Spring Conference on Computer Graphics - SCCG '13, 2013
Spatial selections are a ubiquitous concept in visualization. By localizing particular features, ... more Spatial selections are a ubiquitous concept in visualization. By localizing particular features, they can be analyzed and compared in different views. However, the semantics of such selections are often dependent on other parameter settings and it can be difficult to reconstruct them without additional information. In this paper, we present the concept of contextual snapshots as an effective means for managing spatial selections in visualized data. The selections are automatically associated with the context in which they have been created. Contextual snapshots can be also used as the basis for interactive integrated and linked views, which enable in-place investigation and comparison of multiple visual representations of data. Our approach is implemented as a flexible toolkit with welldefined interfaces for integration into existing systems. We demonstrate the power and generality of our techniques by applying them to several distinct scenarios such as the visualization of simulation data and the analysis of historical documents.
Spatial selections are a ubiquitous concept in visualization. By localizing particular features, ... more Spatial selections are a ubiquitous concept in visualization. By localizing particular features, they can be analysed and compared in different views. However, the semantics of such selections often depend on specific parameter settings and it can be difficult to reconstruct them without additional information. In this paper, we present the concept of contextual snapshots as an effective means for managing spatial selections in visualized data. The selections are automatically associated with the context in which they have been created. Contextual snapshots can also be used as the basis for interactive integrated and linked views, which enable in-place investigation and comparison of multiple visual representations of data. Our approach is implemented as a flexible toolkit with well-defined interfaces for integration into existing systems. We demonstrate the power and generality of our techniques by applying them to several distinct scenarios such as the visualization of simulation data, the analysis of historical documents and the display of anatomical data.
Cryo-Electron Tomography (cryo-ET) is a new 3D imaging technique with unprecedented potential for... more Cryo-Electron Tomography (cryo-ET) is a new 3D imaging technique with unprecedented potential for resolving submicron structural detail. Existing volume visualization methods, however, cannot cope with its very low signal-to-noise ratio. In order to design more powerful transfer functions, we propose to leverage soft segmentation as an explicit component of visualization for noisy volumes. Our technical realization is based on semi-supervised learning where we combine the advantages of two segmentation algorithms. A first weak segmentation algorithm provides good results for propagating sparse user provided labels to other voxels in the same volume. This weak segmentation algorithm is used to generate dense pseudo labels. A second powerful deep-learning based segmentation algorithm can learn from these pseudo labels to generalize the segmentation to other unseen volumes, a task that the weak segmentation algorithm fails at completely. The proposed volume visualization uses the deep-...
Volumetric visualization has many practical applications, particularly in medical imaging. Usabil... more Volumetric visualization has many practical applications, particularly in medical imaging. Usability of volumetric visualization algorithms depends on available means to select areas of interest in volumetric data that are to be visualized. A simple and sucient method is a onedimensional transfer function that assigns colours to intensity values of the data. A drawback of this method is that it produces visual artefacts in specic cases. In this paper we propose a volumetric visualization method that overcomes this drawback by using ltration with volumetric ray casting algorithm. Our method enables users to use simple transfer functions with signicant visual artefacts reduction.
We present a method for producing documentary-style content using real-time scientific visualizat... more We present a method for producing documentary-style content using real-time scientific visualization. We produce molecumentaries, i.e., molecular documentaries featuring structural models from molecular biology. We employ scalable methods instead of the rigid traditional production pipeline. Our method is motivated by the rapid evolution of interactive scientific visualization, which shows great 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, information about the model from heterogeneous sources is compiled into a story graph. Local...
Fibrous structures are ubiquitous in cell biology and play essential structural and functional ro... more Fibrous structures are ubiquitous in cell biology and play essential structural and functional roles in the life cycle of a cell. They are long polymers, such as DNA carrying genetic information, or filaments forming the cytoskeleton, crucial for cell division and maintaining the cell shape. In order to disseminate new findings of such structures to peers or a general audience, animated 3D models of these structures have to be created, as they are too small to be imaged with microscopes. However, this is a tedious task carried out by scientific animators, who manually create expressive visual representations of biological phenomena. In this work, we present a novel concept which simplifies the process of animating multi-scale procedural models of biological fibrous structures. In contrast with existing work in the domain of molecular visualization, our approach can also capture dynamics, which are important to show when communicating biological processes. CCS Concepts • Computing me...
