seanoe:94040 Grandrémy Nina 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. grandremy.n@gmail.com ROMAGNAN Jean-Baptiste 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. Jean.Baptiste.Romagnan@ifremer.fr 2023-10-20 ISO 19115:2003/19139 1.0 PELGAS Bay of Biscay ZooCAM zooplankton Dataset (2016-2019) 2023 2023-10-20 Grandrémy Nina, Bourriau Paul, Danielou Marie-Madeleine, Doray Mathieu, Dupuy Christine, Forest Bertrand, Huret Martin, Le Mestre Sophie, Nowaczyk Antoine, Petitgas Pierre, Pineau Philippe, Rouxel Justin, Tardivel Morgan, Romagnan Jean-Baptiste (2023). PELGAS Bay of Biscay ZooCAM zooplankton Dataset (2016-2019). SEANOE. https://doi.org/10.17882/94040 This dataset is composed of 702,111 zooplankton individuals, zooplankton pieces, non-living particles and imaging artefacts, ranging from 300 µm to 3.39 mm Equivalent Spherical Diameter, individually imaged and measured with the ZooCAM (Colas et al., 2018). 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 2016 to 2019 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. The samples were imaged on board, live, after collection and subsampling, and preserved in 4% buffered formaldehyde seawater. 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 52 morphological and grey level based features (8 bits encoding, 0 = black, 255 = white), including size, automatically extracted on each individual image by the ZooCAM software. Each object was taxonomically identified using the ZooCAM software and 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). Images from 2016-2017 contain ROI bounding box limits, metadata at the bottom of each image, and non-homogenised background within and around the ROI bounding box; Images from 2018 contain non-homogenised background within the ROI bounding box only; images from 2019 have a completely homogeneous and thresholded background around the object.  The differences arose from successive ZooCAM software updates that do not modify the calculation of object’s features. 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 ZooCAM zooplankton dataset) containing all data and metadata associated to each imaged and identified object. Metadata and features are in columns (n =72) and objects are in rows (n = 702,111). - One comma separated file containing the name, type, definition and unit of each field (column) in the .tsv (dataset descriptor zoocam). - 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 zoocam). - A individual_images directory containing images of each object, named according to the object id objid and sorted in subdirectories according to their taxonomic identification, across years and sampling stations. - A Map of the sampling station location over the 2016-2019 period. 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 Jean-Yves Coail, Gérard Guyader and Patrick Berriet (Ifremer – REM-RDT-SIIM) for their contribution to the hardware assembly of the ZooCAM. 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 2016 to 2019. Grandrémy Nina 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. grandremy.n@gmail.com BOURRIAU Paul 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. DANIELOU Marie-Madeleine Unité DYNECO-PELAGOS, Laboratoire d’Ecologie Pélagique, Ifremer Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané, France DORAY Mathieu 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. DUPUY Christine BIOFEEL, UMRi LIENSs, La Rochelle Université / CNRS, 2, rue Olympe de Gouges, 17000 La Rochelle, France FOREST Bertrand Laboratoire Hydrodynamique Marine, Unité RDT, Ifremer Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané, France HURET Martin 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 DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro, Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané, France. Nowaczyk Antoine UMR CNRS 5805 EPOC – OASU, Station Marine d'Arcachon, Université de Bordeaux, 2 Rue du Professeur Jolyet, 33120 Arcachon, France PETITGAS Pierre Departement Ressources Biologiques et Environnement, Ifremer Centre Atlantique - Rue de l'Ile d'Yeu - BP 21105 - 44311 Nantes Cedex 03, France Pineau Philippe BIOFEEL, UMRi LIENSs, La Rochelle Université / CNRS, 2, rue Olympe de Gouges, 17000 La Rochelle, France ROUXEL Justin Laboratoire Détection, Capteurs et Mesures, Unité RDT, Ifremer Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané, France TARDIVEL Morgan Laboratoire Détection, Capteurs et Mesures, Unité RDT, Ifremer Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané, France ROMAGNAN Jean-Baptiste 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. Jean.Baptiste.Romagnan@ifremer.fr SEANOE https://www.seanoe.org/data/00828/94040/illustration.gif Zooplankton Bay of Biscay ZooCAM imaging