Neuronal Morphology Goes Digital: A Research Hub for Cellular and System Neuroscience

Neuron

Volumn 77, Issue 6, 2013, Pages 1017-1038

  Parekh, Ruchi ^a   Ascoli, Giorgio A ^a  

^a GEORGE MASON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCYTIN; CARBOCYANINE; FLUOROGOLD; HORSERADISH PEROXIDASE; LEUKOAGGLUTININ; LUCIFER YELLOW; VIRUS VECTOR;

ANTIBODY LABELING; BRIGHT FIELD MICROSCOPY; CELL LABELING; CELL STRUCTURE; COMPUTER SIMULATION; CONFOCAL MICROSCOPY; DENDRITE; DIGITAL IMAGING; ECOLOGICAL NICHE; HUMAN; IMAGE PROCESSING; IMAGE RECONSTRUCTION; IMAGING SOFTWARE; MULTIPHOTON MICROSCOPY; NERVE CELL; NERVE CELL NETWORK; NERVE FIBER; NEUROANATOMICAL TRACT TRACING; NEUROANATOMY; NEUROIMAGING; NEUROSCIENCE; NONHUMAN; PRIORITY JOURNAL; REFERENCE DATABASE; REVIEW; STRUCTURE ACTIVITY RELATION; VIRTUAL REALITY;

ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTERS; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; NEURONS; NEUROSCIENCES; STAINING AND LABELING;

EID: 84875547168     PISSN: 08966273     EISSN: 10974199     Source Type: Journal    
DOI: 10.1016/j.neuron.2013.03.008     Document Type: Review

References (182)

1. Abbott A., Schiermeier Q. Research prize boost for Europe. Nature 2013, 493:585-586.
2. Alle H., Roth A., Geiger J.R. Energy-efficient action potentials in hippocampal mossy fibers. Science 2009, 325:1405-1408.
3. Andjelic S., Gallopin T., Cauli B., Hill E.L., Roux L., Badr S., Hu E., Tamás G., Lambolez B. Glutamatergic nonpyramidal neurons from neocortical layer VI and their comparison with pyramidal and spiny stellate neurons. J. Neurophysiol. 2009, 101:641-654.
4. Ascoli G.A. Computational Neuroanatomy: Principles and Methods 2002, Humana Press, New York.
5. Ascoli G.A. Mobilizing the base of neuroscience data: the case of neuronal morphologies. Nat. Rev. Neurosci. 2006, 7:318-324.
6. Ascoli G.A. Successes and rewards in sharing digital reconstructions of neuronal morphology. Neuroinformatics 2007, 5:154-160.
7. Ascoli G.A., Krichmar J.L., Scorcioni R., Nasuto S.J., Senft S.L. Computer generation and quantitative morphometric analysis of virtual neurons. Anat. Embryol. (Berl.) 2001, 204:283-301.
8. Ascoli G.A., Alonso-Nanclares L., Anderson S.A., Barrionuevo G., Benavides-Piccione R., Burkhalter A., Buzsáki G., Cauli B., Defelipe J., Fairén A., et al. Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex. Nat. Rev. Neurosci. 2008, 9:557-568. Petilla Interneuron Nomenclature Group.
9. Atunes G., Simones-de-Souza F.M., Roque A.C. Sensitivity of AMPA receptor channel to calcium oscillations: a computational study. Neurocomputing 2003, 52-54:341-346.
10. Bartos M., Vida I., Frotscher M., Meyer A., Monyer H., Geiger J.R., Jonas P. Fast synaptic inhibition promotes synchronized gamma oscillations in hippocampal interneuron networks. Proc. Natl. Acad. Sci. USA 2002, 99:13222-13227.
11. Betzig E., Patterson G.H., Sougrat R., Lindwasser O.W., Olenych S., Bonifacino J.S., Davidson M.W., Lippincott-Schwartz J., Hess H.F. Imaging intracellular fluorescent proteins at nanometer resolution. Science 2006, 313:1642-1645.
12. Billeci L., Magliaro C., Pioggia G., Ahluwalia A. NEuronMOrphological analysis tool: open-source software for quantitative morphometrics. Front. Neuroinform. 2013, 7:2.
13. Borg-Graham L.J. Additional efficient computation of branched nerve equations: adaptive time step and ideal voltage clamp. J. Comput. Neurosci. 2000, 8:209-226.
14. Bower J.M., Beeman D. The Book of GENESIS: Exploring Realistic Neural Models with the GEneral NEural SImulation System 1998, Springer-Verlag, New York.
15. Brecht M., Roth A., Sakmann B. Dynamic receptive fields of reconstructed pyramidal cells in layers 3 and 2 of rat somatosensory barrel cortex. J. Physiol. 2003, 553:243-265.
