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Imaging at the nanoscale and/or at remote locations holds great promise for studies in fields as disparate as the life sciences and materials sciences. One such microscopy technique, stimulated emission depletion (STED) microscopy, is one of several fluorescence based imaging techniques that offers resolution beyond the diffraction-limit. All current implementations of STED microscopy, however, involve the use of free-space beam shaping devices to achieve the Gaussian- and donut-shaped Orbital Angular Momentum (OAM) carrying beams at the desired colors –-- a challenging prospect from the standpoint of device assembly and mechanical stability during operation. A fiber-based solution could address these engineering challenges, and perhaps more interestingly, it may facilitate endoscopic implementation of in vivo STED imaging, a prospect that has thus far not been realized because optical fibers were previously considered to be incapable of transmitting the OAM beams that are necessary for STED. In this thesis, we investigate fiber-based STED systems to enable endoscopic nanoscale imaging. We discuss the design and characteristics of a novel class of fibers supporting and stably propagating Gaussian and OAM modes. Optimization of the design parameters leads to stable excitation and depletion beams propagating in the same fiber in the visible spectral range, for the first time, with high efficiency (>99%) and mode purity (>98%). Using the fabricated vortex fiber, we demonstrate an all-fiber STED system with modes that are tolerant to perturbations, and we obtain naturally self-aligned PSFs for the excitation and depletion beams. Initial experiments of STED imaging using our device yields a 4-fold improvement in lateral resolution compared to confocal imaging. In an experiment in parallel, we show the means of using q-plates as free-space mode converters that yield alignment tolerant STED microscopy systems at wavelengths covering the entire visible spectrum, and hence dyes of interest in such imaging schematics. Our study indicates that the vortex fiber is capable of providing an all-fiber platform for STED systems, and for other imaging systems where the exploitation of spatio-spectral beam shaping is required.

The understanding of the biological processes at the cellular and subcellular level requires the ability to directly visualize them. Fluorescence microscopy played a key role in biomedical imaging because of its high sensitivity and specificity. However, traditional fluorescence microscopy has a limited resolution due to optical diffraction. In recent years, various approaches have been developed to overcome the diffraction limit. Among these techniques, nonlinear structured illumination microscopy (SIM) has been demonstrated a fast and full field superresolution imaging tool, such as Saturated-SIM and Photoswitching-SIM. In this dissertation, I report a new approach that applies nonlinear structured illumination by combining a uniform excitation field and a patterned stimulated emission depletion (STED) field. The nature of STED effect allows fast switching response, negligible stochastic noise during switching, low shot noise and theoretical unlimited resolution, which predicts STED-SIM to be a better nonlinear SIM. After the algorithm development and the feasibility study by simulation, the STED-SIM microscope was tested on fluorescent beads samples and achieved full field imaging over 1 x 10 micron square at the speed of 2s/frame with 4-fold improved resolution. Our STED-SIM technique has been applied on biological samples and superresolution images with tubulin of U2OS cells and granules of neuron cells have been obtained. In this dissertation, an effort to apply a field enhancement mechanism, surface plasmon resonance (SPR), to nonlinear STED-SIM has been made and around 8 time enhancement on STED quenching effect was achieved. Based on this enhancement on STED, 1D SPR enhanced STED-SIM was built and 50 nm resolution of fluorescence beads sample was achieved. Algorithm improvement is required to achieve full field superresolution imaging with SPR enhanced STED-SIM. The application of nonlinear structured illumination in two photon light-sheet microscopy is also studied in this dissertation. Fluorescent cellular imaging of deep internal organs is highly challenging because of the tissue scattering. By combining two photon Bessel beam light-sheet microscopy and nonlinear SIM, 3D live sample imaging at cellular resolution in depth beyond 200 microns has been achieved on live zebrafish. Two-color imaging of pronephric glomeruli and vasculature of zebrafish kidney, whose cellular structures located at the center of the fish body are revealed in high clarity.

