Development of Microscopy Systems for Super-Resolution, Whole-Slide, Hyperspectral, and Confocal Imaging

Optical microscope is an important tool for researchers to study small objects. In this thesis, we will focus on the improvement of traditional microscope systems from several aspects including resolution, field of view, speed, cost, compactness, multimodality. In particular, we will investigate computational imaging methods that bypass the limitations with traditional microscope systems by combining the optical hardware design and image processing algorithm. Examples will include optimizing illumination strategy for the Fourier ptychography (FP), developing field-portable high-resolution microscope using a cellphone lens, investigating pattern-illuminated FP for fluorescence microscopy, demonstrating multimodal microscopic imaging with the use of liquid crystal display, achieving fast and accurate autofocusing for whole slide imaging system

医工学への応用を目指した暗視野反射照明顕微鏡の開発

Tohoku University石川拓司課

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

New acquisition techniques for real objects and light sources in computer graphics

Accurate representations of objects and light sources in a scene model are a crucial prerequisite for realistic image synthesis using computer graphics techniques. This thesis presents techniques for the effcient acquisition of real world objects and real world light sources, as well as an assessment of the quality of the acquired models. Making use of color management techniques, we setup an appearance reproduction pipeline that ensures best-possible reproduction of local light reflection with the available input and output devices. We introduce a hierarchical model for the subsurface light transport in translucent objects, derive an acquisition methodology, and acquire models of several translucent objects that can be rendered interactively. Since geometry models of real world objects are often acquired using 3D range scanners, we also present a method based on the concept of modulation transfer functions to evaluate their accuracy. In order to illuminate a scene with realistic light sources, we propose a method to acquire a model of the near-field emission pattern of a light source with optical prefiltering. We apply this method to several light sources with different emission characteristics and demonstrate the integration of the acquired models into both, global illumination as well as hardware-accelerated rendering systems.Exakte Repräsentationen der Objekte und Lichtquellen in einem Modell einer Szene sind eine unerlässliche Voraussetzung für die realistische Bilderzeugung mit Techniken der Computergraphik. Diese Dissertation beschäftigt sich mit der effizienten Digitalisierung von realen Objekten und realen Lichtquellen. Dabei werden sowohl neue Digitalisierungstechniken als auch Methoden zur Bestimmung der Qualität der erzeugten Modelle vorgestellt. Wir schlagen eine Verarbeitungskette zur Digitalisierung und Wiedergabe der Farbe und Spekularität von Objekten vor, die durch Ausnutzung von Farbmanagementtechniken eine bestmögliche Wiedergabe des Objekts unter Verwendung der gegebenen Ein- und Ausgabegeräte ermöglicht. Wir führen weiterhin ein hierarchisches Modell für den Lichttransport im Inneren von Objekten aus durchscheinenden Materialien sowie eine zugehörige Akquisitionsmethode ein und digitalisieren mehrere reale Objekte. Die dabei erzeugten Modelle können in Echtzeit angezeigt werden. Die Geometrie realer Objekte spielt eine entscheidende Rolle in vielen Anwendungen und wird oftmals unter Verwendung von 3D Scannern digitalisiert. Wir entwickeln daher eine Methode zur Bestimmung der Genauigkeit eines 3D Scanners, die auf dem Konzept der Modulationstransferfunktion basiert. Um eine Szene mit realen Lichtquellen beleuchten zu können, schlagen wir ferner eine Methode zur Erfassung der Nahfeldabstrahlung eine Lichtquelle vor, bei der vor der Digitalisierung ein optischer Filterungsschritt durchgeführt wird. Wir wenden diese Methode zur Digitalisierung mehrerer Lichtquellen mit unterschiedlichen Abstrahlcharakteristika an und zeigen auf, wie die dabei erzeugten Modelle in globalen Beleuchtungsberechnungen sowie bei der Bildsynthese mittels moderner Graphikkarten verwendet werden können

