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Microscopy techniques have been developed and refined over multiple decades, but innovation around single photon modalities has slowed. The advancement of the utility of information acquired, and minimum resolution available is seemingly reaching an asymptote. The fusion of light microscopy and well-studied nonlinear processes has broken through this barrier and enabled the collection of vast amounts of additional information beyond the topographical information relayed by traditional microscopes. Through nonlinear imaging modalities, chemical information can also be extracted from tissue. Nonlinear microscopy also can beat the resolution limit caused by diffraction, and offers up three-dimensional capabilities. The power of nonlinear imaging has been demonstrated by countless research groups, solidifying it as a major player in biomedical imaging. The value of a nonlinear imaging system could be enhanced if a reduction in size would permit the insertion into bodily cavities, as has been demonstrated by linear imaging endoscopes. The miniaturization of single photon imaging devices has led to significant advancements in diagnostics and treatment in the medical field. Much more information can be extracted from a patient if the tissue can be imaged in vivo, a capability that traditional, bulky, table top microscopes cannot offer. The development of new technologies in optics has enabled the miniaturization of many critical components of standard microscopes. It is possible to combine nonlinear techniques with these miniaturized elements into a portable, hand held microscope that can be applied to various facets of the biomedical field. The research demonstrated in this thesis is based on the selection, testing and assembly of several miniaturized optical components for use as a nonlinear imaging device. This thesis is the first demonstration of a fibre delivered, microelectromechanical systems mirror with miniaturized optics housed in a portable, hand held package. Specifically, it is designed for coherent anti-Stokes Raman scattering, second harmonic generation, and two-photon excitation fluorescence imaging. Depending on the modality being exploited, different chemical information can be extracted from the sample being imaged. This miniaturized microscope can be applied to diagnostics and treatments of spinal cord diseases and injuries, atherosclerosis research, cancer tumour identification and a plethora of other biomedical applications. The device that will be revealed in the upcoming text is validated by demonstrating all designed-for nonlinear modalities, and later will be used to perform serialized imaging of myelin of a single specimen over time.

Microscopy techniques have been developed and refined over multiple decades, but innovation around single photon modalities has slowed. The advancement of the utility of information acquired, and minimum resolution available is seemingly reaching an asymptote. The fusion of light microscopy and well-studied nonlinear processes has broken through this barrier and enabled the collection of vast amounts of additional information beyond the topographical information relayed by traditional microscopes. Through nonlinear imaging modalities, chemical information can also be extracted from tissue. Nonlinear microscopy also can beat the resolution limit caused by diffraction, and offers up three-dimensional capabilities. The power of nonlinear imaging has been demonstrated by countless research groups, solidifying it as a major player in biomedical imaging. The value of a nonlinear imaging system could be enhanced if a reduction in size would permit the insertion into bodily cavities, as has been demonstrated by linear imaging endoscopes. The miniaturization of single photon imaging devices has led to significant advancements in diagnostics and treatment in the medical field. Much more information can be extracted from a patient if the tissue can be imaged in vivo, a capability that traditional, bulky, table top microscopes cannot offer. The development of new technologies in optics has enabled the miniaturization of many critical components of standard microscopes. It is possible to combine nonlinear techniques with these miniaturized elements into a portable, hand held microscope that can be applied to various facets of the biomedical field. The research demonstrated in this thesis is based on the selection, testing and assembly of several miniaturized optical components for use as a nonlinear imaging device. This thesis is the first demonstration of a fibre delivered, microelectromechanical systems mirror with miniaturized optics housed in a portable, hand held package. Specifically, it is designed for coherent anti-Stokes Raman scattering, second harmonic generation, and two-photon excitation fluorescence imaging. Depending on the modality being exploited, different chemical information can be extracted from the sample being imaged. This miniaturized microscope can be applied to diagnostics and treatments of spinal cord diseases and injuries, atherosclerosis research, cancer tumour identification and a plethora of other biomedical applications. The device that will be revealed in the upcoming text is validated by demonstrating all designed-for nonlinear modalities, and later will be used to perform serialized imaging of myelin of a single specimen over time.

La microscopie par cohérence optique (OCM) est une technique d'imagerie tomographique basée sur l'interférométrie en lumière blanche permettant d'imager les milieux biologiques à l'échelle microscopique. L'OCM est une méthode particulièrement adaptée à l'imagerie dermatologique, en particulier pour le diagnostic du cancer de la peau, car elle permet d'obtenir des images similaires aux images histologiques sans nécessiter d'effectuer de biopsie.Ces travaux de thèse portent sur le développement de la microscopie par cohérence optique pour l'imagerie de la peau, dans le but de fournir au dermatologue un outil d'imagerie compact, adapté à l'imagerie dermatologique in vivo, et permettant d'obtenir des images à la fois structurelles et fonctionnelles.Un dispositif de microscopie par cohérence optique plein champ (FF-OCM) compact, à éclairage par LED blanche, a tout d'abord été développé, permettant d'obtenir des images tomographiques à très haute résolution (0.7 μm × 1.8 μm) jusqu’à ∼200 μm de profondeur dans la peau. En utilisant une LED de haute puissance, des images de peau in vivo ont pu être obtenues.A partir de ce dispositif de FF-OCM, des méthodes d'imagerie fonctionnelle permettant de cartographier les écoulements sanguins (angiographie) ont été mises en oeuvre. Quatre méthodes, basées sur une analyse du signal interférométrique (temporelle ou fréquentielle), d'images de phase ou d'images d'amplitude ont permis d'imager de l'intralipide s'écoulant dans un modèle de capillaire sanguin.L'imagerie fonctionnelle polarimétrique a aussi été explorée en FF-OCM. Une optimisation du contraste des images polarimétriques a été obtenue en modifiant les composants polarisants d'un montage conventionnel de FF-OCM polarimétrique en fonction de l'échantillon imagé. Cette méthode a été testée sur un échantillon polarisant simple.Finalement, une nouvelle méthode d'OCM, la microscopie par cohérence optique confocale à éclairage « ligne » (LC-OCM) a été étudiée, dans le but de développer un système permettant d'imager la peau in vivo, avec une plus grande profondeur de pénétration dans les tissus que la FF-OCM. Ce système, combinant un filtrage interférométrique et un filtrage confocal, a permis d'obtenir des images de peau in vivo en coupe verticale et en coupe en face, avec une résolution spatiale similaire à celle de la FF-OCM, mais à une profondeur supérieure atteignant 300 μm. / Optical coherence microscopy (OCM) is a technique for tomographic imaging based on white light interferometry, making it possible to image biological media with micrometer-scale spatial resolution. OCM is particularly well-suited to dermatological imaging, especially skin cancer diagnosis, since it provides images that are similar to histological images without the need for biopsy.This PhD thesis focuses on the development of OCM for skin imaging, with the aim of providing a compact, in vivo imaging tool for the dermatologist, capable of acquiring structural and functional images of the skin.A compact, full-field OCM (FF-OCM) system illuminated by a white LED was first developed, making it possible to obtain tomographic images at an ultra-high resolution (0.7 μm × 1.8 μm), up to ∼200 μm in depth within the skin. Using a high power LED, in vivo skin images could be obtained.Using this FF-OCM setup, functional imaging methods for blood flow mapping (angiography) were implemented. Four methods, based on temporal or frequency analysis of the interferometric signal, phase images or amplitude images, have been shown to be able to image intralipid flow within a model blood capillary.Functional polarimetric imaging has also been explored in FF-OCM. Contrast optimization in polarimetric images has been obtained by modifying the polarizing components of the conventional polarization sensitive FF-OCM setup depending on the sample to be imaged. This method has been tested on a simple polarizing sample.Finally, a new OCM method, line-field confocal OCM (LC-OCM), has been studied. The goal here was to develop a system capable of imaging the skin in vivo, with a tissue penetration depth greater than what is possible for FF-OCM. This system, which combines interferometric filtering and confocal filtering, makes it possible to obtain in vivo skin images in vertical and en face slices, with a spatial resolution similar to that of FF-OCM, but with a greater penetration depth of 300 μm.

