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
L5P37C-onlybasal
channels
README
Axon_chans.g *
Axon_chans_tab.g
Axon_comps.g
DiffRm.g *
DS1_141099_rot2_sc_defmesh_axon_onlybasal.p
electrodes_fixbug.g
electrodes_try.g *
Excitatory_fibres.g
Fibres.g *
Firing_rate_modulation.g *
Firing_rate_profile.g *
Golgi_grc_multicomp_ax.g
Gran_chan_tab.g *
Gran_comp_soma_dend_axon.g
Gran_const.g *
Gran_synchan.g *
Harsch-Robinson_modulation.g *
Hgradient.g *
Inhibitory_fibres.g *
L5P_ascout.g
L5P_ascout_exp.g *
L5P_chans.g *
L5P_chans_tab.g
L5P_chans_tab_Temp.g *
L5P_chans_Temp.g *
L5P_comps.g *
L5P_comps+axon+syn.g
L5P_const.g *
L5P_const+axon+syn.g *
L5P_graph.g
L5P_history.g
L5P_onlybasal_make.g
L5P_synchan.g
L5P37C_onlybasal.g
nsynapses.g *
                            
// genesis



/* First include Gran_chan_KCa_tab.g for non-inactivating BK-type 
** Ca-dependent K current.
*/

include ../Granule_cell/Gran_chan_KCa_tab.g 

function make_Granule_chans 

    int i, cdivs
    float zinf, ztau, c, dc, cmin, cmax
    float x, dx, y
    float a, b
    /* The folowing variables are temporary (not temperature) variables
	used to speed up computations */
    float mintau
    float tau
    float temp1
    float temp2

    /* Equations specific to the Granule cell, made by CP */
    /* Inactivating Na current */

    if (!{exists Gran_InNa})
	create tabchannel Gran_InNa
	setfield Gran_InNa Ek {ENa} Gbar 70 Ik 0 Gk 0 Xpower 3 Ypower 1  \
	    Zpower 0

	call Gran_InNa TABCREATE X {tab_xdivs} {tab_xmin} {tab_xmax}
	setfield Gran_InNa X_A->calc_mode 1 X_B->calc_mode 1
	call Gran_InNa TABCREATE Y {tab_xdivs} {tab_xmin} {tab_xmax}
	setfield Gran_InNa Y_A->calc_mode 1 Y_B->calc_mode 1
	call Gran_InNa TABREAD ../Granule_cell/tabInNa37.data
    end

	/* Delayed Rectifier K current */

    if (!{exists Gran_KDr})
	create tabchannel Gran_KDr
	setfield Gran_KDr Ek {EK} Gbar 19 Ik 0 Gk 0 Xpower 4 Ypower 1  \
	    Zpower 0

	call Gran_KDr TABCREATE X {tab_xdivs} {tab_xmin} {tab_xmax}
	setfield Gran_KDr X_A->calc_mode 1 X_B->calc_mode 1
	call Gran_KDr TABCREATE Y {tab_xdivs} {tab_xmin} {tab_xmax}
	setfield Gran_KDr Y_A->calc_mode 1 Y_B->calc_mode 1
	call Gran_KDr TABREAD ../Granule_cell/tabKDr37.data
    end

	/*  K A-current  fast transient potassium channel*/

    if (!{exists Gran_KA})
	create tabchannel Gran_KA
	setfield Gran_KA Ek {EK} Gbar 3.67 Ik 0 Gk 0 Xpower 3 Ypower 1  \
	    Zpower 0

	call Gran_KA TABCREATE X {tab_xdivs} {tab_xmin} {tab_xmax}
	setfield Gran_KA X_A->calc_mode 1 X_B->calc_mode 1
	call Gran_KA TABCREATE Y {tab_xdivs} {tab_xmin} {tab_xmax}
	setfield Gran_KA Y_A->calc_mode 1 Y_B->calc_mode 1
	call Gran_KA TABREAD ../Granule_cell/tabKA37.data
    end

	/* High Voltage Activated HVA Ca current */

    if (!{exists Gran_CaHVA})
	create tabchannel Gran_CaHVA
	setfield Gran_CaHVA Ek {ECa} Gbar 2.91 Ik 0 Gk 0 Xpower 2  \
	    Ypower 1 Zpower 0

	call Gran_CaHVA TABCREATE X {tab_xdivs} {tab_xmin} {tab_xmax}
	setfield Gran_CaHVA X_A->calc_mode 1 X_B->calc_mode 1
	call Gran_CaHVA TABCREATE Y {tab_xdivs} {tab_xmin} {tab_xmax}
	setfield Gran_CaHVA Y_A->calc_mode 1 Y_B->calc_mode 1
	call Gran_CaHVA TABREAD ../Granule_cell/tabCaHVA37.data
    end

	/* Slowly relaxing, mixed Na/K current H 
** Gabbiani et al. used this to model sag in membrane potential during
** hyperpolarizing current pulses 
*/

    if (!{exists Gran_H})
	create tabchannel Gran_H
	setfield Gran_H Ek {EH} Gbar 0.09 Ik 0 Gk 0 Xpower 1 Ypower 0  \
	    Zpower 0

	call Gran_H TABCREATE X {tab_xdivs} {tab_xmin} {tab_xmax}
	setfield Gran_H X_A->calc_mode 1 X_B->calc_mode 1
	call Gran_H TABREAD ../Granule_cell/tabH37.data
    end

	/* non-inactivating BK-type Ca-dependent K current 
   see Moczyd_KC.g
*/
echo diag gran chan 1
make_Moczyd_KC
echo diag gran chan 2



end

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