Using color picker?

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Using color picker?

TessaS
   I'd like to run a particle analysis for eggs with brown, grey, and dark grey spots on them. I have three pictures of each egg (top, bottom, and side) to get a spot count/total area coverage etc, and have been able to go through the process successfully except that because so many of the spots on the eggs over lap/are very close, the program sees them as one large spot or sometimes just as a shadow. I think I need to use the color picker tool to identify what colors are spots and what color the background is, but I can't figure out how to do that!
Help please?