In this work, diatoms from phytoplankton net samples from four stations from a transect southward from Cape Town and five from an eddy at the southern boundary of the Ant-arctic Circumpolar Current, obtained during Polarstern cruise ANTXXVIII-3, were ana-lyzed. Material was cleaned in an acidic water bath and permanent slides, containing diatom frustules, were prepared. The permanent slides were automatically scanned in similar areas using an automated microscopic image acquisition system. The pictures were analyzed using image analysis software developed for detecting and characterizing diatom outlines, as well as manual-ly, in order to test the performance of the software. The test revealed a strong taxonomic bias against large-celled and thinly silicified taxa. Dominant taxa after combining auto-matically and manually obtained diatom counts were Fragilariopsis kerguelensis and the genera Pseudonitzschia and Chaetoceros. For Fragilariopsis kerguelensis, statistically significant morphometric differences between the populations from the transect vs. from the eddy were found, the ecological interpretation of which will require further study.