Emmanuel Beaurepaire

2025 PhD / Master's internships proposals at LOB - check this page.

Postdoc position: large-scale bioimage analysis - check this page. 

Publications

Preprints
BioImageLoader: Easy handling of bioimage datasets for machine learning. Lim et al, arXiv 2023.
2024
Multiplexed orthogonal polarizations harmonic imaging for probing dynamic biological processes
M. Gleeson, S. Escot, X. Solinas, B. Asadipour, W. Supatto, P. Mahou, C. Stringari, E. Beaurepaire
ACS Photonics (2024)
Modeling and predicting second-harmonic generation from protein molecular structure
B. Asadipour, E. Beaurepaire, X. Zhang, A. Chessel, P. Mahou, W. Supatto, M.-C. Schanne-Klein, C. Stringari
Physical Review X (2024)
Understanding the cell fate and behavior of progenitors at the origin of the mouse cardiac mitral valve
B. Farhat, I. Bordeu, B. Jagla, S. Ibrahim, S. Stefanovic, H. Blanc, K. Loulier, B.D. Simons, E. Beaurepaire, J. Livet, M. Pucéat
Developmental Cell (2024)
Non-random spatial organization of telomere varies during the cell cycle and requires LAP2 and BAF
D. Keller, S. Stinus, D. Umlauf, E. Gourbeyre, E. Biot, N. Olivier, P. Mahou, E. Beaurepaire, P. Andrey, L. Crabbe
iScience (2024)
2023
Label-free imaging of red blood cells and oxygenation with color third-order sum-frequency generation microscopy
J. Ferrer Ortas, P. Mahou, S. Escot, C. Stringari, N. B. David, L. Bally-Cuif, N. Dray, M. Négrerie, W. Supatto, E. Beaurepaire
Light: Science & Applications (2023)
Kidney stone classification using multimodal multiphoton microscopy
M. Gleeson, J. Morizet, P. Mahou, M. Daudon, D. Bazin, C. Stringari, M.-C. Schanne-Klein, E. Beaurepaire
ACS Photonics (2023)
Chromatically corrected multicolor multiphoton microscopy
H. Blanc, G. Kaddour, N.B. David, W. Supatto, J. Livet, E. Beaurepaire, P. Mahou
ACS Photonics (2023)
Third harmonic imaging contrast from tubular structures in the presence of index discontinuity
J. Morizet, N. Olivier, P. Mahou, A. Boutillon, C. Stringari, E. Beaurepaire
Scientific Reports (2023)
Fluorescence to measure light intensity
A. Lahlou, H. Sepasi Tehrani, I. Coghill, Y. Shpinov, M. Mandal, MA. Plamont, I. Aujard, Y. Niu, L. Nedbal, D. Lazár, P. Mahou, W. Supatto, E. Beaurepaire, I. Eisenmann, N. Desprat, V. Croquette, R. Jeanneret, T. Le Saux, L. Jullien
Nature Methods (2023)
Apical size and deltaA expression predict adult neural stem cell decisions along lineage progression
L. Mancini, B. Guirao, S. Ortica, M. Labusch, F. Cheysson, V. Bonnet, MS. Phan, S. Herbert, P. Mahou, E. Menant, S. Bedu, JY. Tinevez, C. Baroud, E. Beaurepaire, Y. Bellaiche, L. Bally-Cuif, N. Dray
Science Advances (2023)
NU-Net: A Self-Supervised Smart Filter for Enhancing Blobs in Bioimages
S. Lim, E. Beaurepaire, A. Chessel
IEEE ICCV (2023)
2022
Intravital deep-tumor single-beam 3-photon, 4-photon, and harmonic microscopy
G.-J. Bakker, S. Weischer, J. Ferrer Ortas, J. Heidelin, V. Andresen, M. Beutler, E. Beaurepaire, P. Friedl
eLife (2022)
nAdder: A scale-space approach for the 3D analysis of neuronal traces
M.-S. Phan, K. Matho, E. Beaurepaire, J. Livet, A. Chessel
PLOS Comp Biol (2022)
2021
Modeling nonlinear microscopy near index-mismatched interfaces
J. Morizet, G. Sartorello, N. Dray, C. Stringari, E. Beaurepaire, N. Olivier
