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Current Modules

NamePurposeParametersURLs
BaSiCIllumination correctionReferenceCode - DOI
ASHLARStitching and registrationReferenceCode - DOI
CoreographTMA dearrayingReference - GuideCode - DOI
UnMICSTProbability map generatorReference - GuideCode - DOI
IlastikProbability map generatorReferenceCode - DOI
CypositoryProbability map generator (cytoplasm only)ReferenceCode
S3segmenterWatershed segmentationReference - GuideCode - DOI
mcquantSingle cell quantificationReferenceCode - DOI
naivestatesCell type callingReferenceCode
FastPGCell type callingReferenceCode - DOI
SCIMAPCell type callingReference - GuideCode

Coming soon

Additional module development and evaluation will be enabled through future hackathons hosted by the Cancer Systems Biology Consortium (CSBC).

Suggest a module

Module suggestions can be made by posting to https://forum.image.sc/ and tagging your post with the mcmicro tag.

Add a module

MCMICRO allows for certain module types to be specified dynamically through a configuration file. If you already have a containerized method with a command-line interface, follow our instructions to incorporate your module into the pipeline.