Remove small artifacts from 3d model

Michael_Ef · March 17, 2019, 11:00am

Hello,

I reconstructed a 3d model of prostate glands from histological slides by marching cubes algorithm. In my model I have a lot of small contours that i do not want to have in the model. Is there a way (e.g. a vtk filter) to extract these contours by setting a minimum size for these contours? Similar to the vtkConnectivityFilter where you can extract the largest region!?

Thanks a lot in advance.

Regards Michael

cpinter · March 17, 2019, 12:40pm

The Islands effect in Segment Editor can do this, here’s the code:

github.com

Slicer/Slicer/blob/master/Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorIslandsEffect.py#L121-L208


def splitSegments(self, minimumSize = 0, maxNumberOfSegments = 0, split = True):
  """
  minimumSize: if 0 then it means that all islands are kept, regardless of size
  maxNumberOfSegments: if 0 then it means that all islands are kept, regardless of how many
  """
  # This can be a long operation - indicate it to the user
  qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)


  self.scriptedEffect.saveStateForUndo()


  # Get modifier labelmap
  selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()


  castIn = vtk.vtkImageCast()
  castIn.SetInputData(selectedSegmentLabelmap)
  castIn.SetOutputScalarTypeToUnsignedInt()


  # Identify the islands in the inverted volume and
  # find the pixel that corresponds to the background
  islandMath = vtkITK.vtkITKIslandMath()

This file has been truncated. show original

Is there a good reason for using low-level VTK functions instead of Segment Editor? You’re using Slicer I assume so why not use its features?