Spatial Transcriptomics analysis

Demultiplexing, image alignment, read alignment and barcode/UMI counting of sequencing reads generated by the 10X Genomics Visium assay.

The Spaceranger pipeline processes spatially barcoded RNA-seq data together with brightfield images to align sequencing reads, generate gene-spot matrices and to give spatial context to spot data on the tissue image.

When we run analysis

We run this analysis for 10X Visium projects.

Input data

  • Spaceranger-compatible fastQ files generated by bcl2fastq
  • Brightfield tissue image
  • (Optionally, if needed) Manual brightfield tissue image alignment in Loupe


The pipeline generates standard BAM, MEX, CSV, HDF5, TIFF, PNG, JPEG and HTML files that are augmented with spatial information. These files also include QC metrics that inform of the overall success of the spatial transcriptomics experiments.

For further analysis, visualization, and integration of spatial datasets we suggest any of the following packages:



Last Updated: 23rd March 2022

Please read our sample submission instructions before sending samples:

Sample Submission Guidelines
Method Status


We are currently testing this method. Please contact us to find out more.

Software tool versions

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