Browsing by Author "Vilanova, Anna"

Now showing 1 - 8 of 8
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    Cytosplore: Interactive Visual Single-Cell Profiling of the Immune System
    (The Eurographics Association, 2019) Höllt, Thomas; Pezzotti, Nicola; van Unen, Vincent; Li, Na; Koning, Frits; Eisemann, Elmar; Lelieveldt, Boudewijn P. F.; Vilanova, Anna; Bruckner, Stefan and Oeltze-Jafra, Steffen
    Recent advances in single-cell acquisition technology have led to a shift towards single-cell analysis in many fields of biology. In immunology, detailed knowledge of the cellular composition is of interest, as it can be the cause of deregulated immune responses, which cause diseases. Similarly, vaccination is based on triggering proper immune responses; however, many vaccines are ineffective or only work properly in a subset of those who are vaccinated. Identifying differences in the cellular composition of the immune system in such cases can lead to more precise treatment. Cytosplore is an integrated, interactive visual analysis framework for the exploration of large single-cell datasets. We have developed Cytosplore in close collaboration with immunology researchers and several partners use the software in their daily workflow. Cytosplore enables efficient data analysis and has led to several discoveries alongside high-impact publications.
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    Focus+Context Exploration of Hierarchical Embeddings
    (The Eurographics Association and John Wiley & Sons Ltd., 2019) Höllt, Thomas; Vilanova, Anna; Pezzotti, Nicola; Lelieveldt, Boudewijn P. F.; Hauser, Helwig; Gleicher, Michael and Viola, Ivan and Leitte, Heike
    Hierarchical embeddings, such as HSNE, address critical visual and computational scalability issues of traditional techniques for dimensionality reduction. The improved scalability comes at the cost of the need for increased user interaction for exploration. In this paper, we provide a solution for the interactive visual Focus+Context exploration of such embeddings. We explain how to integrate embedding parts from different levels of detail, corresponding to focus and context groups, in a joint visualization. We devise an according interaction model that relates typical semantic operations on a Focus+Context visualization with the according changes in the level-of-detail-hierarchy of the embedding, including also a mode for comparative Focus+Context exploration and extend HSNE to incorporate the presented interaction model. In order to demonstrate the effectiveness of our approach, we present a use case based on the visual exploration of multi-dimensional images.
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    InkVis: A High-Particle-Count Approach for Visualization of Phase-Contrast Magnetic Resonance Imaging Data
    (The Eurographics Association, 2019) de Hoon, Niels; Lawonn, Kai; Jalba, Andrei; Eisemann, Elmar; Vilanova, Anna; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
    Phase-Contrast Magnetic Resonance Imaging (PC-MRI) measures volumetric and time-varying blood flow data, unsurpassed in quality and completeness. Such blood-flow data have been shown to have the potential to improve both diagnosis and risk assessment of cardiovascular diseases (CVDs) uniquely. Typically PC-MRI data is visualized using stream- or pathlines. However, time-varying aspects of the data, e.g., vortex shedding, breakdown, and formation, are not sufficiently captured by these visualization techniques. Experimental flow visualization techniques introduce a visible medium, like smoke or dye, to visualize flow aspects including time-varying aspects. We propose a framework that mimics such experimental techniques by using a high number of particles. The framework offers great flexibility which allows for various visualization approaches. These include common traditional flow visualizations, but also streak visualizations to show the temporal aspects, and uncertainty visualizations. Moreover, these patient-specific measurements suffer from noise artifacts and a coarse resolution, causing uncertainty. Traditional flow visualizations neglect uncertainty and, therefore, may give a false sense of certainty, which can mislead the user yielding incorrect decisions. Previously, the domain experts had no means to visualize the effect of the uncertainty in the data. Our framework has been adopted by domain experts to visualize the vortices present in the sinuses of the aorta root showing the potential of the framework. Furthermore, an evaluation among domain experts indicated that having the option to visualize the uncertainty contributed to their confidence on the analysis.
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    Interactions for Seamlessly Coupled Exploration of High-Dimensional Images and Hierarchical Embeddings
    (The Eurographics Association, 2023) Vieth, Alexander; Lelieveldt, Boudewijn; Eisemann, Elmar; Vilanova, Anna; Höllt, Thomas; Guthe, Michael; Grosch, Thorsten
    High-dimensional images (i.e., with many attributes per pixel) are commonly acquired in many domains, such as geosciences or systems biology. The spatial and attribute information of such data are typically explored separately, e.g., by using coordinated views of an image representation and a low-dimensional embedding of the high-dimensional attribute data. Facing ever growing image data sets, hierarchical dimensionality reduction techniques lend themselves to overcome scalability issues. However, current embedding methods do not provide suitable interactions to reflect image space exploration. Specifically, it is not possible to adjust the level of detail in the embedding hierarchy to reflect changing level of detail in image space stemming from navigation such as zooming and panning. In this paper, we propose such a mapping from image navigation interactions to embedding space adjustments. We show how our mapping applies the "overview first, details-on-demand" characteristic inherent to image exploration in the high-dimensional attribute space. We compare our strategy with regular hierarchical embedding technique interactions and demonstrate the advantages of linking image and embedding interactions through a representative use case.
