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 Posteriori Error Control for the Binary Mumford-Shah Model

The binary Mumford-Shah model is a widespread tool for image segmentation and can be considered as a basic model in shape optimization with a broad range of applications in computer vision, ranging from basic segmentation and labeling to object reconstruction. This paper presents robust a posteriori error estimates for a natural error quantity, namely the area of the non properly segmented region. To this end, a suitable strictly convex and non-constrained relaxation of the originally non-convex functional is investigated and Repin's functional approach for a posteriori error estimation is used to control the numerical error for the relaxed problem in the $L^2$-norm. In combination with a suitable cut out argument, a fully practical estimate for the area mismatch is derived. This estimate is incorporated in an adaptive meshing strategy. Two different adaptive primal-dual finite element schemes, and the most frequently used finite difference discretization are investigated and compared. Numerical experiments show qualitative and quantitative properties of the estimates and demonstrate their usefulness in practical applications.Comment: 18 pages, 7 figures, 1 tabl

A Fusion Framework for Camouflaged Moving Foreground Detection in the Wavelet Domain

Detecting camouflaged moving foreground objects has been known to be difficult due to the similarity between the foreground objects and the background. Conventional methods cannot distinguish the foreground from background due to the small differences between them and thus suffer from under-detection of the camouflaged foreground objects. In this paper, we present a fusion framework to address this problem in the wavelet domain. We first show that the small differences in the image domain can be highlighted in certain wavelet bands. Then the likelihood of each wavelet coefficient being foreground is estimated by formulating foreground and background models for each wavelet band. The proposed framework effectively aggregates the likelihoods from different wavelet bands based on the characteristics of the wavelet transform. Experimental results demonstrated that the proposed method significantly outperformed existing methods in detecting camouflaged foreground objects. Specifically, the average F-measure for the proposed algorithm was 0.87, compared to 0.71 to 0.8 for the other state-of-the-art methods.Comment: 13 pages, accepted by IEEE TI

Customisable arithmetic hardware designs

Imperial Users onl

Local Stereo Matching Using Adaptive Local Segmentation

We propose a new dense local stereo matching framework for gray-level images based on an adaptive local segmentation using a dynamic threshold. We define a new validity domain of the fronto-parallel assumption based on the local intensity variations in the 4-neighborhood of the matching pixel. The preprocessing step smoothes low textured areas and sharpens texture edges, whereas the postprocessing step detects and recovers occluded and unreliable disparities. The algorithm achieves high stereo reconstruction quality in regions with uniform intensities as well as in textured regions. The algorithm is robust against local radiometrical differences; and successfully recovers disparities around the objects edges, disparities of thin objects, and the disparities of the occluded region. Moreover, our algorithm intrinsically prevents errors caused by occlusion to propagate into nonoccluded regions. It has only a small number of parameters. The performance of our algorithm is evaluated on the Middlebury test bed stereo images. It ranks highly on the evaluation list outperforming many local and global stereo algorithms using color images. Among the local algorithms relying on the fronto-parallel assumption, our algorithm is the best ranked algorithm. We also demonstrate that our algorithm is working well on practical examples as for disparity estimation of a tomato seedling and a 3D reconstruction of a face

SHADHO: Massively Scalable Hardware-Aware Distributed Hyperparameter Optimization

Computer vision is experiencing an AI renaissance, in which machine learning models are expediting important breakthroughs in academic research and commercial applications. Effectively training these models, however, is not trivial due in part to hyperparameters: user-configured values that control a model's ability to learn from data. Existing hyperparameter optimization methods are highly parallel but make no effort to balance the search across heterogeneous hardware or to prioritize searching high-impact spaces. In this paper, we introduce a framework for massively Scalable Hardware-Aware Distributed Hyperparameter Optimization (SHADHO). Our framework calculates the relative complexity of each search space and monitors performance on the learning task over all trials. These metrics are then used as heuristics to assign hyperparameters to distributed workers based on their hardware. We first demonstrate that our framework achieves double the throughput of a standard distributed hyperparameter optimization framework by optimizing SVM for MNIST using 150 distributed workers. We then conduct model search with SHADHO over the course of one week using 74 GPUs across two compute clusters to optimize U-Net for a cell segmentation task, discovering 515 models that achieve a lower validation loss than standard U-Net.Comment: 10 pages, 6 figure

Training Gaussian Mixture Models at Scale via Coresets

How can we train a statistical mixture model on a massive data set? In this work we show how to construct coresets for mixtures of Gaussians. A coreset is a weighted subset of the data, which guarantees that models fitting the coreset also provide a good fit for the original data set. We show that, perhaps surprisingly, Gaussian mixtures admit coresets of size polynomial in dimension and the number of mixture components, while being independent of the data set size. Hence, one can harness computationally intensive algorithms to compute a good approximation on a significantly smaller data set. More importantly, such coresets can be efficiently constructed both in distributed and streaming settings and do not impose restrictions on the data generating process. Our results rely on a novel reduction of statistical estimation to problems in computational geometry and new combinatorial complexity results for mixtures of Gaussians. Empirical evaluation on several real-world datasets suggests that our coreset-based approach enables significant reduction in training-time with negligible approximation error