Study of Computational Image Matching Techniques: Improving Our View of Biomedical Image Data

Image matching techniques are proven to be necessary in various fields of science and engineering, with many new methods and applications introduced over the years. In this PhD thesis, several computational image matching methods are introduced and investigated for improving the analysis of various biomedical image data. These improvements include the use of matching techniques for enhancing visualization of cross-sectional imaging modalities such as Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), denoising of retinal Optical Coherence Tomography (OCT), and high quality 3D reconstruction of surfaces from Scanning Electron Microscope (SEM) images. This work greatly improves the process of data interpretation of image data with far reaching consequences for basic sciences research. The thesis starts with a general notion of the problem of image matching followed by an overview of the topics covered in the thesis. This is followed by introduction and investigation of several applications of image matching/registration in biomdecial image processing: a) registration-based slice interpolation, b) fast mesh-based deformable image registration and c) use of simultaneous rigid registration and Robust Principal Component Analysis (RPCA) for speckle noise reduction of retinal OCT images. Moving towards a different notion of image matching/correspondence, the problem of view synthesis and 3D reconstruction, with a focus on 3D reconstruction of microscopic samples from 2D images captured by SEM, is considered next. Starting from sparse feature-based matching techniques, an extensive analysis is provided for using several well-known feature detector/descriptor techniques, namely ORB, BRIEF, SURF and SIFT, for the problem of multi-view 3D reconstruction. This chapter contains qualitative and quantitative comparisons in order to reveal the shortcomings of the sparse feature-based techniques. This is followed by introduction of a novel framework using sparse-dense matching/correspondence for high quality 3D reconstruction of SEM images. As will be shown, the proposed framework results in better reconstructions when compared with state-of-the-art sparse-feature based techniques. Even though the proposed framework produces satisfactory results, there is room for improvements. These improvements become more necessary when dealing with higher complexity microscopic samples imaged by SEM as well as in cases with large displacements between corresponding points in micrographs. Therefore, based on the proposed framework, a new approach is proposed for high quality 3D reconstruction of microscopic samples. While in case of having simpler microscopic samples the performance of the two proposed techniques are comparable, the new technique results in more truthful reconstruction of highly complex samples. The thesis is concluded with an overview of the thesis and also pointers regarding future directions of the research using both multi-view and photometric techniques for 3D reconstruction of SEM images

Fully automated computer system for diagnosis of corneal diseases. Development of image processing technologies for the diagnosis of Acanthamoeba and Fusarium diseases in confocal microscopy images

Confocal microscopy demonstrated its value in the diagnosis of Acanthamoeba and fungal keratitis which considered sight-threatening corneal diseases. However, it can be difficult to find and train confocal microscopy graders to accurately detect Acanthamoeba cysts and fungal filaments in the images. Use of an automated system could overcome this problem and help to start the correct treatment more quickly. Also, response to treatment can be difficult to assess in infectious keratitis using clinical examination alone, but there is evidence that the morphology of filaments and cysts may change over time with the use of correct treatment. An automated system to analyse confocal microscopy images for such changes would also assist clinicians in determining whether the ulcer is improving, or whether a change of treatment is needed. This research proposes a fully automated novel system with GUI to detect cysts and hyphae (filaments) and measure useful quantitative parameters for them through many stages; Image enhancement, image segmentation, quantitative analysis for detected cysts and hyphae, and registration and tracking of ordered sequence of images. The performance of the proposed segmentation procedure is evaluated by comparing between the manual and the automated traced images of the dataset that was provided by the Manchester Royal Eye Hospital. The positive predictive values rate of cysts for Acanthamoeba images was 76%. For detected hyphae in Fusarium images, many standard measurements were computed. The accuracy of their values was quantified by calculating the percent error rate for each measurement and which ranged from 23% to 49%

Robust convex optimisation techniques for autonomous vehicle vision-based navigation

