G. Allan Johnson


Charles E. Putman University Distinguished Professor of Radiology

Dr. Johnson is the Charles E. Putman University Professor of Radiology, Professor of Physics, and Biomedical Engineering, and Director of the Duke Center for In Vivo Microscopy (CIVM). The CIVM is an NIH/NIBIB national Biomedical Technology Resource Center with a mission to develop novel technologies for preclinical imaging (basic sciences) and apply the technologies to critical biomedical questions. Dr. Johnson was one of the first researchers to bring Paul Lauterbur's vision of magnetic resonance (MR) microscopy to practice as described in his paper, "Nuclear magnetic resonance imaging at microscopic resolution" (J Magn Reson 68:129-137, 1986). Dr. Johnson is involved in both the engineering physics required to extend the resolution of MR imaging and in a broad range of applications in the basic sciences.

Appointments and Affiliations

  • Charles E. Putman University Distinguished Professor of Radiology
  • Professor of Radiology
  • Professor of Biomedical Engineering
  • Professor in the Department of Physics
  • Member of the Duke Cancer Institute

Contact Information

  • Office Location: 141D Bryan Neuroscience Bldg, Research Drive, Durham, NC 27710
  • Office Phone: +1 919 684 7754
  • Email Address: gjohnson@duke.edu
  • Websites:


  • Ph.D. Duke University, 1974

Courses Taught

  • BME 493: Projects in Biomedical Engineering (GE)

