@article{pmid40735541,

title = {Catheter-based polarimetric imaging to complement MRI for deep brain stimulation neurosurgery},

author = {Shadi Masoumi and Maxina Sheft and Mireille Quémener and Alexandre Bédard and Valérie Pineau Noël and Martin Parent and Martin Villiger and Daniel C Côté},

doi = {10.1117/1.NPh.12.3.035001},

issn = {2329-423X},

year  = {2025},

date = {2025-07-01},

journal = {Neurophotonics},

volume = {12},

number = {3},

pages = {035001},

abstract = {SIGNIFICANCE: Deep brain stimulation (DBS) is an established treatment for movement disorders and other neurological conditions. Accurate localization of small deep brain nuclei, such as the subthalamic nucleus (STN) and internal pallidum (GPi), is crucial for successful DBS outcomes. However, magnetic resonance imaging (MRI), commonly used for DBS planning, lacks the resolution and contrast needed to directly delineate these target structures.nnAIM: We aim to explore the potential of catheter-based polarization-sensitive optical coherence tomography (PS-OCT) as a complementary imaging tool for high-resolution visualization of tissue surrounding the DBS insertion trajectory.nnAPPROACH: We simulated DBS implantation surgery at three targets in a post-mortem nonhuman primate head. PS-OCT, using advanced reconstruction algorithms for absolute depth-resolved birefringence, was compared with MRI for its ability to visualize and differentiate structural details.nnRESULTS: PS-OCT provided more detailed and accurate structural information than MRI while maintaining consistency with MRI results. Its compact form factor and imaging paradigm integrate seamlessly into the surgical workflow, offering new insights for intraoperative decision-making.nnCONCLUSIONS: PS-OCT functions as an intraoperative imaging tool, offering valuable guidance during the procedure. These findings establish PS-OCT as a promising complementary tool for DBS, with potential for further clinical validation and  studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40331237,

title = {Retinal changes detected by diffuse reflectance spectroscopy in parkinsonian monkeys},

author = {Jonathan Munro and Elahe Parham and Damon DePaoli and Nicolas Lapointe and Cleophace Akitegetse and Shirley Fecteau and Dominic Sauvageau and Thérèse Di Paolo and Daniel C Côté and Martin Parent},

doi = {10.1117/1.NPh.12.2.025008},

issn = {2329-423X},

year  = {2025},

date = {2025-04-01},

journal = {Neurophotonics},

volume = {12},

number = {2},

pages = {025008},

abstract = {SIGNIFICANCE: Parkinson's disease (PD) is diagnosed when 50% neurodegeneration has occurred. The retina could provide biomarkers that would allow for earlier diagnosis. Retinal spectroscopy is a technique that could be used to find such biomarkers.nnAIM: We aimed to find new diagnostic biomarkers for PD following detailed spectral examinations of the retina.nnAPPROACH: The newly developed Zilia Ocular device was used to perform spectrometric scans of the optic nerve head (ONH) and the retina of four cynomolgus monkeys () before and after the administration of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), a neurotoxin used to produce the gold-standard animal model of PD. From the spectrometric data, the blood oximetry was calculated, and the diffuse reflectance spectra (DRS) were analyzed to find variations between the two experimental conditions. Post-mortem analyses were also performed on the retina of the four parkinsonian monkeys and four additional control animals.nnRESULTS: The analysis of the DRS indicated a lower slope between the 480- and 525-nm wavelengths in both the ONH and the retina. Post-mortem measurements of the retinal layer thicknesses showed that the outer nuclear layer was significantly thinner in MPTP-intoxicated monkeys, compared with controls. Altogether, these results indicate that MPTP altered the optical properties of the ONH and the retina and show that these variations might be explained by MPTP-induced structural changes in the eye fundus, as observed post-mortem.nnCONCLUSIONS: Overall, our results indicate that spectroscopy could be used as a noninvasive method to detect changes in the retina that occur in PD and that such changes could represent retinal biomarkers for improved diagnosis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40083800,

title = {Enhanced spectral resolution and reduced acquisition time in fiber-based wavelength-swept source Raman spectroscopy},

author = {Elahe Parham and Maxime Tousignant-Tremblay and Mireille Quémener and Martin Parent and Daniel C Côté},

