Interactive histology of large-scale biomedical image stacks

Histology is the study of the structure of biological tissue using microscopy techniques. As digital imaging technology advances, high resolution microscopy of large tissue volumes is becoming feasible; however, new interactive tools are needed to explore and analyze the enormous datasets. In this paper we present a visualization framework that specifically targets interactive examination of arbitrarily large image stacks. Our framework is built upon two core techniques: display-aware processing and GPU-accelerated texture compression. With display-aware processing, only the currently visible image tiles are fetched and aligned on-the-fly, reducing memory bandwidth and minimizing the need for time-consuming global pre-processing. Our novel texture compression scheme for GPUs is tailored for quick browsing of image stacks. We evaluate the usability of our viewer for two histology applications: digital pathology and visualization of neural structure at nanoscale-resolution in serial electron micrographs.     

GPU-based interactive cut-surface extraction from high-order finite element fields

We present a GPU-based ray-tracing system for the accurate and interactive visualization of cut-surfaces through 3D simulations of physical processes created from spectral/hp high-order finite element methods. When used by the numerical analyst to debug the solver, the ability for the imagery to precisely reflect the data is critical. In practice, the investigator interactively selects from a palette of visualization tools to construct a scene that can answer a query of the data. This is effective as long as the implicit contract of image quality between the individual and the visualization system is upheld. OpenGL rendering of scientific visualizations has worked remarkably well for exploratory visualization for most solver results. This is due to the consistency between the use of first-order representations in the simulation and the linear assumptions inherent in OpenGL (planar fragments and color-space interpolation). Unfortunately, the contract is broken when the solver discretization is of higher-order. There have been attempts to mitigate this through the use of spatial adaptation and/or texture mapping. These methods do a better job of approximating what the imagery should be but are not exact and tend to be view-dependent. This paper introduces new rendering mechanisms that specifically deal with the kinds of native data generated by high-order finite element solvers. The exploratory visualization tools are reassessed and cast in this system with the focus on image accuracy. This is accomplished in a GPU setting to ensure interactivity.     

利用问题求解理论来研究交互式复杂信息的可视分析行为

面对大数据的挑战,力图将人的推理能力和计算系统的数据处理能力相结合的交 互式可视分析研究变得愈发重要。然而目前仍缺乏有效的认知理论来指导面向复杂信息的可视 分析系统的设计,诸如意义构建等现有的理论框架通常着眼于分析行为的外在特征,未能对此 类行为的内在认知机理进行深入研究。因此提出将问题求解作为一种理论框架来解释交互可视 分析行为的基本认知活动,并建议从非良构问题的角度来描述可视分析过程中用户所面临的主 要挑战,还从问题表征及问题求解策略等角度分析了可视分析系统对分析行为的影响。本研究 在理论上,将认知心理学领域的问题求解理论引入到交互可视分析行为的研究中,该方法对设 计面向复杂信息分析的其他类型交互系统也有启示作用;在实践层面上,从问题求解的支持角 度探索了可视分析系统的设计和评估问题。     

GPU-based remote visualization of dynamic molecular data on the web

Visualization of dynamic data from molecular dynamics simulations is crucial for understanding the functioning of molecules. Many existing visualization tools have mainly focused on supporting a single user working on a desktop computer. Technical advancements in browser features increase the potential for the development of web-based collaborative visualization tools. Although web-based molecular viewers already exist, their support for dynamic molecular data at interactive rates is lacking. To address this gap, we present an efficient web application for visualization of dynamic molecular data using WebGL that exploits HTML5 technologies like WebSockets and Web Workers. GPU-based ray casting techniques offer fast rendering times and produce images with higher visual quality. Efficient data encoding techniques are used to minimize the data transferred to the client; therefore saving bandwidth and improving the transfer times. We demonstrate the feasibility of visualizing large dynamic molecular data with more than one million atoms in the browser at interactive frame rates. Our approach allows scientists at arbitrary locations to concurrently visually analyze the same data. The interactive parameterization of the visualization can be shared among multiple clients, providing the basis for collaborative research. Moreover, the application can be employed for remote simulation monitoring on mobile devices.     

Explanatory and illustrative visualization of special and general relativity

This paper describes methods for explanatory and illustrative visualizations used to communicate aspects of Einstein's theories of special and general relativity, their geometric structure, and of the related fields of cosmology and astrophysics. Our illustrations target a general audience of laypersons interested in relativity. We discuss visualization strategies, motivated by physics education and the didactics of mathematics, and describe what kind of visualization methods have proven to be useful for different types of media, such as still images in popular science magazines, film contributions to TV shows, oral presentations, or interactive museum installations. Our primary approach is to adopt an egocentric point of view: the recipients of a visualization participate in a visually enriched thought experiment that allows them to experience or explore a relativistic scenario. In addition, we often combine egocentric visualizations with more abstract illustrations based on an outside view in order to provide several presentations of the same phenomenon. Although our visualization tools often build upon existing methods and implementations, the underlying techniques have been improved by several novel technical contributions like image-based special relativistic rendering on GPUs, special relativistic 4D ray tracing for accelerating scene objects, an extension of general relativistic ray tracing to manifolds described by multiple charts, GPU-based interactive visualization of gravitational light deflection, as well as planetary terrain rendering. The usefulness and effectiveness of our visualizations are demonstrated by reporting on experiences with, and feedback from, recipients of visualizations and collaborators.     

