3 Step 3: spaceranger

What is spaceranger?

spaceranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images.

The following links and the flowchart provide useful information about spaceranger and how to run it on histology images.

  1. Blog post on running spaceranger on JHPCE
  2. [Website describing the details](https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger_
  3. Installation
  4. Useful links

The output files scalefactors_json.json and tissue_positions_list.csv generated by the spaceranger count module are required for the next image processing steps. These files provide the Visium spot dimensions, spot locations and barcode IDs to reconstruct the spot grid and overlay the histology image for visual inspection.

The individual split images from Step 1 go through the 10x Genomics Loupe browser for manual alignment of the fiducial frame and tissue detection. The output from Loupe Browser along with the split images, their fastqs, slide number, capture area, etc all go into spaceranger which finally provides the Visium spot metrics. This entire process is shown in a brief flowchart below.