http://imagej.273.s1.nabble.com/Make-images-overlap-tp3684297p3684299.html
ImageJ. You can search for it on the plugins page.
> Hi Tomas,
>
> using Fiji, you have at least two options:
>
> 1.
> Open both images and mark corresponding points in both using the point
> selection tool (index number must match) and use the plugin:
>
>
http://pacific.mpi-cbg.de/wiki/index.php/Landmark_Correspondences>
> to map one image into the other using a transformation model of your
> choice (translation + rotation is rigid).
>
>
> 2.
> Import the slides into TrakEM2 and use either of the manual
> alignment/transformation modes. That is less trivial in terms of the
> learning the program and less easy to script but provides a much nicer
> user interface (interactive overlay supporting various overlay modes).
> The underlying engine is the same:
>
>
http://www.ini.uzh.ch/~acardona/trakem2_manual.html#transform_patch>
>
http://www.ini.uzh.ch/~acardona/trakem2_manual.html#landmarks>
> Good luck and best regards,
> Stephan
>
>
>
>
> On Sun, 2011-06-12 at 21:59 +0200, Tomas Karlsson wrote:
> > Dear all.
> >
> > Is there a plugin or macro for making the elements of to images overlap
> ( elements in image 2 being roughly at the same coordinates as in image 1)?
> ( I have searched online but could not find any)
> >
> > The procedure i was thinking of is to load the two images, ask the user
> to select to 2 points ( forming a vector) on the first image, then mark the
> two corresponding points on the second image. Then based on these marked
> points do a translate and a rotate to make the images overlap (i.e.
> Transform the second image so the two vectors overlap) . ( More points can
> be used to improve accuracy).
> >
> > The reason:
> >
> > I am working for a research group that has a protocol for analyzing
> muscle fibers. This protocol requires overlapping fibers from two slides
> with different stainings. Previously this used be done by loading the master
> slide in the microscope, capturing images of the areas of interest. Then
> load the second slide in the microscope, navigate to and capture
> corresponding areas of the second slide. In order to make the fibers of the
> different slides overlap the user needed to rotate the camera or stage since
> its impossible to place the fibers on the slides in a identical angle.
> >
> > Now we have now a fully automated microscope witch supports automated
> tile-scaning but because of the motorized stage and tile-scaning function
> lacks the ability to easily rotate the slides. This however presents the
> opportunity to do tile-scaning and then using software to align the fibers
> of the two slides (i am aware that doing the whole slide might run into
> memory constraints and accuracy problems, but even for a 2x2 tile-scan this
> approach should prove to be a good timesaver, and roughly as accurate).
> >
> > Any help or opinions is appreciated, With best regards,
> >
> > Tomas
>
Joel B. Sheffield, Ph.D