VCBM 16: Eurographics Workshop on Visual Computing for Biology and Medicine

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https://diglib.eg.org/handle/10.2312/2630861

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Monte-Carlo Ray-Tracing for Realistic Interactive Ultrasound Simulation
(The Eurographics Association, 2016) Mattausch, Oliver; Goksel, Orcun; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
Ray-based simulations have been shown to generate impressively realistic ultrasound images in interactive frame rates. Recent efforts used GPU-based surface ray-tracing to simulate complex ultrasound interactions such as multiple reflections and refractions. These methods are restricted to perfectly specular reflections (i.e., following only a single reflective/refractive ray), whereas real tissue exhibits roughness of varying degree at tissue interfaces, causing partly diffuse reflections and refractions. Such surface interactions are significantly more complex and can in general not be handled by such deterministic ray-tracing approaches. However, they can be efficiently computed by Monte-Carlo sampling techniques, where many ray paths are generated with respect to a probability distribution. In this paper we introduce Monte-Carlo ray-tracing for ultrasound. This enables the realistic simulation of ultrasound interactions such as soft shadows and fuzzy reflections. We discuss how to properly weight the contribution of each ray path in order to simulate the behavior of a beamformed ultrasound signal. Tracing many individual rays per transducer element is easily parallelizable on modern GPUs, as opposed to previous approaches based on recursive binary ray-tracing.
PATHONE: From one Thousand Patients to one Cell
(The Eurographics Association, 2016) Corvò, Alberto; Westenberg, Michel A.; Driel, Marc A. van; Wijk, Jarke J.van; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
Digital Pathology is a recent clinical environment in which Electronic Health Records (EHRs), biopsy data and whole-slideimages (WSI) come together to provide pathologists the necessary information for making a diagnosis. Integration of this heterogeneous data into a single application is still one of the challenges in the evolution of pathology to a digital practice. While pathologists can perform diagnoses routinely on digital slides only, this is not the case in clinical research. For such purposes, the link between clinicopathological information of patients and images is essential. For example, image analysis researchers who develop automated diagnostic (support) algorithms need to select a representative set of slides to evaluate their methods. To achieve this, they need applications that combine cohort specification, slide image exploration, and selection of suitable images. We present the visualization tool PATHONE, which enables users to perform these steps on a single screen, integrating cohort and WSI selection.
Aortic Dissection Maps: Comprehensive Visualization of Aortic Dissections for Risk Assessment
(The Eurographics Association, 2016) Mistelbauer, Gabriel; Schmidt, Johanna; Sailer, Anna-Margaretha; Bäumler, Kathrin; Walters, Shannon; Fleischmann, Dominik; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
Aortic dissection is a life threatening condition of the aorta, characterized by separation of its wall layers into a true and false lumen. A subset of patients require immediate surgical or endovascular repair. All survivors of the acute phase need long-term surveillance with imaging to monitor chronic degeneration and dilatation of the false lumen and prevent late adverse events such as rupture, or malperfusion. We introduce four novel plots displaying features of aortic dissections known or presumed to be associated with risk of future adverse events: Aortic diameter, the blood supply (outflow) to the aortic branches from the true and false lumen, the previous treatment, and an estimate of adverse event-free probabilities in one, two and 5 years. Aortic dissection maps, the composite visualization of these plots, provide a baseline for visual comparison of the complex features and associated risk of aortic dissection. These maps may lead to more individualized monitoring and improved, patient-centric treatment planning in the future.
Recent Advances in MRI and Ultrasound Perfusion Imaging
(The Eurographics Association, 2016) Jirík, Radovan; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
Perfusion imaging is an important diagnostic tool used mostly in oncology, neurology and cardiology, to assess the perfusion status of the tissue on a capillary level, e.g. assessment of angiogenesis, ischemic regions and inflammation. This contribution is a review of recent advances in dynamic contrast-enhanced magnetic-resonance and ultrasound imaging.
