CIBC:Seg3D Speedlines

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Basic Introduction to the SpeedLine Tools


The Speedline tools are simple semi-autonomous segmentation methods that perform a similar type of operation to that of the livewire segmentation algorithm (Wikipedia explanation). However, instead of using Dijkstra's algorithm to compute the minimal path between a set of user defined points, we use a fast marching minimal path extraction method available in ITK. This method generates a continuous path and mimics Dijkstra's algorithm by employing nearest neighbor interpolation when minimizing the cost function, although this is not as computationally efficient as Dijkstra.


In this section we discuss in more detail the three different types of speedline tools.

Speedline Iterative Neighbourhood

The iterative neighborhood method is designed for segmenting regions with large discontinuities.

Speedline Gradient Descent

The gradient descent method is suitable for segmenting regions that don't contain any discontinuities.

Speedline Regular Step

Like the gradient descent method, the regular step method is suitable for segmenting regions that don't contain any discontinuities. However, this method enables the user to have more control over the iterative step size by allowing the minimum and maximum step length to be set based on the Step Factor, and the relaxation factor to be explicitly set from the Step Relax value.


Speed Function

In order to to use the speedline tools to perform a segmentation. the image must first be an appropriate speed function. The speed function was computed by applying a gradient magnitude filter and rescaling the values between 1 and epsilon, which is an arbitrary small number close to zero.

Figure 1 illustrates how to create the speed function image in Seg3D.

Speedfunction copy.png

Figure 1


Once the speed function image has been computed it is possible to segment the region between the user defined points. The drawing of the polyline is done interactively and when the user has generated an acceptable segmentation. The line can be filled in by creating a child image, which is done by selecting the plus icon on the volume label. once this new volume label has been created go to the tools panel and press the fill button.

Figure 2 illustrates how to segment a region of the speed function image.

Speedfunction02 copy.png

Figure 2

Unlike the other GUI layouts in Seg3D, the speedline tools contain a checkbox for adding seed points. The reason for this additional GUI component is to enable the user to modify the image brightness and contrast using the left mouse button. Unfortunately, the left mouse button is also used to place the seed points on the image. So to enable the user to modify the brightness and contrast with the speedline tool we added the checkbox.