Editing markers (3D)

Before you start

Markers must be placed in the Main window (see Placing Markers (2D)).

Click Marker in the 3D Visualization window to enter 3D marker mode.

Click edit to enter marker editing mode.

Selecting and hiding/showing markers

Select markers

Select markers for editing using any of the following methods:

  • Select All: Click to select all markers.
  • Click with your mouse: To select a single marker, click it in the tracing window; CTRL-click to select multiple individual markers.
  • Hold down CTRL and drag the mouse to draw a marquee around one or more markers to select them.

Selected markers are displayed within a semi-transparent sphere.

Hiding/Showing all markers of a certain maker type

  1. Click Marker Type Visibility to display a table with the marker types present in the data file.

  2. Click a row in the table to toggle between visible/hidden for that marker type.

  3. Click Marker Type Visibility again to close the table and exit this function.

Hiding/Showing selected markers

Hide/Show selected markers by clicking Hide Selected/ Show Selected .

Click Show All Hidden to make any hidden markers visible

Editing markers

With Marker mode active, click the Edit button and select at least one marker to see the editing options.

Change marker display

Click the Show As drop-down menu and choose how markers are displayed. This affects all markers in the file.

Change marker surface

Click the Surface drop-down menu to choose a surface effect. (This feature is for visualization purposes only, e.g., snapshots for publications; it doesn't affect your data.)

Click to access additional surface specific controls including gradient colors, transparency, and other context dependent settings.

  • Marker Color: Displays markers as the colors they were originally placed as, or the colors chosen from the color picker.

  • Marker Size: Displays the size of markers as a color gradient.

    See Preferences: Markers to learn more about marker sizing.

  • Distance to Puncta : Displays distance (µm) between markers and puncta as a color gradient. Must have puncta present.

  • Distance to Spines: Displays distance (µm) between markers and spines as a color gradient. Must have spines present.

  • Distance to Trees: Displays distance (µm) between markers and trees as a color gradient. Must have trees present.

  • Distance to Varicosities: Displays distance (µm) between markers and varicosities as a color gradient. Must have varicosities present.

Change marker type

Select a different marker type from the Marker Type drop-down menu to apply to the selected markers.

Change marker color

Select a color from the drop-down color picker to change the color of selected markers.

Change marker names

There are multiple ways to change marker names:

  • Click the Change name button and type in the new marker name.
  • Go to File>Preferences>Tracing, Markers section and click the Customize button; double-click a name and type a new name.
  • Right-click over a marker type in the Markers toolbar in the Main (2D) window and select Rename marker.

Change marker transparency

Use the Transparency slider to adjust the transparency of selected markers.

Deleting markers

Press the Delete key on your keyboard or use the Remove button in the Edit Markers panel to delete selected markers. You can't undo this action.

Marker sizing

Changes affect all markers in the file.

The minimal display size for a marker is 1 px.

  • In Pixels:The size is fixed and the same for all markers; zooming in or out has no effect on the display size of the markers. This is the usual method for displaying markers.
  • In Microns: The size of the markers is the same for all markers and is adjusted as you zoom. The markers are scaled along with the tracing.
  • Intrinsic: The intrinsic size for each marker is defined by the diameter of the circular cursor when the marker was placed; therefore the intrinsic value cannot be modified in 3D. Since this size is defined in actual micrometers, the displayed size depends on the zoom level. If you zoom out, you may not see the markers since they are scaled as small as possible. The intrinsic setting allows you to define a different size for each marker.

See also Markers (2D) and Editing markers (2D)