Plankton was sampled with a Continuous Underway Fish Egg Sampler (CUFES, 315µm mesh size) at 4 m below the surface, and a WP2 net (200µm mesh size) from 100m to the surface, or 5 m above the sea floor to the surface when the depth was < 100 m, in the Bay of Biscay. The full images were processed with the ZooCAM software and the embedded Matrox Imaging Library (Colas et a., 2018) which generated regions of interest (ROIs) around each individual object and a set of features measured on the object. The same objects were re-processed to compute features with the scikit-image library http://scikit-image.org. The 1, 286, 590 resulting objects were sorted by a limited number of operators, following a common taxonomic guide, into 93 taxa, using the web application EcoTaxa http://ecotaxa.obs-vlfr.fr. For the purpose of training machine learning classifiers, the images in each class were split into training, validation, and test sets, with proportions 70%, 15% and 15%. The archive contains : taxa.csv.gz Table of the classification of each object in the dataset, with columns : objid : unique object identifier in EcoTaxa (integer number). taxon_level1 : taxonomic name corresponding to the level 1 classification lineage_level1 : taxonomic lineage corresponding to the level 1 classification taxon_level2 : name of the taxon corresponding to the level 2 classification  plankton : if the object is a plankton or not (boolean) set : class of the image corresponding to the taxon (train : training, val : validation, or test) img_path : local path of the image corresponding to the taxon (of level 1), named according to the object id features_native.csv.gz Table of morphological features computed by ZooCAM. All features are computed on the object only, not the background. All area/length measures are in pixels. All grey levels are in encoded in 8 bits (0=black, 255=white). With columns : area : object's surface area_exc : object surface excluding white pixels area_based_diameter : object's Area Based Diameter: 2 * (object_area/pi)^(1/2) meangreyobjet : mean image grey level modegreyobjet : modal object grey level sigmagrey : object grey level standard deviation mingrey : minimum object grey level maxgrey : maximum object grey level sumgrey : object grey level integrated density: object_mean*object_area breadth : breadth of the object along the best fitting ellipsoid minor axis length : breadth of the object along the best fitting ellipsoid majorr axis elongation : elongation index: object_length/object_breadth perim : object's perimeter minferetdiam : minimum object's feret diameter maxferetdiam : maximum object's feret diameter meanferetdiam : average object's feret diameter feretelongation : elongation index: object_maxferetdiam/object_minferetdiam compactness : Isoperimetric quotient: the ration of the object's area to the area of a circle having the same perimeter intercept0, intercept45 , intercept90, intercept135 : the number of times that a transition from background to foreground occurs a the angle 0ø, 45ø, 90ø and 135ø for the entire object convexhullarea : area of the convex hull of the object convexhullfillratio : ratio object_area/convexhullarea convexperimeter : perimeter of the convex hull of the object n_number_of_runs : number of horizontal strings of consecutive foreground pixels in the object n_chained_pixels : number of chained pixels in the object n_convex_hull_points : number of summits of the object's convex hull polygon n_number_of_holes : number of holes (as closed white pixel area) in the object roughness : measure of small scale variations of amplitude in the object's grey levels rectangularity : ratio of the object's area over its best bounding rectangle's area skewness : skewness of the object's grey level distribution kurtosis : kurtosis of the object's grey level distribution fractal_box : fractal dimension of the object's perimeter hist25, hist50, hist75 : grey level value at quantile 0.25, 0.5 and 0.75 of the object's grey levels normalized cumulative histogram valhist25, valhist50, valhist75 : sum of grey levels at quantile 0.25, 0.5 and 0.75 of the object's grey levels normalized cumulative histogram nobj25, nobj50, nobj75 : number of objects after thresholding at the object_valhist25, object_valhist50 and object_valhist75 grey level symetrieh :index of horizontal symmetry symetriev : index of vertical symmetry skelarea : area of the object skeleton thick_r : maximum object's thickness/mean object's thickness cdist : distance between the mass and the grey level object's centroids features_skimage.csv.gz Table of morphological features recomputed with skimage.measure.regionprops on the ROIs produced by ZooCAM. See http://scikit-image.org/docs/dev/api/skimage.measure.html#skimage.measure.regionprops for documentation. inventory.tsv Tree view of the taxonomy and number of images in each taxon, displayed as text. With columns : lineage_level1 : taxonomic lineage corresponding to the level 1 classification taxon_level1 : name of the taxon corresponding to the level 1 classification n : number of objects in each taxon group map.png Map of the sampling locations, to give an idea of the diversity sampled in this dataset. imgs Directory containing images of each object, named according to the object id objid and sorted in subdirectories according to their taxon. Important Note: This submission has been initially submitted to SEA scieNtific Open data Edition (SEANOE) publication service and received the recorded DOI. The metadata elements have been further processed (refined) in EMODnet Ingestion Service in order to conform with the Data Submission Service specifications.

We report stable isotopes data, size measurements and environmental parameters for plankton collected between 2017 to 2019 in the Eastern English Channel and North Sea. Important Note: This submission has been initially submitted to SEA scieNtific Open data Edition (SEANOE) publication service and received the recorded DOI. The metadata elements have been further processed (refined) in EMODnet Ingestion Service in order to conform with the Data Submission Service specifications.

