Our project aims at bringing automated microscopy and image processing methods into routine diatom analysis from the water column, sediment traps and sediment cores in the Southern Ocean. We combined a Metafer slide scanning system with SHERPA, our image analysis software developed specifically for diatom images, to characterize morphometric variation within and among diatom species. This poster gives an overview of the established methodology (presented in detail by the according talk), and its application to three studies in a paleoceanographic, a life cycle and a taxonomic context, respectively.