Open topic with navigation

Using Markers

A variety of marker symbols are available in the Markers toolbar.

When you select a symbol (i.e., marker type), you start the Markers mode. While in Markers mode, contour/neuron tracing is disabled. To return to tracing, turn off the Markers mode by deselecting the last symbol you used in the Markers toolbar.

ClosedHow do I place markers?
  1. Click a symbol in the Markers toolbar to select it.
  2. Click in the Tracing window to place the marker.
ClosedHow do I delete markers?

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.

  • Neurolucida deletes all instances of this marker.
ClosedHow do I assign a new symbol to markers I've already placed?
  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.
ClosedHow do I attach markers to contours?

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

  1. Click Edit>Select Objects.
  2. Click the markers you want to attach to select them.
  3. Right-click and select Attach Markers to Object.
ClosedTell me about all the editing options for markers
  1. Click Edit>Select Objects.
  2. Click a marker to select it.
  3. Right-click and select an action from the menu.
    ClosedMenu options
    ClosedApply Shrinkage

    This is equivalent to using the Tools>Shrinkage Correction command to apply shrinkage to a single marker, or to the entire section.

    ClosedAttach Markers to Object

    Bind a marker or set of markers to an object. Later manipulations of the object 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.

    Closed Attach Markers to Tree

    Bind a set of markers. 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.
    ClosedChange Marker Color

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

    ClosedChange to Marker Type

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

    ClosedCopy Selected Marker

    Copies the selection to the Clipboard.

    ClosedDelete Marker

    Deletes all selected markers.

    ClosedExit Selection Tool

    Returns you to the previous mode.

    ClosedFlip Selected Marker

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

    ClosedHide Selected Marker

    See Hidden Objects for information on working with hidden objects.

    ClosedMark 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.

    ClosedModify 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.
    ClosedMove Selected Marker
    • Drag the marker to a new location.
    ClosedPlace Marker in Section (only available if using sections)

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

    ClosedPlace Markers Into Set

    Creating Object Sets

    ClosedRename Selected Marker

    Applies only to the selected marker.

    ClosedRotate 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.

    ClosedUndo Last Type Change

    Undoes the last change to a marker.

Working with combination markers

Combination markers combine 2, 3, or 4 markers into one marker. Use combination markers for labeling cells and structures that were prepared with two or more staining methods. Working with Combination Markers for details.

See Double Label Analysis in Neurolucida Explorer for an alternative method.

Displaying marker summary and marker names in the Markers toolbar

ClosedMarker summary

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

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

Changing symbol properties

Use the Options>Display Preferences>Markers tab or the right-click menu for changes to individual symbols.

ClosedUsing the right-click menu
  • 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.

ClosedHiding a marker type

Neurolucida makes the marker unavailable in the toolbar and hides markers already placed.

See Hidden Objects for information on hiding and revealing objects.

Customizing the Markers toolbar

ClosedAdding or removing marker types

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

 

 

Neurolucida 11 | MBF Bioscience Support Center | Downloads