def probes(self, gid):
# Cell 0 has three voltage probes:
# 0, 0: end of branch 1
# 0, 1: end of branch 2
# 0, 2: all terminal points
# Values sampled from (0, 0) and (0, 1) should correspond
# to the values sampled from (0, 2).
# Cell 1 has whole cell probes:
# 0, 0: all membrane voltages
# 0, 1: all expsyn state variable 'g'
if gid == 0:
return [
A.cable_probe_membrane_voltage('(location 1 1)'),
A.cable_probe_membrane_voltage('(location 2 1)'),
A.cable_probe_membrane_voltage('(terminal)')
]
elif gid == 1:
return [
A.cable_probe_membrane_voltage_cell(),
A.cable_probe_point_state_cell('expsyn', 'g')
]
else:
return []
def probes(self, gid):
return [
arbor.cable_probe_membrane_voltage('"center"'),
arbor.cable_probe_point_state(1, "expsyn_stdp", "g"),
arbor.cable_probe_point_state(1, "expsyn_stdp", "apost"),
arbor.cable_probe_point_state(1, "expsyn_stdp", "apre"),
arbor.cable_probe_point_state(1, "expsyn_stdp", "weight_plastic")
]
def probes(self, gid):
# Use keyword arguments to check that the wrappers have actually declared keyword arguments correctly.
# Place single-location probes at (location 0 0.01*j) where j is the index of the probe address in
# the returned list.
return [
# probe id (0, 0)
A.cable_probe_membrane_voltage(where='(location 0 0.00)'),
# probe id (0, 1)
A.cable_probe_membrane_voltage_cell(),
# probe id (0, 2)
A.cable_probe_axial_current(where='(location 0 0.02)'),
# probe id (0, 3)
A.cable_probe_total_ion_current_density(where='(location 0 0.03)'),
# probe id (0, 4)
A.cable_probe_total_ion_current_cell(),
# probe id (0, 5)
A.cable_probe_total_current_cell(),
# probe id (0, 6)
A.cable_probe_density_state(where='(location 0 0.06)',
mechanism='hh',
state='m'),
# probe id (0, 7)
A.cable_probe_density_state_cell(mechanism='hh', state='n'),
# probe id (0, 8)
A.cable_probe_point_state(target=0, mechanism='expsyn', state='g'),
# probe id (0, 9)
A.cable_probe_point_state_cell(mechanism='exp2syn', state='B'),
# probe id (0, 10)
A.cable_probe_ion_current_density(where='(location 0 0.10)',
ion='na'),
# probe id (0, 11)
A.cable_probe_ion_current_cell(ion='na'),
# probe id (0, 12)
A.cable_probe_ion_int_concentration(where='(location 0 0.12)',
ion='na'),
# probe id (0, 13)
A.cable_probe_ion_int_concentration_cell(ion='na'),
# probe id (0, 14)
A.cable_probe_ion_ext_concentration(where='(location 0 0.14)',
ion='na'),
# probe id (0, 15)
A.cable_probe_ion_ext_concentration_cell(ion='na'),
# probe id (0, 15)
A.cable_probe_stimulus_current_cell()
]
def probes(self, gid):
if gid < 3:
return []
else:
return [arbor.cable_probe_membrane_voltage('"midpoint"')]
decor.place('"axon_terminal"', arbor.spike_detector(-10), "detector")
# Set cv_policy
soma_policy = arbor.cv_policy_single('"soma"')
dflt_policy = arbor.cv_policy_max_extent(1.0)
policy = dflt_policy | soma_policy
decor.discretization(policy)
# Create a cell
cell = arbor.cable_cell(morph, labels, decor)
# (2) Declare a probe.
probe = arbor.cable_probe_membrane_voltage('"custom_terminal"')
# (3) Create a recipe class and instantiate a recipe
class single_recipe(arbor.recipe):
def __init__(self, cell, probes):
# The base C++ class constructor must be called first, to ensure that
# all memory in the C++ class is initialized correctly.
arbor.recipe.__init__(self)
self.the_cell = cell
self.the_probes = probes
self.the_cat = arbor.default_catalogue()
self.the_cat.extend(arbor.allen_catalogue(), "")
def probes(self, gid):
return [arbor.cable_probe_membrane_voltage('(location 0 0)')]
def probes(self, gid):
return [arbor.cable_probe_membrane_voltage('"root"')]
parser.add_argument('--stimulus_amplitude',
help="amplitude of stimulus in nA",
type=float,
default=1)
parser.add_argument('--cv_policy_max_extent',
help="maximum extent of control volume in μm",
type=float,
default=10)
# parse the command line arguments
args = parser.parse_args()
# set up membrane voltage probes equidistantly along the dendrites
probes = [
arbor.cable_probe_membrane_voltage(f'(location 0 {r})')
for r in np.linspace(0, 1, 11)
]
recipe = Cable(probes, **vars(args))
# create a default execution context and a default domain decomposition
context = arbor.context()
domains = arbor.partition_load_balance(recipe, context)
# configure the simulation and handles for the probes
sim = arbor.simulation(recipe, domains, context)
dt = 0.001
handles = [
sim.sample((0, i), arbor.regular_schedule(dt))
for i in range(len(probes))
]
# (4.4) Override the cell_description method
return self.the_cell
def probes(self, gid):
# (4.5) Override the probes method
return self.the_probes
def global_properties(self, kind):
# (4.6) Override the global_properties method
return self.the_props
# (5) Instantiate recipe with a voltage probe located on "midpoint".
recipe = single_recipe(cell,
[arbor.cable_probe_membrane_voltage('"midpoint"')])
# (6) Create a default execution context and a default domain decomposition.
context = arbor.context()
domains = arbor.partition_load_balance(recipe, context)
