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Postal mailing address for all staff:
     Center for In Vivo Microscopy
     Box 3302, Duke University Medical Center
     Durham, NC  27710

Main phone: 919 684-7755 fax: 919 684-7158

G. ALLAN JOHNSON, PhD
Director - Center for In Vivo Microscopy
Charles E. Putman Distinguished Professor of Radiology
Professor of Biomedical Engineering and Physics
919 684-7754
gjohnson@duke.edu


Dr. Johnson is Director of the Center for In Vivo Microscopy, an NIH/NCRR/NIBIB-funded National Biomedical Technology Resource Center (P41 EB0015897), now into its 23rd year of funding. He received a PhD in Physics from Duke University in 1974 in electron spin resonance under Walter Gordy and has been in the Department of Radiology since 1974, where he is currently Director of Diagnostic Physics. He holds joint appointments in Radiology, Physics, and Biomedical Engineering as the Charles E. Putman University Professor, and he is co-author on over 300 peer-reviewed papers (see PubMed for more information about some of these publications).

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 colleagues in Radiology 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 to be the center of a digital atlasing architecture to share mouse brain data with the scientific research community. A figure from this article is on the cover of the Nov 2010 issue, along with supplemental data. Work on brain atlases has continued resulting in these publications, starting with the most recent:

  • A Badea, GA Johnson Magnetic resonance microscopy. Series: Studies in Health Technology and Informatics 2013; 185:153-184. IOS Press Ebooks, 978-1-61499-239-4 (print) | 978-1-61499-240-0 (online)
  • E Calabrese, A Badea, C Watson, GA Johnson, A quantitative magnetic resonance histology atlas of postnatal rat brain development with regional estimates of growth and variability, Neuroimage 71:196-206, 2013. Supplement
  • E Calabrese, GA Johnson, C Watson, An ontology-based segmentation scheme for tracking postnatal changes in the developing rodent brain with MRI, Neuroimage 67:375-384, 2013. Detailed guide to MRH-based segmentation of all 26 structures available from the Neuroscience Lexicon wiki; Supplement
  • E Calabrese, GA Johnson, Diffusion tensor magnetic resonance histology reveals microstructural changes in the developing rat brain. Neuroimage. 2013 Oct;79:329-39. Supplement
  • A Badea, GA Johnson, Review Article: Magnetic resonance microscopy, Analytical Cellular Pathology Anal Cell Pathol (Amst). 2012 Jan 1;35(4):205-227 PMCID:PMC3508709
  • GA Johnson, E Calabrese, A Badea, G Paxinos, C Watson, A multidimensional magnetic resonance histology atlas of the Wistar rat brain, Neuroimage 62(3): 1848–1856, 2012. PMCID: PMC3408821 Supplement Figure chosen for cover
  • M Hawrylycz, RA Baldock, A Burger, T Hashikawa, GA Johnson, et al., Digital atlasing and standardization in the mouse brain, PLoS Computational Biology 7(2): e1001065, 2011 PMCID: PMC3033370
  • Y Jiang, GA Johnson, Microscopic diffusion tensor atlas of the mouse brain, NeuroImage 56(3): 1235-1243, 2011 Supplement PMCID: PMC3085633


ALEXANDRA BADEA, PhD, Assistant Professor - Radiology

919 684-7654
alexandra.badea@duke.edu

Alexandra uses MR microscopy to image the rodent brain, including its vasculature. She studies the morphometry and 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. Some of her publications are listed below, starting with the most recent:

  • A Badea, GA Johnson, Magnetic resonance microscopy, Analytical Cell Pathol 35(4):205-22, 2012 PMCID:PMC22142643
  • A Badea, S Gewalt, BB Avants, JJ Cook, GA Johnson. Quantitative mouse brain phenotyping based on single and multispectral MR protocols. NeuroImage 63 1633-1645, 2012. NIHMSID#396334
  • D Clark, A Badea, Y Liu, et al. Registration-based segmentation of murine 4D cardiac micro-CT data using symmetric normalization. Phys Med Biol 57:6125-6145, 2012 Supplement
  • GA Johnson, E Calabrese, A Badea, G Paxinos, C Watson, A multidimensional magnetic resonance histology atlas of the Wistar rat brain, Neuroimage 62(3): 1848–1856, 2012 PMCID: PMC3408821 Supplement Cover figure
  • T Wu, MH Bae, M Zhang, R Pan, A Badea. A prior feature SVM-MRF based method for mouse brain segmentation. Neuroimage. 59(3):2298-2306, 2011 NIHMSID#381471
  • DM Bowden, GA Johnson, L Zaborsky, WDK Green, E Moore, A Badea, MF Dubach, FL Bookstein. A symmetrical Waxholm canonical mouse brain for NeuroMaps, J Neurosci Meth 195(2): 170-175, 2011. PMCID: PMC3103134
  • GA Johnson, A Badea, Y Jiang, Quantitative neuromorphometry using MR histology, Toxicol Pathol 39(1):85-91, 2011
  • M Poot, A Badea, RW Williams, MJ Kas, Identifying human disease genes through cross-species gene mapping of evolutionary conserved processes, PLoS ONE 6(5):e18612, 2011 PMCID: PMC3087714
  • AA Sharief, A Badea, AM Dale, GA Johnson, Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy, NeuroImage 39(1): 136-1451, 2008
  • A Badea, GA Johnson, RW Williams, Genetic dissection of the mouse brain using high-field magnetic resonance microscopy. NeuroImage. 45(4):1067-1079, 2009
  • A Badea, GA Johnson, JL Jankowsky, Remote sites of structural atrophy predict later amyloid formation in a mouse model of Alzheimer's disease. Neuroimage 50: 416-427, 2010. Supplement
CRISTIAN BADEA, PhD, Associate Professor - Radiology, BME
919 684-7509
cristian.badea@duke.edu

