Discover in vivo imaging technologies at Gustave Roussy
Author: Marine Beraud
The In Vivo Imaging Unit of the PFIC at Gustave Roussy together with the Revvity team invite you to a half-day session dedicated to in vivo imaging instruments and their preclinical applications.
The event will take place on October 2, 2026, from 12:00 PM to 5:00 PM and will focus on photonic imaging and micro-computed tomography.
The programme will include:
A presentation of in vivo imaging applications
Practical demonstrations on IVIS and Quantum GX3 imaging systems
Planning to attend? To help tailor the presentations and demonstrations to participants’ projects and areas of interest, please complete and return the dedicated form available below, before September 25, 2026.
IMACS is a European postdoctoral programme in biological and medical imaging, led by the Marseille Imaging Institute.
The programme aims to support 17 experienced researchers, recruited by Aix-Marseille University and the University of Tübingen, for a period of 36 months.
Several laboratories that are members of the France-BioImaging Marseille Node are among the host organizations on the Aix-Marseille University side, including:
CIML
Fresnel Institute
IBDM
This programme is a unique opportunity to work in an environment of excellence offering:
high-level research
access to state-of-the-art facilities
personalized and group training
career guidance and support
international mobility
individual exposure to intersectorality
Interested? Applications are now open until November 30, 2026!
Find more information about the eligibility criteria, selection process, host teams and more via the link below.
The France-BioImaging Working Group “Multiplexed Imaging”, in collaboration with the “Cellular Identities and Destinies” exploratory research programme (PEPR Cell-ID), is organizing a workshop from November 30 to December 1, 2026, at Genopolys in Montpellier.
This event will focus on the latest advances, challenges and opportunities in spatial and single-cell biology. It is open to researchers, students and engineers interested in spatial imaging and single-cell multi-omics.
Several speakers have already been invited, including France-BioImaging members:
Florian Mueller – Institut Pasteur, Paris
Marcelo Nollmann – Center for Structural Biology, Montpellier
Perrine Paul-Gilloteaux – University of Nantes
Thomas Walter – Institut Curie/Mines, Paris
The full programme will be published soon!
Interested in attending? Register now via the link below. The deadline is September 30!
Meryem Aloulou is an INSERM researcher at the Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), where she leads a research programme investigating how regulatory T cells orchestrate T–B cell cooperation. She is currently exploring how the nuclear architecture of T cells contributes to the regulation of their identity.
To visualize this architecture, she needed access to an imaging technique that was not available in her laboratory. Through France-BioImaging User Access Support, she was able to visit the IBENS imaging facilityand collaborate with Samira Benadda to move her research project forward.
We had the pleasure of meeting Meryem, who shared her journey with us and presented the results she obtained thanks to this visit.
Could you introduce yourself?
I am originally from Agadir, a coastal city in southern Morocco, where my curiosity about the living world began long before I knew it had a name. What fascinated me from the start, and still does, is the paradox at the heart of immunity: the same system must defend us against pathogens without ever turning against our own tissues. That question brought me to France, where I studied immunology and completed my PhD in Immunology at Université Paris Diderot.
During my PhD, carried out in Professor Renato Monteiro’s laboratory, I investigated Fc receptors and uncovered unexpected mechanisms regulating antibody-mediated immune responses. Our work challenged the traditional view of these receptors as purely activating molecules, revealing that the very same receptors can either amplify or restrain immune responses depending on the biological context. This work highlighted the remarkable adaptability of the immune system and its ability to fine-tune inflammation.
After completing my PhD, I joined the Centre de Physiopathologie de Toulouse Purpan (CPTP) in Toulouse in the laboratory of Dr. Nicolas Fazilleau. There, I turned to the regulation of humoral immunity, where our work revealed an unexpected heterogeneity within follicular regulatory T (Tfr) cells, reshaping our understanding of their role in regulating germinal center responses.
To further broaden my expertise, I spent two years as a visiting researcher in Professor Adrian Liston’s laboratory at the University of Cambridge. I was fascinated by the way Adrian had built his laboratory around a truly interdisciplinary vision, bringing together immunologists, molecular biologists, computational biologists, mathematicians, clinicians… to tackle fundamental questions of immune regulation. Working in this environment transformed the way I approach scientific research and convinced me that the most exciting biological discoveries emerge at the interface of multiple disciplines.
Today, I am an INSERM scientist at the Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), where I have established an independent research program investigating how regulatory T cells orchestrate T–B cell cooperation in health and disease. My goal is twofold: to uncover the mechanisms that govern protective immunity, and to identify biomarkers that improve immune monitoring in vaccination, autoimmune disease, and cancer. To achieve this, I combine fundamental immunology with emerging technologies and translational research.
What is your research project about?
