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To set up and run Space Ranger, please follow the following steps:

  1. Check system requirements
  2. Download Space Ranger
  3. Download References (Optional)
  4. Download Probe Sets (Optional)
  5. Install Space Ranger


We observe sensitivity gains in the analysis with the 2020-A reference compared to the previous cellranger/spaceranger reference. These are mainly due to an updated transcriptome annotation (Ensembl 93 → 98) and improved filtering of readthrough gene annotations. A number of genes (notably IGLC1) are uncounted or undercounted without this filtering step. Below are gains in sensitivity that we observed.

  • 1-3% relative increase in Median UMI Counts per spot
  • 1-2% relative increase in Median Genes per spot
  • 4-7% relative increase in Total Genes Detected
  • 1-3% increase in Reads Mapped Confidently to Transcriptome
  • 0.5% decrease in Reads Mapped Confidently to Intergenic Regions

Details about the specific steps used to correct these annotations can be found in the reference build scripts.

  • Human reference (GRCh38) dataset required for Space Ranger.

    • Human reference (GRCh38) dataset required for Space Ranger.
    Download Human Reference
    File size: 110.178 MB
    md5sum: 26151804338ae4d4b44151232bd64b50
    curl -O "https://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-GRCh38-2020-A.tar.gz"
  • mm10 Reference - 2020-A (June 23, 2020)

    • Mouse reference (mm10) dataset required for Space Ranger.
    Download Mouse Reference
    File size: 110.178 MB
    md5sum: 24ee09ad620a9eb2753763fa068edf1f
    curl -O "https://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-mm10-2020-A.tar.gz"

Download is unavailable on mobile devices.

Probe Sets

The Visium for FFPE and the Visium CytAssist Spatial Gene and Protein Expression for FFPE assays use probes targeting protein coding genes in the human or mouse transcriptomes. Each probe consists of a pair of oligonucleotides hybridized to the targeted transcript and are subsequently ligated.

View more details about probe sets

Human Transcriptome v2
Human Transcriptome v1
Mouse Transcriptome v1

Other downloads

System requirements

System requirements

View the minimum requirements to run Space Ranger pipelines


Space Ranger Installation

View instructions on how to install Space Ranger