Computational Surgery (Lytton et al. 2011)

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Figure 2 in Neocortical simulation for epilepsy surgery guidance: Localization and intervention, by William W. Lytton, Samuel A. Neymotin, Jason C. Wester, and Diego Contreras in Computational Surgery and Dual Training, Springer, 2011
1 . Lytton WW, Neymotin SA, Wester JC, Contreras D (2011) Neocortical simulation for epilepsy surgery guidance: Localization and intervention Computational Surgery and Dual Training
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Gap Junctions:
Simulation Environment: NEURON;
Model Concept(s): Epilepsy;
Implementer(s): Lytton, William [billl at];
intf6_.mod *
misc.mod *
nstim.mod *
stats.mod *
vecst.mod *
declist.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
local.hoc *
misc.h *
nqs_utils.hoc *
nqsnet.hoc *
nrnoc.hoc *
setup.hoc *
simctrl.hoc *
spkts.hoc *
stdgui.hoc *
// $Id: params.hoc,v 1.191 2011/08/17 14:12:24 billl Exp $

//* batch params

//* general params
tstop = 1000
v_init=1000 // so keep v's as set randomly

//* ARTC params
EAM_INTF6=65 // these are deviations above RMP
seadsetting_INTF6 = 2 // fixed inter-cell weights

//* Declarations

dosetexvals=name_declared("wmatex")==0 // whether to set values in wmatex,ratex

declare("wmatex",tstr,"ratex",tstr) // weights,avg. rate of external inputs


declare("vsgrpp",new Vector(CTYPi)) //% X 100 of cells of a type to stim, used in stim,sgrcells
declare("vsgrsidx",new Vector(CTYPi)) //startind index of cell to stim when using topstim
declare("sgrdur",tstop) //duration of stim
declare("sgrhzdel",0.2)//variance in sgrhz for an INTF6
declare("EXGain",15) // gain for external inputs
declare("lcstim",new List()) // list of CSTIM objects
declare("nqwmex",new NQS("ct","sy","w","rate")) // NQS passed to CSTIM init
{sprint(tstr,"d[%d]",numcols) declare("EIBalance",tstr)} // whether to balance rate of external E/I inputs
declare("usens",1) // whether to use NetStims in CSTIM


//* shock-related params

//* setwmatex - set weights of external inputs to INTF6s
proc setwmatex () {  local ct,sy
  if(dosetexvals) {
    for ct=0,CTYPi-1 for sy=0,STYPi-1 wmatex[ct][sy]=0
    for ct=0,CTYPi-1 {
      if(IsLTS(ct)) {
        wmatex[ct][AM2] = 0.2
        wmatex[ct][NM2] = 0.025
      } else {
        wmatex[ct][NM2] = 0.05   
        wmatex[ct][AM2] = 0.25 
      for sy=0,STYPi-1 wmatex[ct][sy] *= EXGain // apply gain control
  for ct=0,CTYPi-1 for sy=0,STYPi-1 if(wmatex[ct][sy]) nqwmex.append(ct,sy,wmatex[ct][sy],ratex[ct][sy])

//* RSparams - setup regular spiking excitatory cells
proc RSparams () { local ii,jj localobj xo,co
  for ltr(co,lcol) for case(&ii,E2,E4,E5R,E5B,E6) if(co.numc[ii]>0) {
    for jj=co.ix[ii],co.ixe[ii] { xo=co.ce.o(jj)
      xo.RMP= -65
      xo.VTH= -40 
      xo.refrac=  50
      xo.Vblock= -25
      xo.tauGA  = 10
      xo.tauGA2 = 20
      xo.tauAM2 = 20
      xo.tauNM2 = 300
      xo.tauRR = 8 
      xo.RRWght = .75 

//* LTSparams - setup low-threshold spiking interneurons
proc LTSparams () { local ii,jj localobj xo,co
  for ltr(co,lcol) for case(&ii,I2L,I4L,I5L,I6L) if(co.numc[ii]>0) {
    for jj=co.ix[ii],co.ixe[ii] { xo=co.ce.o(jj)  
      xo.refrac= 5
      xo.RMP = -65
      xo.VTH= -47

      xo.tauGA  = 10
      xo.tauGA2 = 20
      xo.tauAM2 = 20
      xo.tauNM2 = 300
      xo.tauRR = 1.5
      xo.RRWght = 0.25

//* FSparams - setup fast spiking interneurons
proc FSparams () { local ii,jj localobj xo,co
  for ltr(co,lcol) for case(&ii,I2,I2C,I4,I5,I6,I6C) if(co.numc[ii]>0) {
    for jj=co.ix[ii],co.ixe[ii] { xo=co.ce.o(jj)    
      xo.refrac= 5
      xo.RMP = -63
      xo.VTH= -40

      xo.tauGA  = 10
      xo.tauGA2 = 20
      xo.tauAM2 = 20
      xo.tauNM2 = 300
      xo.tauRR = 1.5
      xo.RRWght = 0.25

