Two projects recently received funding from the Chan-Zuckerberg Initiative (CZI), in which France-BioImaging members take part actively: COMULIS and NEUBIAS. Two community building activities breaking up frontiers to gather scientists around one goal: developing biological imaging.

COMULIS

COMULIS received a 2-year funding from CZI to expand their network both globally and sustainably. Being designed to harness the power of multimodal imaging (MMI) across scales, from basic to clinical diagnostics, this European initiative aims at facilitating access and training a new generation of scientists for whom multimodal imaging will be the new norm. Thanks to this grant, the project will be consolidated and it will help extend the collaborative and innovative network to establish a global multimodal imaging association (COMULISglobe) and ensure long term sustainability.

MMI integrates the best features of combined techniques and overcomes limitations faced when applying single modalities independently. MMI relies on the joint expertise from biologists, physicists, chemists, clinicians, and computer scientists, and depends on coordinated activities and knowledge transfer between technology developers and users. To achieve this inherently interdisciplinary goal, the ultimate goal is toestablish a network of scientists across continents and disciplines, from academia to industry, including transnational research facilities (e.g. synchrotrons, Euro-BioImaging ERIC), to foster and market MMI as a versatile tool in biomedical research and diagnostics.

COMULISglobe will help bridge the gap between biological and clinical imaging, identify, fund, and showcase novel multimodal pipelines, and develop, evaluate, and publish correlation software through dedicated networking activities, including conferences, training schools, open databases, and fellowships for lab exchanges, access to research infrastructures, and conference attendance. And, of course, all outputs of the project will be open access!

Please do not hesitate to join the community and help organize activities or publications – and please share the news, mobility and access grants available at: https://www.comulis.eu/comulisglobe-czi

Thanks to Perrine Paul-Gilloteaux, Bretagne-Loire node of France-BioImaging, for taking part of this amazing project!

NEUBIAS

The international Network of European BioImage Analysts (NEUBIAS), hosted by German BioImaging has also received a 2-year funding from the Chan Zuckerberg Initiative (CZI) as part of their Advancing Imaging through Collaborative Projects program. This grant will secure the sustainability of NEUBIAS, establish strong connections to similar initiatives, and share knowledge about state-of-the-art bioimage analysis tools and methods globally.

Spreading the profession of bioimage analysts and bioimage analysis knowledge internationally are the major aims of NEUBIAS. Modern life-sciences are unthinkable without advanced microscopy imaging techniques and quantitative bioimage analysis. This grant will help ensure novices and experts can access cutting edge techniques, reduce duplications of effort, and support everyone who is working to making new discoveries possible.

NEUBIAS had a tremendous impact on the community by training a powerful generation of bioimage analysts across Europe and beyond. The next step of this project will expand the network internationally and connect to related imaging and image analysis societies around the globe. With that in mind, the project includes travel grant opportunities for early-career bioimage analysts who seek to join NEUBIAS activities, explicitly including scientists outside central Europe. Besides, a dedicated team will work on collecting bioimage analysis teaching materials and make them accessible to the global imaging and life science community.

Great news for both projects that – we hope – will continue to write the great story of bioimaging!

Thanks to Florian Levet, Bordeaux node of France-BioImaging, for being a member of this fantastic project!

Brettanomyces bruxellensis is one of the most damaging spoilage yeasts in the wine industry because of its impact on the beverage’s flavor. Lysiane Brocard, research engineer specialised in plant biology at the Bordeaux Imaging Center (FBI Bordeaux node), recently co-published an article on this yeast cell surface and bioadhesion properties.  

Fruits are transformed into beverages through fermentation processes carried out by microorganisms naturally present in the environment. In wine, yeasts and bacteria play this role and contribute to the development of volatile compounds. Scientists targeted Brettanomyces bruxellensis in this study, a yeast famous for the production of volatile phenols, characterized by horse sweat odors which is – usually – not very enjoyable for the consumer. 

A yeast characterized by bioadhesion abilities

This specific odor comes from volatile compounds, the 4-ethylgaïacol (4EG) and 4-ethylphenol (4 EP), that winemakers try to avoid. Beside adding an unpleasable flavor to the beverage, the issue is that the spoilage yeast is persistent in cellars over several years, resulting in recurrent wine contamination. This suggests a bioadhesion process that helps the microorganism to survive in its environment. To put it simply, bioadhesion is the ability of an organism to adhere on a surface to, then, participate in the formation of a biofilm (which is defined as “a structured community of microorganisms adhered to a surface and producing an extracellular matrix”). 

