# False Color SEM image with Mathematica

I have a question regarding colouring and binary image filtering, but unfortunately, the system doesn't permit the inclusion of images for first-timers. If anyone would like to see the images described below, please email me directly.

I have an image of gold electrodes on a flat substrate obtained with a scanning electron microscope. I would like to colour in all the gold electrodes and particles that appear in the centre of the image, leaving the colour of the background as it is for now. I perform straightforward routines by implementing the following code: Firstly, I rename the image q: q=Image; Then I apply the PeronaMalik Filter to enhance the edges and diffuse the background:

pq = PeronaMalikFilter[q, 20, 0.02, 2]


The background in the image thus obtained looks more diffused and uniform, while the edges of the gold electrodes and particles appear sharp, in contrast to the background. Then I give the following command to colour in the gold

goldq = ImageApply[# {1., 0.843104, 0.} &, q,
Masking -> SelectComponents[Binarize[pq, 0.36], "Area", # > -300 &]]


The result is an image in which the gold electrodes are almost entirely coloured in gold, but there are also large regions that are coloured by gold, which shouldn't be; for instance, the left side of the image, and the top right and bottom right. It seems that these areas receive colour due to the fact that they have the same binary level as the actual gold electrodes, which is an artefact of the scanning, and should definitely have the same zero level as the rest of the background.

Is there any way to correct this gaffe digitally using Mathematica's built-in functions? Is it possible, additionally, to give the background a different colour?

As suggested, here are all three images:

Original image: After filter: After gold:

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You could try another binarizing function. For example:

mask = MorphologicalBinarize[pq, {.5, 0.6}]
ImageSize -> 500]


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I think there is something wrong in your code. Why did you write # > -300 & as criterion for the area. Lets try another approach with only a simple gaussian filter:

img = ImagePad[
ColorConvert[Import["http://i.stack.imgur.com/GdtlA.jpg"],
"Grayscale"], {{0, 0}, {-100, 0}}];
ImageApply[# {1., 0.843104, 0.} &, img,