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
                            
//genesis
/**********************************************************************
** Sets up active membrane Granule cell compartment prototypes 
**  and dendritic spine prototypes.
** Carl Piaf 7th December 1994
** Uses Granule1M.p data file
** Synapses: NONE
** This is a copy of
** /bbf/haddock/carl/Genesis/Granule/True_sa_1_compt_L37/Gran_comp1.g, 
** converted to Genesis 2 by RM
** changed soma to granule/soma on 16/4/96
** Modified bt Reinoud Maex 10/95-4/96
********************************************************************/

/*********************************************************************/
/*function make_Granule_comps 					     */
/*********************************************************************/

function make_Granule_comps 


/* separate function so we can have local variables */

	float len, dia, surf, shell_vol, shell_dia

	/* make spherical soma prototype with sodium currents*/
	len = 0.00e-6
	dia = 1
	surf = dia*dia*{PI}
	shell_dia = dia - 2*{Shell_thick}
	shell_vol = (dia*dia*dia - shell_dia*shell_dia*shell_dia)*{PI}/6.0
//        create neutral granule
	if (!({exists soma}))
		create compartment soma
	end
	// F
	// ohm, correct for sphere
	// V
	// V
	// ohm


	setfield soma Cm {{CM}*surf} Ra {8.0*{RA}/(dia*{PI})}  \
	    Em {EREST_ACT} Vm {RESET_ACT} Rm {{RMs}/surf} inject 0.0  \
	    dia {dia} len {len}

	// Now copy the channels and set maximal conductances */


	copy Gran_InNa soma/InNa
	addmsg soma soma/InNa VOLTAGE Vm
	addmsg soma/InNa soma CHANNEL Gk Ek
	setfield soma/InNa Gbar {{GInNas}*surf}
	copy Gran_KDr soma/KDr
	addmsg soma soma/KDr VOLTAGE Vm
	addmsg soma/KDr soma CHANNEL Gk Ek
	setfield soma/KDr Gbar {{GKDrs}*surf}
	copy Gran_KA soma/KA
	addmsg soma soma/KA VOLTAGE Vm
	addmsg soma/KA soma CHANNEL Gk Ek
	setfield soma/KA Gbar {{GKAs}*surf}
	copy Gran_CaHVA soma/CaHVA
	addmsg soma soma/CaHVA VOLTAGE Vm
	addmsg soma/CaHVA soma CHANNEL Gk Ek
	setfield soma/CaHVA Gbar {{GCaHVAs}*surf}
	copy Gran_H soma/H
	addmsg soma soma/H VOLTAGE Vm
	addmsg soma/H soma CHANNEL Gk Ek
	setfield soma/H Gbar {{GHs}*surf}

	copy Moczyd_KC soma/Moczyd_KC
	addmsg soma soma/Moczyd_KC VOLTAGE Vm
	addmsg soma/Moczyd_KC soma CHANNEL Gk Ek
	setfield soma/Moczyd_KC Gbar {{GMocs}*surf}

	copy AMPA soma/mf_AMPA
	setfield soma/mf_AMPA \
		gmax    {{getfield soma/mf_AMPA gmax} * surf}
	addmsg  soma/mf_AMPA  soma CHANNEL Gk  Ek
	addmsg  soma soma/mf_AMPA  VOLTAGE Vm

	copy AMPA soma/pf_AMPA
	setfield soma/pf_AMPA \
		gmax    {{getfield soma/pf_AMPA gmax} * surf}
	addmsg  soma/pf_AMPA  soma CHANNEL Gk  Ek
	addmsg  soma soma/pf_AMPA  VOLTAGE Vm

	copy NMDA soma/mf_NMDA
	setfield soma/mf_NMDA \
		gmax    {{getfield soma/mf_NMDA gmax} * surf}
	addmsg  soma/mf_NMDA soma/mf_NMDA/Mg_BLOCK CHANNEL Gk Ek
	addmsg  soma/mf_NMDA/Mg_BLOCK soma CHANNEL Gk Ek
	addmsg  soma soma/mf_NMDA/Mg_BLOCK VOLTAGE Vm
	addmsg  soma soma/mf_NMDA VOLTAGE Vm

        copy GABAA soma/GABAA
        setfield soma/GABAA gmax {{getfield soma/GABAA gmax} * surf}
        addmsg  soma/GABAA soma CHANNEL Gk Ek
        addmsg  soma soma/GABAA VOLTAGE Vm

        copy GABAB soma/GABAB
        setfield soma/GABAB gmax {{getfield soma/GABAB gmax} * surf}
        addmsg soma/GABAB soma CHANNEL Gk Ek
        addmsg soma soma/GABAB VOLTAGE Vm

	//lets keep it simple for now

        if (!{exists soma/Ca_pool})
              create Ca_concen soma/Ca_pool
        end
	setfield soma/Ca_pool tau {CaTau} \
                              B {1.0/(2.0*96494*shell_vol*{PI}*100/2012.67)} \
                       	    Ca_base {CCaI} thick {Shell_thick}
// the volume of the Ca-pool may not change in this 1C model

	addmsg soma/Ca_pool soma/Moczyd_KC CONCEN Ca
	addmsg soma/CaHVA soma/Ca_pool I_Ca Ik
	// Possibility of modelling NMDA Ca influx (not done in Gabbiani et al.)
	// Probably not worth the effort (yet).

end


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