Shape: A 3D Modeling Tool for Astrophysics

We present a flexible interactive 3D morpho-kinematical modeling application for astrophysics. Compared to other systems, our application reduces the restrictions on the physical assumptions, data type and amount that is required for a reconstruction of an object's morphology. It is one of the first publicly available tools to apply interactive graphics to astrophysical modeling. The tool allows astrophysicists to provide a-priori knowledge about the object by interactively defining 3D structural elements. By direct comparison of model prediction with observational data, model parameters can then be automatically optimized to fit the observation. The tool has already been successfully used in a number of astrophysical research projects.Comment: 13 pages, 11 figures, accepted for publication in the "IEEE Transactions on Visualization and Computer Graphics

MyBrush: Brushing and Linking with Personal Agency

We extend the popular brushing and linking technique by incorporating personal agency in the interaction. We map existing research related to brushing and linking into a design space that deconstructs the interaction technique into three components: source (what is being brushed), link (the expression of relationship between source and target), and target (what is revealed as related to the source). Using this design space, we created MyBrush, a unified interface that offers personal agency over brushing and linking by giving people the flexibility to configure the source, link, and target of multiple brushes. The results of three focus groups demonstrate that people with different backgrounds leveraged personal agency in different ways, including performing complex tasks and showing links explicitly. We reflect on these results, paving the way for future research on the role of personal agency in information visualization

Data Changes Everything: Challenges and Opportunities in Data Visualization Design Handoff

Complex data visualization design projects often entail collaboration between people with different visualization-related skills. For example, many teams include both designers who create new visualization designs and developers who implement the resulting visualization software. We identify gaps between data characterization tools, visualization design tools, and development platforms that pose challenges for designer-developer teams working to create new data visualizations. While it is common for commercial interaction design tools to support collaboration between designers and developers, creating data visualizations poses several unique challenges that are not supported by current tools. In particular, visualization designers must characterize and build an understanding of the underlying data, then specify layouts, data encodings, and other data-driven parameters that will be robust across many different data values. In larger teams, designers must also clearly communicate these mappings and their dependencies to developers, clients, and other collaborators. We report observations and reflections from five large multidisciplinary visualization design projects and highlight six data-specific visualization challenges for design specification and handoff. These challenges include adapting to changing data, anticipating edge cases in data, understanding technical challenges, articulating data-dependent interactions, communicating data mappings, and preserving the integrity of data mappings across iterations. Based on these observations, we identify opportunities for future tools for prototyping, testing, and communicating data-driven designs, which might contribute to more successful and collaborative data visualization design.Comment: 11 pages, 11 figures. To appear in IEEE Transactions on Visualization and Computer Graphics. To be presented at the IEEE VIS 2019 Conferenc

Simulating the decentralized processes of the human immune system in a virtual anatomy model

BACKGROUND: Many physiological processes within the human body can be perceived and modeled as large systems of interacting particles or swarming agents. The complex processes of the human immune system prove to be challenging to capture and illustrate without proper reference to the spacial distribution of immune-related organs and systems. Our work focuses on physical aspects of immune system processes, which we implement through swarms of agents. This is our first prototype for integrating different immune processes into one comprehensive virtual physiology simulation. RESULTS: Using agent-based methodology and a 3-dimensional modeling and visualization environment (LINDSAY Composer), we present an agent-based simulation of the decentralized processes in the human immune system. The agents in our model - such as immune cells, viruses and cytokines - interact through simulated physics in two different, compartmentalized and decentralized 3-dimensional environments namely, (1) within the tissue and (2) inside a lymph node. While the two environments are separated and perform their computations asynchronously, an abstract form of communication is allowed in order to replicate the exchange, transportation and interaction of immune system agents between these sites. The distribution of simulated processes, that can communicate across multiple, local CPUs or through a network of machines, provides a starting point to build decentralized systems that replicate larger-scale processes within the human body, thus creating integrated simulations with other physiological systems, such as the circulatory, endocrine, or nervous system. Ultimately, this system integration across scales is our goal for the LINDSAY Virtual Human project. CONCLUSIONS: Our current immune system simulations extend our previous work on agent-based simulations by introducing advanced visualizations within the context of a virtual human anatomy model. We also demonstrate how to distribute a collection of connected simulations over a network of computers. As a future endeavour, we plan to use parameter tuning techniques on our model to further enhance its biological credibility. We consider these in silico experiments and their associated modeling and optimization techniques as essential components in further enhancing our capabilities of simulating a whole-body, decentralized immune system, to be used both for medical education and research as well as for virtual studies in immunoinformatics