A challenging problem in biology is the incompleteness of acquired information when visualizing b... more A challenging problem in biology is the incompleteness of acquired information when visualizing biological phenomena. Structural biology generates detailed models of viruses or bacteria at different development stages, while the processes that relate one stage to another are often not clear. Similarly, the entire life cycle of a biological entity might be available as a quantitative model, while only one structural model is available. If the relation between two models is specified at a lower level of detail than the actual models themselves, the two models cannot be interpolated correctly. We propose a method that deals with the visualization of incomplete data information in the developmental or evolutionary states of biological mesoscale models, such as viruses or microorganisms. The central tool in our approach is visual abstraction. Instead of directly interpolating between two models that show different states of an organism, we gradually forward transform the models into a le...
Visual clutter is a major problem in large biological data visualization. It is often addressed t... more Visual clutter is a major problem in large biological data visualization. It is often addressed through the means of level of detail schemes coupled with an appropriate coloring of the visualized structures. Ambient occlusion and shadows are often used to improve the depth perception. However, when used excessively, these techniques are sources of visual clutter themselves. In this paper we present a new approach to screen-space illumination algorithms suitable for use in illustrative visualization. The illumination effect can be controlled so that desired levels of semantic scene organization cast shadows while other remain flat. This way the illumination design can be parameterized to keep visual clutter, originating from illumination, to a minimum, while also guiding the user in a multiscale model exploration. We achieve this by selectively applying occlusion shading based on the inherent semantics of the visualized hierarchically-organized data. The technique is in principle gen...
In visualization systems it is often the case that the changes of the input parameters are not pr... more In visualization systems it is often the case that the changes of the input parameters are not proportional to the visual change of the generated output. In this paper, we propose a model for enabling data-sensitive navigation for user-interface elements. This model is applied to normalize the user input according to the visual change, and also to visually communicate this normalization. In this way, the exploration of heterogeneous data using common interaction elements can be performed in an efficient way. We apply our model to the field of medical visualization and present guided navigation tools for traversing vascular structures and for camera rotation around 3D volumes. The presented examples demonstrate that the model scales to user-interface elements where multiple parameters are set simultaneously.
IEEE Transactions on Visualization and Computer Graphics
We present a method for producing documentary-style content using real-time scientific visualizat... more 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.
Volumetric visualization of medical data is a specific task, as doctors and radiology technicians... more Volumetric visualization of medical data is a specific task, as doctors and radiology technicians are not well trained in the field of computer graphics; therefore, algorithms for visualization of medical data must be as intuitive as possible, so that visualization tools employing them would be helpful in medical environment. Visualization of volumetric data acquired by medical imaging could not be effectively used without defining a proper transfer function, which transforms measured intensities to colours and opacity values. Many visualization methods use complex means for designing transfer functions, which could lead to decreased usability of said methods. We propose a novel approach in volumetric visualization that uses only a simple one-dimensional transfer function for classifying different materials. The goal of our method is to visualize individual tissues from medical data, present them with minimal effort and enable users to observe areas of interest.
Visualization algorithms are parameterized to offer universality in terms of handling various dat... more Visualization algorithms are parameterized to offer universality in terms of handling various data types, showing different aspects of the visualized data, or producing results useful for domain experts from different fields. Hence, input parameters are an important aspect of the visualization process. Their exploration and management are tasks which enable the visualization reusability, portability, and interdisciplinary communication. With increasing availability of visualization systems, which are suitable for a great variety of tasks, their complexity increases as well. This usually involves many input parameters necessary for the meaningful visualization of data. Multiple input parameters form parameter spaces which are too large to be explored by brute-force. Knowing the properties of a parameter space is often beneficial for improving data visualization. Therefore, it is important for domain experts utilizing data visualization to have tools for automatic parameter specificat...
