Tracing contours

Purpose

  • Use closed contours to specify regions of interest. They can be used for measuring structures, systematic random sampling, automatic cell detection,
  • obtain measurements of the area within the contour. automatic cell detection.
  • obtain measurements of the area within the contour. or to specify regions of interest for automatic cell detection.
  • Open contours can be used as 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.
  • 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 Page Up | Page Down keys on your keyboard.

  • End a contour by right-clicking and choosing End Open Contour or Close Contour.

Procedure

  1. Controls for drawing contours are in the Contours section of the Registration ribbon.

  2. Click to draw a freehand shape or select the option to draw a circle- or square-shaped contour from the drop-down menu.

  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.

    • Start typing "contour selection" in the Quick Launch box at the top right of the main BrainMaker software window 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 the contour of choice: Click to place points along the boundaries of a region of interest; when you're done, right-click and select close contour or end open contour.