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Spatial Transcriptomics Self-Training

7 Introduction COSmix

CosMx Spatial Molecular Imager (SMI) by NanoString is a high-plex, high-resolution spatial transcriptomics platform that enables single-molecule detection of RNA and protein targets directly within intact tissue sections. It offers subcellular spatial resolution and the ability to profile hundreds to thousands of genes simultaneously.

CosMx is ideal for studies that require detailed spatial insights into cellular organization, tissue architecture, and cell-to-cell interactions in complex tissues such as tumors, brain, or inflamed tissues.

7.1 🧪 How CosMx Works

  • Uses multiplexed fluorescence in situ hybridization (FISH) chemistry.
  • Targets up to 1000 RNA transcripts (CosMx RNA panel) or up to 64 proteins (CosMx protein panel).
  • Imaging is performed over multiple rounds with subcellular resolution, allowing precise localization of RNA molecules within cells.
  • Cell segmentation is based on morphological stains (e.g., DAPI, membrane markers).

7.2 📁 CosMx Data Output

CosMx generates a rich set of outputs, including:

  • Molecule-level data: Coordinates and intensity of each RNA or protein molecule
  • Cell segmentation maps and cell masks
  • Cell-level expression matrices
  • Spatial coordinates of each cell and molecule
  • High-resolution images of stained tissue

These outputs are used to perform cell-type classification, spatial domain identification, interaction analyses, and more.

7.3 🧠 Applications of CosMx

  • Single-cell spatial transcriptomics in FFPE and fresh frozen tissue
  • Mapping cell types and subtypes in situ
  • Understanding tissue microenvironments and niches
  • Analyzing cell–cell communication and signaling networks
  • Supporting clinical biomarker discovery and pathology research

✅ In this workshop, we’ll guide you through accessing and processing CosMx data, from raw molecule tables and segmentation files to spatial visualization, clustering, and biological interpretation.