| Image Operations | |
| Alt-I | Adjust image contrast automatically |
| Ctrl-I | Show image contrast window |
| S | Hide/reveal segmentation |
| A | Increase segmentation transparency |
| D | Decrease segmentation transparency |
| Tool Selection Commands | |
| 1 | Crosshairs tool |
| 2 | Zoom/pan tool |
| 3 | Polygon tool |
| 4 | Automatic segmentation (SnAP region) tool |
| 5 | Paintbrush tool |
| Slice Window Commands (cursor must be in a slice window) | |
| PgUp | Show next slice in current slice window (mouse must be inside) |
| PgDn | Show previous slice in current slice window |
| Arrow keys | Move cursor left, right, up, down by one voxel |
| Shift+Arrow keys | Move cursor by five voxels |
| 3D Window Commands (cursor must be in the 3D window) | |
| S | Store current viewpoint |
| R | Recall stored viewpoint |
| File Operations | |
| Ctrl-G | Open gray image |
| Ctrl-1 ... Ctrl-5 | Open gray image from recently loaded list (1 = most recent) |
| Ctrl-D | Open segmentation image |
| Ctrl-S | Save segmentation image |
| Ctrl-N | Create new segmentation image (clear segmentation) |
| Ctrl-Q | Exit program |
| Paint Brush Mode | |
| -(_) | Decrease paint brush size |
| +(=) | Increase paint brush size |
| Changing Active/DrawOver Label | |
| ,(<) | Select the previous active label in the list |
| .(>) | Select the next active label in the list |
| Ctrl-,(<) | Select the previous drawover label in the list |
| Ctrl-.(>) | Select the next drawover label in the list |