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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SWiFT Seeing the Wood From the Trees: helping people make sense of their health data
(The Eurographics Association, 2015) Brown, Dan; Duce, David; Franklin, Rachel; Harrison, Rachel; Martin, Clare; Waite, Marion; Katja Bühler and Lars Linsen and Nigel W. John
The aim of the SWIFT project is to determine which visualisations of blood glucose-related data on mobile devices are most usable by people with insulin-dependent diabetes, to improve self-management.
A Two-Level Cascade Classification Algorithm for Real-Time Bifurcation Detection in CTA Images of Blood Vessels
(The Eurographics Association, 2015) Novikov, Alexey A.; Wimmer, Maria; Major, David; Bühler, Katja; Katja Bühler and Lars Linsen and Nigel W. John
We introduce a cascade classification algorithm for bifurcation detection in Computed Tomography Angiography (CTA) scans of blood vessels. The proposed algorithm analyzes the vessel surrounding by a trained classifier first, followed by an accurate segmentation of the vessel outer wall by Morphological Active Contour Without Edges and finally extracts the boundary features of the segmented object and classifies its shape by Approximate K-nearest Neighbour classifier. The algorithm shows encouraging and competitive results for blood vessels from various parts of a human body including head, neck and legs.
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.
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.
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.
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.
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.
Simulation-based Ultrasound Training Supported by Annotations, Haptics and Linked Multimodal Views
(The Eurographics Association, 2015) Law, Yuen C.; Knott, Thomas; Pick, Sebastian; Weyers, Benjamin; Kuhlen, Torsten W.; Katja Bühler and Lars Linsen and Nigel W. John
When learning ultrasound (US) imaging, trainees must learn how to recognize structures, interpret textures and shapes, and simultaneously register the 2D ultrasound images to their 3D anatomical mental models. Alleviating the cognitive load imposed by these tasks should free the cognitive resources and thereby improve the learning process. We argue that the amount of cognitive load that is required to mentally rotate the models to match the images to them is too large and therefore negatively impacts the learning process. We present a 3D visualization tool that allows the user to naturally move a 2D slice and navigate around a 3D anatomical model. The slice is displayed in-place to facilitate the registration of the 2D slice in its 3D context. Two duplicates are also shown externally to the model; the first is a simple rendered image showing the outlines of the structures and the second is a simulated ultrasound image. Haptic cues are also provided to the users to help them maneuver around the 3D model in the virtual space. With the additional display of annotations and information of the most important structures, the tool is expected to complement the available didactic material used in the training of ultrasound procedures.
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.
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.
Simulated Motion Artefact in Computed Tomography
(The Eurographics Association, 2015) Vidal, Franck; Villard, Pierre-Frédéric; Katja Bühler and Lars Linsen and Nigel W. John
We propose a simulation framework to simulate the computed tomography acquisition process. It includes five components: anatomic data, respiration modelling, automatic parametrisation, X-ray simulation, and tomography reconstruction. It is used to generate motion artefacts in reconstructed CT volumes. Our framework can be used to evaluate CT reconstruction algorithm with motion artefact correction in a controlled environment.
Visual Analysis of Medical Image Segmentation Feature Space for Interactive Supervised Classification
(The Eurographics Association, 2015) Molchanov, Vladimir; Chitiboi, Teodora; Linsen, Lars; Katja Bühler and Lars Linsen and Nigel W. John
Classification of image regions is a crucial step in many image segmentation algorithms. Assigning a segment to a certain class can be based on various numerical characteristics such as size, intensity statistics, or shape, which build a multi-dimensional feature space describing the segments. It is commonly unclear and not intuitive, however, how much influence or weight should be assigned to the individual features to obtain a best classification. We propose an interactive supervised approach to the classification step based on a feature-space visualization. Our visualization method helps the user to better understand the structure of the feature space and to interactively optimize feature selection and assigned weights. When investigating labeled training data, the user generates optimal descriptors for each target class. The obtained set of descriptors can then be transferred to classify unlabeled data. We show the effectiveness of our approach by embedding our interactive supervised classification method into a medical image segmentation pipeline for two application scenarios: detecting vertebral bodies in sagittal CT image slices, where we improve the overall accuracy, and detecting the pharynx in head MRI data.
