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
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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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PalmTracer
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News
Multi-dimensional spectral Single Molecule Localization Microscopy
Single molecule localization (SML) and tracking (SPT) techniques, such as (spt)PALM, (u/DNA)PAINT and quantum dot tracking, have given unprecedented insight into the nanoscale molecular organization and dynamics in living cells. They allow monitoring individual proteins with millisecond temporal resolution and high spatial resolution (<30 nm) by precisely localizing the point spread function (PSF) of individual emitters and tracking their position over time. While SPT methods have been extended to study the temporal dynamics and co-organization of multiple proteins, conventional experimental setups are restricted in the number of proteins they can probe simultaneously and usually have to tradeoff between the number of colors, the spatio-temporal resolution, and the field of view. Yet, localizing and tracking several proteins simultaneously at high spatial and temporal resolution within large field of views can provide important biological insights. By employing a dual-objective spectral imaging configuration compatible with live cell imaging combined with dedicated computation tools, we demonstrate simultaneous 3D single particle localization and tracking of multiple distinct species over large field of views to be feasible without compromising spatio-temporal resolution. The dispersive element introduced into the second optical path induces a spectrally dependent displacement, which we used to analytically separate up to five different fluorescent species of single emitters based on their emission spectra. We used commercially available microscope bodies aligned one on top of the other, offering biologists with a very ergonomic and flexible instrument covering a broad range of SMLM applications. Finally, we developed a powerful freely available software, called PALMTracer, which allows to quantitatively assess 3D + t + λ SMLM data. We illustrate the capacity of our approach by performing multi-color 3D DNA-PAINT of fixed samples, and demonstrate simultaneous tracking of multiple receptors in live fibroblast and neuron cultures.
Multi-dimensional spectral Single Molecule Localization Microscopy
Authors: Corey Butler, G. Ezequiel Saraceno, Adel Kechkar, Vincent Studer, Julien P. Dupuis, Laurent Groc, Rémi Galland, Jean-Baptiste Sibarita
Front. Bioinform., 04 March 2022 | https://doi.org/10.3389/fbinf.2022.813494
Contacts: Rémi Galland and Jean-Baptiste Sibarita
+ Cf. Bordeaux Neurocampus website here
Automated high-speed 3D imaging of organoid cultures - Nature Methods, June 2022
Current imaging approaches limit the ability to perform multi-scale characterization of three-dimensional (3D) organotypic cultures (organoids) in large numbers. Here, we present an automated multi-scale 3D imaging platform synergizing high-density organoid cultures with rapid and live 3D single-objective light-sheet imaging. It is composed of disposable microfabricated organoid culture chips, termed JeWells, with embedded optical components and a laser beam-steering unit coupled to a commercial inverted microscope. It permits streamlining organoid culture and high-content 3D imaging on a single user-friendly instrument with minimal manipulations and a throughput of 300 organoids per hour. We demonstrate that the large number of 3D stacks that can be collected via our platform allows training deep learning-based algorithms to quantify morphogenetic organizations of organoids at multi-scales, ranging from the subcellular scale to the whole organoid level. We validated the versatility and robustness of our approach on intestine, hepatic, neuroectoderm organoids and oncospheres.
Authors: Anne Beghin, Gianluca Grenci, Geetika Sahni, Su Guo, Harini Rajendiran, Tom Delaire, Saburnisha Binte Mohamad Raffi, Damien Blanc, Richard de Mets, Hui Ting Ong, Xareni Galindo, Anais Monet, Vidhyalakshmi Acharya, Victor Racine, Florian Levet, Remi Galland, Jean-Baptiste Sibarita and Virgile Viasnoff
Cf. Nature Methods - June 2022 here
Contact: Jean-Baptiste Sibarita
Selected Publications
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« Technical Staff »
BARRY Thierno | Technical staff | thierno.barry.1@u-bordeaux.fr | +33533514700 | |
LEVET Florian | Technical staff | florian.levet@inserm.fr | +33533514747 | ![]() |
NEUHAUS Abdelghani | Technical staff | abdelghani.neuhaus@u-bordeaux.fr | +33533514700 | |
SIBARITA Jean-Baptiste | Technical staff | jean-baptiste.sibarita@u-bordeaux.fr | +33533514706 | ![]() |
« Postdoc »
DELAIRE Tom | Postdoc | tom.delaire@u-bordeaux.fr | +33533514700 | ![]() |
« PhD student »
BETTAREL Laetitia | PhD student | laetitia.bettarel@u-bordeaux.fr | +33533514700 | |
LOHK Christer | PhD student | christer.lohk@u-bordeaux.fr | +33533514700 |