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Abstract: Nonlinear multicontrast microscopy is established in this study as an important tool for understanding biological structure and function of muscle cells. Second harmonic generation, third harmonic generation and multi-photon excitation fluorescence are acquired simultaneously in order to establish the origin of nonlinear signal generation in myocytes, and investigate myocyte structure and functionality during muscle contraction. Using structural cross-correlation image analysis, an algorithm developed specifically for this research, for the first time, third harmonic generation is shown to originate from the mitochondria in myocytes. The second harmonic, which is generated from the anisotropic bands of the sarcomeres, is further shown to be dependent on the crystalline order of the sarcomeres, thereby providing a potential diagnostic tool to evaluate disorder in muscle cells. The combination of the second and third harmonic provides complementary information that can be used to further elucidate the basic principles of muscle contraction. Time-lapse nonlinear microscopic imaging showed structural and functional dynamics in the myocytes. The second harmonic contrast revealed nonsynchronized nanocontractions of sarcomeres in relaxed, non-contracting, cardiomyocytes and Drosophila muscle samples, providing insight into the asynchronous behaviour of individual sarcomeres. Furthermore, macrocontracting samples were found to exhibit a synchronization of nanocontractions, providing new evidence for how muscles contract. Dynamic image correlation analysis, another algorithm developed specifically for this investigation, is used to reveal networks of mitochondria, which show fluctuations of multi-photon excitation fluorescence and third harmonic generation signals. The intensity fluctuations in the networks reveal both slow and fast dynamics; phase shifts of the slow dynamics between different networks are observed. Fast dynamics appear only in the inner networks, suggesting functional difference between interfibrillar and subsarcolemma mitochondria. The groundwork for studying bioenergetics of mitochondria in cardiomyocytes with nonlinear multimodal microscopy is fully developed in this work. The origin of the nonlinear signals and the development of the image analysis techniques provide a solid foundation to further study of muscle contractility and bioenergetics.

Abstract: Nonlinear multicontrast microscopy is established in this study as an important tool for understanding biological structure and function of muscle cells. Second harmonic generation, third harmonic generation and multi-photon excitation fluorescence are acquired simultaneously in order to establish the origin of nonlinear signal generation in myocytes, and investigate myocyte structure and functionality during muscle contraction. Using structural cross-correlation image analysis, an algorithm developed specifically for this research, for the first time, third harmonic generation is shown to originate from the mitochondria in myocytes. The second harmonic, which is generated from the anisotropic bands of the sarcomeres, is further shown to be dependent on the crystalline order of the sarcomeres, thereby providing a potential diagnostic tool to evaluate disorder in muscle cells. The combination of the second and third harmonic provides complementary information that can be used to further elucidate the basic principles of muscle contraction. Time-lapse nonlinear microscopic imaging showed structural and functional dynamics in the myocytes. The second harmonic contrast revealed nonsynchronized nanocontractions of sarcomeres in relaxed, non-contracting, cardiomyocytes and Drosophila muscle samples, providing insight into the asynchronous behaviour of individual sarcomeres. Furthermore, macrocontracting samples were found to exhibit a synchronization of nanocontractions, providing new evidence for how muscles contract. Dynamic image correlation analysis, another algorithm developed specifically for this investigation, is used to reveal networks of mitochondria, which show fluctuations of multi-photon excitation fluorescence and third harmonic generation signals. The intensity fluctuations in the networks reveal both slow and fast dynamics; phase shifts of the slow dynamics between different networks are observed. Fast dynamics appear only in the inner networks, suggesting functional difference between interfibrillar and subsarcolemma mitochondria. The groundwork for studying bioenergetics of mitochondria in cardiomyocytes with nonlinear multimodal microscopy is fully developed in this work. The origin of the nonlinear signals and the development of the image analysis techniques provide a solid foundation to further study of muscle contractility and bioenergetics.

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Neural Networks (NNs) (or 'deep' neural networks (DNNs)) have found great success in many applications across all fields of engineering, and in particular have found recent success in the field of Photonics. In this work we discuss the application of NNs to optical interferometry for the purpose of quantitative phase imaging (QPI). We show that NNs are capable of quantifying the optical pathlength difference in an interferogram with sensitivities that achieve the fundamental limit given by the Cramér-Rao bound (CRB). As an application, we consider a particular QPI technique known as wavelength shifting interferometry (WSI) which obtains the OPL by acquiring multiple interferograms at different, evenly spaced wavenumbers. Traditional phase demodulation algorithms for WSI fail to reach the theoretical OPL sensitivity limit set by the CRB. We have designed NNs which are capable of achieving this bound across a wide range of OPL differences. The NNs are trained on simulated data, and then applied to experimental data. In both simulation and experiment, the NNs outperform the existing analytical demodulation techniques and provide highly sensitive signal demodulation in cases where the analytical approach fails. Thus, NNs provide better performance and more flexibility in the design and use of a WSI system. We expect that the techniques developed in this work can be extended to other two-beam interference based QPI system. / M.S. / Neural Networks (NNs) (or 'deep' neural networks (DNNs)) have found great success in many applications across all fields of engineering, and in particular have found recent success in the field of Photonics. In this work we discuss the application of NNs to making so-called 'phase' images of biological cells and tissues (e.g. red blood cells, sperm cells). This is necessary for many biological samples which are transparent under traditional bright field microscopy. We show that NNs are capable of quantifying the phase of these samples to produce images with higher contrast than possible in a typical microscope image. As an example, we introduce a particular phase microscopy system and study the application of NNs to this system. We show that the NNs are capable of providing solutions for this phase in situations where existing analytical techniques fail. The NNs are also capable of making more precise calculations of the phase than the traditional algorithms in many situations where either technique could be used. Therefore, NNs can provide simultaneously higher performance and more flexibility when designing phase microscopy systems.

