ITK/Release 4/SpatialObjects/2010.11.18-Meeting

Attendees

• Arnaud Gelas
• Vincent Magnotta
• Luis Ibanez

Potential Use for FEM

• A potential FEMMeshSpatialObject could be created
  • Still a "FEMMesh" must be created
• How much refactoring is needed in Numeric/FEM
• IO is a critical need for FEM.
  • One option is to implement a FEMMeshSpatialObject and
    • a Reader Writer for it.
      • We can take the IO code from the Solver in the registration framework (Code/Numerics/FEM/itkFEMSolver.cxx)

Other Modifications

Add TimeStamp

• The actual TimeStamp will probably go in the itk::DataObject
• and will be available to the SpatialObject (given that it derives from itk::DataObject)

Compute Statistics

• A new filter that takes two inputs
  • an Image
  • an SpatialObject (as a mask)
• This filter compute intensity and shape statistics from image pixels that are "inside" of the spatial object.
• Use case: Having thousands of cells (biological ones) represented as itk::SpatialObjects and over each one compute statistics from the image pixels that are inside.
  • Multi-thread over groups of spatial objects.
  • Maybe reusing the LabelMap statistics classes ?
  • Converting the spatial objects to a label map.

Time and Tracking

• Given a group of SpatialObjects at time 1
• Given a group of SpatialObjects at time 2

Need to

• Filter(s) to Establish correspondences between the homologous spatial object of T1 to T1 (find self...)
• What should the output be ?
• Create itkTrajectoriesSpatialObject (3D + time)
  • It derives from the itkGroupSpatialObject
  • It provide links (edges) between objects that are the "same".
    • The links are across 4D.

Conceptual Grouping

• Have ShapedGroupSpatialObjects with Shape information
  • Use Case: Track an organ (composed of spatial objects, each one being cells)
• The shape would be the outline of the group of cell.

Arbitrary Properties

• Add arbitrary (key, value) pairs to label the objects.
  • For example tissue-type (connective, epithelial...).
• This could be done by using the MetaDataDictionary
  • SpatialObjects have MetaDataDictionaries (they inherit it from the itk::Object).
• itk::QuerySpatialObjectFilter that take a Spatial object and select the ones for which the MetaData dictionary has labels with a given value.
• Is the MetaData Dictionary managed by the SpatialObject Reader/Writer ?

Action Items

• Kitware: to create skeletons classes
  • FEMSpatialObject
  • Make sure that it works nicely with the itkSpatialObjectWriter.txx (in ITK/Code/IO)
• Create a filter that takes a collection of spatial objects (in a itkGroupSpatialObject) and generates a label map.
  • Maybe introduce a policy for overlap resolution (?)
  • Arnaud to send this code to Luis
  • Luis to create the filter.