EBImage provides general purpose functionality for high-throughput image processing and analysis in fluorescence microscopy. In the context of microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data (Paut et al., Bioinformatics 26, 979–981, 2010) Registration not required.