SolarView: Low Distortion Radial Embedding with a Focus.

We propose a novel type of low distortion radial embedding which focuses on one specific entity and its closest neighbors. Our embedding preserves near-exact distances to the focus entity and aims to minimize distortion between the other entities. We present an interactive exploration tool SolarView which places the focus entity at the center of a "solar system" and embeds its neighbors guided by concentric circles. SolarView provides an implementation of our novel embedding and several state-of-the-art dimensionality reduction and embedding techniques, which we adapted to our setting in various ways. We experimentally evaluated our embedding and compared it to these state-of-the-art techniques. The results show that our embedding competes with these techniques and achieves low distortion in practice. Our method performs particularly well when the visualization, and hence the embedding, adheres to the solar system design principle of our application. Nonetheless-as with all dimensionality reduction techniques-the distortion may be high. We leverage interaction techniques to give clear visual cues that allow users to accurately judge distortion. We illustrate the use of SolarView by exploring the high-dimensional metric space of bibliographic entity similarities.

Interactive segmentation and visualization of DTI data using a hierarchical watershed representation.

Magnetic resonance diffusion tensor imaging (DTI) measures diffusion of water molecules and is used to characterize orientation of white matter fibers and connectivity of neurological structures. Segmentation and visualization of DT images is challenging, because of low data quality and complexity of anatomical structures. In this paper, we propose an interactive segmentation approach, based on a hierarchical representation of the input DT image through a tree structure. The tree is obtained by successively merging watershed regions, based on the morphological waterfall approach, hence the name watershed tree. Region merging is done according to a combined similarity and homogeneity criterion. We introduce filters that work on the proposed tree representation, and that enable region-based attribute filtering of DTI data. Linked views between the visualizations of the simplified DT image and the tree enable a user to visually explore both data and tree at interactive rates. The coupling of filtering, semiautomatic segmentation by labeling nodes in the tree, and various interaction mechanisms support the segmentation task. Our method is robust against noise, which we demonstrate on synthetic and real DTI data.

eXamine: exploring annotated modules in networks.

BACKGROUND: Biological networks have a growing importance for the interpretation of high-throughput "omics" data. Integrative network analysis makes use of statistical and combinatorial methods to extract smaller subnetwork modules, and performs enrichment analysis to annotate the modules with ontology terms or other available knowledge. This process results in an annotated module, which retains the original network structure and includes enrichment information as a set system. A major bottleneck is a lack of tools that allow exploring both network structure of extracted modules and its annotations. RESULTS: This paper presents a visual analysis approach that targets small modules with many set-based annotations, and which displays the annotations as contours on top of a node-link diagram. We introduce an extension of self-organizing maps to lay out nodes, links, and contours in a unified way. An implementation of this approach is freely available as the Cytoscape app eXamine CONCLUSIONS: eXamine accurately conveys small and annotated modules consisting of several dozens of proteins and annotations. We demonstrate that eXamine facilitates the interpretation of integrative network analysis results in a guided case study. This study has resulted in a novel biological insight regarding the virally-encoded G-protein coupled receptor US28.

SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.

UNLABELLED: SpotXplore is a plugin for Cytoscape for extraction and visualization of differentially expressed subnetworks (hotspots) from gene networks. The hotspot-based visualization approach enables interactive exploration of regulatory interactions in differentially expressed gene sets, and it allows a researcher to explore gene expression in direct relation to the affected cellular gene network. The hotspots provide a view beyond the commonly used metabolic pathways and gene ontologies. AVAILABILITY: http://www.win.tue.nl/∼mwestenb/spotxplore/.

Volumetric attribute filtering and interactive visualization using the Max-Tree representation.

The Max-Tree designed for morphological attribute filtering in image processing, is a data structure in which the nodes represent connected components for all threshold levels in a data set. Attribute filters compute some attribute describing the shape or size of each connected component and then decide which components to keep or to discard. In this paper, we augment the basic Max-Tree data structure such that interactive volumetric filtering and visualization becomes possible. We introduce extensions that allow (1) direct, splatting-based, volume rendering; (2) representation of the Max-Tree on graphics hardware; and (3) fast active cell selection for isosurface generation. In all three cases, we can use the Max-Tree representation for visualization directly, without needing to reconstruct the volumetric data explicitly. We show that both filtering and visualization can be performed at interactive frame rates, ranging between 2.4 and 32 frames per seconds. In contrast, a standard texture-based volume visualization method manages only between 0.5 and 1.8 frames per second. For isovalue browsing, the experimental results show that the performance is comparable to the performance of an interval tree, where our method has the advantage that both filter threshold browsing and isolevel browsing are fast. It is shown that the methods using graphics hardware can be extended to other connected filters.

Suppression of contour perception by band-limited noise and its relation to nonclassical receptive field inhibition.

Band-spectrum noise has been shown to suppress the visual perception of printed letters. The suppression exhibits a specific dependence on the spatial frequency of the noise, and the frequency domain of most effective inhibition has been related to the size of the letters. In this paper, we address two important questions that were left open by previous studies: (1) Is the observed effect specific to text, and which parameters determine the domain of most effective suppression? (2) What is the origin of the effect in terms of underlying neural processes? We conduct a series of psychophysical experiments that demonstrate that the frequency domain of most effective inhibition depends on the stroke width of the letter rather than on the letter size. These experiments also demonstrate that the effect is not specific to the recognition of letters but also applies to other objects and even to single bars. We attribute the observed effect to nonclassical receptive field (non-CRF) inhibition in visual area V1. This mechanism has previously been suggested as the possible origin of various other perceptual effects. We introduce computational models of two types of cell that incorporate non-CRF inhibition, which are based on Gabor energy filters extended by surround suppression of two kinds: isotropic and anisotropic. The computational models confirm previous qualitative explanations of perceptual effects, such as orientation contrast pop-out, reduced saliency of lines embedded in gratings, and reduced saliency of contours surrounded by textures. We apply the computational models to the images used in the psychophysical experiments. The computational results show a dependence of the inhibition effect on the spatial frequency of the noise that is similar to the suppression effect measured in the psychophysical experiments. The experimental results and their explanation give further support to the idea of a possible functional role of non-CRF inhibition in the separation of contour from texture information and the mediation of object contours to higher cortical areas.

Contour detection based on nonclassical receptive field inhibition.

We propose a biologically motivated method, called nonclassical receptive field (non-CRF) inhibition (more generally, surround inhibition or suppression), to improve contour detection in machine vision. Non-CRF inhibition is exhibited by 80% of the orientation-selective neurons in the primary visual cortex of monkeys and has been shown to influence human visual perception as well. Essentially, the response of an edge detector at a certain point is suppressed by the responses of the operator in the region outside the supported area. We combine classical edge detection with isotropic and anisotropic inhibition, both of which have counterparts in biology. We also use a biologically motivated method (the Gabor energy operator) for edge detection. The resulting operator responds strongly to isolated lines, edges, and contours, but exhibits weak or no response to edges that are part of texture. We use natural images with associated ground truth contour maps to assess the performance of the proposed operator for detecting contours while suppressing texture edges. Our method enhances contour detection in cluttered visual scenes more effectively than classical edge detectors used in machine vision (Canny edge detector). Therefore, the proposed operator is more useful for contour-based object recognition tasks, such as shape comparison, than traditional edge detectors, which do not distinguish between contour and texture edges. Traditional edge detection algorithms can, however, also be extended with surround suppression. This study contributes also to the understanding of inhibitory mechanisms in biology.