I'm trying to measure what fraction of an image is covered by filaments. I have tried several combinations of image processing functions without any luck. Any help?
img = Import["https://i.stack.imgur.com/Pvh7c.jpg"];
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Almost
HighlightImage[img,bin = MorphologicalBinarize[
TopHatTransform[GaussianFilter[img, 10], 10], {.01, .02}]]
Fraction about those filaments
N[Total[ImageData[bin], 2]/Times @@ ImageDimensions[bin]]
0.278293
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$\begingroup$ Good answer. You could use
Mean@N@Flatten@ImageData@bin, then you wouldn't have to divide by the number of pixels $\endgroup$ – Niki Estner Jul 5 '17 at 7:44 -
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A HeadStart
by no means it is a complete answer. But one can surely play around with it a bit
img2 = MorphologicalBinarize[GaussianFilter[BrightnessEqualize[img], 2], 0.44] //
Opening[#, 2] & // DeleteSmallComponents[#, 200] &
(* for cropped image i took *)
Length@PixelValuePositions[img2, 1]/(Times@@ImageDimensions[img])
(* ~ 0.20 *)
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1$\begingroup$ I found a little better result using PeronaMaikFilter, LocalAdaptiveBinarize, and DeleteSmallComponents functions $\endgroup$ – JBogoya Jul 4 '17 at 23:16
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$\begingroup$ @JBogoya Great. Good that worked out for you $\endgroup$ – Ali Hashmi Jul 5 '17 at 8:39
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$\begingroup$ @JBogoya You can post your own solution as an answer, it is encouraged here. $\endgroup$ – Alexey Popkov Jul 5 '17 at 9:13
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$\begingroup$ DeleteSmallComponents[ DeleteSmallComponents[LocalAdaptiveBinarize[PeronaMalikFilter[fig, 20], 250], 400] // ColorNegate, 150] // ColorNegate $\endgroup$ – JBogoya Jul 6 '17 at 1:13
MorphologicalBinarize[GaussianFilter[img, 0.2], 0.42] // ColorNegate //MaxFilter[#, 1] &$\endgroup$ – Ali Hashmi Jul 2 '17 at 0:01MorphologicalBinarize[BrightnessEqualize[img],0.43] // Opening[#, 2] & // DeleteSmallComponents[#, 100] &$\endgroup$ – Ali Hashmi Jul 4 '17 at 22:46