Optical Diffraction Tomography for Single Cells

Analyzing the structure of a single cell based on its refractive index (RI) distribution is a common and valued approach, because it does not require any artificial markers. The RI is an inherent structural marker that can be quantified in three dimensions with optical diffraction tomography (ODT), an inverse scattering technique. This work reviews the theory of ODT and its implementation with an emphasis on single-cell analysis, identifying the Rytov approximation as the most efficient descriptor for light propagation. The accuracy of the reconstruction method is verified with in silico data and imaging artifacts associated with the inverse scattering approach are addressed. Furthermore, an experimental ODT setup is presented that consists of a bright-field microscope, a phase-imaging camera, and an optical trap combined with a microfluidic chip. A novel image analysis pipeline is proposed that addresses image corrections and frame alignment of the recorded data prior to the RI reconstruction. In addition, for a rotational axis that is tilted with respect to the image plane, an improved reconstruction algorithm is introduced and applied to single, suspended cells in vitro, achieving sub-cellular resolution

Research studies on advanced optical module/head designs for optical devices

A summary is presented of research in optical data storage materials and of research at the center. The first section contains summary reports under the general headings of: (1) Magnetooptic media: modeling, design, fabrication, characterization, and testing; (2) Optical heads: holographic optical elements; and (3) Optical heads: integrated optics. The second section consist of a proposal entitled, Signal Processing Techniques for Optical Data Storage. And section three presents various publications prepared by the center

Discrete Modeling and Sliding Mode Control of Piezoelectric Actuators

With the ability to generate fine displacements with a resolution down to sub-nanometers, piezoelectric actuators (PEAs) have found wide applications in various nano-positioning systems. However, existence of various effects in PEAs, such as hysteresis and creep, as well as dynamics can seriously degrade the PEA performance or even lead to instability. This raises a great need to model and control PEAs for improved performance, which have drawn remarkable attention in the literature. Sliding mode control (SMC) shows its potential to the control of PEA, by which the hysteresis and other nonlinear effects can be regard as disturbance to the dynamic model and thus rejected or compensated by its switching control. To implement SMC in digital computers, this research is aimed at developing novel discrete models and discrete SMC (DSMC)-based control schemes for PEAs, along with their experimental validation. The first part of this thesis concerns with the modeling and control of one-degree of freedom (DOF) PEA, which can be treated as a single-input-single-output (SISO) system. Specifically, a novel discrete model based on the concept of auto-regressive moving average (ARMA) was developed for the PEA hysteresis; and to compensate for the PEA hysteresis and improve its dynamics, an output tracking integrated discrete proportional-integral-derivative-based SMC (PID-SMC) was developed. On this basis, by making use of the availability of PEA hysteresis models, two control schemes, named “the discrete inversion feedforward based PID-SMC” and “the discrete disturbance observer (DOB)-based PID-SMC”, were further developed. To illustrate the effectiveness of the developed models and control schemes, experiments were designed and conducted on a commercially available one-DOF PEA, as compared with the existing ones. The second part of the thesis presents the extension of the developed modeling and control methods to multi-DOF PEAs. Given the fact that details with regard to the PEA internal configurations is not typically provided by the manufacturer, a state space model based on the black box system identification was developed for the three-DOF PEA. The developed model was then integrated in the output tracking based discrete PID-SMC, with its effectiveness verified through the experiments on a commercially available three-DOF PEA. The superiority of the proposed control method over the conventional PID controller was also experimentally investigated and demonstrated. Finally, by integrating with a DOB in the discrete PID-based SMC, a novel control scheme is resulted to compensate for the nonlinearities of the three-DOF PEA. To verify its effectiveness, the discrete DOB based PID-SMC was applied in the control experiments and compared with the existing SMC. The significance of this research lies in the development of the discrete models and PID-based SMC for PEAs, which is of great help to improve their performance. The successful application of the proposed method in the control of multi-DOF PEA allows the application of SMC to the control of complicated multi-inputs-multi-outputs (MIMO) systems without details regarding the internal configuration. Also, integration of the inversion based feedforward control and the DOB in the SMC design has been proven effective for the tracking control of PEAs

Statistical Performance Evaluation, System Modeling, Distributed Computation, and Signal Pattern Matching for a Compton Medical Imaging System.

