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Vieth, A. (author), Kroes, Thomas (author), Thijssen, Julian (author), Lew, Baldur van (author), Eggermont, Jeroen (author), Basu, Soumyadeep (author), Eisemann, E. (author), Vilanova, Anna (author), Höllt, T. (author), Lelieveldt, B.P.F. (author)Exploration and analysis of high-dimensional data are important tasks in many fields that produce large and complex data, like the financial sector, systems biology, or cultural heritage. Tailor-made visual analytics software is developed for each specific application, limiting their applicability in other fields. However, as diverse as these...journal article 2024
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Li, Chang (author), Thijssen, Julian (author), Kroes, Thomas (author), de Boer, Mitchell (author), Abdelaal, T.R.M. (author), Höllt, T. (author), Lelieveldt, B.P.F. (author)In spatial transcriptomics (ST) data, biologically relevant features such as tissue compartments or cell-state transitions are reflected by gene expression gradients. Here, we present SpaceWalker, a visual analytics tool for exploring the local gradient structure of 2D and 3D ST data. The user can be guided by the local intrinsic...journal article 2023
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Vieth, A. (author), Lelieveldt, B.P.F. (author), Eisemann, E. (author), Vilanova, Anna (author), Höllt, T. (author)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...conference paper 2023
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Basu, S. (author), Eggermont, Jeroen (author), Kroes, Thomas (author), Jorstad, Nikolas (author), Bakken, Trygve (author), Lein, Ed (author), Lelieveldt, B.P.F. (author), Höllt, T. (author)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...conference paper 2023
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Hawrylycz, Michael (author), Martone, Maryann E. (author), Ascoli, Giorgio A. (author), Bjaalie, Jan G. (author), Dong, Hong Wei (author), Ghosh, Satrajit S. (author), Gillis, Jesse (author), Haynor, David R. (author), Lelieveldt, B.P.F. (author)Characterizing cellular diversity at different levels of biological organization and across AU data: Ple modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain...journal article 2023
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Zhang, Yun (author), Miller, Jeremy A. (author), Park, Jeongbin (author), Lelieveldt, B.P.F. (author), Abdelaal, T.R.M. (author), Dzyubachyk, O. (author), Lein, Ed S. (author), Scheuermann, Richard H. (author)With the advent of multiplex fluorescence in situ hybridization (FISH) and in situ RNA sequencing technologies, spatial transcriptomics analysis is advancing rapidly, providing spatial location and gene expression information about cells in tissue sections at single cell resolution. Cell type classification of these spatially-resolved cells...journal article 2023
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Jorstad, Nikolas L. (author), Song, Janet H.T. (author), Exposito-Alonso, David (author), Suresh, Hamsini (author), Castro-Pacheco, Nathan (author), Basu, S. (author), Kroes, T. (author), Höllt, T. (author), Lelieveldt, B.P.F. (author)The cognitive abilities of humans are distinctive among primates, but their molecular and cellular substrates are poorly understood. We used comparative single-nucleus transcriptomics to analyze samples of the middle temporal gyrus (MTG) from adult humans, chimpanzees, gorillas, rhesus macaques, and common marmosets to understand human...journal article 2023
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Brouwer, Thomas P. (author), de Vries, Natasja L. (author), Abdelaal, T.R.M. (author), Li, Zheng (author), Ruano, Dina (author), Fariña, Arantza (author), Lelieveldt, B.P.F. (author), Morreau, Hans (author), Vahrmeijer, Alexander L. (author)BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy in need of effective (immuno)therapeutic treatment strategies. For the optimal application and development of cancer immunotherapies, a comprehensive understanding of local and systemic immune profiles in patients with PDAC is required. Here, our goal was to...journal article 2022
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Popa, A. (author), Gabrieli, F. (author), Kroes, T. (author), Krekeler, A. (author), Alfeld, M.W.E.M. (author), Lelieveldt, B.P.F. (author), Eisemann, E. (author), Höllt, T. (author)Reflectance Imaging Spectroscopy (RIS) is a hyperspectral imaging technique used for investigating the molecular composition of materials. It can help identify pigments used in a painting, which are relevant information for art conservation and history. For every scanned pixel, a reflectance spectrum is obtained and domain experts look for pure...conference paper 2022
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van Unen, Vincent (author), Ouboter, Laura F. (author), Li, Na (author), Schreurs, Mette (author), Abdelaal, T.R.M. (author), Kooy-Winkelaar, Yvonne (author), Beyrend, Guillaume (author), Höllt, T. (author), Maljaars, P. W.Jeroen (author), Mearin, M. Luisa (author), Mahfouz, A.M.E.T.A. (author), Witte, Anne M.C. (author), Clemens, Cornelis H.M. (author), Abraham, Sunje (author), Escher, Johanna C. (author), Lelieveldt, B.P.F. (author), Pascutti, M. Fernanda (author), van der Meulen – de Jong, Andrea E. (author), Koning, Frits (author)Chronic intestinal inflammation underlies inflammatory bowel disease (IBD). Previous studies indicated alterations in the cellular immune system; however, it has been challenging to interrogate the role of all immune cell subsets simultaneously. Therefore, we aimed to identify immune cell types associated with inflammation in IBD using high...journal article 2022
