We present ScatterJn, an ImageJ (and Fiji) plugin for scatterplot-based exploration and analysis of analytical microscopy data. In contrast to commonly used scatterplot tools, it handles more than two input images (or image stacks, respectively) by creating a matrix of pairwise scatterplots. The tool offers the possibility to manually classify pixels by selecting regions of datapoints in the scatterplots as well as in the spatial domain. We demonstrate its functioning using a set of elemental maps acquired by SEM-EDX mapping of a soil sample. The plugin is available at https://savannah.nongnu.org/projects/scatterjn.