Registration of two sequence images of 2d each

Beginner Questions
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1

Hi all,

I am new to SimpleITK, and will appreciate any tips for how to start to deal with my issue:
I have a data of 2 images from brain scan, with slightly different depth (one image is from Zi depth of the brain, and the other is from several Microns in depth, image Zi+1).

I would like to register them such that they will be matched in terms of translation, rotation and appropriate shrink (can include also slight non affine transform).

How would you address this issue?

Thanks
Sivan Schwartz

2

Hello @sivanschwartz,

Based on the details you provided, you should be able to register these images, though some information is unclear:

  1. Are these images of the same object? Not tiles that need to be combined (this discussion).
  2. Are the intensities of the same structures in the two images the same or do they change? This is how we select the appropriate similarity measure to minimize.
  3. Is the transformation rigid, affine or deformable? This is how we select the appropriate transformation model.

For more information about registration, see the registration overview documentation and the SimpleITK notebooks repository, specifically, the registration series 6* notebooks.

Potential turnkey solutions based on SimpleITK:

imaris extensions - XTRegisterSameChannel extension, expects files in imaris format, provides a graphical user interface.
sitk-ibex - supports all file formats supported by SimpleITK + OME-NGFF, provides a command line interface.