The tabbed pane on the right of the graphical interface provides several image viewers to visualize volumetric images.
The multi-level 2D plotter is geared toward simplifying annotation for nuclei or other objects. Select the ROI Editor tab to view the editor. Press the Redraw button to redraw the editor at the selected ROI. To detect and display nuclei in the ROI, select the Detect tab and press the Detect button.
| To Do... | Shortcut |
|---|---|
| Increase/decrease the overview plots' z-plane | Arrow up/right to increase and down/left to decrease |
| Jump to a z-plane in the overview plots corresponding to an ROI plane | "j"+click on the the corresponding ROI plane |
| Preview the ROI at a certain position | Left-click in the overview plot |
| Redraw the editor at the chosen ROI settings | Double right-click in any overview plot |
| To Do... | Shortcut |
|---|---|
| Add a circle | Ctrl+click at the desired location
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| Move the circle's position | shift+click and drag (note that the original position will remain as a solid circle) |
| Resize the circle's radius | Alt+click (option+click on Mac) and drag |
| Copy the circle | "c"+click |
| Duplicate a circle to the same position in another z-plane | "v"+click on the corresponding position in the z-plane to which the circle will be duplicated |
| Cut the circle | "x"+click |
| Delete the circle | "d"+click |
| Cycle between the 3 nuclei detection flags | click within the dotted circles. Red = incorrect, green = correct, and yellow = questionable.
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The multi-planar image plotter allows simplified viewing and editing of annotation labels for an atlas. Existing labels can be painted into adjacent areas, and synchronized planar viewing allows realtime visualization of changes in each plane.
To view the editor, select the Atlas Editor tab. The Redraw button in the ROI tab of the left panel will redraw the editor if necessary. The Registered images section allows selecting any available annotations and label reference files to overlay.
| To Do... | Shortcut |
|---|---|
| See the region name | Mouseover over any label |
| Move the crosshairs and the corresponding planes | Left-click |
| Move planes in the current plot | Scroll or arrow up/down |
| Zoom | Right-click or Ctrl+left-click while moving the mouse up/down |
| Pan | Middle-click or Shift+left-click while dragging the mouse |
| Toggle between 0 and full labels alpha (opacity) | a |
| Halve alpha | shift+a |
| Return to original alpha | press a twice |
Press on the "Edit" button to start painting labels using these controls:
| To Do... | Shortcut |
|---|---|
| Paint over a new area | Left-click, pick a color, then drag over image |
| Use the last picked color to paint over a new area | Alt+Left-click (option-click on Mac) |
| Make the paintbrush smaller/bigger | [/] (brackets) |
| Halve the increment of the paintbrush size | [/] and add shift |
Use the save button in the main window with the atlas window still open to resave
The 3D viewer displays regions of interest, atlas structures, or whole images. MagellanMapper uses the Mayavi data visualizer for 3D voxel or surface rendering. See the Mayavi docs for more shortcuts.
| To Do... | Shortcut |
|---|---|
| Rotate the camera | Left-click and drag |
| Pan the camera | Shift+Left-click or Middle-click and drag |
| Zoom the camera | Scroll, or Ctrl+Left-click and drag up/down |
| Switch to "Joystick" mode. The view becomes a joystick where the center of the view is neutral. Clicking in the view using any of the above controls "moves" the joystick to that position. | j |
| Switch back to the default, "Trackball" mode | t |
TODO: add further description