Filter cells by morphology

Removes debris and artifacts by thresholding morphological measurements. Any parameter left at NA is not applied.

Usage

cr_qc_filter(
  experiment,
  min_area = NA,
  max_area = NA,
  min_circularity = NA,
  max_circularity = NA
)

Arguments

experiment

A cr_experiment.

min_area, max_area

Numeric area thresholds. Cells outside the inclusive interval are removed.

min_circularity, max_circularity

Circularity thresholds (range 0-1).

Value

A modified cr_experiment with fewer cells and a QC log entry.

See also

cr_exclude_small() for a data-derived (quantile) area threshold, and cr_qc_summary() for the log.

Other quality control: cr_apply_gate(), cr_balance_cells(), cr_exclude_small(), cr_qc_doublets(), cr_qc_gate(), cr_qc_gate_impact(), cr_qc_intensity(), cr_qc_manual(), cr_qc_report(), cr_qc_summary(), print.cr_qc_gate()

Examples

exp <- cr_example_experiment(seed = 1, n_cells_per_well = 50)
exp2 <- cr_qc_filter(exp, min_area = 100, max_area = 2000)
cr_n_cells(exp2)
#> [1] 4516