Holographic enhanced remote sensing system

The Holographic Enhanced Remote Sensing System (HERSS) consists of three primary subsystems: (1) an Image Acquisition System (IAS); (2) a Digital Image Processing System (DIPS); and (3) a Holographic Generation System (HGS) which multiply exposes a thermoplastic recording medium with sequential 2-D depth slices that are displayed on a Spatial Light Modulator (SLM). Full-parallax holograms were successfully generated by superimposing SLM images onto the thermoplastic and photopolymer. An improved HGS configuration utilizes the phase conjugate recording configuration, the 3-SLM-stacking technique, and the photopolymer. The holographic volume size is currently limited to the physical size of the SLM. A larger-format SLM is necessary to meet the desired 6 inch holographic volume. A photopolymer with an increased photospeed is required to ultimately meet a display update rate of less than 30 seconds. It is projected that the latter two technology developments will occur in the near future. While the IAS and DIPS subsystems were unable to meet NASA goals, an alternative technology is now available to perform the IAS/DIPS functions. Specifically, a laser range scanner can be utilized to build the HGS numerical database of the objects at the remote work site

Automated computer vision system for real-time drilling cuttings monitoring

In rotary drilling operations, cuttings are continuously transported to the surface by drilling fluid. Real-time monitoring of cuttings and cavings is crucial for early detection and remediation of drilling problems such as stuck pipe, lost circulation, high torque and drag, reduction in rate of penetration, and other wellbore instability issues. These incidents are large contributors to drilling-related Non-Productive Time (NPT). At the current stage, a mud logger performs monitoring manually. This work proposes to use computer vision techniques to automate this procedure. To achieve this application, specific requirements should be established to design an automated machine vision system to maintain drilling safety and speed. Cuttings ramp has been identified as an ideal location to perform the measurement, where cuttings and caving are sliding down a slope at a steady speed. To accomplish this task, an intelligent image processing system must be able to track cuttings speed, measure volume, analyze size, and generate a surface model. Through a detailed review and testing of available 3D sensing techniques, a system consisting of a 2D high-resolution camera and 3D laser profile scanner was designed. By implementing image processing techniques, the cuttings speed on the ramp was estimated which was then synchronized to the 3D depth data from a laser scanner. Finally, the volume of moving cuttings was estimated and a 3D surface profile was reconstructed using point cloud data. Experimental results in the lab environment validated that such a system can be applied to quantify cuttings volume, size distribution, and reconstruct a 3D profile of cuttings and cavings. This measured result can be stored for further analysis. Overall, this work established a foundation for the design of a sophisticated real-time monitoring system for hole cleaning and wellbore risk reduction.Petroleum and Geosystems Engineerin

A concept for a regional coastal zone mission

thesi

Instrument design and optimization of interferometric reflectance imaging sensors for in vitro diagnostics

Thesis (Ph.D.)--Boston UniversityIn the field of drug discovery and disease diagnostics, protein microarrays have generated much enthusiasm for their high-throughput monitoring of biomarkers; however, this technology has yet to translate from research laboratories to commercialization. The hindrance is the considerable uncertainty and skepticism regarding data obtained. The disparity in results from different laboratories performing identical tests is attributed to a lack of assay quality control. Unlike DNA microarrays, protein microarrays have a higher level of bioreceptor immobilization variability and non-specific binding because of the more complex molecular structure and broader physiochemical properties. Traditional assay detection modalities, such as fluorescence microscopy and surface plasmon resonance, are unable to overcome both of these sources of variation. This dissertation describes the hardware and software design and biological validation of three complementary platforms that overcome bioreceptor variability and non-specific binding for diagnostics. In order to quantify the bioreceptor quality, a label-free, nondestructive, low cost, and high-throughput interferometric sensor has been developed as a quality control tool. The quality control tool was combined with a wide-field fluorescence imaging system to improve fluorescence experimental repeatability. Lastly, a novel high-throughput and label-free platform for quality control and specific protein microarray detection is described. This platform overcomes the additional complexities and time required with labeled assays by discriminating between specific and nonspecific detection by including sizing of individual binding events. Protein microarrays may one day emerge as routine clinical laboratory tests; however, it is important that the proper quality control procedures are in place to minimize erroneous results. These platforms provide reliable and repeatable protein microarray measurements for new advancements in disease diagnostics with the potential for drug discovery