Spatial Transcriptomics

Our lab supports spatial transcriptomics studies on the Visium platform (and the coming Visium HD platform) with the help of our CytAssist instrument for fresh-frozen, fixed-frozen, and FFPE tissue sections.
We are open to supporting other platforms. Please contact our expert Hong Qiu (

Visium employs arrays of location-encoded oligonucleotides with poly-T stretches to capture transcripts or probe constructs. The Visium platform enables two types of chemistries:

1.) Poly-A-tail based capture of native transcripts: Suitable for fresh-frozen samples only. These assays are NOT species-specific.
2.) Probe-based “templated ligation”, capture, and amplification: Compatible with fresh-frozen, fixed-frozen, and FFPE tissue. Whole-transcriptome assays are available for human and mouse. Custom probe-sets can be generated for other species, including plants. This assay enables simultaneous analysis of both RNA and protein expression.

The Visium CytAssist is a compact instrument designed to simplify the Visium workflow by facilitating the transfer of transcriptomic probes from standard glass slides onto Visium slides. 

Simplified sample management: The Visium CytAssist enables users to start with tissue sections on standard glass slides, allowing input tissue to be prepared, stained, and imaged using standard histology workflows.

Expanded sample access: Visium CytAssist enables access to fresh frozen sections or FFPE tissues archived in blocks or pre-sectioned onto standard glass slides. Existing samples can be stained with H&E staining or IF antibodies on the glass slides before introduction to the Visium CytAssist workflow.

Maximized spatial insights: Prescreen to find the most biologically relevant tissue sections, and then use the instrument for precise manual alignment of tissue section onto Visium Capture Areas, enabling you to see more of the tissue you care about. 

Tissue profiling with transcriptomics and protein co-detection: Combine whole transcriptome spatial analysis with high-plex protein detection using NGS in the same tissue section to gain a deeper, more holistic understanding of tissue organization.

Visium HD assays offer improved resolution (single-cell resolution), are compatible with FFPE sections and fully compatible with the CytAssist. Each Visium HD slide has two 6.5 x 6.5 mm capture areas.

More information on the CytAssist instrument and the protocols is available here: