Implantable Fluorescence Imager for Deep Neuronal Imaging

This thesis describes the design, fabrication, and characterization of the Implantable Fluorescence Imager (IFI): a camera chip with a needle-like form factor designed for imaging neuronal activity in the deep brain. It is fabricated with a complementary metal oxide semiconductor (CMOS) process, allowing for hundreds or thousands of single- photon-sensitive photodetectors to be densely packed onto a device width comparable to a single-channel fiber optic cannula (~100 μm). The IFI uses a combination of spectral and temporal filters as a fluorescence emission filter, and per-pixel Talbot gratings for 3D light-field imaging. The IFI has the potential to overcome the imaging depth limit of multi-photon microscopes imposed by the scattering and absorption of photons in brain tissue, and the resolution limit of noninvasive imaging techniques, such as functional magnetic resonance imaging and photoacoustic imaging. It competes with graded index lens-based miniaturized microscopes in imaging depth, but offers several comparative advantages. First, its cross sectional area is at least an order of magnitude smaller for an equal field of view. Second, the distribution of pixels along its entire length allows the study of multi- layer or multi-region dynamics. Finally, the scalability advantage of silicon integrated circuit technology in system miniaturization and data bandwidth may allow thousands of such imaging shanks to be simultaneously deployed for large-scale volumetric recording

Narrowband organic light-emitting diodes for fluorescence microscopy and calcium imaging

Funding: Leverhulme Trust (RPG-2017-231), the EPSRC NSF-CBET lead agency agreement (EP/R010595/1, 1706207), the DARPA NESD program (N66001-17-C-4012) and the RS Macdonald Charitable Trust. C.M. acknowledges funding from the European Commission through a Marie Skłodowska Curie individual fellowship (703387). A.M. acknowledges funding through an individual fellowship of the Deutsche Forschungsgemeinschaft (404587082). Y.D. acknowledges support from the Chinese Scholarship Council (CSC). L.T. acknowledges studentship funding through the EPSRC CM-CDT (EP/L015110/1). M.S. acknowledges funding by the Royal Society (Dorothy Hodgkin Fellowship, DH160102).Fluorescence imaging is an indispensable tool in biology, with applications ranging from single‐cell to whole‐animal studies and with live mapping of neuronal activity currently receiving particular attention. To enable fluorescence imaging at cellular scale in freely moving animals, miniaturized microscopes and lensless imagers are developed that can be implanted in a minimally invasive fashion; but the rigidity, size, and potential toxicity of the involved light sources remain a challenge. Here, narrowband organic light‐emitting diodes (OLEDs) are developed and used for fluorescence imaging of live cells and for mapping of neuronal activity in Drosophila melanogaster via genetically encoded Ca2+ indicators. In order to avoid spectral overlap with fluorescence from the sample, distributed Bragg reflectors are integrated onto the OLEDs to block their long‐wavelength emission tail, which enables an image contrast comparable to conventional, much bulkier mercury light sources. As OLEDs can be fabricated on mechanically flexible substrates and structured into arrays of cell‐sized pixels, this work opens a new pathway for the development of implantable light sources that enable functional imaging and sensing in freely moving animals.PostprintPeer reviewe

A 72 × 60 Angle-Sensitive SPAD Imaging Array for Lens-less FLIM

We present a 72 × 60, angle-sensitive single photon avalanche diode (A-SPAD) array for lens-less 3D fluorescence lifetime imaging. An A-SPAD pixel consists of (1) a SPAD to provide precise photon arrival time where a time-resolved operation is utilized to avoid stimulus-induced saturation, and (2) integrated diffraction gratings on top of the SPAD to extract incident angles of the incoming light. The combination enables mapping of fluorescent sources with different lifetimes in 3D space down to micrometer scale. Futhermore, the chip presented herein integrates pixel-level counters to reduce output data-rate and to enable a precise timing control. The array is implemented in standard 180 nm complementary metal-oxide-semiconductor (CMOS) technology and characterized without any post-processing