Cristian's research includes x-ray-based methods for small animal morphological and functional imaging. His interests include CT, digital tomosynthesis, digital subtraction angiography, and image reconstruction algorithms. He designs and implements new systems and methods for in vivo dynamic high-resolution imaging using microCT and x-ray angiography for mouse cardiac phenotyping. The unique microCT system developed at CIVM was used to produce the 1st in vivo cine microCT of the mouse heart with isotropic resolution of 100 microns and temporal resolution of 10 ms. Cristian's work also involves quantitative 4D tumor imaging using digital subtraction angiography and microCT.

Just some of his most recent publications are listed below:

  • C Badea, L Hedlund, GA Johnson, A LabVIEW platform for preclinical imaging using digital subtraction angiography and micro-CT, Journal of Medical Engineering, in press 2013
  • R Bhavane, C Badea, KB Ghaghada, D Clark, D Vela, Anoosha Moturu, Ananth Annapragada, GA Johnson, JT Willerson, A Annapragada, Dual-energy computed tomography imaging of atherosclerotic plaques in a mouse model using a liposomal-iodine nanoparticle contrast agent, Circulation, in press 2013.
  • DP Clark, K Ghaghada, EJ Moding, DG Kirsch, CT Badea, In vivo characterization of tumor vasculature using iodine and gold nanoparticles and dual energy micro-CT, Physics in Medicine and Biology, in press 2013. Supplement
  • C Badea, X Guo, D Clark, S Johnston, C Marshall, C Piantadosi, Dual energy micro-CT of the rodent lung, Am J Physiol-Lung Cell Molec Physiol 302(10):L1088-1097, 2012. PMCID: PMC3362256
  • C Badea, KK Athreya, G Espinosa, DP Clark, AP Ghafoori, Y Yi, DG Kirsch, GA Johnson, A Annapragada, KB Ghaghada, CT imaging of primary lung cancer in mice using a liposomal-iodinated contrast agent, PLoS ONE 7(4): e34496, 2012 PMCID: PMC3317632
  • CT Badea, X Guo, D Clark, SM Johnston, C Marshall, C Piantadosi. Lung imaging in rodents using dual energy micro-CT. Proceedings of SPIE 8317, 83171I, 2012 NIHMSID #421311
  • CT Badea, IN Stanton, SM Johnston, GA Johnson, MJ Therien. Investigations on x-ray luminescence CT for small animal imaging. Proceedings of SPIE 8313, 83130T, 2012 NIHMSID #421296
  • D Clark, GA Johnson, CT Badea, Denoising of 4D cardiac micro-CT data using median-centric bilateral filtration, Proceedings SPIE, 8314, 8314, 83143Z. 2012 NIHMSID #421306
  • D Clark, A Badea, Y Liu, GA Johnson, CT Badea. Registration-based segmentation of murine 4D cardiac micro-CT data using symmetric normalization. Phys Med Biol 57:6125-6145, 2012, Supplement
  • SM Johnston GA Johnson, CT Badea, Temporal and spectral imaging with micro-CT. Medical Physics 39(8):4943-4958, 2012 PMCID:PMC3416878
  • CT Badea, SM Johnston, Y Qi, GA Johnson, 4D micro-CT for cardiac and perfusion applications with view under sampling, Phys Med Biol 56(11): 3351-3369, 2011 PMCID:PMC3180888
  • CT Badea, LW Hedlund, J Cook, BR Berridge, GA Johnson, Micro-CT imaging assessment of dobutamine-induced cardiac stress in rats, J Pharm Toxicol Methods 2011; 63(1):24-29 PMCID:PMC2916074
  • CT Badea, K Ghaghada, G Espinosa, et al. Multi-modality PET-CT imaging of breast cancer in an animal model using nanoparticle x-ray contrast agent and 18F-FDG Proc. SPIE 7965, 796511, 2011
  • CT Badea, SM Johnston, Y Qi, et al., Dual-energy micro-CT for differentiation of iodine- and gold-based nanoparticles temporal and spectral reconstruction algorithms for x-ray CT, Proc. SPIE 7961, 79611X, 2011
  • CT Badea, LW Hedlund, Y Qi, B Berridge, GA Johnson, In vivo imaging of rat coronary arteries using bi-plane digital subtraction angiography, J Pharma Toxicol Methods J Pharmacol Toxicol Methods. 2011 September; 64(2): 151-157 PMCID:PMC3200458
  • KB Ghaghada, CT Badea, L Karumbaiah, N Fettig, RV Bellamkonda, GA Johnson, A Annapragada, Evaluation of tumor microenvironment in an animal model using a nanoparticle contrast agent in CT imaging, Acad Radiol 18(1):20-30, 2011 PMCID:PMC3016875

