Image analysis is hard. To extract meaningful information to meet your analysis goals you often need to work with large, complex, multidimensional and multivariate data. I have found that the following methodology can be used to effectively design software to successfully analyze image data.
Checkpoint can help you convert those large micro CT scans into files that are more manageable. The following explains how to load a stack of TIF image files from a micro CT scanner and convert them into a NifTi (.nii) file type which Checkpoint can load.