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Re: median filter that preserves peaks

Posted by Alexandre Dufour on Sep 06, 2013; 10:25pm
URL: http://imagej.273.s1.nabble.com/median-filter-that-preserves-peaks-tp5004693p5004711.html

Dear Neil,

From a purely signal processing perspective, I suggest you use Fourier- (or better off wavelet-) denoising on such signals. They definitely should preserve your signal dynamics. A good illustration in 1D is given over here (http://www.mathworks.fr/products/demos/shipping/bioinfo/mspreprodemo.html#22)

Alexandre

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Alexandre Dufour, Ph.D.
Institut Pasteur - Quantitative Image Analysis Group
25, rue du Docteur Roux, Paris, France
Research: http://www.bioimageanalysis.org/dufour
Software: http://www.bioimageanalysis.org/icy

On Sep 6, 2013, at 11:18 PM, Neil Fazel <[hidden email]> wrote:

> Thanks. I will look into that.
>
> I have attached a montage of 3 profile plots using 1) the original image, 2) image after applying median filter with radius 0.5, and 3) image after median filter with radius 1. You can see how the Y axis maximum of the plots goes from 3.28 to 3.15 to 3.13; the high frequency component has been reduced (good) at the same time that the peaks have been flattened (bad).
>
> I guess what I'm looking for is a filter that replaces local outliers (i.e. outliers in a neighborhood 2-3 pixels in each direction) with the median, but preserves them if they remain outliers in a larger neighborhood, which indicates that they are not noise but actual peak signal.
>
> Neil
>
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> <median filter flattens peaks somewhat.png>

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