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

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

Silicon Neural Probes for Stimulation of Neurons and the Excitation and Detection of Proteins in the Brain

This thesis describes the development of a number of novel microfabricated neural probes for a variety of specific neuroscience applications. These devices rely on single mode waveguides and grating couplers constructed from silicon nitride thin films, which allows the use of planar lightwave circuits to create advanced device geometries and functions. These probes utilize array waveguide gratings to select an individual emitter from a large array of emitters using the wavelength of incoming light, allowing for spatial multiplexing of optical stimulation. These devices were tested in the laboratory and in living tissue to verify their efficacy. This technology was then modified to create steerable beam forming for stimulation of neurons using optical phase arrays. This technology was also tested for use in fluoresence lifetime imaging microscopy and the first application of pulsed light through the photonic circuits. Finally, this technology was again modified to create laminar illumination patterns for light sheet fluorescence microscopy applications. These devices were further improved by adding embedded microfluidics to the probes. The process of creating embedded microfluidic channels by the dig and seal method is described in detail, including modifications to the procedure that were added to address potential pitfalls in the fabrication process. Next, two projects which combine microfluidics with the optical devices described in the previous chapter are detailed. One project involves combining the use of optical emitters with microfluidic injections containing caged neurotransmitters to stimulate neurons is described. The other project involves microfluidic sampling of the extracellular space for neuropeptides which are detected using ring resonator biosensors. The sensitivity of these biosensors was analyzed in detail, determining both the physical limit of detection and the effect of biological noise due to non-specific binding on the sensors

Analog VLSI Circuits for Biosensors, Neural Signal Processing and Prosthetics

Stroke, spinal cord injury and neurodegenerative diseases such as ALS and Parkinson's debilitate their victims by suffocating, cleaving communication between, and/or poisoning entire populations of geographically correlated neurons. Although the damage associated with such injury or disease is typically irreversible, recent advances in implantable neural prosthetic devices offer hope for the restoration of lost sensory, cognitive and motor functions by remapping those functions onto healthy cortical regions. The research presented in this thesis is directed toward developing enabling technology for totally implantable neural prosthetics that could one day restore lost sensory, cognitive and motor function to the victims of debilitating neural injury or disease. There are three principal components to this work. First, novel integrated biosensors have been designed and implemented to transduce weak extra-cellular electrical potentials and optical signals from cells cultured directly on the surface of the sensor chips, as well as to manipulate cells on the surface of these chips. Second, a method of detecting and identifying stereotyped neural signals, or action potentials, has been mapped into silicon circuits which operate at very low power levels suitable for implantation. Third, as one small step towards the development of cognitive neural implants, a learning silicon synapse has been implemented and a neural network application demonstrated. The original contributions of this dissertation include: * A contact image sensor that adapts to background light intensity and can asynchronously detect statistically significant optical events in real-time; * Programmable electrode arrays for enhanced electrophysiological recording, for directing cellular growth, for site-specific in situ bio-functionalization, and for analyte and particulate collection; * Ultra-low power, programmable floating gate template matching circuits for the detection and classification of neural action potentials; * A two transistor synapse that exhibits spike timing dependent plasticity and can implement adaptive pattern classification and silicon learning