The nucleus is much more than a container for DNA. It is closer to a library: the way the books are arranged on the shelves determines which ones can be read. And in immune cells, we have barely started to look at the shelves
Regulatory T cells are essential for maintaining immune homeostasis. Far from being mere suppressors, they actively orchestrate interactions among T cells, B cells, and dendritic cells to ensure that effective immune responses develop while preventing excessive inflammation and autoimmunity.
Although decades of research have identified the molecular and epigenetic programs controlling regulatory T cells, we still know remarkably little about how the three-dimensional organization of the nucleus contributes to establishing and maintaining their identity.
The spatial organization of chromatin determines which genes are accessible, how they are expressed, and ultimately how a cell acquires its function. Yet this level of regulation remains largely unexplored in regulatory T cells.
To investigate this, we use two complementary populations as experimental models: CD4⁺ and CD8⁺ regulatory T cells. Our previous work revealed important molecular differences between them, leading us to hypothesize that they may also possess distinct nuclear architectures.
Ultimately, we aim to determine whether nuclear architecture represents an additional layer of immune-cell organization that shapes immune-cell function.
You received financial support to access a France-BioImaging facility. Which facility did you visit, and which imaging technology did you use?
I first heard about France-BioImaging through our imaging facility, and the User Access call arrived exactly when our project needed a technology we did not have in Toulouse.
Through the France-BioImaging User Access program, I obtained access to the imaging facility at the Institut de Biologie de l’École Normale Supérieure (IBENS) in Paris.
The project is carried out in close collaboration with Dr. Samira Bennada, Head of the IBENS Imaging Facility, whose expertise in expansion microscopy and quantitative imaging has been instrumental in shaping both experimental design and imaging strategy.
Expansion microscopy relies on a counterintuitive idea: rather than relying solely on a more powerful microscope, the biological specimen itself is physically enlarged. The sample is embedded in a swellable polymer, where molecular labels are anchored before controlled expansion physically separates them while preserving their relative organization.
In our protocol, the sample is physically expanded before imaging, increasing the effective imaging resolution and allowing quantitative visualization of nuclear structures that were previously below the diffraction limit (Figure 1).
Figure 1. Expansion microscopy enhances the visualization of nuclear organization in primary regulatory T cells. DAPI-stained CD4⁺ regulatory T-cell nucleus before expansion (left) and after expansion (middle and right), imaged using a 63× objective. Physical expansion increases the effective imaging resolution from approximately 250 nm to ~30 nm, allowing subnuclear structures that cannot be resolved by conventional fluorescence microscopy to become distinguishable. Right: maximum-intensity projection. Scale bars, 5 µm.
Our project combines expansion microscopy with two complementary imaging modalities: the NSPARC detector for high-resolution confocal imaging of chromatin-associated markers and nuclear compartments, and spinning-disk SoRa microscopy for rapid three-dimensional super-resolution imaging.
Together, these approaches provide a multiscale quantitative imaging pipeline adapted to investigating the nuclear architecture of rare primary regulatory T cells.
Why was this technology relevant or essential for your research project?
Current molecular and genomic approaches have transformed our understanding of regulatory T-cell biology by identifying the genes, transcription factors, and epigenetic programs that define these cells. However, they provide little information about how these molecular components are spatially organized within the nucleus.
Yet, the three-dimensional organization of chromatin is increasingly recognized as a fundamental regulator of gene expression. To understand how regulatory T cells acquire and maintain their identity, we need to investigate not only which molecular players are present, but also how they are arranged in space.
Expansion microscopy is uniquely suited to address this challenge because it enables nanoscale imaging while preserving the native spatial organization of the cell. By physically expanding the specimen, it allows us to visualize and quantitatively analyze subnuclear structures that would otherwise remain below the diffraction limit.
Combined with high-resolution quantitative imaging, this approach allows us to map the spatial organization of chromatin, nuclear compartments, and lineage-defining transcription factors directly in primary regulatory T cells.
Rather than replacing transcriptomic or epigenomic approaches, expansion microscopy complements them by adding a spatial dimension that sequencing alone cannot provide. Ultimately, this integrated strategy will allow us to determine whether distinct nuclear architectures contribute to regulatory T-cell specialization, stability, and function.
Could you walk us through your experience accessing France-BioImaging?
The collaboration started long before the first images were acquired. Together with Samira, we discussed the biological hypothesis, selected the most appropriate nuclear markers, optimized sample preparation, and designed the imaging workflow best suited to answer our biological question.
I still remember seeing the first successfully expanded regulatory T-cell nucleus appear on the screen. It was not yet a biological discovery, but it was the first tangible demonstration that a question we had previously been unable to address had become experimentally accessible. For the first time, we could begin to explore the internal nuclear landscape of these rare primary immune cells at a scale that had previously been beyond our reach.
