Real-Time Image Error Detection in Knife-Edge Scanning Microscope

Research about the microstructure of the brain provides important information to help understand the functions of the brain. In order to investigate large volume, high-resolution data of mouse brains, researchers from Brain Network Lab (BNL) at Texas A&M University (TAMU) have been developing the Knife-Edge Scanning Microscope (KESM) in the past decade. The KESM can simultaneously section and image brain tissues at sub-micrometer resolution. However, malfunctions of the system can cause imaging errors, which make images fail to provide valid information. Moreover, malfunctions, especially due to obstructions (such as tissue fragments) in the light path of the system, result in continued cutting while the obstructions are present. Since KESM is generally not attended by a full-time human operator, this results in data loss. To solve the problem, I developed an image error detection method to automatically find imaging errors in real-time. The method can detect errors by analyzing newly acquired images, report results to human operators and even stop the KESM cutting process if necessary so that data loss is avoided. The basic idea of the method is to solve error detection problem through image change detection algorithm as the images acquired by KESM are well-registered and they do not change too much from one slice to the next when there is no error. As a result, the method can detect imaging errors with 86% accuracy (F1-score) and finish a detection routine within 2 seconds, which is sufficient to achieve real-time detection. By integrating the error detection program into the KESM control system, the method enhanced the robustness of the system and reduced data loss

Measurement of focusing properties for high numerical aperture optics using an automated submicron beamprofiler

The focusing properties of three aspheric lenses with numerical aperture (NA) between 0.53 and 0.68 were directly measured using an interferometrically referenced scanning knife-edge beam profiler with sub-micron resolution. The results obtained for two of the three lenses tested were in agreement with paraxial gaussian beam theory. It was also found that the highest NA aspheric lens which was designed for 830nm was not diffraction limited at 633nm. This process was automated using motorized translation stages and provides a direct method for testing the design specifications of high numerical aperture optics.Comment: 6 pages 4 figure

