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Supporting Material and Data for:

High-Resolution Magnetic Resonance Histology of the Embryonic and Neonatal Mouse: A 4D Atlas and Morphologic Database

Alexandra Petiet, Matthew H. Kaufman, Matthew M. Goddeeris, Jeffrey L. Brandenburg, Susan A. Elmore, G. Allan Johnson

Proceedings of the National Academy of Sciences U S A 105(34):12331-12336, 2008. PMCID: PMC2527911

Engineered mice play an ever-increasing role in defining connections between genotype and phenotypic expression. The potential of magnetic resonance microscopy (MRM) for morphologic phenotyping in the mouse has previously been demonstrated; however, applications have been limited by long scan times, availability of the technology, and a foundation of normative data. This article describes an integrated environment for high-resolution study of normal, transgenic, and mutant mouse models at embryonic and neonatal stages. Three-dimensional images are shown at an isotropic resolution of 19.5 microns (voxel volumes of 8 pL), acquired in 3 h at embryonic days 10.5-19.5 (10 stages) and postnatal days 0-32 (6 stages). A web-accessible atlas encompassing this data was developed, and for critical stages of embryonic development (prenatal days 14.5-18.5), more than 200 anatomical structures have been identified and labeled. Also, matching optical histology and analysis tools are provided to compare multiple specimens at multiple developmental stages. The utility of the approach is demonstrated in characterizing cardiac septal defects in conditional mutant embryos lacking the Smoothened receptor gene.

Finally, a collaborative paradigm is presented that allows sharing of data across the scientific community. This work makes magnetic resonance microscopy of the mouse embryo and neonate broadly available with carefully annotated normative data and an extensive environment for collaborations.

All datasets associated with this publication are available from CIVMSpace, our Web-based data portal.

Use of CIVM Data:

Data downloaded from this site is for academic use only. If you use this data in a publication please send us a request for copyright permission and appropriate acknowledgements. Licenses can be granted for commercial use.
Contact the Center for permission and wording for credits.


This online database is a collection of 3-dimensional MR datasets:
  • Normal C57BL/6 mouse embryos from embryonic day E10.5 to E19.5
  • Normal C57BL/6 mouse neonates from post-natal day 0 to 32
  • Mutant mouse embryos with cardiac septation defects (conditional ablation of the Smoothened receptor gene, Mef2C-AHF-Cre;Smoflox/- mutants)
The database also features:
  • Color-labeled hearts of normal and abnormal mouse embryos
  • Labeled whole bodies of C57BL/6 mouse embryos, viewable in MBAT
  • H&E sections of C57BL/6 mouse embryos matching MR images

System Requirements:

CIVMSpace is designed to work on most platforms and is supported in most browsers.
VoxStation requires a working Java installation.

If you have trouble accessing CIVMSpace or VoxStation, please contact us.

User Guides:

The link from the button below will access CIVMSpace, where you can select any thumbnail to browse slices from the corresponding dataset. To view structure labels, select "Open in VoxStation" from the pull-down menu at the upper right corner of the CIVMSpace page, then the "Go" button to launch VoxStation, a Java Web Start application that lets you view datasets in three planes.

Below is a screen shot for an example of a volume dataset (C57BL/6 normal fetus at E15.5) that can be found in CIVMSpace:

View the Supplementary Data


Related References

  • Petiet A, Hedlund LW, Johnson GA, Staining methods for magnetic resonance microscopy of the rat fetus, Journal of Magnetic Resonance Imaging, 25: 1192-1198 (2007). PMCID: PMC2747382
  • Goddeeris MM, Schwartz R, Klingensmith J, Meyers EN, Independent requirements for Hedgehog signaling by both the anterior heart field and neural crest cells for outflow tract development, Development, 134: 1593-1604 (2007). PMC:PMCID: 2746050
  • Verzi MP, McCulley DJ, De Val S, Dodou E, Black BL, The right ventricle, outflow tract, and ventricular septum comprise a restricted expression domain within the secondary/anterior heart field, Developmental Biology, 287: 134-145 (2005). Open Access
  • Zhang XM, Ramalho-Santos M, McMahon AP, Smoothened mutants revealed redundant roles for Shh and Ihh signaling including regulation of L/R symmetry by the mouse node, Cell, 106: 781-792 (2001). Open access through Science Direct

acknowledgements Acknowledgements

All MR imaging was performed at the Duke Center for In Vivo Microscopy, under NIH/NCRR grant P41 RR005959 and NCI SAIRP grant U24 CA092656. This work was also supported by the Mouse Bioinformatics Research Network (MBIRN) NIH/NCRR grant U24 RR021760.



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