Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data


Name (Type)

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, slide:‘10L13-020’, area: ‘B1’]

id, slide and area are mandatory information!

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,


image (file)

Brightfield tissue H&E image in JPEG or TIFF format.


cytaimage (file)

CytAssist instrument captured eosin stained Brightfield tissue image with fiducial
frame in TIFF format. The size of this image is set at 3k in both dimensions and this image should
not be modified any way before passing it as input to either Space Ranger or Loupe Browser.


darkimage (file)

Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence
image as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files.


colorizedimage (file)

Required for color composite fluorescence microscope image input.
A color composite of one or more fluorescence image channels saved as a single-page,
single-file color TIFF or JPEG.


alignment (file)

OPTIONAL - Path to manual image alignment.


slidefile (file)

OPTIONAL - Path to slide specifications.


reference (directory)

Folder containing all the reference indices needed by Space Ranger

probeset (file)

OPTIONAL - Probe set specification.



Name (Type)

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end


outs (file)

Files containing the outputs of Space Ranger, see official 10X Genomics documentation for a complete list


versions (file)

File containing software versions



10x Genomics EULA

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments.