Table 2.

A summary of computational toolboxes for multiplexed imaging data analysis

Name	Preprocessing	Cell segmentation	Cell phenotyping	Spatial analysis	Language	Code source
RAPID	√				Matlab	https://github.com/nolanlab/RAPID
CODEX Toolkit	√	√			Java	https://github.com/nolanlab/CODEX
REDSEA	√				Matlab	https://github.com/nolanlab/REDSEA
CellProfiler		√			Python	https://github.com/CellProfiler/CellProfiler
Ilastik		√			Python	https://github.com/ilastik/ilastik
CellSeg		√			Python	https://michaellee1.github.io/CellSegSite/
Mesmer		√			Python	https://github.com/vanvalenlab/deepcell-tf
Cellpose		√			Python	https://github.com/mouseland/cellpose
CELESTA			√		R	https://github.com/plevritis-lab/CELESTA
STELLA			√		Python	https://github.com/snap-stanford/stellar
Astir			√		Python	https://github.com/camlab-bioml/astir
Cytofkit			√		R	https://github.com/JinmiaoChenLab/cytofkit
Cytomapper			√		R	https://github.com/BodenmillerGroup/cytomapper
ImaCyte			√	√	Matlab	https://github.com/biovault/ImaCytE
CytoMAP				√	Matlab	https://gitlab.com/gernerlab/cytomap/-/tree/master/CytoMAP
Cytokit	√	√			Python	https://github.com/hammerlab/cytokit
MCMICRO	√	√	√	√	Nextflow, Python	https://mcmicro.org/overview/
SIMPLI		√	√	√	Nextflow	https://github.com/ciccalab/SIMPLI
histoCAT				√	Matlab	https://github.com/BodenmillerGroup/histoCAT
SpatialScore				√	R	https://github.com/nolanlab/SpatialScore
Cell neighborhoods				√	Python	https://github.com/nolanlab/NeighborhoodCoordination
Spatial-LDA				√	Python	https://github.com/calico/spatial_lda
TissueSchematics				√	Python	https://github.com/nolanlab/TissueSchematics
MISTy				√	R	https://github.com/saezlab/mistyR