A LabVIEW® based generic CT scanner control software platform

UGCT, the Centre for X-ray tomography at Ghent University (Belgium) does research on X-ray tomography and its applications. This includes the development and construction of state-of-the-art CT scanners for scientific research. Because these scanners are built for very different purposes they differ considerably in their physical implementations. However, they all share common principle functionality. In this context a generic software platform was developed using LabVIEW (R) in order to provide the same interface and functionality on all scanners. This article describes the concept and features of this software, and its potential for tomography in a research setting. The core concept is to rigorously separate the abstract operation of a CT scanner from its actual physical configuration. This separation is achieved by implementing a sender-listener architecture. The advantages are that the resulting software platform is generic, scalable, highly efficient, easy to develop and to extend, and that it can be deployed on future scanners with minimal effort

Hardware, software, and applications of super-resolution microscopy

Modern microscopy techniques can image beyond the diffraction limit, in three spatial dimensions, and capture sub-cellular resolution videos, providing new biological insight and assisting in drug development. However, such advanced instruments typically require expert engineers and physicists to operate them, limiting their throughput and practicality for answering biological questions. Moreover, analysis of the raw data is complicated and there are significant barriers to publishing and sharing the data with others. This thesis addresses these problems, presenting two tools designed to reduce the level of expertise required to acquire and publish modern microscopy data. The development of a structured illumination microscope (SIM) is described, with a particular emphasis on control and reconstruction software designed to make SIM accessible to biologists who are new to super-resolution microscopy. The microscope's ease-of-use has led to a wide variety of biological investigations, which are presented as case studies to assist readers of this thesis in designing their own SIM experiments. The current practice for publishing 3D data is to show 2D intensity projections or fly-through videos, which present the data only from the author's perspective and do not give readers the opportunity to explore the results themselves. To solve this problem, Chapter 3 introduces my new volumetric rendering program, FPBioimage, which runs in a web browser. By creating a tool that is intuitive and easy to use, FPBioimage enables researchers around the world to immediately view their colleagues' experimental results, even when separated by thousands of miles. Two biological studies are discussed in detail to highlight the ability of these tools to answer the latest questions in cell biology. SIM's combination of high speed and high resolution video capture reveals a pinching phenomenon in the endoplasmic reticulum which was previously unknown, responsible for active flow of luminal proteins. FPBioimage is used to show metal organic frameworks successfully delivering sensitive drugs to cells, establishing a new method of cancer treatment. All software presented in this thesis is freely available, and has been carefully written to be reusable by other researchers. This is evidenced by OMERO, an online microscopy data repository, adopting FPBioimage as their default volumetric renderer. The open-source license under which the software is distributed means that developers can continue to build on the programs, extending the capabilities as new technology becomes available.Integrated Photonic and Electronic Systems Centre for Doctoral Training (IPES CDT

DEVELOPMENT OF A VERSATILE HIGH SPEED NANOMETER LEVEL SCANNING MULTI-PROBE MICROSCOPE

The motivation for development of a multi-probe scanning microscope, presented in this dissertation, is to provide a versatile measurement tool mainly targeted for biological studies, especially on the mechanical and structural properties of an intracellular system. This instrument provides a real-time, three-dimensional (3D) scanning capability. It is capable of operating on feedback from multiple probes, and has an interface for confocal photo-detection of fluorescence-based and single molecule imaging sensitivity. The instrument platform is called a Scanning Multi-Probe Microscope (SMPM) and enables 45 microm by 45 microm by 10 microm navigation of specimen with simultaneous optical and mechanical probing with each probe location being adjustable for collocation or for probing with known probe separations. The 3D positioning stage where the specimen locates was designed to have nanometer resolution and repeatability at 10 Hz scan speed with either open loop or closed loop operating modes. The fine motion of the stage is comprises three orthogonal flexures driven by piezoelectric actuators via a lever linkage. The flexures design is able to scan in larger range especially in z axis and serial connection of the stages helps to minimize the coupling between x, y and z axes. Closed-loop control was realized by the capacitance gauges attached to a rectangular block mounted to the underside of the fine stage upon which the specimen is mounted. The stage's performance was studied theoretically and verified by experimental test. In a step response test and using a simple proportional and integral (PI) controller, standard deviations of 1.9 nm 1.8 nm and 0.41 nm in the x, y and z axes were observed after settling times of 5 ms and 20 ms for the x and y axes. Scanning and imaging of biological specimen and artifact grating are presented to demonstrate the system operation. For faster, short range scanning, novel ultra-fast fiber scanning system was integrated into the xyz fine stage to achieve a super precision dual scanning system. The initial design enables nanometer positioning resolution and runs at 100 Hz scan speed. Both scanning systems are capable of characterization using dimensional metrology tools. Additionally, because the high-bandwidth, ultra-fast scanning system operates through a novel optical attenuating lever, it is physically separate from the longer range scanner and thereby does not introduce additional positioning noise. The dual scanner provides a fine scanning mechanism at relatively low speed and large imaging area using the xyz stage, and focus on a smaller area of interested in a high speed by the ultra-fast scanner easily. Such functionality is beneficial for researchers to study intracellular dynamic motion which requires high speed imaging. Finally, two high end displacement sensor systems, a knife edge sensor and fiber interferometer, were demonstrated as sensing solutions for potential feedback tools to boost the precision and resolution performance of the SMPM

Ono: an open platform for social robotics

In recent times, the focal point of research in robotics has shifted from industrial ro- bots toward robots that interact with humans in an intuitive and safe manner. This evolution has resulted in the subfield of social robotics, which pertains to robots that function in a human environment and that can communicate with humans in an int- uitive way, e.g. with facial expressions. Social robots have the potential to impact many different aspects of our lives, but one particularly promising application is the use of robots in therapy, such as the treatment of children with autism. Unfortunately, many of the existing social robots are neither suited for practical use in therapy nor for large scale studies, mainly because they are expensive, one-of-a-kind robots that are hard to modify to suit a specific need. We created Ono, a social robotics platform, to tackle these issues. Ono is composed entirely from off-the-shelf components and cheap materials, and can be built at a local FabLab at the fraction of the cost of other robots. Ono is also entirely open source and the modular design further encourages modification and reuse of parts of the platform

Development of a Nanoscale-Sensitive DNA Sensor using Functionalized Graphene Substrates and Fluorescence Lifetime Characterization

Fluorescence Lifetime Image Microscopy (FLIM) of nanostructured graphene substrates was used to measure the recently observed nanoscale distance-scaling of the fluorescence lifetime of dyes located in the vicinity of graphene sheets, at distances up to about 30 nm. The results were compared with a Resonant Energy Transfer (RET) theoretical model and used to establish an experimental fluorescence lifetime-to-nanoscale distance conversion function. In the following, this nano-optical relation was used for the design of a Deoxyribonucleic Acid (DNA) biosensor. Graphene was functionalized with fluorescently labeled DNA molecular beacons that unfold during hybridization with complementary DNA, and thereby change the distance of the fluorescent dye from the graphene surface. The spatial distribution of DNA molecular beacons binding to the surface of a graphene flake was studied, as well as the temporal kinetics of the hybridization reaction using time-lapse FLIM measurements. The results showed a vertical ascent of a fluorescent label relative to the graphene surface with a distance extension that is in accordance with the expected molecular length of the specific DNA sequence used. Interestingly, an intermediate state associated to a distance of a few nanometers was identified with a lifespan of about 85 minutes. The developed graphene-based DNA sensor was shown to enable optical detection of nanoscale distances in liquid media. These findings indicate that the fluorescence lifetime-based detection coupled with nanoscale interaction effects may find applications in various biosensing applications such as health and food-quality tracing. For the processing of FLIM data, several fluorescence lifetime calculation algorithms were compared and integrated into a specially designed and implemented analysis software toolbox in MATLAB.Imagens de Microscopia de Tempo de Vida de Fluorescência (FLIM) de substratos de grafeno nano-estruturados foram usadas para a medição da recentemente observada alteração do tempo de vida de fluorescência de corantes quando localizados na vizinhança de grafeno para distâncias até cerca de 30 nm. Os resultados foram comparados com um modelo teórico de Transferência Ressonante de Energia (RET) e utilizados para o estabelecimento de uma função de calibração experimental entre tempo de vida de fluorescência e distâncias à nano-escala. Posteriormente, esta relação nano-ótica foi utilizada para o desenvolvimento de um biossensor de Ácido Desoxirribonucleico (ADN). Substratos de grafeno foram funcionalizados com sinais moleculares (molecular beacons) de ADN que se desdobram durante a hibridização com ADN complementar, alterando a distância do corante fluorescente à superfície de grafeno. A distribuição espacial da ligação de sinais moleculares de ADN à superfície do grafeno foi estudada, bem como a cinética de reação de hibridização, usando medições de FLIM por lapso de tempo. Os resultados mostraram a ascensão vertical dos marcadores fluorescentes relativamente à superfície, com uma deslocamento total que está de acordo com o comprimento molecular esperado para a sequência de ADN utilizada. Curiosamente, um estado intermedio associado a uma distância de alguns nanómetros foi identificado, tendo este uma duração de cerca de 85 minutos. Foi então demonstrado que o sensor de ADN desenvolvido permite a deteção ótica de distâncias à nano-escala em meio líquido. Estes resultados indicaram que a deteção baseada em tempo de vida de fluorescência, acoplada aos efeitos desta interação ótica à nano-escala pode ser utilizada em várias aplicações de biodeteção, tal como na saúde e no rastreamento da qualidade alimentar. Para o tratamento de dados de FLIM, vários algoritmos de cálculo de tempo de vida foram comparados e integrados num programa de análise especificamente desenhado e implementado para o efeito, em ambiente MATLAB.International Iberian Nanotechnology Laboratory – IN