Quantitative imaging of the cell
Our team aims at developing novel imaging and microtechnologies to decipher protein organization and dynamics at high spatial and temporal resolutions. More precisely, four main research areas are dedicating to develop:
1) Novel instruments to improve the penetration depth and the spectral content of high and super-resolution microscopy methods for the imaging of complex and physiologically relevant living samples,
2) Analytical tools for the visualization and the quantification of 3D multi-colour data-sets,
3) Imaging and analysis tools that combine High Content Screening microscopy and super-resolution microscopy approaches to quantify the dynamics and organization of proteins within the living cells and
4) Novel microtechnologies to control the in vitro cellular microenvironment.
Mots clés
Analyses des données, Imagerie cellulaire in vitro ou in vivo, Intelligence artificielle et réalité virtuelle, Microscopie super-résolutiveSelected publications
- Advanced imaging and labelling methods to decipher brain cell organization and function. Daniel Choquet, Matthieu Sainlos, Jean-Baptiste Sibarita. Nat Rev Neurosci. 2021-03-12.
- Nanoscale co-organization and coactivation of AMPAR, NMDAR, and mGluR at excitatory synapses. Julia Goncalves, Tomas M. Bartol, Côme Camus, Florian Levet, Ana Paula Menegolla, Terrence J. Sejnowski, Jean-Baptiste Sibarita, Michel Vivaudou, Daniel Choquet, Eric Hosy. Proc Natl Acad Sci USA. 2020-06-08. : 201922563.
- Author Correction: Structural basis of astrocytic Ca2+ signals at tripartite synapses. Misa Arizono, V. V. G. Krishna Inavalli, Aude Panatier, Thomas Pfeiffer, Julie Angibaud, Florian Levet, Mirelle J. T. Ter Veer, Jillian Stobart, Luigi Bellocchio, Katsuhiko Mikoshiba, Giovanni Marsicano, Bruno Weber, Stéphane H. R. Oliet, U. Valentin Nägerl. Nat Commun. 2020-05-18. 11 (1)
- Structural basis of astrocytic Ca2+ signals at tripartite synapses. Misa Arizono, V. V. G. Krishna Inavalli, Aude Panatier, Thomas Pfeiffer, Julie Angibaud, Florian Levet, Mirelle J. T. Ter Veer, Jillian Stobart, Luigi Bellocchio, Katsuhiko Mikoshiba, Giovanni Marsicano, Bruno Weber, Stéphane H. R. Oliet, U. Valentin Nägerl. Nat Commun. 2020-04-20. 11 (1)
- SpineJ: A software tool for quantitative analysis of nanoscale spine morphology. Florian Levet, Jan Tønnesen, U. Valentin Nägerl, Jean-Baptiste Sibarita. Methods. 2020-03-01. 174 : 49-55.
- SpineJ: A software tool for quantitative analysis of nanoscale spine morphology. Florian Levet, Jan Tønnesen, U. Valentin Nägerl, Jean-Baptiste Sibarita. Methods. 2020-03-01. 174 : 49-55.
- Vangl2 acts at the interface between actin and N-cadherin to modulate mammalian neuronal outgrowth. Steve Dos-Santos Carvalho, Maite M Moreau, Yeri Esther Hien, Michael Garcia, Nathalie Aubailly, Deborah J Henderson, Vincent Studer, Nathalie Sans, Olivier Thoumine, Mireille Montcouquiol. eLife. 2020-01-07. 9
- A super-resolution platform for correlative live single-molecule imaging and STED microscopy. V. V. G. Krishna Inavalli, Martin O. Lenz, Corey Butler, Julie Angibaud, Benjamin Compans, Florian Levet, Jan Tønnesen, Olivier Rossier, Gregory Giannone, Olivier Thoumine, Eric Hosy, Daniel Choquet, Jean-Baptiste Sibarita, U. Valentin Nägerl. Nat Methods. 2019-10-21.
- SpineJ : A software tool for quantitative analysis of nanoscale spine morphology. Florian Levet, Jan Tønnesen, Valentin Nägerl, Jean-Baptiste Sibarita. . 2019-09-10.
