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;
echo making windows for graphics

// now distribured over statements and functions



function add_xgraph (pathname)

	str pathname

        str windowname = "/output" @ {pathname} @ "_window"
	create xform {windowname} [0%, 0%, 33%, 33%] -fg black -bg white
	xshow ^

        str graphname = {windowname} @ {pathname} @ "_graph"
	create xgraph {graphname}

	setfield ^ XUnits sec YUnits Volts
	setfield ^ xmax {tmax} ymin -0.11 ymax 0.04 bg white
	useclock ^ 1	
	xshow ^

// this is added because program crashes when msgs are laid outside hines solver
/*
      	if ({exists {pathname}/soma})
		name = {findsolvefield . {pathname}/soma Vm}
		addmsg . {graphname} PLOT {name} *Soma_Vm *red
	end

      	if ({exists {pathname}/axon[19]})
		name = {findsolvefield .  {pathname}/axon[19] Vm}
		addmsg . {graphname} PLOT {name} *Axon_Vm *blue
	end

      	if ({exists {pathname}/p0b1b2b1b1b1b2b1b2b1b2b1b2b1b1b1b2b1b2b1b2b1b2b1b2b1b2b1b1[8]})
		name = {findsolvefield . {pathname}/p0b1b2b1b1b1b2b1b2b1b2b1b2b1b1b1b2b1b2b1b2b1b2b1b2b1b2b1b1[8] Vm}
		addmsg . {graphname} PLOT {name} *Dend_Vm *black 
	end
*/
        ce {pathname}
      	if ({exists soma})
		name = {findsolvefield solve soma Vm}
		addmsg solve {graphname} PLOT {name} *Soma_Vm *red
	end

      	if ({exists axon[19]})
		name = {findsolvefield solve  axon[19] Vm}
		addmsg solve {graphname} PLOT {name} *Axon_Vm *blue
	end

      	if ({exists p0b1b2b1b1b1b2b1b2b1b2b1b2b1b1b1b2b1b2b1b2b1b2b1b2b1b2b1b1[8]})
		name = {findsolvefield solve p0b1b2b1b1b1b2b1b2b1b2b1b2b1b1b1b2b1b2b1b2b1b2b1b2b1b2b1b1[8] Vm}
		addmsg solve {graphname} PLOT {name} *Dend_Vm *black 
	end

end