Extracellular Action Potential Simulations (Gold et al 2007)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:84589
This package recreates the the principal experiments described in (Gold, Henze and Koch, 2007) and includes the core code necessary to create your own Extracellular Action Potential Simulations.
Reference:
1 . Holt GR, Koch C (1999) Electrical interactions via the extracellular potential near cell bodies. J Comput Neurosci 6:169-84 [PubMed]
2 . Gold C, Henze DA, Koch C, Buzsaki G (2006) On the origin of the extracellular action potential waveform: A modeling study. J Neurophysiol 95:3113-28 [PubMed]
3 . Holt G (1998) A Critical Reexamination of Some Assumptions and Implications of Cable Theory in Neurobiology. PhD thesis
4 . Gold C, Henze DA, Koch C (2007) Using Extracellular Action Potential Recordings to Tune Compartmental Models. Journal of Computational Neuroscience 23:39-58 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Extracellular;
Brain Region(s)/Organism:
Cell Type(s): Hippocampus CA1 pyramidal cell; Myelinated neuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; MATLAB;
Model Concept(s): Extracellular Fields;
Implementer(s): Gold, Carl [carlg at caltech.edu];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal cell;
/
eaps
cells
docs
hoc
mat
mod
output
README.txt
                            
See the "docs" folder for instructions on using the
Extracellular Action Potential Simulation (EAPS) package.

Holt GR, Koch C (1999) Electrical interactions via the extracellular potential near cell bodies. J Comput Neurosci 6:169-84[PubMed]

References and models cited by this paper

References and models that cite this paper

Arvanitaki A (1942) Effects evoked in an axon by the activity of a contiguous one J Neurophysiol 5:89-108 [Journal]

Barr RC, Plonsey R (1992) Electrophysiological interaction through the interstitial space between adjacent unmyelinated parallel fibers. Biophys J 61:1164-75 [PubMed]

Bernander O, Douglas RJ, Martin KA, Koch C (1991) Synaptic background activity influences spatiotemporal integration in single pyramidal cells. Proc Natl Acad Sci U S A 88:11569-73 [PubMed]

Bishop GH, Oleary JL (1942) The polarity of potentials recorded from the superior colliculus J Cell Comp Physiol 19:289-300

Bullock TH (1965) Comparative neurology of transmission Structure and Function in the Nervous Systems of Invertebrates, Bullock TH:Horridge GA, ed. pp.181

Bullock TH (1997) Signals and signs in the nervous system: the dynamic anatomy of electrical activity is probably information-rich. Proc Natl Acad Sci U S A 94:1-6 [PubMed]

Buzsaki G, Penttonen M, Nadasdy Z, Bragin A (1996) Pattern and inhibition-dependent invasion of pyramidal cell dendrites by fast spikes in the hippocampus in vivo. Proc Natl Acad Sci U S A 93:9921-5 [PubMed]

Carter CJ, Cannon M (1980) Maturation of ribosomal precursor RNA in Saccharomyces cerevisiae. A mutant with a defect in both the transport and terminal processing of the 20 S species. J Mol Biol 143:179-99 [PubMed]

Chan CY, Nicholson C (1986) Modulation by applied electric fields of Purkinje and stellate cell activity in the isolated turtle cerebellum. J Physiol 371:89-114 [PubMed]

Clark J, Plonsey R (1968) The extracellular potential field of the single active nerve fiber in a volume conductor. Biophys J 8:842-64

Clark JW, Plonsey R (1970) A mathematical study of nerve fiber interaction. Biophys J 10:937-57

Clark JW, Plonsey R (1971) Fiber interaction in a nerve trunk. Biophys J 11:281-94

Colbert CM, Johnston D (1996) Axonal action-potential initiation and Na+ channel densities in the soma and axon initial segment of subicular pyramidal neurons. J Neurosci 16:6676-86 [PubMed]

COOMBS JS, CURTIS DR, ECCLES JC (1957) The interpretation of spike potentials of motoneurones. J Physiol 139:198-231 [PubMed]

COOMBS JS, CURTIS DR, ECCLES JC (1957) The generation of impulses in motoneurones. J Physiol 139:232-49 [PubMed]

Dalkara T, Krnjevic K, Ropert N, Yim CY (1986) Chemical modulation of ephaptic activation of CA3 hippocampal pyramids. Neuroscience 17:361-70

Debanne D, Guerineau NC, Gahwiler BH, Thompson SM (1997) Action-potential propagation gated by an axonal I(A)-like K+ conductance in hippocampus. Nature 389:286-9 [PubMed]

Douglas RJ, Martin KA, Whitteridge D (1991) An intracellular analysis of the visual responses of neurones in cat visual cortex. J Physiol 440:659-96 [PubMed]

Eccles JC (1964) Presynaptic inhibition The Physiology of synapses :220-238

Faber DS, Korn H (1989) Electrical field effects: their relevance in central neural networks. Physiol Rev 69:821-63

FATT P (1957) Electric potentials occurring around a neurone during its antidromic activation. J Neurophysiol 20:27-60 [Journal] [PubMed]

FREYGANG WH (1958) An analysis of extracellular potentials from single neurons in the lateral geniculate nucleus of the cat. J Gen Physiol 41:543-64

FREYGANG WH, FRANK K (1959) Extracellular potentials from single spinal motoneurons. J Gen Physiol 42:749-60 [PubMed]

FUORTES MG, FRANK K, BECKER MC (1957) Steps in the production of motoneuron spikes. J Gen Physiol 40:735-52 [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 [PubMed]

Holt G (1998) A Critical Reexamination of Some Assumptions and Implications of Cable Theory in Neurobiology. PhD thesis [Journal]

   Extracellular Action Potential Simulations (Gold et al 2007) [Model]

Hubbard JI, Llinas R, Quastel DMJ (1969) Electrophysiological Analysis of Synaptic Transmission

