Spatial transcriptomics
Visium and Visium HD data analysis
Whole-transcriptome spatial data connected to the histology it came from.
What Visium & Visium HD measures
Visium is a sequencing-based spatial transcriptomics platform: RNA from a tissue section is captured on a barcoded slide and sequenced, giving whole-transcriptome expression mapped back onto the H&E image. Standard Visium measures 55 µm spots that each contain several cells, while Visium HD captures RNA on a continuous grid of 2 µm squares that can be binned or assigned to individual cells.
Strengths
- Unbiased, whole-transcriptome coverage
- Expression aligned with the H&E image of the same section
- Visium HD reaches near single-cell resolution
- Mature analysis ecosystem that pairs well with single-cell references
How we can help with Visium & Visium HD data
Processing
Space Ranger runs, image alignment checks and spot or bin quality control.
Domains and clustering
Spatial domains, clustering and spatially variable genes.
Deconvolution
Mapping single-cell references onto spots with tools such as cell2location or RCTD.
Visium HD
Bin aggregation and nucleus-based cell assignment using the H&E image.
Histology linkage
Relating expression patterns to tissue structures and pathology annotations.
Integration
Combining Visium with single-cell RNA-seq, multiplex imaging or other spatial data.
Related technologies
Working with Visium & Visium HD data?
Tell us about your samples, panel and question. The first consultation is free.