Marine high frequency in-situ flow cytometry allows the analysis of phytoplankton at the single cell level, providing huge data sets of abundances and optical properties related to pigment content and size proxy. To give the possibility to the scientists and managers to use these data for research or monitoring purposes, it is essential that best practices are established following FAIRness principles. The TT-CYTO workshop aims to enhance marine flow cytometry data accessibility and reliability, focusing on FAIR (Findable, Accessible, Interoperable, Reusable) principles. Addressing discrepancies in manual gating, it emphasizes establishing common guidelines, leveraging automated neural network processes, and promoting accessible databases. The initiative seeks to standardize practices and improve marine flow cytometry's role as a core variable in ecosystem monitoring.

Key Objectives

The primary objectives of this workshop revolve around unifying the analysis methods used in flow cytometry, ensuring consistency and reliability in delivering datasets promptly. It aims to educate participants in machine learning by creating training sets and delving into the applications of neural networks in this field. Additionally, a key focus is on enhancing databases by converting datasets into FAIR (Findable, Accessible, Interoperable, Reusable) formats, thereby improving accessibility and validation processes. Ultimately, the goal is to streamline flow cytometry practices, empower participants with advanced techniques, and optimize data accessibility for improved scientific outcomes.

Expected Outcomes

Anticipated outcomes from this initiative include an elevated proficiency in identifying Phytoplankton Functional Types (PFTs) and achieving greater uniformity in data interpretation. The workshop aims to generate training sets to facilitate automated clustering processes, enhancing the efficiency of data analysis. Additionally, a synthesis paper will encapsulate the workshop's findings, emphasizing best practices established and outlining forthcoming challenges in the field. Ultimately, the goal is to foster advanced skills in PFT identification, enable streamlined data analysis, and document key insights for future reference and development in this domain.

The expected outcomes of the foresight workshop are:

  • Develop the expertise of the users for identifying and labelling the PFTs and consequently harmonising the flow cytometry data between users.
  • Create training sets for the neural network processes according to the areas of interest.
  • Learn and test the machine learning processes.
  • Validate the workflow from the FCM to databases.
  • Consolidate a network of users to consolidate the future training sets/benchmarked models for automated analysis.
  • A synthesis paper will summarise the results of the workshop. It will highlight 1) the need for harmonising in situ flow cytometry data between users and applying Best Practices for data fairness as mandatory requirements for feeding the next generation ocean models and 2) the next challenges for considering the phytoplankton functional types (PFTs) as an Environmental Biodiversity Variable (EBV).

Expected Impact:

The TT-CYTO workshop is an opportunity to tighten the actual in situ flow cytometry community even if most of us collaborate already together in national or international initiatives such as European programmes. However, the EuroMarine workshop is the unique occasion to be together for 3 days, to share our knowledge and train early career scientists to face new challenges such as using artificial intelligence methodology for analysing data on phytoplankton diversity. The workshop aims to strengthen the community network, support early career scientists, and contribute to the development of more accurate ocean models.


Interested participants can apply by contacting Melilotus.thyssen@mio.osupytheas.fr before the specified deadline.