Image-based single cell analysis is essential to study gene expression levels and subcellular functions with preserving the native spatial locations of biomolecules. However, its low throughput has prevented its wide use to fundamental biology and biomedical applications which require large cellular populations in a rapid and efficient fashion. Here, we report a 2.5D microcopy (2.5DM) that significantly improves the image acquisition rate while maintaining high-resolution and single molecule sensitivity. Unlike serial z-scanning in conventional approaches, volumetric information is simultaneously projected onto a 2D image plane in a single shot by engineering the fluorescence light using a novel phase pattern. The imaging depth can be flexibly adjusted and multiple fluorescent markers can be readily visualized. We further enhance the transmission efficiency of 2.5DM by ~2-fold via configuring the spatial light modulator used for the phase modulation in a polarization-insensitive manner. Our approach provides a uniform focal response within a specific imaging depth, allowing to perform quantitative high-throughput single-molecule RNA measurements for mammalian cells over a 2 x 2 mm2 region within an imaging depth of ~5 µm in less than 10 min and immunofluorescence imaging at a volumetric imaging rate of > 30 Hz with significantly reduced light exposure. With implementation of an adaptive element, our microscope provides an extra degree of freedom in correcting aberrations induced by specimens and optical components, showing its capability of imaging thick specimens with high-fidelity of preserving volumetric information with fast imaging speed. We also demonstrate multimodal imaging that can be switched from 2.5DM to a 3D single-molecule localization imaging platform by encoding the depth information of each emitter into the shape of point spread function, which enables us to obtain a resolution of < 50 nm. Our microscope offers multi-functional capability from fast volumetric high-throughput imaging, multi-color imaging to super-resolution imaging.

Production of high repetition rate, high energy pulses at an eye safe wavelength has become a topic of interest for emerging technologies. 1.5 µm is an eye safe wavelength that is used extensively in telecom and erbium doped fiber amplifiers (EDFA) are common. EDFAs however, have difficulties producing high energy, higher repetition rate pulsed systems with low efficiencies due to quantum defect [1]. A proposed solution is to produce a diamond Raman laser that is seeded with a pulsed 1064 nm source. The thesis covers the design and build of the seed for the diamond Raman laser. The project requires five separate pulsed seed systems to be built, and then combined and further amplified to then be used in a diamond Raman laser. The system needs to be portable and easily reproduced while limiting size, weight, power, costs, and complexity. A common design when building a pulsed laser system, is the Master Oscillator Power Amplifier (MOPA) design. The MOPA design allows for flexibility through a tunable oscillator and multiple amplification stages which is why it is chosen for the initial design. In this thesis, a MOPA is built to provide pulsed output with a 10-20 ns pulse width, > 2 mJ energy, and 10 kHz repetition rate. The design used Nd:YVO4 as the active material in the oscillator and Ytterbium doped fiber amplifiers (YDFA). Pulses are generated using an Acousto-Optic Modulator (AOM) within the oscillator. The thesis covers the build and design of the oscillator and the first fiber amplifier with the second amplifier to be built in future experiments. The system is tested at each stage of the build and issues that arose during testing are documented along with the solutions created to fix the system and ways to enhance it in the future.

The push to study the atomic and molecular dynamics at ever smaller time scales has been the main driving force for developing laser systems with ever shorter pulse durations. Thus far, picosecond lasers and femtosecond lasers have been used with great success in femtochemistry to study molecular dynamics such as molecular rotation and vibration, which all occur in the tens to hundreds of femtosecond. To study electron dynamics however, which are on the order of attoseconds, one needs attosecond laser sources to be able to have the time resolution required to probe ultrafast electron dynamics such as AC Stark shifts, Rabi oscillations and other more complex dynamics such as charge migration. By using few-cycle Titanium:Sapphire femtosecond lasers focused tightly into a generating gas like argon and neon, extreme ultraviolet spectra could be produce through high harmonic generation (HHG). Initial attosecond light sources based on Titanium:Sapphire sources produced HHG spectra up to 150 eV. In order to be able to probe the inner valence shells of atoms and molecules, increasing the cutoff energy of the harmonic spectra becomes necessary. Since the harmonic cutoff energy scales with the square of λ2, longer wavelength driving lasers were developed to increase the harmonic cutoff energies. However, since the harmonic yield at constant laser intensity scales with ~λ-6, thus driving laser photon flux must also increase as the driving laser wavelength increases. It is for this reason that in our lab, a 3 mJ 1.7 µm optical parametric-chirp pulse amplification (OPCPA) laser system was developed and the spectra can reach as high as 450 eV using helium as the generating gas. A number of numerical simulations were done to make suggested improvements to the OPCPA and the DFG seed source. The Titanium:Sapphire amplifiers for the OPCPA were rebuilt from a three-stage system to a two-stage system while producing similar output pulse energies after compression. This laser system will thus be more stable and maintenance will be easier. In this work, an OPCPA system which delivers CEP stable 2 mJ 12-fs pulses centered at 1.7 µm was used to conduct experiments near the water window. This system was used to study below-threshold harmonics produced in Argon, to perform Attosecond Transient Absorption Spectroscopy (ATAS) of Argon at 249 eV and to develop the semi-infinite gas cell which is a high flux soft x-ray source.

