def test_empty(self):
def len(cat):
return sum(1 for _ in cat)
def hash_(cat):
return hash(" ".join(sorted(cat)))
cat = arb.catalogue()
ref = arb.default_catalogue()
other = arb.default_catalogue()
# Test empty constructor
self.assertEqual(0, len(cat),
"Expected no mechanisms in `arbor.catalogue()`.")
# Test empty extend
other.extend(cat, "")
self.assertEqual(hash_(ref), hash_(other),
"Extending cat with empty should not change cat.")
self.assertEqual(0, len(cat),
"Extending cat with empty should not change empty.")
other.extend(cat, "prefix/")
self.assertEqual(
hash_(ref), hash_(other),
"Extending cat with prefixed empty should not change cat.")
self.assertEqual(
0, len(cat),
"Extending cat with prefixed empty should not change empty.")
cat.extend(other, "")
self.assertEqual(
hash_(other), hash_(cat),
"Extending empty with cat should turn empty into cat.")
cat = arb.catalogue()
cat.extend(other, "prefix/")
self.assertNotEqual(
hash_(other), hash_(cat),
"Extending empty with prefixed cat should not yield cat")
def __init__(self, probes, Vms, length, radius, cm, rL, g, gj_g,
cv_policy_max_extent):
"""
probes -- list of probes
Vms -- membrane leak potentials of the two cells
length -- length of cable in μm
radius -- radius of cable in μm
cm -- membrane capacitance in F/m^2
rL -- axial resistivity in Ω·cm
g -- membrane conductivity in S/cm^2
gj_g -- gap junction conductivity in μS
cv_policy_max_extent -- maximum extent of control volume in μm
"""
# 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_probes = probes
self.Vms = Vms
self.length = length
self.radius = radius
self.cm = cm
self.rL = rL
self.g = g
self.gj_g = gj_g
self.cv_policy_max_extent = cv_policy_max_extent
self.the_props = arbor.neuron_cable_properties()
self.the_cat = arbor.default_catalogue()
self.the_props.register(self.the_cat)
def __init__(self, ncells_per_chain, nchains):
arbor.recipe.__init__(self)
self.nchains = nchains
self.ncells_per_chain = ncells_per_chain
self.props = arbor.neuron_cable_properties()
self.cat = arbor.default_catalogue()
self.props.register(self.cat)
def __init__(self, dT, n_pairs):
arbor.recipe.__init__(self)
self.dT = dT
self.n_pairs = n_pairs
self.the_props = arbor.neuron_cable_properties()
self.the_cat = arbor.default_catalogue()
self.the_props.register(self.the_cat)
def __init__(self, n=10):
# 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.ncells = n
self.props = arbor.neuron_cable_properties()
self.cat = arbor.default_catalogue()
self.props.register(self.cat)
def make_catalogue(cls):
"""
Override to return the catalogue required to run this model
"""
try:
import arbor
except ImportError:
raise ImportError("`arbor` unavailable, can't make arbor models.")
return arbor.default_catalogue()
def __init__(self, cell, probes):
# (4.1) 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_props = arbor.neuron_cable_properties()
self.the_cat = arbor.default_catalogue()
self.the_props.register(self.the_cat)
def __init__(self):
A.recipe.__init__(self)
st = A.segment_tree()
i = st.append(A.mnpos, (0, 0, 0, 10), (1, 0, 0, 10), 1)
st.append(i, (1, 3, 0, 5), 1)
st.append(i, (1, -4, 0, 3), 1)
self.the_morphology = A.morphology(st)
self.the_cat = A.default_catalogue()
self.the_props = A.neuron_cable_properties()
self.the_props.register(self.the_cat)
def __init__(self, cell, probes):
# The base C++ class constructor must be called first to ensure that all memory
# in the C++ class is initialised correctly
arbor.recipe.__init__(self)
self.the_cell = cell
self.the_probes = probes
self.the_cat = arbor.default_catalogue()
self.the_props = arbor.cable_global_properties()
def __init__(self, cell):
super().__init__()
self.the_cell = cell
self.vprobe_id = (0, 0)
self.iprobe_id = (0, 1)
self.cprobe_id = (0, 2)
self.the_props = arbor.neuron_cable_properties()
self.the_cat = arbor.default_catalogue()
self.the_props.register(self.the_cat)
def __init__(self, nl_network, pop_indices_vs_gids, pops_vs_components, proj_weights, proj_delays):
# 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.props = arbor.neuron_cable_properties()
self.cat = arbor.default_catalogue()
self.props.register(self.cat)
self.pop_indices_vs_gids = pop_indices_vs_gids
self.pops_vs_components = pops_vs_components
self.nl_network = nl_network
self.proj_weights = proj_weights
self.proj_delays = proj_delays
def __init__(self):
A.recipe.__init__(self)
st = A.segment_tree()
st.append(A.mnpos, (0, 0, 0, 10), (1, 0, 0, 10), 1)
dec = A.decor()
dec.place('(location 0 0.08)', "expsyn")
dec.place('(location 0 0.09)', "exp2syn")
dec.paint('(all)', "hh")
self.cell = A.cable_cell(st, A.label_dict(), dec)
self.cat = A.default_catalogue()
self.props = A.neuron_cable_propetries()
self.props.register(self.cat)
def __init__(self):
arb.recipe.__init__(self)
self.tree = arb.segment_tree()
self.tree.append(arb.mnpos, (0, 0, 0, 10), (1, 0, 0, 10), 1)
self.props = arb.neuron_cable_properties()
try:
self.cat = arb.default_catalogue()
self.props.register(self.cat)
except:
print("Catalogue not found. Are you running from build directory?")