Optica (2021)
Dynamic spatiotemporal coordination of neural stem cell fate decisions occurs through local feedback in the adult vertebrate brain
N. Dray, L. Mancini, U. Binshtok, F. Cheysson, W. Supatto, P. Mahou, S. Bedu, S. Ortica, E. Than-Trong, M. Krecsmarik, S. Herbert, J.-B. Masson, J.-Y. Tinevez, G. Lang, E. Beaurepaire, D. Sprinzak, L. Bally-Cuif
Cell Stem Cell (2021)
Simultaneous NAD(P)H and FAD fluorescence lifetime microscopy of long UVA–induced metabolic stress in reconstructed human skin
T.P.L. Ung, S. Lim, X. Solinas, P. Mahou, A. Chessel, C. Marionnet, T. Bornschlögl, E. Beaurepaire, F. Bernerd, A.-M. Pena, C. Stringari
Scientific Reports (2021)
The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis
A. Johnson,  D.A. Dahhan, N. Gnyliukh, W.A. Kaufmann,  V. Zheden,  T. Costanzo,  P. Mahou, M. Hrtyan, J. Wang, J. Aguilera-Servin, D. van Damme,  E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml
PNAS (2021)
2020
Fast in vivo multiphoton light-sheet microscopy with optimal pulse frequency
V. Maioli, A. Boniface, P. Mahou, J. Ferrer Ortas, L. Abdeladim, E. Beaurepaire, W. Supatto
Biomedical Optics Express (2020)
Fast in vivo imaging of SHG nanoprobes with multiphoton light-sheet microscopy
G. Malkinson, P. Mahou, E. Chaudan, T. Gacoin, A.Y. Sonay, P. Pantazis, E. Beaurepaire, W. Supatto
ACS Photonics (2020)
In utero electroporation of multiaddressable genome-integrating color markers to individualize cortical mouse astrocytes
L. Dumas, S. Clavreul, J. Durand, E. Hernandez-Garzon, L. Abdeladim, R. Barry-Martinet, A. Caballero-Megido, E. Beaurepaire, G. Bonvento, J. Livet, K. Loulier
JoVE (2020)
2019
Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy
L. Abdeladim, K.S. Matho, S. Clavreul, P. Mahou, J.-M. Sintes, X. Solinas, I. Arganda-Carreras, S.G. Turney, J.W. Lichtman, A. Chessel, A.-P. Bemelmans, K. Loulier, W. Supatto, J. Livet, E. Beaurepaire
Nature Communications 10, 1662 (2019)
Cortical astrocytes develop in a plastic manner at both clonal and cellular levels
S. Clavreul, L. Abdeladim, E. Hernández-Garzón, D.Niculescu, J. Durand, S.-H. Ieng, R. Barry, G. Bonvento, E. Beaurepaire, J. Livet, K. Loulier
Nature Communications 10, 4884 (2019)
An actin-based viscoplastic lock ensures progressive body-axis elongation
A. Lardennois, G. Pásti, T. Ferraro, F. Llense, P. Mahou, J. Pontabry, D. Rodriguez, S. Kim, S. Ono, E. Beaurepaire, C. Gally, M. Labouesse
Nature (2019).
High-speed polarization-resolved third-harmonic microscopy
J. Morizet, G. Ducourthial, W. Supatto, A. Boutillon, R. Legouis, M.-C. Schanne-Klein, C. Stringari, E. Beaurepaire
Optica 6 (3), 385-388 (2019).  
Monitoring dynamic collagen reorganization during skin stretching with fast polarization‐resolved second harmonic generation imaging
G. Ducourthial, J.-S. Affagard, M. Schmeltz, X. Solinas, M. Lopez‐Poncelas, C. Bonod‐Bidaud, R. Rubio‐Amador, F. Ruggiero, J.‐M. Allain, E. Beaurepaire, M.‐C. Schanne‐Klein
J. Biophotonics e201800336 (2019).  
Third harmonic generation imaging and analysis of the effect of low gravity on the lacuno-canalicular network of mouse bone
R. Genthial, M. Gerbaix, D. Farlay, L. Vico, E. Beaurepaire, D. Débarre, A. Gourrier
PLoS ONE 14(1): e0209079 (2019).  
