title: A spherical harmonics intensity model for 3D segmentation and 3D shape analysis of heterochromatin foci.
abstract: The genome is partitioned into regions of euchromatin and heterochromatin. The organization of heterochromatin is important for the regulation of cellular processes such as chromosome segregation and gene silencing, and their misregulation is linked to cancer and other diseases. We present a model-based approach for automatic 3D segmentation and 3D shape analysis of heterochromatin foci from 3D confocal light microscopy images. Our approach employs a novel 3D intensity model based on spherical harmonics, which analytically describes the shape and intensities of the foci. The model parameters are determined by fitting the model to the image intensities using least-squares minimization. To characterize the 3D shape of the foci, we exploit the computed spherical harmonics coefficients and determine a shape descriptor. We applied our approach to 3D synthetic image data as well as real 3D static and real 3D time-lapse microscopy images, and compared the performance with that of previous approaches. It turned out that our approach yields accurate 3D segmentation results and performs better than previous approaches. We also show that our approach can be used for quantifying 3D shape differences of heterochromatin foci.
authors.affiliation: Biomedical Computer Vision Group, Department Bioinformatics and Functional Genomics, University of Heidelberg, IPMB, BioQuant, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. Electronic address: simon.eck@bioquant.uni-heidelberg.de.
authors.forename: Simon
authors.initials: S
authors.lastname: Eck
authors.affiliation: Biomedical Computer Vision Group, Department Bioinformatics and Functional Genomics, University of Heidelberg, IPMB, BioQuant, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. Electronic address: s.woerz@dkfz.de.
authors.forename: Stefan
authors.initials: S
authors.lastname: Wörz
authors.affiliation: Research Group Genome Organization and Function, BioQuant and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Müller-Ott
authors.affiliation: Ludwig Maximilians University and Munich Center for Integrated Protein Science (CiPSM), Biomedical Center, 82152 Planegg-Martinsried, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Hahn
authors.affiliation: Biomedical Computer Vision Group, Department Bioinformatics and Functional Genomics, University of Heidelberg, IPMB, BioQuant, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Biesdorf
authors.affiliation: Ludwig Maximilians University and Munich Center for Integrated Protein Science (CiPSM), Biomedical Center, 82152 Planegg-Martinsried, Germany.
authors.forename: Gunnar
authors.initials: G
authors.lastname: Schotta
authors.affiliation: Research Group Genome Organization and Function, BioQuant and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
authors.forename: Karsten
authors.initials: K
authors.lastname: Rippe
authors.affiliation: Biomedical Computer Vision Group, Department Bioinformatics and Functional Genomics, University of Heidelberg, IPMB, BioQuant, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. Electronic address: k.rohr@dkfz.de.
authors.forename: Karl
authors.initials: K
authors.lastname: Rohr
mesh_terms: D006570:Heterochromatin / Q000378:metabolism*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D016018:Least-Squares Analysis; D018613:Microscopy, Confocal / Q000379:methods*
chemical_list: D006570:Heterochromatin
keywords: 3D parametric intensity model; Confocal light microscopy; Pericentric heterochromatin; Spherical harmonics