Here, 54 strains of B. bruxellensis were characterized for their cell surface physico-chemical and bioadhesion properties. And all of them have shown bioadhesion abilities (after only three hours on stainless steel) both on synthetic medium and wine. Enough to highlight the persistence of our favorite horse sweat flavored yeast. 

How did bioimaging help in this project?

Among all the analytical methods used in this study, microscopy helped identify the structure of the biofilms formed with B. bruxellensis. Two imaging techniques were used: confocal microscopy and scanning electron microscopy. The first one offers the advantage of realizing live imaging without being too time-consuming. With fluorescent dyes, the status of cells can be easily determined at the same time as the cell repartitions and concentrations.

Moreover, comparisons have been made thanks to confocal microscopy to determine if some strains of B. bruxellensis could form biofilm with only one cell layer or if they proliferate in three dimensions. To complete these observations, scanning electron microscopy was performed at the Bordeaux Imaging Center (FBI Bordeaux node) with the help of Isabelle Svahn, expert of this type of microscopy. It was a great addition to this study as these observations validated the morphological variability among Brettanomyces strains.

Bioimaging helped a broader project about Brettanomyces led by Isabelle Masneuf-Pomarède who works in the Institut des Sciences de la Vigne et du Vin of Bordeaux. Isabelle studies the persistence and proliferation of Brettanomyces over the years. Isabelle’s PhD student, Paul Le Montagner, carried out most of the experiments published in this paper. Thanks to them for this amazing paper!

Confocal microscopy observations after 3h of bioadhesion of cells on stainless steel
SEM observation of 3h-aged cells adhered on stainless steel

Original article: Paul Le Montagner, Morgan Guilbaud, Cécile Miot-Sertier, Lysiane Brocard, Warren Albertin, Patricia Ballestra, Marguerite Dols-Lafargue, Vincent Renouf, Virginie Moine, Marie-Noëlle Bellon-Fontaine, Isabelle Masneuf-Pomarède, High intraspecific variation of the cell surface physico-chemical and bioadhesion properties in Brettanomyces bruxellensis, Food Microbiology, Volume 112, 2023, 104217, ISSN 0740-0020, https://doi.org/10.1016/j.fm.2023.104217

You are interested in our bioimaging services, including technologies and expertise?

Please contact us at: contact@france-bioimaging.org

An innovative technology to look at thick samples at high resolution? Marc Tramier, a group leader at the Institute of Genetics & Development of the University of Rennes/INSERM/CNRS, and scientific director of MRic (Microscopy Rennes Imaging Centre), is currently working with his team on Random Illumination Microscopy (RIM), a fast and easy to use microscopy technique with low phototoxicity. His facility, which is part of the Bretagne-Loire Node of France-BioImaging, offers RIM as a Euro-BioImaging Proof-of-Concept study, and is now accepting applications for projects. He explains the ideas behind RIM in the article below.

The idea of Random Illumination Microscopy is to use the speckle of the illumination laser in wide field to create a structured illumination pattern at the diffraction limit. By varying the pattern from image to image using a diffracting element (in our case a SLM), scientists are able to acquire a stack of images (around 100 images) on a camera which corresponds to a cumulative homogeneous illumination. By resolving the inverse problem, a super-resolved image is, then, reconstructed, at the focal plane with unprecedented optical sectioning. In comparison to conventional SIM, RIM is able to work in depth inside diffusive samples as the speckle is insensitive to diffusion. 

A transfer full of advantages

The method was first implemented by Thomas Mangeat – that we are happy to welcome in our new Toulouse node! – and collaborators in Toulouse (Mangeat et al., 2021. doi: 10.1016/j.crmeth.2021.100009). In the MRic, after the transfer of the prototype, the facility was able to image microvilli of intestine in c-elegans (depth > 50µm) having a spatial resolution of around 100 nm. This structure is impossible to be revealed by conventional confocal microscopy. Before the use of RIM, only the airyscan approach allowed us to resolve the microvilli but with higher illumination power (photobleaching of the sample) and longer acquisition time (around 10 times more). Now with RIM, we are able to follow microvilli in the living C–elegans at the second time-scale during several minutes.

RIM is one of the powerful methods to achieve super-resolved images in depth at high speed with very low phototoxicity. This makes a very nice compromise of z-sectioning and super-resolution with wide field illumination particularly adapted to thick live samples. Beside reconstruction and data analysis, MRic is offering a user-friendly system, with a complete set of microscopy methods for live sample investigation, from wide-field to light sheet including spinning disk, confocal and airyscan. And of course, this technology is available in open access through France-BioImaging and Euro-BioImaging!

