Placing and editing markers

1. Click a symbol in the Markers toolbar to select it.
2. Click in the Tracing window to place the marker.

To delete the last marker placed, press CTRL-Z.

To delete all markers associated with a symbol, right-click over the symbol in the Markers toolbar and select Delete All Markers of This Type. All instances of this marker are deleted.

1. Right-click over the marker symbol you want to replace in the Markers toolbar.
2. Select Change Traced Marker.
3. In the Change Marker Type window, select a new symbol and click OK.
   • The new symbol is assigned to all existing markers. If the color was changed before this operation, the new color is preserved.

Useful for Marker and Region Analysis in Neurolucida Explorer and for editing contour and markers simultaneously.

1. Click Trace>Edit>Select objects.
2. Click the markers you want to attach to select them.
3. Right-click and select Attach Markers to Object.

1. Click Trace>Edit>Select Objects.
2. Click a marker to select it.
3. Right-click and select an action from the menu.
   Menu options

   Apply Shrinkage

   This is equivalent to using the Trace>Tools>Correct Z shrinkage command to apply shrinkage to a single marker, or to the entire section.

   Attach Markers to Object

   Bind a marker or set of markers to the nearest tree (i.e., nearest to the mouse click) at the root branch. Later manipulations of the tree include the attached markers.

   1. Select all the markers to be attached.
   2. Click the object the markers will be attached to.
   3. Once attached, markers and object are highlighted with small squares.

   Possible application: attach boutons that you have marked to their axon. The axon can then be moved, rotated or scaled while keeping the markers in their appropriate locations.

   Attach Markers to Branches

   Bind a set of markers to the nearest tree branch (i.e., nearest to the mouse click). This action is only visible when you select several markers.

   1. Select all the markers to be attached.
   2. Click the tree the markers will be attached to.
   3. Once attached, markers and tree are highlighted with small squares.

   Change Marker Color

   Choose a new color. Applies only to the selected marker.

   Change to Marker Type

   A marker type is defined as all markers having the same shape. Changing a marker shape means changing a marker type.

   Copy Selected Marker

   Copies the selection to the Clipboard.

   Delete Marker

   Deletes all selected markers.

   Exit Selection Tool

   Returns you to the previous mode.

   Flip Selected Marker

   The program flips the marker around the center defined as the reference point. If you uncheck Flip around origin (reference point), the program flips two or more markers only, using their center as the origin.

   Hide Selected Marker

   See Hidden Objects for information on working with hidden objects.

   Mark as Locus

   Designates a marker as a locus.

   Used by Neurolucida Explorer when performing a locus analysis, measuring the straight-line distance from the locus/loci to all other markers in the file. See Marker & Region Analysis in Neurolucida Explorer.

   Modify Z Position

   • Set Z Values: Specify the absolute Z value for the marker. If multiple markers are selected, the Z value is applied to all the selected markers.
   • Shift Z Values: Moves the marker(s) up (positive value) or down (negative value) a given number of microns.

   Move Selected Marker

   • Drag the marker to a new location.

   Place Marker in Section (only available if using sections)

   Places the selected markers into a new section. See "Using the Serial Section Manager"

   Place Markers Into Set

   See "Creating Object Sets"

   Rename Selected Marker

   Applies only to the selected marker.

   Rotate Selected Marker

   Move the marker(s) around the center point indicated by a green target icon.

   If a single marker is selected, this option has no effect unless the center point is moved.

   Undo Last Type Change

   Undoes the last change to a marker.

See Editing markers (3D)

Number of markers placed for a given marker type/symbol.

• Right-click in the Markers toolbar and select Show Marker Summary.

• Right-click in the Markers toolbar and select Show Marker Names.

• Right-click a symbol in the Markers toolbar and select an option from the menu.

Neurolucida applies the change to all markers associated with that symbol, including the markers already placed.

The marker becomes unavailable in the toolbar and markers that are already placed are hidden.

See Hidden Objects for information on hiding and revealing objects.

Right-click over the Markers toolbar and select Customize Markers Bar.