VCBM 15: Eurographics Workshop on Visual Computing for Biology and Medicine

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https://diglib.eg.org/handle/10.2312/13225

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Automated Slice-Based Artery Identification in Various Field-of-View CTA Scans
(The Eurographics Association, 2015) Major, David; Novikov, Alexey A.; Wimmer, Maria; Hladuvka, Jiri; Bühler, Katja; Katja Bühler and Lars Linsen and Nigel W. John
Automated identification of main arteries in Computed Tomography Angiography (CTA) scans plays a key role in the initialization of vessel tracking algorithms. Automated vessel tracking tools support physicians in vessel analysis and make their workflow time-efficient. We present a fully-automated framework for identification of five main arteries of three different body regions in various field-of-view CTA scans. Our method detects the two common iliac arteries, the aorta and the two common carotid arteries and delivers seed positions in them. After the field-of-view of a CTA scan is identified, artery candidate positions are regressed slice-wise and the best candidates are selected by Naive Bayes classification. Final artery seed positions are detected by picking the most optimal path over the artery classification results from slice to slice. Our method was evaluated on 20 CTA scans with various field-of-views. The high detection performance on different arteries shows its generality and future applicability for automated vessel analysis systems.
Automatic Real-time Annotation of Important Landmarks in Ultrasound-Guided Femoral Nerve Blocks
(The Eurographics Association, 2015) Lindseth, Frank; Leidig, Linda; Smistad, Erik; Katja Bühler and Lars Linsen and Nigel W. John
The main focus of the preliminary work presented here is the automatic real-time annotation (detection and tracking) of the important structures seen in an ultrasound image taken from a femoral nerve block, i.e. the femoral artery, the facias (lata and illiaca) and the femoral nerve.
cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets
(The Eurographics Association, 2015) Muzic, Mathieu Le; Autin, Ludovic; Parulek, Julius; Viola, Ivan; Katja Bühler and Lars Linsen and Nigel W. John
In this article we introduce cellVIEW, a new system to interactively visualize large biomolecular datasets on the atomic level. Our tool is unique and has been specifically designed to match the ambitions of our domain experts to model and interactively visualize structures comprised of several billions atom. The cellVIEW system integrates acceleration techniques to allow for real-time graphics performance of 60 Hz display rate on datasets representing large viruses and bacterial organisms. Inspired by the work of scientific illustrators, we propose a level-of-detail scheme which purpose is two-fold: accelerating the rendering and reducing visual clutter. The main part of our datasets is made out of macromolecules, but it also comprises nucleic acids strands which are stored as sets of control points. For that specific case, we extend our rendering method to support the dynamic generation of DNA strands directly on the GPU. It is noteworthy that our tool has been directly implemented inside a game engine. We chose to rely on a third party engine to reduce software development work-load and to make bleeding-edge graphics techniques more accessible to the end-users. To our knowledge cellVIEW is the only suitable solution for interactive visualization of large bimolecular landscapes on the atomic level and is freely available to use and extend.
Challenges and Technologies for Low Cost Wheelchair Simulation
(The Eurographics Association, 2015) Headleand, Christopher J.; Day, Thomas; Pop, Serban R.; Ritsos, Panagiotis D.; John, Nigel W.; Katja Bühler and Lars Linsen and Nigel W. John
The use of electric wheelchairs is inherently risky, as collisions due to lack of control can result in injury for the user, but also potentially for other pedestrians. Introducing new users to powered chairs via virtual reality (VR) provides one possible solution, as it eliminates the risks inherent to the real world during training. However, traditionally simulator technology has been too expensive to make VR a financially viable solution. Also, current simulators lack the natural interaction possible in the real world, limiting their operational value. We present the early stages of a VR, electric wheelchair simulator built using low-cost, consumer level gaming hardware. The simulator makes use use of the the Leap Motion, to provide a level of interaction with the virtual world which has not previously been demonstrated in wheelchair training simulators. Furthermore, the Occulous Rift provides an immersive experience suitable for our training application.
