Direct recruitment of S1 pyramidal cells and interneurons via ICMS (Overstreet et al., 2013)

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Accession:147460
Study of the pyramidal cells and interneurons recruited by intracortical microstimulation in primary somatosensory cortex. Code includes morphological models for seven types of pyramidal cells and eight types of interneurons, NEURON code to simulate ICMS, and an artificial reconstruction of a 3D slab of cortex implemented in MATLAB.
Reference:
1 . Overstreet CK, Klein JD, Helms Tillery SI (2013) Computational modeling of direct neuronal recruitment during intracortical microstimulation in somatosensory cortex. J Neural Eng 10:066016 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Axon;
Brain Region(s)/Organism:
Cell Type(s): Neocortex U1 L6 pyramidal corticalthalamic GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex bitufted interneuron;
Channel(s): I Na,p; I_Ks;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; MATLAB;
Model Concept(s): Intracortical Microstimulation;
Implementer(s): Overstreet, Cynthia [cynthiakoverstreet at gmail.com];
Search NeuronDB for information about:  Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex U1 L6 pyramidal corticalthalamic GLU cell; I Na,p; I_Ks;
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OverstreetEtAl2013
Pyramidal
NEURON_code
README.txt
AXNODE.mod *
xtra.mod *
anat_type10.hoc
anat_type10sym.hoc
anat_type11.hoc
anat_type12.hoc
anat_type12sym.hoc
anat_type13.hoc
anat_type13sym.hoc
anat_type14.hoc
anat_type14sym.hoc
anat_type15.hoc
anat_type9.hoc
anat_type9sym.hoc
calcrxc.hoc *
field.hoc *
fixnseg.hoc *
initpulsecomp.hoc
initstrdur.hoc
initxcstim.hoc
interpxyz.hoc *
moveandstimtype10.hoc
moveandstimtype10sym.hoc
moveandstimtype11.hoc
moveandstimtype12.hoc
moveandstimtype12sym.hoc
moveandstimtype13.hoc
moveandstimtype13sym.hoc
moveandstimtype14.hoc
moveandstimtype14sym.hoc
moveandstimtype15.hoc
moveandstimtype9.hoc
moveandstimtype9sym.hoc
pulsecompA.hoc
pulsecompB.hoc
rigc.ses *
setpointers.hoc *
stim.hoc *
stimbipolar.hoc *
strdurA.hoc
strdurB.hoc
strdurC.hoc
strdurD.hoc
                            
// $Id: interpxyz.hoc,v 1.2 2005/09/10 23:02:15 ted Exp $
/* Computes xyz coords of nodes in a model cell 
   whose topology & geometry are defined by pt3d data.
   Expects sections to already exist, and that the xtra mechanism has been inserted
 */


// original data, irregularly spaced
objref xx, yy, zz, length
// interpolated data, spaced at regular intervals
objref xint, yint, zint, range

proc grindaway() { local ii, nn, kk, xr
	forall {
	  if (ismembrane("xtra")) {
		// get the data for the section
		nn = n3d()
		xx = new Vector(nn)
		yy = new Vector(nn)
		zz = new Vector(nn)
		length = new Vector(nn)

		for ii = 0,nn-1 {
			xx.x[ii] = x3d(ii)
			yy.x[ii] = y3d(ii)
			zz.x[ii] = z3d(ii)
			length.x[ii] = arc3d(ii)
		}

		// to use Vector class's .interpolate() 
		// must first scale the independent variable
		// i.e. normalize length along centroid
		length.div(length.x[nn-1])

		// initialize the destination "independent" vector
		range = new Vector(nseg+2)
		range.indgen(1/nseg)
		range.sub(1/(2*nseg))
		range.x[0]=0
		range.x[nseg+1]=1

		// length contains the normalized distances of the pt3d points 
		// along the centroid of the section.  These are spaced at 
		// irregular intervals.
		// range contains the normalized distances of the nodes along the 
		// centroid of the section.  These are spaced at regular intervals.
		// Ready to interpolate.

		xint = new Vector(nseg+2)
		yint = new Vector(nseg+2)
		zint = new Vector(nseg+2)
		xint.interpolate(range, length, xx)
		yint.interpolate(range, length, yy)
		zint.interpolate(range, length, zz)

		// for each node, assign the xyz values to x_xtra, y_xtra, z_xtra
//		for ii = 0, nseg+1 {
// don't bother computing coords of the 0 and 1 ends
// also avoid writing coords of the 1 end into the last internal node's coords
		for ii = 1, nseg {
			xr = range.x[ii]
			x_xtra(xr) = xint.x[ii]
			y_xtra(xr) = yint.x[ii]
			z_xtra(xr) = zint.x[ii]
		}
	  }
	}
}

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