16. Broser P.J., Schulte R., Lang S., Roth A., Helmchen F., Waters J., Sakmann B., Wittum G. Nonlinear anisotropic diffusion filtering of three-dimensional image data from two-photon microscopy. J. Biomed. Opt. 2004, 9:1253-1264.
17. Brown K.M., Donohue D.E., D'Alessandro G., Ascoli G.A. A cross-platform freeware tool for digital reconstruction of neuronal arborizations from image stacks. Neuroinformatics 2005, 3:343-360.
18. Brown K.M., Barrionuevo G., Canty A.J., De Paola V., Hirsch J.A., Jefferis G.S.X.E., Lu J., Snippe M., Sugihara I., Ascoli G.A. The DIADEM data sets: representative light microscopy images of neuronal morphology to advance automation of digital reconstructions. Neuroinformatics 2011, 9:143-157.
19. Bui T.V., Cushing S., Dewey D., Fyffe R.E., Rose P.K. Comparison of the morphological and electrotonic properties of Renshaw cells, Ia inhibitory interneurons, and motoneurons in the cat. J. Neurophysiol. 2003, 90:2900-2918.
20. Buonomano D.V. Decoding temporal information: A model based on short-term synaptic plasticity. J. Neurosci. 2000, 20:1129-1141.
21. Cannon R.C., Turner D.A., Pyapali G.K., Wheal H.V. An on-line archive of reconstructed hippocampal neurons. J. Neurosci. Methods 1998, 84:49-54.
22. Cannon R.C., Hasselmo M.E., Koene R.A. From biophysics to behavior: Catacomb2 and the design of biologically-plausible models for spatial navigation. Neuroinformatics 2003, 1:3-42.
23. Cannon R.C., O'Donnell C., Nolan M.F. Stochastic ion channel gating in dendritic neurons: morphology dependence and probabilistic synaptic activation of dendritic spikes. PLoS Comput. Biol. 2010, 6:e1000886.
24. Capowski J.J. Computer-aided reconstruction of neuron trees from several serial sections. Comput. Biomed. Res. 1977, 10:617-629.
25. Carnevale N.T., Hines M.L. The NEURON Book 2006, Cambridge University Press, Cambridge, UK.
26. Cauller L.J., Connors B.W. Synaptic physiology of horizontal afferents to layer I in slices of rat SI neocortex. J. Neurosci. 1994, 14:751-762.
27. Chan C.S., Guzman J.N., Ilijic E., Mercer J.N., Rick C., Tkatch T., Meredith G.E., Surmeier D.J. 'Rejuvenation' protects neurons in mouse models of Parkinson's disease. Nature 2007, 447:1081-1086.
28. Chen K., Aradi I., Thon N., Eghbal-Ahmadi M., Baram T.Z., Soltesz I. Persistently modified h-channels after complex febrile seizures convert the seizure-induced enhancement of inhibition to hyperexcitability. Nat. Med. 2001, 7:331-337.
29. Chiang A.S., Lin C.Y., Chuang C.C., Chang H.M., Hsieh C.H., Yeh C.W., Shih C.T., Wu J.J., Wang G.T., Chen Y.C., et al. Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution. Curr. Biol. 2011, 21:1-11.
30. Chmykhova N.M., Adanina V.O., Karamian O.A., Kozhanov V.M., Vesselkin N.P., Clamann H.P. Comparative study of spinal motoneuron axon collaterals. Brain Res. Bull. 2005, 66:381-386.
31. Costa Lda.F., Zawadzki K., Miazaki M., Viana M.P., Taraskin S.N. Unveiling the neuromorphological space. Front. Comput. Neurosci. 2010, 4:150.
32. Crook S., Gleeson P., Howell F., Svitak J., Silver R.A. MorphML: level 1 of the NeuroML standards for neuronal morphology data and model specification. Neuroinformatics 2007, 5:96-104.
33. Cuntz H., Forstner F., Haag J., Borst A. The morphological identity of insect dendrites. PLoS Comput. Biol. 2008, 4:e1000251.
34. Cuntz H., Forstner F., Borst A., Häusser M. The TREES toolbox-probing the basis of axonal and dendritic branching. Neuroinformatics 2011, 9:91-96.
35. Cutsuridis V., Cobb S., Graham B.P. Encoding and retrieval in a model of the hippocampal CA1 microcircuit. Hippocampus 2010, 20:423-446.
36. DeFelipe J. From the connectome to the synaptome: an epic love story. Science 2010, 330:1198-1201.
37. Denk W., Svoboda K. Photon upmanship: why multiphoton imaging is more than a gimmick. Neuron 1997, 18:351-357.
38. Denk W., Strickler J.H., Webb W.W. Two-photon laser scanning fluorescence microscopy. Science 1990, 248:73-76.
39. Destexhe A., Neubig M., Ulrich D., Huguenard J. Dendritic low-threshold calcium currents in thalamic relay cells. J. Neurosci. 1998, 18:3574-3588.
