voltage propagation in the whole cell

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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xiaosage
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Joined: Sat May 11, 2013 10:01 am

voltage propagation in the whole cell

Post by xiaosage » Tue Mar 24, 2015 9:24 pm

Hello,

I have downloaded a NEURON code and want to add a few lines to visualize the voltage propagation from a synaptic input site to the rest part of the neruon as time evolves. So far I only found some functions such as "Shape/PlotShape", but I am not sure whether they work or not. Can anyone tell me how to do it? Thanks!

ted
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Re: voltage propagation in the whole cell

Post by ted » Tue Mar 24, 2015 10:06 pm

xiaosage wrote:want to . . . visualize the voltage propagation from a synaptic input site to the rest part of the neruon as time evolves.
What kind of a visualization do you want? You could just plot the time course of v in different parts of the model vs. time in the same graph. Then you can compare the detailed time course of v at each of those locations.

xiaosage
Posts: 16
Joined: Sat May 11, 2013 10:01 am

Re: voltage propagation in the whole cell

Post by xiaosage » Tue Mar 24, 2015 11:10 pm

Hi Ted,

Thanks for your reply! I actually want to see the voltage distribution in the whole cell, for example, as the movie shown below

http://cns.iaf.cnrs-gif.fr/files/dendritRE_short.mpg

Thanks!

ted
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Re: voltage propagation in the whole cell

Post by ted » Wed Mar 25, 2015 12:02 pm

Here's how to to generate such a graph by writing hoc code; it's even easier to do this with the GUI's tools.

First you'll need an instance of the PlotShape class, configured as a "shape plot," that will update at every fadvance.

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// this assumes you have already loaded the standard run system
// e.g. by double clicking on nrngui.hoc or some other hoc file
// or by starting NEURON by executing nrngui
// or by including either load_file("nrngui.hoc") or load_file("stdrun.hoc")
// at the top of your program
objref ps
ps = new PlotShape()
fast_flush_list.append(ps)
ps.exec_menu("Shape Plot")
Then you'll need to use the standard run system's movierun() instead of run().

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load_file("movierun.hoc")
Finally, when you're ready to run a simulation, use

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movierun()
If you want to make it run more slowly, specify the frame interval by using a hoc assignment statement that gives the parameter movie_frame_dur_ a value larger than 0.01 (seconds).

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