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.
  • Deadline: February 28th, 2023
  • For users from a unit attached to the INSB who do not usually use Research Infrastructures’ services for their projects
  • For access to technologies and related expertise
  • For access to expertise in data analysis
  • The scientific project must be a project in the process of being finalized

The field of Life Sciences has undergone major developments over the past two decades. The change of scales, both in spatial and temporal resolution, and the integration of data from a wide variety of sources, as induced by the development of technologies, have revolutionized the exploration of life. These technologies call for expensive investments and specific knowhow, carried out by highly qualified personnel, having led to the creation of common infrastructures such as research infrastructures (IRs) open to the entire scientific community.

The Institut des Sciences Biologiques (INSB) from Centre National de la Recherche Scientifique (CNRS) is launching the second edition of a call for projects to fund full access to the national infrastructures in health and biology “INBS Access to national research infrastructures”. This call aims to encourage teams to get a first access to the services offered by Research Infrastructures to help their research project. The objective is to demonstrate the significant impact of these services to improve the quality of their results (resolution, reproducibility, change of scale, etc.) or to help remove technological barriers. We also aim to augment the awareness of our teams to the cutting-edge technologies, methods and expertise offered by these national infrastructures.

Program description

Access to Research Infrastructures is open to the entire French and international scientific community, with contribution to the running costs of equipment being charged to the users on quote, after project feasibility confirmation by the infrastructure. The purpose of this program is to facilitate and finance access to these infrastructures. Target audience are INSB teams new to a technology or method offered by these infrastructures, seeking to validate the contribution that the infrastructures could make to their research topic by removing barriers that impair the completion or finalization of an ongoing project of the team. A new project is not eligible to this call. The list of eligible Research Infrastructures, to which the research team could apply, is available here: Other infrastructures may be considered depending on the proven needs of the project. Several types of access can be supported by this call for projects:

  • Access to technologies and related expertise, upon quote from the infrastructures and confirmation of feasibility in 2023
  • Access to expertise in data analysis, upon quote from the infrastructures and confirmation of feasibility in 2023

In addition to the costs of access to infrastructure, upon a quote emitted by the infrastructure at the second stage of the call, travel/mission costs, as well as consumables that are not covered by the costs of access to infrastructure, may be covered. The funding for each project will be in the range of 10 to 30 K€.

Instructions for submission

This is two-stage submission.

The first stage consists of a letter of intent, prepared by the scientific leader of the project, outlining the project in finalization in which the application fits and highlighting the barriers that could be removed by access to IRs. The novelty for the team of the usage of the technology and methods to which this application would give access has to be underlined. This letter of intent must also be signed by the director of the applicant’s unit. The identification of the infrastructures to access is possible at this stage but not mandatory and the application can focus on the technology and methods needed. An estimated timeline is however welcome.

The letter of intent (maximum of three pages including figures and references, in French or English), signed by the unit director, accompanied by a CV of the project leader (maximum of two pages) must be sent before Tuesday 28th of February 2023 to the following address: These proposals will be screened for eligibility criteria and selected projects will go to the second phase on 8th of March: The second phase consists of a consultation between the INSB and the national Research Infrastructures. This will lead to putting the applicant in contact with the infrastructures that are able to meet the expressed needs, in order to evaluate the feasibility and to establish a quote from their official invoicing cost models.

This stage will lead to the final submission of the project, including the requested budget, signed by the heads of the involved IR(s), no later than Wednesday 22th of march 2023. Funding decision will be sent to the scientific leader beginning of April.

Project eligibility and selection criteria

Access to the infrastructure must be fully implemented before 31/12/2023 (deadline for the engagements of funds by the teams). A scientific and financial report will be asked to the granted team in June 2024.

The scientific project must be a project in the process of being finalized. Access to infrastructure must unlock or accelerate the project. The start of a scientific project is not eligible for this call.

The access to the infrastructure technology or expertise required should be new to the scientific leader.

A project can call to different infrastructures.

In the first stage, budget is not expected, but the project should demonstrate its feasibility from the team side before the end of 2023 if access to the required technologies or expertise is granted (for example identified human resource from the team to undertake the project) and by providing an estimated timeline. The infrastructure(s) will confirm it in the second stage.

Project will be screened for scientific quality of the scientific leader and of the project in finalization, the interest of the targeted method and technology to finalize the project, the novelty of access to the infrastructure. In the second stage, the quote produced by the infrastructure will assess the feasibility and adequacy to the budget.

