Robotic 3D Reconstruction Utilising Structure from Motion

Sensing the real-world is a well-established and continual problem in the field of robotics. Investigations into autonomous aerial and underwater vehicles have extended this challenge into sensing, mapping and localising in three dimensions. This thesis seeks to understand and tackle the challenges of recovering 3D information from an environment using vision alone. There is a well-established literature on the principles of doing this, and some impressive demonstrations; but this thesis explores the practicality of doing vision-based 3D reconstruction using multiple, mobile robotic platforms, the emphasis being on producing accurate 3D models. Typically, robotic platforms such as UAVs have a single on-board camera, restricting which method of visual 3D recovery can be employed. This thesis specifically explores Structure from Motion, a monocular 3D reconstruction technique which produces detailed and accurate, although slow to calculate, 3D reconstructions. It examines how well proof-of-concept demonstrations translate onto the kinds of robotic systems that are commonly deployed in the real world, where local processing is limited and network links have restricted capacity. In order to produce accurate 3D models, it is necessary to use high-resolution imagery, and the difficulties of working with this on remote robotic platforms is explored in some detail

Optical Imaging

Optical Coherence Tomography (OCT)We describe the fundamental concept of optical coherence tomography (OCT) and discuss the two main working principles time domain OCT and frequency domain OCT. Then, we review extended functionalities including spectrally and polarization-resolved OCT as well as Doppler-OCT and show concepts for contrast enhancement. Based on these fundamentals, we demonstrate the potential of OCT for small animal imaging on the basis of exemplary studies on retinal imaging and lung imaging.Optoacoustic ImagingThis chapter deals with the fascinating topic of optoacoustic imaging, a recent powerful addition to the arsenal of in vivo functional and molecular small animal imaging. Due to its hybrid nature, involving optical excitation and ultrasonic detection, optoacoustics overcomes the imaging depth limitations of optical microscopy related to light scattering in living tissues while further benefiting from the compelling advantages of optical contrast. To this end, optoacoustic imaging has been shown capable of delivering multiple types of imaging contrast (structural, functional, kinetic, molecular) within a single imaging modality. It can further deliver images with high spatiotemporal resolution that rivals performance of other well-established whole-body imaging modalities. As such, optoacoustics can play a vital role in biomedical research, from early disease detection and monitoring of dynamic phenomena noninvasively to accelerating drug discovery.Optical ProbesThis chapter is devoted to the properties and application of fluorescence dyes as probes for optical imaging. A variety of agents have been described to date, including nontargeting dyes, vascular agents, targeted conjugates, activatable dyes, and sensing probes. The major classes encompass polymethine dyes and xanthenes dyes, both of which are commercially available in broad variations. Addressing the purpose of optical animal imaging, the most relevant parameters to apply such probes are discussed, thereby supporting the reader in choosing reasonable imaging probes and in preparing bioconjugates for his studies

Optical imaging methods for the study of disease models from the nano to the mesoscale