40. DiGregorio D.A., Nusser Z., Silver R.A. Spillover of glutamate onto synaptic AMPA receptors enhances fast transmission at a cerebellar synapse. Neuron 2002, 35:521-533.
41. Dityatev A.E., Chmykhova N.M., Dityateva G.V., Babalian A.L., Kleinle J., Clamann H.P. Structural and physiological properties of connections between individual reticulospinal axons and lumbar motoneurons of the frog. J. Comp. Neurol. 2001, 430:433-447.
42. Donohue D.E., Ascoli G.A. Automated reconstruction of neuronal morphology: an overview. Brain Res. Brain Res. Rev. 2011, 67:94-102.
43. Eberhard J.P., Wanner A., Wittum G. NeuGen: A tool for the generation of realistic morphology of cortical neurons and neural networks in 3D. Neurocomputing 2006, 70:327-342.
44. Escobar G., Fares T., Stepanyants A. Structural plasticity of circuits in cortical neuropil. J. Neurosci. 2008, 28:8477-8488.
45. Eyre M.D., Antal M., Nusser Z. Distinct deep short-axon cell subtypes of the main olfactory bulb provide novel intrabulbar and extrabulbar GABAergic connections. J. Neurosci. 2008, 28:8217-8229.
46. Feldmeyer D., Egger V., Lubke J., Sakmann B. Reliable synaptic connections between pairs of excitatory layer 4 neurones within a single 'barrel' of developing rat somatosensory cortex. J. Physiol. 1999, 521:169-190.
47. Feldmeyer D., Roth A., Sakmann B. Monosynaptic connections between pairs of spiny stellate cells in layer 4 and pyramidal cells in layer 5A indicate that lemniscal and paralemniscal afferent pathways converge in the infragranular somatosensory cortex. J. Neurosci. 2005, 25:3423-3431.
48. Ferrante M., Blackwell K.T., Migliore M., Ascoli G.A. Computational models of neuronal biophysics and the characterization of potential neuropharmacological targets. Curr. Med. Chem. 2008, 15:2456-2471.
49. Ferrante M., Migliore M., Ascoli G.A. Feed-forward inhibition as a buffer of the neuronal input-output relation. Proc. Natl. Acad. Sci. USA 2009, 106:18004-18009.
50. Franco A., Knafo S., Banon-Rodriguez I., Merino-Serrais P., Fernaud-Espinosa I., Nieto M., Garrido J.J., Esteban J.A., Wandosell F., Anton I.M. WIP is a negative regulator of neuronal maturation and synaptic activity. Cereb. Cortex 2012, 22:1191-1202.
51. Fransén E., Alonso A.A., Dickson C.T., Magistretti J., Hasselmo M.E. Ionic mechanisms in the generation of subthreshold oscillations and action potential clustering in entorhinal layer II stellate neurons. Hippocampus 2004, 14:368-384.
52. Frick A., Feldmeyer D., Helmstaedter M., Sakmann B. Monosynaptic connections between pairs of L5A pyramidal neurons in columns of juvenile rat somatosensory cortex. Cereb. Cortex 2008, 18:397-406.
53. Gan W.-B., Grutzendler J., Wong W.T., Wong R.O.L., Lichtman J.W. Multicolor "DiOlistic" labeling of the nervous system using lipophilic dye combinations. Neuron 2000, 27:219-225.
54. Gasparini S., Migliore M., Magee J.C. On the initiation and propagation of dendritic spikes in CA1 pyramidal neurons. J. Neurosci. 2004, 24:11046-11056.
55. Gerhard F., Pipa G., Lima B., Neuenschwander S., Gerstner W. Extraction of network topology from multi-electrode recordings: is there a small-world effect?. Front Comput Neurosci 2011, 5:4.
56. Gillette T.A., Brown K.M., Ascoli G.A. The DIADEM metric: comparing multiple reconstructions of the same neuron. Neuroinformatics 2011, 9:233-245.
57. Glaser J.R., Glaser E.M. Neuron imaging with Neurolucida-a PC-based system for image combining microscopy. Comput. Med. Imaging Graph. 1990, 14:307-317.
58. Glaser E.M., Vanderloos H. A semi-automatic computer-microscope for the analysis of neuronal morphology. IEEE Trans. Biomed. Eng. 1965, 12:22-31.
