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Volumn 161, Issue 3, 2008, Pages 287-297

JUST (Java User Segmentation Tool) for semi-automatic segmentation of tomographic maps

Author keywords

Electron tomography; Feature extraction; Image processing; Synapsis; Volume segmentation

Indexed keywords

ANIMAL CELL; ARTICLE; CELL ORGANELLE; COMPUTER INTERFACE; COMPUTER PROGRAM; IMAGE ANALYSIS; JAVA USER SEGMENTATION TOOL; NONHUMAN; ORGANELLE SIZE; PRIORITY JOURNAL; TOMOGRAPHY;

EID: 40649127714     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2007.06.011     Document Type: Article
Times cited : (22)

References (35)
  • 2
    • 40649085908 scopus 로고    scopus 로고
    • Amira-User's Guide and Reference Manual, 2001. Zuse Institute Berlin (ZIB) and Indeed-Visual Concepts GmbH, Berlin. .
    • Amira-User's Guide and Reference Manual, 2001. Zuse Institute Berlin (ZIB) and Indeed-Visual Concepts GmbH, Berlin. .
  • 3
    • 0344983351 scopus 로고    scopus 로고
    • Volumetric feature extraction and visualization of tomographic molecular imaging
    • Bajaj C., Yu Z., and Auer M. Volumetric feature extraction and visualization of tomographic molecular imaging. J. Struct. Biol. 144 (2003) 132-143
    • (2003) J. Struct. Biol. , vol.144 , pp. 132-143
    • Bajaj, C.1    Yu, Z.2    Auer, M.3
  • 4
    • 33750976344 scopus 로고    scopus 로고
    • Automated segmentation of molecular subunits in electron cryomicroscopy density maps
    • Baker M.L., Yu Z., Chiu W., and Bajaj C. Automated segmentation of molecular subunits in electron cryomicroscopy density maps. J. Struct. Biol. 156 (2006) 432-441
    • (2006) J. Struct. Biol. , vol.156 , pp. 432-441
    • Baker, M.L.1    Yu, Z.2    Chiu, W.3    Bajaj, C.4
  • 5
    • 26444473610 scopus 로고    scopus 로고
    • An energy-based three-dimensional segmentation approach for the quantitative interpretation of electron tomograms
    • Bartesaghi A., Sapiro G., and Subramaniam S. An energy-based three-dimensional segmentation approach for the quantitative interpretation of electron tomograms. IEEE Trans. Image Proc. 14 (2005) 1314-1323
    • (2005) IEEE Trans. Image Proc. , vol.14 , pp. 1314-1323
    • Bartesaghi, A.1    Sapiro, G.2    Subramaniam, S.3
  • 6
    • 14544297527 scopus 로고    scopus 로고
    • From proteomic inventory to architecture
    • Baumeister W. From proteomic inventory to architecture. FEBS Lett. 579 (2005) 933-937
    • (2005) FEBS Lett. , vol.579 , pp. 933-937
    • Baumeister, W.1
  • 8
    • 0014026167 scopus 로고
    • Cytochemistry of synapses: a selective staining method for electron microscopy
    • Bloom F.E., and Aghajanian G.K. Cytochemistry of synapses: a selective staining method for electron microscopy. Science 154 (1966) 1575-1577
    • (1966) Science , vol.154 , pp. 1575-1577
    • Bloom, F.E.1    Aghajanian, G.K.2
  • 9
    • 33947320938 scopus 로고    scopus 로고
    • Local refinement: An attempt to correct for shrinkage and distortion in electron tomography
    • Cantele F., Zampighi L., Radermacher M., Zampighi G., and Lanzavecchia S. Local refinement: An attempt to correct for shrinkage and distortion in electron tomography. J. Struct. Biol. 158 (2007) 59-70
    • (2007) J. Struct. Biol. , vol.158 , pp. 59-70
    • Cantele, F.1    Zampighi, L.2    Radermacher, M.3    Zampighi, G.4    Lanzavecchia, S.5
  • 10
    • 0035783287 scopus 로고    scopus 로고
    • Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion
    • Frangakis A.S., and Hegerl R. Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion. J. Struct. Biol. 135 (2001) 239-250