CoWRadar: Visual Quantification of the Circle of Willis in Stroke Patients
(The Eurographics Association, 2015) Miao, Haichao; Mistelbauer, Gabriel; Našel, Christian; Gröller, M. Eduard; Katja Bühler and Lars Linsen and Nigel W. John
This paper presents a method for the visual quantification of cerebral arteries, known as the Circle of Willis (CoW). The CoW is an arterial structure that is responsible for the brain's blood supply. Dysfunctions of this arterial circle can lead to strokes. The diagnosis relies on the radiologist's expertise and the software tools used. These tools consist of very basic display methods of the volumetric data without support of advanced technologies in medical image processing and visualization. The goal of this paper is to create an automated method for the standardized description of cerebral arteries in stroke patients in order to provide an overview of the CoW's configuration. This novel display provides visual indications of problematic areas as well as straightforward comparisons between multiple patients. Additionally, we offer a pipeline for extracting the CoW from Time-of-Flight Magnetic Resonance Angiography (TOF-MRA) data sets. An enumeration technique for the labeling of the arterial segments is therefore suggested. We also propose a method for detecting the CoW's main supplying arteries by analyzing the coronal, sagittal and transverse image planes of the data sets. We evaluated the feasibility of our visual quantification approach in a study of 63 TOF-MRA data sets and compared our findings to those of three radiologists. The obtained results demonstrate that our proposed techniques are effective in detecting the arteries of the CoW.
Discovering Medical Knowledge Using Visual Analytics
(The Eurographics Association, 2015) Sturm, Werner; Schreck, Tobias; Holzinger, Andreas; Ullrich, Torsten; Katja Bühler and Lars Linsen and Nigel W. John
Due to advanced technologies, the amount of biomedical data has been increasing drastically. Such large data sets might be obtained from hospitals, medical practices or laboratories and can be used to discover unknown knowledge and to find and reflect hypotheses. Based on this fact, knowledge discovery systems can support experts to make further decisions, explore the data or to predict future events. To analyze and communicate such a vast amount of information to the user, advanced techniques such as knowledge discovery and information visualization are necessary. Visual analytics combines these fields and supports users to integrate domain knowledge into the knowledge discovery process. This article gives a state-of-the-art overview on visual analytics reseach with a focus on the biomedical domain, systems biology and *omics data.
Exploration of 3D Medical Image Data for Interventional Radiology using Myoelectric Gesture Control
(The Eurographics Association, 2015) Hettig, Julian; Mewes, André; Riabikin, Oleksandr; Skalej, Martin; Preim, Bernhard; Hansen, Christian; Katja Bühler and Lars Linsen and Nigel W. John
Human-computer interaction with medical images in a sterile environment is a challenging task. It is often delegated to an assistant or performed directly by the physician with an interaction device wrapped in a sterile plastic sheath. This process is time-consuming and inefficient. To address this challenge, we introduce a gesture-based interface for a medical image viewer that is completely touchlessly controlled by the Myo Gesture Control Armband (Thalmic Labs). Based on a clinical requirement analysis, we propose a minimal gesture set to support basic interaction tasks with radiological images and 3D models. We conducted two user studies and a clinical test to evaluate the interaction device and our new gesture control interface. The evaluation results prove the applicability of our approach and provide an important foundation for future research in physician-machine interaction.