How to apply to use RIM:

Random Illumination Microscopy is part of the Euro-BioImaging Proof-of-Concept study, in collaboration with our Nodes. The Proof-of-Concept study makes it possible to introduce exciting, new imaging technologies to our portfolio that were previously unavailable via our network. We are currently accepting applications to use these technologies as part of the Proof-of-Concept study. Be part of this study – and contribute to community-wide continuous technological innovation!

All scientists, regardless of their affiliation, area of expertise or field of activity can benefit from Euro-BioImaging’s pan-European open access services. Potential users of these new technologies are encouraged to submit project proposals via our website. To do so, you can Login to access our application platform, choose the technology you want to use and the facility you wish to visit, then submit your proposal. All applications will be processed by the Euro-BioImaging Hub. As usual, users will benefit from advice and guidance by technical experts working at the Nodes, training opportunities, and data management services. 

For more information:  info@eurobioimaging.eu 

Thank you Marc Tramier and Marianna Childress, communication officer of Euro-BioImaging, for the original article.

What’s up in multimodal imaging? The FBI CLEM day is renewed for a 2023 edition on March 13 at the Institut Pasteur in Paris.

This event is a great opportunity to discuss about multimodal imaging with expert presentations.
In addition to these talks, poster sessions will intersperse the day.

Registration is free but mandatory.
Please registrate before March 8, 2023 through the following link:
https://docs.google.com/forms/d/e/1FAIpQLScLGEUzzJmeJiZToKjak2myJwJeu3aLwLItt787doaGTKWrSA/viewform?vc=0&c=0&w=1&flr=0

Program down below

From February 6th to February 10th, France-BioImaging organised a group meeting on the project “FBI.data” in Bordeaux. For a week, participants focused on the architecture and the implementation of image data management tools. A user-friendly response to the challenges of never-ending data production. 

New imaging technologies are very greedy in terms of image processing and data management. Beside the image itself, biological imaging generates a huge amount of metadata. The FBI.data project, one of the key missions of France-BioImaging, addresses the questions related to the computational analysis and handling of image data. 

Speeding up the implementation of tools across the infrastructure

Although the distributed FBI.data team meets once per week, the FBI.data Sprint aims at only focusing on data management scenarii and accelerating the project. Two essential aspects have been discussed:

  • First of all, the data management system architecture must be simple for them to be implemented across France-BioImaging nodes. It also has to be compatible with long-term data storage and of course, to be user-friendly – we want to keep it easy for our users! 
  • The second point is all about anticipating as many data management cases as possible. Running through all the needs of bioimaging experts and users, the team lists the specific features of each case and considers the perfect solutions for all of them.

Working for the FAIRisation of data

The FAIRisation of data for Open Science is an initiative fully endorsed by France-BioImaging. Meaning that data are Findable, Accessible, Interoperable and Reusable, the benefits for the bioimaging community are numerous. It improves transparency and reproducibility, enhances quality of results, accelerates scientific progress and method development and finally boosts collaboration within the scientific community. 

OMERO, developed by the University of Dundee & Open Microscopy Environment teams, on which the FBI.data group is working, is one of the software making user data FAIR. Being a microscopy image data management decentralised platform, it helps organise, access and archive data. Besides, it combines image and metadata storage, a viewer and data analysis resources. Furthermore, OMERO is linked to the most valuable tools for bioimaging experts (ImageJ, Napari, QPath, etc.). And users can access their data from anywhere and keep them safe.

But much more has to be set up to have functional solutions: to ease user authentication and management, manage big data transfer, and have an adequate metadata scheme. Accompanying users is one of the mission of the FBI.data team, and the FBI.data Sprint is also the occasion to join efforts from the training working group led by the training mission officer Fabrice Cordelières (Bordeaux Imaging Center) to produce adequate training material on data management.

Sharing efforts and helping the community

The FBI.data working group is composed of:

By joining their skills and experience, they are working together on setting up tools and good practices for the management and FAIRisation of data inside France-BioImaging nodes but also for the entire bioimaging community. With this in mind, the project has collaboration with, among others, the Institut Français de Bioinformatique (IFB) and the Centre National de Ressources Biologiques Marines (EMBRC), and other infrastructure through the MUDIS4LS Equipex+ project. Moreover, the FBI.data project has an open GitLab, providing image data management codes in open source, and a blog with tutorials, recommendations and so much more!