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

CMOS SINGLE-PHOTON AVALANCHE DIODES AND MICROMACHINED OPTICAL FILTERS FOR INTEGRATED FLUORESCENCE SENSING

This dissertation presents a body of work that addresses the two most pressing challenges in the field of integrated fluorescence sensing, namely, the design of integrated optical sensors and the fabrication of high-rejection micro-scale optical filters. Two novel enabling technologies were introduced. They are: the perimeter-gated single-photon avalanche diode (PGSPAD), for on-chip photon counting, and the benzotriazole (BTA)-doped thin-film polymer filter, for on-chip ultraviolet light rejection. Experimental results revealed that the PGSPAD front-end, fabricated in a 0.5 μm standard mixed-signal CMOS process, had the capability of counting photons in the MHz regime. In addition, it was found that a perimeter gate, a structural feature used to suppress edge breakdown in the diode, also maximized the signal-to-noise-ratio in the high-count rate regime whereas it maximized sensitivity at low count rates. On the other hand, BTA-doped filters were demonstrated utilizing three commonly used polymers as hosts. The filters were patternable, utilizing the same procedures traditionally used to pattern the undoped polymer hosts, a key advantage for integration into microsystems. Filter performance was analyzed using a set of metrics developed for optoelectronic characterization of integrated fluorescence sensors; high rejection levels (nearing -40 dB) of UV light were observed in films of only 5 μm in thickness. Ultimately, BTA-doped filters were integrated into a portable sensor, and their use was demonstrated in two types of bioassays

Modeling, Design and Test of an Integrated Optical Neural Recording Device

It has long been a goal of neuroscientists to understand how electrophysiological activity in the nervous system corresponds to, and causes, specific physiological actions. Such knowledge could be used to develop cures for disabilities related to nervous system dysfunction, and to control artificial limbs or restore motion to a paralyzed patient. This has motivated research into technologies, broadly termed brain-machine interfaces, for interfacing with the nervous system. One category of such neural interfaces is implantable neural recording devices, which monitor and record neural signals through a microelectronic device implanted in the body. Typical implantable neural recording devices use a micro-electrode array to record electrical signals simultaneously from a multitude of neurons. Unfortunately, devices employing micro-electrode arrays have several issues from both the biological and circuit design points of view. These issues include tissue damage due to implantation of a micro-electrode array, degradation of recording fidelity over time, limited spatial resolution, the requirement to maintain charge balance in tissue, and the difficulty in implementing low-frequency (large time constant) filter cutoffs with limited chip area. These issues provided the motivation to investigate alternative methods for neural recording - namely optical methods based on fluorescence detection with voltage-sensitive fluorescent proteins. Optical recording methods can alleviate many of the issues with electrical recording, as well as provide other advantages, such as recording targeted to specific neurons/neuron types and higher spatial resolution due to reduced recording site pitch. The major limitations of fully implantable optical recording devices stem from size constraints, the attenuation of light in tissue, which limits imaging depth, and the need for genetically programmed voltage-sensitive fluorescent proteins, which must be introduced to the tissue in the case of chronic recording. This research began with investigating the feasibility of replacing an electrical neural record- ing front end with an optical front end - the conclusion being that producing an initial design was worthwhile. Thus, this thesis presents a prototype optical neural recording device for detecting individual spikes in Layer I of the brain. The device is designed for the fully implantable scenario, where space for typical fluorescence imaging optical components is limited, and a high level of integration is required. The thesis describes: 1) Modeling: a general framework for modeling near-field fluorescence detection systems is presented; the model is then extended and applied to the design of the optical neural recording device for detecting individual spikes in Layer I of the brain, taking into account light attenuation in tissue; 2) Design: the design of a high-sensitivity CMOS imaging chip used in the device; 3) Packaging: the packaging of the CMOS imager with LED dies and an excitation filter; and 4) Testing: the experimental results from testing the packaged device with a fluorescent tissue phantom designed to emulate layer I of the brain. Ideas for future work on such devices are discussed