DEVELOPEMENT OF WIDEFIELD MULTI-CONTRAST OPTICAL METHODS FOR IN VIVO MICROVASCULAR SCALE IMAGING

Traditional in vivo optical imaging methods rely on a single contrast mechanism, thereby limiting one’s ability to characterize more than one biological variable. However, most biological systems are complex and are comprised of multiple variables. Therefore, optical methods that employ multiple contrast mechanisms and are capable of visualizing multiple biological variables would permit a more comprehensive understanding of biological systems. Multi-contrast optical imaging, therefore, has great potential for both fundamental and applied biomedical research. The goal of this dissertation is to develop optical methods to enable multi-contrast imaging in vivo over a wide field of view while retaining a microvascular scale spatial resolution. We present the integration of three types of optical imaging contrast mechanisms: fluorescence (FL), intrinsic optical signals (IOS) and laser speckle contrast (LSC). Fluorescence enables tracking pre-labelled molecules and cells, IOS allow quantification of blood volume and/or intravascular oxygen saturation, and LSC permits assessment of tissue perfusion. Together, these contrast mechanisms can be harnessed to provide a more complete picture of the underlying physiology at the microvascular spatial scale. We developed two such microvascular resolution optical multi-contrast imaging methods, and demonstrated their utility in multiple biomedical applications. First, we developed a multi-contrast imaging system that can interrogate in vivo both neural activity and its corresponding microvascular scale hemodynamics in the brain of a freely moving rodent. To do this, we miniaturized an entire benchtop optical imaging system that would typically occupy 5 x 5 x 5 feet, into just 5 cm3. Our miniaturized microscope weighs only 9 g. The miniature size and light weight permitted us to mount our microscope on a rodent’s head and image brain activity in vivo with multiple contrast mechanisms. We used our microscope to study the functional activation of the mouse auditory cortex, and to investigate the alteration of brain function during arousal from deep anesthesia. Our miniaturized microscope is the world’s first rodent head-mountable imaging system capable of interrogating both neural and hemodynamic brain activity. We envision our microscope to usher an exciting new era in neuroscience research. Second, we developed an optical imaging system to extensively characterize microvascular scale hemodynamics in vivo in an orthotopic breast tumor model. We specifically designed it as a benchtop based system to allow ample space for surgical preparation and small animal manipulation. Using it, we continuously monitored in vivo microvascular scale changes in tissue perfusion, blood volume and intravascular oxygen saturation of an orthotopic breast tumor microenvironment for multiple hours over a field of view encompassing the entire tumor extent. This unique dataset enabled us for the first time to characterize the temporal relationship between different tumor hemodynamic variables at the scale of individual microvessels. We envision our work to inspire a whole new avenue of experimental cancer research where the role of a tumor’s hemodynamic microenvironment is extensively characterized at its native (i.e. microvascular) spatial scale. In summary, this dissertation describes the design, implementation and demonstration of two microvascular resolution, wide-field, multi-contrast optical imaging systems. We believe these methods to be a new tool for broadening our understanding of biology

An Optofluidic Lens Biochip and an x-ray Readable Blood Pressure Microsensor: Versatile Tools for in vitro and in vivo Diagnostics.

Three different microfabricated devices were presented for use in vivo and in vitro diagnostic biomedical applications: an optofluidic-lens biochip, a hand held digital imaging system and an x-ray readable blood pressure sensor for monitoring restenosis. An optofluidic biochip–termed the ‘Microfluidic-based Oil-Immersion Lens’ (mOIL) biochip were designed, fabricated and test for high-resolution imaging of various biological samples. The biochip consists of an array of high refractive index (n = 1.77) sapphire ball lenses sitting on top of an oil-filled microfluidic network of microchambers. The combination of the high optical quality lenses with the immersion oil results in a numerical aperture (NA) of 1.2 which is comparable to the high NA of oil immersion microscope objectives. The biochip can be used as an add-on-module to a stereoscope to improve the resolution from 10 microns down to 0.7 microns. It also has a scalable field of view (FOV) as the total FOV increases linearly with the number of lenses in the biochip (each lens has ~200 microns FOV). By combining the mOIL biochip with a CMOS sensor, a LED light source in 3D printed housing, a compact (40 grams, 4cmx4cmx4cm) high resolution (~0.4 microns) hand held imaging system was developed. The applicability of this system was demonstrated by counting red and white blood cells and imaging fluorescently labelled cells. In blood smear samples, blood cells, sickle cells, and malaria-infected cells were easily identified. To monitor restenosis, an x-ray readable implantable blood pressure sensor was developed. The sensor is based on the use of an x-ray absorbing liquid contained in a microchamber. The microchamber has a flexible membrane that is exposed to blood pressure. When the membrane deflects, the liquid moves into the microfluidic-gauge. The length of the microfluidic-gauge can be measured and consequently the applied pressure exerted on the diaphragm can be calculated. The prototype sensor has dimensions of 1x0.6x10mm and adequate resolution (19mmHg) to detect restenosis in coronary artery stents from a standard chest x-ray. Further improvements of our prototype will open up the possibility of measuring pressure drop in a coronary artery stent in a non-invasively manner.PhDMacromolecular Science and EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/111384/1/toning_1.pd

Development of an integrated microspectrometer using arrayed waveguide grating (AWG)

