5-neuron-model of neocortex for producing realistic extracellular AP shapes (Van Dijck et al. 2012)

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Accession:226812
This is a 5-neuron model of neocortex, containing one tufted layer-5 pyramidal cell, two non-tufted pyramidal cells, and two inhibitory interneurons. It was used to reproduce extracellular spike shapes in a study comparing algorithms for spike sorting and electrode selection. The neuron models are adapted from Dyhrfjeld-Johnsen et al. (2005).
Reference:
1 . Van Dijck G, Seidl K, Paul O, Ruther P, Van Hulle MM, Maex R (2012) Enhancing the yield of high-density electrode arrays through automated electrode selection. Int J Neural Syst 22:1-19 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Extracellular; Neuron or other electrically excitable cell; Realistic Network;
Brain Region(s)/Organism:
Cell Type(s): Neocortex U1 L5B pyramidal pyramidal tract GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: GENESIS;
Model Concept(s):
Implementer(s): Maex, Reinoud [reinoud at bbf.uia.ac.be];
Search NeuronDB for information about:  Neocortex U1 L5B pyramidal pyramidal tract GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell;
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Five-neuron-neocortex
Granule_cell
Axon10.p
Axon20.p
Gran_chan.g
Gran_chan_KA.g *
Gran_chan_KCa.g *
Gran_chan_KCa_tab.g *
Gran_chan_tab.g *
Gran_comp.g
Gran_comp_soma_dend.g
Gran_comp_soma_dend_axon.g
Gran_comp_soma_dend_noH.g
Gran_const.g *
Gran_synchan.g
Gran1M0.p *
Gran1M0_dend.p
Gran1M0_dend_axon.p
Gran1M0_dend10.p
Gran1M0_dend20.p
Gran1M0_dend3D.p
Gran1M0_dend3D_axon.p
Gran1M0_dend3D_axon10_RM2.p
Gran1M0_dend3D_axon20_RM2.p
Gran1M0_dend3D_axon3.p
Gran1M0_dend3D_axon3_RM2.p
Gran1M0_dend3D_axon5_RM2.p
Gran1M0_dend40.p
tabCaHVA37.data
tabH37.data
tabInNa37.data
tabKA37.data
tabKCa37.data
tabKDr37.data
TEST.g
TEST_dend.g
TEST_exp.g
TEST_gapjunction.g
TEST_soma_dend_axon.g
TEST2_gapjunction.g
TEST2exp_gapjunction.g
TEST3_gapjunction.g
TEST4_gapjunction.g
                            
// Morphology file for Golgi cell
// A single compartment neuron with a spherical soma yielding
// an Rin (78 MegaOhm) and a time-constant (24 msec) as tabulated in Midtgaard (1992).
// The resulting Cm is 0.31 nF, assuming a specific membrane capacitance of 0.01 (F/m^2).
// The resulting surface area is 0.31e5 um^2.
// Written by RM (27/11/95).
// changed /library/soma to /library/interneuron/soma on 16/4/96 MAEX

   
*relative

*set_compt_param ELEAK {ELEAK}
*set_compt_param EREST_ACT {EREST_ACT}
   *set_compt_param RM	3.03 // 2.4000	// 24 000 ohm.cm^2
*set_compt_param RA	1.0000 	// 
*set_compt_param CM	0.0100	// 1microF/cm^2


// The entire neuron has now about the same membrane surface area
// as the original single soma compartment. In addition, all
// compartments have the same area.

   
*compt /library/granule/soma
   soma		none		0.000	0.000	0.000	12.25 // 30.0 // 99.33

*compt /library/granule/dend
   dend[0]        soma              0.0       3.75     0.0      5.0
   dend[1]        dend[0]           0.0       3.75     0.0      5.0
   dend[2]        dend[1]           0.0       3.75     0.0      5.0
   dend[3]        dend[2]           0.0       3.75     0.0      5.0
   dend[4]        dend[3]           0.0       3.75     0.0      5.0
   dend[5]        dend[4]           0.0       3.75     0.0      5.0
   dend[6]        dend[5]           0.0       3.75     0.0      5.0
   dend[7]        dend[6]           0.0       3.75     0.0      5.0
   dend[8]        dend[7]           0.0       4.6875   0.0      4.0
   dend[9]        dend[8]           0.0       4.6875   0.0      4.0
   dend[10]       dend[9]           0.0       4.6875   0.0      4.0
   dend[11]       dend[10]          0.0       4.6875   0.0      4.0
   dend[12]       dend[11]          0.0       4.6875   0.0      4.0
   dend[13]       dend[12]          0.0       4.6875   0.0      4.0
   dend[14]       dend[13]          0.0       4.6875   0.0      4.0
   dend[15]       dend[14]          0.0       4.6875   0.0      4.0
   dend[16]       dend[15]          0.0       6.25     0.0      3.0
   dend[17]       dend[16]          0.0       6.25     0.0      3.0
   dend[18]       dend[17]          0.0       6.25     0.0      3.0
   dend[19]       dend[18]          0.0       6.25     0.0      3.0
   dend[20]       dend[19]          0.0       6.25     0.0      3.0
   dend[21]       dend[20]          0.0       6.25     0.0      3.0
   dend[22]       dend[21]          0.0       6.25     0.0      3.0
   dend[23]       dend[22]          0.0       6.25     0.0      3.0
   dend[24]       dend[23]          0.0       9.375    0.0      2.0
   dend[25]       dend[24]          0.0       9.375    0.0      2.0
   dend[26]       dend[25]          0.0       9.375    0.0      2.0
   dend[27]       dend[26]          0.0       9.375    0.0      2.0
   dend[28]       dend[27]          0.0       9.375    0.0      2.0
   dend[29]       dend[28]          0.0       9.375    0.0      2.0
   dend[30]       dend[29]          0.0       9.375    0.0      2.0
   dend[31]       dend[30]          0.0       9.375    0.0      2.0
   dend[32]       dend[31]          0.0      18.75     0.0      1.0
   dend[33]       dend[32]          0.0      18.75     0.0      1.0
   dend[34]       dend[33]          0.0      18.75     0.0      1.0
   dend[35]       dend[34]          0.0      18.75     0.0      1.0
   dend[36]       dend[35]          0.0      18.75     0.0      1.0
   dend[37]       dend[36]          0.0      18.75     0.0      1.0
   dend[38]       dend[37]          0.0      18.75     0.0      1.0
   dend[39]       dend[38]          0.0      18.75     0.0      1.0

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