Digital Morphometry : A Taxonomy Of Morphological Filters And Feature Parameters With Application To Alzheimer\u27s Disease Research

In this thesis the expression digital morphometry collectively describes all those procedures used to obtain quantitative measurements of objects within a two-dimensional digital image. Quantitative measurement is a two-step process: the application of geometrical transformations to extract the features of interest, and then the actual measurement of these features. With regard to the first step the morphological filters of mathematical morphology provide a wealth of suitable geometric transfomations. Traditional radiometric and spatial enhancement techniques provide an additional source of transformations. The second step is more classical (e.g. Underwood, 1970; Bookstein, 1978; and Weibull, 1980); yet here again mathematical morphology is applicable - morphologically derived feature parameters. This thesis focuses on mathematical morphology for digital morphometry. In particular it proffers a taxonomy of morphological filters and investigates the morphologically derived feature parameters (Minkowski functionals) for digital images sampled on a square grid. As originally conceived by Georges Matheron, mathematical morphology concerns the analysis of binary images by means of probing with structuring elements [typically convex geometric shapes] (Dougherty, 1993, preface). Since its inception the theory has been extended to grey-level images and most recently to complete lattices. It is within the very general framework of the complete lattice that the taxonomy of morphological filters is presented. Examples are provided to help illustrate the behaviour of each type of filter. This thesis also introduces DIMPAL (Mehnert, 1994) - a PC-based image processing and analysis language suitable for researching and developing algorithms for a wide range of image processing applications. Though DIMPAL was used to produce the majority of the images in this thesis it was principally written to provide an environment in which to investigate the application of mathematical morphology to Alzheimer\u27s disease research. Alzheimer\u27s disease is a form of progressive dementia associated with the degeneration of the brain. It is the commonest type of dementia and probably accounts for half the dementia of old age (Forsythe, 1990, p. 21 ). Post mortem examination of the brain reveals the presence of characteristic neuropathologic lesions; namely neuritic plaques and neurofibrillary tangles. They occur predominantly in the cerebral cortex and hippocampus. Quantitative studies of the distribution of plaques and tangles in normally aged and Alzheimer brains are hampered by the enormous amount of time and effort required to count and measure these lesions. Here in a morphological algorithm is proposed for the automatic segmentation and measurement of neuritic plaques from light micrographs of post mortem brain tissue

Digital image processing using mathematical morphology

This dissertation is a natural extension of my undergraduate research project entitled, Digital Image Processing”. Whilst my undergraduate project dealt with a number of classical digital image filtering techniques such as spatial convolution and frequency domain filtering via the Fourier transform, this dissertation focuses on an alternative approach employing Mathematical Morphology. In contrast to classical filtering techniques, which often geometrically distort the original image, morphological operations, used sensibly, essentially preserve shape and geometry. Mathematical morphology therefore lends itself to image processing applications requiring the identification of objects and object features within an image. Herein basic morphological operations are developed, firstly within the continuous image domain (Euclidean N-space, Rn), and then in the digital domain (Zn). Particular emphasis is placed on the development of digital morphological operators for both binary and grey-tone images, progressing from the rudimentary operations of dilation and erosion to granulometry and topological processing. Subsequent to the development of the theory, a case study is presented. The case study describes a preliminary investigation into the application of morphological operations to photomicrographs of mouse adrenal cortex cells with the aim of identifying specific cell features

A novel Bayesian approach to adaptive mean shift segmentation of brain images

We present a novel adaptive mean shift (AMS) algorithm for the segmentation of tissues in magnetic resonance (MR) brain images. In particular we introduce a novel Bayesian approach for the estimation of the adaptive kernel bandwidth and investigate its impact on segmentation accuracy. We studied the three class problem where the brain tissues are segmented into white matter, gray matter and cerebrospinal fluid. The segmentation experiments were performed on both multi-modal simulated and real patient T1-weighted MR volumes with different noise characteristics and spatial inhomogeneities. The performance of the algorithm was evaluated relative to several competing methods using real and synthetic data. Our results demonstrate the efficacy of the proposed algorithm and that it can outperform competing methods, especially when the noise and spatial intensity inhomogeneities are high

Unsupervised Segmentation of Head Tissues from Multi-modal MR Images for EEG Source Localization

In this paper, we present and evaluate an automatic unsupervised segmentation method, hierarchical segmenta- tion approach (HSA)–Bayesian-based adaptive mean shift (BAMS), for use in the construction of a patient-specific head conductivity model for electroencephalography (EEG) source localization. It is based on a HSA and BAMS for segmenting the tissues from multi-modal magnetic resonance (MR) head images. The evaluation of the proposed method was done both directly in terms of segmentation accuracy and indirectly in terms of source localization accuracy. The direct evaluation was performed relative to a commonly used reference method brain extraction tool (BET)–FMRIB’s automated segmenta- tion tool (FAST) and four variants of the HSA using both synthetic data and real data from ten subjects. The synthetic data includes multiple realizations of four different noise levels and several realizations of typical noise with a 20 % bias field level. The Dice index and Hausdorff distance were used to measure the segmentation accuracy. The indirect evaluation was performed relative to the reference method BET-FAST using synthetic two-dimensional (2D) multimodal magnetic resonance (MR) data with 3 % noise and synthetic EEG (generated for a prescribed source). The source localiza- tion accuracy was determined in terms of localization error and relative error of potential. The experimental results dem- onstrate the efficacy of HSA-BAMS, its robustness to noise and the bias field, and that it provides better segmentation accuracy than the reference method and variants of the HSA. They also show that it leads to a more accurate localization accuracy than the commonly used reference method and sug- gest that it has potential as a surrogate for expert manual segmentation for the EEG source localization problem

