Simple Neurite Tracer: Key Shortcuts

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Interactive Prompt

  • Y - Confirms the current temporary path. Mnemonic: Yes.
  • N - Discards the current temporary path. Mnemonic: No.
  • F - Finishes a path. Note that you can finish a path by pressing Y twice.
  • C - Cancels a path. Note that you can finish a path by pressing N twice.
  • Esc - Aborts current operation.

Tracing

  • H - Toggles Hessian calculation of Path curvatures.
  • I - Toggles tracing on filtered Image.
  • G - Selects the path nearest to the mouse pointer. Holding Shift+G adds the path nearest to the mouse pointer to the current list of selected paths. Mnemonic: Group paths around pointer.
  • M - Finds the brightest voxel (Maximum) above and below the current x,y position and automatically clicks on it. If multiple maxima exist, their average positioning is used. Note that this feature assumes that neurites are brighter than background.
  • S - Toggles cursor Snapping: If enabled, the plugin will automatically move the cursor to the brightest voxel within the specified x,y,z snapping window1. This facilitates accurate positioning of path points and it is described in more detail in this issue.
  • ^ Control+ Shift-click ( Alt+ Shift-click on MacOS) - Selects a point along the active path to be used as forking point (See step-by-step instructions for more details on joining and branching.)

Navigation and Zoom

  • Shift - Synchronizes XY, ZY and XZ views while moving the cursor when not using cursor snapping.
  • + - Zooms in (Simultaneously on all views) (IJ default)
  • - - Zooms out (Simultaneously on all views) (IJ default)
  • 4 - Displays tracing view(s) at original scale (IJ default)
  • 5 - Displays tracing view(s) at 100% (IJ default)
  • Spacebar - Activates the Pan tool (IJ default)
  • > / < - Previous/Next Z-slice (IJ default)
  • Enter - Shuttles the window focus between the tracing image and the SNT window.

Path Rendering

  • A - Toggles which traced paths should be displayed: All / Selected.
  • Z - Toggles depth-rendering choice of traced paths: Parts in nearby slices / Z-stack projection.

Editing Paths

These shortcuts become available in Edit Mode, activated through the contextual menu (displayed when right-clicking on the image being traced):

  • D or Backspace - Deletes the active node
  • I or Insert - Inserts a new node at cursor position
  • M - Moves active node to cursor position
  • Z - Brings active node to current Z-plane

Legacy 3D Viewer

All shortcuts that are not specific to tracing canvases (XY, ZY and XZ views) should be recognized by the legacy 3D viewer. In addition the following are also implemented:

  • H - Selects the Hand (rotation) tool
  • W - Selects the Wand (selection) tool
  • Esc - Shuttles between the Hand and Wand tool after both have been selected at least once.

Other

There are more complex key and mouse combinations used in:


Tip: SNT was designed so that its shortcuts do not collide with those of ImageJ. SNT hotkeys do not require holding down ^ Control ( Cmd on MacOS). When such a modifier key is pressed, the hotkey will no longer be intercepted by SNT. E.g., During a tracing session pressing S will toggle cursor snapping while Pressing ^ Control+S ( Cmd+Son MacOS) will allow you to save the traced image using IJ's built-in command File ▶ Save.