Citations for Neuronal morphology goes digital ... (Parekh & Ascoli 2013)

Legends: Link to a Model Reference cited by multiple papers


Parekh R, Ascoli GA (2013) Neuronal morphology goes digital: a research hub for cellular and system neuroscience. Neuron 77:1017-38 [PubMed]

References and models cited by this paper

References and models that cite this paper

Abbott A, Schiermeier Q (2013) Research prize boost for Europe. Nature 493:585-6 [Journal] [PubMed]
Alle H, Roth A, Geiger JR (2009) Energy-efficient action potentials in hippocampal mossy fibers. Science 325:1405-8 [Journal] [PubMed]
  • Action potential reconstitution from measured current waveforms (Alle et al. 2009) [Model]
Andjelic S, Gallopin T, Cauli B, Hill EL, Roux L, Badr S, Hu E, Tamás G, Lambolez B (2009) Glutamatergic nonpyramidal neurons from neocortical layer VI and their comparison with pyramidal and spiny stellate neurons. J Neurophysiol 101:641-54 [Journal] [PubMed]
Ascoli GA (2002) Computational neuroanatomy: Principles and methods, Ascoli GA, ed.
Ascoli GA (2006) Mobilizing the base of neuroscience data: the case of neuronal morphologies. Nat Rev Neurosci 7:318-24 [Journal] [PubMed]
Ascoli GA (2007) Successes and rewards in sharing digital reconstructions of neuronal morphology. Neuroinformatics 5:154-60 [PubMed]
Ascoli GA, Krichmar JL, Scorcioni R, Nasuto SJ, Senft SL (2001) Computer generation and quantitative morphometric analysis of virtual neurons. Anat Embryol (Berl) 204:283-301 [PubMed]
Atunes G, Simones-de-souza FM, Roque AC (2003) Sensitivity of AMPA receptor channel to calcium oscillations: a computational study. Neurocomputing 52-54:341-346
Bartos M, Vida I, Frotscher M, Meyer A, Monyer H, Geiger JR, Jonas P (2002) Fast synaptic inhibition promotes synchronized gamma oscillations in hippocampal interneuron networks. Proc Natl Acad Sci U S A 99:13222-7 [Journal] [PubMed]
  • Gamma oscillations in hippocampal interneuron networks (Bartos et al 2002) [Model]
Billeci L, Magliaro C, Pioggia G, Ahluwalia A (2013) NEuronMOrphological analysis tool: open-source software for quantitative morphometrics. Front Neuroinform 7:2 [Journal] [PubMed]
Borg-Graham LJ (2000) Additional efficient computation of branched nerve equations: adaptive time step and ideal voltage clamp. J Comput Neurosci 8:209-26 [PubMed]
Bower JM, Beeman D (1998) The Book Of Genesis: Exploring Realistic Neural Models With The General Neural Simulation System
Brecht M, Roth A, Sakmann B (2003) Dynamic receptive fields of reconstructed pyramidal cells in layers 3 and 2 of rat somatosensory barrel cortex. J Physiol 553:243-65 [Journal] [PubMed]
Broser PJ, Schulte R, Lang S, Roth A, Helmchen F, Waters J, Sakmann B, Wittum G (2004) Nonlinear anisotropic diffusion filtering of three-dimensional image data from two-photon microscopy. J Biomed Opt 9:1253-64 [Journal] [PubMed]
Brown KM, Barrionuevo G, Canty AJ, De Paola V, Hirsch JA, Jefferis GS, Lu J, Snippe M, Sugihara I, Ascoli GA (2011) The DIADEM data sets: representative light microscopy images of neuronal morphology to advance automation of digital reconstructions. Neuroinformatics 9:143-57 [Journal] [PubMed]
Brown KM, Donohue DE, D'Alessandro G, Ascoli GA (2005) A cross-platform freeware tool for digital reconstruction of neuronal arborizations from image stacks. Neuroinformatics 3:343-60 [Journal] [PubMed]
Bui TV, Cushing S, Dewey D, Fyffe RE, Rose PK (2003) Comparison of the morphological and electrotonic properties of Renshaw cells, Ia inhibitory interneurons, and motoneurons in the cat. J Neurophysiol 90:2900-18 [Journal] [PubMed]
Buonomano DV (2000) Decoding temporal information: A model based on short-term synaptic plasticity. J Neurosci 20:1129-41 [PubMed]
Cannon RC, Hasselmo ME, Koene RA (2003) From biophysics to behavior: Catacomb2 and the design of biologically-plausible models for spatial navigation. Neuroinformatics 1:3-42 [Journal] [PubMed]
  • Biologically-plausible models for spatial navigation (Cannon et al 2003) [Model]
Cannon RC, O'Donnell C, Nolan MF (2010) Stochastic ion channel gating in dendritic neurons: morphology dependence and probabilistic synaptic activation of dendritic spikes. PLoS Comput Biol [Journal] [PubMed]
  • Stochastic ion channels and neuronal morphology (Cannon et al. 2010) [Model]
Cannon RC, Turner DA, Pyapali GK, Wheal HV (1998) An on-line archive of reconstructed hippocampal neurons. J Neurosci Methods 84:49-54 [PubMed]
Capowski JJ (1977) Computer-aided reconstruction of neuron trees from several serial sections. Comput Biomed Res 10:617-29 [PubMed]
Cauller LJ, Connors BW (1994) Synaptic physiology of horizontal afferents to layer I in slices of rat SI neocortex. J Neurosci 14:751-62 [PubMed]
Chen K, Aradi I, Thon N, Eghbal-Ahmadi M, Baram TZ, Soltesz I (2001) Persistently modified h-channels after complex febrile seizures convert the seizure-induced enhancement of inhibition to hyperexcitability. Nat Med 7:331-7 [Journal] [PubMed]
  • Febrile seizure-induced modifications to Ih (Chen et al 2001) [Model]
Chmykhova NM, Adanina VO, Karamian OA, Kozhanov VM, Vesselkin NP, Clamann HP (2005) Comparative study of spinal motoneuron axon collaterals. Brain Res Bull 66:381-6 [Journal] [PubMed]
Costa Lda F, Zawadzki K, Miazaki M, Viana MP, Taraskin SN (2010) Unveiling the neuromorphological space. Front Comput Neurosci 4:150 [Journal] [PubMed]
Crook S, Gleeson P, Howell F, Svitak J, Silver RA (2007) MorphML: level 1 of the NeuroML standards for neuronal morphology data and model specification. Neuroinformatics 5:96-104 [PubMed]
Cuntz H, Forstner F, Borst A, Häusser M (2011) The TREES toolbox--probing the basis of axonal and dendritic branching. Neuroinformatics 9:91-6 [Journal] [PubMed]
Cuntz H, Forstner F, Haag J, Borst A (2008) The morphological identity of insect dendrites. PLoS Comput Biol 4:e1000251 [Journal] [PubMed]
Cutsuridis V, Cobb S, Graham BP (2010) Encoding and retrieval in a model of the hippocampal CA1 microcircuit. Hippocampus 20:423-46 [Journal] [PubMed]
  • Encoding and retrieval in a model of the hippocampal CA1 microcircuit (Cutsuridis et al. 2009) [Model]
DeFelipe J (2010) From the connectome to the synaptome: an epic love story. Science 330:1198-201 [Journal] [PubMed]
Denk W, Strickler JH, Webb WW (1990) Two-photon laser scanning fluorescence microscopy. Science 248:73-6 [PubMed]
Denk W, Svoboda K (1997) Photon upmanship: why multiphoton imaging is more than a gimmick. Neuron 18:351-7 [PubMed]
DiGregorio DA, Nusser Z, Silver RA (2002) Spillover of glutamate onto synaptic AMPA receptors enhances fast transmission at a cerebellar synapse. Neuron 35:521-33 [PubMed]
Dityatev AE, Chmykhova NM, Dityateva GV, Babalian AL, Kleinle J, Clamann HP (2001) Structural and physiological properties of connections between individual reticulospinal axons and lumbar motoneurons of the frog. J Comp Neurol 430:433-47 [PubMed]
Donohue DE, Ascoli GA (2011) Automated reconstruction of neuronal morphology: an overview. Brain Res Rev 67:94-102 [Journal] [PubMed]
Eberhard JP, Wanner A, Wittum G (2006) NeuGen: a tool for the generation of realistic morphology of cortical neurons and neural networks in 3D Neurocomputing 70:327-342 [Journal]
Escobar G, Fares T, Stepanyants A (2008) Structural plasticity of circuits in cortical neuropil. J Neurosci 28:8477-88 [Journal] [PubMed]
Eyre MD, Antal M, Nusser Z (2008) Distinct deep short-axon cell subtypes of the main olfactory bulb provide novel intrabulbar and extrabulbar GABAergic connections. J Neurosci 28:8217-29 [Journal] [PubMed]
Feldmeyer D, Egger V, Lubke J, Sakmann B (1999) Reliable synaptic connections between pairs of excitatory layer 4 neurones within a single 'barrel' of developing rat somatosensory cortex. J Physiol 521 Pt 1:169-90 [PubMed]
Feldmeyer D, Roth A, Sakmann B (2005) 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 25:3423-31 [Journal] [PubMed]
Ferrante M, Blackwell KT, Migliore M, Ascoli GA (2008) Computational models of neuronal biophysics and the characterization of potential neuropharmacological targets. Curr Med Chem 15:2456-71 [PubMed]
