France BioImaging (FBI) is organizing a remote training on Light-Sheet Fluorescence Microscopy (LSFM), which enable 3D imaging of biological samples with unprecedented spatio-temporal resolutions and low perturbing effects.

LSFM methods actually cover a large variety of implementations which allow imaging a wide range of sample types, from single cell to whole organs or organisms both live and fixed. These new imaging capabilities are revolutionizing the way we visualize our samples and address biological questions. However, imaging with a light-sheet microscope raises many questions about the choice of the set-up depending on the sample to image, the sample preparation and mounting protocols or the data management (storage, visualization, quantification). Thus, it can be difficult to find its way through the numerous microscope implementations, protocols and tools that have been extensively developed over the last 20 years. We therefore decided to review all those questions in a remote training.

Our goal is to help people who want to jump into the world of 3D imaging and are seeking the best solution for their samples and biological questions. In that perspective, we will provide a comprehensive picture including all the possibilities and challenges regarding LSFM.


The training will be divided in 3 parts:

  1. Theoretical courses on LSFM
  2. Practical demonstrations of several LSFM implementations available throughout the FBI infrastructure
  3. Live online question-and-answer session

For the two first parts, videos will be available on a Youtube FBI channel. The participants will have 3 weeks, from the 15th of February to the 5th of March 2021, to watch those videos and will be invited to ask questions or comment.

FBI experts will then answer all questions during a live interactive video chat on the third week of the training (5th of March where participants will have the opportunity to directly interact with the experts.


1.      Theoretical aspects of LSFM (15th to 26th of February 2021)

Here are the three main questions concerning the imaging with a light-sheet microscope: (1) what LSFM type should I use for my experiment, (2) How do I prepare and mount my sample, and (3) how to visualize and analyze my data sets. The first part of this training will address these three questions through three theoretical courses:

  • Course 1: Theoretical principles and numerous implementations overview of LSFM
    • P. Girard (Institut Jacques Monod, Paris-Centre)
  • Course 2: Sample preparation and mounting principles – highlight on clearing approaches
    • Carol Siret (CIML, Marseille)
  • Course 3: Reconstruction, Visualization and Analysis software overview.
    • Cesar Augusto Valades (Institut Curie, Paris-Centre),

2.      Practical demonstrations of several LSFM implementation and experiments (15th of February to 5th of March 2021)

In the second part of the training we will propose several videos on various systems available in the FBI laboratories and imaging platforms covering diverse types of LSFM design and applications.

Each video will feature a specific set-up and experts will present how to run an experiment on them focusing on three main aspects: (1) sample preparation and mounting methods, (2) image acquisition processes, and (3) visualization of the data-sets.

  • Lattice Light Sheet Microscope(Home-made  and 3i versions)
    • Mathieu Ducros (BIC, Bordeaux)
    • Ludovic Lecomte, Jean Salamero and Cesar Valaldes-Cruz (Institut Curie, Paris-Centre)
  • Single-objective Single Plane Illumination Microscope (soSPIM)Home-made
    • Rémi Galland (IINS, Bordeaux)
  • Dual inverted Single Plane Illumination Microscope (diSPIM)3i (Marianas)
    • Elric Esposito et Julien Fernandes (Institut Pasteur, Paris-Centre)
  • MuviSPIM – Luxendo
    • Sylvain De Rossi (MRI, Montpellier)
  • Ultramicroscope – LaVision Biotech
    • Carol Siret/Mathieu Fallet (CIML, Marseille)

3.      Questions & Answer interactive session (March 5th, 2021)

An online video session will conclude the training where FBI experts will answer all participants’ questions. You can ask questions either in advance in the comment box of the Youtube video, or during the Q&A session in a chat box. The Q&A session will be divided in sections, each related to a specific video.

To register:

In order to register to the Light-Sheet Fluorescence Microscopy remote training, please fill out the registration form available here.

Registration is free but mandatory in order to receive the links to the training videos.

Registration deadline: February 12th, 2021

We look forward to your participation !

A l’occasion de la MorningTech Photonique & Santé organisée par Photonics Bretagne et Biotech Santé Bretagne le 2 février 2021 de 9h30 à 12h00, Marc Tramier, coordinateur du Nœud Bretagne-Loire de France BioImaging présentera “les technologies photoniques des plateformes de Biogenouest au service de l’imagerie pré-clinique“.

Programme et inscriptions:

Registration for France BioImaging Annual Meeting is now open!

France BioImaging is pleased to invite you to participate to France BioImaging 6th Annual Meeting.  For this edition, the meeting will be organized as a two-half days virtual meeting (from 9:00 AM to 1:00 PM) on February 4th & 5th, 2021.

