Metric Semantics by Workflow
Metrics are only meaningful when they match the way cells were detected.
Cell counting and classification
This workflow uses a shared Cell Detection marker such as DAPI or NeuN.
Valid metrics include:
- Total cells
- Marker-positive cells
- Marker-negative cells
- Marker-positive proportion
- Cells/mm2
- Marker-positive cells/mm2
Marker-positive means the detected cell expresses the selected marker. Marker-negative means the detected cell does not express the selected marker.
Independent detection
This workflow detects candidates directly on each marker staining.
Valid metrics include:
- marker-positive cells
- analyzed area
- marker-positive cells/mm2
A positive classification means accepted marker-positive cell. A negative classification means rejected candidate or false positive.
Invalid metrics for independent detection include:
- marker-positive proportion from a shared denominator
- negative cells as a biological population
- all-cell density
Practical rule
If a project has a shared cell detection source, marker-positive proportions can be meaningful.
If each marker detects its own cells independently, use marker-positive counts and densities instead.