Literature DB >> 18449328

Computing a family of skeletons of volumetric models for shape description.

Tao Ju1, Matthew L Baker, Wah Chiu.   

Abstract

Skeletons are important shape descriptors in object representation and recognition. Typically, skeletons of volumetric models are computed using iterative thinning. However, traditional thinning methods often generate skeletons with complex structures that are unsuitable for shape description, and appropriate pruning methods are lacking. In this paper, we present a new method for computing skeletons of volumetric models by alternating thinning and a novel skeleton pruning routine. Our method creates a family of skeletons parameterized by two user-specified numbers that determine respectively the size of curve and surface features on the skeleton. As demonstrated on both real-world models and protein images in bio-medical research, our method generates skeletons with simple and meaningful structures that are particularly suitable for describing cylindrical and plate-like shapes.

Year:  2007        PMID: 18449328      PMCID: PMC2084352          DOI: 10.1016/j.cad.2007.02.006

Source DB:  PubMed          Journal:  Comput Aided Des        ISSN: 0010-4485            Impact factor:   3.027


  3 in total

Review 1.  Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approaches.

Authors:  Wah Chiu; Matthew L Baker; Wen Jiang; Z Hong Zhou
Journal:  Curr Opin Struct Biol       Date:  2002-04       Impact factor: 6.809

2.  Identification of secondary structure elements in intermediate-resolution density maps.

Authors:  Matthew L Baker; Tao Ju; Wah Chiu
Journal:  Structure       Date:  2007-01       Impact factor: 5.006

3.  A new method for analyzing local shape in three-dimensional images based on medial axis transformation.

Authors:  A Bonnassie; F Peyrin; D Attali
Journal:  IEEE Trans Syst Man Cybern B Cybern       Date:  2003
  3 in total
  18 in total

1.  Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking.

Authors:  Mariah R Baker; Ian Rees; Steven J Ludtke; Wah Chiu; Matthew L Baker
Journal:  Structure       Date:  2012-03-07       Impact factor: 5.006

2.  Identification of secondary structure elements in intermediate-resolution density maps.

Authors:  Matthew L Baker; Tao Ju; Wah Chiu
Journal:  Structure       Date:  2007-01       Impact factor: 5.006

3.  Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling.

Authors:  Matthew L Baker; Corey F Hryc; Qinfen Zhang; Weimin Wu; Joanita Jakana; Cameron Haase-Pettingell; Pavel V Afonine; Paul D Adams; Jonathan A King; Wen Jiang; Wah Chiu
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-09       Impact factor: 11.205

4.  Structure of Trypanosoma brucei flagellum accounts for its bihelical motion.

Authors:  Alexey Y Koyfman; Michael F Schmid; Ladan Gheiratmand; Caroline J Fu; Htet A Khant; Dandan Huang; Cynthia Y He; Wah Chiu
Journal:  Proc Natl Acad Sci U S A       Date:  2011-06-20       Impact factor: 11.205

5.  An Iterative Bézier Method for Fitting Beta-sheet Component of a Cryo-EM Density Map.

Authors:  Michael Poteat; Jing He
Journal:  Mol Based Math Biol       Date:  2017-04-27

6.  Intensity-based skeletonization of CryoEM gray-scale images using a true segmentation-free algorithm.

Authors:  Kamal Al Nasr; Chunmei Liu; Mugizi Rwebangira; Legand Burge; Jing He
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2013 Sep-Oct       Impact factor: 3.710

Review 7.  Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography.

Authors:  Juan Chang; Xiangan Liu; Ryan H Rochat; Matthew L Baker; Wah Chiu
Journal:  Adv Exp Med Biol       Date:  2012       Impact factor: 2.622

8.  EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps.

Authors:  Steffen Lindert; René Staritzbichler; Nils Wötzel; Mert Karakaş; Phoebe L Stewart; Jens Meiler
Journal:  Structure       Date:  2009-07-15       Impact factor: 5.006

9.  IDSS: deformation invariant signatures for molecular shape comparison.

Authors:  Yu-Shen Liu; Yi Fang; Karthik Ramani
Journal:  BMC Bioinformatics       Date:  2009-05-22       Impact factor: 3.169

10.  Digital Topology on Adaptive Octree Grids.

Authors:  Ying Bai; Xiao Han; Jerry L Prince
Journal:  J Math Imaging Vis       Date:  2009-06-01       Impact factor: 1.627

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