IEEE Transactions on Visualization and Computer Graphics
Fig. 1. The ultrastructure of a SARS-CoV-2 virion created using our modeling technique. The membr... more Fig. 1. The ultrastructure of a SARS-CoV-2 virion created using our modeling technique. The membrane shape and distribution of the spike proteins are determined from microscopy image data. The internal assembly is a result of an interactive 3D rule specification approach. Left: internal nucleoprotein complex. Middle: RNA condensed within the nucleoprotein. Right: Outer spike distribution.
Proceedings of the 33rd Spring Conference on Computer Graphics - SCCG '17, 2017
In molecular biology, illustrative animations are used to convey complex biological phenomena to ... more In molecular biology, illustrative animations are used to convey complex biological phenomena to broad audiences. However, such animations have to be manually authored in 3D modeling software, a time consuming task that has to be repeated from scratch for every new data set, and requires a high level of expertise in illustration, animation, and biology. We therefore propose metamorphers: a set of operations for defining animation states as well as the transitions to them in the form of re-usable storytelling templates. The re-usability is twofold. Firstly, due to their modular nature, metamorphers can be re-used in different combinations to create a wide range of animations. Secondly, due to their abstract nature, metamorphers can be re-used to recreate an intended animation for a wide range of compatible data sets. Metamorphers thereby mask the low-level complexity of explicit animation specifications by exploiting the inherent properties of the molecular data, such as the position, size, and hierarchy level of a semantic data subset. We demonstrate the re-usability of our technique based on the authoring and application of two animation use-cases to three molecular data sets. CCS CONCEPTS • Human-centered computing → Visualization techniques;
IEEE Transactions on Visualization and Computer Graphics
Fig. 1: A procedurally generated, real-time rendered model of a microtubule assembly inside a cel... more Fig. 1: A procedurally generated, real-time rendered model of a microtubule assembly inside a cell cytoplasm.
Figure 1: The workflow of our method for a model of HIV surrounded with blood plasma proteins. (a... more Figure 1: The workflow of our method for a model of HIV surrounded with blood plasma proteins. (a) The entire dataset is shown. The blood serum (shown in red) is occluding the virus. (b) Clipping objects are added to selectively clip molecules to reveal the HIV capsid. (c) The illustrator decides to show more of the matrix proteins (shown in blue), so their clipping is disabled. However, they are now occluding the view of the capsid. (d) The probabilistic clipping has been used to selectively remove those matrix proteins occluding the capsid, but some of them are left in the scene to indicate the presence of this type of protein on the virus membrane. The capsid has been clipped with view space clipping to reveal its internal structure.
We provide a high-level survey of multiscale molecular visualization techniques, with a focus on ... more 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.
Visualization Multi-Pipeline for Communicating Biology
IEEE Transactions on Visualization and Computer Graphics
We propose a system to facilitate biology communication by developing a pipeline to support the i... more We propose a system to facilitate biology communication by developing a pipeline to support the instructional visualization of heterogeneous biological data on heterogeneous user-devices. Discoveries and concepts in biology are typically summarized with illustrations assembled manually from the interpretation and application of heterogenous data. The creation of such illustrations is time consuming, which makes it incompatible with frequent updates to the measured data as new discoveries are made. Illustrations are typically non-interactive, and when an illustration is updated, it still has to reach the user. Our system is designed to overcome these three obstacles. It supports the integration of heterogeneous datasets, reflecting the knowledge that is gained from different data sources in biology. After pre-processing the datasets, the system transforms them into visual representations as inspired by scientific illustrations. As opposed to traditional scientific illustration these representations are generated in real-time - they are interactive. The code generating the visualizations can be embedded in various software environments. To demonstrate this, we implemented both a desktop application and a remote-rendering server in which the pipeline is embedded. The remote-rendering server supports multi-threaded rendering and it is able to handle multiple users simultaneously. This scalability to different hardware environments, including multi-GPU setups, makes our system useful for efficient public dissemination of biological discoveries.