- A tessellation-based colocalization analysis approach for single-molecule localization microscopy. Florian Levet, Guillaume Julien, Rémi Galland, Corey Butler, Anne Beghin, Anaël Chazeau, Philipp Hoess, Jonas Ries, Grégory Giannone, Jean-Baptiste Sibarita. Nat Commun. 2019-05-30. 10 (1)
- Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software. Daniel Sage, Thanh-An Pham, Hazen Babcock, Tomas Lukes, Thomas Pengo, Jerry Chao, Ramraj Velmurugan, Alex Herbert, Anurag Agrawal, Silvia Colabrese, Ann Wheeler, Anna Archetti, Bernd Rieger, Raimund Ober, Guy M. Hagen, Jean-Baptiste Sibarita, Jonas Ries, Ricardo Henriques, Michael Unser, Seamus Holden. Nat Methods. 2019-04-08. 16 (5) : 387-395.
- Fast Sampling of Implicit Surfaces by Particle Systems. F. Levet, X. Granier, C. Schlick. IEEE International Conference on Shape Modeling and Applications 2006 (SMI'06). .
- Multi-view Sketch-Based FreeForm Modeling. Florian Levet, Xavier Granier, Christophe Schlick. Smart Graphics. . : 204-209.
- Thor: Sketch-Based 3D Modeling by Skeletons. Romain Arcila, Florian Levet, Christophe Schlick. Smart Graphics. . : 232-238.
- Author Correction: Single molecule localisation microscopy reveals how HIV-1 Gag proteins sense membrane virus assembly sites in living host CD4 T cells. Charlotte Floderer, Jean-Baptiste Masson, Elise Boilley, Sonia Georgeault, Peggy Merida, Mohamed El Beheiry, Maxime Dahan, Philippe Roingeard, Jean-Baptiste Sibarita, Cyril Favard, Delphine Muriaux. Sci Rep. 2018-11-22. 8 (1)
- Single molecule localisation microscopy reveals how HIV-1 Gag proteins sense membrane virus assembly sites in living host CD4 T cells. Charlotte Floderer, Jean-Baptiste Masson, Elise Boilley, Sonia Georgeault, Peggy Merida, Mohamed El Beheiry, Maxime Dahan, Philippe Roingeard, Jean-Baptiste Sibarita, Cyril Favard, Delphine Muriaux. Sci Rep. 2018-11-02. 8 (1)
- Bacterial cell wall nanoimaging by autoblinking microscopy. Kevin Floc’h, Françoise Lacroix, Liliana Barbieri, Pascale Servant, Remi Galland, Corey Butler, Jean-Baptiste Sibarita, Dominique Bourgeois, Joanna Timmins. Sci Rep. 2018-09-19. 8 (1)
- A generic widefield topographical and chemical photopatterning method for hydrogels.. Aurelien Pasturel, Pierre-Olivier Strale, Vincent Studer. . 2018-07-20.
- Live single molecule microscopy of HIV-1 assembly in host T cells reveals a spatio-temporal effect of the viral genome.. Charlotte Floderer, Jean-Baptiste Masson, Elise Boiley, Sonia Georgeault, Peggy Merida, Mohamed El Beheiry, Maxime Dahan, Philippe Roigeard, Jean-Baptiste Sibarita, Cyril Favard, Delphine Muriaux. . 2018-02-19.
- Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging. Tomáš Lukeš, Daniela Glatzová, Zuzana Kvíčalová, Florian Levet, Aleš Benda, Sebastian Letschert, Markus Sauer, Tomáš Brdička, Theo Lasser, Marek Cebecauer. Nat Commun. 2017-11-23. 8 (1)
- Localization-based super-resolution imaging meets high-content screening. Anne Beghin, Adel Kechkar, Corey Butler, Florian Levet, Marine Cabillic, Olivier Rossier, Gregory Giannone, Rémi Galland, Daniel Choquet, Jean-Baptiste Sibarita. Nat Meth. 2017-10-30. 14 (12) : 1184-1190.