Computer-Supported Collaborative Production

This paper proposes the concept of collaborative production as a focus of concern within the general area of collaborative work. We position the concept with respect to McGrath's framework for small group dynamics and the more familiar collaboration processes of awareness, coordination, and communication (McGrath 1991). After reviewing research issues and computer-based support for these interacting aspects of collaboration, we turn to a discussion of implications for how to design improved support for collaborative production. We illustrate both the challenges of collaborative production and our design implications with a collaborative map-updating scenario drawn from the work domain of geographical information systems

Integration of Swin UNETR and statistical shape modeling for a semi-automated segmentation of the knee and biomechanical modeling of articular cartilage

Simulation studies like finite element (FE) modeling provide insight into knee joint mechanics without patient experimentation. Generic FE models represent biomechanical behavior of the tissue by overlooking variations in geometry, loading, and material properties of a population. On the other hand, subject-specific models include these specifics, resulting in enhanced predictive precision. However, creating such models is laborious and time-intensive. The present study aimed to enhance subject-specific knee joint FE modeling by incorporating a semi-automated segmentation algorithm. This segmentation was a 3D Swin UNETR for an initial segmentation of the femur and tibia, followed by a statistical shape model (SSM) adjustment to improve surface roughness and continuity. Five hundred and seven magnetic resonance images (MRIs) from the Osteoarthritis Initiative (OAI) database were used to build and validate the segmentation model. A semi-automated FE model was developed using this semi-automated segmentation. On the other hand, a manual FE model was developed through manual segmentation (i.e., the gold standard approach). Both FE models were subjected to gait loading. The predicted mechanical response of manual and semi-automated FE models were compared. In the result, our semi-automated segmentation achieved Dice similarity coefficient (DSC) over 98% for both femur and tibia. The mechanical results (max principal stress, max principal strain, fluid pressure, fibril strain, and contact area) showed no significant differences between the manual and semi-automated FE models, indicating the effectiveness of the proposed semi-automated segmentation in creating accurate knee joint FE models. ( https://data.mendeley.com/datasets/k5hdc9cz7w/1 )

Estimating Cell Count and Distribution in Labeled Histological Samples Using Incremental Cell Search

Cell proliferation is critical to the outgrowth of biological structures including the face and limbs. This cellular process has traditionally been studied via sequential histological sampling of these tissues. The length and tedium of traditional sampling is a major impediment to analyzing the large datasets required to accurately model cellular processes. Computerized cell localization and quantification is critical for high-throughput morphometric analysis of developing embryonic tissues. We have developed the Incremental Cell Search (ICS), a novel software tool that expedites the analysis of relationships between morphological outgrowth and cell proliferation in embryonic tissues. Based on an estimated average cell size and stain color, ICS rapidly indicates the approximate location and amount of cells in histological images of labeled embryonic tissue and provides estimates of cell counts in regions with saturated fluorescence and blurred cell boundaries. This capacity opens the door to high-throughput 3D and 4D quantitative analyses of developmental patterns

Estimating Cell Count and Distribution in Labeled Histological Samples Using Incremental Cell Search

Cell proliferation is critical to the outgrowth of biological structures including the face and limbs. This cellular process has traditionally been studied via sequential histological sampling of these tissues. The length and tedium of traditional sampling is a major impediment to analyzing the large datasets required to accurately model cellular processes. Computerized cell localization and quantification is critical for high-throughput morphometric analysis of developing embryonic tissues. We have developed the Incremental Cell Search (ICS), a novel software tool that expedites the analysis of relationships between morphological outgrowth and cell proliferation in embryonic tissues. Based on an estimated average cell size and stain color, ICS rapidly indicates the approximate location and amount of cells in histological images of labeled embryonic tissue and provides estimates of cell counts in regions with saturated fluorescence and blurred cell boundaries. This capacity opens the door to high-throughput 3D and 4D quantitative analyses of developmental patterns

Integrated Environmental Modelling Framework for Cumulative Effects Assessment

Global warming and population growth have resulted in an increase in the intensity of natural and anthropogenic stressors. Investigating the complex nature of environmental problems requires the integration of different environmental processes across major components of the environment, including water, climate, ecology, air, and land. Cumulative effects assessment (CEA) not only includes analyzing and modeling environmental changes, but also supports planning alternatives that promote environmental monitoring and management. Disjointed and narrowly focused environmental management approaches have proved dissatisfactory. The adoption of integrated modelling approaches has sparked interests in the development of frameworks which may be used to investigate the processes of individual environmental component and the ways they interact with each other. Integrated modelling systems and frameworks are often the only way to take into account the important environmental processes and interactions, relevant spatial and temporal scales, and feedback mechanisms of complex systems for CEA. This book examines the ways in which interactions and relationships between environmental components are understood, paying special attention to climate, land, water quantity and quality, and both anthropogenic and natural stressors. It reviews modelling approaches for each component and reviews existing integrated modelling systems for CEA. Finally, it proposes an integrated modelling framework and provides perspectives on future research avenues for cumulative effects assessment