Re: Q: Getting interspike intervals in neuronal firing patterns

• To: mathgroup at smc.vnet.net
• Subject: [mg3455] Re: Q: Getting interspike intervals in neuronal firing patterns
• From: Harald Berndt <haraldb at nature.berkeley.edu>
• Date: Fri, 8 Mar 1996 01:31:42 -0500
• Organization: University of California Forest Prodcts Lab
• Sender: owner-wri-mathgroup at wolfram.com

```Tobias Cottmann wrote:
>
> Hello,
>
> a friend of mine has some neuronal simulations which return the time
> course of the voltage across a neuronal membrane. These voltages exhibit
> sharp peaks of which he needs to know the position (i.e. the time or the
> time between two spikes).
>
> I'm posting this in comp.soft-sys.math.mathematica and bionet.software
> since he uses Mathematica. So he'd like to have some package finding all
> the peaks in an automated fashion. But if there is any other program which
> is suited to get those intervals it will be fine as well.
>
> We are using Macs and Unix-Machines in our Lab.
>
> Any suggestions will be appreciated.
>
> Tobias

Tobias:

The answer depends on how clean a signal one is dealing with and how
sophisticated one wants to get. For very clean signals and some good,
reliable guess at the interval between the pulses, one might just use
Position[ intervalLookedAt, Max[intervalLookedAt] ] or such like. Even
simpler, if one has single-point spikes clearly above a noise level,
just Chop[] the data with a safe cutoff value and find the Position[]
of the remaining nonzero datapoints.

Using a bit more sophistication and still clean data, try spectral
division deconvolution with a "standard" pulse (Mathematica's
Fourier[] and InverseFourier[] can be adapted for that.
Crosscorrelation with a "standard" pulse also might work.

More "state of the art" (I guess), and probably the best approach for
noisy data is using wavelet transforms for filtering/extraction and
then use some simpler peak finding method. (Wavelet.m is now available
on MathSource, I believe. It was described in TMJ5(1):74-81.

Tschuess,

______________________________________________________________________
Harald Berndt,                                University of California
Research Specialist                         Forest Products Laboratory

Phone:	510-215-4224                                FAX:			510-215-4299

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