A Pelagic Size Structure database (PSSdb) to support biogeochemical modeling: update to first release Article Swipe
Mathilde Dugenne
,
Marco Corrales‐Ugalde
,
Todd O’Brien
,
Fabien Lombard
,
Jean‐Olivier Irisson
,
Lars Stemmann
,
Charles A. Stock
,
Rainer Kiko
,
Jessica Y. Luo
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.5281/zenodo.10150020
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.5281/zenodo.10150020
This dataset is an update to the first release of the Pelagic Size Structure database (PSSdb, https://pssdb.net) scientific project, investigating the global particle size distributions measured from multiple pelagicǂ imaging systems. These devices include the Imaging Flow Cytobot (Olson and Sosik 2007), benchtop scanners like the ZooScan (Gorsky et al. 2010), and the Underwater Vision Profiler (Picheral et al. 2010). The data sources originate from Ecotaxa (https://ecotaxa.obs-vlfr.fr/), Ecopart (https://ecopart.obs-vlfr.fr/), and Imaging FlowCytobot dashboards (https://ifcb.caloos.org/dashboard and https://ifcb-data.whoi.edu/dashboard). Links to the PSSdb code and documentation are available on the PSSdb webpage (https://pssdb.net). This updated version includes the following changes: Duplicate data entries and NaN values have been removed. Data products now include Normalized Biomass Size Spectra (NBSS), and Particle Size Distribution (PSD), two widely used methods to represent plankton and particles size distribution in marine ecology and biogeochemistry. Linear regressions are now performed with log10 transformations of the normalized biovolume/abundance and the size classes. Inclusion of UVP6 and other benchtop plankton Scanner datasets from net tows, which expand the temporal and spatial coverage of the data products. Unbiased portion of the size spectra is selected by a new thresholding method that accounts for both uncertainties on particle sizes, limited by the camera resolution, and particle count, so that only size classes with less than 20% uncertainty are retained, in addition to gaps in the size spectra. This PSSdb dataset is composed of two products, specific to each imaging device: Product 1a includes the size distribution , computed from normalized biovolume, for NBSS, and normalized abundance, for PSD, of plankton and particles within a set of pre-defined size classes (expressed in both biovolume and equivalent circular diameter), averaged by year and month, and in 1-degree longitude/latitude grid cells. Product 1b includes the results of NBSS and PSD regression fit parameters, slopes, intercept, and coefficient of determination (R2), averaged by year and month, and in 1-degree longitude/latitude grid cells. The regression parameters are defined using ordinary least squares linear regressions applied to a log10 transformed normalized biovolume/normalized abundance and biovolume/ diameter size class values. Size spectra parameters were averaged over a maximum of 16 spatial and temporal subsets (0.5°x0.5°x1 week) to avoid over-representation of repeated sampling events (e.g., time-series datasets) within a grid cell. Linear regressions were performed on the linear portion of the log10-transformed NBSS and PSD estimates, between the size classes with a size measurement or particle count uncertainty greater than 20% (Schartau et al. 2010) , and where the maximum NB/PSD is observed and the largest size class before three empty consecutive size classes. For additional information, please see the PDF documentation available below ...
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- Type
- dataset
- Language
- en
- Landing Page
- https://doi.org/10.5281/zenodo.10150020
- OA Status
- green
- Cited By
- 7
- Related Works
- 10
- OpenAlex ID
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- DOI
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https://doi.org/10.5281/zenodo.10150020Digital Object Identifier
- Title
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A Pelagic Size Structure database (PSSdb) to support biogeochemical modeling: update to first releaseWork title
- Type
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datasetOpenAlex work type
- Language
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enPrimary language
- Publication year
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2023Year of publication
- Publication date
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2023-11-17Full publication date if available
- Authors
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Mathilde Dugenne, Marco Corrales‐Ugalde, Todd O’Brien, Fabien Lombard, Jean‐Olivier Irisson, Lars Stemmann, Charles A. Stock, Rainer Kiko, Jessica Y. LuoList of authors in order
- Landing page
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https://doi.org/10.5281/zenodo.10150020Publisher landing page
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YesWhether a free full text is available
- OA status
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greenOpen access status per OpenAlex
- OA URL
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https://doi.org/10.5281/zenodo.10150020Direct OA link when available
- Concepts
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Biogeochemical cycle, Pelagic zone, Database, Oceanography, Computer science, Environmental science, Geology, Chemistry, Environmental chemistryTop concepts (fields/topics) attached by OpenAlex
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7Total citation count in OpenAlex
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2024: 6, 2023: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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