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I am wondering how to filter out bright dots in the picture, which are caused by background noise.

enter image description here

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  • $\begingroup$ Do you want to filter out the "worm" too? $\endgroup$ – Dr. belisarius Jan 24 '13 at 22:47
  • $\begingroup$ What about a median filter? $\endgroup$ – s0rce Jan 25 '13 at 5:53
  • $\begingroup$ Does MinFilter[img, 5] give something acceptable? $\endgroup$ – kglr Jan 25 '13 at 8:50
  • $\begingroup$ If you had an image without any interesting dots (like a test picture), you might be able to find the differences between the two images... $\endgroup$ – cormullion Jan 25 '13 at 10:11
  • $\begingroup$ You mean something like MatrixPlot@ImageData@ColorConvert[image, "GrayScale"]? $\endgroup$ – einbandi Jan 30 '13 at 1:14
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We could do with ground truth data to assess the result. Is this acceptable as a first step?

Manipulate[
    HighlightImage[
         i, 
         result = Binarize[TopHatTransform[i, radius], thr]], 
    {{radius, 4}, 1, 10, 1}, {{thr, .015}, 0, .2}]

enter image description here

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