Spatial transcriptomics
CosMx SMI data analysis
High-plex RNA and protein at single-cell resolution, turned into clear cell types, niches and interactions.
What CosMx measures
CosMx is an imaging-based, in situ platform that measures RNA or protein at single-cell and subcellular resolution in FFPE or fresh frozen tissue. RNA panels range from about a thousand genes up to the whole transcriptome, and protein panels cover dozens of markers, with immunofluorescence morphology markers imaged alongside to support cell segmentation.
Strengths
- Very high plex at single-cell resolution, up to whole-transcriptome RNA
- RNA and protein assays on the same platform
- Subcellular transcript locations for detailed cell–cell interaction analysis
- Field-of-view or larger-area scanning depending on study design
How we can help with CosMx data
Study design
Field-of-view placement, panel choice and sample layout matched to your hypothesis.
Data import and QC
Converting AtoMx exports into analysis-ready objects, with per-cell and per-FOV quality control.
Segmentation review
Checking and refining cell boundaries using morphology markers.
Cell typing
Reference-based and marker-based annotation of cell populations.
Spatial biology
Niches, neighbourhood enrichment, ligand–receptor analysis and spatially resolved differential expression.
Integration
Linking CosMx results with single-cell RNA-seq, histology or other spatial assays.
Related technologies
Working with CosMx data?
Tell us about your samples, panel and question. The first consultation is free.