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Volumn 8, Issue NOV, 2014, Pages

Automated computation of arbor densities: A step toward identifying neuronal cell types

Author keywords

Cell types; Classification; Laminar structures; Reconstruction; Retinal ganglion cells; Stratification

Indexed keywords

JUNCTIONAL ADHESION MOLECULE B;

EID: 84912121216     PISSN: None     EISSN: 16625129     Source Type: Journal    
DOI: 10.3389/fnana.2014.00139     Document Type: Article
Times cited : (21)

References (46)
  • 2
    • 37849043878 scopus 로고    scopus 로고
    • Improved detection of branching points in algorithms for automated neuron tracing from 3D confocal images
    • Al-Kofahi, Y., Dowell-Mesfin, N., Pace, C., Shain, W., Turner, J. N., and Roysam, B. (2008). Improved detection of branching points in algorithms for automated neuron tracing from 3D confocal images. Cytometry A 73, 36-43. doi: 10.1002/cyto.a.20499
    • (2008) Cytometry A , vol.73 , pp. 36-43
    • Al-Kofahi, Y.1    Dowell-Mesfin, N.2    Pace, C.3    Shain, W.4    Turner, J.N.5    Roysam, B.6
  • 4
    • 9744252257 scopus 로고    scopus 로고
    • Quantitative analysis of neuronal morphologies in the mouse retina visualized by using a genetically directed reporter
    • Badea, T. and Nathans, J. (2004). Quantitative analysis of neuronal morphologies in the mouse retina visualized by using a genetically directed reporter. J. Comp. Neurol. 480, 331-351. doi: 10.1002/cne.20304
    • (2004) J. Comp. Neurol , vol.480 , pp. 331-351
    • Badea, T.1    Nathans, J.2
  • 5
    • 79958105763 scopus 로고    scopus 로고
    • Principal curves as skeletons of tubular objects: Locally characterizing the structures of axons
    • Bas, E. and Erdogmus, D. (2011). Principal curves as skeletons of tubular objects: locally characterizing the structures of axons. Neuroinformatics 9, 181-191. doi: 10.1007/s12021-011-9105-2
    • (2011) Neuroinformatics , vol.9 , pp. 181-191
    • Bas, E.1    Erdogmus, D.2
  • 6
    • 0028333470 scopus 로고
    • A new characterization of 3-dimensional simple points
    • Bertrand, G. and Malandain, G. (1994). A new characterization of 3-dimensional simple points. Pattern Recogn. Lett. 15, 169-175. doi: 10.1016/0167-8655(94)90046-9
    • (1994) Pattern Recogn. Lett , vol.15 , pp. 169-175
    • Bertrand, G.1    Malandain, G.2
  • 7
    • 79952376773 scopus 로고    scopus 로고
    • Network anatomy and in vivo physiology of visual cortical neurons
    • Bock, D. D., Lee, W. C. A., Kerlin, A. M., Andermann, M. L., Hood, G., Wetzel, A. W., et al. (2011). Network anatomy and in vivo physiology of visual cortical neurons. Nature 471, 177-182. doi: 10.1038/nature09802
    • (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    Wetzel, A.W.6
  • 8
    • 79958135341 scopus 로고    scopus 로고
    • The diadem data sets: Representative light microscopy images of neuronal morphology to advance automation of digital reconstructions
    • Brown, K., Barrionuevo, G., Canty, A., De Paola, V., Hirsch, J., Jefferis, G., et al. (2011). The diadem data sets: representative light microscopy images of neuronal morphology to advance automation of digital reconstructions. Neuroinformatics 9, 143-157. doi: 10.1007/s12021-010-9095-5
    • (2011) Neuroinformatics , vol.9 , pp. 143-157
