Layer V pyramidal cell model with reduced morphology (Mäki-Marttunen et al 2018)

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Accession:187474
" ... In this work, we develop and apply an automated, stepwise method for fitting a neuron model to data with fine spatial resolution, such as that achievable with voltage sensitive dyes (VSDs) and Ca2+ imaging. ... We apply our method to simulated data from layer 5 pyramidal cells (L5PCs) and construct a model with reduced neuronal morphology. We connect the reduced-morphology neurons into a network and validate against simulated data from a high-resolution L5PC network model. ..."
References:
1 . Hay E, Hill S, Schürmann F, Markram H, Segev I (2011) Models of neocortical layer 5b pyramidal cells capturing a wide range of dendritic and perisomatic active properties. PLoS Comput Biol 7:e1002107 [PubMed]
2 . Hay E, Segev I (2015) Dendritic Excitability and Gain Control in Recurrent Cortical Microcircuits. Cereb Cortex 25:3561-71 [PubMed]
3 . Mäki-Marttunen T, Halnes G, Devor A, Metzner C, Dale AM, Andreassen OA, Einevoll GT (2018) A stepwise neuron model fitting procedure designed for recordings with high spatial resolution: Application to layer 5 pyramidal cells. J Neurosci Methods 293:264-283 [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: Neocortex;
Cell Type(s): Neocortex L5/6 pyramidal GLU cell;
Channel(s): I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I M; I h; I K,Ca; I Calcium; I A, slow;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; NEURON (web link to model); Python; NeuroML;
Model Concept(s):
Implementer(s): Maki-Marttunen, Tuomo [tuomomm at uio.no]; Metzner, Christoph [c.metzner at herts.ac.uk];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I M; I h; I K,Ca; I Calcium; I A, slow;
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reducedhaymodel
single_cell
models
fourcompartment.hoc
                            
begintemplate fourcompartment

public soma, dend, apic
public init

create soma, dend, apic[2]

public somatic, basal, apical
objref somatic, basal, apical

proc init() {

 connect dend(0), soma(0)
 connect apic[0](0), soma(1)
 connect apic[1](0), apic[0](1)

 soma insert pas
 dend insert pas
 apic[0] insert pas
 apic[1] insert pas

 soma {nseg = 1 Ra = 100 diam = 13.47 L = 23.17 cm = 1 V = -80 e_pas = -90}
 dend {nseg = 1 Ra = 100 diam = 10.28 L = 282.13 cm = 2 V = -80 e_pas = -90}
 apic[0] {nseg = 1 Ra = 100 diam = 5.04 L = 700.0 cm = 2 V = -80 e_pas = -90}
 apic[1] {nseg = 1 Ra = 100 diam = 5.04 L = 600.53 cm = 2 V = -80 e_pas = -90}

 soma { 
  insert Ca_LVAst
  insert Ca_HVA
  insert SKv3_1
  insert SK_E2
  insert K_Tst
  insert K_Pst
  insert Nap_Et2
  insert NaTa_t
  insert CaDynamics_E2
  insert Ih
  ek = -85
  ena = 50
  gIhbar_Ih = 0.0002
  g_pas = 0.0000338
  decay_CaDynamics_E2 = 460.0
  gamma_CaDynamics_E2 = 0.000501
  gCa_LVAstbar_Ca_LVAst = 0.00343
  gCa_HVAbar_Ca_HVA = 0.000992
  gSKv3_1bar_SKv3_1 = 0.693
  gSK_E2bar_SK_E2 = 0.0441
  gK_Tstbar_K_Tst = 0.0812
  gK_Pstbar_K_Pst = 0.00223
  gNap_Et2bar_Nap_Et2 = 0.00172
  gNaTa_tbar_NaTa_t = 2.04
 }
 dend {
  insert Ih
  gIhbar_Ih = 0.0002
  g_pas = 0.0000467
 }
 apic[0] {
  insert Ca_LVAst
  insert Ca_HVA
  insert SKv3_1
  insert SK_E2
  insert NaTa_t
  insert Im
  insert CaDynamics_E2
  insert Ih
  ek = -85
  ena = 50
  decay_CaDynamics_E2 = 122
  gamma_CaDynamics_E2 = 0.000509
  gSK_E2bar_SK_E2 = 0.0012
  gSKv3_1bar_SKv3_1 = 0.000261
  gNaTa_tbar_NaTa_t = 0.0213
  gImbar_Im = 0.0000675
  g_pas = 0.0000589
  gIhbar_Ih = 0.0004
  gCa_LVAstbar_Ca_LVAst = 0.0187
  gCa_HVAbar_Ca_HVA = 0.000555
 }
 apic[1] {
  insert Ca_LVAst
  insert Ca_HVA
  insert SKv3_1
  insert SK_E2
  insert NaTa_t
  insert Im
  insert CaDynamics_E2
  insert Ih
  ek = -85
  ena = 50
  decay_CaDynamics_E2 = 122
  gamma_CaDynamics_E2 = 0.000509
  gSK_E2bar_SK_E2 = 0.0012
  gSKv3_1bar_SKv3_1 = 0.000261
  gNaTa_tbar_NaTa_t = 0.0213
  gImbar_Im = 0.0000675
  g_pas = 0.0000589
  gIhbar_Ih = 0.0004
  gCa_LVAstbar_Ca_LVAst = 0.0187
  gCa_HVAbar_Ca_HVA = 0.000555
 }

 somatic = new SectionList()  
 basal = new SectionList()    
 apical = new SectionList()   

 apic[0] apical.append() 
 apic[1] apical.append() 
 dend basal.append()     
 soma somatic.append() 

}

endtemplate fourcompartment

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