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Biological microscopic imaging is receiving increasing interest with the development of new modalities. In this context Synchrotron Radiation (SR) Nano-CT demonstrates a high potential in opening new horizons. We recall the principle of SR micro-CT and its advantages over standard X-ray micro-CT in terms of accuracy and signal to noise ratio. We briefly present data acquisition and reconstruction in absorption and phase CT. While in the first case image reconstruction is based simply on the standard filtered back projection algorithm, in the later case it involves a preliminary step of phase retrieval. Applications of this technique in bone research in conjunction with specific image analysis developments are shown. At the micrometer scale, trabecular and cortical bone have been analyzed in human samples and mice. At the nanometer scale, we present recent data on the osteocyte network which has never before been investigated in 3D. Open problems for the segmentation and quantification of the complex canalicular network are highlighted.