    • Brown, K.1    Barrionuevo, G.2    Canty, A.3    De Paola, V.4    Hirsch, J.5    Jefferis, G.6
  • 9
    • 2542418071 scopus 로고    scopus 로고
    • Power-law for axon diameters at branch point
    • Chklovskii, D. B., and Stepanyants, A. (2003). Power-law for axon diameters at branch point. BMC Neurosci. 4:18. doi: 10.1186/1471-2202-4-18
    • (2003) BMC Neurosci , vol.4 , pp. 18
    • Chklovskii, D.B.1    Stepanyants, A.2
  • 10
    • 84865110867 scopus 로고    scopus 로고
    • Automatic reconstruction of neural morphologies with multi-scale tracking
    • Choromanska, A., Chang, S. F., and Yuste, R. (2012). Automatic reconstruction of neural morphologies with multi-scale tracking. Front. Neural Circuits 6:25. doi: 10.3389/fncir.2012.00025
    • (2012) Front. Neural Circuits , vol.6 , pp. 25
    • Choromanska, A.1    Chang, S.F.2    Yuste, R.3
  • 11
    • 79958088818 scopus 로고    scopus 로고
    • Automated tracing of neurites from light microscopy stacks of images
    • Chothani, P., Mehta, V., and Stepanyants, A. (2011). Automated tracing of neurites from light microscopy stacks of images. Neuroinformatics 9, 263-278. doi: 10.1007/s12021-011-9121-2
    • (2011) Neuroinformatics , vol.9 , pp. 263-278
    • Chothani, P.1    Mehta, V.2    Stepanyants, A.3
  • 12
    • 84878115127 scopus 로고    scopus 로고
    • Structural and molecular interrogation of intact biological systems
    • Chung, K., Wallace, J., Kim, S., Kalyanasundaram, S., Andalman, A., Davidson, T., et al. (2013). Structural and molecular interrogation of intact biological systems. Nature 497, 332-337. doi: 10.1038/nature12107
    • (2013) Nature , vol.497 , pp. 332-337
    • Chung, K.1    Wallace, J.2    Kim, S.3    Kalyanasundaram, S.4    Andalman, A.5    Davidson, T.6
  • 13
    • 33646339118 scopus 로고    scopus 로고
    • Morphological properties of mouse retinal ganglion cells
    • Coombs, J., van der List, D., Wang, G.-Y., and Chalupa, L. (2006). Morphological properties of mouse retinal ganglion cells. Neuroscience 140, 123-136. doi: 10.1016/j.neuroscience.2006.02.079
    • (2006) Neuroscience , vol.140 , pp. 123-136
    • Coombs, J.1    Van Der List, D.2    Wang, G.-Y.3    Chalupa, L.4
  • 14
    • 14044262855 scopus 로고    scopus 로고
    • Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure
    • Denk, W., and Horstmann, H. (2004). Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol. 2:e329. doi: 10.1371/journal.pbio.0020329
    • (2004) PLoS Biol , vol.2 , pp. e329
    • Denk, W.1    Horstmann, H.2
  • 15
    • 84901255614 scopus 로고    scopus 로고
    • Active learning of neuron morphology for accurate automated tracing of neurites. Front
    • Gala, R., Chapeton, J., Jitesh, J., Bhavsar, C., and Stepanyants, A. (2014). Active learning of neuron morphology for accurate automated tracing of neurites. Front. Neuroanat. 8:37. doi: 10.3389/fnana.2014.00037
    • (2014) Neuroanat , vol.8 , pp. 37
    • Gala, R.1    Chapeton, J.2    Jitesh, J.3    Bhavsar, C.4    Stepanyants, A.5
  • 16
    • 0242401835 scopus 로고    scopus 로고
    • A gene expression atlas of the central nervous system based on bacterial artificial chromosomes
    • Gong, S., Zheng, C., Doughty, M., Losos, K., Didkovsky, N., Schambra, U., et al. (2003). A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature 425, 917-925. doi: 10.1038/nature02033