Dr. Badea participates in an annual course sponsored by the National Cancer Institute. See this article in the NCI Cancer Bulletin, Imaging Boot Camp for Cancer Researchers



ZACKARY CLEVELAND, PhD, Research Scientist zack

919 684-7793
zackary.cleveland@duke.edu
zack

Zack grew up in rural Montana and did his undergraduate work in biology and chemistry. His graduate work involved hyperpolarized noble gas NMR, and he focused primarily on elucidating the mechanistic details involved in HP gas relaxation. Zack works under Dr. Bastiaan Driehuys, and his research interests have centered on developing novel 129Xe MR techniques for imaging lung function in rodents and humans. A particular focus has been on visualizing diffusive gas uptake in the lungs by imaging HP 129Xe as it dissolves in the alveolar walls and adjacent capillary blood. He is also studying diffusive gas elimination in rats by first delivering HP 129Xe to the blood using hydrophobic gas exchange membranes and then imaging the gas as it diffuses from the capillary bed into the alveolar spaces.

Zack is the recipient of an NIH/NHLBI K99 award (1K99 HL111217-01A1) Time-resolved 129Xe Ventilation-perfusion MRI in Models of Acute Lung Injury.

Just a few of Zack's selected publications are listed below:

  • ZI Cleveland, HE Moller, LW Hedlund, JC Nouls, MS Freeman, Y Qi, B Driehuys, In vivo MR imaging of pulmonary perfusion and gas exchange in rats via continuous extracorporeal infusion of hyperpolarized 129Xe, PLoS ONE 7(2): e31306, 2012. PMCID: PMC3283644
  • Kaushik SS, Cleveland ZI, Cofer GP, Metz G et al., Diffusion weighted imaging of hyperpolarized 129Xe in patients with COPD, Magn Reson Med, 65(4):1154-1165, 2011
  • Zheng W, Cleveland ZI, Moller HE, Driehuys B. Gradient-induced longitudinal relaxation of hyperpolarized noble gases in the fringe fields of superconducting magnets used for magnetic resonance. J Magn Reson 208(2):284-290, 2011 PMCID:PMC3026078
  • Cleveland ZI, Cofer GP, Metz G, Beaver D, Nouls J, Kaushik S, et al., Hyperpolarized 129Xe MR imaging of alveolar gas uptake in humans, PLoS ONE 5(8): e12192, 2010 PMCID: PMC2922382
  • Branca RT, Cleveland Z, Fubara B, et al., Molecular MRI for sensitive and specific detection of lung metastases, Proc Natl Acad Sci U S A. Feb 23;107(8):3693-3697, 2010 PMCID: PMC2840507
  • B Driehuys, H Moller, J Pollaro, Z Cleveland, LW Hedlund, MR imaging of pulmonary perfusion and Xe gas exchange in rats by intravenous injection of hyperpolarized 129Xe , Radiology 252(2): 386-393, 2009. Free PMC article


GARY COFER, MS, MR Operations Manager
919 684-7677
cof@duke.edu

Gary's multi-faceted functions at the Center include the physical, electronic, and software maintenance of the MR microscopes. He instructs new students and researchers in the nuances of MR imaging processes.

Much of the control software and imaging pulse sequences on the modified GE Signa MR microscopes depends on Gary's expertise and he is involved to the extent necessary to maintain a level of excellence in the images produced.

Several of our MR systems are custom interfaces between a standard GE Signa clinical imaging console and hardware (magnet, gradients, RF amplifiers, preamplifiers and TR switches) appropriate for imaging rats and mice, so Gary is involved with maintaining all these separate pieces. This photo shows that Gary also keeps all the magnets filled with liquid helium and liquid nitrogen, to maintain the superconducting magnetic field.

Paramount to the imaging process are high-quality RF transceiver coils and many coils used have been designed and fabricated by Gary, including single and multi-turn solenoids, Helmholtz pairs, and a periodic wave structure called a birdcage coil. Since monitoring of the animals is directly linked to the imaging process, Gary interacts significantly with physiologic monitoring. Imaging triggers ventilation and the heartbeat triggers the imaging.
JAMES COOK, Computer Programmer  

919 684-7672
james.cook@duke.edu

James supports our computers and software, analyzes some of the lab's data, and runs some of our imaging equipment.



