One embodiment relates to a method of inspecting an array of cells on a substrate. A reference image is generated using a cell image that was previously determined to be defect free. A reference contour image which includes contours of the reference image is also generated. The reference contour image is used to detect defects in the array of cells on the substrate. Another embodiment relates to a system for detecting defects in an array on a substrate. Other embodiments, aspects and features are also disclosed.