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CMEIAS (Center for Microbial Ecology Image Analysis System) Bioimage Informatics software is designed to strengthen microscopy-based approaches for understanding microbial ecology at spatial scales directly relevant to ecological functions performed by individual cells and microcolonies. Copyrighted software components are thoroughly documented and provided as free downloads at . The software tools already released include CMEIAS-Image Tool v. 1.28, CMEIAS Color Segmentation, CMEIAS Quadrat Maker and CMEIAS JFrad Fractal Dimension analysis. The spatial ecology module of the next CMEIAS upgrade currently being developed (version 4.0) is designed to extract data from images for analysis of plotless point-patterns, quadrat-lattice patterns, geostatistical autocorrelation and fractal geometry of cells within biofilms. Examples presented here illustrate how selected CMEIAS attributes can be used to analyze the in situ spatial intensity, pattern of distribution, and colonization behavior of an indigenous population of a rhizobial strain on a sampled image of the rhizoplane landscape of a rice plant grown in field soil. The spatial ecology information gained can provide useful insights that help to predict the most likely performance of the biofertilizer test strain in relation to the growth response of the crop under field conditions.