VCBM: Eurographics Workshop on Visual Computing for Biomedicine

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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.
Colonic Content Assessment from MRI Imaging Using a Semi-automatic Approach
(The Eurographics Association, 2019) Ceballos, Victor; Monclús, Eva; Vázquez, Pere-Pau; Bendezú, Álvaro; Mego, Marianela; Merino, Xavier; Azpiroz, Fernando; Navazo, Isabel; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
The analysis of the morphology and content of the gut is necessary in order to achieve a better understanding of its metabolic and functional activity. Magnetic resonance imaging (MRI) has become an important imaging technique since it is able to visualize soft tissues in an undisturbed bowel using no ionizing radiation. In the last few years, MRI of gastrointestinal function has advanced substantially. However, few studies have focused on the colon, because the analysis of colonic content is time consuming and cumbersome. This paper presents a semi-automatic segmentation tool for the quantitative assessment of the unprepared colon from MRI images. The techniques developed here have been crucial for a number of clinical experiments.
Design Considerations for Immersive Analytics of Bird Movements Obtained by Miniaturised GPS Sensors
(The Eurographics Association, 2017) Nim, Hieu T.; Sommer, Björn; Klein, Karsten; Flack, Andrea; Safi, Kamran; Nagy, Máté; Fiedler, Wolfgang; Wikelski, Martin; Schreiber, Falk; Stefan Bruckner and Anja Hennemuth and Bernhard Kainz and Ingrid Hotz and Dorit Merhof and Christian Rieder
Recent advances in miniaturising sensor tags allow to obtain high-resolution bird trajectories, presenting an opportunity for immersive close-up observation of individual and group behaviour in mid-air. The combination of geographical, environmental, and movement data is well suited for investigation in immersive analytics environments. We explore the benefits and requirements of a wide range of such environments, and illustrate a multi-platform immersive analytics solution, based on a tiled 3D display wall and head-mounted displays (Google Cardboard, HTC Vive and Microsoft Hololens). Tailored to biologists studying bird movement data, the immersive environment provides a novel interactive mode to explore the geolocational time-series data. This paper aims to inform the 3D visualisation research community about design considerations obtained from a real world data set in different 3D immersive environments. This work also contributes to ongoing research efforts to promote better understanding of bird migration and the associated environmental factors at the planet-level scale, thereby capturing the public awareness of environmental issues.
Evaluation of Transfer Function Methods in Direct Volume Rendering of the Blood Vessel Lumen
(The Eurographics Association, 2014) Läthén, Gunnar; Lindholm, Stefan; Lenz, Reiner; Borga, Magnus; Ivan Viola and Katja Buehler and Timo Ropinski
Visualization of contrast enhanced blood vessels in CT angiography data presents a challenge due to varying concentration of the contrast agent. The purpose of this work is to evaluate the correctness (effectiveness) in visualizing the vessel lumen using two different 3D visualization strategies, thereby assessing the feasibility of using such visualizations for diagnostic decisions. We compare a standard visualization approach with a recent method which locally adapts to the contrast agent concentration. Both methods are evaluated in a parallel setting where the participant is instructed to produce a complete visualization of the vessel lumen, including both large and small vessels, in cases of calcified vessels in the legs. The resulting visualizations are thereafter compared in a slice viewer to assess the correctness of the visualized lumen. The results indicate that the participants generally overestimated the size of the vessel lumen using the standard visualization, whereas the locally adaptive method better conveyed the true anatomy. The participants did find the interpretation of the locally adaptive method to be less intuitive, but also noted that this did not introduce any prohibitive complexity in the work flow. The observed trends indicate that the visualized lumen strongly depends on the width and placement of the applied transfer function and that this dependency is inherently local rather than global. We conclude that methods that permit local adjustments, such as the method investigated in this study, can be beneficial to certain types of visualizations of large vascular trees.