- 3D Protein Dynamics in the Cell Nucleus.. Anand P. Singh, Rémi Galland, Megan L. Finch-Edmondson, Gianluca Grenci, Jean-Baptiste Sibarita, Vincent Studer, Virgile Viasnoff, Timothy E. Saunders. Biophysical Journal. 2017-01-01. 112 (1) : 133-142.
- SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data.. Florian Levet, Eric Hosy, Adel Kechkar, Corey Butler, Anne Beghin, Daniel Choquet, Jean-Baptiste Sibarita. Nat Methods. 2015-09-07. 12 (11) : 1065-1071.
- 3D high- and super-resolution imaging using single-objective SPIM.. Remi Galland, Gianluca Grenci, Ajay Aravind, Virgile Viasnoff, Vincent Studer, Jean-Baptiste Sibarita. Nat Methods. 2015-05-11. 12 (7) : 641-644.
- Subrepellent doses of Slit1 promote Netrin-1 chemotactic responses in subsets of axons. Isabelle Dupin, Ludmilla Lokmane, Maxime Dahan, Sonia Garel, Vincent Studer. Neural Dev. 2015-03-20. 10 (1)
- Frequency of Cocaine Self-Administration Influences Drug Seeking in the Rat: Optogenetic Evidence for a Role of the Prelimbic Cortex. Elena Martín-García, Julien Courtin, Prisca Renault, Jean- François Fiancette, Hélène Wurtz, Amélie Simonnet, Florian Levet, Cyril Herry, Véronique Deroche-Gamonet. Neuropsychopharmacol. 2014-03-17. 39 (10) : 2317-2330.
- Directed actin assembly and motility.. Rajaa Boujemaa-Paterski, Rémi Galland, Cristian Suarez, Christophe Guérin, Manuel Théry, Laurent Blanchoin. Methods in Enzymology. 2014-01-01. : 283-300.
- Investigating Axonal Guidance with Microdevice-Based Approaches. I. Dupin, M. Dahan, V. Studer. Journal of Neuroscience. 2013-11-06. 33 (45) : 17647-17655.
- Fabrication of three-dimensional electrical connections by means of directed actin self-organization.. Rémi Galland, Patrick Leduc, Christophe Guérin, David Peyrade, Laurent Blanchoin, Manuel Théry. Nature Mater. 2013-02-10. 12 (5) : 416-421.
- Amplification and Temporal Filtering during Gradient Sensing by Nerve Growth Cones Probed with a Microfluidic Assay. Mathieu Morel, Vasyl Shynkar, Jean-Christophe Galas, Isabelle Dupin, Cedric Bouzigues, Vincent Studer, Maxime Dahan. Biophysical Journal. 2012-10-01. 103 (8) : 1648-1656.
- Compressive fluorescence microscopy for biological and hyperspectral imaging. V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, M. Dahan. Proceedings of the National Academy of Sciences. 2012-06-11. 109 (26) : E1679-E1687.
- Automatic non-parametric capsid segmentation using wavelets transform and graph. Florian Levet, Aurelia Cassany, Michael Kann, Jean-Baptiste Sibarita. 2012 9th IEEE International Symposium on Biomedical Imaging (ISBI). 2012-05-01.
- Reprogramming cell shape with laser nano-patterning.. T. Vignaud, R. Galland, Q. Tseng, L. Blanchoin, J. Colombelli, M. Thery. Journal of Cell Science. 2012-02-22. 125 (9) : 2134-2140.
- Hyperspectral fluorescence microscopy based on compressed sensing. Vincent Studer, Jérome Bobin, Makhlad Chahid, Hamed Mousavi, Emmanuel Candes, Maxime Dahan. Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XIX. 2012-02-09.
- Concentration landscape generators for shear free dynamic chemical stimulation. Mathieu Morel, Jean-Christophe Galas, Maxime Dahan, Vincent Studer. Lab Chip. 2012-01-01. 12 (7) : 1340.
