Microscopy is among the most widely used techniques to quantify and illustrate processes in biology. However, given the diversity of available methods and the rapid pace of technological development, it can be challenging for researchers to gain both a clear overview of microscopy methods, and the practical knowledge of their applications.

This course introduces the fascinating world of optical microscopy applied to marine sciences and aquaculture. Drawing on the expertise of microscopy specialists across the AQUASERV consortium, the course is cross-disciplinary while keeping marine organism imaging as the common thread. Training covers the underlying principles of optical microscopy and shows how to make the best use of imaging technologies available at research infrastructures — from brightfield to advanced approaches such as fluorescence, confocal, and lightsheet microscopy. Through examples from aquaculture and marine biology, participants will follow the complete workflow: learning the fundamentals of microscopy, selecting the right technique for their research question, preparing and imaging marine samples, addressing the unique challenges of marine specimens, and applying modern tools for image analysis and data management.
We aim to develop a course that becomes a reference in the field of marine biology and aquaculture. To ensure continuity and adaptability, we plan on repeating this course regularly, rotating between marine stations and tailoring the practical component to the imaging technologies available on site.

Course Contents

Part 1 (Online: 22 June - 22 July 2026)

• Light Principles
• Fundamentals of Optical Microscopy: know your microscope
• Brightfield imaging and Contrast enhancing techniques - exploring aquatic and marine microorganisms
• Introduction to Fluorescence Microscopy
• Optical sectioning and advanced imaging
• Specialised tools for marine monitoring
• Sample preparation techniques and challenges
• Introduction to image analysis for aquaculture and marine biology
• Conclusion remarks: overview of optical microscopy techniques for marine sciences

Part 2 (Onsite: 1 - 4 September 2026, venue CCMAR, Faro, Portugal)

in person - practicals, demos, consolidating theoretical concepts with a practical approach
 

Course Instructors:

• Carina Mónico, CCMAR, Portugal
• Lucía Sánchez Ruiloba, Instituto de Investigaciones Marinas CSIC, Vigo, Spain
• Sébastien Schaub, LBDV, Institut de la Mer de Villefranche, France
• Xabier Lecube (Plentzia Marine Station, PiE-UPV/EHU, University of the Basque Country, Spain
• Margaux Failla, LBDV, Institut de la Mer de Villefranche, France
• Samah Rekima (IPMC, CNRS, France)
• Kleoniki Keklikoglou (Institute of Marine Biology, Biotechnology and Aquaculture, HCMR, Greece)
• Sophie Le Panse, Station Biologique de Roscoff, France
• Marie Walde, SBR RCC, Sorbonne University, France
• Tania Tato Vidal (Toralla Marine Science Station, ECIMAT, Vigo, Spain)
• Caio Ribeiro, CCMAR, Portugal
• Joana Leal, CCMAR, Portugal
• Teresa Correia, CCMAR, Portugal
• Sandra Rebocho, CCMAR, Portugal
• Paulo Gavaia, CCMAR, Portugal
• Vincent Laizé, CCMAR, Portugal
• Lelde Hermane, CCMAR, Portugal
• others to be announced

Course Coordination:

Carina Monico, Imaging Platform, CCMAR
Sébastien Schaub, LBDV, Institut de la Mer de Villefranche
Claudia Delgado, Marine Training Unit, EMBRC/EMBRC-BE-UGent

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.

Target Audience

Early Career Researchers: MSc students, PhD candidates, and postdoctoral researchers in marine biology, aquaculture, fisheries, and related life sciences.
Research Infrastructure staff: technicians and facility managers seeking to upskill in microscopy and image analysis.
Industry professionals and entrepreneurs: users from aquaculture, blue biotechnology, and environmental monitoring who want to integrate imaging into their workflows.
Senior researchers and group leaders: those who use microscopy but lack formal training in its principles, and who wish to better supervise students, critically assess image data, and refine or expand their experimental workflows.
Transnational Access (TNA) users of the AQUASERV project: researchers preparing or participating in a TNAcall who want to learn microscopy fundamentals to apply these methods in their planned experiments.

Prerequisites

• No previous microscopy training is required.
• Participants should demonstrate a strong interest and motivation in microscopy, whether as current users or as researchers already doing bioimaging, or planning to include microscopy in their future projects.
• Successful completion of the online Part I modules (theory and quizzes) is mandatory for participation in the in-person workshop.
   

Application procedure

Please fill in the Registration form no later than 15 June 2026.

A limited number of seats for the onsite phase is available (20 participants maximum). Selection will be based on motivation and successful completion of the online phase.

Grant opportunities

Pending on external funding the tuition fee for the onsite phase may be reduced.

Learning outcomes

By the end of the course the learner will be able to:

• Explain the fundamental principles of light and optical microscopy.
• Describe the main microscopy techniques, including brightfield and fluorescence microscopy.
• Compare and evaluate the strengths and limitations of key imaging approaches (brightfield, fluorescence,confocal, lightsheet) for different marine samples.
• Prepare and mount a range of marine specimens for microscopy.
• Apply simple tricks and good practices to improve image quality.
• Design a microscopy experiment tailored to a research question in aquaculture or marine biology.
• Operate simple imaging systems and implement key practices for acquiring reproducible image data,independently of the specific microscope available.
• Retrieve and interpret meaningful quantitative data from microscopy images.
• Identify and apply modern open-source tools to address image analysis
   

Cognitive competences:

• Understanding limitations and artefacts in optical microscopy.
• Selecting appropriate workflows for different research applications.
• Integrating microscopy into experimental design in aquaculture and marine biology.
   

Technical skills:

• Operate brightfield, contrast-enhancing, and fluorescence microscopy systems.
• Apply sample preparation techniques suitable for marine specimens.
• Acquire and evaluate microscopy images, recognising the features of high-quality data regardless of themicroscope used.
• Use open-source software tools for basic image processing and analysis.