Detecting & editing somas (3D)

1. Optional: Adjust the detection settings for interactive soma modeling.
   1. Define the Interactive search region. The cursor's width represents the width of the search region.
   Changing the value for Interactive search region

   Hold down CTRL and scroll the mouse wheel to change the cursor size and match the apparent largest cross-section of a soma.

   OR

   Enter a value manually in the Interactive search region field.

   2. Constrain the soma size relative to the length of the region where soma and dendrites join by changing the value of Size constraint. After detection, you may notice that a detected soma appears to flow into the areas where the dendrites originate. To resolve this issue, increase the Size constraint value and detect the soma again.
2. Click a soma to detect it or click the Detect All Somas button in the panel.
3. If you are not satisfied with the detection, delete the soma by clicking the Clear button.
4. Modify the detection settings and detect again.
• Increase the Soma detector sensitivity so that the detector takes into account areas with less contrast between foreground and background.
• Increase the Size constraint value to obtain less flow from the soma to the dendrites, and a more refined soma model.

When a soma's structure is very complex, it might be rendered as a series of contours instead of a volume.

1. Click the Edit button to display the Edit Somas panel.
2. Click the detected soma to select it.
3. Press the Delete key or click the Remove button.

1. Click the Edit button to display the Edit Somas panel.
2. Select somas. Additional options become visible.
   • To select all somas, click the Select All button.
   • To select a single soma, click the soma in the tracing window.
   • To select several somas, hold down CTRL and click each soma that you want to select.
3. Modify color, transparency or smoothness.