Visually comparing brain networks, or connectomes, is an essential task in the field of neuroscience. Especially relevant to the field of clinical neuroscience, group studies that examine differences between populations or changes over time within a population enable neuroscientists to reason about effective diagnoses and treatments for a range of neuropsychiatric disorders. In this paper, we specifically explore how visual analytics tools can be used to facilitate various clinical neuroscience tasks, in which observation and analysis of meaningful patterns in the connectome can support patient diagnosis and treatment. We conduct a survey of visualization tasks that enable clinical neuroscience activities, and further explore how existing connectome visualization tools support or fail to support these tasks. Based on our investigation of these tasks, we introduce a novel visualization tool, NeuroCave, to support group studies analyses. We discuss how our design decisions (the use of immersive visualization, the use of hierarchical clustering and dimensionality reduction techniques, and the choice of visual encodings) are motivated by these tasks. We evaluate NeuroCave through two use cases that illustrate the utility of interactive connectome visualization in clinical neuroscience contexts. In the first use case, we study sex differences using functional connectomes and discover hidden connectome patterns associated with well-known cognitive differences in spatial and verbal abilities. In the second use case, we show how the utility of visualizing the brain in different topological space coupled with clustering information can reveal the brain's intrinsic structure.
Extending the user task definitions presented in @cite_44 through a thorough investigation of connectome visualization projects and surveying neuroscientists that work with group studies, we have identified visual analytics tasks for clinical neuroscientists:
@cite_44
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We introduce NeuroCave, a novel immersive visualization system that facilitates the visual inspection of structural and functional connectome datasets. The representation of the human connectome as a graph enables neuroscientists to apply network-theoretic approaches in order to explore its complex characteristics. With NeuroCave, brain researchers can interact with the connectome— either in a standard desktop environment or while wearing portable VR headsets (such as Oculus Rift, Samsung Gear, or Google Daydream VR platforms)— in any coordinate system or topological space, as well as cluster brain regions into different modules on demand. Furthermore, a default side-by-side layout enables simultaneous, synchronized manipulation in 3D, utilizing modern GPU hardware architecture, and facilitates comparison tasks across different subjects or diagnostic groups or longitudinally within the same subject. Visual clutter is mitigated using a state-of-the-art edge bundling technique and through an interactive lay... Multivariate graphs are prolific across many fields, including transportation and neuroscience. A key task in graph analysis is the exploration of connectivity, to, for example, analyze how signals flow through neurons, or to explore how well different cities are connected by flights. While standard node-link diagrams are helpful in judging connectivity, they do not scale to large networks. Adjacency matrices also do not scale to large networks and are only suitable to judge connectivity of adjacent nodes. A key approach to realize scalable graph visualization are queries: instead of displaying the whole network, only a relevant subset is shown. Query-based techniques for analyzing connectivity in graphs, however, can also easily suffer from cluttering if the query result is big enough. To remedy this, we introduce techniques that provide an overview of the connectivity and reveal details on demand. We have two main contributions: 1 two novel visualization techniques that work in concert for summarizing graph connectivity; and 2 Graffinity, an open-source implementation of these visualizations supplemented by detail views to enable a complete analysis workflow. Graffinity was designed in a close collaboration with neuroscientists and is optimized for connectomics data analysis, yet the technique is applicable across domains. We validate the connectivity overview and our open-source tool with illustrative examples using flight and connectomics data. Diffusion tensor imaging (DTI) is a magnetic resonance imaging method that can be used to measure local information about the structure of white matter within the human brain. Combining DTI data with the computational methods of MR tractography, neuroscientists can estimate the locations and sizes of nerve bundles (white matter pathways) that course through the human brain. Neuroscientists have used visualization techniques to better understand tractography data, but they often struggle with the abundance and complexity of the pathways. In this paper, we describe a novel set of interaction techniques that make it easier to explore and interpret such pathways. Specifically, our application allows neuroscientists to place and interactively manipulate box or ellipsoid-shaped regions to selectively display pathways that pass through specific anatomical areas. These regions can be used in coordination with a simple and flexible query language which allows for arbitrary