SpatialExperimentIO

SpatialExperimentIO reads in imaging-based spatial transcriptomics technology data as SpatialExperiment or SingleCellExperiment objects.

Key Features:

• Xenium support: Reads data from Xenium by 10X Genomics.
• CosMx support: Reads data from CosMx by Nanostring.
• MERSCOPE support: Reads data from MERSCOPE by Vizgen.
• STARmapPLUS support: Reads data from STARmapPLUS from Broad Institute.
• Flexible output formats: Returns data as either SpatialExperiment or SingleCellExperiment objects.

Scientific Applications:

• Imaging-based spatial transcriptomics data import: Enables standardized import of spatial transcriptomics data from multiple imaging-based platforms into Bioconductor object formats for downstream analysis.

Methodology:

The package provides modular data reading functions for each supported technology platform.