Module list
| Name | Purpose | Description/YAML Configs |
|---|---|---|
aggregateData | Combine feature tables | Details |
selectROIs | Define tissue ROIs | Details |
intensityFilter | Filter out-of-focus and counterstain oversaturated cells | Details |
areaFilter | Filter over- and under-segmented cells | Details |
cycleCorrelation | Filter unstable cells | Details |
logTransform | Log10-transform immunomarker signals | Details |
pruneOutliers | Filter channel outliers | Details |
metaQC | Reclassify cells according to QC status | Details |
PCA | Run principle component analysis | Details |
clustering | Identify cell states | Details |
clustermap | Visualize cell state protein expression | Details |
setContrast | Adjust image contrast settings | Details |
frequencyStats | Compute cluster frequency statistics | Details |
curateThumbnails | Visualize example cells from each cluster | Details |
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 https://forum.image.sc/ and tagging your post with the cylinter tag.