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Supplemental Material 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, August 26, 2008

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), >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.

Files in This Data Supplement

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

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.

This online database is a collection of 3-dimensional MR datasets of:
  • 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)
It 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 at

Open PDF user guide in a new window

Open HTML user guide in a new window

View Datasets

From CIVMSpace, 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 select the "Go" button; this will launch VoxStation, a Java Web Start application that lets you view datasets in three planes.

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


Related References

  • Petiet A., Hedlund L. W., Johnson G. A., Staining methods for magnetic resonance microscopy of the rat fetus, Journal of Magnetic Resonance Imaging, 25: 1192-1198 (2007).
  • Goddeeris M. M., Schwartz R., Klingensmith J., Meyers E. N., Independent requirements for Hedgehog signaling by both the anterior heart field and neural crest cells for outflow tract development, Development, 134: 1593-1604 (2007).
  • Verzi Michael P., McCulley David J., De Val Sarah, Dodou Evdokia, Black Brian L., 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).
  • Zhang X. M., Ramalho-Santos M., McMahon A. P., 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).


  • 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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