Alexandra Badea | Scholars@Duke

Alexandra Badea
Associate Professor in Radiology

My research has centered on multivariate image based phenotyping, with a focus on neurological conditions like Alzheimer’s disease. I work on imaging and analysis techniques to provide a comprehensive characterization of the brain. MRI is particularly suitable for brain imaging, and diffusion tensor imaging is an important tool for studying white matter, and the connectivity amongst gray matter regions. Using such techniques, we have developed high resolution, multivariate population atlases for animal models.

I am interested in image segmentation, morphometry and shape analysis, as well as in integrating information from MRI with genetics, and behavior. Our approaches target: 1) phenotyping the neuroanatomy using imaging; 2) uncovering the link between structural and functional changes, the genetic bases, and environmental factors. I am interested in generating methods and tools for comprehensive phenotyping.
The unique setting of the Center for In Vivo Microscopy (CIVM) provides most imaging modalities for small animals: several MRI systems, micro-CT, SPECT, and multi-photon microscopy, which allow us to integrate imaging data from multiple modalities, and across scales. We use high-performance cluster computing to accelerate our image analysis. We use compressed sensing image reconstruction, and process large image arrays using deformable registration, perform segmentation based on multiple image contrasts including diffusion tensor imaging, as well as voxel based analysis, and graph analysis for connectomics. These strategies will help increase the rate at which we grow our current understanding of gray and white matter changes in neurological and psychiatric conditions.

My enthusiasm comes from the possibility to extend from single to integrative multivariate and network based analyses to obtain a comprehensive picture of normal development and aging, stages of disease, and the effects of treatments. I am looking forward to continue working on multivariate image analysis and predictive modeling approaches to help better understand early biomarkers for human disease indirectly through mouse models, as well as directly.

Current Research Interests

Brain Imaging, MRI, Connectivity, Multivariate Biomarkers, Image Analysis, Neurological Conditions, Alzheimer's Disease

Current Appointments & Affiliations

Associate Professor in Radiology, Radiology, Clinical Science Departments 2018
Assistant Professor of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2017
Member of the Center for Brain Imaging and Analysis, Duke-UNC Center for Brain Imaging and Analysis, Institutes and Centers 2018

Contact Information

Box 3302 Duke University Medic, Durham, NC 27710
Center for in Vivo Microscopy, Room 139 Bryan Research Building, Durham, NC 27710
alexandra.badea@duke.edu (919) 684-7654
See my Duke Radiology Page - Click Here
See my Duke University School of Medicine Page - Click Here