59. Gleeson P., Steuber V., Silver R.A. neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron 2007, 54:219-235.
60. Goodman D.F. Code generation: a strategy for neural network simulators. Neuroinformatics 2010, 8:183-196.
61. Gulledge A.T., Stuart G.J. Excitatory actions of GABA in the cortex. Neuron 2003, 37:299-309.
62. Gustafsson M.G.L. Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc. Natl. Acad. Sci. USA 2005, 102:13081-13086.
63. Hadjieconomou D., Rotkopf S., Alexandre C., Bell D.M., Dickson B.J., Salecker I. Flybow: genetic multicolor cell labeling for neural circuit analysis in Drosophila melanogaster. Nat. Methods 2011, 8:260-266.
64. Halavi M., Hamilton K.A., Parekh R., Ascoli G.A. Digital reconstructions of neuronal morphology: three decades of research trends. Front Neurosci 2012, 6:49.
65. Hall D.H., Treinin M. How does morphology relate to function in sensory arbors?. Trends Neurosci. 2011, 34:443-451.
66. Hampel S., Chung P., McKellar C.E., Hall D., Looger L.L., Simpson J.H. Drosophila Brainbow: a recombinase-based fluorescence labeling technique to subdivide neural expression patterns. Nat. Methods 2011, 8:253-259.
67. Harris E., Stewart M. Propagation of synchronous epileptiform events from subiculum backward into area CA1 of rat brain slices. Brain Res. 2001, 895:41-49.
68. Häusser M., Major G., Stuart G.J. Differential shunting of EPSPs by action potentials. Science 2001, 291:138-141.
69. Hayes T.L., Lewis D.A. Magnopyramidal neurons in the anterior motor speech region. Dendritic features and interhemispheric comparisons. Arch. Neurol. 1996, 53:1277-1283.
70. He H.Y., Cline H.T. Diadem X: automated 4 dimensional analysis of morphological data. Neuroinformatics 2011, 9:107-112.
71. Hess S.T., Girirajan T.P.K., Mason M.D. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J. 2006, 91:4258-4272.
72. Hill S.L., Wang Y., Riachi I., Schürmann F., Markram H. Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits. Proc. Natl. Acad. Sci. USA 2012, 109:E2885-E2894.
73. Hines M.L., Carnevale N.T. The NEURON simulation environment. Neural Comput. 1997, 9:1179-1209.
74. Hoffman D.A., Magee J.C., Colbert C.M., Johnston D. K+ channel regulation of signal propagation in dendrites of hippocampal pyramidal neurons. Nature 1997, 387:869-875.
75. Huang B., Babcock H., Zhuang X. Breaking the diffraction barrier: super-resolution imaging of cells. Cell 2010, 143:1047-1058.
76. Jefferis G.S., Potter C.J., Chan A.M., Marin E.C., Rohlfing T., Maurer C.R., Luo L. Comprehensive maps of Drosophila higher olfactory centers: spatially segregated fruit and pheromone representation. Cell 2007, 128:1187-1203.
77. Ikeno H., Kanzaki R., Aonuma H., Takahata M., Mizunami M., Yasuyama K., Matsui N., Yokohari F., Usui S. Development of Invertebrate Brain Platform: management of research resources for invertebrate neuroscience and neuroethology. Neural Information Processing 2008, 905-914. Springer, Berlin. M. Ishikawa, K. Doya, H. Miyamoto, T. Yamakawa (Eds.).
78. Jungblut D., Vlachos A., Schuldt G., Zahn N., Deller T., Wittum G. SpineLab: tool for three-dimensional reconstruction of neuronal cell morphology. J. Biomed. Opt. 2012, 17:076007.
79. Kim H.G., Connors B.W. Apical dendrites of the neocortex: correlation between sodium- and calcium-dependent spiking and pyramidal cell morphology. J. Neurosci. 1993, 13:5301-5311.
80. Kim J., Zhao T., Petralia R.S., Yu Y., Peng H., Myers E., Magee J.C. mGRASP enables mapping mammalian synaptic connectivity with light microscopy. Nat. Methods 2012, 9:96-102.
81. Kita H., Armstrong W. A biotin-containing compound N-(2-aminoethyl)biotinamide for intracellular labeling and neuronal tracing studies: comparison with biocytin. J. Neurosci. Methods 1991, 37:141-150.
82. Klar T.A., Hell S.W. Subdiffraction resolution in far-field fluorescence microscopy. Opt. Lett. 1999, 24:954-956.
83. Köbbert C., Apps R., Bechmann I., Lanciego J.L., Mey J., Thanos S. Current concepts in neuroanatomical tracing. Prog. Neurobiol. 2000, 62:327-351.
84. Koene R.A., Tijms B., van Hees P., Postma F., de Ridder A., Ramakers G.J.A., van Pelt J., van Ooyen A. NETMORPH: a framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies. Neuroinformatics 2009, 7:195-210.
85. Koh I.Y., Lindquist W.B., Zito K., Nimchinsky E.A., Svoboda K. An image analysis algorithm for dendritic spines. Neural Comput. 2002, 14:1283-1310.
