A Survey of Visualization for Live Cell Imaging Pretorius, A. J.; Khan, I. A.; Errington, R. J.
Computer graphics forum,
January 2017, 2017-01-00, 20170101, Letnik:
36, Številka:
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Live cell imaging is an important biomedical research paradigm for studying dynamic cellular behaviour. Although phenotypic data derived from images are difficult to explore and analyse, some ...researchers have successfully addressed this with visualization. Nonetheless, visualization methods for live cell imaging data have been reported in an ad hoc and fragmented fashion. This leads to a knowledge gap where it is difficult for biologists and visualization developers to evaluate the advantages and disadvantages of different visualization methods, and for visualization researchers to gain an overview of existing work to identify research priorities. To address this gap, we survey existing visualization methods for live cell imaging from a visualization research perspective for the first time. Based on recent visualization theory, we perform a structured qualitative analysis of visualization methods that includes characterizing the domain and data, ing tasks, and describing visual encoding and interaction design. Based on our survey, we identify and discuss research gaps that future work should address: the broad analytical context of live cell imaging; the importance of behavioural comparisons; links with dynamic data visualization; the consequences of different data modalities; shortcomings in interactive support; and, in addition to analysis, the value of the presentation of phenotypic data and insights to other stakeholders.
Live cell imaging is an important biomedical research paradigm for studying dynamic cellular behaviour. Although phenotypic data derived from images are difficult to explore and analyse, some researchers have successfully addressed this with visualization. Nonetheless, visualization methods for live cell imaging data have been reported in an ad hoc and fragmented fashion. This leads to a knowledge gap where it is difficult for biologists and visualization developers to evaluate the advantages and disadvantages of different visualization methods, and for visualization researchers to gain an overview of existing work to identify research priorities. To address this gap, we survey existing visualization methods for live cell imaging from a visualization research perspective for the first time.
A central topic in scientific visualization is the transfer function (TF) for volume rendering. The TF serves a fundamental role in translating scalar and multivariate data into color and opacity to ...express and reveal the relevant features present in the data studied. Beyond this core functionality, TFs also serve as a tool for encoding and utilizing domain knowledge and as an expression for visual design of material appearances. TFs also enable interactive volumetric exploration of complex data. The purpose of this state‐of‐the‐art report (STAR) is to provide an overview of research into the various aspects of TFs, which lead to interpretation of the underlying data through the use of meaningful visual representations. The STAR classifies TF research into the following aspects: dimensionality, derived attributes, aggregated attributes, rendering aspects, automation, and user interfaces. The STAR concludes with some interesting research challenges that form the basis of an agenda for the development of next generation TF tools and methodologies.
Add Affinity Designer to your creative skillset while creating innovative designs and illustrations, building a solid foundation for your future with the help of this color guideKey ...FeaturesUnderstand Affinity Designer's interface and setup, discover its capabilities, and develop an efficient workflowHarness the power of an easy and flexible vector and pixel workflow in one applicationLearn practical skills and gain the confidence to power your own creative projectsBook DescriptionAffinity Designer is a widely adopted creative application, and in a reasonably short space of time, it has become a leading design and illustration application. Affinity Designer, along with Affinity Photo and Affinity Publisher, is part of a suite of award-winning creative software applications developed by Serif Europe. Built on the latest technologies, which make it fast and smooth, Affinity Designer is quickly becoming the go-to professional creative application for vector drawing and pixel-based painting.
Up and Running with Affinity Designer is a comprehensive hands-on guide to the Affinity Designer software. Whether you're new to the creative industry, a seasoned professional looking for a proven alternative, or an enthusiastic hobbyist, this book will help you get up to speed in no time. You’ll learn how to create documents and explore workflow best practices while working through practical exercises using the knowledge and skills developed in each chapter to solidify your understanding of the fundamentals. Finally, you’ll bring it all together with real-world practical applications by building a fun logo and professional illustration, forming a base for in-depth exploration in your own projects.
