Prof. Daniel C. Côté Profile

Prof. Daniel C. Côté

Professor at Ctr. de Recherche CERVO

SPIE Involvement:

Author

Publications (31)

Proceedings Article | 13 March 2024 Presentation

Imaging and mapping local neuroanatomy surrounding a deep brain polarization-sensitive OCT catheter

Shadi Masoumi, Georgia Jones, Mireille Quemener, Martin Parent, Martin Villiger, Daniel Cote, Maxina Sheft

Proceedings Volume PC12830, PC128302H (2024) https://doi.org/10.1117/12.3005514

KEYWORDS: Neuroimaging, Brain, Optical coherence tomography, Brain mapping, White matter, Electrodes, Biological imaging, Tissue optics, Birefringence, Associative arrays

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Proceedings Article | 13 March 2024 Presentation

Human brain tissue identification using CARS and DRS for deep brain stimulation surgery

Mireille Quémener, Sébastien Jerczynski, Valérie Pineau Noël, Antoine Rousseau, Elahe Parham, Alexandre Bédard, Thomas Charland, Anthony Drouin, Jonathan Roussel, Valérie Dionne, Thomas Shooner, Anaïs Parrot, Shadi Masoumi, Damon DePaoli, Leo Cantin, Martin Parent, Daniel Côté

Proceedings Volume PC12831, PC1283103 (2024) https://doi.org/10.1117/12.3000974

KEYWORDS: Brain tissue, Surgery, Brain stimulation, Tissue optics, Lead, Principal component analysis, Brain, Standards development, Magnetic resonance imaging, Electrodes

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SPIE Journal Paper | 23 June 2023 Open Access

Millimetric scale two-photon Bessel-Gauss beam light sheet microscopy with three-axis isotropic resolution using an axicon lens

Cléophace Akitegetse, Thomas Charland, Mireille Quémener, Charles Gora, Véronique Rioux, Michel Piché, Yves De Koninck, Martin Lévesque, Daniel C. Côté

NPh, Vol. 10, Issue 03, 035002, (June 2023) https://doi.org/10.1117/12.10.1117/1.NPh.10.3.035002

KEYWORDS: Axicons, Microscopes, Objectives, Brain, Light sources and illumination, Gaussian beams, Imaging systems, Cameras, Fluorescence, Neurophotonics

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Proceedings Article | 17 March 2023 Presentation

Diffuse reflectance spectroscopy for optical guidance in neurosurgery and design of a multimodal optic probe

Alexandre Bédard, Pegah Eslami, Damon Depaoli, Mireille Quémener, Martin Parent, Daniel Côté

Proceedings Volume 12364, 1236407 (2023) https://doi.org/10.1117/12.2649348

KEYWORDS: Diffuse reflectance spectroscopy, Principal component analysis, Brain, Tissues, Tissue optics, Surgery, Safety, Resistance, Electrodes, Computer simulations

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Proceedings Article | 15 March 2023 Presentation

Design and fabrication of a GRIN-axicon for Bessel-Gauss beam generation and applications to fast volumetric imaging (Conference Presentation)

Mireille Quémener, Pierre Girard-Collins, Alexandra Alain-Beaudoin, Nicolas Grégoire, Steeve Morency, Michèle Desjardins, Daniel Côté, Simon Thibault

Proceedings Volume PC12385, PC123850K (2023) https://doi.org/10.1117/12.2648999

KEYWORDS: Axicons, Optics manufacturing, Microscopes, Tissues, Temporal resolution, Optical components, Neuroscience, Neurons, Microscopy, Manufacturing

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Proceedings Article | 7 March 2022 Presentation

High fidelity polarization-sensitive optical coherence tomography through deep learning

Ludovick Bégin, Damon DePaoli, Brett Bouma, Daniel Côté, Martin Villiger

Proceedings Volume PC11963, PC119630F (2022) https://doi.org/10.1117/12.2608232

KEYWORDS: Optical coherence tomography, Reconstruction algorithms, Tissue optics, Speckle, Polarization, Data modeling, Birefringence, Tissues, Signal attenuation, Scattering