combinations of these queries using Boolean logic operators. A representation of the cortical surface is provided for specifying queries of pathways that may be relevant to gray matter structures and for displaying activation information obtained from functional magnetic resonance imaging. By precomputing the pathways and their statistical properties, we obtain the speed necessary for interactive question-and-answer sessions with brain researchers. We survey some questions that researchers have been asking about tractography data and show how our system can be used to answer these questions efficiently. The analysis of brain connectivity is a vast field in neuroscience with a frequent use of visual representations and an increasing need for visual analysis tools. Based on an in-depth literature review and interviews with neuroscientists, we explore high-level brain connectivity analysis tasks that need to be supported by dedicated visual analysis tools. A significant example of such a task is the comparison of different connectivity data in the form of weighted graphs. Several approaches have been suggested for graph comparison within information visualization, but the comparison of weighted graphs has not been addressed. We explored the design space of applicable visual representations and present augmented adjacency matrix and node-link visualizations. To assess which representation best support weighted graph comparison tasks, we performed a controlled experiment. Our findings suggest that matrices support these tasks well, outperforming node-link diagrams. These results have significant implications for the design of brain connectivity analysis tools that require weighted graph comparisons. They can also inform the design of visual analysis tools in other domains, e.g. comparison of weighted social networks or biological pathways. In the field of connectomics, neuroscientists seek to identify cortical connectivity comprehensively. Neuronal boundary detection from the Electron Microscopy (EM) images is often done to assist the automatic reconstruction of neuronal circuit. But the segmentation of EM images is a challenging problem, as it requires the detector to be able to detect both filament-like thin and blob-like thick membrane, while suppressing the ambiguous intracellular structure. In this paper, we propose multi-stage multi-recursive-input fully convolutional networks to address this problem. The multiple recursive inputs for one stage, i.e., the multiple side outputs with different receptive field sizes learned from the lower stage, provide multi-scale contextual boundary information for the consecutive learning. This design is biologically-plausible, as it likes a human visual system to compare different possible segmentation solutions to address the ambiguous boundary issue. Our multi-stage networks are trained end-to-end. It achieves promising results on two public available EM segmentation datasets, the mouse piriform cortex dataset and the ISBI 2012 EM dataset. This classic work on cyclopean perception has influenced a generation of vision researchers, cognitive scientists, and neuroscientists and has inspired artists, designers, and computer graphics pioneers. In Foundations of Cyclopean Perception (first published in 1971 and unavailable for years), Bela Julesz traced the visual information flow in the brain, analyzing how the brain combines separate images received from the two eyes to produce depth perception. Julesz developed novel tools to do this: random-dot stereograms and cinematograms, generated by early digital computers at Bell Labs. These images, when viewed with the special glasses that came with the book, revealed complex, three-dimensional surfaces; this mode of visual stimulus became a paradigm for research in vision and perception. This reprint edition includes all 48 color random-dot designs from the original, as well as the special 3-D glasses required to view them.Foundations of Cyclopean Perception has had a profound impact on the vision studies community. It was chosen as one of the one hundred most influential works in cognitive science in a poll conducted by the University of Minnesota's Center for Cognitive Sciences. Many copies are "permanently borrowed" from college libraries; used copies are sought after online. Now, with this facsimile of the 1971 edition, the book is available again to cognitive scientists, neuroscientists, vision researchers, artists, and designers. Tracing neurons in large-scale microscopy data is crucial to establishing a wiring diagram of the brain, which is needed to understand how neural circuits in the brain process information and generate behavior. Automatic techniques often fail for large and complex datasets, and connectomics researchers may spend weeks or months manually tracing neurons using 2D image stacks. We present a design study of a new virtual reality (VR) system, developed in collaboration with trained neuroanatomists, to trace neurons in microscope scans of the visual cortex of primates. We hypothesize that using consumer-grade VR technology to interact with neurons directly in 3D will help neuroscientists better resolve complex cases and enable them to trace neurons faster and with less physical and mental strain. We discuss both the design process and technical challenges in developing an interactive system to navigate and manipulate terabyte-sized image volumes in VR. Using a number of different datasets, we