Spatial transcriptomics
MERSCOPE (MERFISH) data analysis
Single-molecule spatial transcriptomics across large tissue areas, made interpretable.
What MERSCOPE measures
MERSCOPE uses MERFISH, an imaging-based method that identifies individual RNA molecules in situ through rounds of combinatorial, barcoded hybridization. It measures custom panels of up to around a thousand genes at subcellular resolution across large tissue areas, with cell boundary and nuclear stains used for segmentation.
Strengths
- Subcellular resolution across large tissue areas
- Quantitative single-molecule detection
- Custom gene panels designed around your biology
- Cell boundary stains support segmentation
How we can help with MERSCOPE data
Panel design
Selecting genes that separate the cell types and states you care about.
QC and segmentation
Transcript and cell QC, and segmentation refinement with boundary stains.
Cell typing
Clustering and reference mapping to annotate cell populations.
Spatial analysis
Neighbourhoods, tissue domains and cell–cell proximity.
Integration
Linking MERFISH data with single-cell atlases and histology.
Figures
Clear spatial maps and statistics for papers and grants.
Related technologies
Working with MERSCOPE data?
Tell us about your samples, panel and question. The first consultation is free.