Jefferys JG (1995) Nonsynaptic modulation of neuronal activity in the brain: electric currents and extracellular ions. Physiol Rev 75:689-723 [PubMed]

Katz B, Schmitt OH (1942) A note on interaction between nerve fibers J Physiol 100:369-371

Kocsis JD, Ruiz JA, Cummins KL (1982) Modulation of axonal excitability mediated by surround electric activity: an intra-axonal study. Exp Brain Res 47:151-3

Korn H, Axelrad H (1980) Electrical inhibition of Purkinje cells in the cerebellum of the rat. Proc Natl Acad Sci U S A 77:6244-7

Korn H, Faber DS (1980) Electrical field effect interactions in the vertebrate brain Trends Neurosci 3:6-9

Lorente_de_No_R (1947) Action potential of the motoneurons of the hypoglossus nucleus J Cell Comp Physiol 29:207-287

Mainen ZF, Joerges J, Huguenard JR, Sejnowski TJ (1995) A model of spike initiation in neocortical pyramidal neurons. Neuron 15:1427-39 [PubMed]

   Spike Initiation in Neocortical Pyramidal Neurons (Mainen et al 1995) [Model]

Mainen ZF, Sejnowski TJ (1996) Influence of dendritic structure on firing pattern in model neocortical neurons. Nature 382:363-6 [Journal] [PubMed]

   [2 reconstructed morphologies on NeuroMorpho.Org]
   Pyramidal Neuron Deep, Superficial; Aspiny, Stellate (Mainen and Sejnowski 1996) [Model]

Malmivuo J, Plonsey R (1995) Bioelectromagnetism:Principles and Applications of Bioelectric and Biomagnetic Fields

Manor Y, Koch C, Segev I (1991) Effect of geometrical irregularities on propagation delay in axonal trees. Biophys J 60:1424-37 [PubMed]

Markin VS (2000) [Electric interaction of parallel nonmyelinized nerve fibers. I. Change in the excitability of an adjacent fiber] Biofizika 15:120-9

Markin VS (2000) [Electric interaction of parallel non-myelinized nerve fibers. II. Shared conduction of impulses] Biofizika 15:681-9

Markin VS (2000) [Electric interaction of parallel non-myelinated nerve fibers. 3. Interaction in nerve trunks] Biofizika 18:314-21

Markin VS (2000) [Electric interaction of parallel non-myelinated nerve fibers. IV. Role of anatomic non-uniformities of the nerve trunks] Biofizika 18:512-8

McCaig CD (1988) Nerve guidance: a role for bio-electric fields? Prog Neurobiol 30:449-68

McCaig CD, Zhao M (1997) Physiological electrical fields modify cell behaviour. Bioessays 19:819-26

McNeal DR (1976) Analysis of a model for excitation of myelinated nerve. IEEE Trans Biomed Eng 23:329-37 [PubMed]

Mitzdorf U (1985) Current source-density method and application in cat cerebral cortex: investigation of evoked potentials and EEG phenomena. Physiol Rev 65:37-100 [PubMed]

Nelson PG (1966) Interaction between spinal motoneurons of the cat. J Neurophysiol 29:275-87 [Journal]

Nelson PG, Frank K (1964) Extracellular potential fields of single spinal motoneurons J Neurophysiol 27:913-927 [Journal]

Nicholson C (1995) Extracellular space as the pathway for neuronglial cell interaction Neuroglia, Kettenmann H:Ransom BR, ed. pp.387

Patel NB, Poo MM (1984) Perturbation of the direction of neurite growth by pulsed and focal electric fields. J Neurosci 4:2939-47

Peters A, Palay SL, Webster HF (1991) The Fine Structure of the Nervous System

Plonsey R (1969) Bioelectric Phenomena

Plonsey R, Barr RC (1995) Electric field stimulation of excitable tissue. IEEE Trans Biomed Eng 42:329-36

RALL W (1962) Electrophysiology of a dendritic neuron model. Biophys J 2(2)Pt 2:145-67 [PubMed]

Rall W (1977) Core conductor theory and cable properties of neurons Handbook of Physiology. The Nervous System. Cellular Biology of Neurons, Kandel ER, ed. pp.39

RANCK JB (1963) Specific impedance of rabbit cerebral cortex. Exp Neurol 7:144-52 [PubMed]

Ranck JB (1975) Which elements are excited in electrical stimulation of mammalian central nervous system: a review. Brain Res 98:417-40 [PubMed]

Rapp M, Yarom Y, Segev I (1996) Modeling back propagating action potential in weakly excitable dendrites of neocortical pyramidal cells. Proc Natl Acad Sci U S A 93:11985-90 [PubMed]

Roney KJ, Scheibel AB, Shaw GL (1979) Dendritic bundles: survey of anatomical experiments and physiological theories. Brain Res 180:225-71

Rosenfalck P (1969) Intra- and extracellular potential fields of active nerve and muscle fibres. A physico-mathematical analysis of different models. Thromb Diath Haemorrh Suppl 321:1-168

Rosenthal F (1972) Extracellular potential fields of single PT-neurons. Brain Res 36:251-63

Scott AC, Luzader SD (1979) Coupled solitary waves in neurophysics Physica Scripta 20:395-401

Snow RW, Dudek FE (1984) Electrical fields directly contribute to action potential synchronization during convulsant-induced epileptiform bursts. Brain Res 323:114-8

Sperti L, Gessi T, Volta F (1967) Extracellular potential field of antidromically activated CA1 pyramidal neurons. Brain Res 3:343-61

Stein RB, Pearson KG (1971) Predicted amplitude and form of action potentials recorded from unmyelinated nerve fibres. J Theor Biol 32:539-58

Stevens CF (1966) Neurophysiology: A primer

Stuart GJ, Sakmann B (1994) Active propagation of somatic action potentials into neocortical pyramidal cell dendrites. Nature 367:69-72 [PubMed]

