Advanced microscopy workshop in Bordeaux from November 4th to 7th, 2024.

This advanced training course aims to (1) present the theoretical foundations, (2) clarify and synthesize the various existing approaches to both sample and instrument preparation, and (3) provide an overview of solutions for handling and processing the data acquired. These objectives will be addressed through the prism of two important biological fields of application: Neuroscience and 3D Cell Cultures. Indeed, the versatility of light sheet methods means that questions in these two fields can be addressed at a wide range of scales, from the whole brain or organoid, to the study of the nervous system of small living organisms or brain slices, right down to the single molecule inside spheroids. To address these themes, we will draw on the expertise of the Bordeaux FBI site, whether in neuroscience or in the growth and imaging of 3D cell cultures.

Deadline to apply: 31/05/2024


The course will be structured around 4 main thematic tracks, addressing the issues of sample preparation and data analysis for given samples. Participants will have the choice of following one of these tracks, or navigating between them according to their interests. The tracks will be :

  • P1: Large sample imaging – Clearing & Expansion
  • P2: 3D cellular models Culture & Imaging
  • P3: Neuronal network imaging
  • P4: Image Analysis

The format of the course will include lectures and seminars in the morning, providing a theoretical grounding in the various areas covered (sample preparation, imaging, image processing) and presenting the latest developments in these fields, and practical workshop in the afternoon on the various sites of the Bordeaux node (IINS, BIC, VoxCell).

Invited Speakers

Laura Batty, (Wyss Center for Bio and Neuro Engineering, Geneva Switzerland)

Julien Colombelli, (Institute for Research in Biomedicine, Barcelona Spain)

Adam Glasser (Allen Institute for Neural Dynamics, Seatle USA)

Farida Hellal (Institute for Tissue Engineering and Regenerative Medicine, Munich Germany)

Alfred Millet-Sikking (Calico Life Sciences LLC, San-Francisco USA)

Gaelle Recher (Institut d’optique Graduate School, Bordeaux France)

Ihssane Idrissi / Rémi Galland (Interdisciplinary Institute for Neurosciences, Bordeaux, France)

 Vincent Studer (Interdisciplinary Institute for Neurosciences, Bordeaux France)

Gustavo de Medeiros (Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland)

George Debregas (Jean Perrin Laboratory, Paris France)

Thai Truong (University of Southern California, Los Angeles USA)

Angela Getz / Mathieu Ducros (Bordeaux Imaging Center, Bordeaux France)

Alexandra Fragola (Institut des Sciences Moléculaires d’Orsay, Orsay France)

Emmanuel Faure (Laboratory of Computer Science, Robotics and Microelectronics, Montpellier France)

Johannes Roos (Johannes Kepler University, Linz Austria)

Philippe Girard (IJM, Paris, France)

Carole Siret (CIML, Marseille, France)

Guillaume Maucort (BIC, Bordeaux France)

Workshops on

  • Whole brains imaging by Ultramicroscopy
  • 3D imaging of neuronal expanded samples by Ultramicroscopy
  • 3D entire small animal imaging
  • 3D Cellular models culture and imaging using the soSPIM technology
  • Micro-niche creation for 3D cell culture and 3D imaging using the HS-ISM technique 
  • Neurospheres culture and imaging using the MuViSPIM
  • Brain slices imaging using a Lattice Light Sheet Microscope
  • Single Cell electroporation for Brain slices labelling
  • Functional neuronal network imaging in ZebraFish
  • Orchestrating complex bioimage workflows using the Arkitekt solution
  • Napari for 3D data handling
  • How to segment a 3D dataset in just a few clicks?

Organizing committee

Coordinators: Mathieu Ducros & Rémi Galland

& FBI Work Group on « Multiscale Light-Sheet Microscopy »


France-BioImaging, with its partner the GDR IMABIO, organizes the 4th edition of the FBI-AT: an advanced microscopy workshop to be held in Paris from November 21st to 25th, 2022.

The aim of this France-BioImaging-Advanced Training is to train microscopy users on the most advanced imaging techniques that will allow them to perform molecular studies at the cellular level as well as in thick samples. In particular, recent developments on fluorescent probes will be highlighted. The workshop will benefit from state-of-the-art equipment available on several of the Parisian Node Imaging facilities.

This year’s edition will have plenary lectures given by experts in the microscopy development field. These seminars will be advertised as a series and will be broadcasted for a large audience.  In addition, specific techniques will be introduced.

Hands-on practicals will train attendants on these techniques every afternoon in different sites in Paris including Institut Curie, Institut Pasteur, Institut Cochin, Institut Jacques Monod, Institut de Psychiatrie et Neurosciences de Paris and ENS Paris. Access to this part of training will be restricted to selected and registered trainees.

To guaranty access to set-ups and proper training, each practical session will host only 3-4 persons. The sessions will be run in parallel.

Apply now, attendance will be limited to 25 participants! 

FBI-AT is ideal for researchers with a basic training in microscopy willing to become familiar with advanced techniques to answer their specific biological questions, or to be exposed to new developments that will allow them to tackle new questions in their project. We will consider applications from early career researchers (PhD students, post-docs), technical staff members and more senior scientists.


The workshop contains plenary lectures and specific training sessions. Plenary lectures will be on hybrid mode and largely open.

Invited Speakers

Emmanuel Beaurepaire

Giulia Bertolin

Joerg Bewersdorf

Peter Dedecker

Claire Deo

Marie Erard

Ricardo Henriques

Christophe Leterrier

Sandrine Lévêque-Fort

Gustavo Quintas

Gaelle Recher

Jean-Baptiste Sibarita

Lothar Schermelleh

Practicals on

  • Combining micro UV-irradiation and Single Particle Tracking in living cells
  • SMLM multi-color: from sample preparation to quantification
  • FRET-based molecular tension sensors and FLIM
  • Imaging of cellular ultrastructures with expansion microscopy
  • SIM, STED or STORM ? : from sample prep to 3D imaging
  • 3D STED : Comparing flat cells vs thick samples
  • Culturing and imaging multicolour 3D live brain organoïds
  • Combining fast live 3D imaging with Z resolution preservation
  • Light sources for optogenetics
  • Non-classical genetically modified fluorescent probes for biological imaging
  • Imaging biological structures in 3D using double helix-STORM and 3D-SIM


Florence Niedergang, Lydia Danglot, Chloe Guedj, Mickael Lelek, Pierre Bourdoncle, Audrey Salles, Xavier Baudin, Nicolas Borghi, René-Marc Mege, David Geny, Ludovic Jullien