Line structuring element in any orientations

Beginner Questions
1

Hello,

I’m trying to implement “The Multiscale Bowler-Hat Transform for Vessel Enhancement in 3D Biomedical Images” by creating a custom itk filter.

They use morphological grayscale openings with a combination of spheres and 3D lines structuring elements. The lines structuring elements are oriented in several directions.

I would like to know how to make 3D oriented line structuring elements with ITK.

There is the itkFlatStructuringElement, but I don’t know if the Box function is the one I’m looking for. The documentation is a bit short and the examples on the wiki have been removed with the near ITK 5.0 release.

I also found the LineIterator to draw custom lines using two points. But the result probably won’t be usable by GrayscaleMorphologicalOpeningFilter…

Any pointers on how to proceed ?

Thank you.

2

Hello @Jonas

Welcome to the ITK community! :sunny:

Awesome!

Yes, you are on the right track. Depending on what you want, AddLine, FromImage, or Polygon are likely closer than Box for your application. The itk::FlatStructuringElement source code and the ITK Software Guide have more details or a higher level overview, respectively.

Please let us know how it goes!

3

Hello @Jonas

When I have to create a custom structuring element, I usually go back to the Neighborhood base class.
For a small example, you can see this post I made a while back on the same topic.

HTH,

Tim

1 Like
4

Thank you both for your input.

I want to stay close to the original matlab implementation. They use points uniformly distributed on a sphere to create orientations.

This is what I did :

  • Get a point generated on that sphere and his symmetric equivalent across the center (P1 & P2)
  • Create a boolean image
  • Use a LineIterator to draw the line between P1 and P2 in the image.
  • feed the image to an itkFlatStructuringElement using the FromImage function.

It seems to work. I still have a few things to check, but it’s going in the right direction.
I’ll keep you informed when the full filter is finished :wink:

2 Likes
5

@matt.mccormick
I need your input once more because I’m doing something wrong here…

// A bit of typedef context
typename TInputImage::Pointer input = TInputImage::New();
input->Graft( const_cast<TInputImage*>( this->GetInput() ));
using LineSeType = FlatStructuringElement<3>;
using OpeningLineFilterType =GrayscaleMorphologicalOpeningImageFilter
<TInputImage,TInputImage,LineSeType>;
auto openingLineFilter = OpeningLineFilterType::New();
openingLineFilter->SetInput( input );

// Problematic code portion
LineSeType lineSe;
lineSeImage = line3D(s,v[n],1.0,1.0,1.0);
// Viewing structuring element image for debug purpose
auto castFilter = CastImageFilter<itk::Image<bool,3>,itk::Image<int,3>>::New();
castFilter->SetInput(lineSeImage);
itk::ViewImage<itk::Image<int,3>>::View(castFilter->GetOutput() );
openingLineFilter->SetKernel( lineSe.FromImage(lineSeImage) );
openingLineFilter->Update();
auto imLine = openingLineFilter->GetOutput();
// viewing Opening image for debug purpose
itk::ViewImage::View(imLine);

From my previous post the first 3 steps are doing great. I managed to create a 3D boolean image (odd dimensions as the documentation requires) with the structuring element. As you can see in the picture below.

structuringElement
structuringElement563×589 39.2 KB

But the output of the opening is really bad…There are big overflow values on the image boundaries (3.5 +300) and a constant value inside (128).

going_wrong
going_wrong891×747 4.57 KB

My original picture is this one with a grayscale gradient ( to mimic vessels disappearing in the tissue)

cylindres
cylindres1009×859 20.9 KB

The opening is doing fine with a ball structuring element…My error should comme for the highlighted line.
What did I do wrong ?

6

Since SetKernel takes a reference and FromImage is a static method, try assigning to an instance, e.g.:

LineSeType kernel =  lineSe.FromImage(lineSeImage);
openingLineFilter->SetKernel( kernel )