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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Uncertainty Estimation and Visualization for Multi-modal Image Segmentation
(The Eurographics Association, 2015) Al-Taie, Ahmed; Hahn, Horst K.; Linsen, Lars; Katja Bühler and Lars Linsen and Nigel W. John
Multi-modal imaging allows for the integration of complementary information from multiple medical imaging modalities for an improved analysis. The multiple information channels may lead to a reduction of the uncertainty in the analysis and decision-making process. Recently, efforts have been made to estimate the uncertainty in unimodal image segmentation decisions and visually convey this information to the medical experts that examine the image segmentation results. We propose an approach to extend uncertainty estimation and visualization methods to multi-modal image segmentations. We combine probabilistic uni-modal image segmentation results using the concept of ensemble of classifiers. The uncertainty is computed using a measure that is based on the Kullback- Leibler divergence. We apply our approach for an improved segmentation of Multiple Sclerosis (MS) lesions from multiple MR brain imaging modalities. Moreover, we demonstrate how our approach can be used to estimate and visualize the growth of a brain tumor area for imaging data taken at multiple points in time. Both the MS lesion and the area of tumor growth are detected as areas of high uncertainty due to different characteristics in different imaging modalities and changes over time, respectively.
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.
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.
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.
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.

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