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Volumn 12, Issue 2, 2014, Pages 277-289

VolRoverN: Enhancing surface and volumetric reconstruction for realistic dynamical simulation of cellular and subcellular function

Author keywords

3 D reconstruction; Electron microscopy; Electrophysiology; Neuropil; Reduced model; Serial sections; Skeletonization

Indexed keywords

ANATOMY AND HISTOLOGY; ANIMAL; COMPUTER PROGRAM; COMPUTER SIMULATION; HIPPOCAMPUS; IMAGE PROCESSING; MALE; NERVE CELL; RAT; ULTRASTRUCTURE;

EID: 84899806113     PISSN: 15392791     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12021-013-9205-2     Document Type: Article
Times cited : (18)

References (58)
  • 4
    • 0030283854 scopus 로고    scopus 로고
    • Arbitrary topology shape reconstruction from planar cross sections
    • 10.1006/gmip.1996.0044
    • Bajaj, C.; Coyle, E.; Lin, K. (1996). Arbitrary topology shape reconstruction from planar cross sections. Graphical Models and Image Processing, 58, 524-543.
    • (1996) Graphical Models and Image Processing , vol.58 , pp. 524-543
    • Bajaj, C.1    Coyle, E.2    Lin, K.3
  • 8
    • 79952376773 scopus 로고    scopus 로고
    • Network anatomy and in vivo physiology of visual cortical neurons
    • 1:CAS:528:DC%2BC3MXivFyru7Y%3D 3095821 21390124 10.1038/nature09802
    • Bock, D.D.; Lee, W. CA.; Kerlin, A. M.; Andermann, M.L.; Hood, G.; et al. (2011). Network anatomy and in vivo physiology of visual cortical neurons. Nature, 471, 177-182.
    • (2011) Nature , vol.471 , pp. 177-182
    • Bock, D.D.1    Lee, W.C.A.2    Kerlin, A.M.3    Andermann, M.L.4    Hood, G.5
  • 9
    • 77952540583 scopus 로고
    • Three-dimensional reconstruction of complex shapes based on the Delaunay triangulation
    • Boissonnat, J.; & Geiger, B. (1992). Three-dimensional reconstruction of complex shapes based on the Delaunay triangulation. In Proceedings of SPIE (Vol. 964, pp. 964-975).
    • (1992) Proceedings of SPIE , vol.964 , pp. 964-975
    • Boissonnat, J.1    Geiger, B.2
  • 10
    • 84857691469 scopus 로고    scopus 로고
    • Volume electron microscopy for neuronal circuit reconstruction
    • 1:CAS:528:DC%2BC38Xjt1Grur8%3D 22119321 10.1016/j.conb.2011.10.022
    • Briggman, K.L.; & Bock, D. D. (2012). Volume electron microscopy for neuronal circuit reconstruction. Current Opinion in Neurobiology, 22, 154-161.
    • (2012) Current Opinion in Neurobiology , vol.22 , pp. 154-161
    • Briggman, K.L.1    Bock, D.D.2
  • 11
    • 79952380642 scopus 로고    scopus 로고
    • Wiring specificity in the direction-selectivity circuit of the retina
    • 1:CAS:528:DC%2BC3MXivF2js7c%3D 21390125 10.1038/nature09818
    • Briggman, K.L.; Helmstaedter, M.; Denk, W. (2011). Wiring specificity in the direction-selectivity circuit of the retina. Nature, 471, 183-188.
    • (2011) Nature , vol.471 , pp. 183-188
    • Briggman, K.L.1    Helmstaedter, M.2    Denk, W.3
  • 12
    • 84862556352 scopus 로고    scopus 로고
    • TrakEM2 software for neural circuit reconstruction
    • 1:CAS:528:DC%2BC38XptlSntL0%3D 3378562 22723842 10.1371/journal.pone. 0038011
    • Cardona, A.; Saalfeld, S.; Schindelin, J.; Arganda-Carreras, I.; Preibisch, S.; et al. (2012). TrakEM2 software for neural circuit reconstruction. PLoS One, 7, e38011.
