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Postal mailing address for all staff:

Center for In Vivo Microscopy
Duke University Medical Center, Box 3302
Durham, NC 27710

Courier address: 311 Research Dr. Durham, NC 27710

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


Director - Center for In Vivo Microscopy
Charles E. Putman University Professor of Radiology, Professor of Biomedical Engineering and Physics
919 684-7754

Dr. Johnson is Director of the Center for In Vivo Microscopy, an NIH/NIBIB-funded National Biomedical Technology Resource Center (P41 EB0015897), now into its 2nd decade 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 of 300+ peer-reviewed papers.

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 data. Work on brain atlases has continued with numerous publications. See our Shared Data for more publications that provide access imaging data sets, to help other investigators in their research.

PubMed link
for a list of Dr. Johnson's many publications.



TATIANA ALEXANDER, Administrative Assistant tatiana
919 684-7877

Tatiana takes care of many administrative and financial tasks that keep the Center for In Vivo Microscopy running.

ROBERT "BJ" ANDERSON PhD, Post-doctoral Associate BJ
919 684-7793

BJ grew up in southwest Kansas and attended Kansas State Univ for his undergraduate physics degree. His PhD in physics is from UNC-Chapel Hill, where he developed H1 NMR techniques to study hydrogen storage properties of various carbonaceous nanomaterials. Before joining CIVM, he was a post-doc at the University of Hawaii Neuroscience and MRI Research Program. Unfortunately this required him to spend several years of his prime in Hawaii. But, he had plenty of time to develop tailored RF pulses designed to mitigate various MRI artifacts, while simultaneously accelerating the image acquisition rate in human brain studies.

BJ now works with Dr. Alexandra Badea implementing the registration and segmentation pipeline, focusing on optimizing accuracy and runtime. His current research interests include exploring interesting ways to integrate advanced image processing and machine-learning algorithms into the pipeline. He will also apply his experience with custom MR pulses to various CIVM projects.

Publications pre-CIVM include:

- RJ Anderson, et al., Simultaneous multi-slice spectral-spatial excitations for reduced signal loss susceptibility artifact in BOLD fMRI, Magn Reson Med 12 Dec 2013, [Epub]
- BA Poser, RJ Anderson, P Serano, et al., Simultaneous multi-slice excitation by parallel transmission, Magn Reson Med 2014 Apr;71(4):1416-27
- RJ Anderson, et al., NMR Methods for Characterizing the Pore Structures and Hydrogen Storage Properties of Microporous Carbons, J Amer Chem Soc 132, 8618, 2010
- TP McNicholas, A Wang, K O’Neill, RJ Anderson, et al., H2 storage in microporous carbons from PEEK precursors, J Phys Chem Part C, 114, 13902, 2010
- A Kleinhammes, RJ Anderson, et al., Enhanced binding energy and slow kinetics of H2 in boron-substituted graphitic carbon, J Phys Chem Part C, 114, 13705, 2010


ALEXANDRA BADEA PhD, Assistant Professor - Radiology
919 684-7654

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.

PubMed link for a list of Alex's publications.

CRISTIAN BADEA PhD, Associate Professor - Radiology, Biomedical Engineering, Medical Physics
919 684-7509

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.

PubMed link for a listing of Cristian's publications.

GARY COFER, MS, MR Operations Manager
919 684-7677

Gary's multi-faceted functions at CIVM 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 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.

Paramount to the imaging process are high-quality RF transceiver coils and most 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

With a strong background in computer science, James supports the Center's computers and software, analyzes imaging data, provides technical assistance, and runs some of our imaging equipment. He is instrumental in developing image analysis pipelines to address both internal CIVM needs, as well as needs of our external collaborators in strategies to share image data.

BASTIAAN DRIEHUYS PhD, Associate Professor - Radiology, Biomedical Engineering, Medical Physics
919 684-7786

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 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 HP129Xe, 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.

