doctoral / Doctor of Philosophy

Autism is a life-long neurodevelopmental condition. Autistic individuals have difficulties in communicative and social ability, and repetitive and stereotypic behavior. It has proposed that these symptoms are caused by underconnectivity in the autistic brain. Functional imaging studies have reported functional underconnectivity in autism. In this thesis, the structural connectivity of the autistic brain was studied. White matter contains axon fibers, which connect different cortical and subcortical brain regions. To measure the structural connectivity, Diffusion tensor imaging (DTI) was applied. Since water diffusion in axons inside the white matter is directional, by measuring the magnitude and direction of water diffusion in white matter, the structural integrity of white matter fibers could be estimated. In this thesis, the background of autism as a genetic, neurological and behavioral condition is outlined. The methods needed to acquire and analyze DTI data are illustrated. A meta-analysis on abnormalities found in autistic brain using DTI was conducted and the most consistently reported regions with DTI differences in autism compared to typically developing controls are described. The results of the metaanalysis were localized to white matter tracts likely to be involved, and the possible associations between anatomy and autistic behavioral features are discussed. Finally, a DTI tractography study was conducted in a sample but clinically representative sample of patients with ASD and eighteen major white matter tracts were explored. Underconnectivity in several tracts was identified. It is hoped that the findings reported here will enhance our understanding of widespread underconnectivity in autism. / published_or_final_version / Psychiatry / Master / Master of Philosophy

Diagnostic imaging played a substantial role in the management and treatment of patients during the Severe Acute Respiratory Syndrome (SARS) outbreak when daily chest radiographs were performed as a measure of disease severity and respiratory status. This thesis was performed to address several issues relating to the radiological spectrum of SARS, its temporal pattern on chest radiograph and high resolution computed tomography (HRCT) during the course of disease, and relationships between severity of opacities quantified on chest radiographs and clinical parameters including treatment response. Radiological parameters that could discriminate SARS from non-SARS community-acquired pneumonia (CAP) were also studied. Unifocal unilateral ground glass opacities was the dominant radiographic abnormality at presentation that progressed rapidly to maximal disease within 9.35 ± 4.09 (median 9, range 3-21) days after onset of symptoms with bilateral consolidation in 62.5% of patients. Complete resolution and significant residual disease was noted in 50% and 20% of cases respectively at end of assessment period. There was a temporal pattern of lung abnormalities on HRCT with ground glass opacity and consolidation at presentation. Reticulation developed after the first week and was present in 50% of patients at ?four weeks. HRCT was useful in illustrating parenchymal abnormalities in patients with normal radiographs at presentation. Severity of lung abnormalities quantified on chest radiograph at different time points of disease correlated with clinical and laboratory parameters such as SaO2 and liver transaminases ALT and AST. Significant relationships were also found between radiographic parameters, and O2 supplementation and treatment response. There are discriminating differences in the radiographic pattern, rate of radiographic progression, and zone of involvement between SARS and non-SARS CAP. / published_or_final_version / Medicine / Master / Doctor of Medicine