On High Order Tensor-based Diffusivity Profile Estimation

Diffusion weighted magnetic resonance imaging (dMRI) is used to measure, in vivo, the self-diffusion of water molecules in biological tissues. High order tensors (HOTs) are used to model the apparent diffusion coefficient (ADC) profile at each voxel from the dMRI data. In this paper we propose: (i) A new method for estimating HOTs from dMRI data based on weighted least squares (WLS) optimization; and (ii) A new expression for computing the fractional anisotropy from a HOT that does not suffer from singularities and spurious zeros. We also present an empirical evaluation of the proposed method relative to the two existing methods based on both synthetic and real human brain dMRI data. The results show that the proposed method yields more accurate estimation than the competing methods

Novel chromatin texture features for the classification of Pap smears

This paper presents a set of novel structural texture features for quantifying nuclear chromatin patterns in cells on a conventional Pap smear. The features are derived from an initial segmentation of the chromatin into bloblike texture primitives. The results of a comprehensive feature selection experiment, including the set of proposed structural texture features and a range of different cytology features drawn from the literature, show that two of the four top ranking features are structural texture features. They also show that a combination of structural and conventional features yields a classification performance of 0.954±0.019 (AUC±SE) for the discrimination of normal (NILM) and abnormal (LSIL and HSIL) slides. The results of a second classification experiment, using only normal-appearing cells from both normal and abnormal slides, demonstrates that a single structural texture feature measuring chromatin margination yields a classification performance of 0.815±0.019. Overall the results demonstrate the efficacy of the proposed structural approach and that it is possible to detect malignancy associated changes (MACs) in Papanicoloau stain

Mutual information-based binarisation of multiple images of an object: an application in medical imaging

A new method for image thresholding of two or more images that are acquired in different modalities or acquisition protocols is proposed. The method is based on measures from information theory and has no underlying free parameters nor does it require training or calibration. The method is based on finding an optimal set of global thresholds, one for each image, by maximising the mutual information above the thresholds while minimising the mutual information below the thresholds. Although some assumptions on the nature of images are made, no assumptions are made by the method on the intensity distributions or on the shape of the image histograms. The effectiveness of the method is demonstrated both on synthetic images and medical images from clinical practice. It is then compared against three other thresholding method

Registration evaluation of dynamic breast MR images

The interpretation of dynamic contrast-enhanced breast MR images is predicated on the assumption of minimal voxel movement during the time course of the image acquisition. Misalignment of the dynamic image sequence as a result of movement during image acquisition can lead to potentially misleading diagnostic conclusions. In this paper a new methodology is presented for assessing the degree of in-plane (intra-slice) movement in a dynamic image sequence. The method is demonstrated on data from six subjects. The conclusion is that the method makes it possible to quantitatively qualify the accuracy of computed enhancement curves and more importantly to identify unacceptably poor registration

A Comparative Study of Automated Segmentation Methods for Use in a Microwave Tomography System for Imaging Intracerebral Hemorrhage in Stroke Patients

Microwave technology offers the possibility for pre-hospital stroke detection as we have pre- viously demonstrated using non-imaging diagnostics. The focus in this paper is on image-based diagnostics wherein the technical and computational complexities of image reconstruction are a challenge for clinical realization. Herein we investigate whether information about a patient’s brain anatomy obtained prior to a stroke event can be used to facilitate image-based stroke diag- nostics. A priori information can be obtained by segmenting the patient’s head tissues from mag- netic resonance images. Expert manual segmentation is presently the gold standard, but it is labo- rious and subjective. A fully automatic method is thus desirable. This paper presents an evaluation of several such methods using both synthetic magnetic resonance imaging (MRI) data and real da- ta from four healthy subjects. The segmentation was performed on the full 3D MRI data, whereas the electromagnetic evaluation was performed using a 2D slice. The methods were evaluated in terms of: i) tissue classification accuracy over all tissues with respect to ground truth, ii) the accu- racy of the simulated electromagnetic wave propagation through the head, and iii) the accuracy of the image reconstruction of the hemorrhage. The segmentation accuracy was measured in terms of the degree of overlap (Dice score) with the ground truth. The electromagnetic simulation accu- racy was measured in terms of signal deviation relative to the simulation based on the ground truth. Finally, the image reconstruction accuracy was measured in terms of the Dice score, relative error of dielectric properties, and visual comparison between the true and reconstructed intrace- rebral hemorrhage. The results show that accurate segmentation of tissues (Dice score = 0.97) from the MRI data can lead to accurate image reconstruction (relative error = 0.24) for the intra- cerebral hemorrhage in the subject’s brain. They also suggest that accurate automated segmenta- tion can be used as a surrogate for manual segmentation and can facilitate the rapid diagnosis of intracerebral hemorrhage in stroke patients using a microwave imaging system