Imaging FlowCytobot (IFCB) time-series data from the Baltic Sea and Skagerrak

This dataset contains phytoplankton observations collected to investigate diel vertical migration (DVM) patterns in two distinct marine environments. A detailed description of the dataset can be found in the accompanying article ”High throughput in situ imaging reveals widely occurring diel vertical migration among phytoplankton” in ISME Communications by Karin Garefelt, Bengt Karlson, Michael L. Brosnahan, Kaisa Kraft, Anders Torstensson, Jukka Seppälä, Allan Cembella, Anders F. Andersson. The primary instrument used was the Imaging FlowCytobot (IFCB), which captures images of individual particles in the <10–150 µm size range. Images were classified into taxonomic groups using convolutional neural networks (ResNet18). Biomass for each image was calculated as carbon content (pg C) and converted to concentrations (µg C L⁻¹). The data was collected in two sites: Skagerrak (Tångesund, Sweden): Data collected between August 10 and October 17, 2016. The setup involved an Imaging FlowCytobot (IFCB) mounted on a winch system that continuously profiled the water column across six depths: 3, 6, 8, 11, 13, and 16 meters. Baltic Sea (Utö Atmospheric and Marine Research Station, Finland): Data collected from June to October in 2020 and 2021. Samples were taken from a fixed-depth intake at 4.5 meters. The dataset includes: Phytoplankton Observations: Biomass concentrations for various morpho-taxonomic groups, including dinoflagellates, diatoms, ciliates, and cyanobacteria. Nutrient Measurements (Skagerrak only): Weekly measurements of NO₂, NO₃, NH₄, PO₄, and SiO₃ at multiple depths. This study was supported by the Swedish Research Council FORMAS (grant 2022-01515), the EU Horizon 2020 projects JERICO-NEXT (grant agreement No 654410) and JERICO-S3 (grant Agreement No 871153), and Research Council of Finland (grants No 317297 and 339355). AFA is supported by the Swedish Research Council VR (grant 2021-05563). AC was supported under Helmholtz research program “Changing Earth, Sustaining our Future” (Sub-topic 6.2 Adaptation of marine life) of the Alfred-Wegener-Institut (AWI), Helmholtz Zentrum für Polar- und Meeresforschung, Germany.