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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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.
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.
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.
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.
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.
Visualisation of PET data in the Fly Algorithm
(The Eurographics Association, 2015) Abbood, Zainab Ali; Rocchisani, Jean-Marie; Vidal, Franck; Katja Bühler and Lars Linsen and Nigel W. John
We use the Fly algorithm, an artificial evolution strategy, to reconstruct positron emission tomography (PET) images. The algorithm iteratively optimises the position of 3D points. It eventually produces a point cloud, which needs to be voxelised to produce volume data that can be used with conventional medical image software. However, resulting voxel data is noisy. In our test case with 6,400 points the normalised cross-correlation (NCC) between the reference and the reconstruction is 85.53%; with 25,600 points it is 93.60%. This paper introduces a more robust 3D voxelisation method based on implicit modelling using metaballs to overcome this limitation. With metaballs, the NCC with 6,400 points increases up to 92.21%; and up to 96.26% with 25,600 points.
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.
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.
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.
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.
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.
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.

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