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Re: Using Mathematica for Electrophysiology Data

  • To: mathgroup at smc.vnet.net
  • Subject: [mg110457] Re: Using Mathematica for Electrophysiology Data
  • From: François Blumenfeld <hypotyposis at me.com>
  • Date: Sat, 19 Jun 2010 07:48:05 -0400 (EDT)

Thanks Sjoerd!

This works very well.  I was indeed hoping to return the binning method 
as well, but this is not so important.
The fitting is no problem now that I can build a frequency table from 
the histogram data. (And, yes, I always want to put an uppercase "L" 
in "NonlinearModelFit"!)

To sum up:
Data is imported into Mathematica as a list of time values and a 
matching list of amplitudes; then I apply

{g, {binCounts}} ==
  Reap[
   Histogram[
    listOfAmplitudesInPa,
    Automatic,
    Function[
     {bins, counts}, Sow[{bins, counts}]; counts]]]

which gives me the frequency table for the raw data using 
Mathematica's automatic bin width determination (bin width is, e.g.,  
binCounts[[1, 1, 2]] - binCounts[[1, 1, 1]] ).
Along with fitting of a curve to this data, this is equivalent to the 
procedure we use on raw data with Clampfit and Origin.

Thanks again,

Francois

On Jun 18, 2010, at 12:24 AM, Sjoerd C. de Vries wrote:

> Hi Fran==E7ois,
>
> You could use something like
>
> Reap[Histogram[RandomReal[NormalDistribution[0, 1], 200],
>  Automatic, (Sow[{#1, #2}]; #2) &]]
>
> to get at binning and count data. Don't know about binning method, but
> you could use one of the named binning methods instead of Automatic
> used here if you want to be sure about the method used.
>
> About NonLinearModelFit. If you don't say what you're doing it's hard
> to say what you're doing wrong. One thing I can tell you:
> NonLinearModelFit should be spelled with lowercase L. Perhaps that's
> your problem?
>
> Third question: see first question's answer. Counts are included.
>
> Cheers -- Sjoerd
>
>
> On Jun 16, 11:38 am, Fran==E7ois Blumenfeld <hypotypo... at me.com> wrote:
>> Hi,
>>
>> I'm playing around with Mathematica to analyze some electrophysiology
>> data; this is on my recreation time, so apologies if the following
>> questions are very basic.
>>
>> I've imported data (pairs of time points and amplitudes) from pClamp
>> into Mathematica as lists. The lists are pretty huge (around 150,000
>> elements per list-I've separated times and amplitudes in two lists).
>> I've created a histogram of the amplitudes list, letting Mathematica
>> decide which binning method to use and the width of the bin. Without
>> user input, it actually did a great job at picking bin width and
>> binning method; but I don't know how to retrieve that information:
>> i.e. what bin width was picked and what binning method used for a
>> particular histogram?
>>
>> My second question is about fitting a multivariate Gaussian
>> distribution to a multimodal (usually bimodal) histogram. I've payed
>> around with NonLinearModelFit, but for some reason I don't think I'm
>> doing it correctly. My third question is related to this: how do I
>> retrieve the processed data from the histogram to construct a
>> frequency table? I'm guessing that this might in fact be the
>> intermediate step I need to complete before being able to fit a curve
>> to the histogram data.
>>
>> Any suggestions welcome!
>>
>> Francois Blumenfeld-Kouchner
>
>


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