Sykova E (1997) The extracellular space in the CNS: Its regulation, volume and geometry in normal and pathological neuronal function The Neuroscientist 3:28-41

Tabata T (1990) Ephaptic transmission and conduction velocity of an action potential in Chara internodal cells placed in parallel and in contact with one another Plant Cell Physiol 31:575-579

Terzuolo CA, Araki T (1961) An analysis of intra- versus extracellular potential changes associated with activity of single spinal motoneurons Ann Ny Acad Sci 94:547-558

Tranchina D, Nicholson C (1986) A model for the polarization of neurons by extrinsically applied electric fields. Biophys J 50:1139-56 [PubMed]

Traub RD, Dudek FE, Snow RW, Knowles WD (1985) Computer simulations indicate that electrical field effects contribute to the shape of the epileptiform field potential. Neuroscience 15:947-58

Traub RD, Dudek FE, Taylor CP, Knowles WD (1985) Simulation of hippocampal afterdischarges synchronized by electrical interactions. Neuroscience 14:1033-8 [PubMed]

Trayanova N, Henriquez CS (1991) Examination of the choice of models for computing the extracellular potential of a single fibre in a restricted volume conductor. Med Biol Eng Comput 29:580-4

Trayanova NA, Henriquez CS, Plonsey R (1990) Limitations of approximate solutions for computing the extracellular potential of single fibers and bundle equivalents. IEEE Trans Biomed Eng 37:22-35

Turner RW, Richardson TL (1991) Apical dendritic depolarizations and field interactions evoked by stimulation of afferent inputs to rat hippocampal CA1 pyramidal cells. Neuroscience 42:125-35

van_Harreveld A (1972) The extracellular space in the vertebrate central nervous system The Structure and Function of Nervous Tissue, Bourne GH, ed. pp.447

beim Graben P, Rodrigues S (2013) A biophysical observation model for field potentials of networks of leaky integrate-and-fire neurons Frontiers in Computational Neuroscience 6:1-13 [Journal] [PubMed]

   Biophysical model for field potentials of networks of I&F neurons (beim Graben & Serafim 2013) [Model]

Camunas-Mesa LA, Quiroga RQ (2013) A Detailed and Fast Model of Extracellular Recordings Neural Comput 25(5):1191-1212 [Journal] [PubMed]

   A detailed and fast model of extracellular recordings (Camunas-Mesa & Qurioga 2013) [Model]

Coop AD, Reeke GN (2001) The composite neuron: a realistic one-compartment Purkinje cell model suitable for large-scale neuronal network simulations. J Comput Neurosci 10:173-86 [Journal] [PubMed]

Glabska H, Chintaluri C, Wójcik DK (2017) Collection of Simulated Data from a Thalamocortical Network Model. Neuroinformatics 15:87-99 [Journal] [PubMed]

   Collection of simulated data from a thalamocortical network model (Glabska, Chintaluri, Wojcik 2017) [Model]

Gold C, Henze DA, Koch C (2007) Using Extracellular Action Potential Recordings to Tune Compartmental Models. Journal of Computational Neuroscience 23:39-58 [Journal] [PubMed]

   Extracellular Action Potential Simulations (Gold et al 2007) [Model]

Gold C, Henze DA, Koch C, Buzsaki G (2006) On the origin of the extracellular action potential waveform: A modeling study. J Neurophysiol 95:3113-28 [Journal] [PubMed]

   Extracellular Action Potential Simulations (Gold et al 2007) [Model]

Goldwyn JH, McLaughlin M, Verschooten E, Joris PX, Rinzel J (2014) A model of the medial superior olive explains spatiotemporal features of local field potentials J Neurosci. 34(35):11705-22 [Journal] [PubMed]

   A model of local field potentials generated by medial superior olive neurons (Goldwyn et al 2014) [Model]

Halnes G, Mäki-Marttunen T, Keller D, Pettersen KH, Andreassen OA, Einevoll GT (2016) Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue PLoS Comput Biol 12:e1005193 [Journal] [PubMed]

   Effect of ionic diffusion on extracellular potentials (Halnes et al 2016) [Model]

Miceli S, Ness TV, Einevoll GT, Schubert D (2017) Impedance Spectrum in Cortical Tissue: Implications for Propagation of LFP Signals on the Microscopic Level Eneuro 4:1-15 [Journal]

   Impedance spectrum in cortical tissue: implications for LFP signal propagation (Miceli et al. 2017) [Model]

Nenadic Z, Burdick JW (2006) A control algorithm for autonomous optimization of extracellular recordings. IEEE Trans Biomed Eng 53:941-55 [Journal] [PubMed]

Ness TV, Remme MW, Einevoll GT (2016) Active subthreshold dendritic conductances shape the local field potential. J Physiol 594:3809-25 [Journal] [PubMed]

Parasuram H, Nair B, D`Angelo E, Hines M, Naldi G, Diwakar S (2016) Computational modeling of single neuron extracellular electric potentials and network Local Field Potentials using LFPsim Front. Comput. Neurosci. 10:65 [Journal]

   Modeling single neuron LFPs and extracellular potentials with LFPsim (Parasuram et al. 2016) [Model]

Reznik RI, Barreto E, Sander E, So P (2015) Effects of polarization induced by non-weak electric fields on the excitability of elongated neurons with active dendrites. J Comput Neurosci [Journal] [PubMed]

   Non-Weak E-Fields Pyramidal Neurons (Reznik et. al.,2015) [Model]

Tomsett RJ, Ainsworth M, Thiele A, Sanayei M, Chen X, Gieselmann MA, Whittington MA, Cunningh (2015) Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX): comparing multi-electrode recordings from simulated and biological mammalian cortical tissue. Brain Struct Funct 220(4):2333-53 [Journal] [PubMed]

   Large-scale model of neocortical slice in vitro exhibiting persistent gamma (Tomsett et al. 2014) [Model]

