VCBM 14: Eurographics Workshop on Visual Computing for Biology and Medicine
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Item Visual and Quantitative Analysis of Higher Order Arborization Overlaps for Neural Circuit Research(The Eurographics Association, 2014) Swoboda, Nicolas; Moosburner, Judith; Bruckner, Stefan; Yu, Jai Y.; Dickson, Barry J.; Bühler, Katja; Ivan Viola and Katja Buehler and Timo RopinskiNeuroscientists investigate neural circuits in the brain of the common fruit fly Drosophila melanogaster to discover how complex behavior is generated. Hypothesis building on potential connections between individual neurons is an essential step in the discovery of circuits that govern a specific behavior. Overlaps of arborizations of two or more neurons indicate a potential anatomical connection, i.e. the presence of joint synapses responsible for signal transmission between neurons. Obviously, the number of higher order overlaps (i.e. overlaps of three and more arborizations) increases exponentially with the number of neurons under investigation making it almost impossible to precompute quantitative information for all possible combinations. Thus, existing solutions are restricted to pairwise comparison of overlaps as they are relying on precomputed overlap quantification. Analyzing overlaps by visual inspection of more than two arborizations in 2D sections or in 3D is impeded by visual clutter or occlusion. This work contributes a novel tool that complements existing methods for potential connectivity exploration by providing for the first time the possibility to compute and visualize higher order arborization overlaps on the fly and to interactively explore this information in its spatial anatomical context and on a quantitative level. Qualitative evaluation with neuroscientists and non-expert users demonstrated the utility and usability of the tool.Item A Comparative User Study of a 2D and an Autostereoscopic 3D Display for a Tympanoplastic Surgery(The Eurographics Association, 2014) Baer, Alexandra; Huebler, Antje; Saalfeld, Patrick; Cunningham, Douglas; Preim, Bernhard; Ivan Viola and Katja Buehler and Timo RopinskiThis paper presents the design and execution of a comparative experimental between-participant study with 42 participants. We investigated depth perception comparing a 2D display with a glasses-free 3D autostereoscopic display in detail and conducted a follow-up study with the new 3D zSpace technology including a stylus as input device. This work comprises the design of a tympanoplastic training scenario used as the study's "real world task". Participants had to position a prosthesis implant to reconstruct the ossicular chain and thus a patient's hearing ability. The study revealed an overwhelming support of the 3D autostereoscopic display compared to a 2D display regarding depth judgment, task completion time and the number of required scene and prosthesis interactions.Item 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 RopinskiEfficacy 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.Item Visibility-Driven Processing of Streaming Volume Data(The Eurographics Association, 2014) Solteszova, Veronika; Birkeland, Asmund; Viola, Ivan; Bruckner, Stefan; Ivan Viola and Katja Buehler and Timo RopinskiIn real-time volume data acquisition, such as 4D ultrasound, the raw data is challenging to visualize directly without additional processing. Noise removal and feature detection are common operations, but many methods are too costly to compute over the whole volume when dealing with live streamed data. In this paper, we propose a visibility-driven processing scheme for handling costly on-the-fly processing of volumetric data in real-time. In contrast to the traditional visualization pipeline, our scheme utilizes a fast computation of the potentially visible subset of voxels which significantly reduces the amount of data required to process. As filtering operations modify the data values which may affect their visibility, our method for visibility-mask generation ensures that the set of elements deemed visible does not change after processing. Our approach also exploits the visibility information for the storage of intermediate values when multiple operations are performed in sequence, and can therefore significantly reduce the memory overhead of longer filter pipelines. We provide a thorough technical evaluation of the approach and demonstrate it on several typical scenarios where on-the-fly processing is required.Item Extracting and Visualizing Uncertainties in Segmentations from 3D Medical Data(The Eurographics Association, 2014) Faltin, Peter; Chaisaowong, Kraisorn; Kraus, Thomas; Merhof, Dorit; Ivan Viola and Katja Buehler and Timo RopinskiAssessing surfaces of segmentations extracted from 3D image data for medical purposes requires dedicated extraction and visualization methods. In particular, when assessing follow-up cases, the exact volume and confidence level of the segmentation surface is crucial for medical decision-making. This paper introduces a new processing chain comprising a series of carefully selected and well-matched steps to determine and visualize a segmentation boundary. In a first step, the surface, segmentation confidence and statistical partial volume are extracted. Then, a mesh-based method is applied to determine a refined boundary of the segmented object based on these properties, whilst smoothness, confidence of the surface and partial volume are considered locally. In contrast to existing methods, the proposed approach is able to guarantee the estimated volume for the whole segmentation, which is an important prerequisite for clinical application. Furthermore, a novel visualization method is presented which was specifically designed to simultaneously provide information about 3D morphology, confidence and possible errors. As opposed to