This thesis focuses on super resolution STED optical imaging. STED provides a wealth of new informational content to the acquired images by using stimulated emission to surpass the diffraction limit in optical fluorescence microscopy. To further increase the informational content, a new method to perform multicolor STED imaging by exploiting differences in the photostability and excitation spectra of dyes is presented. In order to extract information from the images, computational algorithms which handle the new type of high resolution informational content are developed. We propose that multicolor super resolution imaging in combination with image analysis can reduce the amount of clinical samples required to perform accurate cancer diagnosis. To date, such diagnosis is based mainly on significant amounts of tissue samples extracted from the suspected tumor site. The sample extraction often requires anesthetics and can lead to complications such as hematoma, infections and even cancer cell ceding along the needle track. We show that by applying multicolor STED and image analysis, the information gained from single cells is greatly increased. We therefore propose that accurate diagnosis can be based on significantly less extracted tissue material, allowing for a more patient friendly sampling. This approach can also be applied when studying blood platelets, where we show how the high informational content can be used to identify platelet specific activational states. Since platelets are involved in many different types of diseases, such analysis could provide means of performing truly minimally invasive diagnostics based on a simple blood test. In addition, our data makes it possible to understand in finer detail the underlying mechanisms rendering cells metastasis competent. We combine the high resolution spatial information provided by STED with information regarding the adhesive forces of cells measured by TFM (Traction Force Microscopy) and the cell stiffness measured by AFM (Atomic Force Microscopy). Such comparisons provide a link between the specific highly resolved protein distributions and different cellular mechanics and functions. This thesis also includes STED imaging and analysis on the spatial organization of neuronal synaptic regulating proteins, implicating the speed with which neuronal signaling can be regulated. / <p>QC 20140207</p>

Two-photon absorption (2PA) has been used for a number of scientific and technological applications, exploiting the fact that the 2PA probability is directly proportional to the square of the incident light intensity (while one-photon absorption bears a linear relation to the incident light intensity). This intrinsic property of 2PA leads to 3D spatial localization, important in fields such as optical data storage, fluorescence microscopy, and 3D microfabrication. The spatial confinement that 2PA enables has been used to induce photochemical and photophysical events in increasingly smaller volumes and allowed nonlinear, 2PA-based, technologies to reach sub-diffraction limit resolutions. The primary focus of this dissertation is the development of novel, efficient 2PA, fluorene-based molecules to be used either as photoacid generators (PAGs) or fluorophores. A second aim is to develop more effective methods of synthesizing these compounds. As a third and final objective, the new molecules were used to develop a write-once-read many (WORM) optical data storage system, and stimulated emission depletion probes for bioimaging. In Chapter I, the microwave-assisted synthesis of triarylsulfonium salt photoacid generators (PAGs) from their diphenyliodonium counterparts is reported. The microwave-assisted synthesis of these novel sulfonium salts afforded reaction times 90 to 420 times faster than conventional thermal conditions, with photoacid quantum yields of new sulfonium PAGs ranging from 0.01 to 0.4. These PAGs were used to develop a fluorescence readout-based, nonlinear three-dimensional (3D) optical data storage system (Chapter II). In this system, writing was achieved by acid generation upon two-photon absorption (2PA) of a PAG (at 710 or 730 nm). Readout was then performed by interrogating two-photon absorbing dyes, after protonation, at 860 nm. Two-photon recording and readout of voxels was demonstrated in five and eight consecutive, crosstalk-free layers within a polymer matrix, generating a data storage capacity of up to 1.8 x 1013 bits/cm3. The possibility of using these PAGs in microfabrication is described in Chapter III, where two-photon induced cationic ring-opening polymerization (CROP) crosslinking of an SU8 resin is employed to produce free-standing microstructures. Chapter IV describes the investigation of one- and two-photon stimulated emission transitions by the fluorescence quenching of a sulfonyl-containing fluorene compound in solution at room temperate using a picosecond pump-probe technique. The nature of stimulated transitions under various fluorescence excitation and quenching conditions were analyzed theoretically, and good agreement with experimental data was demonstrated. Two-photon stimulated transitions S1 to S0 were shown at 1064 nm. The two-photon stimulated emission cross section of the sulfonyl fluorophore was estimated as aproximately 240 - 280 GM, making this compound a good candidate for use in two-photon stimulated emission depletion (STED) microscopy.

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No description available.

