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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

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 25th 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 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 supplemental data. Work on brain atlases has continued, resulting in numerous publications. See our Shared Data for more publications that provide access to imaging data sets, to help other investigators in their research.

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

ROBERT "BJ" ANDERSON PhD, Post-doctoral Associate BJ

919 684-7793

BJ grew up in desolate southwest Kansas and subsequently attended Kansas State University, earning his undergraduate degree in physics. He pursued his PhD in physics at the University of NC at Chapel Hill, where he developed H1 NMR techniques for studying the hydrogen storage properties of various carbonaceous nanomaterials. Before joining CIVM, he had the opportunity to work as a post-doctoral fellow with the University of Hawaii Neuroscience and MRI Research Program. Unfortunately this required him to spend several years of his prime in Hawaii. On the bright side, 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 is new to the Center and will work with Dr. Alexandra Badea implementing the registration and segmentation pipeline, with a focus on optimizing accuracy and runtime of these processes. His current research interests include exploring interesting ways to integrate advanced image processing and machine-learning algorithms into said pipeline. He will also apply his experience with custom MR pulses to various CIVM projects.

Publications pre-CIVM:

  • RJ Anderson, BA Poser, VA Stenger, 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, TP McNicholas, A Kleinhammes, 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, Q Chen, 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, BME, 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.
EVAN CALABRESE PhD, Post-doctoral Associate
919 684-7653
PhD Biomedical Engineering - 2014
MD candidate Medical Scientist Training Program

Evan is part of the Medical Scientist Training Program, which leads to both MD and PhD degrees. He recently completed the PhD part of his program and is now working with the Center as a Post-doctoral Associate, continuing his MR studies involving brain atlases and diffusion tensor imaging.

PubMed link to see a list of Evan's publications, many resulting from his participaton in CIVM collaborations.

At this year's ISMRM meeting in May, Evan received the recognition of being named a 2014 Junior Fellow.


Last year, a monkey brain diffusion tensor image that Evan produced from scans on our MR 7T for collaborators from the University of Wisconsin was a winner in that University's Cool Science Image contest.

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, BME, 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 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.

PubMed link for a list of Bas' publications.


MARK FOSTER, Research Associate
919 684-7784
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Mark, a North Carolina native, recently completed a second undergraduate degree in biology after having pursued a career as a professional musician. At CIVM, he is assisting Dr. Alexandra Badea with rat-atlas initiatives, brain imaging, and data processing for numerous projects. Additionally, he is working on novel visualizations of CIVM data.

TAWYNNA GORDON, Financial Analyst
919 684-7755
tawynna gordon

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 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.

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


TATIANA JOHNSON, Administrative Assistant
919 684-7877
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Tatiana takes care of the many administrative tasks behind the scenes to keep the Center for In Vivo Microscopy running.

photo coming soon

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.

YI QI, MD, Laboratory Research Analyst

919 684-7858

Yi is part of the biological support core and 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’s e-mail, network, ftp, web, and Oracle/SQL database servers.

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 training activities.

Graduate Students

Our graduate students from the departments of Biomedical Engineering and Medical Physics contribute greatly to the work of the Center.


919 684-7507

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, and resulting publications.

PubMed link for a list of Darin's publications.


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

Kyle is just starting the Biomedical Engineering program and is part of the MR team working under the direction of Dr. Chunlei Liu.

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, 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 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' 2 most recent 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 hyperpolarized gas by helping with the development of 129Xe gas MRI technology applied to pulmonary imaging.

Recently 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.


919 684-7687

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.

PubMed link to Matt's publications.


919 684-7884
mu he
MS - Electrical and Computer Engineering 2013
PhD candidate - Biomedical Engineering

Mu is part of the hyperpolarized team under the direction of Dr. Bastiaan Driehuys. She worked on a project with the Center as part of her Master's thesis on "Registration and quantitative analysis of 129Xe ventilation MRI," and worked as a Research Assistant at CIVM before she was accepted into the Duke BME PhD program.

PubMed link to Mu's publications with CIVM

919 684-7687

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.

PubMed link for a list of Shiv's 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.


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

Click this PubMed link for a list of Rohan's publications.

Two of our most recent Medical Physics and Biomedical Engineering graduates:

919 684-7715

BS, Worcester Polytechnic Institute, Worcester MA
PhD Medical Physics - June 2014

Ergys's work at the Center that led to his recent PhD involved 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.

PubMed link to Ergy's publications resulting from his work at the Center for In Vivo Microscopy.

Ergys is now part of the Duke Medical Physics Residency program with the Radiation Oncology department.


919 684-7884

BS and MS, Carnegie Mellon University
PhD - Biomedical Engineering June 2014
Now at the GE Research and Development Center in upstate NY for a summer internship.

As part of the MR team under the direction of Dr. G. Allan Johnson, Luke's studies involved 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.

PubMed link for a listing of Luke's publications.


Garb Coincidences