CanSERV invites applications covering the entire range of the oncology developmental pipeline, from supporting discoveries in fundamental research to translational science and personalized oncology, addressing at least one of the four strategic goals of the Cancer Mission:

• Understanding of Cancer
• Prevention and Early Detection
• Diagnosis and treatment
• Quality of life for patients and their families

Researchers from academia, industry and SMEs may apply for several service categories including:

1. disease models,
2. cutting-edge imaging and structural biology technologies,
3. biomarker research and development,
4. new therapeutic solutions,
5. complex clinical trial design and support,
6. personalized oncology implementation pipelines and recommendations and
7. regulatory support and tools to analyse the socioeconomic dimension of research activities.

Launch of the first call is today, Thursday, October 12, 2023.

Submission deadline is January 4, 2024 at 14.00 CEST.

For more information and call text please visit their CanSERV project website www.canSERV.eu/Calls or contact them at canservprojects@eurobioimaging.eu.

To know which Euro-Imaging’s technologies can help your research project, visit their website www.eurobioimaging.eu/service

In order to answer image data analysis demands, France-BioImaging is launching its first data machine learning competition! The idea? To develop powerful methods that will then end up in creating standards & benchmarks in the field of bioimaging.

The FBI challenge is hinged on a double contribution: from core facilities engineers and from data scientists. The first group will acquire a large number of images to build a dataset, that will later be used by the algorithms. These images will be produced by microscopy engineers & technicians from FBI’s platforms. As for the second contribution, this is where the challenge starts! The challenge will be later published to have a maximum of data scientists to work on the algorithms that best fulfill the analysis task.

The first project is also based on four pillars:

• Open source + FAIR (Findable, Accessible, Interoperable, Reusable)
• Supervised learning, it involves annotated datasets to maintain control over performances.
• In silico annotations, a computer labeling method to avoid manual annotation and its drawbacks.
• Image-to-image analysis tasks, an image analysis tasks which aim to predict an output image from the input one.

We need you!

The first challenge is still under preparation. It will predict the fluorescence image of cell culture from a bright field, phase contrast and/or DIC microscopy label-free image. Nevertheless, we need you to contribute to the dataset that will supply the machine learning! The more images we have, the better the prediction algorithm will be.

If you are interested, please contact Dorian Kauffmann: dorian.kauffmann@france-bioimaging.org.

  FBI opens a call for the recruitment of its next Deputy Director for Internal Affairs

Mission

The Deputy Director for Internal Affairs will help infrastructure management team to oversee several of its key missions: implement a strategic vision for France-BioImaging, encompassing our three pillars, Innovation, Training, Access; develop a roadmap for next generation imaging technologies and services; increase funding opportunities and develop a sustainable cost model; update and improve infrastructure communication goals and actions; develop ours links with the private sector.
The Deputy Director will work closely with the Manager of Internal Affairs to tailor specific activities, prepare strategic decision-making and prioritize needs for initiatives.

Mandate of the Deputy Director for Internal Affairs

• Help to develop and implement the strategic vision of FBI’s core activities, in Innovation, Training and Services; synthesize and prepare elements to assist in decision-making
• Advise the management team to improve cooperation across FBI geographical Nodes; promote the scientific and structuring activities of the infrastructure at the national level, to seek out and federate potential partners, initiate and manage national cooperation programs, and provide expertise and advice.
• Develop a roadmap for technological developments and their implementation as FBI services
• Help to develop funding opportunities and develop a sustainable cost model for Innovation and Services
• Develop links with the private sector, as users of FBI services or partners in FBI core activities including methodological innovations
• Organize a prospective reflection on the development of new initiatives to be carried out to improve FBI communication

Skills

• Senior scientist (DR or equivalent) with a strong motivation and willingness to strengthen FBI core activities in Innovation, Service and Training;
• Knowledge of the national landscape in biological imaging, including in innovation and services;
• Experience in the management of research units or facilities, and projects in the science and innovation domain;
• Demonstrated experience in fund raising operations for research and innovation projects in biological imaging;
• Knowledge of the national and international research infrastructures in Biology and Health environment
• Experience in interdisciplinary scientific and stakeholder networking;
• Demonstrated ability to work collaboratively with diverse stakeholders;
• Excellent communications and public relations skills;
• High proficiency in English language

