Hi,
In tomography you obtain a great number of images (volume), donĀ“t you? I ask you this because I use another program to treat the image, but it does not useful if you has a lot of images in a volume. Imagej is really no friendly to treat images, so I use GIMP2, similar to Photoshop but free. You can use layers easily. If you use 2 layer, for example, and identify differents artefacts or objects in each one you can add them in one and obtain a image to analysis with imageJ. Sorry, maybe this cannot help you