We present ScaleTrotter, a conceptual framework for an interactive, multi-scale visualization of biological mesoscale data and, specifically, genome data. ScaleTrotter allows viewers to smoothly transition from the nucleus of a cell to the atomistic composition of the DNA, while bridging several orders of magnitude in scale. The challenges in creating an interactive visualization of genome data are fundamentally different in several ways from those in other domains like astronomy that require a multi-scale representation as well. First, genome data has intertwined scale levels---the DNA is an extremely long, connected molecule that manifests itself at all scale levels. Second, elements of the DNA do not disappear as one zooms out---instead the scale levels at which they are observed group these elements differently. Third, we have detailed information and thus geometry for the entire dataset and for all scale levels, posing a challenge for interactive visual exploration. Finally, the conceptual scale levels for genome data are close in scale space, requiring us to find ways to visually embed a smaller scale into a coarser one. We address these challenges by creating a new multi-scale visualization concept. We use a scale-dependent camera model that controls the visual embedding of the scales into their respective parents, the rendering of a subset of the scale hierarchy, and the location, size, and scope of the view. In traversing the scales, ScaleTrotter is roaming between 2D and 3D visual representations that are depicted in integrated visuals. We discuss, specifically, how this form of multi-scale visualization follows from the specific characteristics of the genome data and describe its implementation. Finally, we discuss the implications of our work to the general illustrative depiction of multi-scale data.
Also important from Viola and Isenberg's discussion @cite_39 is their concept of , which are traversed in scale space. We also connect the DNA representations at different scales, facilitating a smooth transition between them. In creating this axis of abstraction, we focus primarily on changes of Viola and Isenberg's geometric axis, but without a geometric interpolation of different representations. Instead, we use visual embedding of one scale in another one.
@cite_39
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Abstract Medial axis as a compact representation of shapes has evolved as an essential geometric structure in a number of applications involving 3D geometric shapes. Since exact computation of the medial axis is difficult in general, efforts continue to approximate them. One line of research considers the point cloud representation of the boundary surface of a solid and then attempts to compute an approximate medial axis from this point sample. It is known that the Voronoi vertices converge to the medial axis for a curve in 2D as the sample density approaches infinity. Unfortunately, the same is not true in 3D. Recently, it is discovered that a subset of Voronoi vertices called poles converge to the medial axis in 3D. However, in practice, a continuous approximation as opposed to a discrete one is sought. Recently few algorithms have been proposed which use the Voronoi diagram and its derivatives to compute this continuous approximation. These algorithms are scale or density dependent. Most of them do not have convergence guarantees, and one of them computes it indirectly from the power diagram of the poles. Recently, we proposed a new algorithm that approximates the medial axis straight from the Voronoi diagram in a scale and density independent manner with convergence guarantees. In this paper, we present several experimental results with this algorithm that support our theoretical claims and also show its effectiveness on practical data sets. Abstract We provide a high-level survey of multiscale molecular visualization techniques, with a focus on application-domain questions, challenges, and tasks. We provide a general introduction to molecular visualization basics and describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the general structure of the following survey. First, we discuss methods that support the visual analysis of molecular dynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation. In the second part, we survey multiscale approaches that support the design, analysis, and manipulation of DNA nanostructures and related concepts for abstraction, scale transition, scale-dependent modeling, and navigation of the resulting abstraction spaces. In the third part of the survey, we showcase approaches that support interactive exploration within large structural biology assemblies up to the size of bacterial cells. We describe fundamental rendering techniques as well as approaches for element instantiation, visibility management, visual guidance, camera control, and support of depth perception. We close the survey with a brief listing of important tools that implement many of the discussed approaches and a conclusion that provides some research challenges in the field. We introduce the scale axis transform, a new skelet al shape representation for bounded open sets O ⊂ Rd. The scale axis transform induces a family of skeletons that captures the important features of a shape in a scale-adaptive way and yields a hierarchy of successively simplified skeletons. Its definition is based on the medial axis transform and the simplification of the shape under multiplicative scaling: the s-scaled shape Os is the union of the medial balls of O with radii scaled by a factor of s. The s-scale axis transform of O is the medial axis transform of Os, with radii scaled back by a factor of 1 s. We prove topological properties