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10x Genomics
Visium Spatial Gene Expression

Slide Serial and Capture Area Parameters

The spaceranger count pipeline accepts Slide Serial Number and Capture Area arguments, in order to use the most precise fiducial and spot coordinates for an experiment. From Space Ranger 2.0 onwards it is important to also note the slide version. The following illustrations highlight the key components of a Visium slide as well as the different slide versions.


Visium slide Visium serial number


This table lists the slide version, sample type and workflow compatibility:

Sample Type Supported Slide Versions Capture Areas Supported Workflows
Fresh Frozen (FF) V1
(e.g. V19L01-041)
4 Spatial Gene Expression
V2
(e.g. V20S03-001)
2
Formalin-fixed Paraffin-embedded (FFPE) V1
(e.g. V19L01-041)
4 Spatial Gene Expression
V2
(e.g. V20S03-001)
2
V4
(e.g. V49J01-123)
2 Spatial Gene Expression
CytAssist Compatible
V5
(e.g. V59J01-123)
2 Spatial Gene Expression
CytAssist Compatible

There are three different ways to specify the slide information in spaceranger count run:

Space Ranger Arguments Slide Specific Layout File Pipeline Internet Access Details
--slide
--area
Yes Yes The pipeline will download the layout file associated with the supplied slide serial number.
--slidefile
--slide
--area
Yes No User downloads a slide layout file for a Visium slide before running the pipeline. Download here
--unknown-slide
(one of visium-1, visium-2, or visium-2-large,)
No Optional The pipeline uses a default slide layout file for spot and fiducial coordinates. The typical per-spot difference between the default layout and a specific slide is under 10 microns.

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