  • Computational neuropharmacology of CA1 pyramidal neuron (Ferrante et al. 2008) [Model]
Ferrante M, Migliore M, Ascoli GA (2009) Feed-forward inhibition as a buffer of the neuronal input-output relation. Proc Natl Acad Sci U S A 106:18004-9 [Journal] [PubMed]
  • Dentate Gyrus Feed-forward inhibition (Ferrante et al. 2009) [Model]
Franco A, Knafo S, Banon-Rodriguez I, Merino-Serrais P, Fernaud-Espinosa I, Nieto M, Garrido JJ, Esteban JA, Wandosell F, Anton IM (2012) WIP is a negative regulator of neuronal maturation and synaptic activity. Cereb Cortex 22:1191-202 [Journal] [PubMed]
Fransén E, Alonso AA, Dickson CT, Magistretti J, Hasselmo ME (2004) Ionic mechanisms in the generation of subthreshold oscillations and action potential clustering in entorhinal layer II stellate neurons. Hippocampus 14:368-84 [Journal] [PubMed]
Frick A, Feldmeyer D, Helmstaedter M, Sakmann B (2008) Monosynaptic connections between pairs of L5A pyramidal neurons in columns of juvenile rat somatosensory cortex. Cereb Cortex 18:397-406 [Journal] [PubMed]
Gan WB, Grutzendler J, Wong WT, Wong RO, Lichtman JW (2000) Multicolor "DiOlistic" labeling of the nervous system using lipophilic dye combinations. Neuron 27:219-25 [PubMed]
Gasparini S, Migliore M, Magee JC (2004) On the initiation and propagation of dendritic spikes in CA1 pyramidal neurons. J Neurosci 24:11046-56 [Journal] [PubMed]
  • CA1 pyramidal neuron: dendritic spike initiation (Gasparini et al 2004) [Model]
Gerhard F, Pipa G, Lima B, Neuenschwander S, Gerstner W (2011) Extraction of Network Topology From Multi-Electrode Recordings: Is there a Small-World Effect? Front Comput Neurosci 5:4 [Journal] [PubMed]
Gillette TA, Brown KM, Ascoli GA (2011) The DIADEM metric: comparing multiple reconstructions of the same neuron. Neuroinformatics 9:233-45 [Journal] [PubMed]
GLASER EM, VANDERLOOS H (1965) A SEMI-AUTOMATIC COMPUTER-MICROSCOPE FOR THE ANALYSIS OF NEURONAL MORPHOLOGY. IEEE Trans Biomed Eng 12:22-31 [PubMed]
Glaser JR, Glaser EM (1990) Neuron imaging with Neurolucida--a PC-based system for image combining microscopy. Comput Med Imaging Graph 14:307-17 [PubMed]
Gleeson P, Steuber V, Silver RA (2007) neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron 54:219-35 [Journal] [PubMed]
Goodman DF (2010) Code generation: a strategy for neural network simulators. Neuroinformatics 8:183-96 [Journal] [PubMed]
Gulledge AT, Stuart GJ (2003) Excitatory actions of GABA in the cortex. Neuron 37:299-309 [PubMed]
Gustafsson MG (2005) Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc Natl Acad Sci U S A 102:13081-6 [Journal] [PubMed]
Hadjieconomou D, Rotkopf S, Alexandre C, Bell DM, Dickson BJ, Salecker I (2011) Flybow: genetic multicolor cell labeling for neural circuit analysis in Drosophila melanogaster. Nat Methods 8:260-6 [Journal] [PubMed]
Halavi M, Hamilton KA, Parekh R, Ascoli GA (2012) Digital reconstructions of neuronal morphology: three decades of research trends. Front Neurosci 6:49 [Journal] [PubMed]
Hall DH, Treinin M (2011) How does morphology relate to function in sensory arbors? Trends Neurosci 34:443-51 [Journal] [PubMed]
Hampel S, Chung P, McKellar CE, Hall D, Looger LL, Simpson JH (2011) Drosophila Brainbow: a recombinase-based fluorescence labeling technique to subdivide neural expression patterns. Nat Methods 8:253-9 [Journal] [PubMed]
Harris E, Stewart M (2001) Propagation of synchronous epileptiform events from subiculum backward into area CA1 of rat brain slices. Brain Res 895:41-9 [PubMed]
Häusser M, Major G, Stuart GJ (2001) Differential shunting of EPSPs by action potentials. Science 291:138-41 [Journal] [PubMed]
Hayes TL, Lewis DA (1996) Magnopyramidal neurons in the anterior motor speech region. Dendritic features and interhemispheric comparisons. Arch Neurol 53:1277-83 [PubMed]
He HY, Cline HT (2011) Diadem X: automated 4 dimensional analysis of morphological data. Neuroinformatics 9:107-12 [Journal] [PubMed]
Hess ST, Girirajan TP, Mason MD (2006) Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 91:4258-72 [Journal] [PubMed]
