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):

During embryonic development, cells take on increasingly precise roles in the body as they divide. Be they skin cells, muscle cells or neurons, the different cell types that make up the embryo emerge gradually from a very fine orchestration of their positions and identities, coordinated by the signals they exchange with each other. Like us, the cells need to “talk” to each other to make decisions.

Screaming or whispering: the embryonic cell dilemma

In vertebrate embryos, cells have a very dynamic behaviour. They move around, exchange their neighbours or migrate over long distances. The signals they exchange therefore need to have a long range, which could be characterized as “shouting”. The study of the embryonic development of a sea squirt, a small marine animal with optically transparent embryos, has enabled scientists from several teams at CNRS and INRIA in France, in collaboration with a team from the European Molecular Biology Laboratory (EMBL, Germany), to capture and describe in detail a more discreet mode of cell communication.

The scientists recorded the development of live embryos every two minutes with a new-generation « light-sheet » microscope. They then created software to automatically detect each cell and analyze its position, shape and neighbours up to an advanced stage of development. This work revealed an unusually reproducible mode of development, in which the same cell can be found in the same position across all embryos and where cells move very little in relation to each other. The authors of the study then annotated the films thus made with information on the cell type and the molecular signals emitted by each cell. Using mathematical modelling to integrate the quantitative description of the embryonic geometry with these annotations, their work suggest that cells communicate with very short-range signals. Moreover, the interpretation of these signals is modulated by the area of the contacts between cells. Unlike vertebrates, the cells of ascidian embryos thus have a static and fixed behaviour and the range of their “whispered” signals is very small.

Top: embryonic development of an ascidian from egg to tadpole. The part framed in white is the part of embryogenesis that we have imaged and then segmented (below, segmented cells coloured according to their cell fate). The lower part of the figure illustrates that the light green cells “whisper” instructions to their immediate neighbours by short-range signals.

This study indicates that the dynamics of cell movement varies greatly between animals and that these different modalities could be strongly related to the range of signals that the cells exchange with each other. By extending the repertoire of cellular communication mechanisms, this work opens new perspectives on the understanding of self-organization strategies of living forms.

Article: L. Guignard*, U.-M. Fiuza*, B. Leggio, J. Laussu, E. Faure, G. Michelin, K. Biasuz, L. Hufnagel, G. Malandain, C. Godin#, P. Lemaire# (2020) Contact-area dependent cell communications and the morphological invariance of ascidian embryogenesis (Science, July 10 2020 issue,

Registration is now open for the Virtual Early Career European Microscopy Congress 2020!

Following the cancellation of emc2020, this virtual meeting will provide an opportunity for Early Career Scientists who would have attended and presented at the congress, to still present their work at an International Meeting this year. 

Registration Fees
The registration fees can be found below.

Early Career
You are a student or an Early-Career Researcher (less than 3 years since the completion of your PhD by November 2020).
Thank you to the European Microscopy Society for subsidising to enable free registration for Early Career Researchers.
EMS Member
You are a member of the European Microscopy Society. Member fees are applicable only if your membership status is active at the time of registration. Your membership status will be verified, so you must be sure that your annual subscription is current.

To purchase your tickets, please visit

For help and queries
If you have any questions regarding this event, please do email or visit the website for further information.

2 recent publications using the laser irradiation and photoablation systems available on the MRic facility from the Bretagne-Loire Node are presented here:

  • Esmangart de Bournonville and Le Borgne (IGDR) characterized the assembly and interactions of tricellular junction components in Drosophila epithelial cytokinesis using laser ablation on a SP5 confocal. Their article entitled “Interplay between Anakonda, Gliotactin, and M6 for Tricellular Junction Assembly and Anchoring of Septate Junctions in Drosophila Epithelium” was published last august in Current Biology (
  • Rebecca Smith, post-doc in Sébastien Huet’s team (IGDR) in collaboration with Szilvia Juhász from Gyula Timinszky’s team (Szeged, Hungary) used laser irradiation to study chromatin remodeling following DNA damage. Their paper entitled “The chromatin remodeler ALC1 underlies resistance to PARP inhibitor treatment” has just been accepted in Science Advances.

