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.