205 research outputs found
Image similarity in medical images
Recent experiments have indicated a strong influence of the substrate grain orientation on the self-ordering in anodic porous alumina. Anodic porous alumina with straight pore channels grown in a stable, self-ordered manner is formed on (001) oriented Al grain, while disordered porous pattern is formed on (101) oriented Al grain with tilted pore channels growing in an unstable manner. In this work, numerical simulation of the pore growth process is carried out to understand this phenomenon. The rate-determining step of the oxide growth is assumed to be the Cabrera-Mott barrier at the oxide/electrolyte (o/e) interface, while the substrate is assumed to determine the ratio β between the ionization and oxidation reactions at the metal/oxide (m/o) interface. By numerically solving the electric field inside a growing porous alumina during anodization, the migration rates of the ions and hence the evolution of the o/e and m/o interfaces are computed. The simulated results show that pore growth is more stable when β is higher. A higher β corresponds to more Al ionized and migrating away from the m/o interface rather than being oxidized, and hence a higher retained O:Al ratio in the oxide. Experimentally measured oxygen content in the self-ordered porous alumina on (001) Al is indeed found to be about 3% higher than that in the disordered alumina on (101) Al, in agreement with the theoretical prediction. The results, therefore, suggest that ionization on (001) Al substrate is relatively easier than on (101) Al, and this leads to the more stable growth of the pore channels on (001) Al
Landmark Localization, Feature Matching and Biomarker Discovery from Magnetic Resonance Images
The work presented in this thesis proposes several methods that can be roughly divided into three different categories: I) landmark localization in medical images, II) feature matching for image registration,
and III) biomarker discovery in neuroimaging.
The first part deals with the identification of anatomical landmarks. The motivation stems from the fact that the manual identification and labeling of these landmarks is very time consuming and prone to observer errors, especially when large datasets must be analyzed. In this thesis we present three methods to tackle this challenge: A landmark descriptor based on local self-similarities (SS), a subspace building framework based on manifold learning and a sparse coding landmark descriptor based on data-specific learned dictionary basis.
The second part of this thesis deals with finding matching features between a pair of images. These matches can be used to perform a registration between them. Registration is a powerful tool that allows mapping images in a common space in order to aid in their analysis. Accurate registration can be challenging to achieve using intensity based registration algorithms. Here, a framework is proposed for learning correspondences in pairs of images by matching SS features and random sample and consensus (RANSAC) is employed as a robust model estimator to learn a deformation model based on feature matches.
Finally, the third part of the thesis deals with biomarker discovery using machine learning. In this section a framework for feature extraction from learned low-dimensional subspaces that represent inter-subject
variability is proposed. The manifold subspace is built using data-driven regions of interest (ROI). These regions are learned via sparse regression, with stability selection. Also, probabilistic distribution models for
different stages in the disease trajectory are estimated for different class populations in the low-dimensional manifold and used to construct a probabilistic scoring function.Open Acces
3D shape matching and registration : a probabilistic perspective
Dense correspondence is a key area in computer vision and medical image analysis. It has applications in registration and shape analysis. In this thesis, we develop a technique to recover dense correspondences between the surfaces of neuroanatomical objects over heterogeneous populations of individuals. We recover dense correspondences based on 3D shape matching. In this thesis, the 3D shape matching problem is formulated under the framework of Markov Random Fields (MRFs). We represent the surfaces of neuroanatomical objects as genus zero voxel-based meshes. The surface meshes are projected into a Markov random field space. The projection carries both geometric and topological information in terms of Gaussian curvature and mesh neighbourhood from the original space to the random field space. Gaussian curvature is projected to the nodes of the MRF, and the mesh neighbourhood structure is projected to the edges. 