Image Viewers in MagellanMapper

The tabbed pane on the right of the graphical interface provides several image viewers to visualize volumetric images.

Region of Interest (ROI) Editor

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.

Navigation

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

Annotations

To Do…	Shortcut
Add a circle	Ctrl+click at the desired location Ctrl+1+click to set channel 1 (replace with desired channel)
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. "r"+click to cycle in reverse order.

Atlas Editor

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

3D viewer

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