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The Nanostring CosMX Spatial Molecular Imager (SMI) enables spatial profiling of RNA and proteins at cellular or subcellular resolution with formalin-fixed paraffin embedded (FFPE) or fresh frozen tissue samples. The CosMX technology extends single molecule fluorescent in-situ hybridization (smFISH) by coupling detection probes to a 60-80 nucleotide DNA readout domain. The readout domain contains 4 consecutive regions that hybridize to unique reporters that are read out over sequential imaging rounds. CosMX increases detection efficiency by targeting different regions of the RNA target with up to 5 detection probes, each coupled to the same readout domain. The photocleavable sites in the reporters enable fast fluorescent signal quenching and greatly increase the signal-to-noise ratio.

Pros and cons


  • Commercial kit
  • Single cell resolution
  • High detection efficiency
  • Formalin fixed, paraffin embedded (FFPE) tissue compatible
  • Provides subcellular transcript localization information
  • Compatible with histological staining including DAPI
  • Up to 100 proteins can be quantified with CosMX along side RNAs


  • A curated panel of usually a few hundred genes is required. However, Nanostring provides curated gene panels for common applications such as oncology, neuroscience, and immunology, as well as panel design services.
  • Data size is harder to manage for larger tissue areas and number of samples. Not all spatial analysis methods can scale to hundreds of thousands to millions of cells.

Getting Started

Nanostring has released a CosMX FFPE dataset on their website. A tutorial for processing the output of various spatial transcriptomics technologies, including CosMX, into a SpatialFeatureExperiment(SFE) object for use with Voyager is available below.

The vignette provides technology specific notes for data downloaded from Nanostring. Nanostring provides cell segmentation data as images, while cell centroid coordinates are provided as metadata.

Vignette Colab Notebook Description
Create a SFE object Colab Notebook Download data, create SFE object, CosMX specific notes

Analysis Workflows

The vignettes below demonstrate workflows that can be implemented with Voyager using data generated with the CosMX SMI. The publicly available CosMX dataset profiles 960 genes across 8 non-small-cell lung cancer (NSCLC) samples.

Vignette Colab Notebook Description
CosMX NSCLC analysis Colab Notebook Perform basic QC, data normalization, dimension reduction, spatial autocorrelation metrics, local spatial statistics, non-spatial clustering, differential expression