diff --git a/.github/workflows/basic.yml b/.github/workflows/basic.yml
index 2e321da45dbfa500bf02f969fb2cd85ebfb76f3a..2e903bfc94f577a6ce78f8486973749aedbd8f4b 100644
--- a/.github/workflows/basic.yml
+++ b/.github/workflows/basic.yml
@@ -201,3 +201,4 @@ jobs:
python python/example/single_cell_swc.py python/example/single_cell_detailed.swc
python python/example/single_cell_detailed.py python/example/single_cell_detailed.swc
python python/example/single_cell_detailed_recipe.py python/example/single_cell_detailed.swc
+ python python/example/single_cell_cable.py
\ No newline at end of file
diff --git a/.github/workflows/sanitize.yml b/.github/workflows/sanitize.yml
index 1c36ae74744a788abc7a34712bed848251aeef89..805090d92d13d7acafa657aa8d522900daf701c0 100644
--- a/.github/workflows/sanitize.yml
+++ b/.github/workflows/sanitize.yml
@@ -127,3 +127,4 @@ jobs:
python python/example/single_cell_swc.py python/example/single_cell_detailed.swc
python python/example/single_cell_detailed.py python/example/single_cell_detailed.swc
python python/example/single_cell_detailed_recipe.py python/example/single_cell_detailed.swc
+ python python/example/single_cell_cable.py
\ No newline at end of file
diff --git a/doc/tutorial/index.rst b/doc/tutorial/index.rst
index ce94e4dd038de1392361e83238b2771ec0657ab8..b9fbbc59296c33c805bb8e76c1c9ebb88d3480b8 100644
--- a/doc/tutorial/index.rst
+++ b/doc/tutorial/index.rst
@@ -24,5 +24,6 @@ Tutorials
single_cell_recipe
single_cell_detailed
single_cell_detailed_recipe
+ single_cell_cable
network_ring
mpi
diff --git a/doc/tutorial/single_cell_cable.rst b/doc/tutorial/single_cell_cable.rst
new file mode 100644
index 0000000000000000000000000000000000000000..ccd6e9ef2aa2159a285c3976799ba84a7d833b3e
--- /dev/null
+++ b/doc/tutorial/single_cell_cable.rst
@@ -0,0 +1,77 @@
+.. _tutorialsinglecellcable:
+
+A simple dendrite
+==============================
+
+In this example, we will set up a single dendrite represented by a passive cable.
+On one end the dendrite is stimulated by a short current pulse.
+We will investigate how this pulse travels along the dendrite and calculate the conduction velocity.
+
+.. Note::
+
+ **Concepts covered in this example:**
+
+ 1. Creating a simulation recipe of a single dendrite.
+ 2. Placing probes on the morphology.
+ 3. Running the simulation and extracting the results.
+ 4. Investigating the influence of control volume policies.
+
+The full code
+*************
+
+You can find the full code of the example at ``python/examples/single_cell_cable.py``
+
+Executing the script will run the simulation with default parameters.
+
+
+Walk-through
+**********
+
+We set up a recipe for the simulation of a single dendrite with some parameters.
+
+.. literalinclude:: ../../python/example/single_cell_cable.py
+ :language: python
+ :lines: 11-31
+
+Implementing the ``cell_description`` member function constructs the morphology and sets the properties of the dendrite as well as the current stimulus and the discretization policy.
+
+.. literalinclude:: ../../python/example/single_cell_cable.py
+ :language: python
+ :lines: 63-98
+
+We parse the command line arguments, instantiate the recipe, run the simulation, extract results and plot:
+
+.. literalinclude:: ../../python/example/single_cell_cable.py
+ :language: python
+ :lines: 147-210
+
+The output plot below shows how the current pulse is attenuated and
+gets broader the further it travels along the dendrite from the current
+clamp.
+
+.. figure:: single_cell_cable_result.svg
+ :width: 800
+ :align: center
+
+The conduction velocity in simulation is calculated from the time of the maximum of the membrane potential.
+
+.. literalinclude:: ../../python/example/single_cell_cable.py
+ :language: python
+ :lines: 212-
+
+Please have in mind that the calculated (idealized) conduction velocity is only correct for an infinite cable.
+
+::
+
+ calculated conduction velocity: 0.47 m/s
+ simulated conduction velocity: 0.50 m/s
+
+When we set the control volume policy to cover the full dendrite, all probes will see the same voltage.
+
+.. code-block:: bash
+
+ ./single_cell_cable.py --length 1000 --cv_policy_max_extent 1000
+
+.. figure:: single_cell_cable_result_cv_policy.svg
+ :width: 800
+ :align: center
diff --git a/doc/tutorial/single_cell_cable_result.svg b/doc/tutorial/single_cell_cable_result.svg
new file mode 100644
index 0000000000000000000000000000000000000000..daa686f49416fc5b078f518aeaaf55b98afeb1c8
--- /dev/null
+++ b/doc/tutorial/single_cell_cable_result.svg
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diff --git a/python/example/single_cell_cable.py b/python/example/single_cell_cable.py
new file mode 100755
index 0000000000000000000000000000000000000000..bf3d0ac5b602847890e22e7cc3558678a97f20e3
--- /dev/null
+++ b/python/example/single_cell_cable.py
@@ -0,0 +1,226 @@
+#!/usr/bin/env python3
+
+import arbor
+import argparse
+import numpy as np
+
+import pandas
+import seaborn # You may have to pip install these.