During this year 2020, the MicroPICell facility from the Bretagne Loire Node acquired several imaging systems, some of which offer access to new technologies on the Nantes health research site:

  • a complete Zeiss Lighsheet 7 light sheet microscope associated to an X-Clarity clearing system and an Arivis Vision 4D Offline station,
  • a motorized Nanolive holotomographic microscope,
  • a high-end Nikon confocal microscope (resonant, spectral, FLIM, large field of view),
  • an Akoya CODEX system of multiplex fluorescent tissue labeling.
Holography offers a unique means to measure cells in their native environment: label-free, non-invasive, manipulation-free, and interference-free.

Moreover, the MicroPICell facility, in collaboration with the training organization of the CNRS, is organizing in March 2021 a training on histology: from sample preparation to markers validation by image analysis. This training (lectures, workshops) will take place over 4 days between 03/22/2021 and 04/24/2021.


The pathways leading from cells to embryo are highly complex. They involve among others steps of cell determination, patterning, cellular and organ morphogenesis, processes that are tightly controlled and coordinated in space and time.

However, during the last decade, this field has benefited from major findings in the understanding of epigenetics, gene regulatory networks, mechanobiology, mechanisms of cell specification among others, and also from technical advances such as single cell omics.

This symposium will address state-of-the-art research in this field, both in animals and plants. It will feature keynote and invited lectures, and selected short talks and posters.

The symposium is organized at the initiative of the Multi-Organization Thematic Institute Cell Biology, Development & Evolution (ITMO – BCDE), jointly with the French Society of Developmental Biology (SFBD) and with the French Society of Cell Biology (SBCF). See the composition of the Scientific Organization Committee

The meeting will take place as scheduled on November 16 – 17, 2020. Given the sanitary situation, it will be organized using a mixed format, partly online and partly on site, on the Institut Jacques Monod campus, located in the center of Paris.  Many short talks will be selected by the organizers (applicants will be informed around October 15th). The call for abstracts is now open. Download the submission form on the registration page. Abstract submission by October 1st, 2020.

See the invited faculty

Download the poster of the meeting.

Free registration before October 31st HERE

Congratulations to Emmanuel Beaurepaire, CNRS Research Director from the Laboratory for Optics and Biosciences CNRS-INSERM-Polytechnique, and member of France BioImaging Ile de France Sud Node, who has been awarded the 2020 Life Sciences prize from the European Microscopy Society for his outstanding achievements in: 

the fields of developmental biology and neurobiology by development of novel, cutting-edge light microscopy techniques. Notably, he pushed forward methods of deep-tissue imaging, with important application potential for insights into developing small model systems and for brain imaging, using advanced techniques such as multicolor two-photon excitation, third-harmonic generation imaging, adaptive optics, pulse shaping, etc. 

On August 27th, 2020, Emmanuel presented his work during the award ceremony during the EMS General Assembly, which has been held by visioconference this year.    

The Global BioImaging Exchange of Experience workshop series continues with an online event on “Pre-publication image data: management and processing” which will be held on September 8th and 9th, 2020!

Global BioImaging and ABiS will host a two-half days virtual meeting, featuring high-level speakers from around the world and introducing the topic to the global community. A second meeting is planned, where GBI hope to be able to gather the community in person in Okazaki in spring 2021 and continue fruitful discussions and the scientific networking of our community.

As partner of the Global BioImaging initiative, France BioImaging encourage the FBI community to participate in this 2 half-days virtual meeting and share inputs on solutions related to the management of image data before they reach the publication stage!

Registrations are now open: please follow this link and register!

More information on the event can be found here: EoE V webpage.

Congratulations to Pierre-François Lenne, CNRS research director and group leader at the Institute for Developmental Biology of Marseille-Luminy (IBDM), who was elected member of EMBO. His current research focuses on cell dynamics and mechanics in the context of tissue morphogenesis.

Pierre-François is also FBI Marseille Node representative and scientific manager of the FBI Picsl imaging facility at the IBDM.