Background
Education, Training, & Certifications
- Ph.D., University of Patras (Greece) 2003
Duke Appointment History
- Assistant Professor of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2017 - 2019
- Associate Professor in Neurology, Neurology, Behavioral Neurology, Neurology 2018 - 2019
- Associate Professor in Radiology, Radiology, Clinical Science Departments 2017 - 2018
- Assistant Professor of Radiology, Radiology, Clinical Science Departments 2011 - 2017
- Medical Instructor in the Department of Radiology, Radiology, Clinical Science Departments 2010
Research
Selected Grants
- Brain networks in mouse models of aging awarded by National Institutes of Health 2019 - 2024
- Sex and APOE genotype interact to alter immune regulated metabolism in AD awarded by National Institutes of Health 2019 - 2024
- The Duke Preclinical Research Resources for Quantitative Imaging Biomarkers awarded by National Institutes of Health 2017 - 2022
- Transmission electron microscope (TEM) awarded by National Institutes of Health 2019 - 2020
- Training in Medical Imaging awarded by National Institutes of Health 2003 - 2020
- Using MRI To Visualize Regional Therapy Response In Idiopathic Pulmonary Fibrosis awarded by National Institutes of Health 2015 - 2020
- Sex and APOE genotype interact to alter immune regulated metabolism in AD awarded by National Institutes of Health 2017 - 2019
- Quantitative MR Microscopy of Phenotypic Biomarkers in Alzheimer's Disease awarded by National Institutes of Health 2013 - 2018
- Immune regulated amino acid pathways in Alzheimer's Disease awarded by National Institutes of Health 2016 - 2018
- Serial Block Face Scanning Electron Microscope awarded by National Institutes of Health 2016 - 2018
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Lorenzo, Damaris N., Alexandra Badea, Ruobo Zhou, Peter J. Mohler, Xiaowei Zhuang, and Vann Bennett. “βII-spectrin promotes mouse brain connectivity through stabilizing axonal plasma membranes and enabling axonal organelle transport.” Proc Natl Acad Sci U S A 116, no. 31 (July 30, 2019): 15686–95. https://doi.org/10.1073/pnas.1820649116.
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  - Yang, Rui, Kathryn K. Walder-Christensen, Namsoo Kim, Danwei Wu, Damaris N. Lorenzo, Alexandra Badea, Yong-Hui Jiang, Henry H. Yin, William C. Wetsel, and Vann Bennett. “ANK2 autism mutation targeting giant ankyrin-B promotes axon branching and ectopic connectivity.” Proc Natl Acad Sci U S A 116, no. 30 (July 23, 2019): 15262–71. https://doi.org/10.1073/pnas.1904348116.
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  - Anderson, Robert J., James J. Cook, Natalie Delpratt, John C. Nouls, Bin Gu, James O. McNamara, Brian B. Avants, G Allan Johnson, and Alexandra Badea. “Small Animal Multivariate Brain Analysis (SAMBA) - a High Throughput Pipeline with a Validation Framework.” Neuroinformatics 17, no. 3 (July 2019): 451–72. https://doi.org/10.1007/s12021-018-9410-0.
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  - Tange, Runze, Michael Ketcha, Alexandra Badea, Evan D. Calabrese, Daniel S. Margulies, Joshua T. Vogelstein, Carey E. Priebe, and Daniel L. Sussman. “Connectome Smoothing via Low-Rank Approximations.” Ieee Trans Med Imaging 38, no. 6 (June 2019): 1446–56. https://doi.org/10.1109/TMI.2018.2885968.
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  - Nouls, John C., Rohan S. Virgincar, Alexander G. Culbert, Nathann Morand, Dana W. Bobbert, Anne D. Yoder, Robert S. Schopler, et al. “Applications of 3D printing in small animal magnetic resonance imaging.” J Med Imaging (Bellingham) 6, no. 2 (April 2019): 021605. https://doi.org/10.1117/1.JMI.6.2.021605.
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  - Badea, Alexandra, Kwan L. Ng, Robert J. Anderson, Jiangyang Zhang, Michael I. Miller, and Richard J. O’Brien. “Magnetic resonance imaging of mouse brain networks plasticity following motor learning.” Plos One 14, no. 5 (2019): e0216596. https://doi.org/10.1371/journal.pone.0216596.
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  - Badea, Alexandra, Wenlin Wu, Jordan Shuff, Michele Wang, Robert J. Anderson, Yi Qi, G Allan Johnson, et al. “Identifying Vulnerable Brain Networks in Mouse Models of Genetic Risk Factors for Late Onset Alzheimer's Disease.” Front Neuroinform 13 (2019): 72. https://doi.org/10.3389/fninf.2019.00072.
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  - Wang, Nian, Robert J. Anderson, Alexandra Badea, Gary Cofer, Russell Dibb, Yi Qi, and G Allan Johnson. “Whole mouse brain structural connectomics using magnetic resonance histology.” Brain Struct Funct 223, no. 9 (December 2018): 4323–35. https://doi.org/10.1007/s00429-018-1750-x.