+
+
+class Cable(arbor.recipe):
+ 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.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 num_cells(self):
+ return 1
+
+ def num_sources(self, gid):
+ assert gid == 0
+ return 0
+
+ def cell_kind(self, gid):
+ assert gid == 0
+ return arbor.cell_kind.cable
+
+ 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.mechanism(f'pas/e={self.Vm}', {'g': self.g}))
+
+ decor.place('"start"', arbor.iclamp(args.stimulus_start,
+ args.stimulus_duration,
+ args.stimulus_amplitude))
+
+ policy = arbor.cv_policy_max_extent(self.cv_policy_max_extent)
+ decor.discretization(policy)
+
+ cell = arbor.cable_cell(tree, labels, decor)
+
+ return cell
+
+ def probes(self, gid):
+ assert gid == 0
+ return self.the_probes
+
+ def global_properties(self, kind):
+ return self.the_props
+
+
+def get_rm(g):
+ """Return membrane resistivity in Ohm*m^2
+ g -- membrane conductivity in S/m^2
+ """
+ return 1/g
+
+
+def get_taum(cm, rm):
+ """Return membrane time constant in seconds
+ cm -- membrane capacitance in F/m^2
+ rm -- membrane resistivity in Ohm*m^2
+ """
+ return cm*rm
+
+
+def get_lambdam(a, rm, rL):
+ """Return electronic length in m
+ a -- cable radius in m
+ rm -- membrane resistivity in Ohm*m^2
+ rL -- axial resistivity in Ohm*m
+ """
+ return np.sqrt(a*rm/(2*rL))
+
+
+def get_vcond(lambdam, taum):
+ """Return conductance velocity in m/s
+ lambda -- electronic length in m
+ taum -- membrane time constant
+ """
+ return 2*lambdam/taum
+
+
+def get_tmax(data):
+ """Return time of maximum of membrane voltage"""
+ return data[np.argmax(data[:, 1])][0]
+
+
+if __name__ == "__main__":
+
+ parser = argparse.ArgumentParser(description='Cable')
+
+ parser.add_argument(
+ '--Vm', help="membrane leak potential in mV", type=float, default=-65)
+ parser.add_argument(
+ '--length', help="cable length in μm", type=float, default=1000)
+ parser.add_argument(
+ '--radius', help="cable radius in μm", type=float, default=1)
+ parser.add_argument(
+ '--cm', help="membrane capacitance in F/m^2", type=float, default=0.01)
+ parser.add_argument(
+ '--rL', help="axial resistivity in Ω·cm", type=float, default=90)
+ parser.add_argument(
+ '--g', help="membrane conductivity in S/cm^2", type=float, default=0.001)
+
+ parser.add_argument('--stimulus_start',
+ help="start of stimulus in ms", type=float, default=10)
+ parser.add_argument('--stimulus_duration',
+ help="duration of stimulus in ms", type=float, default=0.1)
+ parser.add_argument('--stimulus_amplitude',
+ help="amplitude of stimulus in nA", type=float, default=1)
+
+ parser.add_argument('--cv_policy_max_extent',
+ help="maximum extent of control volume in μm", type=float,
+ default=10)
+
+ # parse the command line arguments
+ args = parser.parse_args()
+
+ # set up membrane voltage probes equidistantly along the dendrites
+ probes = [arbor.cable_probe_membrane_voltage(
+ f'(location 0 {r})') for r in np.linspace(0, 1, 11)]
+ recipe = Cable(probes, **vars(args))
+
+ # create a default execution context and a default domain decomposition
+ context = arbor.context()
+ domains = arbor.partition_load_balance(recipe, context)
+
+ # configure the simulation and handles for the probes
+ sim = arbor.simulation(recipe, domains, context)
+ dt = 0.001
+ handles = [sim.sample((0, i), arbor.regular_schedule(dt))
+ for i in range(len(probes))]
+
+ # run the simulation for 30 ms
+ sim.run(tfinal=30, dt=dt)
+
+ # retrieve the sampled membrane voltages and convert to a pandas DataFrame
+ data = [sim.samples(handle)[0][0] for handle in handles]
+ data_dict = {str(i): d[:, 1] for i, d in enumerate(data)}
+ data_dict["t"] = data[0][:, 0]
+
+ df = pandas.DataFrame.from_dict(data_dict)
+
+ # plot all probes and save to file
+ for i in range(len(probes)):
+ plot = seaborn.lineplot(data=df, x="t", y=str(
+ i), ci=None, legend="full", label=i)
+
+ plot.set(xlabel="t/ms")
+ plot.set(ylabel="U/mV")
+ plot.set_xlim(9, 14)
+
+ plot.figure.savefig("single_cell_cable_result.svg")
+
+ # calculcate the idealized conduction velocity, cf. cable equation
+ rm = get_rm(args.g*1/(0.01*0.01))
+ taum = get_taum(args.cm, rm)
+ lambdam = get_lambdam(args.radius*1e-6, rm, args.rL*0.01)
+ vcond_ideal = get_vcond(lambdam, taum)
+
+ # take the last and second probe
+ delta_t = (get_tmax(data[-1]) - get_tmax(data[1]))
+
+ # 90% because we took the second probe
+ delta_x = args.length*0.9
+ vcond = delta_x*1e-6/(delta_t*1e-3)
+
+ print(f"calculated conduction velocity: {vcond_ideal:.2f} m/s")
+ print(f"simulated conduction velocity: {vcond:.2f} m/s")