Re: Macro/plugin to align channels ?

Posted by Gabriel Landini on Mar 24, 2009; 10:02am
URL: http://imagej.273.s1.nabble.com/Macro-plugin-to-align-channels-tp3693202p3693206.html

On Monday 23 March 2009 16:39:40 Ignacio Arganda Carreras wrote:
> You may want to give a try to this script:
> http://biocomp.cnb.csic.es/~iarganda/bUnwarpJ/downloads/bunwarpj_stacks.js
> It registers with bUnwarpJ all images in a stack to the first one. If
> you convert your RGB image into a stack and call the script, it should
> work. Just take into account the bUnwarpJ parameters and the fact that
> it is a beta version :P

I see a problem with the suggestion above. Colour aberration is relatively
simple to characterise because it can be measured beforehand.
bUnwarpJ is a very impressive plugin, however, while trying to match the
images it will be unable to tell whether the differences seen between channels
(slices) are due to the aberration or to differences in colour contents across
the channels (unless the object was grey tones).

My suggestion is still to quantify how much the channels diverge with the
beads and then try to compensate this with resizing and translation (if
needed, for example when the field of view is not centred on the optical axis
of the microscope).

Cheers,

Gabriel