The data-set is composed of three tables, Environmental variables, Phytoplankton ( in log+1 abundance)  and the coordinates of the station used in the study. They are the processed data.

The dataset dcm_dtb.txt contains bio-optical measurements and environmental parameters associated with  Deep Chlorophyll Maxima (DCM) acquired by BGC-Argo profiling floats. For each BGC-Argo profile the data files includes the World Meteorological Organization (WMO) and profile numbers, the Data Assembly Center (DAC), the geographical position (LON and LAT), the date of the profile in Julian Day (JULD) and in YYYY-MM-DD format; the region of the profile (REGION, acronyms detailed in the region.txt file), the DCM zonal attribution (ZONE, acronyms detailed in the zone.txt file), the vertical resolution of measurements of the concentration of the chlorophyll a [Chla] and of the backscattering coefficient (bbp) within the 250 first meters, the Mixed Layer Depth (MLD, m), the qualification of the vertical profile (DCM_TYPE) as Deep Biomass Maximum (3), Deep photoAcclimation Maximum (2), or presenting no DCM (1); the depth of the DCM (DCM_DEPTH); the chlorophyll a concentration (CHLA_DCM, mg chla m-3 ) the backscattering coefficient (BBP_DCM, m-1), and the Brunt-Vaisala frequency (N2_DCM) at the DCM depth; the nitracline depth (NCLINE_DEPTH, m) and steepness (NCLINE_STEEP, µmol NO3 m-3 m-1), the mean nitrate concentration within the Mixed Layer (NO3_MEAN_MLD, µmol NO3 m-3), the mean daily Photosynthetically Available Radiation in the Mixed Layer (MEAN_IPAR_MLD, E m -1 d -1), the daily Photosynthetically Available Radiation at the nitracline depth (IPAR_NCLINE, E m-2 d-1);  and the [Chla] measured by satellite (CHLA_SAT, mg chla m-3). The dataset shape_NASTG_ASEW.txt contains the seasonal median, the first and third quartiles of the [Chla] and of the bbp profiles for the North Atlantic Subtropical Gyre and Atlantic SubEquatorial Waters regions. The dataset climato_NASTG_ASEW.txt contains the monthly mean and standard deviations of the DCM depth (DCM_depth), the isolume depth of daily Photosynthetically Available Radiation of 20 E m-2 d-1 (iPAR_20), the nitracline depth, and the Mixed Layer Depth (MLD) for the profiles within the North Atlantic Subtropical Gyre and Atlantic SubEquatorial Waters regions.  The qualification and processing of the BGC-Argo profiles, as well as the DCM detection (DCM_TYPE) and the estimation of the environmental parameters, were applied as described from Cornec, M., Claustre, H., Mignot, A., Guidi, L., Lacour, L., Poteau, A., D’Ortenzio, F.,Gentili, B., Schmechtig, C., (to be updated.) Deep Chlorophyll Maxima in the global ocean: occurrences, drivers and characteristics. Global Biogeochemical Cycles, to be updated The [Chla] satellite variable was obtained by the match of each BGC-Argo profile with a L3S [Chla] product from the Ocean Colour-Climate Change Initiative v4.0 database merging observations from MERIS, MODIS, VIIRS and SeaWiFs, at a monthly and 4x4-km-pixel resolution, up to December 31, 2019 (ftp://oc-cci-data:ELaiWai8ae@oceancolour.org/occci-v4.2/).

'''Short description:''' Le modèle biogéochimique ECO-MARS3D sur la façade Manche Atlantique (PREVIMER_B1-ECOMARS3D-MANGA4000) est un modèle 3D de résolution spatiale 4km qui fournit les concentrations de nutriments et de plancton toutes les heures sur 30 niveaux (fenêtre de prévision à 4 jours). '''Paramètres calculés :''' Les paramètres calculés sont les suivants : * SAL : sea_water_salinity * TEMP : sea_water_temperature * suspended_inorganic_particulate_matter : mass_concentration_of_suspended_matter_in_sea_water * nanopicoplankton_nitrogen : mole_concentration_of_nanoplankton_expressed_as_nitrogen_in_sea_water * diatom_nitrogen : mole_concentration_of_diatoms_expressed_as_nitrogen_in_sea_water * dinoflagellate_nitrogen : mole_concentration_of_dinoflagellates_expressed_as_nitrogen_in_sea_water * microzooplankton_nitrogen : mole_concentration_of_microzooplankton_expressed_as_nitrogen_in_sea_water * mesozooplankton_nitrogen : mole_concentration_of_mesozooplankton_expressed_as_nitrogen_in_sea_water * colonial_phaeocystis_nitrogen : mole_concentration_of_colonial_phaeocystis_expressed_as_nitrogen_in_sea_water * phaeocystis_mucus : concentration_of_phaeocystis_mucus_expressed_as_mass_in_sea_water * ammonium : mole_concentration_of_ammonium_in_sea_water * nitrate : mole_concentration_of_nitrate_in_sea_water * dissolved_silicate : mole_concentration_of_silicate_in_sea_water * dissolved_phosphate : mole_concentration_of_phosphate_in_sea_water * dissolved_oxygen : dissolved_oxygen_in_water_column * cumulative_nanoflagellate_carbon_production : cumulative_nanoflagellate_production_expressed_as_carbon_in_sea_water * cumulative_diatom_carbon_production : cumulative_diatom_production_expressed_as_carbon_in_sea_water * cumulative_dinoflagellate_carbon_production : cumulative_dinoflagellate_production_expressed_as_carbon_in_sea_water * cumulative_phaeocystis_carbon_production : cumulative_phaeocystis_production_expressed_as_carbon_in_sea_water * organic_nitrogen_benth : mole_concentration_of_organic_detritus_expressed_as_nitrogen_in_benthos Les paramètres diagnostiques calculés sont les suivants : * XE : sea_surface_height_above_geoid * maximum_de_diat : maximum_diatom_mass_concentration_in_sea_water * maximum_de_dino : maximum_dinoflagellate_mass_concentration_in_sea_water * maximum_de_nano : maximum_nanoflagellate_mass_concentration_in_sea_water * grad_vert_salinite : maximum_vertical_gradient_of_sea_water_salinity * grad_vert_temp : maximum_vertical_gradient_of_sea_water_temperature * extinction_lumineuse : light_extinction_in_sea_water * prod_diat : cumulated_production_of_diatoms_in_sea_water_column_expressed_in_carbon * prod_dino : cumulated_production_of_dinoflagellates_in_sea_water_column_expressed_in_carbon * prod_nano : cumulated_production_of_nanoflagellates_in_sea_water_column_expressed_in_carbon * chlorophylle_a : chlorophyll_mass_concentration_in_sea_water * prod_cumul_chloro : cumulated_total_production_in_sea_water_column_expressed_in_carbon * maximum_de_phaeocystis : maximum_phaeocystis_mass_concentration_in_sea_water * prod_phaeocystis : cumulated_production_of_phaeocystis_in_sea_water_column_expressed_in_carbon * oxygen_saturation : oxygen_saturation * ammoniumGIRON_tracer_sign: mole_concentration_of_ammonium_in_sea_waterGIRON_tracer_sign * ammoniumGIRON_tracer_age: