Cutting-edges methods in image-based phenotyping and multi-scale tracking of therapeutic agents

The Bretagne-Loire Node is composed of four cellular and tissue imaging platforms: APEX, H2P2, MicroPICell and MRic-of the Bioimaging axis of GIS Biogenouest and research and development teams (belonging to IGDR, Numecan, Cesam, Inria-Rennes, PAnTher@Oniris, LS2N, SFR F. Bonamy) that support the activities of these platforms.

Located in Nantes and Rennes, the four platforms have the IBiSA certification and their expertise in life imaging and pathological anatomy are complementary.

The mission of the node is to provide the latest technological and methodological advances in microscopy for an integrated understanding of cellular and tissue activities in particular for preclinical research.

The Bretagne-Loire Node has expertise in technology transfer and translational research and benefits from a privileged scientific environment due to its affiliation with the University Hospital Centres and the Nantes Veterinary School.

2018 in Numbers

  • 172 hosted projects
  • 31 publications (plus 41 in acknowledgements)
  • 9 training programs
  • 9 patents since 2011

Technological Innovations

Correlative microscopy  (Nature Methods 2017, Burel 2018 )

Multimodal Fluorescent organic nanoassemblies (Small 2018)

High-content screening Fluorescence Life Time, High content screening with large field of views

Label free multimodal imaging (Raman , Infra red, CARS, SHG)

Multiplexing staining

Tech transfer

Roboscopy (Inscoper, Photonlines)

Episcopic microscopy for 3D histology (Kaerlabs)

Most Innovation Systems Available for Booking

Light-sheet microscopy

TEM and cryo-microscopy

Raman microspectrosopy


Structure illumination microscopy, STORM


APEX (Anatomical Pathology Expertise supporting scientific research)

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Facility: APEX (Anatomical Pathology Expertise supporting scientific research)

Head: Marie-Anne Colle 
101 Route de Gachet, 44300 Nantes, France

APEX is a platform characterized by a double expertise in veterinary anatomic pathologic and fluorescence bio-imaging. APEX is set up on veterinary pathologists certified by the European board committee in combination with engineers dedicated to bio-imaging. To face to scientific problems of imaging, APEX suggests new developments in high- technology microscopy such as spectral imaging confocal microscopy, Total Internal Reflection Fluorescence (TIRF), photoactivation localization microscopy (PALM), Airyscan and stochastic optical reconstruction microscopy (STORM) or multiphoton microscopy. With experts in complementary fields as facilitators, APEX originally proposes an integrated offer in veterinary histopathology as well as in tissue and cell phenotyping in a large spectrum of animal species.

Services on this Facility


Microscopy Technologies


MicroPICell (Tissue and cell imaging)

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Facility: MicroPICell (Tissue and cell imaging)

Head: Perrine Paul-Gilloteaux, Emmanuel Scotet
8 Quai Moncousu, 44000 Nantes, France

MicroPICell is an imaging facility specialized in sample preparation (histology), cellular and tissular imaging (photonic microscopy) and data processing and analysis (bioimage analysis). The facility is located within the precinct of the Hotel Dieu hospital, Nantes University. The platform is affiliated to the Structure Federative de Recherche UMS INSERM 016/CNRS 3556/Nantes University and teamed up with Nikon Instrument society and the APEX veterinary facility to create the Center of Excellence Nikon Nantes in 2016. The MicroPICell facility offers a complete integrated cellular imaging service to all users after analysis of the feasibility of their projects. The applications range is then very large, for example cancer research and immunology, regenerative medicine or stem cells research. It is organized in 3 main services: histology, photonic microscopy, image data management and analysis, all these services working closely together on users projects.

Services on this Facility


Image Data Handling


Microscopy Technologies


MRIC (Microscopy Rennes Imaging Center)

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Facility: MRIC (Microscopy Rennes Imaging Center)

Head: Marc Tramier, Claude Prigent
2 Avenue du Professeur Léon Bernard, 35000 Rennes, France

The platform provides regulated access to imaging systems, as well as scientific and technical assistance in the design of projects and experiments. Proposed techniques are: epifluorescence, video microscopy, confocal, spinning disk, multiphoton, lightsheet, TEM, cryo-electron microscopy, high pressure freezing, tomography, immuno-electron microscopy.
Backed by research teams, the platform also has a strong R&D activity dedicated to the design of prototype microscopes. Finally, MRic provides training to microscopy techniques.

Services on this Facility


Microscopy Technologies

R&D team

CeDRE (Cell Division Reverse Engineering)

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R&D team: CeDRE (Cell Division Reverse Engineering)

Head: Jacques Pécréaux
2 Avenue du Professeur Léon Bernard, 35000 Rennes, France
The CeDRE team, led by Jacques Pécréaux (CRCN CNRS) is multidisciplinary, teaming up biologists, physicists and mathematicians. They are interested in mechanical aspects of cell division to understand its dynamical aspects and ultimately the extra-ordinary faithfulness of mitosis. Therefore, the team finely quantifies biological phenomena to recapitulate the results using physical models. In particular, the team performs advanced data analysis and modelling. It includes the fine tracking of spots like the tips of the microtubule, or super-resolution positioning of the centrosomes at a high frame rate (tens of frames per sec.). The obtained tracks are analysed statistically (for example, to classify the dynamics, reduce the dimension using PCA) or using Fourier spectral analysis to fingerprint the underlying mechanisms. To take full advantage of this data analysis, we model the sub-cellular mechanics during mitosis, in particular, the one grounded on microtubules, molecular motors and associated regulators on the one hand. On the other hand, we use agent-based simulations, especially cytosim, to screen for the variety of behaviours without solving the analytical equations. Finally, the team contributes to developing autonomous microscope by enslaving the driving of the microscope to on-the-fly analysis of acquired images, in particular using machine and deep learning.
Facility, R&D team

H2P2 (Histo pathology High precision)

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Facility, R&D team: H2P2 (Histo pathology High precision)

Head & CoHead: Alain Fautrel, Bruno Turlin and Marie-Dominique Galibert
2 Avenue du Professeur Léon Bernard, 35000 Rennes, France

The H2P2 platform performs histology work on human, animal and plant tissues. The facility is equipped with last generation devices to increase analysis reproducibility and ensure rapid automatic processing. We produce Tissues Micro Array (TMA) that can group hundreds of tissulars spots on a single microscope slide. We have developed a thorough expertise in immuno-labeling (more than 500 Ac in our catalog) as well as multiplex staining, a technique that can highlight up to 6 different proteins per slide, fluorescence or chromogenic. To visualize slides we offer several options: epifluorescence microscope, virtual slides from a Hamamatsu scanner with fluorescence and a new generation confocal scanner (3D-Histech) with seven channels in fluorescence.  This latter technology gives the opportunity to scan thick tissues (300µm) after clearing. Slides are analysed in 2D using Halo, an image analysis platform/software (with machine learning) for quantitative tissue analysis in digital pathology.  We perform 3D images routinely and advanced analysis reconstruction with Amira. We also developed extensive expertise in laser capture microdissection, allowing single cells capture. We are developing in situ molecular technologies, as Raman micro spectroscopy imaging on biological samples with statistical analysis of obtained spectra.

Services on this Facility, R&D team


Microscopy Technologies