Layer 5 Pyramidal Neuron (Shai et al., 2015)

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Accession:180373
This work contains a NEURON model for a layer 5 pyramidal neuron (based on Hay et al., 2011) with distributed groups of synapses across the basal and tuft dendrites. The results of that simulation are used to fit a phenomenological model, which is also included in this file.
Reference:
1 . Shai AS, Anastassiou CA, Larkum ME, Koch C (2015) Physiology of layer 5 pyramidal neurons in mouse primary visual cortex: coincidence detection through bursting. PLoS Comput Biol 11:e1004090 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s): Glutamate;
Simulation Environment: NEURON; MATLAB;
Model Concept(s): Dendritic Action Potentials; Active Dendrites;
Implementer(s):
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; Glutamate;
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ShaiEtAl2015
simulationcode
Ca_HVA.mod *
Ca_LVAst.mod *
CaDynamics_E2.mod *
epsp.mod *
glutamate.mod *
Ih.mod *
Im.mod *
K_Pst.mod *
K_Tst.mod *
Nap_Et2.mod *
NaTa_t.mod *
NaTs2_t.mod *
SK_E2.mod *
SKv3_1.mod *
AccessoryFunctions.hoc
DefineSections.hoc
distSynsCluster.hoc
distSynsCluster2.hoc
distSynsUniform.hoc
distSynsUniform2.hoc
distSynsUniformAlpha.hoc
Fig3A.hoc
neuron203.os
O_vd_C.dat
O_vs_C.dat
Run.hoc
varycolor.m
                            

objref tuftList
tuftList = new SectionList()
L5PC.apic[22] {tuftList.subtree()}
L5PC.apic[22] {tuftList.remove()}

forsec tuftList{ 

	if (L/nseg>0.1){
		nseg = int(L/5)+3
	
	}
	//print "nseg is ", nseg

}


// HOTZONE I WILL TAKE TO BE L5PC.APIC[22]
objref hotZoneList
hotZoneList = new SectionList()
L5PC.apic[22] {hotZoneList.append()}

objref axonList
axonList = new SectionList()
L5PC.axon[0]{axonList.append()}
L5PC.axon[1]{axonList.append()}





objref basalList
basalList = new SectionList()
basalList.wholetree()
basalList.remove(tuftList)
basalList.remove(hotZoneList)
basalList.remove()

forsec basalList{ 

	if (L/nseg>0.1){
		nseg = int(L/5)+3
	
	}
	//print "nseg is ", nseg

}


objref allSections
allSections = new SectionList()
allSections.wholetree()
allSections.remove(axonList)



objref shapeG
shapeG = new Shape()
//shapeG.color_list(tuftList,2) //red
//shapeG.color_list(hotZoneList,3) //blue
//shapeG.color_list(basalList,5) // orange
shapeG.color_list(axonList,0)
shapeG.color_list(allSections,1)







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