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]
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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

// copied from Golg_comp_soma_dend_axon.g
 
// include L5P_const+axon+syn.g

function make_Axon_comps

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

	float len, dia, surf


	/* make cylindrical axon prototype */
        len = 1
        dia = 1
        surf = len*dia*{PI}

	if (!({exists /library/L5P-onlybasal/axon}))
		create compartment /library/L5P-onlybasal/axon
	end

        ce /library/L5P-onlybasal

	setfield axon Cm {{CM}*surf} Ra {4.0*{RA}*len/(dia*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 */

        if (!({exists axon/InNa}))
        	copy Axon_InNa axon/InNa
	        addmsg axon axon/InNa VOLTAGE Vm
	        addmsg axon/InNa axon CHANNEL Gk Ek
	end
        setfield axon/InNa Gbar {{GInNa_a}*surf*1} // 1.2}   // 1.2

        if (!({exists axon/KDr}))
        	copy Axon_KDr axon/KDr
	        addmsg axon axon/KDr VOLTAGE Vm
	        addmsg axon/KDr axon CHANNEL Gk Ek
	end
        setfield axon/KDr Gbar {{GKDr_a}*surf*3}   // 2.8 // 2.7 // 1.5

end