5-neuron-model of neocortex for producing realistic extracellular AP shapes (Van Dijck et al. 2012)

 Download zip file 
Help downloading and running models
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]
Citations  Citation Browser
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

// include L5P_const.g


//    str label = "test"

str Excitatory_fibres_history_filename   = {filename} @ "E_"   @ {label} @ ".history"
str Inhibitory_fibres_history_filename   = {filename} @ "I_"   @ {label} @ ".history"

str L5P_history_filename   = {filename} @ "L5P_"   @ {label} @ ".history"



int i
 int size_message_list

   if (!({exists /output/history}))
          create neutral /output/history
   end

   ce /output/history

/*
      echo initializing {Excitatory_fibres_history_filename}
      create spikehistory Excitatory_fibres.history
      setfield Excitatory_fibres.history ident_toggle 0 \ // index
                                    filename {Excitatory_fibres_history_filename} \
                                    initialize 1 leave_open 1 flush 1
      addmsg /Excitatory_fibres/FF/fibre[] /output/history/Excitatory_fibres.history SPIKESAVE
      addmsg /Excitatory_fibres/FBintra/fibre[] /output/history/Excitatory_fibres.history SPIKESAVE
      addmsg /Excitatory_fibres/FBinter/fibre[] /output/history/Excitatory_fibres.history SPIKESAVE
*/


// Inhibitory fibers

/*
      echo initializing {Inhibitory_fibres_history_filename}
      create spikehistory Inhibitory_fibres.history
      setfield Inhibitory_fibres.history ident_toggle 0 \ // index
                                    filename {Inhibitory_fibres_history_filename} \
                                    initialize 1 leave_open 1 flush 1
      addmsg /Inhibitory_fibres/FF/fibre[] /output/history/Inhibitory_fibres.history SPIKESAVE
      addmsg /Inhibitory_fibres/FBintra/fibre[] /output/history/Inhibitory_fibres.history SPIKESAVE
      addmsg /Inhibitory_fibres/FBinter/fibre[] /output/history/Inhibitory_fibres.history SPIKESAVE
*/

// L5P cells

      	echo initializing {L5P_history_filename}
      	create spikehistory L5P.history
      	setfield ^ ident_toggle 0 \ // index
                                   filename {L5P_history_filename} \
                                   initialize 1 leave_open 1 flush 1

	function add_history (pathname)

		str pathname

      		addmsg {pathname}/soma/spike /output/history/L5P.history SPIKESAVE

		create spikegen {pathname}/axon[19]/spike 
		setfield ^  thresh -0.01 abs_refract 0.0015 output_amp 1
   		addmsg {pathname}/axon[1]  ^  INPUT Vm

      		addmsg ^ /output/history/L5P.history SPIKESAVE

        end


//      addmsg /L5Ponlybasal/soma/spike /output/history/L5P.history SPIKESAVE
//      addmsg /L5Pnotuft/soma/spike /output/history/L5P.history SPIKESAVE