A Framework for Fast Initial Exploration of PC-MRI Cardiac Flow
(The Eurographics Association, 2016) Broos, Arjan J. M.; Hoon, Niels H. L. C. de; Koning, Patrick J. H. de; Geest, Rob J. van der; Vilanova, Anna; Jalba, Andrei C.; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
Cardiac flow is still not fully understood, and is currently an active research topic. Using phase-contrast magnetic resonance imaging (PC-MRI) blood flow can be measured. For the inspection of such flow, researchers often rely on methods that require additional scans produced by different imaging modalities to provide context. This requires labor-intensive registration and often manual segmentation before any exploration of the data is performed. This work provides a framework that allows for a quick exploration of cardiac flow without the need of additional imaging and time-consuming segmentation. To achieve this, only the 4D data from one PC-MRI scan is used. A context visualization is derived automatically from the data, and provides context for the flow. Instead of relying on segmentation to deliver an accurate context, the heart's ventricles are approximated by half-ellipsoids that can be placed with minimal user interaction. Furthermore, seeding positions for flow visualization can be placed automatically in areas of interest defined by the user and based on derived flow features. The framework enables a user to do a fast initial exploration of cardiac flow, as is demonstrated by a use case and a user study involving cardiac blood flow researchers.
HIFUtk: Visual Analytics for High Intensity Focused Ultrasound Simulation
(The Eurographics Association, 2017) Modena, Daniela; Dijk, Edmond van; Bošnacki, Dragan; Eikelder, Huub M. M. ten; Westenberg, Michel A.; Stefan Bruckner and Anja Hennemuth and Bernhard Kainz and Ingrid Hotz and Dorit Merhof and Christian Rieder
Magnetic Resonance-guided High Intensity Focused Ultrasound (MR-HIFU) is a novel and non-invasive therapeutic method. It can be used to locally increase the temperature in a target position in the human body. HIFU procedures are helpful for the treatment of soft tissue tumors and bone metastases. In vivo research with HIFU systems poses several challenges, therefore, a flexible and fast computer model for HIFU propagation and tissue heating is crucial. We introduce HIFUtk, a visual analytics environment to define, perform, and visualize HIFU simulations. We illustrate the use of HIFUtk by applying HIFU to a rabbit bone model, focusing on two common research questions related to HIFU. The first question concerns the relation between the ablated region shape and the focal point position, and the second one concerns the effect of shear waves on the temperature distribution in bone. These use cases demonstrate that HIFUtk provides a flexible visual analytics environment to investigate the effects of HIFU in various type of materials.
The iCoCooN: Integration of Cobweb Charts with Parallel Coordinates for Visual Analysis of DCE-MRI Modeling Variations
(The Eurographics Association, 2014) Raidou, Renata G.; Breeuwer, Marcel; Vilanova, Anna; Heide, U. A. van der; Houdt, P. J. van; Ivan Viola and Katja Buehler and Timo Ropinski
Efficacy of radiotherapy treatment depends on the specific characteristics of tumorous tissues. For the determination of these characteristics, clinical practice uses Dynamic Contrast Enhanced (DCE) Magnetic Resonance Imaging (MRI). DCE-MRI data is acquired and modeled using pharmacokinetic modeling, to derive per voxel a set of parameters, indicative of tissue properties. Different pharmacokinetic modeling approaches make different assumptions, resulting in parameters with different distributions. A priori, it is not known whether there are significant differences between modeling assumptions and which assumption is best to apply. Therefore, clinical researchers need to know at least how different choices in modeling affect the resulting pharmacokinetic parameters and also where parameter variations appear. In this paper, we introduce iCoCooN: a visualization application for the exploration and analysis of model-induced variations in pharmacokinetic parameters.We designed a visual representation, the Cocoon, by integrating perpendicularly Parallel Coordinate Plots (PCPs) with Cobweb Charts (CCs). PCPs display the variations in each parameter between modeling choices, while CCs present the relations in a whole parameter set for each modeling choice. The Cocoon is equipped with interactive features to support the exploration of all data aspects in a single combined view. Additionally, interactive brushing allows to link the observations from the Cocoon to the anatomy. We conducted evaluations with experts and also general users. The clinical experts judged that the Cocoon in combination with its features facilitates the exploration of all significant information and, especially, enables them to find anatomical correspondences. The results of the evaluation with general users indicate that the Cocoon produces more accurate results compared to independent multiples.