    • (2001) J. Struct. Biol. , vol.135 , pp. 239-250
    • Frangakis, A.S.1    Hegerl, R.2
  • 11
    • 0036417303 scopus 로고    scopus 로고
    • Segmentation of two- and three-dimensional data from electron microscopy using eigenvector analysis
    • Frangakis A.S., and Hegerl R. Segmentation of two- and three-dimensional data from electron microscopy using eigenvector analysis. J. Struct. Biol. 138 (2002) 105-113
    • (2002) J. Struct. Biol. , vol.138 , pp. 105-113
    • Frangakis, A.S.1    Hegerl, R.2
  • 13
  • 14
    • 0001209075 scopus 로고
    • The granule cells, mossy synapses and Purkinje spine synapses of the cerebellum: light and electron microscope observations
    • Gray E.G. The granule cells, mossy synapses and Purkinje spine synapses of the cerebellum: light and electron microscope observations. J. Anat. Lond. 97 (1963) 101-106
    • (1963) J. Anat. Lond. , vol.97 , pp. 101-106
    • Gray, E.G.1
  • 17
    • 0141865704 scopus 로고    scopus 로고
    • Untangling desmosomal knots with electron tomography
    • He W., Cowin P., and Stokes D.L. Untangling desmosomal knots with electron tomography. Science 302 (2003) 109-113
    • (2003) Science , vol.302 , pp. 109-113
    • He, W.1    Cowin, P.2    Stokes, D.L.3
  • 18
    • 0029879294 scopus 로고    scopus 로고
    • The EM program package: A platform for image processing in biological electron microscopy
    • Hegerl R. The EM program package: A platform for image processing in biological electron microscopy. J. Struct. Biol. 116 (1996) 30-34
    • (1996) J. Struct. Biol. , vol.116 , pp. 30-34
    • Hegerl, R.1
  • 19
    • 0035783171 scopus 로고    scopus 로고
    • Bsoft: Image and molecular processing in electron microscopy
    • Heymann J.B. Bsoft: Image and molecular processing in electron microscopy. J. Struct. Biol. 133 (2001) 156-169
    • (2001) J. Struct. Biol. , vol.133 , pp. 156-169
    • Heymann, J.B.1
  • 20
    • 33845336533 scopus 로고    scopus 로고
    • Bsoft: Image processing and molecular modeling for electron microscopy
    • Heymann J.B., and Belnap D.M. Bsoft: Image processing and molecular modeling for electron microscopy. J. Struct. Biol. 157 (2007) 3-18
    • (2007) J. Struct. Biol. , vol.157 , pp. 3-18
    • Heymann, J.B.1    Belnap, D.M.2
  • 21
    • 0024595352 scopus 로고
    • The cytoskeletal structure of the presynaptic terminal and molecular structure of synapsin 1
    • Hirokawa N., Sobue K., Kanda K., Harada A., and Yorifuji H. The cytoskeletal structure of the presynaptic terminal and molecular structure of synapsin 1. J. Cell. Biol. 108 (1989) 111-126
    • (1989) J. Cell. Biol. , vol.108 , pp. 111-126
    • Hirokawa, N.1    Sobue, K.2    Kanda, K.3    Harada, A.4    Yorifuji, H.5
  • 23
    • 0029879295 scopus 로고    scopus 로고
    • Computer visualization of three-dimensional image data using IMOD
    • Kremer J.R., Mastronarde D.N., and McIntosh J.R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116 (1996) 71-76
    • (1996) J. Struct. Biol. , vol.116 , pp. 71-76
    • Kremer, J.R.1    Mastronarde, D.N.2    McIntosh, J.R.3
  • 24
    • 11144223254 scopus 로고    scopus 로고
    • Conical tomography of freeze-fracture replicas: a method for the study of integral membrane proteins inserted in phospholipid bilayers
    • Lanzavecchia S., Cantele F., Bellon P.L., Zampighi L., Kreman M., Wright E.A., and Zampighi G.A. Conical tomography of freeze-fracture replicas: a method for the study of integral membrane proteins inserted in phospholipid bilayers. J. Struct. Biol. 149 (2005) 87-98
    • (2005) J. Struct. Biol. , vol.149 , pp. 87-98
