These other intensities, which can lead to false positives and large reductions of the SNR, originate generally either from the instrument or from wafer noise, defined below. Examples of instrument-based sources of imaging noise include the shot noise of the charge coupled device, the stray light and glare within the optical columns, and intensity inhomogeneities across the field of view from misalignment, lens imperfections, aberrations, and laser speckle. These sources of error can be significant but are reduced as much as practicable through optical design and design of experiment. In our measurements, speckle is partially removed by using a rotating diffuser at the source plane while aberrations have been reduced through design optimization. Furthermore, systematic instrumental noise effects are largely mitigated by collecting “defect” and (after wafer shifting) “reference” sets of images for differential analysis under nearly the same experimental conditions. These procedures, coupled with a volumetric approach that reduces the effects of random noise, permit a more thorough exploration of the effects of wafer-based intensity noise relative to the defect.