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.
Illustrative PET/CT Visualisation of SIRT-Treated Lung Metastases
(The Eurographics Association, 2016) Merten, Nico; Glaßer, Sylvia; Lassen-Schmidt, Bianca; Großer, Oliver Stephan; Ricke, Jens; Amthauer, Holger; Preim, Bernhard; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
We present an illustrative rendering pipeline which combines anatomical information from CT scans with functional information from PET scans. To treat lung metastases with Selective Internal Radiation Therapies (SIRTs), combined PET/CT recordings are used for treatment planning and intervention validation. We firstly extract surface meshes from the lung lobes and trachea from the CT scan. In addition, the radiation activity of the therapeutic agent 90Y is acquired from the PET data. To convey all this information in one view, we use illustrative rendering techniques, combining Order-Independent Transparencies with Boundary Enhancements and Silhouettes. Our methods are evaluated by clinical and visualisation domain experts. This study indicates an excellent spatial perception and evaluation of tumor position, metabolic and therapeutic agent activity, when transparencies and boundary enhancements are used to render the surrounding lung lobes.
On the Value of Multi-Volume Visualization for Preoperative Planning of Cerebral AVM Surgery
(The Eurographics Association, 2012) Weiler, Florian; Rieder, Christian; David, Carlos A.; Wald, Christoph; Hahn, Horst K.; Timo Ropinski and Anders Ynnerman and Charl Botha and Jos Roerdink
Surgical treatment of cerebral arteriovenous malformations (AVMs) requires thourough preoperative planning for the intervening neurosurgeon. The goal of such planning is to gain a precise understanding of the patho-anatomy of the malformation, specifically about the location and spatial relation of normal and abnormal structures. A key element in this process is the identication and localization of arteries feeding into the lesion, and veins draining it. In this paper, we demonstrate how state-of-the-art techniques from the field of computer graphics and image processing can support neurosurgeons with this task. We address the problem by merging multiple angiographic image sets within a 3D volume rendering pipeline. Datasets from clinical imaging studies were remotely processed at our institute, returned to the institution of origin, and finally visualized in an interactive application, allowing the neurosurgeon to explore the different images simultaneously. Here, we present three case studies along with the medical assessment of an experienced neurosurgeon.
PATHONE: From one Thousand Patients to one Cell
(The Eurographics Association, 2016) Corvò, Alberto; Westenberg, Michel A.; Driel, Marc A. van; Wijk, Jarke J.van; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
Digital Pathology is a recent clinical environment in which Electronic Health Records (EHRs), biopsy data and whole-slideimages (WSI) come together to provide pathologists the necessary information for making a diagnosis. Integration of this heterogeneous data into a single application is still one of the challenges in the evolution of pathology to a digital practice. While pathologists can perform diagnoses routinely on digital slides only, this is not the case in clinical research. For such purposes, the link between clinicopathological information of patients and images is essential. For example, image analysis researchers who develop automated diagnostic (support) algorithms need to select a representative set of slides to evaluate their methods. To achieve this, they need applications that combine cohort specification, slide image exploration, and selection of suitable images. We present the visualization tool PATHONE, which enables users to perform these steps on a single screen, integrating cohort and WSI selection.
RegistrationShop: An Interactive 3D Medical Volume Registration System
(The Eurographics Association, 2014) Smit, Noeska N.; Haneveld, Berend Klein; Staring, Marius; Eisemann, Elmar; Botha, Charl P.; Vilanova, Anna; Ivan Viola and Katja Buehler and Timo Ropinski
In medical imaging, registration is used to combine images containing information from different modalities or to track treatment effects over time in individual patients. Most registration software packages do not provide an easy-to-use interface that facilitates the use of registration. 2D visualization techniques are often used for visualizing 3D datasets. RegistrationShop was developed to improve and ease the process of volume registration using 3D visualizations and intuitive interactive tools. It supports several basic visualizations of 3D volumetric data. Interactive rigid and non-rigid transformation tools can be used to manipulate the volumes and immediate visual feedback for all rigid transformation tools allows the user to examine the current result in real-time. In this context, we introduce 3D comparative visualization techniques, as well as a way of placing landmarks in 3D volumes. Finally, we evaluated our approach with domain experts, who underlined the potential and usefulness of RegistrationShop.