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    Interactive Visual Exploration of Region-based Sensitivities in Fiber Tracking
    (The Eurographics Association, 2023) Siddiqui, Faizan; Höllt, Thomas; Vilanova, Anna; Hansen, Christian; Procter, James; Renata G. Raidou; Jönsson, Daniel; Höllt, Thomas
    Fiber tracking is a powerful technique that provides valuable insights into the complex white matter structure of the human brain. However, the processing pipeline involves many sources of uncertainty, with one notable factor being the user-defined parameters that significantly influence the resulting outputs. Among these parameters, the definition of seed-points is a crucial aspect in most fiber tracking algorithms. These seed-points are determined through regions of interest (ROI) and serve as the initial points for fiber tract generation. In this work, we present an interactive technique that utilizes seed-point sensitivities to guide the definition of regions of interest (ROI). We examine various scenarios where sensitivity information can enhance the ROI definition process and provide user guidelines and recommended actions for each scenario. Building upon this analysis, we have developed a visualization strategy that enables users to explore seed-point sensitivities effectively and facilitate the definition of optimal ROIs. We present results highlighting the benefits of the proposed visual design in the clinical pipelines.
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    ModelWise: Interactive Model Comparison for Model Diagnosis, Improvement and Selection
    (The Eurographics Association and John Wiley & Sons Ltd., 2022) Meng, Linhao; Elzen, Stef van den; Vilanova, Anna; Borgo, Rita; Marai, G. Elisabeta; Schreck, Tobias
    Model comparison is an important process to facilitate model diagnosis, improvement, and selection when multiple models are developed for a classification task. It involves careful comparison concerning model performance and interpretation. Current visual analytics solutions often ignore the feature selection process. They either do not support detailed analysis of multiple multi-class classifiers or rely on feature analysis alone to interpret model results. Understanding how different models make classification decisions, especially classification disagreements of the same instances, requires a deeper model understanding. We present ModelWise, a visual analytics method to compare multiple multi-class classifiers in terms of model performance, feature space, and model explanation. ModelWise adapts visualizations with rich interactions to support multiple workflows to achieve model diagnosis, improvement, and selection. It considers feature subspaces generated for use in different models and improves model understanding by model explanation. We demonstrate the usability of ModelWise with two case studies, one with a small exemplar dataset and another developed with a machine learning expert with real-world perioperative data.
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    NeRF for 3D Reconstruction from X-ray Angiography: Possibilities and Limitations
    (The Eurographics Association, 2023) Maas, Kirsten W. H.; Pezzotti, Nicola; Vermeer, Amy J. E.; Ruijters, Danny; Vilanova, Anna; Hansen, Christian; Procter, James; Renata G. Raidou; Jönsson, Daniel; Höllt, Thomas
    Neural Radiance Field (NeRF) is a promising deep learning technique based on neural rendering for three-dimensional (3D) reconstruction. This technique has overcome several limitations of 3D reconstruction techniques, such as removing the need for 3D ground truth or two-dimensional (2D) segmentations. In the medical context, the 3D reconstruction of vessels from 2D X-ray angiography is a relevant problem. For example, the treatment of coronary arteries could still benefit from 3D reconstruction solutions, as common solutions do not suffice. Challenging areas in the 3D reconstruction from X-ray angiography are the vessel morphology characteristics, such as sparsity, overlap, and the distinction between foreground and background. Moreover, sparse view and limited angle X-ray projections restrict the information available for the 3D reconstructions. Many traditional and machine learning methods have been proposed, but they rely on demanding user interactions or require large amounts of training data. NeRF could solve these limitations, given that promising results have been shown for medical (X-ray) applications. However, to the best of our knowledge, no results have been shown with X-ray angiography projections or consider the vessel morphology characteristics. This paper explores the possibilities and limitations of using NeRF for 3D reconstruction from X-ray angiography. An extensive experimental analysis is conducted to quantitatively and qualitatively evaluate the effects of the X-ray angiographic challenges on the reconstruction quality. We demonstrate that NeRF has the potential for 3D Xray angiography reconstruction (e.g., reconstruction with sparse and limited angle X-ray projections) but also identify explicit limitations (e.g., the overlap of background structures) that must be addressed in future works.
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    A Progressive Approach for Uncertainty Visualization in Diffusion Tensor Imaging
    (The Eurographics Association and John Wiley & Sons Ltd., 2021) Siddiqui, Faizan; Höllt, Thomas; Vilanova, Anna; Borgo, Rita and Marai, G. Elisabeta and Landesberger, Tatiana von
    Diffusion Tensor Imaging (DTI) is a non-invasive magnetic resonance imaging technique that, combined with fiber tracking algorithms, allows the characterization and visualization of white matter structures in the brain. The resulting fiber tracts are used, for example, in tumor surgery to evaluate the potential brain functional damage due to tumor resection. The DTI processing pipeline from image acquisition to the final visualization is rather complex generating undesirable uncertainties in the final results. Most DTI visualization techniques do not provide any information regarding the presence of uncertainty. When planning surgery, a fixed safety margin around the fiber tracts is often used; however, it cannot capture local variability and distribution of the uncertainty, thereby limiting the informed decision-making process. Stochastic techniques are a possibility to estimate uncertainty for the DTI pipeline. However, it has high computational and memory requirements that make it infeasible in a clinical setting. The delay in the visualization of the results adds hindrance to the workflow. We propose a progressive approach that relies on a combination of wild-bootstrapping and fiber tracking to be used within the progressive visual analytics paradigm. We present a local bootstrapping strategy, which reduces the computational and memory costs, and provides fibertracking results in a progressive manner. We have also implemented a progressive aggregation technique that computes the distances in the fiber ensemble during progressive bootstrap computations. We present experiments with different scenarios to highlight the benefits of using our progressive visual analytic pipeline in a clinical workflow along with a use case and analysis obtained by discussions with our collaborators.