Optical scanning sensor system with submicron resolution

In this work, autofocus and optical scanning technologies are brought together in the design of a simplified scanning microscope. The developed system uses an autofocus sensor based on the Foucault knife-edge principle and piezo-based stages for scanning the samples in axial and lateral directions. It is built with a reduced number of components and designed to offer a simple set-up for the analysis of optical aberrations. The traditional way of addressing optical aberrations in scanning system is to improve the optical system such that it works as a paraxial lens. Breaking this paradigm and observing the optics as part of a complex system, it is possible to use simpler optics and correct the resultant errors computationally. These errors are systematic and, as long as they can be measured and modelled, they can be predicted and corrected. This way, the design of the system becomes more flexible and the task of error handling can be divided between optics optimization and computational correction, reducing overall size and weight, raising system dynamics and reducing costs.Laser-Scanning Mikroskopie ist eine im Bereich der Oberflächenmessung wichtige und vielversprechende Technologie für schnelle, genaue und wiederholbare Messungen. Es ist im Grunde eine Technik zur Erhöhung von Kontrast und Auflösung in optischen Abbildungssystemen. Ein Prüfling wird punktweise abgetastet und ein dreidimensionales Bild seiner Oberfläche mit Hilfe eines Rechners erfasst und rekonstruiert. In dieser Arbeit werden Autofokus- und optische Abtastverfahren in der Entwicklung und Konstruktion eines alternativen, vereinfachten Scanning Mikroskops für Oberflächenmessungen im Millimeterbereich mit Sub-Mikrometer Auflösung zusammengebracht. Das entwickelte System verwendet einen auf dem Foucault‘sches Schneidenverfahren basierenden Autofokussensor um die Fokuslage zu bestimmen und einen Piezo-Linearantrieb für die Verschiebung des Objektivs entlang der optischen Achse und das Abtasten des Prüflings in der axialen Richtung. Die laterale Abtastung des Prüflings wird durch den Einsatz eines Piezo-Spiegels realisiert, der um zwei Achsen schwenkbar ist. Das entwickelte Mikroskop hat eine reduzierte Anzahl von optischen Komponenten und bietet einen einfachen und vielseitigen Versuchsaufbau zur Messung und Analyse von Fehlern, die durch die bewusste Verwendung von unkompensierten Optiken auftreten. Die damit verbundenen Abbildungsfehler erzeugen Asymmetrien in den Autofokussensoren und beeinträchtigen die Gesamtleistung. Die herkömmliche Lösung dieser Problematik ist das System durch Addition zusätzlicher Komponenten zu verbessern, sodass es wie ein paraxiales System wirkt. Diese Verbesserung bringt aber die Nachteile von Baugröße, Gewicht und Kosten mit sich. Durch das Brechen des Paradigmas der Verbesserung der Optik bis zu einem paraxialen System und die Betrachtung der Optik als Teil eines komplexen Systems ist es möglich, simplere Optik zu verwenden, und die resultierenden Fehler rechnerisch zu korrigieren. Diese Fehler sind systematisch und können – solange sie modelliert und gemessen werden können – vorhergesagt und korrigiert werden. Damit wird das Design des optischen Systems flexibler und die Aufgabe der Fehlerbehandlung zwischen Optimierung der Optik und rechnerischer Korrektur aufgeteilt. Baugröße, Gewicht und Kosten können dann reduziert werden und die Systemdynamik erhöht sich, ohne Einschränkung der Präzision. Das Ziel ist nicht jeden Abbildungsfehler individuell zu untersuchen, sondern deren Zusammenwirken auf die Messungen zu beobachten und zu modellieren. Verschiedene Strategien für die Behandlung dieser Messfehler werden in dieser Arbeit vorgeschlagen, diskutiert und experimentell validiert.Laser Scanning Microscopy has been used for a long time in the field of surface measurement and is today one of the most promising technologies for fast, accurate and repeatable measurements. It is technique for increasing contrast and resolution in optical imaging systems through the rejection of out-of-focus light. Images are acquired point-by-point and reconstructed with a computer, allowing three-dimensional reconstructions of objects. In this work, autofocus and optical scanning technologies are brought together in the design of an alternative simplified scanning microscope for surface measuring in millimetre range with sub-micrometer resolution. The developed system uses an autofocus sensor based on the Foucault knife-edge principle to generate a defocus signal and a piezo positioning stage for translating the objective and scanning the samples in the axial direction. For the lateral scanning, a piezo driven tip-tilt mirror is used. The developed scanning microscope is built with a reduced number of optical components and designed to offer a simple and versatile set-up for the measurement and analysis of errors induced by optical aberrations due to the use of suboptimal optics. The use of uncompensated lenses has always been avoided in scanning microscopy as it generates asymmetries in the defocus signal and deteriorates its overall performance. The traditional way of solving this problem is to improve the optical system such that it works as a paraxial lens, but that comes with the price of heavy and costly optics. By breaking the paradigm of improving the optics to a paraxial lens and observing the optics as part of a complex system, it is possible to use simpler optics and correct the resultant errors computationally. These errors are systematic and, as long as they can be measured and modelled, they can be predicted and corrected. This way, the design of the optical system becomes much more flexible and the task of error handling can be divided between optics optimization and computational correction, reducing overall size and weight, raising system dynamics and reducing costs, without losing accuracy. The goal is not to study each optical aberration individually, but to measure and model their combined influence in the measurements. Different strategies for addressing these measurement errors caused by the use of uncompensated optics are proposed, discussed and experimentally validate

