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;
// genesis

// RM 17 Sep 2008
// Contains function with as parameters : source, target, connection probability,
// weight and delay.

// A few parameters have been assumed fixed, hence they are not in the argument list
// (such as weight and delay distributions). 
// The connections are laid horizontally, using only the z-coordinate as a criterion,
// Radial connections have been implemented in Excitatory_fibres_connect.g, but not 
// tested yet. 


function connect_horizontally (source, target, probability, weight, delay)

	str source, target
        float probability, weight, delay
// First connection scheme: each fiber runs horizontally and is allowed to make a synapse
// on each compartment in (approximately) the same horizontal plane

	echo connecting {source} to {target} with probability {probability} \
			weight {weight} and delay {delay}

	volumeconnect 	{source} \
                    	{target} \
                    	-relative \
                    	-sourcemask box -1 -1 -1 1 1 1 \
                    	-destmask ellipsoid 0 0 0 1 1 2e-6 \ 
                    	-probability {probability}

	volumeweight 	{source} \
                   	{target} \
			-fixed {weight} \
			-uniform {weight_distribution}

	volumedelay   	{source} \
                    	{target} \
                    	-radial {E_fibre_conduction_velocity} \
			-uniform {delay_distribution}

	volumedelay   	{source} \
                    	{target} \
                    	-fixed {delay}\


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