I am trying to draw profiles along lines of 5-10 pixel width across crystals, but these crystals have cracks. Where these cracks intersect the line, I would like imagej to ignore them, and average only over the width of the line that is not over the crack. Is there a way of drawing round the cracks (and other defects), and to then exclude those regions from the profiles I draw? The functions to do this with ROIs don't seem to work for lines.
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