def inject_soma(mycell):
""" calculate the AP attenuation vs distance after
somatic injection
"""
stim = h.IClamp(0.5, sec = mycell.soma)
stim.delay = 0.1
stim.dur = 2.5
stim.amp = 4.0
# set zero distance
h.distance(sec = mycell.soma)
# Recording: AP waveforms from basal and apical sections
basal_seg = list()
for sec in mycell.allbasalsec:
for seg in sec:
basal_seg.append(seg)
myvectors_basal = simulate_voltage(5, basal_seg)
apical_seg = list()
for sec in mycell.allapicalsec:
for seg in sec:
apical_seg.append(seg)
myvectors_apical = simulate_voltage(5, apical_seg)
# Plotting peak vs distance
peak, dist = list(), list()
for sec, vectors in izip(mycell.allbasalsec, myvectors_basal):
voltage = vectors.voltage
peak.append(np.max(voltage) - voltage[0])
dist.append(-h.distance(0, sec=sec))
peaka, dista = list(), list()
for sec, vectors in izip(mycell.allapicalsec, myvectors_apical):
voltage = vectors.voltage
peak.append(np.max(voltage) - voltage[0])
dist.append(h.distance(0, sec=sec))
plt.plot(dist, peak,'o', markerfacecolor='red')
plt.plot(dista, peaka, 'o', markerfacecolor='red')
#plt.xlim(xmin=-100, xmax=400)
#plt.ylim(ymax=110, ymin=0)
plt.show()
def get_peak(gnabar_hh):
""" this functions returns the peak of the AP in the soma as a function
of gnabar_hh in a CA3 neuron
if gnabar_hh = 0.12 then peak is 96.881
"""
mycell.soma.gnabar_hh = float(gnabar_hh)
spike = simulate_voltage(5, [mycell.soma(0.5)])
# voltage is HocVector obj (see CA3simulations.py)
voltage = spike[0].voltage
peak = np.max(voltage) - voltage[0]
return peak
def get_peak(self, gnabar_hh, sec):
""" returns the AP peak in the cell as a function
of the gnabar_hh in the current section"""
sec.gnabar_hh = float(gnabar_hh)
# attach a simulator to section
stim = self._stimulator(sec = sec)
spike = simulate_voltage(5, [sec(0.5)])
del stim
# voltage is a HocVector obj (see CA3simulations.py)
voltage = spike[0].voltage
peak = np.max(voltage) - voltage[0]
return peak
# let fdistance to take the segment as an argument fsec_apical = lambda section : fdistance( h.distance(0, sec=section) ) #fsec_basal = lambda sec: 0.01 fsec_basal = lambda sec: 0.02 # morphology and biophysics neuron = Neuron(ApicalBasalActive) h.distance(sec=neuron.soma) neuron.get_Active().activatedendrites(fsec_apical, fsec_basal) neuron.soma.gnabar_hh = 0.0 #========================================================================= # Instrumentation: current injection #========================================================================= stim = h.IClamp(0.5, sec = neuron.dend[112]) stim.delay = 2 stim.dur = 0.3 stim.amp = 0.5 #========================================================================= # Recording: AP waveforms from soma and apical dendrite #========================================================================= soma, apical_dend = simulate_voltage(12, [neuron.soma, neuron.dend[112] ]) plt.plot(soma.get_time(), soma.get_voltage(), 'k', lw=1) plt.plot(apical_dend.get_time(), apical_dend.get_voltage(), 'r', lw=1) plt.show()
h.distance(sec=neuron.soma)
neuron.get_Active().activatedendrites(fapical = fsec_apical, fbasal=fsec_basal)
#=========================================================================
# Instrumentation: Somatic current injection
#=========================================================================
stim = h.IClamp(0.5, sec = neuron.soma)
stim.delay = 0.1
stim.dur = 2.5
stim.amp = 4.0
#=========================================================================
# Recording: AP waveforms from basal and apical sections
#=========================================================================
myvectors_basal = simulate_voltage(5, neuron.allbasalsec)
myvectors_apical = simulate_voltage(5, neuron.allapicalsec)
#=========================================================================
# Plotting peak vs distance
#=========================================================================
peak, dist = list(), list()
for sec, vectors in izip(neuron.allbasalsec, myvectors_basal):
voltage = vectors.voltage
peak.append(np.max(voltage) - voltage[0])
dist.append(-h.distance(0, sec=sec))
peaka, dista = list(), list()
for sec, vectors in izip(neuron.allapicalsec, myvectors_apical):
voltage = vectors.voltage
