Slice to Volume registration

I have a 3D microCT image about a tissue sample. And I use a ultramicrotome to get some ultrathin sections(slices) of the tissue. Then I get these slices’ 2D images using electron microscope. How can I use itk to register these 2D images to the 3D image in python. I am new in itk.
The 2D slice images are independent, so just one 2D image registers to the 3D image every time.
Any suggestions will be helpful.

Take a look at relevant repositories on GitHub. Also, TwoProjectionRegistration might be of interest. Look in the wrapping directory to see which classes are available via Python interface, e.g. TwoProjection.

@dzenanz Those repositories look like projected 2D to 3D, that is for use cases such as matching X-ray to CT. Are there any specific solutions that you are aware of that for a 3D single slice to a 3D volume?

@aabbcc Are the EM images acquired with scanning electron microscopy (SEM)?

@blowekamp Yes!