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.. _custom_initialization:
Custom Initialization
=====================
Physical System
---------------
.. image:: img/pyramid.gif
Conceptual Model
----------------
A ball-and-stick approximation to the cell.
.. image:: img/ballstk.gif
The aim of this exercise is to learn how to perform one of the most common types of custom initializaton: initializing to steady state.
We start by making a ball and stick model in which the natural resting potential of the somatic sphere and dendritic cylinder are different. No matter what v_init you choose, default initializaton to a uniform membrane potential results in simulations that show an initial drift of v as the cell settles toward a stable state.
After demonstrating this initial drift, we will implement and test a method for initializing to steady state that leaves membrane potential nonuniform in space but constant in time.
Getting started
~~~~~~~~~~~~~~~
In this exercise you will be creating several files, so you need to be in a working directory for which you have file "write" permission. Start NEURON with exercises/custom_initialization as the working directory.
Computational implementation of the conceptual model
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Use the CellBuilder to make a simple ball and stick model that has these properties:
.. list-table::
:header-rows: 1
* - Soma
- Anatomy
- Compartmentalization
- Biophysics
* - soma
-
length 20 µm
diameter 20 µm
- ``d_lambda = 0.1``
-
``Ra = 160`` ohm cm,
``Cm = 1`` µf / cm\ :sup:`2`
Hodgkin-Huxley channels
* - dend
-
length 1000 µm
diameter 5 µm
- ``d_lambda = 0.1``
-
``Ra = 160`` ohm cm,
``Cm = 1`` µf / cm\ :sup:`2`
passive with Rm = 10,000 ohm cm\ :sup:`2`
Turn Continuous Create ON and save your CellBuilder to a session file.
Using the computational model
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Bring up a RunControl and a voltage axis graph.
Set Tstop to 40 ms and run a simulation.
Use View = plot to see the time course of somatic membrane potential more clearly.
Add ``dend.v(1)`` to the graph (use Plot what?), then run another simulation.
Use Move Text and View = plot as needed to get a better picture.
Add a space plot and use its Set View to change the y axis range to ``-70 -65``.
Run another simulation and watch how drastically v changes from the initial condition.
Save everything to a session file called :file:`all.ses` (use :menuselection:`File --> save session`) and exit NEURON.
Exercise: initializing to steady state
--------------------------------------
In the same directory, make an :file:`init_ss.py` file with the contents:
.. code::
python
from neuron import h, gui
def ss_init(t0=-1e3, dur=1e2, dt=0.025):
"""Initialize to steady state.
Executes as part of h.finitialize()
Appropriate parameters depend on your model
t0 -- how far to jump back (should be < 0)
dur -- time allowed to reach steady state
dt -- initialization time step
"""
h.t = t0
# save CVode state to restore; initialization with fixed dt
old_cvode_state = h.cvode.active()
h.cvode.active(False)
h.dt = dt
while (h.t < t0 + dur):
h.fadvance()
# restore cvode active/inactive state if necessary
h.cvode.active(old_cvode_state)
h.t = 0
if h.cvode.active():
h.cvode.re_init()
else:
h.fcurrent()
h.frecord_init()
fih = h.FInitializeHandler(ss_init)
# model specification
h.load_file('all.ses') # ball and stick model with exptl rig
Now execute :file:`init_ss.py`.
Click on Init & Run and see what happens.
"Special credit" Exercise
-------------------------
Another common initialization is for the initialized model to satisfy a particular criterion. Create an initialization that ensures the resting potential throughout the cell equals ``v_init``.
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