the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Metazoan zooplankton in the Bay of Biscay: 16 years of individual sizes and abundances from the ZooScan and ZooCAM imaging systems
Paul Bourriau
Edwin Daché
Marie-Madeleine Danielou
Mathieu Doray
Christine Dupuy
Bertrand Forest
Laetitia Jalabert
Martin Huret
Sophie Le Mestre
Antoine Nowaczyk
Pierre Petitgas
Philippe Pineau
Justin Rouxel
Morgan Tardivel
Jean-Baptiste Romagnan
Abstract. This paper presents two metazoan zooplankton datasets obtained by imaging samples collected on the Bay of Biscay continental shelf in spring during the PELGAS integrated surveys, over the 2004–2019 period. The samples were collected at night, with a WP2 200 µm mesh size fitted with a Hydrobios (back-run stop) mechanical flowmeter, hauled vertically from the sea floor to the surface with a maximum depth set at 100 m when the bathymetry is deeper. The first dataset originates from samples collected from 2004 to 2016, imaged on land with the ZooScan and is composed of 1,153,507 imaged and measured objects. The second dataset originates from samples collected from 2016 to 2019, imaged on board the R/V Thalassa with the ZooCAM and is composed of 702,111 imaged and measured objects. The imaged objects is composed of zooplankton individuals, zooplankton pieces, non-living particles and imaging artefacts, ranging from 300 µm to 3.39 mm Equivalent Spherical Diameter, individually imaged, measured and identified. Each imaged object is geolocated, associated to a station, a survey, a year and other metadata. Each object is described by a set of morphological and grey level based features (8 bits encoding, 0 = black, 255 = white), including size, automatically extracted on each individual image. Each object was taxonomically identified using the web based application Ecotaxa with built-in, random forest and CNN based, semi-automatic sorting tools followed by expert validation or correction. The objects were sorted in 172 taxonomic and morphological groups. Each dataset features a table combining metadata and data, at the individual object granularity, from which one can easily derive quantitative population and communities descriptors such as abundances, mean sizes, biovolumes, biomasses, and size structure. Each object’s individual image is provided along with the data. These two datasets can be used combined together for ecological studies as the two instruments are interoperable, or as training sets for ZooScan and ZooCAM users.
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Nina Grandremy et al.
Status: open (extended)
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RC1: 'Comment on essd-2023-187', Anonymous Referee #1, 06 Jul 2023
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The compilation of image datasets in the Bay of Biscay of the course of 16 year is a very useful additon to the freely available zooplankton datasets. These datasets can be widely used for ecological or modelling purposes.
General remark: I have wondered about the abbreviation of PELGAS. Maybe it would be a good idea to explain the program either in Methods or Introduction as it is a central part of the data sets.
I find the presentation of the taxa and OTUs in table 1 and 2 a bit difficult. Usually italics are reserved for genera and species names. I suggest to change that in both tables. Additionally it would be good to add the intruments in the header of table 2.
I think it would also be good to add at a more prominent place that environmental and other accompanying data are availabel for the same cruise. So far as I noticed this is only mentioned in the concluding remarks. However, for the usability of these datasets environmetnal data are essential and should be highlighted somewhere earlier in the manuscript.
I have a few orthographic remarks:
Line 40: … objects are composed of…
Line 56: Metazoan planktonic organisms….
Line 77/78: …taxonomic analysts…
Line 86: …these require…
Line 189: quality check of identifications?
Citation: https://doi.org/10.5194/essd-2023-187-RC1 -
AC1: 'Reply on RC1', Nina Grandremy, 26 Sep 2023
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We thank the Anonymous Referee #1 for posting a comment on this manuscript. Please find below a response to each remark.
RC1: "General remark: I have wondered about the abbreviation of PELGAS. Maybe it would be a good idea to explain the program either in Methods or Introduction as it is a central part of the data sets."
We thank Referee #1 for the advice.
