Light microscopy analysis of diatom frustules is widely used in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. Building on automated imaging solutions developed for medical/histological microscopy, we can now implement substantial parts of an automated diatom imaging workflow. Our methods resemble those drafted by the ADIAC (Automated Diatom Identification And Classification) project, and combine a commercial slide-scanning microscope with our automated diatom image analysis software SHERPA for measuring a broad range of morphometric features from individual frustules mounted on permanent slides. Although a fully automated process enabling routine diatom counting is still far from becoming reality, user intervention is minimized by extensive automation and internal quality control of the results. Furthermore care was taken to allow the user to stay in control of the most critical steps (exact segmentation of valve outlines and selection of objects of interest) using interactive functions for reviewing and revising results. We successfully applied our methods to several projects by finding, selecting and measuring up to several ten thousand diatom valves (presented at the poster session), and present our workflow in the hope that it can facilitate research on diatom morphometry.