Micro-scale light emitting diode (micro-LED) is a potentially disruptive display technology because of its outstanding features such as high dynamic range, good sunlight readability, long lifetime, low power consumption, and wide color gamut. To achieve full-color displays, three approaches are commonly used: 1) to assemble individual RGB micro-LED pixels from semiconductor wafers to the same driving backplane through pick-and-place approach, which is referred to as mass transfer process; 2) to utilize monochromatic blue micro-LED with a color conversion film to obtain a white source first, and then employ color filters to form RGB pixels, and 3) to use blue or ultraviolet (UV) micro-LEDs to pump pixelated quantum dots (QDs). This dissertation is devoted to investigating and improving optical performance of these three types of micro-LED displays from device design viewpoints. For RGB micro-LED display, angular color shift may become visually noticeable due to mismatched angular distributions between AlGaInP-based red micro-LED and InGaN-based blue/green counterparts. Based on our simulations and experiments, we find that the mismatched angular distributions are caused by sidewall emission from RGB micro-LEDs. To address this issue, we propose a device structure with top black matrix and taper angle in micro-LEDs, which greatly suppresses the color shift while keeping a reasonably high light extraction efficiency. These findings will shed new light to guide future micro-LED display designs. For white micro-LEDs, the color filters would absorb 2/3 of the outgoing light, which increases power consumption. In addition, color crosstalk would occur due to scattering of the color conversion layer. With funnel-tube array and reflective coating on its inner surface, the crosstalk is eliminated and the optical efficiency is enhanced by ~3X. For quantum dot-converted micro-LED display, its ambient contrast ratio degrades because the top QD converter can be excited by the ambient light. To solve this issue, we build a verified simulation model to quantitatively analyze the ambient reflection of quantum dot-converted micro-LED system and improve its ambient contrast ratio with a top color filter layer.

Passive devices and amplifiers for space division multiplexing are key components for future deployment of this technology and for the development of new applications exploring the spatial diversity of light. Some important devices include photonic lantern (PL) mode multiplexers supporting several modes, fan-in/fan-out (FIFO) devices for multicore fibers (MCFs), and multimode amplifiers capable of amplifying several modes with low differential modal gain penalty. All these components are required to overcome the capacity limit of single mode fiber (SMF) communication systems, driven by the growing data capacity demand. In this dissertation I propose and develop different passive components and amplifiers for space division multiplexing technologies, including PL mode multiplexers with low insertion loss and low mode dependent loss to excite different number of modes into few mode fibers (FMFs). I demonstrate a PL with a graded index core that better matches the mode profiles of a graded index FMF supporting six spatial modes with mode dependent loss (MDL) ranging from 2- to 3-dB over the entire C-band. Multicore fibers can alleviate the capacity limit of single mode fibers by placing multiple single mode cores within the same fiber cladding. However, interfacing single mode fibers to MCFs can be challenging due to physical limitations, in this dissertation I develop and fabricate different types of FIFO devices to couple light into MCFs with high efficiency and having up to 19 cores. I demonstrate high coupling efficiency with insertion loss below 0.5 dB per FIFO into a 4-core MCF and below 1 dB for a 19-core MCF. Multimode erbium doped fiber (EDF) amplifiers are required to amplify each mode within the few mode transmission fiber, the main challenge is to provide an amplifier with low differential modal gain, in this dissertation I present the first coupled-core amplifier concept compatible with FMFs. A 6-core coupled-core EDF can be spliced with low insertion and low MDL to a FMF supporting 6 spatial modes via a slight taper transition. The amplifier introduces 1.8 MDL with gain variation over the entire C-band below 1-dB.