Spring Conference on Computer Graphics - SCCG '13, 2013
Spatial selections are a ubiquitous concept in visualization. By localizing particular features, ... more Spatial selections are a ubiquitous concept in visualization. By localizing particular features, they can be analyzed and compared in different views. However, the semantics of such selections are often dependent on other parameter settings and it can be difficult to reconstruct them without additional information. In this paper, we present the concept of contextual snapshots as an effective means for managing spatial selections in visualized data. The selections are automatically associated with the context in which they have been created. Contextual snapshots can be also used as the basis for interactive integrated and linked views, which enable in-place investigation and comparison of multiple visual representations of data. Our approach is implemented as a flexible toolkit with welldefined interfaces for integration into existing systems. We demonstrate the power and generality of our techniques by applying them to several distinct scenarios such as the visualization of simulation data and the analysis of historical documents.
Spatial selections are a ubiquitous concept in visualization. By localizing particular features, ... more Spatial selections are a ubiquitous concept in visualization. By localizing particular features, they can be analysed and compared in different views. However, the semantics of such selections often depend on specific parameter settings and it can be difficult to reconstruct them without additional information. In this paper, we present the concept of contextual snapshots as an effective means for managing spatial selections in visualized data. The selections are automatically associated with the context in which they have been created. Contextual snapshots can also be used as the basis for interactive integrated and linked views, which enable in-place investigation and comparison of multiple visual representations of data. Our approach is implemented as a flexible toolkit with well-defined interfaces for integration into existing systems. We demonstrate the power and generality of our techniques by applying them to several distinct scenarios such as the visualization of simulation data, the analysis of historical documents and the display of anatomical data.
Cryo-Electron Tomography (cryo-ET) is a new 3D imaging technique with unprecedented potential for... more Cryo-Electron Tomography (cryo-ET) is a new 3D imaging technique with unprecedented potential for resolving submicron structural detail. Existing volume visualization methods, however, cannot cope with its very low signal-to-noise ratio. In order to design more powerful transfer functions, we propose to leverage soft segmentation as an explicit component of visualization for noisy volumes. Our technical realization is based on semi-supervised learning where we combine the advantages of two segmentation algorithms. A first weak segmentation algorithm provides good results for propagating sparse user provided labels to other voxels in the same volume. This weak segmentation algorithm is used to generate dense pseudo labels. A second powerful deep-learning based segmentation algorithm can learn from these pseudo labels to generalize the segmentation to other unseen volumes, a task that the weak segmentation algorithm fails at completely. The proposed volume visualization uses the deep-...
Volumetric visualization has many practical applications, particularly in medical imaging. Usabil... more Volumetric visualization has many practical applications, particularly in medical imaging. Usability of volumetric visualization algorithms depends on available means to select areas of interest in volumetric data that are to be visualized. A simple and sucient method is a onedimensional transfer function that assigns colours to intensity values of the data. A drawback of this method is that it produces visual artefacts in specic cases. In this paper we propose a volumetric visualization method that overcomes this drawback by using ltration with volumetric ray casting algorithm. Our method enables users to use simple transfer functions with signicant visual artefacts reduction.
We present a method for producing documentary-style content using real-time scientific visualizat... more We present a method for producing documentary-style content using real-time scientific visualization. We produce molecumentaries, i.e., molecular documentaries featuring structural models from molecular biology. We employ scalable methods instead of the rigid traditional production pipeline. Our method is motivated by the rapid evolution of interactive scientific visualization, which shows great 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, information about the model from heterogeneous sources is compiled into a story graph. Local...
Fibrous structures are ubiquitous in cell biology and play essential structural and functional ro... more Fibrous structures are ubiquitous in cell biology and play essential structural and functional roles in the life cycle of a cell. They are long polymers, such as DNA carrying genetic information, or filaments forming the cytoskeleton, crucial for cell division and maintaining the cell shape. In order to disseminate new findings of such structures to peers or a general audience, animated 3D models of these structures have to be created, as they are too small to be imaged with microscopes. However, this is a tedious task carried out by scientific animators, who manually create expressive visual representations of biological phenomena. In this work, we present a novel concept which simplifies the process of animating multi-scale procedural models of biological fibrous structures. In contrast with existing work in the domain of molecular visualization, our approach can also capture dynamics, which are important to show when communicating biological processes. CCS Concepts • Computing me...