Organisation

France-BioImaging is a national research infrastructure distributed throughout France that provides researchers with access to the latest innovations in biological imaging and aims to accelerate the transfer of technological and methodological innovations in biological imaging to the 22 platforms
that constitute the infrastructure. The Deputy Director for Internal Affairs will contribute to the development and strengthening of France-Bioimaging.
The Deputy Director for Internal Affairs will work within the national coordination of the France BioImaging infrastructure. He/she will work within a team distributed between Montpellier and Bordeaux, composed of 4 people: the Scientific Director and the Deputy Director for International Affairs, the Internal Affairs Manager, and the External Affairs Manager.

Time Commitment

FBI’s Deputy Director for Internal Affairs should commit approximately 20% of his overall working time to this mission. Virtual coordination meetings (Directors + Managers) occur weekly, and the FBI Executive Board meets virtually monthly. FBI steering committee meets bi-annually. The Deputy Director is appointed for a 5-year mandate and is eligible to renew his service.

Requirements

Frequent travels in France and abroad.

Entry into function is planned as soon as possible / November 15th, 2023.

If you are interested,
please send a short CV and a motivation letter at direction@france-bioimaging.org

You can now apply for two new calls to get free open access to instruments and services at one of our nodes’ core facility!

We are very pleased to share France-BioImaging Activity Report 2021-2022 with the broad community.

Browse through it and discover France-BioImaging activities, our Nodes, our users’ projects, our governance and our achievements in 2021-2022.

FBI Activity Report 2021-2022

Read more publications on Calaméo

You can also view and download the document as a PDF here.

The previous activity report is also available right here, check it out!

Have a great reading!

France-BioImaging primary mission is to develop, promote, disseminate and provide access to innovative instruments and imaging technologies in the field of bioimaging to scientists. Fostering the technological transfers is at the heart of this mission, and for this France-BioImaging relies on a strong association of leading R&D research teams with core facilities.

However, several bottlenecks exist and often hamper or prevent successful technology transfer:

• A lack of human resource leads to difficulties in transferring and stabilizing the technology which is not enough user-friendly
• A technology that is too specific, with not enough user base
• A difficulty to contract with industry through institutional offices for industrial valuation
• In the context of image analysis: the instability of open software economical model, inter-operability, large data handling and algorithm complexity

As a way to tackle these bottlenecks, France-BioImaging launched in January 2021 its first “FBI Internal Call 2021: Technology transfer from the R&D teams to the core facilities” to promote the transfer of new technologies (instrumentation, probes, staining methods, software, data analysis or data visualization) from the R&D teams to the facilities of France-BioImaging, for access and service to end-users. The outcome of the transfer project had to ensure for the prototype to be usable by the end-users until the interpretation of the data. The project had also to include a sustainability plan and a training plan to guide both facility staff and end-users toward autonomy.

The project selection was organized by the National Coordination of France-BioImaging and applications were assessed according to the following evaluation criteria:

• Innovation and originality of the proposal
• Scientific quality, implementation, timeline
• Competitive positioning
• Adequacy of resources with the proposed project
• Economic impact and tech transfer potential and perspectives
• Estimation of the user market and potential for user adoption
• Plan for training and sustainability.

2022 laureates

For the first edition of the “FBI Internal Call 2021: Technology transfer from the R&D teams to the core facilities”, 5 projects were selected:

• Icy@FBI: Jean-Christophe Olivo-Marin (IPDM Node), Broadening the scope of applications of Icy (http://icy.bioimageanalysis.org/) by implementing several key new bioimage analysis components
• BIC-HCS-SMLM: Jean-Baptiste Sibarita (Bordeaux Node), Technological transfer of a Single-Molecule-based High Content Screening platform to the Bordeaux Imaging Center
• CloudFISH: Marcello Nollmann (Montpellier Node), A tool for the analysis of single-molecule RNA and DNA FISH images
• MorphoNet: Emmanuel Faure (Montpellier Node), An interactive online morphological browser to explore complex multi-scale data
• BioImageIT (https://bioimageit.github.io/#/about): Jean Salamero, Sylvain Prigent (IPDM Node), An open source framework for integration of image data management with analysis

