10x Genomics Support/Space Ranger 2.1/Getting Started/

Space Ranger for Visium CytAssist

The Visium CytAssist instrument expands the capability of analyzing formalin-fixed paraffin-embedded (FFPE), fresh frozen (FF), or fixed frozen (FxF) samples. It is compatible with H&E and IF staining, thus adding the ability to preselect the best tissue section for analysis. By introducing slides with two different Capture Area sizes (6.5 mm or 11 mm), the Visium CytAssist workflow offers flexibility in the tissue size used for analysis. It is the only workflow that supports protein expression (PEX) in addition to gene expression (GEX).

Visium CytAssist automates the transfer of molecules from the tissue section on a standard glass slide to the CytAssist Spatial Gene Expression Slide. The FFPE, FxF, or FF tissue sections on standard glass slides follow the direct placement FFPE protocol until the probe hybridization and ligation step. Visium CytAssist mediates the tissue permeabilization to release the ligation products for capture by spatially barcoded oligonucleotides within each Capture Area on the slide. The final product is a sequencing library constructed from barcoded probes that is similar to a Visium for FFPE sequencing library.


The Space Ranger analysis workflow for Visium CytAssist is similar to that for Direct Placement. To utilize the best imaging available for analysis, Space Ranger can take a brightfield or fluorescence microscopy image of the tissue section on the standard glass slide, in addition to the instrument-generated image of the Visium CytAssist slide. After image registration in Space Ranger, spatial gene expression information is mapped in the context of the high-resolution tissue image.

Resources and additional information are available below: