Flow cytometry dataset from the BioSWOT-Med cruise

The BioSWOT-Med campaign (Doglioli et al., 2023; https://doi.org/10.17600/18002392) was conducted aboard R/V L’Atalante from April 20 to May 15, 2023 in the Northwestern Mediterranean Sea, in the region of the North Balearic Front (NBF) to study interactions between fine-scale oceanic circulation and biogeochemical processes. 
We sampled a fine-scale front within the NBF, referred to as ‘F’, and its two adjacent water masses, ‘A’ and ‘B’, using both transect and Lagrangian stations. The transect crossed the front over two days, while the Lagrangian stations consisted of 24-hour sampling periods following the displacement of a water parcel (Doglioli et al., 2025; https://doi.org/10.13155/105690).
An automated CytoSense flow cytometer (CytoBuoy b.v.) was connected to the seawater circuit of the TSG to perform scheduled automated sampling and analysis of pico- and nanophytoplankton at high frequency during the cross-front transect and stations, providing us with real-time, detailed information on the phytoplankton community structure. The data were acquired by using the USB software (Cytobuoy b.v.) and were analyzed with the CytoClus 4 software (Cytobuoy b.v.). During the stations, vertical profiles were also collected using Niskin bottles to characterize phytoplankton communities throughout the water column. From these vertical samples, pico- and nanophytoplankton were analyzed using a CytoFLEX instrument (Beckman Coulter), while microphytoplankton were examined with a TE-2000 Nikon inverted light microscope. Pico- and nanophytoplankton abundances were converted to biomass following the method of Oms et al. (https://doi.org/10.21203/rs.3.rs-6412120/v1), and microphytoplankton abundances were converted to biomass following Leblanc et al., 2012 (https://doi.org/10.5194/essd-4-149-2012). The supporting datasets were used to characterize the frontal region and included drifter trajectories deployed during the cruise, thermosalinograph measurements, SWOT altimetry, and ocean-color chlorophyll.
outputs_cytosense_data: Output files from the automated flow cytometer (CytoClus instrument) clustering procedure. The *Listmode.csv files contain per-cell measurements for each sample (e.g., forward scatter, FWS), whereas the set_statistics* files provide daily summary statistics. The beads_bioswot.csv file contains bead size information used to calibrate the Cytosense and convert FWS measurements into biovolume estimates.
ab2biom_cytosense_data: Forward scatter (FWS, [a.u]), equivalent spherical diameter (ESD, [µm]), biovolume [µm⁻³], carbon contenet (Qc, [fgC/cell]), abundance [cell/mL], and biomass [mmolC m⁻³] derived from outputs_cytosense_data for each of the seven phytoplankton groups identified during the cruise. These dataset spans from 29 April to 13 May and includes all transects and Lagrangian stations. "cyto_stations_AFB.csv" and "cyto_transect_AFB.csv" files contain biomass of, respectively, the cross-front transect dataset collected from 29 April to 30 April and the dataset from the three Lagrangian stations (A2, F2, and B2) collected from 5 May to 7 May. Each record is associated with time, longitude, latitude, conservative temperature [°C], absolute salinity [g kg⁻¹], and photosynthetically available radiation (PAR; [µmol photons m⁻² s⁻¹]).
cytoflex_microscopy_data: Vertical profiles of pico- and nanophytoplankton biomass [mmolC m⁻³] determined by classical flow cytometry (Cytoflex instrument), and microphytoplankton biomass determined by optical microscopy, collected during the three Lagrangian stations (A2, F2, and B2). Each measurement is associated with time and depth.
tsg_data: Temperature (T), conservative temperature (theta) [°C], salinity (S), absolute salinity (SA) [G/KG], and density anomaly (Anrho) [kg m⁻³] measured by the thermosalinograph from 21 April to 14 May (entire duration of the cruise). Each record is associated with time, longitude, and latitude.
stats_data: Output files from ANOSIM and SIMPER analyses performed with the PRIMER software, testing the differentiation among the three Lagrangian stations (A2, F2, and B2).
satellite_data: "dt_europe_allsat_phy_l4_2023*" The European Seas DUACS Level-4 gridded product is used as a reference for conventional multi-mission altimetry-derived ADT over the western Mediterranean Sea (https://doi.org/10.48670/moi-00141). For this work, the 2023 version of the DUACS product is used (i.e. not including SWOT nadir) to evidence the contribution of the SWOT mission over traditional (pre-SWOT) multi-mission altimetry products. "SWOT_L3_LR_SSH_Expert_*" The 2-km ADT derived from SWOT observations allows for the precise identification of the NBF location. Version v1.0.2 of SWOT Level-3 product is used in this study. The SWOT_L3_LR_SSH product, derived from the L2 SWOT KaRIn low rate ocean data products (NASA/JPL and CNES), is produced and made freely available by AVISO and DUACS teams as part of the DESMOS Science Team project". AVISO/DUACS, 2024. SWOT Level-3 KaRIn Low Rate ADT Expert (v1.0.2) [Data set]. CNES. https://doi.org/10.24400/527896/A01-2023.018). To extend high-resolution SWOT observations beyond SWOT swaths, we used a joint-reconstruction of gridded ADT over the western Mediterranean Sea using all available altimetry missions including SWOT data (hereafter referred to as the VarDyn product62). "2023-04-29_4DVARQG_FTLE.nc" and "2023-04-29_4DVARQG_LLADV.nc" VarDyn was chosen as the best representation of fine-scale circulation in the studied area and was used to compute Lyapunov exponents, a Lagrangian diagnostic detecting frontal areas11. The Lagrangian Manifolds and Trajectories Analyzer (LAMTA) computed thousands of numerical particle trajectories advected backward-in-time for 15 days to derive Finite Time Lyapunov Exponents (FTLEs) and advected longitude both with DUACS and VarDyn velocity fields61. "chl_*" Ocean color data from Sentinel-3 product distributed by EUMETSAT (OLCI Level 2 CHL Concentration - Sentinel-3A: https://navigator.eumetsat.int/product/EO:EUM:DAT:0178) is also used to identify the front on May 5.
nutrient_data: Vertical profiles of nitrate "N_discrete_profiles.csv" and phosphate "P_uniq_discrete_profiles.csv" measured during the three Lagrangian stations (A2, F2, and B2). "depth_N_P_discrete_profiles.csv" provides the corresponding depth values. dataset: https://doi.org/10.17882/109892
drifters_data: drifters_data: Trajectories of the drifters "Codes" and "Carthe" ("BIOSWOT*"), and derived strain and vorticity ("w_analysis*") following Molinari et al., 1975 (https://doi.org/10.1175/1520-0485(1975)005%3C0483:CODKPF%3E2.0.CO;2). dataset: https://doi.org/10.17882/100828