def cell_description(self, gid):
"""A high level description of the cell with global identifier gid.
For example the morphology, synapses and ion channels required
to build a multi-compartment neuron.
"""
assert gid == 0
tree = arbor.segment_tree()
tree.append(arbor.mnpos,
arbor.mpoint(0, 0, 0, self.radius),
arbor.mpoint(self.length, 0, 0, self.radius),
tag=1)
labels = arbor.label_dict({'cable': '(tag 1)',
'start': '(location 0 0)'})
decor = arbor.decor()
decor.set_property(Vm=self.Vm)
decor.set_property(cm=self.cm)
decor.set_property(rL=self.rL)
decor.paint('"cable"',
arbor.density(f'pas/e={self.Vm}', {'g': self.g}))
decor.place('"start"', arbor.iclamp(self.stimulus_start, self.stimulus_duration, self.stimulus_amplitude), "iclamp")
policy = arbor.cv_policy_max_extent(self.cv_policy_max_extent)
decor.discretization(policy)
return arbor.cable_cell(tree, labels, decor)
def cable_cell_template(cls, morphology=0, decor=None, labels=None):
import arbor
if not isinstance(cls.morphologies[morphology], str):
raise NotImplementedError(
"Can't use builders for cable cells, must import from file. Please export your morphology builder to an SWC or ASC file and update `cls.morphologies`."
)
if labels is None:
labels = arbor.label_dict()
if decor is None:
decor = arbor.decor()
path = os.path.join(cls.morphology_directory,
cls.morphologies[morphology])
morph, morpho_labels = _try_arb_morpho(path)
labels.update(morpho_labels)
cls._cc_insert_labels(labels, getattr(cls, "labels", {}),
getattr(cls, "tags", {}))
composites = _arb_resolve_composites(cls.section_types, labels)
dflt_policy = arbor.cv_policy_max_extent(40.0)
soma_policy = arbor.cv_policy_fixed_per_branch(1, "(tag 1)")
policy = dflt_policy | soma_policy
decor.discretization(policy)
for label, definition in composites.items():
cls._cc_all(decor, label, definition)
return morph, labels, decor
def cell_description(self, gid):
"""A high level description of the cell with global identifier gid.
For example the morphology, synapses and ion channels required
to build a multi-compartment neuron.
"""
assert gid in [0, 1]
tree = arbor.segment_tree()
tree.append(arbor.mnpos,
arbor.mpoint(0, 0, 0, self.radius),
arbor.mpoint(self.length, 0, 0, self.radius),
tag=1)
labels = arbor.label_dict({
'cell': '(tag 1)',
'gj_site': '(location 0 0.5)'
})
decor = arbor.decor()
decor.set_property(Vm=self.Vms[gid])
decor.set_property(cm=self.cm)
decor.set_property(rL=self.rL)
# add a gap junction mechanism at the "gj_site" location and label that specific mechanism on that location "gj_label"
junction_mech = arbor.junction('gj', {"g": self.gj_g})
decor.place('"gj_site"', junction_mech, 'gj_label')
decor.paint('"cell"',
arbor.density(f'pas/e={self.Vms[gid]}', {'g': self.g}))
if self.cv_policy_max_extent is not None:
policy = arbor.cv_policy_max_extent(self.cv_policy_max_extent)
decor.discretization(policy)
else:
decor.discretization(arbor.cv_policy_single())
return arbor.cable_cell(tree, labels, decor)
decor.paint('"all"', 'pas')
decor.paint('"custom"', 'hh')
decor.paint('"dend"', mech('Ih', {'gbar': 0.001}))
# Place stimuli and spike detectors.
decor.place('"root"', arbor.iclamp(10, 1, current=2), "iclamp0")
decor.place('"root"', arbor.iclamp(30, 1, current=2), "iclamp1")
decor.place('"root"', arbor.iclamp(50, 1, current=2), "iclamp2")
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):
