Characterization of a Single Photon Sensing and Photon Number Resolving CMOS Detector for Astrophysics

Next-generation NASA missions, such as the LUVIOR and HabEx concepts, require single photon counting large-format detectors. Charge Coupled Devices (CCDs) have typically been used for optical applications in similar flagship missions of the past. CCDs have excellent properties in most metrics but have their own challenges for single photon counting applications. First, typical CCDs have a read noise of a few electrons, although recent modifications (EMCCDs) use an on-chip gain to amplify the signal above the read noise. Secondly, the signal is carried by charge that is transferred across the detector array. While CCDs for NASA missions are carefully fabricated to minimize defects, continuous bombardment from high energy radiation in space will damage the detector over the lifetime of the mission. This will degrade the charge transfer efficiency and in turn, reduce the single photon counting ability of the CCD. CMOS devices offer a different architecture that mitigates some of these problems. In CMOS image sensors, each pixel has its own charge to voltage converter and in-pixel amplifier mitigating issues found with charge transfer efficiency. Additional circuits that are critical to operation of the sensor can be incorporated on chip allowing for a parallel readout architecture that increases frame rate and can decrease read noise. This thesis is a collection of work for the characterization of a room temperature characterization, low-noise, single photon counting and photon number resolving CMOS detector. The work performed in this thesis will provide the framework for a technology development project funded by NASA Cosmic Origins (COR) program office. At the end of the two-year project, a megapixel CMOS focal plane array will be demonstrated to satisfy the stated needs of the LUVOIR and HabEx future astrophysics space mission concepts with a launch date near the 2040s

A portable device for time-resolved fluorescence based on an array of CMOS SPADs with integrated microfluidics

[eng] Traditionally, molecular analysis is performed in laboratories equipped with desktop instruments operated by specialized technicians. This paradigm has been changing in recent decades, as biosensor technology has become as accurate as desktop instruments, providing results in much shorter periods and miniaturizing the instrumentation, moving the diagnostic tests gradually out of the central laboratory. However, despite the inherent advantages of time-resolved fluorescence spectroscopy applied to molecular diagnosis, it is only in the last decade that POC (Point Of Care) devices have begun to be developed based on the detection of fluorescence, due to the challenge of developing high-performance, portable and low-cost spectroscopic sensors. This thesis presents the development of a compact, robust and low-cost system for molecular diagnosis based on time-resolved fluorescence spectroscopy, which serves as a general-purpose platform for the optical detection of a variety of biomarkers, bridging the gap between the laboratory and the POC of the fluorescence lifetime based bioassays. In particular, two systems with different levels of integration have been developed that combine a one-dimensional array of SPAD (Single-Photon Avalanch Diode) pixels capable of detecting a single photon, with an interchangeable microfluidic cartridge used to insert the sample and a laser diode Pulsed low-cost UV as a source of excitation. The contact-oriented design of the binomial formed by the sensor and the microfluidic, together with the timed operation of the sensors, makes it possible to dispense with the use of lenses and filters. In turn, custom packaging of the sensor chip allows the microfluidic cartridge to be positioned directly on the sensor array without any alignment procedure. Both systems have been validated, determining the decomposition time of quantum dots in 20 nl of solution for different concentrations, emulating a molecular test in a POC device.[cat] Tradicionalment, l'anàlisi molecular es realitza en laboratoris equipats amb instruments de sobretaula operats per tècnics especialitzats. Aquest paradigma ha anat canviant en les últimes dècades, a mesura que la tecnologia de biosensor s'ha tornat tan precisa com els instruments de sobretaula, proporcionant resultats en períodes molt més curts de temps i miniaturitzant la instrumentació, permetent així, traslladar gradualment les proves de diagnòstic fora de laboratori central. No obstant això i malgrat els avantatges inherents de l'espectroscòpia de fluorescència resolta en el temps aplicada a la diagnosi molecular, no ha estat fins a l'última dècada que s'han començat a desenvolupar dispositius POC (Point Of Care) basats en la detecció de la fluorescència, degut al desafiament que suposa el desenvolupament de sensors espectroscòpics d'alt rendiment, portàtils i de baix cost. Aquesta tesi presenta el desenvolupament d'un sistema compacte, robust i de baix cost per al diagnòstic molecular basat en l'espectroscòpia de fluorescència resolta en el temps, que serveixi com a plataforma d'ús general per a la detecció òptica d'una varietat de biomarcadors, tancant la bretxa entre el laboratori i el POC dels bioassaigs basats en l'anàlisi de la pèrdua de la fluorescència. En particular, s'han desenvolupat dos sistemes amb diferents nivells d'integració que combinen una matriu unidimensional de píxels SPAD (Single-Photon Avalanch Diode) capaços de detectar un sol fotó, amb un cartutx microfluídic intercanviable emprat per inserir la mostra, així com un díode làser UV premut de baix cost com a font d'excitació. El disseny orientat a la detecció per contacte de l'binomi format pel sensor i la microfluídica, juntament amb l'operació temporitzada dels sensors, permet prescindir de l'ús de lents i filtres. Al seu torn, l'empaquetat a mida de l'xip sensor permet posicionar el cartutx microfluídic directament sobre la matriu de sensors sense cap procediment d'alineament. Tots dos sistemes han estat validats determinant el temps de descomposició de "quantum dots" en 20 nl de solució per a diferents concentracions, emulant així un assaig molecular en un dispositiu POC