Feature aligned volume manipulation for illustration and visualization

In this paper we describe a GPU-based technique for creating illustrative visualization through interactive manipulation of volumetric models. It is partly inspired by medical illustrations, where it is common to depict cuts and deformation in order to provide a better understanding of anatomical and biological structures or surgical processes, and partly motivated by the need for a real-time solution that supports the specification and visualization of such illustrative manipulation. We propose two new feature-aligned techniques, namely surface alignment and segment alignment, and compare them with the axis-aligned techniques which was reported in previous work on volume manipulation. We also present a mechanism for defining features using texture volumes, and methods for computing correct normals for the deformed volume in respect to different alignments. We describe a GPU-based implementation to achieve real-time performance of the techniques and a collection of manipulation operators including peelers, retractors, pliers and dilators which are adaptations of the metaphors and tools used in surgical procedures and medical illustrations. Our approach is directly applicable in medical and biological illustration, and we demonstrate how it works as an interactive tool for focus+context visualization, as well as a generic technique for volume graphics.     

Isualization and analysis of large data collections: a case study applied to confocal microscopy data

In this paper we propose an approach in which interactive visualization and analysis are combined with batch tools for the processing of large data collections. Large and heterogeneous data collections are difficult to analyze and pose specific problems to interactive visualization. Application of the traditional interactive processing and visualization approaches as well as batch processing encounter considerable drawbacks for such large and heterogeneous data collections due to the amount and type of data. Computing resources are not sufficient for interactive exploration of the data and automated analysis has the disadvantage that the user has only limited control and feedback on the analysis process. In our approach, an analysis procedure with features and attributes of interest for the analysis is defined interactively. This procedure is used for off-line processing of large collections of data sets. The results of the batch process along with "visual summaries" are used for further analysis. Visualization is not only used for the presentation of the result, but also as a tool to monitor the validity and quality of the operations performed during the batch process. Operations such as feature extraction and attribute calculation of the collected data sets are validated by visual inspection. This approach is illustrated by an extensive case study, in which a collection of confocal microscopy data sets is analyzed.     

Illustrative uncertainty visualization of DTI fiber pathways

Diffusion Tensor Imaging (DTI) and fiber tracking provide unique insight into the 3D structure of fibrous tissues in the brain. However, the output of fiber tracking contains a significant amount of uncertainty accumulated in the various steps of the processing pipeline. Existing DTI visualization methods do not present these uncertainties to the end-user. This creates a false impression of precision and accuracy that can have serious consequences in applications that rely heavily on risk assessment and decision-making, such as neurosurgery. On the other hand, adding uncertainty to an already complex visualization can easily lead to information overload and visual clutter. In this work, we propose Illustrative Confidence Intervals to reduce the complexity of the visualization and present only those aspects of uncertainty that are of interest to the user. We look specifically at the uncertainty in fiber shape due to noise and modeling errors. To demonstrate the flexibility of our framework, we compute this uncertainty in two different ways, based on (1) fiber distance and (2) the probability of a fiber connection between two brain regions. We provide the user with interactive tools to define multiple confidence intervals, specify visual styles and explore the uncertainty with a Focus+Context approach. Finally, we have conducted a user evaluation with three neurosurgeons to evaluate the added value of our visualization.     

智能可视化与可视分析

可视化与可视分析已成为众多领域中结合人类智能与机器智能协同理解、分析数据的常见手段。人工智能可以通过对大数据的学习分析提高数据质量,捕捉关键信息,并选取最有效的视觉呈现方式,从而使用户更快、更准确、更全面地从可视化中理解数据。利用人工智能方法,交互式可视化系统也能更好地学习用户习惯及用户意图,推荐符合用户需求的可视化形式、交互操作和数据特征,从而降低用户探索的学习及时间成本,提高交互分析的效率。人工智能方法在可视化中的应用受到了极大关注,产生了大量学术成果。本文从最新工作出发,探讨人工智能在可视化流程的关键步骤中的作用。包括如何智能地表示和管理数据、如何辅助用户快速创建和定制可视化、如何通过人工智能扩展交互手段及提高交互效率、如何借助人工智能辅助数据的交互分析等。具体而言,本文详细梳理每个步骤中需要完成的任务及解决思路,介绍相应的人工智能方法（如深度网络结构）,并以图表数据为例介绍智能可视化与可视分析的应用,最后讨论智能可视化方法的发展趋势,展望未来的研究方向及应用场景。     

