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
L5P37C-notuft
channels
README
Axon_chans.g *
Axon_chans_tab.g
Axon_comps.g
DiffRm.g *
DS1_141099_rot2_sc_defmesh_axon_notuft.p
electrodes_fixbug.g *
electrodes_try.g *
Excitatory_fibres.g *
Fibres.g *
Firing_rate_modulation.g *
Firing_rate_profile.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.g
L5P_comps+axon+syn.g
L5P_const.g *
L5P_const+axon+syn.g *
L5P_graph.g
L5P_history.g *
L5P_notuft_make.g
L5P_synchan.g
L5P37C_notuft.g
nsynapses.g *
test_position.g *
                            
echo making windows for graphics






//Display of Vm in all compartments of layer 5 pyramidal cell morphology

create xform /cellform [0%, 0%, 40%, 80%]
create xdraw /cellform/draw [0,0,100%,100%]
setfield /cellform/draw xmin -2.5e-4 xmax 2.5e-4 \
                        ymin -8.0e-4 ymax 12.0e-4 \
                        zmin -20e-5 zmax 50e-6 bg white transform y
xshow /cellform
create xcell /cellform/draw/cell
setfield /cellform/draw/cell colmin -0.1 colmax 0.05 path /L5P/##[TYPE=compartment] field Vm
useclock /cellform/draw/cell 1
xcolorscale hot


//Graph of somatic Vm
create xform /data1 [0%, 0%, 33%, 33%] -fg black -bg white
create xgraph /data1/DS1_141099 

setfield /data1/DS1_141099 XUnits sec YUnits Volts
setfield /data1/DS1_141099 xmax {tmax} ymin -0.11 ymax 0.04 bg white
useclock /data1/DS1_141099 1
	
xshow /data1

// for an unknown reason, the following three lines give an execution error
// strangely enough, the same code works for the other neuron models
// I now added thses msgs at the end of the main scipt
// addmsg /L5P/soma /data1/DS1_141099 PLOT Vm *Soma_Vm *red
//  addmsg /L5P/axon[19] /data1/DS1_141099 PLOT Vm *Axon_Vm *blue
// addmsg /L5P/p0b1b2b1b1b1b2b1b2b1b2b1b2b1b1b1b2b1b2b1b2b1b2b1b2b1b2b1b1[8] /data1/DS1_141099 PLOT Vm *Dend_Vm *black 



/*

//Graph of somatic conductances
create xform /data2 [0%, 0%, 100%, 100%]
create xgraph /data2/Conductance

setfield /data2/Conductance XUnits sec YUnits S
setfield /data2/Conductance xmax {tmax} ymin 0 ymax 1e-8 bg white
	
addmsg /L5P/soma/NaF /data2/Conductance PLOT Gk *NaF *red
addmsg /L5P/soma/NaP /data2/Conductance PLOT Gk *NaP *orange
addmsg /L5P/soma/KDr /data2/Conductance PLOT Gk *KDr *blue
addmsg /L5P/soma/KA /data2/Conductance PLOT Gk *KA *black
addmsg /L5P/soma/KC /data2/Conductance PLOT Gk *KC *purple
addmsg /L5P/soma/KAHP /data2/Conductance PLOT Gk *KAHP *green
addmsg /L5P/soma/K2 /data2/Conductance PLOT Gk *K2 *brown
addmsg /L5P/soma/KM /data2/Conductance PLOT Gk *KM *grey
addmsg /L5P/soma/CaT /data2/Conductance PLOT Gk *CaT *yellow
addmsg /L5P/soma/CaL /data2/Conductance PLOT Gk *CaL *pink
addmsg /L5P/soma/H /data2/Conductance PLOT Gk *H *cyan


xshow /data2


//Graph of somatic currents
create xform /data3 [0%, 0%, 100%, 100%]
create xgraph /data3/Currents

setfield /data3/Currents XUnits sec YUnits A
setfield /data3/Currents xmax {tmax} ymin -5e-10 ymax 5e-10 bg white

addmsg /L5P/soma/NaF /data3/Currents PLOT Ik *NaF *red
addmsg /L5P/soma/NaP /data3/Currents PLOT Ik *NaP *orange
addmsg /L5P/soma/KDr /data3/Currents PLOT Ik *KDr *blue
addmsg /L5P/soma/KA /data3/Currents PLOT Ik *KA *black
addmsg /L5P/soma/KC /data3/Currents PLOT Ik *KC *purple
addmsg /L5P/soma/KAHP /data3/Currents PLOT Ik *KAHP *green
addmsg /L5P/soma/K2 /data3/Currents PLOT Ik *K2 *brown
addmsg /L5P/soma/KM /data3/Currents PLOT Ik *KM *grey
addmsg /L5P/soma/CaT /data3/Currents PLOT Ik *CaT *yellow
addmsg /L5P/soma/CaL /data3/Currents PLOT Ik *CaL *pink
addmsg /L5P/soma/H /data3/Currents PLOT Ik *H *cyan
	
xshow /data3

*/

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