The visualisation of disease phenotypes allows scientists to study fundamental mechanisms of disease. Optical imaging methods are useful not only to observe anatomical features of biological samples, but also to infer interactions between molecular species using fluorescence labelling. This thesis presents the development of imaging and analysis tools to study biological questions in three models of disease, with samples ranging from the sub-cellular to the organ scale. First, the role of the alpha-synuclein (a-syn) protein, whose dysfunction is a hallmark of Parkinson’s Disease, was studied with respect to vesicle trafficking at the synapse. Synaptic vesicles are ∼40 nm in diameter; imaging vesicles therefore requires methods with resolution below the diffraction limit. Single-molecule localisation microscopy (SMLM), which circumvents the diffraction limit by separating fluorophore emission in time to localise individual molecules in space with ∼20 nm precision, was thus implemented to study a-syn in purified synaptic boutons. A software package was developed to analyse the colocalisation of a-syn with internalised vesicles, and the clustering of a-syn under differing synaptic calcium levels. The colocalisation of a-syn and internalised vesicles was found to be temperature independent, suggesting that a-syn is involved in non-canonical trafficking mechanisms. Ground truth simulations from a synaptosome model were used to benchmark two cluster analysis methods. Both methods applied on the experimental data showed that a-syn becomes less clustered at low synaptic calcium levels. Second, the spatiotemporal association of ESCRT-II, a protein complex whose role in the budding of the human immunodeficiency virus (HIV) was previously considered dispensable, and the HIV polyprotein Gag was studied during viral egress using novel image analysis tools. A nearest-neighbour analysis showed the ESCRT-II protein EAP45 colocalises with Gag similarly to ALIX, a protein well known to be involved in HIV budding. However, upon deletion of EAP45’s N-terminus, its colocalisation with Gag was significantly impaired, highlighting the importance of this EAP45 domain in linking to Gag. Single particle tracking was used to trace the trajectories of EAP45 and Gag in live cells, and an algorithm was developed to visualise the simultaneous motion of two particles; these analyses revealed three types of potential dynamic interaction between EAP45 and Gag. Finally, an open-source instrument to visualise phenotypes from large organs in 3D was developed for the study of chronic obstructive pulmonary disease (COPD) models. The instrument implements Optical Projection Tomography, a technique which can reconstruct cross-sectional slices of a transparent object from its orthographic projections, using off-the- shelf components and novel ImageJ plugins for artefact correction and volume reconstructions. Excised and cleared mouse lungs were imaged in which high order airways can be discerned with 50 μm resolution. The raw lung data, instructions for building the instrument, the free ImageJ plugins, and a detailed software manual are available in an online repository to encourage the widespread use of OPT for imaging large samples.Gates Cambridg

Matter manipulation with extreme terahertz light: Progress in the enabling THz technology

Terahertz (THz) light has proven to be a fine tool to probe and control quasi-particles and collective excitations in solids, to drive phase transitions and associated changes in material properties, and to study rotations and vibrations in molecular systems. In contrast to visible light, which usually carries excessive photon energy for collective excitations in condensed matter systems, THz light allows for direct coupling to low-energy (meV scale) excitations of interest, The development of light sources of strong-field few-cycle THz pulses in the 2000s opened the door to controlled manipulation of reactions and processes. Such THz pulses can drive new dynamic states of matter, in which materials exhibit properties entirely different from that of the equilibrium. In this review, we first systematically analyze known studies on matter manipulation with strong-field few-cycle THz light and outline some anticipated new results. We focus on how properties of materials can be manipulated by driving the dynamics of different excitations and how molecules and particles can be controlled in useful ways by extreme THz light. Around 200 studies are examined, most of which were done during the last five years. Secondly, we discuss available and proposed sources of strong-field few-cycle THz pulses and their state-of-the-art operation parameters. Finally, we review current approaches to guiding, focusing, reshaping and diagnostics of THz pulses. (C) 2019 The Author(s). Published by Elsevier B.V

Terahertz for subsurface imaging and metrology applications

In the area of metrology and non-destructive testing, Terahertz wavelengths have been widely researched and used. However, the lack of 2D detectors working at room temperature and high power sources prevent the widespread application of Terahertz in industry. In that context, research on the development of new Terahertz equipment is moving at a fast pace. Within the scope of this thesis, applications of newly developed Terahertz technologies were explored using the scanning of single point detectors with the objective to establish the feasibility for their full-field applications in readiness for future 2D detectors. For the first time, a frequency tuneable, all-optical Terahertz source was implemented in multi-wavelength interferometry to overcome one wavelength ambiguity in precise thickness/distance measurements with sub-millimetre resolution. Phase-shifting digital holography is another interferometry technique which allows us to reconstruct not only the amplitude of one object, but also the phase and the depth of it, using existing mathematical algorithms. Digital holography was performed successfully at Terahertz wavelengths using a multiplier/mixer Terahertz source coupled with a single point pyroelectric detector for the applications of non-destructive testing and depth measurements. The novelty is that the phase-stepping technique for digital holography was implemented in THz frequencies for the first time to remove unwanted terms in the reconstructed image in order to improve image quality compare to conventional holography. In the current experiments, recording time for one set of phase-shifting holograms (4 holograms for 4 phase-steps algorithm) was 6 hours. When the technology is ready for 2D detectors, recording time of holograms could be reduced considerably, and the technique will play an important role in full-field applications in industry metrology and/or non-destructive testing and evaluation.EPSR