PubMed link for a list of Bas' publications.

TAWYNNA GORDON, Financial Analyst tawynna
919 684-7755

Tawynna is the grants and financial administrator for the Center. She prepares and maintains 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

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

PubMed link for a listing of Larry's many publications.

JOHN NOULS, PhD, Assistant Professor
919 684-7769
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.

PubMed link
for a list of John's publications.

GEOFFRY SCHRANK, PhD, Physicist and Scientific/Medical Instrument Engineer GSchrank
919 684-7793

Geoff joined the hyperpolarization team from the Physics Department at the University of Utah. He brings experience in designing experiments and equipment to determine the existence and characterization of contaminants in Xe polarizers, and is overseeing the operations, maintenance, and continued development of CIVM's 129Xe hyperpolarization infrastructure in both a preclinical and clinical setting.


YI QI, MD, Laboratory Research Analyst II
919 684-7858

Yi is part of our biological support core and she focuses on 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 has 20+ years of system/network administration experience. She maintains the Center's computer systems, including these operating systems—OS X, IRIX, Linux, Solaris, Windows 2000, and Windows XP.

Lucy also maintains the Center’network, ftp, web, and Oracle/SQL database servers, and Cloud GRID.

SALLY ZIMNEY, MEd, Educational Coordinator
919 684-7758

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 our various training activities.


Our graduate students from the departments of Biomedical Engineering, Computer and Electrical Engineering, and Medical Physics contribute greatly to the work of the Center.
919 684-7507
PhD candidate - Biomedical Engineering

Darin works 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, and resulting publications.

PubMed link for a list of Darin's publications.

919 684-7887
BS - Biomedical Engineering
PhD candidate - Biomedical Engineering

Kyle is in the Biomedical Engineering Medical Imaging Training Program and is part of the MR team working under the direction of Dr. Chunlei Liu, working on susceptibility tensor imaging (STI).

919 684-7839
BS Mechanical Engineering, Brigham Young University
PhD candidate - Biomedical Engineering

As part of the MR team under the direction of Drs. Chunlei Liu and G. Allan Johnson, 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, Russ 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 4D 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.

PubMed link to Russ' publications.

CHRISTOPHER FLOWER, Research Lab Assistant Chris
BS candidate - Physics; entering his junior year

Chris is originally from Baltimore, MD and has spent the last year at Duke working with Dr. Haiyan Gao's Medium Energy Nuclear Physics group developing hyperpolarized 3He gas targets and examining very deep and fundamental properties of nucleons at the Duke Free Electron Laser Lab. At CIVM, he has continued to work with the hyperpolarized gas team by helping with the development of 129Xe gas MRI technology applied to pulmonary imaging.

This past year, Chris was awarded a Pratt Shared Materials Instrumentation Facility (SMiF) Undergraduate User Program grant for "Detection and Characterization of Rb Nanoclusters Present in Spin Exchange Optical Pumping" and will be concurrently working on that project.

919 684-7884
MS - Duke Electrical and Computer Engineering 2013
PhD candidate - Electrical and Computer Engineering

Mu is part of the hyperpolarized team under the direction of Dr. Bastiaan Driehuys. Mu’s research focuses on developing robust post-processing workflow for hyperpolarized gas MR imaging. Since hyperpolarized gas MR imaging has enabled radiation-free imaging of pulmonary function regionally and non-invasively, her current work is to develop image analysis toolkit that can enable pulmonary disease phenotyping.

PubMed link to Mu's CIVM publications.



919 684-7621
BS - Biomedical Engineering, University of Virginia 2007
MS - Engineering, University of Wisconsin 2010
PhD candidate - Medical Physics

Scott is part of the hyperpolarized team under the direction of Dr. Bastiaan Driehuys. His research is focused on optimizing image quality in functional pulmonary MRI applications involving hyperpolarized gases. The hyperpolarized magnetization is non-equilibrium and therefore nonrenewable in vivo, so the prioritization of spatial frequency information is imperative to optimizing the image information obtained by each RF pulse. The goal of Scott's research is to exploit redundancy in undersampled k-space data to allow for the efficient acquisition of high resolution multi-spectral images within a breath hold.