L'amélioration de la visualisation in vivo des lésions précancéreuse (dysplasies) du col utérin est essentielle pour mieux identifier les zones à biopsier et pour optimiser la définition des limites d'exérèse chirurgicale. Dans ce but nous étudions une nouvelle technique d'imagerie polarimétrique en rétrodiffusion, que nous avons mise en oeuvre sur des échantillons ex vivo dans des configurations expérimentales variées afin d'optimiser le diagnostic in vivo. Comme cette optimisation passe par la compréhension des contrastes polarimétriques observés, nous avons réalisé de nombreuses simulations de la propagation de lumière polarisée dans des structures multicouche représentatives des tissus. Ces structures comprennent typiquement une couche comportant des diffuseurs dans une matrice homogène et représentant l'épithélium ou le tissu conjonctif superficiel, et un substrat lambertien totalement dépolarisant pour les couches plus profondes. Ces simulations ont été effectuées au moyen d'un code Monte Carlo que nous avons adapté à notre problématique. Nous avons ainsi montré que la contribution des noyaux cellulaires est très faible en rétrodiffusion. Pour le tissu conjonctif, les fibres de collagène, modélisées par des diffuseurs sphériques de 200 nm de rayon, donnent une contribution plus importante que les noyaux, mais ne reproduisent pas la réponse polarimétrique de type Rayleigh observée dans tous les tissus étudiés, qu'ils soient sains ou pathologiques. En revanche, l'inclusion de diffuseurs de taille nettement inférieure à la longueur d'onde, modélisés par des sphères de 50 nm, permet de reproduire cette réponse de manière très stable. Ces diffuseurs correspondent a priori aux protéines intracellulaires. Dans le cadre de ce modèle, les contrastes observés entre tissus sains et cancéreux s'expliquent essentiellement par une variation de la concentration de ces petits diffuseurs. Ce résultat, encore préliminaire, suggère que l'imagerie polarimétrique en rétrodiffusion peut être sensible non seulement à la morphologie, mais également à l'état physiologique du tissu, ce qui peut s'avérer important pour la détection sélective des dysplasies.

The common way to diagnose hard and soft tissue irregularities in the oral cavity is initially the visual inspection by an experienced dentist followed by further medical examinations, such as radiological imaging and/or histopathological investigation. For the diagnosis of oral hard and soft tissues, the detection of early transformations is mostly hampered by poor visual access, low specificity of the diagnosis techniques, and/or limited feasibility of frequent screenings. Therefore, optical noninvasive diagnosis of oral tissue is promising to improve the accuracy of oral screening. Considering this demand, a rigid handheld endoscopic scanner was developed for optical coherence tomography (OCT). The novelty is the usage of a commercially near-infrared endoscope with fitting optics in combination with an established spectral-domain OCT system of our workgroup. By reaching a high spatial resolution, in vivo images of anterior and especially posterior dental and mucosal tissues were obtained from the oral cavity of two volunteers. The convincing image quality of the endoscopic OCT device is particularly obvious for the imaging of different regions of the human soft palate with highly scattering fibrous layer and capillary network within the lamina propria.

Since optical coherence tomography (OCT) provides three-dimensional high-resolution images of biological tissue, the benefit of polarization contrast in the field of dentistry is highlighted in this study. Polarization-sensitive OCT (PS OCT) with phase-sensitive recording is used for imaging dental and mucosal tissues in the human oral cavity in vivo. An enhanced polarization contrast of oral structures is reached by analyzing the signals of the co- and crosspolarized channels of the swept source PS OCT system quantitatively with respect to reflectivity, retardation, optic axis orientation, and depolarization. The calculation of these polarization parameters enables a high tissue-specific contrast imaging for the detailed physical interpretation of human oral hard and soft tissues. For the proof-of-principle, imaging of composite restorations and mineralization defects at premolars as well as gingival, lingual, and labial oral mucosa was performed in vivo within the anterior oral cavity. The achieved contrast-enhanced results of the investigated human oral tissues by means of polarizationsensitive imaging are evaluated by the comparison with conventional intensity-based OCT.