The point-spread function (PSF) of an imaging system can affect the precision to which geometric features can be measured in digital images. It is shown that the PSF alone, when larger than a certain size relative to the sampling rate, does not cause a loss of precision, but actually improves the precision to which features can be measured. Quantization of the samples in an image is the limiting factor on precision. How much the precision is limited in the face of quantization depends on the size and shape of the PSF. The theory of locales is used extensively to compute bounds on precision as a function of PSF size and shape. Many geometric feature models are considered although almost all of the emphasis is on analysis of the unit step edge. It is shown for the step edge that the size of a PSF has more influence on precision than its shape. The size for which optimal precision occurs is ∼0.7 pixels in "radius". Bounds on precision are also shown for the case of a fixed rectangular sampling PSF with a variable-sized optical PSF and for the case where electronic components introduce asymmetry into the PSF. A method for objective comparison of imaging system PSFs is demonstrated. Other factors influencing precision, including unknown scene contrast and noise, are briefly examined. To illustrate the utility of the results, an experiment is presented showing that approximation of a PSF by a Gaussian PSF results in little loss of precision. Another illustrative experiment shows how the orientation precision of several widely-used first derivative operators are affected by the PSF and shows how the template coefficients can be found to optimize orientation precision for a given PSF.

The primary distinction between an ordinary optical system and one which is both unobscured and reflective is that the elements of the latter must be tilted or decentered with respect to one another. In general, this results in an optical system which has no axis of rotational symmetry, and therefore the classical aberration theory of symmetric systems is no longer applicable. Furthermore, the image becomes anamorphic and keystone distorted, due to the relative tilt between the object and the optical surfaces. The first part of this work is the development of a semi-analytic treatment of the properties (through third order) of systems possessing large tilts and decentrations. The Gaussian properties of both the image and pupil are described in terms of tilt, decentration, magnification, keystone distortion, and anamorphic distortion parameters. In computing these parameters, it is important to take into account the transferred components of the parameters, which are due to the Gaussian properties of the preceding surfaces. The third order properties are computed using the fact that each optical surface, together with its associated entrance pupil, form an optical subsystem which possesses an axis of approximate symmetry. About this axis, the aberration contributions of that surface may be described in the classical wave aberration expansion. The coefficients in this expansion may be corrected for the non-circular appearance of both the object and pupil, using the parametric description of their Gaussian form. the aberration fields due to the various surface contributions are then combined vectorally to yield the resultant aberration field in the image plane. The vector theory is applied to the analysis of several optical systems, and the accuracy of the theory verified by comparison with raytrace data. As a demonstration of the usefulness of the theory to an optical designer, a three mirror unobscured system was designed using a methodology derived from the theory. At each step, the design options are explained, and the probable results are discussed. The residual aberrations of the resulting system are studied, and the selection of another design starting point is discussed from the point of view of the theory.

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Wang, Jianpeng. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references. / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts also in Chinese.

High quality three-dimensional bioluminescence tomographic (BLT) images, if available, would constitute a major advance and provide much more useful information than the two-dimensional bioluminescence images that are frequently used today. To-date, high quality BLT images have not been available, largely because of the poor quality of the data being input into the reconstruction process. Many significant confounds are not routinely corrected for and the noise in this data is unnecessarily large and poorly distributed. Moreover, many of the design choices affecting image quality are not well considered, including choices regarding the number and type of filters used when making multispectral measurements and choices regarding the frequency and uniformity of the sampling of both the range and domain of the BLT inverse problem. Finally, progress in BLT image quality is difficult to gauge owing to a lack of realistic gold-standard references that engage the full complexity and uncertainty within a small animal BLT imaging experiment. Within this dissertation, I address all of these issues. I develop a Cerenkov-based gold-standard wherein a Positron Emission Tomography (PET) image can be used to gauge improvements in the accuracy of BLT reconstruction algorithms. In the process of creating this reference, I discover and describe corrections for several confounds that if left uncorrected would introduce artifacts into the BLT images. This includes corrections for the angle of the animal’s skin surface relative to the camera, for the height of each point on the skin surface relative to the focal plane, and for the variation in bioluminescence intensity as a function of luciferin concentration over time. Once applied, I go on to derive equations and algorithms that when employed are able to minimize the noise in the final images under the constraints of a multispectral BLT data acquisition. These equations and algorithms allow for an optimal choice of filters to be made and for the acquisition time to be optimally distributed among those filtered measurements. These optimizations make use of Barrett’s and Moore-Penrose pseudoinverse matrices which also come into play in a paradigm I describe that can be used to guide choices regarding sampling of the domain and range.

