Method‐dependent differences in zooplankton abundance and size metrics: Microscopy vs. ZooScan

Abstract Image‐based approaches such as ZooScan are increasingly used for high‐throughput zooplankton monitoring. However, quantitative evaluations of methodological differences relative to conventional microscopy remain limited. In this study, zooplankton abundance and size‐based metrics obtained from microscopy and ZooScan image analysis were compared using identical subsamples from 35 net‐collected samples collected between 2022 and 2023. Total zooplankton abundance showed strong agreement between the two methods at the community level ( R 2 = 0.93, p < 0.001), with similarly high consistency for dominant taxonomic groups. In contrast, inferred size structure differed systematically between measurement approaches. Length‐based metrics emphasized larger size classes, whereas equivalent spherical diameter–based metrics derived from ZooScan more strongly represented smaller size classes. Therefore, size‐based results from the two approaches are not directly interchangeable. Although ZooScan produced abundance estimates comparable to those obtained by microscopy for dominant taxa under the identical‐subsample comparison, the choice of size metric substantially influenced inferred size structure, highlighting the importance of accounting for method‐dependent differences in zooplankton size‐based analyses.