Pipeline Overview#
The pipeline consists of the following steps:
Landmark selection: Manual landmarks are selected using the MAGPIE shiny app
Coregistration: Coordinates from modalities are set into the same coordinate system
Creation of spaceranger-style object: A new spaceranger-style object is created for MSI data using coregistered coordinates
Aligning observations across modalities: Observations are matched between modalities so that multi-omics methods requiring common samples can be applied.
Here is a summary of the MAGPIE pipeline:
