Notes

For Fly-Light

• Ensure bridging scripts using ANTs preserve bit-depth (8 & 16 bit)
  • ANTs won't "internally" do the conversion - we'll just have to do it after the fact see here

  • ANTS will output float images which you can convert to other types with the ANTS ConvertImagePixelType tool.

  • Alternatively, convert every transform to a nrrd format that CMTK likes, and use CMTK to apply the transforms
• We tried ANTs Dog without the last level to see how much faster it is, and how much the quality suffers.
  • Conclusion: it's not that much faster, and the quality does not suffer significantly, i.e. not helpful.

TODOs

DONE

• Develop compressed transformation format as discussed with Greg (scaled 16bit integer offsets compressed with GZIP, stored as HDF5), provide converters to nrrd and nii, develop efficient warp tool (for both point coordinates and image volumes) that accepts the compressed format.
  • see Hdf5-Deformation-fields

Jacobians

See /nrs/saalfeld/john/projects/flyChemStainAtlas/testElastixJacobian

Conclusions:

• using cmtk, --jacobian-correct-global and --no-jacobian-correct-global seem to give the same results
  • dfield_total_JacCorrect.nrrd and dfield_total_JacNoCorrect.nrrd are the same
• The ANTs and CMTK routines for computing jacobian are different.
  • dfield_total_JacANTS_stats.csv and dfield_total_JacNoCorrect_stats.csv differ