Editing contours (3D)

See also Tracing contours (2D) and Selecting and editing contours (2D) to place and modify contour shapes in the Main (2D) window.

Before you start

Contours must be traced in the Main window (see Tracing contours).

To edit existing contours in 3D, click the Contour button in the 3D window to enable contour mode, select the contour(s) you want to edit and click the Edit button.

Selecting contours

With Contour mode active, select contours for editing using any of the following methods:

  • Select by type: Use this drop-down menu to select all contours traced with a single contour type; useful when you want to render a series of contours as a wireframe or a shell.
  • Select All: Click the button to select all contours, regardless of the type.
  • Click with your mouse: To select a single contour, click it in the tracing window; CTRL-click to select multiple individual contours.
  • Hold down CTRL and drag the mouse to draw a marquee around one or more contours to select them.

Editing selected contours

With Contour mode active, click the Edit button and select at least one contour to display contour-editing options.

Hiding/Showing selected contours

Hide selected contours with the Hide Selection button to facilitate tracing. Display the hidden contours again with the Show all hidden button.

Resetting contour display when you have made changes

Click the Reset selection to lines button to reset the rendering of the contour to the default line. This may be useful if you previously chose a different option from the Show as drop-down menu.

Deleting contours

Click the Remove button to delete selected contours or press the Delete key on your keyboard.

If you delete a contour, you can't undo this action.

Changing the way that selected contours are displayed

Choose from the show as drop-down menu to change the rendering of selected contours.

Notes on contour display

  • To render as a shell or a wireframe, at least two contours with the same name must be selected.
  • Conversely, if too many contours with the same name are selected before choosing to Show as as shell or wireframe, a message that says the shell cannot be built may be displayed. If there is more than one contour with the same name on the XZ or YZ plane, NeuroInfo software cannot generate a surface rendering. To circumvent this problem:
    • Select fewer contours and try again. You can do this multiple times.
    • Rename contours to have one contour of each name on the XZ or YZ plane.

Changing a contour shape

Click the points button to edit the shape of selected contours.

  • It may be useful to Adjust point display by dragging the slider to more easily visualize the contour points; changing the point size only applies to the display and will NOT affect the tracing data.

  • To modify the shape, click a point and drag it to the desired location.

Editing circular contours

To edit a contour that was drawn with the circle-contour tool, click to select the contour, then click Points. The center point of the circle and one of the outer ring points are highlighted.

  • To move the contour, drag the center point.
  • To resize, drag either point.

Settings and buttons in the Edit Contours panel

Select by type: Choose a contour type from the drop-down menu to select all contours traced with a single contour type. Useful when you want to render a series of contours as a wireframe or a shell.

Select All: Click the button to select all contours, regardless of the type.

Hide selection: Click the button to hide selected contours. This may be useful to facilitate tracing additional structures.

Show all hidden: Click the button to display any hidden contours.

Reset selection to lines: Click to reset the rendering of the contour to the default line. This may be useful if you previously chose a different option from the Show as drop-down menu.

Remove: Click the button to delete selected contours. Alternatively, you can use the Delete key on your keyboard.

If you delete a contour, you can't undo this action.

Points: Click this button to edit the shape of selected contours. Once you are in point-editing mode:

  • Click a point and drag it to the desired location to modify the shape of the contour.
  • Adjust point display: Drag the slider to make the contour points easier to see for editing. Changing the point-display size applies does not affect the tracing data.

Show as: Use the drop-down menu to choose how selected contours are displayed. Line, flat surface, and solid displays can be applied to individual or multiple contours. To show contours as shell or wireframe, a minimum of two contours of the same name must be selected.

Color Picker:The color picker to the right of the Show asmenu can be used to change contour color. To change the color of selected contours, click the arrow near the colored square and choose a color from the color picker.

Transparency: Drag the Transparency slider to increase the transparency of selected contours.

Appearance controls for contours being displayed as shell or wireframe.

These features are for visualization purposes only (e.g., snapshots for publications); it does not affect your data.

Cap Ends: Check the box to cap the ends of contours so they are rendered as a continuous solid object. Leaving the ends uncapped allows you to see inside of the hollow structure.

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

Surface: Use the drop-down menu to choose a surface effect.

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

  • Contour Type: Displays a legend in the 3D window containing the selected contour types and their corresponding colors.

The following surface effects are only available when a minimum of two contours of the same name are shown as shell or wireframe:

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

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

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

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

  • Distance to Varicosities: Displays distance (µm) between contours 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 contours. The image must be one of the following formats: .png, .tif, .jpg, or .bmp.

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