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Proceedings Article | 5 March 2021 Presentation

Endoscopic optic-axis mapping of white matter fiber tracts using polarization-sensitive optical coherence tomography

Damon DePaoli, Daniel Côté, Brett Bouma, Martin Villiger

Proceedings Volume 11629, 116290S (2021) https://doi.org/10.1117/12.2577859

KEYWORDS: Optical coherence tomography, Imaging systems, Endoscopy, Brain mapping, Polarization, Brain, Scattering, Neuroimaging, Magnetic resonance imaging, Light scattering

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Proceedings Article | 5 March 2021 Presentation

Reconstruction of tissue birefringence from polarization-sensitive optical coherence tomography using machine learning

Ludovick Bégin, Damon DePaoli, Brett Bouma, Daniel Côté, Martin Villiger

Proceedings Volume 11646, 1164612 (2021) https://doi.org/10.1117/12.2578448

KEYWORDS: Tissue optics, Birefringence, Optical coherence tomography, Network architectures, Speckle, Polarization, Machine learning, Tissues, Systems modeling, Statistical modeling

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SPIE Journal Paper | 21 January 2021 Open Access

Tools and tutorial on practical ray tracing for microscopy

Valérie Pineau Noël, Shadi Masoumi, Elahe Parham, Gabriel Genest, Ludovick Bégin, Marc-André Vigneault, Daniel Côté

NPh, Vol. 8, Issue 01, 010801, (January 2021) https://doi.org/10.1117/12.10.1117/1.NPh.8.1.010801

KEYWORDS: Ray tracing, Vignetting, Microscopy, Neurophotonics, Optical components, Lenses, Matrices, Geometrical optics, Optical design, Mirrors

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SPIE Journal Paper | 1 May 2020 Open Access

Rise of Raman spectroscopy in neurosurgery: a review

Damon DePaoli, Émile Lemoine, Katherine Ember, Martin Parent, Michel Prud’homme, Léo Cantin, Kevin Petrecca, Frédéric Leblond, Daniel Côté

JBO, Vol. 25, Issue 05, 050901, (May 2020) https://doi.org/10.1117/12.10.1117/1.JBO.25.5.050901

KEYWORDS: Raman spectroscopy, Tissues, Brain, Tissue optics, Remote sensing, Imaging systems, Chromium, Tumors, Signal processing, Biopsy

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SPIE Journal Paper | 10 March 2020 Open Access

Anisotropic light scattering from myelinated axons in the spinal cord

Damon DePaoli, Alicja Gasecka, Mohamed Bahdine, Jean Deschenes, Laurent Goetz, Jimena Perez-Sanchez, Robert Bonin, Yves De Koninck, Martin Parent, Daniel Côté

NPh, Vol. 7, Issue 01, 015011, (March 2020) https://doi.org/10.1117/12.10.1117/1.NPh.7.1.015011

KEYWORDS: Spinal cord, Scattering, Light scattering, Tissue optics, Axons, Monte Carlo methods, Tissues, Optogenetics, Brain, Integrating spheres

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Proceedings Article | 4 March 2019 Presentation

Wide-field intraoperative Raman imaging technique to guide cytoreductive surgery for advanced stages of ovarian cancer (Conference Presentation)

Sandryne David, Guillaume Sheehy, Kayla Simeone, Jean-Phillipe Tremblay, Fred Saad, Anne-Marie Mes-Masson, Daniel Côté, Frédéric Leblond

Proceedings Volume 10890, 108901O (2019) https://doi.org/10.1117/12.2509773

KEYWORDS: Raman spectroscopy, Ovarian cancer, Surgery, Cancer, Tissues, Imaging systems, Tissue optics, Tumor growth modeling, Remote sensing, Optical inspection

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SPIE Journal Paper | 31 January 2019 Open Access

Fluorescence lifetime imaging nanoscopy for measuring Förster resonance energy transfer in cellular nanodomains

