The data set available here is published with 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 150 000 images belonging to 50 different classes (~57 000) + unclassifiable (~94 000) consisting mainly of phytoplankton. The images can be used to validate classifier model performance with data from natural samples.
The images were collected with an Imaging FlowCytobot (IFCB, McLane Research Laboratories, Inc., U.S., Olson and Sosik, 2007) from a continuous deployment in 2021at 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. The images were manually annotated by expert taxonomists. The data was used for validating CNN model performance for natural samples. The sample selection targeted on one sample per week from continuous operation between January to December 2021. Due to scarcity of some classes additional samples were selected from expected seasons. The selected samples were manually inspected: all classifications were assessed (confirmed or corrected) and all identifiable images that were left under the thresholds were labeled. The unidentifiable images that were left without an assigned class were considered as unclassified. 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. Additionally, there is also a folder of the unclassifiable images (not belonging to any of those 50 classes).
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
