def test_place_pwlin_id(self):
# Single branch, discontiguous segments.
s0p = A.mpoint(0, 0, 0, 10)
s0d = A.mpoint(1, 0, 0, 10)
s1p = A.mpoint(3, 0, 0, 10)
s1d = A.mpoint(4, 0, 0, 10)
tree = A.segment_tree()
i = tree.append(A.mnpos, s0p, s0d, 1)
tree.append(i, s1p, s1d, 2)
m = A.morphology(tree)
place = A.place_pwlin(m)
L0 = place.at(A.location(0, 0))
L0s = place.all_at(A.location(0, 0))
self.assertEqual(s0p, L0)
self.assertEqual([s0p], L0s)
Lhalf = place.at(A.location(0, 0.5))
Lhalfs = place.all_at(A.location(0, 0.5))
self.assertTrue(s0d == Lhalf or s1p == Lhalf)
self.assertTrue([s0d, s1p] == Lhalfs)
Chalf = [(s.prox, s.dist)
for s in place.segments([A.cable(0, 0., 0.5)])]
self.assertEqual([(s0p, s0d)], Chalf)
Chalf_all = [(s.prox, s.dist)
for s in place.all_segments([A.cable(0, 0., 0.5)])]
self.assertEqual([(s0p, s0d), (s1p, s1p)], Chalf_all)
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 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 cell_description(self, gid):
tree = arb.segment_tree()
tree.append(arb.mnpos,
arb.mpoint(-3, 0, 0, 3),
arb.mpoint(3, 0, 0, 3),
tag=1)
decor = arb.decor()
decor.place('(location 0 0.5)', arb.gap_junction_site(), "gj")
return arb.cable_cell(tree, arb.label_dict(), decor)
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)'
labels['synapse_site2'] = '(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"', 'hh')
decor.paint('"dend"', 'pas')
# (4) Attach a single synapse.
decor.place('"synapse_site"', 'expsyn')
decor.place('"synapse_site2"', 'expsyn')
# Attach a spike detector with threshold of -10 mV.
decor.place('"root"', arbor.spike_detector(-10))
cell = arbor.cable_cell(tree, labels, decor)
return cell
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):
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()
self.props.catalogue = arb.load_catalogue(cat)
d = arb.decor()
d.paint('(all)', 'dummy')
d.set_property(Vm=0.0)
self.cell = arb.cable_cell(self.tree, arb.label_dict(), d)
def make_cable_cell(gid):
# (1) Build a segment tree
# https://docs.arbor-sim.org/en/latest/concepts/morphology.html
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 = TODO
# Constant radius of 1 μm over the length of the dendrite.
b2 = TODO
# Associate labels to tags
# https://docs.arbor-sim.org/en/latest/concepts/labels.html
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).
# https://docs.arbor-sim.org/en/latest/concepts/labels.html
labels['synapse_site'] = TODO
# Mark the root of the tree.
labels['root'] = TODO
# (3) Create a decor and a cable_cell
# https://docs.arbor-sim.org/en/latest/python/decor.html
decor = arbor.decor()
# Put hh dynamics on soma, and passive properties on the dendrites.
decor.paint('"soma"', 'hh')
decor.paint('"dend"', 'pas')
# (4) Attach a single synapse.
decor.place('"synapse_site"', 'expsyn', 'syn')
# Attach a spike detector with threshold of -10 mV.
decor.place(TODO)
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)', "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 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 cable_cell():
# (1) Create a morphology with a single (cylindrical) segment of length=diameter=6 μm
tree = arbor.segment_tree()
tree.append(
arbor.mnpos,
arbor.mpoint(-3, 0, 0, 3),
arbor.mpoint(3, 0, 0, 3),
tag=1,
)
# (2) Define the soma and its midpoint
labels = arbor.label_dict({'soma': '(tag 1)',
'midpoint': '(location 0 0.5)'})
# (3) Create cell and set properties
decor = arbor.decor()
decor.set_property(Vm=-40)
decor.paint('"soma"', arbor.density('hh'))
decor.place('"midpoint"', arbor.iclamp( 10, 2, 0.8), "iclamp")
decor.place('"midpoint"', arbor.spike_detector(-10), "detector")
return arbor.cable_cell(tree, labels, decor)
def create_arbor_cell(cell, nl_network, gid):
if cell.arbor_cell=='cable_cell':
default_tree = arbor.segment_tree()
radius = evaluate(cell.parameters['radius'], 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'], nl_network.parameters) if 'v_init' in cell.parameters else -70
decor.set_property(Vm=v_init)
decor.paint('"soma"', cell.parameters['mechanism'])
if gid==0:
ic = arbor.iclamp( nl_network.parameters['input_del'], nl_network.parameters['input_dur'], nl_network.parameters['input_amp'])
print_v("Stim: %s"%ic)
decor.place('"center"', ic)
decor.place('"center"', arbor.spike_detector(-10))
# (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"', 'expsyn')
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
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)
def test_place_pwlin_isometry(self):