Understanding the relationship between neural activity and cortical hemodynamics, or neurovascular coupling is the foundation to interpret neuroimaging signals such as functional magnetic resonance imaging (fMRI) which measure local changes in hemodynamics as a proxy for underlying neural activity. Even though the stereotypical stimulus-evoked hemodynamic response pattern with increased concentration of oxy- and total-hemoglobin and decrease in concentration of deoxy-hemoglobin has been well-recognized, the linearity of neurovascular coupling and its variances depending on brain state and tasks haven’t been thoroughly evaluated. To directly assess the cortical neurovascular coupling, simultaneous recordings of neural and hemodynamic activity were imaged by wide-field optical mapping (WFOM) over the bilateral dorsal surface of the mouse brain through a bilateral thinned-skull cranial window. Neural imaging is achieved through wide-field fluorescence imaging in animals expressing genetically encoded calcium sensor (Thy1-GCaMP). Hemodynamics are recorded via simultaneous imaging of multi-spectral reflectance. Significant hemodynamic crosstalk was found in the detected fluorescence signal and the physical model of the contamination, methods of correction as well as electrophysiological verification are presented. A linear model between neural and hemodynamic signals was used to fit spatiotemporal hemodynamics can be predicted by convolving local fluorescence changes with hemodynamic response functions derived through both deconvolution and gamma-variate fitting. Beyond confirming that the resting-state hemodynamics in the awake and anesthetized brain are coupled to underlying neural activity, the patterns of bilaterally symmetric spontaneous neural activity observed by WFOM emulate the functionally connected networks detected by fMRI. This result provides reassurance that resting-state functional connectivity has neural origins. With the access to cortical neural activity at mesoscopic level, we further explore the cortical neural representations preceding and during spontaneous locomotion.

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No description available.

Two-photon microscopy is often used in biological imaging due to its optical sectioning and depth penetration capabilities. These characteristics have made two-photon microscopy especially useful for neurobiological studies where imaging a volume at single cell resolution is typically required. This dissertation focuses on the optimization of two-photon excited fluorescence for volumetric imaging of biological samples, with special attention to imaging the mouse brain. Chapter 2 studies wavefront manipulation as a way of optimizing two-photon excited fluorescence. We show, through numerical simulations and experiments, that the magnitude of the two-photon fluorescence signal originating from cell-sized objects can be used as a metric of beam quality. We also show that the cranial window used in mouse experiment is a major source of aberrations, which can readily be represented in the Zernike basis. Finally, we implement a modal wavefront optimization scheme that optimizes the wavefront based entirely on the magnitude of the fluorescence. Along with this scheme, Zernike functions are found to be a useful basis for correcting aberrations encountered in mouse brain imaging while the Hadamard basis is found to be useful for scattering compensation. Corrections performed in mouse brain using Zernike functions are found to be valid over hundreds of microns, allowing a single correction to be applied to a whole volume. Finally, we show that the wavefront correction system can double as a wavefront encoding system for experiments that require custom point-spread-functions. Chapter 3 aims to significantly improve the volume imaging rate of two-photon microscopy. The imaging speed is improved by combining two-photon excitation with scanning confocally-aligned planar excitation microscopy (SCAPE). Numerical simulations, analytical arguments, and experiments reveal that the standard method of combining nano-joule pulses with 80 MHz repetition rates is inadequate for two-photon light-sheet excitation. We use numerical simulations and experiments to explore the possibility of achieving fast volumetric imaging using line and sheet excitation and find that the sheet excitation scheme is more promising. Given that two-photon excitation requires high photon-flux-densities near the focus, achieving high enough fluorescence has to be balanced with restrictions placed by saturation, photodamage, photobleaching and sample heating effects. Finally, we experimentally study light sheet excitation at various pulse repetition rates with femtosecond pulses and find that repetition rates near 100 kHz allow imaging of nonbiological samples of ~200x300x300 μm^3 volume at 20 volumes per second while balancing the above constraints. This work paves the way for achieving fast, volumetric two-photon imaging of the mouse brain.