Hill SL, Wang Y, Riachi I, Schürmann F, Markram H (2012) Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits. Proc Natl Acad Sci U S A 109:E2885-94 [Journal] [PubMed]
Hines ML, Carnevale NT (1997) The NEURON simulation environment. Neural Comput 9:1179-209 [PubMed]
Hoffman DA, Magee JC, Colbert CM, Johnston D (1997) K+ channel regulation of signal propagation in dendrites of hippocampal pyramidal neurons. Nature 387:869-75 [Journal] [PubMed]
Huang B, Babcock H, Zhuang X (2010) Breaking the diffraction barrier: super-resolution imaging of cells. Cell 143:1047-58 [Journal] [PubMed]
Ikeno H, Kanzaki R, Aonuma H, Takahata M, Mizunami M, Yasuyama K, Matsui N, Yokohari F, Usui (2008) Development of Invertebrate Brain Platform: management of research resources for invertebrate neuroscience and neuroethology Neural Information Processing, Ishikawa M:Doya K:Miyamoto H:Yamakawa T, ed. pp.905
Jefferis GS, Potter CJ, Chan AM, Marin EC, Rohlfing T, Maurer CR, Luo L (2007) Comprehensive maps of Drosophila higher olfactory centers: spatially segregated fruit and pheromone representation. Cell 128:1187-203 [Journal] [PubMed]
Jungblut D, Vlachos A, Schuldt G, Zahn N, Deller T, Wittum G (2012) SpineLab: tool for three-dimensional reconstruction of neuronal cell morphology. J Biomed Opt 17:076007 [Journal] [PubMed]
Kim HG, Connors BW (1993) Apical dendrites of the neocortex: correlation between sodium- and calcium-dependent spiking and pyramidal cell morphology. J Neurosci 13:5301-11 [PubMed]
Kim J, Zhao T, Petralia RS, Yu Y, Peng H, Myers E, Magee JC (2012) mGRASP enables mapping mammalian synaptic connectivity with light microscopy. Nat Methods 9:96-102
Kita H, Armstrong W (1991) A biotin-containing compound N-(2-aminoethyl)biotinamide for intracellular labeling and neuronal tracing studies: comparison with biocytin. J Neurosci Methods 37:141-50 [PubMed]
Klar TA, Hell SW (1999) Subdiffraction resolution in far-field fluorescence microscopy. Opt Lett 24:954-6 [PubMed]
Köbbert C, Apps R, Bechmann I, Lanciego JL, Mey J, Thanos S (2000) Current concepts in neuroanatomical tracing. Prog Neurobiol 62:327-51 [PubMed]
Koene RA, Tijms B, van Hees P, Postma F, de Ridder A, Ramakers GJ, van Pelt J, van Ooyen A (2009) NETMORPH: a framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies. Neuroinformatics 7:195-210 [Journal] [PubMed]
  • NETMORPH: creates NNs with realistic neuron morphologies (Koene et al. 2009, van Ooyen et al. 2014) [Model]
Koh IY, Lindquist WB, Zito K, Nimchinsky EA, Svoboda K (2002) An image analysis algorithm for dendritic spines. Neural Comput 14:1283-310 [Journal] [PubMed]
Kole MH, Ilschner SU, Kampa BM, Williams SR, Ruben PC, Stuart GJ (2008) Action potential generation requires a high sodium channel density in the axon initial segment. Nat Neurosci 11:178-86 [Journal] [PubMed]
  • Na+ channel dependence of AP initiation in cortical pyramidal neuron (Kole et al. 2008) [Model]
Krichmar JL, Nasuto SJ, Scorcioni R, Washington SD, Ascoli GA (2002) Effects of dendritic morphology on CA3 pyramidal cell electrophysiology: a simulation study. Brain Res 941:11-28 [PubMed]
Kvello P, Løfaldli BB, Rybak J, Menzel R, Mustaparta H (2009) Digital, Three-dimensional Average Shaped Atlas of the Heliothis Virescens Brain with Integrated Gustatory and Olfactory Neurons. Front Syst Neurosci 3:14 [Journal] [PubMed]
Lakadamyali M, Babcock H, Bates M, Zhuang X, Lichtman J (2012) 3D multicolor super-resolution imaging offers improved accuracy in neuron tracing. PLoS One 7:e30826 [Journal] [PubMed]
Lanciego JL, Wouterlood FG (2011) A half century of experimental neuroanatomical tracing. J Chem Neuroanat 42:157-83 [Journal] [PubMed]
Lavis LD (2011) Histochemistry: live and in color. J Histochem Cytochem 59:139-45 [Journal] [PubMed]
Le Magueresse C, Alfonso J, Khodosevich K, Arroyo Martín AA, Bark C, Monyer H (2011) "Small axonless neurons": postnatally generated neocortical interneurons with delayed functional maturation. J Neurosci 31:16731-47 [Journal] [PubMed]
