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

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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).
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;
Gap Junctions:
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;
Axon_chans.g *
DiffRm.g *
electrodes_fixbug.g *
electrodes_try.g *
Excitatory_fibres.g *
Fibres.g *
Firing_rate_modulation.g *
Firing_rate_profile.g *
Gran_synchan.g *
Harsch-Robinson_modulation.g *
Hgradient.g *
Inhibitory_fibres.g *
L5P_ascout.g *
L5P_chans.g *
L5P_chans_tab_Temp.g *
L5P_chans_Temp.g *
L5P_comps.g *
L5P_const.g *
L5P_const+axon+syn.g *
L5P_history.g *
nsynapses.g *
test_position.g *
This collection of scripts are used to simulate IV curves from a layer
5 pyramidal cell from rat somatosensory (barrel) cortex as shown in
Fig.11 of

Dyhrfjeld-Johnsen J,Maier J,Schubert D,Staiger J,Luhmann HJ,Stephan
KE, Kotter R.: CoCoDat: a database system for organizing and selecting
quantitative data on single neurons and neuronal microcircuitry. J
Neurosci Methods. 2005 Feb 15;141(2):291-308.

The scripts involved are:

* L5P_mainloop.g - The main simulation script that executes the setup
of the model and runs through the series of current injections.

*L5P_const.g - Constants and values used in the simulation.

*DS1_141099_rot2_sc_defmesh.p - The reconstructed neuron morphology.

*L5P_chans.g - Tabchannel definitions of ion-channels used in the

*L5P_comps.g - Protope compartments used for setting up the model.

*DiffRm.g & Hgradient.g - Functions to set up differentially
distrubuted values for Rm and H-current density.

*L5P_input.g & ExpInjCur.g - Scripts to set up (and provide amplitudes
for) current injection stimulation.

*L5P_graph.g - Creates direct graphical output of membrane potential
for entire morphology, somatic Vm, somatic conductances and somatic
currents. Graphic output can be turned off by commenting out line 40
in the main simulation script.

L5P_ascout.g - Script to write out somatic voltage traces to ASCII
format. ASCII output can be turned off by commenting out line 41 in
the main simulation script.

*DS991014IVPotential.asc - The experimentally recorded IV curves for
the modeled cell.

*plotVmIBloop.m - MATLAB script to plot the simulated and
experimentally recorded IV curves in the same graph for comparison.