Miniature high dynamic range time-resolved CMOS SPAD image sensors

Since their integration in complementary metal oxide (CMOS) semiconductor technology in 2003, single photon avalanche diodes (SPADs) have inspired a new era of low cost high integration quantum-level image sensors. Their unique feature of discerning single photon detections, their ability to retain temporal information on every collected photon and their amenability to high speed image sensor architectures makes them prime candidates for low light and time-resolved applications. From the biomedical field of fluorescence lifetime imaging microscopy (FLIM) to extreme physical phenomena such as quantum entanglement, all the way to time of flight (ToF) consumer applications such as gesture recognition and more recently automotive light detection and ranging (LIDAR), huge steps in detector and sensor architectures have been made to address the design challenges of pixel sensitivity and functionality trade-off, scalability and handling of large data rates. The goal of this research is to explore the hypothesis that given the state of the art CMOS nodes and fabrication technologies, it is possible to design miniature SPAD image sensors for time-resolved applications with a small pixel pitch while maintaining both sensitivity and built -in functionality. Three key approaches are pursued to that purpose: leveraging the innate area reduction of logic gates and finer design rules of advanced CMOS nodes to balance the pixel’s fill factor and processing capability, smarter pixel designs with configurable functionality and novel system architectures that lift the processing burden off the pixel array and mediate data flow. Two pathfinder SPAD image sensors were designed and fabricated: a 96 × 40 planar front side illuminated (FSI) sensor with 66% fill factor at 8.25μm pixel pitch in an industrialised 40nm process and a 128 × 120 3D-stacked backside illuminated (BSI) sensor with 45% fill factor at 7.83μm pixel pitch. Both designs rely on a digital, configurable, 12-bit ripple counter pixel allowing for time-gated shot noise limited photon counting. The FSI sensor was operated as a quanta image sensor (QIS) achieving an extended dynamic range in excess of 100dB, utilising triple exposure windows and in-pixel data compression which reduces data rates by a factor of 3.75×. The stacked sensor is the first demonstration of a wafer scale SPAD imaging array with a 1-to-1 hybrid bond connection. Characterisation results of the detector and sensor performance are presented. Two other time-resolved 3D-stacked BSI SPAD image sensor architectures are proposed. The first is a fully integrated 5-wire interface system on chip (SoC), with built-in power management and off-focal plane data processing and storage for high dynamic range as well as autonomous video rate operation. Preliminary images and bring-up results of the fabricated 2mm² sensor are shown. The second is a highly configurable design capable of simultaneous multi-bit oversampled imaging and programmable region of interest (ROI) time correlated single photon counting (TCSPC) with on-chip histogram generation. The 6.48μm pitch array has been submitted for fabrication. In-depth design details of both architectures are discussed

CMOS IMAGE SENSORS FOR LAB-ON-A-CHIP MICROSYSTEM DESIGN

The work described herein serves as a foundation for the development of CMOS imaging in lab-on-a-chip microsystems. Lab-on-a-chip (LOC) systems attempt to emulate the functionality of a cell biology lab by incorporating multiple sensing modalidites into a single microscale system. LOC are applicable to drug development, implantable sensors, cell-based bio-chemical detectors and radiation detectors. The common theme across these systems is achieving performance under severe resource constraints including noise, bandwidth, power and size. The contributions of this work are in the areas of two core lab-on-a-chip imaging functions: object detection and optical measurements

