def BIO_model_threshold_in_CC(ais_start, ais_end, gna_tot, morpho):
print('AIS start:', ais_start, 'Gna:', gna_tot)
params = params_model_description
pulse_length = 50. * ms
neuron = model_Na_Kv1(params=params,
resting_vm=-75. * mV,
Na_start=ais_start,
Na_end=ais_end,
gna_tot=gna_tot,
density=False,
morpho=morpho)
i_rheo = measure_current_threshold(params, neuron, -75. * mV,
ais_start, ais_end, pulse_length)
print('Rheobase:', i_rheo)
neuron = model_Na_Kv1(params=params,
resting_vm=-75. * mV,
Na_start=ais_start,
Na_end=ais_end,
gna_tot=gna_tot,
density=False,
morpho=morpho)
v_thres, _, _, _ = measure_voltage_threshold(params, neuron, -75. * mV,
ais_start, ais_end,
i_rheo, pulse_length)
print('Voltage threshold:', v_thres)
return v_thres
def BIO_model_threshold_in_CC(x_star, length, gna_dens):
defaultclock.dt = 0.005 * ms
resting_vm = -75. * mV
pulse_length = 50. * ms
# AIS start
start = round(x_star, 2) * um - length / 2
# AIS end
end = start + length
# Removing impossible geometries: the length can not be bigger than two times the middle position
if length / 2 <= round(x_star, 2) * um:
# current threshold
neuron = model_Na_Kv1(params,
resting_vm,
Na_start=start,
Na_end=end,
density=True,
gna_density=gna_dens)
i_rheo = measure_current_threshold(params,
neuron,
resting_vm=resting_vm,
ais_start=start,
ais_end=end,
pulse_length=pulse_length)
print('Rheobase:', i_rheo)
# voltage threshold
neuron = model_Na_Kv1(params,
resting_vm,
Na_start=start,
Na_end=end,
density=True,
gna_density=gna_dens)
vs, va, _, _ = measure_voltage_threshold(params,
neuron,
resting_vm=resting_vm,
ais_start=start,
ais_end=end,
i_rheo=i_rheo,
pulse_length=pulse_length)
print('Threshold:', vs)
res = vs
else: # bottom right triangle
res = nan
return res
def BIO_model_in_CC_Kv(resting_vm, ais_start, ais_end, i_inj, gna_tot):
defaultclock.dt = 0.005*ms
pulse_length = 50.*ms
# current threshold
neuron = model_Na_Kv1(params, resting_vm, Na_start = ais_start, Na_end = ais_end, density=False, gna_tot=gna_tot)
i_rheo = measure_current_threshold(params=params, neuron=neuron, resting_vm=resting_vm, ais_start=ais_start, \
ais_end=ais_end, pulse_length=pulse_length, i_inj=i_inj)
print ('Rheobase:', i_rheo)
# voltage threshold
neuron = model_Na_Kv1(params, resting_vm, Na_start = ais_start, Na_end = ais_end, gna_tot = gna_tot, density=False)
vs, va, _, _ = measure_voltage_threshold(params=params, neuron=neuron, resting_vm=resting_vm, ais_start=ais_start, \
ais_end=ais_end, i_rheo = i_rheo, pulse_length=pulse_length, i_inj=i_inj)
print('Thresholds: soma:', vs, ', AIS:', va)
neuron = model_Na_Kv1(params, resting_vm, Na_start = ais_start, Na_end = ais_end, gna_tot=gna_tot, density=False)
t, v_soma, _, v_ais = calculate_resting_state(neuron, ais_start, ais_end, i_inj)
return i_rheo, vs, va, t, v_soma, v_ais
def BIO_model_in_CC_threshold_density(ais_start, ais_end, gna_dens):
defaultclock.dt = 0.005 * ms
resting_vm = -75. * mV
pulse_length = 50. * ms
print(ais_start, ais_end)
# current threshold
neuron = model_Na_Kv1(params,
resting_vm,
ais_start,
ais_end,
density=True,
gna_density=gna_dens)
i_rheo = measure_current_threshold(params,
neuron,
resting_vm,
ais_start,
ais_end,
pulse_length=pulse_length)
# voltage threshold
neuron = model_Na_Kv1(params,
resting_vm,
ais_start,
ais_end,
density=True,
gna_density=gna_dens)
vs, va, _, _ = measure_voltage_threshold(params,
neuron,
resting_vm,
ais_start,
ais_end,
i_rheo=i_rheo,
pulse_length=pulse_length)
return vs