Visualization-Guided Evaluation of Simulated Minimally Invasive Cancer Treatment
(The Eurographics Association, 2016) Voglreiter, Philip; Hofmann, Michael; Ebner, Christoph; Sequeiros, Roberto Blanco; Portugaller, Horst Rupert; Fütterer, Jurgen; Moche, Michael; Steinberger, Markus; Schmalstieg, Dieter; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
We present a visualization application supporting interventional radiologists during analysis of simulated minimally invasive cancer treatment. The current clinical practice employs only rudimentary, manual measurement tools. Our system provides visual support throughout three evaluation stages, starting with determining prospective treatment success of the simulation parameterization. In case of insufficiencies, Stage 2 includes a simulation scalar field for determining a new configuration of the simulation. For complex cases, where Stage 2 does not lead to a decisive strategy, Stage 3 reinforces analysis of interdependencies of scalar fields via bivariate visualization. Our system is designed to be immediate applicable in medical practice. We analyze the design space of potentially useful visualization techniques and appraise their effectiveness in the context of our design goals. Furthermore, we present a user study, which reveals the disadvantages of manual analysis in the measurement stage of evaluation and highlight the demand for computer-support through our system.
Chameleon - Dynamic Color Mapping for Multi-Scale Structural Biology Models
(The Eurographics Association, 2016) Waldin, Nicholas; Muzic, Mathieu Le; Waldner, Manuela; Gröller, Eduard; Goodsell, David; Ludovic, Autin; Viola, Ivan; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
Visualization of structural biology data uses color to categorize or separate dense structures into particular semantic units. In multiscale models of viruses or bacteria, there are atoms on the finest level of detail, then amino-acids, secondary structures, macromolecules, up to the compartment level and, in all these levels, elements can be visually distinguished by color. However, currently only single scale coloring schemes are utilized that show information for one particular scale only. We present a novel technology which adaptively, based on the current scale level, adjusts the color scheme to depict or distinguish the currently best visible structural information. We treat the color as a visual resource that is distributed given a particular demand. The changes of the color scheme are seamlessly interpolated between the color scheme from the previous views into a given new one. With such dynamic multi-scale color mapping we ensure that the viewer is able to distinguish structural detail that is shown on any given scale. This technique has been tested by users with an expertise in structural biology and has been overall well received.
Illustrative Transitions in Molecular Visualization via Forward and Inverse Abstraction Transform
(The Eurographics Association, 2016) Sorger, Johannes; Mindek, Peter; Klein, Tobias; Johnson, Graham; Viola, Ivan; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
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 level of visual abstraction that matches the level of detail of the modeled relation between them. At this level, the models can be interpolated without conveying false information. After the interpolation to the new state, we apply the inverse transformation to the model’'s original level of abstraction. To show the flexibility of our approach, we demonstrate our method on the basis of molecular data, in particular data of the HIV virion and the mycoplasma bacterium.
Semi-Immersive 3D Sketching of Vascular Structures for Medical Education
(The Eurographics Association, 2016) Saalfeld, Patrick; Stojnic, Aleksandar; Preim, Bernhard; Oeltze-Jafra, Steffen; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
We present a semi-immersive 3D User Interface to sketch complex vascular structures and vessel pathologies by drawing centerlines in 3D. Our framework comprises on-the-fly reconstruction of the corresponding vessel surface and subsequent local surface compression and expansion. Additionally, we allow the enrichment with an illustrative, plausible blood flow visualization. Our framework is designed for medical educators and students to support anatomy and pathology education. Anatomy educators can realize the step-by-step process of creating and explaining complex spatial relationships of interlinked vascular structures and blood flow behavior. Students can view this process and explore the created structures, which helps them in reproducing and memorizing them. To create a surface model based on the sketched centerlines, we employ implicit surfaces. This allows for easy adding, editing, and removing vessel branches and achieve continuous surfaces with smooth transitions at branchings. The blood flow can be interactively added and is realized with a topology-aware particle simulation. We qualitatively evaluated our framework and demonstrate the applicability and usability of our approach.