doi = {10.1117/1.NPh.12.1.015014},

issn = {2329-423X},

year  = {2025},

date = {2025-01-01},

journal = {Neurophotonics},

volume = {12},

number = {1},

pages = {015014},

abstract = {SIGNIFICANCE: We introduce a fast Raman spectroscopy (SSRS) system that reduces acquisition time and enhances data quality, providing a breakthrough in SSRS for real-time applications. We demonstrate its utility in differentiating brain tissue regions based on lipid and protein content.nnAIM: Our primary goal was to develop a fast SSRS system that enables rapid data acquisition for  applications. We aimed to investigate its effectiveness in differentiating brain tissue types by analyzing lipid and protein content, ultimately enhancing classification accuracy and supporting advancements in medical diagnostics.nnAPPROACH: We implemented an optimized circuit and signal processing technique to reduce high-frequency noise and improve signal-to-noise ratio. Brain tissue measurements were validated against staining models, and classification accuracy was tested with principal component analysis (PCA) and support vector machine (SVM).nnRESULTS: Our SSRS system captures spectra in 1 s which is significantly faster than similar systems. This rapid method enables real-time monitoring and accurate classification of brain regions based on lipid-protein content, confirmed by neurofilament and Nissl staining correlations (  and 0.55, respectively). Tissue classification showed 80.20% accuracy using spectral intensity at the wavenumbers associated with C-H,  , and  vibrations and 81.23% accuracy using PCA-derived features (PC1, PC2, and PC3).nnCONCLUSIONS: The fast-SSRS system marks a significant advance in Raman spectroscopy, improving speed and data quality. Our setup captures finer spectral details, facilitating reliable differentiation of tissue types, as verified by staining methods and PCA. This method shows promise for real-time tissue analysis and medical diagnostics, outperforming traditional Raman techniques in speed and data throughput.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39679397,

title = {Absolute depth-resolved optic axis measurement with catheter-based polarization sensitive optical coherence tomography},

author = {Shadi Masoumi and Jaeyul Lee and Georgia L Jones and Mireille Quémener and Martin Parent and Brett E Bouma and Lida P Hariri and Daniel C Côté and Martin Villiger},

doi = {10.1364/BOE.538560},

issn = {2156-7085},

year  = {2024},

date = {2024-12-01},

journal = {Biomed Opt Express},

volume = {15},

number = {12},

pages = {6957--6976},

abstract = {Imaging depth-resolved birefringence and optic axis orientation with polarization sensitive optical coherence tomography (PS-OCT) unveils details of tissue structure and organization that can be of high pathophysiologic, mechanistic, and diagnostic value. For catheter-based PS-OCT, the dynamic rotation of the fiber optic probe, in addition to the polarization effects of the system components, complicates the reliable and robust reconstruction of the sample's optic axis orientation. Addressing this issue, we present a new method for the reconstruction of absolute depth-resolved optic axis orientation in catheter-based PS-OCT by using the intrinsic retardance of the protecting catheter sheath as a stable guide star signal. Throughout the paper, we rigorously inspect the retardance and optic axis orientation of the sheath and validate our method by imaging a birefringent phantom with known optic axis orientation. Reconstructing the optic axis orientation of the phantom, placed at different locations around the catheter, we measured an average absolute deviation (AAD) for the mean optic axis orientation over cross-sectional images of 3.28°, even with significant bending stress on the catheter. This corresponds to an almost three-fold improvement compared to our earlier method (optic axis AAD of 9.41°). We finally highlight the capability of our reconstruction with stereotactic catheter-based PS-OCT of a fresh sheep brain.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38868631,

title = {Human brain tissue identification using coherent anti-Stokes Raman scattering spectroscopy and diffuse reflectance spectroscopy for deep brain stimulation surgery},

author = {Sébastien Jerczynski and Mireille Quémener and Valérie Pineau Noël and Antoine Rousseau and Elahe Parham and Alexandre Bédard and Shadi Masoumi and Thomas Charland and Anthony Drouin and Jonathan Roussel and Valérie Dionne and Thomas Shooner and Anaïs Parrot and Mohamad A Takech and Éric Philippe and Damon DePaoli and Léo Cantin and Martin Parent and Daniel C Côté},

