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We apply an approach from cognitive linguistics by mapping Conceptual Metaphor Theory (CMT) to the visualization domain to address patterns of visual conceptual metaphors that are often used in science infographics. Metaphors play an essential part in visual communication and are frequently employed to explain complex concepts. However, their use is often based on intuition, rather than following a formal process. At present, we lack tools and language for understanding and describing metaphor use in visualization to the extent where taxonomy and grammar could guide the creation of visual components, e.g., infographics. Our classification of the visual conceptual mappings within scientific representations is based on the breakdown of visual components in existing scientific infographics. We demonstrate the development of this mapping through a detailed analysis of data collected from four domains (biomedicine, climate, space, and anthropology) that represent a diverse range of visual conceptual metaphors used in the visual communication of science. This work allows us to identify patterns of visual conceptual metaphor use within the domains, resolve ambiguities about why specific conceptual metaphors are used, and develop a better overall understanding of visual metaphor use in scientific infographics. Our analysis shows that ontological and orientational conceptual metaphors are the most widely applied to translate complex scientific concepts. To support our findings we developed a visual exploratory tool based on the collected database that places the individual infographics on a spatio-temporal scale and illustrates the breakdown of visual conceptual metaphors.

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We developed and validated an instrument to measure the perceived readability in data visualization: PREVis. Researchers and practitioners can easily use this instrument as part of their evaluations to compare the perceived readability of different visual data representations. Our instrument can complement results from controlled experiments on user task performance or provide additional data during in-depth qualitative work such as design iterations when developing a new technique. Although readability is recognized as an essential quality of data visualizations, so far there has not been a unified definition of the construct in the context of visual representations. As a result, researchers often lack guidance for determining how to ask people to rate their perceived readability of a visualization. To address this issue, we engaged in a rigorous process to develop the first validated instrument targeted at the subjective readability of visual data representations. Our final instrument consists of 11 items across 4 dimensions: understandability, layout clarity, readability of data values, and readability of data patterns. We provide the questionnaire as a document with implementation guidelines on osf.io/9cg8j. Beyond this instrument, we contribute a discussion of how researchers have previously assessed visualization readability, and an analysis of the factors underlying perceived readability in visual data representations.

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We propose and study a novel cross-reality environment that seamlessly integrates a monoscopic 2D surface (an interactive screen with touch and pen input) with a stereoscopic 3D space (an augmented reality HMD) to jointly host spatial data visualizations. This innovative approach combines the best of two conventional methods of displaying and manipulating spatial 3D data, enabling users to fluidly explore diverse visual forms using tailored interaction techniques. Providing such effective 3D data exploration techniques is pivotal for conveying its intricate spatial structures-often at multiple spatial or semantic scales-across various application domains and requiring diverse visual representations for effective visualization. To understand user reactions to our new environment, we began with an elicitation user study, in which we captured their responses and interactions. We observed that users adapted their interaction approaches based on perceived visual representations, with natural transitions in spatial awareness and actions while navigating across the physical surface. Our findings then informed the development of a design space for spatial data exploration in cross-reality. We thus developed cross-reality environments tailored to three distinct domains: for 3D molecular structure data, for 3D point cloud data, and for 3D anatomical data. In particular, we designed interaction techniques that account for the inherent features of interactions in both spaces, facilitating various forms of interaction, including mid-air gestures, touch interactions, pen interactions, and combinations thereof, to enhance the users' sense of presence and engagement. We assessed the usability of our environment with biologists, focusing on its use for domain research. In addition, we evaluated our interaction transition designs with virtual and mixed-reality experts to gather further insights. As a result, we provide our design suggestions for the cross-reality environment, emphasizing the interaction with diverse visual representations and seamless interaction transitions between 2D and 3D spaces.

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We introduce DiffFit, a differentiable algorithm for fitting protein atomistic structures into an experimental reconstructed Cryo-Electron Microscopy (cryo-EM) volume map. In structural biology, this process is necessary to semi-automatically composite large mesoscale models of complex protein assemblies and complete cellular structures that are based on measured cryo-EM data. The current approaches require manual fitting in three dimensions to start, resulting in approximately aligned structures followed by an automated fine-tuning of the alignment. The DiffFit approach enables domain scientists to fit new structures automatically and visualize the results for inspection and interactive revision. The fitting begins with differentiable three-dimensional (3D) rigid transformations of the protein atom coordinates followed by sampling the density values at the atom coordinates from the target cryo-EM volume. To ensure a meaningful correlation between the sampled densities and the protein structure, we proposed a novel loss function based on a multi-resolution volume-array approach and the exploitation of the negative space. This loss function serves as a critical metric for assessing the fitting quality, ensuring the fitting accuracy and an improved visualization of the results. We assessed the placement quality of DiffFit with several large, realistic datasets and found it to be superior to that of previous methods. We further evaluated our method in two use cases: automating the integration of known composite structures into larger protein complexes and facilitating the fitting of predicted protein domains into volume densities to aid researchers in identifying unknown proteins. We implemented our algorithm as an open-source plugin (github.com/nanovis/DiffFit) in ChimeraX, a leading visualization software in the field. All supplemental materials are available at osf.io/5tx4q.