Check the France-BioImaging OMERO web portal: https://omero-fbi.fr/

And its gitlab FBI data · GitLab (in2p3.fr)

Learn more about our missions and working packages: https://france-bioimaging.org/about/work-packages/

This is the first edition of our Summer School outside of France, going to South America in synchrony with the IEEE SPS-EMBS ISBI Conference in Colombia.

The spirit of our Summer School was established in French Brittany in 1994 (by Christian ROUX and Jean-Louis COATRIEUX). This Summer School has become a worldwide reference with international lecturers from 20 countries and accessible to young scientists from all around the world. Our Summer School is an open yet privileged place for exchanges and discussions on major on-going research and technologies. Informal and warm, we always select a location and design a program where ample time is dedicated to interactions between lecturers and students.

The Summer School is open to graduate students (MSc., PhD), post doctoral scientists, radiologists, biologists, researchers and engineers in industry.

Being designed in response to imaging challenges, the Roboscope is the product of a collaboration between Marc Tramier’s team (FBI Bretagne-Loire node) with Julia Bonnet-Gélébart, research engineer, Jacques Pécréaux’s team of the Institut Génétique & Développement de Rennes (IGDR), and the Inscoper company, spin-off of the lab. This technology could become a great timesaver for fluorescence microscopy.

Allowing the automation of fluorescence microscope acquisitions, the Roboscope is an embedded technology based on a deep learning algorithm. To be precise, it is a predesigned event-driven acquisition (PEDA) based on a learning automatization of any cellular changes tracked by fluorescence. Catching rare and fast cellular events then becomes possible!

The use of the Roboscope would also save precious time of research, providing users with results without the need to stand by the microscope during acquisition. This technology goes beyond as they will be able to recover the data already classified and with only the specific points of illumination that they have previously triggered. 

A broad range of applications

The teams have almost finished to develop an entire algorithm monitoring the cell cycle progression in mitosis. These events specific to the cellular division correspond to major challenges in the control and treatment of cancer progression (Kops, 2005). As the cell cycle study is needed to understand several biological processes helping the development of targeted drugs, the technology aims to monitor efficiently and automatically simple cell models through their division cycle. 

And this is not its only benefit: this automatized fluorescence microscopy acquisition can be adapted in very diverse fields. From a cell cycle progression analysis to specific analysis, organelles, proteins and biological events can be tracked or activated within cells. A noteworthy advantage of the integrated device that – we hope – will be deployed widely in the future. 

Workflow of a Roboscope experiment. 1. The user annotate a bench of images with different class of interest to be detected. 2. The pre-trained Convolutional Neural Network is adjusted for the experiment by fine tuning and/or transfer learning. 3. The algorithm is transfered on embedded systems to perform real-time image analysis during microscopy acquisition. 4. The biological application with event-driven acquisition is defined and started by the user in order to start, interrupt and parametrize different acquisition sequence following real-time image analysis and event classification.

The next Euro-BioImaging User Forum will be taking place on 21.03.2023 from 2-5 pm CEST, focusing on the topic of “Cardiovascular Research”. 

Register here

Euro-BioImaging is looking forward to featuring some of the excellent science supported by the work of EuBI nodes via presentations from your users. The presentations will be 15 min long and will include the opportunity to briefly introduce your Node. In addition the event will feature two keynote presentations.

Abstracts can be submitted here – https://forms.gle/XriAc5HTMiLAhACG6 
The deadline for abstract submission is on February 6th. 

All users who are working in the area of cardiovascular research are welcome ! The topic is broad as it includes vascular and cardiac development and/or regeneration, development of cardiovascular disease, inflammation in response to cardiovascular injury, etc. The users also do not have to be Euro-BioImaging users.

Euro-Bioimaging is looking forward to receiving your abstracts!

Explore the beauty of the invisible world through the 2023 FBI digital calendar!

Enjoy the diversity of microscopy techniques, models and applications represented, one image at a time. All 12 images used for this calendar were submitted to France-BioImaging Image Contest 2022.

A big thank you again to all the participants!

You can download the A4 print version (one month per page) 2023 FBI digital calendar here:

If you wish to use it as your computer desktop, you can download a PNG version of each month here:

France BioImaging and all the French community aims to develop and promote innovative imaging technologies and methods. But microscopy images can also take an artistic, creative look and make the invisible world beautiful, allowing people to see the visual appeal of the life sciences. 