    • (2012) PLoS One , vol.7 , pp. 38011
    • Cardona, A.1    Saalfeld, S.2    Schindelin, J.3    Arganda-Carreras, I.4    Preibisch, S.5
  • 13
    • 84924618721 scopus 로고    scopus 로고
    • Cambridge University Cambridge 10.1017/CBO9780511541612
    • Carnevale, N.; & Hines, M. (2006). The NEURON book. Cambridge: Cambridge University.
    • (2006) The NEURON Book
    • Carnevale, N.1    Hines, M.2
  • 16
    • 77957017889 scopus 로고    scopus 로고
    • Semi-automated reconstruction of neural circuits using electron microscopy
    • 1:CAS:528:DC%2BC3cXht1WlsL%2FJ 20833533 10.1016/j.conb.2010.08.002
    • Chklovskii, D.B.; Vitaladevuni, S.; Scheffer, L. K. (2010). Semi-automated reconstruction of neural circuits using electron microscopy. Current Opinion in Neurobiology, 20, 667-675.
    • (2010) Current Opinion in Neurobiology , vol.20 , pp. 667-675
    • Chklovskii, D.B.1    Vitaladevuni, S.2    Scheffer, L.K.3
  • 18
    • 84858111150 scopus 로고    scopus 로고
    • Molecular and cellular aspects of mental retardation in the fragile x syndrome: From gene mutation/s to spine dysmorphogenesis
    • De Rubeis, S.; Fernández, E.; Buzzi, A.; Di Marino, D.; Bagni, C. (2012). Molecular and cellular aspects of mental retardation in the fragile x syndrome: from gene mutation/s to spine dysmorphogenesis. In Synaptic plasticity (pp. 517-551).
    • Synaptic Plasticity , pp. 517-551
    • De Rubeis, S.1    Fernández, E.2    Buzzi, A.3    Di Marino, D.4    Bagni, C.5
  • 19
    • 14044262855 scopus 로고    scopus 로고
    • Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure
    • 524270 15514700 10.1371/journal.pbio.0020329
    • Denk, W.; & Horstmann, H. (2004). Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biology, 2, e329.
    • (2004) PLoS Biology , vol.2 , pp. 329
    • Denk, W.1    Horstmann, H.2
  • 20
    • 80052928575 scopus 로고    scopus 로고
    • Topologically correct reconstruction of tortuous contour forests
    • 3190576 22003256 10.1016/j.cad.2011.06.019
    • Edwards, J.; & Bajaj, C. (2011). Topologically correct reconstruction of tortuous contour forests. Computer-Aided Design, 43, 1296-1306.
    • (2011) Computer-Aided Design , vol.43 , pp. 1296-1306
    • Edwards, J.1    Bajaj, C.2
  • 21
    • 17144363197 scopus 로고    scopus 로고
    • Reconstruct: A free editor for serial section microscopy
    • 1:STN:280:DC%2BD2M7osV2msQ%3D%3D 15817063 10.1111/j.1365-2818.2005.01466. x
    • Fiala, J. (2005). Reconstruct: a free editor for serial section microscopy. Journal of Microscopy, 218, 52-61.
    • (2005) Journal of Microscopy , vol.218 , pp. 52-61
    • Fiala, J.1
  • 22
    • 0036082812 scopus 로고    scopus 로고
    • Dendritic spine pathology: Cause or consequence of neurological disorders?
    • 12086707 10.1016/S0165-0173(02)00158-3
    • Fiala, J.; Spacek, J.; Harris, K. (2002). Dendritic spine pathology: cause or consequence of neurological disorders?Brain Research Reviews, 39, 29-54.
    • (2002) Brain Research Reviews , vol.39 , pp. 29-54
    • Fiala, J.1    Spacek, J.2    Harris, K.3
  • 23
    • 84899875539 scopus 로고    scopus 로고
    • Qslim
    • Garland, M. (2004). Qslim. http://mgarland.org/software/qslim.html.
