In this document we walk through how to access, analyze, and work with data exported from the AtoMxâ„¢ Spatial Informatics Platform (SIP), using a study containing liver and liver cancer samples as an example. We will demonstrate the data structure developed for the 1000-plex CosMxâ„¢ RNA assay to enable downstream development of analysis pipelines. The data shown here is in the format exportable from the AtoMx SIP after completing a CosMx Spatial Molecular Imager (SMI) experiment. Specifically, data is stored as both a standalone Seurat object and an equivalent TileDB array. The exported data include: transcript counts/location, field of view images, annotation metadata, and user-initiated data transformations performed in AtoMx SIP prior to export. Applying foundational single-cell spatial analysis techniques, we illustrate the benefits enabled by leveraging the computational efficiency of TileDB and the flexibility of the Seurat objects created for CosMx SMI data.
CosMx SMI is currently the only spatial platform enabling quantification of 1000+ targets at subcellular resolution for maximum biological insight. The CosMx SMI in situ chemistry is designed to enable high-plex and high-resolution with probes and fluorophores designed to reduce optical crowding limitations, allowing multiplexing probes to 1000 unique transcript species and beyond. In addition to high-plex, CosMx SMI also achieves high resolution. Target localization accuracy of ∼50 nm in the XY plane allows for targeting of <1kb transcripts with no loss in performance.