I investigate the use of vertical cavity surface emitting lasers (VCSELs) for portable optical neural imaging. In particular, I attempt to use one laser source to produce the different illumination needed for three techniques, imaging flow, oxygenation, and fluorescence. Our group's goal is to combine these techniques using a single source in a simple imaging format, which can be modified for portable use in awake animals. We exploit tuning properties of VCSELs to implement two distinct operation schemes with different illumination characteristics. Single mode operation provides high speckle contrasts, used to map flow speeds in laser speckle contrast imaging (LSCI). Sweep operation provides low noise, allowing us to image small signal changes with intrinsic optical signal imaging (IOSI), which relate to blood oxygenation. Finally, we use our VCSEL devices for on-chip integrated fluorescence sensing. Future work aims to develop a fully portable format, using CMOS detectors and integrated circuit control.

I investigate the use of vertical cavity surface emitting lasers (VCSELs) for portable optical neural imaging. In particular, I attempt to use one laser source to produce the different illumination needed for three techniques, imaging flow, oxygenation, and fluorescence. Our group's goal is to combine these techniques using a single source in a simple imaging format, which can be modified for portable use in awake animals. We exploit tuning properties of VCSELs to implement two distinct operation schemes with different illumination characteristics. Single mode operation provides high speckle contrasts, used to map flow speeds in laser speckle contrast imaging (LSCI). Sweep operation provides low noise, allowing us to image small signal changes with intrinsic optical signal imaging (IOSI), which relate to blood oxygenation. Finally, we use our VCSEL devices for on-chip integrated fluorescence sensing. Future work aims to develop a fully portable format, using CMOS detectors and integrated circuit control.

An SOI-based platform designed for wideband coupling of light from optical fibers to a 50 nm wide plasmonic slot waveguide is described in this thesis. The device is based on a newly proposed orthogonal junction with coupling efficiencies above 70% near the telecom wavelength. To construct the coupling platform, two such junctions are utilized for input and output, where Si wires are place 90 degree with respect to each of the two ends of a plasmonic section. Analytic studies and FDTD simulations have demonstrated attractive properties such as a smooth micron-wide transmission spectrum that can be spectrally shifted with the design parameters, and the natural phase-matching between the dielectric and plasmonic sections consequent of the waveguide orientations. Fabrication procedures and proof-of-concept characterization work are also presented. The experimentally-tested platform with its unique features would enable applications in on-chip sensing and plasmonic slot-based waveguiding at the 50 nm scale.

Photonic crystal slabs (PCS) are explored in the context of optofluidic refractive index (RI) sensing for portable, label-free, biosensing applications. The accuracy of RI sensors is limited by noise signals that cause a change in RI that cannot be differentiated from the signal of interest. For this reason self-referencing schemes that provide rejection of common mode signals, and an inherent temperature stabilization approach, are explored. A novel referencing method that allows for frequency shifts to be read out in the transmission power spectrum is proposed and characterized. In terms of improving sensing metrics the relevant characteristics of various PCS architectures are explored numerically. In addition, a novel suspended \emph{air-substrate} device that offers greatly improved sensitivity is proposed and characterized. An experimental measurement near the theoretical detection limit for a PCS is demonstrated. In understanding measurement errors the crossed-polarization effect and its practical limitations are explored numerically.

An SOI-based platform designed for wideband coupling of light from optical fibers to a 50 nm wide plasmonic slot waveguide is described in this thesis. The device is based on a newly proposed orthogonal junction with coupling efficiencies above 70% near the telecom wavelength. To construct the coupling platform, two such junctions are utilized for input and output, where Si wires are place 90 degree with respect to each of the two ends of a plasmonic section. Analytic studies and FDTD simulations have demonstrated attractive properties such as a smooth micron-wide transmission spectrum that can be spectrally shifted with the design parameters, and the natural phase-matching between the dielectric and plasmonic sections consequent of the waveguide orientations. Fabrication procedures and proof-of-concept characterization work are also presented. The experimentally-tested platform with its unique features would enable applications in on-chip sensing and plasmonic slot-based waveguiding at the 50 nm scale.

Photonic crystal slabs (PCS) are explored in the context of optofluidic refractive index (RI) sensing for portable, label-free, biosensing applications. The accuracy of RI sensors is limited by noise signals that cause a change in RI that cannot be differentiated from the signal of interest. For this reason self-referencing schemes that provide rejection of common mode signals, and an inherent temperature stabilization approach, are explored. A novel referencing method that allows for frequency shifts to be read out in the transmission power spectrum is proposed and characterized. In terms of improving sensing metrics the relevant characteristics of various PCS architectures are explored numerically. In addition, a novel suspended \emph{air-substrate} device that offers greatly improved sensitivity is proposed and characterized. An experimental measurement near the theoretical detection limit for a PCS is demonstrated. In understanding measurement errors the crossed-polarization effect and its practical limitations are explored numerically.

We present, for the first time, methods to model and control the polarization of the output lightwave of a bidirectional fiber-optic system, in which the lightwave propagates through polarization control elements in both directions. Using the dynamic eigenstate (DES) principle, we built model to simulate the behavior of the polarization evolution. In a bidirectional system with one control element, we extracted system parameters from experimental data and achieved less than 3% angular deviation between modeled and experimental state of polarization (SOP). The theory was further validated by varying the input SOP to the bidirectional system. Our method can be extended to predict the SOP of a system with multiple actuators. Furthermore, combining our deterministic control method and a feedback loop, we are able to control the output SOP to be within a mean angular deviation of 5.5% from the target SOP, with as few as three iterations.

Cancer cells require access to blood vessels for oxygen and nutrients to enable growth and metastasis, making the tumour vasculature an attractive potential target for cancer therapies. Recent evidence suggests that the tumour vasculature plays a significant role in tumour response to high dose radiation therapy; however this effect is not well characterized due to limitations in quantitative imaging of the microvasculature. Speckle variance optical coherence tomography is an emerging imaging modality capable of 3D, non-invasive imaging of in vivo microvasculature. This thesis outlines the work done to test the hypothesis that svOCT imaging can be used to quantitatively monitor the vascular effects of high dose radiotherapy in a preclinical model. This was achieved through the development of a quantification pipeline for longitudinal 3-D svOCT images of microvascular radioresponse.

We present, for the first time, methods to model and control the polarization of the output lightwave of a bidirectional fiber-optic system, in which the lightwave propagates through polarization control elements in both directions. Using the dynamic eigenstate (DES) principle, we built model to simulate the behavior of the polarization evolution. In a bidirectional system with one control element, we extracted system parameters from experimental data and achieved less than 3% angular deviation between modeled and experimental state of polarization (SOP). The theory was further validated by varying the input SOP to the bidirectional system. Our method can be extended to predict the SOP of a system with multiple actuators. Furthermore, combining our deterministic control method and a feedback loop, we are able to control the output SOP to be within a mean angular deviation of 5.5% from the target SOP, with as few as three iterations.

Cancer cells require access to blood vessels for oxygen and nutrients to enable growth and metastasis, making the tumour vasculature an attractive potential target for cancer therapies. Recent evidence suggests that the tumour vasculature plays a significant role in tumour response to high dose radiation therapy; however this effect is not well characterized due to limitations in quantitative imaging of the microvasculature. Speckle variance optical coherence tomography is an emerging imaging modality capable of 3D, non-invasive imaging of in vivo microvasculature. This thesis outlines the work done to test the hypothesis that svOCT imaging can be used to quantitatively monitor the vascular effects of high dose radiotherapy in a preclinical model. This was achieved through the development of a quantification pipeline for longitudinal 3-D svOCT images of microvascular radioresponse.