Selecting and editing contours (2D)

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 contour, click it. If you click another contour The program deselects the currently selected contour and selects the new contour.
    • To add contours to those already selected, hold down the SHIFT key and click additional the contours to select.

    • 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.

Editing contours

Right-click and select a command from the menu.

Allows you to 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.

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.

Same as the Trace>Tools>Correct z shrinkage command. Allows you to apply shrinkage to a single contour, or to the entire section if you used Trace>Edit>Select All Objects or if all tracing objects have been selected.

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.

Bind a contour or set of contours to an object. Later manipulations of the object include the attached contours.

  • Select all contours that you want to attach first.

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.

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 Registration ribbon in the main BrainMaker software window, click the cog icon to open Contour preferences. .

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.

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

Closes the selected open contour.

Copies the selection to the Clipboard.

Deletes all selected contours.

Returns you to the previous mode.

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 the contour around the center defined as the reference point.

  • Flip around origin (reference point) is unchecked: the program flips two or more contours only, using their center as the origin.

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

  • Click to place a new point.

Turns the cursor into a hand.

  • Drag the contour to a new location.

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.

  • 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.

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

See Serial Section Manager.

See Creating Object Sets

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

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.

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

  • 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.

    Selects all contours of the same color.

    Selects all the contours with the same contour name.

    Undoes the last action to a contour.

     

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