Comparison of Imaging Flow Cytometry and Manual Counts for Assessing Ecological Status and Harmful Cyanobacterial Bloom Monitoring

Numerous sampling and analytical methods exist to assess ecological status and to monitor harmful cyanobacterial blooms (HCBs) in freshwater systems. Imaging flow cytometry presents a powerful tool for assessing phytoplankton assemblages, where it reduces processing time while maintaining an intermediate level of taxonomic detail. This increased capacity and reduced processing time makes flow cytometry an effective method for HCB monitoring and large-scale ecological assessment. Here, we compare manual counts and results from the Imaging Flow Cytobot (IFCB) for a project in New York. Preserved and live samples from two lakes in the Finger Lakes region were included in the analysis, with 22 sampling events. Each sample was analyzed using both manual counts and the IFCB. Comparisons between the manual and IFCB counts were analyzed using multidimensional scaling, specifically focusing on differences between functional groups, species classes, and critical water indicators such as HCB species. The differences between live and preserved samples were also compared