Mature use case

Zooscan – EcoTaxa pipeline

Taxonomic identification of zooplankton using Zooscan


To establish an operational image handling service at the iMagine platform that ingests, stores, processes images of marine water samples taken by the Zooscan instrument and uploads the resulting regions of interest to the EcoTaxa platform for later taxonomic Identification.

Development actions during iMagine


Upgrading the ZooProcess software for image analytics with the use of AI (instance segmentation)


Setting up an operational environment at iMagine platform, with ZooProcess –Ecotaxa workflow for processing ZooScan images and storing the resulting data


Connecting this iMagine-hosted environment to the EcoTaxa database, using its API, for ingesting data


Developing guidance and training material for uptake of the new ZooProcess – EcoTaxa workflow services


Reaching out to users for uptake and providing support and training

Expected Results


Plankton is an integral and vital component of pelagic food webs and provides many

ecosystem services, such as oxygen production and carbon storage. Plankton indicators are used within several descriptors of the MSFD and WFD. Datasets showing spatial and longterm trends in concentration of phyto- and zooplankton are essential to understand the dynamics of food availability for commercially exploited species and the effects of climate change. Their description at global scale yields an indication of the health of marine ecosystems and their response to anthropic stressors.


The provision of the ZooScan – EcoTaxa pipeline in iMagine will accelerate and standardise the processing of plankton samples and therefore result in contributing to more numerous and more interoperable zooplankton data to better describe and understand these systems.

Involved Partners

Sorbonne Université

with departments LOV and IMEV, including platform PIQv operating under the EMBRC RI.