A challenging problem in biology is the incompleteness of acquired information when visualizing b... more A challenging problem in biology is the incompleteness of acquired information when visualizing biological phenomena. Structural biology generates detailed models of viruses or bacteria at different development stages, while the processes that relate one stage to another are often not clear. Similarly, the entire life cycle of a biological entity might be available as a quantitative model, while only one structural model is available. If the relation between two models is specified at a lower level of detail than the actual models themselves, the two models cannot be interpolated correctly. We propose a method that deals with the visualization of incomplete data information in the developmental or evolutionary states of biological mesoscale models, such as viruses or microorganisms. The central tool in our approach is visual abstraction. Instead of directly interpolating between two models that show different states of an organism, we gradually forward transform the models into a le...
Visual clutter is a major problem in large biological data visualization. It is often addressed t... more Visual clutter is a major problem in large biological data visualization. It is often addressed through the means of level of detail schemes coupled with an appropriate coloring of the visualized structures. Ambient occlusion and shadows are often used to improve the depth perception. However, when used excessively, these techniques are sources of visual clutter themselves. In this paper we present a new approach to screen-space illumination algorithms suitable for use in illustrative visualization. The illumination effect can be controlled so that desired levels of semantic scene organization cast shadows while other remain flat. This way the illumination design can be parameterized to keep visual clutter, originating from illumination, to a minimum, while also guiding the user in a multiscale model exploration. We achieve this by selectively applying occlusion shading based on the inherent semantics of the visualized hierarchically-organized data. The technique is in principle gen...
In visualization systems it is often the case that the changes of the input parameters are not pr... more In visualization systems it is often the case that the changes of the input parameters are not proportional to the visual change of the generated output. In this paper, we propose a model for enabling data-sensitive navigation for user-interface elements. This model is applied to normalize the user input according to the visual change, and also to visually communicate this normalization. In this way, the exploration of heterogeneous data using common interaction elements can be performed in an efficient way. We apply our model to the field of medical visualization and present guided navigation tools for traversing vascular structures and for camera rotation around 3D volumes. The presented examples demonstrate that the model scales to user-interface elements where multiple parameters are set simultaneously.
IEEE Transactions on Visualization and Computer Graphics
We present a method for producing documentary-style content using real-time scientific visualizat... more 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.
Volumetric visualization of medical data is a specific task, as doctors and radiology technicians... more Volumetric visualization of medical data is a specific task, as doctors and radiology technicians are not well trained in the field of computer graphics; therefore, algorithms for visualization of medical data must be as intuitive as possible, so that visualization tools employing them would be helpful in medical environment. Visualization of volumetric data acquired by medical imaging could not be effectively used without defining a proper transfer function, which transforms measured intensities to colours and opacity values. Many visualization methods use complex means for designing transfer functions, which could lead to decreased usability of said methods. We propose a novel approach in volumetric visualization that uses only a simple one-dimensional transfer function for classifying different materials. The goal of our method is to visualize individual tissues from medical data, present them with minimal effort and enable users to observe areas of interest.
Visualization algorithms are parameterized to offer universality in terms of handling various dat... more Visualization algorithms are parameterized to offer universality in terms of handling various data types, showing different aspects of the visualized data, or producing results useful for domain experts from different fields. Hence, input parameters are an important aspect of the visualization process. Their exploration and management are tasks which enable the visualization reusability, portability, and interdisciplinary communication. With increasing availability of visualization systems, which are suitable for a great variety of tasks, their complexity increases as well. This usually involves many input parameters necessary for the meaningful visualization of data. Multiple input parameters form parameter spaces which are too large to be explored by brute-force. Knowing the properties of a parameter space is often beneficial for improving data visualization. Therefore, it is important for domain experts utilizing data visualization to have tools for automatic parameter specificat...
