In order to survey changes in accumulation of several hundred proteins during the naturally synchronous nuclear division cycle of Physarum polycephalum, we have developed methods for analyzing two-dimensional (2-D) gel electrophoretograms using the general image processing system developed bythe Spatial DataAnalysis Laboratory at Virginia Tech. In this paper we describe fast and accurate methods for removing non-homogeneous background intensity from a 2-D gel image, for resolving overlapping protein spots, and for estimating the total integratedintensity in a protein spot by Gaussian modeling.