    • (2003) Nature , vol.425 , pp. 917-925
    • Gong, S.1    Zheng, C.2    Doughty, M.3    Losos, K.4    Didkovsky, N.5    Schambra, U.6
  • 17
    • 0342323816 scopus 로고    scopus 로고
    • Immunocytochemical analysis of the mouse retina
    • Haverkamp, S. and Wässle, H. (2000). Immunocytochemical analysis of the mouse retina. J. Comp. Neurol. 424, 1-23. doi: 10.1002/1096-9861(20000814)424:11::AID-CNE13.0.CO;2-V
    • (2000) J. Comp. Neurol , vol.424 , pp. 1-23
    • Haverkamp, S.1    Wässle, H.2
  • 18
    • 33750863459 scopus 로고    scopus 로고
    • Automating the collection of ultrathin serial sections for large volume tem reconstructions
    • Hayworth, K. J., Kasthuri, N., Schalek, R., and Lichtman, J. W. (2006). Automating the collection of ultrathin serial sections for large volume tem reconstructions. Microsc. Microanal. 12(Suppl. 2), 86-87. doi: 10.1017/S1431927606066268
    • (2006) Microsc. Microanal , vol.12 , pp. 86-87
    • Hayworth, K.J.1    Kasthuri, N.2    Schalek, R.3    Lichtman, J.W.4
  • 19
    • 84881453258 scopus 로고    scopus 로고
    • Connectomic reconstruction of the inner plexiform layer in the mouse retina
    • Helmstaedter, M., Briggman, K. L., Turaga, S. C., Jain, V., Seung, H. S., and Denk, W. (2013). Connectomic reconstruction of the inner plexiform layer in the mouse retina. Nature 500, 168-174. doi: 10.1038/nature12346
    • (2013) Nature , vol.500 , pp. 168-174
    • Helmstaedter, M.1    Briggman, K.L.2    Turaga, S.C.3    Jain, V.4    Seung, H.S.5    Denk, W.6
  • 20
    • 0026219520 scopus 로고
    • Selection of a convolution function for fourier inversion using gridding
    • Jackson, J. I., Meyer, C. H., Nishimura, D. G., and Macovski, A. (1991). Selection of a convolution function for fourier inversion using gridding. IEEE Trans. Med. Imaging 10, 473-478. doi: 10.1109/42.97598
    • (1991) IEEE Trans. Med. Imaging , vol.10 , pp. 473-478
    • Jackson, J.I.1    Meyer, C.H.2    Nishimura, D.G.3    Macovski, A.4
  • 22
    • 84880920117 scopus 로고    scopus 로고
    • Seedb: A simple and morphology preserving optical clearing agent for neuronal circuit reconstruction
    • Ke, M. T., Fujimoto, S., and Imai, T. (2013). Seedb: a simple and morphology preserving optical clearing agent for neuronal circuit reconstruction. Nat. Neurosci. 16, 1154-1161. doi: 10.1038/nn.3447
    • (2013) Nat. Neurosci , vol.16 , pp. 1154-1161
    • Ke, M.T.1    Fujimoto, S.2    Imai, T.3
  • 23
    • 75349096226 scopus 로고    scopus 로고
    • Laminar restriction of retinal ganglion cell dendrites and axons: Subtype-specific developmental patterns revealed with transgenic markers
    • Kim, I., Zhang, Y., Meister, M., and Sanes, J. (2010). Laminar restriction of retinal ganglion cell dendrites and axons: subtype-specific developmental patterns revealed with transgenic markers. J. Neurosci. 30, 1452-1462. doi: 10.1523/JNEUROSCI.4779-09.2010
    • (2010) J. Neurosci , vol.30 , pp. 1452-1462
    • Kim, I.1    Zhang, Y.2    Meister, M.3    Sanes, J.4
  • 24
    • 41349087571 scopus 로고    scopus 로고
    • Molecular identification of a retinal cell type that responds to upward motion
