[Insight-users] Advices on 3D registration

[Nic]

Hello,
    I would like to register 2 images stacks from one sample (confocal 
microscope, 1 channel only, nucleus staining). Each stack corresponds to one 
side of the sample, one scan was made from the top and the other from the 
bottom, each scan was made until a little past the middle of the sample, in 
order to have in each stack a small common sub-volume I could use for 
registering them (each common volume have around 10-20 µm deep, each stack 
can be 60-80 µm deep); the overlapping part is thus at the bottom of each 
stack. Nucleus are perfectly stained, well shaped and well separated.
I'm currently adapting the "Rigid transform in 3D" (8.6.4), trying to 
initialize the transform with a z translation of the moving stack in order 
to have both overlapping sub-volume a little bit registerated; I'm allowing 
too loading Tiff image stacks, with correct spacing and origin.
According to my acquisition protocol, it is probably possible to neglect 
rotations, or at least to consider only the rotation in the x-y plane (and 
this one could be perhaps approximated with microscope's value on scanfield 
rotation, and a mirroring calculation): should be it a solution to force 
optimisation for versor with a very small step and for translation a greater 
step (tuning is on optimizerScales no ?) ? Or is it possible to use another 
transform that only make 3D translations ?
The idea is finally to have both stacks merged, one stack unchanged, and 
increased by a resampled version of the other from the bottom of the 
unchanged stack until the top of the resampled other stack; z-stepsize are 
same. Is there a way to do it easily ? I think the ImageRegistration8.cxx 
(code of Rigid transform in 3D" (8.6.4) example) do a resampling at end for 
the moving 3D image, but it seems to me it only apply transformation to the 
moving image but don't merge the fixed and moving images.. Or did I miss 
something ?
Thanks a lot in advance ! nic