Advances in characterisation, calibration and data processing speed of optical coherence tomography systems

This thesis describes advances in the characterisation, calibration and data processing of optical coherence tomography (OCT) systems. Femtosecond (fs) laser inscription was used for producing OCT-phantoms. Transparent materials are generally inert to infra-red radiations, but with fs lasers material modification occurs via non-linear processes when the highly focused light source interacts with the materials. This modification is confined to the focal volume and is highly reproducible. In order to select the best inscription parameters, combination of different inscription parameters were tested, using three fs laser systems, with different operating properties, on a variety of materials. This facilitated the understanding of the key characteristics of the produced structures with the aim of producing viable OCT-phantoms. Finally, OCT-phantoms were successfully designed and fabricated in fused silica. The use of these phantoms to characterise many properties (resolution, distortion, sensitivity decay, scan linearity) of an OCT system was demonstrated. Quantitative methods were developed to support the characterisation of an OCT system collecting images from phantoms and also to improve the quality of the OCT images. Characterisation methods include the measurement of the spatially variant resolution (point spread function (PSF) and modulation transfer function (MTF)), sensitivity and distortion. Processing of OCT data is a computer intensive process. Standard central processing unit (CPU) based processing might take several minutes to a few hours to process acquired data, thus data processing is a significant bottleneck. An alternative choice is to use expensive hardware-based processing such as field programmable gate arrays (FPGAs). However, recently graphics processing unit (GPU) based data processing methods have been developed to minimize this data processing and rendering time. These processing techniques include standard-processing methods which includes a set of algorithms to process the raw data (interference) obtained by the detector and generate A-scans. The work presented here describes accelerated data processing and post processing techniques for OCT systems. The GPU based processing developed, during the PhD, was later implemented into a custom built Fourier domain optical coherence tomography (FD-OCT) system. This system currently processes and renders data in real time. Processing throughput of this system is currently limited by the camera capture rate. OCTphantoms have been heavily used for the qualitative characterization and adjustment/ fine tuning of the operating conditions of OCT system. Currently, investigations are under way to characterize OCT systems using our phantoms. The work presented in this thesis demonstrate several novel techniques of fabricating OCT-phantoms and accelerating OCT data processing using GPUs. In the process of developing phantoms and quantitative methods, a thorough understanding and practical knowledge of OCT and fs laser processing systems was developed. This understanding leads to several novel pieces of research that are not only relevant to OCT but have broader importance. For example, extensive understanding of the properties of fs inscribed structures will be useful in other photonic application such as making of phase mask, wave guides and microfluidic channels. Acceleration of data processing with GPUs is also useful in other fields.

Point-wise confidence interval estimation by neural networks: A comparative study based on automotive engine calibration.

In developing neural network techniques for real world applications it is still very rare to see estimates of confidence placed on the neural network predictions. This is a major deficiency, especially in safety-critical systems. In this paper we explore three distinct methods of producing point-wise confidence intervals using neural networks. We compare and contrast Bayesian, Gaussian Process and Predictive error bars evaluated on real data. The problem domain is concerned with the calibration of a real automotive engine management system for both air-fuel ratio determination and on-line ignition timing. This problem requires real-time control and is a good candidate for exploring the use of confidence predictions due to its safety-critical nature.

Statnote 17: using a regression line for prediction and calibration

Two types of prediction problem can be solved using a regression line viz., prediction of the ‘population’ regression line at the point ‘x’ and prediction of an ‘individual’ new member of the population ‘y1’ for which ‘x1’ has been measured. The second problem is probably the most commonly encountered and the most relevant to calibration studies. A regression line is likely to be most useful for calibration if the range of values of the X variable is large, if there is a good representation of the ‘x,y’ values across the range of X, and if several estimates of ‘y’ are made at each ‘x’. It is poor statistical practice to use a regression line for calibration or prediction beyond the limits of the data.

The development of calibration and adaptive filtering procedures for neuromagnetic studies of human visual function

This thesis first considers the calibration and signal processing requirements of a neuromagnetometer for the measurement of human visual function. Gradiometer calibration using straight wire grids is examined and optimal grid configurations determined, given realistic constructional tolerances. Simulations show that for gradiometer balance of 1:104 and wire spacing error of 0.25mm the achievable calibration accuracy of gain is 0.3%, of position is 0.3mm and of orientation is 0.6°. Practical results with a 19-channel 2nd-order gradiometer based system exceed this performance. The real-time application of adaptive reference noise cancellation filtering to running-average evoked response data is examined. In the steady state, the filter can be assumed to be driven by a non-stationary step input arising at epoch boundaries. Based on empirical measures of this driving step an optimal progression for the filter time constant is proposed which improves upon fixed time constant filter performance. The incorporation of the time-derivatives of the reference channels was found to improve the performance of the adaptive filtering algorithm by 15-20% for unaveraged data, falling to 5% with averaging. The thesis concludes with a neuromagnetic investigation of evoked cortical responses to chromatic and luminance grating stimuli. The global magnetic field power of evoked responses to the onset of sinusoidal gratings was shown to have distinct chromatic and luminance sensitive components. Analysis of the results, using a single equivalent current dipole model, shows that these components arise from activity within two distinct cortical locations. Co-registration of the resulting current source localisations with MRI shows a chromatically responsive area lying along the midline within the calcarine fissure, possibly extending onto the lingual and cuneal gyri. It is postulated that this area is the human homologue of the primate cortical area V4.

Range of confidence scale and consumer knowledge calibration

The study examined the effect of range of a confidence scale on consumer knowledge calibration, specifically whether a restricted range scale (25%- 100%) leads to difference in calibration compared to a full range scale (0%-100%), for multiple-choice questions. A quasi-experimental study using student participants (N = 434) was employed. Data were collected from two samples; in the first sample (N = 167) a full range confidence scale was used, and in the second sample (N = 267) a restricted range scale was used. No differences were found between the two scales on knowledge calibration. Results from studies of knowledge calibration employing restricted range and full range confidence scales are thus comparable. © Psychological Reports 2014.

An international round-robin calibration protocol for nanoindentation measurements

Nanoindentation has become a common technique for measuring the hardness and elastic-plastic properties of materials, including coatings and thin films. In recent years, different nanoindenter instruments have been commercialised and used for this purpose. Each instrument is equipped with its own analysis software for the derivation of the hardness and reduced Young's modulus from the raw data. These data are mostly analysed through the Oliver and Pharr method. In all cases, the calibration of compliance and area function is mandatory. The present work illustrates and describes a calibration procedure and an approach to raw data analysis carried out for six different nanoindentation instruments through several round-robin experiments. Three different indenters were used, Berkovich, cube corner, spherical, and three standardised reference samples were chosen, hard fused quartz, soft polycarbonate, and sapphire. It was clearly shown that the use of these common procedures consistently limited the hardness and reduced the Young's modulus data spread compared to the same measurements performed using instrument-specific procedures. The following recommendations for nanoindentation calibration must be followed: (a) use only sharp indenters, (b) set an upper cut-off value for the penetration depth below which measurements must be considered unreliable, (c) perform nanoindentation measurements with limited thermal drift, (d) ensure that the load-displacement curves are as smooth as possible, (e) perform stiffness measurements specific to each instrument/indenter couple, (f) use Fq and Sa as calibration reference samples for stiffness and area function determination, (g) use a function, rather than a single value, for the stiffness and (h) adopt a unique protocol and software for raw data analysis in order to limit the data spread related to the instruments (i.e. the level of drift or noise, defects of a given probe) and to make the H and E r data intercomparable. © 2011 Elsevier Ltd.

Quantifying uncertainty in citizen weather data

The sheer volume of citizen weather data collected and uploaded to online data hubs is immense. However as with any citizen data it is difficult to assess the accuracy of the measurements. Within this project we quantify just how much data is available, where it comes from, the frequency at which it is collected, and the types of automatic weather stations being used. We also list the numerous possible sources of error and uncertainty within citizen weather observations before showing evidence of such effects in real data. A thorough intercomparison field study was conducted, testing popular models of citizen weather stations. From this study we were able to parameterise key sources of bias. Most significantly the project develops a complete quality control system through which citizen air temperature observations can be passed. The structure of this system was heavily informed by the results of the field study. Using a Bayesian framework the system learns and updates its estimates of the calibration and radiation-induced biases inherent to each station. We then show the benefit of correcting for these learnt biases over using the original uncorrected data. The system also attaches an uncertainty estimate to each observation, which would provide real world applications that choose to incorporate such observations with a measure on which they may base their confidence in the data. The system relies on interpolated temperature and radiation observations from neighbouring professional weather stations for which a Bayesian regression model is used. We recognise some of the assumptions and flaws of the developed system and suggest further work that needs to be done to bring it to an operational setting. Such a system will hopefully allow applications to leverage the additional value citizen weather data brings to longstanding professional observing networks.

Reliability-based calibration for a mechanics-based fatigue cracking design procedure

Most pavement design procedures incorporate reliability to account for design inputs-associated uncertainty and variability effect on predicted performance. The load and resistance factor design (LRFD) procedure, which delivers economical section while considering design inputs variability separately, has been recognised as an effective tool to incorporate reliability into design procedures. This paper presents a new reliability-based calibration in LRFD format for a mechanics-based fatigue cracking analysis framework. This paper employs a two-component reliability analysis methodology that utilises a central composite design-based response surface approach and a first-order reliability method. The reliability calibration was achieved based on a number of field pavement sections that have well-documented performance history and high-quality field and laboratory data. The effectiveness of the developed LRFD procedure was evaluated by performing pavement designs of various target reliabilities and design conditions. The result shows an excellent agreement between the target and actual reliabilities. Furthermore, it is clear from the results that more design features need to be included in the reliability calibration to minimise the deviation of the actual reliability from the target reliability.