Table 2.
Comparison of 3D segmentation software features. ✓: has the feature. △: partially has the feature. –: does not have the feature.
| Automatic segmentation | Manual correction/inspection | Multiple platform | Open source | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Predict cell/noncell regions | Segment cell regions into individual cells | Mask | Merge | Delete | Division (2D) | Relink after division | Division (3D) | Undo/redo | Sort by sizes / Remove tiny | Locate cells | |||
| Ilastik29 | ✓ |
✓ watershed 3D |
– | – | – | – | – | – | – | – | – | ✓ | ✓ |
| TrackMate30 | – |
△ 2D SEG (imported from other software) + Link |
– | – | – | – | – | – | – | – | – | ✓ | ✓ |
| Dojo21 | – | – | – |
△ but only within the same slice |
✓ | ✓ | – | – | ✓ | – | – |
△ not in Windows |
✓ |
| UNI–EM24 | ✓ |
✓ watershed 3D |
– |
△ but only within the same slice |
✓ | ✓ | – | – | ✓ | – | – |
△ not in macOS |
✓ |
| NeuTu23 | – | – | – | ✓ | ✓ | – | – |
✓ requires adding seeds |
△ cannot undo after confirming a merge |
– | ✓ |
△ not in Windows |
✓ |
| VAST Lite22 | – | – | – | ✓ | ✓ |
△ but only with straight line |
– | – | – | – | ✓ | – | – |
| Seg2Link | – |
✓ watershed 2D + Link |
✓ | ✓ | ✓ | ✓ | ✓ |
✓ requires annotating boundary |
✓ multiple steps |
✓ | ✓ | ✓ | ✓ |