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    DOI10.15468/5ebhr2

    Sampling event Registered February 28, 2025

    SHARK - Phyto- and Microzooplankton Data Collected by Imaging FlowCytobots (IFCB) in Swedish and Adjacent Waters

    Published by The Swedish Meteorological and Hydrological Institute
    shark.smhi.se
    LicenceCC0 1.0

    Description

    Data is stored in the Swedish Ocean Archive database (SHARK), by the Swedish Meteorological and Hydrological Institute,

    National Oceanographic Data Centre.Monitoring is performed by Swedish Meteorological and Hydrological Institute. The monitoring is financed by monitoring projects.In short, analysis of phyto- and microzooplankton species composition, abundance and biomass is carried out for the following purposes.To describe temporal trends as well as the intensity and occurrence of blooms.To describe the spatial distribution of species.To identify key species (e.g. dominating, harmful, potential non-indigenous and/or invasive species, as well as indicator species).To provide basic data for complex ecosystem analyses, food web studies, modelling as well as for requirements in the frame of the Marine Strategy Framework Directive of the European Union (MSFD European Union 2008) and the EU Water Framework Directive (WFD European Union 2000).In this dataset you will find data from Tangesund oceanographic platform, Swedish Skagerrak coast year 2016 (IFCB110), and from R/V Svea (https://vocab.nerc.ac.uk/collection/C17/current/77SE/) from year 2022 onwards (IFCB134). Other sampling platforms are possible.

    Geographic scope

    Description

    N/A

    Latitude
    From 54.833012 to 65.166347
    Longitude
    From 5.803512 to 23.821384

    Temporal scope

    range
    August 10, 2016 - December 15, 2024

    Taxonomic scope

    Coverage
    ParaliaceaeGymnodiniaceae
    Dinophyceae
    FragilariaceaeMicrocystaceae

    Methodology

    Sampling

    Sampling is performed either using shipboard flow through systems (i.e. FerryBox) where the Imaging FlowCytobot (IFCB) is connected as an addon, or at specific locations with the IFCB is submerged in-situ. Other deployment methods are possible. The IFCB uses flow cytometry technology and high-resolution images to detects particles in a water sample. Shapes in images are identified to best possible taxonomical levels using AI-assisted image analysis software. Volumes are estimated from the organism’s two-dimensional boundary.

    Study extent

    Data are collected within the following marine ecoregions: http://marineregions.org/mrgid/2401, http://marineregions.org/mrgid/2374, http://marineregions.org/mrgid/2379, http://marineregions.org/mrgid/2350

    Method steps

    1. The analysis follows the methods provided

      Machine learning: Sosik, H. M. and Olson, R. J. (2007), Automated taxonomic classification of phytoplankton sampled with imaging-in-flow cytometry. Limnol. Oceanogr: Methods 5, 204–216. http://github.com/hsosik/ifcb-analysis

      Quality control: Hayashi, K., Walton, J., Lie, A., Smith, J. and Kudela M. Using particle size distribution (PSD) to automate imaging flow cytobot (IFCB) data quality in coastal California, USA. In prep. http://github.com/kudelalab/PSD

      Data processing: Anders Torstensson (2024). I 'R' FlowCytobot (iRfcb): Tools for Analyzing and Processing Data from the IFCB. R package version 0.3.10. https://doi.org/10.5281/zenodo.12533225. http://github.com/EuropeanIFCBGroup/iRfcb

    Contacts

    • SHARK SMHI

      Originator
      Metadata author
      Administrative point of contact
      Organization
      Swedish Meterological and Hydrological Institute (SMHI)
      Position
      Data manager
      Roles
      Originator
      Metadata author
      Administrative point of contact
      Email

    GBIF registration

    Registration date
    February 28, 2025
    Metadata last modified
    February 28, 2025
    Publication date
    February 28, 2025
    Hosted by
    GBIF-Sweden
    Installation
    IPT GBIF-Sweden
    Endpoints
    Darwin Core Archive
    EML
    Preferred identifier
    10.15468/5ebhr2
    Alternative identifiers
    GBIF registration details

    Citation

    Swedish Meteorological and Hydrological Institute (2024). SHARK - Phyto- and Microzooplankton Data Collected by Imaging FlowCytobots (IFCB) in Swedish and Adjacent Waters https://doi.org/10.15468/5ebhr2 accessed via GBIF.org on 2025-08-06.