# Single branch, discontiguous segments.
s0p = A.mpoint(0, 0, 0, 10)
s0d = A.mpoint(1, 0, 0, 10)
s1p = A.mpoint(3, 0, 0, 10)
s1d = A.mpoint(4, 0, 0, 10)
tree = A.segment_tree()
i = tree.append(A.mnpos, s0p, s0d, 1)
tree.append(i, s1p, s1d, 2)
m = A.morphology(tree)
iso = A.isometry.translate(2, 3, 4)
place = A.place_pwlin(m, iso)
x0p = iso(s0p)
x0d = iso(s0d)
x1p = iso(s1p)
x1d = iso(s1d)
L0 = place.at(A.location(0, 0))
L0s = place.all_at(A.location(0, 0))
self.assertEqual(x0p, L0)
self.assertEqual([x0p], L0s)
Lhalf = place.at(A.location(0, 0.5))
Lhalfs = place.all_at(A.location(0, 0.5))
self.assertTrue(x0d == Lhalf or x1p == Lhalf)
self.assertTrue([x0d, x1p] == Lhalfs)
Chalf = [(s.prox, s.dist)
for s in place.segments([A.cable(0, 0., 0.5)])]
self.assertEqual([(x0p, x0d)], Chalf)
Chalf_all = [(s.prox, s.dist)
for s in place.all_segments([A.cable(0, 0., 0.5)])]
self.assertEqual([(x0p, x0d), (x1p, x1p)], Chalf_all)
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
#!/usr/bin/env python3
import arbor
import pandas, seaborn # You may have to pip install these.
# (1) Create a morphology with a single (cylindrical) segment of length=diameter=6 μm
tree = arbor.segment_tree()
tree.append(arbor.mnpos,
arbor.mpoint(-3, 0, 0, 3),
arbor.mpoint(3, 0, 0, 3),
tag=1)
# (2) Define the soma and its center
labels = arbor.label_dict({'soma': '(tag 1)', 'center': '(location 0 0.5)'})
# (3) Create cell and set properties
cell = arbor.cable_cell(tree, labels)
cell.set_properties(Vm=-40)
cell.paint('"soma"', 'hh')
cell.place('"center"', arbor.iclamp(10, 2, 0.8))
cell.place('"center"', arbor.spike_detector(-10))
# (4) Make single cell model.
m = arbor.single_cell_model(cell)
# (5) Attach voltage probe sampling at 10 kHz (every 0.1 ms).
m.probe('voltage', '"center"', frequency=10000)
# (6) Run simulation for 30 ms of simulated activity.
m.run(tfinal=30)
d = seg.dist
sections += 'Segment(({}, {}, {}), ({}, {}, {}), {})'.format(p.x, p.y, p.radius, d.x, d.y, d.radius, seg.tag)
last_dist = seg.dist
sections += ']'
string += '\n [{}],'.format(sections)
string += ']\n'
string += '{} = representation.make_morph(tmp)\n\n'.format(name)
return string
# Describe the morphologies
mnpos = arbor.mnpos
# The morphology used for all of the region/locset illustrations
label_tree = arbor.segment_tree()
label_tree.append(mnpos, mpoint(0, 0.0, 0, 2.0), mpoint( 4, 0.0, 0, 2.0), tag=1)
label_tree.append(0, mpoint(4, 0.0, 0, 0.8), mpoint( 8, 0.0, 0, 0.8), tag=3)
label_tree.append(1, mpoint(8, 0.0, 0, 0.8), mpoint(12, -0.5, 0, 0.8), tag=3)
label_tree.append(2, mpoint(12, -0.5, 0, 0.8), mpoint(20, 4.0, 0, 0.4), tag=3)
label_tree.append(3, mpoint(20, 4.0, 0, 0.4), mpoint(26, 6.0, 0, 0.2), tag=3)
label_tree.append(2, mpoint(12, -0.5, 0, 0.5), mpoint(19, -3.0, 0, 0.5), tag=3)
label_tree.append(5, mpoint(19, -3.0, 0, 0.5), mpoint(24, -7.0, 0, 0.2), tag=3)
label_tree.append(5, mpoint(19, -3.0, 0, 0.5), mpoint(23, -1.0, 0, 0.2), tag=3)
label_tree.append(7, mpoint(23, -1.0, 0, 0.2), mpoint(26, -2.0, 0, 0.2), tag=3)
label_tree.append(mnpos, mpoint(0, 0.0, 0, 2.0), mpoint(-7, 0.0, 0, 0.4), tag=2)
label_tree.append(9, mpoint(-7, 0.0, 0, 0.4), mpoint(-10, 0.0, 0, 0.4), tag=2)
label_morph = arbor.morphology(label_tree)
# The label morphology with some gaps (at start of dendritic tree and remove the axon hillock)
