def __init__(self, name='IG', inject=70.0, gbarGABA=1.0):
"""IG model based on Izhikevich type neuron."""
self.sec = h.Section(name)
self.izhi = h.IzhiGS(self.sec(0.5))
self.izhi.celltype = 1 # Regular Spiking
self.izhi.Iin = inject
self.izhi.gbarGraded = gbarGABA
self.netcons = []
def make_kc_with_dynaclamp(kc_name,
kc_file,
inject,
tstart,
tend,
ggn_vm=None):
"""Read KC model from `kc_file`, inject current `inject` nA, apply
dynamic clamp `ggn_vm`, which should be a 2D array with time (ms)
in column 0, and voltage (mV) in column 1.
"""
global model_dict
kc = nu.create_cell(kc_name, filename=kc_file)
model_dict[kc] = None
iclamp = ephys.setup_current_clamp(kc.soma,
pos=0.5,
delay=Q_(tstart, 'ms'),
duration=Q_((tend - tstart), 'ms'),
amplitude=Q_(inject, 'nA'))
model_dict[iclamp] = None
ggn_g_vec = None
if ggn_vm is not None:
syn = h.GradedSyn(kc.soma(0.5))
for attr, value in GGN_KC_SYN_PARAMS.items():
setattr(syn, attr, value)
model_dict[syn] = None
ggn_comp = h.Section('ggn')
model_dict[ggn_comp] = None
h.setpointer(ggn_comp(0.5)._ref_v, 'vpre', syn)
ggn_vm_vec = h.Vector(ggn_vm[:, 1])
tvec = h.Vector(ggn_vm[:, 0])
model_dict[tvec] = None
# vec.play(var_reference, t, continuous) for interpolating
ret = ggn_vm_vec.play(ggn_comp(0.5)._ref_v, tvec, 1)
print('####', ret)
model_dict[ggn_vm_vec] = None
ggn_g_vec = h.Vector()
ggn_g_vec.record(syn._ref_g)
model_dict[ggn_g_vec] = None
kc_vm_vec = h.Vector()
kc_vm_vec.record(kc.soma(0.5)._ref_v)
model_dict[kc_vm_vec] = None
print('Built model')
return (kc_vm_vec, ggn_g_vec)
def create_cable(name,
diameter,
length,
nseg,
RA,
CM=Q_('1.0uF/cm**2'),
mechs=[],
ek=Q_('-80.0mV'),
ena=Q_('60.0mV'),
eca=Q_('60.0mV'),
verbose=False):
"""Create a cable with specified dimeter, length and number of
segments and insert the mechanisms in mechs list.
Parameters:
diameter (um): cable diameter
length (um): cable length
nseg: number of segments to divide the cable into
RA (ohm-cm): specific axial resistance
CM (uF/cm2): specific membrane capacitance.
mechs (Mechanism): list of mechanisms to be inserted into the
section. You may want to update the properties later using
`set_mech_param`.
ek (mV): K+ reversal potential
ena (mV): Na+ reversal potential
eca (mV): Ca2+ reversal potential.
Returns:
cable: a new Section with all the properties and mechanisms.
"""
cable = h.Section(name=name)
cable.diam = diameter.to(ur.um).m
cable.L = length.to(ur.um).m
cable.cm = CM.to('uF/cm**2').m
cable.Ra = RA.to('ohm*cm').m
cable.nseg = nseg
for mech in mechs:
mech.insert_into(cable)
if hasattr(cable, 'ek'):
cable.ek = ek.to('mV').m
if hasattr(cable, 'ena'):
cable.ena = ena.to('mV').m
if hasattr(cable, 'eca'):
cable.eca = eca.to('mV').m
if verbose:
print('Created cable', name, 'with', nseg, 'segments')
for x in cable:
print(
'Segment at', x.x, 'diam=', x.diam, 'area=', x.area(),
'area computed=', np.pi * x.diam * cable.L / cable.nseg, 'ri=',
x.ri(), 'computed ri=', 0.01 * cable.Ra *
(cable.L / 2 / cable.nseg) / (np.pi * (x.diam / 2)**2))
for mech in mechs:
m = getattr(x, mech.name)
print(' Has mechanism', m.name())
sys.stdout.flush()
return cable