Editing somas (3D)

Before you start

1. Detect one or more somas in the 3D environment (see Detecting somas (3D)).

2. Click the Soma button if needed to enable soma detection and/or editing.

3. Then click the Edit button in the Somas panel, and select one or more somas to see the editing options.

Select somas for editing using any of the following methods:

• Select All: Click the button to select all somas.
• Click with your mouse: To select a single marker, click on it; CTRL-click to select multiple somas.
• Hold down CTRL and drag the mouse to draw a marquee around one or more somas to select them.

Deleting somas

Select the soma(s) to delete, then do one of the following:

• Press the Delete key on your keyboard.
• Click the Remove button

You can't undo this action.

Changing soma appearance

1. Click the Edit button to display the Edit Somas panel.

   • If the somas were detected in a specific color channel, select that channel or All channels in order to edit the soma. (Select the color channel either in the Channel panel in the 3D window or in the Image Adjustment tool in the 2D window.)
2. Select somas. Additional options become visible.
   • To select all somas, click the Select All button.
   • To select a single soma, click on it.
   • To select several somas, hold down CTRL and click to select each soma.
3. Modify soma appearance.

   • Show as: Use the drop-down menu to choose how selected somas are displayed.

   • Color Picker: The color picker to the right of the Show as drop-down menu can be used to change the color used to represent somas. To change the color of selected somas, click the arrow near the colored square and choose a color from the color picker.

   • Channel: In images with more than one color channel, use the drop-down menu to associate the selected somas with a specific color channel.

     Changing a soma color-channel does affect the data associated with the image.

   • Transparency: Drag the Transparency slider to increase the transparency of selected somas. (You may want to hide trees instead.)

     

   • Smooth: Check the box and drag the slider to smooth the appearance of selected somas (they will appear less jagged).

     This feature is for visualization purposes only (e.g., snapshots for publications); it does not affect your data.

   • Surface: Use the drop-down menu to choose a surface effect. (This feature is for visualization purposes only, e.g., snapshots for publications; it doesn't affect your data.)

     Click to access additional surface specific controls including gradient colors, transparency, and other context dependent settings.

     • Soma Color: Displays somas as the color they were originally traced as, or as the color chosen from the Color Picker.

     • Distance to Markers: Displays distance (µm) between somas and markers as a color gradient. Must have a marker present.

     • Distance to Puncta : Displays distance (µm) between somas and puncta as a color gradient. Must have a punctum present.

     • Distance to Spines: Displays distance (µm) between somas and spines as a color gradient. Must have a spine present.

     • Distance to Trees: Displays distance (µm) between trees and spines as a color gradient. Must have a tree present.

     • Distance to Varicosities: Displays distance (µm) between trees and varicosities as a color gradient. Must have a varicosity present.

     • Texture: Allows you to select an image from a browser window and apply it to the surface of selected trees. The image must be one of the following formats: .png, .tif, .jpg, or .bmp.

Also see Tracing & editing in 3D