For me, this illustrates one of the greatest strengths of France-BioImaging. It is not simply a network providing access to sophisticated microscopes: it is a network of scientists who help transform an ambitious biological question into a robust imaging strategy.
As an immunologist, working closely with imaging experts has been extremely enriching. This interdisciplinary dialogue has broadened the way I think about my research and opened new perspectives at the interface between immunology, quantitative imaging, and spatial biology.
How did this access contribute to advancing your project? Which results did you obtain?
The project is still ongoing, but the impact of France-BioImaging is already tangible.
Beyond providing access to technologies unavailable at our institute, the collaboration has enabled us to establish a robust multiscale imaging pipelinespecifically adapted to primary regulatory T cells. Together with the IBENS team, we optimized sample preparation, expansion protocols, image acquisition, and quantitative image analysis.
We are nowgenerating the first datasets that will allow us to quantitatively compare the nuclear organization of different regulatory T-cell populations.
Most importantly, this access has transformed what was initially a conceptual hypothesis into a biologically testable question, and has established a technological framework that will support many future projects in our laboratory.
What are the next steps or future perspectives for your research project?
Our immediate objective is to determine whether distinct nuclear architectures are associated with different regulatory T-cell states. Beyond describing nuclear organization, we aim to identify structural features that distinguish specialized Treg populations.
A particularly exciting question is whether nuclear architecture merely reflects cellular state or actively contributes to maintaining the regulatory lineage. We hypothesize that specific features of three-dimensional genome organization provide a structural framework supporting the transcriptional and epigenetic networks underlying Treg stability.
To address this, we will generate multidimensional spatial maps of the Treg nucleus by combining chromatin organization with the spatial distribution of lineage-defining transcription factors and histone modifications. Integrating this nuclear spatial imaging approach with transcriptomic, DNA methylation, and functional analyses will reveal how nuclear organization contributes to Treg stability and function.
More broadly, we envision nuclear architecture as a new dimension of immune-cell characterization, complementing molecular biomarkers and providing innovative ways to assess Treg stability.
Ultimately, this work demonstrates how advanced imaging can bridge structural cell biology and immunology by bringing spatial biology to the nuclear level, opening new perspectives for precision immunology.
What advice would you give to researchers who are considering applying for the France-BioImaging User Access Support?
I would strongly encourage researchers to apply. France-BioImaging offers much more than outstanding imaging technologies: it gives you access to an exceptional community of imaging scientists, and it fosters genuine scientific collaborations.
My advice: start with a clear biological question, not with a specific technology. The facility scientists are true scientific partners who can help refine the experimental design, identify the most appropriate imaging approaches, and develop robust quantitative workflows.
For me, the greatest strength of France-BioImaging is precisely this combination of technological excellence, scientific expertise, and collaborative spirit. It enables researchers to tackle ambitious biological questions that would be difficult to address within a single laboratory.
If I had the opportunity to apply again, I would do it without hesitation.
Like Meryem, you can benefit from France-BioImaging User Access Support to access cutting-edge imaging technologies available across the infrastructure!
The Institut Pasteur (France-BioImaging Paris Centre Node) is organizing a seminar in collaboration with Exciting Instruments on September 21, 2026, in Paris. This event will be dedicated to single-molecule fluorescence methods and how they can complement structural biology and biophysics workflows.
Structural biology methods such as cryo-EM and X-ray crystallography provide powerful snapshots of biomolecular systems. This seminar will explore how smFRET and FCS can add a dynamic layer by revealing conformational changes, biomolecular interactions and heterogeneous populations directly in solution.
On the program
1:30 – 1:45 PM Welcome and Introduction – Dr. Patrick England & Dr. Audrey Salles
1:45 – 2:30 PM See your favorite biomolecules in action – Easy-to-use single-molecule fluorescence tools to observe biomolecular dynamics and interactions – Dr. Roman Renger (Exciting Instruments, Sheffield, United-Kingdom)
2:30 – 3:00 PM Peptides at the membrane interface: quantifying binding, understanding translocation – Dr. Alexandre Chenal (Institut Pasteur, Paris, France)
3:00 – 3:30 PM Coffee Break and discussions
3:30 – 4:00 PM Fantastic biomolecules and how to find them – Dr. Steven Quinn (University of York, United-Kingdom)
4:00 – 4:30 PM Q&A and closing remarks
4:30 – 6:00 PM One to one discussions between Exciting instrument scientists and researchers interested in testing single-molecule fluorescence on their biological system
As we have a limited number of seats, we encourage you to secure your place by registering below.
The France VolumeEM network is organizing its first Scientific Days in Bordeaux (Broca Center – Bordeaux University) on September 28 and 29, 2026.
