electrode_compensation.txt

.. currentmodule:: brian

Electrophysiology: electrode compensation
=========================================
The electrophysiology library also contains methods to compensate for the
electrode voltage in single-electrode current clamp recordings.
To import the electrophysiology library::

  from brian.library.electrophysiology import *

There is a series of example scripts in the examples/electrophysiology folder.

Active Electrode Compensation (AEC)
-----------------------------------
The electrophysiology library includes the Active Electrode Compensation (AEC) technique
described in Brette et al (2008),
`High-resolution intracellular recordings using a real-time computational model of the electrode
<http://www.di.ens.fr/~brette/papers/Brette2008Neuron.html>`__,
Neuron 59(3):379-91.

Given a digital current-clamp recording of the (uncompensated) potential ``v``
(vector of values) and injected current ``i``, the following instructions
calculate the full kernel of the system and the electrode kernel::

  K=full_kernel(v,i,ksize)
  Ke=electrode_kernel_soma(K,start_tail)
  
``ksize`` is the size of the full kernel (number of sampling steps; typical size is
about 15 ms) and ``start_tail`` is the size of the electrode kernel (start point
of the ''tail'' of the full kernel; typical size if about 4 ms). The electrode
should be compensated for capacitance (capacitance neutralization)
but not resistance (bridge compensation). The best choice for the
input current is a series of independent random values, and the last ``ksize``
steps of ``v`` should be null (i.e., the injection should stop before the end).
Here it was assumed that the recording was done at the soma; if it is done in a thin
process such as a dendrite or axon, the function ``electrode_kernel_dendrite``
should be used instead. The full kernel can also be obtained from a step current
injection::

  K=full_kernel_from_step(v,i,ksize)
  Ke=electrode_kernel_soma(K,start_tail)

where ``i`` is a constant value in this case (note that this is not the best choice for
real recordings).

Once the electrode kernel has been found, any recording can be compensated as follows::

  vcomp=AEC_compensate(v,i,ke)

where ``v`` is the raw voltage recording, ``i`` is the injected current
and ``ke`` is the electrode kernel.

Lp compensation
---------------

The Lp compensation is an other electrode compensation method. It is based on 
linear model fitting of an electrode and a neuron in response to an injected 
current. The fitness function is the Lp error between the full model response
and the raw trace, with p<2 to minimize the bias due to the nonlinear voltage
excursions of action potentials.

You can use it like this::

	Vcomp, params = Lp_compensate(I, Vraw, .1*ms)
	
where ``I`` is the injected current, ``Vraw`` is the raw voltage trace, and the
last parameter is the inverse of the sampling frequency. ``I`` and ``Vraw`` must be
1D Numpy arrays with the same length. The ``Lp_compensate`` function returns the
compensated trace ``Vcomp`` and the best parameters ``params``, which is a 2D 
Numpy array where each column contains the parameters R, tau, Vr, Re, taue.
Columns correspond to consecutive slices of the current and the voltage, the compensation
is performed independently on each slice. The duration of the slices can be 
specified with the ``slice_duration`` keyword argument.
Also, the ``p`` parameter can also be specified as a keyword argument.