Are your scaffolds made from hydroxyapatite? Then you have a difficult task. You may try SEM/EDS. If all mineral around is hydroxyapatite you may hope that topography of new mineral will differ from that of scaffolds. You may use BSE (backscattered electrons) which will highlite regions of different mineral density. If scaffolds are made of different material, then the task is an easy one. BSE and EDS will determine new mineral without problems.  

The following paper may possibly help to identify FTIR absorption bands; it refers to crystallised hydroxyapatite and octacalciumphosphate precipitated over phosphosilicate biomineralized glasses:  https://www.researchgate.net/publication/231157513_Network_connectivity_and_bio-mineralization_of_045SiO2-045-xMgO-xK2O-013CaOP2O5_glasses

Article Network Connectivity and Bio-Mineralization of 0.45SiO2–(0.4...

Osteoblast will not just form calcium phosphate on the scaffolds. You could easily checked for Kollagen I (Fast green staining, IF), stain of measure ALP activity ... Osteoblast tend to deposit ALP in the new build matrix, so after removing of your OB with NH4OH (20mM) you could stain ALP and if the cells produced new matrix the ALP in this matrix should stain purple. Deping how thick you material is you could also measure the change in Ca and Phosphat (before and after incubation with OB ) concentration after dissolution of Calciumphosphat with HCl with a Kit from Greiner Diagnostics (Calcium-CPC).

I would suggest performing 2 sets of experiments under strictly equal conditions but one with osteoblasts and another without osteoblasts (the remaining must be the same!) and by means of scanning electron microscopy try to find the differences. In the case of a success, the places of the differences should be investigated by other available techniques. To simplify the differentiation task, ideally, the scaffolds must be prepared from monophasic calcium phosphates, such as 100% of hydroxyapatite, 100% of beta-tricalcium phosphate or 100% of alfa-tricalcium phosphate.

SEM/EDS is the best way to detect the new precipitated minerals on the surface of scaffolds, otherwise you can indirectly detect the new mineral by determining the Ca and P ions concentrationso in the SBF.

It should be noted that when mineralization occurs kind of "lamination" inorganically coated embossed surface modified implant, i.e. coating the substrate topography repeats (3-D profile) while maintaining the implant surface roughness. The study of morphology on the implant formed calcium phosphate coating shows a complex micro-topography of the surface, similar to the bone tissue. It established a significant impact on the nature of the surface microrelief formed calcium phosphate compounds: Ca / P ratio was varied within 0.98-1.05, which corresponded to the structure of brushite; an increase in the Ca / P ratio to 1.3-1.5 indicated in the conversion of brushite calcium phosphate. The occurrence of calcium-deficient apatite (Ca / P

Michael - Check out the following manuscripts for sequential labeling for new mineralization with tetracycline-related fluorescent dyes, both in vitro & in vivo.

Examination of Mineralized Nodule Formation in Living Osteoblastic Cultures Using Fluorescent Dyes. Biotechnol Prog (2006) 22:1697-701.

Yu-Hsiung Wang, Yaling Liu, Peter Maye, David W Rowe

Characterization of eight different tetracyclines: Advances in fluorescence bone labeling. J Anat (2010) 21776-82.

Christoph Pautke, Stephan Vogt, Kilian Kreutzer, Cornelia Haczek, Gabriele Wexel, Andreas Kolk, Andreas B Imhoff, Horst Zitzelsberger, Stefan Milz, Thomas Tischer

Seven-colour fluorochrome labeling of bone growth: Enhancing the number of fluorochromes by spectral image analysis. Int J Oral Max Surg (2005) 34:74-74.

C. Pautke, T. Tischer, S. Vogt, C. Haczek, A. Neff, H. Deppe, M. Schieker, A. Kolk

Article Examination of Mineralized Nodule Formation in Living Osteob...

Article Characterization of eight different tetracyclines: Advances ...

Article Seven-colour fluorochrome labeling of bone growth: Enhancing...