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I am currently working on a summer research project and we have generated 360 slices of a tumor. I now need to compile (if that's the right word) these images into one large 3D image. Is there a way to do this with either a python module or an outside source? I would prefer to use a free software if that is possible.

Walter Zanzig
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  • Please show what you have tried in a [minimal reproducible example](https://stackoverflow.com/help/minimal-reproducible-example) – above_c_level Jun 22 '20 at 15:53

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Perhaps via matplotlib, but anyway may require preprocessing I suppose: https://www.youtube.com/watch?v=5E5mVVsrwZw

In your case, the z axis (3rd dimension) should be specified by your vector of images. Nonetheless, before proceeding, I suppose you would need to extract the shapes of the object you want to reconstruct. For instance, if i take any image of the many 2D you have, I expect to find RGB value for each pixel, but then, for instance if you want to plot a skull like in the video link, as I understand you would need to extract the borders of your object and from each of its frame (2D shape) and then plot their serie. But anyway, the processing may depend on the encoding of the information you have. Perhaps is sufficient to simply plot the series of images.

Some useful link I found: https://www.researchgate.net/post/How_to_reconstruct_3D_images_from_two_or_four_2D_images Python: 3D contour from a 2D image - pylab and contourf

Federico Taranto
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