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Project publications (contract# ANR-11-EQPX-0029)

Research articles
Nature (2019). Lardennois et al. https://doi.org/10.1038/s41586-019-1509-4
An actin-based viscoplastic lock ensures progressive body-axis elongation
Nature Communications 10 (2019). Clavreul et al. https://doi.org/10.1038/s41467-019-12791-5
Cortical astrocytes develop in a plastic manner at both clonal and cellular levels
Nature Communications 10 (2019). Abdeladim et al. doi:10.1038/s41467-019-09552-9
Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy
Optica 6 (2019). Morizet et al. doi:10.1364/OPTICA.6.000385
High-speed polarization-resolved third-harmonic microscopy
J Biophotonics (2019). Ducourthial et al.
Monitoring dynamic collagen reorganization during skin stretching with fast polarization‐resolved SHG imaging
PLoS ONE 14 (2019). Genthial et al.
THG imaging and analysis of the effect of low gravity on the lacuno-canalicular network of mouse bone
Light: Science & Applications 7 (2018). Zhang et al. doi:10.1038/s41377-018-0098-6.
Macroscale fluorescence imaging against autofluorescence under ambient light
Light: Science & Applications 7 (2018). Guesmi et al. doi:10.1038/s41377-018-0012-2.
Dual-color deep-tissue three-photon microscopy with a multiband infrared laser
Cell Reports 25 (2018). Ferreira et al. doi:doi.org/10.1016/j.celrep.2018.10.069.
Chiral Cilia Orientation in the Left-Right Organizer
Development 145 (2018). Fabrèges et al. doi:doi.org/10.1242/dev.152041.
Control of the proportion of inner cells by asymmetric divisions and the ensuing resilience of cloned rabbit embryos
Nucleic Acids Research 46 (2018). Brozovic et al. doi:10.1093/nar/gkx1108.
ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets
Nucleic Acids Research 46 (2018). Delpech et al. doi:10.1093/nar/gky829.
Snapshots of archaeal DNA replication and repair in living cells using super-resolution imaging
Biomaterials Science 27 (2018). Tidu et al. doi:10.1039/c7bm01163f.
Highly concentrated collagen solutions leading to transparent scaffolds of controlled 3D organizations for corneal epithelial cell colonization
Scientific Reports 8 (2018). Faenov et al. doi:10.1038/s41598-018-34717-9.
Advanced high resolution x-ray diagnostic for HEDP experiments
Current Biology 27 (2017). Furlan et al. doi:10.1016/j.cub.2017.09.052.
Life-long neurogenic activity of individual neural stem cells and continuous growth establish an outside-in architecture in the teleost pallium
eLife 6:e25078 (2017). Ferreira et al. doi:10.7554/eLife.25078.
Physical limits of flow sensing in the left-right organizer
eLife 6:e22268 (2017). Dyballa et al. doi:10.7554/eLife.22268.
Distribution of neurosensory progenitor pools during inner ear morphogenesis unveiled by cell lineage reconstruction
Nature Commun. 8, 13929 (2017). Delile et al. doi:10.1038/ncomms13929.
A cell-based computational model of early embryogenesis coupling mechanical behaviour and gene regulation
Small13, 1701442 doi:10.1002/smll.201701442.
Metrology of multiphoton microscopes using second harmonic generation nanoprobes
Opt. Lett. 42 (2017). Burcklen et al. doi:10.1364/OL.42.001927.
High-reflectance magnetron-sputtered scandium-based x-ray multilayer mirrors for the water window
Langmuir 27 (2017). Portier et al. doi:10.1021/acs.langmuir.7b02142.
Stabilization of collagen fibrils by gelatin addition: A study of collagen/gelatin dense phases
Scientific Reportsdoi:10.1038/s41598-017-03359-8.
Multicolor two-photon imaging of endogenous fluorophores in living tissues by wavelength mixing
Scientific Reportsdoi:10.1038/s41598-017-03548-5.
Label-free imaging of bone multiscale porosity and interfaces using third-harmonic generation microscopy
Dynamic multicolor protein labeling in living cells
19, 065506 10.1088/2040-8986/aa6f72.
All-fiber femtosecond laser providing 9 nJ, 50 MHz pulses at 1650 nm for three-photon microscopy
Nature Commun. 7, 8674 (2016). Faure et al. doi:10.1038/ncomms9674.
A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage
Scientific Reports 6, 29863 (2016). Vuillemin et al. doi:10.1038/srep29863.
Efficient second-harmonic imaging of collagen histological slides using Bessel beam excitation
Scientific Reports 6, 26344 (2016). Latour et al. doi:10.1038/srep26344.
Correlative nonlinear optical microscopy and infrared nanoscopy reveals collagen degradation in altered parchments
Opt. Express 24, 16084 (2016). Teulon et al. doi:10.1364/OE.24.016084.
Probing the 3D structure of cornea-like collagen liquid crystals with polarization-resolved SHG microscopy
J. Appl. Phys. 119, 125307 (2016). Burcklen et al. doi:10.1063/1.4944723.
Efficient Cr/B4C multilayer mirrors: Study of interfaces and X-ray reflectance
ChemPhysChem (2016). Querard et al. doi:10.1002/cphc.201500987.
Kinetics of reactive modules adds discriminative dimensions for selective cell imaging
Org Biomol Chem (2016). Li et al. doi:10.1039/c6ob01612j.
Design and characterization of red fluorogenic push–pull chromophores holding great potential for bioimaging and biosensing
Nature Methods 12, 379-80 (2015). Wolf et al. doi:10.1038/nmeth.3371.
Whole-brain functional imaging with two-photon light-sheet microscopy
Development 142, (2015). Dray et al.
Large-scale live imaging of adult neural stem cells in their endogenous niche



Nature Methods 11, 600-1 (2014). Mahou et al. doi:10.1038/nmeth.2963.
Multicolor two-photon light-sheet microscopy
PLoS ONE 9, e104250 (2014). Débarre et al. doi:10.1371/journal.pone.0104250.
Mitigating phototoxicity during multiphoton microscopy of live Drosophila embryos in the 1.0–1.2 µm wavelength range

Reviews and proceedings
Neural cell segmentation in large-scale 3D color fluorescence microscopy images for developmental neuroscience
Fluorescent Protein–photoprotein Fusions and Their Applications in Calcium Imaging

Proc.SPIE 9329Z (2015). Mahou et al. doi:10.1117/12.2079176.
Multiphoton light-sheet microscopy using wavelength mixing: fast multicolor imaging of the beating Zebrafish heart with low photobleaching
Angew Reviews (2015). Alouane et al.
Self-immolative spacers: kinetic aspects, structure-property relationships, and applications
Nat Chem Biol (2014). Gautier et al.
How to control proteins with light in living systems

Some previous references from developing partners:
Nat Rev Mol Cell Biol 2014. Pantazis & Supatto. Advances in whole-embryo imaging: a quantitative transition is underway.
Nat Commun 2014. Bancelin et al. Determination of collagen fibril size via absolute measurements of second-harmonic generation signals.
Neuron 2014. Loulier et al. Multiplex cell and lineage tracking with combinatorial labels.
Phys Rev X 2013. Zimmerley et al. Probing ordered lipid assemblies with polarized third-harmonic-generation microscopy.
Nat Meth 2012. Mahou et al. Multicolor two-photon tissue imaging by wavelength mixing.
Nat Meth 2011. Truong et al. Deep and fast live imaging with two-photon scanned light-sheet microscopy.
Science 2010. Olivier et al. Cell Lineage Reconstruction of Early Zebrafish Embryos Using Label-Free Nonlinear Microscopy.