Free-space optical (FSO) communication has become very popular for wireless applications to complement and, in some cases, replace legacy radio-frequency for advantages like unlicensed band, spatial reuse, and enhanced security. Even though FSO can achieve very high bit-rate (tens of Gbps), range limitation due to high attenuation and weather dependency has always restricted its practical implementation to indoor application like data centers and outdoor application like Project Loon. Building-to-building communication, smart cars, and airborne drones are potential futuristic wireless communication sectors for mobile ad-hoc FSO networking. Increasing social media usage demands high-speed mobile connectivity for applications like video call and live video stream on the go. For these scenarios, implementation of in-band full-duplex FSO (IBFD-FSO) transceivers will potentially double the network capacity to improve performance and reliability of the communication link. In this work, we focus on implementing prototypes of FSO transceivers on mobile platform using both off-the-shelf and customized components. Current goal is to implement a prototype of IBFD-FSO transceiver using VCSEL as transmitter and PIN photodiode as receiver at 900 nm wavelength. We are considering atmospheric attenuation, FSO beam propagation model, geometry, and tiling of the components to optimize the link performance while keeping the package low-cost and mobile, ensuring connectivity to mass population. Eventually, our goal is to have communication between multiple airborne drones through IBFD-FSO transceivers by discovering each other and maintaining established link. Applications of this research is not only limited to the conceived idea of smart cities, but it can also have real impact on disaster management in times of wildfire or hurricane.

Transverse Mode Instabilities (TMIs) stand as a fundamental limitation to power and brightness scaling in laser systems based upon optical fiber technologies. This work comprises experimental and theoretical investigations into fiber laser design that should minimize the effects of Stimulated Thermal Rayleigh Scattering. Theoretical discussions and simulations focus on how fiber parameters affect transverse mode coupling. These include core geometry optimization, pump geometry optimization, in addition to the effects of HOM content and losses on the TMI threshold. Experimentally, a high-power laser facility is commissioned with beam quality diagnostics to quantify the thresholds of the onset of modal interferences and their impacts on beam quality. These diagnostics include high-resolution Fourier Transform Interferometry (FTI) and in-situ power-in-the-bucket measurements. The design and characterization capabilities developed here are crucial to the development of next-generation high-power fiber laser capabilities.

Fluorescence microscopy has long been a valuable tool for biological and medical imaging. Control of optical parameters such as the amplitude, phase, polarization and propagation angle of light gives fluorescence imaging great capabilities ranging from single molecule imaging to long-term observation of living organisms. While numerous fluorescence imaging techniques have been developed over the past decades, there is always an inevitable tradeoff among the spatial resolution, imaging speed, contrast, photodamage and the total cost when it comes to choose the appropriate microscope. A main goal of my dissertation research is to develop state-of-the-art microscope systems that exhibit unprecedented performance in single-molecule fluorescence imaging and live-cell imaging for broader biomedical applications by tailoring the optical illumination beams. In details, I have designed and prototyped: 1) a highly inclined swept illumination for wide-field fluorescence microscope, which greatly improves the sectioning capability with a large field of view and ultrasensitivity; 2) dual inclined line-scan confocal microscope, which reduces photodamage while maintaining the background rejection capability compared to conventional line-scan confocal microscope; 3) a static non-diffracting light-sheet generation by controlling the spatial coherence of light emitting diodes and laser.

Mode-locked lasers have numerous applications in the areas of communications, spectroscopy, and frequency metrology. Harmonically mode-locked semiconductor lasers with external ring cavities offer a unique combination of benefits in that they can produce high repetition rate pulse trains with low timing jitter, achieve narrow axial mode linewidths, have the potential for entire monolithic integration on-chip, feature high wall-plug efficiency due to direct electrical pumping, and can be engineered to operate in different wavelength bands of interest. However, lasers based on InP/InGaAsP quantum well devices which operate in the important telecom C-band have thus far been relatively limited in bandwidth as compared to competing platforms. Broad bandwidth is critical for increasing information carrying capacity and enabling femtosecond pulse production for coherent continuum generation in offset frequency stabilization. The goal of the work in this dissertation is to maximize the bandwidth of semiconductor lasers, bringing them closer to reaching their full potential as all-purpose sources. Dispersion in the laser cavity is a primary limiter of the achievable bandwidth in the laser architectures covered in this dissertation. In the first part of this dissertation, an accurate self-referenced technique based on multi-heterodyne detection is developed for measuring the spectral phase of a mode-locked laser. This technique is used to characterize the dispersion in several semiconductor laser architectures. In the second part, this knowledge is applied to reduce the dispersion in a laser cavity using a programmable pulse shaper, and thus increase the laser's spectral bandwidth. We demonstrate a 10 GHz frequency comb with bandwidth spanning 5 THz, representing a twofold improvement over the previously achievable bandwidth. Finally, this laser is converted to a stand-alone system by reconfiguring it as a coupled opto-electronic oscillator and a novel stabilization scheme is presented.

