gatekeepR separates measurement preparation, correction, threshold estimation, classification, review, and export. This separation makes each decision inspectable, but it does not replace biological validation of a panel or threshold choice.

Threshold methods can be sensitive to support, outliers, density shape, and embedding settings. A returned status and callability flag must be carried into downstream analysis. Small or ambiguous structures remain reviewable rather than being silently promoted to a phenotype.

The package uses simulated examples in its tests and vignettes. Project users should add independent positive and negative controls and record the assay, image-processing, and panel versions in their own provenance layer.