Multi-Atlas Segmentation using Partially Annotated Data: Methods and Annotation Strategies

Multi-atlas segmentation is a widely used tool in medical image analysis, providing robust and accurate results by learning from annotated atlas datasets. However, the availability of fully annotated atlas images for training is limited due to the time required for the labelling task. Segmentation methods requiring only a proportion of each atlas image to be labelled could therefore reduce the workload on expert raters tasked with annotating atlas images. To address this issue, we first re-examine the labelling problem common in many existing approaches and formulate its solution in terms of a Markov Random Field energy minimisation problem on a graph connecting atlases and the target image. This provides a unifying framework for multi-atlas segmentation. We then show how modifications in the graph configuration of the proposed framework enable the use of partially annotated atlas images and investigate different partial annotation strategies. The proposed method was evaluated on two Magnetic Resonance Imaging (MRI) datasets for hippocampal and cardiac segmentation. Experiments were performed aimed at (1) recreating existing segmentation techniques with the proposed framework and (2) demonstrating the potential of employing sparsely annotated atlas data for multi-atlas segmentation

Local selection of features and its applications to image search and annotation

In multimedia applications, direct representations of data objects typically involve hundreds or thousands of features. Given a query object, the similarity between the query object and a database object can be computed as the distance between their feature vectors. The neighborhood of the query object consists of those database objects that are close to the query object. The semantic quality of the neighborhood, which can be measured as the proportion of neighboring objects that share the same class label as the query object, is crucial for many applications, such as content-based image retrieval and automated image annotation. However, due to the existence of noisy or irrelevant features, errors introduced into similarity measurements are detrimental to the neighborhood quality of data objects. One way to alleviate the negative impact of noisy features is to use feature selection techniques in data preprocessing. From the original vector space, feature selection techniques select a subset of features, which can be used subsequently in supervised or unsupervised learning algorithms for better performance. However, their performance on improving the quality of data neighborhoods is rarely evaluated in the literature. In addition, most traditional feature selection techniques are global, in the sense that they compute a single set of features across the entire database. As a consequence, the possibility that the feature importance may vary across different data objects or classes of objects is neglected. To compute a better neighborhood structure for objects in high-dimensional feature spaces, this dissertation proposes several techniques for selecting features that are important to the local neighborhood of individual objects. These techniques are then applied to image applications such as content-based image retrieval and image label propagation. Firstly, an iterative K-NN graph construction method for image databases is proposed. A local variant of the Laplacian Score is designed for the selection of features for individual images. Noisy features are detected and sparsified iteratively from the original standardized feature vectors. This technique is incorporated into an approximate K-NN graph construction method so as to improve the semantic quality of the graph. Secondly, in a content-based image retrieval system, a generalized version of the Laplacian Score is used to compute different feature subspaces for images in the database. For online search, a query image is ranked in the feature spaces of database images. Those database images for which the query image is ranked highly are selected as the query results. Finally, a supervised method for the local selection of image features is proposed, for refining the similarity graph used in an image label propagation framework. By using only the selected features to compute the edges leading from labeled image nodes to unlabeled image nodes, better annotation accuracy can be achieved. Experimental results on several datasets are provided in this dissertation, to demonstrate the effectiveness of the proposed techniques for the local selection of features, and for the image applications under consideration

Provenance, propagation and quality of biological annotation

PhD ThesisBiological databases have become an integral part of the life sciences, being used to store, organise and share ever-increasing quantities and types of data. Biological databases are typically centred around raw data, with individual entries being assigned to a single piece of biological data, such as a DNA sequence. Although essential, a reader can obtain little information from the raw data alone. Therefore, many databases aim to supplement their entries with annotation, allowing the current knowledge about the underlying data to be conveyed to a reader. Although annotations come in many di erent forms, most databases provide some form of free text annotation. Given that annotations can form the foundations of future work, it is important that a user is able to evaluate the quality and correctness of an annotation. However, this is rarely straightforward. The amount of annotation, and the way in which it is curated, varies between databases. For example, the production of an annotation in some databases is entirely automated, without any manual intervention. Further, sections of annotations may be reused, being propagated between entries and, potentially, external databases. This provenance and curation information is not always apparent to a user. The work described within this thesis explores issues relating to biological annotation quality. While the most valuable annotation is often contained within free text, its lack of structure makes it hard to assess. Initially, this work describes a generic approach that allows textual annotations to be quantitatively measured. This approach is based upon the application of Zipf's Law to words within textual annotation, resulting in a single value, . The relationship between the value and Zipf's principle of least e ort provides an indication as to the annotations quality, whilst also allowing annotations to be quantitatively compared. Secondly, the thesis focuses on determining annotation provenance and tracking any subsequent propagation. This is achieved through the development of a visualisation - i - framework, which exploits the reuse of sentences within annotations. Utilising this framework a number of propagation patterns were identi ed, which on analysis appear to indicate low quality and erroneous annotation. Together, these approaches increase our understanding in the textual characteristics of biological annotation, and suggests that this understanding can be used to increase the overall quality of these resources

Effective Graph-Based Content--Based Image Retrieval Systems for Large-Scale and Small-Scale Image Databases

This dissertation proposes two novel manifold graph-based ranking systems for Content-Based Image Retrieval (CBIR). The two proposed systems exploit the synergism between relevance feedback-based transductive short-term learning and semantic feature-based long-term learning to improve retrieval performance. Proposed systems first apply the active learning mechanism to construct users\u27 relevance feedback log and extract high-level semantic features for each image. These systems then create manifold graphs by incorporating both the low-level visual similarity and the high-level semantic similarity to achieve more meaningful structures for the image space. Finally, asymmetric relevance vectors are created to propagate relevance scores of labeled images to unlabeled images via manifold graphs. The extensive experimental results demonstrate two proposed systems outperform the other state-of-the-art CBIR systems in the context of both correct and erroneous users\u27 feedback