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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:

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> 
> 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