Volumetric Data Classification: A Study Direct at 3-D Imagery

This thesis describes research work undertaken in the field of image mining (particularly medical image mining). More specifically, the research work is directed at 3-D image classification according to the nature of a particular Volume Of Interest (VOI) that appears across a given image set. In this thesis the term VOI Based Image Classification (VOIBIC) has been coined to describe this process. VOIBIC entails a number of challenges. The first is the identification and isolation of the VOIs. Two segmentation algorithms are thus proposed to extract a given VOI from an image set: (i) Volume Growing and (ii) Bounding Box. The second challenge that VOIBIC poses is, once the VOI have been identified, how best to represent the VOI so that classification can be effectively and efficiently conducted. Three approaches are considered. The first is founded on the idea of using statistical metrics, the Statistical Metrics based representation. This representation offers the advantage in that it is straightforward and, although not especially novel, provides a benchmark. The second proposed representation is founded on the concept of point series (curves) describing the perimeter of a VOI, the Point Series representation. Two variations of this representation are considered: (i) Spoke based and (ii) Disc based. The third proposed representation is founded on a Frequent Subgraph Mining (FSM) technique whereby the VOI is represented using an Oct-tree structure to which FSM can be applied. The identified frequent subtrees can then be used to define a feature vector representation compatible with many classifier model generation methods. The thesis also considers augmenting the VOI data with meta data, namely age and gender, and determining the effect this has on performance. The presented evaluation used two 3-D MRI brain scan data sets: (i) Epilepsy and (ii) Musicians. The VOI in this case were the lateral ventricles, a distinctive VOI in such MRI brain scan data. For evaluation purposes two scenarios are considered, distinguishing between: (i) epilepsy patients and healthy people and (ii) musicians and non-musicians. The results indicates that the Spoke based point series representation technique produced the best results with a recorded classification accuracy of up to 78.52% for the Epilepsy dataset and 84.91% for the Musician dataset

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Big Data Classification of Ultrasound Doppler Scan Images Using a Decision Tree Classifier Based on Maximally Stable Region Feature Points

The classification of ultrasound scan images is important in monitoring the development of prenatal and maternal structures. This paper proposes a big data classification system for ultrasound Doppler scan images that combines the residual of maximally stable extreme regions and speeded up robust features (SURF) with a decision tree classifier. The algorithm first preprocesses the ultrasound scan images before detecting the maximally stable extremal regions (MSER). A few essential regions are chosen from the MSER regions, along with the residual region that provides the best Region of Interest (ROI). SURF features points that best represent the region are detected using the gradient of the estimated cumulative region of interest. To extract the feature from the pixels that surround the SURF feature points, the Triangular Vertex Transform (TVT) transform is used. A decision tree classifier is used to train the extracted TVT features. The proposed ultrasound scan image classification system is validated using performance parameters such as accuracy, specificity, precision, sensitivity, and F1 score. For validation, a large dataset of 12,400 scan images collected from 1792 patients is used. The proposed method has an F1score of 94.12%, sensitivity, specificity, precision, and accuracy of 93.57%, 93.57%, and 97.96%, respectively. The evaluation results show that the proposed algorithm for classifying Doppler scan images is better than other algorithms that have been used in the past.&nbsp

A new convolutional neural network based on combination of circlets and wavelets for macular OCT classification

Artificial intelligence (AI) algorithms, encompassing machine learning and deep learning, can assist ophthalmologists in early detection of various ocular abnormalities through the analysis of retinal optical coherence tomography (OCT) images. Despite considerable progress in these algorithms, several limitations persist in medical imaging fields, where a lack of data is a common issue. Accordingly, specific image processing techniques, such as time–frequency transforms, can be employed in conjunction with AI algorithms to enhance diagnostic accuracy. This research investigates the influence of non-data-adaptive time–frequency transforms, specifically X-lets, on the classification of OCT B-scans. For this purpose, each B-scan was transformed using every considered X-let individually, and all the sub-bands were utilized as the input for a designed 2D Convolutional Neural Network (CNN) to extract optimal features, which were subsequently fed to the classifiers. Evaluating per-class accuracy shows that the use of the 2D Discrete Wavelet Transform (2D-DWT) yields superior outcomes for normal cases, whereas the circlet transform outperforms other X-lets for abnormal cases characterized by circles in their retinal structure (due to the accumulation of fluid). As a result, we propose a novel transform named CircWave by concatenating all sub-bands from the 2D-DWT and the circlet transform. The objective is to enhance the per-class accuracy of both normal and abnormal cases simultaneously. Our findings show that classification results based on the CircWave transform outperform those derived from original images or any individual transform. Furthermore, Grad-CAM class activation visualization for B-scans reconstructed from CircWave sub-bands highlights a greater emphasis on circular formations in abnormal cases and straight lines in normal cases, in contrast to the focus on irrelevant regions in original B-scans. To assess the generalizability of our method, we applied it to another dataset obtained from a different imaging system. We achieved promising accuracies of 94.5% and 90% for the first and second datasets, respectively, which are comparable with results from previous studies. The proposed CNN based on CircWave sub-bands (i.e. CircWaveNet) not only produces superior outcomes but also offers more interpretable results with a heightened focus on features crucial for ophthalmologists