Department of Computer Science at UH

University of Houston

Department of Computer Science

In Partial Fulfillment of the Requirements for the Degree of
Doctor of Philosophy

Yen Hai Le

Will defend her dissertation

Shape priors for segmentation of mouse brain in gene expression images


The quantification and comparison of gene expression data across images plays a key role in understanding the functional network of various genes. To enable studying of relationships between a large number of images, automated methods that can segment gene expression images into distinct anatomical regions/sub-regions are needed. Automated segmentation of mouse brain gene expression images is a challenging problem mainly due to the complexity of gene expression appearance: (i) the lack of visible edge cues for the anatomical regions, (ii) the inhomogeneous intensity pattern inside each anatomical region, and (iii) the variation of intensity pattern of the same region across images. Therefore, the use of geometric priors and appearance cues can potentially help in accurate segmentation of gene expression images.

The goal of this thesis is to develop segmentation methods that incorporate shape priors and appearance cues and apply them to gene expression image data. The specific objectives are: (i) to incorporate statistical shape information to segment gene expression images; (ii) to learn salient model points that will be selected to provide appearance cues for segmentation methods to handle images with complex appearance (e.g., gene expression images); (iii) to improve the representation ability of statistical shape models to represent a larger range of shapes; and (iv) to evaluate the proposed methods on the segmentation of gene expression images.


Date: Thursday, April 10, 2014
Time: 2:00 - 5:00 PM
Place: HBS 350

Faculty, students, and the general public are invited.
Advisor: Prof. Ioannis A. Kakadiaris
Committee Members: Dr. James P. Carson (UT Austin), Dr. Zhigang Deng, Dr. Christoph Eick, Dr. Tao Ju (Washington University in St. Louis), Dr. Shishir Shah.