BASTIAAN DRIEHUYS, PhD, Associate Professor - Radiology, BME, Medical Physics
919 684-7786
bastiaan.driehuys@duke.edu

Bas' research focuses on developing and applying hyperpolarized (HP) substances in MR imaging (MRI). His background is in the atomic physics of producing hyperpolarized noble gases 3He and 129Xe. Hyperpolarization, which involves aligning nuclei to a high degree, enhances the MRI signal by 5-6 orders of magnitude, which enables high-resolution imaging despite the low density of gases compared to water (the ordinary signal source in MRI).  

With industry and academic experience, Bas' interests span not only in attacking the basic physics problems of these gases, but in their large-scale development and application to biomedical problems. Current work involves high-resolution HP 3He imaging in mouse and rat models of pulmonary diseases, such as asthma, COPD, and fibrosis.

Technical developments focus on advancing HP 129Xe, which has solubility and enormous chemical shift in blood and tissues that show potential to impact a broad range of imaging issues beyond the air spaces.

To realize the full capabilities of HP 129Xe, Bas' integrated team combines atomic physics research, polarizer engineering, and developing MR hardware and techniques to get maximum signal and contrast out of every atom. Efforts have expanded into the clinical arena by running the 1st phase I clinical trial for HP 129Xe MRI sponsored by GE Healthcare, which will lead to developing an integrated functional lung exam capable of revealing both ventilation, pulmonary microstructure, and regional gas exchange.

Selected publications:

  • B Driehuys, S Martinez-Jimenez, ZI Cleveland, et al., Chronic Obstructive Pulmonary Disease: Safety and Tolerability of Hyperpolarized 129Xe MR Imaging in Healthy Volunteers and Patients, Radiology 262(1):279-289, Jan 2012. PMCID: PMC3244666
  • SS Kaushik, ZI Cleveland, GP Cofer, G Metz, D Beaver, J Nouls, M Kraft, J Wolber, KT Kelly, W Auffermann, HP McAdams, B Driehuys, Diffusion weighted imaging of hyperpolarized 129Xe in patients with chronic obstructive pulmonary disease, Magn Reson Med, 65(4):1154-1165, 2011
  • AC Thomas, JC Nouls, B Driehuys, Voltz JW, B Fubara, J Foley, JA Bradbury, DC Zeldin, Ventilation defects observed with hyperpolarized 3He magnetic resonance imaging in a mouse model of acute lung injury, Am J Respir Cell Mol. Biol 44(5):648-54, 2011
  • W Zheng, ZI Cleveland, HE Moller, B Driehuys, Gradient-induced longitudinal relaxation of hyperpolarized noble gases in the fringe fields of superconducting magnets used for magnetic resonance. J Magn Reson 208(2):284-290, 2011
  • RT Branca, ZI Cleveland, B Fubara, et al., Molecular MRI for sensitive and specific detection of lung metastases, Proc Natl Acad Sci USA, 23;107(8):3693-3697, 2010. Free Article
  • ZI Cleveland, GP Cofer, G Metz, D Beaver, J Nouls, S Kaushik, M Kraft, J Wolber, KT Kelly, HP McAdams, B Driehuys, Hyperpolarized 129Xe MR imaging of alveolar gas uptake in humans, PLoS ONE 5(8): e12192. Aug 16 2010 Free article
  • NN Mistry, A Thomas, SS Kaushik, GA Johnson, B Driehuys, Quantitative analysis of hyperpolarized 3He ventilation changes in mice challenged with Methacholine, Magn Reson Med 63:658–666, 2010. Free PMC article
  • B Driehuys, H Moeller, J Pollaro, Z Cleveland, LW Hedlund, MR imaging of pulmonary perfusion and Xenon gas exchange in rats by intravenous injection of hyperpolarized 129Xe , Radiology 252(2): 386-393, 2009. Free PMC article
  • ZI Cleveland, HE Moeller, L Hedlund, B Driehuys. Continuously infusing hyperpolarized 129xe into flowing aqueous solutions using hydrophobic gas exchange membranes. Journal of Physical Chemistry B 113(37):12489-12499, 2009, Free PMC article
  • AC Thomas, EN Potts, BT Chen, DM Slipetz, WM Foster, B Driehuys, A robust protocol for regional evaluation of methacholine challenge in mouse models of allergic asthma using hyperpolarized He-3 MRI. NMR Biomed 22(5):502-515, 2009
  • AH Couture, TB Clegg, B Driehuys, Pressure Shifts and Broadening of the Cs D1 and D2 Lines by He, N2 and Xe at Densities used for Optical Pumping and Spin Exchange Polarization. J Appl Phys 104(14):094912, 2008
  • B Driehuys, J Pollaro, GP Cofer, In vivo MRI using real-time production of hyperpolarized Xe-129. Magn Reson Med 60:14-20, 2008
  • B Driehuys, J Nouls, A Badea, et al., Small-animal imaging with MR microscopy, ILAR Journal 49(1):35-53, 2008
  • B Driehuys, LW Hedlund, Imaging techniques for small animal models of pulmonary disease: MR microscopy, invited paper: Toxicologic Pathology 35(1): 49-58, 2007
  • B Driehuys, J Walker, J Pollaro, et al., Hyperpolarized 3He MR imaging of methacholine challenge in a mouse model of asthma, Magn Reson Med, 58(5):893-900, 2007

TAWYNNA GORDON, Financial Analyst
tawynna
919 684-7755
tawynna.gordon@duke.edu
tawynna gordon

Tawynna is the grants and financial administrator for the Center. She prepares the financial documents to submit to funding agencies, coordinates financial data analysis, handles procurement for both large equipment and research supplies, and keeps the lab running smoothly.