DEVELOPMENT OF A VERSATILE HIGH SPEED NANOMETER LEVEL SCANNING MULTI-PROBE MICROSCOPE

The motivation for development of a multi-probe scanning microscope, presented in this dissertation, is to provide a versatile measurement tool mainly targeted for biological studies, especially on the mechanical and structural properties of an intracellular system. This instrument provides a real-time, three-dimensional (3D) scanning capability. It is capable of operating on feedback from multiple probes, and has an interface for confocal photo-detection of fluorescence-based and single molecule imaging sensitivity. The instrument platform is called a Scanning Multi-Probe Microscope (SMPM) and enables 45 microm by 45 microm by 10 microm navigation of specimen with simultaneous optical and mechanical probing with each probe location being adjustable for collocation or for probing with known probe separations. The 3D positioning stage where the specimen locates was designed to have nanometer resolution and repeatability at 10 Hz scan speed with either open loop or closed loop operating modes. The fine motion of the stage is comprises three orthogonal flexures driven by piezoelectric actuators via a lever linkage. The flexures design is able to scan in larger range especially in z axis and serial connection of the stages helps to minimize the coupling between x, y and z axes. Closed-loop control was realized by the capacitance gauges attached to a rectangular block mounted to the underside of the fine stage upon which the specimen is mounted. The stage's performance was studied theoretically and verified by experimental test. In a step response test and using a simple proportional and integral (PI) controller, standard deviations of 1.9 nm 1.8 nm and 0.41 nm in the x, y and z axes were observed after settling times of 5 ms and 20 ms for the x and y axes. Scanning and imaging of biological specimen and artifact grating are presented to demonstrate the system operation. For faster, short range scanning, novel ultra-fast fiber scanning system was integrated into the xyz fine stage to achieve a super precision dual scanning system. The initial design enables nanometer positioning resolution and runs at 100 Hz scan speed. Both scanning systems are capable of characterization using dimensional metrology tools. Additionally, because the high-bandwidth, ultra-fast scanning system operates through a novel optical attenuating lever, it is physically separate from the longer range scanner and thereby does not introduce additional positioning noise. The dual scanner provides a fine scanning mechanism at relatively low speed and large imaging area using the xyz stage, and focus on a smaller area of interested in a high speed by the ultra-fast scanner easily. Such functionality is beneficial for researchers to study intracellular dynamic motion which requires high speed imaging. Finally, two high end displacement sensor systems, a knife edge sensor and fiber interferometer, were demonstrated as sensing solutions for potential feedback tools to boost the precision and resolution performance of the SMPM

An automated system for chromosome analysis. Volume 1: Goals, system design, and performance

The design, construction, and testing of a complete system to produce karyotypes and chromosome measurement data from human blood samples, and a basis for statistical analysis of quantitative chromosome measurement data is described. The prototype was assembled, tested, and evaluated on clinical material and thoroughly documented

An Automated System for Chromosome Analysis

The design, construction, and testing of a complete system to produce karyotypes and chromosome measurement data from human blood samples, and to provide a basis for statistical analysis of quantitative chromosome measurement data are described

Silicon Carbide And Agile Optics Based Sensors For Power Plant Gas Turbines, Laser Beam Analysis And Biomedicine

Proposed are novel sensors for extreme environment power plants, laser beam analysis and biomedicine. A hybrid wireless-wired extreme environment temperature sensor using a thick single-crystal Silicon Carbide (SiC) chip embedded inside a sintered SiC probe design is investigated and experimentally demonstrated. The sensor probe employs the SiC chip as a Fabry-Perot (FP) interferometer to measure the change in refractive index and thickness of SiC with temperature. A novel temperature sensing method that combines wavelength-tuned signal processing for coarse measurements and classical FP etalon peak shift for fine measurements is proposed and demonstrated. This method gives direct unambiguous temperature measurements with a high temperature resolution over a wide temperature range. An alternative method using blackbody radiation from a SiC chip in a two-color pyrometer configuration for coarse temperature measurement and classical FP laser interferometry via the same chip for fine temperature measurement is also proposed and demonstrated. The sensor design is successfully deployed in an industrial test rig environment with gas temperatures exceeding 1200 C. This sensor is proposed as an alternate to all-electrical thermocouples that are susceptible to severe reliability and lifetime issues in such extreme environments. A few components non-contact thickness measurement system for optical quality semi-transparent samples such as Silicon (Si) and 6H SiC optical chips such as the one used in the design of this sensor is proposed and demonstrated. The proposed system is self-calibrating and ensures a true thickness measurement by taking into account material dispersion in the wavelength band of operation. For the first time, a 100% repeatable all-digital electronically-controlled pinhole laser beam profiling system using a Texas Instruments (TI) Digital Micro-mirror Device (DMD) commonly used in projectors is experimentally demonstrated using a unique liquid crystal image generation system with non-invasive qualities. Also proposed and demonstrated is the first motion-free electronically-controlled beam propagation analyzer system using a TI DMD and a variable focus liquid lens. The system can be used to find all the parameters of a laser beam including minimum waist size, minimum waist location and the beam propagation parameter M2. Given the all-digital nature of DMD-based profiling and all-analog motion-free nature of the Electronically Controlled Variable Focus Lens (ECVFL) beam focus control, the proposed analyzer versus prior-art promises better repeatability, speed and reliability. For the first time, Three Dimensional (3-D) imaging is demonstrated using an electronically controlled Liquid Crystal (LC) optical lens to accomplish a no-moving parts depth section scanning in a modified commercial 3-D confocal microscope. The proposed microscopy system within aberration limits has the potential to eliminate the sample or objective motion-caused mechanical forces that can distort the original sample structure and lead to imaging errors. A signal processing method for realizing high resolution three dimensional (3-D) optical imaging using diffraction limited low resolution optical signals is also proposed

