Chapter 7. Programming Simulations

7.5 Electrodes

Implied Electrodes

In experimental procedures, one must learn to make and insert electrodes to measure the voltage in a cell, some or all parts of it may be too small for penetration or inaccessible because of visibility. For simulations with NEURON, however, voltages and variables at all locations are always available via the interpreter and graphs. Thus the voltage at the mid-point of a section such as "soma" may be examined using such simple statements as
print soma.v
or plotted in a graph by selecting soma.v in the "Plot What" browser available in a graph. The default location again is the midpoint of a section. To specify a point other than the midpoint of the section (0.5), one may explic specify the relative position in the section
(0 <= x => 1): e.g. soma.v(.95).
in the browser edit window when originally loaded or
by selecting the "Change Text" option available upon pressing the Right mouse button while in a graphic window. Clicking the Left button on text to be changed brings up an edit window, allowing the location to be edited. Upon accepting the edit, the next plot will be that appropriate for the new location.

Real Electrodes

Simulated "Electrodes" are available also in NEURON; they are useful for injecting currents into various locations or applying voltage clamps at a point. Such electrodes may be added to the simulation by a hoc program segment (as follows) or with NEURON's graphical tools (as shown later).

Permanent Insertion by program: electrode.hoc

	// assume that the "soma" is the currently accessed section

objref iclamp  	             // declares an object variable name
iclamp = new iclamp(.5)      // insert a current clamp in center of
                                   //currently accessed section
iclamp.del = 0	             // sets current pulse delay = 0 mS
iclamp.dur = 1               // sets current pulse duration = 1 mS
iclamp.amp = 25              // sets current pulse amplitude = 25 nA

Dismissable Insertion by graphical tools

Simulated microelectrodes may be inserted with the graphical interface and disappear wupn dismissal of the corresponding panel. Insertion: on NEURON's main menu choose "Point Processes" .

 This brings up -->

Choosing "Electrode" brings up this electrode panel. ->

.
This panel comes up with "Location" as the default selection which displays the position of the electrode in the lower part of the panel. The location of the electrode is indicated by the position of Blue circle on the accessed compartment, shown in RED to indicate the The location of the electrode may be changed readily by "clicking" anywhere on the cell. The Blue circle will jump there, the section in which it is inserted will turn red, and the precise location of the electrode will be updated (as text) in upper part of the panel. If the sections are difficult to see because the sizes of the sections have very different diameters and lengths, one may improve visability by using the right mouse button to bring up the graphic options and choosing first "Shape Style" and then "Show Diam".

After the electrode has been placed at the desired location, current or voltage control parameters may be set by clicking on the diamond symbol associated with one of the other three options.

I Clamp - or current clamp
V Clamp - for a single Voltage clamp sweep
V Clamp - for a Family of Voltage clamp sweeps

When either of the first two choices is selected, its parameter set appears in the lower part of the panel.


           IClamp                                         VClamp
 .

When the I Clamp is chosen, the delay (del), duration (dur), and amplitude (amp) of a current pulse are displayed. The value of the current (i) at any time during a simulation is shown in the last field for the user's convenience.
When the V Clamp is chosen, a panel with amplitude and duration of three voltage levels is shown. For voltge clamp experiments, one is usually most interested in the form and kinetics of current flowing in a voltage clamped membrane or cell. A graph of the membrane current may be created by simply pressing the button marked "VClamp.i graph".
This graph shows the current flowing through the electrode (which includes the capacitive current); the magnitude of the current depends on the cell morphology, channel types, and channel densities. The default vertical scale will probably be inappropriate for most simulations but one can readily adjust it to the appropriate value with the "view=plot" graphic option. Simply press and hold the right mouse button within the plotting area and choose the " View = Plot" option.

Viewing Point Processes and Electrode parameters

The parameters of any or all Point Processes may be viewed by: by pressing the "Point Processes" button on NEURON's Main Panel, then choosing "Viewers"

Selecting "I Clamp" or "V Clamp" from the choice of point processes brings up a browser list of electrode locations; selection of any (or all) produces a panel(s) showing the assigned current or voltage levels.

For a V Clamp, additional details are available for simulation of non-ideal voltage clamps with realistic amplifiers, access resistance to cells, and circuit delays. control circuit.