Applying Morphological Operations

The morphological operations of dilation, erosion, opening, closing, and smooth can be applied to refine regions of interest and the selected class of a multi-ROI by growing or shrinking labeled regions. The precise effect of these operations is determined by the selected structuring element. If the Use range option is selected, then the operation will be limited to the available range (see Thresholding).

Morphological operations box

Morphological operations

Dilate… Expands a region of interest using the selected structuring element.

Erode… Shrinks a region of interest using the selected structuring element.

Open… Is an erosion followed by a dilation using the same structuring element for both operations. In general, opening is less destructive than erosion. The effect of the operator is to preserve foreground regions that have a similar shape to the structuring element, or that can completely contain the structuring element, while eliminating other foreground pixels.

Close… Is a dilation followed by an erosion using the same structuring element for both operations. The effect of the operator is to preserve background regions that have a similar shape to the structuring element, or that can completely contain the structuring element, while eliminating other background pixels.

Smooth… Smooths a region of interest using the selected structuring element. Smoothing can be required in some cases to remove noise from the surface of an object. An example of smoothing is show in the following screen captures.

Original ROI (left) and smoothed ROI (right)

Settings for morphological operations
  Description

Dimensionality

Lets you apply the selected morphological operation in 3D, in which case the operation will be applied to all axes, or in 2D, in which the case the operation can be applied along the X, Y, or Z axis.

Shape

Lets you choose the shape and size of the neighborhood that will be sampled when calculating the pixel values to be modified (see Structuring Element).

Open

Can be defined as an erosion followed by a dilation using the same structuring element for both operations. In general, opening is less destructive than erosion. The effect of the operator is to preserve foreground regions that have a similar shape to the structuring element, or that can completely contain the structuring element, while eliminating other foreground pixels.

Range

Lets you choose selected slices, a range of image slices and an increment, or a combination of both, to which the selected morphological operation will be applied. For example, if you enter 1,2,3-5,6-15/3, then the operation will be applied to slices 1, 2, 3, 4, 5, 6, 9, 12, and 15.

Kernel size

Lets you choose the size of the neighborhood that will be sampled when calculating the pixel values to be modified (see Structuring Element).
  1. Select the required region of interest or multi-ROI class in the Data Properties and Settings panel.
  2. Select the Use range option in the Range box if want to limit the selected operation to a defined data range (see Defining Intensity Ranges).
  3. Select the required dimensionality for the selected operator — 3D, 2D (X), 2D (Y), or 2D (Z).

    Note Per slice 2D interpretation is generally faster than 3D processing and may give similar results. When setting interpretation to 3D, the filter is applied to the 3D slab with a depth depending on encoded parameters.

  4. Select a shape and size for the structuring element that will used for the selected operator.

    Note Structuring elements are retained in memory, and the last used settings will appear by default.

  5. Choose a range within which the selected operator will be applied, optional.
  6. Click the button — Dilate, Erode, Open, Close, or Smooth — that represents the operation you want to apply.