Visium Analysis
A whole new visual canvas to discover your spatial data
Your journey to whole transcriptome spatial insights
Space Ranger analysis pipelines
Translate sequencing data into gene expression-aligned images
Align reads and process data with Space Ranger
Process Visium Spatial Gene Expression (GEX) and Protein Expression (PEX) data with brightfield and fluorescence images to align reads, generate feature-barcode matrices, and perform secondary analysis including clustering and differential gene expression.
Loupe Browser
10 ways to explore your spatial gene expression data with Loupe Browser
Explore gene expression clusters in the tissue context
Map the expression of thousands of genes onto your microscope H&E or IF image
Identify gene signatures of neighboring regions
Annotate your tissue based on morphology
Define cell types with automated spot deconvolution
Space Ranger performs reference-free spot deconvolution to enable out-of-the-box cell type level analysis in Loupe.Find spatially variable genes in a few clicks
Space Ranger identifies genes with unique spatial patterns, which can be visualized in Loupe for new target gene discovery.Dive deeper into regions of interest
Characterize immune cells with protein co-detection
The Visium Gene and Protein detection kit enables characterization of immune cells in distinct tissues with user friendly protein thresholding in Loupe.Select tissue regions by gene or protein thresholds
Create high-quality figures for publications
Loupe Browser makes it easy to generate SVG and PNG formatted images to share in presentations or publications.
Discover spatial data
Mouse Embryo (FFPE)
Species
MouseTissue
EmbryoNumber of spots
6,434Assay used
Visium CytAssist Spatial Gene Expression
Human Breast Cancer (FFPE)
Species
HumanTissue
BreastNumber of spots
4,169
Mouse Tissue Microarray (FFPE)
Species
MouseTissue
Kidney, BrainNumber of spots
2,805Assay used
Visium CytAssist Spatial Gene Expression
Visium Spatial Platform
The Visium platform enables unbiased molecular profiling of frozen and fixed tissue sections, simple tissue handling, sensitive gene detection, and user-friendly software for visualizing gene expression.