Detect Somas Panel (3D)

See Detecting & editing somas (3D) for step-by-step instructions

Soma Detector Sensitivity

Sensitivity refers to the detector's ability to discriminate between foreground and background (i.e., between bright pixels and dark pixels).

Increasing the sensitivity enables the detector to take into account areas with less contrast between foreground and background.
Decreasing the sensitivity results in the detector ignoring areas with less contrast between foreground and background.

Soma Detection Settings

Interactive search region

Defines the width of a cube used to constrain the search area for interactive detection. Somas larger than the maximum size are detected within the cube; areas of the somas outside of the cube are ignored.

There are two ways to adjust the interactive search region value:

Use the mouse: Hold down CTRL and scroll the mouse wheel to adjust the cursor's size in the tracing window.
Use the Detect Somas panel: Enter a value for Interactive search region

The cursor's width represents the width of the interactive search region.

Size constraint

Constrains the soma size relative to the length of the region where soma and dendrites join. 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.

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