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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

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Unité de Virologie et Immunologie Moléculaires

Zebrafish phenotyping platform

Imaging the host immune system : from dynamic visualization to in-depth view of biological tissues

Created in 2012 within the Infrastructure project TEFOR, our zebrafish phenotyping platform has been established on the INRA campus of Jouy-en-Josas in the environment of plateau de Saclay. It has been recently included in the national infrastructure for infectiology "EMERG’IN". We use zebrafish as a model to understand complex biological processes associated to host-pathogen interactions, inflammation, and diseases linked to the immune system. Using the zebrafish model accelerates understanding of genes function in the framework of infectious diseases research and other contexts.

EMERG’IN : Infrastructure Nationale de Recherche INRA dédiée à la lutte contre les maladies infectieuses animales émergentes ou zoonotiques par l'exploration in vivo.

News & events

Why use zebrafish model?

                     Zebrafish is now recognized as an emergent model for many human pathologies, infectious and inflammatory pathologies as well as for biodistribution studies at the whole body level. Beyond its remarkable optical transparency, this small vertebrate provides an ideal, cheap model to support high content screenings of therapeutic molecules for biodistribution, stability, toxicity, and effectiveness.

                     We provide standardized and customized services to scientific community (academic labs and private companies) for zebrafish phenotyping using 3D and 3D+t microscopy, combining expertise in immunostaining, tissue clearing, infectiology, imaging and data processing. Intravital imaging can now be considered at the level of the whole organism with (sub)cellular resolution. 


Our platform

                     Supported by INRA, the platform involved scientists working on host infection dynamics, phylodynamics applied to host-pathogen systems and development of vaccine strategy. Localized in the L2 zone of the INRA fish facilities at Jouy-en-Josas, (IERP unit), it is mainly dedicated to infectiology experiments on zebrafish at all stages of the life cycle - including adults-, leading to the unique opportunity to develop scientific projects on vaccinology and neurodegenerative diseases.

                     In addition, the environment of the platform provides microscopy equipment in close vicinity of fish aquarium, which promotes real time imaging of fluorescent pathogen invasion and related immune responses upon infection of relevant zebrafish transgenic lines. In this particular context, long-term experiments can also be considered.




  • Zebrafish infectiology and inflammatory models
  • Immunohistochemistry /tissue clearing (Optical clearing agent; CUBIC; iDISCO+)
  • 3D/3D+t microscopy : confocal and two-photon
  • Image analysis : ImageJ, Imaris



                     3D/ 3D+t acquisitions are performed with upright confocal laser scanning microscope (LEICA sp8) equipped with heat chamber and 405nm, 488nm, 552nm lasers in addition to 680 to 1080nm femtosecond IR laser (coherent). Fluorescence can be acquired with PMT and two HyD using conventional or resonant scanners for faster acquisition modes.

                     Stereomicroscopes (MZ10F) and microinjections devices (Narichigue and Femtojet) are used for zebrafish micromanipulation and sample preparations.


Standard and customized services 

Contact us

Scientific management: Christelle Langevin

tel :

Manager: Maxence Frétaud

tel :


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