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Vieth, A. (author), Vilanova, A. (author), Lelieveldt, B.P.F. (author), Eisemann, E. (author), Höllt, T. (author)High-dimensional imaging is becoming increasingly relevant in many fields from astronomy and cultural heritage to systems biology. Visual exploration of such high-dimensional data is commonly facilitated by dimensionality reduction. However, common dimensionality reduction methods do not include spatial information present in images, such as...conference paper 2022
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Sokooti, Hessam (author), Yousefi, Sahar (author), Elmahdy, Mohamed S. (author), Lelieveldt, B.P.F. (author), Staring, M. (author)In this paper we propose a supervised method to predict registration misalignment using convolutional neural networks (CNNs). This task is casted to a classification problem with multiple classes of misalignment: 'correct' 0-3 mm, 'poor' 3-6 mm and 'wrong' over 6 mm. Rather than a direct prediction, we propose a hierarchical approach, where...journal article 2021
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Bakken, Trygve E. (author), Jorstad, Nikolas L. (author), Hu, Qiwen (author), Tian, Wei (author), Kalmbach, Brian E. (author), Eggermont, Jeroen (author), Aevermann, Brian D. (author), Höllt, T. (author), Lelieveldt, B.P.F. (author)The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals<sup>1</sup>. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region,...journal article 2021
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Koolstra, Kirsten (author), Börnert, Peter (author), Lelieveldt, B.P.F. (author), Webb, A. (author), Dzyubachyk, Oleh (author)Objective: To visualize the encoding capability of magnetic resonance fingerprinting (MRF) dictionaries. Materials and methods: High-dimensional MRF dictionaries were simulated and embedded into a lower-dimensional space using t-distributed stochastic neighbor embedding (t-SNE). The embeddings were visualized via colors as a surrogate for...journal article 2021
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Aevermann, Brian (author), Zhang, Yun (author), Novotny, Mark (author), Keshk, Mohamed (author), Bakken, Trygve (author), Miller, Jeremy (author), Hodge, Rebecca (author), Lelieveldt, B.P.F. (author), Lein, Ed (author), Scheuermann, Richard H. (author)Single-cell genomics is rapidly advancing our knowledge of the diversity of cell phenotypes, including both cell types and cell states. Driven by single-cell/-nucleus RNA sequencing (scRNA-seq), comprehensive cell atlas projects characterizing a wide range of organisms and tissues are currently underway. As a result, it is critical that the...journal article 2021
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Kenkhuis, Boyd (author), Somarakis, Antonios (author), de Haan, Lorraine (author), Dzyubachyk, Oleh (author), Ijsselsteijn, Marieke E. (author), de Miranda, Noel F. C. C. (author), Lelieveldt, B.P.F. (author), Dijkstra, Jouke (author), Van Roon-Mom, Willeke (author), Höllt, T. (author), van der Weerd, Louise (author)Brain iron accumulation has been found to accelerate disease progression in amyloid-β(Aβ) positive Alzheimer patients, though the mechanism is still unknown. Microglia have been identified as key players in the disease pathogenesis, and are highly reactive cells responding to aberrations such as increased iron levels. Therefore, using...journal article 2021
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de Jong, Sanne E. (author), van Unen, Vincent (author), Manurung, Mikhael D. (author), Jochems, Simon P. (author), Höllt, T. (author), Pezzotti, N. (author), Eisemann, E. (author), Lelieveldt, B.P.F. (author), Reinders, M.J.T. (author)Controlled human infections provide opportunities to study the interaction between the immune system and malaria parasites, which is essential for vaccine development. Here, we compared immune signatures of malaria-naive Europeans and of Africans with lifelong malaria exposure using mass cytometry, RNA sequencing and data integration, before...journal article 2021
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Ijsselsteijn, Marieke E. (author), Somarakis, Antonios (author), Lelieveldt, B.P.F. (author), Höllt, T. (author), de Miranda, Noel F. C. C. (author)Imaging mass cytometry (IMC) allows the detection of multiple antigens (approximately 40 markers) combined with spatial information, making it a unique tool for the evaluation of complex biological systems. Due to its widespread availability and retained tissue morphology, formalin-fixed, paraffin-embedded (FFPE) tissues are often a material...journal article 2021
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Somarakis, Antonios (author), Ijsselsteijn, Marieke E. (author), Luk, Sietse J. (author), Kenkhuis, Boyd (author), de Miranda, Noel F. C. C. (author), Lelieveldt, B.P.F. (author), Höllt, T. (author)Spatially-resolved omics-data enable researchers to precisely distinguish cell types in tissue and explore their spatial interactions, enabling deep understanding of tissue functionality. To understand what causes or deteriorates a disease and identify related biomarkers, clinical researchers regularly perform large-scale cohort studies,...journal article 2021
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Somarakis, Antonios (author), van Unen, Vincent (author), Koning, Frits (author), Lelieveldt, B.P.F. (author), Höllt, T. (author)Tissue functionality is determined by the characteristics of tissue-resident cells and their interactions within their microenvironment. Imaging Mass Cytometry offers the opportunity to distinguish cell types with high precision and link them to their spatial location in intact tissues at sub-cellular resolution. This technology produces large...journal article 2021