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;
// 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

       echo the number of synapses on L5P is {sum}
       list = (list) @ "the number of synapses on L5P is"
       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
       echo the number of synapses made by E FF fibres is {sum}
       list = (list) @ "the number of synapses made by E FF fibres is" 
       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
       echo the number of synapses made by E FBintra fibres is {sum}
       list = (list) @ "the number of synapses made by E FBintra fibres is" 
       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
       echo the number of synapses made by E FBinter fibres is {sum}
       list = (list) @ "the number of synapses made by E FBinter fibres is" 
       list = (list) @ {sum} @ " " @ {chr 10}
              
       
    echo {list}  > {output} // {source_list}



    list = ""
    output = "E-FF-fibres_nsynapses.dat"

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


    list = ""
    output = "E-FBintra-fibres_nsynapses.dat"

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

/*       
       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

 
       echo the number of synapses on L5P is {sum}
       list = (list) @ "the number of synapses on L5P is"
       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
       echo the number of synapses made by I FF fibres is {sum}
       list = (list) @ "the number of synapses made by E FF fibres is" 
       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
       echo the number of synapses made by I FBintra fibres is {sum}
       list = (list) @ "the number of synapses made by E FBintra fibres is" 
       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
       echo the number of synapses made by I FBintra fibres is {sum}
       list = (list) @ "the number of synapses made by E FBintra fibres is" 
       list = (list) @ {sum} @ " " @ {chr 10}
       
       
       
    echo {list}  > {output} // {source_list}


    list = ""
    output = "I-FF-fibres_nsynapses.dat"

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


    list = ""
    output = "I-FBintra-fibres_nsynapses.dat"

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





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