Visual Analytics for the Exploration and Assessment of Segmentation Errors
(The Eurographics Association, 2016) Raidou, Renata G.; Marcelis, Freek J. J.; Breeuwer, Marcel; Gröller, Eduard; Vilanova, Anna; Wetering, Huub M. M. van de; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
Several diagnostic and treatment procedures require the segmentation of anatomical structures from medical images. However, the automatic model-based methods that are often employed, may produce inaccurate segmentations. These, if used as input for diagnosis or treatment, can have detrimental effects for the patients. Currently, an analysis to predict which anatomic regions are more prone to inaccuracies, and to determine how to improve segmentation algorithms, cannot be performed. We propose a visual tool to enable experts, working on model-based segmentation algorithms, to explore and analyze the outcomes and errors of their methods. Our approach supports the exploration of errors in a cohort of pelvic organ segmentations, where the performance of an algorithm can be assessed. Also, it enables the detailed exploration and assessment of segmentation errors, in individual subjects. To the best of our knowledge, there is no other tool with comparable functionality. A usage scenario is employed to explore and illustrate the capabilities of our visual tool. To further assess the value of the proposed tool, we performed an evaluation with five segmentation experts. The evaluation participants confirmed the potential of the tool in providing new insight into their data and employed algorithms. They also gave feedback for future improvements.
Semi-Automatic Vessel Boundary Detection in Cardiac 4D PC-MRI Data Using FTLE fields
(The Eurographics Association, 2016) Behrendt, Benjamin; Köhler, Benjamin; Gräfe, Daniel; Grothoff, Matthias; Gutberlet, Matthias; Preim, Bernhard; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
Four-dimensional phase-contrast magnetic resonance imaging (4D PC-MRI) is a method to non-invasively acquire in-vivo blood flow, e.g. in the aorta. It produces three-dimensional, time-resolved datasets containing both flow speed and direction for each voxel. In order to perform qualitative and quantitative data analysis on these datasets, a vessel segmentation is often required. These segmentations are mostly performed manually or semi-automatically, based on three-dimensional intensity images containing the maximal flow speed over all time steps. To allow for a faster segmentation, we propose a method that, in addition to intensity, incorporates the flow trajectories into the segmentation process. This is accomplished by extracting Lagrangian Coherent Structures (LCS) from the flow data, which indicate physical boundaries in a dynamical system. To approximate LCS in our discrete images, we employ Finite Time Lyapunov Exponent (FTLE) fields to quantify the rate of separation of neighboring flow trajectories. LCS appear as ridges or valleys in FTLE images, indicating the presence of either a flow structure boundary or physical boundary. We will show that the process of segmenting low-contrast 4D PC-MRI datasets can be simplified by using the generated FLTE data in combination with intensity images.
Unfolding and Interactive Exploration of Protein Tunnels and their Dynamics
(The Eurographics Association, 2016) Kolesár, Ivan; Byska, Jan; Parulek, Julius; Hauser, Helwig; Kozlíková, Barbora; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
The presence of tunnels in protein structures substantially influences their reactivity with other molecules. Therefore, studying their properties and changes over time has been in the scope of biochemists for decades. In this paper we introduce a novel approach for the comparative visualization and exploration of ensembles of tunnels. Our goal is to overcome occlusion problems with traditional tunnel representations while providing users a quick way to navigate through the input dataset and to identify potentially interesting tunnels. First, we unfold the input tunnels to a 2D representation enabling to observe the mutual position of amino acids forming the tunnel surface and the amount of surface they influence. These 2D images are subsequently described by image moments commonly used in image processing. This way we are able to detect similarities and outliers in the dataset, which are visualized as clusters in a scatterplot graph. The same coloring scheme is used in the linked bar chart enabling to detect the position of the cluster members over time. These views provide a way to select a subset of potentially interesting tunnels that can be further explored in detail using the 2D unfolded view and also traditional 3D representation. The usability of our approach is demonstrated by case studies conducted by domain experts.
