Cell Quality Control
Remove low-quality cells based on morphology and intensity metrics.
QC Criteria
| Metric | Default Threshold | Description |
|---|---|---|
| Cell area | 50-5000 px | Remove debris and doublets |
| Nucleus ratio | 0.1-0.9 | Nuclear/cell area ratio |
| Total intensity | >100 | Minimum signal |
| Autofluorescence | <500 | Maximum background |
CLI
celltype-refinery preprocess qc \
--input loaded/ \
--max-removal 0.15 \
--out output/filtered