You can try Fiji imaging software in which stack of two dimensional images may be converted to three or more dimensions

Fiji is probably the most adequate available freeware for this problem. There is also commercially available software like Definiens, which we use.

I would just like to add a few words of caution. Measuring osseointegration with a µCT is a rather difficult technique and there are doubts about its reliability.

The most commonly used parameter to characterize osseointegration is bone-to-implant contact (BIC), the percentage of the implant surface in contact with bone. Especially in the early stages of histological osseointegration the layer of bone on the surfaces is very thin (less than 50 µm) and it is practically “drowned out” by the µCT artefacts in the interface region. See the figure I have uploaded. In the histology on the left you can clearly recognize what is bone on the implant surface and where there is none. In the µCT image of the identical region on the right it is in my opinion impossible to make a clear distinction. For this reason we have stopped to use µCT scans to determine BIC.

To circumvent this problem, in some studies the percentage of bone in a larger zone around the implant is measured (BV/TV). This parameter is less affected by artefacts because those are weaker farther away from the interface. But one has to keep in mind that the amount of bone tissue does not really characterize osseointegration, or rather indirectly. Only if there is a solid contact between bone and implant, can mechanical forces be transferred. More bone in the wider vicinity of the implant does not necessarily mean more contact.

thank you @satish narula sir and @stefan tangl sir. i need to upgrade my computer for the graphics before we analyse i guess. thank you stefan tangl for the comparison with histomorphometry.truly appreciate that.

how to construct 3d image from 2d images?