The aim of this event is to bring together the community around 3D electron microscopy approaches and complementary techniques, such as TomoX, in the fields of life sciences and materials science.
A bonus session will take place on the afternoon of September 29 and will be dedicated to workshops on CryoFIB-SEM, SBF-SEM, array tomography, plasma FIB, cryogenic and room-temperature sample preparation, as well as various image analysis software tools. Places are limited!
Interested in sharing your work? You can submit an abstract to present your research during one of the three thematic sessions!
Abstracts can be submitted via the Sciencesconf website, either during registration or at a later stage, or by email. Please find the submission guidelines here.
If you do not wish to give an oral presentation but would still like to share your work, you can also submit a poster for the Monday evening poster session.
Both oral presentations and posters will be entered into a contest with great prizes to be won!
General information
When: September 28-29, 2026
Where: Broca Center, Bordeaux
The event is free and open to all, but the registration is mandatory.
Developed by Philippe BUN, research engineer at the NEURIMAG imaging facility, part of the France-BioImaging Paris-Centre Node, Fa•Da•Scope is a new software suite designed to support the monitoring and traceability of microscopy set-ups. Initially deployed at NEURIMAG, the tool is now drawing interest from other imaging facilities, including Cyceron in Caen and PRIMACEN in Rouen, both part of the France-BioImaging infrastructure. Discover how Fa•Da•Scope helps bridge the gap between instrument booking and real workstation use.
Shared research facilities often face the same operational gap: a booking tells the facility engineers who was expected to use an instrument, but it rarely documents what happened once the user sat at the workstation. This “last-mile” gap between the calendar and the instrument can create blind spots in traceability, handover and Standard Operating Procedure (SOP) compliance. To address this challenge, Philippe BUN has developed the Facility Data Scope (in short Fa•Da•Scope ••).
Fa•Da•Scope•• is a lightweight software suite designed for shared-instrument environments. For nearly a year, it has been deployed as a software gatekeeper on high-end confocal and widefield systems at the NeurImag imaging facility (IPNP, Inserm, Université Paris Cité). It sits at the workstation between the user and the instrument control software. Before acquisition begins, users interact with a brief, facility-defined interface to manage:
identification and group/project information;
tool and accessory selection;
SOP acknowledgement;
workstation checks and handover comments.
Fa•Da•Scope is not a booking system. It does not replace established platforms or local reservation tools. Instead, it complements them by documenting the exact point of contact where the user, the instrument software, the workstation and the facility rules meet. Fa•Da•Scope is built around three core pillars:
Staff-driven design– Editor module
Facility staff remain in control by configuring system-related questions, tool lists, warnings and mandatory checks through a zero-code interface.
Operational analytics– Insights module with pseudonymizer and spotlight utilities
Dedicated staff toolbox to clean, review and summarize session logs into facility-level indicators. When outputs need to be shared beyond the local staff team, identifiers can be pseudonymized and the resulting metrics transformed into presentation-ready figures.
Privacy-first and lightweight deployment
Fa•Da•Scope is strictly data-blind: it never inspects images, acquisition files or experimental content. Its architecture is designed to remain non-intrusive on high-performance acquisition workstations.
Following routine use at the NeurImag imaging facility and successful testing in one additional shared-facility environment, Fa•Da•Scope is now ready for broader deployment across the research community.
The team is looking to engage with facilities interested in standardizing their workstation metadata, improving instrument stewardship and contributing feedback from different instrument and facility contexts. Demonstrations, installation guidance and support for the initial configuration are provided.
Facilities interested in participating in this broader deployment phase are welcome to contact Philippe BUN at: philippe.bun@inserm.fr
Built around three key pillars – innovation, training and access – France-BioImaging aims to provide the scientific community with access to state-of-the-art microscopy technologies and expertise. To make this possible, innovative developments from R&D teams must be transferred to imaging facilities, where they can become accessible to users.
Since 2021, France-BioImaging has supported this process through dedicated technology transfer calls. Discover the laureates of the 2026 edition and the projects that will help bring new imaging approaches closer to the scientific community.
WEAVE – Web Environment for Annotation, Visualization & Exploration
by Anatole Chessel (LOB, Paris)
FBI facilities produce terabyte-scale 2D, 3D and multi-photon datasets that increasingly outpace local, install-heavy software stacks, (Fiji, QuPath, custom Napari plugins) and are often dependant of the microscope producing company (Zen, LasX, Aivia, Imaris, NIS…). Moving data to a workstation, sharing full-resolution views with collaborators, and overlaying AI-derived annotations on the source pixels remain serious bottlenecks for core facilities and their users.
