Table 1.
Nuclear algorithm settings for the DIA calibration after the Genie classifier
| Algorithm setting | DIA-0 | DIA-1 | DIA-2 |
|---|---|---|---|
| Averaging radius (μ) |
1 |
1 |
1 |
| Curvature threshold |
2.5 |
2.5 |
2.5 |
| Segmentation type |
Cytoplasm rejection |
Cytoplasm rejection |
Cytoplasm rejection |
| Threshold type |
Edge threshold |
Edge threshold |
Edge threshold |
| Lower intensity threshold |
0 |
0 |
0 |
|
Upper intensity threshold |
220 |
230 |
230 |
|
Min. nuclear size (μ2) |
20 |
45 |
40 |
|
Max. nuclear size (μ2) |
1,000,000 |
1,000 |
1,000 |
| Min, roundness |
0.1 |
0.1 |
0.1 |
|
Min. compactness |
0 |
0 |
0.2 |
|
Min. elongation |
0.1 |
0.1 |
0.2 |
| Remove light objects |
removes no nuclei |
removes no nuclei |
removes no nuclei |
|
Weak (1+) threshold |
210 |
210 |
229 |
| Moderate (2+) threshold |
188 |
188 |
188 |
| Strong (3+) threshold |
162 |
162 |
162 |
| Black threshold |
0 |
0 |
0 |
| Edge trimming | Weighted | Weighted | Weighted |
DIA-0 (default), DIA-1 (subjective) and DIA-2 (based on quantified bias). Modified settings are highlighted in bold.