This event, open to all members of the bioimaging community, aims to provide a platform to discuss pivotal subject matters in our field.

The 2021 program of the France BioImaging Annual meeting is built around two pillars:

  • February 4th: “Building and operating an integrated and open infrastructure for bioimaging
  • February 5th: “Latest and future developments in biological imaging

Registration is free but mandatory in order to receive the Zoom link:

Preliminary Program 

We look forward to your participation!

Imaging of proteins, cells, and tissues is critical to understanding health and disease. On December 2nd, 2020, the Chan Zuckerberg Initiative (CZI) announced nearly $32 million in funding to support biomedical imaging researchers, technology development, and the BioImaging North America international network of bioimaging facilities and communities. CZI also opened a new Request for Applications (RFA) aimed at supporting technology development that will allow researchers to see the inner workings of cells, including proteins, at near-atomic resolution to better understand what causes disease and how to develop treatments.

Frontiers of Imaging: Visual Proteomics 

The Frontiers of Imaging initiative, part of CZI’s broader Imaging program, supports the development of disruptive imaging technologies that connect biological scales across organs, cells, and proteins, allowing researchers to directly visualize biological processes at the necessary resolution and context to obtain a mechanistic understanding of health and disease. As part of the Frontiers initiative, the new Visual Proteomics Imaging RFA supports technology development that will allow researchers to see the inner workings of cells, including proteins, at near-atomic resolution. CZI invites scientists to apply for this 2 1/2-year grant opportunity to support the development of hardware, software, and methods. Examples of research themes could include hardware and software development to enhance contrast and resolution for electron tomography, high-resolution correlated light and electron microscopy (CLEM), and FIB-SEM; sample preparation improvements for electron tomography; and development of software or new computational techniques and algorithms for identifying protein molecules inside cells and segmenting sub-cellular structures.

The Visual Proteomics Imaging RFA accept applications until February 17, 2021 at 5 p.m. Pacific Time.

For more information and application instructions, please visit CZI’s online grants management portal.

For administrative and programmatic inquiries, technical assistance, or other questions pertaining to this RFA, please contact:

Learn more about CZI’s Frontiers of Imaging effort.

Congratulations to Emmanuel Beaurepaire (CNRS Research Director from the Laboratory for Optics and Biosciences CNRS-INSERM-Polytechnique), PI of the ERC Synergy Grant project “HOPE”, and to Laurent Groc (CNRS Research Director ; Interdisciplinary Institute for Neuroscience), coordinator of the ERC Synergy Grant projectENSEMBLE“, Laurent Cognet (CNRS Research Director ; Laboratoire photonique numérique et nanosciences) and U. Valentin Nägerl (Professor at University of Bordeaux ; CNRS Research Director ; Interdisciplinary Institute for Neuroscience), both PIs of the ERC Synergy Grant projectENSEMBLE“.

These grants, each worth around 10 million euro over six years, are designed to enable groups of 2 to 4 scientists to tackle some of the world’s most challenging research problems, spanning several scientific disciplines.

The ERC Synergy Grant scheme is part of the EU’s research and innovation programme, Horizon 2020.

ERC Synergy Grant project “HOPE”

Reverse engineering the assembly of the hippocampal scaffold with novel optical and transgenic strategies” 

  • Emmanuel Beaurepaire, Directeur de recherche CNRS au Laboratoire d’optique et biosciences – LOB (CNRS/École polytechnique/INSERM),
  • Rosa Cossart, Directrice de recherche CNRS (Unité INSERM, Aix-Marseille Univ.)
  • Jean Livet, chercheur INSERM à l’Institut de la vision (CNRS, INSERM, Sorbonne Univ.)

At the heart of our brain, a structure plays a key role in memory, and more particularly in the acquisition and maintenance of our memories: the hippocampus. Classically considered as a “cognitive GPS” for space and time, it is also the seat of our episodic memory.

Over the last decade, the neural circuits of the hippocampus have been better described, in particular by the team of Rosa Cossart, director of the Institut de neurobiologie de la méditerranée (Inmed), but the nature, origin and remodeling of these circuits during development and pathologies remain to be understood.

On the other hand, genetic engineering techniques for staining neurons, developed by Jean Livet, Inserm research director at the Institut de la vision, coupled with multi-photon microscopy developed by the team of Emmanuel Beaurepaire, CNRS research director at the Laboratoire d’optique et biosciences – LOB (illustration below / read the 2019 press release in French), have demonstrated their ability to accurately map the complex architecture of neuronal circuits and their evolution during development.