If you need to see someone in the Center, your first stop will probably be with Tawynna.



LAURENCE HEDLUND, PhD, Professor Emeritus of Radiology
919 684-7767
laurence.hedlund@duke.edu

Dr. Hedlund is retired as a Professor of Radiology, but now has the status of Professor Emeritus of Radiology. Larry is still working with the Center, and continues to be responsible for Institutional Animal Care and Use Committee (IACUC) certification of all live animal studies. He also develops physiologic monitoring and support technologies used for live animal imaging.

Selected publications:

  • Z Cleveland, HE Moller, LW Hedlund, JC Nouls, MS Freeman, Y Qi, B Driehuys, In vivo MR imaging of pulmonary perfusion and gas exchange in rats via continuous extracorporeal infusion of hyperpolarized 129Xe, PLoS ONE 7(2): e31306, 2012, Open access article
  • CT Badea, LW Hedlund, J Cook, et al., Micro-CT imaging assessment of dobutamine-induced cardiac stress in rats, J Pharmal Tox Methods. 63(1):24-29, 2011
  • J Nouls, M Fanarjian, L Hedlund, A constant-volume ventilator and gas recapture system for hyperpolarized gas MRI of mouse and rat lungs, Concepts in Magn Reson Part B: Magn Reson Eng, 39B(2): 78-88, 2011, Supplemental data
  • CT Badea, LW Hedlund, Y Qi, B Berridge, GA Johnson, In vivo imaging of rat coronary arteries using bi-plane digital subtraction angiography, J Pharma Toxicol Methods, 64(2): 151-157, 2011
  • CT Badea, SM Johnston, E Subashi, Y Qi, LW Hedlund, GA Johnson, Lung perfusion imaging in small animals using 4D micro-CT at heartbeat temporal resolution, Medical Physics 37(1): 54-62, 2010
  • Z Cleveland, H Moller, L Hedlund, B Driehuys, Continuously infusing hyperpolarized 129Xe into flowing aqueous solutions using hydrophobic gas exchange membranes, J Phys Chem B, 113(37): 12489-99, 2009
  • B Driehuys, H Moeller, J Pollaro, Z Cleveland, LW Hedlund, MR imaging of pulmonary perfusion and Xenon gas exchange in rats by intravenous injection of hyperpolarized 129Xe , Radiology 252(2): 386-393, 2009
  • B Driehuys, J Nouls, A Badea, A Petiet, E Bucholz, K Ghagada, L Hedlund, Small-animal imaging with magnetic resonance microscopy, invited paper, ILAR Journal 49(1):35-53, 2008
  • LW Hedlund, T Gluckman, Basics of Small Animal Handling for In Vivo Imaging, Chapter 24, pp. 377-390, in: Molecular Imaging in Oncology, M Pomper, J Gelovani (Eds), Informa Healthcare, New York, NY, 2008

JOHN NOULS, PhD, Assistant Professor
919 684-7769
john.nouls@duke.edu
PhD, Biomedical Engineering, Duke University
MS, Biomedical Engineering, Geneva University Hospital, Switzerland
Mechanical Engineering, Swiss Federal Institute of Technology

John's parents are Belgian, but he was born in California and grew up in Switzerland. He moved from Europe to North Carolina and worked as a research engineer for a medical imaging company developing hyperpolarized gas technology for MR imaging. His focus was on 3He polarization, handling, and delivery.

John's work concentrates on MR imaging. His research interests cover superconducting technology, hardware in the MR radiofrequency chain, coil design, and radiofrequency simulation. He uses and also develops high-temperature superconducting coils for MR microscopy.

Publications:

