
Michael KroneUniversity of Tübingen | EKU Tübingen · Department of Computer Science
Michael Krone
Dr. rer. nat.
About
99
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25,465
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Introduction
The main focus of my work is on visualizations for the life sciences, especially molecular graphics, visual analysis of molecular dynamics simulations, and visualization of multi-dimensional biomedical data. My research interests include real-time rendering for (scientific) visualization, visual analytics, immersive visualization, and GPU computing (especially using CUDA).
Additional affiliations
Education
October 2002 - December 2008
Publications
Publications (99)
Visualizing small‐world networks such as protein‐protein interaction networks or social networks often leads to visual clutter and limited interpretability. To overcome these problems, we present ProtEGOnist, a visualization approach designed to explore small‐world networks. ProtEGOnist visualizes networks using ego‐graphs that represent local neig...
Molecular docking is a key technique in various fields like structural biology, medicinal chemistry, and biotechnology. It is widely used for virtual screening during drug discovery, computer-assisted drug design, and protein engineering. A general molecular docking process consists of the protein and ligand selection, their preparation, and the do...
The concept of augmented reality (AR) assistants has captured the human imagination for decades, becoming a staple of modern science fiction. To pursue this goal, it is necessary to develop artificial intelligence (AI)-based methods that simultaneously perceive the 3D environment, reason about physical tasks, and model the performer, all in real-ti...
Relational information between different types of entities is often modelled by a multilayer network (MLN) – a network with subnetworks represented by layers. The layers of an MLN can be arranged in different ways in a visual representation, however, the impact of the arrangement on the readability of the network is an open question. Therefore, we...
Line attributes such as width and dashing are commonly used to encode information. However, many questions on the perception of line attributes remain, such as how many levels of attribute variation can be distinguished or which line attributes are the preferred choices for which tasks. We conducted three studies to develop guidelines for using sty...
The concept of augmented reality (AR) assistants has captured the human imagination for decades, becoming a staple of modern science fiction. To pursue this goal, it is necessary to develop artificial intelligence (AI)-based methods that simultaneously perceive the 3D environment, reason about physical tasks, and model the performer, all in real-ti...
Line attributes such as width and dashing are commonly used to encode information. However, many questions on the perception of line attributes remain, such as how many levels of attribute variation can be distinguished or which line attributes are the preferred choices for which tasks. We conducted three studies to develop guidelines for using sty...
Relational information between different types of entities is often modelled by a multilayer network (MLN) -- a network with subnetworks represented by layers. The layers of an MLN can be arranged in different ways in a visual representation, however, the impact of the arrangement on the readability of the network is an open question. Therefore, we...
We present an approach for the visual analysis of multi‐omics data obtained using high‐throughput methods. The term “omics” denotes measurements of different types of biologically relevant molecules like the products of gene transcription (transcriptomics) or the abundance of proteins (proteomics). Current popular visualization approaches often onl...
In recent years, the use of expressive surface visualizations in the representation of vascular structures has gained significant attention. These visualizations provide a comprehensive understanding of complex anatomical structures and are crucial for treatment planning and medical education. However, to aid decision-making, physicians require vis...
Visualization plays a crucial role in molecular and structural biology. It has been successfully applied to a variety of tasks, including structural analysis and interactive drug design. While some of the challenges in this area can be overcome with more advanced visualization and interaction techniques, others are challenging primarily due to the...
Motivation
The increasing amount of data produced by omics technologies has enabled researchers to study phenomena across multiple omics layers. Besides data-driven analysis strategies, interactive visualization tools have been developed for a more transparent analysis. However, most state-of-the-art tools do not reconstruct the impact of a single...
Data are often subject to some degree of uncertainty, whether aleatory or epistemic. This applies both to experimental data acquired with sensors as well as to simulation data. Displaying these data and their uncertainty faithfully is crucial for gaining knowledge. Specifically, the effective communication of the uncertainty can influence the inter...
Flux Sampling (FS) is an unbiased constraint-based modeling method in systems biology that characterizes the admissible metabolic flux space of cells and organisms at a molecular level. It returns information about reaction flux ranges and their probability from a genome-scale metabolic model (GEM), which can be used to predict metabolic phenotypes...
We present an approach for visual analysis of high‐dimensional measurement data with varying sampling rates as routinely recorded in intensive care units. In intensive care, most assessments not only depend on one single measurement but a plethora of mixed measurements over time. Even for trained experts, efficient and accurate analysis of such mul...
BACKGROUND
The visual analysis and delivery of data in the form of visualizations is of great importance in healthcare, as such forms of presentation can reduce errors and improve care, and can also help provide new insights into long-term disease progression. Information visualization and visual analytics also address the complexity of long-term,...
Background
Visual analysis and data delivery in the form of visualizations are of great importance in health care, as such forms of presentation can reduce errors and improve care and can also help provide new insights into long-term disease progression. Information visualization and visual analytics also address the complexity of long-term, time-o...
When studying protein‐ligand interactions, many different factors can influence the behaviour of the protein as well as the ligands. Molecular visualisation tools typically concentrate on the movement of single ligand molecules; however, viewing only one molecule can merely provide a hint of the overall behaviour of the system. To tackle this issue...