demonstrate that, compared to widely used commercial software, consumer-grade VR presents a promising alternative for scientists. Cortical network architecture has predominantly been investigated visually using graph theory representations. In the context of human connectomics, such representations are not however always satisfactory because canonical methods for vertex–edge relationship representation do not always offer optimal insight regarding functional and structural neural connectivity. This article introduces an innovative framework for the depiction of human connectomics by employing a circular visualization method which is highly suitable to the exploration of central nervous system architecture. This type of representation, which we name a ‘connectogram’, has the capability of classifying neuroconnectivity relationships intuitively and elegantly. A multimodal protocol for MRI DTI neuroimaging data acquisition is here combined with automatic image segmentation to (1) extract cortical and non-cortical anatomical structures, (2) calculate associated volumetrics and morphometrics, and (3) determine patient-specific connectivity profiles to generate subject-level and population-level connectograms. The scalability of our approach is demonstrated for a population of 50 adults. Two essential advantages of the connectogram are (1) the enormous potential for mapping and analyzing the human connectome, and (2) the unconstrained ability to expand and extend this analysis framework to the investigation of clinical populations and animal models. The human brain is a complex system whose topological organization can be represented using connectomics. Recent studies have shown that human connectomes can be constructed using various neuroimaging technologies and further characterized using sophisticated analytic strategies, such as graph theory. These methods reveal the intriguing topological architectures of human brain networks in healthy populations and explore the changes throughout normal development and aging and under various pathological conditions. However, given the huge complexity of this methodology, toolboxes for graph-based network visualization are still lacking. Here, using MATLAB with a graphical user interface (GUI), we developed a graph-theoretical network visualization toolbox, called BrainNet Viewer, to illustrate human connectomes as ball-and-stick models. Within this toolbox, several combinations of defined files with connectome information can be loaded to display different combinations of brain surface, nodes and edges. In addition, display properties, such as the color and size of network elements or the layout of the figure, can be adjusted within a comprehensive but easy-to-use settings panel. Moreover, BrainNet Viewer draws the brain surface, nodes and edges in sequence and displays brain networks in multiple views, as required by the user. The figure can be manipulated with certain interaction functions to display more detailed information. Furthermore, the figures can be exported as commonly used image file formats or demonstration video for further use. BrainNet Viewer helps researchers to visualize brain networks in an easy, flexible and quick manner, and this software is freely available on the NITRC website (www.nitrc.org projects bnv ). Thanks to advances in non-invasive technologies such as functional Magnetic Resonance Imaging (fMRI) and Diffusion Tensor Imaging (DTI), highly-detailed maps of brain structure and function can now be collected. In this context, brain connectomics have emerged as a fast growing field that aims at understanding these comprehensive maps of brain connectivity using sophisticated computational models. In this paper we present BRAINtrinsic, an innovative web-based 3D visual analytics tool that allows users to intuitively and iteratively interact with connectome data. Moreover, BRAINtrinsic implements a novel visualization platform that reconstructs connectomes’ intrinsic geometry, i.e., the topological space as informed by brain connectivity, via dimensionality reduction. BRAINtrinsic is implemented with virtual reality in mind and is fully compatible with the Oculus Rift technology. Last, we demonstrate its effectiveness through a series of case studies involving both structural and resting-state MR imaging data. To complement the currently existing definitions and conceptual frameworks of visual analytics, which focus mainly on activities performed by analysts and types of techniques they use, we attempt to define the expected results of these activities. We argue that the main goal of doing visual analytics is to build a mental and or formal model of a certain piece of reality reflected in data. The purpose of the model may be to understand, to forecast or to control this piece of reality. Based on this model-building perspective, we propose a detailed conceptual framework in which the visual analytics process is considered as a goal-oriented workflow producing a model as a result. We demonstrate how this framework can be used for performing an analytical survey of the visual analytics research field and identifying the directions and areas where further research is needed. Cohort comparison studies have traditionally been hypothesis driven and conducted in carefully controlled environments (such as clinical trials). Given two groups of event sequence data, researchers test a single hypothesis (e.g., does the group taking Medication A exhibit more deaths than the group taking Medication B?). Recently, however, researchers have been moving toward more exploratory methods of retrospective analysis with existing data. In this article, we begin by showing that the task of cohort comparison is specific enough to support automatic computation against a bounded set of potential questions and objectives, a method that we refer to as High-Volume Hypothesis Testing (HVHT). From this starting point, we demonstrate that the diversity of these objectives, both across and within different domains, as well as the inherent complexities of real-world datasets, still requires human involvement to determine meaningful insights. We explore how visualization and interaction better support the task of exploratory data analysis and the understanding of HVHT results (how significant they are, why they are meaningful, and whether the entire dataset has been exhaustively explored). Through interviews and case studies with domain experts, we iteratively design and implement visualization and interaction techniques in a visual analytics tool, CoCo. As a result of our evaluation, we propose six design guidelines for enabling users to explore large result sets of HVHT systematically and flexibly in order to glean meaningful insights more quickly. Finally, we illustrate the utility of this method with three case studies in the medical domain. Traditionally, studies of data visualization techniques and systems have evaluated visualizations with respect to usability goals such as effectiveness and efficiency. These studies assess performance-related metrics such as time and correctness of participants completing analytic tasks. Alternatively, several studies in InfoVis recently have evaluated visualizations by investigating user experience goals such as memorability, engagement, enjoyment and fun. These studies employ somewhat different evaluation methodologies to assess these other goals. The growing number of these studies, their alternative methodologies, and disagreements concerning their importance have motivated us to more carefully examine them. In this article, we review this growing collection of visualization evaluations that examine user experience goals and we discuss multiple issues regarding the studies including questions about their motivation and utility. Our aim is to provide a resource for future work that plans to evaluate visualizations using these goals. Analysis of movement is currently a hot research topic in visual analytics. A wide variety of methods and tools for analysis of movement data has been developed in recent years. They allow analysts to look at the data from different perspectives and fulfil diverse analytical tasks. Visual displays and interactive techniques are often combined with computational processing, which, in particular, enables analysis of a larger number of data than would be possible with purely visual methods. Visual analytics leverages methods and tools developed in other areas related to data analytics. particularly statistics, machine learning and geographic information science. We present an illustrated structured survey of the state of the art in visual analytics concerning the analysis of movement data. Besides reviewing the existing works, we demonstrate, using examples. how different visual analytics techniques can support our understanding of various aspects of movement. Abstract In recent years, big brain-initiatives and consortia have created vast resources of publicly available brain data that can be used by neuroscientists for their own research experiments. This includes microscale connectivity data—brain-network graphs with billions of edges—and vast spatial gene expression resources—the representation of tens of thousands genes in brain space. Their joint analysis for higher order relations in structural or functional neuroanatomy would enable the genetic dissection of brain networks on a genome-wide scale. Current experimental workflows involve only time-consuming manual aggregation and extensive graph theoretical analysis of data from different sources, which rarely provide spatial context to operate continuously on different scales. In this paper, we propose BrainTrawler, a task-driven, web-based framework that incorporates visual analytics methods to explore heterogeneous neurobiological data. It facilitates spatial indexing to query large-scale voxel-level connectivity data and gene expression collections in real-time. Relating data to the hierarchical structure of common anatomical atlases enables the retrieval on different anatomical levels. Together with intuitive network visualization, iterative visual queries, and quantitative information this allows the genetic dissection of multimodal networks on local global scales in a spatial context. We demonstrate the relevance of our approach for neuroscience by exploring social-behavior and memory learning related functional neuroanatomy in mice. Time is an exceptional dimension that is common to many application domains such as medicine, engineering, business, or science. Due to the distinct characteristics of time, appropriate visual and analytical methods are required to explore and analyze them. This book starts with an introduction to visualization and historical examples of visual representations. At its core, the book presents and discusses a systematic view of the visualization of time-oriented data along three key questions: what is being