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. > > Thanks in advance, > 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 ==== [MESSAGE SEPARATOR] ====