10x Genomics
Visium Spatial Gene Expression
Space Ranger2.0 (latest), printed on 11/22/2024
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.
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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. |