visualized (data), why something is visualized (user tasks), and how it is presented (visual representation). To support visual exploration, interaction techniques and analytical methods are required that are discussed in separate chapters. A large part of this book is devoted to a structured survey of 101 different visualization techniques as a reference for scientists conducting related research as well as for practitioners seeking information on how their time-oriented data can best be visualized. Confident usage of information visualizations is thought to be influenced by cognitive aspects as well as amount of exposure and training. To support the development of individual competency in visualization processing, it is important to ascertain if we can track users' progress or difficulties they might have while working with a given visualization. In this paper, we extend previous work on predicting in real time a user's learning curve--a mathematical model that can represent a user's skill acquisition ability--when working with a visualization. First, we investigate whether results we previously obtained in predicting users' learning curves during visualization processing generalize to a different visualization. Second, we study to what extent we can make predictions on a user's learning curve without information on the visualization being used. Our models leverage various data sources, including a user's gaze behavior, pupil dilation, and cognitive abilities. We show that these models outperform a baseline that leverages knowledge on user task performance so far. Our best performing model achieves good accuracies in predicting users' learning curves even after observing users' performance on a few tasks only. These results represent an important step toward understanding how to support users in learning a new visualization. Graph visualizations encode relationships between objects. Abstracting the objects into group structures provides an overview of the data. Groups can be disjoint or overlapping, and might be organized hierarchically. However, the underlying graph still needs to be represented for analyzing the data in more depth. This work surveys research in visualizing group structures as part of graph diagrams. A particular focus is the explicit visual encoding of groups, rather than only using graph layout to indicate groups implicitly. We introduce a taxonomy of visualization techniques structuring the field into four main categories: visual node attributes vary properties of the node representation to encode the grouping, juxtaposed approaches use two separate visualizations, superimposed techniques work with two aligned visual layers, and embedded visualizations tightly integrate group and graph representation. The derived taxonomies for group structure and visualization types are also applied to group visualizations of edges. We survey group-only, group–node, group–edge and group–network tasks that are described in the literature as use cases of group visualizations. We discuss results from evaluations of existing visualization techniques as well as main areas of application. Finally, we report future challenges based on interviews we conducted with leading researchers of the field. Programmers are often faced with the necessity to visualize source code and grasp its structure. In a survey we studied how developers deal with this task. Based on our findings, we present the software visualization tool Code Gestalt, which assists programmers in quickly creating class diagrams. We evaluated and refined our concept using two prototypes. As a result, Code Gestalt introduces the tag overlay and thematic relations. These augmentations to class diagrams display similarities in the vocabulary used in the underlying source code. This simple, yet effective toolset empowers the user to explore and visualize software systems. The preliminary results of a user study investigating Code Gestalt indicate good usability. Despite the recent popularity of visual analytics focusing on big data, little is known about how to support users that use visualization techniques to explore multi-dimensional datasets and accomplish specific tasks. Our lack of models that can assist end-users during the data exploration process has made it challenging to learn from the user's interactive and analytical process. The ability to model how a user interacts with a specific visualization technique and what difficulties they face are paramount in supporting individuals with discovering new patterns within their complex datasets. This paper introduces the notion of visualization systems understanding and modeling user interactions with the intent of guiding a user through a task thereby enhancing visual data exploration. The challenges faced and the necessary future steps to take are discussed; and to provide a working example, a grammar-based model is presented that can learn from user interactions, determine the common patterns among a number of subjects using a K-Reversible algorithm, build a set of rules, and apply those rules in the form of suggestions to new users with the goal of guiding them along their visual analytic process. A formal evaluation study with 300 subjects was performed showing that our grammar-based model is effective at capturing the interactive process followed by users and that further research in this area has the potential to positively impact how users interact with a visualization system.