Convert tone pulse into synaptic input (spikes) in NEURON

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henrychen1986
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Convert tone pulse into synaptic input (spikes) in NEURON

Post by henrychen1986 » Wed Nov 25, 2009 7:25 pm

Hi! I am looking for the method to convert a serie of tone pulse into the synaptic input (spikes) in NEURON. I searched in the ModelDB and the Programmer's Reference.
Then I tried to use the v.spikebin by using codes like this:

Code: Select all

spikevec=new Vector()
vrec=new Vector()
vrec.record(&toneA.i) //toneA.i is the value of the tone pulse
spikev = spikevec.spikebin(vrec,0.5)
But it did not give me the conversion I expected. Is there anything wrong in this code? Or should there be any other way to do this conversion?

Thanks in advance,

Henry

ted
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Re: Convert tone pulse into synaptic input (spikes) in NEURON

Post by ted » Thu Nov 26, 2009 10:03 am

What's a "tone pulse"? What are you trying to do: generate a stimulus in the middle of a simulation, or record results and analyze them after the end of a simulation?

henrychen1986
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Joined: Wed Nov 25, 2009 7:07 pm

Re: Convert tone pulse into synaptic input (spikes) in NEURON

Post by henrychen1986 » Fri Nov 27, 2009 5:06 pm

ted wrote:What's a "tone pulse"? What are you trying to do: generate a stimulus in the middle of a simulation, or record results and analyze them after the end of a simulation?
Thank you Ted!

A tone pulse is just a series of square waves with a certain frequency, such as sound wave.

Now I have a sound tone pulse (for example in the unit of dB) to be injected as the input into a synaptic channel, I need to convert it into spike (in the unit of mV) by setting a threshold. In GENESIS, there is a function called 'spikegen'. Now I am looking for a similar function in the NEURON.

Thanks!

-Henry

ted
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Re: Convert tone pulse into synaptic input (spikes) in NEURON

Post by ted » Sat Nov 28, 2009 11:48 am

So you merely want to generate a train of spikes, whose parameters (start time, ISI, number) you control? Or do you have experimental data that you want to pass through a filter whose output is a spike train in which the time of each spike is governed by some aspect of the experimental data (e.g. a positive going threshold crossing)?

henrychen1986
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Joined: Wed Nov 25, 2009 7:07 pm

Re: Convert tone pulse into synaptic input (spikes) in NEURON

Post by henrychen1986 » Sat Nov 28, 2009 5:36 pm

ted wrote:So you merely want to generate a train of spikes, whose parameters (start time, ISI, number) you control? Or do you have experimental data that you want to pass through a filter whose output is a spike train in which the time of each spike is governed by some aspect of the experimental data (e.g. a positive going threshold crossing)?
Merely I want to generate a train of spikes with parameter I can control. Also I would like to check how I can set a threshold crossing. If you can give me some directions on what to look for in the NEURON documentations, I will appreciate that!

ted
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Re: Convert tone pulse into synaptic input (spikes) in NEURON

Post by ted » Sun Nov 29, 2009 10:26 am

henrychen1986 wrote:I want to generate a train of spikes with parameter I can control.
If all you need is a train of events, use a NetStim. You'll want to read about how NEURON uses events to implement spike-triggered synaptic transmission, which is described in chapter 10 of The NEURON Book. You'll also want to read
Hines, M.L. and Carnevale, N.T.
Discrete event simulation in the NEURON environment.
Neurocomputing 58-60:1117-1122, 2004
and the Programmer's Reference documentation of NetStim, NetCon, ExpSyn, Exp2Syn, IntFire1, IntFire2, and IntFire4.

henrychen1986
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Re: Convert tone pulse into synaptic input (spikes) in NEURON

Post by henrychen1986 » Sun Nov 29, 2009 8:14 pm

Thank you very much Ted!

The NetStim can work! And this post is helpful (http://www.neuron.yale.edu/phpBB/viewto ... ered#p6554)

Thanks!

ted
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Re: Convert tone pulse into synaptic input (spikes) in NEURON

Post by ted » Sun Nov 29, 2009 8:44 pm

Glad to be of help. NEURON has many unique features, so it can be difficult for users who are just starting out to know what question to ask, and just as difficult for "experts" to know what is the best answer to a user's question.

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