Workshop report: France BioImaging – Advanced Training on Light-Sheet Microscopy

From November 4th to 7th, 2024, I had the privilege to attend the Advanced Training on Light-Sheet Microscopy‘s Principles and Applications to Neuroscience and 3D Cell Culture at France BioImaging in Bordeaux. This comprehensive training, rich in both theoretical and practical knowledge, provided an exceptional platform for learning and engaging with experts in the field.

Each of the four days was well organized, combining morning lectures with afternoon practical training sessions. The lectures were delivered by renowned national and international experts, ranging from Adam Glasser (Allen Institute for Neural Dynamics, Seattle USA) to George Debrégeas (Jean Perrin Laboratory, Paris France). The course covered a wide array of topics, from the design and construction of microscopes to the different technologies of light-sheet microscopy, sample preparation, and image data analysis pipelines. This blend of theory and hands-on experience offered an excellent opportunity to deepen understanding and acquire practical skills in the field.

The lectures spanned various areas:

• Microscopy Design and Technologies: Understanding the fundamentals of light-sheet microscopy design and the different technologies available.
• Sample Preparation: Emphasizing the choice of the best clearing methods and the complexities involved in preparing samples.
• Image Data Analysis: Exploring the various pipelines used for analyzing microscopy images.
• Live Light-Sheet- and Lattice Light-Sheet microscopy, which addressed the penetration depth of light into tissues without clearing and the bioinformatics solutions available to achieve higher spatial resolution.

The most valuable aspect of the training was the opportunity to interact and think-tank with experts and fellow researchers. Regular coffee and lunch breaks, as well as a social event on the 4th day, facilitated these interactions. The practical sessions, in particular, were invaluable. They provided a chance to ask specific questions to experts and gain hands-on experience in sample preparation, image acquisition, and analysis.

The workshops were the major highlight, structured around 4 main thematic tracks:

1. Large Sample Imaging – Clearing & Expansion
2. 3D Cellular Models Culture & Imaging
3. Neuronal Network Imaging
4. Image Analysis

Participants could choose to follow one track or navigate between them, based on their interests and skills.

The workshops I chose encompassed:

• Workshop P1-2: Focused on the 3D imaging of neuronal expanded samples using the AxL (3i) microscope. This workshop covered practical considerations of sample expansion, imaging by Ultramicroscopy, and 3D data-set management and analysis.
• Workshop P2-3: Presented methods for culturing and imaging 3D neurospheres from rat primary neurons using the MuViSPIM. Discussions included labeling approaches and imaging neuronal connections and functional activity.
• Workshop P4-1: Addressed modern bioimage workflows using the Arkitekt solution. It demonstrated how to orchestrate real-time analysis and microscopy workflows, integrating conventional bioimage software and modern deep learning frameworks.

The France BioImaging Advanced Training 2024 was an enriching experience, blending rigorous academic content with practical applications. The ability to interact with leading experts and peers, coupled with hands-on workshops, significantly enhanced my understanding and skills in light-sheet microscopy. The insights gained from this training will undoubtedly contribute to my ongoing research in neuroscience and 3D cell culture.

JCS-FocalPlane Training Grants are open to all early-career scientists working in the field of cell biology. They can be used to attend training courses in microscopy and bioimage analysis. Drop us an email at focalplane@biologists.com if you have any questions about the grants.

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