Towards the development of a hybrid-integrated chip interferometer for online surface profile measurements

Non-destructive testing and online measurement of surface features are pressing demands in manufacturing. Thus optical techniques are gaining importance for characterization of complex engineering surfaces. Harnessing integrated optics for miniaturization of interferometry systems onto a silicon wafer and incorporating a compact optical probe would enable the development of a handheld sensor for embedded metrology applications. In this work, we present the progress in the development of a hybrid photonics based metrology sensor device for online surface profile measurements. The measurement principle along with test and measurement results of individual components has been presented. For non-contact measurement, a spectrally encoded lateral scanning probe based on the laser scanning microscopy has been developed to provide fast measurement with lateral resolution limited to the diffraction limit. The probe demonstrates a lateral resolution of ∼3.6 μm while high axial resolution (sub-nanometre) is inherently achieved by interferometry. Further the performance of the hybrid tuneable laser and the scanning probe was evaluated by measuring a standard step height sample of 100 nm

Design and Development of an Optical Chip Interferometer For High Precision On-Line Surface Measurement

Advances in manufacturing and with the demand of achieving faster throughput at a lower cost in any industrial setting have put forward the need for embedded metrology. Embedded metrology is the provision of metrology on the manufacturing platform, enabling measurement without the removal of the workpiece. Providing closer integration of metrology upon the manufacturing platform will improve material processing and reliability of manufacture for high added value products in ultra-high-precision engineering. Currently, almost all available metrology instrumentation is either too bulky, slow, destructive in terms of damaging the surfaces with a contacting stylus or is carried out off-line. One technology that holds promise for improving the current state-of-the-art in the online measurement of surfaces is hybrid photonic integration. This technique provides for the integration of individual optoelectronic components onto silicon daughter boards which are then incorporated on a silica motherboard containing waveguides to produce a complete photonic circuit. This thesis presents first of its kind a novel chip interferometer sensor based on hybrid integration technology for online surface and dimensional metrology applications. The complete metrology sensor system is structured into two parts; hybrid photonic chip and optical probe. The hybrid photonic chip interferometer is based on a silica-on-silicon etched integrated-optic motherboard containing waveguide structures and evanescent couplers. Upon the motherboard, electro-optic components such as photodiodes and a semiconductor gain block are mounted and bonded to provide the required functionality. Optical probe is a separate entity attached to the integrated optic module which serves as optical stylus for surface scanning in two measurement modes a) A single-point for measuring distance and thus form/surface topography through movement of the device or workpiece, b) Profiling (lateral scanning where assessment of 2D surface parameters may be determined in a single shot. Wavelength scanning and phase shifting inteferometry implemented for the retrival of phase information eventually providing the surface height measurement. The signal analysis methodology for the two measurement modes is described as well as a theoretical and experimental appraisal of the metrology capabilities in terms of range and resolution. The incremetal development of various hybrid photonic modules such as wavelength encoder unit, signal detection unit etc. of the chip interferometer are presented. Initial measurement results from various componets of metrology sensor and the surface measurement results in two measurement modes validate the applicability of the described sensor system as a potential metrology tool for online surface measurement applications