A Cosmic Watershed: the WVF Void Detection Technique

On megaparsec scales the Universe is permeated by an intricate filigree of clusters, filaments, sheets and voids, the Cosmic Web. For the understanding of its dynamical and hierarchical history it is crucial to identify objectively its complex morphological components. One of the most characteristic aspects is that of the dominant underdense Voids, the product of a hierarchical process driven by the collapse of minor voids in addition to the merging of large ones. In this study we present an objective void finder technique which involves a minimum of assumptions about the scale, structure and shape of voids. Our void finding method, the Watershed Void Finder (WVF), is based upon the Watershed Transform, a well-known technique for the segmentation of images. Importantly, the technique has the potential to trace the existing manifestations of a void hierarchy. The basic watershed transform is augmented by a variety of correction procedures to remove spurious structure resulting from sampling noise. This study contains a detailed description of the WVF. We demonstrate how it is able to trace and identify, relatively parameter free, voids and their surrounding (filamentary and planar) boundaries. We test the technique on a set of Kinematic Voronoi models, heuristic spatial models for a cellular distribution of matter. Comparison of the WVF segmentations of low noise and high noise Voronoi models with the quantitatively known spatial characteristics of the intrinsic Voronoi tessellation shows that the size and shape of the voids are succesfully retrieved. WVF manages to even reproduce the full void size distribution function.Comment: 24 pages, 15 figures, MNRAS accepted, for full resolution, see http://www.astro.rug.nl/~weygaert/tim1publication/watershed.pd

Hyperspectral colon tissue cell classification

A novel algorithm to discriminate between normal and malignant tissue cells of the human colon is presented. The microscopic level images of human colon tissue cells were acquired using hyperspectral imaging technology at contiguous wavelength intervals of visible light. While hyperspectral imagery data provides a wealth of information, its large size normally means high computational processing complexity. Several methods exist to avoid the so-called curse of dimensionality and hence reduce the computational complexity. In this study, we experimented with Principal Component Analysis (PCA) and two modifications of Independent Component Analysis (ICA). In the first stage of the algorithm, the extracted components are used to separate four constituent parts of the colon tissue: nuclei, cytoplasm, lamina propria, and lumen. The segmentation is performed in an unsupervised fashion using the nearest centroid clustering algorithm. The segmented image is further used, in the second stage of the classification algorithm, to exploit the spatial relationship between the labeled constituent parts. Experimental results using supervised Support Vector Machines (SVM) classification based on multiscale morphological features reveal the discrimination between normal and malignant tissue cells with a reasonable degree of accuracy

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

Sparse optical flow regularisation for real-time visual tracking

Optical flow can greatly improve the robustness of visual tracking algorithms. While dense optical flow algorithms have various applications, they can not be used for real-time solutions without resorting to GPU calculations. Furthermore, most optical flow algorithms fail in challenging lighting environments due to the violation of the brightness constraint. We propose a simple but effective iterative regularisation scheme for real-time, sparse optical flow algorithms, that is shown to be robust to sudden illumination changes and can handle large displacements. The algorithm proves to outperform well known techniques in real life video sequences, while being much faster to calculate. Our solution increases the robustness of a real-time particle filter based tracking application, consuming only a fraction of the available CPU power. Furthermore, a new and realistic optical flow dataset with annotated ground truth is created and made freely available for research purposes