Catalogue PIGMA
PELGAS Bay of Biscay ZooCAM zooplankton Dataset (2016-2019)
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.
Simple
- Date (Publication)
- 2023
- Date (Revision)
- 2023-10-20
- Other citation details
- 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
- 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 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.
- Theme
-
- Zooplankton
- Bay of Biscay
- ZooCAM
- imaging
- WP2 200 µm net
- Biological oceanography
- 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 >700k identifications, a few mistakes might remain.
- Date (Publication)
- 2024
- Unique resource identifier
- 10.13155/104256
- Association Type
- Cross reference
- Initiative Type
- Study
- Date (Publication)
- 2023
- Unique resource identifier
- 10.5194/essd-2023-187
- Association Type
- Cross reference
- Initiative Type
- Study
- Date (Publication)
- 2023
- Unique resource identifier
- 10.1016/j.pocean.2022.102949
- Association Type
- Cross reference
- Initiative Type
- Study
- Date (Publication)
- 2023
- Unique resource identifier
- 10.1002/lom3.10577
- Association Type
- Cross reference
- Initiative Type
- Study
- Date (Publication)
- 2018
- Unique resource identifier
- 10.1016/j.pocean.2017.10.014
- Association Type
- Cross reference
- Initiative Type
- Study
- Date (Publication)
- 2018
- Unique resource identifier
- 10.1016/j.pocean.2017.12.004
- Association Type
- Cross reference
- Initiative Type
- Study
- Date (Publication)
- 2024
- Unique resource identifier
- 10.17882/55741
- Association Type
- Cross reference
- Initiative Type
- dataset
- Date (Publication)
- 2024
- Unique resource identifier
- 10.17882/101928
- Association Type
- Cross reference
- Initiative Type
- dataset
- Date (Publication)
- 2018
- Unique resource identifier
- 10.17882/53389
- Association Type
- Cross reference
- Initiative Type
- dataset
- Unique resource identifier
- 10.17600/16002400
- Association Type
- Cross reference
- Initiative Type
- Platform
- Unique resource identifier
- 10.17600/17002000
- Association Type
- Cross reference
- Initiative Type
- Platform
- Unique resource identifier
- 10.17600/18000419
- Association Type
- Cross reference
- Initiative Type
- Platform
- Unique resource identifier
- 10.17600/18001109
- Association Type
- Cross reference
- Initiative Type
- Platform
- Metadata language
- English
- Topic category
-
- Oceans
))
- Distribution format
-
-
TEXTE
(
)
-
CSV
(
)
-
IMAGE
(
)
-
TEXTE
(
)
- OnLine resource
-
Processed data
(
WWW:DOWNLOAD-1.0-link--download
)
PELGAS ZooCAM zooplankton dataset - 377 MB
- OnLine resource
-
dataset descriptor zoocam - 11 KB
(
WWW:DOWNLOAD-1.0-link--download
)
dataset descriptor zoocam - 11 KB
- OnLine resource
-
Processed data
(
WWW:DOWNLOAD-1.0-link--download
)
taxonomy descriptor zoocam - 2 KB
- OnLine resource
-
Raw data
(
WWW:DOWNLOAD-1.0-link--download
)
individual images - 1 GB
- OnLine resource
-
Map of the sampling station location over the 2016-2019 period - 1 MB
(
WWW:DOWNLOAD-1.0-link--download
)
Map of the sampling station location over the 2016-2019 period - 1 MB
- OnLine resource
- DOI of the product ( WWW:LINK-1.0-http--metadata-URL )
- OnLine resource
- Seanoe ( rel-canonical )
- Hierarchy level
- Dataset
- Statement
- WP2 200 µm zooplankton net, ZooCAM, Ecotaxa
- File identifier
- seanoe:94040 XML
- Metadata language
- English
- Character set
- UTF8
- Hierarchy level
- Dataset
- Date stamp
- 2023-10-20
- Metadata standard name
- ISO 19115:2003/19139
- Metadata standard version
- 1.0
Overviews
Spatial extent
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