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Both classifications in combination provide a good mechanistic understanding of phytoplankton community dynamics. In addition, a great advantage of the measurements is the archivability of microscopic images allowing a comprehensive respective data analysis. Two examples of detailed trait and image analysis are demonstrated to investigate single-cell traits for cyanobacteria and chlorophytes/euglenophytes and to follow the fate of a cyanobacterial bloom affected by a fungal infection. © 2020 The Author. Cytometry Part A published by Wiley