Thesis (M.S.)--Rochester Institute of Technology, 2009. / Typescript. Includes bibliographical references (p. 142-143).

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Whereas the Joint Typhoon Warning Center (JTWC) has ten track forecasts to 72 h, only four dynamical model forecasts are available at 96 h and 120 h. Forming a selective consensus (SCON) by proper removal of a likely erroneous track forecast is hypothesized to be more accurate than the non-selective consensus (NCON) of all four models. Conceptual models describing large track error mechanisms, which are related to known tropical cyclone motion processes being misrepresented in the dynamical fields, are applied to forecasts by the Navy Operational Global Atmospheric Prediction System (NOGAPS), U.S. Navy version of the Geophysical Fluid Dynamics Laboratory Model (GFDN), United Kingdom Meteorological Office (UKMO), and National Centers for Environmental Prediction (NCEP) Global Forecast System (GFS) during the 2005 western North Pacific typhoon season. A systematic error in the GFDN was identified in which the model built a false anticyclone downstream of the Tibetan Plateau, which explained over 50% of the large GFDN track errors. In the GFS model, 95% of the large errors occurred due to an incorrect depiction of the vertical structure of the tropical cyclone. The majority of NOGAPS and UKMO large errors were caused by an incorrect depiction of the midlatitude system evolutions. Characteristics of the erroneous forecast tracks and corresponding model fields are documented and illustrative case studies are presented. By applying rules of the Systematic Approach, the average SCON error was 222 n mi (382 n mi) less than NCON (JTWC) in 20% of all 120-h forecasts. / US Air Force (USAF) author.

With the wide-spread adoption of exogenous fluorescent indicators – and more recently genetically encoded fluorescent proteins – over the past two decades, there exists a diverse chemical toolkit with which to probe biological systems. Individual cell types and sub-cellular compartments can be targeted in an increasingly wide range of model organisms. However, imaging these samples is often an exercise in balancing the needs of any given experiment against the constraints of the chosen imaging technology. For example, a volume of brain tissue is host to neurons, glia, vascular compartments and red blood cells that all occupy discrete locations in 3D space, but must work together to support healthy organ function. Single-cell activity on the order of milliseconds can trigger downstream processes that unfold over the course of multiple seconds or even minutes. The development of a technique capable of providing depth-resolved, volumetric imaging with scalable spatiotemporal resolution is crucial to developing a proper understanding of such biological systems. Bottlenecks in the throughput of existing technologies stem from a combination of inefficient illumination and volume acquisition strategies, and insufficient sensor read-out speeds. Light sheet microscopy is a promising solution, but individual designs tend to be highly specialized to specific types of samples and do not easily adapt to a wide range of experimental settings. In this thesis, I detail my work in developing swept, confocally-aligned planar excitation (SCAPE) microscopy from a first-generation prototype into a versatile, easy-to-reproduce, easy-to-use system for high-speed, 3D imaging. The first chapter introduces the challenges of designing optical systems capable of high-speed, volumetric imaging. An introduction to design choices faced in the construction of fluorescence microscopes, and current approaches to 3D imaging are discussed. The second chapter describes the progression from the 1st to 2nd generation SCAPE system. Improvements made through ray-tracing models and an enhanced optomechanical design are described, and results from this system in a number of model organisms are presented. The third chapter presents results from a range of biological applications to which SCAPE microscopy has been applied. Work in imaging the zebrafish heart to demonstrate the system’s improved imaging speed, the C. elegans to show the system’s resolution, and finally a number of examples of large field-of-view and high-resolution structural imaging are all described. Finally, the fourth chapter concludes with an overview of the work that lies ahead to both further develop of SCAPE microscopy, as well as to bring the existing system’s strengths to bear in a wider range of environments.

Existing optic fibre-bundle based imaging probes have been successfully used to image biological signals from tissue in direct contact with the probe tip (Hirano et al. 1996). These fibre-bundle probe systems employed conventional fluorescence microscopy and thus lacked spatial filtering or a scanned light source, two features used by laser scanning confocal microscopes (LSCMs) to improve signal quality. Improving the methods of imaging tissue in its natural state, deep in-vivo and at cellular resolution is an ever-present goal in biological research. Within this study, a novel (580 μm diameter) optic fibre-bundle direct-contact imaging probe, employing a LSCM, was developed to allow for improved imaging of deep biological tissue in-vivo. The new LSCM/probe system possessed a spatial resolution of 10 μm, and a temporal resolution of 1 msec. The LSCM/probe system was compared to a previously used direct-contact probe system that employed a conventional fluorescence microscope. Quantitative and qualitative data indicated that the LSCM/probe system possessed superior image contrast and quality. Furthermore, the LSCM/probe system was approximately 16 times more effective at filtering unwanted contaminating light from regions below the imaging plane (z-axis). The unique LSCM/probe system was applied to an exploratory investigation of calcium activity of both glial and neuronal cells within the whisker portion of the rat primary somatosensory cortex in-vivo. Fluorescence signals of 106 cells were recorded from 12 female Sprague Dawley rats aged between 7-8 weeks. Fluo-3(AM) fluorophore based calcium fluctuations that coincided with 10 - 14 Hz sinusoidal stimulation of rat whiskers for 0.5-1 second were observed in 8.5% of cells (9 of 106). Both increases and decreases in calcium levels that coincided with whisker stimulation were observed. Of the 8.5 % of cells, 2.8% (3 cells) were categorized as glial and 5.7% (6 cells) as neuronal, based on temporal characteristics of the observed activity. The remaining cells (97 of 106) displayed sufficient calcium-based intensity but no fluctuations that coincided with an applied stimulus. This was partially attributed to electronic noise inherent in the prototype system obscuring potential very weak cell signals. The results indicate that the novel LSCM/probe system is an advancement over previously used systems that employed direct-contact imaging probes. The miniature nature of the probe allows for insertion into soft tissue, like a hypodermic needle, and provides access to a range of depths with minimal invasiveness. Furthermore, when combined with selected dyes, the system allows for imaging of numerous forms of activity at cellular resolution.

Thesis (Ph. D.)--West Virginia University, 2006. / Title from document title page. Document formatted into pages; contains xiii, 167 p. : ill. (some col.), map. Includes abstract. Includes bibliographical references (p. 91-94).

Thesis (Ph.D.)--University of Delaware, 2009. / Principal faculty advisor: Gonzalo Arce, Dept. of Electrical & Computer Engineering. Includes bibliographical references.

Thesis (M.S.)--University of Delaware, 2009. / Principal faculty advisor: Dennis W. Prather, Dept. of Electrical & Computer Engineering. Includes bibliographical references.