Radionuclide cancer therapy requires imaging radiotracers that concentrate in tumors and emit high energy charged particles that kill tumor cells. These tracers, such as 131I, generally emit high energy photons that need to be imaged to estimate tumor dose and changes in size during treatment. This research describes the performance of a dual-planar silicon-based Compton imaging system and compares it to a conventional parallel-hole collimated Anger camera with high energy general purpose lead collimator for imaging photons emitted from 131I. The collimated Anger camera imposes a tradeoff between resolution and sensitivity due to the mechanical collimation. As the energy of photons exceed 364keV, increased septal penetration and scattering further degrade the imaging performance. Simulations of the Anger camera and the Compton imaging system demonstrate a 20-fold advantage in detection efficiency and higher spatial resolution for detecting high energy photons by the Compton camera since it decouples the tradeoff. The system performance and comparision are analyzed using the modified uniform Cramer-Rao bound algorithms we developed along with the Monte Carlo calculations and system modeling. The bound show that the effect of Doppler broadening is the limiting factor for Compton camera performance for imaging 364keV photons. Performance of the two systems was compared and analyzed by simulating a 2D disk with uniform activities. For the case in which the two imaging systems detected the same number of events, the proposed Compton imaging system has lower image variance than the Anger camera with HEGP when the FWHM of the desired point source response is less than 1.2 cm. This advantage was also demonstrated by imaging and reconstructing a 2D hot spot phantom. In addition to the performance analysis, the distributed Maximum Likelihood Maximization Expectation algorithm with chessboard data partition was evaluated for speeding up image reconstruction for the Compton imaging system. A 1 x 64 distributed computing system speeded computation by about a factor of 22 compared to a single processor. Finally, a real-time signal processing and pattern matching system employing state-of-the-art digital electronics is described for solving problems of event pile-up raised by high photon count rate in the second detector.Ph.D.Biomedical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/60851/1/lhan_1.pd