<p>On-board imaging is useful for guiding radiation to patients in the treatment position; however, current treatment-room imaging modalities are not sensitive to physiology - features that may differentiate tumor from nearby tissue or identify biological targets, e.g., hypoxia, high tumor burden, or increased proliferation. Single photon emission computed tomography (SPECT) is sensitive to physiology. We propose on-board SPECT for biological target localization.</p><p>Localization performance was studied in computer-simulated and scanner-acquired parallel-hole SPECT images. Numerical observers were forced to localize hot targets in limited search volumes that account for uncertainties common to radiation therapy delivery. Localization performance was studied for spherical targets of various diameters, activity ratios, and anatomical locations. Also investigated were the effects of detector response function compensation (DRC) and observer normalization on target localization. Localization performance was optimized as a function of iteration number and degree of post-reconstruction smoothing. Localization error patterns were analyzed for directional dependencies and were related to the detector trajectory. Localization performance and the effect of the detector trajectory were investigated in a hardware study using a whole-body phantom.</p><p>Typically targets of 6:1 activity were localized as accurately using 4-minute scans as those of 3:1 activity using 20-minute scans. This trend is consistent with the relationship between contrast and noise in the contrast-to-noise ratio (CNR) and implies that higher contrast targets are better candidates for on-board SPECT because of time constraints in the treatment room. Using 4-minute scans, mean localization errors were within 2 mm for superficial targets of 6:1 activity that were proximal to the detector trajectory and of at least 14 mm in diameter. Localization was significantly better (p < 0.05, Wilcoxon signed-rank test) with than without observer normalization and DRC at 5 of 6 superficial tumor sites. Observer normalization improved localization substantially for a target proximal to the much hotter heart. Localization error patterns were shown to be anisotropic and dependent on target position relative to the detector trajectory. Detector views of close approach and of minimal attenuation were predictive of directions with the smallest (magnitude) localization bias and precision. The detector trajectory had a substantial effect on localization performance. In scanner-acquired SPECT images, mean localization errors of a 22-mm-diameter superficial target were 0.8, 1.5, and 6.9 mm respectively using proximal 180°, 360°, and distal 180° detector trajectories, thus demonstrating the benefits of using a proximal 180° detector trajectory.</p><p>In conclusion, the potential performance characteristics of on-board SPECT were investigated using computer-simulation and real-detector studies. Mean localization errors < 2 mm were obtained for proximal, superficial targets with diameters >14 mm and of 6:1 activity relative to background using scan times of approximately 5 minutes. The observed direction-dependent localization errors are related to the detector trajectory and have important implications for radiation therapy. This works shows that parallel-hole SPECT could be useful for localizing certain biological targets.</p> / Dissertation

Semiconductor quantum dots (QDs) and gold nanoparticles (AuNPs) have gained tremendous attention in the last decade as a result of their size-dependent spectroscopic properties. These nanoparticles have been a subject of intense study to bridge the gap between macroscopic and atomic behavior, as well as to generate new materials for novel applications in therapeutics, biological sensing, light emitting devices, microelectronics, lasers, and solar cells. One of the most promising areas for the use of these nanoparticles is in biotechnology, where their size-dependent optical properties are harnessed for imaging and sensing applications. However, these nanoparticles, as synthesized, are often not stable in aqueous media and lack simple and reliable means of covalently linking to biomolecules. The focus of this work is to advance the progress of these nanomaterials for biotechnology by synthesizing them, characterizing their optical properties and rendering them water-soluble and functional while maintaining their coveted optical properties. QDs were synthesized by an organometallic chemical procedure that utilizes coordinating solvents to provide brightly luminescent nanoparticles. The optical interactions of these QDs were studied as a function of concentration to identify particle size-dependent optimal concentrations, where scattering and indirection excitation are minimized and the amount light observed per particle is maximized. Both QDs and AuNPs were rendered water-soluble and stable in a broad range of biologically relevant conditions by using a series of ligands composed of dihydrolipoic acid (DHLA) appended to poly(ethylene glycol) methyl ether. By studying the stability of the surface modified AuNPs, we revealed some interesting information regarding the role of the surface ligand on the nanoparticle stability (i.e. solubility in high salt concentration, resistance to dithiothreitol competition and cyanide decomposition). Furthermore, the nanoparticles were functionalized using a series of bifunctional ligands that contain a dithiol group (DHLA) for surface binding, a PEG segment to instill water-solubility and a terminal functional group for easy bioconjugation (i.e. NH 2 , COOH, or biotin). Finally, a sensing application was demonstrated to detect the presence of microbial DNA (unmethlylated CpG) by using Toll-like receptor 9 proteins as the recognition components and the QDs as the transduction elements via Förster Resonance Energy Transfer.