Thin-film transistor (TFT) liquid crystal displays (LCDs) have become indispensable in our daily lives. Their widespread applications range from smartphones, laptops, TVs to navigational devices, data projectors and wearable displays. Over past decades, massive efforts have been invested in device development, material characterization and manufacturing technology. As a result, the performance of LCDs, such as viewing angle, contrast ratio, color gamut and resolution, have been improved significantly. Nonetheless, there are still urgent needs for fast response time and low power consumption. Fast response time helps reduce motion image blurs and enable color sequential displays. The latter is particularly attractive since it eliminates spatial color filters, which in turn triples optical efficiency and resolution density. The power consumption can be reduced greatly by using color sequential displays, but liquid crystals with submillisecond response time are required to minimize color breakup. The state-of-the-art gray-to-gray response time of nematic LCDs is about 5ms, which is too slow to meet this requirement. With the urgent needs for submillisecond response time, polymer-stabilized blue phase liquid crystal is emerging as a strong candidate for achieving this goal. Compared to conventional nematic LCDs, blue phase LCDs exhibit several revolutionary features: submillisecond gray-to-gray response time, no need for alignment layer, optically isotropic voltage-off state, and large cell gap tolerance. However, some bottlenecks such as high operation voltage, low optical transmittance, noticeable hysteresis and slow TFT charging remain to be overcome before their widespread applications can be realized. This dissertation is dedicated to addressing these challenges from material development and device design viewpoints. First, we started to investigate the device physics of blue phase LCDs. We have built a numerical model based on the refraction effect for simulating the electro-optics of blue phase devices. The model well agrees with experimental data. Based on this model, we explored approaches from device and material viewpoints to achieve low operation voltage. On the device side, with protrusion and etched electrodes, we can reduce the operating voltage to below 10V and enhance the transmittance to over 80%. On the material side, high Kerr constant is indeed helpful for lowering the operation voltage, but we also need to pay attention to the individual ?n and ?? values of liquid crystal host according to the device structures employed. High-?? LC hosts help enhance Kerr constant, leading to a reduced operation voltage; but they may be subject to serious capacitance charging issues due to the huge dielectric anisotropy. Our model provides important guidelines for future device design and material development. To further enhance transmittance and reduce voltage, we have proposed a Z-shaped electrode structure. By optimizing the device structure, we have successfully reduced the operating voltage to ~8V and enhanced optical transmittance to > 95% based on a lower-?? LC host not subjecting to charging issues, showing comparable or even better performance than the mainstream LCDs. This is the first approach to achieve such a high transmittance in blue phase devices without using a directional backlight. By using zigzag structure, the color shift and gray inversion are in unnoticeable range. In addition, hysteresis affects the accuracy of grayscale control and should be suppressed. We have proposed a double exponential model to analyze the electric field effects of blue phase, and found that electrostriction effect is the root cause for hysteresis under strong electric field. To suppress the electrostriction effect in blue phase, a method to stabilize the blue phase lattice via linear photo-polymerization is demonstrated for the first time. By illuminating the mono-functional and the di-functional monomers with a linearly polarized UV beam, we can form anisotropic polymer networks, which in turn lead to anisotropic electrostrictions. In experiments, we found that when the polarization of UV light is perpendicular to the stripe electrodes, the electrostriction effect can be strongly suppressed. The resulting hysteresis is reduced from 6.95% to 0.36% and response time is improved by a factor of two. We foresee this approach will guide future manufacturing process. The approaches and studies presented in this dissertation are expected to advance the blue phase LCDs to a new level and accelerate their emergence as next-generation display technology. It is foreseeable that the widespread application of blue phase LCDs is around the corner.