There is an unprecedented need in neuroscience and medical research for the precise imaging of individual neurons and their interconnectivity in an effort to achieve a more complete understanding of neurological illness and cognitive growth. While several imaging architectures successfully detect active neural tissue, fluorescent imaging through head-mounted microscopes is becoming a standard method of imaging neural circuitry in freely behaving animals. At Boston University, the Gardner Group developed a miniaturized, open-source, single-photon ‘finch-scope’ to spur rapid prototyping in head-mounted miniscope technology. While experimentally convenient, the finch-scope and other miniscope platforms are limited by their native depth of field and may only detect a thin layer of active neurons in a neurological volume. In this Master’s Thesis Project, I will investigate utilizing optical phase masks integrated in the Fourier plane of the finch-scope to invoke a less-diffractive Bessel point spread function. Next, I will experimentally justify the extended depth of field nature of these phase masks by imaging the axial profile of a 10μm fluorescent pinhole object with a modified finch-scope.

We aim to develop an implantable, optical neural imaging device by fabricating lasers and photodiodes onto a gallium arsenide substrate. Some studies suggest that lasers exhibit higher noise than light emitting diodes (LEDs) due to coherence effects – my studies aim to quantify this noise and to guide device development. To this end, I developed a model of a fluorescent imaging device which agreed with experiment. Noise analysis performed in phantom showed that laser sources exhibit temporal and spatial noise up to 10x higher than LED sources, and in vivo noise analysis also demonstrated this trend. I studied a neural injury model called cortical spreading depression in vitro in mouse brain slices and in vivo in the rat brain using laser and LED sources. Signal magnitudes in vitro are on the order of 10% and in vivo results are inconclusive. Future work will aim to reduce coherence related noise.

We aim to develop an implantable, optical neural imaging device by fabricating lasers and photodiodes onto a gallium arsenide substrate. Some studies suggest that lasers exhibit higher noise than light emitting diodes (LEDs) due to coherence effects – my studies aim to quantify this noise and to guide device development. To this end, I developed a model of a fluorescent imaging device which agreed with experiment. Noise analysis performed in phantom showed that laser sources exhibit temporal and spatial noise up to 10x higher than LED sources, and in vivo noise analysis also demonstrated this trend. I studied a neural injury model called cortical spreading depression in vitro in mouse brain slices and in vivo in the rat brain using laser and LED sources. Signal magnitudes in vitro are on the order of 10% and in vivo results are inconclusive. Future work will aim to reduce coherence related noise.

Optogenetic approaches allow the activation or inhibition of genetically prescribed populations of neurons by light. In principle, optogenetics offers not only the ability to elucidate the functions of neural circuitry, but also new approaches to a treatment of neurodegenerative diseases and recovery of vision and auditory perception. Optogenetics already has revolutionized research in neuroscience. However, new methods for delivering light to three-dimensionally distributed structures e.g. in the brain are necessary. A major hurdle for focusing light through biological tissue is the occurring scattering and scrambling of the light. We demonstrate the correction of the scrambling in a multimode fiber by digital optical phase conjugation with a perspective for ptogenetics.

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Cette thèse a pour objectif l’étude d’un lien effectif potentiel entre la motilité cellulaire, la mécanique cellulaire, et l’activité biochimique de ces mêmes cellules. Ce couplage a été étudié dans divers systèmes biologiques, et aussi bien dans des cultures de cellules qu’à l’intérieur de tissus plus complexes. Notamment, nous avons particulièrement cherché à détecter un couplage électromécanique dans des neurones qui pourrait être impliqué dans la propagation du message nerveux.Pour ce faire, nous avons dû développer deux microscopes optiques à la sensibilité extrême. Ces microscopes se composent de deux parties principales. La première sert à détecter des mouvements axiaux plus petits que la longueur d’onde optique, soit en dessous de 100 nanomètres. La deuxième partie permet la détection d’un signal de fluorescence, offrant la possibilité de suivre l’évolution biochimique de la cellule. Avec ces deux microscopes multimodaux, il est donc possible de suivre de manière simultanée un contraste de motilité, un contraste mécanique, un contraste structurel et un contraste biochimique. Si l’un de ces systèmes est basé sur la tomographie de cohérence optique plein champ et permet de faire de telles mesures en 3-D et en profondeur dans les tissus biologiques, le second ne permet que des mesures dans des cultures de cellules, mais est bien plus robuste au bruit mécanique. Dans ce manuscrit, nous allons essentiellement décrire le développement de ces deux appareils, et préciser les contrastes auxquels ils sont sensibles spécifiquement.Nous développerons également deux des applications principales de ces microscopes que nous avons étudié dans le détail au cours de cette thèse. La première application développe l’intérêt d’un de nos microscopes pour la détection sans marquage des principaux composants cellulaires et structuraux de la cornée et de la rétine. La seconde application tend à détecter et à suivre des ondes électromécaniques dans des neurones de mammifères / This PhD project aims to explore the relationship that might exist between the dynamic motility and mechanical behavior of different biological systems and their biochemical activity. In particular,we were interested in detecting the electromechanical coupling that may happen in active neurons, and may assist in the propagation of the action potential. With this goal in mind, we have developed two highly sensitive optical microscopes that combine one modality that detects sub-wavelength axial displacements using optical phase imaging and another modality that uses a fluorescence path. Therefore, these multimodal microscopes can combine a motility, a mechanical,a structural and a biochemical contrast at the same time. One of this system is based ona multimodal combination of full-field optical coherence tomography (FF-OCT) and allows the observation of such contrast inside thick and scattering biological tissues. The other setup provides a higher displacement sensitivity, but is limited to measurements in cell cultures. In this manuscript, we mainly discuss the development of both systems and describe the various contrastst hey can reveal. Finally, we have largely used our systems to investigate diverse functions of the eye and to look for electromechanical waves in cell cultures. The thorough description of both biological applications is also provided in the manuscript