Editing Contours

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

Most commonly used when flipping sections that were mounted upside down (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 drop-down menu in the toolbar.
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, use Options>Display Preferences>Contour tab.

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 Options>Display Preferences>Contour tab are applied to the edited contour.

• 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.

• To change this value, see the Options>General Preferences>Tracing tab.

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

Microlucida flips the contour around the center defined as the reference point.

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

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, use the Options>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.

Serial Section Manager

Creating Object Sets

• Rename the selected contour. Doesn't 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 and lets you control its density.

• Select Fill Cell Bodies from the Options>Display Preferences>Neurons tab to fill the cell bodies.

Selects all the contours of the same color.

Undoes the last action to a contour.