Dynamically reconfigurable bio-inspired hardware

During the last several years, reconfigurable computing devices have experienced an impressive development in their resource availability, speed, and configurability. Currently, commercial FPGAs offer the possibility of self-reconfiguring by partially modifying their configuration bitstream, providing high architectural flexibility, while guaranteeing high performance. These configurability features have received special interest from computer architects: one can find several reconfigurable coprocessor architectures for cryptographic algorithms, image processing, automotive applications, and different general purpose functions. On the other hand we have bio-inspired hardware, a large research field taking inspiration from living beings in order to design hardware systems, which includes diverse topics: evolvable hardware, neural hardware, cellular automata, and fuzzy hardware, among others. Living beings are well known for their high adaptability to environmental changes, featuring very flexible adaptations at several levels. Bio-inspired hardware systems require such flexibility to be provided by the hardware platform on which the system is implemented. In general, bio-inspired hardware has been implemented on both custom and commercial hardware platforms. These custom platforms are specifically designed for supporting bio-inspired hardware systems, typically featuring special cellular architectures and enhanced reconfigurability capabilities; an example is their partial and dynamic reconfigurability. These aspects are very well appreciated for providing the performance and the high architectural flexibility required by bio-inspired systems. However, the availability and the very high costs of such custom devices make them only accessible to a very few research groups. Even though some commercial FPGAs provide enhanced reconfigurability features such as partial and dynamic reconfiguration, their utilization is still in its early stages and they are not well supported by FPGA vendors, thus making their use difficult to include in existing bio-inspired systems. In this thesis, I present a set of architectures, techniques, and methodologies for benefiting from the configurability advantages of current commercial FPGAs in the design of bio-inspired hardware systems. Among the presented architectures there are neural networks, spiking neuron models, fuzzy systems, cellular automata and random boolean networks. For these architectures, I propose several adaptation techniques for parametric and topological adaptation, such as hebbian learning, evolutionary and co-evolutionary algorithms, and particle swarm optimization. Finally, as case study I consider the implementation of bio-inspired hardware systems in two platforms: YaMoR (Yet another Modular Robot) and ROPES (Reconfigurable Object for Pervasive Systems); the development of both platforms having been co-supervised in the framework of this thesis

Fast fluorescence lifetime imaging and sensing via deep learning

Error on title page – year of award is 2023.Fluorescence lifetime imaging microscopy (FLIM) has become a valuable tool in diverse disciplines. This thesis presents deep learning (DL) approaches to addressing two major challenges in FLIM: slow and complex data analysis and the high photon budget for precisely quantifying the fluorescence lifetimes. DL's ability to extract high-dimensional features from data has revolutionized optical and biomedical imaging analysis. This thesis contributes several novel DL FLIM algorithms that significantly expand FLIM's scope. Firstly, a hardware-friendly pixel-wise DL algorithm is proposed for fast FLIM data analysis. The algorithm has a simple architecture yet can effectively resolve multi-exponential decay models. The calculation speed and accuracy outperform conventional methods significantly. Secondly, a DL algorithm is proposed to improve FLIM image spatial resolution, obtaining high-resolution (HR) fluorescence lifetime images from low-resolution (LR) images. A computational framework is developed to generate large-scale semi-synthetic FLIM datasets to address the challenge of the lack of sufficient high-quality FLIM datasets. This algorithm offers a practical approach to obtaining HR FLIM images quickly for FLIM systems. Thirdly, a DL algorithm is developed to analyze FLIM images with only a few photons per pixel, named Few-Photon Fluorescence Lifetime Imaging (FPFLI) algorithm. FPFLI uses spatial correlation and intensity information to robustly estimate the fluorescence lifetime images, pushing this photon budget to a record-low level of only a few photons per pixel. Finally, a time-resolved flow cytometry (TRFC) system is developed by integrating an advanced CMOS single-photon avalanche diode (SPAD) array and a DL processor. The SPAD array, using a parallel light detection scheme, shows an excellent photon-counting throughput. A quantized convolutional neural network (QCNN) algorithm is designed and implemented on a field-programmable gate array as an embedded processor. The processor resolves fluorescence lifetimes against disturbing noise, showing unparalleled high accuracy, fast analysis speed, and low power consumption.Fluorescence lifetime imaging microscopy (FLIM) has become a valuable tool in diverse disciplines. This thesis presents deep learning (DL) approaches to addressing two major challenges in FLIM: slow and complex data analysis and the high photon budget for precisely quantifying the fluorescence lifetimes. DL's ability to extract high-dimensional features from data has revolutionized optical and biomedical imaging analysis. This thesis contributes several novel DL FLIM algorithms that significantly expand FLIM's scope. Firstly, a hardware-friendly pixel-wise DL algorithm is proposed for fast FLIM data analysis. The algorithm has a simple architecture yet can effectively resolve multi-exponential decay models. The calculation speed and accuracy outperform conventional methods significantly. Secondly, a DL algorithm is proposed to improve FLIM image spatial resolution, obtaining high-resolution (HR) fluorescence lifetime images from low-resolution (LR) images. A computational framework is developed to generate large-scale semi-synthetic FLIM datasets to address the challenge of the lack of sufficient high-quality FLIM datasets. This algorithm offers a practical approach to obtaining HR FLIM images quickly for FLIM systems. Thirdly, a DL algorithm is developed to analyze FLIM images with only a few photons per pixel, named Few-Photon Fluorescence Lifetime Imaging (FPFLI) algorithm. FPFLI uses spatial correlation and intensity information to robustly estimate the fluorescence lifetime images, pushing this photon budget to a record-low level of only a few photons per pixel. Finally, a time-resolved flow cytometry (TRFC) system is developed by integrating an advanced CMOS single-photon avalanche diode (SPAD) array and a DL processor. The SPAD array, using a parallel light detection scheme, shows an excellent photon-counting throughput. A quantized convolutional neural network (QCNN) algorithm is designed and implemented on a field-programmable gate array as an embedded processor. The processor resolves fluorescence lifetimes against disturbing noise, showing unparalleled high accuracy, fast analysis speed, and low power consumption