Christian Tardif, Gabriel Nadeau, Simon Labrecque, Daniel Côté, Flavie Lavoie-Cardinal, Paul De Koninck

NPh, Vol. 6, Issue 01, 015002, (January 2019) https://doi.org/10.1117/12.10.1117/1.NPh.6.1.015002

KEYWORDS: Fluorescence resonance energy transfer, Fluorescence lifetime imaging, Stimulated emission depletion microscopy, Spine, Proteins, Receptors, Neurons, Luminescence, Photons, Super resolution microscopy

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SPIE Journal Paper | 17 August 2018 Open Access

Intact primate brain tissue identification using a completely fibered coherent Raman spectroscopy system

Damon DePaoli, Nicolas Lapointe, Younès Messaddeq, Martin Parent, Daniel Côté

NPh, Vol. 5, Issue 03, 035005, (August 2018) https://doi.org/10.1117/12.10.1117/1.NPh.5.3.035005

KEYWORDS: Brain, Raman spectroscopy, Tissues, Electrodes, Signal detection, Fiber lasers, Tissue optics, Laser systems engineering, Signal generators, Spectroscopy

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SPIE Journal Paper | 19 February 2018 Open Access

Designing a large field-of-view two-photon microscope using optical invariant analysis

Jonathan Bumstead, Jasmine Park, Isaac Rosen, Andrew Kraft, Patrick Wright, Matthew Reisman, Daniel Côté, Joseph Culver

NPh, Vol. 5, Issue 02, 025001, (February 2018) https://doi.org/10.1117/12.10.1117/1.NPh.5.2.025001

KEYWORDS: Objectives, Relays, Lenses, Microscopes, Scanners, Polygon scanners, Imaging systems, Mirrors, Image resolution, Laser scanners

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Proceedings Article | 24 April 2017 Presentation

Development of large field-of-view two photon microscopy for imaging mouse cortex (Conference Presentation)

Jonathan Bumstead, Daniel Côté, Joseph Culver

Proceedings Volume 10069, 100690F (2017) https://doi.org/10.1117/12.2251433

KEYWORDS: Diffraction, Relays, Microscopy, Two photon excitation microscopy, Calcium, Brain, Objectives, Monochromatic aberrations, Optical microscopy, Brain imaging

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Proceedings Article | 19 April 2017 Presentation

Subtle changes in myelination due to childhood experiences: label-free microscopy to infer nerve fibers morphology and myelination in brain (Conference Presentation)

Alicja Gasecka, Arnaud Tanti, Pierre-Eric Lutz, Naguib Mechawar, Daniel Cote

Proceedings Volume 10051, 100510K (2017) https://doi.org/10.1117/12.2253507

KEYWORDS: Imaging systems, Nervous system, Brain, Microscopy, Neuroimaging, Nerve, Raman spectroscopy, Cognition, Statistical analysis, Anisotropy

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Proceedings Article | 26 April 2016 Presentation

Network inference from functional experimental data (Conference Presentation)

Patrick Desrosiers, Simon Labrecque, Maxime Tremblay, Mathieu Bélanger, Bertrand De Dorlodot, Daniel Côté

Proceedings Volume 9690, 969019 (2016) https://doi.org/10.1117/12.2212726

KEYWORDS: Neurons, Calcium, Luminescence, Brain mapping, Image segmentation, Microscopy, Statistical analysis, Statistical methods, Information theory, Computer simulations

