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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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Accurate tiling of spatial single-cell data with Tessera

Single-cell spatial transcriptomics reveals how cells organize in healthy and diseased tissues. From these data, tissue segmentation analysis defines discrete compartments that organize cells into functional multicellular units. Existing methods for automated tissue segmentation rely…

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A comprehensive comparison on clustering methods for multi-slide spatially resolved transcriptomics data analysis

Spatial transcriptomics (ST) data, by providing spatial information, enables simultaneous analysis of gene expression distributions and their spatial patterns within tissue. Clustering or spatial domain detection represents an essential methodology for ST data, facilitating the…

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COSIME: Cooperative multi-view integration and Scalable and Interpretable Model Explainer

Single-omics approaches often provide a limited view of complex biological systems, whereas multiomics integration offers a more comprehensive understanding by combining diverse data views. However, integrating heterogeneous data types and interpreting the intricate relationships between…

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Accurate Spatial Heterogeneity Dissection and Gene Regulation Interpretation for Spatial Transcriptomics using Dual Graph Contrastive Learning

Recent advances in spatial transcriptomics have enabled simultaneous preservation of high-throughput gene expression profiles and the spatial context, enabling high-resolution exploration of distinct regional characterization in tissue. To effectively understand the underlying biological mechanisms within…

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Technical and biological sources of noise confound multiplexed enhancer AAV screening

Cis-acting regulatory enhancer elements are valuable tools for gaining cell type-specific genetic access. Leveraging large chromatin accessibility atlases, putative enhancer sequences can be identified and deployed in adeno-associated virus (AAV) delivery platforms. However, a significant…

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High-precision cell-type mapping and annotation of single-cell spatial transcriptomics with STAMapper

Recent advances in single-cell spatial transcriptomics (scST) have enabled the analysis of gene transcription levels in individual cells while preserving their spatial positions. Cell-type mapping and annotation are crucial in understanding the complex interactions between…

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Multiscale Cell-Cell Interactive Spatial Transcriptomics Analysis

Spatial transcriptomics data analysis integrates gene expression profiles with their corresponding spatial locations to identify spatial domains, infer cell-type dynamics, and detect gene expression patterns within tissues. However, the current spatial transcriptomics analysis neglects the…

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Refinement Strategies for Tangram for Reliable Single-Cell to Spatial Mapping

Motivation Single-cell RNA sequencing (scRNA-seq) provides comprehensive gene expression data at a single-cell level but lacks spatial context. In contrast, spatial transcriptomics captures both spatial and transcriptional information but is limited by resolution, sensitivity, or…

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High-fidelity disentangled cellular embeddings for large-scale heterogeneous spatial omics via DECIPHER

The functional role of a cell, shaped by the sophisticated interplay between its molecular identity and spatial context, is often obscured in current spatial modeling. Aiming to model large-scale heterogeneous spatial data in silico properly,…

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A statistical framework for quantifying the nuclear export rate of influenza viral mRNAs

Influenza A virus transcribes viral mRNAs from the eight segmented viral genome when it infects. The kinetics of viral transcription, nuclear export of viral transcripts, and their potential variation between the eight segments are poorly…

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A quantitative spatial atlas of transcriptomic, morphological, and electrophysiological cell type densities in the mouse brain

Brain cells can be classified into transcriptomic, morphological, and electrophysiological types. We derived a quantitative spatial atlas of the distributions of these classes within the mouse brain. To do so, we first generated a 3D…

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Whole-embryo Spatial Transcriptomics at Subcellular Resolution from Gastrulation to Organogenesis

Spatiotemporal patterns of gene expression underlie embryogenesis. Despite progress in single-cell genomics, mapping these patterns across whole embryos with comprehensive gene coverage and at high resolution has remained elusive. Here, we introduce a whole-embryo imaging platform…

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Comparison of imaging-based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed, paraffin-embedded tumor samples

Imaging-based spatial transcriptomics (ST) is evolving rapidly as a pivotal technology in studying the biology of tumors and their associated microenvironments. However, the strengths of the commercially available ST platforms in studying spatial biology have…

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Dendritic cells type 1 control the formation, maintenance, and function of tertiary lymphoid structures in cancer

Tertiary lymphoid structures (TLS) are organized immune cell aggregates that arise in chronic inflammatory conditions. In cancer, TLS are associated with better prognosis and enhanced response to immunotherapy, making these structures attractive therapeutic targets. However,…

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NiCo identifies extrinsic drivers of cell state modulation by niche covariation analysis

Cell states are modulated by intrinsic driving forces such as gene expression noise and extrinsic signals from the tissue microenvironment. The distinction between intrinsic and extrinsic cell state determinants is essential for understanding the regulation…

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Molecular Cartography of the Human and Mouse Down Syndrome Brain

Down syndrome (DS, or Trisomy 21) is one of the most common genetic causes of intellectual disability. DS results in both abnormal neurodevelopment and accelerated neurodegeneration, but the molecular mechanisms underlying abnormal cortical construction and…

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A spatial single-cell atlas of the claustro-insular region uncovers key regulators of neuronal identity and excitability

The claustro-insular region is an evolutionarily conserved and extensively interconnected brain area, critical for functions such as attention, cognitive flexibility, interoception, and affective processing. Despite its importance, its cellular composition and organization remain poorly characterized,…

Publications

Spatial Transcriptomics Reveals Expression Gradients in Developing Wheat Inflorescences at Cellular Resolution

The diversity of plant inflorescence architectures is specified by gene expression patterns. In wheat (Triticum aestivum), the lanceolate-shaped inflorescence (spike) is defined by rudimentary spikelets at the base which initiate first but subsequently lag in…

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Spatial profiling of the interplay between cell type- and vision-dependent transcriptomic programs in the visual cortex

How early sensory experience during “critical periods” of postnatal life affects the organization of the mammalian neocortex at the resolution of neuronal cell types is poorly understood. We previously reported that the functional and molecular…

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Molecular and spatial analysis of ganglion cells on retinal flatmounts: diversity, topography, and perivascularity

Diverse retinal ganglion cells (RGCs) transmit distinct visual features from the eye to the brain. Recent studies have categorized RGCs into 45 types in mice based on transcriptomic profiles, showing strong alignment with morphological and…

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eBook: What Does High-Quality Spatial Genomics Data Look Like?

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