2018
Dual-color deep-tissue three-photon microscopy with a multiband infrared laser
K. Guesmi, L. Abdeladim, S. Tozer, P. Mahou, T. Kumamoto, K. Jurkus, P. Rigaud, K. Loulier, N. Dray, P. Georges, M. Hanna, J. Livet, W. Supatto, E. Beaurepaire, F. Druon
Light: Science & Applications 7, 12 (2018).  
Snapshots of archaeal DNA replication and repair in living cells using super-resolution imaging
F. Delpech, Y. Collien, P. Mahou, E. Beaurepaire, H. Myllykallio, R. Lestini
Nucleic Acids Research 46, 10757-10770 (2018).  
Neural cell segmentation in large-scale 3D color fluorescence microscopy images for developemental neuroscience
F. Nourbakhsh, L. Abdeladim, S. Clavreul, K. Loulier, E. Beaurepaire, J. Livet, A. Chessel
IEEE ICIP (2018).  doi: 10.1109/ICIP.2018.8451702
2017
Multicolor two-photon imaging of endogenous fluorophores in living tissues by wavelength mixing
C. Stringari, L. Abdeladim, G. Malkinson, P. Mahou, X. Solinas, I. Lamarre, S. Brizion, J.-B. Galey, W. Supatto, R. Legouis, A.-M. Pena, E. Beaurepaire
Scientific Reports 7, 3792 (2017).
Metrology of multiphoton microscopes using second harmonic generation nanoprobes
P. Mahou, G. Malkinson, E. Chaudan, T. Gacoin, E. Beaurepaire, W. Supatto
Small 13, 1701442 (2017).
Life-long neurogenic activity of individual neural stem cells and continuous growth establish an outside-in architecture in the teleost pallium
G. Furlan, V. Cuccioli, N. Vuillemin, L. Dirian, A. Janue Muntasell, M. Coolen, N. Dray, S. Bedu, C. Houart, E. Beaurepaire, I. Foucher, L. Bally-Cuif
Current Biology 27, 3288-3301 (2017).
Label-free imaging of bone multiscale porosity and interfaces using third-harmonic generation microscopy
R. Genthial, E. Beaurepaire, M.-C. Schanne-Klein, F. Peyrin, D. Farlay, C. Olivier, Y. Bala, G. Boivin, J.-C. Vial, D. Débarre, A. Gourrier
Scientific Reports 7, 3419 (2017).
All-fiber femtosecond laser providing 9 nJ, 50 MHz pulses at 1650 nm for three-photon microscopy
P. Cadroas, L. Abdeladim, L. Kotov, M. Likhachev, D. Lipatov, D. Gaponov, A. Hideur, M. Tang, J. Livet, W. Supatto, E. Beaurepaire, S. Février
J. Optics 19, 065506 (2017).
2016
Efficient second-harmonic imaging of collagen in histological slides using Bessel beam excitation
N. Vuillemin, P. Mahou, D. Débarre, T. Gacoin, P.-L. Tharaux, M.-C. Schanne-Klein, W.Supatto, E. Beaurepaire
Scientific Reports 6, 29863 (2016).
2015
Whole-brain functional imaging with two-photon light-sheet microscopy
S. Wolf, W. Supatto, G. Debrégeas, P. Mahou, S.G. Kruglik, J.-M. Sintes, E. Beaurepaire, R. Candelier
Nature Methods 12(5), 379–380 (2015).
Large-scale live imaging of adult neural stem cells in their endogenous niche
N. Dray, S. Bedu, N. Vuillemin, A. Alunni, M. Coolen, M. Krecsmarik, W. Supatto, E. Beaurepaire, L. Bally-Cuif
Development 142: 3592-3600 (2015).
