A method of identifying discontinuities in the surface of a substrate is herein disclosed. An object plane of an imaging system is positioned at a focal position associated with a discontinuity and an image is captured, the discontinuity having a relatively higher contrast with respect to the remainder of the surface of the substrate. The discontinuity is thereby more readily discernable than when the focal plane is positioned at the surface of the substrate. Analysis of discontinuities may include the extraction of discontinuity characteristics.