Molecular imaging plays an important role for development of systems biomedicine, which non-invasively extracts pictorial information on physiological and pathological activities at the cellular and molecular levels. Optical molecular tomography is an emerging area of molecular imaging. It locates and quantifies a 3D molecular probe distribution in vivo from data measured on the external surface of a small animal around the visible and infrared range. This approach can facilitate or enable preclinical applications such as cancer studies, involving angiogenesis, tumor growth, cell motility, metastasis, and interaction with a micro-environment. The reconstruction of diffuse light sources is the central task of optical molecular tomography, and generally ill-posed and rather complex. The key element of optical molecular tomography includes the geometrical model, tissue properties, photon characteristics, transport model, and reconstruction algorithm. This dissertation focuses mainly on the development optical molecular tomography methods based on bioluminescence/fluorescence probes to solve some well-known challenges in this field. Our main results are as follows. We developed a new algorithm for estimation of optical parameters based on the phase-approximation model.  Our iterative algorithm takes advantage of both the global search ability of the differential evolution algorithm and the efficiency of the conjugate gradient method. We published the first paper on multispectral bioluminescence tomography (BLT). The multispectral BLT approach improves the accuracy and stability of the BLT reconstruction even if data are highly noisy. We established a well-posed inverse source model for optical molecular tomography. Based on this model, we proposed a differential evolution-based reconstruction algorithm to determine the source locations and strengths accurately and reliably. Furthermore, to enhance the spatial resolution of fluorescence molecular tomography, we proposed fluorescence micro-tomography to image cells in a tissue scaffold based on Monte Carlo simulation on a massive parallel processing architecture. Each of these methods shows better performance in numerical simulation, phantom experiments, and mouse studies than the conventional methods. / Ph. D.

xv, 215 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / In this dissertation, several new methods for the measurement and control of transverse photonic degrees of freedom are developed. We demonstrate a mode sorter for two-dimensional (2-D) parity of transverse spatial states of light based on an out-of-plane Sagnac interferometer. The first experimental 2-D parity sorting measurements of Hermite-Gauss transverse spatial modes are presented. Due to the inherent phase stability of this type of interferometer, it provides a promising tool for the manipulation of higher order transverse spatial modes for the purposes of quantum information processing. We propose two such applications: the production of both spatial-mode entangled Bell states and heralded single photons, tailored to cover the entire Poincaré sphere of first-order transverse modes. In addition to the aforementioned transverse spatial manipulation based on free-space parity sorting, we introduce several more such techniques involving photons propagating in optical fibers. We show that when a photon propagates in a cylindrically symmetric waveguide, its spin angular momentum and its orbital angular momentum (OAM) interact. This spin-orbit interaction (SOI) leads to the prediction of several novel rotational effects: the spatial or time evolution of the photonic polarization vector is controlled by its OAM quantum number or, conversely, its spatial wave function is controlled by its spin. We demonstrate how these phenomena can be used to reversibly transfer entanglement between the spin and OAM degrees of freedom of two-particle states. In order to provide a deeper insight into the cause of the SOI for photons, we also investigate an analogous interaction for electrons in a cylindrical waveguide and find that each of the SOI effects mentioned above remain manifest for the electron case. We show that the SOI dynamics are quantitatively described by a single expression applying to both electrons and photons and explain their common origin in terms of a universal geometric phase associated with the interplay between either particle's spin and OAM. This implies that these SOI-based effects occur for any particle with spin and thereby exist independently of whether or not the particle has mass, charge, or magnetic moment. / Committee in charge: Daniel Steck, Chairperson, Physics; Michael Raymer, Member, Physics; Jens Noeckel, Member, Physics; Steven van Enk, Member, Physics; Andrew Marcus, Outside Member, Chemistry