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Developments in modern bio-imaging techniques have allowed the routine collection of a vast amount of data from various techniques. The challenges lie in how to build accurate and efficient models to draw conclusions from the data and facilitate scientific discoveries. Fortunately, recent advances in statistics, machine learning, and deep learning provide valuable tools. This thesis describes some of our efforts to build scalable Bayesian models for four bio-imaging applications: (1) Stochastic Optical Reconstruction Microscopy (STORM) Imaging, (2) particle tracking, (3) voltage smoothing, (4) detect color-labeled neurons in c elegans and assign identity to the detections.

Dark current is an unwanted source of noise in images produced by digital imagers, the de facto standard of imaging. The two most common types of digital imager architectures, Charged-Coupled Devices (CCDs) and Complementary Metal-Oxide-Semiconductor (CMOS), are both prone to this noise source. To accurately reflect the information from light signals this noise must be removed. This practice is especially vital for scientific purposes such as in astronomical observations. Presented in this dissertation are characterizations of dark current sources that present complications to the traditional methods of correction. In particular, it is observed that pixels in both CCDs and CMOS image sensors produce dark current that is affected by the presence of pre-illuminating the sensor and that these same pixels produce a nonlinear dark current with respect to exposure time. These two characteristics are not conventionally accounted for as it is assumed that the dark current produced will be unaffected by charge accumulated from either illumination or the dark current itself. Additionally, a model reproducing these dark current characteristics is presented. The model incorporates a moving edge of the depletion region, where charge is accumulated, as well as fixed recombination-generation locations. Recombination-generation sites in the form of heavy metal impurities, or lattice defects, are commonly the source of dark current especially in the highest producing pixels, commonly called "hot pixels." The model predicts that pixels with recombination-generation sites near the edge of an empty depletion region will produce less dark current after accumulation of charge, accurately modeling the behavior observed from empirical sources. Finally, it is shown that activation energy calculations will produce inconsistent results for pixels with the presence of recombination-generation sites near the edge of a moving depletion region. Activation energies, an energy associated with the temperature dependence of dark current, are often calculated to characterize aspects of the dark current including types of impurities and sources of dark current. The model is shown to generate data, including changing activation energy values, that correspond with changing activation energy calculations in those pixels observed to be affected by pre-illumination and that produce inconsistent dark current over long exposure times. Rather than only being a complication to dark current correction, the presence of such pixels, and the model explaining their behavior, presents an opportunity to obtain information, such as the depth of these recombination-generation sites, which will aid in refining manufacturing processes for digital imagers.

Thesis (Ph.D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences and the Woods Hole Oceanographic Institution), 2000. / Vita. / Includes bibliographical references (leaves 179-187). / A spectral camera (ALISS - Ambient Light Imaging and Spectral System) was used to image ambient light from high-temperature vents at 9°N East Pacific Rise and the Juan de Fuca Ridge during 1997 and 1998 Alvin dive cruises. ALISS is a low-light digital camera with custom-designed optics. A set of nine lenses, each covered by an individual bandpass filter (50 and 100 nm nominal bandwidths), allows vents to be imaged in nine wavelength bands simultaneously spanning the range of 400-1000 nm. Thus, both spatial and spectral information are obtained. ALISS was used to image three types of vents: black smokers, flange pools, and beehives. The primary source of light is thermal radiation due to the high temperature of the hydrothermal fluid (~350°C). This light is dominant at wavelengths greater than 700 nm. At flange pools, where the fluid is relatively stable, only thermal radiation is present. Black smokers and beehives, however, are subject to mixing with ambient seawater (2°C) leading to mineral precipitation. Data from these types of vents show the existence of non-thermal, temporally varying light in the 400-700 nm region. This light is probably caused by mechanisms related to mixing and precipitation, such as chemiluminescence, crystalloluminescence and triboluminescence. / by Sheri N. White. / Ph.D.