2014
Multicolor two-photon light-sheet microscopy
P. Mahou, J. Vermot, E. Beaurepaire, W. Supatto
Nature Methods 11(6), 600-601 (2014).
Mitigating phototoxicity during multiphoton microscopy of live Drosophila embryos in the 1.0–1.2 µm wavelength range
D. Débarre, N. Olivier, W. Supatto, E. Beaurepaire
PLoS ONE 9(8): e104250 (2014).
Multiplex cell and lineage tracking with combinatorial labels
K. Loulier, R. Barry, P. Mahou, Y. Le Franc, W. Supatto, K.S. Matho, S. Ieng, S. Fouquet, E. Dupin, R. Benosman, A. Chédotal, E. Beaurepaire, X. Morin, J. Livet
Neuron 81(3), 505-520 (2014).

before 2014
44. Probing ordered lipid assemblies with polarized third-harmonic generation microscopy, M. Zimmerley, P. Mahou, D. Débarre, M.-C. Schanne-Klein, E. Beaurepaire, Phys. Rev. X 3, 011002 (2013).
43. Non-invasive monitoring of cell metabolism and lipid production in 3D engineered human adipose tissues using label-free multiphoton microscopyISTEX, T. Chang, M. Zimmerley, K.P. Quinn, I. Lamarre-Jouenne, D.L. Kaplan, E. Beaurepaire, I. Georgakoudi, Biomaterials 34(34) 8607-16 (2013).
42. Multicolor two-photon tissue imaging by wavelength mixing, P. Mahou, M. Zimmerley, K. Loulier, K. Matho, G. Labroille, X. Morin, W. Supatto, J. Livet, D. Débarre, E. Beaurepaire, Nature Methods 9(8) 815-818 (2012).
41. 3D resolved mapping of optical aberrations in thick samples, J. Zeng, P. Mahou, M.-C. Schanne-Klein, E. Beaurepaire, D. Débarre, Biomed. Opt. Express 3(8), 1898-1913 (2012).
40. Third-harmonic generation microscopy with Bessel beams: a numerical study, N. Olivier, D. Débarre, P. Mahou, E. Beaurepaire, Opt. Express 20(22), 24886-24902 (2012).
39. Accuracy of correction in modal sensorless adaptive optics, A. Facomprez, E. Beaurepaire, D. Débarre, Opt. Express 20(3), 2837-2849 (2012).
38. Advances in multiphoton microscopy for imaging embryosISTEX, W. Supatto, T.V. Truong, D. Débarre, E. Beaurepaire, Current Opinion in Genetics & Development 21(5) 538-548 (2011). 
37. Methodology for reconstructing early zebrafish development from in vivo multiphoton microscopy, M. Luengo-Oroz, J. Rubio-Guivernau, E. Faure, T. Savy, L. Duloquin, N. Olivier, D. Pastor, M. Ledesma-Carbayo, D. Débarre, P. Bourgine, E. Beaurepaire, N. Peyriéras, A. Santos, IEEE Trans. Image Processing 21(4), 2335-40 (2012). 
36. Advances in multiphoton microscopy for imaging embryosISTEX, W. Supatto, T.V. Truong, D. Débarre, E. Beaurepaire, Current Opinion in Genetics & Development 21(5) 538-548 (2011). 
35. Combined third-harmonic generation and four-wave mixing microscopy of tissues and embryos, P. Mahou, N. Olivier, G. Labroille, L. Duloquin, J-M. Sintes, N. Peyriéras, R. Legouis, D. Débarre, E. Beaurepaire, Biomed. Opt. Express 2(10), 2837-2849 (2011).
34. Simple characterisation of a deformable mirror inside a high numerical aperture microscope using phase diversity, D. Débarre, T. Vieille, E. Beaurepaire, J. Microsc. 244 (2), 136-143 (2011).
33. Cell lineage reconstruction of early zebrafish embryos using label-free nonlinear microscopy, N. Olivier, M. Luengo-Oroz, L. Duloquin, E. Faure, T. Savy, I. Veilleux, X. Solinas, D. Débarre, P. Bourgine, A. Santos, N. Peyriéras, E. Beaurepaire, Science 339(5994), 967-71 (2010).