Cmos Based Lensless Imaging Systems And Support Circuits

While much progress has been made in various fields of study in past few decades, leading to better understanding of science as well as better quality of life, the role of optical sensing has grown among electrical, chemical, optical, and other physical signal modalities. As an example, fluorescent microscopy has become one of the most important methods in the modern biology. However, broader implementation of optical sensing has been limited due to the expensive and bulky optical and mechanical components of conventional optical sensor systems. To address such bottleneck, this dissertation presents several cost-effective, compact approaches of optical sensor arrays based on solid state devices that can replace the conventional components. As an example, in chapter 2 we demonstrate a chip-scale (<1 mm2 ) sensor, the Planar Fourier Capture Array (PFCA), capable of imaging the far-field without any off-chip optics. The PFCA consists of an array of angle-sensitive pixels manufactured in a standard semiconductor process, each of which reports one component of a spatial two-dimensional (2D) Fourier transform of the local light field. Thus, the sensor directly captures 2D Fourier transforms of scenes. The effective resolution of our prototype is approximately 400 pixels. My work on this project [15] includes a circuit design and layout and the overall testing of the imaging system. In chapter 3 we present a fully integrated, Single Photon Avalanche Detector (SPAD) using only standard low- voltage (1.8V) CMOS devices in a 0.18m process. The system requires one highvoltage AC signal which alternately reverse biases the SPADs into avalanche breakdown and then resets with a forward bias. The proposed self-quenching circuit intrinsically suppresses after-pulse effects, improving signal to noise ratio while still permitting fine time resolution. The required high-voltage AC signal can be generated by resonant structures and can be shared across arrays of SPADs [24]. An ideal light sensor to provide the precise incident intensity, location, and angle of incoming photons is shown in chapter 4. Single photon avalanche diodes (SPADs) provide such desired high (single photon) sensitivity with precise time information, and can be implemented at a pixel scale to form an array to extract spatial information. Furthermore, recent work has demonstrated photodiode-based structures (combined with micro-lenses and diffraction gratings) that are capable of encoding both spatial and angular information of the incident light. In this chapter, we describe the implementation of such grating structure on SPAD to realize a pixel-scale angle-sensitive single photon avalanche diode (A-SPAD) using a standard CMOS process. While the underlying SPAD structure provides the high sensitivity, the diffraction gratings consisting of two sets of metal layers offers the angle-sensitivity. Such unique combination of the SPAD and the diffraction gratings expand the sensing dimensions to pave a path towards a lens-less 3-D imaging and a light-field timeof-flight imaging. In chapter 5, we present a 72 x 60, angle-sensitive single photon avalanche diode (A-SPAD) array for lens-less 3-D fluorescent life time imaging. A-SPAD pixels are comprised of (1) a SPAD to resolve precise timing information, to reject high-powered UV stimulus, and to map the lifetimes of different fluorescent sources and (2) integrated diffraction gratings on top of the SPAD to extract incident angles of incoming light, enabling 3-D localization at a micrometer scale. The chip presented in this work also integrates pixel-level counters as well as shared timing circuitry, and is implemented in conventional 180nm CMOS technology without any post-processing. Contact-based read- out from a revolving MEMS accelerometers is problematic therefore contactless (optical) read-out is preferred. The optical readout requires an image sensor to resolve nanometer-scale shifts of the MEMS image. Traditional imagers record on a rectangular grid which is not well-suited for efficiently imaging rotating objects due to the significant processing overhead required to translate Cartesian coordinates to angular position. Therefore, in chapter 6 we demonstrate a high-speed ( 1kfps), circular, CMOS imaging array for contact-less, optical measurement of rotating inertial sensors. The imager is designed for real-time optical readout and calibration of a MEMS accelerometer revolving at greater than 1000rpm. The imager uses a uniform circular arrangement of pixels to enable rapid imaging of rotational objects. Furthermore, each photodiode itself is circular to maintain uniform response throughout the entire revolution. Combining a high frame rate and a uniform response to motion, the imager can achieve sub-pixel resolution (25nm) of the displacement of micro scale features. In order to avoid fixed pattern noise arising from non-uniform routing within the array we implemented a new global shutter technique that is insensitive to parasitic capacitance. To ease integration with various MEMS platforms, the system has SPI control, on-chip bias generation, sub-array imaging, and digital data read-out. My work on this project [20] includes a circuit design and lay- out and some testing including, a FPGA based controller design of the imaging system. In the previous chapters, compact and cost effective imaging sys- tems have been introduced. Those imaging systems show great potential for wireless implantable systems. A power rectifier for the implant provides a volt- age DC power with a small inductor, for small volume, from a small AC voltage input. In the last chapter we demonstrate an inductively powered, orthogonal current-reuse multi-channel amplifier for power-efficient neural recording. The power rectifier uses the input swing as a self-synchronous charge pump, making it a fully passive, full-wave ladder rectifier. The rectifier supplies 10.37[MICRO SIGN]W at 1.224V to the multi-channel amplifier, which includes bias generation. The prototype device is fabricated in a TSMC 65nm CMOS process, with an active area of 0.107mm2 . The maximum measured power conversion efficiency (PCE) is 16.58% with a 184mV input amplitude. My work on this project [25] in- cludes the rectifier design and overall testing to combine "orthogonal currentreuse neural amplifier" designed by Ben Johnson

