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]
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 code is based on the model published by Dyhrfjeld and available 
at http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=93349.
The original text of its README file is now in README-Dyhrfjeld.

The code of this dir is self-contained.
The tabulated channels are in the channels subdirectory, and should be
machine-independent. If not, the tables should be recreated. This can
be done by starting genesis, and then using
> include defaults
> include L5P_const.g
> include L5P_chans_Temp.g
That should do it.

The Dyhrfjeld model has been extended and modified in several ways,
and some of these changes are reflected in the file names used.

- The temperature is now 37 degrees (instead of 32).
- A 20-compartmental axon has been added.
- Synaptic channels have been added (although NMDA-type and
GABAB-type channels were not used for the paper).
- Afferent fibres have been created and connected to the synaptic channels.
To account for potential differences in the density of inputs along the
axis of the neuron and depth of the cortex (layers), a depth profile can
be defined for their strengts (see Firing_rate_profile.g).
All fibres are Poisson processes and their instantaneous spike rate can
be changed over time as follows:
- the spike rate of subcortical fibres is modulated by an additional
point process with an exponential impulse response, as described by
Harsch and Robinson (Harsch-Robinson_modulation.g);
- the spike rate of intracolumnar feedback fibres is modulated by the
filtered output of the neuron itself.

A few control scripts (test_position.g, nsynapses.g) allow you to
record some parameters of the model.
To simulate this neuron, please type (from within this dir)
genesis L5P37C.g

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