Initially published on Euro BioImaging ERIC website (https://www.eurobioimaging.eu/news/imaging-technologies-used-to-understand-covid-19-infection-/), 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 image.sc 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 https://neubiasacademy.org

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

Speakers

  • 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 www.chanzuckerberg.com.

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 www.globalbioimaging.org.

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.

Visit Bretagne-Loire Node web page

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 RECHERCHE DES CHARGE·ES DE MISSION

• 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.

Contacts: Jean.Salamero@curie.fr, Edouard.Bertrand@igmm.cnrs.fr, caroline.thiriet@france-bioimaging.org

Mission-Officers-FBI_V4-1Download

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 www.eurobioimaging.eu. 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 BIOIMAGING IS PART OF THE GAME

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  (https://www.eurobioimaging.eu/nodes/french-bioimaging-node) and training activities (https://www.eurobioimaging.eu/content/training).

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.

More info on FBI international activities

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.

This 3-day interactive training event will take place at the Institut Pasteur in Paris from the 20th to the 22nd of November 2019.

The program is divided into 2 parts :

Part 1 (Wednesday 20th of November) will include conferences and round tables on personal development in core facilities in the morning, and 3 parallel workshops in the afternoon.

Part 2 (Thursday 21st and Friday 22nd of November) will include workshops in the morning (« How to identify and demonstrate your skills » and « Storytelling, communication and oral fluency ») and extensive discussions with Institut Pasteur core facility staff in the afternoon, on the occasion of visits to technological platforms and animal facilities.

You can either register for the whole event [Part 1 + Part 2] or for Part 1 only.

Part 1 only: you will have to choose by order of preference the workshop you would like to attend in the afternoon of November 20th.

Part1 + Part 2: you will additionally have to choose the Institut Pasteur facilities that you wish to visit, by order of preference (NB : only 20 persons will be selected for Part 2). Each participant will be able to visit 2 different core facilities (at least one of them outside their own field of specialty).

Targeted audience : Any person already working in a core facility or interested by core facility careers, in particular

* Technicians, engineers and scientists working in Life Science core facilities

* Students who are carrying out a traineeship in core facilities or who are considering to become core facility professionals

* Technicians, engineers and scientists who are not currently working in core facilities but are wondering if this could be an opportunity for them in the future

Registration fees :

Part 1 : 80€ for CTLS members, 100€ for non-members.

[Part 1&2] : 120€ for CTLS members, 150€ for non-members.

Bursaries :

 5 bursaries (400 euros each) are available for CTLS members participating to the full workshop (parts 1&2).

For any question, you can email us at ctls2019@pasteur.fr

 Local Organizing Committee :

Nathalie AULNER, Gabriel AYME, Marion BERARD, Evelyne DUFOUR, Patrick ENGLAND, Anna KEHRES, Mariette MATONDO, Mariana MESEL-LEMOINE, Sophie NOVAULT, Patrick WEBER.

The QBI 2020 Conference will be held at the University of Oxford’s Mathematical Institute, Oxford, UK between January 6-9, 2020.

The idea for a conference on Quantitative BioImaging followed from the recognition that there is no conference to date that addresses, in a focused and interdisciplinary manner, the analysis of bioimaging data.

The deadline for the abstract submission for QBI 2020 in Oxford has been extended. The new deadline is now Monday 9 September 2019.

The abstract submission site is:  https://www.quantitativebioimaging.com/qbi2020/abstract-submission/

We seek contributions in any area of quantitative microscopy. Presentations that demonstrate new approaches and methodologies are particularly welcome, including but not limited to algorithmic and software developments, physical modeling approaches, etc. The use of quantitative imaging techniques in biological applications is also of great interest. For submission details, please see the conference website (www.quantitativebioimaging.com).

