PELGAS Bay of Biscay ZooScan zooplankton Dataset (2004-2016)

This dataset is composed of 1,153,507 zooplankton individuals, zooplankton parts, non-living particles and imaging artefacts, ranging from 300 µm to 3.39 mm Equivalent Spherical Diameter, individually imaged and measured with the ZooScan (Gorsky et al., 2010). The objects were sorted in 127 taxonomic and morphological groups. The imaged objects originate from samples collected on the Bay of Biscay continental shelf, in spring, from 2004 to 2016 during the PELGAS ecosystemic surveys (Doray et al., 2018). The samples were collected with a WP2 200 µm mesh size fitted with a Hydrobios (back-run stop) mechanical flowmeter, generally from 100 m depth to the surface, or 5 m above the sea floor (if bottom depth less than 100 m) in vertical hauls, at night. From 2004 to 2006, vertical WP2 net tows were performed in the anchovy core distribution area in the southern Bay of Biscay and North of it until the Loire estuary only. Since 2009, WP2 sampling has been carried out at all PELGAS stations, up to the southern coast of Brittany. The samples were preserved in 4% buffered formaldehyde seawater solution directly after collection, until 2019-2020 where they were imaged with the ZooScan, in the lab, on land. Each imaged object is geolocated, associated to a station, a cruise, a year and other metadata that enable the reconstruction of quantitative zooplankton communities for ecological studies (i.e. Grandrémy et al., 2023a). Each object is described by 46 morphological and grey level based features (8 bits encoding, 0 = black, 255 = white), including size, automatically extracted on each individual image by the Zooprocess. Each object was taxonomically identified using the web based application Ecotaxa with built-in, random forest and CNN based, semi-automatic sorting tools followed by expert validation or correction (Picheral et al., 2017). This dataset is intended to be used for ecological studies as well as machine learning applied to plankton studies.

The archive contains:

- One tab separated file (PELGAS ZooScan zooplankton dataset) containing all data and metadata associated to each imaged and identified object. Metadata and features are in columns (n =71) and objects are in rows (n = 1,153,507).

- One comma separated file containing the name, type, definition and unit of each field (column) in the .tsv (dataset_descriptor_zooscan).

- One comma separated file containing the taxonomic list of the dataset, with counts and nature of the content of the category, i.e. “T” for taxonomical category, and “M” for morphological category (taxonomy_descriptor_zooscan).

- A individual_images directory containing images of each imaged object sorted in subdirectories named according to objects’ identifications object_taxon appended to an Ecotaxa internal taxon numerical id classif_id (i.e. taxon__123456789) across years and sampling stations. Within subdirectories, each object is named after its unique internal Ecotaxa identifier, objid.

- A Map of the sampling station location over the 2004-2016 period

Date (Publication): 2023-03

Date (Revision): 2023-10-20

Other citation details: Grandrémy Nina, Bourriau Paul, Daché Edwin, Danielou Marie-Madeleine, Doray Mathieu, Dupuy Christine, Huret Martin, Jalabert Laetitia, Le Mestre Sophie, Nowaczyk Antoine, Petitgas Pierre, Pineau Philippe, Raphalen Elio, Romagnan Jean-Baptiste (2023). PELGAS Bay of Biscay ZooScan zooplankton Dataset (2004-2016). SEANOE. https://doi.org/10.17882/94052

Credit: The authors acknowledge receiving funding from the Ifremer DEFIPEL project France Filière Pêche projet d’avenir. NG acknowledges being funded by Region Pays de la Loire, FR and Ifremer. The authors wish to thanks the PIQV team (Sorbonne Université – CNRS) for their expertise in zooplankton identification. The authors wish also to thank the many other students, technicians and scientists who participated in the sampling and samples management on board and on land, and the successive crews of the R/V Thalassa involved in the PELGAS cruises from 2004 to 2016.

Author

DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro, Nantes, Centre Atlantique - Rue de l'Ile d'Yeu - BP 21105 - 44311 Nantes Cedex 03, France - Grandrémy Nina

Author

DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro, Nantes, Centre Atlantique - Rue de l'Ile d'Yeu - BP 21105 - 44311 Nantes Cedex 03, France - BOURRIAU Paul

Author

Unité Biologie et Ecologie des Ecosystemes marins Profonds, Laboratoire Environnement Profond, Ifremer Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané, France - DACHé Edwin

Author

Unité DYNECO-PELAGOS, Laboratoire d’Ecologie Pélagique, Ifremer Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané, France - DANIELOU Marie-Madeleine

Author

DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro, Nantes, Centre Atlantique - Rue de l'Ile d'Yeu - BP 21105 - 44311 Nantes Cedex 03, France - DORAY Mathieu

Author

BIOFEEL, UMRi LIENSs, La Rochelle Université / CNRS , 2, rue Olympe de Gouges, 17000 La Rochelle, France - Dupuy Christine

Author

DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro, Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané, France - HURET Martin

Author

Sorbonne Université, CNRS, Laboratoire d’Océanographie de Villefranche, 06230 Villefranche-sur-mer, France - Jalabert Laetitia

Author

DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro, Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané, France - Le Mestre Sophie

Author

UMR CNRS 5805 EPOC – OASU, Station Marine d'Arcachon, Université de Bordeaux, 2 Rue du Professeur Jolyet, 33120 Arcachon, France - Nowaczyk Antoine

Author

Departement Ressources Biologiques et Environnement, Ifremer Centre Atlantique - Rue de l'Ile d'Yeu - BP 21105 - 44311 Nantes Cedex 03, France - PETITGAS Pierre

Author

BIOFEEL, UMRi LIENSs, La Rochelle Université / CNRS , 2, rue Olympe de Gouges, 17000 La Rochelle, France - Pineau Philippe

Author

UMR MARBEC- Laboratoire Halieutique Méditerranée, Ifremer Centre Mediterranée, Station de Sète - Avenue Jean Monnet - CS 30171 - 34203 Sète Cedex - RAPHALEN Elio

Author

DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro, Nantes, Centre Atlantique - Rue de l'Ile d'Yeu - BP 21105 - 44311 Nantes Cedex 03, France - ROMAGNAN Jean-Baptiste

Publisher

SEANOE

Theme

Zooplankton
Bay of Biscay
ZooScan
imaging
WP2 200 µm net
Biological oceanography

ODATIS aggregation parameters and Essential Variable names

Zooplankton

SeaDataNet Parameter Disciplines

Biological oceanography

Centre de données ODATIS

CDS-IS-OASU

Type de jeux de donnée ODATIS

Observational data

Use limitation: CC-BY (Creative Commons - Attribution)

Use constraints: Other restrictions

Other constraints: While all identifications have been reviewed by at least one human operator, we cannot fully guarantee the correctness of each of the >1.15M identifications, a few mistakes might remain.