Biomedical imaging is a key tool for the study of host-pathogen interactions. New techniques are enhancing the quality and flexibility of imaging systems, particularly as a result of developments in laser technologies. This work applies the combination of two advanced laser imaging methods to study the interactions between a virus and the host cells it infects. The first part of this work describes the theory and experimental implementation of coherent anti-Stokes Raman scattering microscopy. This technique-first demonstrated in its current form in 1999-permits the imaging of microscopic samples without the need for fluorescent labelling. Chemical contrast in images arises from the excitation of specific vibrations in the sample molecules themselves. A laser scanning microscope system was set up, based on an excitation source consisting of two titanium-sapphire lasers synchronized with a commercial phase-locked loop system. A custom-built microscope was constructed to provide optimal imaging performance, high detection sensitivity and straightforward adaptation to the specific requirements of biomedical experiments. The system was fully characterized to determine its performance. The second part of this work demonstrates the application of this microscope platform in virology. The microscope was configured to combine two nonlinear imaging modalities: coherent anti-Stokes Raman scattering and two-photon excitation. Mouse fibroblast cells were infected with a genetically modified cytomegalovirus. The modification causes the host cell to express the green fluorescent protein upon infection. The host cell morphology and lipid droplet distribution were recorded by imaging with coherent anti-Stokes Raman scattering, whilst the infection was monitored by imaging the viral protein expression with two-photon excitation. The cytopathic effects typical of cytomegalovirus infection were observed, including expansion of the nucleus, rounding of the cell shape, and the appearance of intracellular viral inclusions. In some cases these effects were accompanied by dense accumulations of lipid droplets at the nuclear periphery. Imaging was performed both with fixed cells and living. It was demonstrated that the lipid droplets in a single live cell could be imaged over a period of 7 hours without causing noticeable laser-induced damage. The system is shown to be a flexible and powerful tool for the investigation of virus replication and its effects on the host cell.

Optical brain imaging is proven to be useful to understand brain function and morphology at cellular and network level. Different optical imaging modalities were developed over the years, with our group developing multi-modal simultaneous imaging using Vertical Cavity Surface Emitting Lasers (VCSELs). This thesis improves and demonstrates the applicability of the imaging system and adapts it to portable imaging. Specifically, it was found that using multiple exposures provide better flow measurements when compared to tracking measurements. An intrinsic parameter to monitor the state of the Blood Brain Barrier (BBB) was also discovered, proving more practical than previous fluorescence methods. We finally demonstrate initial results of imaging flow velocities and fluorescence in awake and moving rodents using VCSELs, achromatic doublets and a CMOS camera. Future work involves developing new prototypes of the portable system for imaging of disease states in awake animals and minimizing movement artefacts for oxygenation measurements.

Optical brain imaging is proven to be useful to understand brain function and morphology at cellular and network level. Different optical imaging modalities were developed over the years, with our group developing multi-modal simultaneous imaging using Vertical Cavity Surface Emitting Lasers (VCSELs). This thesis improves and demonstrates the applicability of the imaging system and adapts it to portable imaging. Specifically, it was found that using multiple exposures provide better flow measurements when compared to tracking measurements. An intrinsic parameter to monitor the state of the Blood Brain Barrier (BBB) was also discovered, proving more practical than previous fluorescence methods. We finally demonstrate initial results of imaging flow velocities and fluorescence in awake and moving rodents using VCSELs, achromatic doublets and a CMOS camera. Future work involves developing new prototypes of the portable system for imaging of disease states in awake animals and minimizing movement artefacts for oxygenation measurements.

<p dir="ltr">Advancements in machine learning are narrowing the gap in visual capabilities between machines and healthcare professionals, resulting in a transformation of the way we understand and address health challenges. Despite these advances, underlying limitations persist in addressing real-world problems, particularly in the precise capture of biological and physiological information. This is primarily because traditional trichromatic cameras fall short of representing reflectance spectra due to their limited spectral information. To overcome these limitations, hyperspectral imaging has emerged as a powerful tool for biomedical applications. By collecting a wealth of information at different wavelengths, hyperspectral imaging provides a comprehensive view of electromagnetic spectra, allowing non-invasive clinical analysis for accurate diagnostics. Snapshot hyperspectral imaging, in particular, is a competitive alternative to traditional cameras as it can capture a hyperspectral image in a single shot without the need for scanning individual wavelengths. Here, we introduce a computational snapshot hyperspectral imaging method, achieved through the integration of a machine learning approach with a streamlined optical system. We design an explainable machine learning algorithm by incorporating optical and biological knowledge into the algorithm. Therefore, the algorithm can reconstruct hyperspectral images with high spectralspatial resolution comparable to those of scientific spectrometers, despite the use of sparse information captured from the optical system. To demonstrate its versatility in biomedical applications, we extract hemodynamic parameters of peripheral microcirculation from embryonic model systems, tissue phantom samples, and human conjunctivas. Furthermore, we validate high accuracy of the results using conventional hyperspectral imaging and functional near-infrared spectroscopy. This learning-powered imaging method, characterized by high resolution and simplified hardware requirements, has the potential to offer solutions for various biomedical challenges by surpassing the constraints of conventional cameras and hyperspectral imaging.</p>

