# make VecStim
vs_cell = VecStimCell("vecstim_cell")
stim2 = vs_cell.make_vecstim(np.array([WARMUP+50]))
# make synapses with spines
syns_4p, heads = cell.add_synapses_with_spine(source=None, secs=cell.secs, number=100, netcon_weight=WEIGHT,
mod_name="Syn4PAChDa", delay=1, **cell.params_4p_syn)
for s, h in zip(syns_4p, heads):
syn_ach = cell.add_synapse(source=stim1, mod_name="SynACh", seg=h(1.0), netcon_weight=0.1, delay=1)
syn_da = cell.add_synapse(source=stim2, mod_name="SynDa", seg=h(1.0), netcon_weight=0.1, delay=1)
cell.set_synaptic_pointers(s, syn_ach, syn_da)
# add mechanisms
cell.make_default_mechanisms()
cell.make_apical_mechanisms(sections='head neck')
# make plots
rec_4psyn = Record(cell.filter_point_processes(mod_name="Syn4PAChDa", name="head[0]"), variables="w")
# init and run
sim = Simulation(init_v=-70, warmup=WARMUP)
sim.run(runtime=200)
# Event delivery
syns_4p[0].make_event(10)
sim.run(runtime=200)
# plot
rec_4psyn.plot()
from neuronpp.utils.record import Record
from neuronpp.utils.simulation import Simulation
path = os.path.dirname(os.path.abspath(__file__))
if __name__ == '__main__':
# Prepare cell
filepath = os.path.join(path, "..",
"commons/mods/sigma3syn")
cell = Cell("cell", compile_paths=filepath)
soma = cell.add_sec("soma", diam=20, l=20, nseg=10)
cell.insert('pas')
cell.insert('hh')
w = 0.003 # LTP
#w = 0.0022 # LTD
syn = cell.add_synapse(source=None, netcon_weight=w, seg=soma(0.5), mod_name="ExcSigma3Exp2Syn")
# prepare plots and spike detector
rec_v = Record(soma(0.5), variables="v")
rec_w = Record(syn, variables="w")
# run
sim = Simulation(init_v=-68, warmup=5)
syn.make_event(5)
sim.run(runtime=50)
# plot
rec_w.plot()
rec_v.plot()
soma = cell.filter_secs("soma")
# Netstim to synapse
stim = NetStimCell("stim").add_netstim(start=WARMUP,
number=REPS,
interval=interval)
syn = cell.add_synapse(source=stim,
netcon_weight=WEIGHT,
mod_name="Syn4P",
delay=1,
seg=cell.filter_secs('apic[1]')(0.5))
# IClamp to soma
iclamp = IClamp(segment=cell.filter_secs("soma")(0.5))
for i in range(REPS):
start_t = WARMUP + delta_t + i * interval
iclamp.stim(delay=start_t, dur=DUR, amp=AMP)
# Record
rec = Record([s(0.5) for s in cell.filter_secs("apic[1],apic[50]")])
# Run
sim = Simulation(init_v=-70, warmup=WARMUP, dt=DT)
total_time = REPS * interval + COOL_DOWN
sim.run(total_time)
# Plot
rec.plot(position="merge")
plt.show()
# 2) Recommended synapse
syn1 = cell.add_synapse(source=stim,
seg=soma(0.5),
netcon_weight=0.01,
mod_name="Syn4P",
delay=1)
# 3) Event synapse
syn2 = cell.add_synapse(source=None,
seg=soma(0.5),
netcon_weight=0.01,
mod_name="Syn4P",
delay=1)
# prepare plots
rec_v = Record(soma(0.5), variables="v")
# run
sim = Simulation(init_v=-55, warmup=20)
# Making external events to the synapse
syn2.make_event(10)
syn2.make_event(20)
syn2.make_event(30)
syn2.make_event(40)
# Example of online update of the graph, however sim.run(runtime=1000) can be call in a single run
for i in range(1000):
sim.run(runtime=1)
rec_v.plot(animate=True)
cell.group_synapses(tag="input_syn", synapses=[s, syn_ach, syn_da])
# add mechanisms
cell.make_default_mechanisms()
cell.make_apical_mechanisms(sections='dend head neck')
soma = cell.filter_secs("soma")
syns = cell.filter_synaptic_group()
syn4p = syns[0]['Syn4PAChDa']
synach = syns[0]['SynACh']
rec_syn = Record(syn4p, variables="w stdp_ach ach_stdp ACh ACh_w")
rec_soma = Record(soma(0.5), variables="v")
sim = Simulation(init_v=-80, warmup=WARMUP, warmup_on_create=True)
event = 0
inter = 5
for i in range(10):
for syn in syns:
syn['Syn4PAChDa'][0].make_event(event)
syn['SynACh'][0].make_event(event)
event += inter
sim.run(runtime=150)
# plot
rec_soma.plot()
rec_syn.plot()
spine_number=10,
spine_secs_names="apic",
spine_seed=13)
soma = cell.filter_secs("soma")
syns = cell.filter_complex_synapses(tag="combe")
# Prepare STDP protocol
stdp = Experiment()
stdp.make_protocol("3xEPSP[int=10] 3xAP[int=10,dur=3,amp=1.6]",
start=1,
isi=10,
epsp_synapse=syns[0],
i_clamp_section=soma)
# Prepare plots
v_soma_rec = Record([soma(0.5), syns[0].parent], variables='v')
cai_head0_rec = Record(syns[0].parent, variables='cai')
# Run
sim = Simulation(init_v=-70,
warmup=20,
with_neuron_gui=True,
constant_timestep=False)
sim.run(runtime=100, debug=True)
# Plot
cai_head0_rec.plot()
v_soma_rec.plot()
v_soma_rec.to_csv("vrec.csv")
cell.insert("hh")
soma = cell.filter_secs("soma")
dend = cell.filter_secs("apic[10]")
syn = cell.add_synapse(source=None, mod_name="ExpSyn", seg=dend(0.5))
# Prepare EPSP and AP (IClamp) protocols
experiment = Experiment(iti=40)
experiment.add_epsp(num=3, synapse=syn, init=20, interval=20, weight=0.02)
experiment.add_iclamp(num=3,
segment=soma(0.5),
init=60,
interval=20,
dur=3,
amp=1.6)
experiment.build()
# Prepare plots
rec = Record([soma(0.5), dend(0.5)], variables='v')
# Run
sim = Simulation(init_v=-70,
warmup=20,
with_neuron_gui=False,
constant_timestep=True)
sim.run(runtime=100)
rec.plot()
v_soma = rec.as_numpy('v', segment_name=soma(.5).name)
v_dend = rec.as_numpy('v', segment_name=dend(.5).name)
