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Overview Stereo-seq Analysis Workflow StereoMap Demo Data

Spatial Omics Investigation: From Sequencing toVisualization

The resolution covers the complete workflow of spatial omics data, from raw reads and image alignment to spatial localization and result visualization.
Spatial Omics Investigation: From Sequencing to Visualization
Stereo-seq Analysis Workflow

SAW: From Stereo-seq Data to Spatial Expression Maps

Download SAW Learn more about SAW
A spatial omics analysis workflow that maps Stereo-seq sequencing data to tissue coordinates and generates spatial expression matrices
SAW processes Stereo-seq sequencing data, maps reads to spatial coordinates, registers spatial expression data with microscopy images, quantifies feature expression, and generates standardized spatial expression matrices
StereoMap

An interactive platform for spatial omics
visualization and exploration

Download StereoMap Learn more about StereoMap
Visualize and explore feature expression and spatial distribution in tissue context
Explore spatial co-expression between features
Cluster cells and binned regions with morphological validation across multiple spatial resolutions
Annotate spatial regions guided by tissue morphology
Group cells by specific gene or protein expression patterns
Re-cluster annotated regions for subpopulation discovery
Perform interactive differential analvsis and filter results across multiple dimensions
Export spatial coorainates and expression matrices of selected regions for downstream analysis
Export HD figures for reports and publications

Demo Data

Rat Brain Demo Data
Rat Brain Demo Data

  • Product: Stereo-seq FF Solutions

  • Kit version: Stereo-seq T FF V1.3

  • Species and Tissue: Rat Brain

  • Embedding method: FF

  • Staining type: ssDNA staining

View details
Mouse Small Intestine Demo Data
Mouse Small Intestine Demo Data

  • Product: Stereo-seq OMNI Solution 

  • Kit version: Stereo-seq N FFPE V1.1

  • Species and Tissue: Mouse Small Intestine 

  • Embedding method: FFPE

  • Staining type: ssDNA staining

View details
STOmics Mouse Embryo Demo Data
Mouse Embryo Demo Data

  • Product: Stereo-seq Large Chip Designs 

  • Kit version: Stereo-seq T FF V1.3 

  • Species and Tissue: Mouse embryo 

  • Embedding method: FF

  • Staining type: H&E staining

View details
STOmics Mouse Spleen Demo Data
Mouse Spleen Demo Data

  • Product: Stereo-CITE Solution

  • Kit version: Stereo-CITE FF V1.1

  • Species and Tissue: Mouse spleen

  • Embedding method: FF

  • Staining type: DAPI staining

View details
STOmics Mouse Testis Demo Data
Mouse Testis Demo Data

  • Product: Stereo-seq Solution - mIF

  • Kit version: Stereo-seq T FF V1.3

  • Species and Tissue: Mouse testis

  • Embedding method: FF

  • Staining type: DAPI+mIF staining

View details
STOmics Mouse Brain Demo Data
Mouse Brain Demo Data

  • Product: Stereo-seq Solution - mIF

  • Kit version: Stereo-seq T FF V1.3

  • Species and Tissue: Mouse brain

  • Embedding method: FF

  • Staining type: DAPI+mIF staining

View details
Mouse Ovary Demo Data

  • Product: Stereo-seq Solutions

  • Kit version: Stereo-seq T FF V1.3

  • Species and Tissue: Mouse ovary

  • Embedding method: FF

  • Staining type: H&E staining

View details
Mouse Tongue Demo Data

  • Product: Stereo-seq Solutions

  • Kit version: Stereo-seq T FF V1.3

  • Species and Tissue: Mouse tongue

  • Embedding method: FF

  • Staining type: H&E staining

View details
Mouse Brain Demo Data

  • Product: Stereo-seq Solutions

  • Kit version: Stereo-seq T FF V1.3

  • Species and Tissue: Mouse brain

  • Embedding method: FF

  • Staining type: H&E staining

View details
Mouse Brain Demo Data

  • Product: Stereo-seq Solutions

  • Kit version: Stereo-seq T FF V1.3

  • Species and Tissue: Mouse brain

  • Embedding method: FF

  • Staining type: Nucleus staining

View details
Mouse Eyeball Demo Data

  • Product: Stereo-seq Solutions

  • Kit version: Stereo-seq T FF V1.3

  • Species and Tissue: Mouse eyeball

  • Embedding method: FF

  • Staining type: H&E staining

View details
Mouse Brain Demo Data

  • Product: Stereo-seq OMNI Solution

  • Kit version: Stereo-seq N FFPE V1.0

  • Species and Tissue: Mouse brain

  • Embedding method: FFPE

  • Staining type: H&E staining

View details
Mouse Lung Demo Data

  • Product: Stereo-seq OMNI Solution

  • Kit version: Stereo-seq N FFPE V1.0

  • Species and Tissue: Mouse lung

  • Embedding method: FFPE

  • Staining type: H&E staining

View details
Mouse Brain Demo Data

  • Product: Stereo-seq OMNI Solution

  • Kit version: Stereo-seq N FFPE V1.0

  • Species and Tissue: Mouse brain

  • Embedding method: FFPE

  • Staining type: H&E staining

View details
Mouse Thymus Demo Data

  • Product: Stereo-CITE Solution

  • Kit version: Stereo-CITE T FF V1.0

  • Species and Tissue: Mouse thymus

  • Embedding method: FF

  • Staining type: DAPI staining

View details
Rat Brain Demo Data

  • Product: Stereo-seq Large Chip Designs 

  • Kit version: Stereo-seq T FF V1.2 

  • Species and Tissue: Rat brain 

  • Embedding method: FF

  • Staining type: DAPI staining

View details
Mouse Brain Demo Data

  • Product: Stereo-seq OMNI Solution

  • Kit version: Stereo-seq N FFPE V1.0

  • Species and Tissue: Mouse brain

  • Embedding method: FFPE

  • Staining type: ssDNA staining

View details
Mouse Olfactory Demo Data

  • Product: Stereo-seq Solutions 

  • Kit version: Stereo-seq T FF V1.2 

  • Species and Tissue: Mouse olfactory 

  • Embedding method: FF 

  • Staining type: DAPI staining

View details
Mouse Kidney Demo Data

  • Product: Stereo-seq Solutions 

  • Kit version: Stereo-seq T FF V1.2 

  • Species and Tissue: Mouse kidney 

  • Embedding type: FF 

  • Staining type: H&E staining 

View details
Mouse Brain Demo Data

  • Product: Stereo-seq Solutions

  • Kit version: Stereo-seq T FF V1.2

  • Species and Tissue: Mouse brain

  • Embedding method: FF

  • Staining type: ssDNA staining

View details
Explore More Demo Data
Analysis Guides
Extend the core workflow with practical guides covering clustering, cell annotation, co-expressed genes, data integration, differential expression, image analysis, normalization, spatial domains, and 3D reconstruction.
Explore the Analysis Guide
Analysis Guides
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