classical visualization approaches that take advantage of color and transparency but need some geometric mapping and interpretation from the observer, the proposed scattered visualization utilizes density and scattering, which are much closer and more intuitively related to the original geometric meaning. The presented method is particularly suitable to assess pleural thickenings from follow-up CT images, which further illustrates the potential of the proposed method.Item Misalignment Correction in Open Cone-Beam CT(The Eurographics Association, 2014) Wieckowski, Adam; Stopp, Fabian; Käseberg, Marc; Keeve, Erwin; Ivan Viola and Katja Buehler and Timo RopinskiCone-beam computed tomography (CBCT) is an established standard for both, medical and industrial volumetric imaging. To compute a 3D volume, multiple 2D x-ray projection images of an object of interest are acquired from different directions. Using the geometric information about the acquisition geometry of each image, the volume is reconstructed. Incorrect geometric information (misalignments) leads to blurring and other artifacts in the resulting reconstruction. The exact acquisition geometry is commonly calculated by the analysis of a scan of a dedicated calibration body (off-line calibration). Such approach requires high repeat accuracy of the scanner mechanics and cannot account for non-systematic deviations. Current methods allowing for misalignment correction without a dedicated phantom, e.g. by iteratively adapting the geometry to minimize the arising artifacts, were developed to work with planar trajectories. It poses a problem for open CBCT systems driving complex trajectories. Therefore, we propose an enhanced method allowing for misalignment correction for general trajectories. We developed a new quality function and a flexible modeling for misalignments. We successfully applied our method to real datasets acquired along planar and non-planar trajectories. The correction with our approach substantially increases the resulting volume quality.Item Uncertainty-aware Ensemble of Classifiers for Segmenting Brain MRI Data(The Eurographics Association, 2014) Al-Taie, Ahmed; Hahn, Horst K.; Linsen, Lars; Ivan Viola and Katja Buehler and Timo RopinskiEstimating and visualizing uncertainty in medical image segmentation has become an active research area due to the necessity of making medical experts aware of possibly wrong segmentation decisions. Still, to our knowledge all these methods are based on a single choice of the underlying segmentation approach. Segmentation using an ensemble of classifiers (or committee machine) use multiple classifiers to increase the performance when compared to applying a single classifier. In this paper, we propose methods to estimate uncertainties in segmentations produced by ensembles of classifiers. We investigate and compare the different combining strategies of the segmentation results of the ensemble members from an uncertainty point of view. We discuss why some combining strategies tend to perform better than others. Also, we visualize the estimated uncertainties using a color mapping in image space and propose a post-segmentations correction step to reclassify the noisy pixels in the final result based on the statistical uncertainty.Item Real-Time Dense Nucleus Selection from Confocal Data(The Eurographics Association, 2014) Wan, Yong; Otsuna, Hideo; Kwan, K. M.; Hansen, Charles; Ivan Viola and Katja Buehler and Timo RopinskiSelecting structures from volume data using direct over-the-visualization interactions, such as a paint brush, is perhaps the most intuitive method in a variety of application scenarios. Unfortunately, it seems difficult to design a universal tool that is effective for all different structures in biology research. In [WOCH12b], an interactive technique was proposed for extracting neural structures from confocal microscopy data. It uses a dual-stroke paint brush to select desired structures directly from volume visualizations. However, the technique breaks down when it was applied to selecting densely packed structures with condensed shapes, such as nuclei from zebrafish eye development research. We collaborated with biologists studying zebrafish eye development and adapted the paint brush tool for real-time nucleus selection from volume data. The morphological diffusion algorithm used in the previous paint brush is restricted to gradient descending directions for improved nucleus boundary definition. Occluded seeds are removed using backward ray-casting. The adapted paint brush is then used in tracking cell movements in a time sequence dataset of a developing zebrafish eye.Item A Survey on Visualizing Magnetic Resonance Spectroscopy Data(The Eurographics Association, 2014) Nunes, Miguel; Laruelo, Andrea; Ken, SoleaKhena; Laprie, Anne; Bühler, Katja; Ivan Viola and Katja Buehler and Timo RopinskiData from Magnetic Resonance Spectroscopy Imaging (MRSI) contains signals about biomarkers concentrations, which are used to achieve new knowledge about biochemical processes. These support doctors in identifying and treat diseases as well as better defining regions of interest. In clinical environment, the lack of appropriate methods and tools to visualize MRSI has made this imaging technique information hard to interpret and include in treatment planning workflows. This paper is doing a review on how MRSI data is analysed in a medical environment as well as new approaches from the rendering and visual analytics areas. We conclude that this topic will be under the spotlight in the coming years, as current research is still facing many challenges on which the visualization community can actively contribute to.Item Personalized X-ray Reconstruction of the Proximal Femur via a New Control Point-based 2D-3D Registration and Residual Complexity Minimization(The Eurographics Association, 