ODTbrain provides image reconstruction algorithms for Optical Diffraction Tomography with a Born and Rytov Approximation-based Inversion to compute the refractive index (n) in 2D and in 3D. This is the documentaion of ODTbrain version 0.4.12.post1+gf7bb8b7.

Documentation

• Introduction
  • Installation
  • Theoretical background
  • Fields of Application
  • How to cite
• Code reference
  • Data conversion methods
    • Sinogram preparation
      • sinogram_as_radon()
      • sinogram_as_rytov()
    • Translation of object function to refractive index
      • odt_to_ri()
      • opt_to_ri()
  • 2D inversion
    • Method summary
    • Backpropagation
      • backpropagate_2d()
    • Fourier mapping
      • fourier_map_2d()
    • Direct sum
      • integrate_2d()
  • 3D inversion
    • Method summary
    • Backpropagation
      • backpropagate_3d()
    • Backpropagation with tilted axis of rotation
      • backpropagate_3d_tilted()
  • 3D Apple core correction
    • apple_core_3d()
    • constraint_nn()
    • constraint_sh()
    • correct()
    • count_to_half()
    • ellipsoid_shell()
    • envelope_gauss()
    • spillover_region()
• Examples
  • 2D examples
    • Mie off-center cylinder
    • Mie cylinder with unevenly spaced angles
    • Mie cylinder with incomplete angular coverage
    • FDTD cell phantom
  • 3D examples
    • Missing apple core correction
    • HL60 cell
    • FDTD cell phantom
    • FDTD cell phantom with tilted axis of rotation
    • FDTD cell phantom with tilted and rolled axis of rotation
    • Mie sphere

• Changelog
• Bilbliography

Indices and tables

• Index

• Module Index

• Search Page