Loading data into the Run Fitness Generator

This actually involves two related tasks: loading data into the Generator, and testing the Generator.

There are four data files. Each one has a name that starts with the letter n and ends with .dat The first part of the file name tells where current was injected, and the second part tells where voltage was recorded. The file we want now is called
nisoma_vsoma.dat
because it shows how current injected at the soma affected membrane potential at the soma.

Read nisoma_vsoma.dat into NEURON's clipboard, then paste it into the iclamp soma Generator.

  1. NEURON Main Menu / Vector / Retrieve from File
  2. Navigate the directory tree and choose nisoma_vsoma.dat
  3. In the iclamp soma Generator, click on Regions / Data from Clipboard
The Generator's graph area should now contain a red trace that shows the time course of membrane potential at the soma elicited by injecting a 0.1 nA x 5 ms current pulse at the soma.

Testing the Generator

Time to test the iclamp soma Generator. Click on its Error Value button. This should launch a simulation, producing a black trace that shows the trajectory of the simulated soma.v(0.5), and reporting an error value (see below).

Adding a second variable to fit

This protocol also produced a recording of dendritic membrane potential, so let's add that as the second variable to fit.

You already know how to do this--click on Fitness / Variable to fit
The name of the variable to add is dendrite_1[9].v(0.5)

If you don't see this new variable in the top panel of the Generator, maybe it's hiding behind something. Grab the bottom margin of the Generator's window and drag down a bit, and you should see a new radio button with "dendrite_1[9].v(0.5)" right next to it.

Having added a new variable, we must also add the corresponding experimental data.

Click on the dendrite_1[9].v(0.5) radio button and the Generator shows an empty graph.

Read nisoma_vdend.dat into NEURON's clipboard, then paste it into the Generator.
Now click on Error Value again and the Generator should look like this:

The experimental data (red) look OK, but the simulation looks like current is being injected into the dendrite.

And it is. We forgot about using protocol parameters to tell IClamp[1] that its amp should be 0 for the "iclamp soma" protocol.

Easy to fix. Click on Fitness / Protocol Constant, then use the "variable name browser" to add IClamp[0].amp.
Do the same for IClamp[1].amp.

Close the Generator and open it again, and notice that both IClamp amp parameters are 0.1.
Enter 0 in the numeric field next to the IClamp[1].amp button, then save the MRF to a session file.

Finally click on the Error Value button and compare the experimental and simulated membrane potentials. Here's what the voltage in the dendrite looks like.

Use the radio buttons to switch back and forth between the graphs of soma.v(0.5) and dendrite_1[9].v(0.5).

Hint: to rescale the vertical axes, use the graphs' "Set View"


Next: specify the model parameters that are to be adjusted.


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