This thesis investigates new convex optimisation techniques for motion and pose estimation. Numerous computer vision problems can be formulated as optimisation problems. These optimisation problems are generally solved via linear techniques using the singular value decomposition or iterative methods under an L2 norm minimisation. Linear techniques have the advantage of offering a closed-form solution that is simple to implement. The quantity being minimised is, however, not geometrically or statistically meaningful. Conversely, L2 algorithms rely on iterative estimation, where a cost function is minimised using algorithms such as Levenberg-Marquardt, Gauss-Newton, gradient descent or conjugate gradient. The cost functions involved are geometrically interpretable and can statistically be optimal under an assumption of Gaussian noise. However, in addition to their sensitivity to initial conditions, these algorithms are often slow and bear a high probability of getting trapped in a local minimum or producing infeasible solutions, even for small noise levels. In light of the above, in this thesis we focus on developing new techniques for finding solutions via a convex optimisation framework that are globally optimal. Presently convex optimisation techniques in motion estimation have revealed enormous advantages. Indeed, convex optimisation ensures getting a global minimum, and the cost function is geometrically meaningful. Moreover, robust optimisation is a recent approach for optimisation under uncertain data. In recent years the need to cope with uncertain data has become especially acute, particularly where real-world applications are concerned. In such circumstances, robust optimisation aims to recover an optimal solution whose feasibility must be guaranteed for any realisation of the uncertain data. Although many researchers avoid uncertainty due to the added complexity in constructing a robust optimisation model and to lack of knowledge as to the nature of these uncertainties, and especially their propagation, in this thesis robust convex optimisation, while estimating the uncertainties at every step is investigated for the motion estimation problem. First, a solution using convex optimisation coupled to the recursive least squares (RLS) algorithm and the robust H filter is developed for motion estimation. In another solution, uncertainties and their propagation are incorporated in a robust L convex optimisation framework for monocular visual motion estimation. In this solution, robust least squares is combined with a second order cone program (SOCP). A technique to improve the accuracy and the robustness of the fundamental matrix is also investigated in this thesis. This technique uses the covariance intersection approach to fuse feature location uncertainties, which leads to more consistent motion estimates. Loop-closure detection is crucial in improving the robustness of navigation algorithms. In practice, after long navigation in an unknown environment, detecting that a vehicle is in a location it has previously visited gives the opportunity to increase the accuracy and consistency of the estimate. In this context, we have developed an efficient appearance-based method for visual loop-closure detection based on the combination of a Gaussian mixture model with the KD-tree data structure. Deploying this technique for loop-closure detection, a robust L convex posegraph optimisation solution for unmanned aerial vehicle (UAVs) monocular motion estimation is introduced as well. In the literature, most proposed solutions formulate the pose-graph optimisation as a least-squares problem by minimising a cost function using iterative methods. In this work, robust convex optimisation under the L norm is adopted, which efficiently corrects the UAV’s pose after loop-closure detection. To round out the work in this thesis, a system for cooperative monocular visual motion estimation with multiple aerial vehicles is proposed. The cooperative motion estimation employs state-of-the-art approaches for optimisation, individual motion estimation and registration. Three-view geometry algorithms in a convex optimisation framework are deployed on board the monocular vision system for each vehicle. In addition, vehicle-to-vehicle relative pose estimation is performed with a novel robust registration solution in a global optimisation framework. In parallel, and as a complementary solution for the relative pose, a robust non-linear H solution is designed as well to fuse measurements from the UAVs’ on-board inertial sensors with the visual estimates. The suggested contributions have been exhaustively evaluated over a number of real-image data experiments in the laboratory using monocular vision systems and range imaging devices. In this thesis, we propose several solutions towards the goal of robust visual motion estimation using convex optimisation. We show that the convex optimisation framework may be extended to include uncertainty information, to achieve robust and optimal solutions. We observed that convex optimisation is a practical and very appealing alternative to linear techniques and iterative methods

SURFACE ENABLED LAB-ON-A-CHIP (LOC) DEVICE FOR PROTEIN DETECTION AND SEPARATION

Sensitive and selective chemical/biological detection/analysis for proteins is essential for applications such as disease diagnosis, species phenotype identification, product quality control, and sample examination. Lab-on-a-chip (LOC) device provides advantages of fast analysis, reduced amount of sample requirements, and low cost, to magnificently facilitate protein detection research. Isoelectric focusing (IEF) is a strong and reliable electrophoretic technique capable of discerning proteins from complex mixtures based on the isoelectric point (pI) differences. It has experienced plenty of fruitful developments during previous decades which has given it the capability of performing with highly robust and reproducible analysis. This progress has made IEF devices an excellent tool for chemical/biological detection/analysis purposes. In recent years, the trends of simple instrument setting, rapid analysis, small sample requirement, and light labor intensity have inspired the LOC concept to be combined with IEF to evolve it into an “easily-handled chip with hours of analysis” from the earlier method of “working with big and heavy machines in a few days.” Although IEF is already a mature technique being applied, further LOC-IEF developments are still experiencing challenges related to its limitations such as miniaturizing the device scale without harming the resolving/discerning ability. With the facilitation of newly technologically advanced/improved fabrication tools, it is completely possible to address challenges and approach new limits of LOC-IEF. In this dissertation, a surface enabled printing technique, which can transfer liquid to a surface with prescribed patterns, was firstly introduced to IEF device fabrication. By employing surface enabled printing, a surface enabled IEF (sIEF) device running at a scale of 100 times smaller than those previously reported was designed and fabricated. Commercial carrier ampholytes (PharmalyteTM) with different pH range were engaged to generate a continuous pH gradient on sIEF device. Device design and optimized fabrication conditions were practically investigated; establishment of pH gradient was verified by fluorescent dyes; dependencies of electric field strength and carrier ampholytes concentration were systematically examined. To further optimize the sIEF system, dependencies of surface treatment and additive chemicals were explored. Fluorescent proteins and peptides were tested for the separation capability of sIEF. Finally, the well optimized sIEF system was used as a tool for real protein (hemoglobin variants and monoclonal antibody isoforms) separations. Hemoglobin variants test results revealed that sIEF is capable of separating amphoteric species with pI difference as small as 0.2. Monoclonal protein tests demonstrated the capability of sIEF to be a ready-to-use tool for protein structural change monitoring. In conclusion, this new sIEF approach has lower applied voltages, smaller sample requirements, a relatively quick fabrication process, and reusability, making it more attractive as a portable, user-friendly platform for qualitative protein detection and separation