Wil O.C. Ward

Derivation of lowland riparian wetland deposit architecture using geophysical image analysis and interface detection

For groundwater-surface water interactions to be understood in complex wetland settings, the architecture of the underlying deposits requires investigation at a spatial resolution sufficient to characterize significant hydraulic pathways. Discrete intrusive sampling using conventional approaches provides insufficient sample density and can be difficult to deploy on soft ground. Here a noninvasive geophysical imaging approach combining three-dimensional electrical resistivity tomography (ERT) and the novel application of gradient and isosurface-based edge detectors is considered as a means of illuminating wetland deposit architecture. The performance of three edge detectors were compared and evaluated against ground truth data, using a lowland riparian wetland demonstration site. Isosurface-based methods correlated well with intrusive data and were useful for defining the geometries of key geological interfaces (i.e., peat/gravels and gravels/Chalk). The use of gradient detectors approach was unsuccessful, indicating that the assumption that the steepest resistivity gradient coincides with the associated geological interface can be incorrect. These findings are relevant to the application of this approach in settings with a broadly layered geology with strata of contrasting resistivities. In addition, ERT revealed substantial structures in the gravels related to the depositional environment (i.e., braided fluvial system) and a complex distribution of low-permeability putty Chalk at the bedrock surface—with implications for preferential flow and variable exchange between river and groundwater systems. These results demonstrate that a combined approach using ERT and edge detectors can provide valuable information to support targeted monitoring and inform hydrological modeling of wetlands.

Three-dimensional vessel segmentation using a novel combinatory filter framework.

Blood vessel segmentation is of great importance in medical diagnostic applications. Filter based methods that make use of Hessian matrices have been found to be very useful for blood vessel segmentation in both 2D and 3D medical images. However, these methods often fail on images that contain high density microvessels and background noise. The errors in the form of missing, undesired broken or incorrectly merged vessels eventually lead to poor segmentation results. In this paper, we present a novel method for 3D vessel segmentation that is also suitable for segmenting microvessels, incorporating the advantages of a line filter and a Hessian-based vessel filter to overcome the problems. The proposed method is shown to be reliable for noisy and inhomogeneous images. Vessels can also be separated based on their scale/thickness so that the method can be used for different medical applications. Furthermore, a quantitative vessel analysis method based on the multifractal analysis is performed on the segmented vasculature and fractal properties are found in all images.

Novel Methods for Microglia Segmentation, Feature Extraction, and Classification

Segmentation and analysis of histological images provides a valuable tool to gain insight into the biology and function of microglial cells in health and disease. Common image segmentation methods are not suitable for inhomogeneous histology image analysis and accurate classification of microglial activation states has remained a challenge. In this paper, we introduce an automated image analysis framework capable of efficiently segmenting microglial cells from histology images and analyzing their morphology. The framework makes use of variational methods and the fast-split Bregman algorithm for image denoising and segmentation, and of multifractal analysis for feature extraction to classify microglia by their activation states. Experiments show that the proposed framework is accurate and scalable to large datasets and provides a useful tool for the study of microglial biology.

Multifractal analysis of microvasculature in health and disease

A growing body of evidence suggests that there is a strong association between neurodegenerative diseases such as Alzheimers Diseases and the abnormality of the cerebral vasculature, in particular the microvessels/capillaries that are responsible for the exchange of nutrients across the blood-brain barrier [1]. Many microvessels are described as being kinked or distorted [2], implying that they are modified by some destructive process. Imaging devices such as microCT can achieve resolutions on the order of several μm, allowing imaging the three dimensional (3D) microvasculature down to the capillary level. However, the main weakness of using microCT for vascular research is considered to be the lack of software for 3D quantification of microvasculature and microvascular image databases for developing and testing algorithms. In this paper we describe a multifractal analysis method for the microvasculature automatically segmented from microCT images of the mouse brain. Due to the lack of a benchmark microCT image database, the method has been tested using a surrogate database - a publicly available retinal vessel database. The results are preliminary indication of the multifractal properties of mouse brain vasculature. A potential solution to automated classification of healthy and disease brains are discussed.

