| Command / Operation | Shortcut | Description |
| N | Create new image or stack | |
| Shift N | Create new text window | |
| Shift V | Create image from system clipboard | |
| O | Open file (any format recognized by ImageJ) | |
| Shift O | Open next image in folder | |
| Shift B | Opens the Blobs.gif example image | |
| W | Close the active window | |
| S | Save active image in Tiff format | |
| R | Revert to saved version of image | |
| P | Print active image | |
| Z | Undo last operation | |
| X | Copy selection to internal clipboard and clear | |
| C | Copy selection to internal clipboard | |
| V | Paste contents of internal clipboard | |
| Backspace | Erase selection to background color | |
| F | Fill selection in foreground color | |
| D | Draw selection | |
| Shift I | Invert image or selection | |
| A | Select entire image | |
| Shift A | Remove selection | |
| Shift E | Restore previous selection | |
| Y | Defines selection properties | |
| T | Add selection to ROI Manager | |
| Shift C | Adjust brightness and contrast | |
| Shift T | Adjust threshold levels | |
| I | Display information about active image | |
| Shift P | Display image properties | |
| Shift K | Open Color Picker | |
| > or → | Go to next stack slice | |
| < or ← | Go to previous stack slice | |
| / | Reslice stack | |
| Shift H | Toggle orthogonal view display | |
| \ | Start/stop stack animation | |
| Shift Z | Open the ‘Channels’ tool | |
| Hyperstacks↑ | > or → | Next hyperstack channel |
| Hyperstacks↑ | < or ← | Previous hyperstack channel |
| Hyperstacks↑ | Ctrl > | Next hyperstack slice |
| Hyperstacks↑ | Ctrl < | Previous hyperstack slice |
| Hyperstacks↑ | Alt > | Next hyperstack frame |
| Hyperstacks↑ | Alt < | Previous hyperstack frame |
| Shift X | Crop active image or selection | |
| Shift D | Duplicate active image or selection | |
| E | Scale image or selection | |
| + or ↑ | Make image larger | |
| − or ↓ | Make image smaller | |
| 4 | Revert to original zoom level | |
| 5 | Zoom to 1:1 | |
| B | Adds active selection to image overlay | |
| Shift S | 3 × 3 unweighted smoothing | |
| Shift R | Repeat previous command | |
| M | Display statistics of active image / selection | |
| H | Display histogram of active image / selection | |
| K | Display density profile plot of active selection | |
| 1 | Select first gel lane | |
| 2 | Select next gel lane | |
| Shift U | Open Control Panel | |
| Shift G | Grab screenshot (with Ctrl if a dialog box is active) | |
| L | List, find and launch commands | |
| ] | Make all windows visible | |
| Tab | Switch to next image window | |
| Main ImageJ window↑ | Enter | Bring ImageJ window to front |