By combining these exceptional multidisciplinary advances, HOPE aims to answer three interdependent questions:

  • Is the architecture of the adult seahorse carried by specific circuits?
  • Are the circuits of the hippocampus pre-wired or shaped by experience?
  • How does this structure reorganize itself in pathological conditions?

HOPE aims to shed new light on the function of the hippocampus and the role of its neuronal circuits through the design of a new, non-invasive and universal method to monitor the growth and construction of brain circuits located deep in the brain, from their neurogenesis to adulthood, under normal and pathological conditions.

Developed by the LOB team, ChroMS is a new microscopy technique combining color, 3D and high resolution, introducing a real revolution in vertebrate brain imaging. © Lamiae ABDELADIM / LOB / Institut de la Vision / CNRS Photothèque

Taken from CNRS Press release:

ERC Synergy Grant project “ENSEMBLE”

“Structure and functions of the brain extracellular space

  • Laurent Groc (Research Director CNRS ; Interdisciplinary Institute for Neuroscience), 
  • Erwan Bézard (Research Director INSERM; Institute of Neurodegenerative Disorders), 
  • Laurent Cognet (Research Director CNRS ; Laboratoire photonique numérique et nanosciences)
  • U. Valentin Nägerl (Professor at University of Bordeaux ; Research Director CNRS ; Interdisciplinary Institute for Neuroscience)

The ENSEMBLE project aims at underpinning the molecular mechanisms of physiological and pathological brain function. This ambitious and innovative endeavor is based on our ability to develop new approaches in high-resolution microscopy at the service of a new conceptual framework in brain cell communication.

Brain, high resolution iimage. Credit: U.V. Nägerl
Credit: U.V. Nägerl

This project has roots in the international leadership of the Bordeaux community in the fields of microscopy, nanophotonics, fundamental and translational neuroscience. The opportunity that is offered to these 4 investigators to break a frontier knowledge was permitted by the continuous support of local institutional actors. The installation of Prof. Valentin Nägerl’s laboratory in 2009 with a “Chaire Accueil” from the Regional Council of Aquitaine, the support of LabEx BRAIN, the Laphia Cluster and the IdEx of the University of Bordeaux provided the ground to build elementary blocks necessary for the challenging adventure of the ERC Synergy project (10 million euros, 6 years).

Taken from Bordeaux Neurocampus Press release:

We are very pleased to announce that FBI Bretagne-Loire Node application to become a Euro BioImaging facility has been evaluated as highly recommended by the EuBI Scientific Advisory Board (SAB) and ratified by the EuBI Board on November 30th, 2020.

The Bretagne Loire Node became a node of the national infrastructure France BioImaging in November 2019 and applied to become a EuBI facility during the last EuBI Call for Nodes (June 2020).

The Bretagne Loire Node brings together four cellular imaging and histology facilities, two in Rennes (MRic and H2P2) and two in Nantes (MicroPIcell and APEX). These facilities have complementary expertise for live imaging and pathological anatomy. The added value of the Bretagne Loire Node is to be able to offer a continuum between biological imaging and medical imaging, through the development of a new line of services as well as methodological and technological transfer to users of microscopy technologies for preclinical studies.

These facilities will now be open to Euro-BioImaging users as part of the French BioImaging Node of Euro-BioImaging.

As part of the Euro-BioImaging research infrastructure, the services provided by these facilities will be open to all scientists, regardless of their discipline or affiliation.

Euro BioImaging press release

The PICsL-FBI microscopy core facility is located on two sites: Centre d’Immunologie de Marseille Luminy (CIML) and Institut de Biologie du Développement de Marseille (IBDM).The PICsL-FBI facility of the CIML called ImagImm (Imaging Immunity) via its microscopy resources – from the molecule to whole organisms – is dedicated to help its users deciphering cellular mechanisms in the fields of immunology.

Major research implications of the ImagImm facility:

  • Technology transfer: spot variation Fluorescence Correlation Spectroscopy (svFCS)

In collaboration with Tomasz Trombik (Faculty of Biotechnology, University of Wroclaw – Wroclaw, Poland), Sophie Brustlein (Institut de Convergences Centuri, AMU,CNRS – Marseille, France) and Nicolas Bertaux (Institut Fresnel, AMU, Centrale Marseille, CNRS – Marseille, France), Sébastien Mailfert and Didier Marguet published the procedure for implementing spot variation Fluorescence Correlation Spectroscopy (svFCS) measurements using a classical fluorescence microscope that has been customized1. This publication is following the technology transfer made in 2018: the svFCS developed by Didier Marguet’s lab was duplicated by Sébastien Mailfert and Sophie Brustlein and built from scratch in 7 days on site, in Poland.