Lee PC, Chuang CC, Chiang AS, Ching YT (2012) High-throughput computer method for 3D neuronal structure reconstruction from the image stack of the Drosophila brain and its applications. PLoS Comput Biol 8:e1002658 [Journal] [PubMed]
Lee PC, He HY, Lin CY, Ching YT, Cline HT (2013) Computer Aided Alignment and Quantitative 4D Structural Plasticity Analysis of Neurons. Neuroinformatics 37: -50
Lee TC, Kashyap RL, Chu CN (1994) Building skeleton models via 3-D medial surface-axis thinning algorithms Comput Vis Graph Image Process 56:462-478
Lemmens MA, Steinbusch HW, Rutten BP, Schmitz C (2010) Advanced microscopy techniques for quantitative analysis in neuromorphology and neuropathology research: current status and requirements for the future. J Chem Neuroanat 40:199-209 [Journal] [PubMed]
Levinthal C, Ware R (1972) Three dimensional reconstruction from serial sections Nature 238:207-210
Lichtman JW, Livet J, Sanes JR (2008) A technicolour approach to the connectome. Nat Rev Neurosci 9:417-22 [Journal] [PubMed]
Liu JK (2011) Learning rule of homeostatic synaptic scaling: presynaptic dependent or not. Neural Comput 23:3145-61 [Journal] [PubMed]
Livet J, Weissman TA, Kang H, Draft RW, Lu J, Bennis RA, Sanes JR, Lichtman JW (2007) Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450:56-62 [Journal] [PubMed]
Longair MH, Baker DA, Armstrong JD (2011) Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes. Bioinformatics 27:2453-4 [Journal] [PubMed]
López-Cruz PL, Bielza C, Larrañaga P, Benavides-Piccione R, DeFelipe J (2011) Models and simulation of 3D neuronal dendritic trees using Bayesian networks. Neuroinformatics 9:347-69 [Journal] [PubMed]
Losavio BE, Liang Y, Santamaría-Pang A, Kakadiaris IA, Colbert CM, Saggau P (2008) Live neuron morphology automatically reconstructed from multiphoton and confocal imaging data. J Neurophysiol 100:2422-9 [Journal] [PubMed]
Luisi J, Narayanaswamy A, Galbreath Z, Roysam B (2011) The FARSIGHT trace editor: an open source tool for 3-D inspection and efficient pattern analysis aided editing of automated neuronal reconstructions. Neuroinformatics 9:305-15 [Journal] [PubMed]
Lytton WW, Sejnowski TJ (1991) Simulations of cortical pyramidal neurons synchronized by inhibitory interneurons. J Neurophysiol 66:1059-79 [Journal] [PubMed]
Macagno ER, Levinthal C, Sobel I (1979) Three-dimensional computer reconstruction of neurons and neuronal assemblies. Annu Rev Biophys Bioeng 8:323-51 [Journal] [PubMed]
Magariños AM, McEwen BS, Saboureau M, Pevet P (2006) Rapid and reversible changes in intrahippocampal connectivity during the course of hibernation in European hamsters. Proc Natl Acad Sci U S A 103:18775-80 [Journal] [PubMed]
Magee JC, Cook EP (2000) Somatic EPSP amplitude is independent of synapse location in hippocampal pyramidal neurons. Nat Neurosci 3:895-903 [Journal] [PubMed]
  • CA1 pyramidal neuron: Synaptic Scaling (Magee, Cook 2000) [Model]
Mainen ZF, Sejnowski TJ (1996) Influence of dendritic structure on firing pattern in model neocortical neurons. Nature 382:363-6 [Journal] [PubMed]
  • Influence of dendritic structure on neocortical neuron firing patterns (Mainen and Sejnowski 1996) [Model]
Margrie TW, Schaefer AT (2003) Theta oscillation coupled spike latencies yield computational vigour in a mammalian sensory system. J Physiol 546:363-74 [PubMed]
Markram H (2006) The blue brain project. Nat Rev Neurosci 7:153-60 [Journal] [PubMed]
Markram H, Lübke J, Frotscher M, Roth A, Sakmann B (1997) Physiology and anatomy of synaptic connections between thick tufted pyramidal neurones in the developing rat neocortex. J Physiol 500 ( Pt 2):409-40 [PubMed]
Martone ME, Tran J, Wong WW, Sargis J, Fong L, Larson S, Lamont SP, Gupta A, Ellisman MH (2008) The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. J Struct Biol 161:220-31 [Journal] [PubMed]
Mattioni M, Cohen U, Le Novère N (2012) Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON. Front Neuroinform 6:20 [Journal] [PubMed]
  • Neuronvisio: a gui with 3D capabilities for NEURON (Mattioni et al. 2012) [Model]