Fiber Stipples for Crossing Tracts in Probabilistic Tractography
(The Eurographics Association, 2015) Reichenbach, Andre; Goldau, Mathias; Hlawitschka, Mario; Katja Bühler and Lars Linsen and Nigel W. John
Given diffusion weighted magnetic resonance (dMRI) data, tractography methods may reconstruct estimations of neural connections of the human brain, so called tractograms. Probabilistic tractography algorithms generate a scalar value for each point of the brain, which describes the confidence of an existing structural connection to a predefined seed region. Recently presented Fiber-Stippling is a promising tool to effectively visualize such scalar values on axis aligned cutting planes. However, Fiber-Stippling only works with principal diffusion directions and cannot handle complex tract configurations, such as overlapping or crossing tracts, which are very important to neuroscience. In this work we present an illustrative technique for probabilistic tracts in such configurations, which is based on Fiber-Stippling. Our technique supports multiple diffusion directions as given by high angular resolution diffusion images (HARDI) and hence can visualize crossing tracts, while preserving all of the advantages of Fiber-Stippling. We solve this by visually supporting the stipples, while not altering the original visualization metaphor. Our work is an important contribution to adequate visualization of neuroanatomy, as crossing tracts are a frequent phenomen inside of the human brain. Moreover, our technique may be customized to crossing line fields in general.
FoldSynth: Interactive 2D/3D Visualisation Platform for Molecular Strands
(The Eurographics Association, 2015) Todd, Stephen; Todd, Peter; Leymarie, Frederic Fol; Latham, William; Kelley, Lawrence A.; Sternberg, Michael; Hugues, Jim; Taylor, Stephen; Katja Bühler and Lars Linsen and Nigel W. John
FoldSynth is an interactive platform designed to help understand the characteristics and commonly used visual abstractions of molecular strands with an emphasis on proteins and DNA. It uses a simple model of molecular forces to give real time interactive animations of the folding and docking processes. The shape of a molecular strand is shown as a 3D visualisation floating above a 2D triangular matrix representing distance constraints, contact maps or other features of residue pairs. As well as more conventional raster plots, contact maps can be shown with vectors representing the grouping of contacts as secondary structures. The 2D visualisation is also interactive and can be used to manipulate a molecule, define constraints, control and view the folding dynamically, or even design new molecules. While the 3D visualisation is more realistic showing a molecule representation approximating the physical behavior and spatial properties, the 2D visualisation offers greater visibility, in that all molecular positions (and pairings) are always in view; the 3D mode may suffer occlusions and create complex views which are typically hard to understand to humans.
Frontmatter: Eurographics Workshop on Visual Computing for Biology and Medicine
(The Eurographics Association, 2015) Bühler, Katja; Linsen, Lars; John, Nigel W.; Katja Bühler and Lars Linsen and Nigel W. John
Haptics-based Modelling of Pigmented Skin Lesions
(The Eurographics Association, 2015) Granados, Alejandro; Bryan, James; Abdalla, Taha; Osborne, Genevieve; Bello, Fernando; Katja Bühler and Lars Linsen and Nigel W. John
Dermatology is under-represented in medical undergraduate education with newly graduated doctors not being able to identify common and important skin conditions. In order to become competent in diagnosing skin lesions, it is important to encounter multiple examples of a condition, as they vary between individuals. Three popular lesions have been identified due to their importance, including nodular melanoma, seborrhoeic keratosis and cherry haemangioma. In this paper we propose a haptics-enabled learning tool for pigmented skin lesions based on haptic texturing. Geometrical modelling, skin deformation and haptics modelling are described. Results of the implementation are presented along with an initial validation study comparing the haptics-based simulator with other methods, including temporary tattoos and silicon made models.
A Haptics-enabled Simulator for Transperineal Ultrasound-Guided Biopsy
(The Eurographics Association, 2015) Ritsos, Panagiotis D.; Edwards, Marc R.; Shergill, Iqbal S.; John, Nigel W.; Katja Bühler and Lars Linsen and Nigel W. John
We present the development of a transperineal prostate biopsy, with high fidelity haptic feedback. We describe our current prototype, which is using physical props and a Geomagic Touch. In addition, we discuss a method for collecting in vitro axial needle forces, for programming haptic feedback, along with implemented an forthcoming features such as a display of 2D ultrasonic images for targeting, biopsy needle bending, prostate bleeding and calcification. Our ultimate goal is to provide an affordable high-fidelity simulation by integrating contemporary off-the-shelf technology components.
