Best practices document for sampling procedures of biological automatic sensors (imaging-in-flow, automated flow cytometry and multispectral fluorometry)

The definition of Best Practices for biological sensors stands as an acute need for the JERICO community, due to the multiplicity of procedures for calibration, operation, sampling and flagging. In the case of novel Biological Sensors, they help to understand plankton dynamics and distribution in coastal waters. Our task within WP5 ST7 is to work on the improvement of the readiness of ship-based and autonomous platform observing networks, guaranteeing their robustness, reliability, and long-term sustainability by working on common operational procedures that we could define together and rely on. This document describes the results of the three polls launched on the JERICO-S3 partners and out of the consortium about three main novel (semi-)automated techniques for observing marine phytoplankton. It reports on the discussions carried out about operational practices summarised from these three polls, during three Workshops on Best Practices for Biological Observations organised by CNRS and CEFAS and held in 2021 and 2022. In addition, we present briefly and discuss the operational practices for sampling procedures related to some targeted innovative biological sensors gathered from various sources. This deliverable therefore seeks to frame these notions in the context of holistic coastal research led by JERICO, for the benefit of the wider scientific community. The first section details the challenges currently faced by marine microbiologists, and the associated issues and solutions. Three polls on three techniques for monitoring plankton were launched and advertised amongst the JERICO community and beyond. We rely on discussions carried out during the corresponding international online workshops, based on the results from dedicated polls, to define some guidelines for defining best practices for the use of three groups of techniques at high spatial and temporal resolution. An example of relevant biological sensors (including in situ imagers, single-cell characterisation devices, or bulk measurement probes) is then briefly described, with associated Best Practices for calibration, maintenance, data collection, and metadata flagging (even though this last part, as well as the description of the sensor, are already described in previous deliverables and publications).

How to cite
Artigas Luis Felipe, Hubert Zéline, Gallot Clémentine, Epinoux Alexandre, Palazot Maialen (2024). Best practices document for sampling procedures of biological automatic sensors (imaging-in-flow, automated flow cytometry and multispectral fluorometry). Ref. JERICO-S3-WP5-D5.6-26092024-V1.0. JERICO S3. https://doi.org/10.13155/103600

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