Alexandra Badea

Assistant Professor of Radiology
Campus mail: Box 3302 Duke University Medical Center, Durham, NC 27710
Phone: (919) 684-7654

My Main Interest

  • 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.

Education and Training

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

My Three Hats

  • I am interested in mouse models of neurological and psychiatric conditions. One of my goals is identifying sensitive biomarkers to track disease progression, and response to treatment. I am therefore exploring new and exciting, mostly MR imaging protocols, and contrasts. My second goal is to integrate imaging biomarkers at different scales, and across modalities, including behavior. I greatly enjoy this quest with mentorship from Drs G Allan Johnson, Carol A Colton , and William C. Wetsel
  • I am director of the Core E for the P41 resource grant where Dr. G Allan Johnson is PI. Wearing this hat makes me focus on visual informatics, help developing atlases, and efficient image processing pipelines for segmentation, classification and voxel based statistical analyses. We aim for using high performance computing. I have the great joy of collaborating with the other cores of the center in this position. At the end we really like to show our images to the world so we are developing these tools using high graphic performance systems. Here is an older example, developed in collaboration with Brooks Adcock, which can be downloaded from and is available from iTunes: Virtual Mouse Brain Ipad App

  • I am in charge of the animal care and use protocols for the Center for In Vivo Microscopy. I help several PIs who have their own protocols as needed, and maintain three protocols on my own, so we can all achieve our goals under the P41 and other individual grants, while keeping in mind animal welfare. I am grateful l for the chance to work with wonderful colleagues, which make sure this is the case.


  • I have co-mentored graduate students: Evan Calabrese (with Dr. G Allan Johnson), and I enjoy working with Natalie Delpratt (with Dr. Kathryn Nightingale) towards her master thesis, and BJ Anderson as a postdoctoral fellow.

    In addition I dedicate part of my summers to mentoring students from high school to graduate school. Some of our young collaborators include: Lauren Kane, Dominique Ferrareli , Abhishek Bollapragada, Camil Craciunescu, Diane Leadbetter, Daniel Brimingham, Diane Kim, and Chandler Berry. I am proud of these young people and how they chose to spend their time and energy. They are going places!

    You can learn more about these young trainees from 2015, and 2014

My Gratitude

  • I am grateful to all my collaborators for being a source of inspiration and motivation. Working with these people makes my day, and gets me through all kinds of moments. It reminds me of the value of what we need to do, and helps me not forget why we ought to keep moving onwards!
  • I owe a lot to CIVM staffers including James Cook, Lucy Upchurch, Gary Cofer and Yi Qi. But students are the beating heart and blood of a university, and the CIVM students I have the privilege to work with are some of the best.
  • Several generous and brave scientists develop open source software. I happen to love ants, although this is not the correct spelling for the project ( We use this software heavily in our pipelines.
  • The office for faculty mentoring
  • Nothing I have done so far would be possible without the support of a loving and fun family.

My Publications

  • G Paxinos, C Watson, E Calabrese, A Badea, GA Johnson, An MRI/DTI Atlas of the Rat Brain, Academic Press, Elsevier, 2015
  • On Google Scholar
  • On Scopus

Press Releases