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We examine visual representations of data that make use of combinations of both 2D and 3D data mappings. Combining 2D and 3D representations is a common technique that allows viewers to understand multiple facets of the data with which they are interacting. While 3D representations focus on the spatial character of the data or the dedicated 3D data mapping, 2D representations often show abstract data properties and take advantage of the unique benefits of mapping to a plane. Many systems have used unique combinations of both types of data mappings effectively. Yet there are no systematic reviews of the methods in linking 2D and 3D representations. We systematically survey the relationships between 2D and 3D visual representations in major visualization publications-IEEE VIS, IEEE TVCG, and EuroVis-from 2012 to 2022. We closely examined 105 articles where 2D and 3D representations are connected visually, interactively, or through animation. These approaches are designed based on their visual environment, the relationships between their visual representations, and their possible layouts. Through our analysis, we introduce a design space as well as provide design guidelines for effectively linking 2D and 3D visual representations.

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We visualize the predictions of multiple machine learning models to help biologists as they interactively make decisions about cell lineage-the development of a (plant) embryo from a single ovum cell. Based on a confocal microscopy dataset, traditionally biologists manually constructed the cell lineage, starting from this observation and reasoning backward in time to establish their inheritance. To speed up this tedious process, we make use of machine learning (ML) models trained on a database of manually established cell lineages to assist the biologist in cell assignment. Most biologists, however, are not familiar with ML, nor is it clear to them which model best predicts the embryo's development. We thus have developed a visualization system that is designed to support biologists in exploring and comparing ML models, checking the model predictions, detecting possible ML model mistakes, and deciding on the most likely embryo development. To evaluate our proposed system, we deployed our interface with six biologists in an observational study. Our results show that the visual representations of machine learning are easily understandable, and our tool, LineageD+, could potentially increase biologists' working efficiency and enhance the understanding of embryos.

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We propose three novel spatial data selection techniques for particle data in VR visualization environments. They are designed to be target- and context-aware and be suitable for a wide range of data features and complex scenarios. Each technique is designed to be adjusted to particular selection intents: the selection of consecutive dense regions, the selection of filament-like structures, and the selection of clusters-with all of them facilitating post-selection threshold adjustment. These techniques allow users to precisely select those regions of space for further exploration-with simple and approximate 3D pointing, brushing, or drawing input-using flexible point- or path-based input and without being limited by 3D occlusions, non-homogeneous feature density, or complex data shapes. These new techniques are evaluated in a controlled experiment and compared with the Baseline method, a region-based 3D painting selection. Our results indicate that our techniques are effective in handling a wide range of scenarios and allow users to select data based on their comprehension of crucial features. Furthermore, we analyze the attributes, requirements, and strategies of our spatial selection methods and compare them with existing state-of-the-art selection methods to handle diverse data features and situations. Based on this analysis we provide guidelines for choosing the most suitable 3D spatial selection techniques based on the interaction environment, the given data characteristics, or the need for interactive post-selection threshold adjustment.

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We investigate the use of 2D black-and-white textures for the visualization of categorical data and contribute a summary of texture attributes, and the results of three experiments that elicited design strategies as well as aesthetic and effectiveness measures. Black-and-white textures are useful, for instance, as a visual channel for categorical data on low-color displays, in 2D/3D print, to achieve the aesthetic of historic visualizations, or to retain the color hue channel for other visual mappings. We specifically study how to use what we call geometric and iconic textures. Geometric textures use patterns of repeated abstract geometric shapes, while iconic textures use repeated icons that may stand for data categories. We parameterized both types of textures and developed a tool for designers to create textures on simple charts by adjusting texture parameters. 30 visualization experts used our tool and designed 66 textured bar charts, pie charts, and maps. We then had 150 participants rate these designs for aesthetics. Finally, with the top-rated geometric and iconic textures, our perceptual assessment experiment with 150 participants revealed that textured charts perform about equally well as non-textured charts, and that there are some differences depending on the type of chart.