2014) Yu, Weimin; Zheng, Guoyan; Ivan Viola and Katja Buehler and Timo RopinskiIn this paper we present a new control point-based 2D-3D registration approach for a deformable registration of a 3D volumetric template to a limited number of 2D calibrated C-arm images and show its application to a personalized X-ray reconstruction of the proximal femur. In our approach, the 2D-3D registration is done with a hierarchical two-stage strategy: the scaled rigid 2D-3D registration stage followed by a regularized deformable b-spline 2D-3D registration stage. In both stages, a set of control points with uniform spacing are placed over the domain of the 3D volumetric template first. The registrations are then driven by computing updated positions of these control points with intensity-based 2D-2D image registrations of C-arm images with the associated digitally reconstructed radiographs (DRRs), which then allows computing the associated registration transformation at each stage. In order to account for intensity nonstationarities and complex spatially-varying intensity distortion in the deformable b-spline 2D-3D registration stage, the intensity-based 2D-2D image registrations at this stage are done based on minimizing the complexity of the residual images between the C-arm images and the associated DRRs. Comprehensive experiments on simulated images, on images of cadaveric femurs and on clinical datasets are designed and conducted to evaluate the performance of the proposed approach. Quantitative and qualitative evaluation results are given, which demonstrate the efficacy of the present approach.Item Interactive Labeling of Toponome Data(The Eurographics Association, 2014) Oeltze-Jafra, Steffen; Pieper, Franz; Hillert, Reyk; Preim, Bernhard; Schubert, Walter; Ivan Viola and Katja Buehler and Timo RopinskiBiological multi-channel microscopy data are often characterized by a high local entropy and phenotypically identical structures covering only a few pixels and forming disjoint regions spread over, e.g., a cell or a tissue section. Toponome data as an example, comprise a fluorescence image (channel) per protein affinity reagent, and capture the location and spatial distribution of proteins in cells and tissues. Biologists investigate such data using a region-of-interest in an image view and a linked view displaying information aggregated or derived from the channels. The cognitive effort of moving the attention back and forth between the views is immense. We present an approach for the in-place annotation of multi-channel microscopy data in 2D views. We combine dynamic excentric labeling and static necklace maps to cope with the special characteristics of these data. The generated annotations support the biologists in visually exploring multi-channel information directly in its spatial context. A label is generated per unique phenotype included in a flexible, moveable focus region. The labels are organized in a circular fashion around the focus region. On demand, a nested labeling can be generated by displaying a second ring of labels which represents the channels characterizing the focused phenotypes. We demonstrate our approach by toponome data of a rhabdomyosarcoma cell line and a prostate tissue section.Item Inlier Detection in Thermal Sensitive Images(The Eurographics Association, 2014) Zadicario, Eyal; Carmi, N.; Ju, Tao; Cohen-Or, Daniel; Ivan Viola and Katja Buehler and Timo RopinskiImage guidance of medical procedures may use thermal images to monitor a treatment. Analysis of the thermal images by the physician may be time consuming and confusing because the thermal image includes multiple outliers. We present a novel inlier detection method for thermal images that results in reliable thermal information to support medical decision making. Outliers in thermal images are particularly challenging to detect using conventional methods, because they are significantly more abundant than inliers and, like inliers, they may be temporally consistent. Our inlier detection method is physically-based: it is motivated by the fact that heat propagation in soft tissues can be modeled using the bio-heat equation. Pixels are classified as inliers only if the temperature pattern in a spatial and temporal neighborhood strongly correlates with the physical model. For improved robustness, the correlation process includes a 2D filter in the spatial domain and a 3D filter in both spatial and temporal domains. Experiments with real data have shown that our method produces results that agree with annotations provided by human experts even in outlier-laden images. Our results show inliers can be detected leaving true heat pixels for the physician to observe, while not overloading him with the need to analyze outliers. The technique has been integrated in a true clinical environment and is being used to aid physicians in analysis of thermal imagesItem 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 RopinskiIn 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.Item Deriving Anatomical Context from 4D Ultrasound(The Eurographics Association, 2014) Müller, Markus; Helljesen, Linn E. S.; Prevost, Raphael; Viola, Ivan; Nylund, Kim; Gilja, Odd Helge; Navab, Nassir; Wein, Wolfgang; Ivan Viola and Katja Buehler and Timo RopinskiReal-time three-dimensional (also known as 4D) ultrasound imaging using matrix array probes has the potential to create large-volume information of entire organs such as the liver without external tracking hardware. This information can in turn be placed into the context of a CT or MRI scan of the same patient. However for such an approach many image processing challenges need to be overcome and sources of error addressed, including reconstruction drift, anatomical deformations, varying appearance of anatomy, and imaging artifacts. In this work, we present a fully automatic system including robust image-based ultrasound tracking, a novel learning-based global initialization of the anatomical context, and joint mono- and multi-modal registration. In an evaluation on 4D US sequences and MRI scans of eight volunteers we achieve automatic reconstruction and registration without any user interaction, assess the registration errors based on physician-defined landmarks, and demonstrate realtime tracking of free-breathing sequences.Item 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 RopinskiFour-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.Item Visualizing Movements of Protein Tunnels in Molecular Dynamics Simulations(The Eurographics Association, 2014) Kozlíková, Barbora; Jurcík, Adam; By ka, Jan; Strnad, Ondrej; Sochor, Jirí; Ivan Viola and Katja Buehler and Timo RopinskiAnalysis and visualization of molecules and their structural features help biochemists and biologists to better understand protein behavior. Studying these structures in molecular dynamics simulations enhances this understanding. In this paper we introduce three approaches for animating specific inner pathways composed of an empty space between atoms, called tunnels. These tunnels facilitate the transport of small molecules, water solvent and ions in many proteins. They help researchers understand the structure-function relationships of proteins and the knowledge of tunnel properties improves the design of new inhibitors. Our methods are derived from selected tunnel representations when each stresses some of the important tunnel properties-width, shape, mapping of physico-chemical properties, etc. Our methods provide smooth animation of the movement of tunnels as they change their length and shape throughout the simulation.Item Survey of Labeling Techniques in Medical Visualizations(The Eurographics Association, 2014) Oeltze-Jafra, Steffen; Preim, Bernhard; Ivan Viola and Katja Buehler and Timo RopinskiAnnotations of relevant structures and regions are crucial in diagnostics, treatment planning, medical team meetings as well as in medical education. They serve to focus discussions, present results of collaborative decision making, record and forward diagnostic findings, support orientation in complex or unfamiliar views on the data, and study anatomy. Different techniques have been presented for labeling the original data in 2D slice views, surface representations of structures extracted from the data, e.g., organs and vasculature, and 3D volume rendered representations of the data. All aim at a clear visual association of labels and structures, visible and legible labels, and a fast and aesthetic labeling while considering individual properties of the data and its representation and tackling various issues, e.g., occlusion of structures by labels, overlapping labels, and crossings of lines connecting labels with structures. We survey the medical labeling work and propose a classification with respect to the employed labeling technique. We give guidelines for choosing a technique dependent on the data representation, e.g., surface rendering or slice view, the type of structures to be labeled, and the individual requirements on an effective label layout.Item 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 RopinskiThe 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.Item Membrane Mapping: Combining Mesoscopic and Molecular Cell Visualization(The Eurographics Association, 2014) Waltemate, Thomas; Sommer, Björn; Botsch, Mario; Ivan Viola and Katja Buehler and Timo RopinskiThree-dimensional cell visualization is an important topic in today's cytology-affiliated community. Cell illustrations and animations are used for scientific as well as for educational purposes. Unfortunately, there exist only few tools to support the cell modeling process on a molecular level. A major problem is the immense intracellular size variation between relatively large mesoscopic cell components and small molecular membrane patches. This makes both modeling and visualization of whole cells a challenging task. In this paper we propose Membrane Mapping as an interactive tool for combining the mesoscopic and molecular level. Based on instantly computed local parameterizations we map patches of molecular membrane structures onto user-selected regions of cell components. By designing an efficient and GPU-friendly mapping technique, our approach allows to visualize and map pre-computed molecular dynamics simulations of membrane patches to mesoscopic structures in real-time. This enables the visualization of whole cells on a mesoscopic level with an interactive magnifier tool for inspecting their molecular structure and dynamic behavior.Item Imaging the Vascular Network of the Human Spleen from Immunostained Serial Sections(The Eurographics Association, 2014) Ulrich, Christine; Lobachev, Oleg; Steiniger, Birte; Guthe, Michael; Ivan Viola and Katja Buehler and Timo RopinskiThe spleen is one of the organs, where the micro-structure and the function on that level are not completely understood. It was for example only recently found that is has an open circulation, which distinguishes it from all other organs. Imaging the complete vascular network from the arteries to open-ended capillaries would greatly facilitate research in this area. The structure of such tissue is best uncovered using immunehistological staining. This can however only be applied to thin tissue sections and larger structures span several slices. Due to the deformation induced when cutting the specimen, standard registration algorithms cannot be used to merge the images into a volume. We propose a specialized matching algorithm to robustly determine corresponding regions in the images. After a rigid alignment of the scans, we use a cubic B-spline to deform and align the images. During this process we minimize the total deformation to produce as accurate results as possible.