doi = {10.1117/1.NPh.11.2.025006},

issn = {2329-423X},

year  = {2024},

date = {2024-04-01},

journal = {Neurophotonics},

volume = {11},

number = {2},

pages = {025006},

abstract = {SIGNIFICANCE: We assess the feasibility of using diffuse reflectance spectroscopy (DRS) and coherent anti-Stokes Raman scattering spectroscopy (CARS) as optical tools for human brain tissue identification during deep brain stimulation (DBS) lead insertion, thereby providing a promising avenue for additional real-time neurosurgical guidance.nnAIM: We developed a system that can acquire CARS and DRS spectra during the DBS surgery procedure to identify the tissue composition along the lead trajectory.nnAPPROACH: DRS and CARS spectra were acquired using a custom-built optical probe integrated in a commercial DBS lead. The lead was inserted to target three specific regions in each of the brain hemispheres of a human cadaver. Spectra were acquired during the lead insertion at constant position increments. Spectra were analyzed to classify each spectrum as being from white matter (WM) or gray matter (GM). The results were compared with tissue classification performed on histological brain sections.nnRESULTS: DRS and CARS spectra obtained using the optical probe can identify WM and GM during DBS lead insertion. The tissue composition along the trajectory toward a specific target is unique and can be differentiated by the optical probe. Moreover, the results obtained with principal component analysis suggest that DRS might be able to detect the presence of blood due to the strong optical absorption of hemoglobin.nnCONCLUSIONS: It is possible to use optical measurements from the DBS lead during surgery to identify WM and GM and possibly the presence of blood in human brain tissue. The proposed optical tool could inform the surgeon during the lead placement if the lead has reached the target as planned. Our tool could eventually replace microelectrode recordings, which would streamline the process and reduce surgery time. Further developments are required to fully integrate these tools into standard clinical procedures.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38898963,

title = {Wavelength-swept spontaneous Raman spectroscopy system improves fiber-based collection efficiency for whole brain tissue classification},

author = {Elahe Parham and Antoine Rousseau and Mireille Quémener and Martin Parent and Daniel C Côté},

doi = {10.1117/1.NPh.11.2.025007},

issn = {2329-423X},

year  = {2024},

date = {2024-04-01},

journal = {Neurophotonics},

volume = {11},

number = {2},

pages = {025007},

abstract = {SIGNIFICANCE: Raman spectroscopy is a valuable technique for tissue identification, but its conventional implementation is hindered by low efficiency due to scattering. Addressing this limitation, we are further developing the wavelength-swept Raman spectroscopy approach.nnAIM: We aim to enhance Raman signal detection by employing a laser capable of sweeping over a wide wavelength range to sequentially excite tissue with different wavelengths, paired with a photodetector featuring a fixed narrow-bandpass filter for collecting the Raman signal at a specific wavelength.nnAPPROACH: We experimentally validate our technique using a fiber-based swept-source Raman spectroscopy setup. In addition, simulations are conducted to assess the efficacy of our approach in comparison with conventional spectrometer-based Raman spectroscopy.nnRESULTS: Our simulations reveal that the wavelength-swept configuration leads to a significantly stronger signal compared with conventional spectrometer-based Raman spectroscopy. Experimentally, our setup demonstrates an improvement of at least 200× in photon detection compared with the spectrometer-based setup. Furthermore, data acquired from different regions of a fixed monkey brain using our technique achieves 99% accuracy in classification via  -nearest neighbor analysis.nnCONCLUSIONS: Our study showcases the potential of wavelength-swept Raman spectroscopy for tissue identification, particularly in highly scattering media, such as the brain. The developed technique offers enhanced signal detection capabilities, paving the way for future  applications in tissue characterization.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38562286,

title = {NBS-SNI, an extension of the network-based statistic: Abnormal functional connections between important structural actors},

author = {Francis Normand and Mehul Gajwani and Daniel C Côté and Antoine Allard},

doi = {10.1162/netn_a_00344},

issn = {2472-1751},

year  = {2024},

date = {2024-01-01},

journal = {Netw Neurosci},

volume = {8},

number = {1},

pages = {44--80},

abstract = {Elucidating the coupling between the structure and the function of the brain and its development across maturation has attracted a lot of interest in the field of network neuroscience in the last 15 years. Mounting evidence supports the hypothesis that the onset of certain brain disorders is linked with the interplay between the structural architecture of the brain and its functional processes, often accompanied with unusual connectivity features. This paper introduces a method called the network-based statistic-simultaneous node investigation (NBS-SNI) that integrates both representations into a single framework, and identifies connectivity abnormalities in case-control studies. With this method, significance is given to the properties of the nodes, as well as to their connections. This approach builds on the well-established network-based statistic (NBS) proposed in 2010. We uncover and identify the regimes in which NBS-SNI offers a gain in statistical resolution to identify a contrast of interest using synthetic data. We also apply our method on two real case-control studies, one consisting of individuals diagnosed with autism and the other consisting of individuals diagnosed with early psychosis. Using NBS-SNI and node properties such as the closeness centrality and local information dimension, we found hypo- and hyperconnected subnetworks and show that our method can offer a 9 percentage points gain in prediction power over the standard NBS.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37362387,

