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(), "")
self.the_props = arbor.cable_global_properties()
self.the_props.set_property(Vm=-65, tempK=300, rL=35.4, cm=0.01)
self.the_props.set_ion(ion='na', int_con=10, ext_con=140, rev_pot=50, method='nernst/na')
self.the_props.set_ion(ion='k', int_con=54.4, ext_con=2.5, rev_pot=-77)
self.the_props.set_ion(ion='ca', int_con=5e-5, ext_con=2, rev_pot=132.5)
self.the_props.register(self.the_cat)
def simulate(self, traj):
cell = arb.cable_cell(self.morphology, self.labels)
cell.compartments_length(20)
cell.set_properties(tempK=self.defaults.tempK,
Vm=self.defaults.Vm,
cm=self.defaults.cm,
rL=self.defaults.rL)
for region, vs in self.regions:
cell.paint(f'"{region}"',
tempK=vs.tempK,
Vm=vs.Vm,
cm=vs.cm,
rL=vs.rL)
for region, ion, e in self.ions:
cell.paint(f'"{region}"', ion, rev_pot=e)
cell.set_ion('ca',
int_con=5e-5,
ext_con=2.0,
method=arb.mechanism('nernst/x=ca'))
tmp = defaultdict(dict)
for key, val in traj.individual.items():
region, mech, valuename = key.split('.')
tmp[(region, mech)][valuename] = val
for (region, mech), values in tmp.items():
cell.paint(f'"{region}"', arb.mechanism(mech, values))
cell.place('"center"', arb.iclamp(200, 1000, 0.15))
model = arb.single_cell_model(cell)
model.probe('voltage', '"center"', frequency=200000)
model.properties.catalogue = arb.allen_catalogue()
model.properties.catalogue.extend(arb.default_catalogue(), '')
model.run(tfinal=1400, dt=0.005)
voltages = np.array(model.traces[0].value[:])
return (((voltages - self.reference)**2).sum(), )
model = arbor.single_cell_model(cell)
# (6) Set the model default properties
model.properties.set_property(Vm=-65, tempK=300, rL=35.4, cm=0.01)
model.properties.set_ion('na',
int_con=10,
ext_con=140,
rev_pot=50,
method='nernst/na')
model.properties.set_ion('k', int_con=54.4, ext_con=2.5, rev_pot=-77)
# Extend the default catalogue with the allen catalogue.
model.catalogue.extend(arbor.allen_catalogue(), "")
# (7) Add probes.
model.probe('voltage', where='"custom_terminal"', frequency=50)
# (8) Run the simulation.
model.run(tfinal=100, dt=0.025)
# (9) Print the spikes.
print(len(model.spikes), 'spikes recorded:')
# Print the spike times.
# (6) Set the model default properties
model.properties.set_property(Vm=-65, tempK=300, rL=35.4, cm=0.01)
model.properties.set_ion('na',
int_con=10,
ext_con=140,
rev_pot=50,
method='nernst/na')
model.properties.set_ion('k', int_con=54.4, ext_con=2.5, rev_pot=-77)
# Extend the default catalogue with the Allen catalogue.
# The function takes a second string parameter that can prefix
# the name of the mechanisms to avoid collisions between catalogues
# in this case we have no collisions so we use an empty prefix string.
model.properties.catalogue.extend(arbor.allen_catalogue(), "")
# (7) Add probes.
# Add voltage probes on the "custom_terminal" locset
# which sample the voltage at 50 kHz
model.probe('voltage', where='"custom_terminal"', frequency=50)
# (8) Run the simulation for 100 ms, with a dt of 0.025 ms
model.run(tfinal=100, dt=0.025)
# (9) Print the spikes.
print(len(model.spikes), 'spikes recorded:')
for s in model.spikes:
def run_arb(fit, swc, current, t_start, t_stop):
tree = arbor.load_swc_allen(swc, no_gaps=False)
# Load mechanism data
with open(fit) as fd:
fit = json.load(fd)
## collect parameters in dict
mechs = defaultdict(dict)
### Passive parameters
ra = float(fit['passive'][0]['ra'])
### Remaining parameters
for block in fit['genome']:
mech = block['mechanism'] or 'pas'
region = block['section']
name = block['name']
if name.endswith('_' + mech):
name = name[:-(len(mech) + 1)]
mechs[(mech, region)][name] = float(block['value'])
# Label regions
labels = arbor.label_dict({
'soma': '(tag 1)',
'axon': '(tag 2)',
'dend': '(tag 3)',
'apic': '(tag 4)',
'center': '(location 0 0.5)'
})
properties = fit['conditions'][0]
T = properties['celsius'] + 273.15
Vm = properties['v_init']
# Run simulation
morph = arbor.morphology(tree)
# Build cell and attach Clamp and Detector
cell = arbor.cable_cell(morph, labels)
cell.place('center', arbor.iclamp(t_start, t_stop - t_start, current))
cell.place('center', arbor.spike_detector(-40))
cell.compartments_length(20)
# read json file and proceed to set parameters and mechanisms
# set global values
print('Setting global parameters')
print(f" * T = {T}K = {T - 273.15}C")
print(f" * Vm = {Vm}mV")
cell.set_properties(tempK=T, Vm=Vm, rL=ra)
# Set reversal potentials
print("Setting reversal potential for")
for kv in properties['erev']:
region = kv['section']
for k, v in kv.items():
if k == 'section':
continue
ion = k[1:]
print(f' * region {region:6} species {ion:5}: {v:10}')
cell.paint(region, arbor.ion(ion, rev_pot=float(v)))
cell.set_ion('ca',
int_con=5e-5,
ext_con=2.0,
method=arbor.mechanism('default_nernst/x=ca'))
# Setup mechanisms and parameters
print('Setting up mechanisms')
## Now paint the cell using the dict
for (mech, region), vs in mechs.items():
print(f" * {region:10} -> {mech:10}: {str(vs):>60}", end=' ')
try:
if mech != 'pas':
m = arbor.mechanism(mech, vs)
cell.paint(region, m)
else:
m = arbor.mechanism('default_pas', {
'e': vs['e'],
'g': vs['g']
})
cell.paint(region, m)
cell.paint(region, cm=vs["cm"] / 100, rL=vs["Ra"])
print("OK")
except Exception as e:
print("ERROR")
print("When trying to set", mech, vs)
print(" ->", e)
exit()
# Run the simulation, collecting voltages
print('Simulation', end=' ')
default = arbor.default_catalogue()
catalogue = arbor.allen_catalogue()
catalogue.extend(default, 'default_')
model = arbor.single_cell_model(cell)
model.properties.catalogue = catalogue
model.probe('voltage', 'center', frequency=200000)
model.run(tfinal=t_start + t_stop, dt=1000 / 200000)
print('DONE')
for t in model.traces:
ts = t.time[:]
vs = t.value[:]
break
spikes = np.array(model.spikes)
count = len(spikes)
print('Counted spikes', count)
return np.array(ts), np.array(vs) + 14
'center': '(location 0 0.5)'})
cell = arb.cable_cell(morphology, labels) # see !\circled{3}!
cell.compartments_length(20) # discretisation strategy: max compartment length
# !\circled{4}! load and assign electro-physical parameters
defaults, regions, ions, mechanisms = utils.load_allen_fit('fit.json')
# set defaults and override by region
cell.set_properties(tempK=defaults.tempK, Vm=defaults.Vm,
cm=defaults.cm, rL=defaults.rL)
for region, vs in regions:
cell.paint('"'+region+'"', tempK=vs.tempK, Vm=vs.Vm, cm=vs.cm, rL=vs.rL)
# set reversal potentials
for region, ion, e in ions:
cell.paint('"'+region+'"', ion, rev_pot=e)
cell.set_ion('ca', int_con=5e-5, ext_con=2.0, method=arb.mechanism('nernst/x=ca'))
# assign ion dynamics
for region, mech, values in mechanisms:
cell.paint('"'+region+'"', arb.mechanism(mech, values))
print(mech)
# !\circled{5}! attach stimulus and spike detector
cell.place('"center"', arb.iclamp(200, 1000, 0.15))
cell.place('"center"', arb.spike_detector(-40))
# !\circled{6}! set up runnable simulation
model = arb.single_cell_model(cell)
model.probe('voltage', '"center"', frequency=200000) # see !\circled{5}!
# !\circled{7}! assign catalogues
model.properties.catalogue = arb.allen_catalogue()
model.properties.catalogue.extend(arb.default_catalogue(), '')
# !\circled{8}! run simulation and plot results
model.run(tfinal=1400, dt=0.005)
utils.plot_results(model)