Zooplankton samples were collected during the successive PELGAS (PELagique GAScogne) integrated surveys carried out over the Bay of Biscay (BoB) French continental shelf, every year in spring from 2004 to 2019 on board the R/V Thalassa. The aim of this survey is to assess small pelagic fish biomass and monitor the pelagic ecosystem to inform ecosystem based fisheries management. Fish data, hydrology, phyto- and zoo-plankton samples and megafauna sightings (marine mammals and seabirds) are concomitantly collected to build long-term spatially resolved time series of the BoB pelagic ecosystem. The PELGAS sampling protocols combines day-time en-route data collection (small pelagic fish and megafauna), with night-time, depth integrated hydrology and plankton sampling at fixed points. Detailed PELGAS survey protocols can be found in Doray et al., 2018c and 2021.
This paragraph will be add to the text at the beginning of the section 2.1 “Sampling”, lines 101-103.
RC1: "I find the presentation of the taxa and OTUs in table 1 and 2 a bit difficult. Usually italics are reserved for genera and species names. I suggest to change that in both tables. Additionally it would be good to add the intruments in the header of table 2."
We understand that italics are not use in a common way here. In the revised manuscript, this font will be suppressed in tables 1 and 2, and taxa and OTUs will be differentiated with different cell colours in both tables. Moreover, the instrument names will be added to the header of table 2.
RC1: I think it would also be good to add at a more prominent place that environmental and other accompanying data are availabel for the same cruise. So far as I noticed this is only mentioned in the concluding remarks. However, for the usability of these datasets environmetnal data are essential and should be highlighted somewhere earlier in the manuscript.
We thank Referee #1 for this interesting remark. Indeed, our zooplankton dataset can be combined with environmental datasets constructed for the same cruise with similar spatio-temporal resolutions which are published in the SEANOE dataportal (Doray et al., 2018a). A comment about the environmental datasets availability will be added at the beginning of the section 2.1 “Sampling” following the PELGAS survey description in the revised manuscript.
RC1: "I have a few orthographic remarks: Line 40: … objects are composed of… / Line 56: Metazoan planktonic organisms…. / Line 77/78: …taxonomic analysts… / Line 86: …these require… / Line 189: quality check of identifications?"
We thank Referee #1 for pointing out these orthographic remarks. It will be corrected in the revised version of the manuscript.
Citation: https://doi.org/10.5194/essd-2023-187-AC1
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AC1: 'Reply on RC1', Nina Grandremy, 26 Sep 2023
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CC1: 'Comment on essd-2023-187', Leo Berline, 29 Sep 2023
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This study is very useful as freely available zooplankton datasets are not very common, especially at this large scale.
I would recommend to clarify/insist on the homogeneity of the two datasets (Zooscan and ZooCAM) in the whole ms.
The title may state this: replace “from the” with “combining” ZooScan and ZooCAM imaging systems.
Some typos and lack of accuracy.
Abstract
L40 “are composed”
I am not familiar to the meaning of ‘interoperable’. Might be worth clarifying.
L76 decent spatio-temporal scale : ‘decent’ is not a scientific word.
L91 ‘open’ = freely available
L113 “...laboratory with the zooscan in 2019.” I suggest to remove ‘in 2019’ which is useless but confusing with the sampling dates.
L138 : I would add “net collection” to insist on the fact that it is the same sample that can be analysed in both ways.
L151-153: “ break free from ..” unclear sentence. I guess authors mean to control the maximum number of object.
L176 ZooCAM sofware?
L184 “that were used”
L191-192. “To be used together” I guess “combined” is the proper word
L190-200 : for 2016, how were the samples splitted between Zooscan and ZooCAM?
L201 comparable: can you better quantify (correlation?)
Fig 2, 3, 4: add reference for the gridding procedure
L252 Table 1, 2. Why not sorting according to abundance? It is more meaningful than taxonomy.
Citation: https://doi.org/10.5194/essd-2023-187-CC1
Nina Grandremy et al.
Nina Grandremy et al.
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