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Quantitative Imaging of the Cell

Team Leader : Jean-Baptiste Sibarita

General objective

General objectives

We develop cutting-edge quantitative imaging methods to decipher protein organization and dynamics with high spatial and temporal resolution and compatible with high-content screening standards. Over the last 10 years, we have successfully developed and combined single-molecule based nanoscopy, dedicated image analysis methods and bioengineering techniques to tackle important biological questions. With no relevant biological question to address within the team itself, our developments are applied in very close collaboration with biology research groups.

Our team has an important academic and industrial technology transfer activity. We develop software and microscopy solutions which we valorize through scientific publications, patents, industrial technology transfers, academic Material Transfer Agreements, and free/collaborative/open source distribution.

Team organization

The Quantitative imaging of the cell team is a R&D team composed of people coming from various disciplines: microscopy, computer science and bioengineering.

Project leaders

Jean-Baptiste Sibarita

Florian Levet

Rémi Galland


Research Projects

3D high- and super-resolution imaging at different scales


Quantitative analysis of super-resolution data


Single-molecule-based High Content Screening


Correlative platform for SMLM & STED nanoscopy


High-content screening imaging of living organoids


Combining deep-learning with geometric and image processing for analysis of microscopy data





  • Single-Molecule Localization Microscopy
  • Light-Sheet Fluorescence Microscopy
  • High Content Screening
  • Bioimage Analysis
  • Geometry Processing
  • Deep Learning
  • Selected Publications

  • F. Levet, J. Tonnesen, U.V. Nagerl, J.B. Sibarita
  • SpineJ: A software tool for quantitative analysis of nanoscale spine morphology Methods (2020)

  • S. Kedia, P. Ramakrishna, P.R. Netrakanti, M. Jose, J.B. Sibarita, S. Nadkarni, D. Nair
  • Real-time nanoscale organization of amyloid precursor protein Nanoscale (2020)

  • D. Jullie, M. Stoeber, J.B. Sibarita, H.L. Zieger, T.M. Bartol, S. Arttamangkul, T.J. Sejnowski, E. Hosy, M. von Zastrow
  • A Discrete Presynaptic Vesicle Cycle for Neuromodulator Receptors Neuron (2020)

  • J. Goncalves, T.M. Bartol, C. Camus, F. Levet, A.P. Menegolla, T.J. Sejnowski, J.B. Sibarita, M. Vivaudou, D. Choquet, E. Hosy
  • Nanoscale co-organization and coactivation of AMPAR, NMDAR, and mGluR at excitatory synapses PNAS (Proceedings of the National Academy of Sciences) (2020)

  • J.S. Ferreira, J.P. Dupuis, B. Kellermayer, N. Benac, C. Manso, D. Bouchet, F. Levet, C. Butler, J.B. Sibarita, L. Groc
  • Distance-dependent regulation of NMDAR nanoscale organization along hippocampal neuron dendrites PNAS (Proceedings of the National Academy of Sciences) (2020)

  • E. Dondi, J.B. Sibarita, N. Varin-Blank, L. Velazquez
  • The adaptor protein APS modulates BCR signalling in mature B cells Cellular Signaling (2020)

  • L. Aoun, A. Farutin, N. Garcia-Seyda, P. Negre, M.S. Rizvi, S. Tlili, S. Song, X. Luo, M. Biarnes-Pelicot, R. Galland, J.B. Sibarita, A. Michelot, C. Hivroz, S. Rafai, M.P. Valignat, C. Misbah, O. Theodoly
  • Amoeboid Swimming Is Propelled by Molecular Paddling in Lymphocytes Biophysical Journal (2020)

  • D. Sage, T.A. Pham, H. Babcock, T. Lukes, T. Pengo, J. Chao, R. Velmurugan, A. Herbert, A. Agrawal, S. Colabrese, A. Wheeler, A. Archetti, B. Rieger, R. Ober, G.M. Hagen, J.B. Sibarita, J. Ries, R. Henriques, M. Unser, S. Holden
  • Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software Nature Methods (2019)

  • A. Mehidi, O. Rossier, M. Schaks, A. Chazeau, F. Biname, A. Remorino, M. Coppey, Z. Karatas, J.B. Sibarita, K. Rottner, V. Moreau, G. Giannone
  • Transient Activations of Rac1 at the Lamellipodium Tip Trigger Membrane Protrusion Current Biology (2019)

  • F. Levet, G. Julien, R. Galland, C. Butler, A. Beghin, A. Chazeau, P. Hoess, J. Ries, G. Giannone, J.B. Sibarita
  • A tessellation-based colocalization analysis approach for single-molecule localization microscopy Nature Communications (2019)

  • V. Inavalli, M.O. Lenz, C. Butler, J. Angibaud, B. Compans, F. Levet, J. Tonnesen, O. Rossier, G. Giannone, O. Thoumine, E. Hosy, D. Choquet, J.B. Sibarita*, U.V. Nagerl*
  • A super-resolution platform for correlative live single-molecule imaging and STED microscopy Nature Methods (2019)

  • M. Letellier, F. Levet, O. Thoumine, Y. Goda
  • Differential role of pre- and postsynaptic neurons in the activity-dependent control of synaptic strengths across dendrites PLoS Biology (2019)


    « Researcher »

    GALLAND Remi Researcher +33533514748

    « Technical Staff »

    BARRY Thierno Technical staff +33533514700
    LEVET Florian Technical staff +33533514747
    NEUHAUS Abdelghani Technical staff +33533514700
    SIBARITA Jean-Baptiste Technical staff +33533514706

    « PhD student »

    DELAIRE Tom PhD student +33533514700
    GALINDO Xareni PhD student +33533514700
    LOHK Christer PhD student +33533514700

    « Student »

    BETTAREL Laetitia Student +33533514700