Editing puncta (3D)

In the 3D Visualization window, click the puncta button to display the Edit puncta panel,

then click the Edit button.

  • To access all puncta-editing options, select the color channel used for puncta detection in the Channel panel.

Select puncta in order to edit them

Select puncta for editing using any of the following methods:

  • Click the Select All button to select all detected puncta.
  • Hold the Ctrl key on your keyboard and drag your mouse to select all puncta in the marquee (selection box) that forms.
  • Click a single punctum with your mouse or hold the Ctrl key on your keyboard and click multiple puncta to select.

Splitting a punctum

To separate two puncta that are modeled as one due to physical proximity, use the Split button.

  1. Zoom, rotate, and pan as needed to view the punctum of interest clearly.
  2. Click to select the punctum you want to split.
  3. Click the Split button.

Merging puncta

To combine two puncta, use the Merge button.

  1. Zoom, rotate, and pan as needed to view the puncta of interest clearly.
  2. Hold the CTRL key on your keyboard and click the two puncta to be merged
    OR press CTRL and drag the mouse to draw a marquee around the puncta to be merged.
  3. Click the Merge button.

You can merge two puncta at a time. Repeat if necessary to merge more than two puncta into a single punctum.

Removing puncta

  1. Select the punctum/puncta.
  2. Click the Remove button or the Delete key on your keyboard to remove the selected punctum/puncta.

You can click Ctrl-Z on your keyboard to un-delete the punctum/puncta.

Changing puncta appearance

These settings affect the appearance of selected puncta, but not the underlying data.

First select the punctum/puncta whose appearance you want to change.

Select appearance options:

  • Show as: Choose a shape from the drop-down menu.

  • Transparency: Use the slider to adjust transparency of selected puncta in their assigned color channel or when all color channels are displayed. The transparency setting specified here will be ignored if a different color channel is displayed, however, the transparency of puncta and any other traced structures associated with undisplayed color channels can be controlled using the Trace Opacity slider in the Channel panel.

  • Smooth: Check the box and drag the slider to enable or disable smoothing.

  • 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.

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

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

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

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