Browsing by Subject "Principal Components Analysis"
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Item Exploration, Registration, and Analysis of High-Throughput 3D Microscopy Data from the Knife-Edge Scanning Microscope(2014-04-25) Sung, ChulAdvances in high-throughput, high-volume microscopy techniques have enabled the acquisition of extremely detailed anatomical structures on human or animal organs. The Knife-Edge Scanning Microscope (KESM) is one of the first instruments to produce sub-micrometer resolution ( ~1 ?m^(3)) data from whole small animal brains. We successfully imaged, using the KESM, entire mouse brains stained with Golgi (neuronal morphology), India ink (vascular network), and Nissl (soma distribution). Our data sets fill the gap of most existing data sets which have only partial organ coverage or have orders of magnitude lower resolution. However, even though we have such unprecedented data sets, we still do not have a suitable informatics platform to visualize and quantitatively analyze the data sets. This dissertation is designed to address three key gaps: (1) due to the large volume (several tera voxels) and the multiscale nature, visualization alone is a huge challenge, let alone quantitative connectivity analysis; (2) the size of the uncompressed KESM data exceeds a few terabytes and to compare and combine with other data sets from different imaging modalities, the KESM data must be registered to a standard coordinate space; and (3) quantitative analysis that seeks to count every neuron in our massive, growing, and sparsely labeled data is a serious challenge. The goals of my dissertation are as follows: (1) develop an online neuro-informatics framework for efficient visualization and analysis of the multiscale KESM data sets, (2) develop a robust landmark-based 3D registration method for mapping the KESM Nissl-stained entire mouse data into the Waxholm Space (a canonical coordinate system for the mouse brain), and (3) develop a scalable, incremental learning algorithm for cell detection in high-resolution KESM Nissl data. For the web-based neuroinformatics framework, I prepared multi-scale data sets at different zoom levels from the original data sets. And then I extended Google Maps API to develop atlas features such as scale bars, panel browsing, and transparent overlay for 3D rendering. Next, I adapted the OpenLayers API, which is a free mapping and layering API supporting similar functionality as the Google Maps API. Furthermore, I prepared multi-scale data sets in vector-graphics to improve page loading time by reducing the file size. To better appreciate the full 3D morphology of the objects embedded in the data volumes, I developed a WebGL-based approach that complements the web-based framework for interactive viewing. For the registration work, I adapted and customized a stable 2D rigid deformation method to map our data sets to the Waxholm Space. For the analysis of neuronal distribution, I designed and implemented a scalable, effective quantitative analysis method using supervised learning. I utilized Principal Components Analysis (PCA) in a supervised manner and implemented the algorithm using MapReduce parallelization. I expect my frameworks to enable effective exploration and analysis of our KESM data sets. In addition, I expect my approaches to be broadly applicable to the analysis of other high-throughput medical imaging data.Item The Religiosity of Vietnamese Americans(2012-07-16) Le, Jennifer LinhReligion is a deeply important tradition in many people's lives, especially for those forced to leave abruptly their homes and loved ones and resettle in a foreign land. Religion not only provides spiritual guidance but also social networks, comfort, and moral standards, among many others things. I chose to study the beliefs and practices of Vietnamese American Buddhists and Catholics as well as the relationship between those two groups in the U.S. The Vietnamese present an interesting case because of their collective status as a well-publicized immigrant, formerly refugee, population that is now well-established in this country. With my research, I was able to test five hypotheses. I wanted to determine the degree of transnationality, tension between the religious groups, conversion, and ancestor worship. Secondarily, I assessed any differences regionally. In order to test my hypotheses, I conducted 60 quantitative surveys. I sampled from the Houston and Minneapolis-St. Paul Vietnamese communities. Transnationality, or ties to the homeland, was more prevalent for Buddhists than Catholics as I had hypothesized. There was a minute degree of tension present, however, generally with older members of the first generation cohort. Traditional Vietnamese ancestor worship was not more prevalent with Buddhists than with Catholics. I was unable to sample enough religious converts in order to test my conversion hypothesis. In terms of differences across regions, all variables other than national identity as well as an indicator of transnationality were statistically insignificant. This data helps fill a nearly 30-year gap in the research in this area and focuses specifically on the Vietnamese population which many studies have been unable to do. In addition to my quantitative study, I also conducted qualitative fieldwork at four primary research and three secondary research sites in the Minneapolis-St. Paul and Houston metropolitan areas. Twenty-five to thirty hours were spent at each primary location observing the members, volunteers, dress, interactions, normative and deviant behaviors during services, socialization, languages spoken, attentiveness, racial diversity, and additional activities provided by the religious organization to the membership. This fieldwork gave me a better understanding of this community in a religious context.