Problems masking out objects in Gimp

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I am trying to use GIMP to cut some objects in my image to use them as a groundtruth for later comparison with some Computer Vision routine. The general ideas is to separate each object from the background. Since they are green plants, the procedure is to select with the "free select" tool, the plant surroundings, later I apply the "Fuzzy Select tool" (the magic wand) on the green channel values, and finally I remove some spurious blobs substracting with the free select tool again. Once a plant is selected, I make a layer mask with this selection. The same is done with the next 3 or 4 plants. Finally I add a black layer as a background and I get my plants cropped from the background. The question is that I have observe that in the final image (PNG exported) some small blobs still appear even when they were not in the selection. It seems like pixels or objects that where selected during the procedure but are not in the final selection.

Trying to see what happened, I can see that, using "mask to selection" do not select those blobs, but, when I remove the mask, and repeat the masking, they are still there! Also, if I "mask to selection", remove the mask, and I use the fuzzy selector to substract those undesired pixels, and finally I mask again. Those pixels dissapear! That means that those pixels are in the selection but I can't see them marked. Anybody have any clue why this is happening and how to avoid it?

I hope my description is clear, and sorry but I am not able to upload an image.

Thanks in advance.

asked 1 min ago

Omg

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Problems masking out objects in Gimp