1,356 research outputs found

    Coupled non-parametric shape and moment-based inter-shape pose priors for multiple basal ganglia structure segmentation

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    This paper presents a new active contour-based, statistical method for simultaneous volumetric segmentation of multiple subcortical structures in the brain. In biological tissues, such as the human brain, neighboring structures exhibit co-dependencies which can aid in segmentation, if properly analyzed and modeled. Motivated by this observation, we formulate the segmentation problem as a maximum a posteriori estimation problem, in which we incorporate statistical prior models on the shapes and inter-shape (relative) poses of the structures of interest. This provides a principled mechanism to bring high level information about the shapes and the relationships of anatomical structures into the segmentation problem. For learning the prior densities we use a nonparametric multivariate kernel density estimation framework. We combine these priors with data in a variational framework and develop an active contour-based iterative segmentation algorithm. We test our method on the problem of volumetric segmentation of basal ganglia structures in magnetic resonance (MR) images. We present a set of 2D and 3D experiments as well as a quantitative performance analysis. In addition, we perform a comparison to several existent segmentation methods and demonstrate the improvements provided by our approach in terms of segmentation accuracy

    Factorisation-Based Image Labelling

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    Segmentation of brain magnetic resonance images (MRI) into anatomical regions is a useful task in neuroimaging. Manual annotation is time consuming and expensive, so having a fully automated and general purpose brain segmentation algorithm is highly desirable. To this end, we propose a patched-based labell propagation approach based on a generative model with latent variables. Once trained, our Factorisation-based Image Labelling (FIL) model is able to label target images with a variety of image contrasts. We compare the effectiveness of our proposed model against the state-of-the-art using data from the MICCAI 2012 Grand Challenge and Workshop on Multi-Atlas Labelling. As our approach is intended to be general purpose, we also assess how well it can handle domain shift by labelling images of the same subjects acquired with different MR contrasts

    Contrastive Registration for Unsupervised Medical Image Segmentation

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    Medical image segmentation is a relevant task as it serves as the first step for several diagnosis processes, thus it is indispensable in clinical usage. Whilst major success has been reported using supervised techniques, they assume a large and well-representative labelled set. This is a strong assumption in the medical domain where annotations are expensive, time-consuming, and inherent to human bias. To address this problem, unsupervised techniques have been proposed in the literature yet it is still an open problem due to the difficulty of learning any transformation pattern. In this work, we present a novel optimisation model framed into a new CNN-based contrastive registration architecture for unsupervised medical image segmentation. The core of our approach is to exploit image-level registration and feature-level from a contrastive learning mechanism, to perform registration-based segmentation. Firstly, we propose an architecture to capture the image-to-image transformation pattern via registration for unsupervised medical image segmentation. Secondly, we embed a contrastive learning mechanism into the registration architecture to enhance the discriminating capacity of the network in the feature-level. We show that our proposed technique mitigates the major drawbacks of existing unsupervised techniques. We demonstrate, through numerical and visual experiments, that our technique substantially outperforms the current state-of-the-art unsupervised segmentation methods on two major medical image datasets.Comment: 11 pages, 3 figure

    Hybrid Bayesian Eigenobjects: Combining Linear Subspace and Deep Network Methods for 3D Robot Vision

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    We introduce Hybrid Bayesian Eigenobjects (HBEOs), a novel representation for 3D objects designed to allow a robot to jointly estimate the pose, class, and full 3D geometry of a novel object observed from a single viewpoint in a single practical framework. By combining both linear subspace methods and deep convolutional prediction, HBEOs efficiently learn nonlinear object representations without directly regressing into high-dimensional space. HBEOs also remove the onerous and generally impractical necessity of input data voxelization prior to inference. We experimentally evaluate the suitability of HBEOs to the challenging task of joint pose, class, and shape inference on novel objects and show that, compared to preceding work, HBEOs offer dramatically improved performance in all three tasks along with several orders of magnitude faster runtime performance.Comment: To appear in the International Conference on Intelligent Robots (IROS) - Madrid, 201