of the scale axis transform and we describe the evolution s → Os by defining the multiplicative distance function to the shape and studying properties of the corresponding steepest ascent flow. All our theoretical results hold for any dimension. In addition, using a discrete approximation, we present several examples of two-dimensional scale axis transforms that illustrate the practical relevance of our new framework. Three-dimensional geometric data play fundamental roles in many computer vision applications. However, their scale-dependent nature, i.e. the relative variation in the spatial extents of local geometric structures, is often overlooked. In this paper we present a comprehensive framework for exploiting this 3D geometric scale variability. Specifically, we focus on detecting scale-dependent geometric features on triangular mesh models of arbitrary topology. The key idea of our approach is to analyze the geometric scale variability of a given 3D model in the scale-space of a dense and regular 2D representation of its surface geometry encoded by the surface normals. We derive novel corner and edge detectors, as well as an automatic scale selection method, that acts upon this representation to detect salient geometric features and determine their intrinsic scales. We evaluate the effectiveness and robustness of our method on a number of models of different topology. The results show that the resulting scale-dependent geometric feature set provides a reliable basis for constructing a rich but concise representation of the geometric structure at hand. In this paper, we introduce the concept of spatial transfer functions as a unified approach to volume modeling and animation. A spatial transfer function is a function that defines the geometrical transformation of a scalar field in space, and is a generalization and abstraction of a variety of deformation methods. It facilitates a field based representation, and can thus be embedded into a volumetric scene graph under the algebraic framework of constructive volume geometry. We show that when spatial transfer functions are treated as spatial objects, constructive operations and conventional transfer functions can be applied to such spatial objects. We demonstrate spatial transfer functions in action with the aid of a collection of examples in volume visualization, sweeping, deformation and animation. In association with these examples, we describe methods for modeling and realizing spatial transfer functions, including simple procedural functions, operational decomposition of complex functions, large scale domain decomposition and temporal spatial transfer functions. We also discuss the implementation of spatial transfer functions in the vlib API and our efforts in deploying the technique in volume animation. The medial axis of a geometric shape captures its connectivity. In spite of its inherent instability, it has found applications in a number of areas that deal with shapes. In this survey paper, we focus on results that shed light on this instability and use the new insights to generate simplified and stable modifications of the medial axis. Various algorithms have been proposed to create planar abstractions of 3D models, but there has been no systematic effort to evaluate the effectiveness of such abstractions in terms of perception of the abstracted surfaces. In this work, we perform a large crowd-sourced study involving approximately 70k samples to evaluate how well users can orient gauges on planar abstractions of commonly occurring models. We test four styles of planar abstractions against ground truth surface representations, and analyze the data to discover a wide variety of correlations between task error and measurements relating to surface-specific properties such as curvature, local thickness and medial axis distance, and abstraction-specific properties. We use these discovered correlations to create linear models to predict error in surface understanding at a given point, for both surface representations and planar abstractions. Our predictive models reveal the geometric causes most responsible for error, and we demonstrate their potential use to build upon existing planar abstraction techniques in order to improve perception of the abstracted surface. We describe the theoretical frame for a method of creating and describing rounded objects of arbitrary topology in CAD, and its implementation for UNIGRAFIX, a polygon-based modeler developed at UC Berkeley that generates black-and-white, smooth-shaded images on several output devices. The mathematical foundation for building triangular patches interpolating cubic edges and blending with geometric continuity is given, and various approaches are discussed. To represent curvature information, we extended the UNIGRAFIX language to UniCubix, and we implemented uci, an interactive shell that interprets a UniCubix description and converts it into UNIGRAFIX wireframes or polyhedral nets that approximate curved patches. Uci also provides a prototype of a global smoothing operation, that takes a polyhedral object of arbitrary topology and creates the UniCubix representation of a smooth object interpolating the input vertices. This letter introduces a robust representation of 3-D shapes, named DeepPano, learned with deep convolutional neural networks (CNN). Firstly, each 3-D shape is converted into a panoramic view, namely a cylinder projection around its principle axis. Then, a variant of CNN is specifically designed for learning the deep representations directly from such views. Different from typical CNN, a row-wise max-pooling layer is inserted between the convolution and fully-connected layers, making the learned representations