32. Multimodal nonlinear imaging of the human cornea, F. Aptel, N. Olivier, A. Deniset-Besseau, J.-M. Legeais, K. Plamann, M.-C. Schanne-Klein, E. Beaurepaire, Invest. Ophthalmol. Vis. Sci. 51(5), 2459-65 (2010).
31. Harmonic microscopy of isotropic and anisotropic microstructure of the human cornea, N. Olivier, F. Aptel, K. Plamann, M.-C. Schanne-Klein, E. Beaurepaire, Opt. Express 18(5), 5028-40 (2010).
30. Dispersion-based pulse shaping for multiplexed two-photon fluorescence microscopy, G. Labroille, R. S. Pillai, X. Solinas, C. Boudoux, N. Olivier, E. Beaurepaire, M. Joffre, Opt Lett 35(20), 3444 (2010).
29. Multiphoton microscopy of engineered dermal substitutes: assessment of 3-D collagen matrix remodeling induced by fibroblast contraction, A.-M. Pena, D. Fagot, C. Olive, J.-F. Michelet, J.-B. Galey, F. Leroy, E. Beaurepaire, J.-L. Martin, A. Colonna, M. C. Schanne-Klein, J Biomed Opt 15(05), 056018 (2010).
28. Dynamic aberration correction for multiharmonic microscopy, N. Olivier, D. Débarre, E. Beaurepaire, Opt. Lett. 34(20), 3145-7 (2009).
27. Multiplexed two-photon microscopy of dynamic biological samples with shaped broadband pulses, R.S. Pillai, C. Boudoux, G. Labroille, N. Olivier, I. Veilleux, E. Farge, M. Joffre, E. Beaurepaire, Opt. Express 17(15), 12741-52 (2009).
26. Two-photon microscopy with simultaneous standard and extended depth of field using an acoustic gradient-index lens, N. Olivier, A. Mermillod-Blondin, C.B. Arnold, E. Beaurepaire, Opt. Lett. 34(11), 1684-6 (2009).
25. Third-harmonic generation microscopy with focus-engineered beams: a numerical study, N. Olivier, E. Beaurepaire, Opt. Express 16, 14703 (2008)
24. Tissue deformation modulates Twist expression to determine anterior midgut differentiation in Drosophila embryos, N. Desprat, W. Supatto, P.-A. Pouille, E. Beaurepaire, E. Farge, Dev. Cell 15, 470 (2008)
23. Mechanical factors activate beta-catenin-dependent oncogene expression in APC1638N/+  mouse colon, J. Whitehead, D. Vignjevic, C. Fütterer, E. Beaurepaire, S. Robine, E. Farge, HFSP J. 2, 286 (2008)
22. Quantitative characterization of biological liquids for third-harmonic generation microscopy, D. Débarre, E. Beaurepaire, Biophys. J. 92, 603 (2007)
21. Signal epidetection in third-harmonic generation microscopy of turbid media, D. Débarre, N. Olivier, E. Beaurepaire, Opt. Express 15, 8913 (2007)
20. Three-dimensional investigation and scoring of extracellular matrix remodeling during lung fibrosis using multiphoton microscopy, A.-M. Pena, A. Fabre, D. Débarre, J. Marchal-Somme, B. Crestani, J.-L. Martin, E. Beaurepaire, M.-C. Schanne-Klein, Microsc. Research Techn. 70, 162 (2007)
19. Second harmonic imaging and scoring of collagen in fibrotic tissues, M. Strupler, A.-M. Pena, M. Hernest, P.-L. Tharaux, J.-L. Martin, E. Beaurepaire, M.-C. Schanne-Klein, Opt. Express 15, 4054 (2007)
18. Micrometer-scale ex vivo multiphoton imaging of unstained arterial wall structure, T. Boulesteix, A.-M. Pena, N. Pagès, G. Godeau, M.-P. Sauviat, E. Beaurepaire, M.-C. Schanne-Klein, Cytometry A 69, 20 (2006)