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  - Nouls, John C., Alexandra Badea, Robert B. J. Anderson, Gary P. Cofer, and G. Allan Johnson. “Diffusion tensor imaging using multiple coils for mouse brain connectomics.” Nmr Biomed 31, no. 6 (June 2018): e3921. https://doi.org/10.1002/nbm.3921.
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  - Badea, Alexandra, Alaa Kamnaksh, Robert J. Anderson, Evan Calabrese, Joseph B. Long, and Denes V. Agoston. “Repeated mild blast exposure in young adult rats results in dynamic and persistent microstructural changes in the brain.” Neuroimage Clin 18 (2018): 60–73. https://doi.org/10.1016/j.nicl.2018.01.007.
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  - Graña, Gilberto David, Kendall A. Hutson, Alexandra Badea, Andrew Pappa, William Scott, and Douglas C. Fitzpatrick. “The organization of frequency and binaural cues in the gerbil inferior colliculus.” The Journal of Comparative Neurology 525, no. 9 (June 2017): 2050–74. https://doi.org/10.1002/cne.24155.
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  - Anderson, Robert J., James J. Cook, Natalie A. Delpratt, John C. Nouls, Bin Gu, James O. McNamara, Brian B. Avants, G Allan Johnson, and Alexandra Badea. “An HPC Pipeline with Validation Framework for Small Animal Multivariate Brain Analysis (SAMBA).” Corr abs/1709.10483 (2017).
  - Badea, Alexandra, Lauren Kane, Robert J. Anderson, Yi Qi, Mark Foster, Gary P. Cofer, Neil Medvitz, et al. “The fornix provides multiple biomarkers to characterize circuit disruption in a mouse model of Alzheimer's disease.” Neuroimage 142 (November 15, 2016): 498–511. https://doi.org/10.1016/j.neuroimage.2016.08.014.
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  - Bhagat, Srishti L., Sunny Qiu, Zachary F. Caffall, Yehong Wan, Yuanji Pan, Ramona M. Rodriguiz, William C. Wetsel, Alexandra Badea, Ute Hochgeschwender, and Nicole Calakos. “Mouse model of rare TOR1A variant found in sporadic focal dystonia impairs domains affected in DYT1 dystonia patients and animal models.” Neurobiol Dis 93 (September 2016): 137–45. https://doi.org/10.1016/j.nbd.2016.05.003.
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  - Wang, Xiaoming, Alexandra L. Bey, Brittany M. Katz, Alexandra Badea, Namsoo Kim, Lisa K. David, Lara J. Duffney, et al. “Altered mGluR5-Homer scaffolds and corticostriatal connectivity in a Shank3 complete knockout model of autism.” Nat Commun 7 (May 10, 2016): 11459. https://doi.org/10.1038/ncomms11459.
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  - Calabrese, Evan, Alexandra Badea, Gary Cofer, Yi Qi, and G Allan Johnson. “A Diffusion MRI Tractography Connectome of the Mouse Brain and Comparison with Neuronal Tracer Data.” Cereb Cortex 25, no. 11 (November 2015): 4628–37. https://doi.org/10.1093/cercor/bhv121.
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  - Calabrese, Evan, Alexandra Badea, Christopher L. Coe, Gabriele R. Lubach, Yundi Shi, Martin A. Styner, and G Allan Johnson. “A diffusion tensor MRI atlas of the postmortem rhesus macaque brain.” Neuroimage 117 (August 15, 2015): 408–16. https://doi.org/10.1016/j.neuroimage.2015.05.072.
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  - Borg, Jana Schaich, Mai-Anh Vu, Cristian Badea, Alexandra Badea, G Allan Johnson, and Kafui Dzirasa. “Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas.” Eneuro 2, no. 4 (July 2015). https://doi.org/10.1523/ENEURO.0017-15.2015.
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  - Lorenzo, Damaris Nadia, Alexandra Badea, Jonathan Davis, Janell Hostettler, Jiang He, Guisheng Zhong, Xiaowei Zhuang, and Vann Bennett. “A PIK3C3-ankyrin-B-dynactin pathway promotes axonal growth and multiorganelle transport.” J Cell Biol 207, no. 6 (December 22, 2014): 735–52. https://doi.org/10.1083/jcb.201407063.
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  - Calabrese, Evan, Alexandra Badea, Christopher L. Coe, Gabriele R. Lubach, Martin A. Styner, and G Allan Johnson. “Investigating the tradeoffs between spatial resolution and diffusion sampling for brain mapping with diffusion tractography: time well spent?” Hum Brain Mapp 35, no. 11 (November 2014): 5667–85. https://doi.org/10.1002/hbm.22578.
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  - Johnson, G Allan, Evan Calabrese, Peter B. Little, Laurence Hedlund, Yi Qi, and Alexandra Badea. “Quantitative mapping of trimethyltin injury in the rat brain using magnetic resonance histology.” Neurotoxicology 42 (May 2014): 12–23. https://doi.org/10.1016/j.neuro.2014.02.009.