McIntyre CC, Grill WM (2002) Extracellular stimulation of central neurons: influence of stimulus waveform and frequency on neuronal output. J Neurophysiol 88:1592-604 [Journal] [PubMed]
McIntyre CC, Grill WM, Sherman DL, Thakor NV (2004) Cellular effects of deep brain stimulation: model-based analysis of activation and inhibition. J Neurophysiol 91:1457-69 [Journal] [PubMed]
Meijering E (2010) Neuron tracing in perspective. Cytometry A 77:693-704 [Journal] [PubMed]
Meijering E, Jacob M, Sarria JC, Steiner P, Hirling H, Unser M (2004) Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. Cytometry A 58:167-76 [Journal] [PubMed]
Meyer AH, Katona I, Blatow M, Rozov A, Monyer H (2002) In vivo labeling of parvalbumin-positive interneurons and analysis of electrical coupling in identified neurons. J Neurosci 22:7055-64 [Journal] [PubMed]
Michaelsen K, Murk K, Zagrebelsky M, Dreznjak A, Jockusch BM, Rothkegel M, Korte M (2010) Fine-tuning of neuronal architecture requires two profilin isoforms. Proc Natl Acad Sci U S A 107:15780-5 [Journal] [PubMed]
Micheva KD, Smith SJ (2007) Array tomography: a new tool for imaging the molecular architecture and ultrastructure of neural circuits. Neuron 55:25-36 [Journal] [PubMed]
Mukamel EA, Nimmerjahn A, Schnitzer MJ (2009) Automated analysis of cellular signals from large-scale calcium imaging data. Neuron 63:747-60 [Journal] [PubMed]
Myatt DR, Hadlington T, Ascoli GA, Nasuto SJ (2012) Neuromantic - from semi-manual to semi-automatic reconstruction of neuron morphology. Front Neuroinform 6:4 [Journal] [PubMed]
Narro ML, Yang F, Kraft R, Wenk C, Efrat A, Restifo LL (2007) NeuronMetrics: software for semi-automated processing of cultured neuron images. Brain Res 1138:57-75 [Journal] [PubMed]
Nolte C, Matyash M, Pivneva T, Schipke CG, Ohlemeyer C, Hanisch UK, Kirchhoff F, Kettenmann H (2001) GFAP promoter-controlled EGFP-expressing transgenic mice: a tool to visualize astrocytes and astrogliosis in living brain tissue. Glia 33:72-86 [PubMed]
Oberlaender M, de Kock CP, Bruno RM, Ramirez A, Meyer HS, Dercksen VJ, Helmstaedter M, Sakmann B (2012) Cell type-specific three-dimensional structure of thalamocortical circuits in a column of rat vibrissal cortex. Cereb Cortex 22:2375-91 [Journal] [PubMed]
Packer AM, Yuste R (2011) Dense, unspecific connectivity of neocortical parvalbumin-positive interneurons: a canonical microcircuit for inhibition? J Neurosci 31:13260-71 [Journal] [PubMed]
Peng H, Long F, Myers G (2011) Automatic 3D neuron tracing using all-path pruning. Bioinformatics 27:i239-47 [Journal] [PubMed]
Peng H, Ruan Z, Long F, Simpson JH, Myers EW (2010) V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nat Biotechnol 28:348-53 [Journal] [PubMed]
Peng YR, He S, Marie H, Zeng SY, Ma J, Tan ZJ, Lee SY, Malenka RC, Yu X (2009) Coordinated changes in dendritic arborization and synaptic strength during neural circuit development. Neuron 61:71-84 [Journal] [PubMed]
Perez-Rosello T, Baker JL, Ferrante M, Iyengar S, Ascoli GA, Barrionuevo G (2011) Passive and active shaping of unitary responses from associational/commissural and perforant path synapses in hippocampal CA3 pyramidal cells. J Comput Neurosci 31:159-82 [Journal] [PubMed]
Poirazi P, Brannon T, Mel BW (2003) Arithmetic of subthreshold synaptic summation in a model CA1 pyramidal cell. Neuron 37:977-87 [PubMed]
  • CA1 pyramidal neuron: as a 2-layer NN and subthreshold synaptic summation (Poirazi et al 2003) [Model]
Pool M, Thiemann J, Bar-Or A, Fournier AE (2008) NeuriteTracer: a novel ImageJ plugin for automated quantification of neurite outgrowth. J Neurosci Methods 168:134-9 [Journal] [PubMed]
Poolos NP, Migliore M, Johnston D (2002) Pharmacological upregulation of h-channels reduces the excitability of pyramidal neuron dendrites. Nat Neurosci 5:767-74 [Journal] [PubMed]
  • CA1 pyramidal neuron: effects of Lamotrigine on dendritic excitability (Poolos et al 2002) [Model]
Ray S, Bhalla US (2008) PyMOOSE: Interoperable Scripting in Python for MOOSE. Front Neuroinform 2:6 [Journal] [PubMed]
