Browsing by Author "Lelieveldt, Boudewijn"

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    Cytosplore Simian Viewer: Visual Exploration for Multi-Species Single-Cell RNA Sequencing Data
    (The Eurographics Association, 2023) Basu, Soumyadeep; Eggermont, Jeroen; Kroes, Thomas; Jorstad, Nikolas; Bakken, Trygve; Lein, Ed; Lelieveldt, Boudewijn; Höllt, Thomas; Hansen, Christian; Procter, James; Renata G. Raidou; Jönsson, Daniel; Höllt, Thomas
    With the rapid advances in single-cell sequencing technologies, novel types of studies into the cell-type makeup of the brain have become possible. Biologists often analyze large and complex single-cell transcriptomic datasets to enhance knowledge of the intricate features of cellular and molecular tissue organization. A particular area of interest is the study of whether cell types and their gene regulation are conserved across species during evolution. However, in-depth comparisons across species of such high-dimensional, multi-modal single-cell data pose considerable visualization challenges. This paper introduces Cytosplore Simian Viewer, a visualization system that combines various views and linked interaction methods for comparative analysis of single-cell transcriptomic datasets across multiple species. Cytosplore Simian Viewer enables biologists to help gain insights into the cell type and gene expression differences and similarities among different species, particularly focusing on comparing human data to other species. The system validation in discovery research on real-world datasets demonstrates its utility in visualizing valuable results related to the evolutionary development of the middle temporal gyrus.
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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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    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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    Visual Analysis of Tissue Images at Cellular Level
    (The Eurographics Association, 2021) Somarakis, Antonios; Ijsselsteijn, Marieke E.; Kenkhuis, Boyd; Unen, Vincent van; Luk, Sietse J.; Koning, Frits; Weerd, Louise van der; Miranda, Noel F. C. C. de; Lelieveldt, Boudewijn P. F.; Höllt, Thomas; Oeltze-Jafra, Steffen and Raidou, Renata Georgia
    The detailed analysis of tissue composition is crucial for the understanding of tissue functionality. For example, the location of immune cells related to a tumour area is highly correlated with the effectiveness of immunotherapy. Therefore, experts are interested in presence of cells with specific characteristics as well as the spatial patterns they form. Recent advances in single-cell imaging modalities, producing high-dimensional, high-resolution images enable the analysis of both of these features. However, extracting useful insight on tissue functionality from these high-dimensional images poses serious and diverse challenges to data analysis. We have developed an interactive, data-driven pipeline covering the main analysis challenges experts face, from the pre-processing of images via the exploration of tissue samples to the comparison of cohorts of samples. All parts of our pipeline have been developed in close collaboration with domain experts and are already a vital part in their daily analysis routine.