Development of a microfluidic device for gaseous formaldehyde sensing = Développement d\u27un dispositif microfluidique pour la détection de formaldéhyde à l\u27état gazeux

Formaldehyd (HCHO) ist eine chemische Verbindung, die bei der Herstellung einer großen Zahl von Haushaltsprodukten verwendet wird.Charakteristisch ist seine hohe Flüchtigkeit aufgrund einer niedrigen Siedetemperatur ($T = - 19\ ℃$). Daher ist HCOH fast überall als Luftschadstoff in Innenräumen vorhanden. Die Miniaturisierung analytischer Systeme zu Handheld-Gerät hat das Potenzial, nicht nur effizientere, sondern auch empfindlichere Instrumente für die Echtzeitüberwachung dieses gefährlichen Luftschadstoffs zu ermöglichen. Die vorliegende Doktorarbeit präsentiert die Entwicklung eines Mikrofluidik-Geräts für die Erfassung von HCHO basierend auf der Hantzsch-Reaktion.Hierbei wurde der Schwerpunkt auf die Komponente für Fluoreszenzdetektion gelegt. Es wurde eine umfangreiche Literaturrecherche durchgeführt, die es erlaubt, den Stand der Technik auf dem Gebiet der Miniaturisierung des Fluoreszenzsensors zusammenzufassen. Auf Grund dieser Studie wurde ein modulares Fluoreszenzdetektionskonzept vorgeschlagen, das um einen CMOS-Bildsensor (CIS) herum entwickelt wurde. Zwei dreischichtige Fluidikzellenkonfigurationen (Konfiguration 1: Quarz - SU-8 3050 - Quarz und Konfiguration 2: Silizium - SU-8 3050 - Quarz) wurden in Betracht gezogen und parallel unter den gleichen experimentellen Bedingungen getestet. Die Verfahren der Mikrofabrikation der fluidischen Zellen wurden detailliert beschrieben, einschließlich des Integrationsprozesses der Standardkomponenten und der experimentellen Verfahren. Der CIS-basierte Fluoreszenzdetektor bewies seine Leistungsfähigkeit, eine anfängliche HCHO-Konzentration von 10 µg/L vollständig in 3,5-Diacetyl-1,4-dihydrolutidin (DDL- derivatisiert) sowohl für die Quarz- als auch für die Silizium-Fluidikzellen zu detektieren. Beide Systemewiesenein Abfragevolumen von 3,5 µL auf. Ein offensichtlich höheres Signal-Rausch-Verhältnis (SNR) wurde für die Silizium-Fluidzelle ($\text{SNR}_{\text{silicon}} = 6.1$) im Vergleich zur Quarz-Fluidzelle ($\text{SNR}_{\text{quartz}} = 4.9$) beobachtet. Die Verstärkung der Signalintensität in der Silizium-Fluidzelle ist wahrscheinlich auf den Silizium-Absorptionskoeffizienten bei der Anregungswellenlänge zurückzuführen,$a\left( \lambda_{\text{abs}} = 420\ nm \right) = 5 \bullet 10^{4}\text{cm}^{- 1}$. Dieser Koeffizient ist ungefähr fünfmal höher als der Absorptionskoeffizient bei der Fluoreszenzemissionswellenlänge $a\left(\lambda_{\text{em}} = 515\ nm \right) = 9.25 \bullet 10^{3}\text{cm}^{- 1}$. HCHO wird aufgrund seiner relativ hohen Konstanten für das Henry-Gesetz sehr schnell in ein flüssiges Reagenz aufgenommen. Somit hängt die Auswahl des molekularen Einfangverfahrens (Schwallströmung, Ringströmung