Ultra-high Throughput Real-time Instruments for Capturing Fast Signals and Rare Events

Wide-band signals play important roles in the most exciting areas of science, engineering, and medicine. To keep up with the demands of exploding internet traffic, modern data centers and communication networks are employing increasingly faster data rates. Wide-band techniques such as pulsed radar jamming and spread spectrum frequency hopping are used on the battlefield to wrestle control of the electromagnetic spectrum. Neurons communicate with each other using transient action potentials that last for only milliseconds at a time. And in the search for rare cells, biologists flow large populations of cells single file down microfluidic channels, interrogating them one-by-one, tens of thousands of times per second. Studying and enabling such high-speed phenomena pose enormous technical challenges. For one, parasitic capacitance inherent in analog electrical components limits their response time. Additionally, converting these fast analog signals to the digital domain requires enormous sampling speeds, which can lead to significant jitter and distortion. State-of-the-art imaging technologies, essential for studying biological dynamics and cells in flow, are limited in speed and sensitivity by finite charge transfer and read rates, and by the small numbers of photo-electrons accumulated in short integration times. And finally, ultra-high throughput real-time digital processing is required at the backend to analyze the streaming data. In this thesis, I discuss my work in developing real-time instruments, employing ultrafast optical techniques, which overcome some of these obstacles. In particular, I use broadband dispersive optics to slow down fast signals to speeds accessible to high-bit depth digitizers and signal processors. I also apply telecommunication multiplexing techniques to boost the speeds of confocal fluorescence microscopy. The photonic time stretcher (TiSER) uses dispersive Fourier transformation to slow down analog signals before digitization and processing. The act of time-stretching effectively boosts the performance of the back-end electronics and digital signal processors. The slowed down signals reach the back-end electronics with reduced bandwidth, and are therefore less affected by high-frequency roll-off and distortion. Time-stretching also increases the effective sampling rate of analog-to-digital converters and reduces aperture jitter, thereby improving resolution. Finally, the instantaneous throughputs of digital signal processors are enhanced by the stretch factor to otherwise unattainable speeds. Leveraging these unique capabilities, TiSER becomes the ideal tool for capturing high-speed signals and characterizing rare phenomena. For this thesis, I have developed techniques to improve the spectral efficiency, bandwidth, and resolution of TiSER using polarization multiplexing, all-optical modulation, and coherent dispersive Fourier transformation. To reduce the latency and improve the data handling capacity, I have also designed and implemented a real-time digital signal processing electronic backend, achieving 1.5 tera-bit per second instantaneous processing throughput. Finally, I will present results from experiments highlighting TiSER's impact in real-world applications. Confocal fluorescence microscopy is the most widely used method for unveiling the molecular composition of biological specimens. However, the weak optical emission of fluorescent probes and the tradeoff between imaging speed and sensitivity is problematic for acquiring blur-free images of fast phenomena and cells flowing at high speed. Here I introduce a new fluorescence imaging modality, which leverages techniques from wireless communication to reach record pixel and frame rates. Termed Fluorescence Imaging using Radio-frequency tagged Emission (FIRE), this new imaging modality is capable of resolving never before seen dynamics in living cells - such as action potentials in neurons and metabolic waves in astrocytes - as well as performing high-content image assays of cells and particles in high-speed flow