Module: Segmentation Three Phases ()

Description:

Segments an unsigned int image into three phases depending on the image intensities and local gradients.

Detailed explanation:

3-phase segmentation is a multistage process that divides (segments) the voxels in an image into three distinct phases. It uses a modified form of converging active contours.

In the main mode of operation four intensity thresholds and two gradient thresholds are defined. (All gradients used are Sobel gradients.)

Thresholds

Variable	Name	Use
Ti i=1...4	threshold1 ... threshold4	Intensity thresholds
Gin	in_gradient_threshold	Gradient threshold for intermediate phase
Ghl	hl_gradient_threshold	Gradient threshold for high and low phases

In the first stage of the process all voxels are segmented into four categories, based on their intensity value I, and local (Sobel) gradient G:

Initial assignment

Condition	Assignment
I < T1 and G < Ghl	void
T2 < I <T3 and G < Gin	intermediate
I > T4 and G < Glh	solid
else	undecided

Then, starting from the three known phases: "void", "solid" and "intermediate", we grow into the "undecided" region using the converging active contours algorithm.

In normal operation G_hl is left at 65535, and only the G_in is set. The last threshold is set to reduce mislabelling of voxels on edges between the void and solid phase, but with intermediate intensity value. If we did not use the gradient threshold we would have all interfaces between void and solid lined with an intermediate layer. Good values for this threshold are in the order of 100's or 1000's depending on the relative intensities in the image.

Additionally you can use tight thresholds and unassigned voxels to finetune your segmentation.

Connections:

Data [required]
The uniform scalar input field to be processed. Limitation: only 16-bit unsigned data with less than 2 billion voxels are currently supported.

Ports:

Void Threshold

The intensity threshold for the void phase.

Lower Intermediate Threshold

The lower intensity limit for the intermediate phase.

Upper Intermediate Threshold

The upper intensity limit for the intermediate phase.

Solid Threshold

The intensity threshold for the solid phase.

Intermediate Gradient Threshold

The gradient threshold for the intermediate phase. Voxels where the gradient is greater than this are initially thresholded as undecided.

Low/High Gradient Threshold

The gradient threshold for the high and low intensity phases. Voxels where the gradient is greater than this are initially thresholded as undecided

Use Tight Thresholds

Use an additional set of thresholds with which to perform partial segmentation by connectivity. Much faster and often higher quality.

Tight Void Threshold

Voxels having values below this threshold are conditionally set to void before the second stage. Regions set to void in this stage remain void only if they connect to regions set definitely to void in the initial threshold. Should be higher than Void Threshold but lower than Tight Lower Intermediate Threshold.

Tight Lower Intermediate Threshold

Voxels having values above this threshold and below Tight Upper Intermediate Threshold will be conditionally set to intermediate before the second stage. Regions set to intermediate in this stage remain intermediate only if they connect to regions set to intermediate in the initial threshold. Should be between Tight Void Threshold and Lower Intermediate Threshold.

Tight Upper Intermediate Threshold

Voxels having values above Tight Lower Intermediate Threshold and below this threshold will be conditionally set to intermediate before the second stage. Regions set to intermediate in this stage remain intermediate only if they connect to regions set to intermediate in the initial threshold. Should be between Upper Intermediate Threshold and Tight Solid Threshold.

Tight Solid Threshold

Voxels having values above this threshold are conditionally set to solid before the second stage. Regions set to solid in this stage remain solid only if they connect to regions set definitely to solid in the initial threshold. Should be chosen to lie between Tight Upper Intermediate Threshold and Solid Threshold.

Tight Intermediate Gradient Threshold

The gradient threshold for the intermediate phase for the second stage. Voxels where the gradient is greater than this remain undecided after the second connectivity thresholding stage. Should be greater than or equal to Intermediate Gradient Threshold.

Tight Low/High Gradient Threshold

The gradient threshold for the high and low intensity phases for the second stage. Voxels where the gradient is greater than this remain undecided after the second thresholding. Should be greater than or equal to Low/High Gradient Threshold.

Unassigned Phase

If the segmentation is taking place in a multiply-connected domain, then it's possible to have some isolated components of the domain that don't have any seed values. These regions will always end up as undecided. If you are using a multiply connected domain, e.g. as part of a multi-stage segmentation, then you may wish to assign a particular phase to these regions, in which case "" is common. For all normal segmentations this should be left to which will means that unassigned voxels cause an error.

Pore Speed Factor

Values lower than retard the growth of this phase and values greater than speed it up

Intermediate Speed Factor

Values lower than retard the growth of this phase and values greater than speed it up.

Grain Speed Factor

Values lower than retard the growth of this phase and values greater than speed it up.

Use Intensity

Use intensity in region growing speed calculation.

Intensity Exponent

Large exponents increase speed sensitivity just near the average of Void Threshold and Lower Intermediate Threshold.

Gradient Divisor

The higher this value is, the less influence the gradient will have on the front propagation speed.

Gradient Exponent

Larger exponents increase the speed sensitivity to the gradients.

Number of Acceleration Steps

For the acceleration of CAC segmentation. Sets the number of times that the segmentation will be interrupted to perform the acceleration. is safest, often gives good results.

Acceleration Gradient Threshold

For the acceleration of perfect segmentation. Sets the (smoothed) gradient value below which we say that the voxel is in a homogeneous region that can be considered a single cluster for the purposes of accelerating segmentation.