Over the past three decades in cellular neuroscience there has been a shift towards the view of the 'tripartite synapse', where, astrocytes -- as well as the pre-synapse and post-synapse -- are involved in synaptic signalling. The migration of astrocytes to form branched networks in the brain is, therefore, of great interest in understanding brain development and neuronal function. Migration is a complex interplay between cytoskeletal reorganisation and cell mechanical stiffness. In order to improve understanding of this process, correlative measurements of cytoskeletal organisation and mechanical stiffness are required. To investigate astrocyte migration a technique combining atomic force microscopy (AFM) with stimulated emission depletion (STED) microscopy was developed. First a custom STED microscope was developed. To facilitate the design of this system the theoretical performance of a range of STED techniques (cw-STED, time-gated STED, pulsed STED and RESOLFT) were compared, identifying that pulsed STED theoretically has the highest photon efficiency. A pulsed STED microscope, which uses adaptive optics, was then designed, developed and characterised. The microscope was found to achieve resolutions below 50 nm. The STED microscope was combined with a commercial AFM to study live cells. Using the recently developed SiR-actin and SiR-tubulin dyes and AFM probes optimised for live cell mechanical property studies, images of the actin and tubulin cytoskeleton were correlated with AFM topography and mechanical stiffness measurements. It was found that, in astrocytes, actin contributes significantly both to astrocyte stiffness and topography. Investigations of migrating cells showed differences in actin organisation and mechanical stiffness between the basis and leading edge of migration. A further study was performed, investigating the effects of the gap-junction protein connexin30, which is expressed during the early stages of brain development, on migration. This protein was found to inhibit the actin reorganisation and mechanical stiffness changes observed in basal conditions. Overall the combination of mechanosensitive AFM measurements with advanced microscopy, such as super-resolution, on live cells is a promising approach which will enable a range of investigations, for instance when studying cell structural remodeling during brain development or tumorigenesis.

?-Conjugated systems have been the focus of study in recent years in order to understand their charge transport and optical properties for use in organic electronic devices, fluorescence bioimaging, sensors, and 3D optical data storage (ODS), among others. As a result, several molecular building blocks have been designed, allowing new frontiers to be realized. While various successful building blocks have been fine-tuned at both the electronic and molecular structure level to provide advanced photophysical and optoelectronic characteristics, the azulene framework has been under-appreciated despite its unique electronic and optical properties. Among several attributes, azulenes are vibrant blue naturally occurring hydrocarbons that exhibit large dipolar character, coupled with stimuli-responsive behavior in acidic environments. Additionally, the non-toxic nature and the accompanying eco-friendly feature of some azulenes, namely guaiazulene, may set the stage to further explore a more "green" route towards photonic and conductive materials. The first part of this dissertation focuses on exploiting guaiazulene as a natural building block for the synthesis of chromophores with varying stimuli-responsiveness. Results described in Chapter 1 show that extending the conjugation of guaiazulene through its seven-membered ring methyl group with aromatic substituents dramatically impacts the optical properties of the guaiazulenium carbocation. Study of these ?–stabilized tropilium ions enabled establishing photophysical structure-property trends for guaiazulene-terminated ?-conjugated analogs under acidic conditions, including absorption, emission, quantum yield, and optical band gap patterns. These results were exploited in the design of a photosensitive polymeric system with potential application in the field of three dimensional (3D) optical data storage (ODS). Chapter 2 describes the use of guaiazulene reactive sites (C-3 and C-4 methyl group) to generate a series of cyclopenta[ef]heptalenes that exhibit strong stimuli-responsive behavior. The approach presents a versatile route that allows for various substrates to be incorporated into the resulting cyclopenta[ef]heptalenes, especially after optimization that led to devising a one-pot reaction toward such tricyclic systems. Examining the UV-vis absorption profiles in neutral and acidic media showed that the extension of conjugation at C(4) of the cyclopenta[ef]heptalene skeleton results in longer absorption maxima and smaller optical energy gaps. Additionally, it was concluded that these systems act as sensitizers of a UV-activated (< 300 nm) photoacid generator (PAG), via intermolecular photoinduced electron transfer (PeT), upon which the PAG undergoes photodecomposition resulting in the generation of acid. In a related study, the guaiazulene methyl group at C-4 was employed to study the linear and nonlinear optical properties of 4-styrylguaiazulenes, having the same ?–donor with varying ?-spacer. It was realized that the conjugation length correlates with the extent of bathochromic shift of the protonated species. On the other hand, a trend of decreasing quantum yield was established for this set of 4-styrylguaiazulenes, which can be explained by the increasingly higher degree of flexibility. The second part of this dissertation presents a comprehensive investigation of the linear photophysical, photochemical, and nonlinear optical properties of diketopyrrolopyrrole (DPP)-based derivatives, including two-photon absorption (2PA), femtosecond transient absorption, stimulated emission spectroscopy, and superfluorescence phenomena. The synthetic feasibility, ease of modification, outstanding robustness, and attractive spectroscopic properties of DPPs have motivated their study for fluorescence microscopy applications, concluding that the prepared DPP's are potentially suitable chromophores for high resolution stimulated emission depletion (STED) microscopy.