Lab-on-CMOS Sensors and Real-time Imaging for Biological Cell Monitoring

Monitoring biological cell growth and viability is essential for in vivo biomedical diagnosis and therapy, and in vitro studies of pharmaceutical efficacy and material toxicity. Conventional monitoring techniques involve the use of dyes and markers that can potentially introduce side effects into the cell culture and often function as end-point assays. This eliminates the opportunity to track fast changes and to determine temporal correlation between measurements. Particularly in drug screening applications, high-temporal resolution cell viability data could inform decisions on drug application protocols that could lead to better treatment outcomes. This work presents development of a lab-on-chip (LoC) sensor for real-time monitoring of biological cell viability and proliferation, to provide a comprehensive picture of the changes cells undergo during their lifecycle. The LoC sensor consists of a complementary metal-oxide-semiconductor (CMOS) chip that measures the cell-to-substrate coupling of adherent cells that are cultured directly on top. This technique is non-invasive, does not require biochemical labeling, and allows for automated and unsupervised cell monitoring. The CMOS capacitance sensor was designed to addresses the ubiquitous challenges of sensitivity, noise coupling, and dynamic range that affect existing sensors. The design includes on-chip digitization, serial data output, and programmable control logic in order to facilitate packaging requirements for biological experiments. Only a microcontroller is required for readout, making it suitable for applications outside the traditional laboratory setting. An imaging platform was developed to provide time-lapse images of the sensor surface, which allowed for concurrent visual and capacitance observation of the cells. Results showed the ability of the LoC sensor to detect single cell binding events and changes in cell morphology. The sensor was used in in vitro experiments to monitor chemotherapeutic agent potency on drug-resistant and drug-sensitive cancer cell lines. Concentrations higher than 5 μM elicited cytotoxic effects on both cell lines, while a dose of 1 μM allowed discrimination of the two cell types. The system demonstrates the use of real-time capacitance measurements as a proof-of-concept tool that has potential to hasten the drug development process

Wearable, low-power CMOS ISFETs and compensation circuits for on-body sweat analysis

Complementary metal-oxide-semiconductor (CMOS) technology has been a key driver behind the trend of reduced power consumption and increased integration of electronics in consumer devices and sensors. In the late 1990s, the integration of ion-sensitive field-effect transistors (ISFETs) into unmodified CMOS helped to create advancements in lab-on-chip technology through highly parallelised and low-cost designs. Using CMOS techniques to reduce power and size in chemical sensing applications has already aided the realisation of portable, battery-powered analysis platforms, however the possibility of integrating these sensors into wearable devices has until recently remained unexplored. This thesis investigates the use of CMOS ISFETs as wearable electrochemical sensors, specifically for on-body sweat analysis. The investigation begins by evaluating the ISFET sensor for wearable applications, identifying the key advantages and challenges that arise in this pursuit. A key requirement for wearable devices is a low power consumption, to enable a suitable operational life and small form factor. From this perspective, ISFETs are investigated for low power operation, to determine the limitations when trying to push down the consumption of individual sensors. Batteryless ISFET operation is explored through the design and implementation of a 0.35 \si{\micro\metre} CMOS ISFET sensing array, operating in weak-inversion and consuming 6 \si{\micro\watt}. Using this application-specific integrated circuit (ASIC), the first ISFET array powered by body heat is demonstrated and the feasibility of using near-field communication (NFC) for wireless powering and data transfer is shown. The thesis also presents circuits and systems for combatting three key non-ideal effects experienced by CMOS ISFETs, namely temperature variation, threshold voltage offset and drift. An improvement in temperature sensitivity by a factor of three compared to an uncompensated design is shown through measured results, while adding less than 70 \si{\nano\watt} to the design. A method of automatically biasing the sensors is presented and an approach to using spatial separation of sensors in arrays in applications with flowing fluids is proposed for distinguishing between signal and sensor drift. A wearable device using the ISFET-based system is designed and tested with both artificial and natural sweat, identifying the remaining challenges that exist with both the sensors themselves and accompanying components such as microfluidics and reference electrode. A new ASIC is designed based on the discoveries of this work and aimed at detecting multiple analytes on a single chip. %Removed In the latter half of the thesis, Finally, the future directions of wearable electrochemical sensors is discussed with a look towards embedded machine learning to aid the interpretation of complex fluid with time-domain sensor arrays. The contributions of this thesis aim to form a foundation for the use of ISFETs in wearable devices to enable non-invasive physiological monitoring.Open Acces

Image processing on reconfigurable hardware for continuous monitoring of fluorescent biomarkers in cell cultures

