def make_ebner_network(input_size, input_cell_num):
def cell_ebner_ach_da():
cell = Ebner2019AChDACell("ebner_ach_da",
compile_paths="agents/commons/mods/4p_ach_da_syns "
"agents/commons/mods/ebner2019")
soma = cell.add_sec("soma", diam=20, l=20, nseg=10)
cell.add_sec("apic", diam=2, l=50, nseg=100)
cell.connect_secs(child="apic", parent="soma", child_loc=0, parent_loc=1)
cell.make_default_mechanisms()
cell.make_spike_detector(soma(0.5))
return cell
def cell_ebner():
cell = Ebner2019Cell("ebner", compile_paths="agents/commons/mods/ebner2019")
cell.add_sec("soma", diam=20, l=20, nseg=10)
cell.add_sec("apic", diam=2, l=50, nseg=100)
cell.connect_secs(child="apic", parent="soma", child_loc=0, parent_loc=1)
cell.make_default_mechanisms()
return cell
input_syn_per_cell = int(np.ceil(input_size / input_cell_num))
inp = Population(name="input")
inp.add_cells(num=input_cell_num, cell_function=cell_ebner)
con = inp.connect(rule="one", syn_num_per_cell_source=input_syn_per_cell)
con.set_source(None)
con.set_target(inp.cells)
con.add_synapse("Syn4P").add_netcon(weight=UniformTruncatedDist(low=0.01, high=0.1))
con.build()
hid = Population(name="hid")
hid.add_cells(num=4, cell_function=cell_ebner_ach_da)
con = hid.connect(syn_num_per_cell_source=1, cell_connection_proba=0.5)
con.set_source([c.filter_secs("soma")(0.5) for c in inp.cells])
con.set_target(hid.cells)
con.add_synapse("Syn4PAChDa").add_netcon(weight=UniformTruncatedDist(low=0.01, high=0.1)) \
.add_point_process_params(ACh_tau=50, Da_tau=100, A_Da=1e-35, A_ACh=1e-35)
con.add_synapse("SynACh").add_netcon(weight=0.3)
con.add_synapse("SynDa").add_netcon(weight=1.0)
con.set_synaptic_function(func=lambda syns: Ebner2019AChDACell.set_synaptic_pointers(*syns))
con.group_synapses()
con.build()
reward = [s['SynACh'][0] for s in hid.syns]
punish = [s['SynDa'][0] for s in hid.syns]
out = Population(name="output")
out.add_cells(num=2, cell_function=cell_ebner_ach_da)
con = out.connect(syn_num_per_cell_source=1, cell_connection_proba=1)
con.set_source([c.filter_secs("soma")(0.5) for c in hid.cells])
con.set_target(out.cells)
con.add_synapse("Syn4PAChDa").add_netcon(weight=UniformTruncatedDist(low=0.01, high=0.1)) \
.add_point_process_params(ACh_tau=50, Da_tau=100, A_Da=1e-3, A_ACh=1e-3)
con.add_synapse("SynACh").add_netcon(weight=0.3)
con.add_synapse("SynDa").add_netcon(weight=1.0)
con.set_synaptic_function(func=lambda syns: Ebner2019AChDACell.set_synaptic_pointers(*syns))
con.group_synapses()
con.build()
reward += [s['SynACh'][0] for s in out.syns]
punish += [s['SynDa'][0] for s in out.syns]
return inp, out, reward, punish
def cell_ebner_ach_da():
cell = Ebner2019AChDACell("ebner_ach_da",
compile_paths="agents/commons/mods/4p_ach_da_syns "
"agents/commons/mods/ebner2019")
soma = cell.add_sec("soma", diam=20, l=20, nseg=10)
cell.add_sec("apic", diam=2, l=50, nseg=100)
cell.connect_secs(child="apic", parent="soma", child_loc=0, parent_loc=1)
cell.make_default_mechanisms()
cell.make_spike_detector(soma(0.5))
return cell
from neuronpp.utils.record import Record
from neuronpp.utils.simulation import Simulation
from neuronpp.core.cells.netstim_cell import NetStimCell
from neuronpp.core.cells.vecstim_cell import VecStimCell
from neuronpp.cells.ebner2019_ach_da_cell import Ebner2019AChDACell
path = os.path.dirname(os.path.abspath(__file__))
WEIGHT = 0.0035 # µS, conductance of (single) synaptic potentials
WARMUP = 200
if __name__ == '__main__':
# define cell
cell = Ebner2019AChDACell(name="cell")
filepath = os.path.join(path, "..",
"commons/morphologies/swc/my.swc")
cell.load_morpho(filepath=filepath)
# make NetStim stims
ns_cell = NetStimCell("netstim_cell")
stim1 = ns_cell.make_netstim(start=WARMUP + 1, number=1)
# 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)
from neuronpp.cells.ebner2019_ach_da_cell import Ebner2019AChDACell
from neuronpp.utils.synaptic_debugger import SynapticDebugger
WEIGHT = 0.0035 # From Ebner et al. 2019
if __name__ == '__main__':
# Prepare cell
cell = Ebner2019AChDACell("cell")
soma = cell.add_sec("soma", diam=20, l=20, nseg=10)
syn = cell.add_synapse(source=None,
netcon_weight=WEIGHT,
seg=soma(0.5),
mod_name="Syn4PAChDa",
**cell.params_4p_syn,
ACh_tau=1,
Da_tau=20,
A_Da=1e-3)
syn_ach = cell.add_synapse(source=None,
seg=soma(0.5),
netcon_weight=1.0,
mod_name="SynACh")
syn_da = cell.add_synapse(source=None,
seg=soma(0.5),
netcon_weight=1.0,
mod_name="SynDa")
cell.set_synaptic_pointers(syn, syn_ach, syn_da)
cell.make_default_mechanisms()