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10x Genomics
Visium Spatial Gene Expression

Slide Serial and Capture Area Parameters

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.

Visium slide layout

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.

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