By the end of this Affinity Designer book, you'll have gained the knowledge and confidence to use Affinity Designer as part of your creative toolset.What you will learnExplore the interface and unique UX characteristics of Affinity DesignerDiscover features that allow you to manipulate and transform objectsApply color, shading, and effects to create unique compositionsEmploy layers to organize and simplify complex projectsUse grids, guides, and snapping features as design aidsAdapt to Affinity Designer s custom workspaces and keyboard shortcutsExplore the workflow and design best practices for more predictable and successful outcomesIdentify potential stumbling blocks in your design process and learn how to avoid themWho this book is forThis Affinity Designer book is for graphic designers, artists, illustrators, and hobbyists. Anyone curious about Affinity Designer's unique toolset and vector and pixel workflows or looking for cost-effective alternatives to the Adobe suite will find this book useful. Experience in working with other similar tools will be helpful, but not necessary.
Tumors are heterogeneous tissues consisting of multiple regions with distinct characteristics. Characterization of these intra‐tumor regions can improve patient diagnosis and enable a better targeted ...treatment. Ideally, tissue characterization could be performed non‐invasively, using medical imaging data, to derive per voxel a number of features, indicative of tissue properties. However, the high dimensionality and complexity of this imaging‐derived feature space is prohibiting for easy exploration and analysis ‐ especially when clinical researchers require to associate observations from the feature space to other reference data, e.g., features derived from histopathological data. Currently, the exploratory approach used in clinical research consists of juxtaposing these data, visually comparing them and mentally reconstructing their relationships. This is a time consuming and tedious process, from which it is difficult to obtain the required insight. We propose a visual tool for: (1) easy exploration and visual analysis of the feature space of imaging‐derived tissue characteristics and (2) knowledge discovery and hypothesis generation and confirmation, with respect to reference data used in clinical research. We employ, as central view, a 2D embedding of the imaging‐derived features. Multiple linked interactive views provide functionality for the exploration and analysis of the local structure of the feature space, enabling linking to patient anatomy and clinical reference data. We performed an initial evaluation with ten clinical researchers. All participants agreed that, unlike current practice, the proposed visual tool enables them to identify, explore and analyze heterogeneous intra‐tumor regions and particularly, to generate and confirm hypotheses, with respect to clinical reference data.
Weather conditions affect multiple aspects of human life such as economy, safety, security, and social activities. For this reason, weather forecast plays a major role in society. Currently weather ...forecasts are based on Numerical Weather Prediction (NWP) models that generate a representation of the atmospheric flow. Interactive visualization of geo‐spatial data has been widely used in order to facilitate the analysis of NWP models. This paper presents a visualization system for the analysis of spatio‐temporal patterns in short‐term weather forecasts. For this purpose, we provide an interactive visualization interface that guides users from simple visual overviews to more advanced visualization techniques. Our solution presents multiple views that include a timeline with geo‐referenced maps, an integrated webmap view, a forecast operation tool, a curve‐pattern selector, spatial filters, and a linked meteogram. Two key contributions of this work are the timeline with geo‐referenced maps and the curve‐pattern selector. The latter provides novel functionality that allows users to specify and search for meaningful patterns in the data. The visual interface of our solution allows users to detect both possible weather trends and errors in the weather forecast model. We illustrate the usage of our solution with a series of case studies that were designed and validated in collaboration with domain experts.
In many cases, only the combination of geometric and volumetric data sets is able to describe a single phenomenon under observation when visualizing large and complex data. When semi‐transparent ...geometry is present, correct rendering results require sorting of transparent structures. Additional complexity is introduced as the contributions from volumetric data have to be partitioned according to the geometric objects in the scene. The A‐buffer, an enhanced framebuffer with additional per‐pixel information, has previously been introduced to deal with the complexity caused by transparent objects. In this paper, we present an optimized rendering algorithm for hybrid volume‐geometry data based on the A‐buffer concept. We propose two novel components for modern GPUs that tailor memory utilization to the depth complexity of individual pixels. The proposed components are compatible with modern A‐buffer implementations and yield performance gains of up to eight times compared to existing approaches through reduced allocation and reuse of fast cache memory. We demonstrate the applicability of our approach and its performance with several examples from molecular biology, space weather and medical visualization containing both, volumetric data and geometric structures.
