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,

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.


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:

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:

The F1000R Gateway NEUBIAS aims to fill an important gap in the field of Bioimage Analysis: To improve and standardize how to publish reproducible and reusable components and workflows, and to gather resources and training material to help BioImage Analysts grow as a professional community of experts.

The primary aim of this gateway is to be the hub for the exchange of knowledge about bioimage analysis and its related fields, by offering a common place to publish this knowledge. This includes newly developed bioimage analysis strategies, practical applications in challenging topics, and cutting-edge development in Bioimage Analysis. The Gateway accepts all topics that contribute to the enhancement of the capability of bioimage analysis, spanning image processing, analysis, visualization and statistical methods, bioimage analysis workflows, software packages, machine learning based approaches, data mining, architecture and storage management, and more. The submission, publication, review and indexation process are fully detailed here


NEUBIAS, COST Action CA15124, will support the F1000R article publication charges for a selected number of original articles presenting research results/methods/software on topics of bioimage analysis (see figure above).
The first Call for Papers opens on June 15th and closes on July 15th, 2020.


1) You provide, in the following form, the title, abstract and complementary description for the article you aim to publish.

2) Your proposal is evaluated by the Advisory Board of the Gateway (

3) Upon acceptance by the Advisory Board and prior to the submission of your full manuscript, NEUBIAS will waive the publication charges in direct communication with F1000R.

15th of July 2020: Call is closing,
1st of August 2020: Notification of acceptance of NEUBIAS support,
August-September 2020: granted authors write and submit their contributions,
30th of September 2020: Deadline to submit the full version of your article to the Neubias F1000R gateway.

IMPORTANT NOTE: The approval of your proposal is necessary before submission of your article. Articles submitted to F1000R before being approved will not be considered to be responding to this Call and will not be eligible for financial support. This policy ensures the same treatment of all the submissions; the pre-inquiry has to be submitted by all the authors, and the provided information will be used for assessment. The board will not review the full submissions before their publication.

NEUBIAS has a fixed budget for this Call, therefore only medium and short articles will be considered. The final number of articles to be supported depends on the numbers of submissions of each type.
We aim to support around 20 articles, distributed tentatively in two categories:
11 Short Articles (up to 1000 words)
9 Medium Articles (up to 2500 words)

Please check for Articles guidelines, types and formats in F1000R at

The Chan Zuckerberg Initiative invites applications for five-year grants to support the work of Imaging Scientists employed in imaging core facilities at non-profit universities or research institutes across the world. Learn about the grantees from the first cycle and view the first RFA.

The Chan Zuckerberg Initiative (CZI) seeks to support the work of up to 15 Imaging Scientists who will work at the interface of biology, microscopy hardware, and imaging software at imaging core facilities across the world. “Imaging Scientists” might be engineers, physicists, mathematicians, computer scientists, or biologists who have focused on technology development in either light or electron microscopy, medical imaging, or data analysis fields. The primary goal of the program is to increase interactions between biologists and technology experts. The Imaging Scientists will have expertise in imaging hardware or software. A successful “Imaging Program” will employ an Imaging Scientist who: a) works collaboratively with experimental biologists on projects at the imaging core; b) participates in courses that disseminate advanced microscopy methods and analysis; c) trains students and postdocs in imaging technology; d) participates in a network of CZI Imaging Scientists to identify needs and drive advances in the imaging field; e) attends twice-yearly CZI scientific workshops and meetings in imaging and adjacent biomedical areas. Each grant will fund salary and fringe benefits for an Imaging Scientist at the imaging core, a modest travel and teaching budget, plus 15% indirect costs. The award period is three years plus an additional two years, awarded as a separate grant, if the Imaging Program passes a review at year three.

More info on the RFA:

Application deadline: July 30th, 2020

Initially published on Euro BioImaging ERIC website (, on May 27th, 2020

[FBI Bordeaux Node] is contributing to an important study led by the University of Bordeaux to understand COVID-19 infection and inflammatory response using fully differentiated human bronchial epithelium as model. Fluorescent imaging techniques such as immune fluorescence and RNAscope technology will be used in this highly relevant physiological system to determine if a particular cell type is (preferentially) infected by the virus. Dr Harald Wodrich, INSERM Research Director at the University of Bordeaux, explains.

The study, called ANACONDA, is funded by the French ANR Flash COVID-19 call. It combines the unique expertise of four local partners: Dr. Thomas Trian, from the Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, who had previously developed a model of differentiated airway epithelia to study asthma, Prof. Denis Malvy, head of the tropical and infectious diseases unit at the CHU and regional coordinator of the SARS-CoV-2 response, Marie-Line Andreola and Harald Wodrich, from the MFP CNRS UMR 5234 at the University of Bordeaux, experts on highly pathogenic RNA-viruses and virus microscopy, and the Bordeaux Imaging Center for virus imaging at the cellular level.

Interdisciplinary collaboration

The objective of the study is to understand the contribution of the bronchial epithelium to the immune response triggered by SARS-CoV-2 infection and causing high morbidity. SARS-CoV-2 infection will be analysed according to the presence of respiratory diseases such as COPD. Different risk factors (age, gender, tobacco consumption and diabetes) will also be taken into account. Specimens are obtained from the thoracic surgery unit of the CHU of Bordeaux, and virus propagation and infection assays are done in the BSL3 facility of the UMS TBM core of Bordeaux University under the supervision of Dr. Marie-Line Andreola. 

Fluorescent imaging technology & RNAscope

Within this study, imaging in only performed on fixed material because the BSL3 is not equipped with the necessary imaging infrastructure to follow live SARS-CoV-2. Dr. Wodrich, an experienced user of the Bordeaux Imaging Center’s facilities, uses classical indirect immune fluorescence to label viral proteins and identify infected cells. In addition antibodies against cellular markers are used and specific cell types in the differentiated epithelium are identified (E.g. antibodies against acetylated tubulin, Muc5AC, keratin V and SCGB1A1 to detect ciliated airway epithelial cells, mucus cells, basal cells and club cells respectively).

RNAscope technology is also an important part of this study. RNAscope works with the principle of RNA in situ fluorescence hybridisation (RNA-FISH) and will be used to detect SARS-CoV-2 genomes but also viral mRNAs to follow viral replication and gene expression. 

Part of a unique network of European research infrastructures

The Bordeaux Imaging Center (BIC) is one of the hot spots for fluorescence microscopy in France. More than just a platform providing high-end microscopes, it is also involved in R&D. Their experienced and dedicated staff provides a lot of local support with image acquisition and image analysis. This will be especially important for reconstructing 3-D images of infected epithelia to trace virus propagation.

As part of France BioImaging, the Bordeaux Imaging Center is a Euro-BioImaging Node, part of the ESFRI research infrastructure of high-quality imaging facilities across Europe, committed to open access to imaging instruments and sharing expertise, training opportunities and data management services.

All scientists, regardless of their affiliation, area of expertise or field of activity can benefit from these pan-European open access services by contacting Euro-BioImaging.

The final results of this important study will be published in a scientific journal and all imaging data will hopefully be shared with the community in an open access repository.