Eligible expenses are:

  • Billing from the infrastructure based on quote presented at the second stage
  • Mission fees to access the infrastructures
  • Consumables needed to prepare samples for access if not provided by the infrastructures

MicroPICell core facility offers access and services to a broad range of bioimaging technology and expertise, specialized in cell and tissue imaging. Based in Nantes, the core facility is now certified ISO 9001 and NFX 50-900, demonstrating their investment in providing quality services to its users.

The ISO 9001 :2015 and NFX 50-900 :2016 standards ensures good practices in terms of organization and management of a life science core facility. These standards are focusing, among other criteria, on the ability to fulfill its scientific and technological research missions, to consistently provide products and services that meet customer and legal requirements and finally, aims to increase the satisfaction of its customers through the effective application of its management system.

A supported process

To implement the first standard, experts from MicroPICell core facility have been trained in the management of the required quality system. The core facility staff have then been supported, in close collaboration with the GIS Biogenouest, by the head of the IBISA quality mission in order to build and implement the quality system according to both standards. This “Groupement d’intérêt scientifique” also has a quality network, Iquare, to which the core facility participates in, to exchange, share and be advised in the implementation of the quality system. The NFX 50-900 :2016 standard has been applied on R&D projects such as the establishment of a digital histology center delivering deep learning data processing, smart microdissection or the imaging of thick samples in collaboration with the company Kaer Labs.

Guaranteeing quality to users

This double certification is a recognition of the core facility’s quality approach, and allows MicroPICell to guarantee to their industrial and academic users that the implemented tools and procedures meet the requirements of the standards. This quality approach facilitates day-to-day management and internal communication at the platform and with the various parties concerned. Above all, it is a way of continuously improving bioimaging core facilities and ensuring that the missions are carried out efficiently.

In coordination with the African BioImaging Consortium and Imaging Africa, two recently created initiatives, France-BioImaging wishes to extend its partnership with colleagues in Africa that have interest in using advanced microscopy approaches for their own research programs and projects. With this in mind and in the framework of the Horizon Europe Programme, France-BioImaging designed two calls to strengthen collaboration between African and French researchers in biology.

The call description and eligibility criteria are available here.

  •  Call 1: External Access 

The application form to be completed by the applicant is available here and must be submitted through the submission form below.

  •  Call 2: Twinning program African BioImaging-France-BioImaging communities 

The application form to be completed by the applicant is available here and must be submitted through the submission form below. 

Deadline for submission of proposals:   April 30th at 23h59 CET. 

En coordination avec l’African BioImaging Consortium et Imaging Africa, deux initiatives récemment créées, France-BioImaging (FBI) souhaite étendre son partenariat avec des collègues en Afrique qui ont un intérêt à utiliser des approches avancées de microscopie pour leurs propres programmes et projets de recherche. Dans cette optique et dans le cadre du programme Horizon Europe, France-BioImaging a conçu deux appels pour renforcer la collaboration entre les chercheurs africains et français en biologie.

La description des appels et les critères d’éligibilité sont disponibles ici.


  •  Appel à projet 1 : Accès externe 

Le formulaire à remplir est disponible ici et doit être soumis via le formulaire ci-dessous.

  •  Appel à projet 2 : Programme de jumelage/échanges des Communautés en BioImagerie Africaines et Françaises 

Le formulaire à remplir est disponible ici et doit être soumis via le formulaire ci-dessous.

Date limite de soumission des projets:   30 avril à 23h59 CET. 

Proposal submission


 Call 1: External Access/Accès externe 
Africa-France Joint Initiative for Biological Imaging 2022 - Call 1
Maximum upload size: 104.86MB

 Call 2: Twinning program African BioImaging-France-BioImaging communities/Programme de jumelage/échanges des Communautés en BioImagerie Africaines et Françaises 
Africa-France Joint Initiative for Biological Imaging 2022 - Call 2
Maximum upload size: 104.86MB

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


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:

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:

Initiated a few years ago, the Inria-IPL-NAVISCOPE (“Image guided NAvigation and Visualization data sets in live cell imaging and microscopy”) project aims at overcoming challenges of bioimaging observation. Virtual and augmented reality could become the new way to visualize and analyze microscope image renders.

