Une liste à jour des publications est disponible sur mes profils Google Scholar, ResearchGate et ORCID.


  • Delafontaine-Martel, P., Lemieux, P., Descoteaux, M., Petit, L., Lesage, F., & Lefebvre, J. (2021). Localization and imaging of white matter fiber crossings in whole mouse brains using diffusion MRI and serial blockface OCT. In SPIE (Ed.), Neural Imaging and Sensing 2021 (BO201) Special: Vol. SPIE (accepté, présentation à venir).


  • delas Penas K, Dmitrieva M, Lefebvre J, et al. Extracting Axial Depth and Trajectory Trend Using Astigmatism, Gaussian Fitting, and CNNs for Protein Tracking. In: 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI). IEEE; 2020. doi:10.1109/isbi45749.2020.9098364
  • Dmitrieva M, Lefebvre J, delas Penas K, et al. Short Trajectory Segmentation with 1D UNET Framework: Application to Secretory Vesicle Dynamics. In: 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI). IEEE; 2020. doi:10.1109/isbi45749.2020.9098426
  • Lefebvre J, Javer A, Dmitrieva M, et al. Single-Molecule Localization Microscopy Reconstruction Using Noise2Noise for Super-Resolution Imaging of Actin Filaments. In: 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI). IEEE; 2020. doi:10.1109/isbi45749.2020.9098713


  • Lefebvre J, Delafontaine-Martel P, Lesage F. A Review of Intrinsic Optical Imaging Serial Blockface Histology (ICI-SBH) for Whole Rodent Brain Imaging. Photonics. Published online June 11, 2019:66. doi:10.3390/photonics6020066


  • Castonguay A, Lefebvre J, Lesage F, Pouliot P. Comparing three-dimensional serial optical coherence tomography histology to MRI imaging in the entire mouse brain. J Biomed Opt. Published online January 8, 2018:1. doi:10.1117/1.jbo.23.1.016008
  • Lefebvre J, Delafontaine-Martel P, Pouliot P, Girouard H, Descoteaux M. Fully automated dual-resolution serial optical coherence tomography aimed at diffusion MRI validation in whole mouse brains. Neurophoton. Published online November 3, 2018:1. doi:10.1117/1.nph.5.4.045004
  • Lefebvre J, Castonguay A, Lesage F. Imaging whole mouse brains with a dual resolution serial swept-source optical coherence tomography scanner. In: Luo Q, Ding J, eds. Neural Imaging and Sensing 2018. SPIE; 2018. doi:10.1117/12.2288521
  • Delafontaine-Martel P, Lesage F, Damseh R, Lefebvre J, Castonguay A, Tardif P-L. Large scale serial two-photon microscopy to investigate local vascular changes in whole rodent brain models of Alzheimer’s disease. In: Periasamy A, So PT, Xie XS, König K, eds. Multiphoton Microscopy in the Biomedical Sciences XVIII. SPIE; 2018. doi:10.1117/12.2290060
  • Lefebvre J. Neuro-imagerie multimodale et multirésolution de cerveaux de souris combinant l’histologie sérielle par tomographie en cohérence optique et l’IRM de diffusion. Published online 2018.
  • Castonguay A, Lefebvre J, Lesage F. Serial OCT reveals age-dependent cardiac fiber orientation change (Conference Presentation). In: Tearney GJ, Gregory KW, Marcu L, eds. Diagnostic and Therapeutic Applications of Light in Cardiology 2018. SPIE; 2018. doi:10.1117/12.2289092
  • Delafontaine-Martel P, Lefebvre J, Tardif P-L, Lévy BI, Pouliot P, Lesage F. Whole brain vascular imaging in a mouse model of Alzheimer’s disease with two-photon microscopy. J Biomed Opt. Published online July 11, 2018:1. doi:10.1117/1.jbo.23.7.076501