    • (2004)
    • Garland, M.1
  • 24
    • 0024473444 scopus 로고
    • Dendritic spines of CA 1 pyramidal cells in the rat hippocampus: Serial electron microscopy with reference to their biophysical characteristics
    • 1:STN:280:DyaL1MzmtFKltg%3D%3D 2769375
    • Harris, K.; & Stevens, J. (1989). Dendritic spines of CA 1 pyramidal cells in the rat hippocampus: serial electron microscopy with reference to their biophysical characteristics. The Journal of Neuroscience, 9, 2982.
    • (1989) The Journal of Neuroscience , vol.9 , pp. 2982
    • Harris, K.1    Stevens, J.2
  • 25
    • 33751347587 scopus 로고    scopus 로고
    • Uniform serial sectioning for transmission electron microscopy
    • 1:CAS:528:DC%2BD28Xht12htLzM 17122034 10.1523/JNEUROSCI.3994-06.2006
    • Harris, K.M.; Perry, E.; Bourne, J.; Feinberg, M.; Ostroff, L.; et al. (2006). Uniform serial sectioning for transmission electron microscopy. The Journal of Neuroscience, 26, 12101-12103.
    • (2006) The Journal of Neuroscience , vol.26 , pp. 12101-12103
    • Harris, K.M.1    Perry, E.2    Bourne, J.3    Feinberg, M.4    Ostroff, L.5
  • 26
    • 33750863459 scopus 로고    scopus 로고
    • Automating the collection of ultrathin serial sections for large volume tem reconstructions
    • 10.1017/S1431927606066268
    • Hayworth, K.; Kasthuri, N.; Schalek, R.; Lichtman, J. (2006). Automating the collection of ultrathin serial sections for large volume tem reconstructions. Microscopy and Microanalysis, 12, 86-87.
    • (2006) Microscopy and Microanalysis , vol.12 , pp. 86-87
    • Hayworth, K.1    Kasthuri, N.2    Schalek, R.3    Lichtman, J.4
  • 27
    • 84857688652 scopus 로고    scopus 로고
    • Computational methods and challenges for large-scale circuit mapping
    • 1:CAS:528:DC%2BC38Xjt1Gksbg%3D 3406305 22221862 10.1016/j.conb.2011.11. 010
    • Helmstaedter, M.; & Mitra, P. P. (2012). Computational methods and challenges for large-scale circuit mapping. Current Opinion in Neurobiology, 22, 162-169.
    • (2012) Current Opinion in Neurobiology , vol.22 , pp. 162-169
    • Helmstaedter, M.1    Mitra, P.P.2
  • 28
    • 79960844955 scopus 로고    scopus 로고
    • High-accuracy neurite reconstruction for high-throughput neuroanatomy
    • 1:CAS:528:DC%2BC3MXos1Omtr0%3D 21743472 10.1038/nn.2868
    • Helmstaedter, M.; Briggman, K.; Denk, W. (2011). High-accuracy neurite reconstruction for high-throughput neuroanatomy. Nature Neuroscience, 14, 1081-1088.
    • (2011) Nature Neuroscience , vol.14 , pp. 1081-1088
    • Helmstaedter, M.1    Briggman, K.2    Denk, W.3
  • 29
    • 84860653775 scopus 로고    scopus 로고
    • STEPS: Efficient simulation of stochastic reaction-diffusion models in realistic morphologies
    • 10.1186/1752-0509-6-36
    • Hepburn, I.; Chen, W.; Wils, S.; De Schutter, E. (2012). STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies. BMC Systems Biology, 6, 1752-0509.
    • (2012) BMC Systems Biology , vol.6 , pp. 1752-0509
    • Hepburn, I.1    Chen, W.2    Wils, S.3    De Schutter, E.4
  • 30
    • 77951870906 scopus 로고    scopus 로고
    • Ssecrett and neurotrace: Interactive visualization and analysis tools for large-scale neuroscience data sets
    • 2909612 20650718 10.1109/MCG.2010.56
    • Jeong, W.; Beyer, J.; Hadwiger, M.; Blue, R.; Law, C.; et al. (2010). Ssecrett and neurotrace: interactive visualization and analysis tools for large-scale neuroscience data sets. IEEE Computer Graphics and Applications, 30, 58.
