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

// this is a copy of the channels of the granule cell model
// used also for the axons in Maex & De Schutter 2007

/*********************************************************************
**               The current equations themselves 
*********************************************************************/


float offset = 0.010

function make_Axon_chans_tab

    	float temperature = 5
    	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

	if ({!{exists /library}})
          	create neutral /library 
          	disable /library
   	end

        ce /library

	if ({!{exists L5P-onlybasal}})
          	create neutral L5P-onlybasal 
   	end

        ce L5P-onlybasal

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

	create tabchannel Axon_InNa
	setfield Axon_InNa Ek {ENa} Gbar 70 Ik 0 Gk 0 Xpower 3 Ypower 1  \
	    Zpower 0

	call Axon_InNa TABCREATE X {tab_xdivs} {tab_xmin} {tab_xmax}

	setfield Axon_InNa X_A->calc_mode 1 X_B->calc_mode 1

	call Axon_InNa TABCREATE Y {tab_xdivs} {tab_xmin} {tab_xmax}

	setfield Axon_InNa Y_A->calc_mode 1 Y_B->calc_mode 1

        call Axon_InNa TABREAD tabAxonInNa.dat

        call Axon_InNa TABFILL X 3000 0
        call Axon_InNa TABFILL Y 3000 0


// Delayed Rectifier K current 

	create tabchannel Axon_KDr
	setfield Axon_KDr Ek {EK} Gbar 19 Ik 0 Gk 0 Xpower 4 Ypower 1  \
	    Zpower 0

	call Axon_KDr TABCREATE X {tab_xdivs} {tab_xmin} {tab_xmax}

	setfield Axon_KDr X_A->calc_mode 1 X_B->calc_mode 1

	call Axon_KDr TABCREATE Y {tab_xdivs} {tab_xmin} {tab_xmax}

	setfield Axon_KDr Y_A->calc_mode 1 Y_B->calc_mode 1

        call Axon_KDr TABREAD tabAxonKDr.dat

        call Axon_KDr TABFILL X 3000 0
        call Axon_KDr TABFILL Y 3000 0

end

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