    • Kim, I., Zhang, Y., Yamagata, M., Meister, M., and Sanes, J. (2008). Molecular identification of a retinal cell type that responds to upward motion. Nature 452, 478-482. doi: 10.1038/nature06739
    • (2008) Nature , vol.452 , pp. 478-482
    • Kim, I.1    Zhang, Y.2    Yamagata, M.3    Meister, M.4    Sanes, J.5
  • 25
    • 84900523778 scopus 로고    scopus 로고
    • Space-time wiring specificity supports direction selectivity in the retina
    • Kim, J. S., Greene, M. J., Zlateski, A., Lee, K., Richardson, M., Turaga, S. C., et al. (2014). Space-time wiring specificity supports direction selectivity in the retina. Nature 509, 331-336. doi: 10.1038/nature13240
    • (2014) Nature , vol.509 , pp. 331-336
    • Kim, J.S.1    Greene, M.J.2    Zlateski, A.3    Lee, K.4    Richardson, M.5    Turaga, S.C.6
  • 26
    • 22644437764 scopus 로고    scopus 로고
    • Diversity of ganglion cells in the mouse retina: Unsupervised morphological classification and its limits
    • Kong, J. H., Fish, D. R., Rockhill, R. L., and Masland, R. H. (2005). Diversity of ganglion cells in the mouse retina: unsupervised morphological classification and its limits. J. Comp. Neurol. 489, 293-310. doi: 10.1002/cne.20631
    • (2005) J. Comp. Neurol , vol.489 , pp. 293-310
    • Kong, J.H.1    Fish, D.R.2    Rockhill, R.L.3    Masland, R.H.4
  • 27
    • 0032203257 scopus 로고    scopus 로고
    • Gradient-based learning applied to document recognition
    • LeCun, Y., Bottou, L., Bengio, Y., and Haffner, P. (1998). Gradient-based learning applied to document recognition. Proc. IEEE 86, 2278-2324. doi: 10.1109/5.726791
    • (1998) Proc. IEEE , vol.86 , pp. 2278-2324
    • Lecun, Y.1    Bottou, L.2    Bengio, Y.3    Haffner, P.4
  • 28
    • 43249113370 scopus 로고    scopus 로고
    • Least squares conformal maps for automatic texture atlas generation
    • Levy, B., Petitjean, S., Ray, N., and Maillot, J. (2002). Least squares conformal maps for automatic texture atlas generation. ACM Trans. Graphic. 21, 362-371. doi: 10.1145/566654.566590
    • (2002) ACM Trans. Graphic , vol.21 , pp. 362-371
    • Levy, B.1    Petitjean, S.2    Ray, N.3    Maillot, J.4
  • 29
    • 57349177834 scopus 로고    scopus 로고
    • Live neuron morphology automatically reconstructed from multiphoton and confocal imaging data
    • Losavio, B. E., Liang, Y., Santamaria-Pang, A., Kakadiaris, I. A., Colbert, C. M., and Saggau, P. (2008). Live neuron morphology automatically reconstructed from multiphoton and confocal imaging data. J. Neurophysiol. 100, 2422-2429. doi: 10.1152/jn.90627.2008
    • (2008) J. Neurophysiol , vol.100 , pp. 2422-2429
    • Losavio, B.E.1    Liang, Y.2    Santamaria-Pang, A.3    Kakadiaris, I.A.4    Colbert, C.M.5    Saggau, P.6
  • 30
    • 79958130994 scopus 로고    scopus 로고
    • 3-D image pre-processing algorithms for improved automated tracing of neuronal arbors
    • Narayanaswamy, A., Wang, Y., and Roysam, B. (2011). 3-D image pre-processing algorithms for improved automated tracing of neuronal arbors. Neuroinformatics 9, 219-231. doi: 10.1007/s12021-011-9116-z
    • (2011) Neuroinformatics , vol.9 , pp. 219-231
    • Narayanaswamy, A.1    Wang, Y.2    Roysam, B.3
  • 31
    • 79959470488 scopus 로고    scopus 로고
    • Automatic 3D neuron tracing using all-path pruning