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  - Ashbrook, David G., Anna Delprato, Claudia Grellmann, Marieke Klein, Richard Wetzel, Rupert W. Overall, and Alexandra Badea. “Transcript co-variance with Nestin in two mouse genetic reference populations identifies Lef1 as a novel candidate regulator of neural precursor cell proliferation in the adult hippocampus.” Front Neurosci 8 (2014): 418. https://doi.org/10.3389/fnins.2014.00418.
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  - Johnson, G Allan, Alexandra Badea, Evan Calabrese, Chunlei Liu, and Luke Xie. “Magnetic resonance histology: cool images– but who cares?” Toxicology Letters 221 (August 2013): S50–S50. https://doi.org/10.1016/j.toxlet.2013.06.183.
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  - Clark, D., A. Badea, G. A. Johnson, and C. T. Badea. “Constructing a 4D murine cardiac micro-CT atlas for automated segmentation and phenotyping applications.” Progress in Biomedical Optics and Imaging Proceedings of Spie 8669 (June 3, 2013). https://doi.org/10.1117/12.2007043.
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  - Calabrese, Evan, Alexandra Badea, Charles Watson, and G Allan Johnson. “A quantitative magnetic resonance histology atlas of postnatal rat brain development with regional estimates of growth and variability.” Neuroimage 71 (May 2013): 196–206. https://doi.org/10.1016/j.neuroimage.2013.01.017.
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  - Badea, Alexandra, and G Allan Johnson. “Magnetic resonance microscopy.” Stud Health Technol Inform 185 (2013): 153–84.
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  - Badea, Alexandra, Sally Gewalt, Brian B. Avants, James J. Cook, and G Allan Johnson. “Quantitative mouse brain phenotyping based on single and multispectral MR protocols.” Neuroimage 63, no. 3 (November 15, 2012): 1633–45. https://doi.org/10.1016/j.neuroimage.2012.07.021.
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  - Clark, Darin, Alexandra Badea, Yilin Liu, G Allan Johnson, and Cristian T. Badea. “Registration-based segmentation of murine 4D cardiac micro-CT data using symmetric normalization.” Phys Med Biol 57, no. 19 (October 7, 2012): 6125–45. https://doi.org/10.1088/0031-9155/57/19/6125.
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  - Driehuys, B., J. Nouls, A. Badea, E. Bucholz, K. Ghaghada, A. Petiet, and L. W. Hedlund. “Small animal imaging with magnetic resonance microscopy.” Ilar Journal 53, no. 1 (September 11, 2012): 35–53.
  - Johnson, G Allan, Evan Calabrese, Alexandra Badea, George Paxinos, and Charles Watson. “A multidimensional magnetic resonance histology atlas of the Wistar rat brain.” Neuroimage 62, no. 3 (September 2012): 1848–56. https://doi.org/10.1016/j.neuroimage.2012.05.041.
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  - Wu, Teresa, Min Hyeok Bae, Min Zhang, Rong Pan, and Alexandra Badea. “A prior feature SVM-MRF based method for mouse brain segmentation.” Neuroimage 59, no. 3 (February 2012): 2298–2306. https://doi.org/10.1016/j.neuroimage.2011.09.053.
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  - Badea, Alexandra, and G Allan Johnson. “Magnetic resonance microscopy.” Anal Cell Pathol (Amst) 35, no. 4 (2012): 205–27. https://doi.org/10.3233/ACP-2011-0050.
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  - Poot, Martin, Alexandra Badea, Robert W. Williams, and Martien J. Kas. “Identifying human disease genes through cross-species gene mapping of evolutionary conserved processes.” Plos One 6, no. 5 (May 4, 2011): e18612. https://doi.org/10.1371/journal.pone.0018612.
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  - Bowden, Douglas M., G Allan Johnson, Laszlo Zaborsky, William D. K. Green, Eider Moore, Alexandra Badea, Mark F. Dubach, and Fred L. Bookstein. “A symmetrical Waxholm canonical mouse brain for NeuroMaps.” J Neurosci Methods 195, no. 2 (February 15, 2011): 170–75. https://doi.org/10.1016/j.jneumeth.2010.11.028.
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  - Johnson, G Allan, Alexandra Badea, and Yi Jiang. “Quantitative neuromorphometry using magnetic resonance histology.” Toxicol Pathol 39, no. 1 (January 2011): 85–91. https://doi.org/10.1177/0192623310389622.
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  - Johnson, G Allan, Alexandra Badea, Jeffrey Brandenburg, Gary Cofer, Boma Fubara, Song Liu, and Jonathan Nissanov. “Waxholm space: an image-based reference for coordinating mouse brain research.” Neuroimage 53, no. 2 (November 1, 2010): 365–72. https://doi.org/10.1016/j.neuroimage.2010.06.067.