We enjoyed the diversity of the images submitted with many different microscopy techniques, models and applications represented. A big thank you to all the participants!

The National Coordination Team and the Executive Board are proud to announce the winners of the FBI Image Contest 2022:

  • 1st Place: Carole SIRET, Van de Pavert Team, Centre d’Immunologie de Marseille-Luminy

Little Monster

The embryonic formation of lymph nodes, small organs essential for the immune response, is now known. Using light sheet microscopy, scientists were able to determine the dynamics at work in this 13.5-day-old mouse embryo. In blue, the lymphoid cells (LTi), derived from the haematogenous endothelium, a specific tissue of the embryo. They pass into the liver where they proliferate before migrating through the body to give rise to lymph nodes. The 3D information obtained thus makes it possible to follow the interactions of lymph nodes with their environment, in particular with nerve cells, in green, and blood vessels, in white. The lymphatic endothelial cells and some macrophages are visible in red.

Lightsheet Microscopy

  • 2nd Place: Magalie BENARD, Plateforme de Recherche en IMAgerie CEllulaire de Normandie (PRIMACEN), Research infrastructure HeRacLeS, Inserm US 51, CNRS UAR 2026,

“The communication link with others”

Image of a cellular interconnection between two human tumor cells whose cytoskeleton has been labeled with anti-tubulin (ATTO-647N), anti-vimentin (AlexaFluor594) antibodies and with Phalloidin probe (AlexaFluor488). Scale bar 1µm.

Confocal microscopy

  • 3rd Place: Frédéric FERCOQ, Parasites et Protistes Libres (PPL), Museum National d’Histoire Naturelle

“Sepia”

Stage 25 cuttlefish embryo (Sepia officinalis) observed under a confocal microscope.
The cuttlefish was cleared and the tissue autofluorescence was captured.

This image was produced in collaboration with Laure BONNAUD-PONTICELLI and Luis MOLINA from the BOREA laboratory.

Confocal microscopy

Congratulations to the winners!


Explore all the images submitted here:

As stated in the Terms & Conditions of the contest, foreign participants non-affiliated to a French institution are featured in the gallery, but were not evaluated as part of the contest.

Since 2019, the “Cristal collectif” medal rewards teams supporting research with their technical expertise, the collective dimension, their innovation and outreach. Both nationally and internationally recognised, the Bordeaux Imaging Center (BIC) from the France-BioImaging node of Bordeaux received this award for providing access to innovating technologies and for the quality of its training. The BIC was commended for its investment in training, especially for its partnership with the International School of Neurosciences, a unique partnership in Europe. The CNRS also has particularly highlighted the core facility’s activities of research and development in implementing new techniques and image analysis. Among its achievements, the BIC has succeeded to optimize a homemade Lattice Light Sheet, which has the benefit of being a good compromise between resolution, acquisition speed, imaging depth and low phototoxicity.

© Gautier Dufau

Laureates :

  • Lysiane Brocard, Plant Unit manager
  • Fabrice Cordelières, Image analysis manager
  • Mathieu Ducros, R&D Lattice Light Sheet Microscopy manager
  • Mónica Fernández Monreal, R&D CLEM manager
  • Étienne Gontier, Electronic Unit manager
  • Sabrina Lacomme, Transmission Electron Microscopy manager
  • Florian Levet, R&D software manager
  • Sébastien Marais, Confocal and Two-photon Microscopy manager
  • Magali Mondin, Super-resolution Microscopy manager
  • Melina Petrel, Cryo-preparation and immunomarking manager
  • Christel Poujol, Photonic Unit manager
  • Isabelle Svahn, Scanning Electron Microscopy manager
  • Jérémie Teillon, Clarification and Light-Sheet Microscopy manager

More information: www.cnrs.fr/fr/talent/index

Imagerie-Gif core facility, from our Ile-de-France Sud node, is pleased to announce the acquisition of a Scanning Ion Beam Electron Microscope (FIB-SEM) and a Lattice Structured Illumination Microscope (SIM) Elyra 7. For the occasion, the core facility is organizing “3D Res/volution“, a scientific event on high-resolution 3D imaging on December 15, 2022 from 2:00 pm to 5:00 pm at B21 amphitheatre. This event will be a great opportunity to introduce to you the possibilities of these 2 new systems available at Imagerie-Gif.

Free but mandatory registration: https://evento.renater.fr/survey/3d-res-volution-day-8pdzetbi