graphs in extracelllular stimulation

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shwetakgp
Posts: 36
Joined: Sun Jun 16, 2013 1:21 am

Re: graphs in extracelllular stimulation

Post by shwetakgp » Thu Aug 22, 2013 11:53 am

dear ted,
i wanted to make a dsic electrode so that i can vary its dimensions so that i can vary its dimensions and see the effects. i hope that is feasible....
in the code which you earlier send me asking these paprameters
given the orientation of the electrode's axis,
calculate angular orientation of this radius section . . .
. . . knowing its angular orientation, and its length in um,
calculate the coordinates (xx, yy, zz) of its end point . .
i have not been given any orientation of the elctrode and my cell is 2 dimensional as i have included dendritc area instead of coordinates of dendrites. i have not been provided with the 3 d coordiantes of dendrites yet. please let me know how should my electrode be oriented? any possible orientation would do.

i dont know... i m trying very hard to learn about this software but i am not able to make any code independently. please tell me what should i do as i am very inclined to venture in this field

shwetakgp
Posts: 36
Joined: Sun Jun 16, 2013 1:21 am

Re: graphs in extracelllular stimulation

Post by shwetakgp » Fri Aug 23, 2013 10:25 am

please reply to my query

ted
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Re: graphs in extracelllular stimulation

Post by ted » Fri Aug 23, 2013 3:31 pm

shwetakgp wrote:i wanted to make a dsic electrode so that i can vary its dimensions so that i can vary its dimensions and see the effects. i hope that is feasible....
The instructions I gave about creating a bunch of sections that radiate outward from a point will produce a set of sections that exist only for cosmetic purposes. That is, they will give a visual suggestion of the location, orientation, and size of the disc electrode. I thought that I had already made clear, many messages ago, the fact that you yourself have to control the extracellular potential at each point in your model, either directly by using numerical values that are precalculated and stored in Vectors before a simulation, or indirectly by using Vector play to drive the xtra mechanism's is variable after setting the xtra.rx value at each internal node of the model to the appropriate transfer resistance.

And how would you know what rx values are appropriate for a particular cell and electrode? If the electrode is a point source, or a bipolar pair of point sources, the code provided with xtra.mod allows NEURON to calculate the rx values for you. For any other electrode geometry, you have to come up with those yourself, or derive an algebraic function that NEURON can then use to calculate rx. Your recent messages indicated that you had done one or the other of these things.
i m trying very hard to learn about this software but i am not able to make any code independently. please tell me what should i do as i am very inclined to venture in this field
I appreciate your energy and enthusiasm, and those qualities will be essential for your future success, but perhaps NEURON is not the right tool for you to use--it requires significant programming skill. COMSOL can calculate the extracellular field in a volume conductor, but it is an expensive commercial product, does not have any features that make simulating neurons easy, and I imagine that it too requires programming skill. Perhaps you need to collaborate with someone else who is geographically close to you and has the programming abilities that would help you make progress.

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