(90 refs)

Gold C, Henze DA, Koch C, Buzsaki G (2006) On the origin of the extracellular action potential waveform: A modeling study. J Neurophysiol 95:3113-28[PubMed]

References and models cited by this paper

References and models that cite this paper

Borg-graham L (1999) Interpretations of data and mechanisms for hippocampal pyramidal cell models Cerebral Cortex cortical Models, Jones E:Ulinski P:Peters A, ed. pp.19

Buzsaki G, Kandel A (1998) Somadendritic backpropagation of action potentials in cortical pyramidal cells of the awake rat. J Neurophysiol 79:1587-91 [Journal] [PubMed]

Buzsaki G, Penttonen M, Nadasdy Z, Bragin A (1996) Pattern and inhibition-dependent invasion of pyramidal cell dendrites by fast spikes in the hippocampus in vivo. Proc Natl Acad Sci U S A 93:9921-5 [PubMed]

Christie BR, Eliot LS, Ito K, Miyakawa H, Johnston D (1995) Different Ca2+ channels in soma and dendrites of hippocampal pyramidal neurons mediate spike-induced Ca2+ influx. J Neurophysiol 73:2553-7 [Journal] [PubMed]

Colbert CM, Johnston D (1996) Axonal action-potential initiation and Na+ channel densities in the soma and axon initial segment of subicular pyramidal neurons. J Neurosci 16:6676-86 [PubMed]

Colbert CM, Magee JC, Hoffman DA, Johnston D (1997) Slow recovery from inactivation of Na+ channels underlies the activity-dependent attenuation of dendritic action potentials in hippocampal CA1 pyramidal neurons. J Neurosci 17:6512-21 [PubMed]

Colbert CM, Pan E (2002) Ion channel properties underlying axonal action potential initiation in pyramidal neurons. Nat Neurosci 5:533-8 [PubMed]

Csicsvari J, Henze DA, Jamieson B, Harris KD, Sirota A, Bartho P, Wise KD, Buzsaki G (2003) Massively parallel recording of unit and local field potentials with silicon-based electrodes. J Neurophysiol 90:1314-23 [Journal] [PubMed]

Csicsvari J, Hirase H, Czurko A, Mamiya A, Buzsaki G (1999) Oscillatory coupling of hippocampal pyramidal cells and interneurons in the behaving Rat. J Neurosci 19:274-87 [PubMed]

Destexhe A, Pare D (1999) Impact of network activity on the integrative properties of neocortical pyramidal neurons in vivo. J Neurophysiol 81:1531-47 [Journal] [PubMed]

Fisher RE, Gray R, Johnston D (1990) Properties and distribution of single voltage-gated calcium channels in adult hippocampal neurons. J Neurophysiol 64:91-104 [Journal] [PubMed]

Frick A, Magee J, Johnston D (2004) LTP is accompanied by an enhanced local excitability of pyramidal neuron dendrites. Nat Neurosci 7:126-35 [PubMed]

Frick A, Magee J, Koester HJ, Migliore M, Johnston D (2003) Normalization of Ca2+ signals by small oblique dendrites of CA1 pyramidal neurons. J Neurosci 23:3243-50 [PubMed]

Gray CM, Maldonado PE, Wilson M, McNaughton B (1995) Tetrodes markedly improve the reliability and yield of multiple single-unit isolation from multi-unit recordings in cat striate cortex. J Neurosci Methods 63:43-54 [PubMed]

Gulyas AI, Megias M, Emri Z, Freund TF (1999) Total number and ratio of excitatory and inhibitory synapses converging onto single interneurons of different types in the CA1 area of the rat hippocampus. J Neurosci 19:10082-97 [PubMed]

   [67 reconstructed morphologies on NeuroMorpho.Org]

Halliwell JV, Adams PR (1982) Voltage-clamp analysis of muscarinic excitation in hippocampal neurons. Brain Res 250:71-92 [PubMed]

Harris KM, Stevens JK (1989) Dendritic spines of CA 1 pyramidal cells in the rat hippocampus: serial electron microscopy with reference to their biophysical characteristics. J Neurosci 9:2982-97 [PubMed]

Henze DA, Borhegyi Z, Csicsvari J, Mamiya A, Harris KD, ki G (2000) Intracellular features predicted by extracellular recordings in the hippocampus in vivo. J Neurophysiol 84:390-400 [Journal] [PubMed]

Henze DA, Buzsaki G (2001) Action potential threshold of hippocampal pyramidal cells in vivo is increased by recent spiking activity. Neuroscience 105:121-30 [PubMed]

Hines ML, Carnevale NT (1997) The NEURON simulation environment. Neural Comput 9:1179-209 [PubMed]

Hines ML, Carnevale NT (2000) Expanding NEURON's repertoire of mechanisms with NMODL. Neural Comput 12:995-1007 [PubMed]

Hines ML, Carnevale NT (2001) NEURON: a tool for neuroscientists. Neuroscientist 7:123-35 [Journal] [PubMed]

   Spatial gridding and temporal accuracy in NEURON (Hines and Carnevale 2001) [Model]

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 [PubMed]

Holt G (1998) A Critical Reexamination of Some Assumptions and Implications of Cable Theory in Neurobiology. PhD thesis [Journal]

   Extracellular Action Potential Simulations (Gold et al 2007) [Model]

Holt GR, Koch C (1999) Electrical interactions via the extracellular potential near cell bodies. J Comput Neurosci 6:169-84 [Journal] [PubMed]

   Extracellular Action Potential Simulations (Gold et al 2007) [Model]

Jaffe DB, Ross WN, Lisman JE, Lasser-Ross N, Miyakawa H, Johnston D (1994) A model for dendritic Ca2+ accumulation in hippocampal pyramidal neurons based on fluorescence imaging measurements. J Neurophysiol 71:1065-77 [Journal] [PubMed]

