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

Class-Based Feature Matching Across Unrestricted Transformations

We develop a novel method for class-based feature matching across large changes in viewing conditions. The method is based on the property that when objects share a similar part, the similarity is preserved across viewing conditions. Given a feature and a training set of object images, we first identify the subset of objects that share this feature. The transformation of the feature's appearance across viewing conditions is determined mainly by properties of the feature, rather than of the object in which it is embedded. Therefore, the transformed feature will be shared by approximately the same set of objects. Based on this consistency requirement, corresponding features can be reliably identified from a set of candidate matches. Unlike previous approaches, the proposed scheme compares feature appearances only in similar viewing conditions, rather than across different viewing conditions. As a result, the scheme is not restricted to locally planar objects or affine transformations. The approach also does not require examples of correct matches. We show that by using the proposed method, a dense set of accurate correspondences can be obtained. Experimental comparisons demonstrate that matching accuracy is significantly improved over previous schemes. Finally, we show that the scheme can be successfully used for invariant object recognition

An Adaptive Locally Connected Neuron Model: Focusing Neuron

This paper presents a new artificial neuron model capable of learning its receptive field in the topological domain of inputs. The model provides adaptive and differentiable local connectivity (plasticity) applicable to any domain. It requires no other tool than the backpropagation algorithm to learn its parameters which control the receptive field locations and apertures. This research explores whether this ability makes the neuron focus on informative inputs and yields any advantage over fully connected neurons. The experiments include tests of focusing neuron networks of one or two hidden layers on synthetic and well-known image recognition data sets. The results demonstrated that the focusing neurons can move their receptive fields towards more informative inputs. In the simple two-hidden layer networks, the focusing layers outperformed the dense layers in the classification of the 2D spatial data sets. Moreover, the focusing networks performed better than the dense networks even when 70$\%$ of the weights were pruned. The tests on convolutional networks revealed that using focusing layers instead of dense layers for the classification of convolutional features may work better in some data sets.Comment: 45 pages, a national patent filed, submitted to Turkish Patent Office, No: -2017/17601, Date: 09.11.201

A supervised clustering approach for fMRI-based inference of brain states

We propose a method that combines signals from many brain regions observed in functional Magnetic Resonance Imaging (fMRI) to predict the subject's behavior during a scanning session. Such predictions suffer from the huge number of brain regions sampled on the voxel grid of standard fMRI data sets: the curse of dimensionality. Dimensionality reduction is thus needed, but it is often performed using a univariate feature selection procedure, that handles neither the spatial structure of the images, nor the multivariate nature of the signal. By introducing a hierarchical clustering of the brain volume that incorporates connectivity constraints, we reduce the span of the possible spatial configurations to a single tree of nested regions tailored to the signal. We then prune the tree in a supervised setting, hence the name supervised clustering, in order to extract a parcellation (division of the volume) such that parcel-based signal averages best predict the target information. Dimensionality reduction is thus achieved by feature agglomeration, and the constructed features now provide a multi-scale representation of the signal. Comparisons with reference methods on both simulated and real data show that our approach yields higher prediction accuracy than standard voxel-based approaches. Moreover, the method infers an explicit weighting of the regions involved in the regression or classification task

Learning-based Image Enhancement for Visual Odometry in Challenging HDR Environments

One of the main open challenges in visual odometry (VO) is the robustness to difficult illumination conditions or high dynamic range (HDR) environments. The main difficulties in these situations come from both the limitations of the sensors and the inability to perform a successful tracking of interest points because of the bold assumptions in VO, such as brightness constancy. We address this problem from a deep learning perspective, for which we first fine-tune a Deep Neural Network (DNN) with the purpose of obtaining enhanced representations of the sequences for VO. Then, we demonstrate how the insertion of Long Short Term Memory (LSTM) allows us to obtain temporally consistent sequences, as the estimation depends on previous states. However, the use of very deep networks does not allow the insertion into a real-time VO framework; therefore, we also propose a Convolutional Neural Network (CNN) of reduced size capable of performing faster. Finally, we validate the enhanced representations by evaluating the sequences produced by the two architectures in several state-of-art VO algorithms, such as ORB-SLAM and DSO

Medical imaging analysis with artificial neural networks

Given that neural networks have been widely reported in the research community of medical imaging, we provide a focused literature survey on recent neural network developments in computer-aided diagnosis, medical image segmentation and edge detection towards visual content analysis, and medical image registration for its pre-processing and post-processing, with the aims of increasing awareness of how neural networks can be applied to these areas and to provide a foundation for further research and practical development. Representative techniques and algorithms are explained in detail to provide inspiring examples illustrating: (i) how a known neural network with fixed structure and training procedure could be applied to resolve a medical imaging problem; (ii) how medical images could be analysed, processed, and characterised by neural networks; and (iii) how neural networks could be expanded further to resolve problems relevant to medical imaging. In the concluding section, a highlight of comparisons among many neural network applications is included to provide a global view on computational intelligence with neural networks in medical imaging