Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images
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Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images Sabarish Babu,1 Pao-Chuan Liao,1 Min C. Shin,1 and Leonid V. Tsap2 1 Department
of Computer Science, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA 2 Systems Research Group, Electronics Engineering Department, University of California Lawrence Livermore National Laboratory, Livermore, CA 94551, USA Received 27 April 2005; Revised 12 October 2005; Accepted 21 December 2005 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. Copyright © 2006 Hindawi Publishing Corporation. All rights reserved.
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INTRODUCTION
1.1. Motivation Tracking and visualizing chromosomes gives biologists valuable information regarding their three-dimensional (3D) structure and behavior. Previously, segmentation of banded chromosomes frozen in metaphase of mitosis was important for classification especially in the karyotyping process. This process facilitates the classification and detection of chromosomal abnormalities such as Klinefelter’s, Down’s, and Turner’s syndrome. Chromosome analysis is important in such situations as prenatal amniocentesis examination, detection of malignant diseases, and monitoring environmental gene mutations. In this paper, we propose a new method for (1) an automatic recovery of chromosomes in a sequence of 2D fluorescence volume image slices, and (2) visualizing the resulting chromosomes in 3D. Such 3D visualization provides biologists with information that cannot be obtained by 2D images alone. Commonly used imaging systems rely on reconstruction of an image from its projections through the process of computed tomography (CT) which generates fluorescent optical sections also known as volume image slices.
In medical imaging, for example, X-ray plates, CT scans, magnetic resonance imaging (MRI), and various types of positron emission tomography (PET) all record 2D projections of 3D objects [1]. Hence, tracking the contour of an object
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