Kamondi A, Acsady L, Buzsaki G (1998) Dendritic spikes are enhanced by cooperative network activity in the intact hippocampus. J Neurosci 18:3919-28 [PubMed]

Klee R, Ficker E, Heinemann U (1995) Comparison of voltage-dependent potassium currents in rat pyramidal neurons acutely isolated from hippocampal regions CA1 and CA3. J Neurophysiol 74:1982-95 [Journal] [PubMed]

Koch C (1999) Biophysics Of Computation: Information Processing in Single Neurons

Koch C, Segev I (1998) Methods In Neuronal Modeling

Lancaster B, Nicoll RA (1987) Properties of two calcium-activated hyperpolarizations in rat hippocampal neurones. J Physiol 389:187-203 [PubMed]

Lopez-Aguado L, Ibarz JM, Herreras O (2001) Activity-dependent changes of tissue resistivity in the CA1 region in vivo are layer-specific: modulation of evoked potentials. Neuroscience 108:249-62

Magee JC (1998) Dendritic hyperpolarization-activated currents modify the integrative properties of hippocampal CA1 pyramidal neurons. J Neurosci 18:7613-24 [PubMed]

Magee JC, Johnston D (1995) Characterization of single voltage-gated Na+ and Ca2+ channels in apical dendrites of rat CA1 pyramidal neurons. J Physiol 487 ( Pt 1):67-90 [PubMed]

Mainen ZF, Joerges J, Huguenard JR, Sejnowski TJ (1995) A model of spike initiation in neocortical pyramidal neurons. Neuron 15:1427-39 [PubMed]

   Spike Initiation in Neocortical Pyramidal Neurons (Mainen et al 1995) [Model]

Major G, Larkman AU, Jonas P, Sakmann B, Jack JJ (1994) Detailed passive cable models of whole-cell recorded CA3 pyramidal neurons in rat hippocampal slices. J Neurosci 14:4613-38 [PubMed]

Martina M, Jonas P (1997) Functional differences in Na+ channel gating between fast-spiking interneurones and principal neurones of rat hippocampus. J Physiol 505 ( Pt 3):593-603 [PubMed]

Martina M, Vida I, Jonas P (2000) Distal initiation and active propagation of action potentials in interneuron dendrites. Science 287:295-300 [PubMed]

Maxwell JC (1881) A Treatise on Electricity, Magnetism

Megias M, Emri Z, Freund TF, Gulyas AI (2001) Total number and distribution of inhibitory and excitatory synapses on hippocampal CA1 pyramidal cells. Neuroscience 102:527-40 [PubMed]

   [18 reconstructed morphologies on NeuroMorpho.Org]

Moffitt MA, McIntyre CC (2005) Model-based analysis of cortical recording with silicon microelectrodes. Clin Neurophysiol 116:2240-50 [PubMed]

Mountcastle VB, Talbot WH, Sakata H, Hyvarinen J (1969) Cortical neuronal mechanisms in flutter-vibration studied in unanesthetized monkeys. Neuronal periodicity and frequency discrimination. J Neurophysiol 32:452-84 [Journal] [PubMed]

Plonsey R (1969) Bioelectric Phenomena

Poirazi P, Brannon T, Mel BW (2003a) Arithmetic of subthreshold synaptic summation in a model CA1 pyramidal cell. Neuron 37:977-987 [Journal] [PubMed]

   CA1 pyramidal neuron: as a 2-layer NN and subthreshold synaptic summation (Poirazi et al 2003) [Model]

Poolos NP, Johnston D (1999) Calcium-activated potassium conductances contribute to action potential repolarization at the soma but not the dendrites of hippocampal CA1 pyramidal neurons. J Neurosci 19:5205-12 [PubMed]

Quirk MC, Blum KI, Wilson MA (2001) Experience-dependent changes in extracellular spike amplitude may reflect regulation of dendritic action potential back-propagation in rat hippocampal pyramidal cells. J Neurosci 21:240-8 [PubMed]

Quiroga RQ, Nadasdy Z, Ben-Shaul Y (2004) Unsupervised spike detection and sorting with wavelets and superparamagnetic clustering. Neural Comput 16:1661-87 [PubMed]

RALL W (1962) Electrophysiology of a dendritic neuron model. Biophys J 2(2)Pt 2:145-67 [PubMed]

Rosenfalck P (1969) Intra- and extracellular potential fields of active nerve and muscle fibres. A physico-mathematical analysis of different models. Thromb Diath Haemorrh Suppl 321:1-168

Spruston N, Johnston D (1992) Perforated patch-clamp analysis of the passive membrane properties of three classes of hippocampal neurons. J Neurophysiol 67:508-29 [Journal] [PubMed]

Storm JF (1988) Temporal integration by a slowly inactivating K+ current in hippocampal neurons. Nature 336:379-81 [PubMed]

Stuart G, Spruston N (1998) Determinants of voltage attenuation in neocortical pyramidal neuron dendrites. J Neurosci 18:3501-10 [PubMed]

   [13 reconstructed morphologies on NeuroMorpho.Org]
   Pyramidal Neuron Deep: attenuation in dendrites (Stuart, Spruston 1998) [Model]

Toledo-Rodriguez M, Blumenfeld B, Wu C, Luo J, Attali B, Goodman P, Markram H (2004) Correlation maps allow neuronal electrical properties to be predicted from single-cell gene expression profiles in rat neocortex. Cereb Cortex 14:1310-27 [PubMed]

Trayanova N, Henriquez CS (1991) Modification of a cylindrical bidomain model for cardiac tissue. Math Biosci 104:59-72

Tsubokawa H (2005) Control of Na+ spike backpropagation by intracellular signaling in the pyramidal neuron dendrites. Mol Neurobiol 22:129-41

Weber E (1950) Electro Magnetic Fields: Theory, Applications

Williamson A, Alger BE (1990) Characterization of an early afterhyperpolarization after a brief train of action potentials in rat hippocampal neurons in vitro. J Neurophysiol 63:72-81 [Journal] [PubMed]