    • Lanzavecchia, S.1    Cantele, F.2    Bellon, P.L.3    Zampighi, L.4    Kreman, M.5    Wright, E.A.6    Zampighi, G.A.7
  • 25
    • 14844330221 scopus 로고    scopus 로고
    • Structural studies by electron: from cells to molecules
    • Lučić V., Förster F., and Baumeister W. Structural studies by electron: from cells to molecules. Annu. Rev. Biochem. 74 (2005) 833-865
    • (2005) Annu. Rev. Biochem. , vol.74 , pp. 833-865
    • Lučić, V.1    Förster, F.2    Baumeister, W.3
  • 26
    • 1842681953 scopus 로고    scopus 로고
    • Direct continuities between cisternae at different levels of the Golgi complex in glucose-stimulated mouse islet beta cells
    • Marsh B.J., Volkmann N., McIntosh J.R., and Howell K.E. Direct continuities between cisternae at different levels of the Golgi complex in glucose-stimulated mouse islet beta cells. PNAS 101 (2004) 5565-5570
    • (2004) PNAS , vol.101 , pp. 5565-5570
    • Marsh, B.J.1    Volkmann, N.2    McIntosh, J.R.3    Howell, K.E.4
  • 27
    • 0035030787 scopus 로고    scopus 로고
    • The emergence of electron tomography as an important tool for investigating cellular ultrastructure
    • McEwen B.F., and Marko M. The emergence of electron tomography as an important tool for investigating cellular ultrastructure. J. Histochem. Cytochem. 49 (2001) 553-564
    • (2001) J. Histochem. Cytochem. , vol.49 , pp. 553-564
    • McEwen, B.F.1    Marko, M.2
  • 28
    • 27644477833 scopus 로고    scopus 로고
    • 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography
    • Nicastro D., McIntosh J.R., and Baumeister W. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography. Proc. Natl. Acad. Sci. USA 102 (2005) 15889-15894
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 15889-15894
    • Nicastro, D.1    McIntosh, J.R.2    Baumeister, W.3
  • 31
    • 4644328746 scopus 로고    scopus 로고
    • Methods for generating high-resolution structural models from electron microscope tomography data
    • Ress D.B., Harlow M.L., Marshall R.M., and McMahan U.L. Methods for generating high-resolution structural models from electron microscope tomography data. Structure 12 (2004) 1763-1774
    • (2004) Structure , vol.12 , pp. 1763-1774
    • Ress, D.B.1    Harlow, M.L.2    Marshall, R.M.3    McMahan, U.L.4
  • 32
    • 0026172104 scopus 로고
    • Watersheds in digital space: an efficient algorithm based on immersion simulations
    • Vincent L., and Soille P. Watersheds in digital space: an efficient algorithm based on immersion simulations. IEEE Trans. Pattern Anal. Mach. Intell. 13 (1991) 583-598
    • (1991) IEEE Trans. Pattern Anal. Mach. Intell. , vol.13 , pp. 583-598
    • Vincent, L.1    Soille, P.2
  • 33
    • 0036424944 scopus 로고    scopus 로고
    • A novel three-dimensional variant of the watershed transform for segmentation of electron density maps
    • Volkmann N. A novel three-dimensional variant of the watershed transform for segmentation of electron density maps. J. Struct. Biol. 138 (2002) 123-129
    • (2002) J. Struct. Biol. , vol.138 , pp. 123-129
    • Volkmann, N.1
  • 35
    • 33749525657 scopus 로고    scopus 로고
    • Conical tomography III: synaptic vesicles docked to the active zone are hemi-fused
    • Zampighi G., Zampighi L., Fain N., Lanzavecchia S., Simon S., and Wright E.M. Conical tomography III: synaptic vesicles docked to the active zone are hemi-fused. Biophys. J. 91 (2006) 2910-2918
    • (2006) Biophys. J. , vol.91 , pp. 2910-2918
    • Zampighi, G.1    Zampighi, L.2    Fain, N.3    Lanzavecchia, S.4    Simon, S.5    Wright, E.M.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.