Edit Spines Panel (3D)

Procedure overview

See Editing spines (3D), Spines in 3D and the tutorial (PDF) for step-by-step instructions.

  • To open the Edit Spines Panel, click the Spines button in the 3D environment and then the Edit button. Click the Edit button a second time to exit editing mode.
  • If spines are associated with a single color-channel (that is, if a color channel was selected prior to spine detection), select that color channel to access all of the spine-editing functions. Select the color channel in either the Channel panel in the 3D environment or in the Image Adjustment tool in the 2D window.

Spine editing tools

Edit Spines (# spines): To see all the options, select spines first. The number of spines selected will be indicated in the panel title:

Select/Hide buttons

  • Click Select All to select all detected spines. Selected spines are displayed with wireframes.

    Note that you can select individual spines by clicking on them. Hold the Ctrl key and either click multiple spines or drag with the mouse to select all spines in the marquee that appears.

  • Hide/Show Selection button:

    • Hide Selection: Click to hide all selected spines.

    • Show All Hidden: Click to show all hidden spines.

Spine editing buttons

Split: Separate two spines that are modeled as one spine due to physical proximity.

  1. Click the spine to split to select it.
  2. Click the Split button.
  3. If necessary, this can be repeated.

Merge: Combine separate spines into a single spine.

  1. Press and hold CTRL and click each spine to be merged OR hold CTRL and drag the mouse to draw a marquee around the spines to be merged.
  2. Click the Merge button.

You can merge only two spine objects at a time.

Points: Click to display the five points that represent the selected spines and enable editing of these points.

Click and drag the point or points as necessary to obtain a more accurate spine model.

Remove: Click to delete selected spine(s). Alternatively, press the Delete key on your keyboard to delete selected spines.

You can't undo this action.

Appearance controls

Type drop-down menu

Use the Type drop-down menu to manually classify spines:

  1. Select the spine(s) whose Type you want to change.
  2. Select a type from the Type drop-down menu in the panel. This will override any previous spine-type classification.

Color picker

The color picker to the right of the Type menu can be used to change the color used to represent spines:

  1. Select the spine(s) you want to color differently.
  2. Click the arrow near the colored square to access the Color picker.
  3. Select a new color.

Show As drop-down menu

The Show as drop-down menu offers choices for display of detected spines. It does not change the spine-type assigned.

  1. Select the spine(s) you want to show a different way.
  2. Click the arrow next to the Show as drop-down menu and choose one of the display options, Solid, Wireframe, or Stick.

Channel drop-down menu

Use the Channel drop-down menu in multi color-channel images to associate spines with a (different) color channel.

Learn more about using individual color channels in the 3D environment.

  1. If the spines are associated with a color-channel, select that color channel in either the Channel panel in the 3D environment or in the Image Adjustment tool in the 2D window.
  2. Select the spines that you want to associate with a (different) color channel.
  3. Choose the new color channel from the Channel drop-down menu

Transparency slider

Slide the Transparency slider to adjust the display of selected spine(s).

If you set transparency to 100% (far right of the slider), the spine(s) will become invisible and can only be selected using the Select All button—slide the transparency setting back and forth to make them visible again.

Smooth checkbox

  1. Select the spines you want to smooth.
  2. Click the Smooth checkbox.
  3. Drag the slider to enable or disable smoothing.

Surface drop-down menu

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.

  • Spine Color: Displays spines as the colors they were originally traced as, the colors chosen from the color picker, or classification colors if the spines have been classified.

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

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

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

  • Texture: Select an image with the texture you want to apply to the surface of selected spines from the Load Texture Image window that opens. The image must be one of the following formats: .png, .tif, .jpg, or .bmp.