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

author = {Cléophace Akitegetse and Thomas Charland and Mireille Quémener and Charles Gora and Véronique Rioux and Michel Piché and Yves De Koninck and Martin Lévesque and Daniel C Côté},

doi = {10.1117/1.NPh.10.3.035002},

issn = {2329-423X},

year  = {2023},

date = {2023-07-01},

journal = {Neurophotonics},

volume = {10},

number = {3},

pages = {035002},

abstract = {SIGNIFICANCE: Typical light sheet microscopes suffer from artifacts related to the geometry of the light sheet. One main inconvenience is the non-uniform thickness of the light sheet obtained with a Gaussian laser beam.nnAIM: We developed a two-photon light sheet microscope that takes advantage of a thin and long Bessel-Gauss beam illumination to increase the sheet extent without compromising the resolution.nnAPPROACH: We use an axicon lens placed directly at the output of an amplified femtosecond laser to produce a long Bessel-Gauss beam on the sample. We studied the dopaminergic system and its projections in a whole cleared mouse brain.nnRESULTS: Our light sheet microscope allows an isotropic resolution of  in all three axes of the scanned volume while keeping a millimetric-sized field of view, and a fast acquisition rate of up to . With slight modifications to the optical setup, the sheet extent can be increased to 6 mm.nnCONCLUSION: The proposed system's sheet extent and resolution surpass currently available systems, enabling the fast imaging of large specimens.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36400379,

title = {Endoscopic imaging of white matter fiber tracts using polarization-sensitive optical coherence tomography},

author = {Damon DePaoli and Daniel C Côté and Brett E Bouma and Martin Villiger},

doi = {10.1016/j.neuroimage.2022.119755},

issn = {1095-9572},

year  = {2022},

date = {2022-12-01},

journal = {Neuroimage},

volume = {264},

pages = {119755},

abstract = {Polarization sensitive optical coherence tomography (PSOCT) has been shown to image and delineate white matter fibers in a label-free manner by revealing optical birefringence within the myelin sheath using a microscope setup. In this proof-of-concept study, we adapt recent advancements in endoscopic PSOCT to perform depth-resolved imaging of white matter structures deep inside intact porcine brain tissue ex-vivo, through a small, rotational fiber probe. The probe geometry is comparable to microelectrodes currently used in neurosurgical interventions. The presented imaging system is mobile, robust, and uses biologically safe levels of optical radiation making it well suited for clinical translation. In neurosurgery, where accuracy is imperative, endoscopic PSOCT through a narrow-gauge fiber probe could provide intra-operative feedback on the location of critical white matter structures.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid34133116,

title = {Versatile Microfluidic Platform for Automated Live-Cell Hyperspectral Imaging Applied to Cold Climate Cyanobacterial Biofilms},

author = {Tianyang Deng and Damon DePaoli and Ludovick Bégin and Nan Jia and Leon Torres de Oliveira and Daniel C Côté and Warwick F Vincent and Jesse Greener},

doi = {10.1021/acs.analchem.0c05446},

issn = {1520-6882},

year  = {2021},

date = {2021-06-01},

journal = {Anal Chem},

abstract = {Microfluidic bioanalytical platforms are driving discoveries from synthetic biology to the health sciences. In this work, we present a platform for  live-cell imaging and automated species detection in mixed cyanobacterial biofilms from cold climate environments. Using a multimodal microscope with custom optics applied to a chip with six parallel growth channels, we monitored biofilm dynamics via continuous imaging at natural irradiance levels. Machine learning algorithms were applied to the collected hyperspectral images for automatic segmentation of mixed-species biofilms into individual species of cyanobacteria with similar filamentous morphology. The coupling of microfluidic technology with modern multimodal imaging and computer vision systems provides a versatile platform for the study of cause-and-effect scenarios of cyanobacterial biofilms, which are important elements of many ecosystems, including lakes and rivers of the polar regions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}