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;
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Five-neuron-neocortex
L5P37C-onlybasal
channels
README
Axon_chans.g *
Axon_chans_tab.g
Axon_comps.g
DiffRm.g *
DS1_141099_rot2_sc_defmesh_axon_onlybasal.p
electrodes_fixbug.g
electrodes_try.g *
Excitatory_fibres.g
Fibres.g *
Firing_rate_modulation.g *
Firing_rate_profile.g *
Golgi_grc_multicomp_ax.g
Gran_chan_tab.g *
Gran_comp_soma_dend_axon.g
Gran_const.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+syn.g
L5P_const.g *
L5P_const+axon+syn.g *
L5P_graph.g
L5P_history.g
L5P_onlybasal_make.g
L5P_synchan.g
L5P37C_onlybasal.g
nsynapses.g *
                            
// genesis

int sum, nsynapses
str list 
str output 

include ../Fibres/Fibres_make.g

    list = ""
    output = "L5P_AMPA_nsynapses.dat"

       sum = 0
       foreach name ({el /L5P/p#[][TYPE=compartment]})
//         echo {name}
         ce {name}/AMPA
         nsynapses = {getfield . nsynapses}
         sum = {sum} + {nsynapses}
//         list = (list) @ {name} @ " " @ {nsynapses} @ " " @ {chr 10}
       end

       list = (list) @ {sum} @ " " @ {chr 10}
       
       
       ce /Excitatory_fibres/FF
       sum = 0
       for (i = 0; i < {number_FF_fibres}; i = {i} + 1)
            sum = {sum} + {getsyncount fibre[{i}]}
       end
       list = (list) @ {sum} @ " " @ {chr 10}
       
       
       ce /Excitatory_fibres/FBintra
       sum = 0
       for (i = 0; i < {number_FBintra_fibres}; i = {i} + 1)
            sum = {sum} + {getsyncount fibre[{i}]}
       end
       list = (list) @ {sum} @ " " @ {chr 10}
       
       
       ce /Excitatory_fibres/FBinter
       sum = 0
       for (i = 0; i < {number_FBinter_fibres}; i = {i} + 1)
            sum = {sum} + {getsyncount fibre[{i}]}
       end
       list = (list) @ {sum} @ " " @ {chr 10}
              
       
    echo {list}  > {output} // {source_list}


    list = ""
    output = "L5P_GABAA_nsynapses.dat"

       sum = 0
       foreach name ({el /L5P/p#[][TYPE=compartment]})
//         echo {name}
         ce {name}/GABA
         nsynapses = {getfield . nsynapses}
         sum = {sum} + {nsynapses}
//         list = (list) @ {name} @ " " @ {nsynapses} @ " " @ {chr 10}
       end

       list = (list) @ {sum} @ " " @ {chr 10}
       
       
       ce /Inhibitory_fibres/FF
       sum = 0
       for (i = 0; i < {number_FF_fibres}; i = {i} + 1)
            sum = {sum} + {getsyncount fibre[{i}]}
       end
       list = (list) @ {sum} @ " " @ {chr 10}
       
       
       ce /Inhibitory_fibres/FBintra
       sum = 0
       for (i = 0; i < {number_FBintra_fibres}; i = {i} + 1)
            sum = {sum} + {getsyncount fibre[{i}]}
       end
       list = (list) @ {sum} @ " " @ {chr 10}
       
       
       ce /Inhibitory_fibres/FBinter
       sum = 0
       for (i = 0; i < {number_FBinter_fibres}; i = {i} + 1)
            sum = {sum} + {getsyncount fibre[{i}]}
       end
       list = (list) @ {sum} @ " " @ {chr 10}
       
       
       
    echo {list}  > {output} // {source_list}