EMBO announced the list of newest elected members on July 7th, 2020.

EMBO’s tradition of recognising outstanding life scientists as Members dates back to 1963, when an initial group of 150 Members were selected by EMBO’s Council. Since then, EMBO Members have been invited to nominate and elect exceptional researchers to join the community, which now exceeds 1,800 Members and Associate Members. Elections for EMBO Members are held annually. The new EMBO Members join a growing list of renowned researchers elected before them, which includes 88 Nobel laureates.

“The new Members have contributed to the success of research in the life sciences in Europe and around the world,” said EMBO Director Maria Leptin. “As EMBO Members they can help to shape the future through EMBO’s work to support talented researchers, bring ideas together, and promote an international research environment conducive to excellent science.”

EMBO Members actively participate in EMBO initiatives, for example by serving on EMBO Council and committees, by mentoring young scientists, or supporting activities such as the promotion of sound science policy. Members also guide and support the organisation in ensuring the highest quality in the selection of future members, postdoctoral fellows, and courses and workshops.

Source: EMBO press release

More info on EMBO:

Due to the current sanitary measures and uncertainty about future COVID-19 developments, the LSFM workshop to be held in Bordeaux in December has been cancelled. The organizers are currently working on a virtual format of the workshop. More details to come soon.

This workshop will be held in Bordeaux from December 1st to December 4th 2020 and aims to give an overview of the Light Sheet Fluorescence Microscopy techniques and their application possibilities, taking advantage of the available technologies and expertise within the France BioImaging research infrastructure and the broad light-sheet microscopy community. This workshop is organized by the members of the FBI Multiscale Light-sheet Imaging Working Group.

About the workshop

  • The workshop will last 3 ½ days
  • The workshop is built on the basis of an alternation between theoretical and practical sessions. Both will be in English and provided by national expert trainers.
  • On day 2 a mini-symposium will be organized to present the last developments in different LSFM domains (instrumentation, sample preparation and data analysis) done by international experts. This mini-symposium will be open to a larger audience in order to promote LSFM approaches to the local research community. Registration is free but mandatory (this does not apply to workshop participants). Register now
  • The workshop will encompass various theoretical aspects of LSFM from sample preparation, to image acquisition and first post-processing steps (3D reconstruction, visualization).
  • The workshop will span various scales that can be imaged with LSFM based on at least 4 different LSFM set-ups
  • It will be included in the future “FBI training passport” and corresponds to a level III module (“à la carte”). Therefore, “trainees” must demonstrate knowledge of Level I (basic imaging) and Level II (optical principles) imaging.


  • Describe the general principle of light-sheet microscopy
  • Present the three main instrumentations that have been developed depending of the sample scale to be imaged (1 to 100 µm; 100 µm to mm; mm to cm)
  • Give an overview of the sample preparation techniques
  • Present the challenges raised by the data management and analysis of LSFM data
  • Present the future of light-sheet microscopy


This workshop is ideal for researchers, engineers, technicians, PhD students, and post-docs from public institutes and private companies with a prior knowledge in fluorescence microscopy techniques, and willing to become familiar with advanced techniques to answer specific biological questions.

Number of participants is limited to 20.

Practical workshops:

The practical workshops main objectives are to:

  • Provide an overview by experts of the 3 main implementations of LSFM depending of the sample size to be imaged:
    • Ultramicroscope (LaVision Biotech) – BIC
    • Invi Lattice Pro (Luxendo)
    • Z1 (Zeiss) – to be confirmed
    • LLS – BIC;
    • soSPIM – IINS
  • Give an overview of existing solutions for 3D reconstruction, Multiview merging and 3D+t visualization.

Participation fee

Academia: 200€
Industry: 600€

Preliminary program:

The workshop will last 3 ½  days with theoretical courses the morning and practical workshops the afternoon on 4 different set-up spanning the different sample sizes that can be imaged with LSFM:

  • Zeiss – Z1 (to be confirmed)
  • Luxendo – Invi Lattice Pro
  • LaVision – Ultramicroscope II
  • Lattice Light-sheet microscope – BIC
  • soSPIM – IINS

3 theoretical sessions will encompass various domains of LSFM:

  • General principle
  • Sample preparation
  • Data management

A mini-symposium will be organized to highlight recent national and international developments in LSFM.