86. Kole M.H., Ilschner S.U., Kampa B.M., Williams S.R., Ruben P.C., Stuart G.J. Action potential generation requires a high sodium channel density in the axon initial segment. Nat. Neurosci. 2008, 11:178-186.
87. Krichmar J.L., Nasuto S.J., Scorcioni R., Washington S.D., Ascoli G.A. Effects of dendritic morphology on CA3 pyramidal cell electrophysiology: a simulation study. Brain Res. 2002, 941:11-28.
88. Kvello P., Løfaldli B.B., Rybak J., Menzel R., Mustaparta H. Digital, three-dimensional average shaped atlas of the heliothis virescens brain with integrated gustatory and olfactory neurons. Front Syst. Neurosci. 2009, 3:14.
89. Lakadamyali M., Babcock H., Bates M., Zhuang X., Lichtman J. 3D multicolor super-resolution imaging offers improved accuracy in neuron tracing. PLoS ONE 2012, 7:e30826.
90. Lanciego J.L., Wouterlood F.G. A half century of experimental neuroanatomical tracing. J. Chem. Neuroanat. 2011, 42:157-183.
91. Lavis L.D. Histochemistry: live and in color. J. Histochem. Cytochem. 2011, 59:139-145.
92. Le Magueresse C., Alfonso J., Khodosevich K., Arroyo Martín A.A., Bark C., Monyer H. "Small axonless neurons": postnatally generated neocortical interneurons with delayed functional maturation. J. Neurosci. 2011, 31:16731-16747.
93. Lee T.-C., Kashyap R.L., Chu C.N. Building skeleton models via 3-D medial surface/axis thinning algorithms. Comput. Vis. Graph. Image Process. 1994, 56:462-478.
94. Lee P.C., Chuang C.C., Chiang A.S., Ching Y.T. High-throughput computer method for 3D neuronal structure reconstruction from the image stack of the Drosophila brain and its applications. PLoS Comput. Biol. 2012, 8:e1002658.
95. Lee P.C., He H.Y., Lin C.Y., Ching Y.T., Cline H.T. Computer aided alignment and quantitative 4D structural plasticity analysis of neurons. Neuroinformatics 2013.
96. Lemmens M.A.M., Steinbusch H.W.M., Rutten B.P.F., Schmitz C. Advanced microscopy techniques for quantitative analysis in neuromorphology and neuropathology research: current status and requirements for the future. J. Chem. Neuroanat. 2010, 40:199-209.
97. Levinthal C., Ware R. Three dimensional reconstruction from serial sections. Nature 1972, 238:207-210.
98. Lichtman J.W., Livet J., Sanes J.R. A technicolour approach to the connectome. Nat. Rev. Neurosci. 2008, 9:417-422.
99. Liu J.K. Learning rule of homeostatic synaptic scaling: presynaptic dependent or not. Neural Comput. 2011, 23:3145-3161.
100. Livet J., Weissman T.A., Kang H., Draft R.W., Lu J., Bennis R.A., Sanes J.R., Lichtman J.W. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 2007, 450:56-62.
101. Longair M.H., Baker D.A., Armstrong J.D. Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes. Bioinformatics 2011, 27:2453-2454.
102. López-Cruz P.L., Bielza C., Larrañaga P., Benavides-Piccione R., DeFelipe J. Models and simulation of 3D neuronal dendritic trees using Bayesian networks. Neuroinformatics 2011, 9:347-369.
103. Losavio B.E., Liang Y., Santamaría-Pang A., Kakadiaris I.A., Colbert C.M., Saggau P. Live neuron morphology automatically reconstructed from multiphoton and confocal imaging data. J. Neurophysiol. 2008, 100:2422-2429.
104. Luisi J., Narayanaswamy A., Galbreath Z., Roysam B. The FARSIGHT trace editor: an open source tool for 3-D inspection and efficient pattern analysis aided editing of automated neuronal reconstructions. Neuroinformatics 2011, 9:305-315.
105. Lytton W.W., Sejnowski T.J. Simulations of cortical pyramidal neurons synchronized by inhibitory interneurons. J. Neurophysiol. 1991, 66:1059-1079.
106. Macagno E.R., Levinthal C., Sobel I. Three-dimensional computer reconstruction of neurons and neuronal assemblies. Annu. Rev. Biophys. Bioeng. 1979, 8:323-351.
107. Magariños A.M., McEwen B.S., Saboureau M., Pevet P. Rapid and reversible changes in intrahippocampal connectivity during the course of hibernation in European hamsters. Proc. Natl. Acad. Sci. USA 2006, 103:18775-18780.