17. Optical in situ size determination of single lanthanide-ion doped oxide nanoparticles, D. Casanova, D. Giaume, E. Beaurepaire, T. Gacoin, J.-P. Boilot, A. Alexandrou, Appl. Phys. Lett. 89, 253103 (2006)
16. Imaging lipid bodies in cells and tissues using third-harmonic generation microscopy, D. Débarre, W. Supatto, A.-M. Pena, A. Fabre, T. Tordjmann, L. Combettes, M.-C. Schanne-Klein, E. Beaurepaire, Nature Methods 3, 47 (2006)
15. Fourier-transform coherent anti-Stokes Raman scattering microscopy, J. P. Ogilvie, E. Beaurepaire, A. Alexandrou, M. Joffre, Opt. Lett. 31, 480 (2006)
14. Use of coherent control for selective two-photon fluorescence microscopy in live organisms, J. P. Ogilvie, D. Débarre, X. Solinas, J.-L. Martin, E. Beaurepaire, M. Joffre, Opt. Express 14, 759 (2006)
13. Structure sensitivity in third-harmonic generation microscopy, D. Débarre, W. Supatto, E. Beaurepaire, Opt. Lett. 30, 2134 (2005)
12. Femtosecond pulse-induced microprocessing of live Drosophila embryos, W. Supatto, D. Débarre, E. Farge, E. Beaurepaire, Med. Laser Applic. 20, 207 (2005)
11. In vivo modulation of morphogenetic movements in Drosophila embryos with femtosecond laser pulses, W. Supatto, D. Débarre, B. Moulia, E. Brouzés, J.-L. Martin, E. Farge, E. Beaurepaire, Proc. Nat. Acad. Sci. USA 102, 1047 (2005)
10. Functionalized fluorescent oxide nanoparticles: artificial toxins for sodium channel targeting and imaging at the single-molecule level, E. Beaurepaire, V. Buissette, M.-P. Sauviat, D. Giaume, K. Lahlil, A. Mercuri, D. Casanova, A. Huignard, J.-L. Martin, T. Gacoin, J.-P. Boilot, A. Alexandrou, Nano Letters 4, 2079 (2004)
9. Second-harmonic microscopy of unstained living cardiac myocytes: measurements of sarcomere length with 20 nm accuracy, T. Boulesteix, E. Beaurepaire, M.-P. Sauviat, M.-C. Schanne-Klein, Opt. Lett. 29, 2031 (2004)
8. Velocimetric third-harmonic generation microscopy: micrometer-scale quantification of morphogenetic movements in unstained embryos, D. Débarre, W. Supatto, E. Farge, B. Moulia, M.-C. Schanne-Klein, E. Beaurepaire, Opt. Lett. 29, 2881 (2004)
7. Epifluorescence collection in two-photon microscopy, E. Beaurepaire, J. Mertz, Appl. Opt. 41, 5376 (2002)
6. High resolution full-field optical coherence tomography with a Linnik microscope, L. Dubois, L. Vabre, A. C. Boccara, E. Beaurepaire, Appl. Opt. 41, 805 (2002)
5. Ultra-deep two-photon excitation in turbid mediaISTEX, E. Beaurepaire, M. Oheim, J. Mertz, Opt. Commun. 188, 25 (2001)
4. Odor-evoked calcium signals in dendrites of rat mitral cells, S. Charpak, J. Mertz, E. Beaurepaire, L. Moreaux, K. Delaney, Proc. Nat. Acad. Sci. USA 98, 1230 (2001)
3. Two-photon microscopy in brain tissue: parameters influencing the imaging depthISTEX, M. Oheim, E. Beaurepaire, E. Chaigneau, J. Mertz, S. Charpak, J. Neurosci. Meth. 111, 29 (2001); 112, 205 (2001).
2. Combined scanning optical coherence and two-photon-excited fluorescence microscopy, E. Beaurepaire, L. Moreaux, F. Amblard, J. Mertz, Opt. Lett. 24, 969 (1999)
1. Full-field optical coherence microscopy, E. Beaurepaire, C. Boccara, M. Lebec, L. Blanchot, H. Saint-Jalmes, Opt. Lett. 23, 244 (1998)