Space Ranger1.3, printed on 03/03/2025
The spaceranger count pipeline accepts slide serial and capture area arguments, in order to use the most precise fiducial and spot coordinates for an experiment.
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There are three different ways to specify the slide information in spaceranger count run:
| Space Ranger Arguments | Access to Slide Layout | Internet Access | Details |
|---|---|---|---|
--slide,--area |
Yes | Yes | The pipeline will download the layout file associated with the supplied serial number. |
--slidefile,--slide,--area |
Yes | No | User downloads a layout file for a Visium slide before running the pipeline. Download here |
--unknown-slide |
No | Optional | The pipeline uses a default layout file for spot and fiducial coordinates. The typical per-spot difference between the default layout and a specific slide is under 10 microns. |