The data set available here is published along with an article “Kraft et al. (2022). Towards operational phytoplankton recognition with automated high-throughput imaging, near real-time data processing, and convolutional neural networks. Front Mar. Sci. 9. Doi: 10.3389/fmars.2022.867695” and if used for further purposes, the article should be cited accordingly. The data set contains approximately 63 000 images belonging to 50 different classes, consisting mainly of phytoplankton. The images can be used to e.g. train a classifier to identify phytoplankton images.
The images were collected with an Imaging FlowCytobot (IFCB, McLane Research Laboratories, Inc., U.S., Olson and Sosik, 2007) from different locations in the Baltic Sea. In 2017 and 2018 the data were collected from a continuous deployment at the Utö Atmospheric and Marine Research Station (59°46.84’ N, 21°22.13’ E; Laakso et al., 2018; Kraft et al., 2021) operated by Finnish Environment Institute and Finnish Meteorological Institute (n=62). In 2016 and 2019 water samples were collected using the Alg@line ferrybox systems of M/S Finnmaid and Silja Serenade (Ruokanen et al., 2003; Kaitala et al., 2014) and manually ran in the laboratory (n=52). The images were manually annotated by expert taxonomists. The class list and labeled image set is a continuous work in progress, thus there may be a need for revision in future. The data set available with this doi will not be revised. More detailed explanation and example images can be found from the publication Kraft et al. 2022.
The zipped folder contains 50 different folders, and the images are located in the class-specific folders. The image names may refer to an old class (e.g. folder Cryptophyceae-Teleaulax contains images with names Cryptophyceae_drop, Cryptophyceae_small, Teleaulax sp.) that has been joined with another one / revised otherwise.
The work utilized SYKE and FMI marine research infrastructure as a part of the national FINMARI RI consortium. The work was partly funded by Tiina and Antti Herlin Foundation (personal grant for KK), Academy of Finland project FASTVISION (grant no. 321980), Academy of Finland project FASTVISION-plus (grant no. 339355), JERICO-S3 project, funded by the European Commission’s H2020 Framework Programme under grant agreement No. 871153, and PHIDIAS project, funded by the European Union's Connecting Europe Facility under grant agreement INEA/CEF/ICT/A2018/1810854.
The class list separated in taxonomic groups
Cyanophyceae
Aphanizomenon flosaquae
Aphanothece paralleliformis
Chroococcales
Chroococcus sp.
Dolichospermum sp. / Anabaenopsis sp.
Dolichospermum sp. / Anabaenopsis sp. coiled
Merismopedia sp.
Nodularia spumigena
Oscillatoriales
Snowella sp. / Woronichinia sp.
Cryptophyceae
Cryptomonadales
Cryptophyceae / Teleaulax sp.
Euglenophyceae
Euglenophyceae
Eutreptiella sp.
Dinophyceae
Amylax triacantha
Dinophyceae
Dinophysis acuminata
Gonyaulax verior
Gymnodiniales
Gymnodinium like cells
Heterocapsa rotundata
Heterocapsa triquetra
Peridiniella catenata chain
Peridiniella catenata single
Prorocentrum cordatum
Diatomophyceae
Centrales
Ceratoneis closterium
Chaetoceros sp. chain
Chaetoceros sp. single
Cyclotella choctawhatcheeana
Licmophora sp.
Melosira arctica
Nitzschia paleacea
Pauliella taeniata
Pennales thick
Pennales thin
Skeletonema marinoi
Thalassiosira levanderi
Chrysophyceae
Pseudopedinella sp.
Uroglenopsis sp.
Chlorophyta
Chlorococcales
Cymbomonas tetramitiformis
Monoraphidium contortum
Oocystis sp.
Pyramimonas sp.
Other
Katablepharis remigera
Ciliates
Ciliata
Mesodinium rubrum
Additional classes
Beads
Heterocyte
