/
spike_extract_frequency.hoc
139 lines (103 loc) · 5.09 KB
/
spike_extract_frequency.hoc
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// frequence meter
objref rec, nil , inter_spike, spike_indx, somaVm_late, somaD1_late, somaD2_late, somaT_late, abdVm_late
objref abdD1_late, abdD2_late,nabdVm_late, nabdD1_late, nabdD2_late, abdT_late, nabdT_late
spike_indx = new Vector()
inter_spike = new Vector() // a vector to store spike time intervals
soma rec = new NetCon(&v(0.5), nil) // create a netcon that watch the soma to reach a threshold
rec.threshold = -35 // record time indexes when V crosses threshold
rec.record(spike_indx)
nb_spikes_rejected = 8// ignore the first 10-1 = 9 interspike intervals
nbr=nb_spikes_rejected
nb_spikes_recorded= 4// nb +1 of ISI from which instantaneous frequency will be calculated
nbrec=nb_spikes_recorded
nb_min = nb_spikes_rejected + nb_spikes_recorded // ignore recordings with fewer spikes than this sum (3)
proc freqmeter () {local t1, t2
mean_freq = 0
nbspikes = spike_indx.size() // calculate the number of spikes
print "spike times are ", spike_indx.printf //
t1 = spike_indx.x[nbr] // nbr th spike time
t2 = spike_indx.x[nbr+1] // nbr+1 th spike time
print "t1 et t2 " , t1 ," " , t2
index1 = somaT.indwhere(">=", t1+40) // time before the extracted spike
index2 = somaT.indwhere(">=", t2+40) //time after the extracted spike
print "index1 is ", index1
print "index2 is ", index2
if (nbspikes > nb_min) {
somaVm_late = new Vector()
somaD1_late = new Vector()
somaD2_late = new Vector()
somaT_late = new Vector()
abdVm_late = new Vector()
abdD1_late = new Vector()
abdD2_late = new Vector()
abdT_late = new Vector()
nabdVm_late = new Vector()
nabdD1_late = new Vector()
nabdD2_late = new Vector()
nabdT_late = new Vector()
inter_spike.copy(spike_indx,nb_spikes_rejected,nb_min) // copy the vector to a new vector starting by the n th intervals
sub_nbspikes=inter_spike.size() // nb of spikes in the sub sample
inter_spike.deriv // calculate spike time intervals (ISI)
// inter_spike.printf
moy = inter_spike.mean() // calculate mean ISI
// sd = inter_spike.stdev() // Calculate ISI STANDARD DEVIATION
// sem = inter_spike.stderr() // calculate ISI sem
// time_total = inter_spike.sum() // calculate total time between the first and last spike
// mean_freq = (sub_nbspikes/time_total)*500 // mean firing frequency
// print "nb of spikes is ",sub_nbspikes, "mean ISI is " , moy, "sd is " , sd, "sem is ", sem
print " mean ISI is ", moy
somaVm_late.copy(somaVm,index1,index2) // copy the spikes of interest from the different compartment
somaD1_late.copy(somaD1,index1,index2)
somaD2_late.copy(somaD2,index1,index2)
somaT_late.copy(somaT,index1,index2)
abdVm_late.copy(abdVm,index1,index2)
abdD1_late.copy(abdD1,index1,index2)
abdD2_late.copy(abdD2,index1,index2)
abdT_late.copy(abdT, index1,index2)
nabdVm_late.copy(nabdVm,index1,index2)
nabdD1_late.copy(nabdD1,index1,index2)
nabdD2_late.copy(nabdD2,index1,index2)
nabdT_late.copy(nabdT, index1,index2)
strdef somaName
sprint (somaName, "%s%d%s%d%s%d%s%d%s", "I_soma_SD", soma.gbar_Na12, "_AIS", SIprox.gbar_Na12, "_AIS_length_", ais_length, "_ABD_length_", abd_length, ".txt")
print "soma file is ", somaName
soma_analysis()
fsomaSum.aopen(somaSum)
fsomaSum.printf("\n %s\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t ", somaName, soma.gbar_Na12, SIprox.gbar_kdrDA, SIprox.gbar_Na12, abd_length, ais_length, iTh, threshold, AP, HW, peakIS, peakSD)
fsomaSum.close()
fISI.aopen(ISISum)
fISI.printf("\n %s\t%g\t%g\t%g\t%g\t%g\t", somaName,ais_length, abd_length, soma.gbar_Na12, SIprox.gbar_Na12, moy)
fISI.close()
strdef ABDname
sprint (ABDname, "%s%d%s%d%s%d%s%d%s", "I_ABD_SD", soma.gbar_Na12, "_AIS", SIprox.gbar_Na12, "_AIS_length_", ais_length, "_ABD_length_", abd_length, ".txt")
print "ABD file is ", ABDname
abd_analysis()
fabdSum.aopen(abdSum)
fabdSum.printf("\n %s\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t ", ABDname, soma.gbar_Na12, SIprox.gbar_kdrDA, SIprox.gbar_Na12, abd_length, ais_length, iTh, threshold, AP, HW, peakIS, peakSD)
fabdSum.close()
strdef nABDname
sprint (nABDname, "%s%d%s%d%s%d%s%d%s", "I_nABD_SD", soma.gbar_Na12, "_AIS", SIprox.gbar_Na12, "_AIS_length_", ais_length, "_ABD_length_", abd_length, ".txt")
print "nABD file is ", nABDname
nabd_analysis()
fnabdSum.aopen(nabdSum)
fnabdSum.printf("\n %s\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t ", nABDname, soma.gbar_Na12, SIprox.gbar_kdrDA, SIprox.gbar_Na12, abd_length, ais_length, iTh, threshold, AP, HW, peakIS, peakSD)
fnabdSum.close()
chdir("data")
fsoma.wopen(somaName)
fabd.wopen(ABDname)
fnabd.wopen(nABDname)
for n=0, somaVm_late.size()-1{
fsoma.printf("%g %g %g %g \n", somaT_late.x(n), somaVm_late.x(n), somaD1_late.x(n), somaD2_late.x(n))
fabd.printf("%g %g %g %g \n", abdT_late.x(n), abdVm_late.x(n), abdD1_late.x(n), abdD2_late.x(n))
fnabd.printf("%g %g %g %g \n", nabdT_late.x(n), nabdVm_late.x(n), nabdD1_late.x(n), nabdD2_late.x(n))
}
fsoma.close()
fabd.close()
fnabd.close()
print "controle spike extract1"
} else {
print "not enough spikes, increase duration of simulation "
quit()
}
print "controle spike extract2"
}