Selecting and editing contours (2D)

Also see Select objects/ Select all (editing mode)

Selecting contours

  1. Click Trace>Edit>Select Objects to open the Edit panel.

  2. In the Edit panel, choose Select under Editing Mode and select Only Contours from the Select Objects drop-down menu.

  3. There are several ways to select contours; selected contours are highlighted with small squares.

    • To select a contour, click it.

    • To add contour(s) to the selection, hold down the SHIFT key and click additional contour(s).

    • To add or remove contours from a group of selected objects, hold down the CTRL key.

      • Clicking an unselected contour adds it to the selected group.

      • Clicking a selected contour removes it.

    • Click the Select All button to select all contours.

Select all

Click Select All to select all contours in the file.

Selecting with your mouse

  • Click Select objects button, then click a contour to select it.

    • Selected contours are highlighted by small squares filled with a solid color.

  • To select multiple objects, do one of the following:

    • Drag the mouse to draw a rectangle around the objects

    • Hold the SHIFT or CTRL key and click the objects.

  • To add or remove objects from a group of selected objects, hold the CTRL key and click an object.

  • To remove a group of objects, drag your mouse from the lower right to the upper left to draw a rectangle around the objects.

Selecting with the Freehand Selection tool

The Freehand selection tool is useful for selecting all of the contours in oddly shaped regions—you draw the selection area.

The tool is in "Rubber line lasso" mode by default. Right click after selecting the tool, but before using it, to switch to "Continuous lasso" mode.

  • Click the Freehand selection button

    • Rubber line lasso mode (default): Click to place the points of the region in which you want to select objects.

    • Continuous lasso mode (available via right-click): Click and drag the mouse to define the selection region.

  • Right-click and select Close lasso or click Close and select from the Trace ribbon.

Editing contours

Right-click and select a command from the context-sensitive menu. The commands displayed when your cursor is directly on a contour are different from those available when the cursor is not on a contour. The most commonly used commands are described here:

Add to start of contour: Append to the first point of the contour rather than the last.

When selected, you exit the editing mode and return to tracing at the last point of the selected contour, indicated by a flashing circular cursor.

Append to selected contour: Only available for open contours.

When selected, you exit the editing mode and return to tracing at the last point of the selected contour, indicated by a flashing circular cursor.

Apply shrinkage: This is the same as the Correct z shrinkage command. Use it to apply shrinkage to selected contours.

Most commonly used when flipping sections that were mounted upside down (see Flipping a single section with a completed tracing).

Can be used to correct for known amounts of shrinkage, if you want measurements to reflect the parameters of the tissue before processing. However, this would usually be applied to an entire data stack, rather than to a few contours.

Attach internal markers: Bind a contour or set of contours to a selected contour.

A good application of this tool would be to attach boutons that you have marked to their axon. The axon can then be moved, rotated or scaled while keeping the contours in their appropriate locations.

Change contour type: The contour types currently assigned are listed in the Contour names drop-down menu.
A contour type is defined as a group of contours with the same name.

To assign a name to a contour type that will be used repeatedly, from the Trace ribbon, Contours section, in the main Neurolucida software window, click the cog icon to open the Contour Settings window. .

If a contour name (which is case-sensitive) is changed to exactly match an existing contour name, contours with the old contour name are assigned to the new contour type, and all changes to the new contour type made in contour preferences are applied to the edited contour.

Change contour to color: You can choose a new color for the contour and the fill (if you used Set contour density to fill the contour).

Close selected contour: Closes the selected open contour.

Copy selected contour: Copies the selection to the Clipboard.

Delete selected contour: Deletes all selected contours.

Exit selection tool: Returns you to the previous mode.

Fix Z values: Corrects large deviations in the Z values of a contour. The Z discrepancy that is corrected by Fix Z Values is the same as the Z value that triggers a Z Position Out of Range warning during tracing.

When Fix Z Values is selected, any move in Z position larger than this specified value is automatically corrected. The Z values shown in Ortho View do not change until you exit the editing mode.

Flip selected contour: Flip the contour(s). In the Flip Selected window that opens, choose how you want to flip the contour(s).

Hide selected contour: The contour is hidden; see Hidden Objects for information on working with hidden objects.

Insert point in selected contour: Click to place a new point.

Move selected contour: Turns the cursor into a hand; you can then drag the contour to a new location.

Modify thickness: You can also use the slider in the Edit Tool panel.

To display the thickness, go to File > Preferences > Display Preferences > View tab and check Display Thickness.

Modify Z position

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

Place contour in section: (Only available if using sections) Places the selected contours into a new section.

Place contours into set: See Creating Object Sets

Rename selected contour: Rename the selected contour. Note that this action does not create a new contour type.

Rotate selected contour: Rotates the contour or group of contours around the center point indicated by a green target icon.

  • Drag the green target icon to change the location of the rotation center.

Set contour density: Applies a cross-hatch fill; you control its density.

Set to cell body: Changes the selected contours to cell bodies. If applied to an open contour, this command closes the contour.

Useful for analyses in Neurolucida Explorer.

click the cog icon in the Neurons group of the ribbon to open preferences . Then select Fill Cell Bodies from the Neuron preferences to fill the cell bodies.

Select everything this color: Selects all contours of the same color.

Select everything of this contour type: Selects all the contours with the same contour name.

Undo last: Undoes the last action to a contour.

 

Also see Tracing contours (2D), Hidden objects, Editing contours (3D)