WEAVE is a browser-based portal that solves these in one stack: zero-install visualization of OME-Zarr, CZI and multi-photon TIFF data at any scale; collaborative ROI annotation with hard-linked statistics; an AI inference layer for routine quantification tasks; and native interoperability with the new FBI.data transfer infrastructure being deployed across the FBI Ile-de-France node.
Built on the Awdacity stack (initiated with INRIA and Pasteur Institute) co-developed with the LOB advanced microscopy team and the MIMA2 facility, WEAVE will be physically implanted at the MORPHOSCOPE imaging facility (École Polytechnique) and the MIMA2 platform (Micalis, INRAE) within 12 months as a service for participating nodes users, ready for adoption across other nodes and integration with FBI.data solutions.
XRM4ALL – X-ray Microscopy for all and beyond
by Nicolas Brouilly (IBDM, Marseille)
The project combines two X-ray Microscopy (XRM) developments at PICsL. First, it will establish an XRM-guided targeting service for FBI and the RIME (Réseau d’Imagerie par Microscopie Electronique) users, enabling non destructive 3D localization of regions of interest in resin blocks before ultramicrotomy. This service will be structured through standardized submission, sample handling, automated reconstruction workflows, and data sharing through OMERO, with immediate deployment followed by progressive optimization.
Second, the project will develop an Expansion Microscopy (ExM) approach for XRM imaging, together with a membrane labelling strategy, to provide volumetric visualization of cellular compartments. To compensate for contrast dilution during expansion, we propose using an ExM-compatible membrane labelling probe conjugated to undecagold for post-expansion silver enhancement.
Altogether, this innovative method will allow increasing the resolution of micro- and nano-XRM imaging modalities for biological samples.
SCALE
by Florian Muller (Institut Pasteur, Paris)
Demand is rising for spatial gene-expression mapping in complex 3D models such as organoids, organ-on-chip, and thick tissue sections. While commercial solutions offer turn-key workflows, they remain costly and are often incompatible with non-standard sample formats or thick tissue. We propose transferring the SCALE workflow to the Pasteur BioImaging (PBI) core facility as a service. SCALE integrates hydrogel-embedded tissue clearing with two detection modalities – multispectral HCR and automated sequential smFISH (AutoFISH) – on existing PBI microscopes.
The project has two objectives: first, utilizing multispectral imaging to visualize 10 genes simultaneously; and second, deploying automated sequential smFISH (AutoFISH) to target >40 genes in the same sample. Building on ongoing R&D projects, this 12-month transfer will establish an affordable, open-access spatial transcriptomics service optimized for 3D biology.
Dark2Light – TRAST microscopy: imaging dark states
by Elisa Bombarda (LBP, Strasbourg)
TRAnsient STate (TRAST) microscopy is an innovative fluorescence approach that probes non – or weakly fluorescent (“dark”) transient states through time-averaged fluorescence detection under modulated excitation. Arising from intersystem crossing, trans-cis isomerization, or photo-induced charge transfer, these dark states typically exhibit long lifetimes, enabling TRAST to access μs-ms dynamics far beyond the ps-ns timescale of fluorescence. TRAST can thus probe cellular microenvironments, rare molecular events and slow processes that remain inaccessible to conventional fluorescence methods.
Combining the high sensitivity of fluorescence detection with the strong environmental responsiveness of long-lived dark states, TRAST is applicable to a broad range of fluorophores, including weak emitters, with promising applications in biology, medicine and nanotechnology. The project will establish the first TRAST setup in France (the second in Europe), providing a unique technology for the scientific community.
The IPAM (Imagerie Préclinique Appliquée de Montpellier) imaging facility, part of the France-BioImaging Montpellier node, is proud to announce the installation of France’s first IVIM Technology intravital microscopy system (IVM-C3), at the Institut de Génomique Fonctionnelle (IGF, CNRS, Inserm, University of Montpellier).
Intravital microscopy (IVM) is a cutting-edge imaging technique that enables real-time, cellular-level visualization of biological processes in small animal models (e.g. mice, rats). It provides a direct window into cellular dynamics of soft tissues within their native physiological environment, and longitudinal imaging sessions (from days to months) in which animals are their own control.
This system enables a broad range of preclinical applications, including:
Real-time vascular permeability measurements,
Tracking of cell intravasation and extravasation (tumor cells, immune cells),
Immune cell imaging within native tissue microenvironments,
The IPAM facility warmly acknowledges the financial support by the Région Occitanie (PRIO-FEDER project) and the PEI-Muse program (Université de Montpellier).
The IPAM facility now offers access to this system (CNRS auditable fees), available to the national and international academic community as well as industrial partners.
For inquiries and collaboration requests, contact: ipam@ipam.cnrs.fr.
