[Insight-users] Advices on 3D registration

[Luis Ibanez]

Hi Nic,

Thanks for the detailed description of your problem.

A couple of questions:


1) When you acquired the volume from the bottom (in the second
    acquisition), are the slices organized in such a way that
    the first slice in your stack is actually the last slice of
    the sample as view from the direction of the first acquisition.

2) Were the acquisitions made by actually flipping the sample in
    the microscope between the two readings  ?


If the answers to (1) and (2) are true, what you may want to do
is initialize the rotation as a 180 degrees along the *SAME*
axis that you physically rotated the sample in-between the two
acquisitions, *AND* set the center of rotation to the physical
position of the middle of the first stack, *AND* initialize
the translation of the registration to the distance between the
centers of both stacks.

 From you data, it seems that the thickness of the full sample
is about:

               80um + 80um - 20um   = 140um

There for the distance between the physical centers of both
acquired blocks is about 60um.



Since you probably were very careful placing the sample in the
microscopy, you should set the parameter scaling in such a way
that rotations should be minimal, and the optimizer will
concentrate mostly on correcting for translations.



Once you solve the registration, you can join the two images into
a full image by resampling both the FIXED and the MOVING images
into an image grid equal aligned with the fixed image, but physically
extended downwards in order to include the physical region where the
second stack is located.


Please let us know if you have further questions,


    Thanks


       Luis


===========
Nic wrote:
> 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
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