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We present a method for producing documentary-style content using real-time scientific visualization. We introduce molecumentaries, i.e., molecular documentaries featuring structural models from molecular biology, created through adaptable methods instead of the rigid traditional production pipeline. Our work is motivated by the rapid evolution of scientific visualization and it potential in science dissemination. Without some form of explanation or guidance, however, novices and lay-persons often find it difficult to gain insights from the visualization itself. We integrate such knowledge using the verbal channel and provide it along an engaging visual presentation. To realize the synthesis of a molecumentary, we provide technical solutions along two major production steps: (1) preparing a story structure and (2) turning the story into a concrete narrative. In the first step, we compile information about the model from heterogeneous sources into a story graph. We combine local knowledge with external sources to complete the story graph and enrich the final result. In the second step, we synthesize a narrative, i.e., story elements presented in sequence, using the story graph. We then traverse the story graph and generate a virtual tour, using automated camera and visualization transitions. We turn texts written by domain experts into verbal representations using text-to-speech functionality and provide them as a commentary. Using the described framework, we synthesize fly-throughs with descriptions: automatic ones that mimic a manually authored documentary or semi-automatic ones which guide the documentary narrative solely through curated textual input.

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We developed and validated a rating scale to assess the aesthetic pleasure (or beauty) of a visual data representation: the BeauVis scale. With our work we offer researchers and practitioners a simple instrument to compare the visual appearance of different visualizations, unrelated to data or context of use. Our rating scale can, for example, be used to accompany results from controlled experiments or be used as informative data points during in-depth qualitative studies. Given the lack of an aesthetic pleasure scale dedicated to visualizations, researchers have mostly chosen their own terms to study or compare the aesthetic pleasure of visualizations. Yet, many terms are possible and currently no clear guidance on their effectiveness regarding the judgment of aesthetic pleasure exists. To solve this problem, we engaged in a multi-step research process to develop the first validated rating scale specifically for judging the aesthetic pleasure of a visualization (osf.io/fxs76). Our final BeauVis scale consists of five items, "enjoyable," "likable," "pleasing," "nice," and "appealing." Beyond this scale itself, we contribute (a) a systematic review of the terms used in past research to capture aesthetics, (b) an investigation with visualization experts who suggested terms to use for judging the aesthetic pleasure of a visualization, and (c) a confirmatory survey in which we used our terms to study the aesthetic pleasure of a set of 3 visualizations.

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Microscopy image observation is commonly performed on 2D screens, which limits human capacities to grasp volumetric, complex, and discrete biological dynamics. With the massive production of multidimensional images (3D + time, multi-channels) and derived images (e.g., restored images, segmentation maps, and object tracks), scientists need appropriate visualization and navigation methods to better apprehend the amount of information in their content. New modes of visualization have emerged, including virtual reality (VR)/augmented reality (AR) approaches which should allow more accurate analysis and exploration of large time series of volumetric images, such as those produced by the latest 3D + time fluorescence microscopy. They include integrated algorithms that allow researchers to interactively explore complex spatiotemporal objects at the scale of single cells or multicellular systems, almost in a real time manner. In practice, however, immersion of the user within 3D + time microscopy data represents both a paradigm shift in human-image interaction and an acculturation challenge, for the concerned community. To promote a broader adoption of these approaches by biologists, further dialogue is needed between the bioimaging community and the VR&AR developers.

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We present a case study on a journey about a personal data collection of carnivorous plant species habitats, and the resulting scientific exploration of location data biases, data errors, location hiding, and data plausibility. While initially driven by personal interest, our work led to the analysis and development of various means for visualizing threats to insight from geo-tagged social media data. In the course of this endeavor we analyzed local and global geographic distributions and their inaccuracies. We also contribute Motion Plausibility Profiles-a new means for visualizing how believable a specific contributor's location data is or if it was likely manipulated. We then compared our own repurposed social media dataset with data from a dedicated citizen science project. Compared to biases and errors in the literature on traditional citizen science data, with our visualizations we could also identify some new types or show new aspects for known ones. Moreover, we demonstrate several types of errors and biases for repurposed social media data. Please note that people with color impairments may consider our alternative paper version.

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In Augmented Reality (AR), users perceive virtual content anchored in the real world. It is used in medicine, education, games, navigation, maintenance, product design, and visualization, in both single-user and multi-user scenarios. Multi-user AR has received limited attention from researchers, even though AR has been in development for more than two decades. We present the state of existing work at the intersection of AR and Computer-Supported Collaborative Work (AR-CSCW), by combining a systematic survey approach with an exploratory, opportunistic literature search. We categorize 65 papers along the dimensions of space, time, role symmetry (whether the roles of users are symmetric), technology symmetry (whether the hardware platforms of users are symmetric), and output and input modalities. We derive design considerations for collaborative AR environments, and identify under-explored research topics. These include the use of heterogeneous hardware considerations and 3D data exploration research areas. This survey is useful for newcomers to the field, readers interested in an overview of CSCW in AR applications, and domain experts seeking up-to-date information.