Histology-Based Evaluation of Optical Coherence Tomographic Characteristics of the Cerebral Artery Wall via Virtual Inflating
(The Eurographics Association, 2015) Glaßer, Sylvia; Hoffmann, Thomas; Boese, Axel; Voß, Samuel; Kalinski, Thomas; Skalej, Martin; Preim, Bernhard; Katja Bühler and Lars Linsen and Nigel W. John
With an increased rate of cerebrovascular diseases, the need for an advanced vessel wall analysis increases as well. In this work, we provide new information of cerebral artery walls extracted with optical coherence tomography (OCT) ex vivo. We present first results of cerebral vessel wall characteristics combined with histological image data. As a prerequisite for this combination, a new image processing method called virtual inflation was developed. This method accounts for the missing blood pressure causing collapsing of the vessels as well as geometrical shape deformations due to catheter probing and histological imaging. We sample the vessel wall thickness locally based on the (deflated) vessel-lumen border instead of the vessel's centerline. The virtual inflation allows for co-aligning of the different image modalities. It is embedded in a multiple coordinated view framework where correspondences between the data can be highlighted via brushing and linking. In combination with histologic image data, we provide OCT signal characteristics of the human cerebral artery wall.
Illustrative Multi-volume Rendering for PET/CT Scans
(The Eurographics Association, 2015) Lawonn, Kai; Smit, Noeska; Preim, Bernhard; Vilanova, Anna; Katja Bühler and Lars Linsen and Nigel W. John
In this paper we present illustrative visualization techniques for PET/CT datasets. PET/CT scanners acquire both PET and CT image data in order to combine functional metabolic information with structural anatomical information. Current visualization techniques mainly rely on 2D image fusion techniques to convey this combined information to physicians. We introduce an illustrative 3D visualization technique, specifically designed for use with PET/CT datasets. This allows the user to easily detect foci in the PET data and to localize these regions by providing anatomical contextual information from the CT data. Furthermore, we provide transfer function specifically designed for PET data that facilitates the investigation of interesting regions. Our technique allows users to get a quick overview of regions of interest and can be used in treatment planning, doctor-patient communication and interdisciplinary communication. We conducted a qualitative evaluation with medical experts to validate the utility of our method in clinical practice.
Image Registration Methods for Patient-Specific Virtual Physiological Human Models
(The Eurographics Association, 2015) Oliveira, Julia E. E. de; Giessler, Paul; Deserno, Thomas M.; Katja Bühler and Lars Linsen and Nigel W. John
In this paper, current status of image registration is reviewed with respect to physiological, morphological and anatomical aspects. There are ample choices of recent techniques for image registration which can be used, and a technique suitable for image registration of the pelvis region supporting the femoral nerve block was applied for the development of patient-specific models. Virtual physiological human (VPH) model and magnetic resonance image (MRI) are used for patient-specific image registration. Results are presented in the form of image registration with respect to the skin of the models.
Instant Visualization of Secondary Structures of Molecular Models
(The Eurographics Association, 2015) Hermosilla, Pedro; Guallar, V.; Vinacua, Alvar; Vázquez, Pere-Pau; Katja Bühler and Lars Linsen and Nigel W. John
Molecular Dynamics simulations are of key importance in the drug design field. Among all possible representations commonly used to inspect these simulations, Ribbons has the advantage of giving the expert a good overview of the conformation of the molecule. Although several techniques have been previously proposed to render ribbons, all of them have limitations in terms of space or calculation time, making them not suitable for real-time interaction with simulation software. In this paper we present a novel adaptive method that generates ribbons in real-time, taking advantage of the tessellation shader. The result is a fast method that requires no precomputation, and that generates high quality shapes and shading.