raise
d = arb.decor()
d.paint('(all)', arb.density('pas'))
d.set_property(Vm=0.0)
self.cell = arb.cable_cell(self.tree, arb.label_dict(), d)
def __init__(self):
A.recipe.__init__(self)
st = A.segment_tree()
st.append(A.mnpos, (0, 0, 0, 10), (1, 0, 0, 10), 1)
dec = A.decor()
dec.place('(location 0 0.08)', A.synapse("expsyn"), "syn0")
dec.place('(location 0 0.09)', A.synapse("exp2syn"), "syn1")
dec.place('(location 0 0.1)', A.iclamp(20.), "iclamp")
dec.paint('(all)', A.density("hh"))
self.cell = A.cable_cell(st, A.label_dict(), dec)
self.props = A.neuron_cable_properties()
self.props.catalogue = A.default_catalogue()
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 __init__(self, probes,
Vm, length, radius, cm, rL, g,
stimulus_start, stimulus_duration, stimulus_amplitude,
cv_policy_max_extent):
"""
probes -- list of probes
Vm -- membrane leak potential
length -- length of cable in μm
radius -- radius of cable in μm
cm -- membrane capacitance in F/m^2
rL -- axial resistivity in Ω·cm
g -- membrane conductivity in S/cm^2
stimulus_start -- start of stimulus in ms
stimulus_duration -- duration of stimulus in ms
stimulus_amplitude -- amplitude of stimulus in nA
cv_policy_max_extent -- maximum extent of control volume in μm
"""
# (4.1) 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_probes = probes
self.Vm = Vm
self.length = length
self.radius = radius
self.cm = cm
self.rL = rL
self.g = g
self.stimulus_start = stimulus_start
self.stimulus_duration = stimulus_duration
self.stimulus_amplitude = stimulus_amplitude
self.cv_policy_max_extent = cv_policy_max_extent
self.the_props = arbor.neuron_cable_properties()
self.the_cat = arbor.default_catalogue()
self.the_props.register(self.the_cat)
def __init__(self, cell, probes):
# The base C++ class constructor must be called first to ensure that all memory
# in the C++ class is initialised correctly
arbor.recipe.__init__(self)
self.the_cell = cell
self.the_probes = probes
self.the_cat = arbor.default_catalogue()
self.the_props = arbor.cable_global_properties()
self.the_props.set_property(Vm=-45, cm=0.01, rL=12000)
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)
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(), )
'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)
def __init__(self, n_cell):
A.recipe.__init__(self)
self.n_cell = n_cell
self.cat = A.default_catalogue()
self.props = A.neuron_cable_propetries()
self.props.register(self.cat)
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
# (6) Run simulation for 30 ms of simulated activity.
m.run(tfinal=500)
# (7) Print spike times, if any.
if len(m.spikes) > 0:
print('{} spikes:'.format(len(m.spikes)))
for s in m.spikes:
print('{:3.3f}'.format(s))
else:
print('no spikes')
# (8) Plot the recorded voltages over time.
print("Plotting results ...")
seaborn.set_theme() # Apply some styling to the plot
df = pandas.DataFrame({'t/ms': m.traces[0].time, 'U/mV': m.traces[0].value})
seaborn.relplot(data=df, kind="line", x="t/ms", y="U/mV",
ci=None).savefig('single_cell_model_result_7_0.svg')
# (9) Optionally, you can store your results for later processing.
df.to_csv('single_cell_model_result_7_0.csv', float_format='%g')
cat = arbor.default_catalogue()
# Get mechanism_info for the 'expsyn' mechanism.
mech = cat['Leak']
# Query the mechanism_info for information about parameters.
print(mech.parameters.keys())
print(mech.parameters['gmax'].default)