    • (2010) IEEE Computer Graphics and Applications , vol.30 , pp. 58
    • Jeong, W.1    Beyer, J.2    Hadwiger, M.3    Blue, R.4    Law, C.5
  • 31
    • 84872491808 scopus 로고    scopus 로고
    • Semi-automated neuron boundary detection and nonbranching process segmentation in electron microscopy images
    • Jurrus, E.; Watanabe, S., Giuly, R.J., Paiva, A.R., Ellisman, M.H., et al. (2012). Semi-automated neuron boundary detection and nonbranching process segmentation in electron microscopy images. Neuroinformatics, 11(1), 1-25.
    • (2012) Neuroinformatics , vol.11 , Issue.1 , pp. 1-25
    • Jurrus, E.1    Watanabe, S.2    Giuly, R.J.3    Paiva, A.R.4    Ellisman, M.H.5
  • 32
    • 55149086309 scopus 로고    scopus 로고
    • Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces
    • 2819163 20151023 10.1137/070692017
    • Kerr, R., Bartol, T., Kaminsky, B., Dittrich, M., Chang, J., et al. (2008). Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces. SIAM Journal on Scientific Computing, 30, 3126.
    • (2008) SIAM Journal on Scientific Computing , vol.30 , pp. 3126
    • Kerr, R.1    Bartol, T.2    Kaminsky, B.3    Dittrich, M.4    Chang, J.5
  • 34
    • 84870657123 scopus 로고    scopus 로고
    • Extracellular sheets and tunnels modulate glutamate diffusion in hippocampal neuropil
    • 3540825 22740128 10.1002/cne.23181
    • Kinney, J.P., Spacek, J., Bartol, T.M., Bajaj, C.L., Harris, K.M., et al. (2013). Extracellular sheets and tunnels modulate glutamate diffusion in hippocampal neuropil. Journal of Comparative Neurology, 521, 448-464.
    • (2013) Journal of Comparative Neurology , vol.521 , pp. 448-464
    • Kinney, J.P.1    Spacek, J.2    Bartol, T.M.3    Bajaj, C.L.4    Harris, K.M.5
  • 35
    • 80755143593 scopus 로고    scopus 로고
    • Large-scale automated histology in the pursuit of connectomes
    • 1:CAS:528:DC%2BC3MXhsFSlt7nJ 3758571 22072665 10.1523/JNEUROSCI.4077-11. 2011
    • Kleinfeld, D., Bharioke, A., Blinder, P., Bock, D., Briggman, K.L., et al. (2011). Large-scale automated histology in the pursuit of connectomes. The Journal of Neuroscience, 31, 16125-16138.
    • (2011) The Journal of Neuroscience , vol.31 , pp. 16125-16138
    • Kleinfeld, D.1    Bharioke, A.2    Blinder, P.3    Bock, D.4    Briggman, K.L.5
  • 36
    • 41149120500 scopus 로고    scopus 로고
    • Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling
    • 1:CAS:528:DC%2BD1cXjvFCjs7k%3D 18353998 10.1523/JNEUROSCI.3189-07.2008
    • Knott, G.; Marchman, H.; Wall, D.; Lich, B. (2008). Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling. The Journal of Neuroscience, 28, 2959-2964.
    • (2008) The Journal of Neuroscience , vol.28 , pp. 2959-2964
    • Knott, G.1    Marchman, H.2    Wall, D.3    Lich, B.4
  • 37
    • 84884283576 scopus 로고    scopus 로고
    • Beyond counts and shapes: Studying pathology of dendritic spines in the context of the surrounding neuropil through serial section electron microscopy
    • 22561733 10.1016/j.neuroscience.2012.04.061
    • Kuwajima, M.; Spacek, J.; Harris, K.M. (2012). Beyond counts and shapes: studying pathology of dendritic spines in the context of the surrounding neuropil through serial section electron microscopy. Neuroscience, 251, 75-89.
