Alexandra Badea


Associate Professor in Radiology

My interest lies primarily in using MR microscopy to image the rodent brain, including its vasculature, so as to provide comprehensive morphometric phenotyping. I study the morphometry of the rodent brain, its anatomical variability in normal states, and also in human disease models. These studies require several steps: imaging protocols for optimal contrast, brain segmentation, registration, statistical analysis, and atlasing. Ultimately we should be able to quantify changes during normal development, aging, disease progression and to assess treatment effect in a quantitative fashion. By combining imaging data with behavioral and genetic tools we have a truly interdisciplinary approach in our translational studies.

Appointments and Affiliations

  • Associate Professor in Radiology
  • Assistant Professor of Biomedical Engineering

Contact Information


  • Ph.D. University of Patras (Greece), 2003

Representative Publications

  • Wu, T; Bae, MH; Zhang, M; Pan, R; Badea, A, A prior feature SVM-MRF based method for mouse brain segmentation., Neuroimage, vol 59 no. 3 (2012), pp. 2298-2306 [10.1016/j.neuroimage.2011.09.053] [abs].
  • Poot, M; Badea, A; Williams, RW; Kas, MJ, Identifying human disease genes through cross-species gene mapping of evolutionary conserved processes., Plos One, vol 6 no. 5 (2011) [10.1371/journal.pone.0018612] [abs].
  • Bowden, DM; Johnson, GA; Zaborsky, L; Green, WDK; Moore, E; Badea, A; Dubach, MF; Bookstein, FL, A symmetrical Waxholm canonical mouse brain for NeuroMaps., Journal of Neuroscience Methods, vol 195 no. 2 (2011), pp. 170-175 [10.1016/j.jneumeth.2010.11.028] [abs].
  • Johnson, GA; Badea, A; Jiang, Y, Quantitative neuromorphometry using magnetic resonance histology., Toxicologic Pathology (Sage), vol 39 no. 1 (2011), pp. 85-91 [10.1177/0192623310389622] [abs].
  • Johnson, GA; Badea, A; Brandenburg, J; Cofer, G; Fubara, B; Liu, S; Nissanov, J, Waxholm space: an image-based reference for coordinating mouse brain research., Neuroimage, vol 53 no. 2 (2010), pp. 365-372 [10.1016/j.neuroimage.2010.06.067] [abs].
  • Badea, A; Johnson, GA; Jankowsky, JL, Remote sites of structural atrophy predict later amyloid formation in a mouse model of Alzheimer's disease., Neuroimage, vol 50 no. 2 (2010), pp. 416-427 [10.1016/j.neuroimage.2009.12.070] [abs].
  • Badea, A; Johnson, GA; Williams, RW, Genetic dissection of the mouse CNS using magnetic resonance microscopy., Curr Opin Neurol, vol 22 no. 4 (2009), pp. 379-386 [10.1097/WCO.0b013e32832d9b86] [abs].
  • Bae, MH; Pan, R; Wu, T; Badea, A, Automated segmentation of mouse brain images using extended MRF., Neuroimage, vol 46 no. 3 (2009), pp. 717-725 [10.1016/j.neuroimage.2009.02.012] [abs].
  • Badea, A; Johnson, GA; Williams, RW, Genetic dissection of the mouse brain using high-field magnetic resonance microscopy., Neuroimage, vol 45 no. 4 (2009), pp. 1067-1079 [10.1016/j.neuroimage.2009.01.021] [abs].
  • Sharief, AA; Badea, A; Dale, AM; Johnson, GA, Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy., Neuroimage, vol 39 no. 1 (2008), pp. 136-145 [10.1016/j.neuroimage.2007.08.028] [abs].
  • Driehuys, B; Nouls, J; Badea, A; Bucholz, E; Ghaghada, K; Petiet, A; Hedlund, LW, Small animal imaging with magnetic resonance microscopy., Ilar Journal, vol 49 no. 1 (2008), pp. 35-53 [10.1093/ilar.49.1.35] [abs].
  • Badea, A; Ali-Sharief, AA; Johnson, GA, Morphometric analysis of the C57BL/6J mouse brain., Neuroimage, vol 37 no. 3 (2007), pp. 683-693 [10.1016/j.neuroimage.2007.05.046] [abs].
  • Johnson, GA; Ali-Sharief, A; Badea, A; Brandenburg, J; Cofer, G; Fubara, B; Gewalt, S; Hedlund, LW; Upchurch, L, High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology., Neuroimage, vol 37 no. 1 (2007), pp. 82-89 [10.1016/j.neuroimage.2007.05.013] [abs].
  • Badea, A; Nicholls, PJ; Johnson, GA; Wetsel, WC, Neuroanatomical phenotypes in the reeler mouse., Neuroimage, vol 34 no. 4 (2007), pp. 1363-1374 [10.1016/j.neuroimage.2006.09.053] [abs].
  • Ali, AA; Dale, AM; Badea, A; Johnson, GA, Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain., Neuroimage, vol 27 no. 2 (2005), pp. 425-435 [10.1016/j.neuroimage.2005.04.017] [abs].
  • Badea, A; Kostopoulos, GK; Ioannides, AA, Surface visualization of electromagnetic brain activity., Journal of Neuroscience Methods, vol 127 no. 2 (2003), pp. 137-147 [abs].