2023 laureates

The call was renewed for another edition in 2022! Here are the 7 laureates:

• UV_FLIM NA: Yves Mely (Alsace Node), Microscope for live cell imaging of fully functional nucleic acids by Fluorescence Lifetime Imaging Microscopy coupled to Ultra-Violet excitation
• RIM-Ouest: Marc Tramier (Bretagne-Loire Node), Random Illumination Microscopy transfer in Rennes
• TempFoCash: Laurent Bourdieu (Paris-Centre Node), 3D-ultrafast optical functional activity recordings based of TEMPoral FOcusing and Custom Access Serial Holography
• Side C.A.R.S.: Elric Esposito (Paris-Centre Node), Stand-alone temporal synchronization module for CARS microscopy
• 3D LIGHTiss: Laurent Malaquin (Toulouse Node), Development of an Embedded Optical Lens MicroPhysiological System for Mesoscopic Live Deep 3D High-Resolution Imaging
• MAPS: Cyril Favard (Montpellier Node), Multicolor imaging and Absolute positioning using Planar all dielectric Surface enhanced TIRF microscopy
• FBI-MIN: Emmanuel Margeat (Montpellier node), Implementation of a RASTMIN / p-MINFLUX microscope

Each selected project was awarded with a 80k€ grant for salary and/or equipment, and several positions are currently available: https://france-bioimaging.org/jobs/

This event, organized by the Bioimaging axis and the Image analysis working group of Biogenouest, will take place at Pôle Numérique Rennes Villejean, on October 4th, 2023.

It will be divided into 4 parts:

Three lectures:

• Jean-Yves Tinevez, Image Analysis Hub core facility, Institut Pasteur
• Francesca Galassi, Empenn team, INRIA Rennes – Bretagne Atlantique
• FBI.Data project, France-BioImaging

Two small-group workshops followed by plenary feedback sessions

A pitch session to present image processing issues on your platform

A poster session over lunch

Please register before September 29th, 2023 on the following link: docs.google.com/forms/d/e/1FAIpQLSfkyXjNvYInLjU0v0WPOd10PFsufjDy3uoVpnhr9avNMVJZzw/viewform

This visit was the perfect occasion to have a look on the broad range of technologies and expertise both nodes are providing in open access to their users. They cover a multitude of imaging techniques in electron microscopy, light microscopy and cytometry and working on various models going from the single cell to small animals. Besides, they both provide excellent services in – of course – imaging expertise, but also in sample preparation and bioimage analysis.

Furthermore, we discussed about the future of the nodes and their promising perspectives. The core facilities and R&D teams are working towards novel innovative imaging technologies that, we hope, will be in open access very soon!

Thank you to all of the following core facilities and R&D teams for the warm welcome:

• MRI
• PIBBS
• IPAM
• OV-CI
• MIMA2
• Morphoscope
• ImCy
• Imagerie-Gif
• PFIC

We were happy to meet everyone! Until next time!

Photos from our visit at the Montpellier node:

Photos from our visit at the Ile-de-France Sud node:

We are happy to announce that our 1st Africa-France Joint Initiative for Biological Imaging calls, in coordination with the African BioImaging Consortium and Imaging Africa, is funding 11 projects!

As a reminder, these two calls (“External access” and “Twinning exchange”) have been primarily designed to strengthen collaboration between African and French researchers and engineers in all fields in biology, health and agro-ecology, where the contribution of the rapidly expanding technologies of digital imaging has become essential. The ambition of these calls is in line with the anticipation of bilateral research funding programs between Europe and Africa in the framework of the Horizon Europe Program.

Multiple scientists from the entire African continent have responded to the calls, covering 8 countries: Senegal, Togo, Nigeria, Ivory Coast, Burkina Faso, Morocco, Uganda and South Africa. Besides, we are very glad that 5 of our nodes (Paris-Centre, Montpellier, Bordeaux, Ile-de-France Sud and Bretagne-Loire) are going to work in the framework of the Africa-France Joint Initiative for Biological Imaging.