Despite incredible progresses in microscopy, imaging biomolecular dynamics in cells remains a challenge. A lack of sensitivity, limited recording speed, photobleaching and phototoxicity associated have restrained, for a long time, our capacity to study biomolecules in their natural environments. As microscopy image is commonly observed on 2D screens, it can narrow human capacities to grasp volumetric, complex, and discrete biological dynamics. Following new modes of visualization including virtual reality (VR)/augmented reality (AR) approaches, the NAVISCOPE project allows more accurate analysis and exploration of large time series of volumetric images, such as those produced by the latest 3D + time fluorescence microscopy.

Why should cell biologists be interested in this project?

The project to which 4 FBI-teams from the BI-IPDM node participate, aims at engineering a technology made with and for biologists. For VR/AR approaches to be adopted by the broader bioimaging community, it is, indeed, important that they are evaluated by the biologists, on their own datasets. 

The potentials of VR/AR technologies for scientists are numerous: navigating into multidimensional, large data sets with another view angle or perception, interacting with these data especially by selecting subregions, quantifying features of interests, etc. New VR/AR approaches also provide specific quantification tools to show distances, angles, counting, local density, and histogram profiler or include a selection of regions of interest for further analysis such as the 3D Timelines. Moreover, because communication with analysis software coded in Java or Python is now integrated, more post-treatment analysis is possible on selected features, providing a multifaceted and accessible tool for biologists.

A promising future ahead

In practice, immersion of the user within 3D + time microscopy data still represents an acculturation challenge for the concerned community. Thus, to promote a broader adoption of these approaches by biologists, further dialogue is needed between the bioimaging community and the VR&AR developers. Nonetheless, future innovation can already be foreseen as there are multiple way to upgrade this technology. For example, using eye-tracking (Günther et al., 2020) or haptic interfaces (Petit et al., 2020) can improve human perception by providing local sensations, which would improve the selection of responses in a 3D + time space. Besides, a better integration of multiple channels with high pixel resolution or the addition of vector representations could add information about the orientation, movement of molecules or organization of structures such as cytoskeleton elements or membrane lipids. The prospects initiated by the NAVISCOPE projects are, as mentioned above, endless and could be a technology that reshapes the way we see biology at the hearth.

Full article on:

Challenges of intracellular visualization using virtual and augmented reality

Valades-Cruz Cesar Augusto, Leconte Ludovic, Fouche Gwendal, Blanc Thomas, Van Hille Nathan, Fournier Kevin, Laurent Tao, Gallean Benjamin, Deslandes Francois, Hajj Bassam, Faure Emmanuel, Argelaguet Ferran, Trubuil Alain, Isenberg Tobias, Masson Jean-Baptiste, Salamero Jean, Kervrann Charleseub

Front. Bioinform. 2:997082.

As the 2022 edition of the France-BioImaging Image Contest admissions is coming to an end, we wanted to highlight our previous winners and their projects. Here is a quick throwback to our 2021 winners.

Before getting to the heart of the matter, we want to remind you that you still have time (before November 11th) to submit your best images and try to win your registration fees for one 2023 microscopy-related event! Please make sure you upload your images on the following link:

FBI Image Contest 2022 – Last days to submit your images!

Last year, we enjoyed the winning images submitted for their artistic take and their quality. Thanks to Léna Meneux, Eunice HoYee Chan, Camille Boutin et Nicolas Brouilly for their beautiful images!

1st place: Léna Meneux, Eye Team, Institut des Neurosciences de Montpellier

"The eye of the storm"

Sensory fibers of a mouse cornea imaged with a confocal microscope. The corneal nerves converge toward the centre forming a vortex. This particular transgenic mouse model allows stochastic expression of fluorescent proteins, unravelling the heterogeneity of the fiber origines inside the corneal epithelium.
Acknowledgements to Karine Loulier for the mouse model and Laetitia Hudececk for her help during the acquisition.

In the Institut des Neurosciences de Montpellier since 2020, Léna is a PhD student working in the team Eye lead by Dr. Frédéric Michon. This team is investigating the mechanisms related to the preservation and the integrity of the anterior part of the eye, including the lacrimal gland, the tears and the cornea. Léna’s project focuses on the cellular and molecular effects of the corneal innervation on the corneal homeostasis. The project goes further as they aim at highlighting new targets able to prevent and/or repair corneal damage. 