    Generative Models for Preprocessing of Hospital Brain Scans

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    I will in this thesis present novel computational methods for processing routine clinical brain scans. Such scans were originally acquired for qualitative assessment by trained radiologists, and present a number of difficulties for computational models, such as those within common neuroimaging analysis software. The overarching objective of this work is to enable efficient and fully automated analysis of large neuroimaging datasets, of the type currently present in many hospitals worldwide. The methods presented are based on probabilistic, generative models of the observed imaging data, and therefore rely on informative priors and realistic forward models. The first part of the thesis will present a model for image quality improvement, whose key component is a novel prior for multimodal datasets. I will demonstrate its effectiveness for super-resolving thick-sliced clinical MR scans and for denoising CT images and MR-based, multi-parametric mapping acquisitions. I will then show how the same prior can be used for within-subject, intermodal image registration, for more robustly registering large numbers of clinical scans. The second part of the thesis focusses on improved, automatic segmentation and spatial normalisation of routine clinical brain scans. I propose two extensions to a widely used segmentation technique. First, a method for this model to handle missing data, which allows me to predict entirely missing modalities from one, or a few, MR contrasts. Second, a principled way of combining the strengths of probabilistic, generative models with the unprecedented discriminative capability of deep learning. By introducing a convolutional neural network as a Markov random field prior, I can model nonlinear class interactions and learn these using backpropagation. I show that this model is robust to sequence and scanner variability. Finally, I show examples of fitting a population-level, generative model to various neuroimaging data, which can model, e.g., CT scans with haemorrhagic lesions

    A Survey on Deep Learning in Medical Image Analysis

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    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

    Reasoning with Uncertainty in Deep Learning for Safer Medical Image Computing

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    Deep learning is now ubiquitous in the research field of medical image computing. As such technologies progress towards clinical translation, the question of safety becomes critical. Once deployed, machine learning systems unavoidably face situations where the correct decision or prediction is ambiguous. However, the current methods disproportionately rely on deterministic algorithms, lacking a mechanism to represent and manipulate uncertainty. In safety-critical applications such as medical imaging, reasoning under uncertainty is crucial for developing a reliable decision making system. Probabilistic machine learning provides a natural framework to quantify the degree of uncertainty over different variables of interest, be it the prediction, the model parameters and structures, or the underlying data (images and labels). Probability distributions are used to represent all the uncertain unobserved quantities in a model and how they relate to the data, and probability theory is used as a language to compute and manipulate these distributions. In this thesis, we explore probabilistic modelling as a framework to integrate uncertainty information into deep learning models, and demonstrate its utility in various high-dimensional medical imaging applications. In the process, we make several fundamental enhancements to current methods. We categorise our contributions into three groups according to the types of uncertainties being modelled: (i) predictive; (ii) structural and (iii) human uncertainty. Firstly, we discuss the importance of quantifying predictive uncertainty and understanding its sources for developing a risk-averse and transparent medical image enhancement application. We demonstrate how a measure of predictive uncertainty can be used as a proxy for the predictive accuracy in the absence of ground-truths. Furthermore, assuming the structure of the model is flexible enough for the task, we introduce a way to decompose the predictive uncertainty into its orthogonal sources i.e. aleatoric and parameter uncertainty. We show the potential utility of such decoupling in providing a quantitative “explanations” into the model performance. Secondly, we introduce our recent attempts at learning model structures directly from data. One work proposes a method based on variational inference to learn a posterior distribution over connectivity structures within a neural network architecture for multi-task learning, and share some preliminary results in the MR-only radiotherapy planning application. Another work explores how the training algorithm of decision trees could be extended to grow the architecture of a neural network to adapt to the given availability of data and the complexity of the task. Lastly, we develop methods to model the “measurement noise” (e.g., biases and skill levels) of human annotators, and integrate this information into the learning process of the neural network classifier. In particular, we show that explicitly modelling the uncertainty involved in the annotation process not only leads to an improvement in robustness to label noise, but also yields useful insights into the patterns of errors that characterise individual experts
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