Finally, the projects have been selected for the need to access imaging resources in response to key challenges that African researchers are facing. Among them, scientists tackle issues in several topics going from infectious diseases to marine biology, but also cancer research, plant biology and climate change. 

Here are the selected projects

Call 1 “External Access”:

• Production of digitised teaching tools (anatomical and histological sections) for bachelor’s and master’s students – Aliou NDIAYE, Département de Biologie végétale, Université Cheikh Anta DIOP, Dakar, Sénégal – with Montpellier node

• VCAPE – Effects of climatic variability on the anatomical properties of Pterocarpus erinaceus Poir. wood in Togo – Kossi Novinyo SEGLA, Laboratoire de recherche forestière, Université de Lomé, Togo – with Montpellier node

• TRITUICAFH – The role of imaging techniques to understand the initial cellular aspects on functionalized hydrogels – David Olubiyi OBADA, Multifunctional Materials Laboratory, Department of Mechanical Engineering, Ahmadu Bello University, Nigeria – with Paris-Centre node

• AfluBio – Botanical quality of plant raw materials used in African pharmacopoeia products: histological study and localisation of active biomolecules by autofluorescence – Akoua Clémentine YAO, Plateforme Microscopie électronique et Bioproductions, Centre Suisse de recherches Scientifiques en Côte d’Ivoire (CSRS) / Université NANGUI ABROGOUA, Côte d’Ivoire – with Bordeaux node

• Ultrastructural Evaluation of Tramadol-induced Testicular Toxicity in Wistar Rats – Adebanji AKINGBABE, Department of Anatomy EKSU, Ekiti State University, Nigeria – with Ile-de-France Sud node

• MeCap – Histological analysis of Carica papaya roots infested by Meloidogyne javanica – Laëtitia COULIBALY, Laboratoire Mixte International (LMI) crée entre l’Institut de l‘Environnement et de Recherches Agricoles (INERA) et l’Institut de Recherche pour le Développement (IRD) à Bobo Dioulasso, Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso – with Montpellier node

• OTOSHAPE – Study of otolith shape as a tool for determining the structure of sole (Cynoglossus senegalensis) stocks using ImageJ: towards sustainable management of fishery resources – Khady DIOUF, Laboratoire de Biologie marine, Institut fondamental d’Afrique noire cheikh Anta Diop / Université Cheikh Anta Diop de Dakar, Senegal – with Bretagne-Loire node

• Study of the interface of native endomycorrhizae using high-resolution microanalysis methods – Malik NDIAYE, Laboratoire de biotechnologies végétales, UCAD, Senegal – with Montpellier node

Call 2 “Twinning Exchange”:

• Twinning between the electron microscopy core facility of the Centre National de la Recherche Scientifique et Technique (CNRST) of Rabat (Morocco) and the Plateforme d’imagerie cellulaire et tissulaire (PICT) from the Institut Curie Paris – Mohamed EL BOUJI, Centre National pour la Recherche Scientifique et Technique (CNRST), Laboratoire de microscopie électronique en transmission – division UATRS, Rabat, Morocco – with Paris-Centre node

• Africa-France Open BioImaging Initiative (AFOBII) – William WASSWA, Mbarara University of Science and Technology (MUST), Medical Imaging and Artificial Intelligence Lab (MIAL), Mbarara, Uganda – with Paris-Centre node

• Exchange of expertise in light sheet microscopy (lattice and others) and serial block face electron microscopy. Comparison of strategies to prepare challenging samples and EDX in biological samples – Madelaine FRAZENBURG, Microscopy Unit, University of Stellenbosch, Cape Town, South Africa – with Paris-Centre node

Congratulations to all the laureates! We are eager to welcome you on our core facilities!

Stay tuned to know more about these project’s unfolding!

High-content screening (HCS) is a technology used in drug discovery and research to analyze cell phenotype. HCS has created new opportunities for studying biological phenomena as it combines high-throughput screening methods with automated microscopy on microplate format. Using automated cell manipulations and microscopy platforms, it is possible to easily screen the effects of selected drugs on the model’s phenotype. This technology, available at France-BioImaging at Montpellier Ressources Imaging (MRI), has been used in a recent study identifying therapeutic drugs for a fatal neurodegenerative disorder, the Giant Axonal Neuropathy (GAN). Benoît Bordignon and Cédric Hassen-Khodja, screening experts at the MRI and co-authors in this recent publication, tell you more about the reasons why the HCS technology was essential!