  • Moose/PyMOOSE: interoperable scripting in Python for MOOSE (Ray and Bhalla 2008) [Model]
Reiner A, Veenman CL, Medina L, Jiao Y, Del Mar N, Honig MG (2000) Pathway tracing using biotinylated dextran amines. J Neurosci Methods 103:23-37 [PubMed]
Rodriguez A, Ehlenberger D, Kelliher K, Einstein M, Henderson SC, Morrison JH, Hof PR, Wearne SL (2003) Automated reconstruction of three-dimensional neuronal morphology from laser scanning microscopy images. Methods 30:94-105 [PubMed]
Ropireddy D, Ascoli GA (2011) Potential Synaptic Connectivity of Different Neurons onto Pyramidal Cells in a 3D Reconstruction of the Rat Hippocampus. Front Neuroinform 5:5 [Journal] [PubMed]
Ropireddy D, Bachus SE, Ascoli GA (2012) Non-homogeneous stereological properties of the rat hippocampus from high-resolution 3D serial reconstruction of thin histological sections. Neuroscience 205:91-111 [Journal] [PubMed]
Roysam B, Shain W, Ascoli GA (2009) The central role of neuroinformatics in the National Academy of Engineering's grandest challenge: reverse engineer the brain. Neuroinformatics 7:1-5 [Journal] [PubMed]
Rust MJ, Bates M, Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3:793-5 [Journal] [PubMed]
Rybak J, Kuß A, Lamecker H, Zachow S, Hege HC, Lienhard M, Singer J, Neubert K, Menzel R (2010) The Digital Bee Brain: Integrating and Managing Neurons in a Common 3D Reference System. Front Syst Neurosci 4:
Sah P, Bekkers JM (1996) Apical dendritic location of slow afterhyperpolarization current in hippocampal pyramidal neurons: implications for the integration of long-term potentiation. J Neurosci 16:4537-42 [PubMed]
Samsonovich AV, Ascoli GA (2005) Statistical determinants of dendritic morphology in hippocampal pyramidal neurons: A hidden Markov model. Hippocampus 15:166-83 [Journal] [PubMed]
Sasaki T, Matsuki N, Ikegaya Y (2012) Effects of axonal topology on the somatic modulation of synaptic outputs. J Neurosci 32:2868-76 [Journal] [PubMed]
Schiller J, Major G, Koester HJ, Schiller Y (2000) NMDA spikes in basal dendrites of cortical pyramidal neurons. Nature 404:285-9 [Journal] [PubMed]
Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9:671-5 [PubMed]
Scorcioni R, Polavaram S, Ascoli GA (2008) L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies. Nat Protoc 3:866-76 [Journal] [PubMed]
Seidl AH, Rubel EW, Harris DM (2010) Mechanisms for adjusting interaural time differences to achieve binaural coincidence detection. J Neurosci 30:70-80 [Journal] [PubMed]
Senft SL (2011) A brief history of neuronal reconstruction. Neuroinformatics 9:119-28 [Journal] [PubMed]
Silberberg G, Markram H (2007) Disynaptic inhibition between neocortical pyramidal cells mediated by Martinotti cells. Neuron 53:735-46 [Journal] [PubMed]
Smith RG (1992) NeuronC: a computational language for investigating functional architecture of neural circuits. J Neurosci Methods 43:83-108 [PubMed]
Snider J, Pillai A, Stevens CF (2010) A universal property of axonal and dendritic arbors. Neuron 66:45-56 [Journal] [PubMed]
Softky WR, Koch C (1993) The highly irregular firing of cortical cells is inconsistent with temporal integration of random EPSPs. J Neurosci 13:334-50 [PubMed]
Solinas SM, Maex R, De Schutter E (2006) Dendritic amplification of inhibitory postsynaptic potentials in a model Purkinje cell. Eur J Neurosci 23:1207-18 [Journal] [PubMed]
Spruston N (2008) Pyramidal neurons: dendritic structure and synaptic integration. Nat Rev Neurosci 9:206-21 [Journal] [PubMed]
Spruston N, Jaffe DB, Johnston D (1994) Dendritic attenuation of synaptic potentials and currents: the role of passive membrane properties. Trends Neurosci 17:161-6 [PubMed]
Stepanyants A, Chklovskii DB (2005) Neurogeometry and potential synaptic connectivity. Trends Neurosci 28:387-94 [Journal] [PubMed]
Stepanyants A, Hirsch JA, Martinez LM, Kisvárday ZF, Ferecskó AS, Chklovskii DB (2008) Local potential connectivity in cat primary visual cortex. Cereb Cortex 18:13-28 [Journal] [PubMed]