oder membranbasierte Strömungswechselwirkung) von derLeistungsfähigkeit des Fluoreszenzdetektors ab. Ein vorläufiges Konzept, das auf der Verwendung einer Gas-Flüssigkeitsmembran-basierten Wechselwirkung zum ständigen Abfangen des gasförmigen HCHO basiert, wurde eingeführt. Hierzu wurden kompatible Materialien und Herstellungsmethoden identifiziert. Darüber hinaus wurden CFD-Simulationen durchgeführt, um die Mikrokanallänge unter verschiedenen hydrodynamischen Bedingungen abzuschätzen, die für eine vollständige HCHO-Derivatisierung erforderlich sind. Eine Verbesserung und Vereinfachung auf der Grundlage von sehrnempfindlichen Fluoreszenzdetektoren mit niedrigen Detektionsgrenzen könnte zukünftig basierend z. B. auf Schwallströmung oder Ringströmung möglich sein

Advances in Bioengineering

The technological approach and the high level of innovation make bioengineering extremely dynamic and this forces researchers to continuous updating. It involves the publication of the results of the latest scientific research. This book covers a wide range of aspects and issues related to advances in bioengineering research with a particular focus on innovative technologies and applications. The book consists of 13 scientific contributions divided in four sections: Materials Science; Biosensors. Electronics and Telemetry; Light Therapy; Computing and Analysis Techniques

Miniaturization of fluorescence sensing in optofluidic devices

International audienceSuccessful development of a micro-total-analysis system (μTAS, lab-on-a-chip) is strictly related to the degree of miniaturization, integration, autonomy, sensitivity, selectivity, and repeatability of its detector. Fluorescence sensing is an optical detection method used for a large variety of biological and chemical assays, and its full integration within lab-on-a-chip devices remains a challenge. Important achievements were reported during the last few years, including improvements of previously reported methodologies, as well as new integration strategies. However, a universal paradigm remains elusive. This review considers achievements in the field of fluorescence sensing miniaturization, starting from off-chip approaches, representing miniaturized versions of their lab counter-parts, continuing gradually with strategies that aim to fully integrate fluorescence detection on-chip, and reporting the results around integration strategies based on optical-fiber-based designs,optical layer integrated designs, CMOS-based fluorescence sensing, and organic electronics. Further successful development in this field would enable the implementation of sensing networks in specific environments that, when coupled to Internet of-Things (IoT) and artificial intelligence (AI), could provide real-time data collection and, therefore, revolutionize fields like health, environmental, and industrial sensing