<p dir="ltr">Single molecule localization microscopy (SMLM) has become an essential tool in imaging nanoscale biological structures. It breaks the diffraction limit by utilizing photo-switchable or photo-convertible fluorophores to obtain isolated single molecule emission patterns (i.e. PSFs) and subsequently localize the molecule’s position with a precision down to ~ 20 to 80 nm laterally-axially. However, optical aberrations compromise its spatial resolution. Additionally, conventional SMLM algorithms require sparse activation to reduce emission pattern overlap, which restricts imaging speed and temporal resolution, thus limiting its utility in dynamic live cell imaging. In this study, we first conducted a comprehensive quantitative analysis of the theoretical precision limits for position and wavefront distortion measurements in the presence of aberrations, which enhances our understanding of aberration effects in SMLM and lays the groundwork for developing more effective aberration correction methods. To improve temporal resolution, we developed a high-density single molecule localization algorithm that utilizes deep learning to analyze molecule blinking data. This approach allows us to achieve high localization precision and resolve structures at tens of nanometers resolution, even with highly overlapped blinking data. Validated by both simulated and high-density experimental data, our algorithm successfully resolves the complex structures of various cellular organelles and captures rapid dynamic movements in live cells. This work addresses the knowledge gap about aberrations in SMLM and expands its applications to more dynamic and detailed studies of cellular processes.</p>

A methodology is presented for creating tomographic reconstructions from various projection data, and the relevance of the results to applications in atmospheric science and biomedical imaging is analyzed. The fundamental differences between transform and iterative methods are described and the properties of the imaging configurations are addressed. The presented results are particularly suited for highly ill-conditioned inverse problems in which the imaging data are restricted as a result of poor angular coverage, limited detector arrays, or insufficient access to an imaging region. The class of reconstruction algorithms commonly used in sparse tomography, the algebraic reconstruction techniques, is presented, analyzed, and compared. These algorithms are iterative in nature and their accuracy depends significantly on the initialization of the algorithm, the so-called initial guess. A considerable amount of research was conducted into novel initialization techniques as a means of improving the accuracy. The main body of this paper is comprised of three smaller papers, which describe the application of the presented methods to atmospheric and medical imaging modalities. The first paper details the measurement of mesospheric airglow emissions at two camera sites operated by Utah State University. Reconstructions of vertical airglow emission profiles are presented, including three-dimensional models of the layer formed using a novel fanning technique. The second paper describes the application of the method to the imaging of polar mesospheric clouds (PMCs) by NASA’s Aeronomy of Ice in the Mesosphere (AIM) satellite. The contrasting elements of straight-line and diffusive tomography are also discussed in the context of ill-conditioned imaging problems. A number of developing modalities in medical tomography use near-infrared light, which interacts strongly with biological tissue and results in significant optical scattering. In order to perform tomography on the diffused signal, simulations must be incorporated into the algorithm, which describe the sporadic photon migration. The third paper presents a novel Monte Carlo technique derived from the optical scattering solution for spheroidal particles designed to mimic mitochondria and deformed cell nuclei. Simulated results of optical diffusion are presented. The potential for improving existing imaging modalities through continual development of sparse tomography and optical scattering methods is discussed.

Various biomedical technologies like CT, MRI and PET scanners provide detailed cross-sectional views of the human anatomy. The image information obtained from these scanning devices is typically represented as large data sets whose sizes vary from several hundred megabytes to about one hundred gigabytes. As these data sets cannot be stored on one's local hard drive, SDSC provides a large data repository to store such data sets. These data sets need to be accessed by researchers around the world to collaborate in their research. But the size of these data sets make them difficult to be transmitted over the current network. This thesis presents a 3-D Haar wavelet algorithm which enables these data sets to be transformed into smaller hierarchical representations. These transformed data sets are transmitted over the network and reconstructed to a 3-D volume on the client's side through progressive refinement of the images and 3-D texture mapping techniques.

