The Region Class

The Region is the basic unit of the SpatialMap. It stores processed image information - segmented cells, X-Y coordinates, and feature expression values - and their metadata. The hierarchical structure is flexible and SpatialMaps will perform analyses on independent regions, groups of regions, or subsets of regions.

Beyond these basic slots, regions may contain a suite of downstream analyses, including cell neighborhood analyses or dimensionality reductions. Regions also support fetching or storing raw image data for viewing in R.

Slots

Data

Typically contains expression data, markers X cells

NormalizedData

Normalized Data

ScaledData

Scaled (centered and scaled) data

bgData

Any cell level information pertaining to background. Used for QC etc.

coordinates

Coordinates of cells in the currently-active segmentation

cellMetadata

Stores cell information - clustering, etc.

channelInfo

Stores information about the microscope channel for each marker

featureInfo

Stores feature information - antibodies, barcodes, gene information, etc.

neighborhoods

A list of cell-cell interaction 'neighborhoods'

images

Stores links or actual image data. Note that this feature could explode the size of the SpatialMap

tiles

Stores information pertaining to any images that were stitched to form this Region. A mapping of cells to tiles