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We present V-Mail, a framework of cross-platform applications, interactive techniques, and communication protocols for improved multi-person correspondence about spatial 3D datasets. Inspired by the daily use of e-mail, V-Mail seeks to enable a similar style of rapid, multi-person communication accessible on any device; however, it aims to do this in the new context of spatial 3D communication, where limited access to 3D graphics hardware typically prevents such communication. The approach integrates visual data storytelling with data exploration, spatial annotations, and animated transitions. V-Mail "data stories" are exported in a standard video file format to establish a common baseline level of access on (almost) any device. The V-Mail framework also includes a series of complementary client applications and plugins that enable different degrees of story co-authoring and data exploration, adjusted automatically to match the capabilities of various devices. A lightweight, phone-based V-Mail app makes it possible to annotate data by adding captions to the video. These spatial annotations are then immediately accessible to team members running high-end 3D graphics visualization systems that also include a V-Mail client, implemented as a plugin. Results and evaluation from applying V-Mail to assist communication within an interdisciplinary science team studying Antarctic ice sheets confirm the utility of the asynchronous, cross-platform collaborative framework while also highlighting some current limitations and opportunities for future work.

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We present Multiscale Unfolding, an interactive technique for illustratively visualizing multiple hierarchical scales of DNA in a single view, showing the genome at different scales and demonstrating how one scale spatially folds into the next. The DNA's extremely long sequential structure-arranged differently on several distinct scale levels-is often lost in traditional 3D depictions, mainly due to its multiple levels of dense spatial packing and the resulting occlusion. Furthermore, interactive exploration of this complex structure is cumbersome, requiring visibility management like cut-aways. In contrast to existing temporally controlled multiscale data exploration, we allow viewers to always see and interact with any of the involved scales. For this purpose we separate the depiction into constant-scale and scale transition zones. Constant-scale zones maintain a single-scale representation, while still linearly unfolding the DNA. Inspired by illustration, scale transition zones connect adjacent constant-scale zones via level unfolding, scaling, and transparency. We thus represent the spatial structure of the whole DNA macro-molecule, maintain its local organizational characteristics, linearize its higher-level organization, and use spatially controlled, understandable interpolation between neighboring scales. We also contribute interaction techniques that provide viewers with a coarse-to-fine control for navigating within our all-scales-in-one-view representations and visual aids to illustrate the size differences. Overall, Multiscale Unfolding allows viewers to grasp the DNA's structural composition from chromosomes to the atoms, with increasing levels of "unfoldedness," and can be applied in data-driven illustration and communication.

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We present the VIS30K dataset, a collection of 29,689 images that represents 30 years of figures and tables from each track of the IEEE Visualization conference series (Vis, SciVis, InfoVis, VAST). VIS30K's comprehensive coverage of the scientific literature in visualization not only reflects the progress of the field but also enables researchers to study the evolution of the state-of-the-art and to find relevant work based on graphical content. We describe the dataset and our semi-automatic collection process, which couples convolutional neural networks (CNN) with curation. Extracting figures and tables semi-automatically allows us to verify that no images are overlooked or extracted erroneously. To improve quality further, we engaged in a peer-search process for high-quality figures from early IEEE Visualization papers. With the resulting data, we also contribute VISImageNavigator (VIN, visimagenavigator.github.io), a web-based tool that facilitates searching and exploring VIS30K by author names, paper keywords, title and abstract, and years.

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We present a method for the browsing of hierarchical 3D models in which we combine the typical navigation of hierarchical structures in a 2D environment-using clicks on nodes, links, or icons-with a 3D spatial data visualization. Our approach is motivated by large molecular models, for which the traditional single-scale navigational metaphors are not suitable. Multi-scale phenomena, e. g., in astronomy or geography, are complex to navigate due to their large data spaces and multi-level organization. Models from structural biology are in addition also densely crowded in space and scale. Cutaways are needed to show individual model subparts. The camera has to support exploration on the level of a whole virus, as well as on the level of a small molecule. We address these challenges by employing HyperLabels: active labels that-in addition to their annotational role-also support user interaction. Clicks on HyperLabels select the next structure to be explored. Then, we adjust the visualization to showcase the inner composition of the selected subpart and enable further exploration. Finally, we use a breadcrumbs panel for orientation and as a mechanism to traverse upwards in the model hierarchy. We demonstrate our concept of hierarchical 3D model browsing using two exemplary models from meso-scale biology.

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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.

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We discuss the concept of directness in the context of spatial interaction with visualization. In particular, we propose a model that allows practitioners to analyze and describe the spatial directness of interaction techniques, ultimately to be able to better understand interaction issues that may affect usability. To reach these goals, we distinguish between different types of directness. Each type of directness depends on a particular mapping between different spaces, for which we consider the data space, the visualization space, the output space, the user space, the manipulation space, and the interaction space. In addition to the introduction of the model itself, we also show how to apply it to several real-world interaction scenarios in visualization, and thus discuss the resulting types of spatial directness, without recommending either more direct or more indirect interaction techniques. In particular, we will demonstrate descriptive and evaluative usage of the proposed model, and also briefly discuss its generative usage.

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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.

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