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