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;
//Genesis - ascii output file

   str asc_name = "network" @ {label} // "L5P_test"
   create asc_file /output/{asc_name}


function add_ascout (pathname) 

	str pathname

	addmsg {pathname}/soma /output/{asc_name} SAVE Vm
//	Addmsg /L5P/axon[0] /output/{asc_name} SAVE Vm
   	addmsg {pathname}/axon[1] /output/{asc_name} SAVE Vm
//	addmsg /L5P/p0b1b2b1b1b1b2b1b2b1b2b1b2b1b1b1b2b1b2b1b2b1b2b1b2b1b2b1b1[8] /output/{asc_name} SAVE Vm
//	addmsg /L5P/p4b2b1[15] /output/{asc_name} SAVE Vm

/*
    if ({exists {pathname}/soma/NaF})
        addmsg {pathname}/soma/NaF /output/{asc_name} SAVE Ik
    end
    if ({exists {pathname}/soma/InNa})
        addmsg {pathname}/soma/InNa /output/{asc_name} SAVE Ik
    end
    if ({exists {pathname}/axon/InNa})
        addmsg {pathname}/axon[0]/InNa /output/{asc_name} SAVE Ik
        addmsg {pathname}/axon[1]/InNa /output/{asc_name} SAVE Ik
        addmsg {pathname}/axon[2]/InNa /output/{asc_name} SAVE Ik
        addmsg {pathname}/axon[6]/InNa /output/{asc_name} SAVE Ik
        addmsg {pathname}/axon[10]/InNa /output/{asc_name} SAVE Ik
        addmsg {pathname}/axon[19]/InNa /output/{asc_name} SAVE Ik
    end

    addmsg {pathname}/p0b1b1b1[3]  /output/{asc_name} SAVE Vm
    if ({exists {pathname}/p0b1b1b1[3]/NaF})
        addmsg {pathname}/p0b1b1b1[3]/NaF /output/{asc_name} SAVE Ik
    end
*/
end



/*
   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

   echo   asc_file_name is {asc_file_name}   
   echo   filename is {filename}
   echo   label is {label}