mole_concentration_of_ammonium_in_sea_waterGIRON_tracer_age * nitrateGIRON_tracer_sign: mole_concentration_of_nitrate_in_sea_waterGIRON_tracer_sign * nitrateGIRON_tracer_age: mole_concentration_of_nitrate_in_sea_waterGIRON_tracer_age * nanopicoplankton_nitrogenGIRON_tracer_sign: mole_concentration_of_nanoplankton_expressed_as_nitrogen_in_sea_waterGIRON_tracer_sign * nanopicoplankton_nitrogenGIRON_tracer_age: mole_concentration_of_nanoplankton_expressed_as_nitrogen_in_sea_waterGIRON_tracer_age * diatom_nitrogenGIRON_tracer_sign: mole_concentration_of_diatoms_expressed_as_nitrogen_in_sea_waterGIRON_tracer_sign * diatom_nitrogenGIRON_tracer_age: mole_concentration_of_diatoms_expressed_as_nitrogen_in_sea_waterGIRON_tracer_age * dinoflagellate_nitrogenGIRON_tracer_sign: mole_concentration_of_dinoflagellates_expressed_as_nitrogen_in_sea_waterGIRON_tracer_sign * dinoflagellate_nitrogenGIRON_tracer_age: mole_concentration_of_dinoflagellates_expressed_as_nitrogen_in_sea_waterGIRON_tracer_age * microzooplankton_nitrogenGIRON_tracer_sign: mole_concentration_of_microzooplankton_expressed_as_nitrogen_in_sea_waterGIRON_tracer_sign * microzooplankton_nitrogenGIRON_tracer_age: mole_concentration_of_microzooplankton_expressed_as_nitrogen_in_sea_waterGIRON_tracer_age * mesozooplankton_nitrogenGIRON_tracer_sign: mole_concentration_of_mesozooplankton_expressed_as_nitrogen_in_sea_waterGIRON_tracer_sign * mesozooplankton_nitrogenGIRON_tracer_age: mole_concentration_of_mesozooplankton_expressed_as_nitrogen_in_sea_waterGIRON_tracer_age * detrital_nitrogenGIRON_tracer_sign: mole_concentration_of_organic_detritus_expressed_as_nitrogen_in_sea_waterGIRON_tracer_sign * detrital_nitrogenGIRON_tracer_age: mole_concentration_of_organic_detritus_expressed_as_nitrogen_in_sea_waterGIRON_tracer_age * colonial_phaeocystis_nitrogenGIRON_tracer_sign: mole_concentration_of_colonial_phaeocystis_expressed_as_nitrogen_in_sea_waterGIRON_tracer_sign * colonial_phaeocystis_nitrogenGIRON_tracer_age: mole_concentration_of_colonial_phaeocystis_expressed_as_nitrogen_in_sea_waterGIRON_tracer_age * phaeocystis_cells_nitrogenGIRON_tracer_sign: mole_concentration_of_phaeocystis_cells_expressed_as_nitrogen_in_sea_waterGIRON_tracer_sign * phaeocystis_cells_nitrogenGIRON_tracer_age: mole_concentration_of_phaeocystis_cells_expressed_as_nitrogen_in_sea_waterGIRON_tracer_age * organic_nitrogen_benthGIRON_tracer_sign: mole_concentration_of_organic_detritus_expressed_as_nitrogen_in_benthosGIRON_tracer_sign * organic_nitrogen_benthGIRON_tracer_age: mole_concentration_of_organic_detritus_expressed_as_nitrogen_in_benthosGIRON_tracer_age * phytoplankton_sign_N_GIRON: nitrogen_fraction_in_phytoplankton_from_source_GIRON * phytoplankton_age_N_GIRON: age_of_nitrogen_fraction_in_phytoplankton_from_source_GIRON * ammoniumLOIRE_tracer_sign: mole_concentration_of_ammonium_in_sea_waterLOIRE_tracer_sign * ammoniumLOIRE_tracer_age: mole_concentration_of_ammonium_in_sea_waterLOIRE_tracer_age * nitrateLOIRE_tracer_sign: mole_concentration_of_nitrate_in_sea_waterLOIRE_tracer_sign * nitrateLOIRE_tracer_age: mole_concentration_of_nitrate_in_sea_waterLOIRE_tracer_age * nanopicoplankton_nitrogenLOIRE_tracer_sign: mole_concentration_of_nanoplankton_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_sign * nanopicoplankton_nitrogenLOIRE_tracer_age: mole_concentration_of_nanoplankton_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_age * diatom_nitrogenLOIRE_tracer_sign: mole_concentration_of_diatoms_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_sign * diatom_nitrogenLOIRE_tracer_age: mole_concentration_of_diatoms_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_age * dinoflagellate_nitrogenLOIRE_tracer_sign: mole_concentration_of_dinoflagellates_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_sign * dinoflagellate_nitrogenLOIRE_tracer_age: mole_concentration_of_dinoflagellates_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_age * microzooplankton_nitrogenLOIRE_tracer_sign: mole_concentration_of_microzooplankton_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_sign * microzooplankton_nitrogenLOIRE_tracer_age: mole_concentration_of_microzooplankton_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_age * mesozooplankton_nitrogenLOIRE_tracer_sign: mole_concentration_of_mesozooplankton_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_sign * mesozooplankton_nitrogenLOIRE_tracer_age: mole_concentration_of_mesozooplankton_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_age * detrital_nitrogenLOIRE_tracer_sign: mole_concentration_of_organic_detritus_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_sign * detrital_nitrogenLOIRE_tracer_age: mole_concentration_of_organic_detritus_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_age * colonial_phaeocystis_nitrogenLOIRE_tracer_sign: mole_concentration_of_colonial_phaeocystis_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_sign * colonial_phaeocystis_nitrogenLOIRE_tracer_age: mole_concentration_of_colonial_phaeocystis_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_age * phaeocystis_cells_nitrogenLOIRE_tracer_sign: mole_concentration_of_phaeocystis_cells_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_sign * phaeocystis_cells_nitrogenLOIRE_tracer_age: mole_concentration_of_phaeocystis_cells_expressed_as_nitrogen_in_sea_waterLOIRE_tracer_age * organic_nitrogen_benthLOIRE_tracer_sign: mole_concentration_of_organic_detritus_expressed_as_nitrogen_in_benthosLOIRE_tracer_sign * organic_nitrogen_benthLOIRE_tracer_age: mole_concentration_of_organic_detritus_expressed_as_nitrogen_in_benthosLOIRE_tracer_age * phytoplankton_sign_N_LOIRE: nitrogen_fraction_in_phytoplankton_from_source_LOIRE * phytoplankton_age_N_LOIRE: age_of_nitrogen_fraction_in_phytoplankton_from_source_LOIRE * ammoniumSEINE_tracer_sign: mole_concentration_of_ammonium_in_sea_waterSEINE_tracer_sign * ammoniumSEINE_tracer_age: mole_concentration_of_ammonium_in_sea_waterSEINE_tracer_age * nitrateSEINE_tracer_sign: mole_concentration_of_nitrate_in_sea_waterSEINE_tracer_sign * nitrateSEINE_tracer_age: mole_concentration_of_nitrate_in_sea_waterSEINE_tracer_age * nanopicoplankton_nitrogenSEINE_tracer_sign: mole_concentration_of_nanoplankton_expressed_as_nitrogen_in_sea_waterSEINE_tracer_sign * nanopicoplankton_nitrogenSEINE_tracer_age: mole_concentration_of_nanoplankton_expressed_as_nitrogen_in_sea_waterSEINE_tracer_age * diatom_nitrogenSEINE_tracer_sign: mole_concentration_of_diatoms_expressed_as_nitrogen_in_sea_waterSEINE_tracer_sign * diatom_nitrogenSEINE_tracer_age: mole_concentration_of_diatoms_expressed_as_nitrogen_in_sea_waterSEINE_tracer_age * dinoflagellate_nitrogenSEINE_tracer_sign: mole_concentration_of_dinoflagellates_expressed_as_nitrogen_in_sea_waterSEINE_tracer_sign * dinoflagellate_nitrogenSEINE_tracer_age: mole_concentration_of_dinoflagellates_expressed_as_nitrogen_in_sea_waterSEINE_tracer_age * microzooplankton_nitrogenSEINE_tracer_sign: mole_concentration_of_microzooplankton_expressed_as_nitrogen_in_sea_waterSEINE_tracer_sign * microzooplankton_nitrogenSEINE_tracer_age: mole_concentration_of_microzooplankton_expressed_as_nitrogen_in_sea_waterSEINE_tracer_age * mesozooplankton_nitrogenSEINE_tracer_sign: mole_concentration_of_mesozooplankton_expressed_as_nitrogen_in_sea_waterSEINE_tracer_sign * mesozooplankton_nitrogenSEINE_tracer_age: mole_concentration_of_mesozooplankton_expressed_as_nitrogen_in_sea_waterSEINE_tracer_age * detrital_nitrogenSEINE_tracer_sign: mole_concentration_of_organic_detritus_expressed_as_nitrogen_in_sea_waterSEINE_tracer_sign * detrital_nitrogenSEINE_tracer_age: mole_concentration_of_organic_detritus_expressed_as_nitrogen_in_sea_waterSEINE_tracer_age * colonial_phaeocystis_nitrogenSEINE_tracer_sign: mole_concentration_of_colonial_phaeocystis_expressed_as_nitrogen_in_sea_waterSEINE_tracer_sign * colonial_phaeocystis_nitrogenSEINE_tracer_age: mole_concentration_of_colonial_phaeocystis_expressed_as_nitrogen_in_sea_waterSEINE_tracer_age * phaeocystis_cells_nitrogenSEINE_tracer_sign: mole_concentration_of_phaeocystis_cells_expressed_as_nitrogen_in_sea_waterSEINE_tracer_sign * phaeocystis_cells_nitrogenSEINE_tracer_age: mole_concentration_of_phaeocystis_cells_expressed_as_nitrogen_in_sea_waterSEINE_tracer_age * organic_nitrogen_benthSEINE_tracer_sign: mole_concentration_of_organic_detritus_expressed_as_nitrogen_in_benthosSEINE_tracer_sign * organic_nitrogen_benthSEINE_tracer_age: mole_concentration_of_organic_detritus_expressed_as_nitrogen_in_benthosSEINE_tracer_age * phytoplankton_sign_N_SEINE: nitrogen_fraction_in_phytoplankton_from_source_SEINE * phytoplankton_age_N_SEINE: age_of_nitrogen_fraction_in_phytoplankton_from_source_SEINE

This benchmark dataset contains the physical data used as predictors to reconstruct global chlorophyll-a concentrations (Chl, a proxy of phytoplankton biomass) in Roussillon et al., as well as the reference satellite Chl target fields. The nine physical predictors' data (Short-Wave radiations, Sea Surface Temperature, Sea Level Anomaly, Zonal and meridional surface currents, Zonal and meridional surface wind stress, Bathymetry, Binary continental mask) were extracted from publicly available datasets over [1998-2015] and resampled to the same spatio-temporel resolution as Chl, i.e. monthly on a 1°x1° grid between 50°N and 50°S. Missing values were gap-filled using the heat diffusion equation. Each variable was normalized by substracting its mean from the original values and dividing by its standard deviation over [1998-2015]. This dataset was used to train and validate the Multi-Mode Convolutional Neural network (CNNMM8) introduced in Roussillon et al. ; reconstructed monthly Chl fields over the [2012-2015] test period are also provided here. We hope this benchmark dataset can help to promote the improvements of methods as well as the emergence of new ideas, as building datasets is sometimes more time-consuming than the implementation of machine learning tools themselves. This would also facilitate the quantitative comparison of models performances' on the exact same datasets.