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  - Badea, Alexandra, G Allan Johnson, and Joanna L. Jankowsky. “Remote sites of structural atrophy predict later amyloid formation in a mouse model of Alzheimer's disease.” Neuroimage 50, no. 2 (April 2010): 416–27. https://doi.org/10.1016/j.neuroimage.2009.12.070.
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  - Badea, Alexandra, G Allan Johnson, and Robert W. Williams. “Genetic dissection of the mouse CNS using magnetic resonance microscopy.” Curr Opin Neurol 22, no. 4 (August 2009): 379–86. https://doi.org/10.1097/WCO.0b013e32832d9b86.
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  - Bae, Min Hyeok, Rong Pan, Teresa Wu, and Alexandra Badea. “Automated segmentation of mouse brain images using extended MRF.” Neuroimage 46, no. 3 (July 2009): 717–25. https://doi.org/10.1016/j.neuroimage.2009.02.012.
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  - Badea, A., G. A. Johnson, and R. W. Williams. “Genetic dissection of the mouse brain using high-field magnetic resonance microscopy.” Neuroimage 45, no. 4 (May 1, 2009): 1067–79. https://doi.org/10.1016/j.neuroimage.2009.01.021.
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  - Driehuys, Bastiaan, John Nouls, Alexandra Badea, Elizabeth Bucholz, Ketan Ghaghada, Alexandra Petiet, and Laurence W. Hedlund. “Small animal imaging with magnetic resonance microscopy.” Ilar J 49, no. 1 (2008): 35–53. https://doi.org/10.1093/ilar.49.1.35.
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  - Sharief, Anjum A., Alexandra Badea, Anders M. Dale, and G Allan Johnson. “Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy.” Neuroimage 39, no. 1 (January 1, 2008): 136–45. https://doi.org/10.1016/j.neuroimage.2007.08.028.
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  - Badea, A., A. A. Ali-Sharief, and G. A. Johnson. “Morphometric analysis of the C57BL/6J mouse brain.” Neuroimage 37, no. 3 (September 1, 2007): 683–93. https://doi.org/10.1016/j.neuroimage.2007.05.046.
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  - Johnson, G Allan, Anjum Ali-Sharief, Alexandra Badea, Jeffrey Brandenburg, Gary Cofer, Boma Fubara, Sally Gewalt, Laurence W. Hedlund, and Lucy Upchurch. “High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology.” Neuroimage 37, no. 1 (August 1, 2007): 82–89. https://doi.org/10.1016/j.neuroimage.2007.05.013.
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  - Badea, Alexandra, Peter J. Nicholls, G Allan Johnson, and William C. Wetsel. “Neuroanatomical phenotypes in the reeler mouse.” Neuroimage 34, no. 4 (February 15, 2007): 1363–74. https://doi.org/10.1016/j.neuroimage.2006.09.053.
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  - Ali, Anjum A., Anders M. Dale, Alexandra Badea, and G Allan Johnson. “Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain.” Neuroimage 27, no. 2 (August 2005): 425–35. https://doi.org/10.1016/j.neuroimage.2005.04.017.
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  - Badea, Alexandra, George K. Kostopoulos, and Andreas A. Ioannides. “Surface visualization of electromagnetic brain activity.” Journal of Neuroscience Methods 127, no. 2 (August 2003): 137–47. https://doi.org/10.1016/s0165-0270(03)00100-6.
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- Conference Papers
  - Johnson, G. A., R. J. Anderson, J. J. Cook, C. Long, and A. Badea. “Image-processing pipelines: Applications in magnetic resonance histology.” In Progress in Biomedical Optics and Imaging Proceedings of Spie, Vol. 9784, 2016. https://doi.org/10.1117/12.2203525.
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  - Johnson, G Allan, Alexandra Badea, Evan Calabrese, Chunlei Liu, and Luke Xie. “Magnetic resonance histology—Applications in toxicology.” In Toxicology Letters, 229:S31–32. Elsevier BV, 2014. https://doi.org/10.1016/j.toxlet.2014.06.148.
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  - Bowsher, J. E., H. Yuan, L. W. Hedlund, T. G. Turkington, G. Akabani, A. Badea, W. C. Kurylo, et al. “Utilizing MRI information to estimate F18-FDG distributions in rat flank tumors.” In Ieee Nuclear Science Symposium Conference Record, 4:2488–92, 2004.
Teaching & Mentoring
Recent Courses
Teaching Activities
- NEUROSCI Research Independent Study
  
  NEUROSCI 493
  NEUROSCI 494
  NEUROSCI 495
  NEUROSCI 496

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Education, Training, & Certifications

Duke Appointment History

Selected Grants

Selected Publications

Academic Articles

Conference Papers

Recent Courses

Teaching Activities