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Functional connectivity maps of neuronal networks are critical tools to understand how neurons form circuits, how information is encoded and processed by neurons, how memory is shaped, and how these basic processes are altered under pathological conditions. Current light microscopy allows to observe calcium or electrical activity of thousands of neurons simultaneously, yet assessing comprehensive connectivity maps directly from such data remains a non-trivial analytical task. There exist simple statistical methods, such as cross-correlation and Granger causality, but they only detect linear interactions between neurons. Other more involved inference methods inspired by information theory, such as mutual information and transfer entropy, identify more accurately connections between neurons but also require more computational resources. We carried out a comparative study of common connectivity inference methods. The relative accuracy and computational cost of each method was determined via simulated fluorescence traces generated with realistic computational models of interacting neurons in networks of different topologies (clustered or non-clustered) and sizes (10-1000 neurons). To bridge the computational and experimental works, we observed the intracellular calcium activity of live hippocampal neuronal cultures infected with the fluorescent calcium marker GCaMP6f. The spontaneous activity of the networks, consisting of 50-100 neurons per field of view, was recorded from 20 to 50 Hz on a microscope controlled by a homemade software. We implemented all connectivity inference methods in the software, which rapidly loads calcium fluorescence movies, segments the images, extracts the fluorescence traces, and assesses the functional connections (with strengths and directions) between each pair of neurons. We used this software to assess, in real time, the functional connectivity from real calcium imaging data in basal conditions, under plasticity protocols, and epileptic conditions.

Proceedings Article | 26 April 2016 Presentation

Light distribution properties in spinal cord for optogenetic stimulation (Conference Presentation)

Alicja Gąsecka, Mohamed Bahdine, Nicolas Lapointe, Veronique Rioux, Jimena Perez-Sanchez, Robert Bonin, Yves De Koninck, Daniel Côté

Proceedings Volume 9690, 96902N (2016) https://doi.org/10.1117/12.2213899

KEYWORDS: Spinal cord, Optical fibers, Optogenetics, Tissue optics, Light scattering, Signal attenuation, Monte Carlo methods, 3D modeling, Neuroscience, Brain

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Proceedings Article | 26 April 2016 Presentation

Fiber-based tissue identification for electrode placement in deep brain stimulation neurosurgery (Conference Presentation)

Damon DePaoli, Nicolas Lapointe, Laurent Goetz, Martin Parent, Michel Prudhomme, Léo Cantin, Tigran Galstian, Younès Messaddeq, Daniel Côté

Proceedings Volume 9690, 96900G (2016) https://doi.org/10.1117/12.2213353

KEYWORDS: Electrodes, Brain stimulation, Tissues, Brain, In vitro testing, Optical design, Optical fibers, Biosensing, Tissue optics, Blood vessels

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SPIE Journal Paper | 21 March 2012 Open Access

Live animal myelin histomorphometry of the spinal cord with video-rate multimodal nonlinear microendoscopy

Erik Belanger, Joël Crépeau, Sophie Laffray, Réal Vallée, Yves De Koninck, Daniel Côté

JBO, Vol. 17, Issue 02, 021107, (March 2012) https://doi.org/10.1117/12.10.1117/1.JBO.17.2.021107

KEYWORDS: Axons, Spinal cord, Objectives, CARS tomography, Optical filters, In vivo imaging, Bandpass filters, Luminescence, Microscopes, Signal to noise ratio

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SPIE Journal Paper | 1 February 2011 Open Access

Multimodal coherent anti-Stokes Raman scattering microscopy reveals microglia-associated myelin and axonal dysfunction in multiple sclerosis-like lesions in mice

Jaime Imitola, Stine Rasmussen, Yingru Liu, Tanuja Chitnis, Samia Khoury, Daniel Côté, X. Sunney Xie, Charles Lin, Richard Sidman

JBO, Vol. 16, Issue 02, 021109, (February 2011) https://doi.org/10.1117/12.10.1117/1.3533312

KEYWORDS: Reflectivity, Axons, CARS tomography, Spinal cord, Tissues, Microscopy, Visualization, Confocal microscopy, Green fluorescent protein, Microscopes

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SPIE Journal Paper | 1 July 2008 Open Access

Combined optical intensity and polarization methodology for analyte concentration determination in simulated optically clear and turbid biological media

Michael Wood, Daniel Côté, I. Alex Vitkin

JBO, Vol. 13, Issue 04, 044037, (July 2008) https://doi.org/10.1117/12.10.1117/1.2968198

KEYWORDS: Polarization, Glucose, Absorption, Plasma, Data modeling, Monte Carlo methods, Scattering, Biomedical optics, Blood, Optical activity

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Proceedings Article | 15 February 2008 Paper