Research engineer at Institut Cochin, Raphaël Braud-Mussi leads the development of OpenCID, an open platform designed to simplify the management, processing and sharing of biomedical data. Initially created to support imaging data workflows at Institut Cochin, OpenCID has progressively expanded to other types of biomedical data and is now being deployed beyond its original environment.
In this interview, Raphaël shares the ambitions behind the project, its benefits for researchers and imaging facilities, and the potential synergies with BioImage Cloud within the France-BioImaging ecosystem.
To begin with, could you briefly introduce yourself?
Hi, I’m Raphaël Braud-Mussi. I’m a research engineer at Institut Cochin in Paris, where I lead the development of OpenCID, a platform developed with an open collaboration model that helps thousands of scientists manage and process their biological data.
I started at the institute in 2023, working on interoperability between OMERO and our in-house image database, and integrating deep learning tools for image segmentation. Before that, I studied mathematics and computer science at Université Paris Cité, then completed a master’s degree in image processing and computer vision at Université de Montpellier.
What’s driven me throughout is a genuine interest in building tools that make researchers’ work more efficient and OpenCID is exactly that kind of project
What are you currently working on?
Right now, the team and I are focused on the next major version of OpenCID. The core of the platform has been entirely rebuilt in Python, which ensures portability across server environments and makes it easier for the broader community to contribute to the codebase.
This new version will also include a redesigned web interface with more fluid and intuitive workflows for researchers. We’re planning to deploy it at Institut Cochin this summer, with a rollout to other institutes starting in September.
My role is to make sure everything runs as expected across environments and to coordinate the deployment with each site. Beyond that release, we already have a roadmap of new features to continue expanding what the platform can do; we’re currently managing over 350 TB of data at Cochin with a data flow exceeding 10 TB per month, so scalability stays a constant priority.
Could you explain what OpenCID is and what need it addresses?
OpenCID started as an internal project at Institut Cochin called CID. The Cochin Image Database is designed to help researchers manage their imaging data. As the user base grew, we expanded the platform to include processing pipelines directly accessible through the web interface, removing the need for researchers to install software locally.
Institut Cochin hosts a large number of core facilities across different disciplines, so once the imaging management layer was stable, we extended OpenCID to handle other types of biomedical data (genomic, proteomic, cytometry…) produced by those facilities as well.
Today, OpenCID is openly available upon request and allows research institutes to manage and process large volumes of biomedical data entirely through a web interface. It’s built to scale, and its open nature makes it easier for the community to adopt and contribute to it.
In practical terms, how does OpenCID work for users?
Three words: simplicity, efficiency, usability
Let me give you a concrete example. You’re a biologist who needs to acquire microscopy images and RNA sequencing data for your project. Traditionally, getting that data from the core facility to your workstation means copying files onto an external hard drive or by using a shared space on your network, a process that eats into your time slot on the acquisition machine and breaks your workflow.
With OpenCID, everything is streamlined. Once your acquisition is done, leave the machine to the next user. Then log into OpenCID, select the machine you used and your data folder directly from the web interface, and import your files into the database in just a few steps, accessible from anywhere, at any time. From there, you can run your processing pipelines (segmentation, deconvolution…) and download your results with a couple of clicks, without ever installing software locally, whether you’re working remotely, attending a congress, or even on the beach.
Who can currently benefit from OpenCID?
OpenCID is currently deployed at Institut Cochin, where it serves users across multiple core facilities, including IMAG’IC for bioimaging. External users who acquire data at the institute can also import and retrieve their own data through the platform, even if they are not based at Cochin. The platform is designed to go well beyond a single institute.
Any research institute interested in deploying OpenCID can reach out to the team at cid.u1016@inserm.fr to get started. The solution is ready for deployment, and we are genuinely happy to support new sites through the process. For those who want to explore first, we can also provide access to our GitLab repository, where the documentation and the full deployment procedure are available.
What are the main benefits of OpenCID for researchers, engineers and imaging facilities?
For researchers, OpenCID simplifies the management of an entire team’s data and supports a genuine open science workflow. Every dataset can be shared and downloaded based on access rights defined by the team leader, and an automated open science link generator allows any dataset to be connected to a DOI, making data citation and publication straightforward.
Beyond that, OpenCID is designed to help research teams meet the requirements of Data Management Plans, which are now mandatory for most public funding bodies. By centralizing data storage, traceability, and sharing in a single platform, OpenCID makes it significantly easier to demonstrate compliance with FAIR data principles, findable, accessible, interoperable, and reusable, without adding administrative burden to the team. (https://hal.science/hal-04834159v1/file/INSTITUT_COCHIN_ENTITY_DMP_-_CID_V1.pdf)
For engineers, OpenCID brings structure and accessibility to data management. Processing pipelines can run workflows on a workstation connected to the OpenCID system, allowing engineers to launch analyses on a dedicated machine and continue working on other tasks in the meantime. Results are made available directly on the web interface as soon as the workflow completes. And thanks to our fully Python-based codebase, integrating new workflows is straightforward, either by requesting an addition from the team, or by contributing directly if you are comfortable doing so.