With non-invasive properties and high sensitivities, portable optical biosensors are extremely desirable for point-of-care (POC) applications. Lab-on-a-chip technology such as microfluidics has been treated as an ideal approach to integrate complex sample processing and analysis units with optical detection elements. Spectroscopic sensing (such as fluorescence, Raman and absorption spectroscopy) remains the most highly developed, widely applied, optical technique. However, conventional spectroscopic sensing systems still rely on bulky and expensive dispersive components such as spectrophotometers in a well established laboratory. The work in this thesis is to develop an integrated dispersive component in combination with a microfluidic chip, providing a portable and inexpensive platform for on-chip spectroscopic sensing. In this study, an arrayed waveguide grating (AWG) design developed for telecommunication is re-engineered and utilized to realise a compact, dispersive optical component operating in the visible spectral region. The AWG devices operating in the visible region (λ_c=680 nm) are designed and fabricated with flame hydrolysis deposited (FHD) silica waveguide material. The micro-spectrometer in this proof of concept study has a small (1 cm x 1 cm) footprint and 8 output channels centred on different wavelengths. A series of fabrication issues and challenges are investigated and discussed for the specific AWG device. Subsequently, a sample cuvette is formed by using lithographic technique and dry etching process. Following this, a PDMS chip with microfluidic channels is bonded with the AWG device, leading to an integrated AWG-microfluidic platform. To the best of the author’s knowledge, this is the first work to integrate a visible AWG device and a microfluidic chip towards spectroscopic sensing. The monolithic integrated AWG microspectrometer–microfluidic platform is demonstrated for fluorescence spectroscopic analysis. Signals from the output channels detected on a camera chip can be used to re-create the complete fluorescence spectrum of an analyte. By making fluorescence measurements of (i) mixed quantum dot solutions, (ii) an organic fluorophore (Cy5) and (iii) the propidium iodide (PI)-DNA assay, the results obtained illustrate the unique advantages of the AWG platform for simultaneous, quantitative multiplex detection and its capability to detect small spectroscopic shifts. Although the current system is designed for fluorescence spectroscopic analysis, in principle, it can be implemented for other types of analysis, such as Raman spectroscopy. Fabricated using established semiconductor industry methods, this miniturised platform holds great potential to create a handheld, low cost biosensor with versatile detection capability. Also, the AWG device design is modified with focusing properties that enable localised spectroscopic measurements. Micro-beads based, multiplexed fluorescence detection is performed with the AWG + CCD system and the results have demonstrated capabilities of using the adapted AWG device for localised, multiplexed fluorescence detections, opening up potential applications in the field of cell sorting and single cell analysis. Furthermore, the AWG-microfluidic device is investigated for absorption spectroscopy measurement. As a test system, the pH dependence of the absorption spectra of bromophenol blue is measured to illustrate how an AWG device could be used as a colorimetric pH sensor. Overall, it is believed that the AWG technology holds great potential to realise a compact, integrated spectroscopic biosensor for point-of-care applications

Review on X-ray detectors based on scintillators and CMOS technology

This article describes the theoretical basis, design and implementation of X-ray microdetectors based on scintillating materials and CMOS technology. The working principle of such microdetectors consists in the absorption of X-rays by scintillators, which produce visible light. The visible light is then detected and converted into electric signals by means of photodetectors. In order to understand such detectors, several issues related to its implementation are presented in this article, namely: Production of X-rays and interaction between them and matter - the first step necessary to the detection of X-rays is that they must be absorbed by some material, in this case by a scintillator; Radiation detectors - there are several types of detectors, namely: pn junctions, photoconductors, based on thermal effects and scintillators; Fabrication of scintillator arrays - after the X-ray radiation is absorbed by a scintillator, this material emits visible light whose intensity is proportional to the total energy of the absorbed X-rays; Optical interfaces between scintillators and photodetectors - the visible light generated by scintillators must arrive to the photodetectors, so, it is necessary to have an interface between the scintillators and the photodetectors that ideally does not introduce losses; Photodetectors and interface electronics - the visible light is absorbed by the photodetectors and converted into electrical signals, which are finally converted into digital images by means of interface electronics. The article presents some promising patents on X-ray detectors based on scintillators and CMOS technology.Fundação para a Ciência e a Tecnologia (FCT) - Bolsa SFRH/BSAB/1014/201

NASA Tech Briefs, October 1990

Topics: New Product Ideas; NASA TU Services; Electronic Components and Circuits; Electronic Systems; Physical' Sciences; Materials; Computer Programs; Mechanics; Machinery; Fabrication Technology; Mathematics and Information Sciences; Life Sciences

MEMS Technology for Biomedical Imaging Applications

Biomedical imaging is the key technique and process to create informative images of the human body or other organic structures for clinical purposes or medical science. Micro-electro-mechanical systems (MEMS) technology has demonstrated enormous potential in biomedical imaging applications due to its outstanding advantages of, for instance, miniaturization, high speed, higher resolution, and convenience of batch fabrication. There are many advancements and breakthroughs developing in the academic community, and there are a few challenges raised accordingly upon the designs, structures, fabrication, integration, and applications of MEMS for all kinds of biomedical imaging. This Special Issue aims to collate and showcase research papers, short commutations, perspectives, and insightful review articles from esteemed colleagues that demonstrate: (1) original works on the topic of MEMS components or devices based on various kinds of mechanisms for biomedical imaging; and (2) new developments and potentials of applying MEMS technology of any kind in biomedical imaging. The objective of this special session is to provide insightful information regarding the technological advancements for the researchers in the community