    • (2012) Neuroscience , vol.251 , pp. 75-89
    • Kuwajima, M.1    Spacek, J.2    Harris, K.M.3
  • 38
    • 84875418121 scopus 로고    scopus 로고
    • Automated transmission-mode scanning electron microscopy (tsem) for large volume analysis at nanoscale resolution
    • 1:CAS:528:DC%2BC3sXlslCgtLk%3D 3608656 23555711 10.1371/journal.pone. 0059573
    • Kuwajima, M.; Mendenhall, J.M.; Lindsey, L.F.; Harris, K.M. (2013). Automated transmission-mode scanning electron microscopy (tsem) for large volume analysis at nanoscale resolution. PloS One, 8, e59573.
    • (2013) PloS One , vol.8 , pp. 59573
    • Kuwajima, M.1    Mendenhall, J.M.2    Lindsey, L.F.3    Harris, K.M.4
  • 39
    • 1842588624 scopus 로고    scopus 로고
    • From Maxwell's equations to the cable equation and beyond
    • 1:STN:280:DC%2BD2c7lvVOktg%3D%3D 15050381 10.1016/j.pbiomolbio.2003.08. 001
    • Lindsay, K.; Rosenberg, J.; Tucker, G. (2004). From Maxwell's equations to the cable equation and beyond. Progress in Biophysics and Molecular Biology, 85, 71-116.
    • (2004) Progress in Biophysics and Molecular Biology , vol.85 , pp. 71-116
    • Lindsay, K.1    Rosenberg, J.2    Tucker, G.3
  • 40
    • 79952625895 scopus 로고    scopus 로고
    • Dendritic changes in visual pathways in glaucoma and other neurodegenerative conditions
    • 1:CAS:528:DC%2BC3MXjsV2nsLk%3D 21310146 10.1016/j.exer.2011.01.014
    • Liu, M.; Duggan, J.; Salt, T.E.; Cordeiro, M.F. (2011). Dendritic changes in visual pathways in glaucoma and other neurodegenerative conditions. Experimental Eye Research, 92, 244-250.
    • (2011) Experimental Eye Research , vol.92 , pp. 244-250
    • Liu, M.1    Duggan, J.2    Salt, T.E.3    Cordeiro, M.F.4
  • 41
    • 66249148685 scopus 로고    scopus 로고
    • Semi-automated reconstruction of neural processes from large numbers of fluorescence images
    • 10.1371/journal.pone.0005655
    • Lu, J.; Fiala, J.; Lichtman, J. (2009). Semi-automated reconstruction of neural processes from large numbers of fluorescence images. PLoS One, 4, 5655.
    • (2009) PLoS One , vol.4 , pp. 5655
    • Lu, J.1    Fiala, J.2    Lichtman, J.3
  • 42
    • 77956990482 scopus 로고    scopus 로고
    • Ultrastructural analysis of hippocampal neuropil from the connectomics perspective
    • 1:CAS:528:DC%2BC3cXht1WisrzP 3215280 20869597 10.1016/j.neuron.2010.08. 014
    • Mishchenko, Y.; Hu, T.; Spacek, J.; Mendenhall, J.; Harris, K.; et al. (2010). Ultrastructural analysis of hippocampal neuropil from the connectomics perspective. Neuron, 67, 1009-1020.
    • (2010) Neuron , vol.67 , pp. 1009-1020
    • Mishchenko, Y.1    Hu, T.2    Spacek, J.3    Mendenhall, J.4    Harris, K.5
  • 44
    • 79953161238 scopus 로고    scopus 로고
    • The endoplasmic reticulum and protein trafficking in dendrites and axons
    • 21215635 10.1016/j.tcb.2010.12.003
    • Ramírez, O. A.; & Couve, A. (2011). The endoplasmic reticulum and protein trafficking in dendrites and axons. Trends in Cell Biology, 21, 219-227.
    • (2011) Trends in Cell Biology , vol.21 , pp. 219-227
    • Ramírez, O.A.1    Couve, A.2
  • 45
    • 84863192622 scopus 로고    scopus 로고
    • Elastic volume reconstruction from series of ultra-thin microscopy sections
    • 22688414 10.1038/nmeth.2072
    • Saalfeld, S.; Fetter, R.; Cardona, A.; Tomancak, P. (2012). Elastic volume reconstruction from series of ultra-thin microscopy sections. Nature Methods, 9, 717-720.