The image she submitted for the 2021 France-BioImaging Image Contest (The eye of the storm) represents the sensory fibers of a mouse cornea. This innervation follows a typical pattern where all the nerves converge toward the centre forming a vortex. This particular transgenic mouse model allows random expression of fluorescent proteins, unravelling the heterogeneity of the fibers’ origin inside the corneal epithelium. As cornea is the most innervated tissue in the whole body, this model shows the differences between fibers. In pathological context, for example wound injury, it is thus possible to follow a specific fiber during the healing process.

France-Bioimaging sponsored her participation to the FOM (Focus on Microscopy) 2022 congress where she presented her project through a poster. Even though the congress was online, it gave her the opportunity to share her results with experts and as a consequence, to gather advice on her ongoing experiments.

2nd place: Eunice HoYee Chan, Muscle Dynamics Team, Developmental Biology Institute of Marseille (IBDM)

Myofibrils isolated from Drosophila indirect flight muscle labelled with titin (yellow) and actin (blue). Image captured from confocal microscope. We are studying the role of titin protein in muscle mechanics and organisation during development

"Sarcomeric bouquet"

Myofibrils isolated from Drosophila indirect flight muscle labelled with titin (yellow) and actin (blue). Image captured from confocal microscope. We are studying the role of titin protein in muscle mechanics and organisation during development.

Research engineer in Frank Schnorrer's team at Institut de Biologie du Développement de Marseille (IBDM), Eunice focuses her research on Drosophila muscle dynamic and organisation during development using advanced biophysical and imaging techniques.

The image she submitted named “Sarcomeric bouquet" was from one of her very first muscle myofibrils isolation experiment. She dissected flight muscles from flies and labelled the individualised myofibrils with Llama nanobodies conjugated with different epitopes. Those labelled myofibrils were then subjected to various imaging methods including standard confocal microscopy, super resolution microscopy and cryo electron-tomogram. Using these novel labelling tools and imaging techniques, her team could study the dynamic and organisation of muscles during development in details.

France-BioImaging sponsored her registration to the 49th European Muscle Conference in Prague (22-26 September 2022). As she is new to the muscle field, this conference offered a great opportunity to have a broad view on different kind of state-of-the-art imaging techniques. Besides, she gave a presentation during the conference, highlighting her work and initiating discussion.

3rd Place: Camille Boutin, Biology of multiciliated cells Team, Developmental Biology Institute of Marseille (IBDM) & Nicolas Brouilly, PICsL Imaging facility, Electron Microscopy department

Lamellar structure in a differentiating multiciliated cell observed by transmission electron microscopy with a Tecnai G2 200kV FEI.


Lamellar structure in a differentiating multiciliated cell observed by transmission electron microscopy with a Tecnai G2 200kV FEI.

Camille is a researcher in Laurent Kodjabachian’s group at the Institut de Biologie du Développement de Marseille (IBDM). She develops projects as a principal investigator on the compartmentalization and sizing of multiciliated cells. With this in mind, she routinely uses confocal and super-resolution microscopy but also scanning and transmission electron microscopy and tomography.

Nicolas is in charge of the Electron Microscopy Unit of the Plateforme d’imagerie commune du site de Luminy (PICsL). In addition to the routine sample preparation and 2D TEM imaging, this imaging facility offers, to internal and external users, advanced sample preparation (cryo-methods, immunolabelling...) and advanced imaging (tomography, CLEM, serial blockface…).

To understand the production of multiple centrioles in multiciliate cells, they focused on the deuterosome, a membrane-less organelle that has been described 50 years ago but whose composition, organisation and function remain unknown to this day. In this context they have developed an inducible multiciliated cells line. This image was taken during the initial characterisation of this cell line by transmission electron microscopy.

Thanks to the France-Bioimaging Image Contest, Nicolas participated to the COST COMULIS Conference that was held by the Cyprus Institute in Nikosia. It was a great opportunity to exchange with the people at the cutting edge of the multi-modal imaging field. The program covered subjects such as the sample preparation for multi-modal imaging, image analysis and integrated industrial partners.

Published on August 23rd, 2022 in EMBO reports, this article questions the way that core facilities should be recognized in the scientific literature and their key contributions to data lifecycle. An initiative endorsed by France-BioImaging.

Core facilities are an integral part of the life science research landscape as providers of centralised access to technological resources and expertise. This article’s working group has estimated that between 40 and 80% of imaging, proteomics and genomics data at their institutes are generated at core facilities. The contribution of core facilities to scientific research and innovation must thus be accordingly recognised. In that respect, the most straightforward way is an acknowledgement. Unfortunately, the lack of formal rules still leaves core facilities being inadequately recognised. 

