Micro computed tomography (micro-CT) has been used for in vivo animal study owing to its noninvasive and high spatial resolution capability. However, the sizes of existing detectors for micro-CT systems are too small to obtain whole-body images of a small animal object with $sim$10 micron resolution and a part of its bones or other organs should be extracted. So, we have introduced the zoom-in micro-tomography technique which can obtain high-resolution images of a local region of an live animal object without extracting samples. In order to verify our zoom-in technique, we performed in vivo animal bone study. We prepared some SD (Sprague-Dawley) rats for making osteoporosis models. They were divided into control and ovariectomized groups. Again, the ovariectomized group is divided into two groups fed with normal food and with calcium-free food. And we took 3D tomographic images of their femurs with 20 micron resolution using our zoom-in tomography technique and observed the bone changes for 12 weeks. We selected ROI (region of interest) of a femur image and applied 2D FDT (fuzzy distance transform) to measure the trabecular bone thickness. The measured results showed obvious bone changes and big differences between control and ovariectomized groups. However, we found that the reliability of the measurement depended on the selection of ROI in a bone image for thickness calculation. So, we extended the method to 3D FDT technique. We selected 3D VOI (volume of interest) in the obtained 3D tomographic images and applied 3D FDT algorithm. The results showed that the 3D technique could give more accurate and reliable measurement.