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.

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.

NEUBIAS Academy is a new initiative, aimed to provide sustainable material and activities focused on Training in Bioimage Analysis. NEUBIAS Academy capitalizes on the success of NEUBIAS’ 15 Training Schools (2016-2020) that have supported over 400 trainees (Early Career Scientists, Facility Staff and Bioimage Analysts), but could not satisfy the high and increasing demand (almost 1000 applicants). A team of about 20 members will interact with a larger pool of hundreds of trainers, analysts and developers to bring knowledge and bleeding-edge updates to the community.

NEUBIAS Academy @ Home: Online events

NEUBIAS aims to support the community with a new series of live online events targeting all levels of Bioimage Analysis Technology, with intensive activity to best serve the community during the currently challenging period of confinement:

Live Online Courses will provide interactivity with the audience (e.g. exercises in virtual breakout rooms), 

Live Webinars will target a larger audience with specific topics, software tools, theoretical content or critical updates, from introductions to concepts to very advanced implementations. Questions and Answers will be moderated by experts. Webinars will be recorded and made available on Youtube NEUBIAS Channel, and a thread per event will be opened in the Forum to report Q&As and to welcome further questions/comments.

Starting list of confirmed events:

14-15 April: IJ/Fiji Macro Programming, online course. Register now !

21 April: Introduction to Machine Learning and DeepImageJ  Register now !

22 April: Bioimage Analysis with Icy Register now !

29 April: Quantitative Pathology and Bioimage Analysis: QuPath v0.2.0

30 April: Advanced Image Processing with MorphoLibJ

You’ll find more information on

The Fluorescence Microscopy Workshop will include a symposium (17th march) with a series of seminars to explore the latest technological and scientific developments in fluorescence microscopy. This year, talks around both acquisition and analysis in living imaging will be designed with scientific and commercial presentations. This edition promises a lot of intense scientific discussions on these topics. 

This symposium, which will take place in the auditorium of the François Jacob building, represents a unique opportunity to hear from the leading experts in fluorescence microscopy about their latest research findings.

To coincide with this event, various companies will also be invited to display their state-of-the-art technological equipment with demonstrations on the campus 12companies have accepted the invitation to come and present either their technology or their materials.  

This 5th edition of FMW benefits from direct financial supports from invited companies and the C2RT for the organization. We strongly encourage PhD students and post-docs to participate to this workshop

Keynote : Emmanuel G. Reynaud, UCD Centre for Biomedical Engineering, Dublin
Light Sheet Microscopy for the masses


  • Edouard Bertrand, IGMM, Montpellier
  • Rut Carballido-Lopez, Micalis, INRAE
  • Akos Diosdi, Biological Research Centre (BRC), Szeged, Hungary 
  • Capucine Grandjean, Institut Pasteur
  • Romain Levayer, Institut Pasteur
  • Jean-Léon Maitre, Institut Curie
  • Jean-Christophe Olivo-Marin, Institut Pasteur
  • Ralph Palmisano, Optical Imaging Center Erlangen (OICE)
  • Anna Pepe, Institut Pasteur
  • Perrine Paul-Gilloteaux, MicroPICell, Université de Nantes

Invited Companies for demonstrations 

Abbelight, Abberior, Amira, Andor, Bruker, Coherent, DRVISION/Aivia, Leica, Nikon, Olympus,Syglass, Zeiss

Registration is free but mandatory : WWW.PASTEUR.FR/EN/FMWV

The organizing committee :

  • Education department : Thierry Lang, Virginie Ponticelli, Hervé Waxin
  • UTechS Photonic BioImaging (Imagopole)/C2RT : Nathalie Aulner, Julien Fernandes, Lesly Raulin,  Audrey Salles 
  • Image Analysis Hub/C2RT : Stéphane Rigaud

On January 28th, 2020, the Chan Zuckerberg Initiative (CZI) announced over $1.3 million in funding to support Global BioImaging (GBI), an international network of bioimaging facilities and communities. These networks of core imaging centers help researchers better understand and identify the biological mechanisms of health and disease using cutting-edge technology. 

While imaging of molecules, cells, and tissues remains central to both biomedical research and clinical practice, progress in the imaging field has been slowed by uneven access to advanced microscopy methods. The grant supports GBI’s efforts to strengthen community building and training worldwide to address the practical challenges of operating open access tools for imaging technologies in the life sciences. 

