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Module list

NamePurposeDescription/YAML Configs
aggregateDataCombine feature tablesDetails
selectROIsDefine tissue ROIsDetails
intensityFilterFilter out-of-focus and counterstain oversaturated cellsDetails
areaFilterFilter over- and under-segmented cellsDetails
cycleCorrelationFilter unstable cellsDetails
logTransformLog10-transform immunomarker signalsDetails
pruneOutliersFilter channel outliersDetails
metaQCReclassify cells according to QC statusDetails
PCARun principle component analysisDetails
clusteringIdentify cell statesDetails
clustermapVisualize cell state protein expressionDetails
setContrastAdjust image contrast settingsDetails
frequencyStatsCompute cluster frequency statisticsDetails
curateThumbnailsVisualize example cells from each clusterDetails

Suggest a module

The CyLinter team is collaborating with NCI-sponsored consortia (CSBC and PS-ON) to host hackathons to improve and automate existing methods for microscopy quality control like those instantiated by the CyLinter pipeline. CyLinter modules are also being added incrementally by a diverse developer community seeded by the NCI Human Tissue Atlas Network. See what modules are currently available here. Module suggestions can be made by posting to and tagging your post with the cylinter tag.

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