Re: help with registration please

Posted by William Simpson on Mar 16, 2011; 10:30am
URL: http://imagej.273.s1.nabble.com/help-with-registration-please-tp3685383p3685387.html

Hi Stephan,

> You can do that but the structures that you see in one plane aren't
> actually there.  That is, they do not have the expected topological and
> geometric properties.  Simpler, you have parallaxes depending on
> internal 3d-shears and tilts in the tissue, but all structures are
> mapped into the same plane.  The consequence is that you see structure A
> move left and structure B move right.  You would need to separate both
> structures which is complicated from the 2d projection.  Conventional 2d
> registration will randomly prefer either A or B (if at all), align it
> and bring the other structure out of place by that.
Points taken. Only problem: we do not have 3D information, just the
images taken at different times and from slightly different (unknown)
aspects.
:-(

> Find what I could do with the new elastic stack align plugin that I have
> announced yesterday:
>
> http://picpaste.com/elastic-align-3LE3c0GU.gif
>
> with the parameters:
>
> http://picpaste.com/align-parameters-hm2JNSsM.png
>
> It is clearly visible at various points that structures at various
> depths move in different directions due to 3d deformation of the tissue.

Thanks very much! Much better than our attempt.

Thanks very much Stephan for your help.

Bill