def cell_description(self, gid):
tree = arbor.segment_tree()
tree.append(arbor.mnpos,
arbor.mpoint(-3, 0, 0, 3),
arbor.mpoint(3, 0, 0, 3),
tag=1)
labels = arbor.label_dict({
'soma': '(tag 1)',
'center': '(location 0 0.5)'
})
decor = arbor.decor()
decor.set_property(Vm=-40)
decor.paint('(all)', arbor.density('hh'))
decor.place('"center"', arbor.spike_detector(-10), "detector")
decor.place('"center"', arbor.synapse('expsyn'), "synapse")
mech = arbor.mechanism('expsyn_stdp')
mech.set("max_weight", 1.)
syn = arbor.synapse(mech)
decor.place('"center"', syn, "stpd_synapse")
cell = arbor.cable_cell(tree, labels, decor)
return cell
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 make_cable_cell(gid):
# (1) Build a segment tree
tree = arbor.segment_tree()
# Soma (tag=1) with radius 6 μm, modelled as cylinder of length 2*radius
s = tree.append(arbor.mnpos,
arbor.mpoint(-12, 0, 0, 6),
arbor.mpoint(0, 0, 0, 6),
tag=1)
# Single dendrite (tag=3) of length 50 μm and radius 2 μm attached to soma.
b0 = tree.append(s,
arbor.mpoint(0, 0, 0, 2),
arbor.mpoint(50, 0, 0, 2),
tag=3)
# Attach two dendrites (tag=3) of length 50 μm to the end of the first dendrite.
# Radius tapers from 2 to 0.5 μm over the length of the dendrite.
b1 = tree.append(b0,
arbor.mpoint(50, 0, 0, 2),
arbor.mpoint(50 + 50 / sqrt(2), 50 / sqrt(2), 0, 0.5),
tag=3)
# Constant radius of 1 μm over the length of the dendrite.
b2 = tree.append(b0,
arbor.mpoint(50, 0, 0, 1),
arbor.mpoint(50 + 50 / sqrt(2), -50 / sqrt(2), 0, 1),
tag=3)
# Associate labels to tags
labels = arbor.label_dict()
labels['soma'] = '(tag 1)'
labels['dend'] = '(tag 3)'
# (2) Mark location for synapse at the midpoint of branch 1 (the first dendrite).
labels['synapse_site'] = '(location 1 0.5)'
# Mark the root of the tree.
labels['root'] = '(root)'
# (3) Create a decor and a cable_cell
decor = arbor.decor()
# Put hh dynamics on soma, and passive properties on the dendrites.
decor.paint('"soma"', arbor.density('hh'))
decor.paint('"dend"', arbor.density('pas'))
# (4) Attach a single synapse.
decor.place('"synapse_site"', arbor.synapse('expsyn'), 'syn')
# Attach a spike detector with threshold of -10 mV.
decor.place('"root"', arbor.spike_detector(-10), 'detector')
cell = arbor.cable_cell(tree, labels, decor)
return cell
def make_cable_cell(gid):
# Build a segment tree
tree = arbor.segment_tree()
# Soma with radius 5 μm and length 2 * radius = 10 μm, (tag = 1)
s = tree.append(arbor.mnpos,
arbor.mpoint(-10, 0, 0, 5),
arbor.mpoint(0, 0, 0, 5),
tag=1)
# Single dendrite with radius 2 μm and length 40 μm, (tag = 2)
b = tree.append(s,
arbor.mpoint(0, 0, 0, 2),
arbor.mpoint(40, 0, 0, 2),
tag=2)
# Label dictionary for cell components
labels = arbor.label_dict()
labels['soma'] = '(tag 1)'
labels['dend'] = '(tag 2)'
# Mark location for synapse site at midpoint of dendrite (branch 0 = soma + dendrite)
labels['synapse_site'] = '(location 0 0.6)'
# Gap junction site at connection point of soma and dendrite
labels['gj_site'] = '(location 0 0.2)'
# Label root of the tree
labels['root'] = '(root)'
# Paint dynamics onto the cell, hh on soma and passive properties on dendrite
decor = arbor.decor()
decor.paint('"soma"', arbor.density("hh"))
decor.paint('"dend"', arbor.density("pas"))
# Attach one synapse and gap junction each on their labeled sites
decor.place('"synapse_site"', arbor.synapse('expsyn'), 'syn')
decor.place('"gj_site"', arbor.junction('gj'), 'gj')
# Attach spike detector to cell root
decor.place('"root"', arbor.spike_detector(-10), 'detector')
cell = arbor.cable_cell(tree, labels, decor)
return cell
def create_arbor_cell(self, cell, gid, pop_id, index):
if cell.arbor_cell == "cable_cell":
default_tree = arbor.segment_tree()
radius = (evaluate(cell.parameters["radius"],
self.nl_network.parameters)
if "radius" in cell.parameters else 3)
default_tree.append(
arbor.mnpos,
arbor.mpoint(-1 * radius, 0, 0, radius),
arbor.mpoint(radius, 0, 0, radius),
tag=1,
)
labels = arbor.label_dict({
"soma": "(tag 1)",
"center": "(location 0 0.5)"
})
labels["root"] = "(root)"
decor = arbor.decor()
v_init = (evaluate(cell.parameters["v_init"],
self.nl_network.parameters)
if "v_init" in cell.parameters else -70)
decor.set_property(Vm=v_init)
decor.paint('"soma"', arbor.density(cell.parameters["mechanism"]))
decor.place('"center"', arbor.spike_detector(0), "detector")
for ip in self.input_info:
if self.input_info[ip][0] == pop_id:
print_v("Stim: %s (%s) being placed on %s" %
(ip, self.input_info[ip], pop_id))
for il in self.input_lists[ip]:
cellId, segId, fract, weight = il
if cellId == index:
if self.input_info[ip][
1] == 'i_clamp': # TODO: remove hardcoding of this...
ic = arbor.iclamp(
self.nl_network.parameters["input_del"],
self.nl_network.parameters["input_dur"],
self.nl_network.parameters["input_amp"],
)
print_v("Stim: %s on %s" % (ic, gid))
decor.place('"center"', ic, "iclamp")
# (2) Mark location for synapse at the midpoint of branch 1 (the first dendrite).
labels["synapse_site"] = "(location 0 0.5)"
# (4) Attach a single synapse.
decor.place('"synapse_site"', arbor.synapse("expsyn"), "syn")
default_cell = arbor.cable_cell(default_tree, labels, decor)
print_v("Created a new cell for gid %i: %s" % (gid, cell))
print_v("%s" % (default_cell))
return default_cell