- Engineering the surface properties of microfluidic stickers. Bertrand Levaché, Ammar Azioune, Maurice Bourrel, Vincent Studer, Denis Bartolo. Lab Chip. 2012-01-01. 12 (17) : 3028.
- Neurexin-neuroligin adhesions capture surface-diffusing AMPA receptors through PSD-95 scaffolds.. M. Mondin, V. Labrousse, E. Hosy, M. Heine, B. Tessier, F. Levet, C. Poujol, C. Blanchet, D. Choquet, O. Thoumine. Journal of Neuroscience. 2011-09-21. 31 (38) : 13500-13515.
- Analysis of gene expression at the single-cell level using microdroplet-based microfluidic technology. Pascaline Mary, Luce Dauphinot, Nadège Bois, Marie-Claude Potier, Vincent Studer, Patrick Tabeling. Biomicrofluidics. 2011-06-01. 5 (2) : 024109.
- Fast and Easy Enzyme Immobilization by Photoinitiated Polymerization for Efficient Bioelectrochemical Devices. Emmanuel Suraniti, Vincent Studer, Neso Sojic, Nicolas Mano. Anal. Chem.. 2011-04-01. 83 (7) : 2824-2828.
- Multi-confocal fluorescence correlation spectroscopy.. Antoine Delon. Front Biosci. 2011-01-01. E3 (2) : 476-488.
- Photopatterning of ultrathin electrochemiluminescent redox hydrogel films. Milena Milutinovic, Emmanuel Suraniti, Vincent Studer, Nicolas Mano, Dragan Manojlovic, Neso Sojic. Chem. Commun.. 2011-01-01. 47 (32) : 9125.
- Multi-confocal fluorescence correlation spectroscopy.. Antoine Delon. Front Biosci. 2011-01-01. E3 (2) : 476-488.
- Multi-confocal fluorescence correlation spectroscopy.. Antoine Delon. Front Biosci. 2011-01-01. E3 (2) : 476-488.
- Dynamic superresolution imaging of endogenous proteins on living cells at ultra-high density.. Gregory Giannone, Eric Hosy, Florian Levet, Audrey Constals, Katrin Schulze, Alexander I. Sobolevsky, Michael P. Rosconi, Eric Gouaux, Robert Tampé, Daniel Choquet, Laurent Cognet. Biophysical Journal. 2010-08-01. 99 (4) : 1303-1310.
- Measuring, in solution, multiple-fluorophore labeling by combining fluorescence correlation spectroscopy and photobleaching.. Antoine Delon, Irène Wang, Emeline Lambert, Silva Mache, Régis Mache, Jacques Derouard, Vincent Motto-Ros, Rémi Galland. J. Phys. Chem. B. 2010-03-04. 114 (8) : 2988-2996.
- Active connectors for microfluidic drops on demand. Jean-Christophe Galas, Denis Bartolo, Vincent Studer. New J. Phys.. 2009-07-31. 11 (7) : 075027.
- Activity-dependent tuning of inhibitory neurotransmission based on GABAAR diffusion dynamics. . Neuron.. 2009-06-11. 62 (5) : 670-82.
- Microfluidic stickers for cell- and tissue-based assays in microchannels. Mathieu Morel, Denis Bartolo, Jean-Christophe Galas, Maxime Dahan, Vincent Studer. Lab Chip. 2009-01-01. 9 (7) : 1011-1013.
- Microfluidic droplet-based liquid-liquid extraction. Pascaline Mary, Vincent Studer, Patrick Tabeling. Anal. Chem.. 2008-04-01. 80 (8) : 2680-2687.
- A novel fluorescence-based array biosensor: principle and application to DNA hybridization assays.. E. Schultz, R. Galland, D. Du Bouëtiez, T. Flahaut, A. Planat-Chrétien, F. Lesbre, A. Hoang, H. Volland, F. Perraut. Biosensors and Bioelectronics. 2008-02-01. 23 (7) : 987-994.
