How can I convert a 2d image stack into a 3d model while maintaining color?

Question

I have a stack of 2D .tiff images that I'd like to convert into a 3D model, while maintaining color and a relatively decent level of resolution. I need to be able to import this 3D model into a 3D modeling program (like Blender, http://www.blender.org/) to use it together with other models.

Thus far, I've been pretty easily able to export it as a .stl surface from ImageJ. I don't want a surface, though, because it has no color and I can't see anything past the surface. Essentially everything that's black in the image should be transparent and non-black things should be visible in the model.

EDIT: For further details/solutions specific to Blender see this related question.

Answer 1

Blender includes an addon called Import Images as Planes which will create a plane the same aspect ratio as the image and have the image setup as a texture on the plane ready to show up in the final render. It's not enabled by default but is easy to turn on in the preferences.

While any images containing alpha channels can easily be used directly in making parts of the plane transparent you also have ways to filter the image into black and white to use as a mask to make areas of the plane transparent.

If you need any blender specific help you would be better off asking at blender.stackexchange

Edit:

Using the blender internal render engine (cycles doesn't support voxels yet) you can setup a texture using voxel data that uses the images directly. You can then use a boolean modifier to cut away part of the object to reveal the insides.

The important material settings are volume and set density to 0.0 then in the texture select voxel data and turn on density under influence.

Answer 2

Your stack of 2D bitmaps is really a 3D bitmap, also known as a Voxel. Searching for "blender voxel image sequence" yield numerous interesting results.