PubMed link to Scott's publications.

919 684-7715
BS - MIT, Physics, 2012
PhD candidate - Medical Physics

Heng began working in CIVM as part of a rotation through several research laboratories, and is now in our laboratory under the direction of Dr. Cristian Badea to help develop a next generation spectral computed tomography for cancer imaging and therapy.

His contributions resulted in a recent paper: DP Clark, M Touch, W Barber, CT Badea, Simultaneous Imaging of Multiple Contrast Agents Using Full-Spectrum Micro-CT. Proceedings SPIE Medical Imaging Vol. 9412:941222, 2015.

919 536-2214
BE, Biomedical Engineering, University of Mumbai, India
MS - Biomedical Engineering
PhD candidate - Biomedical Engineering

Rohan's is a member of the hyperpolarized gas MRI team led by Dr. Bastiaan Driehuys. 129Xe has the unique property that it interacts with biological media in vivo, and in this process exhibits chemical shifts sensitive to the local tissue microenvironment. Rohan's research involves understanding and characterizing these subtle signal changes, as well as extending 129Xe MR imaging and spectroscopy to different mouse models of disease to identify early signatures of disease onset and progression.

PubMed link for a list of Rohan's publications.



EVAN CALABRESE PhD, MD candidate Medical Scientist Training Program evan
PhD Biomedical Engineering - 2014

Evan is part of the Medical Scientist Training Program, which leads to both MD and PhD degrees. He completed the PhD part of the program in 2014, was a Post-doctoral Associate in CIVM for a year, and is now back in Medical School finishing his MD degree.

Evan's PhD dissertation was "Diffusion Tensor Imaging Biomarkers of Brain Development and Disease" and his contributions to brain studies at CIVM resulted in many publications. See this PubMed link, which includes a recent Open Access article and one publication that generated a Duke press release.

BE, Medical Electronics, VTU, Bangalore, India
MS, Biomedical Engineering, Duke University
PhD - Biomedical Engineering, November 2014

Shiv contributed greatly to the work of the MR hyperpolarized gases team,with interests in developing pulse sequences, accelerated imaging and reconstruction, and developing diffusion-weighted 129XeMRI. PubMed link for a list of his publications.

Shiv's defended his dissertation in Nov 2014 on "Simultaneous Imaging of Hyperpolarized 129Xe Ventilation and Gas Exchange for Early Detection of Interstitial Lung Disease" and continued on in the lab as a Post-doctoral Associate.

Shiv is now a Research Scientist at the Medical College of Wisconsin in Milwaukee.

PhD - Medical Physics, March 2014

Matt was part of the hyperpolarized team under direction of Dr. Bastiaan Driehuys. His research focused on mathematical modeling of our polarizer performance, in-vivo SPION imaging studies with both 129Xe and 3He, brown fat spectroscopy, and construction of a 1-liter hyperpolarized gas resolution phantom. PubMed link to Matt's publications.

In March 2015, he defended his dissertation on "The Efficiency Limits of Spin Exchange Optical Pumping Methods of 129Xe Hyperpolarization: Implications for In Vivo MRI Applications."

Matt is now working in New Mexico with the Los Alamos National Laboratory.

BS and MS, Carnegie Mellon University
PhD - Biomedical Engineering June 2014

After graduation from the Duke BME program in 2014, Luke spent a year as a post-doctoral associate in CIVM, continuing his studies identifying age-related nephropathy in Sprague-Dawley rats using MR 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.

PubMed link for Luke's publications.

Luke is now a Research Associate in the Department of Radiology Research at the University of Utah in Salt Lake City.



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