108. Magee J.C., Cook E.P. Somatic EPSP amplitude is independent of synapse location in hippocampal pyramidal neurons. Nat. Neurosci. 2000, 3:895-903.
109. Mainen Z.F., Sejnowski T.J. Influence of dendritic structure on firing pattern in model neocortical neurons. Nature 1996, 382:363-366.
110. Margrie T.W., Schaefer A.T. Theta oscillation coupled spike latencies yield computational vigour in a mammalian sensory system. J. Physiol. 2003, 546:363-374.
111. Markram H. The blue brain project. Nat. Rev. Neurosci. 2006, 7:153-160.
112. Markram H., Lübke J., Frotscher M., Roth A., Sakmann B. Physiology and anatomy of synaptic connections between thick tufted pyramidal neurones in the developing rat neocortex. J. Physiol. 1997, 500:409-440.
113. Martone M.E., Tran J., Wong W.W., Sargis J., Fong L., Larson S., Lamont S.P., Gupta A., Ellisman M.H. The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. J. Struct. Biol. 2008, 161:220-231.
114. Mattioni M., Cohen U., Le Novère N. Neuronvisio: a graphical user interface with 3D capabilities for NEURON. Front. Neuroinform. 2012, 6:20.
115. McIntyre C.C., Grill W.M. Extracellular stimulation of central neurons: influence of stimulus waveform and frequency on neuronal output. J. Neurophysiol. 2002, 88:1592-1604.
116. McIntyre C.C., Grill W.M., Sherman D.L., Thakor N.V. Cellular effects of deep brain stimulation: model-based analysis of activation and inhibition. J. Neurophysiol. 2004, 91:1457-1469.
117. Meijering E. Neuron tracing in perspective. Cytometry A 2010, 77:693-704.
118. Meijering E., Jacob M., Sarria J.-C.F., Steiner P., Hirling H., Unser M. Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. Cytometry A 2004, 58:167-176.
119. Meyer A.H., Katona I., Blatow M., Rozov A., Monyer H. In vivo labeling of parvalbumin-positive interneurons and analysis of electrical coupling in identified neurons. J. Neurosci. 2002, 22:7055-7064.
120. Michaelsen K., Murk K., Zagrebelsky M., Dreznjak A., Jockusch B.M., Rothkegel M., Korte M. Fine-tuning of neuronal architecture requires two profilin isoforms. Proc. Natl. Acad. Sci. USA 2010, 107:15780-15785.
121. Micheva K.D., Smith S.J. Array tomography: a new tool for imaging the molecular architecture and ultrastructure of neural circuits. Neuron 2007, 55:25-36.
122. Mukamel E.A., Nimmerjahn A., Schnitzer M.J. Automated analysis of cellular signals from large-scale calcium imaging data. Neuron 2009, 63:747-760.
123. Myatt D.R., Hadlington T., Ascoli G.A., Nasuto S.J. Neuromantic - from semi-manual to semi-automatic reconstruction of neuron morphology. Front. Neuroinform. 2012, 6:4.
124. Narro M.L., Yang F., Kraft R., Wenk C., Efrat A., Restifo L.L. NeuronMetrics: software for semi-automated processing of cultured neuron images. Brain Res. 2007, 1138:57-75.
125. Nolte C., Matyash M., Pivneva T., Schipke C.G., Ohlemeyer C., Hanisch U.-K., Kirchhoff F., Kettenmann H. GFAP promoter-controlled EGFP-expressing transgenic mice: a tool to visualize astrocytes and astrogliosis in living brain tissue. Glia 2001, 33:72-86.
126. Oberlaender M., de Kock C.P., Bruno R.M., Ramirez A., Meyer H.S., Dercksen V.J., Helmstaedter M., Sakmann B. Cell-type specific three-dimensional structure of thalamocortical circuits in a column of rat vibrissal cortex. Cereb. Cortex 2012, 22:2375-2391.
127. Packer A.M., Yuste R. Dense, unspecific connectivity of neocortical parvalbumin-positive interneurons: a canonical microcircuit for inhibition?. J. Neurosci. 2011, 31:13260-13271.
128. Peng Y.R., He S., Marie H., Zeng S.Y., Ma J., Tan Z.J., Lee S.Y., Malenka R.C., Yu X. Coordinated changes in dendritic arborization and synaptic strength during neural circuit development. Neuron 2009, 61:71-84.
129. Peng H., Ruan Z., Long F., Simpson J.H., Myers E.W. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nat. Biotechnol. 2010, 28:348-353.
130. Peng H., Long F., Myers G. Automatic 3D neuron tracing using all-path pruning. Bioinformatics 2011, 27:i239-i247.
131. Perez-Rosello T., Baker J.L., Ferrante M., Iyengar S., Ascoli G.A., Barrionuevo G. Passive and active shaping of unitary responses from associational/commissural and perforant path synapses in hippocampal CA3 pyramidal cells. J. Comput. Neurosci. 2011, 31:159-182.