“Imaging of molecules, cells, and tissues is integral to understanding disease, and core imaging facilities that use the latest microscopy tools to further the research of hundreds of biomedical scientists are fundamental to progress,” said CZI Head of Science, Cori Bargmann. “By bolstering the development of Global BioImaging’s central hub and investing in training and data exchange between imaging centers and communities, we hope to increase global collaboration and accelerate potentially life-saving scientific breakthroughs.”  

The three-year grant will support Global BioImaging’s core activities, allowing the organization to develop a self-sustaining administrative framework. CZI funding will also allow Global BioImaging to expand its worldwide network; intensify training, job shadowing, and outreach efforts; and strengthen links to the biomedical imaging community. In addition, funds will support nations to strengthen the scientific foundations of imaging in their own countries. Global BioImaging’s community includes members from the United States, Europe, Australia, Singapore, Canada, Mexico, India, Japan, South Africa, and more.

“Discussions with imaging scientists have confirmed a strong need for training material and courses for staff that work at imaging centers, information on best practices for data handling, and increased opportunities for collaboration,” said CZI Imaging Program Lead, Stephani Otte. “We are excited to help meet these needs and spur scientific discovery in this critical area of biomedicine.”

CZI’s continued investment in the imaging field is part of its ambitious mission of supporting the science and technology that will make it possible to cure, prevent, or manage all diseases by the end of this century. Through its Imaging Scientists program, CZI supports imaging scientists and staff scientists working at core facilities in the U.S., increasing collaboration between biologists and technology experts and improving the imaging tools that scientists use. 

About the Chan Zuckerberg Initiative

Founded by Dr. Priscilla Chan and Mark Zuckerberg in 2015, the Chan Zuckerberg Initiative (CZI) is a new kind of philanthropy that’s leveraging technology to help solve some of the world’s toughest challenges — from eradicating disease, to improving education, to reforming the criminal justice system. Across three core Initiative focus areas of Science, Education, and Justice & Opportunity, we’re pairing engineering with grant-making, impact investing, and policy and advocacy work to help build an inclusive, just and healthy future for everyone. For more information, please visit

About Global BioImaging

Global BioImaging is an international network of imaging infrastructures and communities, which is coordinated by the international organization EMBL (European Molecular Biology Laboratory, Heidelberg, Germany). Recognizing that scientific, technical and data challenges are universal and not restricted by geographical boundaries, Global BioImaging brings together imaging facility managers and technical staff, and scientists and science policy officers from around the globe, to join forces and build capacity internationally. It provides a unique opportunity for international discussion and cooperation to tackle the practical challenges as well as the strategic questions linked to operating open access, cutting-edge imaging centers. By doing so, Global BioImaging supports the international scientific community to build the infrastructure they need to boost fundamental and applied research and drive breakthrough discoveries in the life sciences and beyond. For more information, please visit

Following the final decision of France BioImaging Institutional Committee on October 29th, 2019, we are delighted to announce that a new node is joining France BioImaging: the Bretagne-Loire Node.

The new Bretagne-Loire Node is composed of four cellular and tissue imaging platforms: APEX, H2P2, MicroPICell and MRic-of the Bioimaging axis of GIS Biogenouest and research and development teams (belonging to IGDR, Numecan, Cesam, Inria-Rennes, PAnTher@Oniris, LS2N) that support the activities of these platforms.

Located in Nantes and Rennes, the four platforms have the IBiSA certification and their expertise in life imaging and pathological anatomy are complementary.

The mission of the node is to provide the latest technological and methodological advances in microscopy for an integrated understanding of cellular and tissue activities in particular for preclinical research. 

The Bretagne-Loire Node has expertise in technology transfer and translational research and benefits from a privileged scientific environment due to its affiliation with the University Hospital Centres and the Nantes Veterinary School.

This integration is completing the node candidate evaluation process started in 2016.

Welcome to the FBI Bretagne-Loire Node!

L’infrastructure nationale “France-BioImaging”, membre de l’ERIC-EuroBioImaging nouvellement créé, va élargir son périmètre et renforcera ses activités sur 2020-2025. Cette amplification nécessite un meilleur partage des tâches au sein de la gouvernance.


