imcRtools

imcRtools supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data by providing spatial analysis approaches for single-cell data after image segmentation and measurement.

Key Features:

• Data import and formatting: Reads in single-cell data after image segmentation and measurement and formats data for channel spillover correction.
• Spatial graph construction: Detects cell-cell interactions via spatial graph construction, with visualization of cells as nodes and interactions as edges.
• Spatial clustering: Summarizes direct neighbours per cell to enable spatial clustering.
• Cell-cell interaction analysis: Counts, averages and compares interactions between cell types against random permutations per image or grouping level to detect attraction or avoidance patterns.

Scientific Applications:

• Imaging mass cytometry analysis: Analyzes imaging mass cytometry data for spatially resolved single-cell analysis including community analysis, cellular neighborhood detection and cell-cell interaction testing.
• Highly multiplexed imaging: Adapts to other highly multiplexed imaging technologies beyond imaging mass cytometry for spatial profiling of biological molecules in tissues at single-cell resolution.

Methodology:

Spatial graph construction for cell-cell interaction detection; neighbour summarization for spatial clustering; permutation-based comparison of cell type interactions against random distributions.