  • Lefebvre J. OCT Mouse Brain Templates. Published online July 13, 2017. doi:10.17632/33WFGXPMP8.1
  • Castonguay A, Lefebvre J, Pouliot P, Avti P, Moeini M, Lesage F. Serial optical coherence scanning reveals an association between cardiac function and the heart architecture in the aging rodent heart. Biomed Opt Express. Published online October 16, 2017:5027. doi:10.1364/boe.8.005027
  • Lefebvre J, Castonguay A, Lesage F. White matter segmentation by estimating tissue optical attenuation from volumetric OCT massive histology of whole rodent brains. In: Brown TG, Cogswell CJ, Wilson T, eds. Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXIV. SPIE; 2017. doi:10.1117/12.2251173
  • Lefebvre J, Castonguay A, Pouliot P, Descoteaux M, Lesage F. Whole mouse brain imaging using optical coherence tomography: reconstruction, normalization, segmentation, and comparison with diffusion MRI. Neurophoton. Published online July 11, 2017:041501. doi:10.1117/1.nph.4.4.041501


  • Tardif P-L, Bertrand M-J, Abran M, et al. Validating Intravascular Imaging with Serial Optical Coherence Tomography and Confocal Fluorescence Microscopy. IJMS. Published online December 15, 2016:2110. doi:10.3390/ijms17122110
  • Castonguay A, Lefebvre J, Tardif P-L, Delafontaine-Martel P, Pouliot P, Lesage F. Serial OCT scanner : comparing 3D histology to In vivo imaging in the entire mouse brain. In: ; 2016.


  • Lesage F, Castonguay A, Tardif PL, Lefebvre J, Li B. Investigating the impact of blood pressure increase to the brain using high resolution serial histology and image processing. In: Papadakis M, Goyal VK, Van De Ville D, eds. Wavelets and Sparsity XVI. SPIE; 2015. doi:10.1117/12.2189110
  • Gagnon L, Sakad i  S, Lesage F, et al. Quantifying the Microvascular Origin of BOLD-fMRI from First Principles with Two-Photon Microscopy and an Oxygen-Sensitive Nanoprobe. Journal of Neuroscience. Published online February 25, 2015:3663-3675. doi:10.1523/jneurosci.3555-14.2015


  • Desjardins M, Berti R, Lefebvre J, Dubeau S, Lesage F. Aging-related differences in cerebral capillary blood flow in anesthetized rats. Neurobiology of Aging. Published online August 2014:1947-1955. doi:10.1016/j.neurobiolaging.2014.01.136
  • Lefebvre J. Développement d’outils de vectorisation d’angiographies obtenues par microscopie 2-photons dans le contexte du vieillissement du cerveau. Published online 2014.
  • Gagnon L, Sakadzic S, Lesage F, et al. Folded cortical orientation influences the amplitude of BOLD-fMRI: evidence from simulations and experimental data. In: ; 2014.
  • Sakadžić S, Mandeville ET, Gagnon L, et al. High-Resolution Optical Microscopy Imaging of Cortical Oxygen Delivery and Consumption. In: CLEO: 2014. OSA; 2014. doi:10.1364/cleo_at.2014.af2b.3
  • Sakadžić S, Mandeville ET, Gagnon L, et al. Large arteriolar component of oxygen delivery implies a safe margin of oxygen supply to cerebral tissue. Nat Commun. Published online December 2014. doi:10.1038/ncomms6734
  • Desjardins M, Berti R, Lefebvre J, Dubeau S, Lesage F. Microscopic Dynamics of Cerebral Capillary Blood Flow in Aged Anesthetized Rats. In: Biomedical Optics 2014. OSA; 2014. doi:10.1364/biomed.2014.bt3a.3
  • Sakadžić S, Mandeville ET, Gagnon L, et al. Oxygen Distribution in Cortical Microvasculature Reveals a Novel Mechanism for Maintaining a Safe Tissue Oxygenation. In: Biomedical Optics 2014. OSA; 2014. doi:10.1364/biomed.2014.bw1a.2
  • Gagnon L, Sakadžić S, Lesage F, et al. Underpinning the microvascular origin of BOLD-fMRI with two-photon microscopy. In: Biomedical Optics 2014. OSA; 2014. doi:10.1364/biomed.2014.bt4a.1


  • Baraghis E, Bolduc V, Lefebvre J, et al. Measurement of cerebral microvascular compliance in a model of atherosclerosis with optical coherence tomography. Biomed Opt Express. Published online October 13, 2011:3079. doi:10.1364/boe.2.003079