In addition to contributed talks we will feature minisymposia on:

  • Imaging in Immunology
  • Volumetric Imaging
  • New frontiers in single molecule microscopy
  • Correlative microscopy
  • Spatial Statistics in Microscopy
  • Bioimage Informatics
  • Modern machine learning approaches to image analysis and uncertainty quantification in microscopy
  • Tissue multiplexing techniques and applications in oncology

The planned conference workshops are:

  • Spatial statistics in bioimaging analysis
  • Introduction to scientific programming for image analysts
  • Cluster and photon counting analysis
  • Single molecule localization microscopy flight simulator

A new feature of the conference is a challenges session:

  • Challenges in subcellular trafficking

A plenary discussion panel on

  • Uses and misuses of machine learning

The keynote speakers of the conference are: 

  • Jennifer Lippincott-Schwartz, Janelia Farm
  • Wolfgang Baumeister, Max Planck Institute, Munich

Other confirmed speakers to date are: Dylan Owen, University College London; Melike Lakadamyali, University of Pennsylvanial; Steve Presse, Arizona State; Kristin Grussmayer, EPFL; Aleksandra Radenovic, EPFL; Christian Soeller, University of Exeter; Alexander Jesacher, Innsbruck; Dirk-Peter Herten, Heidelberg; Michael Dustin, Oxford; Gerhard Schütz, Vienna; Fred Maxfield, New York; Daniel Wuestner, Odense; Christoph Wuelfing, Bristol; Thibault Lagache, Columbia University, New York; Thierry Pecot, Hollings Cancer Center at the Medical University of South Carolina; Ilaria Testa, Stockholm; Gail McConnell, Strathclyde; Charles Kervrann, Rennes; Edward Cohen, Imperial College, London; Anish Abraham, College Station; Jean-Baptiste Sibarita, University of Bordeaux; Thomas Walter, Institute Curie, Paris; Luke Lavis, Janelia Farm; Lei Tian, Boston; Andrew York, San Francisco; Bernd Bodenmiller, Zuerich; Josephine Bunch, National Physical Laboratory, UK; Jan-Otto Hooghoudt, Aalborg University; Rasmus Waagepetersen, Aalborg University; Lucy Collinson, London; Roarke Horstmeyer, Durham, NC, USA; Badri Roysam, Houston; Sandrine Leveque-Fort, Paris; Frederick Klauschen, Institute of Pathology, Charite – University Medicine Berlin; Shanon Seger, Hoffman La-Roche, Switzerland, Marino Zerial, Dresden.

Our student and post-doc section is planning the following events:

  • Meet the experts
  • Career opportunities in academia and industry

Please see the conference website (www.quantitativebioimaging.com) for more information, including list of the confirmed speakers. The site will be updated as new programmatic information becomes available.

To obtain email updates, please sign up for membership of the QBI Society at www.quantitativebioimaging.com. Membership is free of charge.

Subscribe to our newsletters and be the first to know more about the QBI 2020 conference. Register here if not a member already.

Après le succès de Bordeaux en 2017 et à l’occasion de son soixantième anniversaire, la Société Française des Microscopies (Sfµ) a choisi la ville de Poitiers pour accueillir la seizième édition de son colloque. Suite aux traditionnels ateliers de formation qui se dérouleront le lundi 1er juillet 2019, le colloque se tiendra du 2 au 5 juillet 2019 dans les locaux de l’Ecole Nationale Supérieure d’Ingénieurs de Poitiers (ENSIP).

Le colloque de la Sfµ a vocation à rassembler la plus large communauté autour des études développant ou faisant usage des microscopies (électronique, optique, à champ proche, sonde atomique tomographique, …). Le programme scientifique s’articulera autour de douze symposia : quatre orientés Sciences du Vivant (SDV), quatre dédiés aux Sciences des Matériaux (SDV) et quatre symposia communs (SDV/SDM) à l’image de l’interdisciplinarité qui caractérise notre société. Les thèmes abordés dans plusieurs symposia seront l’occasion de pérenniser notre partenariat avec le GN-MEBA qui tiendra ses journées semestrielles à la même période à Poitiers. Le programme scientifique du colloque et la liste des conférenciers et conférencières invités sont consultables ici.

Il est encore temps….. N’hésitez pas à déposer vos résumés !!!!
Après avoir créé un compte dans l’espace Sfμ, vous pourrez soumettre vos contributions: https://colloque.sfmu.fr/fr/inscription/soumission/

Les inscriptions au colloque sont ouvertes à un tarif préférentiel jusqu’au 15 mai 2019: https://colloque.sfmu.fr/fr/inscription/frais/

Le 25 mai 2019, l’Institut Cochin vous invite à découvrir ses outils innovants d’imagerie biologique et leurs applications en recherche biomédicale.