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Filter for noisy single molecule photobleach step data

Thu, 03/29/2012 - 07:24 am

Hi,

I am working on the single molecule photobleach data to determine the intensity between each step. However, the data are really noisy and it's hard to clearly identify the steps. Is any people familiar with this topic and know how to deal it with Igor? In the meantime, I read papers and found some people use the Chung kennedy (CK） nonlinear filter which worked pretty well. I am wondering where can I find the package for this filter?

thanks,
xiang

741

Hello Xiang,

I've implemented a Chung Kennedy filter a while ago, but unfortunately lost the code somehow. I remember that the algorithm is quite simple, going over each point of the trace in turn while calculating some sort of average of the points to left and right of the current point of interest. I think I implemented it based on the brief description in the following paper: http://dx.doi.org/10.1039/c0cp01729a.

I remember that there were some simple typo's in the equations involving the subscript indices, but nothing major.

I'd recommend you to have a go at implementing it, and feel free to post back if you run into trouble.

March 29, 2012 at 11:26 pm - Permalink

xw7659

Thanks, Peter. You are always supportive !

I am going to study that paper and see how can I get this done. Meanwhile, I googled and found a code for Matlab from Dr.Michael Strano from MIT. The link is here: http://web.mit.edu/stranogroup/NoRSE.txt
If I can't use Igor to accomplish it, I may just copy and paste that code to Matlab.

I will see what I can do.

thanks,
xiang

March 30, 2012 at 08:48 am - Permalink