L’objectif de ce travail a porté sur l’élaboration d’une sonde bimodale ADP–TEP (absorption à deux photons–tomographie par emission de positons) pour des applications en imagerie médicale.Dans un premier temps, le projet a consisté en le design, la synthèse et l’évaluation des propriétés photophysiques d’une nouvelle série de chromophores diaziniques A–p–D (A : groupement électro-attracteur, p : lien conjugué, D : groupement électro-donneur). Des études de relation structure-propriétés photophysiques impliquant des modulations sur chacune des sous-structures (groupements A et D, lien p-conjugué) ont été réalisées puis étudiées en UV et en fluorescence. Suite à l’obtention de ces premiers résultats, des mesures d’absorption à deux photons ont été effectuées sur ces fluorophores.Dans un second temps, les fluorophores ont été modifiés afin de greffer des parties hydrophiles. Des propriétés photophysiques encourageantes ont été obtenues et des premiers tests en imagerie bi-photonique ont été réalisés.L’insertion du fluor radiomarqué est envisagée via l’insertion d’un groupement –BF2. Pour cela des structures chélatantes, « mimes de BODIPY », incorporant une pyrimidine ou un triazole ont été élaborées. Des premiers essais ont été conduits mais n’ont pas permis l’obtention des composés borés correspondants. / The purpose of this subject has been the synthesis of a bimodal probe using TPA–PET techniques for a potential application in biological imaging.In this context, we have synthesized a new range of A–π –D fluorophores incorporating diazine (p-deficient heterocycle) as electron-withdrawing moiety, N,N-dimethylaniline as electron-donating part and fluorene as p-conjugated linker. In order to increase the conjugation along the scaffold, ethynyl and/or triazole bridges have been introduced on both sides of the fluorene. The UV/Vis and photoluminescence properties have been measured. Further to those results two-photon absorption cross-section of our fluorophores (dTPA) has been obtained. Following these promising results, hydrophilic compounds using PEG groups have been prepared and photoluminescence properties have been carried out. In order to use the boron center as a site for radiofluorination, the synthesis of "BODIPY-like" probes has been considered. A new series of pyrimidine and triazole ligand have been synthesized but the corresponding boron complexes haven’t been obtained.

L'étude de la dynamique des protéines est essentielle pour comprendre les processus biologiques. Notre laboratoire a développé une nouvelle classe de protéines fluorescentes semi-synthétiques, appelée Fluorescence-Activating and absorption-Shifting Tag (FAST). Cette thèse de doctorat présente le développement de nouveaux systèmes FAST avec diverses propriétés pour l'imagerie multiplexée. Nous avons développé une série de fluorogènes permettant de modifier la couleur de FAST de vert-jaune à orange et rouge. Au delà de l’application de l’imagerie multi-couleurs, ces fluorogènes permettant un échange dynamique des couleurs grâce à la liaison réversible de FAST, ouvrant de nouvelles perspectives pour le développement de méthodes d’imagerie sélective reposant sur la dynamique de systèmes réactifs. Pour étendre davantage les propriétés spectrales de FAST vers le rouge lointain, nous avons développé une nouvelle série de fluorogènes rouges, pour lesquels nous avons sélectionné par une stratégie d'évolution dirigée basée sur le yeast display et la cytométrie en flux de nouveaux tags protéiques capables d’interagir avec ces fluorogènes et d’activer leur fluorescence. Nous avons enfin développé de nouveaux fluorogènes capables de former des complexes fluorescents avec FAST, mais incapables de traverser la membrane plasmique, ce qui permet de détecter sélectivement les protéines membranaires. / Studying protein activities could help us to understand the complex mechanisms controlling cells and organisms. Our laboratory recently developed Fluorescence-Activating and absorption-Shifting Tag (FAST), a small fluorogen-based reporter enabling to fluorescently label fusion proteins in living cells. My PhD thesis presents the developments of new FAST systems with various properties for multiplexed imaging. We report a collection of fluorogens enabling to tune the fluorescence color of FAST from green-yellow to orange and red. Beyond allowing multicolor imaging of FAST-tagged proteins in live cells, these fluorogens enable dynamic color switching because of FAST’s reversible labeling, opening great prospects for the design of selective imaging methods relying on dynamic systems. In order to further expand the spectral properties of FAST to red, we also designed and developed a library of red fluorogenic dyes, for which we engineered specific protein binders by applying a directed evolution strategy based on the yeast display technology and high-throughput fluorescence activating cell sorting (FACS). We finally developed novel fluorogens able to form fluorescent complexes with FAST, but incapable of crossing the plasma membrane, which makes it possible to selectively detect FAST-tagged cell-surface proteins.