3D shape matching between two surface meshes is then performed by solving an energy function minimisation problem formulated with MRFs. The outcome of the 3D shape matching is dense point-to-point correspondences. However, the minimisation of the energy function is NP hard. In this thesis, we use belief propagation to perform the probabilistic inference for 3D shape matching. A sparse update loopy belief propagation algorithm adapted to the 3D shape matching is proposed to obtain an approximate global solution for the 3D shape matching problem. The sparse update loopy belief propagation algorithm demonstrates significant efficiency gain compared to standard belief propagation. The computational complexity and convergence property analysis for the sparse update loopy belief propagation algorithm are also conducted in the thesis. We also investigate randomised algorithms to minimise the energy function. In order to enhance the shape matching rate and increase the inlier support set, we propose a novel clamping technique. The clamping technique is realized by combining the loopy belief propagation message updating rule with the feedback from 3D rigid body registration. By using this clamping technique, the correct shape matching rate is increased significantly. Finally, we investigate 3D shape registration techniques based on the 3D shape matching result. Based on the point-to-point dense correspondences obtained from the 3D shape matching, a three-point based transformation estimation technique is combined with the RANdom SAmple Consensus (RANSAC) algorithm to obtain the inlier support set. The global registration approach is purely dependent on point-wise correspondences between two meshed surfaces. It has the advantage that the need for orientation initialisation is eliminated and that all shapes of spherical topology. The comparison of our MRF based 3D registration approach with a state-of-the-art registration algorithm, the first order ellipsoid template, is conducted in the experiments. These show dense correspondence for pairs of hippocampi from two different data sets, each of around 20 60+ year old healthy individuals
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
Recommended from our members
ScatterNet Hybrid Frameworks for Deep Learning
Image understanding is the task of interpreting images by effectively solving the individual tasks of object recognition and semantic image segmentation. An image understanding system must have the capacity to distinguish between similar looking image regions while being invariant in its response to regions that have been altered by the appearance-altering transformation. The fundamental challenge for any such system lies within this simultaneous requirement for both invariance and specificity.
Many image understanding systems have been proposed that capture geometric properties such as shapes, textures, motion and 3D perspective projections using filtering, non-linear modulus, and pooling operations. Deep learning networks ignore these geometric considerations and compute descriptors having suitable invariance and stability to geometric transformations using (end-to-end) learned multi-layered network filters. These deep learning networks in recent years have come to dominate the previously separate fields of research in machine learning, computer vision, natural language understanding and speech recognition.
Despite the success of these deep networks, there remains a
fundamental lack of understanding in the design and optimization of these networks which makes it difficult to develop them. Also, training of these networks requires large labeled datasets which in numerous applications may not be available.
In this dissertation, we propose the ScatterNet Hybrid Framework for Deep Learning that is inspired by the circuitry of the visual cortex. The framework uses a hand-crafted front-end, an unsupervised learning based middle-section, and a supervised back-end to rapidly learn hierarchical features from unlabelled data. Each layer in the proposed framework is automatically optimized to produce the desired computationally efficient architecture. The term `Hybrid' is coined because the framework uses both unsupervised as well as supervised learning.
We propose two hand-crafted front-ends that can extract locally invariant features from the input signals. Next, two ScatterNet Hybrid Deep Learning (SHDL) networks (a generative and a deterministic) were introduced by combining the proposed front-ends with two unsupervised learning modules which learn hierarchical features. These hierarchical features were finally used by a supervised learning module to solve the task of either object recognition or semantic image segmentation. The proposed front-ends have also been shown to improve the performance and learning of current Deep Supervised Learning Networks (VGG, NIN, ResNet) with reduced computing overhead
Object Recognition
Vision-based object recognition tasks are very familiar in our everyday activities, such as driving our car in the correct lane. We do these tasks effortlessly in real-time. In the last decades, with the advancement of computer technology, researchers and application developers are trying to mimic the human's capability of visually recognising. Such capability will allow machine to free human from boring or dangerous jobs
A survey of visual preprocessing and shape representation techniques
Many recent theories and methods proposed for visual preprocessing and shape representation are summarized. The survey brings together research from the fields of biology, psychology, computer science, electrical engineering, and most recently, neural networks. It was motivated by the need to preprocess images for a sparse distributed memory (SDM), but the techniques presented may also prove useful for applying other associative memories to visual pattern recognition. The material of this survey is divided into three sections: an overview of biological visual processing; methods of preprocessing (extracting parts of shape, texture, motion, and depth); and shape representation and recognition (form invariance, primitives and structural descriptions, and theories of attention)
- …