//* setNMParams(col,celltype,mg0 factor,maxnmc) 
proc setNMParams () { local ct,mgf,maxnmc,idx localobj col,ce
  col=$o1 ce=col.ce ct=$2 mgf=$3 maxnmc=$4
  for idx=col.ix[ct],col.ixe[ct] {
    ce.o(idx).mg0 = 3.57 * mgf
    ce.o(idx).maxnmc = maxnmc

//* setNMIParams(col[,mg0 factor,maxnmc])
proc setNMI () { local mgf,maxnmc,ct localobj col
  if(numarg()>1) mgf=$2 else mgf=1 
  if(numarg()>2) maxnmc=$3 else maxnmc=1
  for ct=0,CTYPi-1 if(ice(ct)) setNMParams(col,ct,mgf,maxnmc)

//* schizon - turn on schizo params
proc schizon () { local c,ct
  for c=0,numcols-1 {
    for case(&ct,E2,E5R,E5B) setNMParams(col[c],ct,0.75,0.9)
//* schizon - turn off schizo params
proc schizoff () { local c,ct
  for c=0,numcols-1 {
    for case(&ct,E2,E5R,E5B) setNMParams(col[c],ct,1,1)

proc rewt () {} // nothing needs to be done since copy directly into wd0[][][]

//* setcstim - set external inputs to COLUMNs using CSTIM
proc setcstim () { local i,seed
  for i=0,lcol.count-1 {
    if(dbgcols)seed=inputseed else seed=(i+1)*inputseed
    lcstim.append(new CSTIM(lcol.o(i),seed,sgrdur,sgrhzdel,EIBalance[i],usens))
  print "set external inputs"

//* clrshock -- clear all shock params and actual shocks
proc clrshock () { local i,j,k
  for i=0,numcols-1 for j=0,CTYPi-1 for k=0,STYPi-1 {

//* setshockparms -- setup matrices for shock params used by setshock
proc setshockparms () { local i,x,tm
  for i=0,0 {
    wshock[i][E4][AM2] = 6.25
    durshock[i][E4][AM2] = 1
    prctshock[i][E4][AM2] = 80
    nshock[i][E4][AM2] = 1
    isishock[i][E4][AM2] = 0
    startshock[i][E4][AM2] = 50
  // clrshock() setshockparms() setshock() time()
  if (0) for i=0,13 for ctt(&x) if (ice(x)) for case(&tm,300) {
    wshock[i][x][NM2] = 25
    durshock[i][x][NM2] = 10
    prctshock[i][x][NM2] = 1000
    nshock[i][x][NM2] = 1
    isishock[i][x][NM2] = 0
    startshock[i][x][NM2] = tm
  if (0) for i=0,3 for case(&x,E2,E5B,E5R,E4,E6) for case(&tm,550) {
    wshock[i][x][AM2] = 20.25
    durshock[i][x][AM2] = 1
    prctshock[i][x][AM2] = 100
    nshock[i][x][AM2] = 1
    isishock[i][x][AM2] = 0
    startshock[i][x][AM2] = tm

proc setshockp () { local i,x,cty,col,syty,wt,tm,prct
  cty=$1 col=$2 syty=$3 wt=$4 tm=$5
  if (argtype(6)==0) prct=$6 else prct=100
  wshock[col][cty][syty] = wt
  durshock[col][cty][syty] = 1
  prctshock[col][cty][syty] = prct
  nshock[col][cty][syty] = 1
  isishock[col][cty][syty] = 0
  startshock[col][cty][syty] = tm

//* setshock([clear vq first]) - set stims to L4 , NB: DEFAULT IS TO CLEAR vq FIRST
proc setshock () { local clr,i,j,k,l,tt,set
  if(numarg()>0) clr=$1 else clr=1
  for i=0,numcols-1 {
    set=0 // whether setting new spikes
    if(clr) {col[i].cstim.vq.clear() col[i].ce.o(0).clrvspks()} // clear shocks to this column?
    for j=0,CTYPi-1 for k=0,STYPi-1 if(wshock[i][j][k]>0 && nshock[i][j][k]>0) {
      set = 1
      tt = startshock[i][j][k] // time
      for l=0,nshock[i][j][k]-1 {
        tt += isishock[i][j][k] // inc by ISI
    if(set) {
      print col[i].cstim.vq.size(-1)

//* function calls


{RSparams() LTSparams() FSparams()}

if (!jcn) rjinet() //means no jitcon

if(disinhib) inhiboff()

setcstim() // random inputs from other areas

// how to shock:
// setup params for shock << timing, weights, bursts, isi, etc.
// {clrshock() setshockparms() setshock()}

Lytton WW, Neymotin SA, Wester JC, Contreras D (2011) Neocortical simulation for epilepsy surgery guidance: Localization and intervention Computational Surgery and Dual Training

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