IEEE Transactions on Visualization and Computer Graphics
Fig. 1. The ultrastructure of a SARS-CoV-2 virion created using our modeling technique. The membr... more Fig. 1. The ultrastructure of a SARS-CoV-2 virion created using our modeling technique. The membrane shape and distribution of the spike proteins are determined from microscopy image data. The internal assembly is a result of an interactive 3D rule specification approach. Left: internal nucleoprotein complex. Middle: RNA condensed within the nucleoprotein. Right: Outer spike distribution.
Proceedings of the 33rd Spring Conference on Computer Graphics - SCCG '17, 2017
In molecular biology, illustrative animations are used to convey complex biological phenomena to ... more In molecular biology, illustrative animations are used to convey complex biological phenomena to broad audiences. However, such animations have to be manually authored in 3D modeling software, a time consuming task that has to be repeated from scratch for every new data set, and requires a high level of expertise in illustration, animation, and biology. We therefore propose metamorphers: a set of operations for defining animation states as well as the transitions to them in the form of re-usable storytelling templates. The re-usability is twofold. Firstly, due to their modular nature, metamorphers can be re-used in different combinations to create a wide range of animations. Secondly, due to their abstract nature, metamorphers can be re-used to recreate an intended animation for a wide range of compatible data sets. Metamorphers thereby mask the low-level complexity of explicit animation specifications by exploiting the inherent properties of the molecular data, such as the position, size, and hierarchy level of a semantic data subset. We demonstrate the re-usability of our technique based on the authoring and application of two animation use-cases to three molecular data sets. CCS CONCEPTS • Human-centered computing → Visualization techniques;
IEEE Transactions on Visualization and Computer Graphics
Fig. 1: A procedurally generated, real-time rendered model of a microtubule assembly inside a cel... more Fig. 1: A procedurally generated, real-time rendered model of a microtubule assembly inside a cell cytoplasm.
Figure 1: The workflow of our method for a model of HIV surrounded with blood plasma proteins. (a... more Figure 1: The workflow of our method for a model of HIV surrounded with blood plasma proteins. (a) The entire dataset is shown. The blood serum (shown in red) is occluding the virus. (b) Clipping objects are added to selectively clip molecules to reveal the HIV capsid. (c) The illustrator decides to show more of the matrix proteins (shown in blue), so their clipping is disabled. However, they are now occluding the view of the capsid. (d) The probabilistic clipping has been used to selectively remove those matrix proteins occluding the capsid, but some of them are left in the scene to indicate the presence of this type of protein on the virus membrane. The capsid has been clipped with view space clipping to reveal its internal structure.
We provide a high-level survey of multiscale molecular visualization techniques, with a focus on ... more 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.
Visualization Multi-Pipeline for Communicating Biology
IEEE Transactions on Visualization and Computer Graphics
We propose a system to facilitate biology communication by developing a pipeline to support the i... more We propose a system to facilitate biology communication by developing a pipeline to support the instructional visualization of heterogeneous biological data on heterogeneous user-devices. Discoveries and concepts in biology are typically summarized with illustrations assembled manually from the interpretation and application of heterogenous data. The creation of such illustrations is time consuming, which makes it incompatible with frequent updates to the measured data as new discoveries are made. Illustrations are typically non-interactive, and when an illustration is updated, it still has to reach the user. Our system is designed to overcome these three obstacles. It supports the integration of heterogeneous datasets, reflecting the knowledge that is gained from different data sources in biology. After pre-processing the datasets, the system transforms them into visual representations as inspired by scientific illustrations. As opposed to traditional scientific illustration these representations are generated in real-time - they are interactive. The code generating the visualizations can be embedded in various software environments. To demonstrate this, we implemented both a desktop application and a remote-rendering server in which the pipeline is embedded. The remote-rendering server supports multi-threaded rendering and it is able to handle multiple users simultaneously. This scalability to different hardware environments, including multi-GPU setups, makes our system useful for efficient public dissemination of biological discoveries.
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Papers by Peter Mindek