Improving the visibility of ocean data from new technologies: A case study of high frequency flow cytometry Internal


Activity Overview

Type: Foresight Workshop
Start Date: March 22, 2018
End Date: March 23, 2018
Venue: University Aix-Marseille (AMU), France
Contact: Véronique Créach
E-mail: euromarine.marseille2018 [at]
Funding Call: EuroMarine 2017 call for FWS and WG proposals
Total Budget: €7,500
Funds Granted: €7,500

Manager(s): Véronique Créach

During the last 10 years, scientists have developed collaboration around the North Sea, Channel, Baltic and Mediterranean Sea, sharing experience and knowledge on online flow cytometry measurement. The recently funded EU network of coastal observations called JERICO-NEXT aims to integrate biogeochemical and biological observations for ecological assessment. In the case of flow cytometry, the quantity of data produced as well as their different format compared to the traditional approach, makes the integration even more difficult.

If you are interested in attending, please contact: euromarine [dot] marseille2018atcefas [dot] co [dot] uk 


During the Foresight workshop, the terms of reference, metadata, and quality control processes needed to create the framework of a new database for storing flow cytometry data will be discussed. This will be done with the collaboration of other scientists involved in SeaDataCloud which is a standardized infrastructure for managing large and diverse data sets collected by the oceanographic fleets and the automatic observation systems. Following a two-day workshop organised by JERICO-NEXT entitled ” Algal bloom dynamics and phytoplankton automated observations”, the foresight workshop will be able not only to connect experts
in phytoplankton ecology and data managers but also potential users such as monitoring agencies, and remote sensing scientist and modellers. Open to JERICO-NEXT and SeaDataCloud partners as well as other flow cytometer users and students, it will consist of a series of presentations, discussions with other scientific communities and demonstrations of the current data collection, analysis process.

Expected outcomes

The synthesis of the workshop will be summarised in a position paper which will be used as a road map for future harmonised methods for data classification and analysis on flow cytometry, as well as integration with existing ocean data portals.




The foresight workshop attracted 43 participants from 12 different countries and 21 research organisations, each of whom was interested in addressing the challenges surrounding data processing, quality control and standardisation which are often hidden within the development and application of new technologies. The workshop aimed to update the scientists in phytoplankton ecology around the North Sea, Channel, Baltic and Mediterranean Sea, in terms of data handling and processing by demonstrating the different computer tools available. It informed them of a new vocabulary developed during the H2020 project SeaDataCloud defining the phytoplankton functional types and stored in BODC. It showed the capability of European Infrastructures such as SeaDataNet and EMODnet biology to integrate the new data (initiative from the H2020 project JERICO-NEXT). The event was also an opportunity to inform other scientific communities related to monitoring, modelling and remote sensing about the progress in situ biological observations, and their availability in the near future.


By the end of the three day workshop, the participants had agreed to continue to develop computer tools to rapidly process the data and to establish a network of experts to:

  • Validate the outputs of automatic processes
  • Establish quality controlled standardisation processes and metadata
  • Determine  a data format which could be used by stakeholders and stored in data infrastructure platforms (institution, national and European) 

The attendees agreed to meet regularly (every two years) to keep each other up to date on the evolution of technology and change in user needs.

They also applied for ETN funding (2019-2020) and agreed to continue to pursue relevant H2020 and COST programmes. 

A paper "Establishing a new vocabulary and database for high frequency flow cytometry" was outlined and will be worked on as a prelude to the development of a road map for future harmonised methods for data classification and analysis on flow cytometry, as well as integration with existing ocean data portals.