I’m working on brain vessels segmentation. I need manually annotated data from clinicians, so I wrote a module that uses some effects from the Segment Editor. Their current pipeline for segmentation is:
- MITK: Intensity threshold of the vessels image and surface generation
- MeshLab: mesh cleaning by removing small (diameter) islands and manually selected ones
My Slicer module is very similar, but works on a
Segmentation node with label map as master representation. I use
Remove small islands and the
Scissors effect, but my feature requests are:
- Being able to remove an island by clicking on it in the 3D view. I guess this shouldn’t be too hard since one can already move the 2D crosshair by placing the mouse on the 3D mesh and pressing Shift
- Add an option to use islands diameters (longest distance between points on the surface) instead of number of voxels for the
Remove small islands. This one might be harder, I don’t know whether that filter is available on VTK.
An elongated, thin island (long diameter, small volume) is more likely to be a vessel than a spherical island (small diameter, high volume). That’s why this difference is important for my case.