  • RS Virgincar, ZI Cleveland, SS Kaushik, MS Freeman, J Nouls, GP Cofer, S Martinez-Jimenezc, M He, M Kraft, J Wolberg, HP McAdams, B Driehuys, Quantitative analysis of hyperpolarized 129Xe ventilation imaging in healthy volunteers and subjects with chronic obstructive pulmonary disease, NMR in Biomedicine, NMR in Biomedicine 26 (4): 424-435, 2013.
  • SS Kaushik, ZI Cleveland, GP Cofer, G Metz, D Beaver, J Nouls, et al., Diffusion weighted imaging of hyperpolarized 129Xe in patients with chronic obstructive pulmonary disease, Magn Reson Med 65(4):1154-65, 2011, if access available through Wiley Online Library
  • J Nouls, M Fanarjian, L Hedlund, A constant-volume ventilator and gas recapture system for hyperpolarized gas MRI of mouse and rat lungs, Concepts in Magnetic Resonance Part B: Magnetic Resonance Engineering, 39B(2): 78–88, 2011, Supplementary data
  • AC Thomas, JC Nouls, B Driehuys, et al., Ventilation defects observed with hyperpolarized 3He magnetic resonance imaging in a mouse model of acute lung injury, Am J Respir Cell Mol. Biol 44(5):648-54, 2011, data supplement If have access, journal text is available
  • ZI Cleveland, GP Cofer, G Metz , D Beaver, J Nouls, et al., Hyperpolarized 129Xe MR imaging of alveolar gas uptake in humans, PLoS ONE 5(8): e12192. 16 Aug 2010 Free article
  • GP Howles, JC Nouls, Y Qi, GA Johnson, Rapid production of specialized animal handling devices using computer-aided design and solid freeform fabrication, J Magn Reson Imag 30(2):466-471, 2009, Supplemental data Free PMC article
  • B Driehuys, J Nouls, A Badea, et al., Small-animal imaging with magnetic resonance microscopy, invited paper, ILAR Journal Noninvasive Bioimaging of Laboratory Animals 49(1):35-53, 2008. Free PMC article
  • JC Nouls, MG Izenson, HP Greeley, GA Johnson, Design of a superconducting volume coil for MR microscopy of the mouse brain, J Magn Reson 191 (2):231-238, 2008.

BECKY PRATT, Administrative Assistant Becky

919 684-7887
bpratt.duke@gmail.com

Becky takes care of the many tasks behind the scenes that keep the lab running.



YI QI, MD, Laboratory Research Analyst

919 684-7858
yi.qi@duke.edu

Yi is part of the biological support core and focuses on the surgery and setup of small animals for most of our imaging modalities, including micro-CT, MR, and digital subtraction angiography studies. Throughout the studies, Yi monitors the anesthesia, heart rate, temperature, and ventilation of the animals using custom-written LabVIEW programs.



LUCY UPCHURCH, Computer Systems and Network Manager
919 684-7781
lucy.upchurch@duke.edu

Lucy has over 20 years of system/network administration experience. She maintains over 75 computer systems, including these operating systems—OS X, IRIX, Linux, Solaris, Windows 2000, and Windows XP. Lucy also maintains the Center’s e-mail, network, ftp, web, and Oracle/SQL database servers.

SALLY ZIMNEY, MEd, Educational Coordinator
919 684-7758
sally.zimney@duke.edu

Sally has experience in technical and marketing writing, editing, graphics, and instructional design. She uses these skills to enhance all forms of communication, journal articles, grants, and reports that deal with the Center and the activities of the people who work here. Sally is the contact person to initiate projects with the Center, interfaces with long- and short-term visitors to the Center, and handles all aspects of training activities.

Graduate Students

Our graduate students contribute greatly to the work of the Center as Graduate Research Assistants.

EVAN CALABRESE
evan
919 684-7653
evan.calabrese@duke.edu
evan
MD candidate
PhD candidate - Biomedical Engineering

Evan is part of the Medical Scientist Training Program, which leads to both MD and PhD degrees.

One of his studies with MR imaging involves longitudinal diffusion tensor imaging of blast-induced traumatic brain injury in a mouse model, and he works on the Center's initiatives for creating brain atlases.

Publications:

  • E Calabrese, GA Johnson, C Watson, An ontology-based segmentation scheme for tracking postnatal changes in the developing rodent brain with MRI, Neuroimage, 67:375-384, 2013. Detailed guide to MRH-based segmentation of all 26 structures Neuroscience Lexicon wiki; Supplement
  • E Calabrese, A Badea, C Watson, GA Johnson, A quantitative magnetic resonance histology atlas of postnatal rat brain development with regional estimates of growth and variability, Neuroimage 71:196-206, 2013. Supplement
  • E Calabrese, GA Johnson, Diffusion tensor magnetic resonance histology reveals microstructural changes in the developing rat brain. Neuroimage. 2013 Oct;79:329-39. Supplement
  • E Gyengesi, E Calabrese, MC Sherrier, GA Johnson, G Paxinos, Charles Watson. Semi-automated 3D segmentation of major tracts in the rat brain: comparing DTI with standard histological methods. Brain Struct Funct online 2013 Mar 1.
  • PT Wei , D Leong, E Calabrese, L White, T Pierce, S Platt, J Provenzale, Diffusion tensor imaging of neural tissue organization: correlations between radiologic and histologic parameters. Neuroradiol J. 2013 Nov;26(5):501-10.

DARIN CLARK
Darin

919 684-7507
darin.clark@duke.edu

PhD candidate - Biomedical Engineering

Darin is working under the direction of Dr. Cristian Badea. His studies include 4D bilateral filtration of cardiac CT data, which provides a powerful denoising and regularization scheme for post-processing 4D cardiac micro-CT data in the mouse.