WP2 200 µm net Biological oceanography Zooplankton ODATIS aggregation parameters and Essential Variable names 2024-09-16 geonetwork.thesaurus.external.theme.NVS.OD1 Biological oceanography SeaDataNet Parameter Disciplines 2021-04-07 geonetwork.thesaurus.external.parameter.NVS.P08 CDS-OASU Centre de données ODATIS 2024-10-16 geonetwork.thesaurus.local.theme.odatis_centre_donnees /Observational data/in-situ Type de jeux de donnée ODATIS 2024-10-15 geonetwork.thesaurus.local.theme.type_jeux_donnee CC-BY (Creative Commons - Attribution) While all identifications have been reviewed by at least one human operator, we cannot fully guarantee the correctness of each of the >700k identifications, a few mistakes might remain. Rapport DEFIPEL. Développement d’une approche de gestion intégrée de la filière petits pélagiques française. 2024 Ifremer Huret Martin Lehuta Sigrid Romagnan Jean-Baptiste Doray Mathieu Daures Fabienne Travers-Trolet Morgane 10.13155/104256 Metazoan zooplankton in the Bay of Biscay: 16 years of individual sizes and abundances from the ZooScan and ZooCAM imaging systems 2023 Copernicus GmbH GRANDREMY NINA BOURRIAU PAUL DACHÉ EDWIN DANIELOU MARIE-MADELEINE DORAY MATHIEU DUPUY CHRISTINE FOREST BERTRAND JALABERT LAETITIA HURET MARTIN LE MESTRE SOPHIE NOWACZYK ANTOINE PETITGAS PIERRE PINEAU PHILIPPE ROUXEL JUSTIN TARDIVEL MORGAN ROMAGNAN JEAN-BAPTISTE 10.5194/essd-2023-187 Hydrology and small pelagic fish drive the spatio–temporal dynamics of springtime zooplankton assemblages over the Bay of Biscay continental shelf 2023 Elsevier BV GRANDREMY NINA ROMAGNAN JEAN-BAPTISTE DUPUY CHRISTINE DORAY MATHIEU HURET MARTIN PETITGAS PIERRE 10.1016/j.pocean.2022.102949 The ZooScan and the ZooCAM zooplankton imaging systems are intercomparable: A benchmark on the Bay of Biscay zooplankton 2023 ASLO Grandremy Nina Dupuy Christine Petitgas Pierre Le Mestre Sophie Bourriau Paul Nowaczyk Antoine Forest Bertrand Romagnan Jean-Baptiste 10.1002/lom3.10577 The ZooCAM, a new in-flow imaging system for fast onboard counting, sizing and classification of fish eggs and metazooplankton 2018 Pergamon-elsevier Science Ltd COLAS FLORENT TARDIVEL MORGAN PERCHOC JONATHAN LUNVEN MICHEL FOREST BERTRAND GUYADER GERARD DANIELOU MARIE-MADELEINE LE MESTRE SOPHIE BOURRIAU PAUL ANTAJAN ELVIRE SOURISSEAU MARC HURET MARTIN PETITGAS PIERRE ROMAGNAN JEAN-BAPTISTE 10.1016/j.pocean.2017.10.014 Monitoring small pelagic fish in the Bay of Biscay ecosystem, using indicators from an integrated survey 2018 Pergamon-elsevier Science Ltd DORAY MATHIEU PETITGAS PIERRE HURET MARTIN DUHAMEL ERWAN ROMAGNAN JEAN-BAPTISTE AUTHIER MATTHIEU DUPUY CHRISTINE SPITZ JEROME 10.1016/j.pocean.2017.12.004 ZooScanNet: plankton images captured with the ZooScan 2024 SEANOE Elineau Amanda Desnos Corinne Jalabert Laetitia Olivier Marion Romagnan Jean-Baptiste Costa Brandao Manoela Lombard Fabien Llopis Natalia Courboulès Justine Caray-Counil Louis Serranito Bruno Irisson Jean-Olivier Picheral Marc Gorsky Gaby Stemmann Lars 10.17882/55741 ZooCAMNet : plankton images captured with the ZooCAM 2024 SEANOE Romagnan Jean-Baptiste Panaïotis Thelma Bourriau Paul Danielou Marie-Madeleine Doray Mathieu Dupuy Christine Forest Bertrand Grandremy Nina Huret Martin Le Mestre Sophie Nowaczyk Antoine Petitgas Pierre Pineau Philippe Rouxel Justin Tardivel Morgan Irisson Jean-Olivier 10.17882/101928 Gridded maps of pelagic ecosystem parameters collected in the Bay of Biscay during the PELGAS integrated survey 2018 SEANOE Doray Mathieu Huret Martin Authier Matthieu Duhamel Erwan Romagnan Jean-Baptiste Dupuy Christine Spitz Jérôme Sanchez Florence Berger Laurent Dorémus Ghislain Bourriau Paul Grellier Patrick Pennors Laurence Masse Jacques Petitgas Pierre 10.17882/53389 10.17600/16002400 10.17600/17002000 10.17600/18000419 10.17600/18001109 oceans -7.390009 -0.007196 42.663116 48.731617 TEXTE CSV IMAGE https://www.seanoe.org/data/00828/94040/data/101092.tsv WWW:DOWNLOAD-1.0-link--download Processed data PELGAS ZooCAM zooplankton dataset - 377 MB https://www.seanoe.org/data/00828/94040/data/101093.csv WWW:DOWNLOAD-1.0-link--download dataset descriptor zoocam - 11 KB https://www.seanoe.org/data/00828/94040/data/101094.csv WWW:DOWNLOAD-1.0-link--download Processed data taxonomy descriptor zoocam - 2 KB https://www.seanoe.org/data/00828/94040/data/101095.zip WWW:DOWNLOAD-1.0-link--download Raw data individual images - 1 GB https://www.seanoe.org/data/00828/94040/data/101096.png WWW:DOWNLOAD-1.0-link--download Map of the sampling station location over the 2016-2019 period - 1 MB https://doi.org/10.17882/94040 WWW:LINK-1.0-http--metadata-URL DOI of the product https://www.seanoe.org/data/00828/94040/ rel-canonical Seanoe WP2 200 µm zooplankton net, ZooCAM, Ecotaxa