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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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Some questions : 1. What are the run-time constraints on the algorithm? 2. Can we assume that the 2D image occupies a whole plane in the 3d volume? 3. How large can be the rotation and the scale? 4. Can you do a long pre-processing step? P.S - please supply images! –  Andrey Oct 27 '12 at 23:45
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dsp.stackexchange.com/q/679/29 is similar, but you're trying to match pixels to voxels, not 2D points to 3D points, right? –  endolith Oct 28 '12 at 15:13
    
@endolith you are right, I am trying to match pixels to voxels. –  chippies Oct 29 '12 at 6:56
    
@Andrey Sorry, I cannot supply images, while this is for research, the images are confidential. (1) For run-time, I don't mind if it takes a few days. I have a Core i7 2600k if that helps you to estimate running time. (2) The 2D image does occupy a whole plane through the sample. (3) rotation is probably less than 10 degrees, scale change 2D:3D is probably between 0.8:1 and 0.9:1. (4) What is the long preprocessing step? I could do it. –  chippies Oct 29 '12 at 7:02
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1 Answer

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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