Multimodal optical microscopy for monitoring fast neuronal activity and signaling

S. Pagès, I. Veilleux, P. De Koninck, D. Côté

Proceedings Volume 6860, 68601X (2008) https://doi.org/10.1117/12.764161

KEYWORDS: Second-harmonic generation, Calcium, Neurons, Luminescence, Video, Mirrors, Action potentials, Microscopes, Reflectivity, Scanners

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SPIE Journal Paper | 1 January 2008 Open Access

In vivo confocal and multiphoton microendoscopy

Pilhan Kim, Mehron Pouris'haag, Daniel Cote, Charles Lin, Seok-Hyun Yun

JBO, Vol. 13, Issue 01, 010501, (January 2008) https://doi.org/10.1117/12.10.1117/1.2839043

KEYWORDS: Confocal microscopy, Luminescence, Endoscopes, In vivo imaging, GRIN lenses, Image resolution, Imaging systems, Endoscopy, Second-harmonic generation, Objectives

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Proceedings Article | 8 November 2007 Paper

All-fiber Raman laser tuned over 60nm

E. Bélanger, M. Bernier, D. Côté, R. Vallée

Proceedings Volume 6796, 67960V (2007) https://doi.org/10.1117/12.778711

KEYWORDS: Raman spectroscopy, Reflectivity, Fiber lasers, Tunable lasers, Fiber Bragg gratings, High power lasers, Laser damage threshold, Laser resonators, Ranging, Prisms

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Proceedings Article | 26 October 2007 Paper

Two different mechanical tuning devices of fiber Bragg gratings

E. Bélanger, M. Bernier, J. Bérubé, B. Déry, S. Gagnon, D. Côté, R. Vallée

Proceedings Volume 6796, 67962Q (2007) https://doi.org/10.1117/12.778922

KEYWORDS: Fiber Bragg gratings, Polymers, Epoxies, Optical fibers, Glasses, Metals, Reflectivity, Diamond, Wavelength tuning, Optical filters

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SPIE Journal Paper | 1 May 2007 Open Access

Combined magnetic resonance and bioluminescence imaging of live mice

Mathieu Allard, Daniel Coté, Lorinda Davidson, Jun Dazai, Mark Henkelman

JBO, Vol. 12, Issue 03, 034018, (May 2007) https://doi.org/10.1117/12.10.1117/1.2745298

KEYWORDS: Tissues, Monte Carlo methods, Magnetic resonance imaging, Bioluminescence, Magnetism, Optical properties, Luminescence, Image segmentation, Tomography, Data modeling

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Proceedings Article | 13 October 2005 Paper

Three-dimensional light-tissue interaction models for bioluminescence tomography

D. Côté, M. Allard, R. Henkelman, I. Vitkin

Proceedings Volume 5969, 59691D (2005) https://doi.org/10.1117/12.628677

KEYWORDS: Tissues, Photons, Bioluminescence, 3D modeling, Scattering, Light scattering, Optical properties, Monte Carlo methods, Brain, Tomography

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Proceedings Article | 27 August 2005 Paper

Characterization of the modeled fluence distribution for non-ideal cylindrical diffusers in intraluminal and interstitial settings

Augusto Rendon, Daniel Cote, Leonid Vesselov, Lothar Lilge

Proceedings Volume 5863, 58630T (2005) https://doi.org/10.1117/12.633090

KEYWORDS: Diffusers, Optical properties, Tissue optics, Tissues, Photons, Monte Carlo methods, Electroluminescence, Absorption, Photodynamic therapy, Information technology

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SPIE Journal Paper | 1 January 2004 Open Access

Balanced detection for low-noise precision polarimetric measurements of optically active, multiply scattering tissue phantoms

Daniel Cote, I. Alex Vitkin

JBO, Vol. 9, Issue 01, (January 2004) https://doi.org/10.1117/12.10.1117/1.1629683

KEYWORDS: Scattering, Glucose, Polarization, Tissue optics, Mie scattering, Polarimetry, Monte Carlo methods, Optical testing, Sensors, Optical activity

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