Images that are created from selected ROIs (e.g. by simply duplicating) do also show the surrounding area of the nucleus (ROI). This can lead to "irritations" in the analysis due to changed brightness.
By copying the ROI and pasting it into an empty (black) image will solve this issue.
Since there seems to be no easy way of copying the interior of a selection programatically, check all pixels whether they are contained within the ROI. If they are, leave them, otherwise, set them to black.
Images that are created from selected ROIs (e.g. by simply duplicating) do also show the surrounding area of the nucleus (ROI). This can lead to "irritations" in the analysis due to changed brightness. By copying the ROI and pasting it into an empty (black) image will solve this issue.