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)
args = parser.parse_args()
inputs = args.inputs
celltemplate = args.celltemplate
syncount = args.syncount
onset = args.onset
tau = args.tau
gmax = args.gmax
diascale = args.diascale
dialim = args.dialim
mechs = {'pas': {'g': 3e-5, 'e': -51.0}}
# {'name': 'caiiag', 'gbar': 2.5e-5},
# {'name': 'ka', 'gbar': 0.03}]
h.xopen(celltemplate)
ggn = nu.create_cell(args.cellname,
filename=args.celltemplate,
mechparams=mechs)
if (args.diascale is not None) and (args.dialim is not None):
count = 0
ggn.soma.push()
ordered_tree = h.SectionList()
ordered_tree.wholetree()
h.pop_section()
for sec in ordered_tree:
sec.push()
for ii, seg in enumerate(sec):
if seg.diam < dialim:
seg.diam = seg.diam * diascale
# print('Changed diameter of segment', ii, seg.x, 'of section', sec.name(), 'to', seg.diam)
count += 1
h.pop_section()
def setup_model(args):
"""Setup the model with synapses and recording tables."""
cell_template = args['celltemplate']
input_regions = args['inputs']
syn_counts = args['syncounts']
onset = args['onset']
tau = args['tau']
gsyn = args['gsyn']
mechs = {
'pas': {
'g': Q_(args['gpas'], 'S/cm**2'),
'e': Q_(args['Em'], 'mV')
}
}
if args['gk'] > 0:
mechs['ka'] = {'gbar': Q_(args['gk'], 'S/cm**2')}
if args['gca'] > 0:
mechs['cam'] = {'gbar': Q_(args['gca'], 'S/cm**2')}
h.xopen(cell_template)
ggn = nu.create_cell(args['cellname'],
filename=args['celltemplate'],
mechparams=mechs)
for sec in ggn.allsec():
sec.Ra = args['RA']
g0 = nu.nrngraph(ggn)
g, nmap = ng.renumber_nodes(g0, ggn.soma.name())
# Pick out nodes with sections associated with them (not terminal dummy nodes)
sec_nodes = [n for n in g.nodes() if g.node[n]['orig'] is not None]
# Select the nodes for synapse insertion
if args['synfile'] is not None: # This option is to allow replication
syn_nodes = []
sec_node_map = get_section_node_map(g)
with open(args['synfile']) as fd:
for line in fd:
try:
secname = line.strip()
syn_nodes.append(sec_node_map[secname])
except KeyError:
print('Could not fidn section "{}"'.format(secname))
raise
else:
syn_nodes_by_sid = ng.select_random_nodes_by_sid(
g.subgraph(sec_nodes), args['inputs'], args['syncounts'])
syn_nodes = list(
np.concatenate(
[v for v in syn_nodes_by_sid.values() if len(v) > 0]))
# If np.concatenate arg contains empty list, the result gets converted to float
syn_secs = []
synapses = []
for syn_node in syn_nodes:
sec = g.node[syn_node]['orig']
syn_secs.append(sec)
syn = insert_alphasynapse(sec(1.0),
onset=args['onset'],
gmax=args['gsyn'],
tau=args['tau'])
synapses.append(syn)
if args['recfile'] is not None:
rec_nodes = []
sec_node_map = get_section_node_map(g)
with open(args['recfile']) as fd:
for line in fd:
try:
secname = line.strip()
rec_nodes.append(sec_node_map[secname])
except KeyError:
print('Could not fidn section "{}"'.format(secname))
raise
else:
if args['recbyreg']:
rec_regions = [1, 3, 4, 5, 6, 7, 8]
rec_nodes_by_sid = ng.select_random_nodes_by_sid(
g.subgraph(sec_nodes), rec_regions,
[args['reccount']] * len(rec_regions))
rec_nodes = np.concatenate(
[v for v in rec_nodes_by_sid.values() if len(v) > 0])
rec_nodes = list(rec_nodes)
else:
rec_nodes = list(
np.random.choice(sec_nodes,
size=args['reccount'],
replace=False))
rec_nodes = list(set(rec_nodes + syn_nodes))
rec_secs = [g.node[n]['orig'] for n in rec_nodes]
t_vec = h.Vector()
t_vec.record(h._ref_t)
v_vecs = setup_recording(rec_secs)
syn_vecs = []
for syn in synapses:
vec = h.Vector()
vec.record(syn._ref_i)
syn_vecs.append(vec)
return {
'cell': ggn,
'cellgraph': g,
'synapses': synapses,
'synsecs': syn_secs,
'synnodes': syn_nodes,
'recsecs': rec_secs,
'recnodes': rec_nodes,
'tvec': t_vec,
'vvecs': v_vecs,
'synvecs': syn_vecs
}
dest='rec',
default=0)
args = parser.parse_args()
inputs = args.inputs
celltemplate = args.celltemplate
syncount = args.syncount
onset = args.onset
gmax = args.gmax
diascale = args.diascale
dialim = args.dialim
maxrate = args.maxrate / 1000.0 # s^-1 to per ms^-1
mechs = {'pas': {'g': '{} S/cm**2'.format(args.gpas), 'e': '-51.0mV'}}
h.xopen(celltemplate)
ggn = nu.create_cell(args.cellname,
mechparams=mechs,
Ra='{}ohm*cm'.format(args.RA),
filename=args.celltemplate)
if (args.diascale is not None) and (args.dialim is not None):
count = 0
ggn.soma.push()
ordered_tree = h.SectionList()
ordered_tree.wholetree()
h.pop_section()
for sec in ordered_tree:
sec.push()
for ii, seg in enumerate(sec):
if seg.diam < dialim:
seg.diam = seg.diam * diascale
count += 1
h.pop_section()
print('Scaled diameters of', count, 'sections whose diameters were <',
'vslope': Q_('5.0mV').to('mV').m,
'e': Q_('-80mV').to('mV').m,
'gbar': Q_('1e-3uS').to('uS').m,
'tau': Q_('4.0ms').to('ms').m
}
# Note: I increased threshold to avoid transmission during low frequency stimulus
# where KC can have sustained depolarization.
kc_ggn_syn_params = {
'threshold': Q_('-10.0mV').to('mV').m,
'delay': Q_('1.0ms').to('ms').m,
'e': Q_('0.0mV').to('mV').m,
'tau1': Q_('13.333ms').to('ms').m,
'tau2': Q_('13.333ms').to('ms').m,
'gmax': Q_('5pS').to('uS').m
}
kc = nu.create_cell(args.kc, filename=args.kcfile)
kc_solo = nu.create_cell(args.kc, filename=args.kcfile)
ggn = nu.create_cell(args.ggn, filename=args.ggnfile)
model = make_ggn_kc_conn(ggn, kc, ggn_kc_syn_params)
tstart = 0.5e3
tend = 3.1e3
if len(args.freq) > 1:
inject = make_driving_current(kc.soma, 0.5, args.amp[0], 1.0, tstart,
tend)
inject_solo = make_driving_current(kc_solo.soma, 0.5, args.amp[0], 1.0,
tstart, tend)
else:
inject = ephys.setup_current_clamp(kc.soma,
delay=Q_(tstart, 'ms'),
duration=Q_((tend - tstart), 'ms'),
amplitude=Q_(args.amp[0], 'nA'),