Interactive Position-dependent Customization of Transfer Function Classification Parameters in Volume Rendering
(The Eurographics Association, 2015) Brix, Tobias; Scherzinger, Aaron; Völker, Andreas; Hinrichs, Klaus; Katja Bühler and Lars Linsen and Nigel W. John
In direct volume rendering (DVR) and related techniques a basic operation is the classification of data values by mapping (mostly scalar) intensities to color values using a transfer function. However, in some cases this kind of mapping might not suffice to achieve satisfying rendering results, for instance when intensity homogeneities occur in the volume data due to technical restrictions of the scanner technology. In this case it might be desirable to customize one or more parameters of the visualization depending on the position within the volume. In this paper we propose a novel approach for an interactive position-dependent customization of arbitrary parameters of the transfer function classification. Our method can easily be integrated into existing volume rendering pipelines by incorporating an additional operation during the classification step. It allows the user to interactively modify the rendering result by specifying reference points within the data set and customizing their associated visualization parameters while receiving direct visual feedback. Since the additional memory requirements of our method do not depend on the size of the visualized data our approach is applicable to large data sets, for instance in the field of ultra microscopy.
Motion-moderated Transfer Function for Volume Rendering 4D CMR Data
(The Eurographics Association, 2015) Walton, Simon; Chen, Min; Holloway, Cameron; Katja Bühler and Lars Linsen and Nigel W. John
Cardiovascular Magnetic Resonance (CMR) produces time-varying volume data by combining conventional MRI techniques with ECG gating. It allows physicians to inspect the dynamics of a beating heart, such as myocardium motion and blood flows. Because the material intensity changes over time in a typical CMR scan, this poses a challenging problem in specifying an effective transfer function for depicting the geometry of a beating heart or other moving objects. In this paper, we propose to moderate the traditional transfer function based on intensity and intensity gradient. This enables us to depict the exterior boundary of a beating heart in a temporally consistent manner. We examine several different ways of moderating an intensity-based transfer function, and evaluate these designs in conjunction with practical CMR data. We present a ray-casting pipeline which includes optional flow estimation and a mechanism to assist temporal coherence in animation.
Parametric-based Reconstruction Of 3D Mesh Models; Towards the Generation of a Parametric Human Foot Biomodel
(The Eurographics Association, 2015) Agathos, Alexander; Azariadis, Philip; Katja Bühler and Lars Linsen and Nigel W. John
In this work a new reconstruction technique is presented based on Parametric-Based Deformation. The new method uses a template 3D mesh model which is deformed according to user-defined semantic parameters in order to derive a new 3D object. The proposed methodology is divided in three stages: template construction (production of a template mesh model), regression (the template model is deformed to match sample models) and prediction (new instance mesh models are derived based on user parameters). The proposed method has been successfully applied for the reconstruction of human and animal skeletal models. A practical and novel reconstruction methodology has been developed and implemented for the reconstruction of the human foot given a bi-planar X-ray. The purpose of this methodology is to support the parametric generation of human foot biomodels in an automated way. The generated biomodels are employed by simulation tools based on Finite Element Analysis to test the stress factors that the foot is undertaking during its contact with the ground or a footwear sole structure.
QuantiScale: A Study in Redesigning Interactions for Multi-Touch
(The Eurographics Association, 2015) Ritter, Felix; Issawi, Jumana Al; Benten, Simon; Katja Bühler and Lars Linsen and Nigel W. John
We investigate the performance of QuantiScale, a new multi-touch interaction technique for the quantification of distances in medical images and discuss the benefits and prospects of redesigning interactions with multi-touch devices. Taking advantage of the multi-touch capabilities, QuantiScale behaves like a tape measure, but automatically adjusts the view onto the measured object to improve precision and speed. The technique has been studied in a real-world scenario measuring the diameter of structures for the diagnostic reading of medical images and provides hints for the replacement of traditional mouse-based interaction with gestural interaction. Results of the quantitative evaluation indicate a high measurement precision particularly for small objects. Participants experienced QuantiScale as being more fun, natural, and intuitive in comparison to mouse-based interaction even though the subjective preference for speed and precision was still in favor of the mouse.

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