Pyramidal Neuron Deep: attenuation in dendrites (Stuart, Spruston 1998)

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Accession:3677
Stuart, G. and Spruston, N. Determinants of voltage attenuation in neocortical pyramidal neuron dendrites. Journal of Neuroscience 18:3501-3510, 1998.
Reference:
1 . Stuart G, Spruston N (1998) Determinants of voltage attenuation in neocortical pyramidal neuron dendrites. J Neurosci 18:3501-10 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell;
Channel(s): I h;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Parameter Fitting;
Implementer(s): Spruston, Nelson [Spruston at Northwestern.edu];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; I h;
/* access dend1[7]   -- somatic recording site at 0.5    */
/* access dend1[134] -- dendritic recording site at 0.01 */

graphicson = 1 	/* 1 graphics on, -1 graphics off */
lserroron = 1  /* compare simulation to real data if > 0 */
writeout = 0    /* equals 1 if output should be written to a file */
makeplot = 0

xopen("$(NEURONHOME):lib:hoc:noload.hoc")
xopen("mystdrun.hoc")
xopen("ri22geo5.hoc")
xopen("ri22init.hoc")
xopen("ri22func.hoc")
nrnmainmenu()
nrnmainmenu()
tstop=100
long=1
short=1
both=0
syn=0
nurm=0 /* 4 is preferred for nonuniform Rm */
nuri=0
initq=8
init_params()
Cm=1.0          /* specific membrane capacitance in uF/cm^2 */
Rm=20805      /* specific membrane resistivity in ohm-cm^2 */
Vrestsoma=Vrest
Vrestdend=Vrest

areascale=0.9

read_expt_data()
insert_pass(global_ra)		/* initialize passive membrane */

if (nurm<1) {
	init_pass(Cm)	/* initialize passive membrane */
}
if (nurm>2) {
	init_nurm4(Cm)	/* initialize passive membrane */
}
if (qblock<1) {
  if (initq>0) {
    initq1()
  }
  if (initq>7) {
    initq8()
  }
}		
/* initnakhh()	*/	/* initialize active HH Na/K conductances */
if (graphicson>0) {
  newPlotV(-83,-78)
}
init()			/* initialize v and active states */

if (qblock<1) {
  print "stabilizing"
  stabilize_cc(600,5)
}

proc vectors() {
somarawvec.play(&somarawv,vecdt)
dendrawvec.play(&dendrawv,vecdt)
somarawvec.play_remove()
dendrawvec.play_remove()
somarawvec.add(Vrestsoma)
dendrawvec.add(Vrestdend)
/* somarawvec.add(somaticv()) */
/* dendrawvec.add(dendriticv()) */
somarawvec.play(&somarawv,vecdt)
dendrawvec.play(&dendrawv,vecdt)
 if (qblock<1) {
  Vrestsoma=somaticv()
  Vrestdend=dendriticv()
 }
graphItem.size(0,tstop,-82,-78)
}

wopen("data.out")
fprint("ri22geo5\n")
fprint("Surface area of dendrites scaled for spines (spinescale)\n")
fprint("Surface area of all compartments scaled by an additional\n")
fprint(" factor (areascale) to match input resistance\n")
/* fprint("Surface area of soma (including dend[0-9]) scaled up by an\n") */
/* fprint(" additional factor of 1.5 to check effects of error in soma SA\n")*/
fprint("Ri     spinescale     areascale      long          long pulse    short vdend    short        short pulse\n")
fprint("                                     atten.        ms error      peak time      atten.       vdend ms error\n")
fprint("---    ---------      ---------      ---------     -----------   -----------    ---------    -------------\n")

for (ra=175;ra<=175;ra=ra+2) {
  global_ra=ra
  print"******************************************************************\n"
  printf("Ra=%d\n",ra)
  long=1
  short=0
  read_expt_data()
  vectors()
  t=0
  tstop=400
  graphItem.size(0,tstop,-82,-78)
  init()
  if (nurm<1) {
  	init_pass(Cm)	/* initialize passive membrane */
  }
  if (nurm>2) {
  	init_nurm4(Cm)	/* initialize passive membrane */
  }
  somastep_cc(-0.05, 51.3, 201.4, 400, 5.0)
  while (abs(rn-target)>0.0001*(target)) {
    findsf(target)
	if (nurm<1) {
		init_pass(Cm)	/* initialize passive membrane */
	}
	if (nurm>2) {
		init_nurm4(Cm)	/* initialize passive membrane */
	}
    /* stabilize_cc(600,5) */
   /* Vrestsoma=dend1[7].v(0.5) */
   /* Vrestdend=dend1[134].v(0.01) */
    t=0
    somastep_cc(-0.05, 51.3, 201.4, 400, 5.0)
        /* send stim, delay, duration, tmax, dt */
  }
  t=0
  mserrsoma=0
  mserrdend=0
  somastep_cc(-0.05, 51.3, 201.4, 400, 0.5)
  ssatten=maxvdend/maxvsoma
  longerr=mserr
  long=0
  short=1
  read_expt_data()
  vectors()
  t=0
  tstop=100
  mserrsoma=0
  mserrdend=0
  graphItem.size(0,tstop,-82,-78)
  init()
  somastep_cc(-2.0, 5.06, 1.008, 100, 0.1)
  shortatten=peakvdend/peakvsoma
  shorterr=mserrdend
  printf("spinescale = %f\n",spinescale)
  printf("areascale = %f\n",areascale)
  printf("Input resistance = %f Mohms\n",rn)
  printf("Max. voltage change at somatic electrode = %f mV\n\n",maxvsoma)
  printf("Max. voltage change at dendritic electrode = %f mV\n\n",maxvdend)
  if (long>0) {
	printf("Attenuation = %f \n\n",maxvdend/maxvsoma)
  }
  if (short>0) {
	printf("Dend peak at %f ms \n",peakvdendt)
	printf("Attenuation = %f \n\n",peakvdend/peakvsoma)
  }
  printf("MS Error = %f \n\n",mserr)
  /* write Ra and maxv to output file */
  fprint("%3d     %f      %f       %f      %f      %f      %f      %f\n",ra,spinescale,areascale,ssatten,longerr,peakvdendt,shortatten,shorterr)
}
print"******************************************************************\n"
print"DONE\n"