Yu, Tsz Tat. / "December 2010." / Thesis (M.Phil.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 143-147). / Abstracts in English and Chinese. / Abstract --- p.2 / 摘要 --- p.4 / Acknowledgements --- p.5 / List of Figures --- p.6 / List of Tables --- p.12 / List of Abbreviations --- p.13 / Table of Contents --- p.14 / Chapter Chapter 1 --- Introduction --- p.17 / Chapter Chapter 2 --- Literature Review / Chapter 2.1 --- Surface Plasmon Wave --- p.19 / Chapter 2.2 --- Excitation of Surface Plasmon --- p.23 / Chapter 2.3 --- Surface Plasmon Coupling --- p.24 / Chapter 2.4 --- Surface Plasmon Resonance Detection Techniques --- p.33 / Chapter 2.5 --- Applications of SPR biosensors --- p.39 / Chapter Chapter 3 --- Theory of irradiance modulator / Chapter 3.1 --- Polarization --- p.44 / Chapter 3.2 --- Optical polarizer --- p.45 / Chapter 3.3 --- Liquid Crystal Modulator --- p.49 / Chapter 3.4 --- Irradiance Modulator --- p.52 / Chapter Chapter 4 --- LCM characterization / Chapter 4.1 --- Single LCM Transmittance driven by pure square wave --- p.66 / Chapter 4.2 --- Single LCM Reflectance driven by 50:50 STAM wave --- p.70 / Chapter 4.3 --- Multiple LCMs Reflectance driven by 90:10 STAM wave --- p.73 / Chapter Chapter 5 --- Background of phase measurement / Chapter 5.1 --- From holography to shearography --- p.77 / Chapter 5.2 --- From static Mach-Zehnder interferometer to differential-phase Mach-ZehnderZ interferometer --- p.81 / Chapter 5.3 --- From differential-phase imaging to pixel-referencing imaging --- p.86 / Chapter Chapter 6 --- Pixel-referencing data processing / Chapter 6.1 --- Background --- p.89 / Chapter 6.2 --- Procedures --- p.94 / Chapter 6.3 --- Experimental results --- p.98 / Chapter 6.4 --- Sensor resolution --- p.116 / Chapter 6.5 --- Performance comparison between single-beam LCM and Mach Zehnder configuration --- p.119 / Chapter Chapter 7 --- Discussions / Chapter 7.1 --- Experiment precautions --- p.136 / Chapter 7.2 --- Linear curve fitting --- p.137 / Chapter 7.3 --- Hardware limitation: Low frame rate --- p.138 / Chapter 7.4 --- Matching oil and glass slide --- p.139 / Chapter Chapter 8. --- Conclusions --- p.141 / References --- p.143 / Appendix / Chapter A1 --- "Concentration, Refractive Index and Dielectric constant of Sodium Chloride Solution (20°C)" --- p.148 / Chapter A2 --- Liquid Crystal Modulator Specification --- p.149 / Chapter A3 --- "Digital-to-analogue Converter Device (NI, PCI6036E) Datasheet" --- p.150 / Chapter A4 --- "CCD Camera (Lumenera, Infinity) Datasheet" --- p.151 / Chapter A5 --- Flow chart of SPR phase extraction --- p.152 / Chapter A6 --- Codes of SPR phase extraction in modules --- p.153