Off-axis Holografie im aberrationskorrigierten Transmissionselektronenmikroskop

Die off-axis Elektronenholografie im Transmissionselektronenmikroskop (TEM) erlaubt die quantitative Rekonstruktion der komplexen Objektaustrittswelle mit atomarer Auflösung. Die Auswertung der Phase dieser Welle ermöglicht die Unterscheidung der Atomsorten bzw. das Zählen der Atome in Projektionsrichtung sowie die Bestimmung von Atompositionen. Damit ist ein TEM über die einfache Abbildung hinaus ein sehr leistungsstarkes Messgerät zur quantitativen Analyse kleinster Strukturen bis hin zur atomaren Skala. Die Prozedur von der Aufnahme eines hochaufgelösten Elektronenhologramms über die Rekonstruktion bis zur bildfehlerkorrigierten Objektwelle ist jedoch sehr umfangreich und teils sehr anfällig für Artefakte. Diese Arbeit zeigt unter kritischer Betrachtung der einzelnen Einflüsse, wie dieser Weg zu beschreiten ist, um schlussendlich zu einer artefaktfreien, interpretierbaren Objektwelle zu gelangen. Im letzten Jahrzehnt haben Bildfehler-Korrektoren die höchstauflösende Transmissions-elektronenmikroskopie auf instrumenteller Seite revolutioniert. Auch die off-axis Holografie kann eine ganze Reihe von Vorteilen aus diesem elektronenoptischen Zusatzsystem ziehen. Neben der Analyse dieser einzelnen Verbesserungen, insbesondere der Phasensignalauflösung, wird gezeigt, wie es das Cs-korrigierte TEM zu optimieren gilt, um schließlich bestmögliche Ergebnisse für quantitative Objektanalyse zu erzielen. Zwei Anwendungsbeispiele zeigen experimentelle Ergebnisse der Elektronenholografie mit Cs-korrigierten Mikroskopen. Bei der Analyse ferroelektrischer Nanoschichten erweisen sich die einzigartigen Möglichkeiten der holografischen Auswertung im Zusammenspiel mit der nunmehr hervorragenden Signalauflösung als äußerst nützlich, um die ferroelektrische Polarisation zu ermitteln. Die Objektwellenrekonstruktion der Korngrenze in einer Goldfolie demonstriert weitere Verbesserungen für die Holografie, wenn zusätzlich eine neuartige Elektronenquelle mit höherem Richtstrahlwert zum Einsatz kommt. Einzelne Goldatome werden mit einem Signal-Rausch-Verhältnis von ca. 10 in Amplitude und Phase messbar.Off-axis electron holography in a transmission electron microscope (TEM) allows reconstructing the complex object exit-wave quantitatively with atomic resolution. Analyzing the phase shift of this wave gives access to the atomic species and enables counting the number of atoms in projection direction as well as determining atom positions. Therefore, a TEM is a very powerful measuring device for quantitative analysis of smallest structures down to the atomic scale beyond simple microscopic imaging. The procedure of the recording of a high-resolution electron hologram, its reconstruction, and after numerical aberration correction finally ending up with the object-exit wave, is quite comprehensive and partially susceptible to artifacts. This work shows how to manage this procedure in order to obtain an interpretable object exit-wave, which is free of artifacts. In instrumentation within the last decade aberration correctors have revolutionized high-resolution electron microscopy. Also off-axis holography can benefit from this electron optical add-on module. Besides the exploration of each improvement, in particular the phase detection limit, this work demonstrates, how to optimize the Cs-corrected TEM in order to get best possible results for quantitative object analysis. Two application examples show experimental results of electron holography with Cs-corrected microscopes. For the investigation of ferroelectric nanolayers, the unique possibilities of the holographic evaluation together with the strongly improved signal resolution turn out to be very useful when determining the ferroelectric polarization. The object wave reconstruction of the grain boundary in a gold film demonstrates further improvements for holography, when additionally using a new electron gun with improved brightness. Single gold atoms become measurable with a signal-noise-ratio of about 10 in amplitude and phase

Reconstruction of 3D scenes from pairs of uncalibrated images. Creation of an interactive system for extracting 3D data points and investigation of automatic techniques for generating dense 3D data maps from pairs of uncalibrated images for remote sensing applications.

Much research effort has been devoted to producing algorithms that contribute directly or indirectly to the extraction of 3D information from a wide variety of types of scenes and conditions of image capture. The research work presented in this thesis is aimed at three distinct applications in this area: interactively extracting 3D points from a pair of uncalibrated images in a flexible way; finding corresponding points automatically in high resolution images, particularly those of archaeological scenes captured from a freely moving light aircraft; and improving a correlation approach to dense disparity mapping leading to 3D surface reconstructions. The fundamental concepts required to describe the principles of stereo vision, the camera models, and the epipolar geometry described by the fundamental matrix are introduced, followed by a detailed literature review of existing methods. An interactive system for viewing a scene via a monochrome or colour anaglyph is presented which allows the user to choose the level of compromise between amount of colour and ghosting perceived by controlling colour saturation, and to choose the depth plane of interest. An improved method of extracting 3D coordinates from disparity values when there is significant error is presented. Interactive methods, while very flexible, require significant effort from the user finding and fusing corresponding points and the thesis continues by presenting several variants of existing scale invariant feature transform methods to automatically find correspondences in uncalibrated high resolution aerial images with improved speed and memory requirements. In addition, a contribution to estimating lens distortion correction by a Levenberg Marquard based method is presented; generating data strings for straight lines which are essential input for estimating lens distortion correction. The remainder of the thesis presents correlation based methods for generating dense disparity maps based on single and multiple image rectifications using sets of automatically found correspondences and demonstrates improvements obtained using the latter method. Some example views of point clouds for 3D surfaces produced from pairs of uncalibrated images using the methods presented in the thesis are included.Al-Baath UniversityThe appendices files and images are not available online

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Epidemiology of injuries in high-level youth sport in Luxembourg [Abstract]

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