132. Poirazi P., Brannon T., Mel B.W. Arithmetic of subthreshold synaptic summation in a model CA1 pyramidal cell. Neuron 2003, 37:977-987.
133. Pool M., Thiemann J., Bar-Or A., Fournier A.E. NeuriteTracer: a novel ImageJ plugin for automated quantification of neurite outgrowth. J. Neurosci. Methods 2008, 168:134-139.
134. Poolos N.P., Migliore M., Johnston D. Pharmacological upregulation of h-channels reduces the excitability of pyramidal neuron dendrites. Nat. Neurosci. 2002, 5:767-774.
135. Ray S., Bhalla U.S. PyMOOSE: Interoperable scripting in Python for MOOSE. Front. Neuroinform. 2008, 2:6.
136. Reiner A., Veenman C.L., Medina L., Jiao Y., Del Mar N., Honig M.G. Pathway tracing using biotinylated dextran amines. J. Neurosci. Methods 2000, 103:23-37.
137. Rodriguez A., Ehlenberger D.B., Kelliher K.T., Einstein M., Henderson S.C., Morrison J.H., Hof P.R., Wearne S.L. Automated reconstruction of three-dimensional neuronal morphology from laser scanning microscopy images. Methods 2003, 30:94-105.
138. Ropireddy D., Ascoli G.A. Potential synaptic connectivity of different neurons onto pyramidal cells in a 3D reconstruction of the rat hippocampus. Front. Neuroinform. 2011, 5:5.
139. Ropireddy D., Bachus S.E., Ascoli G.A. Non-homogeneous stereological properties of the rat hippocampus from high-resolution 3D serial reconstruction of thin histological sections. Neuroscience 2012, 205:91-111.
140. Roysam B., Shain W., Ascoli G.A. The central role of neuroinformatics in the National Academy of Engineering's grandest challenge: reverse engineer the brain. Neuroinformatics 2009, 7:1-5.
141. Rust M.J., Bates M., Zhuang X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 2006, 3:793-795.
142. Rybak J., Kuß A., Lamecker H., Zachow S., Hege H.C., Lienhard M., Singer J., Neubert K., Menzel R. The digital bee brain: integrating and managing neurons in a common 3D reference system. Front Syst. Neurosci. 2010, 4:30.
143. Sah P., Bekkers J.M. Apical dendritic location of slow afterhyperpolarization current in hippocampal pyramidal neurons: implications for the integration of long-term potentiation. J. Neurosci. 1996, 16:4537-4542.
144. Samsonovich A.V., Ascoli G.A. Statistical determinants of dendritic morphology in hippocampal pyramidal neurons: A hidden Markov model. Hippocampus 2005, 15:166-183.
145. Sasaki T., Matsuki N., Ikegaya Y. Effects of axonal topology on the somatic modulation of synaptic outputs. J. Neurosci. 2012, 32:2868-2876.
146. Schiller J., Major G., Koester H.J., Schiller Y. NMDA spikes in basal dendrites of cortical pyramidal neurons. Nature 2000, 404:285-289.
147. Schneider C.A., Rasband W.S., Eliceiri K.W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 2012, 9:671-675.
148. Scorcioni R., Polavaram S., Ascoli G.A. L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies. Nat. Protoc. 2008, 3:866-876.
149. Seidl A.H., Rubel E.W., Harris D.M. Mechanisms for adjusting interaural time differences to achieve binaural coincidence detection. J. Neurosci. 2010, 30:70-80.
150. Senft S.L. A brief history of neuronal reconstruction. Neuroinformatics 2011, 9:119-128.
151. Silberberg G., Markram H. Disynaptic inhibition between neocortical pyramidal cells mediated by Martinotti cells. Neuron 2007, 53:735-746.
152. Smith R.G. NeuronC: a computational language for investigating functional architecture of neural circuits. J. Neurosci. Methods 1992, 43:83-108.
153. Snider J., Pillai A., Stevens C.F. A universal property of axonal and dendritic arbors. Neuron 2010, 66:45-56.
154. Softky W.R., Koch C. The highly irregular firing of cortical cells is inconsistent with temporal integration of random EPSPs. J. Neurosci. 1993, 13:334-350.
155. Solinas S.M., Maex R., De Schutter E. Dendritic amplification of inhibitory postsynaptic potentials in a model Purkinje cell. Eur. J. Neurosci. 2006, 23:1207-1218.
156. Spruston N. Pyramidal neurons: dendritic structure and synaptic integration. Nat. Rev. Neurosci. 2008, 9:206-221.
157. Spruston N., Jaffe D.B., Johnston D. Dendritic attenuation of synaptic potentials and currents: the role of passive membrane properties. Trends Neurosci. 1994, 17:161-166.