Millimeter-wave imaging has gathered attention in recent years for its ability to penetrate clothing, thin layers of soils, and certain construction materials. However, image quality remains a challenge that needs to be addressed. One way of improving image quality is by increasing the dimensions of the collecting aperture. A sparse array can be used to synthesize a larger aperture with a limited set of relatively small detectors. In this research we design, build, and test a test-bed having an active source at 94 GHz and an array of coherent detectors, mounted on arms that extend radially on a rotary table. Using this test bed a circular area with a maximum diameter of 900 mm can be scanned. The signal is down-converted using heterodyne receivers with digital in-phase and quadrature detection. Signal correlation is performed using the digitized data, which is stored for post-processing, electronic focusing, and image reconstruction. Near-field imaging using interferometric reconstructions is achieved using electronic focusing. Imaging tests show the ability of the system to generate imagery of concealed and unconcealed objects at distances between 400 and 700 mm. A study of the effects of redundant and nonredundant configurations on image quality for 4 common detector configurations is presented. In this document we show that an active sparse-aperture imaging system using digital correlators is a viable way to generate millimeter-wave images.

A large fleet (in the hundreds) of high quality telescopes are used for tracking and imaging of launch vehicles during ascent from Cape Canaveral Air Force Station and Kennedy Space Center. A maintenance tool has been development for use with these telescopes. The tool requires rankings of telescope condition in terms of the ability to generate useful imagery. It is thus a case of ranking telescope conditions on the basis of the perceptual image quality of their imagery. Perceptual image quality metrics that are well-correlated to observer opinions of image quality have been available for several decades. However, these are quite limited in their applications, not being designed to compare various optical systems. The perceptual correlation of the metrics implies that a constant image quality curve (such as the boundary between two qualitative categories labeled as excellent and good) would have a constant value of the metric. This is not the case if the optical system parameters (such as object distance or aperture diameter) are varied. No published data on such direct variation is available and this dissertation presents an investigation made into the perceptual metric responses as system parameters are varied. This investigation leads to some non-intuitive conclusions. The perceptual metrics are reviewed as well as more common metrics and their inability to perform in the necessary manner for the research of interest. Perceptual test methods are also reviewed, as is the human visual system. iv Image formation theory is presented in a non-traditional form, yielding the surprising result that perceptual image quality is invariant under changes in focal length if the final displayed image remains constant. Experimental results are presented of changes in perceived image quality as aperture diameter is varied. Results are analyzed and shortcomings in the process and metrics are discussed. Using the test results, predictions are made about the form of the metric response to object distance variations, and subsequent testing was conducted to validate the predictions. The utility of the results, limitations of applicability, and the immediate ability to further generalize the results is presented.

The science and technology of X-rays has only been part of human achievement for the past 100 years, while the study of image formation in general has endured for as long as 1000 years. The ability to conceive, design, and fabricate X-ray imagers, moreover, has existed for only the past 70 years, and X-ray astronomical telescopes have been in use for a mere 35 years. Considering that aplanatic, normal incidence telescope designs required more than 400 years to perfect, it is most interesting to note that the development of ‘aplanatic’ grazing incidence telescopes has taken only about 40 years. In order to improve and expand the field of X-ray astronomy, and imaging in general, we find that these days a comprehensive systems engineering approach to X-ray image formation must be undertaken. While some industrial interests have taken steps in this direction, any academic approach is lacking from within the archival literature to date, and there are virtually no established university courses. Indeed, it would seem that top level, optical-systems-engineering is exclusively reserved for those seasoned professionals who have accumulated (though somewhat artistically) the “know-how” to efficiently conceive and implement excellent optical designs. Such expert knowledge is not and should not be mysterious. To this end, we attempt to formulate a highly comprehensive approach to X-ray optical systems engineering and implement it within the context of the Wolter Type-I and Type-II (grazing incidence) telescopes currently utilized for practical X-ray/EUV astronomy. In addition, we will transform the classical paraboloid-hyperboloid designs into ‘aplanatic’ and ‘isoplanatic’, hyperboloid-hyperboloid systems, where certain coma conditions are minimized. As will be shown, one gains little improvement in performance when choosing a quasi-aplanatic mirror design over a classical one, owing to scatter and other image degradation effects. Next we will show that a generalized hyperboloid-hyperboloid design can be comprehensively optimized for any imaging requirement, where the operational field-of-view is weighted according to spatial information content. Our H-H design has been optimized for the GOES Solar X-ray Imager mission and adopted by NASA and NOAA. It is currently undergoing fabrication by Raytheon Optical Systems Inc. who is under subcontract to the Lockheed-Martin Solar and Astrophysics Laboratory. Our design is expected to result in an 80% increase in optical system performance over the original SXI baseline design.

