One particular tool that was developed with mouse imaging as the target is the mouse "chopper" which is available in the pxitclmousesegment and pxitclmouseregister applications. This allows the segmentation of hind limb mouse CT images (images of the lower half of the mouse, from the kidneys down to the tail) into regions of interest for the quantification of both microSPECT and microCT angiography images.
A detailed tutorial for using the Mouse Chopper tool by Patti Cavaliere is available in pdf format (4.7 MB). This tutorial assumes that the user is using Linux, although once the mouseregister application is opened the rest of the steps apply on other platfroms as well. The tutorial also assumes minimal exposure to BioImage Suite so it is a good introduction to the novice user.