    • (2012) Nature Methods , vol.9 , pp. 717-720
    • Saalfeld, S.1    Fetter, R.2    Cardona, A.3    Tomancak, P.4
  • 49
    • 0033756376 scopus 로고    scopus 로고
    • Overview on the structure, composition, function, development, and plasticity of hippocampal dendritic spines
    • 1:STN:280:DC%2BD3M7hvFyntw%3D%3D 11075821 10.1002/1098-1063(2000)10: 5<501: AID-HIPO1>3.0.CO;2-T
    • Sorra, K.E.; & Harris, K.M. (2000). Overview on the structure, composition, function, development, and plasticity of hippocampal dendritic spines. Hippocampus, 10, 501-511.
    • (2000) Hippocampus , vol.10 , pp. 501-511
    • Sorra, K.E.1    Harris, K.M.2
  • 51
    • 84979981857 scopus 로고    scopus 로고
    • Shape transformation using variational implicit functions
    • Turk, G.; & O'Brien, J. (1999). Shape transformation using variational implicit functions. In SIGGRAPH'99 (pp. 335-342).
    • (1999) SIGGRAPH'99 , pp. 335-342
    • Turk, G.1    O'Brien, J.2
  • 52
    • 77954891060 scopus 로고    scopus 로고
    • Synapse pathology in psychiatric and neurologic disease
    • 2857788 20425036 10.1007/s11910-010-0104-8
    • van Spronsen, M.; & Hoogenraad, C.C. (2010). Synapse pathology in psychiatric and neurologic disease. Current Neurology and Neuroscience Reports, 10, 207-214.
    • (2010) Current Neurology and Neuroscience Reports , vol.10 , pp. 207-214
    • Van Spronsen, M.1    Hoogenraad, C.C.2
  • 53
    • 28444442292 scopus 로고    scopus 로고
    • Adaptive and quality quadrilateral/hexahedral meshing from volumetric data
    • 2740490 19750180 10.1016/j.cma.2005.02.016
    • Zhang, Y.; & Bajaj, C. (2006). Adaptive and quality quadrilateral/hexahedral meshing from volumetric data. Computer Methods in Applied Mechanics and Engineering, 195, 942-960.
    • (2006) Computer Methods in Applied Mechanics and Engineering , vol.195 , pp. 942-960
    • Zhang, Y.1    Bajaj, C.2
  • 54
    • 37349014019 scopus 로고    scopus 로고
    • Application of new multiresolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity
    • 10.1137/050647670
    • Zhang, X.; Bajaj, C.L.; Kwon, B.; Dolinsky, T.J.; Nielsen, J.E.; et al. (2006). Application of new multiresolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity. Multiscale Modeling & Simulation, 5, 1196-1213.
    • (2006) Multiscale Modeling & Simulation , vol.5 , pp. 1196-1213
    • Zhang, X.1    Bajaj, C.L.2    Kwon, B.3    Dolinsky, T.J.4    Nielsen, J.E.5
  • 56
    • 61749090052 scopus 로고    scopus 로고
    • Surface smoothing and quality improvement of quadrilateral/hexahedral meshes with geometric flow
    • 10.1002/cnm.1067
    • Zhang, Y.; Bajaj, C.; Xu, G. (2009). Surface smoothing and quality improvement of quadrilateral/hexahedral meshes with geometric flow. Communications in Numerical Methods in Engineering, 25, 1-18.
    • (2009) Communications in Numerical Methods in Engineering , vol.25 , pp. 1-18
    • Zhang, Y.1    Bajaj, C.2    Xu, G.3
  • 57
    • 84862900534 scopus 로고    scopus 로고
    • Macromolecular structure modeling from 3D em using VolRover 2.0
    • 1:CAS:528:DC%2BC38XosVaksrg%3D 3511818 22696407 10.1002/bip.22052
    • Zhang, Q.; Bettadapura, R.; Bajaj, C. (2012). Macromolecular structure modeling from 3D EM using VolRover 2.0. Biopolymers, 97, 709-731.
    • (2012) Biopolymers , vol.97 , pp. 709-731
    • Zhang, Q.1    Bettadapura, R.2    Bajaj, C.3


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