Controls
Windows vs. Mac: Controls below assume a Windows keyboard with Alt and Ctrl keys. On a Mac, Option should be substituted for Alt, and Command for Ctrl.
The Segmentor interface contains three primary views: the 3D view, 2D slice view, and Region table. Mouse-based interactions with the 3D and 2D slice views depend upon the current mode, which can be selected from the mode toolbar above the 2D slice view. The mode labels in the 3D and 2D slice views indicate the current mode. Additional actions can be applied to the current region being edited via the action toolbar to the right of the mode toolbar. Various visualization settings can be controlled using the view toolbar to the right of the 2D slice view. These interface components are highlighted in the image below.
Independent of the mode, the user can middle-click or Ctrl + left-click any region to select it as the current region for editing.
The two primary modes are navigation mode and edit mode. In addition to using the mode toolbar, users can switch between these two modes using the space bar. Interactions and keyboard shortcuts for all modes are described in more detail below.
Navigation - Translate:
middle-click and drag - Zoom:
right-click and drag - Rotate:
left-click and drag - Rotate around view up vector:
Alt + left-click and drag - Rotate around view right vector:
Ctrl + left-click and drag
Edit - Paint (with current label):
left-clickorleft-click and drag - Overwrite (enables painting over other labels):
Alt + left-clickorleft-click and drag - Erase (voxels with current label) :
right-clickorright-click and drag
Brush size can be adjusted by pressing Ctrl + left arrow key or Ctrl + right arrow key, or via the Settings menu.
Add - Add region:
left-clickin empty voxel (2D slice view only)
Merge - Merge with current region:
Left-clickany region
Grow/shrink - Grow current region:
left-clickoutside current region (2D slice view only) - Shrink current region:
left-clickinside current region (2D slice view only)
Growing and shrinking is based on the voxel intensity of the current cursor position.
Visibility - Toggle region visibility:
left-clickany region
Actions are editing operations applied to the current region.
Fill Fill any holes in the region, applied to current z-slice only.
Update Update region by creating new regions for any unconnected components (e.g. the result of manual splitting).
Clean Clean region by removing any unconnected components and filling any holes in 3D.
Split Automatically split region into two parts.
Split multiple Open dialog to to split region into multiple parts.
Done Toggle 'done' status for region.
Voxel overlay Toggle voxel overlay visualization in 2D slice view. Overlay opacity can be adjusted by pressing the left arrow key and right arrow key, or via the Settings menu.
Outlines Toggle region outline visualization in 2D slice view.
Rescale full Adjust window/level settings to full range of current z-slice intensities.
Rescale partial Adjust window/level settings to condensed range of current z-slice intensities, producing a higher contrast image.
Auto rescale Toggle automatically adjusting window/level settings (full or partial, whichever was most recently selected) to current z-slice intensities when z changes.
Smooth normals Toggle smooth normals in 3D view.
Smooth surface Toggle smooth surfaces in 3D view.
Show plane Toggle display of current slice plane representation in 3D view.
Filter regions Toggle filtering regions based on their visibility.
Clear visibility Turn off visibility for all regions (current region will still be shown).
Show plane regions Turn on visibility for all regions that intersect the current slice plane.
Show neighbors Turn on visibility for all regions close to the current region.
Show the x-slice (yz plane) at the current position. Press in succession to 'flip' view.
Show the y-slice (xz plane) at the current position. Press in succession to 'flip' view.
Show the z-slice (xy plane) at the current position. Press in succession to 'flip' view.
Reset view (i)Adjust zoom such that the full volume/slice is visible.
- Move clipping plane:
Ctrl + right-click and dragorup arrowanddown arrow - Zoom to point:
f - Undo:
Ctrl + z - Redo:
Ctrl + y - Toggle 2D/3D view:
t - Show 2D and 3D view:
r
- Mouse-over cells in the Id, Color, or Size columns to highlight that region in the 3D view
- Click cells in the Id column to select and fly to that region
- Click cells in the Color column to select the color for that region
- Regions edited by the user are indicated in the Refining column
- Click the check box in the Done column to indicate regions for which editing is complete, which will render them as grey in the 3D and 2D slice views
- Click the button in the Remove column to remove that region