Many biochemical and biomedical applications such as protein engineering or drug design are concerned with finding functionally similar proteins, however, this remains to be a challenging task. We present a new imaged-based approach for identifying and visually comparing proteins with similar function that builds on the hierarchical clustering of M...
Motivation
The increasing amount of data produced by omics technologies has significantly improved the understanding of how biological information is transferred across different omics layers and to which extent it is involved in the manifestation of a given phenotype. Besides data-driven analysis strategies, interactive visualization tools have be...
This work focuses on particle-based ΛCDM (cold dark matter) simulations. The features of interest are clusters of dark matter particles, called halos. Halos are governed by the laws of motion and gravitation, and they may, consequently, merge over time. In this paper, we present visualization methods for the topology of the resulting tree-like accu...
Proteins perform a large variety of functions in living organisms, thus playing a key role in biology. As of now, available learning algorithms to process protein data do not consider several particularities of such data and/or do not scale well for large protein conformations. To fill this gap, we propose two new learning operations enabling deep...
Visualization has evolved into a mature scientific field and it has also become widely accepted as a standard approach in diverse fields, including physics, life sciences, and business intelligence. However, despite its successful development, there are still many open research questions that require customized implementations in order to explore a...
Visualization of molecular structures is one of the most common tasks carried out by structural biologists, typically using software, such as Chimera, COOT, PyMOL, or VMD. In this Perspective article, we outline how past developments in computer graphics and data visualization have expanded the understanding of biomolecular function, and we summari...
We present MegaMol, a low-overhead prototyping framework for interactive visualization of large scientific data sets. We give a brief summary of related work for context and then focus on a comprehensive overview of the core architecture of the framework. This is followed by the existing and novel features and techniques in MegaMol that define its...
In this paper, we review the advances in molecular visualization over the last 12 years and put the development of the community in context with our own efforts in the DFG Collaborative Research Center (CRC) 716. This includes advances in the field of molecular surface computation and rendering, interactive extraction of protein cavities, and compa...
WebGL 2.0 makes it possible to implement efficient volume rendering that runs in browsers using 3D textures and complex fragment shaders. However, a typical bottleneck for web-based volume rendering is the size of the volumetric data sets. Transferring these data to the client for rendering can take a substantial amount of time, depending on the ne...
Realistic simulations of detailed, biophysics-based, multi-scale models often require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are typically designed to allow for high flexibility and generality in model development. Flexibility and model development, h...
Bioinformatics-related research produces huge heterogeneous amounts of data. This wealth of information includes data describing metabolic mechanisms and pathways, proteomics, transcriptomics, and metabolomics. Often, the visualization and exploration of related structural - usually molecular - data plays an important role in the aforementioned con...
Immersive technologies like stereo rendering, virtual reality, or augmented reality (AR) are often used in the field of molecular visualisation. Modern, comparably lightweight and affordable AR headsets like Microsoft’s HoloLens open up new possibilities for immersive analytics in molecular visualisation. A crucial factor for a comprehensive analys...
In simulations of salt dissolving in water, viscous fingers emerge. Comparing a number of simulation runs with different parameters allows domain scientists to gain insight into this dissolution process. Researchers have developed a tool that allows interactive visual analysis of ensembles of such simulations at different levels of detail in an ada...
Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow for a high flexibility and generality in model development. Flexibility and model development, however, are of...
This article discusses our experience in creating MegaMol, an open-source visualization framework for large particle-based data.
Two-dimensional height fields are the most common data structure used for storing and rendering of terrain in offline rendering and especially real-time computer graphics. By its very nature, a height field cannot store terrain structures with multiple vertical layers such as overhanging cliffs, caves, or arches. This restriction does not apply to...
Smoothed particle hydrodynamics (SPH) is a popular mesh-free, particle-based fluid simulation approach for a wide range of applications. There are several numerical variants of SPH along with a variety of models for aspects such as boundary conditions, compressibility or incompressibility, and surface tension. Different combinations of these models...
Visualizations for computational biology have been developing for over 50 years. With recent advances in both computational biology and computer graphics techniques, these fields have witnessed rapid technological advances in the last decade. Thus, coping with the large number of scientific articles from both fields is a challenging task. Furthermo...
The solvent-excluded surface (SES) is a popular molecular representation that gives the boundary of the molecular volume with respect to a specific solvent. SESs depict which areas of a molecule are accessible by a specific solvent, which is represented as a spherical probe. Despite the popularity of SESs, their generation is still a compute-intens...
Two-dimensional heightfields are the most common data structure used for storing and rendering of terrain in offline rendering and especially real-time computer graphics. By its very nature, a heightfield cannot store terrain structures with multiple vertical layers such as overhanging cliffs, caves, or arches. This restriction does not apply to vo...
Chapter 3 presented several options for the different calculations required for particle-based ray casting. These include different approaches of glyph silhouette approximation and support geometry generation. Basically, all the different approaches shift workload between different stages of the graphics pipeline, i.e., between geometry upload on t...
