Tuberculosis is a major concern in low- and middle-income countries, but may be diagnosed using standard chest x-rays. Conventional film-screen x-ray detectors require more maintenance than digital x-ray detectors and need a good supply chain of developer chemicals and film, which make them difficult to maintain in low-infrastructure areas of the world. Current digital x-ray technology is prohibitively expensive for this market, although it brings the possibility of tele-radiology and tele-medicine, quicker diagnosis time, and virtually no cost per test compared to other diagnostics for tuberculosis. This thesis examines the requirements on a small-sized, low-cost digital x-ray detector for this application. Two small x-ray detectors were integrated into x-ray systems, then characterized for detector performance using metrics known as modulation transfer function, noise power spectrum, and detective quantum efficiency. The system designs and the results of the experiments are shown. Details are also shown about the setup of the x-ray lab, including the door interlock system for a lead-lined x-ray cabinet. To determine whether a smaller x-ray detector is diagnostically accurate enough for tuberculosis diagnosis compared to full-size chest radiography equipment, a medical study was designed and run using a web-based survey of radiologists in Pakistan, where tuberculosis is a recognized disease. In an attempt to compare x-ray detector performance, MATLAB code was written to measure the modulation transfer function, noise power spectrum, and detective quantum efficiency of x-ray systems. The details about this code, and challenges in simulating the performance of physically different detectors are explained in the thesis.

abstract: One of the single-most insightful, and visionary talks of the 20th century, “There’s plenty of room at the bottom,” by Dr. Richard Feynman, represented a first foray into the micro- and nano-worlds of biology and chemistry with the intention of direct manipulation of their individual components. Even so, for decades there has existed a gulf between the bottom-up molecular worlds of biology and chemistry, and the top-down world of nanofabrication. Creating single molecule nanoarrays at the limit of diffraction could incentivize a paradigm shift for experimental assays. However, such arrays have been nearly impossible to fabricate since current nanofabrication tools lack the resolution required for precise single-molecule spatial manipulation. What if there existed a molecule which could act as a bridge between these top-down and bottom-up worlds? At ~100-nm, a DNA origami macromolecule represents one such bridge, acting as a breadboard for the decoration of single molecules with 3-5 nm resolution. It relies on the programmed self-assembly of a long, scaffold strand into arbitrary 2D or 3D structures guided via approximately two hundred, short, staple strands. Once synthesized, this nanostructure falls in the spatial manipulation regime of a nanofabrication tool such as electron-beam lithography (EBL), facilitating its high efficiency immobilization in predetermined binding sites on an experimentally relevant substrate. This placement technology, however, is expensive and requires specialized training, thereby limiting accessibility. The work described here introduces a method for bench-top, cleanroom/lithography-free, DNA origami placement in meso-to-macro-scale grids using tunable colloidal nanosphere masks, and organosilane-based surface chemistry modification. Bench-top DNA origami placement is the first demonstration of its kind which facilitates precision placement of single molecules with high efficiency in diffraction-limited sites at a cost of $1/chip. The comprehensive characterization of this technique, and its application as a robust platform for high-throughput biophysics and digital counting of biomarkers through enzyme-free amplification are elucidated here. Furthermore, this technique can serve as a template for the bottom-up fabrication of invaluable biophysical tools such as zero mode waveguides, making them significantly cheaper and more accessible to the scientific community. This platform has the potential to democratize high-throughput single molecule experiments in laboratories worldwide. / Dissertation/Thesis / Doctoral Dissertation Biomedical Engineering 2019

No / As existing video processing technology is primarily developed in the pixel domain yet digital video is stored in compressed format, any application of those techniques to compressed videos would require decompression. For discrete cosine transform (DCT)-based MPEG compressed videos, the computing cost of standard row-by-row and column-by-column inverse DCT (IDCT) transforms for a block of 8 8 elements requires 4096 multiplications and 4032 additions, although practical implementation only requires 1024 multiplications and 896 additions. In this paper, we propose a new algorithm to extract videos directly from MPEG compressed domain (DCT domain) without full IDCT, which is described in three extraction schemes: 1) video extraction in 2 2 blocks with four coefficients; 2) video extraction in 4 4 blocks with four DCT coefficients; and 3) video extraction in 4 4 blocks with nine DCT coefficients. The computing cost incurred only requires 8 additions and no multiplication for the first scheme, 2 multiplication and 28 additions for the second scheme, and 47 additions (no multiplication) for the third scheme. Extensive experiments were carried out, and the results reveal that: 1) the extracted video maintains competitive quality in terms of visual perception and inspection and 2) the extracted videos preserve the content well in comparison with those fully decompressed ones in terms of histogram measurement. As a result, the proposed algorithm will provide useful tools in bridging the gap between pixel domain and compressed domain to facilitate content analysis with low latency and high efficiency such as those applications in surveillance videos, interactive multimedia, and image processing.