title: A pipeline for neuron reconstruction based on spatial sliding volume filter seeding.
abstract: Neuron's shape and dendritic architecture are important for biosignal transduction in neuron networks. And the anatomy architecture reconstruction of neuron cell is one of the foremost challenges and important issues in neuroscience. Accurate reconstruction results can facilitate the subsequent neuron system simulation. With the development of confocal microscopy technology, researchers can scan neurons at submicron resolution for experiments. These make the reconstruction of complex dendritic trees become more feasible; however, it is still a tedious, time consuming, and labor intensity task. For decades, computer aided methods have been playing an important role in this task, but none of the prevalent algorithms can reconstruct full anatomy structure automatically. All of these make it essential for developing new method for reconstruction. This paper proposes a pipeline with a novel seeding method for reconstructing neuron structures from 3D microscopy images stacks. The pipeline is initialized with a set of seeds detected by sliding volume filter (SVF), and then the open curve snake is applied to the detected seeds for reconstructing the full structure of neuron cells. The experimental results demonstrate that the proposed pipeline exhibits excellent performance in terms of accuracy compared with traditional method, which is clearly a benefit for 3D neuron detection and reconstruction.
authors.affiliation: Biocomputing Research Center, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Dong
authors.identifier: 0000-0002-7887-2111
authors.initials: D
authors.lastname: Sui
authors.affiliation: Biocomputing Research Center, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Kuanquan
authors.identifier: 0000-0003-1347-3491
authors.initials: K
authors.lastname: Wang
authors.affiliation: Department of Computer Science and Engineering, Incheon National University, Incheon 402-751, Republic of Korea.
authors.forename: Jinseok
authors.initials: J
authors.lastname: Chae
authors.affiliation: Biocomputing Research Center, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China.
authors.forename: Yue
authors.identifier: 0000-0002-4515-8931
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Biocomputing Research Center, School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China ; School of Physics & Astronomy, University of Manchester, Manchester M13 9PL, UK.
authors.forename: Henggui
authors.initials: H
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D001369:Axons / Q000473:pathology; D003071:Cognition; D003198:Computer Simulation; D003712:Dendrites / Q000502:physiology; D006801:Humans; D021621:Imaging, Three-Dimensional; D018613:Microscopy, Confocal; D008959:Models, Neurological; D009474:Neurons / Q000378:metabolism / Q000502:physiology*; D009832:Olfactory Nerve / Q000473:pathology; D015203:Reproducibility of Results; D012984:Software
references.citation: Microsc Microanal. 2003 Aug;9(4):296-310
references.pmid: 12901764
references.citation: PLoS One. 2009 May 21;4(5):e5655
references.pmid: 19479070
references.citation: Cytometry A. 2010 Jul;77(7):693-704
references.pmid: 20583273
references.citation: Neuroinformatics. 2008 Spring;6(1):1-3
references.pmid: 18253866
references.citation: Neuroinformatics. 2009 Dec;7(4):213-32
references.pmid: 20012509
references.citation: Annu Int Conf IEEE Eng Med Biol Soc. 2012;2012:118-21
references.pmid: 23365846
references.citation: Bioinformatics. 2010 Jun 15;26(12):i38-46
references.pmid: 20529931
references.citation: J Neurosci Methods. 2009 Mar 30;178(1):197-204
references.pmid: 19059434
references.citation: Bioinformatics. 2010 Jun 15;26(12):i64-70
references.pmid: 20529938
references.citation: J Microsc. 1994 Feb;173(Pt 2):103-14
references.pmid: 8169949
references.citation: J Microsc. 2013 Apr;250(1):42-9
references.pmid: 23458490
references.citation: Neuroimage. 2004 Dec;23(4):1283-98
references.pmid: 15589093
references.citation: IEEE Trans Med Imaging. 2010 Aug;29(8):1463-73
references.pmid: 20525532
references.citation: Neuroimage. 2006 Oct 1;32(4):1608-20
references.pmid: 16861006
references.citation: IEEE Trans Med Imaging. 2002 Feb;21(2):61-75
references.pmid: 11929106
references.citation: Cytometry A. 2004 Apr;58(2):167-76
references.pmid: 15057970
references.citation: Med Image Anal. 1998 Jun;2(2):143-68
references.pmid: 10646760
references.citation: Neuroinformatics. 2007 Fall;5(3):189-203
references.pmid: 17917130
references.citation: IEEE Trans Inf Technol Biomed. 2002 Jun;6(2):171-87
references.pmid: 12075671
references.citation: Med Image Anal. 2008 Dec;12(6):666-75
references.pmid: 18440853
references.citation: Neuroinformatics. 2011 Sep;9(2-3):193-217
references.pmid: 21399937