seanoe:94052 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 ZooScan zooplankton Dataset (2004-2016) 2023-03 2023-10-20 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 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 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. 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 DACHé Edwin 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 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 HURET Martin DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro, Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané, France Jalabert Laetitia Sorbonne Université, CNRS, Laboratoire d’Océanographie de Villefranche, 06230 Villefranche-sur-mer, 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 RAPHALEN Elio UMR MARBEC- Laboratoire Halieutique Méditerranée, Ifremer Centre Mediterranée, Station de Sète - Avenue Jean Monnet - CS 30171 - 34203 Sète Cedex 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/00829/94052/illustration.gif Zooplankton Bay of Biscay ZooScan 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 >1.15M 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 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 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 Digital zooplankton image analysis using the ZooScan integrated system 2010 Oxford Univ Press GORSKY GABY OHMAN MARK D. PICHERAL MARC GASPARINI STEPHANE STEMMANN LARS ROMAGNAN JEAN-BAPTISTE CAWOOD ALISON PESANT STEPHANE GARCIA-COMAS CARMEN PREJGER FRANCK 10.1093/plankt/fbp124 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 10.17600/4040040 10.17600/5040030 10.17600/6040040 10.17600/7040040 10.17600/8040040 10.17600/9040030 10.17600/10040040 10.17600/11040030 10.17600/12040030 10.17600/13040020 10.17600/14001800 10.17600/15001900 10.17600/16002400 oceans -5.361529 -0.32979 43.196993 48.472763 TEXTE CSV IMAGE https://www.seanoe.org/data/00829/94052/data/101138.tsv WWW:DOWNLOAD-1.0-link--download Quality controlled data PELGAS ZooScan zooplankton dataset - 753 MB https://www.seanoe.org/data/00829/94052/data/101139.csv WWW:DOWNLOAD-1.0-link--download dataset descriptor zooscan - 5 KB https://www.seanoe.org/data/00829/94052/data/101140.csv WWW:DOWNLOAD-1.0-link--download Quality controlled data taxonomy descriptor zooscan - 2 KB https://www.seanoe.org/data/00829/94052/data/101141.zip WWW:DOWNLOAD-1.0-link--download Raw data individual images - 6 GB https://doi.org/10.17882/94052 WWW:LINK-1.0-http--metadata-URL DOI of the product https://www.seanoe.org/data/00829/94052/ rel-canonical Seanoe WP2 200 µm zooplankton net, ZooScan, Ecotaxa