Robust Cardiac Function Assessment in 4D PC-MRI Data
(The Eurographics Association, 2014) Köhler, Benjamin; Preim, Uta; Gutberlet, Matthias; Fischbach, Katharina; Preim, Bernhard; Ivan Viola and Katja Buehler and Timo Ropinski
Four-dimensional phase-contrast magnetic resonance imaging (4D PC-MRI) is a relatively young image modality that allows the non-invasive acquisition of time-resolved, three-dimensional blood flow information. Stroke volumes and regurgitation fractions are two of the main measures to assess the cardiac function and severity of pathologies. The flow volumes in forward and backward direction through a plane inside the vessel are required for their quantification. Unfortunately, the calculations are highly sensitive towards the plane's angulation since orthogonally passing flow is considered. This often leads to physiologically implausible results. In this work, a robust quantification method is introduced to overcome this problem. Collaborating radiologists and cardiologists were carefully observed while estimating stroke volumes in various healthy volunteer and patient datasets with conventional quantification. This facilitated the automatization of their approach which, in turn, allows to derive statistical information about the plane angulation sensitivity. Moreover, the experts expect a continuous decrease of the stroke volume along the vessel course after a peak value above the aortic valve. Conventional methods are often unable to produce this behavior. Thus, we present a procedure to fit a function that ensures such physiologically plausible results. In addition, the technique was adapted for the robust quantification of regurgitation fractions. The performed qualitative evaluation shows the capability of our method to support diagnosis, a parameter evaluation confirms the robustness. Vortex flow was identified as main cause for quantification uncertainties.
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.
Temporal Interpolation of 4D PC-MRI Blood-flow Measurements Using Bidirectional Physics-based Fluid Simulation
(The Eurographics Association, 2016) Hoon, Niels H. L. C. de; Jalba, Andrei C.; Eisemann, Elmar; Vilanova, Anna; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
Magnetic Resonance Imaging (MRI) enables volumetric and time-varying measurements of blood-flow data. Such data have shown potential to improve diagnosis and risk assessment of various cardiovascular diseases. Hereby, a unique way of analysing patient-specific haemodynamics becomes possible. However, these measurements are susceptible to artifacts, noise and a coarse spatio-temporal resolution. Furthermore, typical flow visualization techniques rely on interpolation. For example, using pathlines requires a high quality temporal resolution. While numerical simulations, based on mathematical flow models, address some of these limitations, the involved modelling assumptions (e.g., regarding the inflow and mesh) do not provide patientspecific data to the degree actual measurements would. To overcome this issue, data assimilation techniques can be applied to use measured data in order to steer a physically-based simulation of the flow, combining the benefits of measured data and simulation. Our work builds upon such an existing solution to increase the temporal resolution of the measured data, but achieves significantly higher fidelity. We avoid the previous damping and interpolation bias towards one of the measurements, by simulating bidrectionally (forwards and backwards through time) and using sources and sinks. Our method is evaluated and compared to the, currently-used, conventional interpolation scheme and forward-only simulation using measured and analytical flow data. It reduces artifacts, noise, and interpolation error, while being closer to laminar flow, as is expected for flow in vessels.
