Florian Levet
Team: Quantitative imaging of the cell
Engineer/Technician | Ingénieur de recherche (IR) | INSERM
Florian Levet
PI | INSERM Research Engineer | PhD, HDR
Bioimage Analysis & Software Development
Team: Quantitative Imaging of the Cell (QIC)
Affiliations: Interdisciplinary Institute for Neuroscience (IINS) & Bordeaux Imaging Center (BIC)
I work at the interface between microscopy, image analysis and cell biology. I develop methods that transform complex microscopy data into quantitative and interpretable representations - from single molecules and synapses to whole 3D cellular systems.
Achievements
SINGLE-MOLECULE LOCALIZATION MICROSCOPY DATA
Point cloud analysis
I developed tessellation-based approaches to segment and quantify localization microscopy data and to measure molecular co-organization. SR-Tesseler and Coloc-Tesseler introduced this geometric view of SMLM data; the same philosophy later became part of PoCA, where visualization, interaction and quantification are combined in a common environment.
NEURONAL MORPHOLOGY
Connecting molecular organization to morphology
Protein spatial organization is most informative when interpreted in the context of the surrounding morphology. This requires geometry-based methods to quantify dendrites, spines and synapses, as well as correlative microscopy approaches that map nanoscale protein localization onto the global cellular structure.
3D IMAGING
3D nuclei segmentation and style transfer
With the development of light-sheet microscopy in the team, we began acquiring hundreds of 3D spheroids, creating a need for robust and scalable nuclei segmentation. We first manually annotated seven 3D image stacks to train a dedicated StarDist 3D model. As increasingly diverse spheroid datasets were acquired using different imaging modalities and fluorescent labels, we then explored style-transfer approaches to adapt existing annotated datasets and limit the need for new manual annotations.
Current directions
Learning representations
Learning representations with well-structured embedding spaces that separate biological structures and support segmentation, instance identification and classification with limited annotation.
Geometry & topology
Combining geometry and topology to identify structural components, describe their spatial organization and compute quantitative features from complex biological systems.
PoCA multimodal platform
Extending PoCA from point-cloud analysis into a scalable environment for multimodal bioimage analysis, combining images, segmentations, meshes, graphs and quantitative features across large datasets.
Software, open science & community
Software development is not a separate technical activity in my work; it is one of the ways methods become usable, testable and transferable. This is also why I am involved in broader efforts around bioimage-analysis practice, community resources and collaborative development.
Open software
PoCA, SR-Tesseler and related tools turn methodological developments into open software that can be explored, tested and reused by other groups.
Community
Through GloBIAS and related initiatives, I contribute to efforts around training, reproducibility, best practices and the organization of the international bioimage-analysis community.
Collaboration
Many of the methods originate from concrete microscopy questions. I therefore work closely with imaging specialists and biologists, from synaptic nano-organization to complex 3D cellular systems.
COMMUNITY / GLOBIAS
Strengthening the foundations of bioimage analysis
GloBIAS brings together bioimage analysts, software developers, imaging scientists and educators to strengthen bioimage analysis as a scientific and professional field. Its activities focus on knowledge exchange, training, best practices and standards, community building, and coordinated efforts around emerging methodological and computational challenges.
GloBIAS: strengthening the foundations of bioimage analysis
Agustin A. Corbat, Christa G. Walther, Laura R. de la Ballina, Nicholas D. Condon, Alessandro A. Felder, Martin Schätz, Bettina Schmerl, Ko Sugawara, Clara Prats, Anna Klemm, Kota Miura, Paula Sampaio, Christian Tischer, Florian Levet*, Rocco D’Antuono*, Beth A. Cimini*, Robert Haase*
Nature Methods (2026). * co-corresponding authors
GloBIAS survey results – An insight into the global bioimage analysis community
Laura R. de la Ballina, Christa G. Walther, Nicholas D. Condon, Alessandro A. Felder, Martin Schätz, Bettina Schmerl, Ko Sugawara, Clara Prats, Anna Klemm, Kota Miura, Paula Sampaio, Christian Tischer, Shuichi Onami, Rocco D'Antuono, Beth A. Cimini, Robert Haase, Agustin A. Corbat, Florian Levet
Journal of Microscopy (2026).
Publications
GloBIAS survey results – An insight into the global bioimage analysis community
Laura R. de la Ballina, Christa G. Walther, Nicholas D. Condon, Alessandro A. Felder, Martin Schätz, Bettina Schmerl, Ko Sugawara, Clara Prats, Anna Klemm, Kota Miura, Paula Sampaio, Christian Tischer, Shuichi Onami, Rocco D'Antuono, Beth A Cimini, Robert Haase, Agustin A. Corbat, Florian Levet
Journal of Microscopy.
2026-07-27
10.1111/jmi.70153
Presynaptic actin nanostructures: A reproducibility case study
Rensu P. Theart, Florian Levet, Paul Hernández‐Herrera, Christophe Leterrier, Laura R. de la Ballina
Journal of Microscopy.
