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

Automated Image Registration And Mosaicking For Multi-Sensor Images Acquired By A Miniature Unmanned Aerial Vehicle Platform

Algorithms for automatic image registration and mosaicking are developed for a miniature Unmanned Aerial Vehicle (MINI-UAV) platform, assembled by Air-O-Space International (AOSI) L.L.C.. Three cameras onboard this MINI-UAV platform acquire images in a single frame simultaneously at green (550nm), red (650 nm), and near infrared (820nm) wavelengths, but with shifting and rotational misalignment. The area-based method is employed in the developed algorithms for control point detection, which is applicable when no prominent feature details are present in image scenes. Because the three images to be registered have different spectral characteristics, region of interest determination and control point selection are the two key steps that ensure the quality of control points. Affine transformation is adopted for spatial transformation, followed by bilinear interpolation for image resampling. Mosaicking is conducted between adjacent frames after three-band co-registration. Pre-introducing the rotation makes the area-based method feasible when the rotational misalignment cannot be ignored. The algorithms are tested on three image sets collected at Stennis Space Center, Greenwood, and Oswalt in Mississippi. Manual evaluation confirms the effectiveness of the developed algorithms. The codes are converted into a software package, which is executable under the Microsoft Windows environment of personal computer platforms without the requirement of MATLAB or other special software support for commercial-off-the-shelf (COTS) product. The near real-time decision-making support is achievable with final data after its installation into the ground control station. The final products are color-infrared (CIR) composite and normalized difference vegetation index (NDVI) images, which are used in agriculture, forestry, and environmental monitoring

The Method of Automatic Knuckle Image Acquisition for Continuous Verification Systems

The paper proposes a method of automatic knuckle image acquisition for continuous verification systems. The developed acquisition method is dedicated for verification systems in which the person being verified uses a computer keyboard. This manner of acquisition enables registration of the knuckle image without interrupting the user’s work for the time of acquisition. This is an important advantage, unprecedented in the currently known methods. The process of the automatic location of the finger knuckle can be considered as a pattern recognition approach and is based on the analysis of symmetry and similarity between the reference knuckle patterns and live camera image. The effectiveness of the aforesaid approach has been tested experimentally. The test results confirmed its high effectiveness. The effectiveness of the proposed method was also determined in a case where it is a part of a multi-biometric method

Incorporating spatial and temporal information for microaneurysm detection in retinal images

The retina of the human eye has the potential to reveal crucial information about several diseases such as diabetes. Several signs such as microaneurysms (MA) manifest themselves as early indicators of Diabetic Retinopathy (DR). Detection of these early signs is important from a clinical perspective in order to suggest appropriate treatment for DR patients. This work aims to improve the detection accuracy of MAs in colour fundus images. While it is expected that multiple images per eye are available in a clinical setup, proposed segmentation algorithms in the literature do not make use of these multiple images. This work introduces a novel MA detection algorithm and a framework for combining spatial and temporal images. A new MA detection method has been proposed which uses a Gaussian matched filter and an ensemble classifier with 70 features for the detection of candidates. The proposed method was evaluated on three public datasets (171 images in total) and has shown improvement in performance for two of the sets when compared to a state-of-the-art method. For lesion-based performance, the proposed method has achieved Retinopathy Online Challenge (ROC) scores of 0.3923, 2109 and 0.1523 in the MESSIDOR, DIARETDB1 and ROC datasets respectively. Based on the ensemble algorithm, a framework for the information combination is developed and consists of image alignment, detecting candidates with likelihood scores, matching candidates from aligned images, and finally fusing the scores from the aligned image pairs. This framework is used to combine information both spatially and temporally. A dataset of 320 images that consists of both spatial and temporal pairs was used for the evaluation. An improvement of performance by 2% is shown after combining spatial information. The framework is applied to temporal image pairs and the results of combining temporal information are analyzed and discussed

