In this research work, a software and hardware prototype for real—time 3D visualisation is developed. The proposed system takes two input videos to interpolate virtual in—between views, which are then combined into 3D videos after processing for viewing on a 3D monitor. The core section of this research work is based on view morphing, a type of image based rendering. The image based rendering is a technique used to render a scene from a number of source images. According to the knowledge of geometric information of captured scenes, the image based rendering technique can be classified into three categories: rendering without geometry, rendering with implicit geometry and rendering with explicit geometry. The view morphing technique, a subset of the second category, requires less geometric information and a few source images of captured scenes. These reduce the complexities of both computation and hardware configuration of the proposed system, moreover, the quality of interpolated virtual in—between views by view morphing technique is good enough for visualisation applications. In this thesis, the research work is presented from two aspects: the algorithmic and the system's points of view separately. The algorithmic development and optimisation consist of the procedures of automatically interpolating virtual in—between views from two source images. The work begun with two cameras calibration with the objective of finding out the geometric relationship in 3D space between the two cameras. Image rectification is followed to project two source images into two parallel planes. This enables to obtain physically valid virtual in—between views and also reduces the computational cost for correspondence estimation. Subsequently, stereo matching is applied to establish feature correspondences between the two rectified source images. A novel feature based correspondence estimation algorithm is proposed to raise the level of the computational efficiency and the reliability. After that, interval interpolation is used to synthesise virtual in—between views. Finally, image derectification is applied to obtain final interpolated virtual in—between views. A novel pseudo real—time 3D visualisation system is proposed in the system development and optimisation. The proposed system has been developed using the TI (Texas Instruments) DM642 EVM board which is a standalone Digital Media Processing board. The system also includes a stereo video capture module consisting of two PAL cameras and the X3D-19 DISPLAY AD 3D display unit for visualisation of 3D video output. The core algorithm utilises images captured from the cameras and generates 6 virtual in—between views using interpolation techniques. The combined views (eight views of 2D images) are displayed on the 3D monitor using a proprietary method developed specifically for X31) monitors. The advantage of the proposed system is that real 3D impressions are able to be visualised in front of the 3D monitor in near real—time without any special glasses. The proposed system has been evaluated on a number of real scenes. The experimental results indicate that the performance of the proposed 3D visualisation system is about 4.7 FPS.

abstract: Gene circuit engineering facilitates the discovery and understanding of fundamental biology and has been widely used in various biological applications. In synthetic biology, gene circuits are often constructed by two main strategies: either monocistronic or polycistronic constructions. The Latter architecture can be commonly found in prokaryotes, eukaryotes, and viruses and has been largely applied in gene circuit engineering. In this work, the effect of adjacent genes and noncoding regions are systematically investigated through the construction of batteries of gene circuits in diverse scenarios. Data-driven analysis yields a protein expression metric that strongly correlates with the features of adjacent transcriptional regions (ATRs). This novel mathematical tool helps the guide for circuit construction and has the implication for the design of synthetic ATRs to tune gene expression, illustrating its potential to facilitate engineering complex gene networks. The ability to tune RNA dynamics is greatly needed for biotech applications, including therapeutics and diagnostics. Diverse methods have been developed to tune gene expression through transcriptional or translational manipulation. Control of RNA stability/degradation is often overlooked and can be the lightweight alternative to regulate protein yields. To further extend the utility of engineered ATRs to regulate gene expression, a library of RNA modules named degradation-tuning RNAs (dtRNAs) are designed with the ability to form specific 5’ secondary structures prior to RBS. These modules can modulate transcript stability while having a minimal interference on translation initiation. Optimization of their functional structural features enables gene expression level to be tuned over a wide dynamic range. These engineered dtRNAs are capable of regulating gene circuit dynamics as well as noncoding RNA levels and can be further expanded into cell-free system for gene expression control in vitro. Finally, integrating dtRNA with synthetic toehold sensor enables improved paper-based viral diagnostics, illustrating the potential of using synthetic dtRNAs for biomedical applications. / Dissertation/Thesis / Doctoral Dissertation Biomedical Engineering 2020

abstract: Synthetic gene networks have evolved from simple proof-of-concept circuits to complex therapy-oriented networks over the past fifteen years. This advancement has greatly facilitated expansion of the emerging field of synthetic biology. Multistability is a mechanism that cells use to achieve a discrete number of mutually exclusive states in response to environmental inputs. However, complex contextual connections of gene regulatory networks in natural settings often impede the experimental establishment of the function and dynamics of each specific gene network. In this work, diverse synthetic gene networks are rationally designed and constructed using well-characterized biological components to approach the cell fate determination and state transition dynamics in multistable systems. Results show that unimodality and bimodality and trimodality can be achieved through manipulation of the signal and promoter crosstalk in quorum-sensing systems, which enables bacterial cells to communicate with each other. Moreover, a synthetic quadrastable circuit is also built and experimentally demonstrated to have four stable steady states. Experiments, guided by mathematical modeling predictions, reveal that sequential inductions generate distinct cell fates by changing the landscape in sequence and hence navigating cells to different final states. Circuit function depends on the specific protein expression levels in the circuit. We then establish a protein expression predictor taking into account adjacent transcriptional regions’ features through construction of ~120 synthetic gene circuits (operons) in Escherichia coli. The predictor’s utility is further demonstrated in evaluating genes’ relative expression levels in construction of logic gates and tuning gene expressions and nonlinear dynamics of bistable gene networks. These combined results illustrate applications of synthetic gene networks to understand the cell fate determination and state transition dynamics in multistable systems. A protein-expression predictor is also developed to evaluate and tune circuit dynamics. / Dissertation/Thesis / Doctoral Dissertation Biomedical Engineering 2017