Fluorescence microscopy is a widespread tool in biological research. It is the primary modality for bioimaging and empowers the study and analysis of multitudes of biological processes. It can be applied to fixed biosamples, that is samples with frozen biological features by mean of chemical linkers, or live biosamples providing useful insights on the spatio-temporal behavior of fluorescently stained biomarkers. Current fluorescent microscopy techniques use digital image sensors which are used to leverage quantitative studies instead qualitative outcomes. However, state-of-the-art techniques are not suitable for integration in small, contained and (semi-)autonomous systems. They remain costly, bulky and rather quantitatively inefficient methods for monitoring fluorescent biomarkers, which is not on par with the design constraints found in modern Lab-on-a-Chip or Point-of-Use systems requiring the use of miniaturized and integrated fluroscence microscopy. In this thesis, I summarize my research and engineering efforts in bringing an embedded image processing system capable of monitoring fluorescent biomarkers in cell cultures in a continuous and real-time manner. Three main areas related to the problem at hand were explored in the course of this work: simulation, segmentation algorithms and embedded image processing. n the area of simulation, a novel approach for generating synthetic fluorescent 2D images of cell cultures is presented. This approach is dichotomized in a first part focusing on the modeling and generation of synthetic populations of cells (i.e. cell cultures) at the level of single fluorescent biomarkers and in a second part simulating the imaging process occurring in a traditional digital fluorescent microscope to produce realistic images of the synthetic cell cultures. The objective of the proposed approach aims at providing synthetic data at will in order to test and validate image processing systems and algorithms. Various image segmentation algorithms are considered and compared for the purpose of segmenting fluorescent spots in microscopic images. The study presented in this thesis includes a novel image thresholding technique for spot extraction along with three well-known spot segmentation techniques. The comparison is undertaken on two aspects. The segmentation masks provided by the methods are used to extract further metrics related to the fluorescent signals in order to (i) evaluate how well the segmentation masks can provide data for classifying real fluorescent biological samples from negative control samples and (ii) quantitatively compare the segmentations masks based on simulated data from the previously stated simulation tool. Finally, the design of an embedded image processing system based on FPGA technologies is showcased. A semi-autonomous smart camera is conceived for the continuous monitoring of fluorescent biomarkers based on one of the segmentation methods incorporated in the previously stated comparison. Keeping the focus on the need for integration in fluorescence microscopy, the image processing core at the heart of the smart camera results from the use of a novel image processing suite; a suite of IP cores developed under the constraints dictated by the bioimaging needs of fluorescence microscopy for use in FPGA and SoC technologies. As a proof of concept, the smart camera is applied to the monitoring of the kinetics of the uptake of fluorescent silica nano-particles in cell cultures

Challenges and Solutions to Next-Generation Single-Photon Imagers

Detecting and counting single photons is useful in an increasingly large number of applications. Most applications require large formats, approaching and even far exceeding 1 megapixel. In this thesis, we look at the challenges of massively parallel photon-counting cameras from all performance angles. The thesis deals with a number of performance issues that emerge when the number of pixels exceeds about 1/4 of megapixels, proposing characterization techniques and solutions to mitigate performance degradation and non-uniformity. Two cameras were created to validate the proposed techniques. The first camera, SwissSPAD, comprises an array of 512 x 128 SPAD pixels, each with a one-bit memory and a gating mechanism to achieve 5ns high precision time windows with high uniformity across the array. With a massively parallel readout of over 10 Gigabit/s and positioning of the integration time window accurate to the pico-second range, fluorescence lifetime imaging and fluorescence correlation spectroscopy imaging achieve a speedup of several orders of magnitude while ensuring high precision in the measurements. Other possible applications include wide-field time-of-flight imaging and the generation of quantum random numbers at highest bit-rates. Lately super-resolution microscopy techniques have also used SwissSPAD. The second camera, LinoSPAD, takes the concepts of SwissSPAD one step further by moving even more 'intelligence' to the FPGA and reducing the sensor complexity to the bare minimum. This allows focusing the optimization of the sensor on the most important metrics of photon efficiency and fill factor. As such, the sensor consists of one line of SPADs that have a direct connection each to the FPGA where complex photon processing algorithms can be implemented. As a demonstration of the capabilities of current lowcost FPGAs we implemented an array of time-to-digital converters that can handle up to 8.5 billion photons per second, measuring each one of them and accounting them in high precision histograms. Using simple laser diodes and a circuit to generate light pulses in the picosecond range, we demonstrate a ubiquitous 3D time-of-flight sensor. The thesis intends to be a first step towards achieving the world's first megapixel SPAD camera, which, we believe, is in grasp thanks to the architectural and circuital techniques proposed in this thesis. In addition, we believe that the applications proposed in this thesis offer a wide variety of uses of the sensors presented in this thesis and in future ones to come