- Integrating whole transcriptome assays on a lab-on-a-chip for single cell gene profiling. N. Bontoux, L. Dauphinot, T. Vitalis, V. Studer, Y. Chen, J. Rossier, M-C. Potier. Lab Chip. 2008-01-01. 8 (3) : 443.
- Microfluidic stickers. Denis Bartolo, Guillaume Degré, Philippe Nghe, Vincent Studer. Lab Chip. 2008-01-01. 8 (2) : 274-279.
- Visualization and quantification of vesicle trafficking on a three-dimensional cytoskeleton network in living cells. Racine V, Sachse M, Salamero J, Fraisier V, Trubuil A, Sibarita JB.. J Microsc.. 2007 Mar. 225 (Pt 3) : 214-28.
- Improved skeleton extraction and surface generation for sketch-based modeling. Florian Levet, Xavier Granier. Proceedings of Graphics Interface 2007 on - GI '07. 2007-01-01.
- 3D Sketching with Profile Curves. Florian Levet, Xavier Granier, Christophe Schlick. Smart Graphics. 2006-01-01. : 114-125.
- Experimental observation of induced-charge electro-osmosis around a metal wire in a microchannel. Jeremy A. Levitan, Shankar Devasenathipathy, Vincent Studer, Yuxing Ben, Todd Thorsen, Todd M. Squires, Martin Z. Bazant. Colloids and Surfaces A: Physicochemical and Engineering Aspects. 2005-10-01. 267 (1-3) : 122-132.
- Characterization of pneumatically activated microvalves by measuring electrical conductance. J.-C. Galas, V. Studer, Y. Chen. Microelectronic Engineering. 2005-03-01. 78-79 : 112-117.
- Exploring the high sensitivity of SU-8 resist for high resolution electron beam patterning. A PEPIN. Microelectronic Engineering. 2004-06-01. 73-74 : 233-237.
- On-chip optical components and microfluidic systems. Q KOU. Microelectronic Engineering. 2004-06-01. 73-74 : 876-880.
- A microfluidic mammalian cell sorter based on fluorescence detection. V STUDER. Microelectronic Engineering. 2004-06-01. 73-74 : 852-857.
- A nanoliter-scale nucleic acid processor with parallel architecture. Jong Wook Hong, Vincent Studer, Giao Hang, W French Anderson, Stephen R Quake. Nat Biotechnol. 2004-03-14. 22 (4) : 435-439.
- An integrated AC electrokinetic pump in a microfluidic loop for fast and tunable flow control. Vincent Studer, Anne Pépin, Yong Chen, Armand Ajdari. Analyst. 2004-01-01. 129 (10) : 944-949.
- Scaling properties of a low-actuation pressure microfluidic valve. Vincent Studer, Giao Hang, Anna Pandolfi, Michael Ortiz, W. French Anderson, Stephen R. Quake. Journal of Applied Physics. 2004-01-01. 95 (1) : 393-398.
- Fabrication of microfluidic devices for AC electrokinetic fluid pumping. V. Studer, A. Pépin, Y. Chen, A. Ajdari. Microelectronic Engineering. 2002-07-01. 61-62 : 915-920.
- Nanoimprint lithography for the fabrication of DNA electrophoresis chips. A. Pépin, P. Youinou, V. Studer, A. Lebib, Y. Chen. Microelectronic Engineering. 2002-07-01. 61-62 : 927-932.
- Room-temperature and low-pressure nanoimprint lithography. A. Lebib, Y. Chen, E. Cambril, P. Youinou, V. Studer, M. Natali, A. Pépin, H.M. Janssen, R.P. Sijbesma. Microelectronic Engineering. 2002-07-01. 61-62 : 371-377.
- Nanoembossing of thermoplastic polymers for microfluidic applications. V. Studer, A. Pépin, Y. Chen. Appl. Phys. Lett.. 2002-05-13. 80 (19) : 3614-3616.
Team leader
Team member(s)
Chercheurs, Praticiens hospitaliers...
Rémi Galland
Galland
(Researcher)
Ingénieur(e)s, technicien(ne)s
Post-doctorant(s)
Corey Butler
Butler
Doctorant(s)