Contouring (Interactive)

The interactive contouring logic can be used to manually contour 2D particle images and class averages or 3D volume(s) in a shape-specific manner.

Contouring defines the boundary between particle and unwanted particle regions or background-noise - an important step to increase the signal-to-noise ratio and/or to focus image processing on a certain region.

As input data a stack of 2D images or a 3D volume is required. Push the PLAY button once to import the data resulting in a blue hourglass. Then click the notepad to start the contouring process in a new window. In the main area, the current slice of the 2D/3D stack to be contoured is shown. At the bottom the current slice and previews of the previous and the following image are shown. Areas to be excluded are overlaid with a mesh, areas to be included are clear. To apply the selection of contoured images the process has to be saved by clicking the SAVE button and then executed with the RUN button.

Different masks (“layers”) can be defined to obtain more flexible masks, which may be combined in different ways, also with masks from other contouring sessions.

Three different modes are available for contouring, which all act on the slice of the 2D/3D stack shown in the main window:

Parameters Description
Bezier-Mode A continuous line can be drawn with the cursor by keeping the left mouse button pressed, thereby defining the boundary between particle and background-noise.
Poly-Line By single mouse clicks the contouring area is connected by lines. By double-clicking the right mouse button inside the selected area the mode can be finished resulting in a clear contoured and a shaded non-contoured area.
Drawing-Mode By holding the left mouse button areas that should be excluded can be marked.
Invert-Mask Invert the definition of areas to be included or excluded for the current slice.

Use the plus (+) button on the bottom left to add separate masks (“layers”), the minus (-) button to delete selected masks. Overlapping areas of different selected masks can be combined in three different ways: Union (all areas of all selected masks are combined), Intersection (only overlaps of masks are combined) and Difference (only none overlapping parts are combined). Only masks with checked boxes will be later applied for contouring of the respective slice.

  • Zoom in: CTRL + mouse wheel up
  • Zoom out: CTRL + mouse wheel down
  • next image: mouse wheel up
  • previous image: mouse wheel down
  • contouring several areas in one image: SHIFT + selection in Bezier-mode
  • excluding specific areas from contouring: CTRL + selection in Bezier-mode
Input Description
Io::in Input stack of 2D images/3D volume to be contoured
Io::input::layer Masks (layers) from previous Contouring run
Output Description
Io::layer All masks created as separate layers to be used in another Contouring run
Io::mask Mask as applied to the image stack
Io::out Stack of 2D images/3D volume contoured with selected mask/combination of masks