Three-dimensional surface representation of DNA replication sites using finite-element-based deformable models

摘要

Abstract: Surface reconstruction and representation is an important aspect of Biomedical Image Analysis. With respect to the shape and organization of DNA within a cell nucleus, the development of improved technology for visualizing genome organization and function as it exists within a cell nucleus has led to increasing interest in understanding the genome and its expression in three dimensions. In this context, it is necessary to be able to visualize the cell nucleus within which the DNA replication occurs. Here we discuss the implementation of a 3D surface reconstruction system for shape analysis of nuclei in mammalian cells obtained through laser confocal microscopy. Finite elements based deformable models are used for the surface reconstruction. The deformable models developed are based on thin shell element formulation. An initial global shape is assigned, and deformation forces based on distance and elasticity constraints are used to fit the final shape. The deformations energy functionals are the spline deformation energy functionals. These models are applied to images of a mammalian cell nucleus to extract shape information. Based on the segmented shape, volume and surface area are computed for the nucleus. Relevance of this method in shape analysis of biomedical images is examined. The biological data for the experiments were obtained from Dr. Ronald Berezeney from the Biomedical Imaging Group.!10