The Central Arctic Ocean is a sensitive marine ecosystem, often nutrient and light limited, rapidly changing due to climate change. As the annual Arctic summer sea-ice cover decreases, it is essential to understand how environmental changes will affect phytoplankton biodiversity. Taxonomic identification of phytoplankton is traditionally done with microscopy. However, this is time consuming, requires high taxonomical knowledge and is bias-prone. Imaging Flow Cytometry (IFC) combines flow cytometry with the imagery and functional insights of microscopy. The aims of this thesis were to compare the efficiency of microscopy and IFC to quantify Arctic phytoplankton species and to assess the applicability of IFC for natural samples. An analysis of nano‑ and microphytoplankton communities from samples taken during the ArcWatch-1 expedition to the central Arctic Ocean was performed with both methodologies. Overall, IFC underestimated the abundance of the major groups when compared to microscopy. In general, identification with IFC was achieved to the same taxonomical level as in microscopy. IFC proved to be a valuable tool for discerning alive cells due to the presence of Chl a fluorescence, as well as in identifying feeding habits. The analysis of samples from late summer indicated a flagellate based ecosystem, followed by diatoms in abundance.
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