Tracing contours

Purpose

  • Use closed contours to specify regions of interest. They can be used for measuring structures or to specify regions of interest for automatic cell detection.
  • Open contours can be used as delineations or reference lines to indicate layers in a reconstruction. This may be useful for measuring structures with Neurolucida Explorer software.

See also Automatic contour tracing, Selecting and editing contours (2D), and Editing contours (3D).

Before you start

  • Bring a specimen into view, make sure that a reference point has been placed.
  • If you are tracing a live image, enable Joy Track mode.
  • Enable AutoMove if you plan to trace contours that are larger than the field of view.

Procedure Notes

At any time during contour tracing, you can:

  • Adjust the thickness of the contour by scrolling the mouse wheel.

  • Press Ctrl-Z to erase the last drawn points one by one back to the beginning of the contour.

  • Focus with the joystick or the Page Up | Page Down keys on your keyboard.

    If your microscope has a built-in Z-motor system, you can focus using the microscope focus knobs and the focal depth changes are reported to Neurolucida software.

  • End a contour by right-clicking and choosing:

    • Close Contour

    • End Open Contour

Procedure

  1. Click Contour in the Trace ribbon to enter contour-drawing mode.

  2. Choose Freehand, Draw circle, or Draw square from the drop-down menu to determine the contour shape you want to draw. (The default shape is Freehand, but if you select circle or square, it will "stick" and become the default contour shape until you choose a different shape.)

  3. Choose a contour name before you begin drawing a contour using one of the following methods:

    • Choose a name from the Contour name drop-down menu; click to show the drop down menu, then click on the name for the contour you want to draw. If you don't choose a name, the first contour name in the list is used.

    • Click Contour selection to display the Contour Selection panel that includes a list of available contour names (typically anatomical names that you will use for your annotations).

      • Select the name for the contour you want to draw from the Contour Selection panel by clicking it.

      • You can change the name and/or color of the listed contours in Contour preferences; accessible from the cog icon in the ribbon or File > Preferences > Tracing > Contours. To change the name and/or color of a contour, click the name and type a new name; double-click the color picker and select the color you want.

  4. Select a tracing method by right-clicking in the tracing window. The method chosen is strictly a matter of preference and can be changed at any time during the tracing by right-clicking and selecting a different method.

  5. Trace or place your contour:

    • Freehand tool: click to place points along the boundaries of a region of interest. Right-click and choose one of the following to complete the contour:

      • Close Contour

      • End Open Contour

    • Draw circle tool: click to place the center of the circle, move your mouse to extend the circle and click again to finalize the contour.

    • Draw square tool, click to a corner of the square, move your mouse in any direction to extend the square, and click again to finalize the contour.