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Human and animal tissues consist of heterogeneous cell types that organize and interact in highly structured manners. Bulk and single-cell sequencing technologies remove cells from their original microenvironments, resulting in a loss of…
Spatial transcriptomics is a modern sequencing technology that allows the measurement of the activity of thousands of genes in a tissue sample and map where the activity is occurring. This technology has enabled the study of the so-called…
In order to understand the complexities of cellular biology, researchers are interested in two important metrics: the genetic expression information of cells and their spatial coordinates within a tissue sample. However, state-of-the art…
Spatial transcriptomics measures the expression of thousands of genes in a tissue sample while preserving its spatial structure. This class of technologies has enabled the investigation of the spatial variation of gene expressions and their…
Cellular identity and function are linked to both their intrinsic genomic makeup and extrinsic spatial context within the tissue microenvironment. Spatial transcriptomics (ST) offers an unprecedented opportunity to study this, providing in…
Mapping spatial distributions of transcriptomic cell types is essential to understanding the brain, with its exceptional cellular heterogeneity and the functional significance of its spatial organization. Spatial transcriptomics techniques…
For the Bio+Med-Vis Challenge 2024, we propose a visual analytics system as a redesign for the scatter pie chart visualization of cell type proportions of spatial transcriptomics data. Our design uses three linked views: a view of the…
Genomics methods have uncovered patterns in a range of biological systems, but obscure important aspects of cell behavior: the shape, relative locations of, movement of, and interactions between cells in space. Spatial technologies that…
Single-cell RNA-sequencing technologies may provide valuable insights to the understanding of the composition of different cell types and their functions within a tissue. Recent technologies such as spatial transcriptomics, enable the…
Background: Spatial transcriptomics have emerged as a powerful tool in biomedical research because of its ability to capture both the spatial contexts and abundance of the complete RNA transcript profile in organs of interest. However,…
Spatial transcriptomics is an emerging technology that aligns histopathology images with spatially resolved gene expression profiling. It holds the potential for understanding many diseases but faces significant bottlenecks such as…
Understanding the evolution of cellular microenvironments in spatiotemporal data is essential for deciphering tissue development and disease progression. While experimental techniques like spatial transcriptomics now enable high-resolution…
Spatial transcriptomics (ST) enables the visualization of gene expression within the context of tissue morphology. This emerging discipline has the potential to serve as a foundation for developing tools to design precision medicines.…
Spatial transcriptomics has the potential to transform our understanding of RNA expression in tissues. Classical array-based technologies produce multiple-cell-scale measurements requiring deconvolution to recover single cell information.…
Cardiovascular disease arises from interactions between inherited risk, molecular programmes, and tissue-scale remodelling that are observed clinically through imaging. Health systems now routinely generate large volumes of cardiac MRI, CT…
Spatial transcriptomics (ST) provides spatially resolved measurements of gene expression, enabling characterization of the molecular landscape of human tissue beyond histological assessment as well as localized readouts that can be aligned…
Conventional histopathology has long been essential for disease diagnosis, relying on visual inspection of tissue sections. Immunohistochemistry aids in detecting specific biomarkers but is limited by its single-marker approach, restricting…
Spatial Transcriptomics (ST) profiles thousands of gene expression values at discrete spots with precise coordinates on tissue sections, preserving spatial context essential for clinical and pathological studies. With rising sequencing…
The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and…
Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells are largely based on transcriptomic single-cell…