2026-07-24
10.1111/jmi.70138
GloBIAS: strengthening the foundations of bioimage analysis
Agustin A. Corbat, Christa G. Walther, Laura R. de la Ballina, Nicholas D. Condon, Alessandro A. Felder, Martin Schätz, Bettina Schmerl, Ko Sugawara, Clara Prats, Anna Klemm, Kota Miura, Paula Sampaio, Christian Tischer, Florian Levet, Rocco D’Antuono, Beth A. Cimini, Robert Haase
Nature Methods.
2026-04-22
10.1038/s41592-026-03060-7
Membrane-associated effluxosomes coordinate multi-metal resistance in Mycobacterium tuberculosis
Pierre Dupuy, Yves-Marie Boudehen, Marion Faucher, John A Buglino, Allison Fay, Sylvain Cantaloube, Yasmina Grimoire, Julien Marcoux, Florian Levet, Laetitia Bettarel, Bertille Voisin, Jérôme Rech, Jean-Yves Bouet, Olivier Saurel, Jean-Baptiste Sibarita, Michael Glickman, Claude Gutierrez, Olivier Neyrolles
The EMBO Journal.
2026-02-13
10.1038/s44318-026-00715-1
In-depth single molecule localization microscopy using adaptive optics and single objective light-sheet microscopy
Marine Cabillic, Hisham Forriere, Laetitia Bettarel, Corey Butler, Abdelghani Neuhaus, Ihssane Idrissi, Miguel Edouardo Sambrano-Lopez, Julian Rossbroich, Lucas-Raphael Müller, Jonas Ries, Gianluca Grenci, Virgile Viasnoff, Florian Levet, Jean-Baptiste Sibarita, Rémi Galland
Nat Commun.
2025-09-24
10.1038/s41467-025-62198-8
High-affinity detection of biotinylated endogenous neuroligin-1 at excitatory and inhibitory synapses using a tagged knock-in mouse
Charles Ducrot, Adèle Drouet, Béatrice Tessier, Chloé Desquines, Tiffany Cloâtre, Rania-Cérine Mazouzi, Florian Levet, Alexandre Favereaux, Mathieu Letellier, Olivier Thoumine
Proc. Natl. Acad. Sci. U.S.A..
2025-05-27
10.1073/pnas.2411669122
Arkitekt: streaming analysis and real-time workflows for microscopy
Johannes Roos, Stéphane Bancelin, Tom Delaire, Alexander Wilhelmi, Florian Levet, Maren Engelhardt, Virgile Viasnoff, Rémi Galland, U. Valentin Nägerl, Jean-Baptiste Sibarita
Nat Methods.
2024-09-18
10.1038/s41592-024-02404-5
Protocol for matching protein localization to synapse morphology in primary rat neurons by correlative super-resolution microscopy
Tiffany Cloâtre, Magali Mondin, Jean-Baptiste Sibarita, Florian Levet, Olivier Thoumine
STAR Protocols.
2024-09-01
10.1016/j.xpro.2024.103160
Neuroligin-1 dependent phosphotyrosine signaling in excitatory synapse differentiation
Zsófia Szíber, Adèle Drouet, Magali Mondin, Florian Levet, Olivier Thoumine
Front. Mol. Neurosci..
2024-05-15
10.3389/fnmol.2024.1359067
Multi-synaptic boutons are a feature of CA1 hippocampal connections in the stratum oriens
Mark Rigby, Federico W. Grillo, Benjamin Compans, Guilherme Neves, Julia Gallinaro, Sophie Nashashibi, Sally Horton, Pedro M. Pereira Machado, Maria Alejandra Carbajal, Gema Vizcay-Barrena, Florian Levet, Jean-Baptiste Sibarita, Angus Kirkland, Roland A. Fleck, Claudia Clopath, Juan Burrone
Cell Reports.
2023-05-01
10.1016/j.celrep.2023.112397
PoCA: a software platform for point cloud data visualization and quantification
Florian Levet, Jean-Baptiste Sibarita
Nat Methods.
2023-03-03
10.1038/s41592-023-01811-4
A framework for evaluating the performance of SMLM cluster analysis algorithms
Daniel J. Nieves, Jeremy A. Pike, Florian Levet, David J. Williamson, Mohammed Baragilly, Sandra Oloketuyi, Ario de Marco, Juliette Griffié, Daniel Sage, Edward A. K. Cohen, Jean-Baptiste Sibarita, Mike Heilemann, Dylan M. Owen
Nat Methods.
2023-02-01
10.1038/s41592-022-01750-6
MID3A: Microscopy Image Denoising meets Differentiable Data Augmentation
Felix Fuentes-Hurtado, Tom Delaire, Florian Levet, Jean-Baptiste Sibarita, Virgile Viasnoff
2022 International Joint Conference on Neural Networks (IJCNN).
2022-07-18
10.1109/IJCNN55064.2022.9892954
Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification
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, Virgile Viasnoff
Nat Methods.
2022-06-13
10.1038/s41592-022-01508-0
A synaptomic analysis reveals dopamine hub synapses in the mouse striatum
Vincent Paget-Blanc, Marlene E. Pfeffer, Marie Pronot, Paul Lapios, Maria-Florencia Angelo, Roman Walle, Fabrice P. Cordelières, Florian Levet, Stéphane Claverol, Sabrina Lacomme, Mélina Petrel, Christelle Martin, Vincent Pitard, Véronique De Smedt Peyrusse, Thomas Biederer, David Perrais, Pierre Trifilieff, Etienne Herzog
Nat Commun.
