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Emmanuel Beaurepaire

Research director - CNRS
Room: 84-2018, 05-2016A
Phone: (+33) 1 69 33 5021

emmanuel.beaurepaire at polytechnique.edu

Current research activity:
Advanced microscopies & tissue physiology
Multiphoton microscopy of developing tissues
Large-scale multicolor microscopy • In-depth 3-photon/THG imaging • 2P-light-sheet • Imaging brain development
Equipex Morphoscope


PhD theses advised or co-advised

Postdoc positions available in multiphoton microscopy - see Postdoc proposals at LOB.

ORCID iD iconorcid.org/0000-0002-2082-8214 - ResearcherID: C-6343-2014 - Google Scholar

Dynamic spatiotemporal coordination of neural stem cell fate decisions through local feedback in the adult vertebrate brain, Dray et al, bioRxiv
A scale-space approach for 3D neuronal traces analysis, Phan et al, bioRxiv
In utero electroporation of multiaddressable genome-integrating color markers to individualize cortical mouse astrocytes, Dumas et al, JoVE
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)
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). 
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
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).
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).
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).
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 microscopy, 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 embryos, 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 embryos, 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 media, 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 depth, 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)

PhD theses advised or co-advised

  • Bahar Asadipour (in progress)
  • Hugo Blanc (in progress)
  • Júlia Ferrer Ortas (in progress)
  • Joséphine Morizet (feb 2020) Polarized THG microscopy for the study of biocystals. Currently: postdoc at Polytechnique LOB.
  • Lamiae Abdeladim (sep 2018) Large volume multicolor nonlinear microsopy of brain tissue. Currently: postdoc at UC Berkeley.
  • Nelly Vuillemin (dec 2015) Wavefront control in nonlinear microscopy. Currently: bioimage analyst at McGill University.
  • Pierre Mahou (dec 2012) NL microsc.: multicolor, Bessel beams, and light-sheet illumination. Currently: tenured engineer at Polytechnique.
  • Guillaume Labroille (dec 2011) 3D multiphoton imaging of biological tissues using shaped pulses. Currently: CTO at CAILabs.
  • Nicolas Olivier (dec 2009) Contrast mechanisms and wavefront control in coherent NL microscopy. Currently: tenured scientist at CNRS.
  • Delphine Débarre (sep 2006) THG microscopy for biological applications. Currently: tenured scientist at CNRS.
  • Willy Supatto (sep 2005) Quantitative multiphoton imaging and femtosecond pulse-induced ablation for studying mechano-sensitive gene expression in wild-type Drosophila embryos. Currently: tenured scientist at CNRS.



  • 2020 European microscopy award for the life sciences (European Microscopy Society).
  • 2019 Castaing prize for the life sciences (Societe Francaise des Microscopies).
  • 2015 Dargelos prize (Ecole Polytechnique / AX).
  • 2010 CNRS award for scientific excellence.