Get routinely quick acquisition of numerous samples with HCS

As mentioned before, High-Content Screening uses automated cell manipulations and automated microscopy platforms to easily visualize the modification of the phenotype. In other words, it allows image acquisitions and analysis of a large number of samples, and collects data of biological parameters of interest directly for statistical analysis. Image acquisition and analysis are done in batches and rapidly, which limit potential bias as the process will be identical from one well to another. A huge advantage that prevents issues and saves time!

Imaging can help therapeutic research

Giant axonal neuropathy (GAN) is a fatal neurodegenerative disorder for which there is currently no treatment. Affecting the nervous system, GAN starts in infancy with motor deficits that rapidly evolve toward total loss of ambulation. Using the gan zebrafish model that reproduces the loss of motility as seen in patients, scientists conducted the first pharmacological screening for the GAN pathology. They combined behavioral, in silico, and high-content imaging analyses to identify drugs restoring locomotion, axonal outgrowth, and stabilizing neuromuscular junctions in the gan zebrafish. 

This is when imaging becomes essential! To validate at cellular level the last 103 selected hits, they have developed a custom-made High-Content Screening method to check if the phenotype was also restored at the cellular level in gan zebrafish, in particular on neuromuscular junction (NMJ) and axonal function. The postsynaptic nature of the drug’s cellular targets provides direct evidence for the pivotal role the neuromuscular junction holds in the restoration of motility. 

The results of this study identify the first drug candidates that can now be integrated in a repositioning approach to fasten therapy for the GAN disease.

Scientists working on this study therefore created an automated image analysis protocol using HCS to quantify neuromuscular junctions’ number/size and measure axon length in treated gan zebrafish. Thus, image data treatment had a central place in this study. And this is just an example! This novel high-content imaging methodology represents a useful automated procedure that can be transferred to other neuromuscular conditions for mechanistic studies and drug screening.

Thanks to Benoît Bordignon and Cédric Hassen-Khodja for providing very helpful insights of the study!

Get access to one of our services!

You need HCS or another imaging technology or expertise that France-BioImaging provides? To get open access, please login via Euro-BioImaging website! You just have to choose the technology you want to use, then submit your proposal. All applications will be processed by the Euro-BioImaging Hub in close relation with France-BioImaging. And of course, all scientists regardless of their affiliation, area of expertise or field of activity can benefit from open access services! Users whose projects will be validated by Euro-BioImaging will benefit from a waiver for the access cost on France-BioImaging core facilities (france-bioimaging.org/access)

Lescouzères, L., Hassen‐Khodja, C., Baudot, A., Bordignon, B., & Bomont, P. (2023). A multilevel screening pipeline in zebrafish identifies therapeutic drugs for GAN. EMBO Molecular Medicine, e16267. https://doi.org/10.15252/emmm.202216267

COMULISglobe aims at consolidating and extending a collaborative and innovative network that promotes MultiModal Imaging and analysis across scales (MMI) from biological research to clinical diagnostics. To this aim, they 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. COMULIS have two calls and support schemes open:

1. Global Showcases: This call can fund up to 3 showcase projects (with up to 12k Euros each) that tackle an outstanding biomedical research question using two or more imaging modalities across countries. Eligible expenses are travel costs for lab exchanges, consumables, instrumentation access, supplies, or sample mailing fees. Please send your 2-page applications to andreas.walter@hs-aalen.de by July 23rd, 2023. Projects need to take place between September 1st, 2023 and April, 30th,2025.
Find more info here: https://www.comulis.eu/comulisglobeshowcase-projects

2. Lab Exchanges/Mobility Grants: These lab exchange fellowships are aimed at supporting individual mobility, strengthening the existing networks and fostering collaborations by allowing PhD students, Early Career Investigators (ECIs), facility staff and experienced researchers in the field of MultiModal Imaging to visit an institution, laboratory or industry in another country. The lab exchange will be offered on regular competitive calls throughout the duration of the CZI grant.
Find more info here: https://www.comulis.eu/comulisglobe-lab-exchange