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

//float EK=-0.085
float Gbar = 1.0

float offset = 0.01

int tab_ydivs = {tab_xdivs}
float tab_ymin = {CCaI}
float tab_ymax = {Ca_tab_max}
float Temp = 22
float temperature = 5

/* non-inactivating BK-type Ca-dependent K current
** Moczydlowski and Latorre 1983, J Gen Physiol 82, 511-542.
** Uses original parameters. 
** Includes Paul Smolen's bug fix. 
*/
/* scaled for units: V, sec, mM */
function make_Moczyd_KC
	int i, j
	float ginf, itau, c, dc, cmin, cmax
	float x, dx, y, dy
	float a, b
	float ZFbyRT = 23210/(273.15 + (Temp))

	if (!({exists Moczyd_KC}))
		create tab2Dchannel Moczyd_KC
		setfield Moczyd_KC Ek {EK} Gbar {Gbar}  \
		    Xindex {VOLT_C1_INDEX} Xpower 1 Ypower 0 Zpower 0

		call Moczyd_KC TABCREATE X {tab_xdivs} {tab_xmin}  \
		    {tab_xmax} {tab_ydivs} {tab_ymin} {tab_ymax}
	end
echo diag Moczyd_KC 1
	dx = ({tab_xmax} - {tab_xmin})/{tab_xdivs}
	dy = (tab_ymax - tab_ymin)/tab_ydivs
	x = {tab_xmin} - {offset}
	for (i = 0; i <= ({tab_xdivs}); i = i + 1)
		y = tab_ymin
		for (j = 0; j <= (tab_ydivs); j = j + 1)
			/* \
			     Must check that the following are scaled correctly!!  \
			    */
			a = 2.5e3/(1 + ((1.5e-3*{exp {-0.085e3*x}})/y))
			b = 1.5e3/(1 + (y/(150e-6*{exp {-0.077e3*x}})))
			itau = a + b
			ginf = a/itau
			setfield Moczyd_KC X_A->table[{i}][{j}] {temperature * a}
			setfield Moczyd_KC X_B->table[{i}][{j}] {temperature * itau}
			y = y + dy
		end
		x = x + dx
	end
    setfield Moczyd_KC X_A->calc_mode {LIN_INTERP}
    setfield Moczyd_KC X_B->calc_mode {LIN_INTERP}
echo diag Moczyd_KC 3
create neutral comp
setfield comp x -0.10
setfield comp y 0.10
addmsg comp Moczyd_KC VOLTAGE x
addmsg comp Moczyd_KC CONCEN y
echo diag Moczyd_KC 4
end


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