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Vizgen is developing the next generation of genomics tools to expand on the capabilities of spatially resolved transcriptomics. Our technology will aide the acceleration of biological research and discovery to advance human health. Access supporting resources by selecting the category below.
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Publications
Spatio-relational inductive biases in spatial cell-type deconvolution
Abstract Spatial transcriptomic technologies profile gene expression in-situ, facilitating the spatial characterisation of molecular phenomena within tissues, yet often at multi-cellular resolution. Computational approaches have been developed to infer fine-grained cell-type compositions across locations, but they…
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WebAtlas pipeline for integrated single cell and spatial transcriptomic data
Abstract Single cell and spatial transcriptomics illuminate complementary features of tissues. However, online dissemination and exploration of integrated datasets is challenging due to the heterogeneity and scale of data. We introduce the WebAtlas pipeline for…
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A Hypothalamic Circuit Underlying the Dynamic Control of Social Homeostasis
Summary Social grouping increases survival in many species, including humans1,2. By contrast, social isolation generates an aversive state (loneliness) that motivates social seeking and heightens social interaction upon reunion3-5. The observed rebound in social interaction…
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MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial transcriptomics data in Bioconductor
Abstract Imaging-based spatial transcriptomics technologies have achieved subcellular resolution, enabling detection of individual molecules in their native tissue context. Data associated with these technologies promises unprecedented opportunity towards understanding cellular and subcellular biology. However, in…
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Mapping cells through time and space with moscot
Abstract Single-cell genomics technologies enable multimodal profiling of millions of cells across temporal and spatial dimensions. Experimental limitations prevent the measurement of all-encompassing cellular states in their native temporal dynamics or spatial tissue niche. Optimal…
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Integrated multimodal cell atlas of Alzheimer’s disease
Abstract Alzheimer’s disease (AD) is the most common cause of dementia in older adults. Neuropathological and imaging studies have demonstrated a progressive and stereotyped accumulation of protein aggregates, but the underlying molecular and cellular mechanisms…
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Integrated multimodal cell atlas of Alzheimer’s disease
Abstract Alzheimer’s disease (AD) is the most common cause of dementia in older adults. Neuropathological and imaging studies have demonstrated a progressive and stereotyped accumulation of protein aggregates, but the underlying molecular and cellular mechanisms…
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A universal differential expression prediction tool for single-cell and spatial genomics data
ABSTRACT With the growing complexity of single-cell and spatial genomics data, there is an increasing importance of unbiased and efficient exploratory data analysis tools. One common exploratory data analysis step is the prediction of genes…
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Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling
SUMMARY Gut inflammation involves contributions from immune and non-immune cells, whose interactions are shaped by the spatial organization of the healthy gut and its remodeling during inflammation. The crosstalk between fibroblasts and immune cells is…
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SpatialData: an open and universal data framework for spatial omics
Abstract Spatially resolved omics technologies are transforming our understanding of biological tissues. However, handling uni- and multi-modal spatial omics datasets remains a challenge owing to large volumes of data, heterogeneous data types and the lack…
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