<p dir="ltr">The movement of Cerebrospinal Fluid (CSF) within the brain's ventricles and the subarachnoid spaces of both the cranium and spine is crucial for the health and functioning of the central nervous system. Recent research has emphasized CSF movement's importance in metabolic waste clearance and its effect on the pathophysiology of neurodegenerative and neurodevelopmental disorders. Additionally, CSF movement is significantly enhanced during Non-rapid eye movement (NREM) sleep. Despite the critical role of CSF in maintaining brain health, a comprehensive understanding of the mechanisms driving its movement across different states of wakefulness and sleep is lacking. In this work, multimodal imaging was utilized to simultaneously monitor CSF movement and brain hemodynamics via functional Magnetic Resonance Imaging (MRI), neural activity through Electroencephalography (EEG), and non-neuronal systemic physiology via peripheral functional Near-Infrared Spectroscopy (fNIRS). Our findings reveal that CSF movement is influenced by multiple physiological forces concurrently. During wakefulness, both low-frequency vasomotion and respiration interact to regulate CSF movement. Furthermore, systemic physiological changes significantly impact CSF movement during light NREM sleep, even in the presence of autonomic neural activity. Notably, during deep NREM3 sleep, CSF movement magnitude increases independent of the magnitude of brain hemodynamics, suggesting a decrease in impedance to CSF movement and an enhanced exchange between CSF and interstitial fluid (ISF) in the brain. Building on these observations, significant enhancement of CSF movement was also achieved via simple respiratory interventions, thereby demonstrating their potential to be used as clinical protocols across pathologies characterized by reduced CSF movement.</p>

The photothermal effect is a way in which chemical contrast can be measured as an optical pathlength or phase change. When a chemical species in a sample absorbs optical energy at a particular wavelength, this absorption raises the temperature at these points in the sample via the photothermal effect. This temperature change changes the local refractive index in the sample. Quantitative phase imaging is an interferometric technique for measuring the optical pathlength of sample features. Quantitative phase imaging is capable of detecting the photothermally-induced refractive index change, and is thus a powerful method for performing photothermal imaging. In this work, a thermal wave model is derived from Fourier's law of conduction in conjunction with a medium's heat capacity to derive the diffusion of temperature in a medium. This diffusion theory is transformed to a thermal wave model by applying a temporally modulated thermal source. Analytical expressions for the temperature field surrounding such a modulated thermal source are derived in multiple dimensions. The thermal wave equation is also simulated using a custom finite difference numerical method, and the simulated results are compared to the theoretical expressions with good agreement. The experimental apparatus for inducing such a thermal point source in a medium of water is described using the quantitative phase imaging system of spectral modulation interferometry. The spectral modulation interferometry system is aligned with a visible light pumping laser in two configurations for point source measurement and cell imaging. Label-free chemical imaging is then performed by pumping a field of cellular samples with wide-field illumination, and the resulting photothermal signal is detected by temporal analysis of the optical pathlength changes, generating the two-dimensional photothermal image. The measured photothermal cell image is qualitatively compared to predicted photothermal image based on the application of the thermal wave model in the spatial frequency domain. The chemical specificity of this technique is also verified by simultaneously pumping absorbing and non-absorbing biological cells in the same field-of-view. / Generating image contrast is a fundamental challenge in optical microscopy. Samples of interest in optical microscopy typically do not have visible absorption contrast without modification. A method of contrast that could provide information about a sample's absorption at different optical wavelengths would be useful for characterizing a sample's chemical content. The photothermal effect is an effect in which the small absorption of light by microscopic samples can be detected as a temperature change. With quantitative phase imaging, this temperature change can be measured by detecting the change in optical density of a sample due to its increase in temperature. Thus, quantitative phase imaging can be used to detect the small absorption of light by microscopic samples and generate two-dimensional images with chemical contrast. This work describes the theory of how thermal energy produced by optical absorption diffuses through a sample immersed in water. A thermal wave model is derived theoretically and compared to a custom simulation of the thermal wave physics with strong agreement. This thermal theory is verified with the quantitative phase imaging system used in this work to characterize the photothermal imaging technique. The photothermal imaging method is then applied to cellular samples, which are pumped with green light. The photothermal image is then generated and compared qualitatively to the image predicted by the thermal theory. The chemical imaging ability of the technique is then demonstrated by simultaneous imaging of absorbing and non-absorbing cells.

