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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 *
                            
//Genesis - ascii output file

   str asc_name = "L5P_out"
   create asc_file /output/{asc_name}
   addmsg /L5P/soma /output/{asc_name} SAVE Vm
   addmsg /L5P/axon[0] /output/{asc_name} SAVE Vm
   addmsg /L5P/axon[10] /output/{asc_name} SAVE Vm
   addmsg /L5P/p0b1b2b1b1b1b2b1b2b1b2b1b2b1b1b1b2b1b2b1b2b1b2b1b2b1b2b1b1[8] /output/{asc_name} SAVE Vm

/*
   addmsg /L5P/p8[1]      /output/{asc_name} SAVE Vm
   addmsg /L5P/p8[1]/AMPA /output/{asc_name} SAVE Gk
   addmsg /L5P/p8[1]/AMPA /output/{asc_name} SAVE Ik 
   addmsg /L5P/p8[1]/GABA /output/{asc_name} SAVE Gk
  addmsg /L5P/p8[1]/GABA /output/{asc_name} SAVE Ik 
*/
   str asc_file_name = {filename} @ "L5P_" @ {label} @ "_somaVm.dat"
   setfield /output/{asc_name} filename {asc_file_name} initialize 1 append 0 leave_open 1 
   useclock /output/{asc_name} 1

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