Dynamic biological processes in living cells, including those associated with plasma membrane organization, occur on various spatial and temporal scales, ranging from nanometers to micrometers and microseconds to minutes, respectively. Such a broad range of biological processes challenges conventional microscopy approaches. The published protocol includes a specific performance check of the svFCS setup and the guidelines for molecular diffusion measurements by svFCS on the plasma membrane of living cells under physiological conditions. Additionally, a procedure for disrupting plasma membrane raft nanodomains by cholesterol oxidase treatment is provided and how these changes in the lateral organization of the plasma membrane might be revealed by svFCS analysis. This fluorescence-based method can provide unprecedented details on the lateral organization of the plasma membrane with the appropriate spatial and temporal resolution.

Figure 1: Schematic view of excitation and emission optical paths of the svFCS setup and pictures of the setup. The svFCS setup contains four modules: (1) the output of a fibered 488 nm laser is collimated, (2) a combination of a half-wave plate and polarizing beamsplitter sets the optical power, (3) the laser beam focused on the sample after traveling through a tube-lens free motorized microscope, and (4) the fluorescence is detected through a confocal-like detection path onto an avalanche photodiode coupled to a single photon counting module, which delivers a signal to a hardware correlator. Simplicity gives the system its sensitivity, robustness, and ease of use.
  • SAPHIR : a Shiny application to analyze tissue section images

In collaboration with Hugues Lelouard (CIML, Inserm, CNRS, AMU) and Elodie Germani, Mathieu Fallet published a powerful method for both basic and medical research to study cell populations in tissues using immunofluorescence. Image acquisitions performed by confocal microscopy notably allow excellent lateral resolution and more than 10 parameter measurement when using spectral or multiplexed imaging. Analysis of such complex images can be very challenging and easily lead to bias and misinterpretation. They developed the Shiny Analytical Plot of Histological Images Results (SAPHIR), an R shiny application for histo-cytometry using scatterplot representation of data extracted by segmentation. It offers many features, such as filtering of spurious data points, selection of cell subsets on scatterplot, visualization of scatterplot selections back into the image, statistics of selected data and data annotation. This application allows to quickly characterize labeled cells, from their phenotype to their number and location in the tissue, as well as their interaction with other cells.

Figure 2: Flow chart of tissue image analysis from image acquisition and segmentation (left side) to extract data analysis with SAPHIR (right side)
  • Wound healing in C. elegans

In collaboration with Nathalie Pujol and Jonathan Ewbank (CIML, Inserm, CNRS, AMU), Mathieu Fallet and Sébastien Mailfert participated in the project on the immune response by showing that wounding provokes a reorganization of plasma membrane subdomains3.  The skin protects animals from infection and physical damage. In Caenorhabditis elegans, wounding the epidermis triggers an immune reaction and a repair response, but it is not clear how these are coordinated. Previous work implicated the microtubule cytoskeleton in the maintenance of epidermal integrity (Chuang et al., 2016). Taffoni et al. show the reorganization of the plasma membrane subdomains by a simple wounding system. This is followed by recruitment of the microtubule plus end-binding protein EB1/EBP-2 around the wound and actin ring formation, dependent on ARP2/3 branched actin polymerization. They show that microtubule dynamics are required for the recruitment and closure of the actin ring, and for the trafficking of the key signaling protein SLC6/SNF-12 toward the injury site. Without SNF-12 recruitment, there is an abrogation of the immune response. These results suggest that microtubule dynamics coordinate the cytoskeletal changes required for wound repair and the concomitant activation of innate immunity.

Figure 3: Time line of events


  1. Mailfert, S., Wojtowicz, K., Brustlein, S., Blaszczak, E., Bertaux, N., Łukaszewicz, M., Marguet, D., Trombik, T. Spot Variation Fluorescence Correlation Spectroscopy for Analysis of Molecular Diffusion at the Plasma Membrane of Living Cells, JoVE, 165, 1-19 (2020).
  2. Germani, E., Lelouard, H., Fallet, M. SAPHIR: a Shiny application to analyze tissue section images, F1000Research, Faculty of 1000, 9, 1276-1285 (2020).
  3. Taffoni, C., Omi, S., Huber, C., Mailfert, S., Fallet, M., Rupprecht, J-F,. Ewbank, J., Pujol., N. Microtubule plus-end dynamics link wound repair to the innate immune response, eLIFE, 9, e45047 (2020)

Congratulations to Patrick LEMAIRE, CNRS Research Director from the
Centre de recherche en biologie cellulaire de Montpellier (CRBM) – CNRS / Université de Montpellier, member of France BioImaging Montpellier Node, who has been awarded the Mottart prize.