In the News

Representative Publications

  • Calabrese, E; Badea, A; Cofer, G; Qi, Y; Johnson, GA, A Diffusion MRI Tractography Connectome of the Mouse Brain and Comparison with Neuronal Tracer Data., Cereb Cortex, vol 25 no. 11 (2015), pp. 4628-4637 [10.1093/cercor/bhv121] [abs].
  • Calabrese, E; Badea, A; Coe, CL; Lubach, GR; Shi, Y; Styner, MA; Johnson, GA, A diffusion tensor MRI atlas of the postmortem rhesus macaque brain., Neuroimage, vol 117 (2015), pp. 408-416 [10.1016/j.neuroimage.2015.05.072] [abs].
  • Calabrese, E; Hickey, P; Hulette, C; Zhang, J; Parente, B; Lad, SP; Johnson, GA, Postmortem diffusion MRI of the human brainstem and thalamus for deep brain stimulator electrode localization., Hum Brain Mapp, vol 36 no. 8 (2015), pp. 3167-3178 [10.1002/hbm.22836] [abs].
  • Johnson, GA, Magnetic resonance histology., J Magn Reson Imaging, vol 42 no. 1 (2015), pp. 1-2 [10.1002/jmri.24774] [abs].
  • Paxinos, G; Watson, C; Calabrese, E; Badea, A; Johnson, G, An MRI/DTI Atlas of the Rat Brain (2015) [abs].
  • Xie, L; Qi, Y; Subashi, E; Liao, G; Miller-DeGraff, L; Jetten, AM; Johnson, GA, 4D MRI of polycystic kidneys from rapamycin-treated Glis3-deficient mice., NMR Biomed, vol 28 no. 5 (2015), pp. 546-554 [10.1002/nbm.3281] [abs].
  • Subashi, E; Qi, Y; Johnson, GA, Dynamic contrast-enhanced MR microscopy identifies regions of therapeutic response in a preclinical model of colorectal adenocarcinoma., Med Phys, vol 42 no. 5 (2015), pp. 2482-2488 [10.1118/1.4917525] [abs].
  • Xie, L; Dibb, R; Cofer, GP; Li, W; Nicholls, PJ; Johnson, GA; Liu, C, Susceptibility tensor imaging of the kidney and its microstructural underpinnings., Magn Reson Med, vol 73 no. 3 (2015), pp. 1270-1281 [10.1002/mrm.25219] [abs].
  • Papp, EA; Leergaard, TB; Calabrese, E; Johnson, GA; Bjaalie, JG, Addendum to “Waxholm Space atlas of the Sprague Dawley rat brain” [NeuroImage 97 (2014) 374-386]., Neuroimage, vol 105 (2015), pp. 561-562 [10.1016/j.neuroimage.2014.10.017] [abs].
  • Borg, JS; Vu, M-A; Badea, C; Badea, A; Johnson, GA; Dzirasa, K, Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas., eNeuro, vol 2 no. 4 (2015) [10.1523/ENEURO.0017-15.2015] [abs].
  • Calabrese, E; Badea, A; Coe, CL; Lubach, GR; Styner, MA; Johnson, GA, Investigating the tradeoffs between spatial resolution and diffusion sampling for brain mapping with diffusion tractography: time well spent?, Hum Brain Mapp, vol 35 no. 11 (2014), pp. 5667-5685 [10.1002/hbm.22578] [abs].
  • Johnson, GA; Badea, A; Calabrese, E; Liu, C; Xie, L, Magnetic resonance histology—Applications in toxicology, Toxicology Letters, vol 229 (2014), pp. S31-S32 [10.1016/j.toxlet.2014.06.148] [abs].
  • Xie, L; Subashi, E; Qi, Y; Knepper, MA; Johnson, GA, Four-dimensional MRI of renal function in the developing mouse., NMR Biomed, vol 27 no. 9 (2014), pp. 1094-1102 [10.1002/nbm.3162] [abs].
  • Papp, EA; Leergaard, TB; Calabrese, E; Johnson, GA; Bjaalie, JG, Waxholm Space atlas of the Sprague Dawley rat brain., Neuroimage, vol 97 (2014), pp. 374-386 [10.1016/j.neuroimage.2014.04.001] [abs].
  • Calabrese, E; Du, F; Garman, RH; Johnson, GA; Riccio, C; Tong, LC; Long, JB, Diffusion tensor imaging reveals white matter injury in a rat model of repetitive blast-induced traumatic brain injury., J Neurotrauma, vol 31 no. 10 (2014), pp. 938-950 [10.1089/neu.2013.3144] [abs].
  • Johnson, GA; Calabrese, E; Little, PB; Hedlund, L; Qi, Y; Badea, A, Quantitative mapping of trimethyltin injury in the rat brain using magnetic resonance histology., Neurotoxicology, vol 42 (2014), pp. 12-23 [10.1016/j.neuro.2014.02.009] [abs].
  • Gyengesi, E; Calabrese, E; Sherrier, MC; Johnson, GA; Paxinos, G; Watson, C, Semi-automated 3D segmentation of major tracts in the rat brain: comparing DTI with standard histological methods., Brain Struct Funct, vol 219 no. 2 (2014), pp. 539-550 [10.1007/s00429-013-0516-8] [abs].
  • Calabrese, E; Johnson, GA, Diffusion tensor magnetic resonance histology reveals microstructural changes in the developing rat brain., Neuroimage, vol 79 (2013), pp. 329-339 [10.1016/j.neuroimage.2013.04.101] [abs].
  • Pandit, P; Johnston, SM; Qi, Y; Story, J; Nelson, R; Johnson, GA, The utility of micro-CT and MRI in the assessment of longitudinal growth of liver metastases in a preclinical model of colon carcinoma., Acad Radiol, vol 20 no. 4 (2013), pp. 430-439 [10.1016/j.acra.2012.09.030] [abs].
  • Calabrese, E; Johnson, GA; Watson, C, An ontology-based segmentation scheme for tracking postnatal changes in the developing rodent brain with MRI., Neuroimage, vol 67 (2013), pp. 375-384 [10.1016/j.neuroimage.2012.11.037] [abs].
  • Subashi, E; Moding, EJ; Cofer, GP; MacFall, JR; Kirsch, DG; Qi, Y; Johnson, GA, A comparison of radial keyhole strategies for high spatial and temporal resolution 4D contrast-enhanced MRI in small animal tumor models., Med Phys, vol 40 no. 2 (2013) [10.1118/1.4774050] [abs].
  • Badea, A; Johnson, GA, Magnetic resonance microscopy., Stud Health Technol Inform, vol 185 (2013), pp. 153-184 [abs].