invariant to the rotation around a principle axis. Our approach achieves state-of-the-art retrieval classification results on two large-scale 3-D model datasets (ModelNet-10 and ModelNet-40), outperforming typical methods by a large margin. In visual analytics, sensemaking is facilitated through interactive visual exploration of data. Throughout this dynamic process, users combine their domain knowledge with the dataset to create insight. Therefore, visual analytic tools exist that aid sensemaking by providing various interaction techniques that focus on allowing users to change the visual representation through adjusting parameters of the underlying statistical model. However, we postulate that the process of sensemaking is not focused on a series of parameter adjustments, but instead, a series of perceived connections and patterns within the data. Thus, how can models for visual analytic tools be designed, so that users can express their reasoning on observations (the data), instead of directly on the model or tunable parameters? Observation level (and thus “observation”) in this paper refers to the data points within a visualization. In this paper, we explore two possible observation-level interactions, namely exploratory and expressive, within the context of three statistical methods, Probabilistic Principal Component Analysis (PPCA), Multidimensional Scaling (MDS), and Generative Topographic Mapping (GTM). We discuss the importance of these two types of observation level interactions, in terms of how they occur within the sensemaking process. Further, we present use cases for GTM, MDS, and PPCA, illustrating how observation level interaction can be incorporated into visual analytic tools. A good image object detection algorithm is accurate, fast, and does not require exact locations of objects in a training set. We can create such an object detector by taking the architecture of the Viola-Jones detector cascade and training it with a new variant of boosting that we call MIL-Boost. MILBoost uses cost functions from the Multiple Instance Learning literature combined with the AnyBoost framework. We adapt the feature selection criterion of MILBoost to optimize the performance of the Viola-Jones cascade. Experiments show that the detection rate is up to 1.6 times better using MILBoost. This increased detection rate shows the advantage of simultaneously learning the locations and scales of the objects in the training set along with the parameters of the classifier. This paper improves recent methods for large scale image search. State-of-the-art methods build on the bag-of-features image representation. We, first, analyze bag-of-features in the framework of approximate nearest neighbor search. This shows the sub-optimality of such a representation for matching descriptors and leads us to derive a more precise representation based on 1) Hamming embedding (HE) and 2) weak geometric consistency constraints (WGC). HE provides binary signatures that refine the matching based on visual words. WGC filters matching descriptors that are not consistent in terms of angle and scale. HE and WGC are integrated within the inverted file and are efficiently exploited for all images, even in the case of very large datasets. Experiments performed on a dataset of one million of images show a significant improvement due to the binary signature and the weak geometric consistency constraints, as well as their efficiency. Estimation of the full geometric transformation, i.e., a re-ranking step on a short list of images, is complementary to our weak geometric consistency constraints and allows to further improve the accuracy. This technical report presents and extends a recent paper we have proposed for large scale image search. State-of-the-art methods build on the bag-of- features image representation. We first analyze bag-of-features in the framework of approximate nearest neighbor search. This shows the sub-optimality of such a representation for matching descriptors and leads us to derive a more precise representation based on 1) Hamming embedding (HE) and 2) weak geometric consistency constraints (WGC). HE provides binary signatures that refine the matching based on visual words. WGC filters matching descriptors that are not consistent in terms of angle and scale. HE and WGC are integrated within an inverted file and are efficiently exploited for all images, even in the case of very large datasets. Experiments performed on a dataset of one million of images show a significant improvement due to the binary signature and the weak geometric consistency constraints, as well as their efficiency. Estimation of the full geometric transformation, i.e., a re-ranking step on a short list of images, is complementary to our weak geometric consistency constraints and allows to further improve the accuracy. Abstract In which order can a product be assembled or disassembled? How many hands are required? How many degrees of freedom? What parts should be withdrawn to allow the removal of a specified subassembly? To answer such questions automatically, important theoretical issues in geometric reasoning must be addressed. This paper investigates the planning of assembly algorithms specifying (dis) assembly operations on the components of a product and the ordering of these operations. It also presents measures to evaluate the complexity of these algorithms and techniques to estimate the inherent complexity of a product. The central concept underlying these planning and complexity evaluation techniques is that of a “non-directional blocking graph”, a qualitative representation of the internal structure of an assembly product. This representation describes the combinatorial set of parts