Module: Watershed Segmentation ()

Description:

This module performs an accurate segmentation of different phases by applying a watershed on the high gradient magnitude.

After having specified the number of phases to segment, click on the Skip button and follow the instructions.

Actions to perform are:

• Specify the number of phases
  If only one phase is specified, a fake label will internally be computed from the eroded negative of the specified phase. Thus, the spread of the specified phase during the watershed computation is limited by the erosion.
• Compute the 3D gradient magnitude
  Internally the gradient_canny3d is used. Alternatively, the gradient magnitude can be set by connecting a gradient magnitude scalar field to the portGradient.
• Threshold the gradient mask
  Use the slider to threshold the gradient mask, ie define areas where markers can't be set.
• Specify each marker for the phases
  Each marker can be set either using the min and max threhold sliders, or by specifying the phase marker as a binary image through the portPhase.
• Apply the watershed computation
  The watershed algorithm is performed from the previously set markers, with the gradient magnitude as height image.
• Visualize the final phases
  A colorwash module is connected to the slice, to offer simultaneously phases segmentation and original data visualization.

Connections:

Data [required]
Image data to be processed.

Gradient [optional]
[Step 2] Connect your own gradient magnitude scalar field to this port to skip gradient magnitude computation.

Phase 0 [optional]
[Step 4 and next] Connect your own phases markers to these ports to skip phase marker thresholdings.

Ports:

Slice Number

This port controls the slice number of the Ortho Slice connected to the input data.

Slice Orientation

This port controls the orientation of the Ortho Slice connected to the input data.

Info

This port displays information about the current action.

Action

This port contains the 3 buttons "Back", "Skip" and "Apply" triggering the actions to perform.

Number of Phases

[Step 1] This port indicates the number of phases to segment.

Auto

[Step 3] If the auto checkbox is toggled when applying the gradient thresholding, the user does not define the gradient mask manually (The Gradient Threshold port is hidden). It is automatically detected by an automatic thresholding of the high values.

Gradient Threshold

[Step 3] If the auto checkbox is not toggled, this port controls the high gradient magnitude threshold used as a mask during markers selection.

Max Phase 0

[Step 4 and next] This port controls the minimim and maximum threshold values during markers thresholding.