Wilson MA, McNaughton BL (1993) Dynamics of the hippocampal ensemble code for space. Science 261:1055-8 [PubMed]

Yoshida A, Oda M, Ikemoto Y (1991) Kinetics of the Ca(2+)-activated K+ channel in rat hippocampal neurons. Jpn J Physiol 41:297-315

Berzhanskaya J, Chernyy N, Gluckman BJ, Schiff SJ, Ascoli GA (2013) Modulation of hippocampal rhythms by subthreshold electric fields and network topology. J Comput Neurosci 34(3):369-389 [Journal] [PubMed]

   Modulation of hippocampal rhythms by electric fields and network topology (Berzhanskaya et al. 2013) [Model]

Camunas-Mesa LA, Quiroga RQ (2013) A Detailed and Fast Model of Extracellular Recordings Neural Comput 25(5):1191-1212 [Journal] [PubMed]

   A detailed and fast model of extracellular recordings (Camunas-Mesa & Qurioga 2013) [Model]

Carnevale NT, Morse TM (1996-2009) Research reports that have used NEURON Web published citations at the NEURON website [Journal]

Diwakar S, Lombardo P, Solinas S, Naldi G, D`Angelo E (2011) Local field potential modeling predicts dense activation in cerebellar granule cells clusters under LTP and LTD control PLoS ONE 6(7):e21928 [Journal]

   Reconstructing cerebellar granule layer evoked LFP using convolution (ReConv) (Diwakar et al. 2011) [Model]

Fink CG, Gliske S, Catoni N, Stacey WC (2015) Network Mechanisms Generating Abnormal and Normal Hippocampal High-Frequency Oscillations: A Computational Analysis eNeuro 2(3):ENEURO.0024-15.2015 [Journal] [PubMed]

   Normal ripples, abnormal ripples, and fast ripples in a hippocampal model (Fink et al. 2015) [Model]

Frey U, Egert U, Heer F, Hafizovic S, Hierlemann A (2009) Microelectronic system for high-resolution mapping of extracellular electric fields applied to brain slices. Biosens Bioelectron 24:2191-8 [Journal] [PubMed]

Giugliano M, Gambazzi L, Ballerini L, Prato M, Campidelli S (2012) Carbon nanotubes as electrical interfaces to neurons Nanotechnology for Biology and Medicine, Parpura V, Silva GA, ed. pp.187 [Journal]

   Carbon nanotubes as electrical interfaces to neurons (Giugliano et al. 2008) [Model]

Glabska H, Chintaluri C, Wójcik DK (2017) Collection of Simulated Data from a Thalamocortical Network Model. Neuroinformatics 15:87-99 [Journal] [PubMed]

   Collection of simulated data from a thalamocortical network model (Glabska, Chintaluri, Wojcik 2017) [Model]

Gold C, Henze DA, Koch C (2007) Using Extracellular Action Potential Recordings to Tune Compartmental Models. Journal of Computational Neuroscience 23:39-58 [Journal] [PubMed]

   Extracellular Action Potential Simulations (Gold et al 2007) [Model]

Huys QJ, Ahrens MB, Paninski L (2006) Efficient estimation of detailed single-neuron models. J Neurophysiol 96:872-90 [Journal] [PubMed]

   Efficient estimation of detailed single-neuron models (Huys et al. 2006) [Model]

Mechler F, Victor JD (2012) Dipole characterization of single neurons from their extracellular action potentials. J Comput Neurosci 32:73-100 [Journal] [PubMed]

   Dipole Localization Kit (Mechler & Victor, 2012) [Model]

Ness TV, Remme MW, Einevoll GT (2016) Active subthreshold dendritic conductances shape the local field potential. J Physiol 594:3809-25 [Journal] [PubMed]

Parasuram H, Nair B, D`Angelo E, Hines M, Naldi G, Diwakar S (2016) Computational modeling of single neuron extracellular electric potentials and network Local Field Potentials using LFPsim Front. Comput. Neurosci. 10:65 [Journal]

   Modeling single neuron LFPs and extracellular potentials with LFPsim (Parasuram et al. 2016) [Model]

Wang K, Riera J, Enjieu-Kadji H, Kawashima R (2013) The Role of Extracellular Conductivity Profiles in Compartmental Models for Neurons: Particulars for Layer 5 Pyramidal Cells Neural Comput 25(7):1807-52 [Journal] [PubMed]

   Modeling conductivity profiles in the deep neocortical pyramidal neuron (Wang K et al. 2013) [Model]

Xu J, Clancy CE (2008) Ionic mechanisms of endogenous bursting in CA3 hippocampal pyramidal neurons: a model study. PLoS ONE 3:e2056 [Journal] [PubMed]

   Ionic mechanisms of bursting in CA3 pyramidal neurons (Xu and Clancy 2008) [Model]

(74 refs)

Holt G (1998) A Critical Reexamination of Some Assumptions and Implications of Cable Theory in Neurobiology. PhD thesis

References and models cited by this paper

References and models that cite this paper

Gold C, Henze DA, Koch C (2007) Using Extracellular Action Potential Recordings to Tune Compartmental Models. Journal of Computational Neuroscience 23:39-58 [Journal] [PubMed]

   Extracellular Action Potential Simulations (Gold et al 2007) [Model]

Gold C, Henze DA, Koch C, Buzsaki G (2006) On the origin of the extracellular action potential waveform: A modeling study. J Neurophysiol 95:3113-28 [Journal] [PubMed]

   Extracellular Action Potential Simulations (Gold et al 2007) [Model]

Holt GR, Koch C (1999) Electrical interactions via the extracellular potential near cell bodies. J Comput Neurosci 6:169-84 [Journal] [PubMed]

   Extracellular Action Potential Simulations (Gold et al 2007) [Model]