    • Peng, H., Long, F., and Myers, G. (2011). Automatic 3D neuron tracing using all-path pruning. Bioinformatics 27, i239-i247. doi: 10.1093/bioinformatics/btr237
    • (2011) Bioinformatics , vol.27 , pp. i239-i247
    • Peng, H.1    Long, F.2    Myers, G.3
  • 32
    • 77954196544 scopus 로고    scopus 로고
    • Automatic reconstruction of 3d neuron structures using a graph-augmented deformable model
    • Peng, H., Ruan, Z., Atasoy, D., and Sternson, S. (2010). Automatic reconstruction of 3d neuron structures using a graph-augmented deformable model. Bioinformatics 26, i38-i46. doi: 10.1093/bioinformatics/btq212
    • (2010) Bioinformatics , vol.26 , pp. i38-i46
    • Peng, H.1    Ruan, Z.2    Atasoy, D.3    Sternson, S.4
  • 33
    • 7744235523 scopus 로고    scopus 로고
    • New methods for the computer-assisted 3-D reconstruction of neurons from confocal image stacks
    • Schmitt, S., Evers, J. F., Duch, C., Scholz, M., and Obermayer, K. (2004). New methods for the computer-assisted 3-D reconstruction of neurons from confocal image stacks. Neuroimage 23, 1283-1298. doi: 10.1016/j.neuroimage.2004.06.047
    • (2004) Neuroimage , vol.23 , pp. 1283-1298
    • Schmitt, S.1    Evers, J.F.2    Duch, C.3    Scholz, M.4    Obermayer, K.5
  • 34
    • 77954201127 scopus 로고    scopus 로고
    • Reconstruction of the neuromuscular junction connectome
    • Srinivasan, R., Li, Q., Zhou, X., Lu, J., Lichtman, J., and Wong, S. T. (2010). Reconstruction of the neuromuscular junction connectome. Bioinformatics 26, i64-i70. doi: 10.1093/bioinformatics/btq179
    • (2010) Bioinformatics , vol.26 , pp. i64-i70
    • Srinivasan, R.1    Li, Q.2    Zhou, X.3    Lu, J.4    Lichtman, J.5    Wong, S.T.6
  • 35
    • 20744456035 scopus 로고    scopus 로고
    • Neurogeometry and potential synaptic connectivity
    • Stepanyants, A., and Chklovskii, D. B. (2005). Neurogeometry and potential synaptic connectivity. Trends Neurosci. 28, 387-394. doi: 10.1016/j.tins.2005.05.006
    • (2005) Trends Neurosci , vol.28 , pp. 387-394
    • Stepanyants, A.1    Chklovskii, D.B.2
  • 36
    • 84903177431 scopus 로고    scopus 로고
    • A genetic and computational approach to structurally classify neuronal types
    • Sümbül, U., Song, S., McCulloch, K., Becker, M., Lin, B., Sanes, J. R., et al. (2014). A genetic and computational approach to structurally classify neuronal types. Nat. Commun. 5:3512. doi: 10.1038/ncomms4512
    • (2014) Nat. Commun , vol.5 , pp. 3512
    • Sümbül, U.1    Song, S.2    McCulloch, K.3    Becker, M.4    Lin, B.5    Sanes, J.R.6
  • 37
    • 0036663895 scopus 로고    scopus 로고
    • Large-scale morphological survey of rat retinal ganglion cells
    • Sun, W., Li, X., and He, S. (2002). Large-scale morphological survey of rat retinal ganglion cells. Visual Neurosci. 19, 483-493. doi: 10.1017/S0952523802194107
    • (2002) Visual Neurosci , vol.19 , pp. 483-493
    • Sun, W.1    Li, X.2    He, S.3
  • 38
    • 84866715770 scopus 로고    scopus 로고
    • (2012). “Automated reconstruction of tree structures using path classifiers and mixed integer programming,”
    • Providence, RI
    • Turetken, E., Benmansour, F., and Fua, P. (2012). “Automated reconstruction of tree structures using path classifiers and mixed integer programming,” in IEEE Conference on Computer Vision and Pattern Recognition (CVPR) (Providence, RI), 566-573.
