Space Ranger2.0, printed on 11/12/2024
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.
Start by choosing a computing option to set up and run Space Ranger.
Space Ranger requires FASTQ files as input. If you are starting with raw sequence BCL files, first demultiplex them to FASTQ using either spaceranger mkfastq, bcl-convert or bcl2fastq from Illumina.
Identify the appropriate Space Ranger pipeline based on sample type, species and imaging modality. Pipeline constraints like species-specific (humans indicated by # ) and sample type-specific (FFPE indicated by * ) are highlighted.
| 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) |
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| 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) |
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| 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) |
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| Tissue section on standard glass slide (FFPE, FF$ or Fized Frozen$) | Human, Mouse |
CytAssist Captured Brightfield Image | Supported | spaceranger count(CytAssist GEX) $ - Probe based whole transcriptome profiling |
| Microscope Captured Fluorescence or Brightfield Image | Supported (Optionally, use manual image registration and/or manual fiducial alignment in Loupe Browser) |