Confirmed speakers:

  • Willy Supatto – Laboratoire D’Optique et Biosciences, Palaiseau – France
  • Christopher Dunsby – Faculty of Medicine, Imperial College, London – UK
  • Laura Batti – Wyss Center, Genève – Switzerland
  • Nicolas Renier – Laboratory of Structural Plasticity, ICM, Paris – France
  • Martin Weigert – EPFL, Lausanne

On the last day two round tables will be proposed to discuss about two hot topics in light-sheet fluorescent microscopy:

  • Clearing protocols
  • Live imaging: challenges and solutions

Participants are invited to bring their own samples if possible to test during an optional practical workshop on the last day.

A diner in Bordeaux is planned on day 2.


The workshop will be held on the premises of the Bordeaux Imaging Center and the Interdisciplinary Institute for Neuroscience, in the Centre Broca Nouvelle Aquitaine, in Bordeaux, France.


Hotel booking is left to the participant’s initiative.

Here is a list of other hotels located in the historic center of Bordeaux city (quartiers des “Grands hommes”, “Quinconces”, “Hôtel de ville” and “Mériadeck”). All are close to the tramway stops of line A (direction Le Haillan-Rostan / Pin Galant – Stops: Hôpital Pellegrin, Saint-Augustin, François Mitterand):

Hôtel de France **

Hôtel Gambetta **

Hôtel la Porte Dijeaux **

Hôtel des 4 Sœurs **

Hôtel de l’Opéra **

Hôtel Le Chantry **

Citadines Centre Mériadeck Bordeaux ***

Hôtel Ibis style Bordeaux Mériadeck ***

La Maison du Lierre ***

Hôtel Ibis Mériadeck ***

Best Western Bordeaux-Bayonne Etche Ona ***

Adagio Bordeaux Gambetta ****

Mama Shelter

Local Organisers

Dr. Mathieu Ducros, Bordeaux Imaging Center

Dr. Rémi Galland, Interdisciplinary Institute for Neuroscience

Questions about the LSFM workshop can be addressed directly to the local organisation team :


CZI’s new Deep Tissue Imaging RFA aims to advance the field of deep tissue imaging and support the development of technologies that will allow researchers to view information at cellular resolution, in complex tissue and through skin and bone, in living organisms. CZI invites scientists to apply for this 2 1/2-year grant opportunity, and grants will be for $1 million in total costs per grantee

In the first phase of the RFA, grantees will develop a pilot project. Successful outcomes could include the development of imaging technologies and biological probes needed to visualize and label important cellular processes throughout the body, or new computational techniques and algorithms for deep tissue signal extraction and analysis. In the second phase of the RFA, successful grantees will be eligible to apply for four-year, $10 million technology development grant awards. Final determination of awards and numbers will depend on the quality of the applications received. 

Scientific Scope

The long-term goal of this initiative is to drive technology development aimed at visualizing cellular structure and function throughout the body. During this pilot phase, they especially seek proposals that support the development of tools for visualizing cellular level processes in deep tissue. This funding opportunity is explicitly aimed at technology development. It is not intended to support question-driven basic or translational research, clinical trials, or drug development.

Examples of research themes:

·         Bioacoustic probe, hardware, and/or method development

·         Biomagnetic probe, hardware, and/or method development

·         Biochemical probe or method development

·         Multi-photon hardware or method development

·         Deep imaging tissue techniques with potential human applicability

The Deep Tissue Imaging RFA will accept Letters of Intent starting Thursday, July 9, 2020 at 9 a.m. Pacific time until Thursday, August 6, 2020 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.

CZI’s Imaging Scientists Cycle 2 RFA is also currently open until July 30, 2020 at 5 p.m. Pacific Time. Read more about CZI’s Imaging program.

More information about CZI’s Deep Tissue Imaging RFA: