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Duke Center for In Vivo Microscopy (CIVM) is an NIH/NIBIB National Biomedical Technology Resource Center. We develop novel methods for preclinical imaging and apply those methods to important biomedical problems.

Our small animal imaging program includes MRI, CT, x-ray, ultrasound, confocal, optical, and SPECT, all at the highest possible spatial resolution. Set up a collaboration or service project, and see information below to access some of our data.

Interested in working at CIVM? A post-doctoral position is available.

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One of the Winners
University of Wisconsin 2013 Cool Science Image Contest
Monkey brain diffusion tensor image

From scans on our MR 7T equipment as part of a collaboration with the Univ. of Wisconsin (C Coe, G Lubach, A Alexander), UNC (M Styner), and CIVM (E Calabrese, GA Johnson).

Click here for detail about the image and to see the other winners.

. SHARED DATA: Many of our publications include supplements that share our data with other researchers. Just a few are listed below.

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.

  MR Brain Data and Atlases

  • Waxholm Space (C57BL/6 mouse brain, 3 MR contrasts), supplement Neuroimage 53: 365-372, 2010
  • Mouse brain segmentation pipeline (actively stained C57BL/6 mouse), supplement NeuroImage 63:1633-1645, 2012
  • Adult Wistar rat atlas, supplement NeuroImage 62: 1848-1856, 2012
  • Developing rat brain (regional changes in volume, postnatal days 0-80), supplement NeuroImage 67:375-384, 2013
  • Developing rat brain (9 time points, 8 MR contrasts, 26 brain regions), supplement Neuroimage 71C:196-206, 2013

 MR - Kidney Data

  • MRI of quantitative susceptibility mapping in mouse model deficient of angiotensin receptor type 1 (AT1) to identify kidney inflammation and fibrosis, supplement NMR Biomed 26(12): 1853-1863, 2013

CT and SPECT Data

  • Mouse micro-CT pipeline (for registration-based segmentation / analysis of 4D cardiac data), supplement Phys Med Biol 57:6125-6145, 2012
  • Mouse tumor model (filtered datasets of tumor vasculature using iodine and gold nanoparticles), supplement Phys Med Biol 58:1683-1704, 2013
  • Comparision of micro-CT and SPECT for cardiac function, supplement Mol Img Biol, 2013 Sept 14 [Epub]


CIVM continues to expand our range of technical capabilities and applications, such as these examples:

Dynamic 4D CT perfusion
Tractography from
40-day-old rat
3Helium mouse lung
3D isotropic acquisition at 156-micron resolution




C Badea, L Hedlund, GA Johnson, A LabVIEW platform for preclinical imaging using digital subtraction angiography and micro-CT, J Med Eng Vol 2013, Article ID 581617, 1-13. Open access

EJ Moding, DP Clark, Y Qi, Y Li, YMa, K Ghaghada, GA Johnson, DG Kirsch, CT Badea, Dual energy micro-CT imaging of radiation-induced vascular changes in primary mouse sarcomas, Intl J Rad Oncol Biol Phys 85(5):1353-9, 2013. PMCID: PMC3625949 Elsevier


C Liu, W Li, Imaging neural architecture of the brain based on its multipole magnetic response. Neuroimage 67:193-202, 2013. PMCID: PMC3640835 ScienceDirect

Virtual Mouse Brain application for iPad developed by CIVM

  • Download to iPad from App Store for $4.99
  • View high-resolution MR images with interactive mouse brain atlas
  • Mouse neuroanatomy with 3D and 2D views of 35+ anatomical structures that can be highlighted
  • Swipe through MRI slices on all 3 planes


E Subashi, G Cofer, JS MacFall, Y Qi, GA Johnson, A comparison of keyhole strategies for high spatial and temporal resolution 4D contrast-enhanced MRI in small animal tumor models, Med Phys 40(2): 022304, 2013. PMCID: PMC3562278 Abstract


RS Virgincar, ZI Cleveland, SS Kaushik, MS Freeman, J Nouls, GP Cofer, S Martinez-Jimenez, M He, M Kraft, J Wolberg, HP McAdams, B Driehuys, Quantitative analysis of hyperpolarized 129Xe ventilation imaging in healthy volunteers and subjects with COPD, NMR in Biomedicine 26(4): 424-435,2013. PMCID: PMC3362235

Y Feng, RM Davis, WS Warren. Accessing long-lived nuclear singlet states between chemically equivalent spins without breaking symmetry, Nature Physics 8: 831-837, 2012. PMCID: PMC3596050


JW Wilson, S Degan, WS Warren, MC Fischer. Optical clearing of archive-compatible paraffin embedded tissue for multiphoton microscopy. Biomed Opt Express Nov 1;3(11):2752-60. 2012. PMCID: PMC3493235


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