Darin's work also contributes to many of our CT collaborations.


Publications:

  • C Badea, X Guo, D Clark, S Johnston, C Marshall, C Piantadosi, Dual energy micro-CT of the rodent lung, Am J Physiol-Lung Cell Molec Physiol 302(10):L1088-1097, 2012. PMCID: PMC3362256
  • C Badea, KK Athreya, G Espinosa, DP Clark, AP Ghafoori, Y Yi, DG Kirsch, GA Johnson, A Annapragada, KB Ghaghada, CT imaging of primary lung cancer in mice using a liposomal-iodinated contrast agent, PLoS ONE 7(4): e34496, 2012 PMCID: PMC3317632
  • CT Badea, X Guo, D Clark, SM Johnston, C Marshall, C Piantadosi. Lung imaging in rodents using dual energy micro-CT. Proceedings of SPIE 8317, 83171I, 2012.
  • R Bhavane, C Badea, KB Ghaghada, D Clark, D Vela, Anoosha Moturu, Ananth Annapragada, GA Johnson, JT Willerson, A Annapragada, Dual-energy computed tomography imaging of atherosclerotic plaques in a mouse model using a liposomal-iodine nanoparticle contrast agent, Circ Cardiovasc Imaging 6(2):285-294, 2013. PMCID: PMC3760185
  • DP Clark, K Ghaghada, EJ Moding, DG Kirsch, CT Badea, In vivo characterization of tumor vasculature using iodine and gold nanoparticles and dual energy micro-CT, Physics in Medicine and Biology, Phys Med Biol 58(6):1683-1704, 2013. Supplement

RUSSELL DIBB
Russ
919 684-7839
russell.dibb@duke.edu

BS Mechanical Engineering, Brigham Young University
PhD candidate - Biomedical Engineering

As part of the MR team, Russell works to exploit the usefulness of signal phase information acquired from gradient echo MRI of the brain. The signal phase reveals anatomic structures, tissue compositions, and potential markers for brain pathologies that may not typically be visible in corresponding magnitude images.

Using a multi-echo sequence, Russell acquires gradient echo image volumes at multiple time points within a single scan, then employs several mathematical tools to transform that data into enhanced magnitude, phase, and susceptibility images with reduced noise. Russell's 4-D datasets also allow him to investigate T2* in the adult mouse brain. Russell also investigates the effect of magnetic field strength and contrast agent concentration on the susceptibility of brain tissues.


MATTHEW FREEMAN
matt

919 684-7687
msf19@duke.edu

PhD candidate - Medical Physics

Matt is part of the hyperpolarized team under direction of Dr. Bastiaan Driehuys. His research focuses on the translation of hyperpolarized gas MR imaging to the brain, specifically looking at imaging 129Xe in the dissolved phase for the purposes of Alzheimer's Disease diagnosis and monitoring. Matt's work so far has focused on the mathematical modeling of our polarizer performance, in-vivo SPION imaging studies with both 129Xe and 3He, brown fat spectroscopy, and the construction of a 1-liter hyperpolarized gas resolution phantom. Currently Matt is designing a dual-tuned RF coil capable of transmitting at the proton and xenon resonances in our beloved 2T magnet, Onnes. This photo shows Matt with our preclinical polarizer.


Publications:

  • ZI Cleveland, HE Moller, LW Hedlund, JC Nouls, MS Freeman, Y Qi, B Driehuys, In vivo MR imaging of pulmonary perfusion and gas exchange in rats via continuous extracorporeal infusion of hyperpolarized 129Xe, PLoS ONE 7(2): e31306, 2012. PMCID: PMC3283644
  • M Freeman, K Claytor, Y Qi, S Degan, Z Ma, WS Warren, B Driehuys, RT Branca, Hyperpolarized 129Xe And 3He MRI for sensitive detection of iron oxide contrast in the mouse lung Am J Respir Crit Care Med 185: A2250, 2012.
  • MS Freeman, ZI Cleveland, Y Qi, B Driehuys, Enabling hyperpolarized 129Xe MR spectroscopy and imaging of pulmonary gas transfer to the red blood cells in transgenic mice expressing human hemoglobin, Magnetic Resonance in Medicine, 2013 Nov;70(5):1192-1199.
  • RS Virgincar, ZI Cleveland, SS Kaushik, MS Freeman, J Nouls, GP Cofer, S Martinez-Jimenezc, M He, M Kraft, J Wolberg, HP McAdams, B Driehuys, Quantitative analysis of hyperpolarized 129Xe ventilation imaging in healthy volunteers and subjects with chronic obstructive pulmonary disease, NMR in Biomedicine 26(4): 424-435, 2013.
SIVARAM KAUSHIK
919 684-7687
ssk13@duke.edu

BE, Medical Electronics, VTU, Bangalore, India
MS, Biomedical Engineering, Duke University
PhD candidate - Biomedical Engineering

Sivaram hails from Bangalore, the Silicon Valley of India. He completed his Masters in Biomedical Engineering at Duke in 2009, with research focused on image processing and quantitative analysis of hyperpolarized gas MRI. He stayed in the Center as a research associate for 1 year, during which time he was also responsible for the operation of the Xenon polarizers for a phase I clinical trial. His PhD research continues to focus on hyperpolarized gas MRI.

