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I have been searching for software that can handle the task of registering a 2D image to a 3D volume. The 3D volume is a microCT scan, while the 2D image is taken from a plane passing through the sample. I am looking for something that can locate the plane of the 2D image within this 3D volume, i.e. get the 3D translation, rotation and scale transform betwee the image and volume.

First prize is for pre-compiled free Windows software, but if that isn't possible then any libraries that can handle this task. I see that ITK from Kitware provides registration tools, but I don't see any discussion of my specific task, which doesn't seem to a common one.

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The software Amira from Visage Imaging has some excellent built-in registration features. I never tried that exact problem, though.

It is unfortunately pretty pricy, but you can download a free trial version of it from the website to give it a try. http://www.vsg3d.com/amira/overview

I also found some well implemented registration algorithms in the software MedInria, an open source and free software specially developed for medical image analysis. http://med.inria.fr

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Have you been able to solve this? Im interested in the solution too. There are a couple of articles about this topic. But it is a very difficult problem to solve because there are so many local minima.

This thread on mathworks has some matlab code that the OP said worked after she edited it.

Elastix has some nice registration functions that you could call. If you have a good initial guess and strong constraints it might work.

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