Detecting somas (3D)

Before you start

• Open an image stack or single images.
• In the 3D environment, select your preferred image display (3D Volume [default] or Image Slice).
• Click the Soma button to display the Detect Somas panel.

Detecting somas

1. Optional: Adjust the detection settings for interactive soma modeling.

   1. Define the Interactive search region. The cursor width represents the width of the search region.

      Change the value for Interactive search region one of the following ways:

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

      • Enter a value 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. Optional: To associate somas with a specific color channel, select a single channel using either the Channel panel on the left side of the 3D environment window or the Image Adjustment tool (on the Image and Workspace ribbons) in the 2D window.

3. Click a soma to detect it or click the Detect All Somas button in the panel.

4. If you are not satisfied with the detection, delete the soma by clicking the Clear button.

5. Modify the detection settings and detect again.

• Increase the Soma detector sensitivity so that the detector considers 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.

  Somas with very complex structures may be rendered as series of contours rather than as volumes.

6. Optional: Click the 3D Settings button to save your settings for later use. Learn more here.