10x Genomics Support/Space Ranger/Tutorials/

Slide Parameters

Visium slides have features that Space Ranger users should be familiar with, particularly the slide serial number and the capture area associated with each sample, which are typically provided as parameters to spaceranger count.

There are currently four types of slides available that can be grouped into three product categories:

  • Visium HD is specific to assays that use the Visium HD slide (6.5 mm). Only compatible with the Visium CytAssist instrument.
  • Visium v2 includes assays that use the Visium CytAssist Spatial Gene Expression slides (v2, 6.5 mm and v2, 11 mm). Only compatible with the Visium CytAssist instrument.
  • Visium v1 refers to direct placement assays that use Visium Spatial Gene Expression slides (v1, 6.5 mm).
Visium Slides

The slide serial number is the unique identifier printed on the label of each Visium slide. The serial number starts with a prefix indicating the slide type:

  • V1: Visium Spatial Gene Expression Slide (v1, 6.5 mm)
  • V4: Visium CytAssist Spatial Gene Expression Slide (v2, 6.5 mm)
  • V5: Visium CytAssist Spatial Gene Expression Slide (v2, 11 mm)
  • H1: Visium HD Slide (6.5 mm)

The slide serial number is either specified to spaceranger count with the --slide argument or through the CytAssist image metadata (--cytaimage).

Capture areas are active regions for capturing expression data on a Visium slide. Slides either have two or four capture areas. Slide areas are named consecutively from top to bottom:

  • A1, B1, C1, D1 for Visium Spatial Gene Expression slides, v1, 6.5 mm
  • A, B for Visium CytAssist Spatial Gene Expression slide, v2, 11 mm
  • A1, D1 for Visium CytAssist Spatial Gene Expression slides, v2, 6.5 mm, and Visium HD slides, 6.5 mm
Capture Areas

The capture area is either specified to spaceranger count with the --area argument or through the CytAssist image metadata (--cytaimage).

In most cases, Space Ranger will use the --slide and --area arguments to retrieve the corresponding slide layout file automatically. However, if Space Ranger is being run on a computer that is not connected to the internet, you also need to provide the slide layout file to spaceranger count with the --slidefile argument. Slide layout files can be downloaded from the Space Ranger Download Center.

If the slide serial number and capture area are unknown, you can run spaceranger count using the --unknown-slide option, and Space Ranger will use a generic slide layout file.

If the --unknown-slide option is used with Visium HD, data quality may be affected. Due to the high resolution and manufacturing variability of Visium HD slides, it is strongly recommended to specify the actual slide used.