**ABOUT PROJECT** This is a synthetic high-resolution (35 micron) CT atlas generated using adult specimens of more than 30 different inbred mice strains. Atlas, as well as the accompanying R image processing pipeline (based on Advanced Symmetric Normalization library) can be used to orient specimens in canonical coordinates, segmented cranium, hemi-mandibles and endocranial space. More information about strains used, template generation and image processing and analysis pipeline can be found in [Maga AM, Tustison NJ, Avants BB. 2017. A population level atlas of Mus musculus craniofacial skeleton and automated image-based shape analysis. J Anat 231:433–443.][1] All figures and procedures in the paper can be reproduced by cloning the [github repository][2] and following the instructions. **Inbred strains used to generate the template:** 129S1.SvImJ, 129X1.SvJ, A.J, AKR.J, BALB.cByJ, BALB.cJ, BTBR , C3H.HeJ, C3H.HeouJ, C57BL.10J, C57BL.6J, C57BL.6NJ, C57L.J, CAST.EiJ, CBA.CaJ, CBA.J, DBA.1J, DBA.2J, FVB.NJ, MRL.MpJ, NOD.ShiLtJ, NU.J, NZW.LacJ, SJL.J, and TALLYHO.JngJ. **F1 crosses used to generate the template:** B6AF1, B6D2F1, CAF1, CB6F1, and NZBWF1. [1]: http://dx.doi.org/10.1111/joa.12645 [2]: https://github.com/muratmaga/mouse_CT_atlas