  • Johnson, GA; Badea, A; Calabrese, E; Liu, C; Xie, L, Magnetic resonance histology: cool images- but who cares?, TOXICOLOGY LETTERS, vol 221 (2013), pp. S50-S50 [10.1016/j.toxlet.2013.06.183] [abs].
  • Badea, A; Gewalt, S; Avants, BB; Cook, JJ; Johnson, GA, Quantitative mouse brain phenotyping based on single and multispectral MR protocols., Neuroimage, vol 63 no. 3 (2012), pp. 1633-1645 [10.1016/j.neuroimage.2012.07.021] [abs].
  • Johnson, GA; Calabrese, E; Badea, A; Paxinos, G; Watson, C, A multidimensional magnetic resonance histology atlas of the Wistar rat brain., Neuroimage, vol 62 no. 3 (2012), pp. 1848-1856 [10.1016/j.neuroimage.2012.05.041] [abs].
  • Liu, C; Li, W; Wu, B; Jiang, Y; Johnson, GA, 3D fiber tractography with susceptibility tensor imaging., Neuroimage, vol 59 no. 2 (2012), pp. 1290-1298 [10.1016/j.neuroimage.2011.07.096] [abs].
  • Guo, X; Johnston, SM; Qi, Y; Johnson, GA; Badea, CT, 4D micro-CT using fast prospective gating., Phys Med Biol, vol 57 no. 1 (2012), pp. 257-271 [10.1088/0031-9155/57/1/257] [abs].
  • Lipinski, RJ; Hammond, P; O'Leary-Moore, SK; Ament, JJ; Pecevich, SJ; Jiang, Y; Budin, F; Parnell, SE; Suttie, M; Godin, EA; Everson, JL; Dehart, DB; Oguz, I; Holloway, HT; Styner, MA; Johnson, GA; Sulik, KK, Ethanol-induced face-brain dysmorphology patterns are correlative and exposure-stage dependent., PLoS One, vol 7 no. 8 (2012) [10.1371/journal.pone.0043067] [abs].
  • Badea, A; Johnson, GA, Magnetic resonance microscopy., Anal Cell Pathol (Amst), vol 35 no. 4 (2012), pp. 205-227 [10.3233/ACP-2011-0050] [abs].
  • Veraart, J; Leergaard, TB; Antonsen, BT; Van Hecke, W; Blockx, I; Jeurissen, B; Jiang, Y; Van der Linden, A; Johnson, GA; Verhoye, M; Sijbers, J, Population-averaged diffusion tensor imaging atlas of the Sprague Dawley rat brain., Neuroimage, vol 58 no. 4 (2011), pp. 975-983 [10.1016/j.neuroimage.2011.06.063] [abs].
  • Liu, C; Li, W; Johnson, GA; Wu, B, High-field (9.4 T) MRI of brain dysmyelination by quantitative mapping of magnetic susceptibility., Neuroimage, vol 56 no. 3 (2011), pp. 930-938 [10.1016/j.neuroimage.2011.02.024] [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., J Neurosci Methods, vol 195 no. 2 (2011), pp. 170-175 [10.1016/j.jneumeth.2010.11.028] [abs].
  • Hawrylycz, M; Baldock, RA; Burger, A; Hashikawa, T; Johnson, GA; Martone, M; Ng, L; Lau, C; Larson, SD; Nissanov, J; Puelles, L; Ruffins, S; Verbeek, F; Zaslavsky, I; Boline, J, Digital atlasing and standardization in the mouse brain., PLoS Comput Biol, vol 7 no. 2 (2011) [10.1371/journal.pcbi.1001065] [abs].
  • Johnson, GA; Badea, A; Jiang, Y, Quantitative neuromorphometry using magnetic resonance histology., Toxicol Pathol, 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].
  • Pandit, P; Qi, Y; Story, J; King, KF; Johnson, GA, Multishot PROPELLER for high-field preclinical MRI., Magn Reson Med, vol 64 no. 1 (2010), pp. 47-53 [10.1002/mrm.22376] [abs].
  • Jiang, Y; Johnson, GA, Microscopic diffusion tensor imaging of the mouse brain., Neuroimage, vol 50 no. 2 (2010), pp. 465-471 [10.1016/j.neuroimage.2009.12.057] [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].
  • Mistry, NN; Qi, Y; Hedlund, LW; Johnson, GA, Ventilation/perfusion imaging in a rat model of airway obstruction., Magn Reson Med, vol 63 no. 3 (2010), pp. 728-735 [10.1002/mrm.22221] [abs].
  • Petiet, A; Johnson, GA, Active staining of mouse embryos for magnetic resonance microscopy., Methods Mol Biol, vol 611 (2010), pp. 141-149 [10.1007/978-1-60327-345-9_11] [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].
  • 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].
  • 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].
  • 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].
  • Johnson, GA; Cofer, GP; Gewalt, SL; Hedlund, LW, Morphologic phenotyping with MR microscopy: the visible mouse., Radiology, vol 222 no. 3 (2002), pp. 789-793 [10.1148/radiol.2223010531] [abs].
  • Johnson, GA; Hedlund, LW, Image based phenotyping: The visible mouse, FASEB JOURNAL, vol 16 no. 5 (2002), pp. A1091-A1091 [abs].
  • Johnson, GA; Cofer, GP; Gewalt, SL; Hedlund, LW, An engineering approach to image-based phenotyping, 2002 IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING, PROCEEDINGS (2002), pp. 381-383 [abs].
  • Johnson, GA; Benveniste, H; Engelhardt, RT; Qiu, H; Hedlund, LW, Magnetic resonance microscopy in basic studies of brain structure and function., Ann N Y Acad Sci, vol 820 (1997), pp. 139-147 [10.1111/j.1749-6632.1997.tb46193.x] [abs].
  • Johnson, GA; Benveniste, H; Black, RD; Hedlund, LW; Maronpot, RR; Smith, BR, Histology by magnetic resonance microscopy., Magn Reson Q, vol 9 no. 1 (1993), pp. 1-30 [abs].
  • Johnson, GA; Thompson, MB; Drayer, BP, Three-dimensional MRI microscopy of the normal rat brain., Magn Reson Med, vol 4 no. 4 (1987), pp. 351-365 [10.1002/mrm.1910040406] [abs].
  • Johnson, GA; Thompson, MB; Gewalt, SL; Hayes, CE, Nuclear magnetic resonance imaging at microscopic resolution, Journal of Magnetic Resonance (1969), vol 68 no. 1 (1986), pp. 129-137 [abs].