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Forgot to mention, there are also real-time hardware correlators available
from Correlator.com (no financial interest) for about $2K without drivers. We
have developed a LabView driver for it that does control / display / on line
fitting of the FCS curve to various simple models etc. The driver is available
free from us as a LabView executable (LabView not required on your PC).
We also have a separate Maximum Entropy based FCS fitting routine (MEMFCS) for
continuous distributions (described in Sengupta et al., Biophys. J., vol. 84,
2003, 1977) - again available free.
Sudipta
On Tue, 14 Jun 2011 14:40:26 -0700, David Baddeley wrote
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> It's been a while since I used matlab, but the other classic way to
> speed up correlation is to use FFTs - ie: corr =
> ifftshift(real(ifft(fft(x)*fft(flipud(x)))))
>
> you can also replace fft(flipud(x)) with ifft(x) (subject to
> normalisation), which will avoid a couple of memory allocations.
>
> this method should be significantly faster (O(nlogn)) than a
> standard correlation (O(n^2)), but you might need to mess around a
> bit with normalisation and cut out just the bit of the curve
> corresponding to +ve lags.
>
> I have a funny feeling that this might already be available as a
> function
> (potentially called fftcorr), but can't be sure.
>
> cheers,
> David
>
> ----- Original Message ----LISTS.UMN.EDU
> Sent: Wed, 15 June, 2011 1:08:38 AM
> Subject: Re: FCS - Matlab code
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Have you looked at this? (I found it with google)
>
> http://www.mathworks.com/matlabcentral/fileexchange/22358
>
> Cheers
> On 14/06/2011, at 12:27 PM, Alessandro Esposito wrote:
>
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > *****
> >
> > Dear all,
> > I was trying to write code for FCS analysis in Matlab, but noticed that
> > computing the ACF directly is computationally very expensive. I've read
papers
>
> > about the math needed to make the problem computationally efficient, but
not
> > intending to develop new FCS methods I am not that keen committing too
much
> > time into that.
> >
> > Does anyone have Matlab code for FCS analysis. If you have a toolbox
great, if
>
> > you have just the optimized functions to compute the correlation functions
for
>
> > FCS and FCCS, it will be anyway VERY helpful.
> >
> > Cheers,
> >
> > Alessandro
> > www.quantitative-microscopy.org
Dr. Sudipta Maiti
Associate Professor
Dept. of Chemical Sciences
Tata Institute of Fundamental Research
Homi Bhabha Raod, Colaba, Mumbai 400005
Ph. 91-22-2278-2716 / 2539
Fax: 91-22-2280-4610
alternate e-mail: [log in to unmask]
url: biophotonics.wetpaint.com
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