For imaging facilities, OpenCID provides a centralized and reliable solution to handle the constant flow of data produced by acquisition machines, with no need for users to manage everything manually.
Ultimately, every one of these benefits points to the same goal: reducing friction at every step of the research workflow, so that scientists and engineers can focus on what actually matters; science
Could OpenCID be deployed across other imaging facilities?
As mentioned earlier, this is precisely our current priority. OpenCID is already being deployed beyond Institut Cochin, we are actively working with sites such as INRAE Montpellier and Institut Max Planck in Cologne, and more are in discussion.
The community-driven nature of the platform is a key enabler here: it lowers the barrier to adoption and allows each site to adapt the solution to their specific environment. Our affiliation with France-BioImaging also gives us a strong network to reach imaging facilities across the country and beyond.
Building a community around OpenCID is not just a goal, it is part of the project’s long-term vision.
What feedback have you received since OpenCID has been implemented?
It has been three years of sustained development rethinking the entire CID project from the ground up. Now that version 2.0 is ready and continuously updated, the feedback from users has been very encouraging.
A big part of that trust comes from how we handle support. The team commits to addressing any issue within 24 hours, whether we identify a bug proactively or a user reports one directly. That responsiveness has built a real relationship with our user base.
User feedback is also a direct input into our roadmap. We actively seek opinions on the platform, and many of the features we have built or are planning came directly from conversations with researchers and engineers in the field.
What are the next steps for OpenCID?
The next steps for OpenCID are threefold: reinforcing the team, completing the current deployment rollout, and delivering several new features that are already in progress.
On the technical side, we are currently in the testing phase for Zarr format support, which will be a significant step forward for open science interoperability. We are also developing an online 3D object viewer, which will allow researchers to visualize volumetric data directly from the web interface without any local software. Both features are on track to be released soon.
The project is at a stage where it needs additional engineers to sustain both maintenance and new development in parallel, and that is precisely what we are actively working to address.
FBI.data recently launched BioImage Cloud. In the future, do you see possible synergies between OpenCID and BioImage Cloud?
OpenCID and BioImage Cloud have been developed with different but complementary goals. BioImage Cloud focuses on streamlining the transfer of imaging datasets from acquisition to national cloud storage, while OpenCID provides a broader platform for data management, processing, and sharing, regardless of data type or format.
Given that both projects are part of the France-BioImaging ecosystem and share the same underlying objectives, making research data FAIR, accessible, and manageable, I genuinely see potential for synergy. One concrete avenue would be to explore how OpenCID’s data management layer could interface with FBI.data transfer infrastructure, effectively combining the strengths of both solutions. A proof of concept in that direction would be worth considering.
More broadly, I think the community benefits from having multiple approaches being explored in parallel. The most important thing is that researchers end up with tools that actually work for them.
In spring 2026, the IGBMC imaging facility, ICI, located in Illkirch, acquired two new light-sheet microscopes thanks to France-BioImaging and the BIOGEN project, supported by the French National Research Agency (ANR-24-INBS-0005 FBI BIOGEN).
One of the strategic priorities of BIOGEN is to strengthen the national offer in multiscale light-sheet microscopy for the scientific community. By addressing major imaging bottlenecks such as sensitivity, acquisition speed and phototoxicity, light-sheet microscopy opens up new possibilities for the observation of live and delicate biological samples.
At the ICI facility, two complementary systems have been acquired, each designed to address specific imaging needs.
The lattice light-sheet 7 microscope enables the observation of fast dynamic processes over long periods of time, with very low phototoxicity and photobleaching compared to confocal microscopy. It is particularly well suited for fast volumetric imaging of live samples, without requiring specific sample preparation.
The lattice SIM microscope, installed on a dedicated system, provides live super-resolution imaging, offering an excellent balance between acquisition speed and resolution gain.
Lattice light-sheet 7
Lattice SIM
Together, these two instruments significantly reinforce IGBMC’s technological offer by covering a broad range of biological questions, from fast cellular dynamics to super-resolved imaging of subcellular structures.
Light-sheet microscopy is particularly relevant for live and fragile samples, such as living cells, small organoids or early-stage embryos. The systems available at IGBMC are compatible with several common experimental formats, including dishes, multi-chamber slides and multi-well plates, making them easy to integrate into existing workflows.
These technologies are especially suited for projects focusing on intracellular dynamics, cell division, calcium signalling, developmental biology and, more broadly, quantitative cell biology requiring fast and minimally invasive imaging.