The objectives of this research were (1) to develop scales of preferred image sharpness for thermal dye transfer prints and (2) to relate these scales to an objective measurement of image quality. Interval scales were developed using two different indirect scaling techniques, paired comparison and rank ordering, for three groups of participants (novice photographers, advanced amateur photographers, and Kodak image quality experts). Differences between scales developed through the separate scaling procedures were minor, suggesting that either procedure would produce a reliable and valid interval scale. Given the time required to perform the method of paired comparisons, the method of rank ordering would likely be the preferred procedure. The results from multiple range tests of the interval scales found that higher levels of image sharpening (filter levels 1.5x to 2.5x) were generally preferred. However, for some conditions, particularly the portrait, lower levels of sharpening were generally preferred. While it appears that the preferred level of image sharpness may be somewhat dependent upon scene content, participants always preferred a small amount of sharpening to none at all. For all conditions examined, stimuli that received no sharpening were the least preferred. In relating interval scales to an objective measure of image quality, scale values developed from within a level of addressability were highly correlated with values of modified MTFA for all participant groups. These correlations show that a strong relationship exists between preferred levels of image sharpness and increasing levels of luminance modulation for edges in thermal prints. However, values of modified MTFA were not well correlated with interval scale values developed from experts participants for the between levels of addressability portion of the experiment. Values of MTFA were considered modified due to limits that were imposed on the bounds of integration. These results suggest that the preferences of experts may not represent those of the average consumer for desired levels of thermal print sharpness. / Ph. D.

This dissertation research had three primary objectives. The first was to develop and evaluate a metric of image quality that incorporates a model of suprathreshold contrast and is based upon the perceived magnitude of suprathreshold contrast. The second objective was to determine the effects that common display characteristics, such as MTF shape, noise, and field of view, have on a display observer's ability to perceive egocentric motion from a display. The third and final objective was to provide a discussion of the use of image quality metrics for the evaluation of displays that are designed to facilitate motion perception. To meet these objectives, two experiments were conducted. The first experiment investigated the effects of the display Field of View, Dynamic Contrast Range, Noise Level, and Bandwidth on perceived image quality. The second study investigated the effects of these same display parameters as well as the effect of terrain type on observers’ sensitivity to changes in the speed of image motion. Existing visual psychophysical data were used to propose the two additional image quality metrics, the Perceived Contrast Magnitude (PCM) and the Weighted Perceived Contrast Magnitude (WPCM). Each of these metrics provides some additional model parameters to the Modulation Transfer Function Area (MTFA). However, based upon the studies that were conducted in this dissertation, it appears that the Integrated Contrast Sensitivity (ICS) and Square Root Integral (SQRI) provide significantly better estimates of perceived image quality than do MTFA, PCM, or WPCM. Results indicate that the display parameters of Bandwidth, Field of View, and Noise Level, plus several interactions significantly influenced the observers’ sensitivity to changes in the speed of images. One interaction indicated that observers were more sensitive to changes in the speed of images when the scene contained a lot of contextual information or when the scene was viewed through a display with reasonably high bandwidth and low noise level. However, when the bandwidth of the system was decreased, the noise level was increased, and the contextual information in the image was reduced, the observer's sensitivity to changes in motion was degraded when viewing the image through a small field of view display (20 deg) but it was not degraded when viewing the image through a larger field of view display (47 deg). Based upon the evidence collected in this dissertation, it appears that displays designed to support motion perception should have a relatively large field of view with partitions to facilitate relative motion perception. The factors of Dynamic Contrast Range and Field of View were shown to have different effects on the perception of image quality than they have on the perception of changes in the speed of an image. Therefore, the use of image quality metrics for the evaluation and design of displays that must support the veridical perception of motion should be questioned. Instead, it appears that a task specific evaluation technique should be developed for the evaluation of these displays. / Ph. D.

The effects of physical image quality on reading and on perceived image quality from CRT and hard copy were studied in this experiment. The results showed that as the image quality of a display increased, indicated by an increase in the value of the MTFA, the reading speed increased and subjective image quality V; ratings increased. This change in reading speed and perceived image quality occurred in the hard copy as well as in the soft copy condition. Image quality, therefore, is concluded to be the major determinant of subjects' performance with respect to displayed information. This implies that if the image quality the displayed text ls the same on the display techniques used, subjects will read from CRT displays as fast as from hard copy displays. / Master of Science