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This document will describe how to inspect conductances and mechanisms and read out anything from them.

Inspecting conductances

xolotl does not return the m and h (activation and inactivation) variables from channels by default. This decision was made because it is not often that this is needed, and omitting these variables makes the code run faster and saves memory. If you do want to pull these values out, this is what you have to do.

Inspecting activation variables in most conductances

If the channel you want to inspect follows the standard Hodgkin-Huxley formalism (most channels in xolotl do), and its integration routines use the built in conductance::integrate methods, then you can use the channelProbe mechanism to read out values. Like so:

% create a neuron with some channels
x = xolotl.examples.neurons.BurstingNeuron;

% let's probe the NaV channel

% now read out the activation variables and plot them
[V,~,M] = x.integrate;

Plotting M and comparing to the voltage shows us the activation and inactivation variables for the sodium channel lines up nicely with the spikes.

Inspecting activation variables in custom conductances

Custom conductances may not use the Hodgkin-Huxley formalism, may have their own integration routines, and may contain their own internal variables. To read out internal variables from these channels, you have to do two things. First, your custom conductance must respond to getState requests and return every variable of interest. Add something like this to your conductance:

double customChannel::getState(int idx) {
    if (idx == 1) {return variable_1;}  
    else if (idx == 2) {return variable_2;}
    else {return std::numeric_limits<double>::quiet_NaN();}

and modify a copy of ChannelProbe to read out these variables:

int ChannelProbe::getState(double *mech_states, int idx) {
    // read out custom variables
    mech_states[idx] = channel->getState(1);
    mech_states[idx] = channel->getState(2);
    return idx;

Inspecting mechanisms

Inspecting mechanisms is similar to the process described earlier.