Depth-of-Field Rendering by Pyramidal Image Processing

We present an image-based algorithm for interactive rendering depth-of-field effects in images with depth maps. While previously published methods for interactive depth-of-field rendering suffer from various rendering artifacts such as color bleeding and sharpened or darkened silhouettes, our algorithm achieves a significantly improved image quality by employing recently proposed GPU-based pyramid methods for image blurring and pixel disocclusion. Due to the same reason, our algorithm offers an interactive rendering performance on modern GPUs and is suitable for real-time rendering for small circles of confusion. We validate the image quality provided by our algorithm by side-by-side comparisons with results obtained by distributed ray tracing.     

Interactive level-of-detail selection using image-based quality metric for large volume visualization

For large volume visualization, an image-based quality metric is difficult to incorporate for level-of-detail selection and rendering without sacrificing the interactivity. This is because it is usually time-consuming to update view-dependent information as well as to adjust to transfer function changes. In this paper, we introduce an image-based level-of-detail selection algorithm for interactive visualization of large volumetric data. The design of our quality metric is based on an efficient way to evaluate the contribution of multiresolution data blocks to the final image. To ensure real-time update of the quality metric and interactive level-of-detail decisions, we propose a summary table scheme in response to runtime transfer function changes and a GPU-based solution for visibility estimation. Experimental results on large scientific and medical data sets demonstrate the effectiveness and efficiency of our algorithm     

The State of the Art in Visual Analysis Approaches for Ocean and Atmospheric Datasets

The analysis of ocean and atmospheric datasets offers a unique set of challenges to scientists working in different application areas. These challenges include dealing with extremely large volumes of multidimensional data, supporting interactive visual analysis, ensembles exploration and visualization, exploring model sensitivities to inputs, mesoscale ocean features analysis, predictive analytics, heterogeneity and complexity of observational data, representing uncertainty, and many more. Researchers across disciplines collaborate to address such challenges, which led to significant research and development advances in ocean and atmospheric sciences, and also in several relevant areas such as visualization and visual analytics, big data analytics, machine learning and statistics. In this report, we perform an extensive survey of research advances in the visual analysis of ocean and atmospheric datasets. First, we survey the task requirements by conducting interviews with researchers, domain experts, and end users working with these datasets on a spectrum of analytics problems in the domain of ocean and atmospheric sciences. We then discuss existing models and frameworks related to data analysis, sense‐making, and knowledge discovery for visual analytics applications. We categorize the techniques, systems, and tools presented in the literature based on the taxonomies of task requirements, interaction methods, visualization techniques, machine learning and statistical methods, evaluation methods, data types, data dimensions and size, spatial scale and application areas. We then evaluate the task requirements identified based on our interviews with domain experts in the context of categorized research based on our taxonomies, and existing models and frameworks of visual analytics to determine the extent to which they fulfill these task requirements, and identify the gaps in current research. In the last part of this report, we summarize the trends, challenges, and opportunities for future research in this area. (see http://www.acm.org/about/class/class/2012 )     

VISMiner：一个交互式可视化数据挖掘原型系统

交互式可视化数据挖掘是利用可视化技术进行联机数据挖掘的技术。基于SOM的交互式可视化数据挖掘原型系统VISMiner的主要目的是将数据挖掘与数据可视化及OLAP进行集成,允许用户以交互的方式从SOM的标记图或距离图中选定感兴趣区域加以深入分析。     

GraSp: Combining Spatially‐aware Mobile Devices and a Display Wall for Graph Visualization and Interaction

Going beyond established desktop interfaces, researchers have begun re‐thinking visualization approaches to make use of alternative display environments and more natural interaction modalities. In this paper, we investigate how spatially‐aware mobile displays and a large display wall can be coupled to support graph visualization and interaction. For that purpose, we distribute typical visualization views of classic node‐link and matrix representations between displays. The focus of our work lies in novel interaction techniques that enable users to work with personal mobile devices in combination with the wall. We devised and implemented a comprehensive interaction repertoire that supports basic and advanced graph exploration and manipulation tasks, including selection, details‐on‐demand, focus transitions, interactive lenses, and data editing. A qualitative study has been conducted to identify strengths and weaknesses of our techniques. Feedback showed that combining mobile devices and a wall‐sized display is useful for diverse graph‐related tasks. We also gained valuable insights regarding the distribution of visualization views and interactive tools among the combined displays.     

Enabling design and interactive selection of haptic modes

The ever increasing size and complexity of volumetric data in a wide range of disciplines makes it useful to augment volume visualization tools with alternative modalities. Studies have shown that introducing haptics can significantly increase both exploration speed and precision. It is also capable of conveying material properties of data and thus has great potential to improve user performance in volume data exploration. In this paper we describe how recent advances in volume haptics can be used to build haptic modes—building blocks for haptic schemes. These modes have been used as base components of a toolkit allowing for more efficient development of haptic prototypes and applications. This toolkit allows interactive construction, configuration and fine-tuning of both visual and haptic representations of the data. The technology is also used in a pilot study to determine the most important issues and aspects in haptic volume data interaction and exploration, and how the use of haptic modes can facilitate the implementation of effective haptic schemes.     

Elements of early vision for computer graphics

Visually based techniques in computer graphics have blossomed. Important advances in perceptually driven rendering, realistic image display, high-fidelity visualization, and appearance-preserving geometric simplification have all been realized by applying knowledge of the limitations and capabilities of human visual processing. Much of this work is grounded in the physiology and psychophysics of early vision, which focuses on how visual mechanisms transduce and code the patterns of light arriving at the eye. The article surveys some of the fundamental findings in the study of early vision including basic visual anatomy and physiology, optical properties of the eye, light sensitivity and visual adaptation, and spatial vision     

An Overview of 3D Software Visualization

Software visualization studies techniques and methods for graphically representing different aspects of software. Its main goal is to enhance, simplify and clarify the mental representation a software engineer has of a computer system. During many years, visualization in 2D space has been actively studied, but in the last decade, researchers have begun to explore new 3D representations for visualizing software. In this article, we present an overview of current research in the area, describing several major aspects like: visual representations, interaction issues, evaluation methods and development tools. We also perform a survey of some representative tools to support different tasks, i.e., software maintenance and comprehension, requirements validation and algorithm animation for educational purposes, among others. Finally, we conclude identifying future research directions.     

Pattern discovery: A progressive visual analytic design to support categorical data analysis

When using data-mining tools to analyze big data, users often need tools to support the understanding of individual data attributes and control the analysis progress. This requires the integration of data-mining algorithms with interactive tools to manipulate data and analytical process. This is where visual analytics can help. More than simple visualization of a dataset or some computation results, visual analytics provides users an environment to iteratively explore different inputs or parameters and see the corresponding results. In this research, we explore a design of progressive visual analytics to support the analysis of categorical data with a data-mining algorithm, Apriori. Our study focuses on executing data mining techniques step-by-step and showing intermediate result at every stage to facilitate sense-making. Our design, called Pattern Discovery Tool, targets for a medical dataset. Starting with visualization of data properties and immediate feedback of users’ inputs or adjustments, Pattern Discovery Tool could help users detect interesting patterns and factors effectively and efficiently. Afterward, further analyses such as statistical methods could be conducted to test those possible theories.     

Interactive Lenses for Visualization: An Extended Survey

The elegance of using virtual interactive lenses to provide alternative visual representations for selected regions of interest is highly valued, especially in the realm of visualization. Today, more than 50 lens techniques are known in the closer context of visualization, far more in related fields. In this paper, we extend our previous survey on interactive lenses for visualization. We propose a definition and a conceptual model of lenses as extensions of the classic visualization pipeline. An extensive review of the literature covers lens techniques for different types of data and different user tasks and also includes the technologies employed to display lenses and to interact with them. We introduce a taxonomy of lenses for visualization and illustrate its utility by dissecting in detail a multi‐touch lens for exploring large graph layouts. As a conclusion of our review, we identify challenges and unsolved problems to be addressed in future research.     

SEE: a Spatial Exploration Environment based on adirect-manipulation paradigm

The need to provide effective tools for analyzing and querying spatial data is becoming increasingly important with the explosion of data in applications such as geographic information systems, image databases, CAD, and remote sensing. The SEE (Spatial Exploration Environment) is the first effort at applying direct-manipulation visual information seeking (VIS) techniques to spatial data analysis by visually querying as well as browsing spatial data and reviewing the visual results for trend analysis. The SEE system incorporates a visual query language (SVIQUEL) that allows users to specify the relative spatial position (both topology and direction) between objects using direct manipulation. The quantitative SVIQVEL sliders (S-sliders) are complemented by the qualitative active-picture-for-querying (APIQ) interface that allows the user to specify qualitative relative position queries. APIQ provides qualitative visual representations of the quantitative query specified by the S-sliders. This increases the utility of the system for spatial browsing and spatial trend discovery with no particular query in mind. The SVIQUEL queries are processed using a k-Bucket index structure specifically tuned for incremental processing of the multidimensional range queries that represent the class of queries that can be expressed by SVIQUEL. We have also designed a tightly integrated map visualization that helps to preserve the spatial context and a bar visualization that provides a qualitative abstraction of aggregates