A novel neural network approach to cDNA microarray image segmentation

This is the post-print version of the Article. The official published version can be accessed from the link below. Copyright @ 2013 Elsevier.Microarray technology has become a great source of information for biologists to understand the workings of DNA which is one of the most complex codes in nature. Microarray images typically contain several thousands of small spots, each of which represents a different gene in the experiment. One of the key steps in extracting information from a microarray image is the segmentation whose aim is to identify which pixels within an image represent which gene. This task is greatly complicated by noise within the image and a wide degree of variation in the values of the pixels belonging to a typical spot. In the past there have been many methods proposed for the segmentation of microarray image. In this paper, a new method utilizing a series of artificial neural networks, which are based on multi-layer perceptron (MLP) and Kohonen networks, is proposed. The proposed method is applied to a set of real-world cDNA images. Quantitative comparisons between the proposed method and commercial software GenePix(®) are carried out in terms of the peak signal-to-noise ratio (PSNR). This method is shown to not only deliver results comparable and even superior to existing techniques but also have a faster run time.This work was funded in part by the National Natural Science Foundation of China under Grants 61174136 and 61104041, the Natural Science Foundation of Jiangsu Province of China under Grant BK2011598, the International Science and Technology Cooperation Project of China under Grant No. 2011DFA12910, the Engineering and Physical Sciences Research Council (EPSRC) of the U.K. under Grant GR/S27658/01, the Royal Society of the U.K., and the Alexander von Humboldt Foundation of Germany

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

Multi-model fitting based on minimum spanning tree

This paper presents a novel approach to the computation of primitive geometrical structures, where no prior knowledge about the visual scene is available and a high level of noise is expected. We based our work on the grouping principles of proximity and similarity, of points and preliminary models. The former was realized using Minimum Spanning Trees (MST), on which we apply a stable alignment and goodness of fit criteria. As for the latter, we used spectral clustering of preliminary models. The algorithm can be generalized to various model fitting settings, without tuning of run parameters. Experiments demonstrate the significant improvement in the localization accuracy of models in plane, homography and motion segmentation examples. The efficiency of the algorithm is not dependent on fine tuning of run parameters like most others in the field

Cognitive fusion of thermal and visible imagery for effective detection and tracking of pedestrians in videos

BACKGROUND INTRODUCTION In this paper, we present an efficient framework to cognitively detect and track salient objects from videos. In general, colored visible image in red-green-blue (RGB) has better distinguishability in human visual perception, yet it suffers from the effect of illumination noise and shadows. On the contrary, the thermal image is less sensitive to these noise effects though its distinguishability varies according to environmental settings. To this end, cognitive fusion of these two modalities provides an effective solution to tackle this problem. METHODS First, a background model is extracted followed by two stage background-subtraction for foreground detection in visible and thermal images. To deal with cases of occlusion or overlap, knowledge based forward tracking and backward tracking are employed to identify separate objects even the foreground detection fails. RESULTS To evaluate the proposed method, a publicly available color-thermal benchmark dataset OTCBVS is employed here. For our foreground detection evaluation, objective and subjective analysis against several state-of-the-art methods have been done on our manually segmented ground truth. For our object tracking evaluation, comprehensive qualitative experiments have also been done on all video sequences. CONCLUSIONS Promising results have shown that the proposed fusion based approach can successfully detect and track multiple human objects in most scenes regardless of any light change or occlusion problem

Large-scale Binary Quadratic Optimization Using Semidefinite Relaxation and Applications

In computer vision, many problems such as image segmentation, pixel labelling, and scene parsing can be formulated as binary quadratic programs (BQPs). For submodular problems, cuts based methods can be employed to efficiently solve large-scale problems. However, general nonsubmodular problems are significantly more challenging to solve. Finding a solution when the problem is of large size to be of practical interest, however, typically requires relaxation. Two standard relaxation methods are widely used for solving general BQPs--spectral methods and semidefinite programming (SDP), each with their own advantages and disadvantages. Spectral relaxation is simple and easy to implement, but its bound is loose. Semidefinite relaxation has a tighter bound, but its computational complexity is high, especially for large scale problems. In this work, we present a new SDP formulation for BQPs, with two desirable properties. First, it has a similar relaxation bound to conventional SDP formulations. Second, compared with conventional SDP methods, the new SDP formulation leads to a significantly more efficient and scalable dual optimization approach, which has the same degree of complexity as spectral methods. We then propose two solvers, namely, quasi-Newton and smoothing Newton methods, for the dual problem. Both of them are significantly more efficiently than standard interior-point methods. In practice, the smoothing Newton solver is faster than the quasi-Newton solver for dense or medium-sized problems, while the quasi-Newton solver is preferable for large sparse/structured problems. Our experiments on a few computer vision applications including clustering, image segmentation, co-segmentation and registration show the potential of our SDP formulation for solving large-scale BQPs.Comment: Fixed some typos. 18 pages. Accepted to IEEE Transactions on Pattern Analysis and Machine Intelligenc