Photon-counting detectors are important to many areas of astronomy. A new generation, based on microchannel plate intensifiers, is already in use, and so understanding the fundamental problems of image-analysis techniques which are used by both current and new generation devices is necessary. We examine the "pattern noise" problem which causes modulation of the image. We find that it has a number of sources and suggest methods whereby it may be reduced. The problems discussed have applications to all fields (like CCD photometry and astrometry) which employ few-pixel, image-analysis techniques.