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-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

// 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



/*
// Excitatory fibers

      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/FF_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/FF_fibre[] /output/history/Inhibitory_fibres.history SPIKESAVE

*/



// L5P cells

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

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


/* added 16 June 2008 because soma spikes do not always cross zero level,
but axon spikes do */

   ce /L5P
   create spikegen axon[10]/spike
   setfield axon[10]/spike thresh -0.01  \
                       abs_refract 0.0015 \
                       output_amp 1
   addmsg axon[10] axon[10]/spike INPUT Vm
   addmsg /L5P/axon[10]/spike /output/history/L5P.history SPIKESAVE






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