Illustrative PET/CT Visualisation of SIRT-Treated Lung Metastases
(The Eurographics Association, 2016) Merten, Nico; Glaßer, Sylvia; Lassen-Schmidt, Bianca; Großer, Oliver Stephan; Ricke, Jens; Amthauer, Holger; Preim, Bernhard; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
We present an illustrative rendering pipeline which combines anatomical information from CT scans with functional information from PET scans. To treat lung metastases with Selective Internal Radiation Therapies (SIRTs), combined PET/CT recordings are used for treatment planning and intervention validation. We firstly extract surface meshes from the lung lobes and trachea from the CT scan. In addition, the radiation activity of the therapeutic agent 90Y is acquired from the PET data. To convey all this information in one view, we use illustrative rendering techniques, combining Order-Independent Transparencies with Boundary Enhancements and Silhouettes. Our methods are evaluated by clinical and visualisation domain experts. This study indicates an excellent spatial perception and evaluation of tumor position, metabolic and therapeutic agent activity, when transparencies and boundary enhancements are used to render the surrounding lung lobes.
Visual Analysis and Comparison of Multiple Sequence Alignments
(The Eurographics Association, 2016) Hess, Martin; Jente, Daniel; Wiemeyer, Josef; Hamacher, Kay; Goesele, Michael; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
Multiple Sequence Alignments (MSA) of a set of DNA, RNA or protein sequences form the fundamental basis for various biological applications such as evolutionary heritage and protein structure prediction. The quality of an MSA is crucial in order to provide useful and correct results. The analysis of MSAs is, however, still a challenging task since constructing MSAs is an NP hard problem and thus the optimal MSA is usually unknown. Additionally, MSA quality analysis is often completely ignored, especially by non-expert users, due to the lack of tools for the visual comparison and the intuitive quality assessment of alignments. In this paper, we present an interactive visual approach to simultaneously assess the quality of multiple alternative MSAs of the same set of sequences. We provide a direct assessment of the alignment quality using different highlighting techniques in combination with automatic quality measures and editing capabilities. An in-depth evaluation of our approach highlights its benefits for MSA quality assessment.
A Feasibility Study on Automated Protein Aggregate Characterization Utilizing a Hybrid Classification Model
(The Eurographics Association, 2016) Eschweiler, Dennis; Gadermayr, Michael; Unger, Jakob; Nippold, Markus; Falkenburger, Björn; Merhof, Dorit; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
The characterization of cytoplasmic protein aggregates based on time-lapse fluorescence microscopy imaging data is important for research in neuro-degenerative diseases such as Parkinson. As the manual assessment is time-consuming and subject to significant variability, incentive for the development of an objective automated system is provided. We propose and evaluate a pipeline consisting of cell-segmentation, tracking and classification of neurological cells. Focus is specifically on the novel and challenging classification task which is covered by relying on feature extraction followed by a hybrid classification approach incorporating a support vector machine focusing on mainly stationary information and a hidden Markov model to incorporate temporal context. Several image representations are experimentally evaluated to identify cell properties that are important for discrimination. Relying on the proposed approach, classification accuracies up to 80 % are reached. By extensively analyzing the outcomes, we discuss about strengths and weaknesses of our method as a quantitative assessment tool.
Volume Visualization Using Principal Component Analysis
(The Eurographics Association, 2016) Alakkari, Salaheddin; Dingliana, John; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
In this paper, we investigate the use of Principal Component Analysis (PCA) for image-based volume visualization. Firstly we compute a high-dimensional eigenspace using training images, pre-rendered using a standard ray-caster, from a spherically distributed range of camera positions. Then, our system is able to synthesize arbitrary views of the dataset with minimal computation at runtime. We propose a perceptually-adaptive technique to minimize data size and computational complexity whilst preserving perceptual quality of the visualization, in comparison to corresponding ray-cast images. Results indicate that PCA is able to sufficiently learn the full view-independent volumetric model through a finite number of training images and generalize the computed eigenspace to produce high quality images from arbitrary viewpoints, on demand. The approach has potential application in client-server volume visualization or where results of a computationally-complex 3D imaging process need to be interactively visualized on a display device of limited specification.