This thesis focuses on designing and synthesis of novel molecular imaging probes based on non-covalent funtionalisation of pure single-walled carbon nanotubes (SWNTs). Several synthetic strategies for the supramolecular chemistry functionalisation of SWNTs, cytotoxicity measurements and cellular imaging of supramolecularly functionalised carbon nanotube probes are discussed. Chapter one is a literature review as the thesis Introduction. This describes aspects of the physical and chemical properties, structural importance and synthesis methods of single-walled carbon nanotubes (SWNTs), also opens the discussion of the different functionalisation methods to enhance the solubility and biocompatibility of SWNTs for biomedical applications. Several approaches for the design of functionalisation SWNTs for molecular imaging reported in the current literature are highlighted. Techniques and facilities for accessing cell imaging ability and behavior of these synthesized molecular imaging probes, including confocal laser scanning microscopy (CLSM) and fluorescence-lifetime imaging microscopy (FLIM) are described briefly. Chapter two explores the synthesis of specifically designed naphthalene diimide (NDI). These molecules are known to form 3 dimensional (3D) helical organic nanotubes through hydrogen bonding. In this work an iodine-tagged NDI was allowed to self-assemble onto the surface of SWNTs. The cavities of the NDI organic nanotubes can accommodate SWNTs strands in their hydrophobic interior as observed high-resolution transmission electron microscopy (HR TEM). A new hybrid material, NDI@SWNT, was prepared and characterised as dispersed in organic solvents and aqueous media and in the solid state by HR TEM, tapping mode atomic force microscopy (TM AFM), scanning electron microscopy (SEM), circular dichroism, Raman and fluorescence spectroscopies (steady-state single and two-photon techniques). These measurements indicate that amino acid-functionalised NDI interacts strongly with SWNTs in dispersions and forms a donor-acceptor complex denoted NDI@SWNT. The interaction of this nanohybrid with cancer cells was explored using fluorescence microscopies. Chapter three describes the synthesis of series of molecular imaging agents based on two cancer targeting peptides (bombesin and RGDfK). Two types of NDIpeptide conjugates (Iodine-tagged NDI-Bombesin and Tryptophan-NDI-RGDfK) were designed and synthesized through EDC-coupling method. New compounds synthesized were characterised by mass spectroscopy and also HPLC. Fluorescence lifetime imaging microcopy and confocal laser scanning microscopy were utilised for investigating cellular behaviors (stability, fluorescence intensity and localization) of these molecular imaging probes. Chapter four describes the synthesis of amphiphilic conjugated thiophenes (dodecathiophene, denoted as T12). In this system, the thiophene backbone structure was chosen as a biocompatible coating for carbon nanotubes as simple molecular mechanics modeling suggested that it would be perfectly fitted to the curvature of SWNTs. T12 showed very good capability for debundling of SWNTs and forming corresponding solution dispersions of T12@SWNTs describes the potential of T12@SWNTs as a stable fluorescent bioimaging nano-probe for tracking cancer cells. Chapter five describes the successful filling of SWNTs with Cu2+ by radiochemistry methods (using 'hot' 64Cu ions anchored onto NaOAc) and also by a 'cold' optimised procedure for excess Cu(OAc)2. Filling with other metal ions was also tested, for example KReO4 and Zr(OAc)4. The filling experiments with Zr(OAc)4 in solution did not prove successful at normal pH but results were promising when pH was adjusted to ca. 2 by adding H2SO4. Any significant leakage of metal ions from open SWNTs was avoided by a simultaneous encapsulation of C70 molecules at the ends of SWNTs. Functionalisation of SWNTs by the supramolecular wrapping the surface of SWNTs in aqueous media with a naturally occurring glucan (β-1,3-1,4-Dglucan, denoted here as β-D-glucan) was also explored. Several boronic acid fluorophores were successfully synthesized and tested for the labeling of β-D-glucan @SWNTs by molecular recognition between boronic acids and this polysaccharide. Their cellular translocation behaviour and fluorescence properties were investigated by confocal fluorescence imaging and fluorescence lifetime imaging. Both methods show that localisation in sub-cellular (MCF-7 cells) regions and that the glucan coating significantly enhances the cell membrane translocation of SWNTs. Chapter six reports an efficient and economical strategy of supramolecular complex formulation of thermally reduced graphene. Naphthalene diimide (NDI) was used to form a stable and energy transfer complex which showed efficient quenching and significant red-shift of fluorescence of NDI when adsorbed onto graphene surfaces. The effect of thermally reducing annealing procedure to convert graphene oxides in graphene-nanoflake like materials was investigated. A new hybrid material (denoted here as NDI@TRG) synthesized was characterised by transmission electron microscopy (TEM), Raman spectroscopy, thermogravimetric analysis (TGA) and fluorescence microscopy in the dispersed phase Chapter seven contains full experimental details for the work described in this thesis. The Appendix contains details of the crystallographic data and supplementary information on cell imaging photos and fluorescence lifetime point decay data for SWNT nanocomposites.