Fluorescence in situ hybridization (FISH) is the most widely used molecular technique to visualize chromosomal abnormalities. Here, we describe a novel 3D modeling approach to allow precise shape estimation and localization of FISH signals in the nucleus of human embryonic stem cells (hES) undergoing progressive but defined aneuploidy. The hES cell line WA09 acquires an extra copy of chromosome 12 in culture with increasing passages. Both diploid and aneuploid nuclei were analyzed to quantitate the differences in the localization of centromeric FISH signals for chromosome 12 as it transitions from euploidy to aneuploidy. We employed superquadric modeling primitives coupled with principal component analysis to determine the 3D position of FISH signals within the nucleus. A novel aspect of our modeling approach is that it allows comparison of FISH signals across multiple cells by normalizing the position of the centromeric signals relative to a reference landmark in oriented nuclei. Using this model we present evidence of changes in the relative positioning of centromeres in trisomy-12 cells when compared to diploid cells from the same population. Our analysis also suggests a significant change in the spatial distribution of at least one of the FISH signals in the aneuploid chromosome complements implicating that an overall change in centromere position may occur in trisomy-12 due to the addition of an extra chromosome. These studies underscore the unique utility of our modeling algorithms in quantifying FISH signals in three dimensions.

In this study, we describe the utility of the zebrafish model of in-vivo blood vessel formation as a tool for chemical risk assessment. Time-lapse confocal imaging of embryonic vasculature in the zebrafish is used in conjunction with digital image analysis to monitor and quantify the effect of toxins on vascular development. Non-rigid registration is used to capture changes in vascular morphology over time. Vascular formation in healthy normal and arsenic treated embryos was evaluated for differences in vascular structure using the algorithms developed. Although, the temporal progression of vascular development was similar, significant differences were observed in vessel structure between the toxin treated and healthy fish. This study revealed, for the first time, that vital vascular structures in fish maybe affected by exposure to arsenic. This technique allowed visualization of vascular abnormalities in embryos showing no external signs of malformations.