# (7) Create and run simulation and set up 10 kHz (every 0.1 ms) sampling on the probe.
# The probe is located on cell 0, and is the 0th probe on that cell, thus has probe_id (0, 0).
sim = arbor.simulation(recipe, domains, context)
sim.record(arbor.spike_recording.all)
handle = sim.sample((0, 0), arbor.regular_schedule(0.1))
sim.run(tfinal=30)
# (8) Collect results.
parser.add_argument('--stimulus_start',
help="start of stimulus in ms", type=float, default=10)
parser.add_argument('--stimulus_duration',
help="duration of stimulus in ms", type=float, default=0.1)
parser.add_argument('--stimulus_amplitude',
help="amplitude of stimulus in nA", type=float, default=1)
parser.add_argument('--cv_policy_max_extent',
help="maximum extent of control volume in μm", type=float,
default=10)
# parse the command line arguments
args = parser.parse_args()
# set up membrane voltage probes equidistantly along the dendrites
probes = [arbor.cable_probe_membrane_voltage(
f'(location 0 {r})') for r in np.linspace(0, 1, 11)]
recipe = Cable(probes, **vars(args))
# create a default execution context and a default domain decomposition
context = arbor.context()
domains = arbor.partition_load_balance(recipe, context)
# configure the simulation and handles for the probes
sim = arbor.simulation(recipe, domains, context)
dt = 0.001
handles = [sim.sample((0, i), arbor.regular_schedule(dt))
for i in range(len(probes))]
# run the simulation for 30 ms
sim.run(tfinal=30, dt=dt)
default=0.001)
parser.add_argument('--gj_g',
help="gap junction conductivity in μS",
type=float,
default=0.01)
parser.add_argument('--cv_policy_max_extent',
help="maximum extent of control volume in μm",
type=float)
# parse the command line arguments
args = parser.parse_args()
# set up membrane voltage probes at the position of the gap junction
probes = [arbor.cable_probe_membrane_voltage('"gj_site"')]
recipe = TwoCellsWithGapJunction(probes, **vars(args))
# create a default execution context and a default domain decomposition
context = arbor.context()
domains = arbor.partition_load_balance(recipe, context)
# configure the simulation and handles for the probes
sim = arbor.simulation(recipe, domains, context)
dt = 0.01
handles = []
for gid in [0, 1]:
handles += [
sim.sample((gid, i), arbor.regular_schedule(dt))
for i in range(len(probes))
def cell_description(self, gid):
# (4.4) Override the cell_description method
return self.the_cell
def probes(self, gid):
# (4.5) Override the probes method
return self.the_probes
def global_properties(self, kind):
# (4.6) Override the global_properties method
return self.the_props
# (5) Instantiate recipe with a voltage probe located on "midpoint".
recipe = single_recipe(cell, [arbor.cable_probe_membrane_voltage('"midpoint"')])
# (6) Create a default execution context and a default domain decomposition.
context = arbor.context()
domains = arbor.partition_load_balance(recipe, context)
# (7) Create and run simulation and set up 10 kHz (every 0.1 ms) sampling on the probe.
# The probe is located on cell 0, and is the 0th probe on that cell, thus has probe_id (0, 0).
sim = arbor.simulation(recipe, domains, context)
sim.record(arbor.spike_recording.all)
handle = sim.sample((0, 0), arbor.regular_schedule(0.1))
sim.run(tfinal=30)
# (8) Collect results.
decor.place('"center"', arbor.iclamp(100, 300, value))
# Spike detection at center of soma.
decor.place('"center"', arbor.spike_detector(-26))
#define CV policy and add it to decor
#policy = arbor.cv_policy_every_segment('(all)')
policy = arbor.cv_policy_fixed_per_branch(1, '(all)')
#policy = arbor.cv_policy_max_extent(1.0)
decor.discretization(policy)
# (4) Create cell.
dd1_cell = arbor.cable_cell(morph, labels, decor)
# (5) Create probes for membrane voltage and calcium ion concentration.
voltage_probe = arbor.cable_probe_membrane_voltage('"center"')
ca_conc_probe = arbor.cable_probe_ion_int_concentration('"center"', "ca")
# Instantiate recipe
# Pass the probe in a list because that it what single_recipe expects.
#recipe = single_recipe(dd1_cell, [voltage_probe]) #, ca_conc_probe])
recipe = single_recipe(dd1_cell, [voltage_probe, ca_conc_probe])
context = arbor.context()
domains = arbor.partition_load_balance(recipe, context)
sim = arbor.simulation(recipe, domains, context)
# Instruct the simulation to record the spikes
# Label dictionary
labels = arbor.label_dict()
labels['centre'] = '(location 0 0.5)'
# Decorations
decor = arbor.decor()
decor.set_property(Vm=-40)
decor.paint('(all)', 'hh')
decor.place('"centre"', arbor.iclamp(10, 2, 0.8))
decor.place('"centre"', arbor.spike_detector(-10))
cell = arbor.cable_cell(tree, labels, decor)
# (3) Instantiate recipe with a voltage probe.
recipe = single_recipe(cell, [arbor.cable_probe_membrane_voltage('"centre"')])
# (4) Instantiate simulation and set up sampling on probe id (0, 0).
context = arbor.context()
domains = arbor.partition_load_balance(recipe, context)
sim = arbor.simulation(recipe, domains, context)
sim.record(arbor.spike_recording.all)
handle = sim.sample((0, 0), arbor.regular_schedule(0.1))
# (6) Run simulation for 30 ms of simulated activity and collect results.
sim.run(tfinal=30)
spikes = sim.spikes()
data, meta = sim.samples(handle)[0]
