Photon microscopy

The Photon microscopy facility is specialised in photonic microscopy from the sub-cellular level to the whole embryo level and has expertise in flow cytometry, cell sorting, and data analysis. The CIF is supported by a team of three engineers (1 IR-CNRS, 2 IE-CNRS), who ensure maintenance and quality control of the equipment, provide user training, assistance and scientific animation and participate in technological and methodological developments. 

A number of photonic devices (confocal microscopy, spinning disc microscopy, video-microscopy, multiphoton microscopy, FLIM-LIFA, macro-apotome, multilaser flow cytometers, cell sorter) are available. Motorized stages, heating and CO2-chambers, cloning and microplate sampling devices are on hand, answering user’s needs for the study of a large variety of model organisms (zebrafish, C. elegans, drosophila, mouse, chicken, xenopus, A. thaliana). Dedicated image analysis tools (Huygens, Metamorph, Volocity, FLOJO) are provided. State-of the art imaging techniques such as F-techniques, fluorescence lifetime imaging, spectral imaging and live cell imaging as well as sorting of rare cell populations and multicolour analysis are accessible.

Equipment access is open via online booking for public and private research laboratories (IBPS, campus P6, public research organisms, industry).

The CIF is strongly implicated in training for imaging and flow cytometry and associated techniques for students, researchers and technicians on the local, regional, national and international level.

The platform’s training, support and methodological development missions are carried out through scientific collaborations, valorization of research (publications, conferences) and teaching.



Presentation of offers:

Offers may include conception monitoring, follow-up, realization, analysis and result analysis of possible experimental strategies on our equipment.

Type of offers :

  • Observation sessions for autonomous users : Autonomous use of equipment, attribution of a user account, data availability.
  • Engineer-assisted observation session : Image acquisition monitored by an engineer, attribution of a user account, data availability.
  • Long-term collaborative project


  • 3D-imaging from cell to whole organism
  • Live cell and tissue imaging
  • Photomanipulation (FRAP, Photoconversion, photoablation)
  • Spectral imaging
  • Restauration et image analysis: Co-localization analysis, deconvolution (wide-field confocal, spinning disc, multiphoton), 3D-reconstitution

Methodological development

  • Optimisation of the axial resolution : we work on the optimisation of sample preparation in combination with image restoration in order to improve the axial resolution of photonic devices. We study the resolution improvement in thick fixed samples (mouse brain and zebrafish) marked by immuno-labelling or fluorescent proteins. Furthermore, we study the importance of systematic deconvolution of image data. (more)
  • Live cell imaging improvement, evaluation of photo-toxicity :
    Live cell imaging is a tool of choice for tracing cellular mechanisms, however, light exposure may disturb these mechanisms due to photo-toxicity. It is a crucial question how to evaluate the impact of light on cellular processes? Which light regime is the less photo-toxic and thus the most adapted for the experiment to be carried out? In this context, we have developed a tool based on ratiometric imaging to estimate photo-toxicity during life cell imaging. (more)
  • Development of tools for spatial analysis: The facility has aproved expertise in the analysis of co-localisation events (Bolte and Cordelières, 2006, Cordelières and Bolte, 2014). In the past, ImageJ-based plugins such as “JaCoP were used. This tool has a restricted power for co-localisation analysis, because it is exclusively based on intensities. We recently developed a novel advanced tool based on the detection of objects and the analysis of spatial relationships between them. This fully automatized tool is called “DiAna” (Distance Analysis) and has been conceived in collaboration with Dr. Thomas Boudier (Image & Pervasive Access Lab, IPAL, Singapore). (more)


  • Dr. Stephen R. Davidson, Leicester (Angleterre)
  • Dr. Marc Tramier, Université de Rennes