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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. Starting with Space Ranger v2.0, 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.

Capture AreasSlide Serial Number

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

Sample TypeSupported Slide VersionsCapture AreasSupported Workflows
Fresh Frozen (FF)V1
(e.g. V19L01-041)
4Spatial Gene Expression
(e.g. V20S03-001)
2Spatial Gene Expression
Formalin-fixed Paraffin-embedded (FFPE)V1
(e.g. V19L01-041)
4Spatial Gene Expression
V2 (e.g. V20S03-001)2Spatial Gene Expression
(e.g. V49J01-123)
2Spatial Gene Expression

CytAssist Compatible
(e.g. V59J01-123)
2Spatial Gene Expression

CytAssist Compatible
CytAssist also supports Fresh Frozen (FF) and Fixed Frozen (FxF) sample types on V4 and V5 slides using probes against whole transcriptome.

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

Space Ranger ArgumentsSlide
Pipeline Internet AccessDetails
YesYesThe pipeline will download the
layout file associated with
the supplied slide serial number.
YesNoUser downloads a slide layout
file for a Visium slide
before running the pipeline. Download here
(one of
--visium-2, or
YesNoThe 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.