Plankton was sampled with various nets, from bottom or 500m depth to the surface, in many oceans of the world. Samples were imaged with a ZooScan. The full images were processed with ZooProcess which generated regions of interest (ROIs) around each individual object and a set of associated features measured on the object (see Gorsky et al 2010 for more information). The same objects were re-processed to compute features with the scikit-image toolbox http://scikit-image.org. The 1,451,745 resulting objects were sorted by a limited number of operators, following a common taxonomic guide, into 98 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 folder ZooScanNet_data.tar 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 metadata of each object including the different features processed by ZooProcess. 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: - objid: unique object identifier in EcoTaxa (integer number) And 48 features: - area - mean - stddev - mode - min/max - perim. - width,height  - major,minor - circ. - feret - intden - median - skew,kurt - %area - area_exc - fractal - skelarea - slope - histcum1,2,3 - nb1,2,3 - symetrieh,symetriev - symetriehc,symetrievc - convperim,convarea - fcons - thickr:  - esd - elongation - range - centroids - sr - perimareaexc - feretareaexc - perimferet/perimmajor - circex - cdexc See the “ZooScan” sheet - OBJECT metadata, annotation and measurements - , at https://doi.org/10.5281/zenodo.14704250 for definitions. features_skimage.csv.gz Table of morphological features recomputed with skimage.measure.regionprops on the ROIs produced by ZooProcess. 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 class          2. Second folder ZooScanNet_imgs.tar contains : imgs Directory containing images of each object, named according to the object id objid and sorted in subdirectories according to their taxon.         3. And : map.png Map of the sampling locations, to give an idea of the diversity sampled in this dataset.  

Coastal Surveillance Through Observation of Ocean Color (COASTlOOC) oceanographic expeditions were conducted in 1997 and 1998 to examine the relationship between the optical properties of seawater and related biological and chemical properties across the coastal-to-open ocean gradient in various European seas. A total of 379 stations were visited along the coasts of the Gulf of Lion in the Mediterranean Sea (n = 61), Adriatic Sea (n = 39), Baltic Sea (n = 57), North Sea (n = 99), English Channel (n = 85) and Atlantic Ocean (n = 38). Particular emphasis was dedicated to the collection of a comprehensive set of apparent (AOPs) and inherent (IOPs) optical properties to support the development of ocean color remote sensing algorithms. The data were collected in situ using traditional ship-based sampling, but also from a helicopter, which is a very efficient means for that type of coastal sampling. The dataset collected during the COASTlOOC campaigns is unique in that it is fully consistent in terms of operators, protocols, and instrumentation. This rich and historical dataset is still today frequently requested and used by other researchers. Therefore, we present the result of an effort to compile and standardize a dataset which will facilitate its use in future development and evaluation of new bio-optical models adapted for optically-complex waters. 

The PHYTOBS-MARCOBOLO dataset comprises long-term time series on marine microphytoplankton, from 2003 to 2021, along the entire French metropolitan coastline. Microphytoplankton data cover microscopic taxonomic identifications and counts. The PHYTOBS-MARCOBOLO dataset corresponds to a dataset extracted from the PHYTOBS network (DOI:10.17882/85178). The PHYTOBS network provides the scientific community and stakeholders with validated and qualified data on the biomass, abundance and composition of marine microphytoplankton in coastal and lagoon waters, with the aim of supporting scientific research. PHYTOBS-MARCOBOLO is a dataset used as part of the Horizon Europe MARCO-BOLO project (https://marcobolo-project.eu/), in which we are currently working to understand and analyze multi-decadal trends in coastal and marine biodiversity on a European scale. The PHYTOBS-MARCOBOLO dataset gathers data from 18 sampling sites, selected from the PHYTOBS-Network dataset according to requirements of time series quality and geographical location of sampling sites established as part of the MARCO-COLO project. This dataset was also formatted according to a template imposed for the European project.

The Sir Alister Hardy Foundation for Ocean Science (SAHFOS) is an international charity that operates the Continuous Plankton Recorder (CPR) Survey. The dataset covers the North Atlantic and the North Sea on since 1958.