Shiv's primary areas of interests are developing pulse sequences, accelerated imaging and reconstruction, and developing diffusion-weighted 129Xe MRI.

Publications:

  • SS Kaushik, ZI Cleveland, GP Cofer, et al., Diffusion weighted imaging of hyperpolarized 129Xe in patients with chronic obstructive pulmonary disease, Magn Reson Med, 65(4):1154-1165, 2011. PMCID:PMC3351270
  • AC Thomas, SS Kaushik, J Nouls, EN Potts, DM Slipetz, WM Foster, B Driehuys, Effects of corticosteroid treatment on airway inflammation, mechanics, and hyperpolarized 3He MR imaging in an allergic mouse model, J Appl Physiol 112:1437-1444, 2012. PMCID: PMC3362235
  • RS Virgincar, ZI Cleveland, SS Kaushik, MS Freeman, J Nouls, GP Cofer, S Martinez-Jimenez, M He, M Kraft, J Wolberg, HP McAdams, B Driehuys, Quantitative analysis of hyperpolarized 129Xe ventilation imaging in healthy volunteers and subjects with chronic obstructive pulmonary disease, NMR in Biomedicine 26 (4): 424-435, 2013.

ERGYS SUBASHI
919 684-7715
ergys.subashi@duke.edu

BS, Worcester Polytechnic Institute, Worcester MA
PhD candidate - Medical Physics

Ergys is exploring the feasibility of the integration of different modalities and/or MR contrast mechanisms to extract functional and quantitative parameters in tumors. Dynamic contrast enhanced and diffusion MRI currently appear to offer the greatest potential for functional/quantitative tumor imaging. CT perfusion techniques also seem suitable for this application. The incorporation of high-resolution structural imaging (as done previously by other students in our lab) offers the possibility to correlate the observed functional measures to anatomical landmarks.


Publications:

  • CT Badea, SM Johnston, E Subashi, Y Qi, LW Hedlund, GA Johnson, Lung perfusion imaging in small animals using 4D micro-CT at heartbeat temporal resolution, Medical Physics 37(1): 54-62, Jan. 2010. PMC: PMCID:PMC2801733
  • E Subashi, G Cofer, J MacFall, Y Qi, GA Johnson, A comparison of keyhole strategies for high spatial and temporal resolution 4D contrast-enhanced MRI in small animal tumor models, Medical Physics 40(2): 022304, 2013. PMCID: PMC3562278


ROHAN VIRGINCAR rohan

919 536-2214
rohan.virgincar@duke.edu

BE, Biomedical Engineering, University of Mumbai, India
MS candidate - Biomedical Engineering

Rohan is from the Indian state of Goa, the ‘pearl of the east.’ Working with the hyperpolarized gas MRI team, his core activities involve developing image analysis tools to quantify hyperpolarized 129Xe, 3He, and 1H MR images, and operating and maintaining gas polarizers. His research also includes small animal imaging and pulse sequence programming.


Publications:

  • RS Virgincar, ZI Cleveland, SS Kaushik, MS Freeman, J Nouls, GP Cofer, S Martinez-Jimenez, M He, M Kraft, J Wolberg, HP McAdams, B Driehuys, Quantitative analysis of hyperpolarized 129Xe ventilation imaging in healthy volunteers and subjects with chronic obstructive pulmonary disease, NMR in Biomedicine 26 (4): 424-435, 2013.
LUKE XIE
Luke

919 684-7884
luke.xie@duke.edu

line

BS and MS, Carnegie Mellon University
PhD candidate - Biomedical Engineering

Luke is part of the MR team. One of his studies involves identifying age-related nephropathy in Sprague-Dawley rats using magnetic resonance histology (MRH). High-resolution MRH can be used to assess renal architecture, and the onset nephropathy due to aging of the kidney. This work established the foundation of MR histology in high-throughput quantitative measurements and screening for safety effects.

Publications:

  • L Xie, R Cianciolo, B Hulette, H Won Lee, Y Qi, G Cofer, GA Johnson, Magnetic resonance histology of age-related nephropathy in the Sprague Dawley rat, Toxicologic Pathology 40(5):764-778, 2012. Supplement PMCID: PMC22504322
  • L Xie, MA Sparks, W Li, Y Qi, C Liu, TM Coffman, GA Johnson, Quantitative susceptibility mapping of kidney inflammation and fibrosis in Type 1 Angiotensin Receptor-deficient mice, NMR in Biomedicine 26(12): 1853-1863, 2013. Supplement
  • GA Johnson, A Badea, E Calabrese, C Liu, L Xie, Magnetic resonance histology: cool images—but who cares? Toxicology Letters 221: S50, 2013, abstract W15-1

 


Garb Coincidences

 

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