VCBM 2016: Frontmatter
(Eurographics Association, 2016) Stefan Bruckner; Bernhard Preim; Anna Vilanova; Helwig Hauser; Anja Hennemuth; Arvid Lundervold; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
A Framework for Fast Initial Exploration of PC-MRI Cardiac Flow
(The Eurographics Association, 2016) Broos, Arjan J. M.; Hoon, Niels H. L. C. de; Koning, Patrick J. H. de; Geest, Rob J. van der; Vilanova, Anna; Jalba, Andrei C.; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
Cardiac flow is still not fully understood, and is currently an active research topic. Using phase-contrast magnetic resonance imaging (PC-MRI) blood flow can be measured. For the inspection of such flow, researchers often rely on methods that require additional scans produced by different imaging modalities to provide context. This requires labor-intensive registration and often manual segmentation before any exploration of the data is performed. This work provides a framework that allows for a quick exploration of cardiac flow without the need of additional imaging and time-consuming segmentation. To achieve this, only the 4D data from one PC-MRI scan is used. A context visualization is derived automatically from the data, and provides context for the flow. Instead of relying on segmentation to deliver an accurate context, the heart's ventricles are approximated by half-ellipsoids that can be placed with minimal user interaction. Furthermore, seeding positions for flow visualization can be placed automatically in areas of interest defined by the user and based on derived flow features. The framework enables a user to do a fast initial exploration of cardiac flow, as is demonstrated by a use case and a user study involving cardiac blood flow researchers.
Real-Time Guidance and Anatomical Information by Image Projection onto Patients
(The Eurographics Association, 2016) Edwards, Marc R.; Pop, Serban R.; John, Nigel W.; Ritsos, Panagiotis D.; Avis, Nick; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
The Image Projection onto Patients (IPoP) system is work in progress intended to assist medical practitioners perform procedures such as biopsies, or provide a novel anatomical education tool, by projecting anatomy and other relevant information from the operating room directly onto a patient's skin. This approach is not currently used widely in hospitals but has the benefit of providing effective procedure guidance without the practitioner having to look away from the patient. Developmental work towards the alpha-phase of IPoP is presented including tracking methods for tools such as biopsy needles, patient tracking, image registration and problems encountered with the multi-mirror effect.
Graxels: Information Rich Primitives for the Visualization of Time-Dependent Spatial Data
(The Eurographics Association, 2016) Stoppel, Sergej; Hodneland, Erlend; Hauser, Helwig; Bruckner, Stefan; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
Time-dependent volumetric data has important applications in areas as diverse as medicine, climatology, and engineering. However, the simultaneous quantitative assessment of spatial and temporal features is very challenging. Common visualization techniques show either the whole volume in one time step (for example using direct volume rendering) or let the user select a region of interest (ROI) for which a collection of time-intensity curves is shown. In this paper, we propose a novel approach that dynamically embeds quantitative detail views in a spatial layout. Inspired by the concept of small multiples, we introduce a new primitive graxel (graph pixel). Graxels are view dependent primitives of time-intensity graphs, generated on-the-fly by aggregating per-ray information over time and image regions. Our method enables the detailed feature-aligned visual analysis of time-dependent volume data and allows interactive refinement and filtering. Temporal behaviors like frequency relations, aperiodic or periodic oscillations and their spatial context are easily perceived with our method. We demonstrate the power of our approach using examples from medicine and the natural sciences.
How to Evaluate Medical Visualizations on the Example of 3D Aneurysm Surfaces
(The Eurographics Association, 2016) Glaßer, Sylvia; Saalfeld, Patrick; Berg, Philipp; Merten, Nico; Preim, Bernhard; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
For the evaluation of medical visualizations, a ground truth is often missing. Therefore, the evaluation of medical visualizations is often restricted to qualitative comparisons w.r.t user preferences but neglects more objective measures such as accuracies or task completion times. In this work, we provide a pipeline with statistical tests for the evaluation of the user performance within an experimental setup. We demonstrate the adaption of the pipeline for the specific example of cerebral aneurysm surface visualization. Therefore, we developed three visualization techniques to compare the aneurysm volumes. Then, we present a single-factor, within-subject user study, which allows for the evaluation of these visualization techniques as well as the identification of the most suitable one. The evaluation includes a qualitative as well as a comprehensive quantitative analysis to determine statistically significant differences. As a result, a color-coded map surface view is identified as best suited to depict the aneurysm volume changes. The presentation of the different stages of the evaluation pipeline allows for an easy adaption to other application areas of medical visualization. As a result, we provide orientation to enrich qualitative evaluations by the presented quantitative analyses.

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