In the previous chapters, direct depictions of particle data sets were discussed. In this chapter, some examples for application-driven abstractions are given and discussed. The general idea is to create visualizations that show a special feature or property of the data. This can make the analysis of the data much easier. Often, the abstract visual...
Be scenarios and requirements sketched out in the introduction have been a widespread application case in visualization for at least 30 years now [Max, 1983]. As such, the widely accepted solutions presented in this lecture shall be briefly put into historical context. Very well- known and early examples for particle visualization were all applied...
This lecture has shown practical approaches for the rendering of particle data. The introduction described application areas and data and gave a brief historical overview of evolving hardware and the corresponding improvements in technique. First, the basic hybrid image/object-order GPU-based glyph ray casting was detailed, also showing approaches...
Applying the techniques presented earlier in Chapters 3 and 4, we can assume that rendering speed issues are resolved. We can visualize data as fast as possible, i.e., we can interactively view data sets with billions of particles on a single desktop machine. However, when viewing such large data sets problems with the visual quality occur, which a...
Finding the neighboring particles of a particle is a common problem for many computational tasks. Mostly, a fixed- radius nearest neighbor search is required. That is, all neighboring particles that are within a certain distance have to be found (see Figure 6.1). A common application is the detection of interacting particles. This is not only neces...
The acceleration strategies described in Chapter 4 enable us to render several hundreds of thousands of particles at interactive rates. However, these techniques are only profitable for dense data featuring inherent occlusion and, thus, potential for culling. When dealing with even more particles or sparse data, we need to resort to explicit data s...
Point-based visualization seems like a natural choice for particle-based data sets. In fact, this approach is an optimal representation of the data, as it is true to the original simulation results. The basic idea is that each element in the data set, in the case of data sets from MD simulations atoms or rigid molecules, is depicted by a compact gr...
Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of thre...
In this report, we review the current state of the art of web-based visualization applications. Recently, an increasing number of web-based visualization applications have emerged. This is due to the fact that new technologies offered by modern browsers greatly increased the capabilities for visualizations on the web. We first review these technica...
In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we pre...
Visualization of dynamic data from molecular dynamics simulations is crucial for understanding the functioning of molecules. Many existing visualization tools have mainly focused on supporting a single user working on a desktop computer. Technical advancements in browser features increase the potential for the development of web-based collaborative...
We present Molecular Surface Maps, a novel, view-independent, and concise representation for molecular surfaces. It transfers the well-known world map metaphor to molecular visualization. Our application maps the complex molecular surface to a simple 2D representation through a spherical intermediate, the Molecular Surface Globe. The Molecular Surf...
Scientific data is typically analyzed using visualizations. Large high-resolution displays can facilitate the analysis process since they offer more screen real estate than desktop monitors, which allows visualizing more data in greater detail and working collaboratively. On the other hand, mobile devices like smartphones and tablets are getting mo...
In many disciplines, such as computer aided drug design, multiple simulation runs are performed with varying parameters, yielding ensembles of data sets. Comparative visualisation of these simulation results can help understanding the influence of different parameters. However, researchers might need to compare large numbers of variants. Single des...
Visualization of dynamic data from molecular dynamics simulations is crucial for understanding the functioning of molecules. Many existing visualization tools have mainly focused on supporting a single user working on a desktop computer. Technical advancements in browser features increase the potential for the development of web-based collaborative...
Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of thre...
Scientific visualization is an application area for virtual reality environments like stereoscopic displays or CAVEs. Especially interactive molecular visualizations that show the complex threedimensional structures found in structural biology are often investigated using such environments. In contrast to VR applications like simulators, molecular...
Visualization applications nowadays not only face increasingly larger datasets, but have to solve increasingly complex research questions. They often require more than a single algorithm and consequently a software solution will exceed the possibilities of simple research prototypes. Well-established systems intended for such complex visual analysi...
We reflect on the reproducibility of our work presented at EuroVis 2014 [SKR * 14], which applies deformable models to compare molecular surfaces. We discuss both negative and positive aspects of our work in terms of reproducibility and put the aspects in a wider, more general context, in particular for the more critical points. Categories and Subj...
Intrinsically disordered regions (IDRs) in proteins are still not well understood, but are increasingly recognised as important in key biological functions, as well as in diseases. IDRs often confound experimental structure determination --- however, they are present in many of the available 3D structures, where they exhibit a wide range of conform...
The potential of web browsers as a platform for remote visualization has long been recognized. One of the motivations behind remote visualization has mainly been large data that cannot be easily transferred to the client. Further impeding factors for local visualization at the client side included lack of compute power or capabilities as well as la...
We present a novel line drawing algorithm that illustrates surfaces in real-time to convey their shape. We use line integral convolution (LIC) and employ ambient occlusion for illustrative surface rendering. Furthermore, our method depicts salient regions based on the illumination gradient. Our method works on animated surfaces in a frame-coherent...
The comparison of molecular surface attributes is of interest for computer aided drug design and the analysis of biochemical simulations. Due to the non-rigid nature of molecular surfaces, partial shape matching is feasible for mapping two surfaces onto each other. We present a novel technique to obtain a mapping relation between two surfaces using...