2022-06-03
10.1038/s41467-022-30776-9
Editorial: Methods and Tools for Bioimage Analysis
Florian Levet, Virginie Uhlmann, Florian Jug
Front. Comput. Sci..
2022-05-30
10.3389/fcomp.2022.931939
CaMKII activation persistently segregates postsynaptic proteins via liquid phase separation
Tomohisa Hosokawa, Pin-Wu Liu, Qixu Cai, Joana S. Ferreira, Florian Levet, Corey Butler, Jean-Baptiste Sibarita, Daniel Choquet, Laurent Groc, Eric Hosy, Mingjie Zhang, Yasunori Hayashi
Nat Neurosci.
2021-04-29
10.1038/s41593-021-00843-3
Developing open-source software for bioimage analysis: opportunities and challenges
Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase
F1000Res.
2021-04-19
10.12688/f1000research.52531.1
Distance-dependent regulation of NMDAR nanoscale organization along hippocampal neuron dendrites
Joana S. Ferreira, Julien P. Dupuis, Blanka Kellermayer, Nathan Bénac, Constance Manso, Delphine Bouchet, Florian Levet, Corey Butler, Jean-Baptiste Sibarita, Laurent Groc
Proc Natl Acad Sci USA.
2020-09-14
10.1073/pnas.1922477117
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
10.1073/pnas.1922563117
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
10.1038/s41467-020-16453-9
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
10.1038/s41467-020-15648-4
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
10.1016/j.ymeth.2020.01.020
Synaptic and supra-synaptic organisation of the dopaminergic projection to the striatum.
Marlene Pfeffer, Marie Pronot, Maria Florencia Angelo, Roman Walle, Fabrice P Cordelieres, Florient Levet, Stephane Claverol, Sabrina Lacome, Melina Petrel, Christelle Martin, Vincent Pitard, Veronique Desmedt-Peyrusse, Thomas Biederer, Pierre Trifilieff, Etienne Herzog
.
2020-02-18
10.1101/2020.02.18.952978
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
10.1038/s41592-019-0611-8
SpineJ : A software tool for quantitative analysis of nanoscale spine morphology
Florian Levet, Jan Tønnesen, Valentin Nägerl, Jean-Baptiste Sibarita
.
2019-09-10
10.1101/764548
Differential role of pre- and postsynaptic neurons in the activity-dependent control of synaptic strengths across dendrites
Mathieu Letellier, Florian Levet, Olivier Thoumine, Yukiko Goda
PLoS Biol.
2019-06-05
10.1371/journal.pbio.2006223
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
10.1038/s41467-019-10007-4
Differential Nanoscale Topography and Functional Role of GluN2-NMDA Receptor Subtypes at Glutamatergic Synapses
Blanka Kellermayer, Joana S. Ferreira, Julien Dupuis, Florian Levet, Dolors Grillo-Bosch, Lucie Bard, Jeanne Linarès-Loyez, Delphine Bouchet, Daniel Choquet, Dmitri A. Rusakov, Pierre Bon, Jean-Baptiste Sibarita, Laurent Cognet, Matthieu Sainlos, Ana Luisa Carvalho, Laurent Groc
Neuron.
2018-10-01
10.1016/j.neuron.2018.09.012
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).
10.1109/smi.2006.13
Multi-view Sketch-Based FreeForm Modeling
Florian Levet, Xavier Granier, Christophe Schlick
Smart Graphics.
10.1007/978-3-540-73214-3_21
Thor: Sketch-Based 3D Modeling by Skeletons
Romain Arcila, Florian Levet, Christophe Schlick
Smart Graphics.
10.1007/978-3-540-85412-8_22
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
10.1038/s41467-017-01857-x
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
10.1038/nmeth.4486
Nanoscale organization of synaptic adhesion proteins revealed by single-molecule localization microscopy
Ingrid Chamma, Florian Levet, Jean-Baptiste Sibarita, Matthieu Sainlos, Olivier Thoumine
Neurophoton.
2016-11-03
10.1117/1.NPh.3.4.041810
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
10.1038/nmeth.3579
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
10.1038/npp.2014.66
Target-specific vulnerability of excitatory synapses leads to deficits in associative memory in a model of intellectual disorder
X. Houbaert, C.-L. Zhang, F. Gambino, M. Lepleux, M. Deshors, E. Normand, F. Levet, M. Ramos, P. Billuart, J. Chelly, E. Herzog, Y. Humeau
Journal of Neuroscience.
2013-08-21
10.1523/JNEUROSCI.1457-13.2013
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
10.1523/jneurosci.6439-10.2011
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
10.1523/jneurosci.6439-10.2011
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
10.1016/j.bpj.2010.06.005
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
10.1145/1268517.1268524
3D Sketching with Profile Curves
Florian Levet, Xavier Granier, Christophe Schlick
Smart Graphics.
2006-01-01
10.1007/11795018_11
