Tracing the Cell Body as a 3D Structure (soma)

If you trace the cell body using the Cell Body tracing tool, Neurolucida records the tracing as a two-dimensional structure.

To trace a cell body as a 3D structure

1. Name a contour type for the cell body: from the Trace ribbon bar, click the cog icon to open Contour preferences .
2. Click Trace>Contour Mapping and select the contour type named after the cell body in the drop-down menu.
3. Recalibrate the Z position of the stage to match the Z position of the processes where the cell body is first visible.
4. Focus on the highest part of the cell body and outline it in sharp focus.
5. When done with the outline, right-click and select Close Contour.
6. Focus a little deeper and outline the cell body again.
   • Draw outlines at several Z positions, like the hoops around a barrel.
7. When you have finished tracing the outlines for the soma, trace the processes.
8. If the cell body appears in multiple sections, repeat this process in all the sections in which it appears.