Recovery and visualization of 3D structure of chromosomes from tomographic reconstruction images

Authors:
Sabarish Babu;Pao-Chuan Liao;Min C. Shin;Leonid V. Tsap
Affiliations:
Department of Computer Science, University of North Carolina at Charlotte, University City Boulevard, Charlotte, NC;Department of Computer Science, University of North Carolina at Charlotte, University City Boulevard, Charlotte, NC;Department of Computer Science, University of North Carolina at Charlotte, University City Boulevard, Charlotte, NC;Systems Research Group, Electronics Engineering Department, University of California Lawrence Livermore National Laboratory, Livermore, CA
Venue:
EURASIP Journal on Applied Signal Processing
Year:
2006

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Abstract

The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell. Structure is very important for biologists as it affects chromosome functions, behavior of the cell, and its state. Analysis of chromosome structure is significant in the detection of diseases, identification of chromosomal abnormalities, study of DNA structural conformation, in-depth study of chromosomal surface morphology, observation of in vivo behavior of the chromosomes over time, and in monitoring environmental gene mutations. The methodology incorporates thresholding based on a histogram analysis with a polyline splitting algorithm, contour extraction via active contours, and detection of the 3D chromosome structure by establishing corresponding regions throughout the slices. Visualization using point cloud meshing generates a 3D surface. The 3D triangular mesh of the chromosomes provides surface detail and allows a user to interactively analyze chromosomes using visualization software.