Nenadic Z, Burdick JW (2006) A control algorithm for autonomous optimization of extracellular recordings. IEEE Trans Biomed Eng 53:941-55 [Journal] [PubMed]

Parasuram H, Nair B, D`Angelo E, Hines M, Naldi G, Diwakar S (2016) Computational modeling of single neuron extracellular electric potentials and network Local Field Potentials using LFPsim Front. Comput. Neurosci. 10:65 [Journal]

   Modeling single neuron LFPs and extracellular potentials with LFPsim (Parasuram et al. 2016) [Model]

Roessert C, Dean P, Porrill J (2015) At the Edge of Chaos: How Cerebellar Granular Layer Network Dynamics Can Provide the Basis for Temporal Filters PLOS Computational Biology [Journal] [PubMed]

   Basis for temporal filters in the cerebellar granular layer (Roessert et al. 2015) [Model]

Tomsett RJ, Ainsworth M, Thiele A, Sanayei M, Chen X, Gieselmann MA, Whittington MA, Cunningh (2015) Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX): comparing multi-electrode recordings from simulated and biological mammalian cortical tissue. Brain Struct Funct 220(4):2333-53 [Journal] [PubMed]

   Large-scale model of neocortical slice in vitro exhibiting persistent gamma (Tomsett et al. 2014) [Model]

Wilson CJ, Beverlin B, Netoff T (2011) Chaotic desynchronization as the therapeutic mechanism of deep brain stimulation. Front Syst Neurosci 5:50 [Journal] [PubMed]

Zandt BJ, Visser S, van Putten MJAM, ten Haken B (2014) A neural mass model based on single cell dynamics to model pathophysiology Journal of Computational Neuroscience 37(3):549-68 [Journal] [PubMed]

   Neural mass model based on single cell dynamics to model pathophysiology (Zandt et al 2014) [Model]

(9 refs)

Gold C, Henze DA, Koch C (2007) Using Extracellular Action Potential Recordings to Tune Compartmental Models. Journal of Computational Neuroscience 23:39-58[PubMed]

References and models cited by this paper

References and models that cite this paper

Bedard C, Kroger H, Destexhe A (2006) Model of low-pass filtering of local field potentials in brain tissue. Phys Rev E Stat Nonlin Soft Matter Phys 73:051911 [Journal] [PubMed]

Borg-graham L (1999) Interpretations of data and mechanisms for hippocampal pyramidal cell models Cerebral Cortex cortical Models, Jones E:Ulinski P:Peters A, ed. pp.19

Buzsaki G, Kandel A (1998) Somadendritic backpropagation of action potentials in cortical pyramidal cells of the awake rat. J Neurophysiol 79:1587-91 [Journal] [PubMed]

Colbert CM, Magee JC, Hoffman DA, Johnston D (1997) Slow recovery from inactivation of Na+ channels underlies the activity-dependent attenuation of dendritic action potentials in hippocampal CA1 pyramidal neurons. J Neurosci 17:6512-21 [PubMed]

Colbert CM, Pan E (2002) Ion channel properties underlying axonal action potential initiation in pyramidal neurons. Nat Neurosci 5:533-8 [PubMed]

De_No RL (1947) Action potential of the motoneurons of the hypoglossus nucleus J Cell Comp Phsiol 29:207-287

Forsyth DA, Ponce J (2002) Computer vision: A modern approach

Gold C, Girardin C, Martin K, Koch C (2006) Unpublished experiments

Gold C, Henze DA, Koch C, Buzsaki G (2006) On the origin of the extracellular action potential waveform: A modeling study. J Neurophysiol 95:3113-28 [Journal] [PubMed]

   Extracellular Action Potential Simulations (Gold et al 2007) [Model]

Hayes RD, Byrne JH, Cox SJ, Baxter DA (2005) Estimation of single-neuron model parameters from spike train data Neurocomputing 66:517-529

Henze DA, Borhegyi Z, Csicsvari J, Mamiya A, Harris KD, ki G (2000) Intracellular features predicted by extracellular recordings in the hippocampus in vivo. J Neurophysiol 84:390-400 [Journal] [PubMed]

Hines ML, Carnevale NT (1997) The NEURON simulation environment. Neural Comput 9:1179-209 [PubMed]

Hines ML, Carnevale NT (2001) NEURON: a tool for neuroscientists. Neuroscientist 7:123-35 [Journal] [PubMed]

   Spatial gridding and temporal accuracy in NEURON (Hines and Carnevale 2001) [Model]

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 [PubMed]

Holt G (1998) A Critical Reexamination of Some Assumptions and Implications of Cable Theory in Neurobiology. PhD thesis [Journal]

   Extracellular Action Potential Simulations (Gold et al 2007) [Model]

Holt GR, Koch C (1999) Electrical interactions via the extracellular potential near cell bodies. J Comput Neurosci 6:169-84 [Journal] [PubMed]

   Extracellular Action Potential Simulations (Gold et al 2007) [Model]

Huys QJ, Ahrens MB, Paninski L (2006) Efficient estimation of detailed single-neuron models. J Neurophysiol 96:872-90 [Journal] [PubMed]

   Efficient estimation of detailed single-neuron models (Huys et al. 2006) [Model]

Jackson JD (1962) Classical Electrodynamics

Keren N, Peled N, Korngreen A (2005) Constraining compartmental models using multiple voltage recordings and genetic algorithms. J Neurophysiol 94:3730-42 [Journal] [PubMed]

Klee R, Ficker E, Heinemann U (1995) Comparison of voltage-dependent potassium currents in rat pyramidal neurons acutely isolated from hippocampal regions CA1 and CA3. J Neurophysiol 74:1982-95 [Journal] [PubMed]

Koch C (1999) Biophysics Of Computation: Information Processing in Single Neurons

