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

enter image description here

  • $\begingroup$ Do you want to filter out the "worm" too? $\endgroup$ Jan 24, 2013 at 22:47
  • $\begingroup$ What about a median filter? $\endgroup$
    – s0rce
    Jan 25, 2013 at 5:53
  • $\begingroup$ Does MinFilter[img, 5] give something acceptable? $\endgroup$
    – kglr
    Jan 25, 2013 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, 2013 at 10:11
  • $\begingroup$ You mean something like MatrixPlot@ImageData@ColorConvert[image, "GrayScale"]? $\endgroup$
    – einbandi
    Jan 30, 2013 at 1:14

1 Answer 1


We could do with ground truth data to assess the result. Is this acceptable as a first step?

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

enter image description here


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