10x Genomics Support/Space Ranger/Analysis/

Run spaceranger count

The spaceranger count pipeline is compatible with most Visium data, including Visium HD. The pipeline inputs a reference, a microscope slide image, and FASTQ files to generate feature-barcode matrices, identify clusters, and perform differential gene expression.

Count for Visium HD Spatial Gene Expression

For FFPE tissues prepared with the Visium CytAssist.

Count for Visium CytAssist, Spatial Gene and Protein Expression

For FFPE tissues prepared with the Visium CytAssist.

Count for Visium CytAssist, Spatial Gene Expression

For Fresh Frozen, Fixed Frozen or FFPE tissues prepared with the Visium CytAssist.

Count for Visium Spatial Gene Expression for FFPE

For FFPE tissues directly placed on the Visium slide.

Count for Visium Spatial Gene Expression

For fresh frozen tissues directly placed on the Visium slide.