Biomedical research has been revolutionised by the development of high throughput systems which enable thousands of experiments to be carried out simultaneously, leading to the generation of vast amounts of microscopy data. At the same time smaller scale experiments are increasingly dependent on accurate quantification of relatively small changes since the intricate network of interactions within a cell often counteracts attempts to per- turb the function of any single protein or pathway. This has motivated the development of algorithms and software packages to assist with the analysis of biological imaging data. This thesis develops and applies image analysis tools to multiple biological problems, and also illustrates the whole process required to label live samples so they can be imaged in the first place, thus giving an appreciation of the practical difficulties of biomedical research. We begin with the development of a kymograph tool, which is used for the spatio- temporal subcellular quantification of the chromosomal passenger complex, a complex of proteins involved in regulating mitosis. Following this we start to consider inter-cellular signalling interactions in a study of the IGF2 pathway in clumped cells. A random forest classification framework using cell-based image features is developed, and shown to be able to distinguish between cells with different levels of activation. Importantly the random forest feature importance measures are shown to be useful in helping to identify biologi- cally relevant differences. Finally we apply the random forest classifier to the analysis of immunofiuoresence images of Ewing's sarcoma tumour biopsies, which are associated with clinical outcome data, allowing us to develop a framework for integrating imaging data with patient prognosis data. The samples originate from multiple sources, making this a very challenging data set due to a lack of normalisation, but we are still able to obtain clinically useful results, in addition to identifying areas where further research is required.

Magnetic nanoparticles have attracted a great attention due to their diverse potential applications in biology and technology and a substantial number of synthetic methods have been developed to produce these materials. Chemical synthesis approaches have been a particular focus of the field, because of their ability to tune the size, shape and composition, as well as surface of the nanoparticles. To produce magnetic nanoparticles for biomedical applications, one of the primary requirements is to make nanoparticles that are dispersible and stable in aqueous medium under physiological conditions. The focus of this thesis has been the development of methods to synthesise magnetic nanoparticles of different compositions and shape that are dispersible and stable in water. Monodisperse water-dispersible magnetic Co nanoparticles were fabricated using a facile reduction method in water in the presence of hydrophilic polymers. The size and shape of the nanoparticles were both tunable by varying the conditions of synthesis. The size of the spherical nanoparticles would be tuned between 2-7.5 nm by changing the concentration of the polymer. The synthesis approach could also be used to produce nanorods of 15 x 36 nm. The spherical nanoparticles were superparamagnetic at room temperature and were stable in water and in electrolyte solutions of up to 0.23 mM NaCI. The preliminary use of the Co nanoparticles as a MRI contrast enhancer was tested and provided evidence that these materials have considerable potential in this application. Using a similar method, water-dispersible and colloidal stable CoPt nanoparticles were prepared. The effect of structure, functional group and combinations of stabilising ligands on the morphology of the nanoparticles was investigated. It was found that multiple-thiol functional groups play a critical role in the formation of hollow nanoparticles. The size of hollow nanoparticles could be tuned in the range of7-54 nm by changing the concentration and molecular weight of the ligands. The hollow nanoparticles were water-dispersible and superparamagnetic at room temperature. They were stable in wide range of pH from I to 12.5 and at electrolyte concentrations as high as 2 M NaCI. An experiment on tracking stem cells labelled with the CoPt hollow nanoparticles indicated that MRl can effectively detect low numbers of labelled cells due to the enhanced contrast provided by the nanoparticles. CoPt hollow nanoparticles may, thus, have potential applications in MRI. CoFe and cobalt ferrite nanoparticles were synthesised by thermal decomposition in organic solvent to take advantage of the superior control over monodispersity and morphology of the nanoparticles afforded by solvent based syntheses. In the case of CoFe nanoparticles, a layer of Pt was also deposited on the nanoparticles to make core/shell structures. Varying reaction conditions, such as reaction time, had an insignificant effect on monodispersity, size and shape of Co Fe nanoparticles. However, these parameters had a substantial impact on the cobalt ferrite nanoparticles. Cobalt ferrite nanoparticles with sizes in a broad range from 4 nm to over 30 nm and diverse shapes including spherical, cubic and star-like, were synthesised by changing surfactant concentration and reaction time. Ligand exchange using hydrophilic silane and/or polymer ligands were demonstrated to be efficacious on CoFe, CoFelPt and cobalt ferrite nanoparticles. After ligand exchange, the nanoparticles were reasonably stable in water. The work presented in this thesis demonstrates that chemical synthesis is an efficient route to the production of magnetic nanoparticles of diverse composition and shape and so magnetic properties. Moreover, these materials were found to be stable in aqueous solutions. However, it is clear that the application of such magnetic nanoparticles in biology and medicine will require substantial further effort in the development of ligand shells able to withstand the rigours of the biological environment. Given the success of chemical synthesis demonstrated in this thesis, the development of ligand shell systems is now a major challenge of the field.

Plasma formation in liquids has due to the tremendous application potential been a fast developing topic in the past two decades. Here a study on sub-kV plasma formation in conducting liquids is presented. In this environment the temporal evolution from initiation of power input into the liquid can be separated into different phases. First of all, an Ohmic heating phase leads to vapour formation in the electrode proximity. This will be investigated experimentally as well as with a computer model. The present experimental studies demonstrate not only the complexity of this multi parameter system but also reveal the influence of specific parameters, such as conductivity and applied voltage. Those results have lead to incorporation and refinement of the model. Consecutively the advanced model enabled further understanding of the system and effects involved effects, e.g. superheating of the liquid before evaporation. When formed the vapour regime leads to isolation of the electrode from the liquid. Since electrode surface properties play an important role on discharge formation study of these lead to detection and information on salt as a surface contaminant after evaporation. For plasma formation those small salt crystals play a crucial role in discharge formation processes. After generation of a low density vapour environment formation of a plasma is observed within it. Regimes with stochastic discharge appearance as well as continuous discharges have been observed and ultimately lead to characterisation of the discharge type as well as determination of the electron density. Pronounced differences for positive and negative polarity are also highlighted. The rich chemistry with its reactive species in the liquid phase is then used for investigation of cancer cell treatment efficiency and compared with conventional x-ray treatment and there are indications of higher efficiency, in particular relating to range effects.

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Shear stress generated by biological fluid flows in vivo plays an important role in the regulation of numerous cellular processes; these include apoptosis, cellular proliferation and differentiation, regulation of metabolism and of inflammatory responses. The effects of shear stress are particularly prevalent in cells of the cardiovascular and skeletal systems due to the haemodynamic and interstitial fluid flows respectively. The limited scope for controlling in vivo shear stress has required the research to be conducted in vitro. Within the thesis, stable cavitation microstreaming was harnessed as a method for mimicking in vivo shear stress with the aim of developing a generic method for stressing cells. Stable cavitation microstreaming is a steady fluid flow generated by the transfer of acoustic energy into a time averaged steady momentum flux as a result of viscous damping in the boundary layer of an oscillating gas bubble. Microstreaming was generated around Expancel encapsulated microbubbles (EMBs) in purpose built microfluidic devices. The devices provided controlled environments for the generation of microstreaming. Important features of the final device include adherence of microbubbles to an internal surface of the device, the minimisation of primary acoustic radiation forces and the ability to perform high throughput biological experiments on adhered cells in the device. The microstreaming flow was characterized by micro particle image velocimetry (μPIV), showing that flows possess good repeatability and controllability. H9c2 cardiomyocytes, adhered opposite to the microbubbles at a separation distance of approximately 150 μm, were stressed with microstreaming and their viability was measured. This was carried out in order to assess the applicability of the device to biomedical research. This research is thought to be the first in depth analysis of the controllability and repeatability of microstreaming in the context of stressing cells. Furthermore, it is thought to be the first demonstration of inflicting controlled cell death by stable cavitation microstreaming at a distance of 150 μm.