This dataset consists of a quantitative imaging dataset of ZooScan-imaged mesoplankton (> 200 µm), collected with high-speed net aboard the schooner Tara during the Tara Pacific Expedition (2016-2018). Samples were collected at the surface, generally on a daily frequency, across the Atlantic and Pacific Oceans from open-ocean stations (151 samples; open-ocean label: [i00_oa###]) and from stations in coastal waters of 32 Pacific islands (54 samples; island label: [i##_oa###]). The full description and discussion of this dataset can be found in the associated data paper Mériguet et al. (in rev). This dataset consists of 256 352 plankton individuals, plankton parts, non-living particles and imaging artefacts, ranging from 300 µm to a few mm, individually imaged and measured with the ZooScan (Gorsky et al., 2010). The objects were classified into 159 taxonomic and morphological groups. All images and their taxonomic annotations are available in the open-access EcoTaxa (Picheral et al., 2017) project at this link: https://ecotaxa.obs-vlfr.fr/prj/11292. The 'EcoTaxa ZooScan Tara Pacific HSN 300 microns export' dataset contains the EcoTaxa tsv exports which associate each object with these metadata (station name, sampling coordinates, sampling date and time, etc., the main metadata are found in the Classic Metadata ZooScan Tara Pacific HSN 330 microns.csv table) and describe it by numerous morphological features extracted from each individual object by ZooProcess. The csv table named 'Export EcoTaxa ZooScan read me.csv' defines the 160 metadata and data found in the EcoTaxa tsv export. The 'Descriptors ZooScan Tara Pacific HSN 330 microns.csv' table combined the data from which we calculated quantitative descriptors of the planktonic communities: abundance (ind.m-3), biovolume (mm3.m-3; as a proxy of biomass) calculated from the area, riddled area and ellipsoidal measurement of each object (see Vandromme et al., 2012 for the 3 calculations of biovolume), and Shannon diversity index. This was done for all taxonomic annotations and for several levels of grouping; living or non-living, plankton groups and trophic association. The individual biovolumes of organisms were arranged in Normalised Biomass Size Spectra (NBSS) as described by Platt (1978), with size expressed as Equivalent Spherical Diameter (ESD, µm). NBSS calculations were made for all taxonomic annotations and for the different levels of grouping. There are available for each station in the NBSS ZooScan Tara Pacific HSN 330 microns csv tables. Important Note: This submission has been initially submitted to SEA scieNtific Open data Edition (SEANOE) publication service and received the recorded DOI. The metadata elements have been further processed (refined) in EMODnet Ingestion Service in order to conform with the Data Submission Service specifications.

The Eurofleets+ IOPD research cruise took place from 28/06/2022 till 10/07/2022 in the Uummannaq region in West Greenland where a total of five fjords and the connecting shelf area were sampled. This data upload "Data from IOPD cruise Part 2 Water sample analysis and plankton identifications" contains: -Nutrient data of NH4, NO2, NO3, NOX, PO4 and DSi. -Chlorophyll a data. -Fatty acid profiles (in relative abundance) of the microzooplankton and mesozooplankton community. At certain stations the dominant species was picked out to have a separate fatty acid profile. -Phytoplankton identifications and counts by a FlowCam. - Zooplankton identifications of MultiNet samples by microscopy. A maximum of 10 specimen per species, per net, per sampling station were measured. - Zooplankton identifications of the Video Plankton Recorder data, accompanied with depth, temperature, salinity, turbidity, and fluorescence data from the CTD and FLNTU sensors mounted on the VPR. Important Note: This submission has been initially submitted to SEA scieNtific Open data Edition (SEANOE) publication service and received the recorded DOI. The metadata elements have been further processed (refined) in EMODnet Ingestion Service in order to conform with the Data Submission Service specifications.

Although zooplankton was extensively studied in the North Sea, knowledge about winter zooplankton assemblages is still scarce, despite potential influence of zooplankton overwintering stocks on seasonal plankton succession and productivity. Furthermore, several economically and ecologically important fish species reproduce during winter contributing to the zooplankton community as passive members (eggs) or predators (larvae). To shed some light on winter zooplankton distribution, abundance and composition in the Southern North Sea and Eastern English Channel, we defined assemblages based on mesozoo- and ichthyoplankton data sampled between January and February 2008 using fuzzy-clustering and indicator species. Mesozoo- and ichthyoplankton (eggs+larvae) were integrated in a common analysis by using a spatial grid adapted to the datasets and defined by means of a geostatistical method developed in agronomics. Potential environmental drivers of assemblage distribution were evaluated by means of GLMM and comparison with data from 2022 facilitated insight about the inter-annual representativeness of the assemblages. Five zooplankton assemblages were found varying with regard to total zooplankton abundance, dominant and indicator taxa. Spatial variability of abiotic (dissolved nutrients, salinity, depth, temperature, organic matter in suspension, chlorophyll a), biotic variables (phyto- and microplankton composition), water masses and fish spawning grounds were revealed as potential drivers of assemblage distribution. Assemblages off the Rhine-Scheldt estuary and in the German Bight harbored the biggest zooplankton overwintering stocks that might influence the grazing pressure on phytoplankton spring production. Assemblages off the Rhine-Scheldt estuary and covering the English Channel and the Southern Bight were found to be of high importance for herring and plaice larvae. Although further analyses suggested inter-annual representativeness of the assemblages found (2008 vs 2022), the assessment of further years would be necessary to account for potential inter-annual variability. Future studies could profit from the assessment of microzooplankton facilitating insight in fish larvae feeding potential and zooplankton overwintering strategies. Important Note: This submission has been initially submitted to SEA scieNtific Open data Edition (SEANOE) publication service and received the recorded DOI. The metadata elements have been further processed (refined) in EMODnet Ingestion Service in order to conform with the Data Submission Service specifications.

Abundance data (individuals.100 m-3) of planktonic cnidarians collected during the Camadas Finas III oceanographic cruise along the North Brazilian continental shelf between the Amazon and Oyapok river mouths and equatorial Atlantic oceanic waters between 8°N, 51°W and 3.5°S, 37°W. Data was obtained during the oceanographic cruise Camadas Finas III, aboard the research vessel NHo. Cruzeiro do Sul - H38 (DHN/Brazilian Navy), performed in 9-31 October 2012. Planktonic cnidarians were sorted from zooplankton samples collected at at 44 stations in oblique hauls, using Bongo nets with 120 and 300 µm mesh and 0.3 and 0.6 m mouth diameter, respectively. The water column was sampled from near the bottom to the surface over the continental shelf and from 200 m to the surface in the offshore. The net was towed at approximately 2 knots, at various times of day and night. Important Note: This submission has been initially submitted to SEA scieNtific Open data Edition (SEANOE) publication service and received the recorded DOI. The metadata elements have been further processed (refined) in EMODnet Ingestion Service in order to conform with the Data Submission Service specifications.

MARRE Project Zooplankton biomass Aegean sea 2020

The (JGOFS)-[http://ijgofs.whoi.edu/]), 2, focus on small scale biogeochemical processes, in particular at a daily scale, 3, study the influence of nitrogen, phosphorus and iron on oceanic fertility and 4, conduct a calibration/validation operation for the SeaWIFS (Sea-viewing Wide Field-of-View Sensor) color sensor. To reach these objectives, the studied areas, as well as the cruise plan, were designed : To investigate different trophic regimes, to investigate systems characterized by different degrees of limitation in nitrogen and phosphorus and to study stable ("steady state") systems for a sufficiently long period. The cruise track encompassed a variety of trophic systems ranging from eutrophic conditions associated to the Moroccan upwelling to the typical ultra-oligotrophic conditions of the eastern Mediterranean sea during summer stratification. Two main types of stations were occupied : 9 short (4-hour) stations. These sites were occupied around the solar noon and were essentially designed to conduct objectives 1 (JGOFS process studies) and 4 (SeaWIFS validation/calibration) 3 "long" (5-day) stations, where all four objectives were investigated with a particular emphasis on objectives 2 (processes at a daily scale) and 3 (nutrient resources and oceanic fertility). Between each station, continuous multiparametric (hydrological, optical, biological and chemical) surface acquisitions were performed. Important Note: This submission has been initially submitted to SEA scieNtific Open data Edition (SEANOE) publication service and received the recorded DOI. The metadata elements have been further processed (refined) in EMODnet Ingestion Service in order to conform with the Data Submission Service specifications.

The California Current system (CCS) comprise two large regions, one subarctic from central California to British Columbia, and other subtropical from Point Conception, California to the tip of Baja California peninsula. To progress in the knowledge of the subtropical part of the CCS, was created the IMECOCAL program, which means “Mexican Research of the California Current”. The data base presented here is a product of the zooplankton collection during ten IMECOCAL cruises. Zooplankton samples were collected with oblique net tows in the upper 200 m (or from 10 m above the sea floor in shallow stations), using a Bongo net of 500 µm mesh width and mouth diameter of 0.7 m. Four cruises correspond to the four seasons of 2005 and the rest are summer cruises preformed during 2002-2008. Hyperiid amphipods were identified using mainly the taxonomic key for Hyperiidea of the world oceans (Vinogradov et al., 1996). The total number of samples analyzed were 482 but hyperiids were absent in 18. The positive samples were 75% of the oceanic stations collected during nighttime, and the rest were from neritic stations (11% nighttime and 14% daytime). The total number of species found are 125, with strong dominance of Vibilia armata, Lestrigonus schizogeneios, Primno brevidens, and Eupronoe minuta. The abundances of these and other common species changes seasonally as described by Lavaniegos & Hereu (2009), and interannually as observed in summer of the period 2002-2008 for the northern Baja California region (Lavaniegos, 2017) and the Gulf of Ulloa and offshore region (Lavaniegos, under review). Important Note: This submission has been initially submitted to SEA scieNtific Open data Edition (SEANOE) publication service and received the recorded DOI. The metadata elements have been further processed (refined) in EMODnet Ingestion Service in order to conform with the Data Submission Service specifications.