range var plot using GUI

Using the graphical user interface to build and exercise models. Includes customizing the GUI by writing a little bit of hoc.
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range var plot using GUI

Post by mingu31 » Fri Aug 14, 2009 11:43 am


I was going through 'CellBuilder tutorial' on Documentation page of Neurone website.
In the second tutorial "Managing a model cell with complex anatomy", on Step 5 I wan't sure how you got the second graph (RangeVarPlot) by using GUI.
http://www.neuron.yale.edu/neuron/stati ... model.html

Many thanks!

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Re: range var plot using GUI

Post by ted » Fri Aug 14, 2009 12:21 pm

Good question. This should really be in the "Hot tips" area.

NEURON Main Menu / Graph / Shape plot
Click on menu box (in upper left corner of the Shape plot's canvas) and select "Space Plot" from the menu.
Place cursor next to one end of the path that you are interested in.
Press left button on mouse and hold down while dragging cursor over the path of interest.
Release mouse button.

After you have set up all the paths you want, close the Shape plot window.
The Space Plot window will persist.

Use Movie Run to see the Space Plot evolve smoothly in time.
NEURON Main Menu / Tools / Movie Run
Launch simulations by clicking on the Movie Run tool's Init & Run button.

1. You can add multiple paths to a single space plot, but one or two is usually enough.
2. By default a Space Plot shows voltage along a path, but any other range variable can be plotted. To specify which range variable will be plotted, use the Shape plot's "Plot what?" tool.
Click on the Shape plot's menu box and select Plot what? from the menu.
Click in the white "edit field" and type the name of the range variable.
For example, if your model is neurondemo's pyramidal cell, you might want to see a plot of i_cap (membrane capacitive current).
Click the Accept button, and the label on the Shape plot will change from v to the name of the range variable you entered.
Now you can create a Space Plot as described above. Try a path that runs from the most distal apical branch termination (upper left in the shape plot) to the distal end of the axon (lower right).

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