    • IEEE Conference on Computer Vision and Pattern Recognition (CVPR) , pp. 566-573
    • Turetken, E.1    Benmansour, F.2    Fua, P.3
  • 39
    • 79958172203 scopus 로고    scopus 로고
    • Automated reconstruction of dendritic and axonal trees by global optimization with geometric priors
    • Turetken, E., Gonzlez, G., Blum, C., and Fua, P. (2011). Automated reconstruction of dendritic and axonal trees by global optimization with geometric priors. Neuroinformatics 9, 279-302. doi: 10.1007/s12021-011-9122-1
    • (2011) Neuroinformatics , vol.9 , pp. 279-302
    • Turetken, E.1    Gonzlez, G.2    Blum, C.3    Fua, P.4
  • 40
    • 59049087943 scopus 로고    scopus 로고
    • Tracer coupling patterns of the ganglion cell subtypes in the mouse retina
    • Völgyi, B., Chheda, S., and Bloomfield, S. (2009). Tracer coupling patterns of the ganglion cell subtypes in the mouse retina. J. Comp. Neurol. 512, 664-687. doi: 10.1002/cne.21912
    • (2009) J. Comp. Neurol , vol.512 , pp. 664-687
    • Völgyi, B.1    Chheda, S.2    Bloomfield, S.3
  • 41
    • 79958104510 scopus 로고    scopus 로고
    • A broadly applicable 3-D neuron tracing method based on open-curve snake
    • Wang, Y., Narayanaswamy, A., Tsai, C., and Roysam, B. (2011). A broadly applicable 3-D neuron tracing method based on open-curve snake. Neuroinformatics 9, 193-217. doi: 10.1007/s12021-011-9110-5
    • (2011) Neuroinformatics , vol.9 , pp. 193-217
    • Wang, Y.1    Narayanaswamy, A.2    Tsai, C.3    Roysam, B.4
  • 42
    • 33845924630 scopus 로고    scopus 로고
    • Retrograde neuronal tracing with a deletion-mutant rabies virus
    • Wickersham, I. R., Finke, S., Conzelmann, K. K., and Callaway, E. M. (2006). Retrograde neuronal tracing with a deletion-mutant rabies virus. Nat. Methods 4, 47-49. doi: 10.1038/nmeth999
    • (2006) Nat. Methods , vol.4 , pp. 47-49
    • Wickersham, I.R.1    Finke, S.2    Conzelmann, K.K.3    Callaway, E.M.4
  • 43
    • 33847159648 scopus 로고    scopus 로고
    • Monosynaptic restriction of transsynaptic tracing from single, genetically targeted neurons
    • Wickersham, I. R., Lyon, D. C., Barnard, R. J., Mori, T., Finke, S., Conzelmann, K. K., et al. (2007). Monosynaptic restriction of transsynaptic tracing from single, genetically targeted neurons. Neuron 53, 639-647. doi: 10.1016/j.neuron.2007.01.033
    • (2007) Neuron , vol.53 , pp. 639-647
    • Wickersham, I.R.1    Lyon, D.C.2    Barnard, R.J.3    Mori, T.4    Finke, S.5    Conzelmann, K.K.6
  • 44
    • 80052165284 scopus 로고    scopus 로고
    • Anisotropic path searching for automatic neuron reconstruction
    • Xie, J., Zhao, T., Lee, T., Myers, E., and Peng, H. (2011). Anisotropic path searching for automatic neuron reconstruction. Med. Image Anal. 15, 680-689. doi: 10.1016/j.media.2011.05.013
    • (2011) Med. Image Anal , vol.15 , pp. 680-689
    • Xie, J.1    Zhao, T.2    Lee, T.3    Myers, E.4    Peng, H.5
  • 45
    • 34147198443 scopus 로고    scopus 로고
    • Automated neurite extraction using dynamic programming for highthroughput screening of neuron-based assays
    • Zhang, Y., Zhou, X., Degterev, A., Lipinski, M., Adjeroh, D., Yuan, J., et al. (2007). Automated neurite extraction using dynamic programming for highthroughput screening of neuron-based assays. Neuroimage 35, 1502-1515. doi: 10.1016/j.neuroimage.2007.01.014
    • (2007) Neuroimage , vol.35 , pp. 1502-1515
    • Zhang, Y.1    Zhou, X.2    Degterev, A.3    Lipinski, M.4    Adjeroh, D.5    Yuan, J.6
  • 46
    • 79958161539 scopus 로고    scopus 로고
    • Automated reconstruction of neuronal morphology based on local geometrical and global structural models
    • Zhao, T., Xie, J., Amat, F., Clack, N., Ahammad, P., Peng, H., et al. (2011). Automated reconstruction of neuronal morphology based on local geometrical and global structural models. Neuroinformatics 9, 247-261. doi: 10.1007/s12021-011-9120-3
    • (2011) Neuroinformatics , vol.9 , pp. 247-261
    • Zhao, T.1    Xie, J.2    Amat, F.3    Clack, N.4    Ahammad, P.5    Peng, H.6


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