Humans have unique cognitive abilities among primates, including language, but their molecular, cellular, and circuit substrates are poorly understood. We used comparative single nucleus transcriptomics in adult humans, chimpanzees, gorillas,...

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...

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,...

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...

Microglia have been identified as key players in Alzheimer’s disease pathogenesis, and other neurodegenerative diseases. Iba1, and more specifically TMEM119 and P2RY12 are gaining ground as presumedly more specific microglia...

Background The composition of the tumor immune microenvironment (TIME) associated with good prognosis generally also predicts the success of immunotherapy, and both entail the presence of pre-existing tumor-specific T cells....

The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei...

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...

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...

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...

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...

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...

Geological analysis of 3D Digital Outcrop Models (DOMs) for reconstruction of ancient habitable environments is a key aspect of the upcoming ESA ExoMars 2022 Rosalind Franklin Rover and the NASA...

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...

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...

The relationship between human cytomegalovirus (HCMV) infections and accelerated immune senescence is controversial. Whereas some studies reported a CMV-associated impaired capacity to control heterologous infections at old age other studies...

Helminth infections induce strong type 2 and regulatory responses, but the degree of heterogeneity of such cells is not well characterized. Using mass cytometry, we profiled these cells in Europeans...

In recent years the t-distributed Stochastic Neighbor Embedding (t-SNE) algorithm has become one of the most used and insightful techniques for exploratory data analysis of high-dimensional data. It reveals clusters...

Induction of antigen-specific regulatory T cells (Tregs) in vivo is the holy grail of current immune-regulating therapies in autoimmune diseases, such as type 1 diabetes. Tolerogenic dendritic cells (tolDCs) generated...

These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry...

Elucidating the cellular architecture of the human cerebral cortex is central to understanding our cognitive abilities and susceptibility to disease. Here we used single-nucleus RNA-sequencing analysis to perform a comprehensive...

Objective A comprehensive understanding of anticancer immune responses is paramount for the optimal application and development of cancer immunotherapies. We unravelled local and systemic immune profiles in patients with colorectal...

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...

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,...

High-dimensional mass cytometry (CyTOF) allows the simultaneous measurement of multiple cellular markers at single cell level, providing a comprehensive view of cell compositions. However, the power of CyTOF to explore...

Mass cytometry (CyTOF) is a valuable technology for high-dimensional analysis at the single cell level. Identification of different cell populations is an important task during the data analysis. Many clustering...

The fetus is thought to be protected from exposure to foreign antigens, yet CD45RO+ T cells reside in the fetal intestine. Here we combined functional assays with mass cytometry, single-cell...

Purpose: The tumor immune microenvironment determines clinical outcome. Whether the original tissue in which a primary tumor develops influences this microenvironment is not well understood. Experimental Design: We applied high-dimensional...

Multi-parametric flow and mass cytometry allows exceptional high-resolution exploration of the cellular composition of the immune system. A large panel of computational tools have been developed to analyze the high-dimensional...

Auto-reactive CD8 T-cells play an important role in the destruction of pancreatic β-cells resulting in type 1 diabetes (T1D). However, the phenotype of these auto-reactive cytolytic CD8 T-cells has not...

A bipartite graph is a powerful abstraction for modeling relationships between two collections. Visualizations of bipartite graphs allow users to understand the mutual relationships between the elements in the two...

Innate lymphoid cells (ILCs) are abundant in mucosal tissues and involved in tissue homeostasis and barrier function. While several ILC subsets have been identified, it is unknown if additional heterogeneity...

Technological advances in mass spectrometry imaging (MSI) have contributed to growing interest in 3D MSI. However, the large size of 3D MSI data sets has made their efficient analysis and...

The relationship between human cytomegalovirus (HCMV) infections and accelerated immune senescence is controversial. Whereas some studies reported a CMV-associated impaired capacity to control heterologous infections at old age other studies...

Deep neural networks are now rivaling human accuracy in several pattern recognition problems. Compared to traditional classifiers, where features are handcrafted, neural networks learn increasingly complex features directly from the...

Single-cell analysis through mass cytometry has become an increasingly important tool for immunologists to study the immune system in health and disease. Mass cytometry creates a high-dimensional description vector for...

Mass cytometry allows high-resolution dissection of the cellular composition of the immune system. However, the high-dimensionality, large size, and non-linear structure of the data poses considerable challenges for data analysis....