Operational since March 2026, these two systems are now part of the technological offer of the IGBMC imaging facility and the France-BioImaging Alsace node. They strengthen access to advanced light-sheet microscopy within the national network and open new opportunities for projects requiring fast, high-resolution and minimally invasive live imaging.
Researchers interested in using these microscopes, or in developing collaborative projects within the France-BioImaging network, are invited to contact the IGBMC imaging facility at: ici@igbmc.fr
Three new invited speakers have been announced for SFBS 2026, further enriching the scientific programme dedicated to super-resolution microscopy for biological imaging.
Good news: the deadline for early bird registration and abstract submission has been extended to June 30, 2026! Apply here before June 30, 2026
Giuseppe Vicidomini
Dr Giuseppe Vicidomini obtained his degree in Computer Science in 2003 and completed his PhD in Computer Science in 2008, both at the University of Genoa under the supervision of Prof. Alberto Diaspro.
He subsequently joined the Max Planck Institute for Biophysical Chemistry as a postdoctoral fellow in the Department of NanoBiophotonics, led by Prof. Stefan W. Hell, where he pioneered gated-STED microscopy, a single-photon temporal-detection approach that enabled nanometric resolution at reduced light doses, facilitating the widespread application of STED microscopy to live-cell imaging.
In 2011, he joined the Italian Institute of Technology (IIT), where he further advanced STED microscopy by developing time-resolved approaches now implemented in all major commercial STED systems.
In 2016, Dr Vicidomini established the Molecular Microscopy and Spectroscopy (MMS) laboratory at IIT and launched an independent research programme based on single-photon avalanche diode (SPAD) array detectors. This work led to the establishment of photon-resolved microscopy, a new imaging paradigm that assigns spatial and temporal information to individual photons, enabling advances in super-resolution imaging, fluorescence lifetime microscopy, spectroscopy, and single-molecule analysis.
His research has generated multiple patents, technology licensing agreements, and the spin-off company Genoa Instruments, of which he is co-founder and scientific advisor. Established to commercialise photon-resolved microscopy technologies, Genoa Instruments is accelerating its adoption within the life-science community. In parallel, SPAD array detector concepts and methodologies developed in his laboratory have been incorporated into commercial microscopy platforms from Nikon, Abberior, and PicoQuant.
Dr Vicidomini was Principal Investigator of the ERC Consolidator Grant BrightEyes, which established the foundations of photon-resolved microscopy and enabled the development of a new generation of non-invasive imaging and spectroscopy tools for studying biomolecular processes in living systems. He currently leads the ERC Proof-of-Concept project BrightMind, which integrates photon-resolved microscopy with artificial intelligence and smart microscopy concepts to create adaptive imaging systems for autonomous data acquisition and information extraction.
Xiaoshuai Huang
Xiaoshuai Huang is a Principal Investigator at the Institute of Advanced Clinical Medicine, Peking University. He earned his B.S. from Wuhan University in 2013 and his Ph.D. from Peking University in 2018, followed by a postdoctoral fellowship at the same institution until 2020.
Dr. Huang’s research operates at the intersection of optical physics and cell biology, focusing on engineering next-generation super-resolution microscopy platforms to decode complex three-dimensional subcellular dynamics.
Since establishing his independent laboratory, he has systematically addressed the critical bottlenecks of live-cell volumetric imaging, specifically speed, axial resolution, reconstruction fidelity, and multimodal contrast. Under his leadership, the laboratory has developed flagship platforms such as 3D-MP-SIM and 4Pi-SIM, with landmark findings published as leading or co-corresponding author in premier journals including Nature Photonics, Nature Methods, and Nature Cell Biology.
Anne-Sophie Hafner
Dr Hafner studies the dynamic composition of synapses, the molecular basis of memory encoding in the brain.
Her lab uses omics-approaches combined with FACs-based synapse purification, as well as metabolic labelling, super-resolution, and live-imaging and also computational modeling to elucidate changes in synapse composition associated with learning, aging and diseases.
Recently, her lab identified a novel promising pathway that likely contributes to Alzheimer’s disease onset. In 2022, she received an ERC Starting Grant from the European Research Council for her project MemCode, to investigate the mechanisms of long-term memory storage in the brain, and in 2026 an ERC proof of concept for her project OligoBlockers, to generate a new innovative therapy to stop Alzheimer’s disease progression at early stages.
Don’t miss this opportunity to meet these experts during SFBS 2026! Join us in Bordeaux from October 19 to 21, 2026!
Would you like to share your work at SFBS 2026? Good news: the abstract submission deadline has been extended! Apply before June 30, 2026 for a chance to give a talk or present a poster.