Koch C, Segev I (1998) Methods In Neuronal Modeling

Lopez-Aguado L, Ibarz JM, Herreras O (2001) Activity-dependent changes of tissue resistivity in the CA1 region in vivo are layer-specific: modulation of evoked potentials. Neuroscience 108:249-62

Magee JC, Johnston D (1995) Characterization of single voltage-gated Na+ and Ca2+ channels in apical dendrites of rat CA1 pyramidal neurons. J Physiol 487 ( Pt 1):67-90 [PubMed]

Mainen ZF, Joerges J, Huguenard JR, Sejnowski TJ (1995) A model of spike initiation in neocortical pyramidal neurons. Neuron 15:1427-39 [PubMed]

   Spike Initiation in Neocortical Pyramidal Neurons (Mainen et al 1995) [Model]

Malmivuo J, Plonsey R (1995) Bioelectromagnetism:Principles and Applications of Bioelectric and Biomagnetic Fields

Migliore M, Shepherd GM (2002) Emerging rules for the distributions of active dendritic conductances. Nature Review Neuroscience 3:362-70 [Journal] [PubMed]

   Modulation of temporal integration window (Migliore, Shepherd 2002) [Model]

Plonsey R (1969) Bioelectric Phenomena

Quiroga RQ, Nadasdy Z, Ben-Shaul Y (2004) Unsupervised spike detection and sorting with wavelets and superparamagnetic clustering. Neural Comput 16:1661-87 [PubMed]

RALL W (1962) Electrophysiology of a dendritic neuron model. Biophys J 2(2)Pt 2:145-67 [PubMed]

Schwarz WM (1973) Intermediate Electromagnetic Theory

Spruston N, Johnston D (1992) Perforated patch-clamp analysis of the passive membrane properties of three classes of hippocampal neurons. J Neurophysiol 67:508-29 [Journal] [PubMed]

Stuart G, Spruston N, Hausser M (2001) Dendrites

Toledo-Rodriguez M, Blumenfeld B, Wu C, Luo J, Attali B, Goodman P, Markram H (2004) Correlation maps allow neuronal electrical properties to be predicted from single-cell gene expression profiles in rat neocortex. Cereb Cortex 14:1310-27 [PubMed]

Vanier MC, Bower JM (1999) A comparative survey of automated parameter-search methods for compartmental neural models. J Comput Neurosci 7:149-71 [Journal] [PubMed]

Varona P, Ibarz JM, Lopez-Aguado L, Herreras O (2000) Macroscopic and subcellular factors shaping population spikes. J Neurophysiol 83:2192-208 [PubMed]

Almog M, Korngreen A (2014) A Quantitative Description of Dendritic Conductances and Its Application to Dendritic Excitation in Layer 5 Pyramidal Neurons J Neurosci 34(1):182-196 [Journal]

   Ionic mechanisms of dendritic spikes (Almog and Korngreen 2014) [Model]

Anwar H, Roome CJ, Nedelescu H, Chen W, Kuhn B, De Schutter E (2014) Dendritic diameters affect the spatial variability of intracellular calcium dynamics in computer models Frontiers in Cellular Neuroscience 8(168):1-14 [Journal] [PubMed]

   [1 reconstructed morphology on NeuroMorpho.Org]
   Calcium dynamics depend on dendritic diameters (Anwar et al. 2014) [Model]

beim Graben P, Rodrigues S (2013) A biophysical observation model for field potentials of networks of leaky integrate-and-fire neurons Frontiers in Computational Neuroscience 6:1-13 [Journal] [PubMed]

   Biophysical model for field potentials of networks of I&F neurons (beim Graben & Serafim 2013) [Model]

Camunas-Mesa LA, Quiroga RQ (2013) A Detailed and Fast Model of Extracellular Recordings Neural Comput 25(5):1191-1212 [Journal] [PubMed]

   A detailed and fast model of extracellular recordings (Camunas-Mesa & Qurioga 2013) [Model]

Carnevale NT, Morse TM (1996-2009) Research reports that have used NEURON Web published citations at the NEURON website [Journal]

Diwakar S, Lombardo P, Solinas S, Naldi G, D`Angelo E (2011) Local field potential modeling predicts dense activation in cerebellar granule cells clusters under LTP and LTD control PLoS ONE 6(7):e21928 [Journal]

   Reconstructing cerebellar granule layer evoked LFP using convolution (ReConv) (Diwakar et al. 2011) [Model]

Frey U, Egert U, Heer F, Hafizovic S, Hierlemann A (2009) Microelectronic system for high-resolution mapping of extracellular electric fields applied to brain slices. Biosens Bioelectron 24:2191-8 [Journal] [PubMed]

Glabska H, Chintaluri C, Wójcik DK (2017) Collection of Simulated Data from a Thalamocortical Network Model. Neuroinformatics 15:87-99 [Journal] [PubMed]

   Collection of simulated data from a thalamocortical network model (Glabska, Chintaluri, Wojcik 2017) [Model]

Mechler F, Victor JD (2012) Dipole characterization of single neurons from their extracellular action potentials. J Comput Neurosci 32:73-100 [Journal] [PubMed]

   Dipole Localization Kit (Mechler & Victor, 2012) [Model]

Parasuram H, Nair B, D`Angelo E, Hines M, Naldi G, Diwakar S (2016) Computational modeling of single neuron extracellular electric potentials and network Local Field Potentials using LFPsim Front. Comput. Neurosci. 10:65 [Journal]

   Modeling single neuron LFPs and extracellular potentials with LFPsim (Parasuram et al. 2016) [Model]

Wang K, Riera J, Enjieu-Kadji H, Kawashima R (2013) The Role of Extracellular Conductivity Profiles in Compartmental Models for Neurons: Particulars for Layer 5 Pyramidal Cells Neural Comput 25(7):1807-52 [Journal] [PubMed]

   Modeling conductivity profiles in the deep neocortical pyramidal neuron (Wang K et al. 2013) [Model]

(47 refs)