04/09/2026
AQUASERV's first on-site training brings marine microscopy specialists together at CCMAR
From optical theory to 3D imaging: researchers spent four days in Faro learning how to choose, and use the right microscope for different marine samples.
At the start of September, CCMAR in Faro hosted "Microscopy for Marine Biology: From Fundamentals to Applications", the first on-site training course to come out of AQUASERV's dedicated training call, and a milestone for the project's growing training programme.
The course followed a month-long online theoretical module (available here) with four days of hands-on practicals, demonstrations and discussion in Faro, from 1 to 4 September. Participants moved across six imaging platforms — Widefield, Confocal, Axiozoom/Apotome, Lightsheet (SPIM), Tomocube (Holotomography) and live sample staining — building a practical understanding of how each technique serves a different research question.
Matching the tool to the sample
Rather than looking for a single "best" microscope, the course encouraged participants to think in trade-offs: resolution against speed, deph against sensitivity, and always with the sample itself in mind.
The practical sessions also offered the opportunity to work directly with advanced imaging technologies available through research infrastructures. One example was the use of light-sheet microscopy to capture fast biological dynamics in vivo. During the course, participants imaged the movement of erythrocytes through the caudal blood vessels of a live zebrafish at 100 frames per second, demonstrating how advanced microscopy can reveal biological processes in real time.
With the confocal microscope, participants explored the natural fluorescence of different macroalgae in 3D, revealing how fluorescent pigments are distributed within green, brown and red algae. In Asparagopsis, combining spectral imaging with fluorescence lifetime imaging (FLIM) allowed them to distinguish up to five overlapping endogenous fluorescent components within the same sample.
The course also gave participants the opportunity to explore cutting-edge technologies such as the Tomocube holotomography system, demonstrating how refractive index imaging can quantify specimen morphology without any staining at all, a valuable option when working with delicate marine samples. Sessions on conjugate planes and Köhler illumination gave the group a firmer theoretical footing, turning what can often feel like trial-and-error troubleshooting into a more fundamental knowledge, that students can apply to any microscope they use.
Stephany Osei, one of the participants, expressed her gratitude for the knowledge gained and the connections made during the training, sharing that it was an experience that would stick with her forever.
A course built by the consortium
The training drew on expertise from across the AQUASERV partnership, with instructors from CCMAR, the Institut de la Mer de Villefranche (LBDV), the CSIC's Toralla Marine Science Station (ECIMAT, Vigo), the Plentzia Marine Station (PiE-UPV/EHU), the IPMC-CNRS, the Hellenic Centre for Marine Research (HCMR), the Station Biologique de Roscoff and Sorbonne University all contributing sessions.
The course was coordinated by Carina Mónico (CCMAR Imaging Platform), Sébastien Schaub (LBDV, Institut de la Mer de Villefranche) and Cláaudia Delgado (EMBRC Marine Training Unit / EMBRC-BE-UGent), and made possible thanks to funding secured through AQUASERV's staff and user training scheme, with the University of South Bohemia's Laboratory of Machine Vision in Aquaculture and Water Protection among the institutions that supported their team's participation.
“This course was an excellent opportunity to meet colleagues from imaging facilities across different marine stations. We all learned a lot from each other by sharing expertise, imaging protocols and procedures, new tools, and networking opportunities. The blended format of the course also allowed us to create useful training resources that we can continue to use in our own facilities, helping our users gain the fundamental microscopy knowledge they need to address their current research questions and to inspire ideas for future projects. The course has already generated new interest in TNA and staff mobility opportunities, with staff exchanges and collaborations developing directly from the course participants.
"It took a lot of work and a strong joint effort to make all of this possible, but seeing the participants' enthusiasm, dedication and "wow" moments made it completely worthwhile. One of the best things is that future editions will be much easier to run, because the material and experience is already in place."
"My dream is to reach students from all four corners of the world, particularly those with more limited access to microscopy training, and to share this knowledge as widely as possible." - Carina Mónico
What’s next
Given the response from participants, a second edition of the course is already being planned for 2027, and the online theoretical module remains freely available in the meantime.
This is exactly the kind of training AQUASERV was built to support: researchers applying for funding, designing a course together, and passing on specialist skills across the consortium. It's the first course to be delivered through this route and it won't be the last.
Curious about microscopy, imaging, or other specialised research technologies available through AQUASERV? Explore the service catalogue to find out how to access top-tier research infrastructure and future training opportunities.
This course has been funded with support from the European Commission. The AQUASERV project has received funding from the European Union’s HORIZON Research and Innovation Actions under grant agreement N° 101131121. We thank all the sposors that contributed to this course: Tomoclube, Enzifarma, FILSAT, Leica Microsystems, Alfagene, ThermoFisher Scientific, and Câmara Municipal de Faro.