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10x Genomics
Visium Spatial Gene Expression

Choosing a Space Ranger Pipeline

Space Ranger provides a set of analysis pipelines that allows for processing of Visium Spatial Gene Expression (GEX) data with brightfield and fluorescence images to align reads, generate Feature Barcode (FB) matrices and perform secondary analysis including clustering and differential gene expression.

Sample Type Species Imaging Type Automatic Fiducial Alignment Compatible Analysis Pipelines
Individual fresh frozen (FF) tissue section Human#,
Mouse,
Others
Brightfield Image Supported spaceranger count
(Spatial GEX)

spaceranger count
(Targeted GEX)

spaceranger targeted-compare#
(Targeted GEX)

spaceranger targeted-depth#
(Targeted GEX)

spaceranger mkref
(For custom references)
Fluorescence Image Not Supported
(must use manual fiducial alignment in Loupe Browser)
Individual formalin fixed paraffin embedded (FFPE) tissue section
Human, Mouse Brightfield Image Supported spaceranger count
(Spatial GEX)
Fluorescence Image Not Supported
(must use manual fiducial alignment in Loupe Browser)
Individual tissue sections from multiple samples (FF or FFPE*) Human,
Mouse,
Others
Brightfield Image Supported spaceranger count
(Spatial GEX)

spaceranger count
(Spatial GEX*)

spaceranger aggr
(samples processed using same protocol only)

spaceranger mkref
(For custom references)
Fluorescence Image Not Supported
(must use manual fiducial alignment in Loupe Browser)
Tissue section on standard glass slide (FFPE) Human,
Mouse
CytAssist Captured Brightfield Image Supported spaceranger count
(CytAssist GEX)
Microscope Captured Fluorescence or Brightfield Image Supported

(Optionally, use manual image registration
and/or manual fiducial alignment in Loupe Browser)