single_cell_cable.rst

.. _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: 11-71

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: 72-113

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: 151-226

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: 228-243

Keep 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

Output:

.. figure:: single_cell_cable_result_cv_policy.svg
    :width: 800
    :align: center