Semantic Context Forests for Learning-Based Knee Cartilage Segmentation in 3D MR Images

The automatic segmentation of human knee cartilage from 3D MR images is a useful yet challenging task due to the thin sheet structure of the cartilage with diffuse boundaries and inhomogeneous intensities. In this paper, we present an iterative multi-class learning method to segment the femoral, tibial and patellar cartilage simultaneously, which effectively exploits the spatial contextual constraints between bone and cartilage, and also between different cartilages. First, based on the fact that the cartilage grows in only certain area of the corresponding bone surface, we extract the distance features of not only to the surface of the bone, but more informatively, to the densely registered anatomical landmarks on the bone surface. Second, we introduce a set of iterative discriminative classifiers that at each iteration, probability comparison features are constructed from the class confidence maps derived by previously learned classifiers. These features automatically embed the semantic context information between different cartilages of interest. Validated on a total of 176 volumes from the Osteoarthritis Initiative (OAI) dataset, the proposed approach demonstrates high robustness and accuracy of segmentation in comparison with existing state-of-the-art MR cartilage segmentation methods.Comment: MICCAI 2013: Workshop on Medical Computer Visio

Long-Term Quantitative Microscopy: From Microbial Population Dynamics to Growth of Plant Roots

Quantitative optical measurements at the micron scale have been crucial to the study of multiple biological processes, including bacterial chemotaxis, eukaryotic gene expression and y development. Extending measurements to long time scales allows complete observation of processes that are otherwise studied piecemeal, such as development and evolution. This thesis describes the development of two types of microscope for making long term, quantitative measurements, and the tools for image analysis. The rst device is a digital holographic microscope for measuring microbial population dynamics. It allows three dimensional localization of hundreds of cells within a mm3 sized volume, at micron resolution and an acquisition period of minutes. The technique is simple and inexpensive, which enabled us to construct ten replicate devices for parallel measurements. Each device incorporates precise and programmable control of light and temperature for the microbial ecosystem. Experiments were performed with the green algae Chlamydomonas reinhardtii and the ciliate Tetrahymena reinhardtii, both together and in isolation, and continued for as long as 90 days. The population dynamics exhibited a striking degree of repeatability, despite the presence of added noise in the illumination, spatial gradients of cell density, convection currents and phenotypic changes of both species. The second device is a thin light sheet fluorescence microscope for tracking nuclei in growing roots of the flowering plant Arabidopsis thaliana. The device incorporates a chamber designed to maintain optical quality while providing conditions for root growth. Optical feedback to a translation stage is used to maintain the root tip in the fi eld of view as the root grows by centimeters over several days. Data from a three day experiment is presented to demonstrate the technique. Over 1,000 nuclei were tracked simultaneously, and hundreds of cell divisions were automatically identif ed. The device was also used to image the regeneration of a root tip after surgical excision. The data corroborate earlier investigations at a more detailed level than was previously possible

Doctor of Philosophy

dissertationGenotype Phenotype Association (GPA) is a means to identify candidate genes and genetic variants that may contribute to phenotypic variation. Technological advances in DNA sequencing continue to improve the efficiency and accuracy of GPA. Currently, High Throughput Sequencing (HTS) is the preferred method for GPA as it is fast and economical. HTS allows for population-level characterization of genetic variation, required for GPA studies. Despite the potential power of using HTS in GPA studies, there are technical hurdles that must be overcome. For instance, the excessive error rate in HTS data and the sheer size of population-level data can hinder GPA studies. To overcome these challenges, I have written two software programs for the purpose of HTS GPA. The first toolkit, GPAT++, is designed to detect GPA using small genetic variants. Unlike pervious software, GPAT++'s association test models the inherent errors in HTS, preventing many spurious GPA. The second toolkit, Whole Genome Alignment Metrics (WHAM), was designed for GPA using large genetic variants (structural variants). By integrating both structural variant identification and association testing, WHAM can identify shared structural variants associated with a phenotype. Both GPAT++ and WHAM have been successfully applied to real-world GPA studie

Program and Abstracts of the Annual Meeting of the Georgia Academy of Science, 2011

The annual meeting of the Georgia Academy of Science took place March 23–24, 2011, at Gainesville State College, Oakwood, Georgia. Presentations were provided by members of the Academy who represented the following sections: I. Biological Sciences, II. Chemistry, III. Earth & Atmospheric Sciences, IV. Physics, Mathematics, Computer Science, Engineering & Technology, V. Biomedical Sciences, VI. Philosophy & History of Science, VII. Science Education, and VIII. Anthropology

Proceedings of 2011 Kentucky Water Resources Annual Symposium

This conference was planned and conducted as part of the state water resources research annual program with the support and collaboration of the Department of the Interior, U.S. Geological Survey and the University of Kentucky Research Foundation, under Grant Agreement Number 06HQGR0087. The views and conclusions contained in this document and presented at the symposium are those of the abstract authors and presenters and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the U.S. Government or other symposium organizers and sponsors