interactions in polynomial space. It is obtained by identifying physical criticalities where geometric interferences among parts change. It is generated from an input geometric description of the product. The main application considered in the paper is the creation of smart environments to help designers create products that are easier to manufacture and service. Other possible applications include planning for rapid prototyping and autonomous robots. We present a simple, efficient, and stable method for computing-with any desired precision-the medial axis of simply connected planar domains. The domain boundaries are assumed to be given as polynomial spline curves. Our approach combines known results from the field of geometric approximation theory with a new algorithm from the field of computational geometry. Challenging steps are (1) the approximation of the boundary spline such that the medial axis is geometrically stable, and (2) the efficient decomposition of the domain into base cases where the medial axis can be computed directly and exactly. We solve these problems via spiral biarc approximation and a randomized divide & conquer algorithm. In the first part of this paper, we reduce two geometric optimization problems to convex programming: finding the largest axis-aligned box in the intersection of a family of convex sets, and finding the translation and scaling that minimizes the Hausdorff distance between two polytopes. These reductions imply that important cases of these problems can be solved in expected linear time. In the second part of the paper, we use convex programming to give a new, short proof of an interesting Helly-type theorem, first conjectured by Gru¨nbaum and Motzkin. In this paper, we analyze and analytically describe the specific statistical changes brought into the covariance structure of signal by the interpolation process. We show that interpolated signals and their derivatives contain specific detectable periodic properties. Based on this, we propose a blind, efficient, and automatic method capable of finding traces of resampling and interpolation. The proposed method can be very useful in many areas, especially in image security and authentication. For instance, when two or more images are spliced together, to create high quality and consistent image forgeries, almost always geometric transformations, such as scaling, rotation, or skewing are needed. These procedures are typically based on a resampling and interpolation step. By having a method capable of detecting the traces of resampling, we can significantly reduce the successful usage of such forgeries. Among other points, the presented method is also very useful in estimation of the geometric transformations factors. Semantic image segmentation is a basic street scene understanding task in autonomous driving, where each pixel in a high resolution image is categorized into a set of semantic labels. Unlike other scenarios, objects in autonomous driving scene exhibit very large scale changes, which poses great challenges for high-level feature representation in a sense that multi-scale information must be correctly encoded. To remedy this problem, atrous convolution[14]was introduced to generate features with larger receptive fields without sacrificing spatial resolution. Built upon atrous convolution, Atrous Spatial Pyramid Pooling (ASPP)[2] was proposed to concatenate multiple atrous-convolved features using different dilation rates into a final feature representation. Although ASPP is able to generate multi-scale features, we argue the feature resolution in the scale-axis is not dense enough for the autonomous driving scenario. To this end, we propose Densely connected Atrous Spatial Pyramid Pooling (DenseASPP), which connects a set of atrous convolutional layers in a dense way, such that it generates multi-scale features that not only cover a larger scale range, but also cover that scale range densely, without significantly increasing the model size. We evaluate DenseASPP on the street scene benchmark Cityscapes[4] and achieve state-of-the-art performance. This paper presents a large scale general purpose image database with human annotated ground truth. Firstly, an all-in-all labeling framework is proposed to group visual knowledge of three levels: scene level (global geometric description), object level (segmentation, sketch representation, hierarchical decomposition), and low-mid level (2.1D layered representation, object boundary attributes, curve completion, etc.). Much of this data has not appeared in previous databases. In addition, And-Or Graph is used to organize visual elements to facilitate top-down labeling. An annotation tool is developed to realize and integrate all tasks. With this tool, we've been able to create a database consisting of more than 636,748 annotated images and video frames. Lastly, the data is organized into 13 common subsets to serve as benchmarks for diverse evaluation endeavors. This paper proposes a novel content-based image watermarking method based on invariant regions of an image. The invariant regions are self-adaptive image patches that deform with geometric transformations. Three different invariant-region detection methods based on the scale-space representation of an image were considered for watermarking. At each invariant region, the watermark is embedded after geometric normalization according to the shape of the region. By binding watermarking with invariant regions, resilience against geometric transformations can be readily obtained. Experimental results show that the proposed method is robust against various image processing steps, including geometric transformations, cropping, filtering, and JPEG compression.