Table 1. Software tools for spatial analysis.

Software	Platform	Input	Output	Reference
histoCAT	MATLAB, standalone program	Imaging mass cytometry	User-guided cell neighborhood for selected cells, enrichments/depletion of cell-cell interactions based on comparison to spatially randomized data	[13]
Pelkmans lab	Module compatible with CellProfiler	Cell cultures	Local cell density, population size, cell islet edges	[14–17]
Cell-graph	Standalone tool	H&E stained tissue samples	Multiple graph metrics, e.g. clustering coefficient, network diameter	[9]
PySpacell	Python	Cell cultures	Statistical tests of magnitude and scale of spatial effects	[18]
SpatialDE	Python	Spatial transcriptomics datasets	Statistical tests of genes with spatial variation, spatial gene-clustering	[19]
trendsceek	R	Spatial transcriptomics datasets	Statistical tests of genes with spatial variation	[20]
cytoMAP	MATLAB	Histo-cytometry data	Multi-scale characterization of tissue structure	[21]
MuSIC	Cytoscape	Immunofluorescence and affinity purification mass spectrometry data	Intracellular protein positions and distances	[22]