In this presentation we will demonstrate the application of quantitative microscopy to the analysis of a number of microbial models common to bacteriology, virology, mycology, and parasitology. The quantitative microscopy tool box consists of an automated digital microscope, an array of stains and fluorescent probes, and s/w for multi-parameter processing and analysis of acquired images resulting in both qualitative and quantitative data outcomes. Applications using live and fixed microorganisms will be highlighted via individual case studies, including quantitating plaque assay viral titers in 96-well plates using montage and stitching; calculating bio volume and morphology characteristics of bacterial and fungal matrices using z-stacking; and monitoring effects of phagocytic inhibition on uptake of bacteria and yeast.