Quality Control
This chapter presents the visual quality control (QC) review of all axon segmentations across the 8 corpus callosum regions. Every axon detected by AxonDeepSeg was visually inspected and either retained or excluded.
Methodology¶
For each image, the following QC pipeline was applied:
Morphometrics computation with instance segmentation using AxonDeepSeg v5.4.0
Automated flagging based on: border-touching, invalid g-ratio, no myelin, sub-pixel artifacts (d < 0.05 um), myelin-dominant (g < 0.3), low solidity (< 0.75), myelin >> axon (mt/ad > 1.0)
Visual review of every axon closeup, confirming auto-flags and checking for missed problems
Exclusion decision with per-axon justification
Overall summary¶
Total axons detected: 6825
Total excluded: 1618 (23.7%)
Total retained: 5207
Exclusions by category¶
Border-touching: 972 (truncated at image edges)
Sub-pixel artifacts: 335 (axon diameter < 0.05 um)
Invalid g-ratio: 116 (g >= 1.0 or negative myelin)
Merge errors: 105 (solidity < 0.75, irregular shapes)
Myelin-dominant: 90 (g < 0.3, myelin >> axon)
Per-image summary¶
| Sample | Slice | Total | Excluded | Retained | % Excluded |
|---|---|---|---|---|---|
| Region 1 | 1 | 496 | 60 | 436 | 12.1% |
| Region 1 | 3 | 445 | 72 | 373 | 16.2% |
| Region 1 | 7 | 496 | 94 | 402 | 19.0% |
| Region 2 | 1 | 308 | 46 | 262 | 14.9% |
| Region 2 | 3 | 369 | 52 | 317 | 14.1% |
| Region 2 | 5 | 364 | 55 | 309 | 15.1% |
| Region 3 | 1 | 276 | 57 | 219 | 20.7% |
| Region 3 | 3 | 166 | 66 | 100 | 39.8% |
| Region 3 | 5 | 276 | 59 | 217 | 21.4% |
| Region 4 | 1 | 144 | 83 | 61 | 57.6% |
| Region 4 | 5 | 180 | 72 | 108 | 40.0% |
| Region 4 | 7 | 200 | 78 | 122 | 39.0% |
| Region 5 | 1 | 214 | 70 | 144 | 32.7% |
| Region 5 | 3 | 216 | 67 | 149 | 31.0% |
| Region 5 | 5 | 281 | 70 | 211 | 24.9% |
| Region 6 | 1 | 271 | 68 | 203 | 25.1% |
| Region 6 | 3 | 279 | 86 | 193 | 30.8% |
| Region 6 | 5 | 331 | 81 | 250 | 24.5% |
| Region 7 | 1 | 329 | 72 | 257 | 21.9% |
| Region 7 | 3 | 323 | 80 | 243 | 24.8% |
| Region 7 | 5 | 322 | 62 | 260 | 19.3% |
| Region 8 | 1 | 195 | 68 | 127 | 34.9% |
| Region 8 | 3 | 255 | 75 | 180 | 29.4% |
| Region 8 | 5 | 89 | 25 | 64 | 28.1% |
Recommended filters¶
Based on the visual review, the following automated filters capture all exclusions:
image_border_touching == Truegratio >= 1.0orgratio <= 0myelin_area <= 0ormyelin_thickness <= 0axon_diam < 0.05 umgratio < 0.3solidity < 0.75myelin_thickness / axon_diam > 1.0
The full exclusion database is available as exclusion_database.csv.