• France BioImaging (FBI) est l’infrastructure nationale pour l’imagerie biologique, ayant pour tutelle principale le CNRS.
• Les chargé·es de mission ont des activités opérationnelles internes à
l’infrastructure (IR), en cohérence avec la feuille de route stratégique
approuvée par le comité de pilotage.
• Les chargé·es de missions recevront un « mandat-lettre de mission » de
la direction de FBI, approuvé par le bureau exécutif.
• Ils/Elles sont nommé·es par le Bureau Exécutif pour 5 ans maximum.
• Ils/Elles participent aux réunions du Bureau Exécutif de FBI (1 par mois),
selon l’ordre du jour.
• Les personnes intéressées doivent avoir un poste dans une EPST et doivent fournir un CV et une déclaration de candidature et les envoyer à la direction de FBI (voir contacts ci dessous).

Les différents profils et livrables sont détailés dans le PDF ci-dessous.

Les personnes hors périmètre FBI peuvent candidater.


On October 29th, 2019, the European Commission has officially established Euro-BioImaging as a European Research Infrastructure Consortium (ERIC1) for state-of-the-art imaging services in biological and biomedical research, allowing the foundation of the Euro-BioImaging ERIC and the implementation of a full range of imaging services to life scientists across Europe.

With its ERIC status, Euro-BioImaging is now legally recognised as a European research infrastructure2 for biological and biomedical imaging. Euro-BioImaging offers life scientists open access to imaging instruments, expertise, training opportunities, and data management services that they do not find at their home institutions or among their collaboration partners. All scientists, regardless of affiliation, area of expertise, or field of activity, can benefit from these pan-European open access services. Euro-BioImaging will ensure excellent research and development across the life sciences in Europe. All Euro-BioImaging services are accessible via Establishment of the Euro-BioImaging ERIC builds on over 10 years of preparatory work with active engagement of 25 national imaging communities, funded by the European Commission and coordinated by the European Molecular Biology Laboratory (EMBL). 

Finland will host the Statutory Seat, the access gateway, and manage the overall coordination of Euro-BioImaging, while EMBL will coordinate access to biological imaging, and Italy will coordinate access to biomedical imaging. EMBL will also coordinate Euro-BioImaging’s data services via the BioImage Archive to store and share imaging data.

Euro-BioImaging offers state-of-the-art imaging services through its internationally renowned facilities, called Nodes. These Nodes are distributed across Euro-BioImaging’s 15 founding members: Austria, Bulgaria, Czech Republic, Denmark, EMBL, Finland, France, Hungary, Israel, Italy, Norway, Netherlands, Portugal, Sweden, and the UK. Belgium will participate as an observer.


France officially became a founding member of the Euro-Bioimaging research infrastructure in March 2019. As an active collaborator in the development of the future infrastructure since its inception (2009) and during the preparatory phases of the Euro BioImaging ESFRI project (2010 – 2018) and as a previous “Node Candidate” of the project since 2013, France BioImaging represents today the only French Node and the single entry point in Biological Imaging in this new European research infrastructure. FBI core facilities will be participating directly in the activities carried out by the EuBI ERIC, opening their premises to EuBI users for access  ( and training activities (

Also, the involvement of France BioImaging, and therefore of the French biological imaging community, at the European level directly contributes to promote the French expertise in biological imaging and strengthens the role of France as an essential partner for future initiatives/projects in Europe.

The European Commission implementing decision (EU) 2019/1854 of 29 October 2019 setting up the European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences — Euro-BioImaging European Research Infrastructure Consortium (Euro-BioImaging ERIC) has been published in the Official Journal of European Union on 6 November 2019. Read the Commission Decision here.

1: What is an ERIC? A European Research Infrastructure Consortium, or ERIC, is a specific legal form to facilitate the establishment and operation of research infrastructures of European interest. ERIC status endows research infrastructures with a legal personality recognised in all EU Member States.

2: What are research infrastructures? Research infrastructures are facilities, resources, and related services used by the scientific community to conduct research and foster innovation. They include major scientific equipment, resources such as collections, archives or scientific data, e-infrastructures such as data and computing systems, and communication networks. Their development has been coordinated through the European Strategic Forum on Research Infrastructures (ESFRI) since 2002. ESFRI is a strategic instrument to develop the scientific integration of Europe and to strengthen its international outreach.