3-D Scene Reconstruction from Aerial Imagery

3-D scene reconstructions derived from Structure from Motion (SfM) and Multi-View Stereo (MVS) techniques were analyzed to determine the optimal reconnaissance flight characteristics suitable for target reconstruction. In support of this goal, a preliminary study of a simple 3-D geometric object facilitated the analysis of convergence angles and number of camera frames within a controlled environment. Reconstruction accuracy measurements revealed at least 3 camera frames and a 6 convergence angle were required to achieve results reminiscent of the original structure. The central investigative effort sought the applicability of certain airborne reconnaissance flight profiles to reconstructing ground targets. The data sets included images collected within a synthetic 3-D urban environment along circular, linear and s-curve aerial flight profiles equipped with agile and non-agile sensors. S-curve and dynamically controlled linear flight paths provided superior results, whereas with sufficient data conditioning and combination of orthogonal flight paths, all flight paths produced quality reconstructions under a wide variety of operational considerations

Handbook of Vascular Biometrics

This open access handbook provides the first comprehensive overview of biometrics exploiting the shape of human blood vessels for biometric recognition, i.e. vascular biometrics, including finger vein recognition, hand/palm vein recognition, retina recognition, and sclera recognition. After an introductory chapter summarizing the state of the art in and availability of commercial systems and open datasets/open source software, individual chapters focus on specific aspects of one of the biometric modalities, including questions of usability, security, and privacy. The book features contributions from both academia and major industrial manufacturers

Computer analysis for registration and change detection of retinal images

The current system of retinal screening is manual; It requires repetitive examination of a large number of retinal images by professional optometrists who try to identify the presence of abnormalities. As a result of the manual and repetitive nature of such examination, there is a possibility for error in diagnosis, in particular in the case when the progression of disease is slight. As the sight is an extremely important sense, any tools which can improve the probability of detecting disease could be considered beneficial. Moreover, the early detection of ophthalmic anomalies can prevent the impairment or loss of vision. The study reported in this Thesis investigates computer vision and image processing techniques to analyse retinal images automatically, in particular for diabetic retinopathy disease which causes blindness. This analysis aims to automate registration to detect differences between a pair of images taken at different times. These differences could be the result of disease progression or, occasionally, simply the presence of artefacts. The resulting methods from this study, will be therefore used to build a software tool to aid the diagnosis process undertaken by ophthalmologists. The research also presents a number of algorithms for the enhancement and visualisation of information present within the retinal images, which under normal situations would be invisible to the viewer; For instance, in the case of slight disease progression or in the case of similar levels of contrast between images, making it difficult for the human eye to see or to distinguish any variations. This study also presents a number of developed methods for computer analysis of retinal images. These methods include a colour distance measurement algorithm, detection of bifurcations and their cross points in retina, image registration, and change detection. The overall analysis in this study can be classified to four stages: image enhancement, landmarks detection, registration, and change detection. The study has showed that the methods developed can achieve automatic, efficient, accurate, and robust implementation

Automated annotation and visualisation of high-resolution spatial proteomic mass spectrometry imaging data using HIT-MAP.

Spatial proteomics has the potential to significantly advance our understanding of biology, physiology and medicine. Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) is a powerful tool in the spatial proteomics field, enabling direct detection and registration of protein abundance and distribution across tissues. MALDI-MSI preserves spatial distribution and histology allowing unbiased analysis of complex, heterogeneous tissues. However, MALDI-MSI faces the challenge of simultaneous peptide quantification and identification. To overcome this, we develop and validate HIT-MAP (High-resolution Informatics Toolbox in MALDI-MSI Proteomics), an open-source bioinformatics workflow using peptide mass fingerprint analysis and a dual scoring system to computationally assign peptide and protein annotations to high mass resolution MSI datasets and generate customisable spatial distribution maps. HIT-MAP will be a valuable resource for the spatial proteomics community for analysing newly generated and retrospective datasets, enabling robust peptide and protein annotation and visualisation in a wide array of normal and disease contexts