Methods for imaging mass cytometry data analysis

Documentation for package ‘imcRtools’ version 1.13.0

aggregateNeighbors	Function to aggregate all neighbors of each cell.
binAcrossPixels	Aggregate consecutive pixels per single-metal spot
buildSpatialGraph	Builds an interaction graph based on the cells' locations
countInteractions	Summarizes cell-cell interactions within grouping levels (e.g. images)
detectCommunity	Detect the spatial community of each cell
detectSpatialContext	Detect the spatial context of each cell based on its neighborhood
filterPixels	Filter pixels based on their assigned masses
filterSpatialContext	Filter spatial contexts
findBorderCells	Find cells at the image border
minDistToCells	Function to calculate minimal distance to cells of interest
patchDetection	Function to detect patches containing defined cell types
patchSize	Function to compute the area of c3ll patches
plotSpatial	Visualizes the spatial locations and interactions of cells
plotSpatialContext	Plot spatial context graph
plotSpotHeatmap	Summarizes and visualizes the pixel intensities per spot and channel
readImagefromTXT	Reads one or multiple .txt files into a CytoImageList object
readSCEfromTXT	Generates a SingleCellExperiment from .txt files
read_cpout	Reads in single-cell data generated by the ImcSegmentationPipeline
read_steinbock	Reads in single-cell data generated by the steinbock pipeline
show_cpout_features	Display all features measured by CellProfiler.
testInteractions	Tests if cell types interact more or less frequently than random