Diffusion Tensor Imaging (DTI) group studies often require the comparison of two groups of 3D diffusion tensor fields. The total number of datasets involved in the study and the multivariate...

Spatial and temporal brain transcriptomics has recently emerged as an invaluable data source for molecular neuroscience. The complexity of such data poses considerable challenges for analysis and visualization. We present...

Progressive Visual Analytics aims at improving the interactivity in existing analytics techniques by means of visualization as well as interaction with intermediate results. One key method for data analysis is...

A diffusion tensor imaging group study consists of a collection of volumetric diffusion tensor datasets (i.e., an ensemble) acquired from a group of subjects. The multivariate nature of the diffusion...

In recent years, dimensionality-reduction techniques have been developed and are widely used for hypothesis generation in Exploratory Data Analysis. However, these techniques are confronted with overcoming the trade-off between computation...

To understand how the immune system works, one needs to have a clear picture of its cellular compositon and the cells’ corresponding properties and functionality. Mass cytometry is a novel...

Inflammatory intestinal diseases are characterized by abnormal immune responses and affect distinct locations of the gastrointestinal tract. Although the role of several immune subsets in driving intestinal pathology has been...

Hydrocarbon reservoir simulation models produce large amounts of heterogeneous data, combining multiple variables of different dimensionality, such as two or three-dimensional geospatial estimates with abstract estimates simulated for the complete...

We present a novel integrated visualization system that enables the interactive visual analysis of ensemble simulations and estimates of the sea surface height and other model variables that are used...

Ocean forecasts nowadays are created by running ensemble simulations in combination with data assimilation techniques. Most of these techniques resample the ensemble members after each assimilation cycle. This means that...

We present a novel integrated visualization system that enables interactive visual analysis of ensemble simulations of the sea surface height that is used in ocean forecasting. The position of eddies...

We present a novel integrated visualization system that enables interactive visual analysis of ensemble simulations used in ocean forecasting, i.e, simulations of sea surface elevation. Our system enables the interactive...

Seismic interpretation is an important step in building subsurface models, which are needed to efficiently exploit fossil fuel reservoirs. However, seismic features are seldom unambiguous, resulting in a high degree...

The most important resources to fulfill today's energy demands are fossil fuels, such as oil and natural gas. When exploiting hydrocarbon reservoirs, a detailed and credible model of the subsurface...

In this paper, a method for interactive direct volume rendering is proposed that computes ambient occlusion effects for visualizations that combine both volumetric and geometric primitives, specifically tube shaped geometric...

Increasing demands in world-wide energy consumption and oil depletion of large reservoirs have resulted in the need for exploring smaller and more complex oil reservoirs. Planning of the reservoir valorization...

This paper presents a novel method for interactive exploration of industrial CT volumes such as cast metal parts, with the goal of interactively detecting, classifying, and quantifying features using a...

In this chapter, we present research that deals with the rendering and processing of seismic volumes and unstructured reservoir grids. We focus on approaches that facilitate interactive workflows, i.e., real-time...

Diffusion-Weighted Magnetic Resonance Imaging (DWI) enables the in-vivo visualization of fibrous tissues such as white matter in the brain. Diffusion-Tensor Imaging (DTI) specifically models the DWI diffusion measurements as a...

Spatial transcriptomics (ST) enables profiling the expression of hundreds of genes in tissue sections, down to the level of single cells in their tissue environment. For single cells, these high-dimensional...

High-dimensional mass cytometry (CyTOF) permits the simultaneous measurement of many cellular markers, providing a system-wide view of immune phenotypes at the single-cell level1. Yet, the maximum number of markers that...

Mass cytometry allows high-resolution dissection of the cellular composition of the immune system. However, the high-dimensionality, large size, and non-linear structure of the data poses considerable challenges for data analysis....

Despite its importance to the world community for a variety of socio-economical reasons and the presence of extensive coral reef gardens along its shores, the Red Sea remains one of...

This work presents a new workflow for the interpretation of seismic volume data, as well as a novel approach to interactively tracing seismic horizons. Instead of interpreting the seismic cube...

The most important resources to fulfill today's energy demands are fossil fuels, such as oil and natural gas. When exploiting hydrocarbon reservoirs, a detailed and credible model of the subsurface...

Using programmable graphics hardware (GPU) is the de-facto standard for real time volume rendering nowadays. In addition to that, GPUs are often used for non-graphical tasks to accelerate complex computations...