Retinal vasculature classification using novel multifractal features.

Retinal blood vessels have been implicated in a large number of diseases including diabetic retinopathy and cardiovascular diseases, which cause damages to retinal blood vessels. The availability of retinal vessel imaging provides an excellent opportunity for monitoring and diagnosis of retinal diseases, and automatic analysis of retinal vessels will help with the processes. However, state of the art vascular analysis methods such as counting the number of branches or measuring the curvature and diameter of individual vessels are unsuitable for the microvasculature. There has been published research using fractal analysis to calculate fractal dimensions of retinal blood vessels, but so far there has been no systematic research extracting discriminant features from retinal vessels for classifications. This paper introduces new methods for feature extraction from multifractal spectra of retinal vessels for classification. Two publicly available retinal vascular image databases are used for the experiments, and the proposed methods have produced accuracies of 85.5% and 77% for classification of healthy and diabetic retinal vasculatures. Experiments show that classification with multiple fractal features produces better rates compared with methods using a single fractal dimension value. In addition to this, experiments also show that classification accuracy can be affected by the accuracy of vessel segmentation algorithms.

Surface Reconstruction from Point Clouds Using a Novel Variational Model

Multi-view reconstruction has been an active research topic in the computer vision community for decades. However, state of the art 3D reconstruction systems have lacked the speed, accuracy, and ease to use properties required by the industry. The work described in this paper is part of the effort to produce a multi-view reconstruction system for a UK company. A novel variational level set method is developed for reconstructing an accurate implicit surface for a set of unorganised points (point cloud). The variational model consists of three energy terms to ensure accurate and smooth surface reconstruction whilst preserving the fine details of the point cloud and increasing speed. The model also completely eliminated the need for reinitialisation associated with the level set method. Implementation details of the variational model using gradient descent optimisation are given, and the roles of its three energy terms are illustrated through numerical experiments. Experiments show that the proposed method outperformed the state of the art surface reconstruction approaches.

Tracking tracer motion in a 4‐D electrical resistivity tomography experiment

A new framework for automatically tracking subsurface tracers in electrical resistivity tomography (ERT) monitoring images is presented. Using computer vision and Bayesian inference techniques, in the form of a Kalman filter, the trajectory of a subsurface tracer is monitored by predicting and updating a state model representing its movements. Observations for the Kalman filter are gathered using the maximally stable volumes algorithm, which is used to dynamically threshold local regions of an ERT image sequence to detect the tracer at each time step. The application of the framework to the results of 2-D and 3-D tracer monitoring experiments show that the proposed method is effective for detecting and tracking tracer plumes in ERT images in the presence of noise, without intermediate manual intervention.

Introducing diffusion tensor to high order variational model for image reconstruction

Second order total variation (SOTV) models have advantages for image restoration over their first order counterparts including their ability to remove the staircase artefact in the restored image. However, such models tend to blur the reconstructed image when discretised for numerical solution [1–5]. To overcome this drawback, we introduce a new tensor weighted second order (TWSO) model for image restoration. Specifically, we develop a novel regulariser for the SOTV model that uses the Frobenius norm of the product of the isotropic SOTV Hessian matrix and an anisotropic tensor. We then adapt the alternating direction method of multipliers (ADMM) to solve the proposed model by breaking down the original problem into several subproblems. All the subproblems have closed-forms and can be solved efficiently. The proposed method is compared with state-of-the-art approaches such as tensor-based anisotropic diffusion, total generalised variation, and Eulers elastica. We validate the proposed TWSO model using extensive experimental results on a large number of images from the Berkeley BSDS500. We also demonstrate that our method effectively reduces both the staircase and blurring effects and outperforms existing approaches for image inpainting and denoising applications.

Analysis of three-dimensional vasculature using multifractal theory

This paper investigates the use of multifractal formalism for characterising 3D brain vasculature of 2 different mammalian species. Multifractal properties were found across all the 3D vascular models. Variations in the analysis results appear to correspond with vessel density ans morphology. The implication of the research is that multifractal analysis could potentially provide a useful tool for clinical assessment of diseases that are known to alter density and structure of brain microvasculature.