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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

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Quantitative analysis of super-resolution data

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Single-molecule-based High Content Screening

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Correlative platform for SMLM & STED nanoscopy

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High-content screening imaging of living organoids

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

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Expertise

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

    « Researcher »

    GALLAND Remi Researcher remi.galland@u-bordeaux.fr +33533514748

    « Technical Staff »

    LEVET Florian Technical staff florian.levet@inserm.fr +33533514747
    SAMBRANO LOPEZ Miguel Eduardo Technical staff miguel-eduardo.sambrano-lopez@u-bordeaux.fr +33533514700
    SIBARITA Jean-Baptiste Technical staff jean-baptiste.sibarita@u-bordeaux.fr +33533514706

    « PhD student »

    CABILLIC marine PhD student marine.cabillic@u-bordeaux.fr +33533514746
    DELAIRE Tom PhD student tom.delaire@u-bordeaux.fr +33533514700
    FORRIERE Hisham PhD student hisham.forriere@etu.u-bordeaux.fr +33533514750
    GALINDO Xareni PhD student xareni.galindo@u-bordeaux.fr +33533514700

    « Student »

    IDRISSI Ihssane Student ihssane.idrissi@etu.u-bordeaux.fr +33533514700

    Jobs

    Software engineer in super-resolution microscopy

    Open software engineer position on ANR STABLE-FP. Within the team "Quantitative Imaging of the Cell", the engineer will be tasked to develop quantitative analysis tools for high content analysis of single molecule localization microscopy data, helping to design new photo-convertible fluorescent proteins for SMLM. The expected missions are: i) to develop an analysis platform to characterize fluorophore photophysics from the single molecule localization data, under various experimental conditions; ii) to help performing and optimizing the screening using the HCS-SMLM platform developed in the team.

    This work builds on 2 of our Nature Methods paper [1,2] and is part of an interdisciplinary project conducted with the teams of Daniel Choquet (IINS, Bordeaux), Dominique Bourgeois (IBS, Grenoble) and the Bordeaux Imaging Center.

    For project details and all other inquiries, please contact;

    Dr. Jean-Baptiste Sibarita
    E-mail : jean-baptiste.sibarita@u-bordeaux.fr
    Tel : +33 (0) 5 33 51 47 06

    [1] Beghin, A., et al., Localization-based super-resolution imaging meets high-content screening. Nat Methods, 2017. 14(12): p. 1184-1190.

    [2] Levet, F., et al., SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data. Nat Methods, 2015. 12(11): p. 1065-71.

    Postdoc in Deep Learning and Image Processing

    Open Postdoc position on ANR NANO-SYNATLAS. Our goal with this project is to provide a better understanding on how specific protein-protein interactions regulate synapse dynamics and organization. Within the team "Quantitative Imaging of the Cell", the Postdoc will be tasked to process the abundant image and single molecule localization data acquired by our PALM/STED correlative platform 1 by developing a complete analysis toolbox. This toolbox will allow: (i) efficient segmentation and classification of synapse morphology by using Deep Learning, (ii) automatic quantification of protein organization and dynamics extracted from SMLM data, and (iii) fusion of the nanoscale morpho-dynamic information and creation of an analytical models of the synapse through geometric analysis, parametrization and normalization.

    This work builds on several of our highly successful recent methods (2 Nature Methods 1,2, 1 Nature Communications 3, 1 Methods 4) and is part of an interdisciplinary project conducted with the team of Olivier Thoumine (IINS, Bordeaux).

    For project details and all other inquiries, please contact;

    Dr. Florian Levet
    E-mail : florian.levet@u-bordeaux.fr
    Tel : +33 (0) 5 33 51 47 47

    1.           Inavalli, V.V.G.K. et al. A super-resolution platform for correlative live single-molecule imaging and STED microscopy Nat. Methods 16,  (2019). DOI:10.1038/s41592-019-0611-8

    2.           Levet, F. et al. SR-Tesseler: A method to segment and quantify localization-based super-resolution microscopy data Nat. Methods 12,  (2015). DOI:10.1038/nmeth.3579

    3.           Levet, F. et al. A tessellation-based colocalization analysis approach for single-molecule localization microscopy Nat. Commun. 10, 1–12 (2019). DOI:10.1038/s41467-019-10007-4

    4.           Levet, F., Tønnesen, J., Nägerl, U.V. & Sibarita, J.B. SpineJ: A software tool for quantitative analysis of nanoscale spine morphology Methods 0–1 (2020).doi:10.1016/j.ymeth.2020.01.020. DOI:10.1016/j.ymeth.2020.01.020