158. Stepanyants A., Chklovskii D.B. Neurogeometry and potential synaptic connectivity. Trends Neurosci. 2005, 28:387-394.
159. Stepanyants A., Hof P.R., Chklovskii D.B. Geometry and structural plasticity of synaptic connectivity. Neuron 2002, 34:275-288.
160. Stepanyants A., Hirsch J.A., Martinez L.M., Kisvárday Z.F., Ferecskó A.S., Chklovskii D.B. Local potential connectivity in cat primary visual cortex. Cereb. Cortex 2008, 18:13-28.
161. Stuart G.J., Häusser M. Dendritic coincidence detection of EPSPs and action potentials. Nat. Neurosci. 2001, 4:63-71.
162. Sulkowski M.J., Iyer S.C., Kurosawa M.S., Iyer E.P., Cox D.N. Turtle functions downstream of Cut in differentially regulating class specific dendrite morphogenesis in Drosophila. PLoS ONE 2011, 6:e22611.
163. Svoboda K. The past, present, and future of single neuron reconstruction. Neuroinformatics 2011, 9:97-98.
164. Teeter C.M., Stevens C.F. A general principle of neural arbor branch density. Curr. Biol. 2011, 21:2105-2108.
165. Teschemacher A.G., Paton J.F.R., Kasparov S. Imaging living central neurones using viral gene transfer. Adv. Drug Deliv. Rev. 2005, 57:79-93.
166. Traynelis S.F., Silver R.A., Cull-Candy S.G. Estimated conductance of glutamate receptor channels activated during EPSCs at the cerebellar mossy fiber-granule cell synapse. Neuron 1993, 11:279-289.
167. Trojanowski J.Q., Gonatas J.O., Gonatas N.K. Horseradish peroxidase (HRP) conjugates of cholera toxin and lectins are more sensitive retrogradely transported markers than free HRP. Brain Res. 1982, 231:33-50.
168. Troyer T.W., Levin J.E., Jacobs G.A. Construction and analysis of a database representing a neural map. Microsc. Res. Tech. 1994, 29:329-343.
169. Ugolini G. Advances in viral transneuronal tracing. J. Neurosci. Methods 2010, 194:2-20.
170. van Ooyen A. Using theoretical models to analyse neural development. Nat. Rev. Neurosci. 2011, 12:311-326.
171. Vyas A., Jadhav S., Chattarji S. Prolonged behavioral stress enhances synaptic connectivity in the basolateral amygdala. Neuroscience 2006, 143:387-393.
172. Wang Y., Narayanaswamy A., Tsai C.L., Roysam B. A broadly applicable 3-D neuron tracing method based on open-curve snake. Neuroinformatics 2011, 9:193-217.
173. Wann D.F., Woolsey T.A., Dierker M.L., Cowan W.M. An on-line digital-computer system for the semiautomatic analysis of Golgi-impregnated neurons. IEEE Trans. Biomed. Eng. 1973, 20:233-247.
174. Watanabe S., Hoffman D.A., Migliore M., Johnston D. Dendritic K+ channels contribute to spike-timing dependent long-term potentiation in hippocampal pyramidal neurons. Proc. Natl. Acad. Sci. USA 2002, 99:8366-8371.
175. Wearne S.L., Rodriguez A., Ehlenberger D.B., Rocher A.B., Henderson S.C., Hof P.R. New techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales. Neuroscience 2005, 136:661-680.
176. Wei H., El Jundi B., Homberg U., Stengl M. Implementation of pigment-dispersing factor-immunoreactive neurons in a standardized atlas of the brain of the cockroach Leucophaea maderae. J. Comp. Neurol. 2010, 518:4113-4133.
177. Wen Q., Chklovskii D.B. A cost-benefit analysis of neuronal morphology. J. Neurophysiol. 2008, 99:2320-2328.
178. Wilson T. Trends in confocal microscopy. Trends Neurosci. 1989, 12:486-493.
179. Wolf E., Birinyi A., Pomahazi S. A fast 3-dimensional neuronal tree reconstruction system that uses cubic polynomials to estimate dendritic curvature. J. Neurosci. Methods 1995, 63:137-145.
180. Yabuta N.H., Callaway E.M. Functional streams and local connections of layer 4C neurons in primary visual cortex of the macaque monkey. J. Neurosci. 1998, 18:9489-9499.
181. Zador A.M., Dubnau J., Oyibo H.K., Zhan H., Cao G., Peikon I.D. Sequencing the connectome. PLoS Biol. 2012, 10:e1001411.
182. Zubler F., Douglas R. A framework for modeling the growth and development of neurons and networks. Front Comput Neurosci 2009, 3:25.