Towards Clinical Deployment of Automated Anatomical Regions-Of-Interest
(The Eurographics Association, 2014) Lindholm, Stefan; Forsberg, Daniel; Ynnerman, Anders; Knutsson, Hans; Andersson, Mats; Lundström, Claes; Ivan Viola and Katja Buehler and Timo Ropinski
The purpose of this work is to investigate, and improve, the feasibility of advanced Region Of Interest (ROI) selection schemes in clinical volume rendering. In particular, this work implements and evaluates an Automated Anatomical ROI (AA-ROI) approach based on the combination of automatic image registration (AIR) and Distance- Based Transfer Functions (DBTFs), designed for automatic selection of complex anatomical shapes without relying on prohibitive amounts of interaction. Domain knowledge and clinical experience has been included in the project through participation of practicing radiologists in all phases of the project. This has resulted in a set of requirements that are critical for Direct Volume Rendering applications to be utilized in clinical practice and a prototype AA-ROI implementation that was developed to addresses critical points in existing solutions. The feasibility of the developed approach was assessed through a study where five radiologists investigated three medical data sets with complex ROIs, using both traditional tools and the developed prototype software. Our analysis indicate that advanced, registration based ROI schemes could increase clinical efficiency in time-critical settings for cases with complex ROIs, but also that their clinical feasibility is conditional with respect to the radiologists trust in the registration process and its application to the data.
Tractography in Context: Multimodal Visualization of Probabilistic Tractograms in Anatomical Context
(The Eurographics Association, 2012) Berres, Anne; Goldau, Mathias; Tittgemeyer, Marc; Scheuermann, Gerik; Hagen, Hans; Timo Ropinski and Anders Ynnerman and Charl Botha and Jos Roerdink
Multi-modal display of neurological data in anatomical context is a challenging issue in biomedical visualization. We present an application-driven approach, which solves the visibility issues arising from the simultaneous presentation of probabilistic tractograms and anatomical context. The tractogram (a scalar field indicating a connectivity score between voxels) is visualized by nested surface layers, providing an overview of long-range connectivity. Unique dataset features are reflected by value-based opacity and further enhanced by depth cues. An illustrative, three-dimensional rendering of the cortex complemented with textured slices is provided as anatomical context. The presented methods are based on a detailed requirements analysis with domain experts. Two user studies were performed to evaluate our methods and the techniques were improved based on their feedback. Our methods can be applied to a wide range of data, as they can be adapted to the range and requirements of data very easily.
A Visual Analytics Approach for Patient Stratification and Biomarker Discovery
(The Eurographics Association, 2019) Alemzadeh, Shiva; Kromp, Florian; Preim, Bernhard; Taschner-Mandl, Sabine; Bühler, Katja; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
We introduce discoVA as a visual analytics tool for the refinement of risk stratification of cancer patients and biomarker discovery. Currently, tools for the joint analysis of multiple biological and clinical information in this field are insufficient or lacking. Our tool fills this gap by enabling bio-medical experts to explore datasets of cancer patient cohorts. By using multiple coordinated visualization techniques, nested visual queries on various data types can be performed to generate/prove a hypothesis by identifying discrete sub-cohorts. We demonstrated the utility of discoVA by a case study involving bio-medical researchers.
Visual Analytics for the Exploration and Assessment of Segmentation Errors
(The Eurographics Association, 2016) Raidou, Renata G.; Marcelis, Freek J. J.; Breeuwer, Marcel; Gröller, Eduard; Vilanova, Anna; Wetering, Huub M. M. van de; Stefan Bruckner and Bernhard Preim and Anna Vilanova and Helwig Hauser and Anja Hennemuth and Arvid Lundervold
Several diagnostic and treatment procedures require the segmentation of anatomical structures from medical images. However, the automatic model-based methods that are often employed, may produce inaccurate segmentations. These, if used as input for diagnosis or treatment, can have detrimental effects for the patients. Currently, an analysis to predict which anatomic regions are more prone to inaccuracies, and to determine how to improve segmentation algorithms, cannot be performed. We propose a visual tool to enable experts, working on model-based segmentation algorithms, to explore and analyze the outcomes and errors of their methods. Our approach supports the exploration of errors in a cohort of pelvic organ segmentations, where the performance of an algorithm can be assessed. Also, it enables the detailed exploration and assessment of segmentation errors, in individual subjects. To the best of our knowledge, there is no other tool with comparable functionality. A usage scenario is employed to explore and illustrate the capabilities of our visual tool. To further assess the value of the proposed tool, we performed an evaluation with five segmentation experts. The evaluation participants confirmed the potential of the tool in providing new insight into their data and employed algorithms. They also gave feedback for future improvements.

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