Data for High throughput in situ imaging reveals complex ecological behavior of giant marine mixotrophic protists

Supporting data for the paper "High throughput in situ imaging reveals complex ecological behavior of giant marine mixotrophic protists".
Plankton data was collected with ISIIS during the VISUFRONT cruise, in July 2013. Sampling consisted of repeated transects across and along the Ligurian Front. The ISIIS is deployed in a tow-yo fashion behind the boat, oscillating between the surface and a given depth (100 m or 150 m depending on transects). Raw images were segmented with Apeep (https://github.com/jiho/apeep). During segmentation, a set of features are computed with the scikit-image toolbox (http://scikit-image.org) for each object. Detected objects were then sorted with a CNN classifier. Besides plankton, ISIIS records environmental data: temperature, salinity, oxygen, fluorescence and irradiance.


The dataset contains:
- A description of files in README.Md

- Plankton data in ecotaxa_export_all_rhizaria_cc.tsv

- Environmental data is in isiis_images_env.parquet

Supporting data for the paper "High throughput in situ imaging reveals complex ecological behavior of giant marine mixotrophic protists".
Plankton data was collected with ISIIS during the VISUFRONT cruise, in July 2013. Sampling consisted of repeated transects across and along the Ligurian Front. The ISIIS is deployed in a tow-yo fashion behind the boat, oscillating between the surface and a given depth (100 m or 150 m depending on transects). Raw images were segmented with Apeep (https://github.com/jiho/apeep). During segmentation, a set of features are computed with the scikit-image toolbox (http://scikit-image.org) for each object. Detected objects were then sorted with a CNN classifier. Besides plankton, ISIIS records environmental data: temperature, salinity, oxygen, fluorescence and irradiance.


The dataset contains:
- A description of files in README.Md

- Plankton data in ecotaxa_export_all_rhizaria_cc.tsv

- Environmental data is in isiis_images_env.parquet

Disciplines

Biological oceanography

Keywords

plankton, mixotrophic protist, preferred orientation, buoyancy control, in situ imaging

Location

43.66N, 43.29S, 7.794E, 7.315W

Devices

In Situ Ichthyoplankton Imaging System (ISIIS)

R. K. Cowen, C. M. Guigand, In situ ichthyoplankton imaging system (ISIIS): system design and preliminary results. Limnology and Oceanography: Methods 6, 126–132 (2008).

Data

FileSizeFormatProcessingAccess
Description of other files of the dataset
6 KoTEXT
Plankton data exported from EcoTaxa. Each row corresponds to one organism.
1 GoTEXTQuality controlled data
Environmental data. Each row corresponds to one ISIIS image.
76 MoparquetProcessed data
How to cite
Panaïotis Thelma, Biard Tristan, Caray--counil Louis, Faillettaz Robin, Luo Jessica Y, Guigand Cédric M, Cowen Robert K, Irisson Jean-Olivier (2023). Data for High throughput in situ imaging reveals complex ecological behavior of giant marine mixotrophic protists. SEANOE. https://doi.org/10.17882/96266

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