A Statistical Method for Surface Detection
(The Eurographics Association, 2015) Smith, Samuel; Williams, Ian; Katja Bühler and Lars Linsen and Nigel W. John
This work presents a new method for 3D surface detection using a statistical dual-region filter. The method improves over traditional 3D surface detection techniques by resolving interfaces between different stochastic textures, while maintaining the accuracy for gradient based interfaces. Segmentation is commonly applied to 3D image formats such as MRI and CT data to aid high level visualisation and anatomical model creation. Often segmentation is a process which is reliant on accurate surface information and typically gradient-based surface detection methods are applied. These gradient methods identify sharp changes in the image intensity profile, however are known to fail when high levels of noise are present. Often within MRI and CT data, the regions to be segmented are areas of stochastic texture, such as soft tissue structures, this can resemble intensity boundaries corrupted by noise where the intensity profile across the regions remains constant, rendering gradient-based operators less effective. To overcome these issues, we present a surface detection method that employs a dual-region neighbourhood mask, alongside a statistical comparison test. Within this method we assess eight different statistical tests which measure the similarity between the neighbourhood mask regions. The tests presented are mean based, variance based, non-parametric or distribution based. Results from this method show that when a high degree of similarity is found between image regions a non-surface point is detected, and likewise where a low degree of similarity from the tests is found signifies a surface location. Through this process, improved surface segmentation is achieved even in the presence of stochastic texture. We present results to show significant improvements over the 3D Canny method of surface detection and also the 3D Steerable filter method, notably in the detection of surfaces between regions of stochastic texture with high intensity variance. This improvement is further illustrated by our method achieving fewer missed interfaces, more complete surfaces and a measured reduction in spurious surface responses. We employ a Monte-Carlo analysis, involving the development of a synthetic texture interface datasets and the corresponding ground truth solutions. Receiver Operator Characteristic and Precision Recall quantitative performance measures are used to compare against existing state of the art filter methods, and application in real CT and MRI data shows where the improvements can be found.
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.
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.
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.
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.
A Survey of Cardiac 4D PC-MRI Data Processing
(The Eurographics Association, 2015) Köhler, Benjamin; Born, Silvia; Pelt, Roy F. P. van; Preim, Uta; Preim, Bernhard; Katja Bühler and Lars Linsen and Nigel W. John
Cardiac 4D PC-MRI acquisitions gained increasing clinical interest in recent years. They allow to non-invasively obtain extensive information about patient-specific hemodynamics and thus have a great potential to improve the diagnosis of cardiovascular diseases. A dataset contains time-resolved, three-dimensional blood flow directions and strengths, facilitating comprehensive qualitative and quantitative data analysis. The quantification of measures such as stroke volumes helps to assess the cardiac function and monitor disease progression. Qualitative analysis allows to investigate abnormal flow characteristics, such as vortices, that are correlated to different pathologies. Processing the data comprises complex image processing methods as well as flow analysis and visualization. In this work, we mainly focus on the aorta. We provide an overview from data measurement and preprocessing to current visualization and quantification methods so that other researchers can quickly catch up with the topic and take on new challenges to further investigate the potential of 4D PC-MRI.
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.
Schematic Electrode Map for Navigation in Neuro Data Sets
(The Eurographics Association, 2015) Berge, Christian Schulte zu; Weiss, Jakob; Navab, Nassir; Katja Bühler and Lars Linsen and Nigel W. John
Neuro resection surgery is one of the last resorts when treating epilepsy patients where conservative treatment shows no effect on seizure reduction. However, due to the severity of the surgery, the resection planning has to be as precise as possible in order to avoid harming any critical anatomy. The tight time constraints in clinal routine demand for a highly optimized workflow. In this work, we therefore introduce a novel visualization in order to simplify the navigation in the complex multi-modal neuro data sets and support the clinician with the planning procedure. We propose a schematic electrode map based on a force-directed graph model providing an intuitive overview over the topology of the implanted depth electrode configuration. To further facilitate the planning workflow, our carefully designed electrode glyph supports different scalar, nominal and binary annotations augmenting the view with additional information. Brushing and linking techniques allow for easy mapping of the EEG data to the corresponding anatomy, as well as for straight-forward navigation within the visualization of the anatomical and functional imaging modalities in order to identify the origin and spread of the seizure. Our results show that the proposed graph layouting method successfully removes occlusions of the projected electrodes while maintaining the original topology of the depth electrode configuration. Initial discussions with clinicians and the application to clinical data further show the effectiveness of our methods.

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