Can ITK extract the skeleton for a 3D mask?

Beginner Questions
1

Now, I need to extract the skeleton for a 3D mask. And I find the itkBinaryThinningImageFilter is useful for 2D mask, and it doesn’t work for a 3D mask.

Can ITK extract the skeleton for a 3D mask?

2

itkBinaryThinningImageFilter works for 3D volumes. Does it take too long to run or do you experience other issue?

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3

You could also take a look at ITKThickness3D remote module. Enabling Module_Thickness3D when configuring ITK should make that module available.

4

Yes, it take about 280s for a 512512498 volume in release version, while it take about 9 s by Python (skimage.morphology.skeletonize_3d).

My code is:

        constexpr unsigned int Dimension = 3;
        using PixelType = float;

        using ImageType = itk::Image< PixelType, Dimension >;
        using ImageReaderType = itk::ImageFileReader<ImageType>;
        ImageReaderType::Pointer reader = ImageReaderType::New();
        reader->SetFileName("..\\mask.mha");
        reader->Update();
        ImageType::Pointer itkImage = reader->GetOutput();
        using BinaryThinningImageFilterType = itk::BinaryThinningImageFilter<ImageType, ImageType>;
        BinaryThinningImageFilterType::Pointer binaryThinningImageFilter = BinaryThinningImageFilterType::New();
        binaryThinningImageFilter->SetInput(itkImage);
        binaryThinningImageFilter->Update();

Why ITK take so long time to calculate the skeleton? Is there any method to make the time shorter?

5

Thank you for your suggestion. I am try to use this module. In addition, after obtaining the skeleton of a volume, how can I get the network of the skeleton?

In python, the skan module can obtain the skeleton graph. Thus, we can obtain the cross section image along the medial axis.

6

You can use SGEXT, a library that I develop and maintain, which uses a less noisy skeletonization algorithm, and also generates a graph (what you called a network) from it. Also includes tools to manipulate graphs, and other modules specific to my research.

I am right now parallelizing the 3D thinning algorithm to make it faster. The library is not yet in a super-easy to use state (it will be), but I encourage you to try it if you need its functionality. In the short future it will also be completely wrapped to use in python (right now is at 70%).

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7

Thank you very much. We will test the SGEXT in our project.

8

Sounds great. Is it going to be available in ITK, too?

9

I would love too, but too much effort for the gain to be honest, not in my list of priorities. Also, DGtal has a GPL license, which will limit the benefits of having it in ITK.

Having said that, I would really love to integrate a digital topology module in ITK, @Niels_Dekker contribution of range neighbor iterators would greatly ease up its development.

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