With his team members, Patrick Lemaire is studying the embryonic development of a small marine invertebrate, the sea squirt Phallusia mammillata, chosen for the simplicity and transparency of its embryos. His latest work has combined microscopy, image analysis and mathematical modeling approaches to describe, cell by cell, the embryogenesis of this animal and to analyze the role of communication between cells.

To learn more about the study:

The webconference organized by ITMO Molecular and Structural Bases of Life (BMSV) of the Aviesan Alliance entitled “Physics-Biology interface” will take place on Thursday, December 17th 2020.

Advances in biology opened up new areas of research that are developing at the interface with physics.

Physicists make a major contribution to this interface, with the development of new instruments allowing the massive data acquisition, the manipulation of single molecules and the observation of biological phenomena at increasingly higher temporal and spatial resolutions. These developments offer new perspectives for solving previously unaffordable biological questions.

Furthermore, theoretical approaches from physics are now necessary to tackle new problems: those linked to cellular heterogeneity, to the way it is regulated, filtered or even exploited; or those linked to newly identified cell compartments, devoid of membranes and very dynamic, which are revolutionizing our vision of cellular organization and functioning.

A detailed understanding of all these complex phenomena requires new conceptual frameworks developed in physics (quantum, statistics, signal theory, thermodynamics out of equilibrium, study of polymers and colloids, etc.) which will make it possible to model living things from the atomic scale to integrated cellular systems.

This conference is therefore dedicated to the interface between biology and physics and aims to promote interactions between the two communities by illustrating the currently emerging questions and new scientific challenges.


  • Patricia Bassereau – Institut Curie – Paris
  • Martin Blackledge – Institut de Biologie Structurale – Grenoble
  • Céline Boutin – IRAMIS-NIMBE
  • Pascal Hersen – Institut Curie – Paris
  • Eric Hosy – Institut Interdisciplinaire de Neurosciences – Bordeaux
  • Arnaud Hubstenberger – Institut de Biologie Valrose – Nice
  • Martin Lenz – Laboratoire de Physique Théorique et Modèles Statistiques – Orsay
  • Marcello Nollmann – Centre de Biochimie Structurale – Montpellier

Registration deadline: December 3rd, 2020

Le programme de ce WEB-JST (Flyer téléchargeable ici) comprend quatre présentations orales (20’ + 10’ de questions) en microscopies photonique et électronique, en traitement d’image et en imagerie chimique ainsi que L’AG du réseau présentant les actions menées durant l’année écoulée.

COMULIS is an EU-funded COST Action that aims at fueling urgently needed collaborations in the field of correlated multimodal imaging (CMI), promoting and disseminating its benefits through showcase pipelines, and paving the way for its technological advancement and implementation as a versatile tool in biological and preclinical research. CMI combines two or more modalities to gather holistic information about the same specimen. It creates a composite view of the sample with multidimensional information about its macro, meso- and microscopic structure, dynamics, function and chemical composition. Since no single technique can reveal all these details, CMI is the only way to understand biomedical processes mechanistically.

In order to encourage correlated multi-modal imaging projects, COMULIS Short Term Scientific Missions (STSMs) provides travel grants to individuals wishing to explore new imaging techniques. The grants are presented in the form of a lump sum of up to 3,500 Euros (depending on the duration of the mission), to cover travel and subsistence. COMULIS COST accepts applications on a continuous basis from Early Career Investigators and Experienced Imaging Scientists who would like to travel internationally to collaborate with a Host facility on a Correlated Multi-modal imaging project. There is a rapid review process and around 10 grants are awarded every year.

In addition, COMULIS STSM can provide funding for core facility staff to learn a new imaging  technique or work with new software tools to bring the expertise back to their own facility.

Applications can be submitted any time & will be reviewed at the end of each month.

More info and application procedure:

The image depicts a spheroid of human stem cells (green) and its actin cytoskeleton (purple), produced by Philippe Cohen during its PhD at Treefrog. This nice picture serves as an illustration for an article covering the use of stem cells for regenerative medicine.
Acquisition was made by Philippe Cohen on a scanning confocal microscope and 3D rendering was done by Jérémie Teillon using Agave software.
Agave is a free 3D visualization software, using light path-trace light rendering.

The Bordeaux Imaging Center team offers training and support on 3D commercial softwares such as Imaris and Arivis as well as other freeware such as Agave. Don’t hesitate to contact them ( if you are interested  in 3D rendering and visualization of your microscopy data!

Agave software:
Article (in French):