Stepanyants A, Hof PR, Chklovskii DB (2002) Geometry and structural plasticity of synaptic connectivity. Neuron 34:275-88 [PubMed]
Stuart GJ, Häusser M (2001) Dendritic coincidence detection of EPSPs and action potentials. Nat Neurosci 4:63-71 [Journal] [PubMed]
Sulkowski MJ, Iyer SC, Kurosawa MS, Iyer EP, Cox DN (2011) Turtle functions downstream of Cut in differentially regulating class specific dendrite morphogenesis in Drosophila. PLoS One 6:e22611 [Journal] [PubMed]
Svoboda K (2011) The past, present, and future of single neuron reconstruction. Neuroinformatics 9:97-8 [Journal] [PubMed]
Teeter CM, Stevens CF (2011) A general principle of neural arbor branch density. Curr Biol 21:2105-8 [Journal] [PubMed]
Teschemacher AG, Paton JF, Kasparov S (2005) Imaging living central neurones using viral gene transfer. Adv Drug Deliv Rev 57:79-93 [Journal] [PubMed]
Traynelis SF, Silver RA, Cull-Candy SG (1993) Estimated conductance of glutamate receptor channels activated during EPSCs at the cerebellar mossy fiber-granule cell synapse. Neuron 11:279-89 [PubMed]
Trojanowski JQ, Gonatas JO, Gonatas NK (1982) Horseradish peroxidase (HRP) conjugates of cholera toxin and lectins are more sensitive retrogradely transported markers than free HRP. Brain Res 231:33-50 [PubMed]
Troyer TW, Levin JE, Jacobs GA (1994) Construction and analysis of a database representing a neural map. Microsc Res Tech 29:329-43 [Journal] [PubMed]
Ugolini G (2010) Advances in viral transneuronal tracing. J Neurosci Methods 194:2-20 [Journal] [PubMed]
van Ooyen A (2011) Using theoretical models to analyse neural development. Nat Rev Neurosci 12:311-26 [Journal] [PubMed]
Vyas A, Jadhav S, Chattarji S (2006) Prolonged behavioral stress enhances synaptic connectivity in the basolateral amygdala. Neuroscience 143:387-93 [Journal] [PubMed]
Wang Y, Narayanaswamy A, Tsai CL, Roysam B (2011) A broadly applicable 3-D neuron tracing method based on open-curve snake. Neuroinformatics 9:193-217 [Journal] [PubMed]
Wann DF, Woolsey TA, Dierker ML, Cowan WM (1973) An on-line digital-computer system for the semiautomatic analysis of Golgi-impregnated neurons. IEEE Trans Biomed Eng 20:233-47 [Journal] [PubMed]
Watanabe S, Hoffman DA, Migliore M, Johnston D (2002) Dendritic K+ channels contribute to spike-timing dependent long-term potentiation in hippocampal pyramidal neurons. Proc Natl Acad Sci U S A 99:8366-71 [Journal] [PubMed]
  • CA1 pyramidal neuron: conditional boosting of dendritic APs (Watanabe et al 2002) [Model]
Wearne SL, Rodriguez A, Ehlenberger DB, Rocher AB, Henderson SC, Hof PR (2005) New techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales. Neuroscience 136:661-80 [Journal] [PubMed]
Wei H, el Jundi B, Homberg U, Stengl M (2010) Implementation of pigment-dispersing factor-immunoreactive neurons in a standardized atlas of the brain of the cockroach Leucophaea maderae. J Comp Neurol 518:4113-33 [Journal] [PubMed]
Wen Q, Chklovskii DB (2008) A cost-benefit analysis of neuronal morphology. J Neurophysiol 99:2320-8 [Journal] [PubMed]
Wilson T (1989) Trends in confocal microscopy. Trends Neurosci 12:486-93 [PubMed]
Wolf E, Birinyi A, Pomahazi S (1995) A fast 3-dimensional neuronal tree reconstruction system that uses cubic polynomials to estimate dendritic curvature. J Neurosci Methods 63:137-45 [PubMed]
Yabuta NH, Callaway EM (1998) Functional streams and local connections of layer 4C neurons in primary visual cortex of the macaque monkey. J Neurosci 18:9489-99 [PubMed]
Zador AM, Dubnau J, Oyibo HK, Zhan H, Cao G, Peikon ID (2012) Sequencing the connectome. PLoS Biol 10:e1001411 [Journal] [PubMed]
Zubler F, Douglas R (2009) A framework for modeling the growth and development of neurons and networks. Front Comput Neurosci 3:25 [Journal] [PubMed]
Galati DF, Hiester BG, Jones KR (2016) Computer Simulations Support a Morphological Contribution to BDNF Enhancement of Action Potential Generation. Front Cell Neurosci 10:209 [Journal] [PubMed]
  • BDNF morphological contributions to AP enhancement (Galati et al. 2016) [Model]
(183 refs)