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We present a framework for cell tracking in a highly cluttered environment in live cell imaging from mouse brain cortex. Our goal is to track cells over a long period of time for intracellular calciumion concentration in order to detect important cellular events such as neural activity and cell division. Since traditional object tracking approach such as segmentation followed by tracking is not applicable...
In this paper, we present a study on the relationships between Chronic Lymphocytic Leukemia (CLL) related clinical attributes using network visualization and analysis techniques. This work is the first step of our long-term project to identify novel biomarkers for CLL, working in coordination with the NCI-funded CLL Research Consortium (cll.ucsd.edu). By computing Spearman correlation coefficients...
We are developing a new framework for discovery of genes involved in the breast carcinogenesis process. Among families that have a predisposition to breast cancer, approximately 25% have inherited mutations in either breast cancer associated (ldquoBRCArdquo) genes BRCA1 or BRCA2, but the predisposing mutated genes in the majority of the families are unknown. BRCA1 and BRCA2 gene products both regulate...
In this paper we report an ongoing project for identifying human cytomegalovirus (HCMV) micro RNAs (miRNA) expressed in infected human cells using the new massive parallel sequencing technology with the Solexa Sequencer. We developed a data processing pipeline for analyzing such data including mapping segments to genomes, detecting highly expressed sequences and their loci, comparing sequences to...
Developments in optical microscopy imaging have generated large high-resolution data sets that have spurred medical researchers to conduct investigations into mechanisms of disease, including cancer at cellular and subcellular levels. The work reported here demonstrates that a suitable methodology can be conceived that isolates modality-dependent effects from the larger segmentation task and that...
We present an application problem of examining phenotype differences in wildtype and retinoblastoma (Rb) knockout specimens of mouse placenta. The lack of the Rb gene causes uncontrolled tissue growth which forces infiltrations into critical sections of mouse placenta that lead to fetal death. We briefly describe our method for volume visualization of mouse placenta tissue level intermixing at a microscopic...
In this paper, a framework of fast registration algorithm for large microscopy images is presented. The rationale behind this approach is that the rigid transform gives the global mapping between the two images while the nonrigid components further refines the local matching of the pixels by taking care of local nonrigid distortion and variation. Therefore, to estimate rigid transform, the global...
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