G. Allan Johnson

G. Allan Johnson

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

Contact Information

Education

  • Ph.D. Duke University, 1974

Research Interests

Dr. Johnson's research involves magnetic resonance histology (MRH), the application of MR microscopy to study tissue architecture. Using MRH for morphologic phenotyping in the mouse was first suggested by Dr. Johnson and his colleagues in this article (Radiology 2002;222:789-793 2002). A publication of our Waxholm Space (WHS) atlas of the C57BL mouse brain was created in conjunction with the International Neuroinformatics Coordinating Facility (INCF) digital brain atlasing program (http://software.incf.org/software/waxholm-space) to be the center of a digital atlasing architecture to share mouse brain data with the scientific research community.

Specialties

Medical Imaging

Courses Taught

  • BME 493: Projects in Biomedical Engineering (GE)
  • BME 494: Projects in Biomedical Engineering (GE)
  • MEDPHY 791: Independent Study in Medical Physics
  • PHYSICS 493: Research Independent Study

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., Cerebral Cortex, vol 25 no. 11 (2015), pp. 4628-4637 [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 [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., Human Brain Mapping, vol 36 no. 8 (2015), pp. 3167-3178 [abs].
  • Johnson, GA, Magnetic resonance histology., Journal of Magnetic Resonance Imaging, vol 42 no. 1 (2015), pp. 1-2 [abs].
  • Borg, JS; Vu, MA; 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) [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 in Biomedicine, vol 28 no. 5 (2015), pp. 546-554 [abs].
  • Subashi, E; Qi, Y; Johnson, GA, Dynamic contrast-enhanced MR microscopy identifies regions of therapeutic response in a preclinical model of colorectal adenocarcinoma., Medical physics, vol 42 no. 5 (2015), pp. 2482-2488 [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, Magnetic Resonance in Medicine, 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 [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?, Human Brain Mapping, vol 35 no. 11 (2014), pp. 5667-5685 [abs].
  • Xie, L; Subashi, E; Qi, Y; Knepper, MA; Johnson, GA, Four-dimensional MRI of renal function in the developing mouse., Nmr in Biomedicine, vol 27 no. 9 (2014), pp. 1094-1102 [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].
  • 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 [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., Journal of Neurotrauma, vol 31 no. 10 (2014), pp. 938-950 [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 [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].
  • 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].
  • 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., Academic Radiology, 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., Medical physics, vol 40 no. 2 (2013) [10.1118/1.4774050] [abs].
  • Badea, A; Johnson, GA, Magnetic resonance microscopy., Studies in health technology and informatics, vol 185 (2013), pp. 153-184 [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 Structure and Function (2013), pp. 1-12 [10.1007/s00429-013-0516-8] [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].
  • O'Leary-Moore, SK; Johnson, GA; Calabrese, E; Budin, F; Oguz, I; Styner, MA; Parnell, SE; Sulik, KK, DIFFUSION TENSOR IMAGING (DTI)-BASED ANALYSIS OF FIBER TRACT ABNORMALITIES IN A MOUSE MODEL OF PRENATAL ALCOHOL EXPOSURE, Alcoholism: Clinical and Experimental Research, vol 36 (2012), pp. 312A-312A [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., Physics in Medicine and Biology, vol 57 no. 1 (2012), pp. 257-271 [10.1088/0031-9155/57/1/257] [abs].
  • Badea, A; Johnson, GA, Magnetic resonance microscopy., Analytical Cellular Pathology, vol 35 no. 4 (2012), pp. 205-227 [10.3233/ACP-2011-0050] [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].
  • 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, WD; 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].
  • 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 computational biology, vol 7 no. 2 (2011) [10.1371/journal.pcbi.1001065] [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., Magnetic Resonance in Medicine, 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., Magnetic Resonance in Medicine, 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 in molecular biology (Clifton, N.J.), vol 611 (2010), pp. 141-149 [abs].
  • Badea, A; Johnson, GA; Williams, RW, Genetic dissection of the mouse CNS using magnetic resonance microscopy., Current Opinion in Neurology, vol 22 no. 4 (2009), pp. 379-386 [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 [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 [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 [abs].
  • Johnson, GA; Hedlund, LW, Image based phenotyping: The visible mouse, The FASEB journal : official publication of the Federation of American Societies for Experimental Biology, vol 16 no. 5 (2002), pp. A1091-A1091 [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; Cofer, GP; Gewalt, SL; Hedlund, LW; IEEE, ; IEEE, , 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., Annals of the New York Academy of Sciences, vol 820 (1997), pp. 139-147 [abs].
  • Johnson, GA; Benveniste, H; Black, RD; Hedlund, LW; Maronpot, RR; Smith, BR, Histology by magnetic resonance microscopy., Magnetic resonance quarterly, vol 9 no. 1 (1993), pp. 1-30 [abs].
  • Johnson, GA; Thompson, MB; Drayer, BP, Three-dimensional MRI microscopy of the normal rat brain., Magnetic Resonance in Medicine, vol 4 no. 4 (1987), pp. 351-365 [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].