We present an A‐buffer based algorithm that achieves performance gains of up to eight times relative existing techniques. The algorithm contains two novel components which improve the utilization of the local cache memory on the GPU. This is particularly important for scenes with non‐uniform depth complexities and rapidly decreasing depth complexity histograms (DCHs).
We present a user‐assisted video stabilization algorithm that is able to stabilize challenging videos when state‐of‐the‐art automatic algorithms fail to generate a satisfactory result. Current ...methods do not give the user any control over the look of the final result. Users either have to accept the stabilized result as is, or discard it should the stabilization fail to generate a smooth output. Our system introduces two new modes of interaction that allow the user to improve the unsatisfactory stabilized video. First, we cluster tracks and visualize them on the warped video. The user ensures that appropriate tracks are selected by clicking on track clusters to include or exclude them. Second, the user can directly specify how regions in the output video should look by drawing quadrilaterals to select and deform parts of the frame. These user‐provided deformations reduce undesirable distortions in the video. Our algorithm then computes a stabilized video using the user‐selected tracks, while respecting the user‐modified regions. The process of interactively removing user‐identified artifacts can sometimes introduce new ones, though in most cases there is a net improvement. We demonstrate the effectiveness of our system with a variety of challenging hand held videos.
A pathological vessel dilation in the brain, termed cerebral aneurysm, bears a high risk of rupture, and is associated with a high mortality. In recent years, incidental findings of unruptured ...aneurysms have become more frequent, mainly due to advances in medical imaging. The pathological condition is often treated with a stent that diverts the blood flow from the aneurysm sac back to the original vessel. Prior to treatment, neuroradiologists need to decide on the optimal stent configuration and judge the long‐term rupture risk, for which blood flow information is essential. Modern patient‐specific simulations can model the hemodynamics for various stent configurations, providing important indicators to support the decision‐making process. However, the necessary visual analysis of these data becomes tedious and time‐consuming, because of the abundance of information. We introduce a comprehensive comparative visualization that integrates morphology with blood flow indicators to facilitate treatment assessment. To deal with the visual complexity, we propose a details‐on‐demand approach, combining established medical visualization techniques with innovative glyphs inspired by information visualization concepts. In an evaluation we have obtained informal feedback from domain experts, gauging the value of our visualization.
Identification and characterization of cancer subtypes are important areas of research that are based on the integrated analysis of multiple heterogeneous genomics datasets. Since there are no tools ...supporting this process, much of this work is done using ad‐hoc scripts and static plots, which is inefficient and limits visual exploration of the data. To address this, we have developed StratomeX, an integrative visualization tool that allows investigators to explore the relationships of candidate subtypes across multiple genomic data types such as gene expression, DNA methylation, or copy number data. StratomeX represents datasets as columns and subtypes as bricks in these columns. Ribbons between the columns connect bricks to show subtype relationships across datasets. Drill‐down features enable detailed exploration. StratomeX provides insights into the functional and clinical implications of candidate subtypes by employing small multiples, which allow investigators to assess the effect of subtypes on molecular pathways or outcomes such as patient survival. As the configuration of viewing parameters in such a multi‐dataset, multi‐view scenario is complex, we propose a meta visualization and configuration interface for dataset dependencies and data‐view relationships. StratomeX is developed in close collaboration with domain experts. We describe case studies that illustrate how investigators used the tool to explore subtypes in large datasets and demonstrate how they efficiently replicated findings from the literature and gained new insights into the data.
The environmental and noise impact of airports often causes extensive political discussion which in some cases even lead to transnational tensions. Analyzing local approach and departure patterns ...around an airport is difficult since it depends on a variety of complex variables like weather, local and general regulations and many more. Yet, understanding these movements and the expected amount of flights during arrival and departure is of great interest to both casual and expert users, as planes have a higher impact on the areas beneath during these phases. We present a Visual Analytics framework that enables users to develop an understanding of local flight behavior through visual exploration of historical data and interactive manipulation of prediction models with direct feedback, as well as a classification quality visualization using a random noise metaphor. We showcase our approach using real world data from the Zurich International Airport region, where aircraft noise has led to an ongoing conflict between Germany and Switzerland. The use cases, findings and expert feedback demonstrate how our approach helps in understanding the situation and to substantiate the otherwise often subjective discourse on the topic.
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