Tracing cell bodies

See also Tracing trees, Tracing neurons (2D), Editing trees (2D)

Before you start

Before you start tracing, you might find it useful to read Preparing to trace. In most cases, starting with the cell body and working outward produces the best results.

Cell body tracing procedure

  1. Select Trace>Mode>Neuron.
  2. Click Cell Body.
  3. Trace the cell body (this is similar to tracing a contour):
    1. Choose a focal plane (e.g., focal plane near the center of the cell body).
    2. Click to place the first point.
    3. Continue to click to place the next points to trace the contour of the cross-section.
    4. After you've placed the last point, right-click and select Finish Cell Body.
  4. Either stop with one cross-section to represent the cell body in two dimensions, or continue tracing cross-sections of the cell body at different focal planes to obtain a three-dimensional representation.

    Tracing a 2D cell body

    Trace a single cross-section at a single Z plane, preferably around the middle of your cell.

    Tracing a 3D cell body

    Trace multiple separate cell bodies (one cell body at each Z plane).

    A few considerations:

    • The more contours you have, the more accurate your reconstruction will be. But having more than one cell body is primarily cosmetic and won’t affect most analyses.
    • Even though the different cell bodies are drawn with different colors, they will be displayed as a single cell body in the 3D window and in Neurolucida Explorer.
    • Very dark cells (e.g., Golgi) tend to block the transmitted light over a much larger area in Z than they actually occupy. This tends to give them a very “stretched” or “smeared” appearance in Z when viewed in the 3D window.
    • Sholl analysis will be centered around the centroid of all cell bodies. Usually a single cell body contour traced around the middle of your cell is sufficient.
    • The only branched structure analysis data that will be changed by having multiple cell body contours are those related to the cell body in Analyze>Structure>Branched Structure Analysis>Neuron Summary.
  5. Trace the trees emanating from the cell body.

 

Unlike contours that can be open or closed shapes, cell bodies are always a closed shape.