This article proposes that the recognition of core facilities should be deployed via two actions and implemented in two phases: first, with the systematic acknowledgement of core facilities in all scientific publications, and second, by including core facilities and their staff in data citations (Cousijn et al, 2018).

The first step can be accomplished at the manuscript-submission stage by asking the corresponding author to confirm if any data (and associated metadata) used in the manuscript originated from a core facility, and if yes, to identify the associated core facility. EMBO Press has recently included a question in the author checklist to confirm whether the work in the publication “benefited from core facilities” and that the core facility be acknowledged accordingly.

The next step would be to make it compulsory for authors to respond to such a query and explicitly identify the core facility and relevant data (and associated metadata). The MDAR (Materials, Design, Analysis, Reporting) form (Macleod et al, 2021), wherein one needs to provide information about data availability in the Analysis section, could likewise include a question to explicitly identify core facilities involved. Eventually, the information in the author checklist could be automatically fed into the acknowledgement section.

Acknowledging will have two key positive consequences: on the sustainability of core facilities and on their staff careers. In the absence of a high number of publications, particularly as lead or corresponding authors, acknowledgements are used as a measure of a core facility and its staff’s output and impact. Second, it further motivates and incentivizes core facility staff to actively contribute to scientific research. 

The acknowledgement of a core facility goes beyond professional courtesy: identifying the origin of data (and associated metadata) is essential for data traceability and reproducibility particularly since core facilities are major generators of data in life science research. 

Thanks to Jean SALAMERO, our “Action inter-infrastructures” mission officer, for contributing to this article. 

Full article on:

Acknowledging and citing core facilities

Katja Kivinen, Henri G A M van Luenen, Myriam Alcalay, Christoph Bock, Joanna Dodzian, Katerina Hoskova, Danielle Hoyle, Ondrej Hradil, Sofie Kjellerup Christensen, Bernhard Korn, Theodoros Kosteas, Mònica Morales, Krzysztof Skowronek, Vasiliki Theodorou, Geert Van Minnebruggen, Jean Salamero, Lavanya Premvardhan

EMBO reports (2022) 23: e55734

Developed by the Serpico Inria-CNRS-Institut Curie Joint Team, member of the IPDM-BioImage Informatics node of France-BioImaging (FBI), this open-source framework could be a huge step forward in bioimaging management and analysis.

Bioimaging has a broad range of applications, addressing a variety of biological models at diverse scales of life. Thus, descriptions of novel computational approaches are often focused on target case studies. To tackle any scenario in biological imaging is a major challenge, that needs the conception and the development of a unified solution.

With this in mind, the BioImageIT project aims at providing a middleware that integrates data management with analysis using existing softwares (Omero, BioFormats, Fiji, napari, Scipy, pytorch…). The mission of BioImageIT was to design a graphical user interface (GUI) that allows any scientist without coding skills to annotate and analyze datasets using various software. By being user-centered, open-source and cross-platform (Windows, MacOS, Linux), BioImageIT created a management tool that is definitely accessible and well documented.

Started in late 2019, the project, funded by France-BioImaging, is now being deployed in 10 FBI imaging facilities. As it is a first step, the BioImageIT project have the ambition to expand the dissemination of the middleware throughout France and even further, Europe.

BioImageIT overview. a, Schematic view of BioImageIT architecture. The BioImageIT core is composed of data management and data processing functionalities. Users can access plugins by a script editor, Jupyter or the BioImageIT graphical interface (GUI). Data management functionalities exploit local files, remote files or databases such as OMERO. Data processing can perform computations in remote jobs, containers, or local runners. Image analysis is provided by plugins written in different languages. Developers can implement their own plugins in BioImageIT and design their own Graphical Interface. (b-i) LLSM processing workflow gathered in BioImageIT. Hela cell line expressing CD-M6PR-eGFP were stained with Tubulin TrackerTM Deep Red for Microtubules. b, Due to the geometry of LLS scanning, raw 3D images are skewed. c, g, First, realignment (deskew) of raw stacks is performed using Pycudadecon. d, h, Richardson Lucy deconvolution is performed using Pycudadecon. e, CD-M6PR-eGFP vesicles are tracked using Trackmate(FiJi). f, i, Deconvolved stacks and tracks are rendered using napari.

Prigent, S., Valades-Cruz, C.A., Leconte, L. et al. BioImageIT: Open-source framework for integration of image data management with analysis. Nat Methods (2022).